From 97b985af85cdd10497082253cf2b4232b2bd0eeb Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 30 Aug 2018 16:17:10 +0200
Subject: [PATCH] new line characters unified to use linux standard
---
.../cdplugin/copypaste/CopyAction.java | 180 +-
.../copypaste/CopyPasteAbstractAction.java | 370 +-
.../cdplugin/copypaste/CopyPastePlugin.java | 260 +-
.../cdplugin/copypaste/CopyPluginAction.java | 122 +-
.../cdplugin/copypaste/PasteAction.java | 164 +-
.../cdplugin/copypaste/PastePluginAction.java | 120 +-
.../cdplugin/copypaste/package-info.java | 18 +-
.../mapviewer/cdplugin/info/InfoFrame.java | 544 +--
.../mapviewer/cdplugin/info/InfoPlugin.java | 342 +-
.../mapviewer/cdplugin/info/package-info.java | 14 +-
.../CopyPasteAbstractActionTest.java | 256 +-
.../cache/ApplicationLevelCache.java | 298 +-
.../annotation/cache/CachableInterface.java | 606 +--
.../annotation/cache/CacheException.java | 50 +-
.../annotation/cache/FtpClientFactory.java | 42 +-
.../annotation/cache/GeneralCache.java | 306 +-
.../cache/GeneralCacheInterface.java | 24 +-
.../cache/GeneralCacheWithExclusion.java | 196 +-
.../cache/PermanentDatabaseLevelCache.java | 1170 +++---
.../PermanentDatabaseLevelCacheInterface.java | 102 +-
.../annotation/cache/QueryCacheInterface.java | 160 +-
.../annotation/cache/SourceNotAvailable.java | 98 +-
.../annotation/cache/WebPageDownloader.java | 382 +-
.../annotation/cache/XmlSerializer.java | 222 +-
.../annotation/cache/package-info.java | 54 +-
.../mapviewer/annotation/data/Article.java | 390 +-
.../data/ArticleCitationComparator.java | 38 +-
.../lcsb/mapviewer/annotation/data/Chebi.java | 494 +--
.../annotation/data/ChebiRelation.java | 212 +-
.../mapviewer/annotation/data/Chemical.java | 630 +--
.../data/ChemicalDirectEvidence.java | 74 +-
.../lcsb/mapviewer/annotation/data/Drug.java | 670 +--
.../mapviewer/annotation/data/EntrezData.java | 304 +-
.../lcsb/mapviewer/annotation/data/Go.java | 172 +-
.../lcsb/mapviewer/annotation/data/MeSH.java | 366 +-
.../lcsb/mapviewer/annotation/data/MiRNA.java | 266 +-
.../mapviewer/annotation/data/Target.java | 460 +-
.../mapviewer/annotation/data/TargetType.java | 106 +-
.../annotation/data/package-info.java | 10 +-
.../annotation/services/ChEMBLParser.java | 1386 +++---
.../annotation/services/ChemicalParser.java | 1530 +++----
.../services/ChemicalSearchException.java | 96 +-
.../annotation/services/DrugAnnotation.java | 668 +--
.../services/DrugSearchException.java | 96 +-
.../services/DrugbankHTMLParser.java | 1546 +++----
.../services/DrugbankXMLParser.java | 806 ++--
.../services/ExternalServiceStatus.java | 182 +-
.../services/ExternalServiceStatusType.java | 130 +-
.../annotation/services/IExternalService.java | 60 +-
.../annotation/services/MeSHParser.java | 660 +--
.../annotation/services/MiRNAParser.java | 1368 +++---
.../services/MiRNASearchException.java | 94 +-
.../annotation/services/MiriamConnector.java | 556 +--
.../services/MissingAnnotation.java | 80 +-
.../services/MissingRequiredAnnotations.java | 128 +-
.../services/ProblematicAnnotation.java | 34 +-
.../annotation/services/PubmedParser.java | 766 ++--
.../services/PubmedSearchException.java | 76 +-
.../annotation/services/TaxonomyBackend.java | 418 +-
.../services/TaxonomySearchException.java | 60 +-
.../WrongResponseCodeIOException.java | 86 +-
.../annotators/AnnotatorException.java | 96 +-
.../annotators/BiocompendiumAnnotator.java | 690 +--
.../annotators/ChebiSearchException.java | 64 +-
.../annotators/GoSearchException.java | 60 +-
.../services/annotators/UniprotAnnotator.java | 610 +--
.../annotators/UniprotSearchException.java | 60 +-
.../services/annotators/package-info.java | 18 +-
.../AbstractReferenceGenomeConnector.java | 790 ++--
.../genome/FileNotAvailableException.java | 96 +-
.../genome/ReferenceGenomeConnector.java | 316 +-
.../ReferenceGenomeConnectorException.java | 100 +-
.../genome/UcscReferenceGenomeConnector.java | 948 ++---
.../services/genome/package-info.java | 8 +-
.../annotation/services/package-info.java | 12 +-
.../annotation/AllAnnotationTests.java | 36 +-
.../annotation/AnnotationTestFunctions.java | 592 +--
.../annotation/cache/AllCacheTests.java | 38 +-
.../cache/ApplicationLevelCacheTest.java | 242 +-
.../annotation/cache/BigFileCacheTest.java | 1198 +++---
.../cache/CachableInterfaceMock.java | 28 +-
.../cache/CachableInterfaceTest.java | 270 +-
.../annotation/cache/GeneralCacheTest.java | 274 +-
.../cache/GeneralCacheWithExclusionTest.java | 266 +-
.../annotation/cache/MockCacheInterface.java | 66 +-
.../PermanentDatabaseLevelCacheTest.java | 1014 ++---
.../cache/SourceNotAvailableTest.java | 60 +-
.../cache/WebPageDownloaderTest.java | 196 +-
.../annotation/data/AllDataTests.java | 48 +-
.../data/ArticleCitationComparatorTest.java | 94 +-
.../annotation/data/ArticleTest.java | 54 +-
.../annotation/data/ChebiRelationTest.java | 54 +-
.../mapviewer/annotation/data/ChebiTest.java | 138 +-
.../data/ChemicalDirectEvidenceTest.java | 62 +-
.../annotation/data/ChemicalTest.java | 134 +-
.../mapviewer/annotation/data/DrugTest.java | 236 +-
.../annotation/data/EntrezDataTest.java | 102 +-
.../mapviewer/annotation/data/GoTest.java | 56 +-
.../mapviewer/annotation/data/MeSHTest.java | 180 +-
.../mapviewer/annotation/data/MiRNATest.java | 90 +-
.../mapviewer/annotation/data/TargetTest.java | 130 +-
.../annotation/data/TargetTypeTest.java | 64 +-
.../annotation/services/AllServicesTests.java | 68 +-
.../annotation/services/ChEMBLParserTest.java | 2514 +++++------
.../services/ChemicalParserTest.java | 1330 +++---
.../services/ChemicalSearchExceptionTest.java | 60 +-
.../services/DrugAnnotationTest.java | 130 +-
.../services/DrugbankHTMLParserTest.java | 1664 ++++----
.../services/DrugbankXMLParserTest.java | 292 +-
.../services/ExternalServiceStatusTest.java | 68 +-
.../ExternalServiceStatusTypeTest.java | 66 +-
.../annotation/services/MeSHParserTest.java | 694 +--
.../annotation/services/MiRNAParserTest.java | 668 +--
.../services/MiRNASearchExceptionTest.java | 78 +-
.../services/MiriamConnectorTest.java | 744 ++--
.../services/ModelAnnotatorTest.java | 918 ++--
.../annotation/services/PubmedParserTest.java | 850 ++--
.../services/TaxonomyBackendTest.java | 680 +--
.../annotators/AllAnnotatorTests.java | 60 +-
.../annotators/AnnotatorExceptionTest.java | 64 +-
.../BiocompendiumAnnotatorTest.java | 722 ++--
.../services/genome/AllGenomeTests.java | 22 +-
.../UcscReferenceGenomeConnectorTest.java | 1948 ++++-----
.../lcsb/mapviewer/common/Configuration.java | 856 ++--
.../common/EventStorageLoggerAppender.java | 278 +-
.../mapviewer/common/FrameworkVersion.java | 182 +-
.../common/HttpConnectionMethodType.java | 40 +-
.../mapviewer/common/IProgressUpdater.java | 54 +-
.../java/lcsb/mapviewer/common/MimeType.java | 172 +-
.../lcsb/mapviewer/common/ObjectUtils.java | 104 +-
.../main/java/lcsb/mapviewer/common/Pair.java | 166 +-
.../mapviewer/common/SystemClipboard.java | 126 +-
.../lcsb/mapviewer/common/TextFileUtils.java | 128 +-
.../java/lcsb/mapviewer/common/XmlParser.java | 754 ++--
.../common/comparator/BooleanComparator.java | 54 +-
.../common/comparator/ColorComparator.java | 58 +-
.../common/comparator/DoubleComparator.java | 112 +-
.../common/comparator/EnumComparator.java | 58 +-
.../common/comparator/IntegerComparator.java | 54 +-
.../common/comparator/PointComparator.java | 116 +-
.../common/comparator/SetComparator.java | 132 +-
.../common/comparator/StringComparator.java | 112 +-
.../comparator/StringListComparator.java | 112 +-
.../common/comparator/package-info.java | 10 +-
.../exception/InvalidArgumentException.java | 112 +-
.../exception/InvalidClassException.java | 76 +-
.../exception/InvalidStateException.java | 112 +-
.../exception/InvalidXmlSchemaException.java | 112 +-
.../exception/NotImplementedException.java | 70 +-
.../common/exception/package-info.java | 10 +-
.../common/geometry/ColorParser.java | 154 +-
.../common/geometry/CompositeStroke.java | 82 +-
.../common/geometry/DoubleDimension.java | 72 +-
.../geometry/EllipseTransformation.java | 306 +-
.../common/geometry/PointTransformation.java | 124 +-
.../common/geometry/TextAlignment.java | 50 +-
.../common/geometry/package-info.java | 24 +-
.../lcsb/mapviewer/common/package-info.java | 10 +-
.../lcsb/mapviewer/common/AllCommonTests.java | 54 +-
.../mapviewer/common/CommonTestFunctions.java | 72 +-
.../mapviewer/common/ConfigurationTest.java | 254 +-
.../EventStorageLoggerAppenderTest.java | 122 +-
.../common/HttpConnectionMethodTypeTest.java | 58 +-
.../lcsb/mapviewer/common/MimeTypeTest.java | 64 +-
.../mapviewer/common/ObjectUtilsTest.java | 116 +-
.../java/lcsb/mapviewer/common/PairTest.java | 140 +-
.../mapviewer/common/SystemClipboardTest.java | 196 +-
.../mapviewer/common/TextFileUtilsTest.java | 156 +-
.../lcsb/mapviewer/common/XmlParserTest.java | 948 ++---
.../common/comparator/AllComparatorTests.java | 42 +-
.../comparator/BooleanComparatorTest.java | 72 +-
.../comparator/ColorComparatorTest.java | 76 +-
.../comparator/DoubleComparatorTest.java | 88 +-
.../comparator/IntegerComparatorTest.java | 70 +-
.../comparator/PointComparatorTest.java | 94 +-
.../comparator/StringComparatorTest.java | 88 +-
.../comparator/StringListComparatorTest.java | 112 +-
.../comparator/StringSetComparatorTest.java | 122 +-
.../common/exception/AllExceptionTests.java | 24 +-
.../InvalidArgumentExceptionTest.java | 78 +-
.../exception/InvalidClassExceptionTest.java | 58 +-
.../exception/InvalidStateExceptionTest.java | 78 +-
.../InvalidXmlSchemaExceptionTest.java | 78 +-
.../NotImplementedExceptionTest.java | 58 +-
.../common/geometry/AllGeometryTests.java | 34 +-
.../common/geometry/ColorParserTest.java | 136 +-
.../common/geometry/CompositeStrokeTest.java | 52 +-
.../geometry/EllipseTransformationTest.java | 164 +-
.../geometry/LineTransformationTest.java | 428 +-
.../geometry/PointTransformationTest.java | 88 +-
.../common/geometry/TextAlignmentTest.java | 58 +-
.../run/ImageToCellDesignerBackground.java | 270 +-
.../lcsb/mapviewer/run/LegendGenerator.java | 340 +-
.../lcsb/mapviewer/run/PdMapAnnotations.java | 164 +-
.../mapviewer/run/ReactomeComparison.java | 814 ++--
.../lcsb/mapviewer/run/ReactomeExport.java | 1218 +++---
.../java/lcsb/mapviewer/run/Statistics.java | 776 ++--
.../run/UnknownReactionInReactome.java | 598 +--
.../lcsb/mapviewer/run/VibineSnippet.java | 210 +-
.../java/lcsb/mapviewer/run/package-info.java | 20 +-
.../mapviewer/run/PdMapAnnotationsTest.java | 80 +-
.../CellDesignerElementCollection.java | 482 +--
.../CellDesignerParserException.java | 114 +-
.../celldesigner/CellDesignerXmlParser.java | 1418 +++----
.../model/celldesigner/CommonXmlParser.java | 212 +-
.../celldesigner/InvalidGroupException.java | 118 +-
.../model/celldesigner/LayerXmlParser.java | 1070 ++---
.../alias/AbstractAliasXmlParser.java | 174 +-
.../alias/AliasCollectionXmlParser.java | 482 +--
.../alias/CompartmentAliasXmlParser.java | 380 +-
.../alias/ComplexAliasXmlParser.java | 574 +--
.../celldesigner/alias/package-info.java | 12 +-
.../celldesigner/annotation/package-info.java | 10 +-
.../CompartmentCollectionXmlParser.java | 216 +-
.../compartment/CompartmentXmlParser.java | 342 +-
.../compartment/package-info.java | 12 +-
.../ComplexCellDesignerAliasConverter.java | 140 +-
.../DegradedCellDesignerAliasConverter.java | 214 +-
.../DrugCellDesignerAliasConverter.java | 184 +-
.../IonCellDesignerAliasConverter.java | 238 +-
.../PhenotypeCellDesignerAliasConverter.java | 188 +-
.../ProteinCellDesignerAliasConverter.java | 462 +-
.../ReactionCellDesignerConverter.java | 46 +-
...pleMoleculeCellDesignerAliasConverter.java | 168 +-
.../geometry/helper/CellDesignerAnchor.java | 290 +-
.../CellDesignerEllipseTransformation.java | 96 +-
.../CellDesignerLineTransformation.java | 270 +-
.../CellDesignerPointTransformation.java | 180 +-
.../CellDesignerPolygonTransformation.java | 220 +-
.../CellDesignerRectangleTransformation.java | 116 +-
.../geometry/helper/PolylineDataFactory.java | 122 +-
.../geometry/helper/package-info.java | 12 +-
.../celldesigner/geometry/package-info.java | 12 +-
.../model/celldesigner/package-info.java | 16 +-
.../reaction/ReactionCollectionXmlParser.java | 226 +-
.../reaction/ReactionFromXml.java | 3520 ++++++++--------
.../reaction/ReactionLineData.java | 824 ++--
.../reaction/ReactionParserException.java | 204 +-
.../celldesigner/reaction/ReactionToXml.java | 2214 +++++-----
.../reaction/ReactionXmlParser.java | 152 +-
.../reaction/SelfReactionException.java | 62 +-
.../UnknownModifierClassException.java | 108 +-
.../celldesigner/reaction/package-info.java | 12 +-
.../species/InternalModelSpeciesData.java | 428 +-
.../celldesigner/species/ProteinMapping.java | 310 +-
.../species/SpeciesCollection.java | 346 +-
.../celldesigner/species/package-info.java | 12 +-
.../structure/CellDesignerChemical.java | 250 +-
.../structure/CellDesignerComplexSpecies.java | 340 +-
.../structure/CellDesignerDegraded.java | 102 +-
.../structure/CellDesignerDrug.java | 102 +-
.../structure/CellDesignerGene.java | 244 +-
.../structure/CellDesignerGenericProtein.java | 142 +-
.../CellDesignerIonChannelProtein.java | 104 +-
.../structure/CellDesignerPhenotype.java | 104 +-
.../CellDesignerReceptorProtein.java | 104 +-
.../structure/CellDesignerSimpleMolecule.java | 118 +-
.../structure/CellDesignerSpecies.java | 1094 ++---
.../CellDesignerTruncatedProtein.java | 106 +-
.../structure/CellDesignerUnknown.java | 100 +-
.../structure/fields/ConnectScheme.java | 224 +-
.../structure/fields/EditPoints.java | 348 +-
.../structure/fields/LineProperties.java | 178 +-
.../structure/fields/SingleLine.java | 66 +-
.../celldesigner/structure/fields/View.java | 188 +-
.../structure/fields/package-info.java | 10 +-
.../celldesigner/structure/package-info.java | 10 +-
.../celldesigner/types/ModifierType.java | 404 +-
.../celldesigner/types/ModifierTypeUtils.java | 610 +--
.../celldesigner/types/OperatorType.java | 188 +-
.../celldesigner/types/OperatorTypeUtils.java | 184 +-
.../celldesigner/types/package-info.java | 12 +-
.../celldesigner/AllCellDesignerTests.java | 88 +-
.../CellDesignerElementCollectionTest.java | 86 +-
.../CellDesignerParserExceptionTest.java | 104 +-
.../CellDesignerTestFunctions.java | 456 +-
.../celldesigner/ComplexParserTests.java | 850 ++--
.../InvalidGroupExceptionTest.java | 54 +-
.../celldesigner/LayerXmlParserTest.java | 898 ++--
.../NestedComplexParsingTests.java | 176 +-
.../ReconDataInCellDesignerXmlParserTest.java | 152 +-
.../alias/AliasCollectionXmlParserTest.java | 728 ++--
.../celldesigner/alias/AllAliasTests.java | 28 +-
.../alias/CompartmentAliasXmlParserTest.java | 532 +--
.../alias/ComplexAliasXmlParserTest.java | 178 +-
.../alias/SpeciesAliasXmlParserTest.java | 672 +--
.../annotation/AllAnnotationTests.java | 26 +-
.../annotation/NoteFieldTest.java | 64 +-
.../compartment/AllCompartmentTests.java | 28 +-
.../CompartmentCollectionXmlParserTest.java | 216 +-
.../compartment/CompartmentParserTests.java | 162 +-
.../compartment/CompartmentXmlParserTest.java | 296 +-
...bstractCellDesignerAliasConverterTest.java | 168 +-
.../geometry/AllGeometryTests.java | 52 +-
...enseRnaCellDesignerAliasConverterTest.java | 118 +-
.../CellDesignerAliasConverterTest.java | 102 +-
...egradedCellDesignerAliasConverterTest.java | 114 +-
...ProteinCellDesignerAliasConverterTest.java | 116 +-
.../ReactionCellDesignerConverterTest.java | 60 +-
.../RnaCellDesignerAliasConverterTest.java | 118 +-
.../geometry/helper/AllHelperTests.java | 36 +-
.../helper/CellDesignerAnchorTest.java | 62 +-
...CellDesignerEllipseTransformationTest.java | 290 +-
.../CellDesignerLineTransformationTest.java | 436 +-
.../CellDesignerPointTransformationTest.java | 132 +-
...CellDesignerPolygonTransformationTest.java | 142 +-
...llDesignerRectangleTransformationTest.java | 72 +-
.../helper/PolylineDataFactoryTest.java | 74 +-
.../reaction/AllReactionTests.java | 40 +-
.../ReactionCollectionXmlParserTest.java | 378 +-
.../reaction/ReactionFromXmlTest.java | 1334 +++---
.../reaction/ReactionLineDataTest.java | 110 +-
.../reaction/ReactionParserExceptionTest.java | 84 +-
.../reaction/ReactionParserTests.java | 3742 ++++++++---------
.../reaction/ReactionToXmlTest.java | 530 +--
.../UnknownModifierClassExceptionTest.java | 64 +-
.../celldesigner/species/AllSpeciesTests.java | 42 +-
.../species/AntisenseRnaXmlParserTest.java | 316 +-
.../species/ComplexParserTest.java | 704 ++--
.../species/InternalModelSpeciesDataTest.java | 102 +-
.../species/ProteinMappingTest.java | 162 +-
.../species/SpeciesCollectionTest.java | 242 +-
.../SpeciesCollectionXmlParserTest.java | 916 ++--
.../species/SpeciesSbmlParserTest.java | 2286 +++++-----
.../structure/AllStructureTests.java | 76 +-
.../structure/CellDesignerChemicalTest.java | 80 +-
.../structure/CompartmentTest.java | 344 +-
.../structure/ComplexSpeciesTest.java | 296 +-
.../structure/ConnectSchemeTest.java | 90 +-
.../celldesigner/structure/DegradedTest.java | 140 +-
.../celldesigner/structure/DrugTest.java | 140 +-
.../celldesigner/structure/ElementTest.java | 258 +-
.../structure/GenericProteinTest.java | 138 +-
.../structure/IonChannelProteinTest.java | 140 +-
.../structure/LinePropertiesTest.java | 68 +-
.../structure/ModificationResidueTest.java | 306 +-
.../celldesigner/structure/PhenotypeTest.java | 140 +-
.../celldesigner/structure/ProteinTest.java | 270 +-
.../structure/ReceptorProteinTest.java | 140 +-
.../structure/SimpleMoleculeTest.java | 140 +-
.../celldesigner/structure/SpeciesTest.java | 716 ++--
.../structure/TruncatedProteinTest.java | 140 +-
.../celldesigner/structure/UnknownTest.java | 140 +-
.../celldesigner/structure/ViewTest.java | 72 +-
.../structure/fields/AllFieldsTests.java | 24 +-
.../CellDesignerModificationResidueTest.java | 60 +-
.../celldesigner/types/AllTypesTests.java | 30 +-
.../celldesigner/types/ModifierTypeTest.java | 62 +-
.../types/ModifierTypeUtilsTest.java | 526 +--
.../celldesigner/types/OperatorTypeTest.java | 62 +-
.../types/OperatorTypeUtilsTest.java | 222 +-
.../model/sbgnml/SbgnmlXmlConverter.java | 168 +-
.../console/SbgnmlConsoleConverter.java | 240 +-
.../sbgnml/console/SbgnmlRunOptions.java | 500 +--
.../console/gui/GraphicalInterface.java | 640 +--
.../sbgnml/console/gui/package-info.java | 14 +-
.../model/sbgnml/console/package-info.java | 8 +-
.../converter/model/sbgnml/package-info.java | 6 +-
.../model/sbgnml/structures/Process.java | 474 +--
.../model/sbgnml/structures/package-info.java | 6 +-
.../model/sbgnml/AllSbgnmlTests.java | 34 +-
.../CellDesigner2SbgnmlConversionTest.java | 180 +-
.../model/sbgnml/CellDesignerToSbgnTest.java | 124 +-
.../model/sbgnml/SbgnmlXmlExporterTest.java | 138 +-
.../graphics/AbstractImageGenerator.java | 2322 +++++-----
.../converter/graphics/ConverterParams.java | 236 +-
.../converter/graphics/DrawingException.java | 76 +-
.../converter/graphics/ImageGenerators.java | 356 +-
.../converter/graphics/JpgImageGenerator.java | 168 +-
.../converter/graphics/MapGenerator.java | 810 ++--
.../graphics/NormalImageGenerator.java | 130 +-
.../converter/graphics/PdfImageGenerator.java | 230 +-
.../converter/graphics/PngImageGenerator.java | 184 +-
.../converter/graphics/SvgImageGenerator.java | 190 +-
.../bioEntity/BioEntityConverter.java | 500 +--
.../bioEntity/BioEntityConverterImpl.java | 404 +-
.../bioEntity/element/ElementConverter.java | 34 +-
.../BottomSquareCompartmentConverter.java | 192 +-
.../compartment/CompartmentConverter.java | 410 +-
.../LeftSquareCompartmentConverter.java | 196 +-
.../compartment/OvalCompartmentConverter.java | 214 +-
.../PathwayCompartmentConverter.java | 170 +-
.../RightSquareCompartmentConverter.java | 206 +-
.../SquareCompartmentConverter.java | 230 +-
.../TopSquareCompartmentConverter.java | 188 +-
.../element/compartment/package-info.java | 10 +-
.../bioEntity/element/package-info.java | 10 +-
.../element/species/ComplexConverter.java | 380 +-
.../element/species/DegradedConverter.java | 270 +-
.../element/species/DrugConverter.java | 244 +-
.../element/species/IonConverter.java | 220 +-
.../element/species/PhenotypeConverter.java | 172 +-
.../SBGNNucleicAcidFeatureConverter.java | 264 +-
.../element/species/package-info.java | 12 +-
.../graphics/bioEntity/package-info.java | 10 +-
.../bioEntity/reaction/ReactionConverter.java | 888 ++--
.../bioEntity/reaction/package-info.java | 14 +-
.../geometry/ArrowTransformation.java | 934 ++--
.../graphics/geometry/FontFinder.java | 494 +--
.../geometry/RectangleTooSmallException.java | 52 +-
.../graphics/geometry/package-info.java | 12 +-
.../graphics/layer/LayerConverter.java | 308 +-
.../graphics/layer/package-info.java | 12 +-
.../converter/graphics/package-info.java | 54 +-
.../graphics/placefinder/PlaceFinder.java | 964 ++---
.../graphics/placefinder/package-info.java | 12 +-
.../converter/graphics/AllGraphicsTests.java | 52 +-
.../converter/graphics/ConverterTest.java | 172 +-
.../graphics/ImageGeneratorsTest.java | 90 +-
.../converter/graphics/MapGeneratorTest.java | 170 +-
.../graphics/NormalImageGeneratorTest.java | 294 +-
.../graphics/PdfImageGeneratorTest.java | 204 +-
.../species/AllSpeciesConverterTests.java | 22 +-
.../bioEntity/reaction/AllReactionTests.java | 22 +-
.../reaction/ReactionConverterTest.java | 788 ++--
.../graphics/geometry/AllGeometryTests.java | 22 +-
.../geometry/ArrowTransformationTest.java | 118 +-
.../graphics/geometry/FontFinderTest.java | 290 +-
.../placefinder/AllPlaceFinderTest.java | 294 +-
.../model/sbml/GenericSbmlParserTest.java | 208 +-
.../sbml/GenericSbmlToXmlParserTest.java | 168 +-
.../SbmlPareserForInvalidReactionTest.java | 116 +-
.../converter/ComplexZipConverter.java | 798 ++--
.../converter/ComplexZipConverterParams.java | 260 +-
.../converter/ConverterException.java | 110 +-
.../mapviewer/converter/ConverterParams.java | 248 +-
.../lcsb/mapviewer/converter/IConverter.java | 164 +-
.../converter/InvalidCoordinatesFile.java | 102 +-
.../converter/InvalidInputDataExecption.java | 136 +-
.../converter/InvalidOverviewFile.java | 102 +-
.../mapviewer/converter/OverviewParser.java | 918 ++--
.../annotation/XmlAnnotationParser.java | 386 +-
.../mapviewer/converter/package-info.java | 14 +-
.../converter/zip/ImageZipEntryFile.java | 84 +-
.../converter/zip/InputFileType.java | 86 +-
.../converter/zip/LayoutZipEntryFile.java | 164 +-
.../converter/zip/ModelZipEntryFile.java | 400 +-
.../mapviewer/converter/zip/ZipEntryFile.java | 170 +-
.../converter/zip/ZipEntryFileFactory.java | 336 +-
.../mapviewer/converter/zip/package-info.java | 10 +-
.../commands/ClearColorModelCommand.java | 92 +-
.../mapviewer/commands/ColorExtractor.java | 210 +-
.../commands/CommandExecutionException.java | 110 +-
.../lcsb/mapviewer/commands/CopyCommand.java | 848 ++--
.../commands/CreateHierarchyCommand.java | 770 ++--
.../commands/InvalidModelException.java | 52 +-
.../lcsb/mapviewer/commands/ModelCommand.java | 460 +-
.../commands/ModelCommandStatus.java | 44 +-
.../lcsb/mapviewer/commands/MoveCommand.java | 152 +-
.../commands/MoveElementsCommand.java | 362 +-
.../mapviewer/commands/NewModelCommand.java | 104 +-
.../SetFixedHierarchyLevelCommand.java | 122 +-
.../mapviewer/commands/SubModelCommand.java | 282 +-
.../lcsb/mapviewer/commands/package-info.java | 14 +-
.../AddElementFormerSymbolsCommand.java | 148 +-
.../AddElementMiriamDataCommand.java | 148 +-
.../AddElementPropertyListEntryCommand.java | 182 +-
.../properties/AddElementSynonymsCommand.java | 146 +-
.../ChangeElementAbbreviationCommand.java | 100 +-
.../properties/ChangeElementColorCommand.java | 98 +-
.../ChangeElementFontSizeCommand.java | 102 +-
.../ChangeElementFormerSymbolCommand.java | 128 +-
.../ChangeElementFormulaCommand.java | 102 +-
.../ChangeElementFullNameCommand.java | 102 +-
.../ChangeElementMiriamDataCommand.java | 136 +-
.../properties/ChangeElementNameCommand.java | 94 +-
.../properties/ChangeElementNotesCommand.java | 102 +-
.../ChangeElementPropertyCommand.java | 240 +-
...ChangeElementPropertyListEntryCommand.java | 254 +-
.../ChangeElementSymbolCommand.java | 102 +-
.../ChangeElementSynonymCommand.java | 128 +-
.../RemoveElementFormerSymbolsCommand.java | 146 +-
.../RemoveElementMiriamDataCommand.java | 148 +-
...RemoveElementPropertyListEntryCommand.java | 184 +-
.../RemoveElementSynonymsCommand.java | 146 +-
.../commands/properties/package-info.java | 16 +-
.../mapviewer/commands/AllCommandsTests.java | 42 +-
.../commands/CommandTestFunctions.java | 130 +-
.../mapviewer/commands/CopyCommandTest.java | 778 ++--
.../commands/MoveElementsCommandTest.java | 554 +--
.../commands/SubModelCommandTest.java | 336 +-
.../properties/AllPropertyCommandTests.java | 46 +-
.../ChangeElementAbbreviationCommandTest.java | 150 +-
.../ChangeElementColorCommandTest.java | 156 +-
.../ChangeElementFontSizeCommandTest.java | 150 +-
.../ChangeElementFormerSymbolCommandTest.java | 88 +-
.../ChangeElementFormulaCommandTest.java | 150 +-
.../ChangeElementFullNameCommandTest.java | 150 +-
.../ChangeElementMiriamDataCommandTest.java | 176 +-
.../ChangeElementNameCommandTest.java | 154 +-
.../ChangeElementNotesCommandTest.java | 150 +-
.../ChangeElementSymbolCommandTest.java | 150 +-
.../ChangeElementSynonymCommandTest.java | 180 +-
.../java/lcsb/mapviewer/model/Project.java | 1250 +++---
.../lcsb/mapviewer/model/ProjectStatus.java | 206 +-
.../mapviewer/model/cache/BigFileEntry.java | 232 +-
.../mapviewer/model/cache/CacheQuery.java | 368 +-
.../lcsb/mapviewer/model/cache/CacheType.java | 204 +-
.../lcsb/mapviewer/model/cache/FileEntry.java | 344 +-
.../model/cache/UploadedFileEntry.java | 136 +-
.../mapviewer/model/cache/package-info.java | 10 +-
.../mapviewer/model/graphics/ArrowType.java | 202 +-
.../model/graphics/ArrowTypeData.java | 368 +-
.../graphics/ArrowTypeDataComparator.java | 142 +-
.../mapviewer/model/graphics/LineType.java | 266 +-
.../model/graphics/PolylineData.java | 1070 ++---
.../graphics/PolylineDataComparator.java | 218 +-
.../model/graphics/package-info.java | 12 +-
.../lcsb/mapviewer/model/log/GenericLog.java | 308 +-
.../lcsb/mapviewer/model/log/LogType.java | 120 +-
.../lcsb/mapviewer/model/log/ObjectLog.java | 126 +-
.../lcsb/mapviewer/model/log/SystemLog.java | 40 +-
.../mapviewer/model/log/package-info.java | 10 +-
.../lcsb/mapviewer/model/map/BioEntity.java | 402 +-
.../lcsb/mapviewer/model/map/Comment.java | 714 ++--
.../map/ElementInFewParentsException.java | 48 +-
.../model/map/InconsistentModelException.java | 56 +-
.../lcsb/mapviewer/model/map/MiriamData.java | 622 +--
.../model/map/MiriamRelationType.java | 224 +-
.../lcsb/mapviewer/model/map/MiriamType.java | 1472 +++----
.../model/map/MiriamTypeNameComparator.java | 46 +-
.../mapviewer/model/map/OverviewImage.java | 462 +-
.../model/map/OverviewImageComparator.java | 196 +-
.../model/map/OverviewImageLink.java | 154 +-
.../map/OverviewImageLinkComparator.java | 150 +-
.../mapviewer/model/map/OverviewLink.java | 330 +-
.../model/map/OverviewLinkComparator.java | 124 +-
.../model/map/OverviewModelLink.java | 362 +-
.../map/OverviewModelLinkComparator.java | 176 +-
.../model/map/OverviewSearchLink.java | 148 +-
.../lcsb/mapviewer/model/map/SearchIndex.java | 376 +-
.../compartment/BottomSquareCompartment.java | 158 +-
.../model/map/compartment/Compartment.java | 808 ++--
.../compartment/CompartmentComparator.java | 238 +-
.../compartment/LeftSquareCompartment.java | 160 +-
.../map/compartment/OvalCompartment.java | 122 +-
.../map/compartment/PathwayCompartment.java | 120 +-
.../compartment/RightSquareCompartment.java | 204 +-
.../map/compartment/TopSquareCompartment.java | 160 +-
.../model/map/compartment/package-info.java | 6 +-
.../model/map/kinetics/SbmlFunction.java | 306 +-
.../model/map/kinetics/SbmlKinetics.java | 410 +-
.../map/kinetics/SbmlKineticsComparator.java | 92 +-
.../model/map/kinetics/SbmlParameter.java | 242 +-
.../model/map/kinetics/SbmlUnit.java | 256 +-
.../map/kinetics/SbmlUnitTypeFactor.java | 262 +-
.../model/map/layout/BlockDiagram.java | 38 +-
.../model/map/layout/ColorSchema.java | 806 ++--
.../model/map/layout/ElementGroup.java | 154 +-
.../model/map/layout/GeneVariation.java | 554 +--
.../map/layout/GeneVariationColorSchema.java | 184 +-
.../model/map/layout/GenericColorSchema.java | 88 +-
.../layout/InvalidColorSchemaException.java | 96 +-
.../model/map/layout/LayoutComparator.java | 116 +-
.../model/map/layout/LayoutStatus.java | 118 +-
.../model/map/layout/ReferenceGenome.java | 442 +-
.../layout/ReferenceGenomeGeneMapping.java | 292 +-
.../model/map/layout/ReferenceGenomeType.java | 74 +-
.../model/map/layout/graphics/Layer.java | 802 ++--
.../map/layout/graphics/LayerComparator.java | 262 +-
.../model/map/layout/graphics/LayerOval.java | 524 +--
.../layout/graphics/LayerOvalComparator.java | 136 +-
.../model/map/layout/graphics/LayerRect.java | 490 +--
.../layout/graphics/LayerRectComparator.java | 136 +-
.../model/map/layout/graphics/LayerText.java | 674 +--
.../layout/graphics/LayerTextComparator.java | 156 +-
.../map/layout/graphics/package-info.java | 12 +-
.../model/map/layout/package-info.java | 12 +-
.../map/model/ElementSubmodelConnection.java | 288 +-
.../ElementSubmodelConnectionComparator.java | 162 +-
.../model/map/model/ModelComparator.java | 700 +--
.../map/model/ModelSubmodelConnection.java | 264 +-
.../ModelSubmodelConnectionComparator.java | 146 +-
.../model/map/model/SubmodelConnection.java | 438 +-
.../model/SubmodelConnectionComparator.java | 202 +-
.../model/map/model/SubmodelType.java | 92 +-
.../model/map/model/package-info.java | 10 +-
.../model/map/modifier/Catalysis.java | 122 +-
.../model/map/modifier/Inhibition.java | 122 +-
.../model/map/modifier/Modulation.java | 122 +-
.../map/modifier/PhysicalStimulation.java | 124 +-
.../mapviewer/model/map/modifier/Trigger.java | 122 +-
.../model/map/modifier/UnknownCatalysis.java | 124 +-
.../model/map/modifier/UnknownInhibition.java | 124 +-
.../model/map/modifier/package-info.java | 12 +-
.../mapviewer/model/map/package-info.java | 14 +-
.../model/map/reaction/AbstractNode.java | 364 +-
.../map/reaction/AbstractNodeComparator.java | 114 +-
.../model/map/reaction/AndOperator.java | 134 +-
.../map/reaction/AssociationOperator.java | 128 +-
.../map/reaction/DissociationOperator.java | 126 +-
.../model/map/reaction/Modifier.java | 128 +-
.../model/map/reaction/NandOperator.java | 124 +-
.../model/map/reaction/NodeOperator.java | 528 +--
.../map/reaction/NodeOperatorComparator.java | 202 +-
.../model/map/reaction/OrOperator.java | 136 +-
.../mapviewer/model/map/reaction/Product.java | 126 +-
.../model/map/reaction/Reactant.java | 124 +-
.../model/map/reaction/Reaction.java | 1784 ++++----
.../map/reaction/ReactionComparator.java | 374 +-
.../model/map/reaction/ReactionNode.java | 190 +-
.../map/reaction/ReactionNodeComparator.java | 152 +-
.../model/map/reaction/SplitOperator.java | 126 +-
.../map/reaction/TruncationOperator.java | 126 +-
.../model/map/reaction/UnknownOperator.java | 126 +-
.../model/map/reaction/package-info.java | 24 +-
.../type/BooleanLogicGateReaction.java | 146 +-
.../map/reaction/type/CatalysisReaction.java | 134 +-
.../reaction/type/DissociationReaction.java | 136 +-
.../type/HeterodimerAssociationReaction.java | 136 +-
.../map/reaction/type/InhibitionReaction.java | 134 +-
.../type/KnownTransitionOmittedReaction.java | 136 +-
.../type/ModifierReactionNotation.java | 30 +-
.../map/reaction/type/ModulationReaction.java | 134 +-
.../type/NegativeInfluenceReaction.java | 136 +-
.../type/PhysicalStimulationReaction.java | 134 +-
.../type/PositiveInfluenceReaction.java | 136 +-
.../model/map/reaction/type/ReactionRect.java | 106 +-
.../type/ReducedModulationReaction.java | 136 +-
.../map/reaction/type/ReducedNotation.java | 30 +-
.../ReducedPhysicalStimulationReaction.java | 136 +-
.../reaction/type/ReducedTriggerReaction.java | 136 +-
.../type/SimpleReactionInterface.java | 24 +-
.../type/StateTransitionReaction.java | 134 +-
.../reaction/type/TranscriptionReaction.java | 134 +-
.../reaction/type/TranslationReaction.java | 136 +-
.../map/reaction/type/TransportReaction.java | 148 +-
.../map/reaction/type/TriggerReaction.java | 134 +-
.../map/reaction/type/TruncationReaction.java | 136 +-
.../type/TwoProductReactionInterface.java | 24 +-
.../type/TwoReactantReactionInterface.java | 24 +-
.../type/UnknownCatalysisReaction.java | 134 +-
.../type/UnknownInhibitionReaction.java | 134 +-
.../UnknownNegativeInfluenceReaction.java | 136 +-
.../UnknownPositiveInfluenceReaction.java | 134 +-
.../UnknownReducedModulationReaction.java | 136 +-
...ownReducedPhysicalStimulationReaction.java | 136 +-
.../type/UnknownReducedTriggerReaction.java | 136 +-
.../type/UnknownTransitionReaction.java | 136 +-
.../model/map/reaction/type/package-info.java | 12 +-
.../map/species/AntisenseRnaComparator.java | 158 +-
.../mapviewer/model/map/species/Chemical.java | 232 +-
.../model/map/species/ChemicalComparator.java | 146 +-
.../mapviewer/model/map/species/Complex.java | 398 +-
.../model/map/species/ComplexComparator.java | 200 +-
.../mapviewer/model/map/species/Degraded.java | 124 +-
.../model/map/species/DegradedComparator.java | 108 +-
.../mapviewer/model/map/species/Drug.java | 126 +-
.../model/map/species/DrugComparator.java | 108 +-
.../model/map/species/ElementComparator.java | 404 +-
.../model/map/species/GeneComparator.java | 160 +-
.../model/map/species/GenericProtein.java | 116 +-
.../map/species/GenericProteinComparator.java | 108 +-
.../lcsb/mapviewer/model/map/species/Ion.java | 128 +-
.../model/map/species/IonChannelProtein.java | 116 +-
.../species/IonChannelProteinComparator.java | 108 +-
.../model/map/species/IonComparator.java | 108 +-
.../model/map/species/Phenotype.java | 128 +-
.../map/species/PhenotypeComparator.java | 110 +-
.../mapviewer/model/map/species/Protein.java | 250 +-
.../model/map/species/ProteinComparator.java | 178 +-
.../model/map/species/ReceptorProtein.java | 114 +-
.../species/ReceptorProteinComparator.java | 108 +-
.../model/map/species/RnaComparator.java | 158 +-
.../model/map/species/SimpleMolecule.java | 128 +-
.../map/species/SimpleMoleculeComparator.java | 108 +-
.../mapviewer/model/map/species/Species.java | 974 ++---
.../model/map/species/SpeciesComparator.java | 314 +-
.../model/map/species/TruncatedProtein.java | 114 +-
.../species/TruncatedProteinComparator.java | 108 +-
.../mapviewer/model/map/species/Unknown.java | 126 +-
.../model/map/species/UnknownComparator.java | 108 +-
.../species/field/PositionToCompartment.java | 154 +-
.../model/map/species/field/package-info.java | 12 +-
.../model/map/species/package-info.java | 18 +-
.../model/map/statistics/SearchHistory.java | 338 +-
.../model/map/statistics/SearchType.java | 58 +-
.../model/map/statistics/package-info.java | 10 +-
.../lcsb/mapviewer/model/package-info.java | 42 +-
.../lcsb/mapviewer/model/plugin/Plugin.java | 226 +-
.../model/plugin/PluginDataEntry.java | 180 +-
.../mapviewer/model/user/BasicPrivilege.java | 366 +-
.../user/ConfigurationElementEditType.java | 110 +-
.../user/ConfigurationElementTypeGroup.java | 52 +-
.../model/user/ConfigurationOption.java | 192 +-
.../mapviewer/model/user/ObjectPrivilege.java | 198 +-
.../mapviewer/model/user/PrivilegeType.java | 302 +-
.../java/lcsb/mapviewer/model/user/User.java | 832 ++--
.../model/user/UserAnnotationSchema.java | 1080 ++---
.../model/user/UserClassAnnotators.java | 350 +-
.../user/UserClassRequiredAnnotations.java | 460 +-
.../model/user/UserClassValidAnnotations.java | 384 +-
.../mapviewer/model/user/package-info.java | 10 +-
.../modelutils/map/ClassNameComparator.java | 36 +-
.../modelutils/map/ClassTreeNode.java | 308 +-
.../map/ClassTreeNodeNameComparator.java | 50 +-
.../modelutils/map/package-info.java | 10 +-
.../test/java/lcsb/mapviewer/AllTests.java | 32 +-
.../lcsb/mapviewer/ModelTestFunctions.java | 64 +-
.../lcsb/mapviewer/model/AllModelTests.java | 48 +-
.../mapviewer/model/ProjectStatusTest.java | 60 +-
.../lcsb/mapviewer/model/ProjectTest.java | 522 +--
.../mapviewer/model/cache/AllCacheTests.java | 32 +-
.../model/cache/BigFileEntryTest.java | 132 +-
.../mapviewer/model/cache/CacheQueryTest.java | 138 +-
.../mapviewer/model/cache/CacheTypeTest.java | 100 +-
.../model/cache/UploadedFileEntryTest.java | 66 +-
.../model/graphics/AllGraphicsTests.java | 36 +-
.../graphics/ArrowTypeDataComparatorTest.java | 144 +-
.../model/graphics/ArrowTypeDataTest.java | 158 +-
.../model/graphics/ArrowTypeTest.java | 58 +-
.../model/graphics/LineTypeTest.java | 60 +-
.../graphics/PolylineDataComparatorTest.java | 224 +-
.../model/graphics/PolylineDataTest.java | 842 ++--
.../lcsb/mapviewer/model/log/AllLogTests.java | 28 +-
.../lcsb/mapviewer/model/log/LogTypeTest.java | 58 +-
.../mapviewer/model/log/ObjectLogTest.java | 130 +-
.../mapviewer/model/log/SystemLogTest.java | 54 +-
.../lcsb/mapviewer/model/map/AllMapTests.java | 98 +-
.../lcsb/mapviewer/model/map/CommentTest.java | 180 +-
.../map/ElementInFewParentsExceptionTest.java | 56 +-
.../map/InconsistentModelExceptionTest.java | 56 +-
.../model/map/LayoutComparatorTest.java | 278 +-
.../mapviewer/model/map/MiriamDataTest.java | 270 +-
.../model/map/MiriamRelationTypeTest.java | 76 +-
.../map/MiriamTypeNameComparatorTest.java | 92 +-
.../mapviewer/model/map/MiriamTypeTest.java | 272 +-
.../map/OverviewImageComparatorTest.java | 184 +-
.../map/OverviewImageLinkComparatorTest.java | 194 +-
.../model/map/OverviewImageLinkTest.java | 126 +-
.../model/map/OverviewImageTest.java | 164 +-
.../model/map/OverviewLinkComparatorTest.java | 186 +-
.../mapviewer/model/map/OverviewLinkTest.java | 146 +-
.../map/OverviewModelLinkComparatorTest.java | 214 +-
.../model/map/OverviewModelLinkTest.java | 196 +-
.../model/map/OverviewSearchLinkTest.java | 174 +-
.../mapviewer/model/map/SearchIndexTest.java | 256 +-
.../map/compartment/AllCompartmentTests.java | 40 +-
.../BottomSquareCompartmentTest.java | 190 +-
.../CompartmentComparatorTest.java | 444 +-
.../map/compartment/CompartmentTest.java | 828 ++--
.../LeftSquareCompartmentTest.java | 192 +-
.../map/compartment/OvalCompartmentTest.java | 142 +-
.../compartment/PathwayCompartmentTest.java | 180 +-
.../RightSquareCompartmentTest.java | 218 +-
.../compartment/TopSquareCompartmentTest.java | 200 +-
.../model/map/layout/AllLayoutTests.java | 50 +-
.../model/map/layout/ColorSchemaTest.java | 294 +-
.../model/map/layout/ElementGroupTest.java | 132 +-
.../layout/GeneVariationColorSchemaTest.java | 248 +-
.../model/map/layout/GeneVariationTest.java | 202 +-
.../map/layout/GenericColorSchemaTest.java | 162 +-
.../InvalidColorSchemaExceptionTest.java | 114 +-
.../model/map/layout/LayoutStatusTest.java | 60 +-
.../model/map/layout/LayoutTest.java | 362 +-
.../ReferenceGenomeGeneMappingTest.java | 108 +-
.../model/map/layout/ReferenceGenomeTest.java | 178 +-
.../map/layout/ReferenceGenomeTypeTest.java | 70 +-
.../map/layout/graphics/AllGraphicsTests.java | 38 +-
.../layout/graphics/LayerComparatorTest.java | 400 +-
.../graphics/LayerOvalComparatorTest.java | 284 +-
.../map/layout/graphics/LayerOvalTest.java | 330 +-
.../graphics/LayerRectComparatorTest.java | 282 +-
.../map/layout/graphics/LayerRectTest.java | 324 +-
.../model/map/layout/graphics/LayerTest.java | 316 +-
.../graphics/LayerTextComparatorTest.java | 302 +-
.../map/layout/graphics/LayerTextTest.java | 392 +-
.../model/map/model/AllModelTests.java | 42 +-
...ementSubmodelConnectionComparatorTest.java | 258 +-
.../model/ElementSubmodelConnectionTest.java | 188 +-
.../model/map/model/ModelComparatorTest.java | 852 ++--
.../model/map/model/ModelDataTest.java | 602 +--
...ModelSubmodelConnectionComparatorTest.java | 220 +-
.../model/ModelSubmodelConnectionTest.java | 204 +-
.../SubmodelConnectionComparatorTest.java | 378 +-
.../model/map/model/SubmodelTypeTest.java | 60 +-
.../model/map/modifier/AllModifierTests.java | 36 +-
.../model/map/modifier/CatalysisTest.java | 168 +-
.../model/map/modifier/InhibitionTest.java | 170 +-
.../model/map/modifier/ModulationTest.java | 170 +-
.../map/modifier/PhysicalStimulationTest.java | 170 +-
.../model/map/modifier/TriggerTest.java | 170 +-
.../map/modifier/UnknownCatalysisTest.java | 170 +-
.../map/modifier/UnknownInhibitionTest.java | 170 +-
.../reaction/AbstractNodeComparatorTest.java | 104 +-
.../model/map/reaction/AllReactionTests.java | 62 +-
.../model/map/reaction/AndOperatorTest.java | 200 +-
.../map/reaction/AssociationOperatorTest.java | 170 +-
.../reaction/DissociationOperatorTest.java | 170 +-
.../model/map/reaction/ModifierTest.java | 146 +-
.../model/map/reaction/NandOperatorTest.java | 170 +-
.../reaction/NodeOperatorComparatorTest.java | 312 +-
.../model/map/reaction/NodeOperatorMock.java | 60 +-
.../model/map/reaction/NodeOperatorTest.java | 420 +-
.../model/map/reaction/OrOperatorTest.java | 170 +-
.../model/map/reaction/ProductTest.java | 144 +-
.../model/map/reaction/ReactantTest.java | 146 +-
.../map/reaction/ReactionComparatorTest.java | 596 +--
.../reaction/ReactionNodeComparatorTest.java | 274 +-
.../model/map/reaction/ReactionTest.java | 856 ++--
.../model/map/reaction/SplitOperatorTest.java | 168 +-
.../map/reaction/TruncationOperatorTest.java | 168 +-
.../map/reaction/UnknownOperatorTest.java | 170 +-
.../reaction/type/AllReactionTypeTests.java | 64 +-
.../type/BooleanLogicGateReactionTest.java | 256 +-
.../type/DissociationReactionTest.java | 258 +-
.../HeterodimerAssociationReactionTest.java | 254 +-
.../KnownTransitionOmittedReactionTest.java | 254 +-
.../type/NegativeInfluenceReactionTest.java | 254 +-
.../type/PositiveInfluenceReactionTest.java | 254 +-
.../map/reaction/type/ReactionRectTest.java | 58 +-
.../type/ReducedModulationReactionTest.java | 252 +-
...educedPhysicalStimulationReactionTest.java | 252 +-
.../type/ReducedTriggerReactionTest.java | 252 +-
.../type/StateTransitionReactionTest.java | 250 +-
.../type/TranscriptionReactionTest.java | 250 +-
.../type/TranslationReactionTest.java | 250 +-
.../reaction/type/TransportReactionTest.java | 252 +-
.../reaction/type/TruncationReactionTest.java | 254 +-
.../UnknownNegativeInfluenceReactionTest.java | 252 +-
.../UnknownPositiveInfluenceReactionTest.java | 252 +-
.../UnknownReducedModulationReactionTest.java | 252 +-
...educedPhysicalStimulationReactionTest.java | 252 +-
.../UnknownReducedTriggerReactionTest.java | 252 +-
.../type/UnknownTransitionReactionTest.java | 252 +-
.../model/map/species/AllSpeciesTests.java | 98 +-
.../species/AntisenseRnaComparatorTest.java | 190 +-
.../map/species/ChemicalComparatorTest.java | 148 +-
.../map/species/ComplexComparatorTest.java | 766 ++--
.../model/map/species/ComplexTest.java | 362 +-
.../map/species/DegradedComparatorTest.java | 166 +-
.../model/map/species/DegradedTest.java | 160 +-
.../model/map/species/DrugComparatorTest.java | 150 +-
.../mapviewer/model/map/species/DrugTest.java | 160 +-
.../map/species/ElementComparatorTest.java | 642 +--
.../model/map/species/ElementTest.java | 808 ++--
.../species/GenericProteinComparatorTest.java | 168 +-
.../model/map/species/GenericProteinTest.java | 136 +-
.../IonChannelProteinComparatorTest.java | 168 +-
.../map/species/IonChannelProteinTest.java | 138 +-
.../model/map/species/IonComparatorTest.java | 166 +-
.../mapviewer/model/map/species/IonTest.java | 160 +-
.../map/species/PhenotypeComparatorTest.java | 172 +-
.../model/map/species/PhenotypeTest.java | 188 +-
.../ReceptorProteinComparatorTest.java | 168 +-
.../map/species/ReceptorProteinTest.java | 138 +-
.../species/SimpleMoleculeComparatorTest.java | 242 +-
.../model/map/species/SimpleMoleculeTest.java | 160 +-
.../map/species/SpeciesComparatorTest.java | 626 +--
.../model/map/species/SpeciesTest.java | 68 +-
.../TruncatedProteinComparatorTest.java | 168 +-
.../map/species/TruncatedProteinTest.java | 138 +-
.../map/species/UnknownComparatorTest.java | 168 +-
.../model/map/species/UnknownTest.java | 160 +-
.../map/species/field/AllFieldTests.java | 36 +-
.../species/field/ModificationStateTest.java | 80 +-
.../field/PositionToCompartmentTest.java | 78 +-
.../map/statistics/AllStatisticsTests.java | 26 +-
.../map/statistics/SearchHistoryTest.java | 126 +-
.../model/map/statistics/SearchTypeTest.java | 56 +-
.../mapviewer/model/user/AllUserTests.java | 44 +-
.../model/user/BasicPrivilegeTest.java | 130 +-
.../ConfigurationElementEditTypeTest.java | 62 +-
.../user/ConfigurationElementTypeTest.java | 62 +-
.../model/user/ConfigurationTest.java | 98 +-
.../model/user/ObjectPrivilegeTest.java | 226 +-
.../model/user/PrivilegeTypeTest.java | 68 +-
.../model/user/UserAnnotationSchemaTest.java | 464 +-
.../model/user/UserClassAnnotatorsTest.java | 142 +-
.../UserClassRequiredAnnotationsTest.java | 194 +-
.../user/UserClassValidAnnotationsTest.java | 160 +-
.../lcsb/mapviewer/model/user/UserTest.java | 222 +-
.../modelutils/map/AllMapUtilTests.java | 28 +-
.../modelutils/map/ClassTreeNodeTest.java | 86 +-
.../map/RequireAnnotationMapTest.java | 58 +-
.../lcsb/mapviewer/wikipathway/Activator.java | 68 +-
.../mapviewer/wikipathway/ImportExport.java | 442 +-
.../wikipathway/XML/BiopaxParser.java | 528 +--
.../wikipathway/XML/CyclicEdgeException.java | 76 +-
.../wikipathway/XML/DataNodeParser.java | 400 +-
.../wikipathway/XML/EdgeLineParser.java | 184 +-
.../mapviewer/wikipathway/XML/EdgeParser.java | 1158 ++---
.../wikipathway/XML/ElementGpmlParser.java | 278 +-
.../wikipathway/XML/GPMLToModel.java | 102 +-
.../mapviewer/wikipathway/XML/GpmlParser.java | 1314 +++---
.../XML/GraphicalPathwayElementParser.java | 154 +-
.../XML/InvalidElbowConnectorException.java | 60 +-
.../wikipathway/XML/LabelParser.java | 356 +-
.../wikipathway/XML/PointDataParser.java | 136 +-
.../wikipathway/XML/ReferenceParser.java | 324 +-
.../wikipathway/XML/ShapeParser.java | 392 +-
.../wikipathway/XML/StateParser.java | 342 +-
.../XML/UnknownAttributeValueException.java | 58 +-
.../XML/UnknownChildClassException.java | 60 +-
.../XML/UnknownMergingMethodException.java | 58 +-
.../wikipathway/XML/package-info.java | 10 +-
.../mapviewer/wikipathway/model/DataNode.java | 428 +-
.../wikipathway/model/Direction.java | 160 +-
.../mapviewer/wikipathway/model/Edge.java | 938 ++---
.../model/GpmlInteractionType.java | 270 +-
.../model/GpmlLineConnectorType.java | 146 +-
.../wikipathway/model/GpmlLineType.java | 170 +-
.../model/GpmlModificationType.java | 272 +-
.../wikipathway/model/GpmlStateType.java | 174 +-
.../mapviewer/wikipathway/model/Graph.java | 1166 ++---
.../model/GraphicalPathwayElement.java | 506 +--
.../mapviewer/wikipathway/model/Group.java | 270 +-
.../wikipathway/model/Interaction.java | 780 ++--
.../wikipathway/model/InteractionMapping.java | 1028 ++---
.../mapviewer/wikipathway/model/Label.java | 344 +-
.../wikipathway/model/MergeMapping.java | 398 +-
.../wikipathway/model/PathwayElement.java | 334 +-
.../wikipathway/model/PointData.java | 402 +-
.../wikipathway/model/ReferenceMapping.java | 540 +--
.../mapviewer/wikipathway/model/Shape.java | 448 +-
.../mapviewer/wikipathway/model/State.java | 518 +--
.../model/UnknownTypeException.java | 56 +-
.../wikipathway/model/biopax/BiopaxData.java | 184 +-
.../BiopaxOpenControlledVocabulary.java | 170 +-
.../model/biopax/BiopaxPublication.java | 344 +-
.../model/biopax/package-info.java | 14 +-
.../wikipathway/model/package-info.java | 30 +-
.../mapviewer/wikipathway/package-info.java | 20 +-
.../lcsb/mapviewer/wikipathway/utils/Geo.java | 652 +--
.../wikipathway/utils/package-info.java | 10 +-
.../wikipathway/AllWikipathwaysTests.java | 44 +-
.../ComplexReactionToModelTest.java | 432 +-
.../wikipathway/ReactionElbowsTest.java | 1750 ++++----
.../ReactionGpmlInputToModelTest.java | 2834 ++++++-------
.../ReactionGpmlOutputToModelTest.java | 2888 ++++++-------
.../wikipathway/ReactionGpmlToModelTest.java | 2108 +++++-----
.../WikipathwaysTestFunctions.java | 468 +--
.../wikipathway/XML/AllXmlTests.java | 44 +-
.../wikipathway/XML/BiopaxParserTest.java | 124 +-
.../mapviewer/wikipathway/XML/BugTest.java | 138 +-
.../wikipathway/XML/DataNodeParserTest.java | 118 +-
.../wikipathway/XML/EdgeLineParserTest.java | 110 +-
.../XML/ElementGpmlParserTest.java | 108 +-
.../wikipathway/XML/GpmlParserTest.java | 300 +-
.../wikipathway/XML/LabelParserTest.java | 144 +-
.../wikipathway/XML/ModelContructorTest.java | 90 +-
.../wikipathway/XML/ModelToGPMLTest.java | 188 +-
.../wikipathway/XML/ReferenceParserTest.java | 316 +-
.../wikipathway/XML/ShapeParserTest.java | 430 +-
.../wikipathway/XML/StateParserTest.java | 88 +-
.../wikipathway/model/AllModelTests.java | 44 +-
.../wikipathway/model/DataNodeTest.java | 54 +-
.../mapviewer/wikipathway/model/EdgeTest.java | 54 +-
.../wikipathway/model/GraphTest.java | 56 +-
.../wikipathway/model/GroupTest.java | 54 +-
.../wikipathway/model/InteractionTest.java | 54 +-
.../wikipathway/model/LabelTest.java | 54 +-
.../wikipathway/model/PointDataTest.java | 54 +-
.../wikipathway/model/ShapeTest.java | 54 +-
.../wikipathway/model/StateTest.java | 54 +-
.../model/biopax/AllBiopaxTests.java | 22 +-
.../model/biopax/BiopaxDataTest.java | 56 +-
.../BiopaxOpenControlledVocabularyTest.java | 56 +-
.../model/biopax/BiopaxPublicationTest.java | 56 +-
.../persist/ApplicationContextLoader.java | 150 +-
.../java/lcsb/mapviewer/persist/DbUtils.java | 624 +--
.../persist/SpringApplicationContext.java | 128 +-
.../lcsb/mapviewer/persist/dao/BaseDao.java | 660 +--
.../persist/dao/ConfigurationDao.java | 104 +-
.../mapviewer/persist/dao/ProjectDao.java | 212 +-
.../persist/dao/cache/BigFileEntryDao.java | 110 +-
.../persist/dao/cache/CacheQueryDao.java | 116 +-
.../persist/dao/cache/CacheTypeDao.java | 90 +-
.../dao/cache/UploadedFileEntryDao.java | 68 +-
.../persist/dao/cache/package-info.java | 10 +-
.../persist/dao/graphics/PolylineDao.java | 42 +-
.../persist/dao/graphics/package-info.java | 10 +-
.../mapviewer/persist/dao/log/LogDao.java | 90 +-
.../persist/dao/log/package-info.java | 10 +-
.../mapviewer/persist/dao/map/CommentDao.java | 266 +-
.../mapviewer/persist/dao/map/LayoutDao.java | 202 +-
.../mapviewer/persist/dao/map/ModelDao.java | 222 +-
.../persist/dao/map/ReactionDao.java | 42 +-
.../dao/map/layout/ReferenceGenomeDao.java | 70 +-
.../layout/ReferenceGenomeGeneMappingDao.java | 42 +-
.../persist/dao/map/layout/package-info.java | 10 +-
.../persist/dao/map/package-info.java | 10 +-
.../persist/dao/map/species/ElementDao.java | 42 +-
.../persist/dao/map/species/package-info.java | 10 +-
.../dao/map/statistics/SearchHistoryDao.java | 56 +-
.../dao/map/statistics/package-info.java | 10 +-
.../mapviewer/persist/dao/package-info.java | 10 +-
.../persist/dao/plugin/PluginDao.java | 48 +-
.../dao/plugin/PluginDataEntryDao.java | 86 +-
.../persist/dao/user/PrivilegeDao.java | 42 +-
.../mapviewer/persist/dao/user/UserDao.java | 144 +-
.../persist/dao/user/package-info.java | 10 +-
.../persist/mapper/Point2DMapper.java | 252 +-
.../persist/mapper/package-info.java | 10 +-
.../lcsb/mapviewer/persist/package-info.java | 12 +-
.../lcsb/mapviewer/persist/AllDbTests.java | 38 +-
.../persist/ApplicationContextLoaderTest.java | 162 +-
.../lcsb/mapviewer/persist/DbUtilsTest.java | 138 +-
.../persist/PersistTestFunctions.java | 592 +--
.../persist/SpringApplicationContextTest.java | 58 +-
.../mapviewer/persist/dao/AllDaoTests.java | 54 +-
.../mapviewer/persist/dao/BaseDaoTest.java | 90 +-
.../persist/dao/ConfigurationDaoTest.java | 100 +-
.../mapviewer/persist/dao/ProjectDaoTest.java | 622 +--
.../persist/dao/cache/AllCacheDbTests.java | 30 +-
.../persist/dao/cache/CacheQueryDaoTest.java | 84 +-
.../persist/dao/cache/CacheTypeDaoTest.java | 248 +-
.../dao/cache/UploadedFileEntryDaoTest.java | 116 +-
.../dao/graphics/AllGraphicsDaoTests.java | 22 +-
.../dao/graphics/PolylineDataTest.java | 138 +-
.../persist/dao/log/AllLogTests.java | 24 +-
.../mapviewer/persist/dao/log/LogDaoTest.java | 94 +-
.../persist/dao/map/AllMapDaoTests.java | 40 +-
.../persist/dao/map/FeedbackTest.java | 86 +-
.../persist/dao/map/ModelDaoTest.java | 996 ++---
.../dao/map/layout/AllLayoutTests.java | 32 +-
.../map/layout/ReferenceGenomeDaoTest.java | 142 +-
.../ReferenceGenomeGeneMappingDaoTest.java | 124 +-
.../dao/map/layout/alias/AllAliasTests.java | 30 +-
.../map/statistics/SearchHistoryDaoTest.java | 80 +-
.../map/statistics/StatisticsAllTests.java | 22 +-
.../persist/dao/user/AllUserTests.java | 24 +-
.../persist/dao/user/UserDaoTest.java | 490 +--
.../persist/mapper/Point2DMapperTest.java | 120 +-
.../lcsb/mapviewer/api/BaseController.java | 186 +-
.../java/lcsb/mapviewer/api/BaseRestImpl.java | 780 ++--
.../mapviewer/api/ObjectExistsException.java | 76 +-
.../api/ObjectNotFoundException.java | 76 +-
.../lcsb/mapviewer/api/QueryException.java | 76 +-
.../ConfigurationController.java | 236 +-
.../configuration/ConfigurationRestImpl.java | 636 +--
.../mapviewer/api/files/FileController.java | 116 +-
.../mapviewer/api/files/FileRestImpl.java | 214 +-
.../genomics/ReferenceGenomeController.java | 246 +-
.../api/genomics/ReferenceGenomeRestImpl.java | 570 +--
.../mapviewer/api/mesh/MeshController.java | 88 +-
.../lcsb/mapviewer/api/mesh/MeshRestImpl.java | 86 +-
.../java/lcsb/mapviewer/api/package-info.java | 8 +-
.../api/plugins/PluginController.java | 200 +-
.../mapviewer/api/plugins/PluginRestImpl.java | 278 +-
.../api/projects/ProjectController.java | 416 +-
.../api/projects/ProjectRestImpl.java | 1876 ++++-----
.../chemicals/ChemicalController.java | 110 +-
.../projects/chemicals/ChemicalRestImpl.java | 440 +-
.../projects/comments/CommentController.java | 364 +-
.../projects/comments/CommentRestImpl.java | 688 +--
.../api/projects/drugs/DrugController.java | 112 +-
.../api/projects/drugs/DrugRestImpl.java | 414 +-
.../api/projects/mirnas/MiRnaController.java | 112 +-
.../api/projects/mirnas/MiRnaRestImpl.java | 342 +-
.../bioEntities/BioEntitiesController.java | 160 +-
.../bioEntities/BioEntitiesRestImpl.java | 194 +-
.../elements/ElementsController.java | 78 +-
.../elements/ElementsRestImpl.java | 692 +--
.../reactions/ReactionsController.java | 74 +-
.../reactions/ReactionsRestImpl.java | 630 +--
.../models/functions/FunctionsController.java | 88 +-
.../models/functions/FunctionsRestImpl.java | 212 +-
.../parameters/ParametersController.java | 88 +-
.../models/parameters/ParametersRestImpl.java | 190 +-
.../publications/PublicationsController.java | 76 +-
.../publications/PublicationsRestImpl.java | 592 +--
.../models/units/UnitsController.java | 88 +-
.../projects/models/units/UnitsRestImpl.java | 150 +-
.../projects/overlays/OverlayController.java | 352 +-
.../mapviewer/api/users/UserController.java | 446 +-
.../java/lcsb/mapviewer/api/AllRestTests.java | 48 +-
.../lcsb/mapviewer/api/RestTestFunctions.java | 638 +--
.../api/projects/AllProjectTests.java | 44 +-
.../api/projects/ProjectRestImplTest.java | 686 +--
.../projects/comments/AllCommentTests.java | 22 +-
.../comments/CommentRestImplTest.java | 186 +-
.../mapviewer/api/users/AllUserTests.java | 22 +-
.../mapviewer/api/users/UserRestImplTest.java | 288 +-
.../AuthenticationTokenExpireException.java | 28 +-
.../services/InvalidTokenException.java | 28 +-
.../mapviewer/services/SecurityException.java | 36 +-
.../services/UserAccessException.java | 28 +-
.../services/impl/CommentService.java | 664 +--
.../services/impl/ConfigurationService.java | 348 +-
.../impl/ExternalServicesService.java | 338 +-
.../mapviewer/services/impl/LogService.java | 236 +-
.../services/impl/Md5PasswordEncoder.java | 116 +-
.../services/impl/MiriamService.java | 108 +-
.../services/impl/ProjectService.java | 2824 ++++++-------
.../services/impl/ReferenceGenomeService.java | 302 +-
.../services/impl/SearchHistoryService.java | 102 +-
.../services/impl/SearchService.java | 1680 ++++----
.../mapviewer/services/impl/package-info.java | 12 +-
.../services/interfaces/ICommentService.java | 178 +-
.../interfaces/IConfigurationService.java | 236 +-
.../interfaces/IExternalServicesService.java | 84 +-
.../services/interfaces/ILayoutService.java | 990 ++---
.../services/interfaces/ILdapService.java | 122 +-
.../services/interfaces/ILogService.java | 270 +-
.../services/interfaces/IMiriamService.java | 64 +-
.../services/interfaces/IProjectService.java | 272 +-
.../interfaces/IReferenceGenomeService.java | 294 +-
.../interfaces/ISearchHistoryService.java | 50 +-
.../services/interfaces/ISearchService.java | 628 +--
.../services/interfaces/package-info.java | 12 +-
.../overlay/AnnotatedObjectTreeRow.java | 592 +--
.../services/overlay/ChebiTreeRow.java | 250 +-
.../services/overlay/IconManager.java | 288 +-
.../mapviewer/services/overlay/IconType.java | 136 +-
.../services/overlay/package-info.java | 14 +-
.../services/search/DbSearchCriteria.java | 336 +-
.../services/search/ElementMatcher.java | 226 +-
.../services/search/IDbSearchService.java | 112 +-
.../search/chemical/ChemicalService.java | 588 +--
.../search/chemical/IChemicalService.java | 28 +-
.../search/chemical/package-info.java | 16 +-
.../services/search/drug/DrugService.java | 750 ++--
.../services/search/drug/IDrugService.java | 42 +-
.../services/search/drug/package-info.java | 16 +-
.../services/search/mirna/IMiRNAService.java | 28 +-
.../services/search/mirna/MiRNAService.java | 410 +-
.../services/search/mirna/package-info.java | 16 +-
.../services/search/package-info.java | 16 +-
.../services/utils/ColorSchemaXlsxReader.java | 694 +--
.../services/utils/CreateProjectParams.java | 1664 ++++----
.../mapviewer/services/utils/EmailSender.java | 626 +--
.../utils/InvalidPrivilegeException.java | 48 +-
.../utils/ReferenceGenomeExistsException.java | 52 +-
.../services/utils/SearchIndexer.java | 356 +-
.../services/utils/data/BuildInLayout.java | 224 +-
.../utils/data/ColorSchemaColumn.java | 322 +-
.../services/utils/data/ColorSchemaType.java | 42 +-
.../services/utils/data/ExportColumn.java | 228 +-
.../services/utils/data/ExportFileType.java | 92 +-
.../services/utils/data/package-info.java | 12 +-
.../services/utils/package-info.java | 10 +-
.../mapviewer/services/AllServicesTests.java | 38 +-
.../services/ServiceTestFunctions.java | 854 ++--
.../services/impl/AllImplServiceTests.java | 40 +-
.../services/impl/CommentServiceTest.java | 380 +-
.../impl/ConfigurationServiceTest.java | 280 +-
.../impl/ExternalServicesServiceTest.java | 134 +-
.../services/impl/FailServiceMock.java | 32 +-
.../services/impl/LayoutServiceTest2.java | 498 +--
.../services/impl/LdapServiceTest.java | 272 +-
.../services/impl/Md5PasswordEncoderTest.java | 94 +-
.../services/impl/OkServiceMock.java | 32 +-
.../services/impl/SearchServiceTest.java | 1226 +++---
.../services/impl/UserServiceTest.java | 458 +-
.../services/overlay/AllOverlayTests.java | 28 +-
.../overlay/AnnotatedObjectTreeRowTest.java | 62 +-
.../services/overlay/ChebiTreeRowTest.java | 58 +-
.../services/overlay/IconManagerTest.java | 94 +-
.../services/search/AllSearchTests.java | 40 +-
.../search/chemical/ChemicalServiceTest.java | 140 +-
.../search/drug/AllSearchDrugTests.java | 26 +-
.../services/search/drug/DrugServiceTest.java | 600 +--
.../search/mirna/MiRNAServiceTest.java | 96 +-
.../services/utils/AllUtilsTests.java | 30 +-
.../utils/ColorSchemaReaderXlsTest.java | 270 +-
.../utils/ColorSchemaReaderXlsxTest.java | 270 +-
.../services/utils/EmailSenderTest.java | 78 +-
.../bean/utils/CssContentTypeFilter.java | 104 +-
.../mapviewer/bean/utils/CustomFilter.java | 102 +-
.../CustomHttpServletResponseWrapper.java | 496 +--
.../bean/utils/IPrimefacesUtils.java | 262 +-
.../JsfAjaxAccessControlAllowFilter.java | 88 +-
.../mapviewer/bean/utils/PrimefacesUtils.java | 248 +-
.../mapviewer/bean/utils/StartupBean.java | 384 +-
.../bean/utils/VersionResourceHandler.java | 222 +-
.../bean/utils/XFrameAccessControlFilter.java | 122 +-
.../mapviewer/bean/utils/package-info.java | 10 +-
.../converter/MiriamTypeConverter.java | 118 +-
.../mapviewer/converter/package-info.java | 12 +-
.../java/lcsb/mapviewer/events/Event.java | 22 +-
.../java/lcsb/mapviewer/events/Listener.java | 120 +-
.../mapviewer/events/ObjectAddedEvent.java | 80 +-
.../mapviewer/events/ObjectModifiedEvent.java | 78 +-
.../mapviewer/events/ObjectRemovedEvent.java | 80 +-
.../lcsb/mapviewer/events/package-info.java | 10 +-
.../MvAuthenticationFailureHandler.java | 72 +-
.../MvAuthenticationSuccessHandler.java | 136 +-
...vUsernamePasswordAuthenticationFilter.java | 86 +-
.../lcsb/mapviewer/security/package-info.java | 12 +-
1180 files changed, 150240 insertions(+), 150240 deletions(-)
diff --git a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyAction.java b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyAction.java
index c1da55c096..a3570d3324 100644
--- a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyAction.java
+++ b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyAction.java
@@ -1,90 +1,90 @@
-package lcsb.mapviewer.cdplugin.copypaste;
-
-import jp.sbi.celldesigner.MainWindow;
-import jp.sbi.celldesigner.plugin.PluginListOf;
-import jp.sbi.celldesigner.plugin.PluginReaction;
-import jp.sbi.celldesigner.plugin.PluginSBase;
-import jp.sbi.celldesigner.plugin.PluginSpecies;
-import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
-import lcsb.mapviewer.common.SystemClipboard;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-
-import org.apache.log4j.Logger;
-
-/**
- * CD Plugin action resposible for translating annotation stored in notes to xml
- * format stored in annotations.
- *
- * @author Piotr Gawron
- *
- */
-public class CopyAction extends CopyPasteAbstractAction {
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(CopyAction.class.getName());
-
- /**
- * Method that perform annotation of a celldesigner species listed in
- * speciesList.
- *
- * @param plug
- * - a plugin object
- * @param speciesList
- * - list of species to annotate
- * @param win
- * - main window of cell designer
- */
- public void performAnnotation(CopyPastePlugin plug, PluginListOf speciesList, MainWindow win) {
-
- // if list is empty then just return from the method
- if (speciesList.size() == 0) {
- return;
- }
-
- SystemClipboard sc = new SystemClipboard();
-
- this.setWindow(win);
- this.setPlug(plug);
-
- int size = speciesList.size();
-
- PluginSBase chosenElement = null;
- String id = "";
- for (int i = 0; i < size; i++) {
- PluginSBase element = speciesList.get(i);
- if (element instanceof PluginSpeciesAlias) {
- PluginSpeciesAlias alias = (PluginSpeciesAlias) element;
- PluginSpecies species = alias.getSpecies();
-
- if (chosenElement == null) {
- chosenElement = species;
- id = species.getId();
- } else if (id.compareTo(species.getId()) < 0) {
- chosenElement = species;
- id = species.getId();
- }
- } else if (element instanceof PluginReaction) {
- PluginReaction reaction = (PluginReaction) element;
- if (chosenElement == null) {
- chosenElement = reaction;
- id = reaction.getId();
- } else if (id.compareTo(reaction.getId()) < 0) {
- chosenElement = reaction;
- id = reaction.getId();
- }
- } else {
- logger.warn("Unknown class type :" + element.getClass());
- }
- }
-
- if (chosenElement != null) {
- try {
- sc.setClipboardContents(getCopyString(chosenElement.getAnnotationString(), chosenElement.getNotesString()));
- } catch (InvalidXmlSchemaException e) {
- logger.warn("Problem with creating copy-paste String", e);
- }
- }
- }
-
-}
+package lcsb.mapviewer.cdplugin.copypaste;
+
+import jp.sbi.celldesigner.MainWindow;
+import jp.sbi.celldesigner.plugin.PluginListOf;
+import jp.sbi.celldesigner.plugin.PluginReaction;
+import jp.sbi.celldesigner.plugin.PluginSBase;
+import jp.sbi.celldesigner.plugin.PluginSpecies;
+import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
+import lcsb.mapviewer.common.SystemClipboard;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+
+import org.apache.log4j.Logger;
+
+/**
+ * CD Plugin action resposible for translating annotation stored in notes to xml
+ * format stored in annotations.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CopyAction extends CopyPasteAbstractAction {
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(CopyAction.class.getName());
+
+ /**
+ * Method that perform annotation of a celldesigner species listed in
+ * speciesList.
+ *
+ * @param plug
+ * - a plugin object
+ * @param speciesList
+ * - list of species to annotate
+ * @param win
+ * - main window of cell designer
+ */
+ public void performAnnotation(CopyPastePlugin plug, PluginListOf speciesList, MainWindow win) {
+
+ // if list is empty then just return from the method
+ if (speciesList.size() == 0) {
+ return;
+ }
+
+ SystemClipboard sc = new SystemClipboard();
+
+ this.setWindow(win);
+ this.setPlug(plug);
+
+ int size = speciesList.size();
+
+ PluginSBase chosenElement = null;
+ String id = "";
+ for (int i = 0; i < size; i++) {
+ PluginSBase element = speciesList.get(i);
+ if (element instanceof PluginSpeciesAlias) {
+ PluginSpeciesAlias alias = (PluginSpeciesAlias) element;
+ PluginSpecies species = alias.getSpecies();
+
+ if (chosenElement == null) {
+ chosenElement = species;
+ id = species.getId();
+ } else if (id.compareTo(species.getId()) < 0) {
+ chosenElement = species;
+ id = species.getId();
+ }
+ } else if (element instanceof PluginReaction) {
+ PluginReaction reaction = (PluginReaction) element;
+ if (chosenElement == null) {
+ chosenElement = reaction;
+ id = reaction.getId();
+ } else if (id.compareTo(reaction.getId()) < 0) {
+ chosenElement = reaction;
+ id = reaction.getId();
+ }
+ } else {
+ logger.warn("Unknown class type :" + element.getClass());
+ }
+ }
+
+ if (chosenElement != null) {
+ try {
+ sc.setClipboardContents(getCopyString(chosenElement.getAnnotationString(), chosenElement.getNotesString()));
+ } catch (InvalidXmlSchemaException e) {
+ logger.warn("Problem with creating copy-paste String", e);
+ }
+ }
+ }
+
+}
diff --git a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractAction.java b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractAction.java
index 108d99b8d0..a84a45a303 100644
--- a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractAction.java
+++ b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractAction.java
@@ -1,186 +1,186 @@
-package lcsb.mapviewer.cdplugin.copypaste;
-
-import java.util.HashSet;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-
-import jp.sbi.celldesigner.MainWindow;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.XmlParser;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
-
-/**
- * This abstract class defines common function for {@link CopyAction} and
- * {@link PasteAction}.
- *
- * @author Piotr Gawron
- *
- */
-public class CopyPasteAbstractAction extends XmlParser {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(CopyPasteAbstractAction.class);
-
- /**
- * Prefix used for serialization/deserialization of {@link MiriamData} to
- * string stored in system clipboard.
- */
- private static final String PREFIX = "[MIRIAM]";
- /**
- * Plugin object which ran this action. This object is used to update
- * information about species
- */
- private CopyPastePlugin plug;
- /**
- * Object of CellDesigner main form.
- */
- private MainWindow window;
-
- /**
- * Serializes {@link MiriamData} into string that will be stored into system
- * clipboard.
- *
- * @param md
- * object to serialize
- * @return string representation of {@link MiriamData}
- */
- protected String serialize(MiriamData md) {
- return PREFIX + "\t" + md.getRelationType().getStringRepresentation() + "\t" + md.getDataType().getUris().get(0) + "\t" + md.getResource();
- }
-
- /**
- * Deserialize {@link MiriamData} from string creted by
- * {@link #serialize(MiriamData)} method.
- *
- * @param string
- * string representation of {@link MiriamData}
- * @return {@link MiriamData} obtained from input string
- */
- protected MiriamData deserialize(String string) {
- if (string == null) {
- return null;
- }
- String[] tmp = string.split("\t");
-
- // CHECKSTYLE:OFF
- if (tmp.length == 4) {
- if (PREFIX.equals(tmp[0])) {
- String relation = tmp[1];
- String uri = tmp[2];
- String resource = tmp[3];
- MiriamType mt = MiriamType.getTypeByUri(uri);
- MiriamRelationType mrt = MiriamRelationType.getTypeByStringRepresentation(relation);
- if (mt == null || mrt == null) {
- return null;
- }
- return new MiriamData(mrt, mt, resource);
- }
- }
- // CHECKSTYLE:ON
- return null;
- }
-
- /**
- * Returns serialized string of annotations and notes.
- *
- * @param annotationString
- * xml string representing annotations in CellDesigner
- * @param notesString
- * flat notes String
- * @return serialized string
- * @throws InvalidXmlSchemaException
- * thrown when xmlString is invalid
- */
- protected String getCopyString(String annotationString, String notesString) throws InvalidXmlSchemaException {
- XmlAnnotationParser xap = new XmlAnnotationParser();
- Set<MiriamData> set = xap.parse(annotationString);
- StringBuilder result = new StringBuilder();
- for (MiriamData md : set) {
- result.append(serialize(md) + "\n");
- }
- result.append(notesString);
- return result.toString();
- }
-
- /**
- * Deserialize string created by {@link #getCopyString(String, String)}
- * method. Used to create {@link MiriamData} set and notes from clipboard.
- *
- * @param value
- * string for deserialization
- *
- * @return {@link Pair} of {@link MiriamData} set and notes string
- */
- protected Pair<Set<MiriamData>, String> getAnnotationDataFromClipboardString(String value) {
- if (value == null) {
- return new Pair<Set<MiriamData>, String>(null, null);
- }
- String[] rows = value.split("\n");
-
- StringBuilder sb = new StringBuilder("");
-
- boolean miriam = true;
-
- Set<MiriamData> set = new HashSet<MiriamData>();
- for (int i = 0; i < rows.length; i++) {
- String row = rows[i];
- if (miriam) {
- MiriamData md = deserialize(row);
- if (md != null) {
- set.add(md);
- } else {
- miriam = false;
- }
- }
- if (!miriam) {
- sb.append(row);
- sb.append("\n");
- }
- }
- String notes = sb.toString().trim();
-
- return new Pair<Set<MiriamData>, String>(set, notes);
- }
-
- /**
- * @return the plug
- * @see #plug
- */
- protected CopyPastePlugin getPlug() {
- return plug;
- }
-
- /**
- * @param plug
- * the plug to set
- * @see #plug
- */
- protected void setPlug(CopyPastePlugin plug) {
- this.plug = plug;
- }
-
- /**
- * @return the window
- * @see #window
- */
- protected MainWindow getWindow() {
- return window;
- }
-
- /**
- * @param window
- * the window to set
- * @see #window
- */
- protected void setWindow(MainWindow window) {
- this.window = window;
- }
-
+package lcsb.mapviewer.cdplugin.copypaste;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+
+import jp.sbi.celldesigner.MainWindow;
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
+
+/**
+ * This abstract class defines common function for {@link CopyAction} and
+ * {@link PasteAction}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CopyPasteAbstractAction extends XmlParser {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(CopyPasteAbstractAction.class);
+
+ /**
+ * Prefix used for serialization/deserialization of {@link MiriamData} to
+ * string stored in system clipboard.
+ */
+ private static final String PREFIX = "[MIRIAM]";
+ /**
+ * Plugin object which ran this action. This object is used to update
+ * information about species
+ */
+ private CopyPastePlugin plug;
+ /**
+ * Object of CellDesigner main form.
+ */
+ private MainWindow window;
+
+ /**
+ * Serializes {@link MiriamData} into string that will be stored into system
+ * clipboard.
+ *
+ * @param md
+ * object to serialize
+ * @return string representation of {@link MiriamData}
+ */
+ protected String serialize(MiriamData md) {
+ return PREFIX + "\t" + md.getRelationType().getStringRepresentation() + "\t" + md.getDataType().getUris().get(0) + "\t" + md.getResource();
+ }
+
+ /**
+ * Deserialize {@link MiriamData} from string creted by
+ * {@link #serialize(MiriamData)} method.
+ *
+ * @param string
+ * string representation of {@link MiriamData}
+ * @return {@link MiriamData} obtained from input string
+ */
+ protected MiriamData deserialize(String string) {
+ if (string == null) {
+ return null;
+ }
+ String[] tmp = string.split("\t");
+
+ // CHECKSTYLE:OFF
+ if (tmp.length == 4) {
+ if (PREFIX.equals(tmp[0])) {
+ String relation = tmp[1];
+ String uri = tmp[2];
+ String resource = tmp[3];
+ MiriamType mt = MiriamType.getTypeByUri(uri);
+ MiriamRelationType mrt = MiriamRelationType.getTypeByStringRepresentation(relation);
+ if (mt == null || mrt == null) {
+ return null;
+ }
+ return new MiriamData(mrt, mt, resource);
+ }
+ }
+ // CHECKSTYLE:ON
+ return null;
+ }
+
+ /**
+ * Returns serialized string of annotations and notes.
+ *
+ * @param annotationString
+ * xml string representing annotations in CellDesigner
+ * @param notesString
+ * flat notes String
+ * @return serialized string
+ * @throws InvalidXmlSchemaException
+ * thrown when xmlString is invalid
+ */
+ protected String getCopyString(String annotationString, String notesString) throws InvalidXmlSchemaException {
+ XmlAnnotationParser xap = new XmlAnnotationParser();
+ Set<MiriamData> set = xap.parse(annotationString);
+ StringBuilder result = new StringBuilder();
+ for (MiriamData md : set) {
+ result.append(serialize(md) + "\n");
+ }
+ result.append(notesString);
+ return result.toString();
+ }
+
+ /**
+ * Deserialize string created by {@link #getCopyString(String, String)}
+ * method. Used to create {@link MiriamData} set and notes from clipboard.
+ *
+ * @param value
+ * string for deserialization
+ *
+ * @return {@link Pair} of {@link MiriamData} set and notes string
+ */
+ protected Pair<Set<MiriamData>, String> getAnnotationDataFromClipboardString(String value) {
+ if (value == null) {
+ return new Pair<Set<MiriamData>, String>(null, null);
+ }
+ String[] rows = value.split("\n");
+
+ StringBuilder sb = new StringBuilder("");
+
+ boolean miriam = true;
+
+ Set<MiriamData> set = new HashSet<MiriamData>();
+ for (int i = 0; i < rows.length; i++) {
+ String row = rows[i];
+ if (miriam) {
+ MiriamData md = deserialize(row);
+ if (md != null) {
+ set.add(md);
+ } else {
+ miriam = false;
+ }
+ }
+ if (!miriam) {
+ sb.append(row);
+ sb.append("\n");
+ }
+ }
+ String notes = sb.toString().trim();
+
+ return new Pair<Set<MiriamData>, String>(set, notes);
+ }
+
+ /**
+ * @return the plug
+ * @see #plug
+ */
+ protected CopyPastePlugin getPlug() {
+ return plug;
+ }
+
+ /**
+ * @param plug
+ * the plug to set
+ * @see #plug
+ */
+ protected void setPlug(CopyPastePlugin plug) {
+ this.plug = plug;
+ }
+
+ /**
+ * @return the window
+ * @see #window
+ */
+ protected MainWindow getWindow() {
+ return window;
+ }
+
+ /**
+ * @param window
+ * the window to set
+ * @see #window
+ */
+ protected void setWindow(MainWindow window) {
+ this.window = window;
+ }
+
}
\ No newline at end of file
diff --git a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPastePlugin.java b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPastePlugin.java
index cffc826371..8e2d09a645 100644
--- a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPastePlugin.java
+++ b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPastePlugin.java
@@ -1,131 +1,131 @@
-package lcsb.mapviewer.cdplugin.copypaste;
-
-import java.awt.KeyEventDispatcher;
-import java.awt.KeyboardFocusManager;
-import java.awt.event.KeyEvent;
-
-import jp.sbi.celldesigner.MainWindow;
-import jp.sbi.celldesigner.plugin.CellDesignerPlugin;
-import jp.sbi.celldesigner.plugin.PluginSBase;
-
-import org.apache.log4j.Logger;
-
-/**
- * This class represent a plugin to cell designer with copy past functionality
- * that allows to copy and paste notes and annotations of species.
- *
- * It overrides:
- * <ul>
- * <li>ALT + CTRL + C shortcut - copy annotations from selected element into
- * system clipboard, if many elements are selected then copy from the one with
- * the lowest id,</li>
- * <li>ALT + CTRL + V shortcut - paste annotations from clipboard into selected
- * element(s), if many elements are selected then all elements will be modified,
- * </li>
- * </ul>
- *
- * @author Piotr Gawron
- *
- */
-public class CopyPastePlugin extends CellDesignerPlugin {
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(CopyPastePlugin.class.getName());
- /**
- * Main window of cell designer.
- */
- private MainWindow win;
-
- /**
- * Paste action.
- */
- private PastePluginAction ppa;
-
- /**
- * Paste action.
- */
- private CopyPluginAction cpa;
-
- /**
- * Default constructor. Creates menu and InfoFrame.
- */
- public CopyPastePlugin() {
- try {
- // PropertyConfigurator.configure("D:/log4j.properties");
- logger.debug("Loading copy-paste plugin...");
-
- win = MainWindow.getLastInstance();
-
- ppa = new PastePluginAction(this, win);
- cpa = new CopyPluginAction(this, win);
-
- // create keyboard listener for shortcuts
- KeyboardFocusManager.getCurrentKeyboardFocusManager().addKeyEventDispatcher(new KeyEventDispatcher() {
- public boolean dispatchKeyEvent(KeyEvent e) {
- switch (e.getID()) {
- case KeyEvent.KEY_PRESSED:
- if (e.getKeyCode() == java.awt.event.KeyEvent.VK_V//
- && e.isControlDown()//
- && e.isAltDown()//
- ) {
- ppa.myActionPerformed(null);
- return true;
- } else if (e.getKeyCode() == java.awt.event.KeyEvent.VK_C//
- && e.isControlDown()//
- && e.isAltDown()//
- ) {
- cpa.myActionPerformed(null);
- return true;
- } else {
- return false;
- }
- default:
- return false;
- }
- }
- });
-
- } catch (Exception exception) {
- logger.error(exception, exception);
- }
- }
-
- // CHECKSTYLE:OFF
- @Override
- public void SBaseAdded(PluginSBase arg0) {
-
- }
-
- @Override
- public void SBaseChanged(PluginSBase arg0) {
-
- }
-
- @Override
- public void SBaseDeleted(PluginSBase arg0) {
- }
-
- // CHECKSTYLE:ON
-
- @Override
- public void addPluginMenu() {
- }
-
- @Override
- public void modelClosed(PluginSBase arg0) {
-
- }
-
- @Override
- public void modelOpened(PluginSBase arg0) {
-
- }
-
- @Override
- public void modelSelectChanged(PluginSBase arg0) {
-
- }
-
+package lcsb.mapviewer.cdplugin.copypaste;
+
+import java.awt.KeyEventDispatcher;
+import java.awt.KeyboardFocusManager;
+import java.awt.event.KeyEvent;
+
+import jp.sbi.celldesigner.MainWindow;
+import jp.sbi.celldesigner.plugin.CellDesignerPlugin;
+import jp.sbi.celldesigner.plugin.PluginSBase;
+
+import org.apache.log4j.Logger;
+
+/**
+ * This class represent a plugin to cell designer with copy past functionality
+ * that allows to copy and paste notes and annotations of species.
+ *
+ * It overrides:
+ * <ul>
+ * <li>ALT + CTRL + C shortcut - copy annotations from selected element into
+ * system clipboard, if many elements are selected then copy from the one with
+ * the lowest id,</li>
+ * <li>ALT + CTRL + V shortcut - paste annotations from clipboard into selected
+ * element(s), if many elements are selected then all elements will be modified,
+ * </li>
+ * </ul>
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CopyPastePlugin extends CellDesignerPlugin {
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(CopyPastePlugin.class.getName());
+ /**
+ * Main window of cell designer.
+ */
+ private MainWindow win;
+
+ /**
+ * Paste action.
+ */
+ private PastePluginAction ppa;
+
+ /**
+ * Paste action.
+ */
+ private CopyPluginAction cpa;
+
+ /**
+ * Default constructor. Creates menu and InfoFrame.
+ */
+ public CopyPastePlugin() {
+ try {
+ // PropertyConfigurator.configure("D:/log4j.properties");
+ logger.debug("Loading copy-paste plugin...");
+
+ win = MainWindow.getLastInstance();
+
+ ppa = new PastePluginAction(this, win);
+ cpa = new CopyPluginAction(this, win);
+
+ // create keyboard listener for shortcuts
+ KeyboardFocusManager.getCurrentKeyboardFocusManager().addKeyEventDispatcher(new KeyEventDispatcher() {
+ public boolean dispatchKeyEvent(KeyEvent e) {
+ switch (e.getID()) {
+ case KeyEvent.KEY_PRESSED:
+ if (e.getKeyCode() == java.awt.event.KeyEvent.VK_V//
+ && e.isControlDown()//
+ && e.isAltDown()//
+ ) {
+ ppa.myActionPerformed(null);
+ return true;
+ } else if (e.getKeyCode() == java.awt.event.KeyEvent.VK_C//
+ && e.isControlDown()//
+ && e.isAltDown()//
+ ) {
+ cpa.myActionPerformed(null);
+ return true;
+ } else {
+ return false;
+ }
+ default:
+ return false;
+ }
+ }
+ });
+
+ } catch (Exception exception) {
+ logger.error(exception, exception);
+ }
+ }
+
+ // CHECKSTYLE:OFF
+ @Override
+ public void SBaseAdded(PluginSBase arg0) {
+
+ }
+
+ @Override
+ public void SBaseChanged(PluginSBase arg0) {
+
+ }
+
+ @Override
+ public void SBaseDeleted(PluginSBase arg0) {
+ }
+
+ // CHECKSTYLE:ON
+
+ @Override
+ public void addPluginMenu() {
+ }
+
+ @Override
+ public void modelClosed(PluginSBase arg0) {
+
+ }
+
+ @Override
+ public void modelOpened(PluginSBase arg0) {
+
+ }
+
+ @Override
+ public void modelSelectChanged(PluginSBase arg0) {
+
+ }
+
}
\ No newline at end of file
diff --git a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPluginAction.java b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPluginAction.java
index 5b6ce570dc..8fee9aee00 100644
--- a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPluginAction.java
+++ b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPluginAction.java
@@ -1,62 +1,62 @@
-package lcsb.mapviewer.cdplugin.copypaste;
-
-import java.awt.event.ActionEvent;
-
-import jp.sbi.celldesigner.MainWindow;
-import jp.sbi.celldesigner.plugin.PluginAction;
-import jp.sbi.celldesigner.plugin.PluginListOf;
-
-import org.apache.log4j.Logger;
-
-/**
- * This class represent action that copy species/reaction annotations and notes
- * into clipboard.
- *
- * @author Piotr Gawron
- *
- */
-public class CopyPluginAction extends PluginAction {
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(PasteAction.class.getName());
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Plugin that access this action.
- */
- private CopyPastePlugin plug = null;
- /**
- * Main window of CellDesigner.
- */
- private MainWindow window;
-
- /**
- * Default constructor.
- *
- * @param plugin
- * {@link #plug}
- * @param win
- * {@link #window}
- */
- public CopyPluginAction(CopyPastePlugin plugin, MainWindow win) {
- this.plug = plugin;
- this.window = win;
- }
-
- @Override
- public void myActionPerformed(ActionEvent e) {
- try {
- CopyAction annotateAction = new CopyAction();
- PluginListOf list = plug.getSelectedAllNode();
- annotateAction.performAnnotation(plug, list, window);
- } catch (Exception ex) {
- logger.error(ex, ex);
- }
- }
-
+package lcsb.mapviewer.cdplugin.copypaste;
+
+import java.awt.event.ActionEvent;
+
+import jp.sbi.celldesigner.MainWindow;
+import jp.sbi.celldesigner.plugin.PluginAction;
+import jp.sbi.celldesigner.plugin.PluginListOf;
+
+import org.apache.log4j.Logger;
+
+/**
+ * This class represent action that copy species/reaction annotations and notes
+ * into clipboard.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CopyPluginAction extends PluginAction {
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(PasteAction.class.getName());
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Plugin that access this action.
+ */
+ private CopyPastePlugin plug = null;
+ /**
+ * Main window of CellDesigner.
+ */
+ private MainWindow window;
+
+ /**
+ * Default constructor.
+ *
+ * @param plugin
+ * {@link #plug}
+ * @param win
+ * {@link #window}
+ */
+ public CopyPluginAction(CopyPastePlugin plugin, MainWindow win) {
+ this.plug = plugin;
+ this.window = win;
+ }
+
+ @Override
+ public void myActionPerformed(ActionEvent e) {
+ try {
+ CopyAction annotateAction = new CopyAction();
+ PluginListOf list = plug.getSelectedAllNode();
+ annotateAction.performAnnotation(plug, list, window);
+ } catch (Exception ex) {
+ logger.error(ex, ex);
+ }
+ }
+
}
\ No newline at end of file
diff --git a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/PasteAction.java b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/PasteAction.java
index 1829de262f..d554598646 100644
--- a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/PasteAction.java
+++ b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/PasteAction.java
@@ -1,82 +1,82 @@
-package lcsb.mapviewer.cdplugin.copypaste;
-
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-
-import jp.sbi.celldesigner.MainWindow;
-import jp.sbi.celldesigner.plugin.PluginListOf;
-import jp.sbi.celldesigner.plugin.PluginReaction;
-import jp.sbi.celldesigner.plugin.PluginSBase;
-import jp.sbi.celldesigner.plugin.PluginSpecies;
-import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.SystemClipboard;
-import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
-import lcsb.mapviewer.model.map.MiriamData;
-
-/**
- * CD Plugin action resposible for translating annotation stored in notes to xml
- * format stored in annotations.
- *
- * @author Piotr Gawron
- *
- */
-public class PasteAction extends CopyPasteAbstractAction {
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(PasteAction.class.getName());
-
- /**
- * Method that perform annotation of a celldesigner species listed in
- * speciesList.
- *
- * @param plug
- * - a plugin object
- * @param speciesList
- * - list of species to annotate
- * @param win
- * - main window of cell designer
- */
- public void performAnnotation(CopyPastePlugin plug, PluginListOf speciesList, MainWindow win) {
-
- XmlAnnotationParser xap = new XmlAnnotationParser();
-
- // if list is empty then just return from the method
- if (speciesList.size() == 0) {
- return;
- }
-
- SystemClipboard sc = new SystemClipboard();
- String value = sc.getClipboardContents();
-
- Pair<Set<MiriamData>, String> data = getAnnotationDataFromClipboardString(value);
- String notes = data.getRight();
- Set<MiriamData> set = data.getLeft();
-
- this.setWindow(win);
- this.setPlug(plug);
-
- int size = speciesList.size();
- for (int i = 0; i < size; i++) {
- PluginSBase element = speciesList.get(i);
- if (element instanceof PluginSpeciesAlias) {
- PluginSpeciesAlias alias = (PluginSpeciesAlias) element;
- PluginSpecies species = alias.getSpecies();
- species.setNotes(notes);
- species.setAnnotationString(xap.dataSetToXmlString(set));
- plug.notifySBaseChanged(element);
- plug.notifySBaseChanged(species);
- } else if (element instanceof PluginReaction) {
- PluginReaction reaction = (PluginReaction) element;
- reaction.setNotes(notes);
- reaction.setAnnotationString(xap.dataSetToXmlString(set));
- plug.notifySBaseChanged(element);
- } else {
- logger.warn("Unknown class type :" + element.getClass());
- }
- }
- }
-
-}
+package lcsb.mapviewer.cdplugin.copypaste;
+
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+
+import jp.sbi.celldesigner.MainWindow;
+import jp.sbi.celldesigner.plugin.PluginListOf;
+import jp.sbi.celldesigner.plugin.PluginReaction;
+import jp.sbi.celldesigner.plugin.PluginSBase;
+import jp.sbi.celldesigner.plugin.PluginSpecies;
+import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.SystemClipboard;
+import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
+import lcsb.mapviewer.model.map.MiriamData;
+
+/**
+ * CD Plugin action resposible for translating annotation stored in notes to xml
+ * format stored in annotations.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class PasteAction extends CopyPasteAbstractAction {
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(PasteAction.class.getName());
+
+ /**
+ * Method that perform annotation of a celldesigner species listed in
+ * speciesList.
+ *
+ * @param plug
+ * - a plugin object
+ * @param speciesList
+ * - list of species to annotate
+ * @param win
+ * - main window of cell designer
+ */
+ public void performAnnotation(CopyPastePlugin plug, PluginListOf speciesList, MainWindow win) {
+
+ XmlAnnotationParser xap = new XmlAnnotationParser();
+
+ // if list is empty then just return from the method
+ if (speciesList.size() == 0) {
+ return;
+ }
+
+ SystemClipboard sc = new SystemClipboard();
+ String value = sc.getClipboardContents();
+
+ Pair<Set<MiriamData>, String> data = getAnnotationDataFromClipboardString(value);
+ String notes = data.getRight();
+ Set<MiriamData> set = data.getLeft();
+
+ this.setWindow(win);
+ this.setPlug(plug);
+
+ int size = speciesList.size();
+ for (int i = 0; i < size; i++) {
+ PluginSBase element = speciesList.get(i);
+ if (element instanceof PluginSpeciesAlias) {
+ PluginSpeciesAlias alias = (PluginSpeciesAlias) element;
+ PluginSpecies species = alias.getSpecies();
+ species.setNotes(notes);
+ species.setAnnotationString(xap.dataSetToXmlString(set));
+ plug.notifySBaseChanged(element);
+ plug.notifySBaseChanged(species);
+ } else if (element instanceof PluginReaction) {
+ PluginReaction reaction = (PluginReaction) element;
+ reaction.setNotes(notes);
+ reaction.setAnnotationString(xap.dataSetToXmlString(set));
+ plug.notifySBaseChanged(element);
+ } else {
+ logger.warn("Unknown class type :" + element.getClass());
+ }
+ }
+ }
+
+}
diff --git a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/PastePluginAction.java b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/PastePluginAction.java
index e0c7289c45..16e44f3ff2 100644
--- a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/PastePluginAction.java
+++ b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/PastePluginAction.java
@@ -1,61 +1,61 @@
-package lcsb.mapviewer.cdplugin.copypaste;
-
-import java.awt.event.ActionEvent;
-
-import jp.sbi.celldesigner.MainWindow;
-import jp.sbi.celldesigner.plugin.PluginAction;
-import jp.sbi.celldesigner.plugin.PluginListOf;
-
-import org.apache.log4j.Logger;
-
-/**
- * This class represent action that paste annotations and notes from clipboard
- * into selected species/reactions.
- *
- * @author Piotr Gawron
- *
- */
-public class PastePluginAction extends PluginAction {
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(PasteAction.class.getName());
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- /**
- * Plugin that access this action.
- */
- private CopyPastePlugin plug = null;
- /**
- * Main window of CellDesigner.
- */
- private MainWindow window;
-
- /**
- * Default constructor.
- *
- * @param plugin
- * {@link #plug}
- * @param win
- * {@link #window}
- */
- public PastePluginAction(CopyPastePlugin plugin, MainWindow win) {
- this.plug = plugin;
- this.window = win;
- }
-
- @Override
- public void myActionPerformed(ActionEvent e) {
- try {
- PasteAction annotateAction = new PasteAction();
- PluginListOf list = plug.getSelectedAllNode();
- annotateAction.performAnnotation(plug, list, window);
- } catch (Exception ex) {
- logger.error(ex, ex);
- }
- }
-
+package lcsb.mapviewer.cdplugin.copypaste;
+
+import java.awt.event.ActionEvent;
+
+import jp.sbi.celldesigner.MainWindow;
+import jp.sbi.celldesigner.plugin.PluginAction;
+import jp.sbi.celldesigner.plugin.PluginListOf;
+
+import org.apache.log4j.Logger;
+
+/**
+ * This class represent action that paste annotations and notes from clipboard
+ * into selected species/reactions.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class PastePluginAction extends PluginAction {
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(PasteAction.class.getName());
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ /**
+ * Plugin that access this action.
+ */
+ private CopyPastePlugin plug = null;
+ /**
+ * Main window of CellDesigner.
+ */
+ private MainWindow window;
+
+ /**
+ * Default constructor.
+ *
+ * @param plugin
+ * {@link #plug}
+ * @param win
+ * {@link #window}
+ */
+ public PastePluginAction(CopyPastePlugin plugin, MainWindow win) {
+ this.plug = plugin;
+ this.window = win;
+ }
+
+ @Override
+ public void myActionPerformed(ActionEvent e) {
+ try {
+ PasteAction annotateAction = new PasteAction();
+ PluginListOf list = plug.getSelectedAllNode();
+ annotateAction.performAnnotation(plug, list, window);
+ } catch (Exception ex) {
+ logger.error(ex, ex);
+ }
+ }
+
}
\ No newline at end of file
diff --git a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/package-info.java b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/package-info.java
index 161c4ee44c..aea1cfceea 100644
--- a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/package-info.java
+++ b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/package-info.java
@@ -1,9 +1,9 @@
-/**
- * In this package there is implementation of simple plugin that allows to copy
- * and paste annotations and notes from CellDesigner elements into other
- * CellDesigner elements. It uses system clipboard to store data. More
- * information can be found in
- * {@link lcsb.mapviewer.cdplugin.copypaste.CopyPastePlugin}.
- */
-package lcsb.mapviewer.cdplugin.copypaste;
-
+/**
+ * In this package there is implementation of simple plugin that allows to copy
+ * and paste annotations and notes from CellDesigner elements into other
+ * CellDesigner elements. It uses system clipboard to store data. More
+ * information can be found in
+ * {@link lcsb.mapviewer.cdplugin.copypaste.CopyPastePlugin}.
+ */
+package lcsb.mapviewer.cdplugin.copypaste;
+
diff --git a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/InfoFrame.java b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/InfoFrame.java
index a09fe36500..f480bc4101 100644
--- a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/InfoFrame.java
+++ b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/InfoFrame.java
@@ -1,272 +1,272 @@
-package lcsb.mapviewer.cdplugin.info;
-
-import java.awt.Component;
-import java.awt.Container;
-import java.awt.Dimension;
-import java.awt.Font;
-import java.awt.GridLayout;
-import java.awt.Toolkit;
-import java.util.ArrayList;
-
-import javax.swing.Box;
-import javax.swing.BoxLayout;
-import javax.swing.JFrame;
-import javax.swing.JLabel;
-import javax.swing.JPanel;
-import javax.swing.JScrollPane;
-import javax.swing.JTextArea;
-import javax.swing.JTextField;
-
-import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
-
-import org.apache.log4j.Logger;
-
-/**
- * This class represent a frame that visualise MIRIAM data and notes for a
- * species. Only one instance of JFrame is stored in the class (only one window
- * of this type can be created).
- *
- * @author Piotr Gawron
- *
- */
-public final class InfoFrame {
-
- /**
- * What should be the distance between description of different aliases.
- */
- private static final int DISTANCE_BETWEEN_PANELS = 5;
-
- /**
- * How many columns should be in the info panel grid.
- */
- private static final int GRID_INFO_COL_NUMBER = 2;
-
- /**
- * How many rows should be in the info panel grid.
- */
- private static final int GRID_INFO_ROW_NUMBER = 3;
-
- /**
- * Frame height.
- */
- private static final int FRAME_HEIGHT = 200;
-
- /**
- * Frame width.
- */
- private static final int FRAME_WIDTH = 200;
-
- /**
- * Font size of the caption label.
- */
- private static final int CAPTION_FONT_SIZE = 18;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(InfoFrame.class.getName());
-
- /**
- * Instance of the JFrame representation of windows.
- */
- private JFrame frame = null;
-
- /**
- * Singleton instance of this class (there can be only one instance of the
- * frame).
- */
- private static InfoFrame instance = null;
-
- /**
- * Font used for captions.
- */
- private Font captionFont = new Font("Default", Font.PLAIN, CAPTION_FONT_SIZE);
-
- /**
- * List of selected aliases.
- */
- private ArrayList<PluginSpeciesAlias> species = new ArrayList<PluginSpeciesAlias>();
-
- /**
- * Default constructor.
- */
- private InfoFrame() {
- int width = FRAME_WIDTH;
- int height = FRAME_HEIGHT;
-
- // check the resolution of the screen
- Toolkit tk = Toolkit.getDefaultToolkit();
- Dimension screenSize = tk.getScreenSize();
- int screenHeight = screenSize.height;
- int screenWidth = screenSize.width;
-
- // if the resultion of the screen changed in a meantime adjust position to
- // be
- // visible on the screen
- width = Math.min(width, screenWidth);
- height = Math.min(height, screenHeight);
-
- int posX = (screenWidth - width) / 2;
- int posY = (screenHeight - height) / 2;
-
- frame = new JFrame("Element information");
- frame.setSize(width, height);
- frame.setLocation(posX, posY);
- frame.setAlwaysOnTop(true);
- frame.setVisible(false);
- }
-
- /**
- * Returns singleton instance of the class.
- *
- * @return singleton instance of this class
- */
- public static InfoFrame getInstance() {
- if (InfoFrame.instance == null) {
- instance = new InfoFrame();
- }
- return instance;
- }
-
- /**
- * Set visible flag for {@link #frame}.
- *
- * @param visible
- * should the frame be visible or not
- */
- public void setVisible(boolean visible) {
- frame.setVisible(visible);
- }
-
- /**
- * This method assign a set of species to this form.
- *
- * @param species
- * - species to be shown in the form
- */
- public void setSpecies(ArrayList<PluginSpeciesAlias> species) {
- this.species = species;
- updateSpecies();
- }
-
- /**
- * Updates information about species in the form.
- */
- protected void updateSpecies() {
- int panels = species.size() + 1;
-
- JPanel controlArea = new JPanel(new GridLayout(panels, 1));
- controlArea.setLayout(new BoxLayout(controlArea, BoxLayout.Y_AXIS));
- // for every species create a panel and add it to general form
- for (PluginSpeciesAlias sp : this.species) {
- JPanel panel = getPanelViewForSpecies(sp);
- controlArea.add(panel);
- }
- // after adding all species add a text area which is "invisible", the main
- // purpose of it is to fill the empty space in the form
- JTextArea text = new JTextArea();
- text.setEditable(false);
- text.setBackground(frame.getBackground());
- controlArea.add(text);
-
- Container content = frame.getContentPane();
- content.removeAll();
-
- // the whole panel should be scrollable
- JScrollPane scrollBar = new JScrollPane(controlArea, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
- scrollBar.setPreferredSize(new Dimension(0, 0));
- content.add(scrollBar);
-
- frame.validate();
- }
-
- /**
- * This method create a panel for a species with all information to be
- * presented.
- *
- * @param species
- * CellDesigner species alias
- * @return {@link JPanel} object with information about species
- */
- private JPanel getPanelViewForSpecies(PluginSpeciesAlias species) {
- JPanel result = new JPanel();
- result.setLayout(new BoxLayout(result, BoxLayout.Y_AXIS));
-
- // create a caption
- JPanel tmpPanel = new JPanel(new GridLayout(GRID_INFO_ROW_NUMBER, GRID_INFO_COL_NUMBER));
- JLabel label = new JLabel("Element: ", JLabel.RIGHT);
- label.setFont(captionFont);
- tmpPanel.add(label, Component.RIGHT_ALIGNMENT);
- JTextField textField = new JTextField(species.getSpecies().getName(), JLabel.LEFT);
- textField.setFont(captionFont);
- textField.setEditable(false);
- tmpPanel.add(textField, Component.LEFT_ALIGNMENT);
-
- tmpPanel.add(new JLabel("Alias id: ", JLabel.RIGHT), Component.RIGHT_ALIGNMENT);
- textField = new JTextField(species.getAliasID(), JLabel.LEFT);
- textField.setEditable(false);
- tmpPanel.add(textField, Component.LEFT_ALIGNMENT);
-
- tmpPanel.add(new JLabel("Species id: ", JLabel.RIGHT), Component.RIGHT_ALIGNMENT);
- textField = new JTextField(species.getSpecies().getId(), JLabel.LEFT);
- textField.setEditable(false);
- tmpPanel.add(textField, Component.LEFT_ALIGNMENT);
-
- result.add(tmpPanel);
-
- // add empty space between labels
- result.add(Box.createRigidArea(new Dimension(DISTANCE_BETWEEN_PANELS, DISTANCE_BETWEEN_PANELS)));
-
- return result;
- }
-
- /**
- * Returns info if the frame is visible.
- *
- * @return info if the frame is visible
- */
- public boolean isVisible() {
- return frame.isVisible();
- }
-
- /**
- * Sets frame title.
- *
- * @param title
- * title of the frame
- */
- public void setTitle(String title) {
- frame.setTitle(title);
- }
-
- /**
- * Returns frame title.
- *
- * @return frame title
- */
- public JFrame getFrame() {
- return frame;
- }
-
- /**
- * Set {@link JFrame#defaultCloseOperation}.
- *
- * @param type
- * new {@link JFrame#defaultCloseOperation} value
- */
- public void setDefaultCloseOperation(int type) {
- frame.setDefaultCloseOperation(type);
- }
-
- /**
- * Set {@link JFrame#setAlwaysOnTop(boolean)}.
- *
- * @param always
- * new {@link JFrame#isAlwaysOnTop()} value
- */
- public void setAlwaysOnTop(boolean always) {
- frame.setAlwaysOnTop(always);
- }
-
-}
+package lcsb.mapviewer.cdplugin.info;
+
+import java.awt.Component;
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.GridLayout;
+import java.awt.Toolkit;
+import java.util.ArrayList;
+
+import javax.swing.Box;
+import javax.swing.BoxLayout;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+import javax.swing.JTextField;
+
+import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
+
+import org.apache.log4j.Logger;
+
+/**
+ * This class represent a frame that visualise MIRIAM data and notes for a
+ * species. Only one instance of JFrame is stored in the class (only one window
+ * of this type can be created).
+ *
+ * @author Piotr Gawron
+ *
+ */
+public final class InfoFrame {
+
+ /**
+ * What should be the distance between description of different aliases.
+ */
+ private static final int DISTANCE_BETWEEN_PANELS = 5;
+
+ /**
+ * How many columns should be in the info panel grid.
+ */
+ private static final int GRID_INFO_COL_NUMBER = 2;
+
+ /**
+ * How many rows should be in the info panel grid.
+ */
+ private static final int GRID_INFO_ROW_NUMBER = 3;
+
+ /**
+ * Frame height.
+ */
+ private static final int FRAME_HEIGHT = 200;
+
+ /**
+ * Frame width.
+ */
+ private static final int FRAME_WIDTH = 200;
+
+ /**
+ * Font size of the caption label.
+ */
+ private static final int CAPTION_FONT_SIZE = 18;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(InfoFrame.class.getName());
+
+ /**
+ * Instance of the JFrame representation of windows.
+ */
+ private JFrame frame = null;
+
+ /**
+ * Singleton instance of this class (there can be only one instance of the
+ * frame).
+ */
+ private static InfoFrame instance = null;
+
+ /**
+ * Font used for captions.
+ */
+ private Font captionFont = new Font("Default", Font.PLAIN, CAPTION_FONT_SIZE);
+
+ /**
+ * List of selected aliases.
+ */
+ private ArrayList<PluginSpeciesAlias> species = new ArrayList<PluginSpeciesAlias>();
+
+ /**
+ * Default constructor.
+ */
+ private InfoFrame() {
+ int width = FRAME_WIDTH;
+ int height = FRAME_HEIGHT;
+
+ // check the resolution of the screen
+ Toolkit tk = Toolkit.getDefaultToolkit();
+ Dimension screenSize = tk.getScreenSize();
+ int screenHeight = screenSize.height;
+ int screenWidth = screenSize.width;
+
+ // if the resultion of the screen changed in a meantime adjust position to
+ // be
+ // visible on the screen
+ width = Math.min(width, screenWidth);
+ height = Math.min(height, screenHeight);
+
+ int posX = (screenWidth - width) / 2;
+ int posY = (screenHeight - height) / 2;
+
+ frame = new JFrame("Element information");
+ frame.setSize(width, height);
+ frame.setLocation(posX, posY);
+ frame.setAlwaysOnTop(true);
+ frame.setVisible(false);
+ }
+
+ /**
+ * Returns singleton instance of the class.
+ *
+ * @return singleton instance of this class
+ */
+ public static InfoFrame getInstance() {
+ if (InfoFrame.instance == null) {
+ instance = new InfoFrame();
+ }
+ return instance;
+ }
+
+ /**
+ * Set visible flag for {@link #frame}.
+ *
+ * @param visible
+ * should the frame be visible or not
+ */
+ public void setVisible(boolean visible) {
+ frame.setVisible(visible);
+ }
+
+ /**
+ * This method assign a set of species to this form.
+ *
+ * @param species
+ * - species to be shown in the form
+ */
+ public void setSpecies(ArrayList<PluginSpeciesAlias> species) {
+ this.species = species;
+ updateSpecies();
+ }
+
+ /**
+ * Updates information about species in the form.
+ */
+ protected void updateSpecies() {
+ int panels = species.size() + 1;
+
+ JPanel controlArea = new JPanel(new GridLayout(panels, 1));
+ controlArea.setLayout(new BoxLayout(controlArea, BoxLayout.Y_AXIS));
+ // for every species create a panel and add it to general form
+ for (PluginSpeciesAlias sp : this.species) {
+ JPanel panel = getPanelViewForSpecies(sp);
+ controlArea.add(panel);
+ }
+ // after adding all species add a text area which is "invisible", the main
+ // purpose of it is to fill the empty space in the form
+ JTextArea text = new JTextArea();
+ text.setEditable(false);
+ text.setBackground(frame.getBackground());
+ controlArea.add(text);
+
+ Container content = frame.getContentPane();
+ content.removeAll();
+
+ // the whole panel should be scrollable
+ JScrollPane scrollBar = new JScrollPane(controlArea, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
+ scrollBar.setPreferredSize(new Dimension(0, 0));
+ content.add(scrollBar);
+
+ frame.validate();
+ }
+
+ /**
+ * This method create a panel for a species with all information to be
+ * presented.
+ *
+ * @param species
+ * CellDesigner species alias
+ * @return {@link JPanel} object with information about species
+ */
+ private JPanel getPanelViewForSpecies(PluginSpeciesAlias species) {
+ JPanel result = new JPanel();
+ result.setLayout(new BoxLayout(result, BoxLayout.Y_AXIS));
+
+ // create a caption
+ JPanel tmpPanel = new JPanel(new GridLayout(GRID_INFO_ROW_NUMBER, GRID_INFO_COL_NUMBER));
+ JLabel label = new JLabel("Element: ", JLabel.RIGHT);
+ label.setFont(captionFont);
+ tmpPanel.add(label, Component.RIGHT_ALIGNMENT);
+ JTextField textField = new JTextField(species.getSpecies().getName(), JLabel.LEFT);
+ textField.setFont(captionFont);
+ textField.setEditable(false);
+ tmpPanel.add(textField, Component.LEFT_ALIGNMENT);
+
+ tmpPanel.add(new JLabel("Alias id: ", JLabel.RIGHT), Component.RIGHT_ALIGNMENT);
+ textField = new JTextField(species.getAliasID(), JLabel.LEFT);
+ textField.setEditable(false);
+ tmpPanel.add(textField, Component.LEFT_ALIGNMENT);
+
+ tmpPanel.add(new JLabel("Species id: ", JLabel.RIGHT), Component.RIGHT_ALIGNMENT);
+ textField = new JTextField(species.getSpecies().getId(), JLabel.LEFT);
+ textField.setEditable(false);
+ tmpPanel.add(textField, Component.LEFT_ALIGNMENT);
+
+ result.add(tmpPanel);
+
+ // add empty space between labels
+ result.add(Box.createRigidArea(new Dimension(DISTANCE_BETWEEN_PANELS, DISTANCE_BETWEEN_PANELS)));
+
+ return result;
+ }
+
+ /**
+ * Returns info if the frame is visible.
+ *
+ * @return info if the frame is visible
+ */
+ public boolean isVisible() {
+ return frame.isVisible();
+ }
+
+ /**
+ * Sets frame title.
+ *
+ * @param title
+ * title of the frame
+ */
+ public void setTitle(String title) {
+ frame.setTitle(title);
+ }
+
+ /**
+ * Returns frame title.
+ *
+ * @return frame title
+ */
+ public JFrame getFrame() {
+ return frame;
+ }
+
+ /**
+ * Set {@link JFrame#defaultCloseOperation}.
+ *
+ * @param type
+ * new {@link JFrame#defaultCloseOperation} value
+ */
+ public void setDefaultCloseOperation(int type) {
+ frame.setDefaultCloseOperation(type);
+ }
+
+ /**
+ * Set {@link JFrame#setAlwaysOnTop(boolean)}.
+ *
+ * @param always
+ * new {@link JFrame#isAlwaysOnTop()} value
+ */
+ public void setAlwaysOnTop(boolean always) {
+ frame.setAlwaysOnTop(always);
+ }
+
+}
diff --git a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/InfoPlugin.java b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/InfoPlugin.java
index 7aee33c4db..dfe0ec3728 100644
--- a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/InfoPlugin.java
+++ b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/InfoPlugin.java
@@ -1,172 +1,172 @@
-package lcsb.mapviewer.cdplugin.info;
-
-import java.awt.KeyEventDispatcher;
-import java.awt.KeyboardFocusManager;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.KeyEvent;
-import java.util.ArrayList;
-
-import javax.swing.Timer;
-
-import jp.sbi.celldesigner.plugin.CellDesignerPlugin;
-import jp.sbi.celldesigner.plugin.PluginListOf;
-import jp.sbi.celldesigner.plugin.PluginSBase;
-import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
-
-import org.apache.log4j.Logger;
-
-/**
- * This class represent a plugin to CellDesigner that add info text box with
- * informations about species. Plugin run in pooling mode (there is no other way
- * in CellDesigner...).
- *
- * It overrides <i>CTRL + T shortcut</i> - shows/hide info text window.
- *
- * @author Piotr Gawron
- *
- */
-public class InfoPlugin extends CellDesignerPlugin {
-
- /**
- * What is the time between two consecutive checks if the set of selected
- * elements changed.
- */
- private static final int DELAY_BETWEEN_ON_SELECT_LISTENER_CHECKS = 250;
-
- /**
- * Maximum number of elements that will be described in the text box.
- */
- private static final int MAX_VISIBLE_ELEMENTS = 5;
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(InfoPlugin.class.getName());
-
- /**
- * Listener called when set of selected elements in cell designer changed.
- */
- private ActionListener onChangeSelectListener;
-
- /**
- * Frame where visualization is generated.
- */
- private InfoFrame frame;
-
- /**
- * Default constructor. Creates menu and InfoFrame.
- */
- public InfoPlugin() {
- try {
- // load logger information
-
- // PropertyConfigurator.configure("D:/log4j.properties");
- logger.debug("Loading info plugin...");
-
- frame = InfoFrame.getInstance();
-
- // create keyboard listener for shortcuts
- KeyboardFocusManager.getCurrentKeyboardFocusManager().addKeyEventDispatcher(new KeyEventDispatcher() {
- public boolean dispatchKeyEvent(KeyEvent e) {
- if (KeyEvent.KEY_PRESSED == e.getID()) {
- // if someone hits CTRL+T then open/hide info window
- if (e.getKeyCode() == java.awt.event.KeyEvent.VK_T && e.getModifiers() == java.awt.event.InputEvent.CTRL_MASK) {
- frame.setVisible(!frame.isVisible());
- return true;
- }
- }
- return false;
- }
- });
-
- // create a listener for refreshing selected elements
- onChangeSelectListener = new ActionListener() {
-
- /**
- * This string contains a simple hash of all species shown in the last
- * run of this listener. Due to this information we don't have to
- * refresh this information at every run.
- */
- private String selectedElementsId = "";
-
- @Override
- public void actionPerformed(ActionEvent arg0) {
-
- // if there is no open model then getSelectedAllNode() will throw an
- // exception...
- PluginListOf list = null;
- try {
- list = getSelectedAllNode();
- } catch (Exception e) {
- return;
- }
- try {
- ArrayList<PluginSpeciesAlias> v = new ArrayList<PluginSpeciesAlias>();
- String newId = "";
- // max five elements should be shown in infofrmae
- for (int i = 0; i < Math.min(list.size(), MAX_VISIBLE_ELEMENTS); i++) {
- if (list.get(i) instanceof PluginSpeciesAlias) {
- PluginSpeciesAlias alias = (PluginSpeciesAlias) list.get(i);
- v.add(alias);
- newId += alias.getSpecies().getName();
- }
- }
- // if the cache is exactly the same as in the previous run then
- // don't update infoframe
- if (!selectedElementsId.equals(newId)) {
- selectedElementsId = newId;
- frame.setSpecies(v);
- }
- } catch (Exception exception) {
- logger.error(exception, exception);
- }
-
- }
- };
-
- Timer timer = new Timer(DELAY_BETWEEN_ON_SELECT_LISTENER_CHECKS, onChangeSelectListener);
- timer.start();
-
- } catch (Exception exception) {
- logger.error("Unhandled exception. ", exception);
- }
- }
-
- // CHECKSTYLE:OFF
- @Override
- public void SBaseAdded(PluginSBase arg0) {
-
- }
-
- @Override
- public void SBaseChanged(PluginSBase arg0) {
-
- }
-
- @Override
- public void SBaseDeleted(PluginSBase arg0) {
- }
-
- // CHECKSTYLE:ON
-
- @Override
- public void addPluginMenu() {
- }
-
- @Override
- public void modelClosed(PluginSBase arg0) {
-
- }
-
- @Override
- public void modelOpened(PluginSBase arg0) {
-
- }
-
- @Override
- public void modelSelectChanged(PluginSBase arg0) {
-
- }
-
+package lcsb.mapviewer.cdplugin.info;
+
+import java.awt.KeyEventDispatcher;
+import java.awt.KeyboardFocusManager;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyEvent;
+import java.util.ArrayList;
+
+import javax.swing.Timer;
+
+import jp.sbi.celldesigner.plugin.CellDesignerPlugin;
+import jp.sbi.celldesigner.plugin.PluginListOf;
+import jp.sbi.celldesigner.plugin.PluginSBase;
+import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
+
+import org.apache.log4j.Logger;
+
+/**
+ * This class represent a plugin to CellDesigner that add info text box with
+ * informations about species. Plugin run in pooling mode (there is no other way
+ * in CellDesigner...).
+ *
+ * It overrides <i>CTRL + T shortcut</i> - shows/hide info text window.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class InfoPlugin extends CellDesignerPlugin {
+
+ /**
+ * What is the time between two consecutive checks if the set of selected
+ * elements changed.
+ */
+ private static final int DELAY_BETWEEN_ON_SELECT_LISTENER_CHECKS = 250;
+
+ /**
+ * Maximum number of elements that will be described in the text box.
+ */
+ private static final int MAX_VISIBLE_ELEMENTS = 5;
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(InfoPlugin.class.getName());
+
+ /**
+ * Listener called when set of selected elements in cell designer changed.
+ */
+ private ActionListener onChangeSelectListener;
+
+ /**
+ * Frame where visualization is generated.
+ */
+ private InfoFrame frame;
+
+ /**
+ * Default constructor. Creates menu and InfoFrame.
+ */
+ public InfoPlugin() {
+ try {
+ // load logger information
+
+ // PropertyConfigurator.configure("D:/log4j.properties");
+ logger.debug("Loading info plugin...");
+
+ frame = InfoFrame.getInstance();
+
+ // create keyboard listener for shortcuts
+ KeyboardFocusManager.getCurrentKeyboardFocusManager().addKeyEventDispatcher(new KeyEventDispatcher() {
+ public boolean dispatchKeyEvent(KeyEvent e) {
+ if (KeyEvent.KEY_PRESSED == e.getID()) {
+ // if someone hits CTRL+T then open/hide info window
+ if (e.getKeyCode() == java.awt.event.KeyEvent.VK_T && e.getModifiers() == java.awt.event.InputEvent.CTRL_MASK) {
+ frame.setVisible(!frame.isVisible());
+ return true;
+ }
+ }
+ return false;
+ }
+ });
+
+ // create a listener for refreshing selected elements
+ onChangeSelectListener = new ActionListener() {
+
+ /**
+ * This string contains a simple hash of all species shown in the last
+ * run of this listener. Due to this information we don't have to
+ * refresh this information at every run.
+ */
+ private String selectedElementsId = "";
+
+ @Override
+ public void actionPerformed(ActionEvent arg0) {
+
+ // if there is no open model then getSelectedAllNode() will throw an
+ // exception...
+ PluginListOf list = null;
+ try {
+ list = getSelectedAllNode();
+ } catch (Exception e) {
+ return;
+ }
+ try {
+ ArrayList<PluginSpeciesAlias> v = new ArrayList<PluginSpeciesAlias>();
+ String newId = "";
+ // max five elements should be shown in infofrmae
+ for (int i = 0; i < Math.min(list.size(), MAX_VISIBLE_ELEMENTS); i++) {
+ if (list.get(i) instanceof PluginSpeciesAlias) {
+ PluginSpeciesAlias alias = (PluginSpeciesAlias) list.get(i);
+ v.add(alias);
+ newId += alias.getSpecies().getName();
+ }
+ }
+ // if the cache is exactly the same as in the previous run then
+ // don't update infoframe
+ if (!selectedElementsId.equals(newId)) {
+ selectedElementsId = newId;
+ frame.setSpecies(v);
+ }
+ } catch (Exception exception) {
+ logger.error(exception, exception);
+ }
+
+ }
+ };
+
+ Timer timer = new Timer(DELAY_BETWEEN_ON_SELECT_LISTENER_CHECKS, onChangeSelectListener);
+ timer.start();
+
+ } catch (Exception exception) {
+ logger.error("Unhandled exception. ", exception);
+ }
+ }
+
+ // CHECKSTYLE:OFF
+ @Override
+ public void SBaseAdded(PluginSBase arg0) {
+
+ }
+
+ @Override
+ public void SBaseChanged(PluginSBase arg0) {
+
+ }
+
+ @Override
+ public void SBaseDeleted(PluginSBase arg0) {
+ }
+
+ // CHECKSTYLE:ON
+
+ @Override
+ public void addPluginMenu() {
+ }
+
+ @Override
+ public void modelClosed(PluginSBase arg0) {
+
+ }
+
+ @Override
+ public void modelOpened(PluginSBase arg0) {
+
+ }
+
+ @Override
+ public void modelSelectChanged(PluginSBase arg0) {
+
+ }
+
}
\ No newline at end of file
diff --git a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/package-info.java b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/package-info.java
index ce1ad1d979..311f2ff3bd 100644
--- a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/package-info.java
+++ b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/package-info.java
@@ -1,7 +1,7 @@
-/**
- * In this package there is implementation of a simple plugin that presents
- * informations about CellDesigner elements. More information can be found in
- * {@link lcsb.mapviewer.cdplugin.info.InfoPlugin}.
- */
-package lcsb.mapviewer.cdplugin.info;
-
+/**
+ * In this package there is implementation of a simple plugin that presents
+ * informations about CellDesigner elements. More information can be found in
+ * {@link lcsb.mapviewer.cdplugin.info.InfoPlugin}.
+ */
+package lcsb.mapviewer.cdplugin.info;
+
diff --git a/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractActionTest.java b/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractActionTest.java
index 4711ede11d..19366d3934 100644
--- a/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractActionTest.java
+++ b/CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractActionTest.java
@@ -1,128 +1,128 @@
-package lcsb.mapviewer.cdplugin.copypaste;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-
-import java.util.Set;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class CopyPasteAbstractActionTest {
- Logger logger = Logger.getLogger(CopyPasteAbstractActionTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testPaste() throws Exception {
- try {
- CopyPasteAbstractAction pa = new PasteAction();
- String clipboardString = "[MIRIAM]\t" + MiriamRelationType.BQ_BIOL_IS.getStringRepresentation() + "\t" + MiriamType.CHEBI.getUris().get(0)
- + "\tCHEBI:12345\nasd";
- Pair<Set<MiriamData>, String> res = pa.getAnnotationDataFromClipboardString(clipboardString);
- assertNotNull(res);
- assertNotNull(res.getLeft());
- assertEquals(1, res.getLeft().size());
- assertNotNull(res.getRight());
- assertEquals("asd", res.getRight());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopyPaste() throws Exception {
- try {
- CopyPasteAbstractAction pa = new PasteAction();
- String annString = "<rdf:RDF xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" "
- + "xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\" "
- + "xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\">\n"//
- + "<rdf:Description rdf:about=\"#s1\">" + "<bqmodel:is>" + "<rdf:Bag>" + "<rdf:li rdf:resource=\"urn:miriam:hgnc:SNCA\"/>" + "</rdf:Bag>"
- + "</bqmodel:is>" + "</rdf:Description>" + "</rdf:RDF>";
-
- String str = pa.getCopyString(annString, "notes");
-
- Pair<Set<MiriamData>, String> res = pa.getAnnotationDataFromClipboardString(str);
- assertNotNull(res);
- assertNotNull(res.getLeft());
- assertEquals(1, res.getLeft().size());
- assertNotNull(res.getRight());
- assertEquals("notes", res.getRight());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSerializeMiriam() throws Exception {
- try {
- CopyPasteAbstractAction pa = new PasteAction();
- MiriamData md = new MiriamData(MiriamType.CHEBI, "CH:12");
-
- String string = pa.serialize(md);
- MiriamData md2 = pa.deserialize(string);
- assertEquals(md, md2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDeserializeMiriam() throws Exception {
- try {
- CopyPasteAbstractAction pa = new PasteAction();
-
- MiriamData md = pa.deserialize("ASDASDAS");
- assertNull(md);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDeserializeMiriam2() throws Exception {
- try {
- CopyPasteAbstractAction pa = new PasteAction();
-
- MiriamData md = pa.deserialize(null);
- assertNull(md);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDeserializeMiriam3() throws Exception {
- try {
- CopyPasteAbstractAction pa = new PasteAction();
-
- MiriamData md = pa.deserialize("[MIRIAM]\tinvalid\ttype\tresource");
- assertNull(md);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.cdplugin.copypaste;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+
+import java.util.Set;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class CopyPasteAbstractActionTest {
+ Logger logger = Logger.getLogger(CopyPasteAbstractActionTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testPaste() throws Exception {
+ try {
+ CopyPasteAbstractAction pa = new PasteAction();
+ String clipboardString = "[MIRIAM]\t" + MiriamRelationType.BQ_BIOL_IS.getStringRepresentation() + "\t" + MiriamType.CHEBI.getUris().get(0)
+ + "\tCHEBI:12345\nasd";
+ Pair<Set<MiriamData>, String> res = pa.getAnnotationDataFromClipboardString(clipboardString);
+ assertNotNull(res);
+ assertNotNull(res.getLeft());
+ assertEquals(1, res.getLeft().size());
+ assertNotNull(res.getRight());
+ assertEquals("asd", res.getRight());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyPaste() throws Exception {
+ try {
+ CopyPasteAbstractAction pa = new PasteAction();
+ String annString = "<rdf:RDF xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" "
+ + "xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\" "
+ + "xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\">\n"//
+ + "<rdf:Description rdf:about=\"#s1\">" + "<bqmodel:is>" + "<rdf:Bag>" + "<rdf:li rdf:resource=\"urn:miriam:hgnc:SNCA\"/>" + "</rdf:Bag>"
+ + "</bqmodel:is>" + "</rdf:Description>" + "</rdf:RDF>";
+
+ String str = pa.getCopyString(annString, "notes");
+
+ Pair<Set<MiriamData>, String> res = pa.getAnnotationDataFromClipboardString(str);
+ assertNotNull(res);
+ assertNotNull(res.getLeft());
+ assertEquals(1, res.getLeft().size());
+ assertNotNull(res.getRight());
+ assertEquals("notes", res.getRight());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSerializeMiriam() throws Exception {
+ try {
+ CopyPasteAbstractAction pa = new PasteAction();
+ MiriamData md = new MiriamData(MiriamType.CHEBI, "CH:12");
+
+ String string = pa.serialize(md);
+ MiriamData md2 = pa.deserialize(string);
+ assertEquals(md, md2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDeserializeMiriam() throws Exception {
+ try {
+ CopyPasteAbstractAction pa = new PasteAction();
+
+ MiriamData md = pa.deserialize("ASDASDAS");
+ assertNull(md);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDeserializeMiriam2() throws Exception {
+ try {
+ CopyPasteAbstractAction pa = new PasteAction();
+
+ MiriamData md = pa.deserialize(null);
+ assertNull(md);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDeserializeMiriam3() throws Exception {
+ try {
+ CopyPasteAbstractAction pa = new PasteAction();
+
+ MiriamData md = pa.deserialize("[MIRIAM]\tinvalid\ttype\tresource");
+ assertNull(md);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/ApplicationLevelCache.java b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/ApplicationLevelCache.java
index 9bd95528fa..988858a11d 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/ApplicationLevelCache.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/ApplicationLevelCache.java
@@ -1,149 +1,149 @@
-package lcsb.mapviewer.annotation.cache;
-
-import java.util.HashMap;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-import org.w3c.dom.Node;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.XmlParser;
-import lcsb.mapviewer.model.cache.CacheType;
-
-/**
- * Implementation of cache that stores everything in application memory. Data is
- * lost when application restarts. It implements singleton pattern. All method
- * are synchronized (so there are no issues when few thread are trying to access
- * data at the same time),
- *
- * @author Piotr Gawron
- *
- */
-public final class ApplicationLevelCache extends XmlParser implements QueryCacheInterface {
-
- /**
- * How many values should be stored in cache before we even try to consider
- * releasing object due to huge memory usage.
- */
- static final int MIN_CACHED_VALUES_BEFORE_CLEAN = 100;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ApplicationLevelCache.class);
-
- /**
- * Cached nodes stored locally and identified by string.
- */
- private static Map<String, Node> cachedQueryNodes = new HashMap<String, Node>();
-
- /**
- * Cached strings stored locally and identified by string.
- */
- private static Map<String, String> cachedQueryString = new HashMap<String, String>();
-
- /**
- * Global instance of cache.
- */
- private static ApplicationLevelCache cache = null;
-
- /**
- * Returns single instance of global application cache (singleton pattern).
- *
- * @return single instance of global application cache
- */
- public static ApplicationLevelCache getInstance() {
- if (Configuration.isApplicationCacheOn()) {
- if (cache == null) {
- cache = new ApplicationLevelCache();
- }
- return cache;
- } else {
- return null;
- }
- }
-
- /**
- * Default constructor. Prevents instantiation.
- */
- private ApplicationLevelCache() {
-
- }
-
- @Override
- public synchronized Node getXmlNodeByQuery(String query, CacheType type) {
- Node result = null;
- result = cachedQueryNodes.get(type.getId() + "\n" + query);
- return result;
- }
-
- @Override
- public synchronized String getStringByQuery(String query, CacheType type) {
- String result = null;
- result = cachedQueryString.get(type.getId() + "\n" + query);
- return result;
- }
-
- @Override
- public synchronized void setCachedQuery(String query, CacheType type, Object object) {
- setCachedQuery(query, type, object, 0);
- }
-
- @Override
- public synchronized void setCachedQuery(String query, CacheType type, Object object, int validDays) {
- performMemoryBalance();
-
- if (object instanceof String) {
- cachedQueryString.put(type.getId() + "\n" + query, (String) object);
- } else if (object instanceof Node) {
- cachedQueryNodes.put(type.getId() + "\n" + query, (Node) object);
- } else if (object == null) {
- cachedQueryString.put(type.getId() + "\n" + query, (String) object);
- } else {
- throw new CacheException("Unknown object type: " + object.getClass());
- }
- }
-
- /**
- * Method that clean cache if memory usage is too high.
- */
- synchronized void performMemoryBalance() {
- long cacheCount = 0;
- cacheCount += cachedQueryString.size();
- cacheCount += cachedQueryNodes.size();
- // check memory usage only if we have some data to clear
- if (cacheCount > MIN_CACHED_VALUES_BEFORE_CLEAN) {
- Runtime runtime = Runtime.getRuntime();
- long maxMem = runtime.maxMemory();
- long useMem = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory();
- // if free memory is less than 10% then we clear cache
- if (useMem > maxMem * Configuration.getMemorySaturationRatioTriggerClean()) {
- logger.info("Cache will be cleared");
- logger.info("Memory usage: " + useMem + " out of " + maxMem + " is used. Exceeded: "
- + maxMem * Configuration.getMemorySaturationRatioTriggerClean());
- logger.info("Elements in cache: " + cacheCount);
- clearCache();
- System.gc();
- }
- }
- }
-
- @Override
- public synchronized void removeByQuery(String query, CacheType type) {
- cachedQueryString.remove(type.getId() + "\n" + query);
- cachedQueryNodes.remove(type.getId() + "\n" + query);
- }
-
- @Override
- public synchronized void clearCache() {
- logger.info("Clearing application cache");
- cachedQueryNodes.clear();
- cachedQueryString.clear();
- }
-
- @Override
- public void invalidateByQuery(String query, CacheType type) {
- removeByQuery(query, type);
- }
-
-}
+package lcsb.mapviewer.annotation.cache;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+import org.w3c.dom.Node;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.model.cache.CacheType;
+
+/**
+ * Implementation of cache that stores everything in application memory. Data is
+ * lost when application restarts. It implements singleton pattern. All method
+ * are synchronized (so there are no issues when few thread are trying to access
+ * data at the same time),
+ *
+ * @author Piotr Gawron
+ *
+ */
+public final class ApplicationLevelCache extends XmlParser implements QueryCacheInterface {
+
+ /**
+ * How many values should be stored in cache before we even try to consider
+ * releasing object due to huge memory usage.
+ */
+ static final int MIN_CACHED_VALUES_BEFORE_CLEAN = 100;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ApplicationLevelCache.class);
+
+ /**
+ * Cached nodes stored locally and identified by string.
+ */
+ private static Map<String, Node> cachedQueryNodes = new HashMap<String, Node>();
+
+ /**
+ * Cached strings stored locally and identified by string.
+ */
+ private static Map<String, String> cachedQueryString = new HashMap<String, String>();
+
+ /**
+ * Global instance of cache.
+ */
+ private static ApplicationLevelCache cache = null;
+
+ /**
+ * Returns single instance of global application cache (singleton pattern).
+ *
+ * @return single instance of global application cache
+ */
+ public static ApplicationLevelCache getInstance() {
+ if (Configuration.isApplicationCacheOn()) {
+ if (cache == null) {
+ cache = new ApplicationLevelCache();
+ }
+ return cache;
+ } else {
+ return null;
+ }
+ }
+
+ /**
+ * Default constructor. Prevents instantiation.
+ */
+ private ApplicationLevelCache() {
+
+ }
+
+ @Override
+ public synchronized Node getXmlNodeByQuery(String query, CacheType type) {
+ Node result = null;
+ result = cachedQueryNodes.get(type.getId() + "\n" + query);
+ return result;
+ }
+
+ @Override
+ public synchronized String getStringByQuery(String query, CacheType type) {
+ String result = null;
+ result = cachedQueryString.get(type.getId() + "\n" + query);
+ return result;
+ }
+
+ @Override
+ public synchronized void setCachedQuery(String query, CacheType type, Object object) {
+ setCachedQuery(query, type, object, 0);
+ }
+
+ @Override
+ public synchronized void setCachedQuery(String query, CacheType type, Object object, int validDays) {
+ performMemoryBalance();
+
+ if (object instanceof String) {
+ cachedQueryString.put(type.getId() + "\n" + query, (String) object);
+ } else if (object instanceof Node) {
+ cachedQueryNodes.put(type.getId() + "\n" + query, (Node) object);
+ } else if (object == null) {
+ cachedQueryString.put(type.getId() + "\n" + query, (String) object);
+ } else {
+ throw new CacheException("Unknown object type: " + object.getClass());
+ }
+ }
+
+ /**
+ * Method that clean cache if memory usage is too high.
+ */
+ synchronized void performMemoryBalance() {
+ long cacheCount = 0;
+ cacheCount += cachedQueryString.size();
+ cacheCount += cachedQueryNodes.size();
+ // check memory usage only if we have some data to clear
+ if (cacheCount > MIN_CACHED_VALUES_BEFORE_CLEAN) {
+ Runtime runtime = Runtime.getRuntime();
+ long maxMem = runtime.maxMemory();
+ long useMem = Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory();
+ // if free memory is less than 10% then we clear cache
+ if (useMem > maxMem * Configuration.getMemorySaturationRatioTriggerClean()) {
+ logger.info("Cache will be cleared");
+ logger.info("Memory usage: " + useMem + " out of " + maxMem + " is used. Exceeded: "
+ + maxMem * Configuration.getMemorySaturationRatioTriggerClean());
+ logger.info("Elements in cache: " + cacheCount);
+ clearCache();
+ System.gc();
+ }
+ }
+ }
+
+ @Override
+ public synchronized void removeByQuery(String query, CacheType type) {
+ cachedQueryString.remove(type.getId() + "\n" + query);
+ cachedQueryNodes.remove(type.getId() + "\n" + query);
+ }
+
+ @Override
+ public synchronized void clearCache() {
+ logger.info("Clearing application cache");
+ cachedQueryNodes.clear();
+ cachedQueryString.clear();
+ }
+
+ @Override
+ public void invalidateByQuery(String query, CacheType type) {
+ removeByQuery(query, type);
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/CachableInterface.java b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/CachableInterface.java
index 953f91175e..251ea03a32 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/CachableInterface.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/CachableInterface.java
@@ -1,303 +1,303 @@
-package lcsb.mapviewer.annotation.cache;
-
-import java.io.IOException;
-
-import org.apache.commons.lang3.StringEscapeUtils;
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.w3c.dom.Node;
-
-import lcsb.mapviewer.common.XmlParser;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.cache.CacheType;
-import lcsb.mapviewer.persist.dao.cache.CacheTypeDao;
-
-/**
- * Interface used for retrieving data that are no longer valid in the cache
- * (their expire date was reached).
- *
- * @author Piotr Gawron
- *
- */
-public abstract class CachableInterface extends XmlParser {
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(CachableInterface.class);
-
- /**
- * Refresh cache data from original source.
- *
- * @param query
- * text used to identify the resource
- * @return newly obtained data from the source
- * @throws SourceNotAvailable
- * thrown when original source is unavailable
- */
- public Object refreshCacheQuery(Object query) throws SourceNotAvailable {
- String result = null;
- try {
- if (query instanceof String) {
- String name = (String) query;
- if (name.startsWith("http")) {
- result = getWebPageContent(name);
- } else {
- throw new InvalidArgumentException("Don't know what to do with string \"" + query + "\"");
- }
- } else {
- throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
- }
- } catch (IOException e) {
- throw new SourceNotAvailable(e);
- }
- return result;
- }
-
- /**
- * String containing class name of the class that extends
- * {@link CachableInterface}. String name is used because cache layer doesn't
- * have access to every possible cacheable interface, therefore it cannot enlist
- * it.
- */
- private String cacheIdentifier;
-
- /**
- * Type of the cache elements associated with this interface.
- */
- private CacheType cacheType;
-
- /**
- * Cache mechanism used to speed up computation.
- */
- @Autowired
- private GeneralCacheInterface cache;
-
- /**
- * Cache mechanism used to speed up computation.
- */
- @Autowired
- private CacheTypeDao cacheTypeDao;
-
- /**
- * This object downloads web pages.
- */
- private WebPageDownloader webPageDownloader = new WebPageDownloader();
-
- /**
- * Default constructor.
- *
- * @param clazz
- * type that defines this interface
- */
- public CachableInterface(final Class<? extends CachableInterface> clazz) {
- this.cacheIdentifier = clazz.getCanonicalName();
- }
-
- /**
- * Puts some string value into cache.
- *
- * @param key
- * string that identifies value
- * @param result
- * value to put into cache
- */
- protected final void setCacheValue(String key, String result) {
- if (cache != null) {
- cache.setCachedQuery(key, getCacheType(), result);
- }
- }
-
- protected final void setCacheValue(String key, String result, int validDays) {
- if (cache != null) {
- cache.setCachedQuery(key, getCacheType(), result, validDays);
- }
- }
-
- /**
- * Retrieves string from cache.
- *
- * @param key
- * string that identifies xml node
- * @return string from cache
- */
- protected final String getCacheValue(String key) {
- if (cache != null) {
- return cache.getStringByQuery(key, getCacheType());
- } else {
- return null;
- }
- }
-
- /**
- * @return the cacheType
- * @see #cacheType
- */
- public final CacheType getCacheType() {
- if (cacheType == null) {
- cacheType = getCacheTypeDao().getByClassName(cacheIdentifier);
- }
- return cacheType;
- }
-
- /**
- * Retrieves xml node from cache.
- *
- * @param key
- * string that identifies xml node
- * @return xml node from cache
- */
- protected final Node getCacheNode(String key) {
- if (cache != null) {
- return cache.getXmlNodeByQuery(key, getCacheType());
- } else {
- return null;
- }
- }
-
- /**
- * Saves xml node in the cache.
- *
- * @param id
- * identifier of the node
- * @param item
- * node to save
- */
- protected void setCacheNode(String id, Node item) {
- if (cache != null) {
- cache.setCachedQuery(id, getCacheType(), item);
- }
- }
-
- /**
- * @return the cache
- * @see #cache
- */
- public final GeneralCacheInterface getCache() {
- return cache;
- }
-
- /**
- * @param cache
- * the cache to set
- * @see #cache
- */
- public final void setCache(GeneralCacheInterface cache) {
- this.cache = cache;
- }
-
- /**
- * Returns a content of the web page for a given url using GET request.
- *
- * @param accessUrl
- * web page url address
- * @return content of the web page
- * @throws IOException
- * thrown when there are problems with connection to ChEMBL database
- */
- protected final String getWebPageContent(String accessUrl) throws IOException {
- return getWebPageContent(accessUrl, "GET", null);
- }
-
- /**
- * Returns a content of the web page for a given url. If postData is not null,
- * the page will be accessed using POST request. Otherwise GET will be used.
- *
- * @param accessUrl
- * web page url address
- * @param httpRequestMethod
- * type of HTTP request (GET, POST, PUT, PATCH, DELETE, ...)
- * @param postData
- * string to be sent in the body of the request
- * @return content of the web page
- * @throws IOException
- * thrown when there are problems with connection to ChEMBL database
- */
- protected final String getWebPageContent(String accessUrl, String httpRequestMethod, String data) throws IOException {
- // check if we have the page in our internal cache
-
- String cacheKey = accessUrl;
- if (data != null) {
- cacheKey += data;
- }
-
- String result = getCacheValue(cacheKey);
- if (result == null) {
- result = webPageDownloader.getFromNetwork(accessUrl, httpRequestMethod, data);
- if (result != null) {
- setCacheValue(cacheKey, result);
- }
- }
- return result;
- }
-
- /**
- * Removes html tags from text.
- *
- * @param text
- * text text to clean
- * @return text without html tags
- */
- public String cleanHtml(String text) {
- int startIndex;
- int endIndex;
- // and now clean the description from html tags (should be somehow
- // improved...)
-
- StringBuilder result = new StringBuilder();
-
- int oldEndIndex = 0;
- startIndex = text.indexOf("<");
- while (startIndex >= 0) {
- endIndex = text.indexOf(">", startIndex);
- result.append(text.substring(oldEndIndex, startIndex));
- if (endIndex < 0) {
- logger.warn("Problem with html code: " + text);
- oldEndIndex = text.length();
- break;
- } else {
- oldEndIndex = endIndex + 1;
- }
-
- startIndex = text.indexOf("<", oldEndIndex);
- }
-
- result.append(text.substring(oldEndIndex));
- return StringEscapeUtils.unescapeHtml4(result.toString().replaceAll("[\n\r]+", " "));
- }
-
- /**
- * @return the cacheTypeDao
- * @see #cacheTypeDao
- */
- public CacheTypeDao getCacheTypeDao() {
- return cacheTypeDao;
- }
-
- /**
- * @param cacheTypeDao
- * the cacheTypeDao to set
- * @see #cacheTypeDao
- */
- public void setCacheTypeDao(CacheTypeDao cacheTypeDao) {
- this.cacheTypeDao = cacheTypeDao;
- }
-
- /**
- * @return the webPageDownloader
- * @see #webPageDownloader
- */
- protected WebPageDownloader getWebPageDownloader() {
- return webPageDownloader;
- }
-
- /**
- * @param webPageDownloader
- * the webPageDownloader to set
- * @see #webPageDownloader
- */
- protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
- this.webPageDownloader = webPageDownloader;
- }
-
-}
+package lcsb.mapviewer.annotation.cache;
+
+import java.io.IOException;
+
+import org.apache.commons.lang3.StringEscapeUtils;
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.w3c.dom.Node;
+
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.cache.CacheType;
+import lcsb.mapviewer.persist.dao.cache.CacheTypeDao;
+
+/**
+ * Interface used for retrieving data that are no longer valid in the cache
+ * (their expire date was reached).
+ *
+ * @author Piotr Gawron
+ *
+ */
+public abstract class CachableInterface extends XmlParser {
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(CachableInterface.class);
+
+ /**
+ * Refresh cache data from original source.
+ *
+ * @param query
+ * text used to identify the resource
+ * @return newly obtained data from the source
+ * @throws SourceNotAvailable
+ * thrown when original source is unavailable
+ */
+ public Object refreshCacheQuery(Object query) throws SourceNotAvailable {
+ String result = null;
+ try {
+ if (query instanceof String) {
+ String name = (String) query;
+ if (name.startsWith("http")) {
+ result = getWebPageContent(name);
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with string \"" + query + "\"");
+ }
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
+ }
+ } catch (IOException e) {
+ throw new SourceNotAvailable(e);
+ }
+ return result;
+ }
+
+ /**
+ * String containing class name of the class that extends
+ * {@link CachableInterface}. String name is used because cache layer doesn't
+ * have access to every possible cacheable interface, therefore it cannot enlist
+ * it.
+ */
+ private String cacheIdentifier;
+
+ /**
+ * Type of the cache elements associated with this interface.
+ */
+ private CacheType cacheType;
+
+ /**
+ * Cache mechanism used to speed up computation.
+ */
+ @Autowired
+ private GeneralCacheInterface cache;
+
+ /**
+ * Cache mechanism used to speed up computation.
+ */
+ @Autowired
+ private CacheTypeDao cacheTypeDao;
+
+ /**
+ * This object downloads web pages.
+ */
+ private WebPageDownloader webPageDownloader = new WebPageDownloader();
+
+ /**
+ * Default constructor.
+ *
+ * @param clazz
+ * type that defines this interface
+ */
+ public CachableInterface(final Class<? extends CachableInterface> clazz) {
+ this.cacheIdentifier = clazz.getCanonicalName();
+ }
+
+ /**
+ * Puts some string value into cache.
+ *
+ * @param key
+ * string that identifies value
+ * @param result
+ * value to put into cache
+ */
+ protected final void setCacheValue(String key, String result) {
+ if (cache != null) {
+ cache.setCachedQuery(key, getCacheType(), result);
+ }
+ }
+
+ protected final void setCacheValue(String key, String result, int validDays) {
+ if (cache != null) {
+ cache.setCachedQuery(key, getCacheType(), result, validDays);
+ }
+ }
+
+ /**
+ * Retrieves string from cache.
+ *
+ * @param key
+ * string that identifies xml node
+ * @return string from cache
+ */
+ protected final String getCacheValue(String key) {
+ if (cache != null) {
+ return cache.getStringByQuery(key, getCacheType());
+ } else {
+ return null;
+ }
+ }
+
+ /**
+ * @return the cacheType
+ * @see #cacheType
+ */
+ public final CacheType getCacheType() {
+ if (cacheType == null) {
+ cacheType = getCacheTypeDao().getByClassName(cacheIdentifier);
+ }
+ return cacheType;
+ }
+
+ /**
+ * Retrieves xml node from cache.
+ *
+ * @param key
+ * string that identifies xml node
+ * @return xml node from cache
+ */
+ protected final Node getCacheNode(String key) {
+ if (cache != null) {
+ return cache.getXmlNodeByQuery(key, getCacheType());
+ } else {
+ return null;
+ }
+ }
+
+ /**
+ * Saves xml node in the cache.
+ *
+ * @param id
+ * identifier of the node
+ * @param item
+ * node to save
+ */
+ protected void setCacheNode(String id, Node item) {
+ if (cache != null) {
+ cache.setCachedQuery(id, getCacheType(), item);
+ }
+ }
+
+ /**
+ * @return the cache
+ * @see #cache
+ */
+ public final GeneralCacheInterface getCache() {
+ return cache;
+ }
+
+ /**
+ * @param cache
+ * the cache to set
+ * @see #cache
+ */
+ public final void setCache(GeneralCacheInterface cache) {
+ this.cache = cache;
+ }
+
+ /**
+ * Returns a content of the web page for a given url using GET request.
+ *
+ * @param accessUrl
+ * web page url address
+ * @return content of the web page
+ * @throws IOException
+ * thrown when there are problems with connection to ChEMBL database
+ */
+ protected final String getWebPageContent(String accessUrl) throws IOException {
+ return getWebPageContent(accessUrl, "GET", null);
+ }
+
+ /**
+ * Returns a content of the web page for a given url. If postData is not null,
+ * the page will be accessed using POST request. Otherwise GET will be used.
+ *
+ * @param accessUrl
+ * web page url address
+ * @param httpRequestMethod
+ * type of HTTP request (GET, POST, PUT, PATCH, DELETE, ...)
+ * @param postData
+ * string to be sent in the body of the request
+ * @return content of the web page
+ * @throws IOException
+ * thrown when there are problems with connection to ChEMBL database
+ */
+ protected final String getWebPageContent(String accessUrl, String httpRequestMethod, String data) throws IOException {
+ // check if we have the page in our internal cache
+
+ String cacheKey = accessUrl;
+ if (data != null) {
+ cacheKey += data;
+ }
+
+ String result = getCacheValue(cacheKey);
+ if (result == null) {
+ result = webPageDownloader.getFromNetwork(accessUrl, httpRequestMethod, data);
+ if (result != null) {
+ setCacheValue(cacheKey, result);
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Removes html tags from text.
+ *
+ * @param text
+ * text text to clean
+ * @return text without html tags
+ */
+ public String cleanHtml(String text) {
+ int startIndex;
+ int endIndex;
+ // and now clean the description from html tags (should be somehow
+ // improved...)
+
+ StringBuilder result = new StringBuilder();
+
+ int oldEndIndex = 0;
+ startIndex = text.indexOf("<");
+ while (startIndex >= 0) {
+ endIndex = text.indexOf(">", startIndex);
+ result.append(text.substring(oldEndIndex, startIndex));
+ if (endIndex < 0) {
+ logger.warn("Problem with html code: " + text);
+ oldEndIndex = text.length();
+ break;
+ } else {
+ oldEndIndex = endIndex + 1;
+ }
+
+ startIndex = text.indexOf("<", oldEndIndex);
+ }
+
+ result.append(text.substring(oldEndIndex));
+ return StringEscapeUtils.unescapeHtml4(result.toString().replaceAll("[\n\r]+", " "));
+ }
+
+ /**
+ * @return the cacheTypeDao
+ * @see #cacheTypeDao
+ */
+ public CacheTypeDao getCacheTypeDao() {
+ return cacheTypeDao;
+ }
+
+ /**
+ * @param cacheTypeDao
+ * the cacheTypeDao to set
+ * @see #cacheTypeDao
+ */
+ public void setCacheTypeDao(CacheTypeDao cacheTypeDao) {
+ this.cacheTypeDao = cacheTypeDao;
+ }
+
+ /**
+ * @return the webPageDownloader
+ * @see #webPageDownloader
+ */
+ protected WebPageDownloader getWebPageDownloader() {
+ return webPageDownloader;
+ }
+
+ /**
+ * @param webPageDownloader
+ * the webPageDownloader to set
+ * @see #webPageDownloader
+ */
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ this.webPageDownloader = webPageDownloader;
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/CacheException.java b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/CacheException.java
index 505b07ca27..b171e2a1cc 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/CacheException.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/CacheException.java
@@ -1,25 +1,25 @@
-package lcsb.mapviewer.annotation.cache;
-
-/**
- * Thrown when query to the database is of wrong type.
- *
- * @author Piotr Gawron
- *
- */
-public class CacheException extends RuntimeException {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Constructor receives some kind of message.
- *
- * @param string
- * message associated with exception
- */
- public CacheException(final String string) {
- super(string);
- }
-
-}
+package lcsb.mapviewer.annotation.cache;
+
+/**
+ * Thrown when query to the database is of wrong type.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CacheException extends RuntimeException {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Constructor receives some kind of message.
+ *
+ * @param string
+ * message associated with exception
+ */
+ public CacheException(final String string) {
+ super(string);
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/FtpClientFactory.java b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/FtpClientFactory.java
index e05ead8ba0..1d18378679 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/FtpClientFactory.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/FtpClientFactory.java
@@ -1,21 +1,21 @@
-package lcsb.mapviewer.annotation.cache;
-
-import org.apache.commons.net.ftp.FTPClient;
-
-/**
- * Factory class used for creating {@link FTPClient} objects.
- *
- * @author Piotr Gawron
- *
- */
-public class FtpClientFactory {
-
- /**
- * Creates new instance of {@link FTPClient}.
- *
- * @return new instance of {@link FTPClient}
- */
- public FTPClient createFtpClient() {
- return new FTPClient();
- }
-}
+package lcsb.mapviewer.annotation.cache;
+
+import org.apache.commons.net.ftp.FTPClient;
+
+/**
+ * Factory class used for creating {@link FTPClient} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class FtpClientFactory {
+
+ /**
+ * Creates new instance of {@link FTPClient}.
+ *
+ * @return new instance of {@link FTPClient}
+ */
+ public FTPClient createFtpClient() {
+ return new FTPClient();
+ }
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/GeneralCache.java b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/GeneralCache.java
index 6c98ed1aa4..27a9b4cbdb 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/GeneralCache.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/GeneralCache.java
@@ -1,153 +1,153 @@
-package lcsb.mapviewer.annotation.cache;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.annotation.Transactional;
-import org.w3c.dom.Node;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.cache.CacheType;
-
-/**
- * Cache used by the application. It contains two sub-classes responsible for
- * application level cache (for single run of the application) and database
- * level cache (for information that were gathered since the beginning).
- *
- * @author Piotr Gawron
- *
- */
-@Transactional(value = "txManager")
-public class GeneralCache implements GeneralCacheInterface {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(GeneralCache.class);
-
- /**
- * Application level cache. More information can be found
- * {@link ApplicationLevelCache here}.
- */
- private QueryCacheInterface cache1 = ApplicationLevelCache.getInstance();
-
- /**
- * Database level cache. More information can be found
- * {@link PermanentDatabaseLevelCache here}.
- */
- @Autowired
- private QueryCacheInterface cache2;
-
- @Override
- public void clearCache() {
- if (cache1 != null) {
- cache1.clearCache();
- }
- if (cache2 != null) {
- cache2.clearCache();
- }
- }
-
- @Override
- public Node getXmlNodeByQuery(String query, CacheType type) {
- if (type == null) {
- throw new InvalidArgumentException("Cache type cannot be null");
- }
-
- Node result = null;
- if (cache1 != null) {
- result = cache1.getXmlNodeByQuery(query, type);
- }
- if (result == null && cache2 != null) {
- result = cache2.getXmlNodeByQuery(query, type);
- if (result != null && cache1 != null) {
- cache1.setCachedQuery(query, type, result);
- }
- }
- return result;
- }
-
- @Override
- public String getStringByQuery(String query, CacheType type) {
- if (type == null) {
- throw new InvalidArgumentException("Cache type cannot be null");
- }
- String result = null;
- if (cache1 != null) {
- result = cache1.getStringByQuery(query, type);
- }
- if (result == null && cache2 != null) {
- result = cache2.getStringByQuery(query, type);
- if (result != null && cache1 != null) {
- cache1.setCachedQuery(query, type, result);
- }
- }
- return result;
- }
-
- @Override
- public void setCachedQuery(String query, CacheType type, Object object) {
- if (type == null) {
- throw new InvalidArgumentException("Cache type cannot be null");
- }
- setCachedQuery(query, type, object, type.getValidity());
- }
-
- @Override
- public void setCachedQuery(String query, CacheType type, Object object, int validDays) {
- if (type == null) {
- throw new InvalidArgumentException("Cache type cannot be null");
- }
- if (cache1 != null) {
- cache1.setCachedQuery(query, type, object, validDays);
- }
- if (cache2 != null) {
- cache2.setCachedQuery(query, type, object, validDays);
- }
- }
-
- @Override
- public void removeByQuery(String query, CacheType type) {
- if (type == null) {
- throw new InvalidArgumentException("Cache type cannot be null");
- }
- if (cache1 != null) {
- cache1.removeByQuery(query, type);
- }
- if (cache2 != null) {
- cache2.removeByQuery(query, type);
- }
- }
-
- @Override
- public void invalidateByQuery(String query, CacheType type) {
- if (type == null) {
- throw new InvalidArgumentException("Cache type cannot be null");
- }
- if (cache1 != null) {
- cache1.invalidateByQuery(query, type);
- }
- if (cache2 != null) {
- cache2.invalidateByQuery(query, type);
- }
-
- }
-
- /**
- * @return the cache2
- * @see #cache2
- */
- public QueryCacheInterface getCache2() {
- return cache2;
- }
-
- /**
- * @param cache2
- * the cache2 to set
- * @see #cache2
- */
- public void setCache2(QueryCacheInterface cache2) {
- this.cache2 = cache2;
- }
-
-}
+package lcsb.mapviewer.annotation.cache;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+import org.w3c.dom.Node;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.cache.CacheType;
+
+/**
+ * Cache used by the application. It contains two sub-classes responsible for
+ * application level cache (for single run of the application) and database
+ * level cache (for information that were gathered since the beginning).
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Transactional(value = "txManager")
+public class GeneralCache implements GeneralCacheInterface {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(GeneralCache.class);
+
+ /**
+ * Application level cache. More information can be found
+ * {@link ApplicationLevelCache here}.
+ */
+ private QueryCacheInterface cache1 = ApplicationLevelCache.getInstance();
+
+ /**
+ * Database level cache. More information can be found
+ * {@link PermanentDatabaseLevelCache here}.
+ */
+ @Autowired
+ private QueryCacheInterface cache2;
+
+ @Override
+ public void clearCache() {
+ if (cache1 != null) {
+ cache1.clearCache();
+ }
+ if (cache2 != null) {
+ cache2.clearCache();
+ }
+ }
+
+ @Override
+ public Node getXmlNodeByQuery(String query, CacheType type) {
+ if (type == null) {
+ throw new InvalidArgumentException("Cache type cannot be null");
+ }
+
+ Node result = null;
+ if (cache1 != null) {
+ result = cache1.getXmlNodeByQuery(query, type);
+ }
+ if (result == null && cache2 != null) {
+ result = cache2.getXmlNodeByQuery(query, type);
+ if (result != null && cache1 != null) {
+ cache1.setCachedQuery(query, type, result);
+ }
+ }
+ return result;
+ }
+
+ @Override
+ public String getStringByQuery(String query, CacheType type) {
+ if (type == null) {
+ throw new InvalidArgumentException("Cache type cannot be null");
+ }
+ String result = null;
+ if (cache1 != null) {
+ result = cache1.getStringByQuery(query, type);
+ }
+ if (result == null && cache2 != null) {
+ result = cache2.getStringByQuery(query, type);
+ if (result != null && cache1 != null) {
+ cache1.setCachedQuery(query, type, result);
+ }
+ }
+ return result;
+ }
+
+ @Override
+ public void setCachedQuery(String query, CacheType type, Object object) {
+ if (type == null) {
+ throw new InvalidArgumentException("Cache type cannot be null");
+ }
+ setCachedQuery(query, type, object, type.getValidity());
+ }
+
+ @Override
+ public void setCachedQuery(String query, CacheType type, Object object, int validDays) {
+ if (type == null) {
+ throw new InvalidArgumentException("Cache type cannot be null");
+ }
+ if (cache1 != null) {
+ cache1.setCachedQuery(query, type, object, validDays);
+ }
+ if (cache2 != null) {
+ cache2.setCachedQuery(query, type, object, validDays);
+ }
+ }
+
+ @Override
+ public void removeByQuery(String query, CacheType type) {
+ if (type == null) {
+ throw new InvalidArgumentException("Cache type cannot be null");
+ }
+ if (cache1 != null) {
+ cache1.removeByQuery(query, type);
+ }
+ if (cache2 != null) {
+ cache2.removeByQuery(query, type);
+ }
+ }
+
+ @Override
+ public void invalidateByQuery(String query, CacheType type) {
+ if (type == null) {
+ throw new InvalidArgumentException("Cache type cannot be null");
+ }
+ if (cache1 != null) {
+ cache1.invalidateByQuery(query, type);
+ }
+ if (cache2 != null) {
+ cache2.invalidateByQuery(query, type);
+ }
+
+ }
+
+ /**
+ * @return the cache2
+ * @see #cache2
+ */
+ public QueryCacheInterface getCache2() {
+ return cache2;
+ }
+
+ /**
+ * @param cache2
+ * the cache2 to set
+ * @see #cache2
+ */
+ public void setCache2(QueryCacheInterface cache2) {
+ this.cache2 = cache2;
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/GeneralCacheInterface.java b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/GeneralCacheInterface.java
index ca2c5d9dce..91b4b8307f 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/GeneralCacheInterface.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/GeneralCacheInterface.java
@@ -1,12 +1,12 @@
-package lcsb.mapviewer.annotation.cache;
-
-/**
- * General cache service used by the application. It allows user to store data
- * that requires plenty of time to compute or download and access it later on.
- *
- * @author Piotr Gawron
- *
- */
-public interface GeneralCacheInterface extends QueryCacheInterface {
-
-}
+package lcsb.mapviewer.annotation.cache;
+
+/**
+ * General cache service used by the application. It allows user to store data
+ * that requires plenty of time to compute or download and access it later on.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface GeneralCacheInterface extends QueryCacheInterface {
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/GeneralCacheWithExclusion.java b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/GeneralCacheWithExclusion.java
index 412043bd98..84676a13df 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/GeneralCacheWithExclusion.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/GeneralCacheWithExclusion.java
@@ -1,98 +1,98 @@
-package lcsb.mapviewer.annotation.cache;
-
-import org.apache.log4j.Logger;
-import org.w3c.dom.Node;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.cache.CacheType;
-
-/**
- * This implementation of cache works as a normal cache except of the fact that
- * first few query requests are ignored (return null). It's used when refreshing
- * data from cache. Object of this class is injected into a
- * {@link CachableInterface} and after that normal call is performed. First
- * query to database will be ignored (so it won't be taken from cache), the rest
- * will go to cache.
- *
- * @author Piotr Gawron
- *
- */
-public class GeneralCacheWithExclusion implements GeneralCacheInterface {
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(GeneralCacheWithExclusion.class);
-
- /**
- * How many queries should be ignored.
- */
- private int counter = 0;
-
- /**
- * Original cache object.
- */
- private GeneralCacheInterface cache;
-
- /**
- * Constructor that creates cache.
- *
- * @param originalCache
- * {@link #cache}
- * @param exclusionCount
- * {@link #counter}
- */
- public GeneralCacheWithExclusion(GeneralCacheInterface originalCache, int exclusionCount) {
- if (originalCache == null) {
- throw new InvalidArgumentException("Cache passed as argument cannot be null");
- }
- this.counter = exclusionCount;
- this.cache = originalCache;
- }
-
- @Override
- public Node getXmlNodeByQuery(String identifier, CacheType type) {
- if (counter > 0) {
- counter--;
- logger.debug("Ignoring cache query due to cache refresh: " + identifier + ", " + type);
- return null;
- }
- return cache.getXmlNodeByQuery(identifier, type);
- }
-
- @Override
- public String getStringByQuery(String identifier, CacheType type) {
- if (counter > 0) {
- counter--;
- logger.debug("Ignoring cache query due to cache refresh: " + identifier + ", " + type);
- return null;
- }
- return cache.getStringByQuery(identifier, type);
- }
-
- @Override
- public void setCachedQuery(String identifier, CacheType type, Object value) {
- cache.setCachedQuery(identifier, type, value);
- }
-
- @Override
- public void setCachedQuery(String identifier, CacheType type, Object value, int validDays) {
- cache.setCachedQuery(identifier, type, value, validDays);
- }
-
- @Override
- public void clearCache() {
- cache.clearCache();
-
- }
-
- @Override
- public void removeByQuery(String identifier, CacheType type) {
- cache.removeByQuery(identifier, type);
- }
-
- @Override
- public void invalidateByQuery(String identifier, CacheType type) {
- cache.invalidateByQuery(identifier, type);
- }
-}
+package lcsb.mapviewer.annotation.cache;
+
+import org.apache.log4j.Logger;
+import org.w3c.dom.Node;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.cache.CacheType;
+
+/**
+ * This implementation of cache works as a normal cache except of the fact that
+ * first few query requests are ignored (return null). It's used when refreshing
+ * data from cache. Object of this class is injected into a
+ * {@link CachableInterface} and after that normal call is performed. First
+ * query to database will be ignored (so it won't be taken from cache), the rest
+ * will go to cache.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class GeneralCacheWithExclusion implements GeneralCacheInterface {
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(GeneralCacheWithExclusion.class);
+
+ /**
+ * How many queries should be ignored.
+ */
+ private int counter = 0;
+
+ /**
+ * Original cache object.
+ */
+ private GeneralCacheInterface cache;
+
+ /**
+ * Constructor that creates cache.
+ *
+ * @param originalCache
+ * {@link #cache}
+ * @param exclusionCount
+ * {@link #counter}
+ */
+ public GeneralCacheWithExclusion(GeneralCacheInterface originalCache, int exclusionCount) {
+ if (originalCache == null) {
+ throw new InvalidArgumentException("Cache passed as argument cannot be null");
+ }
+ this.counter = exclusionCount;
+ this.cache = originalCache;
+ }
+
+ @Override
+ public Node getXmlNodeByQuery(String identifier, CacheType type) {
+ if (counter > 0) {
+ counter--;
+ logger.debug("Ignoring cache query due to cache refresh: " + identifier + ", " + type);
+ return null;
+ }
+ return cache.getXmlNodeByQuery(identifier, type);
+ }
+
+ @Override
+ public String getStringByQuery(String identifier, CacheType type) {
+ if (counter > 0) {
+ counter--;
+ logger.debug("Ignoring cache query due to cache refresh: " + identifier + ", " + type);
+ return null;
+ }
+ return cache.getStringByQuery(identifier, type);
+ }
+
+ @Override
+ public void setCachedQuery(String identifier, CacheType type, Object value) {
+ cache.setCachedQuery(identifier, type, value);
+ }
+
+ @Override
+ public void setCachedQuery(String identifier, CacheType type, Object value, int validDays) {
+ cache.setCachedQuery(identifier, type, value, validDays);
+ }
+
+ @Override
+ public void clearCache() {
+ cache.clearCache();
+
+ }
+
+ @Override
+ public void removeByQuery(String identifier, CacheType type) {
+ cache.removeByQuery(identifier, type);
+ }
+
+ @Override
+ public void invalidateByQuery(String identifier, CacheType type) {
+ cache.invalidateByQuery(identifier, type);
+ }
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCache.java b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCache.java
index 92d56f5401..0ebe051926 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCache.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCache.java
@@ -1,586 +1,586 @@
-package lcsb.mapviewer.annotation.cache;
-
-import java.lang.reflect.Constructor;
-import java.util.Calendar;
-import java.util.concurrent.Callable;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-import java.util.concurrent.Future;
-import java.util.concurrent.ScheduledThreadPoolExecutor;
-import java.util.concurrent.ThreadFactory;
-
-import javax.annotation.PostConstruct;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.context.ApplicationContext;
-import org.springframework.context.ApplicationContextAware;
-import org.springframework.transaction.annotation.Transactional;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-
-import lcsb.mapviewer.common.XmlParser;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.model.cache.CacheQuery;
-import lcsb.mapviewer.model.cache.CacheType;
-import lcsb.mapviewer.persist.DbUtils;
-import lcsb.mapviewer.persist.dao.cache.CacheQueryDao;
-
-/**
- * Implementation of database level cache (
- * {@link PermanentDatabaseLevelCacheInterface}). The bean implements
- * {@link ApplicationContextAware} to be able to inject dependencies into
- * {@link CachableInterface} classes that are responsible for specific parts of
- * the cache. Every single task in this implementation is performed in new
- * transaction (and separate thread).
- *
- * @author Piotr Gawron
- *
- */
-@Transactional(value = "txManager")
-public class PermanentDatabaseLevelCache extends XmlParser
- implements PermanentDatabaseLevelCacheInterface, ApplicationContextAware {
-
- /**
- * This class represents new thread task for querying database.
- *
- * @author Piotr Gawron
- *
- */
- private final class QueryTask implements Callable<CacheQuery> {
-
- /**
- * Identifier of cached entry.
- *
- * @see CacheQuery#query
- */
- private String query;
-
- /**
- * Type of cached entry.
- *
- * @see CacheQuery#type
- */
- private CacheType type;
-
- /**
- * Default constructor.
- *
- * @param query
- * {@link #query}
- * @param type
- * {@link #type}
- */
- private QueryTask(String query, CacheType type) {
- logger.debug("Query task start");
- this.query = query;
- this.type = type;
- }
-
- @Override
- public CacheQuery call() throws Exception {
- logger.debug("Query task call");
- try {
- dbUtils.createSessionForCurrentThread();
- logger.debug("Query task session started");
- CacheQuery entry = getCacheQueryDao().getByQuery((String) query, type);
- logger.debug("Query task data retrieved");
- return entry;
- } finally {
- dbUtils.closeSessionForCurrentThread();
- }
- }
-
- }
-
- /**
- * This class represents new thread task for refreshing element in db.
- *
- * @author Piotr Gawron
- *
- */
- private final class RefreshTask implements Callable<CacheQuery> {
-
- /**
- * Identifier of cached entry.
- *
- * @see CacheQuery#query
- */
- private String query;
-
- /**
- * Type of cached entry.
- *
- * @see CacheQuery#type
- */
- private CacheType type;
-
- /**
- * Default constructor.
- *
- * @param query
- * {@link #query}
- * @param type
- * {@link #type}
- */
- private RefreshTask(String query, CacheType type) {
- logger.debug("Refresh task start (query: " + query + ")");
- this.query = query;
- this.type = type;
- }
-
- @Override
- public CacheQuery call() throws Exception {
- logger.debug("Refresh task call");
- CachableInterface cachableInterface = null;
- try {
- Constructor<?> ctor;
- Class<?> clazz = Class.forName(type.getClassName());
- ctor = clazz.getConstructor();
- Object object = ctor.newInstance();
- if (object instanceof CachableInterface) {
- cachableInterface = (CachableInterface) object;
- } else {
- logger.fatal(
- "Invalid class type: " + object.getClass() + ". Class cannot be cast into " + CachableInterface.class);
- }
- applicationContext.getAutowireCapableBeanFactory().autowireBean(object);
-
- } catch (Exception e) {
- logger.fatal("Problem with creating cache query updater", e);
- }
- if (cachableInterface != null) {
- cachableInterface.setCache(new GeneralCacheWithExclusion(cachableInterface.getCache(), 1));
- dbUtils.createSessionForCurrentThread();
- logger.debug("Refresh task session started");
- try {
- Object result = cachableInterface.refreshCacheQuery(query);
- if (result == null) {
- removeByQuery(query, type);
- } else {
- setCachedQuery(query, type, result);
-
- }
- } catch (SourceNotAvailable e) {
- logger.error("Cannot refresh cache", e);
- } catch (InvalidArgumentException e) {
- removeByQuery(query, type);
- logger.error("Problem with refreshing. Invalid data to refresh", e);
- } catch (Exception e) {
- logger.error("Severe problem in cache", e);
- } finally {
- // close the transaction for this thread
- dbUtils.closeSessionForCurrentThread();
- logger.debug("Refresh task session closed");
- }
- }
- logger.debug("Refresh task finish");
- final Future<CacheQuery> task = service.submit(new QueryTask(query, type));
- return task.get();
- }
-
- }
-
- /**
- * This class represents new thread task for adding entry to database.
- *
- * @author Piotr Gawron
- *
- */
- private final class AddTask implements Callable<CacheQuery> {
-
- /**
- * Identifier of cached entry.
- *
- * @see CacheQuery#query
- */
- private String query;
-
- /**
- * Type of cached entry.
- *
- * @see CacheQuery#type
- */
- private CacheType type;
-
- /**
- * Value to cache.
- *
- * @see CacheQuery#value
- */
- private String value;
-
- /**
- * How long should the entry be valid in days.
- *
- */
- private int validDays;
-
- /**
- * Default constructor.
- *
- * @param query
- * {@link #query}
- * @param type
- * {@link #type}
- * @param value
- * {@link #value}
- */
- private AddTask(String query, CacheType type, String value, int validDays) {
- logger.debug("Add task start");
- this.query = query;
- this.type = type;
- this.value = value;
- this.validDays = validDays;
- }
-
- @Override
- public CacheQuery call() throws Exception {
- logger.debug("Add task call");
- try {
- dbUtils.createSessionForCurrentThread();
- CacheQuery entry = getCacheQueryDao().getByQuery((String) query, type);
-
- if (entry == null) {
- entry = new CacheQuery();
- entry.setQuery((String) query);
- entry.setAccessed(Calendar.getInstance());
- } else {
- entry.setAccessed(Calendar.getInstance());
- }
- entry.setValue(value);
- entry.setType(type);
- Calendar expires = Calendar.getInstance();
- expires.add(Calendar.DAY_OF_MONTH, validDays);
- entry.setExpires(expires);
-
- getCacheQueryDao().add(entry);
- return entry;
- } finally {
- dbUtils.closeSessionForCurrentThread();
- }
- }
-
- }
-
- /**
- * This class represents new thread task for removing entry from database.
- *
- * @author Piotr Gawron
- *
- */
- private final class RemoveTask implements Callable<CacheQuery> {
-
- /**
- * Identifier of cached entry.
- *
- * @see CacheQuery#query
- */
- private String query;
-
- /**
- * Type of cached entry.
- *
- * @see CacheQuery#type
- */
- private CacheType type;
-
- /**
- * Default constructor.
- *
- * @param query
- * {@link #query}
- * @param type
- * {@link #type}
- */
- private RemoveTask(String query, CacheType type) {
- logger.debug("Remove task start");
- this.query = query;
- this.type = type;
- }
-
- @Override
- public CacheQuery call() throws Exception {
- logger.debug("Remove task call");
- try {
- dbUtils.createSessionForCurrentThread();
- CacheQuery entry = getCacheQueryDao().getByQuery((String) query, type);
- if (entry != null) {
- getCacheQueryDao().delete(entry);
- }
- return entry;
- } finally {
- dbUtils.closeSessionForCurrentThread();
- }
- }
-
- }
-
- /**
- * This class represents new thread task for invalidating entry in database.
- *
- * @author Piotr Gawron
- *
- */
- private final class InvalidateTask implements Callable<CacheQuery> {
-
- /**
- * Identifier of cached entry.
- */
- private String query;
-
- /**
- * Type of cached entry.
- */
- private CacheType type;
-
- /**
- * Default constructor.
- *
- * @param query
- * {@link #query}
- * @param type
- * {@link #type}
- */
- private InvalidateTask(String query, CacheType type) {
- logger.debug("Invalidate task start");
- this.query = query;
- this.type = type;
- }
-
- @Override
- public CacheQuery call() throws Exception {
- logger.debug("Invalidate task call");
- dbUtils.createSessionForCurrentThread();
- try {
- Calendar date = Calendar.getInstance();
-
- date.add(Calendar.DATE, -1);
-
- CacheQuery entry = getCacheQueryDao().getByQuery(query, type);
- if (entry != null) {
- entry.setExpires(date);
- getCacheQueryDao().update(entry);
- cacheRefreshService.submit(new RefreshTask(query, type));
- }
- return entry;
- } finally {
- // close session even when we had a problem
- dbUtils.closeSessionForCurrentThread();
- }
- }
-
- }
-
- /**
- * Spring application context.
- */
- private static ApplicationContext applicationContext;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(PermanentDatabaseLevelCache.class);
-
- /**
- * Data access object for query entries accessed by string key.
- */
- @Autowired
- private CacheQueryDao cacheQueryDao;
-
- /**
- * Utility that help to manage the sessions in custom multithreaded
- * implementation.
- */
- @Autowired
- private DbUtils dbUtils;
-
- /**
- * Service used for executing database tasks in separate thread.
- */
- private ExecutorService service;
-
- /**
- * This service is used for execution and queue of the refresh entries in the
- * database.
- */
- private ExecutorService cacheRefreshService;
-
- /**
- * Post init spring method used for initialization of {@link #service} used for
- * execution of db tasks.
- */
- @PostConstruct
- public void init() {
- // the executor is a daemon thread so that it will get killed automatically
- // when the main program exits
- service = Executors.newScheduledThreadPool(1, new ThreadFactory() {
- @Override
- public Thread newThread(Runnable r) {
- Thread t = new Thread(r);
- t.setDaemon(true);
- return t;
- }
- });
- cacheRefreshService = Executors.newScheduledThreadPool(1, new ThreadFactory() {
- @Override
- public Thread newThread(Runnable r) {
- Thread t = new Thread(r);
- t.setDaemon(true);
- return t;
- }
- });
-
- // put in the queue empty task to make sure that everything was initialized
- // (additional managing thread was created)
- service.submit(new Callable<Object>() {
- @Override
- public Object call() throws Exception {
- return null;
- }
- });
- cacheRefreshService.submit(new Callable<Object>() {
- @Override
- public Object call() throws Exception {
- return null;
- }
- });
- }
-
- @Override
- public void clearCache() {
- cacheQueryDao.clearTable();
- }
-
- @Override
- public Node getXmlNodeByQuery(String query, CacheType type) {
- final Future<CacheQuery> task = service.submit(new QueryTask(query, type));
- CacheQuery entry = executeTask(task);
-
- if (entry == null) {
- return null;
- }
- try {
- Document document = getXmlDocumentFromString(entry.getValue());
- Calendar currentDate = Calendar.getInstance();
- if (currentDate.after(entry.getExpires())) {
- cacheRefreshService.submit(new RefreshTask(query, type));
- }
- Node result = null;
- if (document != null) {
- result = document.getFirstChild();
- }
- return result;
- } catch (InvalidXmlSchemaException e) {
- logger.warn("Invalid xml for query: " + query);
- logger.warn("xml: " + entry.getValue());
- removeByQuery(query, type);
- return null;
- }
- }
-
- @Override
- public String getStringByQuery(String query, CacheType type) {
- Calendar currentDate = Calendar.getInstance();
- final Future<CacheQuery> task = service.submit(new QueryTask(query, type));
- CacheQuery entry = executeTask(task);
- if (entry == null) {
- return null;
- }
- if (currentDate.before(entry.getExpires())) {
- return entry.getValue();
- } else {
- cacheRefreshService.submit(new RefreshTask(query, type));
- return entry.getValue();
- }
- }
-
- @Override
- public void setCachedQuery(String query, CacheType type, Object object) {
- setCachedQuery(query, type, object, type.getValidity());
- }
-
- @Override
- public void setCachedQuery(String query, CacheType type, Object object, int validDays) {
- String value = null;
- if (object instanceof String) {
- value = (String) object;
- } else if (object instanceof Node) {
- value = nodeToString((Node) object, true);
- } else if (object == null) {
- value = null;
- } else {
- throw new CacheException("Unknown object type: " + object.getClass());
- }
- if (value == null) {
- removeByQuery(query, type);
- } else {
- final Future<CacheQuery> task = service.submit(new AddTask(query, type, value, validDays));
- executeTask(task);
- }
- }
-
- @Override
- public void removeByQuery(String query, CacheType type) {
- final Future<CacheQuery> task = service.submit(new RemoveTask(query, type));
- executeTask(task);
- }
-
- @Override
- public void invalidateByQuery(String query, CacheType type) {
- final Future<CacheQuery> task = service.submit(new InvalidateTask(query, type));
- executeTask(task);
- }
-
- /**
- * Executes and returns result of the task provided in the parameter. This
- * method is blocking (it's waiting for the results).
- *
- * @param task
- * task to be executed
- * @return value returned by the task
- */
- private CacheQuery executeTask(final Future<CacheQuery> task) {
- try {
- return task.get();
- } catch (InterruptedException e1) {
- logger.error(e1, e1);
- } catch (ExecutionException e1) {
- logger.error(e1, e1);
- }
- return null;
- }
-
- @Override
- public void setApplicationContext(ApplicationContext arg0) {
- applicationContext = arg0;
- }
-
- @Override
- public int getRefreshPendingQueueSize() {
- return ((ScheduledThreadPoolExecutor) cacheRefreshService).getQueue().size();
- }
-
- @Override
- public boolean refreshIsBusy() {
- return getRefreshPendingQueueSize() != 0 || getRefreshExecutingTasksSize() != 0;
- }
-
- @Override
- public int getRefreshExecutingTasksSize() {
- return ((ScheduledThreadPoolExecutor) cacheRefreshService).getActiveCount();
- }
-
- @Override
- public CacheQueryDao getCacheQueryDao() {
- return cacheQueryDao;
- }
-
- @Override
- public void setCacheQueryDao(CacheQueryDao cacheQueryDao) {
- this.cacheQueryDao = cacheQueryDao;
- }
-
+package lcsb.mapviewer.annotation.cache;
+
+import java.lang.reflect.Constructor;
+import java.util.Calendar;
+import java.util.concurrent.Callable;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
+import java.util.concurrent.ScheduledThreadPoolExecutor;
+import java.util.concurrent.ThreadFactory;
+
+import javax.annotation.PostConstruct;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.ApplicationContext;
+import org.springframework.context.ApplicationContextAware;
+import org.springframework.transaction.annotation.Transactional;
+import org.w3c.dom.Document;
+import org.w3c.dom.Node;
+
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.model.cache.CacheQuery;
+import lcsb.mapviewer.model.cache.CacheType;
+import lcsb.mapviewer.persist.DbUtils;
+import lcsb.mapviewer.persist.dao.cache.CacheQueryDao;
+
+/**
+ * Implementation of database level cache (
+ * {@link PermanentDatabaseLevelCacheInterface}). The bean implements
+ * {@link ApplicationContextAware} to be able to inject dependencies into
+ * {@link CachableInterface} classes that are responsible for specific parts of
+ * the cache. Every single task in this implementation is performed in new
+ * transaction (and separate thread).
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Transactional(value = "txManager")
+public class PermanentDatabaseLevelCache extends XmlParser
+ implements PermanentDatabaseLevelCacheInterface, ApplicationContextAware {
+
+ /**
+ * This class represents new thread task for querying database.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ private final class QueryTask implements Callable<CacheQuery> {
+
+ /**
+ * Identifier of cached entry.
+ *
+ * @see CacheQuery#query
+ */
+ private String query;
+
+ /**
+ * Type of cached entry.
+ *
+ * @see CacheQuery#type
+ */
+ private CacheType type;
+
+ /**
+ * Default constructor.
+ *
+ * @param query
+ * {@link #query}
+ * @param type
+ * {@link #type}
+ */
+ private QueryTask(String query, CacheType type) {
+ logger.debug("Query task start");
+ this.query = query;
+ this.type = type;
+ }
+
+ @Override
+ public CacheQuery call() throws Exception {
+ logger.debug("Query task call");
+ try {
+ dbUtils.createSessionForCurrentThread();
+ logger.debug("Query task session started");
+ CacheQuery entry = getCacheQueryDao().getByQuery((String) query, type);
+ logger.debug("Query task data retrieved");
+ return entry;
+ } finally {
+ dbUtils.closeSessionForCurrentThread();
+ }
+ }
+
+ }
+
+ /**
+ * This class represents new thread task for refreshing element in db.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ private final class RefreshTask implements Callable<CacheQuery> {
+
+ /**
+ * Identifier of cached entry.
+ *
+ * @see CacheQuery#query
+ */
+ private String query;
+
+ /**
+ * Type of cached entry.
+ *
+ * @see CacheQuery#type
+ */
+ private CacheType type;
+
+ /**
+ * Default constructor.
+ *
+ * @param query
+ * {@link #query}
+ * @param type
+ * {@link #type}
+ */
+ private RefreshTask(String query, CacheType type) {
+ logger.debug("Refresh task start (query: " + query + ")");
+ this.query = query;
+ this.type = type;
+ }
+
+ @Override
+ public CacheQuery call() throws Exception {
+ logger.debug("Refresh task call");
+ CachableInterface cachableInterface = null;
+ try {
+ Constructor<?> ctor;
+ Class<?> clazz = Class.forName(type.getClassName());
+ ctor = clazz.getConstructor();
+ Object object = ctor.newInstance();
+ if (object instanceof CachableInterface) {
+ cachableInterface = (CachableInterface) object;
+ } else {
+ logger.fatal(
+ "Invalid class type: " + object.getClass() + ". Class cannot be cast into " + CachableInterface.class);
+ }
+ applicationContext.getAutowireCapableBeanFactory().autowireBean(object);
+
+ } catch (Exception e) {
+ logger.fatal("Problem with creating cache query updater", e);
+ }
+ if (cachableInterface != null) {
+ cachableInterface.setCache(new GeneralCacheWithExclusion(cachableInterface.getCache(), 1));
+ dbUtils.createSessionForCurrentThread();
+ logger.debug("Refresh task session started");
+ try {
+ Object result = cachableInterface.refreshCacheQuery(query);
+ if (result == null) {
+ removeByQuery(query, type);
+ } else {
+ setCachedQuery(query, type, result);
+
+ }
+ } catch (SourceNotAvailable e) {
+ logger.error("Cannot refresh cache", e);
+ } catch (InvalidArgumentException e) {
+ removeByQuery(query, type);
+ logger.error("Problem with refreshing. Invalid data to refresh", e);
+ } catch (Exception e) {
+ logger.error("Severe problem in cache", e);
+ } finally {
+ // close the transaction for this thread
+ dbUtils.closeSessionForCurrentThread();
+ logger.debug("Refresh task session closed");
+ }
+ }
+ logger.debug("Refresh task finish");
+ final Future<CacheQuery> task = service.submit(new QueryTask(query, type));
+ return task.get();
+ }
+
+ }
+
+ /**
+ * This class represents new thread task for adding entry to database.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ private final class AddTask implements Callable<CacheQuery> {
+
+ /**
+ * Identifier of cached entry.
+ *
+ * @see CacheQuery#query
+ */
+ private String query;
+
+ /**
+ * Type of cached entry.
+ *
+ * @see CacheQuery#type
+ */
+ private CacheType type;
+
+ /**
+ * Value to cache.
+ *
+ * @see CacheQuery#value
+ */
+ private String value;
+
+ /**
+ * How long should the entry be valid in days.
+ *
+ */
+ private int validDays;
+
+ /**
+ * Default constructor.
+ *
+ * @param query
+ * {@link #query}
+ * @param type
+ * {@link #type}
+ * @param value
+ * {@link #value}
+ */
+ private AddTask(String query, CacheType type, String value, int validDays) {
+ logger.debug("Add task start");
+ this.query = query;
+ this.type = type;
+ this.value = value;
+ this.validDays = validDays;
+ }
+
+ @Override
+ public CacheQuery call() throws Exception {
+ logger.debug("Add task call");
+ try {
+ dbUtils.createSessionForCurrentThread();
+ CacheQuery entry = getCacheQueryDao().getByQuery((String) query, type);
+
+ if (entry == null) {
+ entry = new CacheQuery();
+ entry.setQuery((String) query);
+ entry.setAccessed(Calendar.getInstance());
+ } else {
+ entry.setAccessed(Calendar.getInstance());
+ }
+ entry.setValue(value);
+ entry.setType(type);
+ Calendar expires = Calendar.getInstance();
+ expires.add(Calendar.DAY_OF_MONTH, validDays);
+ entry.setExpires(expires);
+
+ getCacheQueryDao().add(entry);
+ return entry;
+ } finally {
+ dbUtils.closeSessionForCurrentThread();
+ }
+ }
+
+ }
+
+ /**
+ * This class represents new thread task for removing entry from database.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ private final class RemoveTask implements Callable<CacheQuery> {
+
+ /**
+ * Identifier of cached entry.
+ *
+ * @see CacheQuery#query
+ */
+ private String query;
+
+ /**
+ * Type of cached entry.
+ *
+ * @see CacheQuery#type
+ */
+ private CacheType type;
+
+ /**
+ * Default constructor.
+ *
+ * @param query
+ * {@link #query}
+ * @param type
+ * {@link #type}
+ */
+ private RemoveTask(String query, CacheType type) {
+ logger.debug("Remove task start");
+ this.query = query;
+ this.type = type;
+ }
+
+ @Override
+ public CacheQuery call() throws Exception {
+ logger.debug("Remove task call");
+ try {
+ dbUtils.createSessionForCurrentThread();
+ CacheQuery entry = getCacheQueryDao().getByQuery((String) query, type);
+ if (entry != null) {
+ getCacheQueryDao().delete(entry);
+ }
+ return entry;
+ } finally {
+ dbUtils.closeSessionForCurrentThread();
+ }
+ }
+
+ }
+
+ /**
+ * This class represents new thread task for invalidating entry in database.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ private final class InvalidateTask implements Callable<CacheQuery> {
+
+ /**
+ * Identifier of cached entry.
+ */
+ private String query;
+
+ /**
+ * Type of cached entry.
+ */
+ private CacheType type;
+
+ /**
+ * Default constructor.
+ *
+ * @param query
+ * {@link #query}
+ * @param type
+ * {@link #type}
+ */
+ private InvalidateTask(String query, CacheType type) {
+ logger.debug("Invalidate task start");
+ this.query = query;
+ this.type = type;
+ }
+
+ @Override
+ public CacheQuery call() throws Exception {
+ logger.debug("Invalidate task call");
+ dbUtils.createSessionForCurrentThread();
+ try {
+ Calendar date = Calendar.getInstance();
+
+ date.add(Calendar.DATE, -1);
+
+ CacheQuery entry = getCacheQueryDao().getByQuery(query, type);
+ if (entry != null) {
+ entry.setExpires(date);
+ getCacheQueryDao().update(entry);
+ cacheRefreshService.submit(new RefreshTask(query, type));
+ }
+ return entry;
+ } finally {
+ // close session even when we had a problem
+ dbUtils.closeSessionForCurrentThread();
+ }
+ }
+
+ }
+
+ /**
+ * Spring application context.
+ */
+ private static ApplicationContext applicationContext;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(PermanentDatabaseLevelCache.class);
+
+ /**
+ * Data access object for query entries accessed by string key.
+ */
+ @Autowired
+ private CacheQueryDao cacheQueryDao;
+
+ /**
+ * Utility that help to manage the sessions in custom multithreaded
+ * implementation.
+ */
+ @Autowired
+ private DbUtils dbUtils;
+
+ /**
+ * Service used for executing database tasks in separate thread.
+ */
+ private ExecutorService service;
+
+ /**
+ * This service is used for execution and queue of the refresh entries in the
+ * database.
+ */
+ private ExecutorService cacheRefreshService;
+
+ /**
+ * Post init spring method used for initialization of {@link #service} used for
+ * execution of db tasks.
+ */
+ @PostConstruct
+ public void init() {
+ // the executor is a daemon thread so that it will get killed automatically
+ // when the main program exits
+ service = Executors.newScheduledThreadPool(1, new ThreadFactory() {
+ @Override
+ public Thread newThread(Runnable r) {
+ Thread t = new Thread(r);
+ t.setDaemon(true);
+ return t;
+ }
+ });
+ cacheRefreshService = Executors.newScheduledThreadPool(1, new ThreadFactory() {
+ @Override
+ public Thread newThread(Runnable r) {
+ Thread t = new Thread(r);
+ t.setDaemon(true);
+ return t;
+ }
+ });
+
+ // put in the queue empty task to make sure that everything was initialized
+ // (additional managing thread was created)
+ service.submit(new Callable<Object>() {
+ @Override
+ public Object call() throws Exception {
+ return null;
+ }
+ });
+ cacheRefreshService.submit(new Callable<Object>() {
+ @Override
+ public Object call() throws Exception {
+ return null;
+ }
+ });
+ }
+
+ @Override
+ public void clearCache() {
+ cacheQueryDao.clearTable();
+ }
+
+ @Override
+ public Node getXmlNodeByQuery(String query, CacheType type) {
+ final Future<CacheQuery> task = service.submit(new QueryTask(query, type));
+ CacheQuery entry = executeTask(task);
+
+ if (entry == null) {
+ return null;
+ }
+ try {
+ Document document = getXmlDocumentFromString(entry.getValue());
+ Calendar currentDate = Calendar.getInstance();
+ if (currentDate.after(entry.getExpires())) {
+ cacheRefreshService.submit(new RefreshTask(query, type));
+ }
+ Node result = null;
+ if (document != null) {
+ result = document.getFirstChild();
+ }
+ return result;
+ } catch (InvalidXmlSchemaException e) {
+ logger.warn("Invalid xml for query: " + query);
+ logger.warn("xml: " + entry.getValue());
+ removeByQuery(query, type);
+ return null;
+ }
+ }
+
+ @Override
+ public String getStringByQuery(String query, CacheType type) {
+ Calendar currentDate = Calendar.getInstance();
+ final Future<CacheQuery> task = service.submit(new QueryTask(query, type));
+ CacheQuery entry = executeTask(task);
+ if (entry == null) {
+ return null;
+ }
+ if (currentDate.before(entry.getExpires())) {
+ return entry.getValue();
+ } else {
+ cacheRefreshService.submit(new RefreshTask(query, type));
+ return entry.getValue();
+ }
+ }
+
+ @Override
+ public void setCachedQuery(String query, CacheType type, Object object) {
+ setCachedQuery(query, type, object, type.getValidity());
+ }
+
+ @Override
+ public void setCachedQuery(String query, CacheType type, Object object, int validDays) {
+ String value = null;
+ if (object instanceof String) {
+ value = (String) object;
+ } else if (object instanceof Node) {
+ value = nodeToString((Node) object, true);
+ } else if (object == null) {
+ value = null;
+ } else {
+ throw new CacheException("Unknown object type: " + object.getClass());
+ }
+ if (value == null) {
+ removeByQuery(query, type);
+ } else {
+ final Future<CacheQuery> task = service.submit(new AddTask(query, type, value, validDays));
+ executeTask(task);
+ }
+ }
+
+ @Override
+ public void removeByQuery(String query, CacheType type) {
+ final Future<CacheQuery> task = service.submit(new RemoveTask(query, type));
+ executeTask(task);
+ }
+
+ @Override
+ public void invalidateByQuery(String query, CacheType type) {
+ final Future<CacheQuery> task = service.submit(new InvalidateTask(query, type));
+ executeTask(task);
+ }
+
+ /**
+ * Executes and returns result of the task provided in the parameter. This
+ * method is blocking (it's waiting for the results).
+ *
+ * @param task
+ * task to be executed
+ * @return value returned by the task
+ */
+ private CacheQuery executeTask(final Future<CacheQuery> task) {
+ try {
+ return task.get();
+ } catch (InterruptedException e1) {
+ logger.error(e1, e1);
+ } catch (ExecutionException e1) {
+ logger.error(e1, e1);
+ }
+ return null;
+ }
+
+ @Override
+ public void setApplicationContext(ApplicationContext arg0) {
+ applicationContext = arg0;
+ }
+
+ @Override
+ public int getRefreshPendingQueueSize() {
+ return ((ScheduledThreadPoolExecutor) cacheRefreshService).getQueue().size();
+ }
+
+ @Override
+ public boolean refreshIsBusy() {
+ return getRefreshPendingQueueSize() != 0 || getRefreshExecutingTasksSize() != 0;
+ }
+
+ @Override
+ public int getRefreshExecutingTasksSize() {
+ return ((ScheduledThreadPoolExecutor) cacheRefreshService).getActiveCount();
+ }
+
+ @Override
+ public CacheQueryDao getCacheQueryDao() {
+ return cacheQueryDao;
+ }
+
+ @Override
+ public void setCacheQueryDao(CacheQueryDao cacheQueryDao) {
+ this.cacheQueryDao = cacheQueryDao;
+ }
+
}
\ No newline at end of file
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCacheInterface.java b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCacheInterface.java
index 438685d1fe..6faff6f509 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCacheInterface.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCacheInterface.java
@@ -1,51 +1,51 @@
-package lcsb.mapviewer.annotation.cache;
-
-import lcsb.mapviewer.persist.dao.cache.CacheQueryDao;
-
-/**
- * Interface describing database level cache. It has the same functionality as
- * {@link QueryCacheInterface}. It allows to cache data within application
- * scope. After application restarts everything is lost.
- *
- * @author Piotr Gawron
- *
- */
-public interface PermanentDatabaseLevelCacheInterface extends QueryCacheInterface {
-
- /**
- * Returns how many tasks are pending for refreshing.
- *
- * @return how many tasks are pending for refreshing.
- */
- int getRefreshPendingQueueSize();
-
- /**
- * Returns true if refreshing of entries in database is in progress.
- *
- * @return true if refreshing of entries in database is in progress.
- */
- boolean refreshIsBusy();
-
- /**
- * Returns approximate number of refresh tasks that are currently executed.
- *
- * @return approximate number of refresh tasks that are currently executed.
- */
- int getRefreshExecutingTasksSize();
-
- /**
- * Returns {@link CacheQueryDao} used by the cache.
- *
- * @return {@link CacheQueryDao} used by the cache
- */
- CacheQueryDao getCacheQueryDao();
-
- /**
- * Sets {@link CacheQueryDao}.
- *
- * @param cacheQueryDao
- * new {@link CacheQueryDao} used by the cache
- */
- void setCacheQueryDao(CacheQueryDao cacheQueryDao);
-
-}
+package lcsb.mapviewer.annotation.cache;
+
+import lcsb.mapviewer.persist.dao.cache.CacheQueryDao;
+
+/**
+ * Interface describing database level cache. It has the same functionality as
+ * {@link QueryCacheInterface}. It allows to cache data within application
+ * scope. After application restarts everything is lost.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface PermanentDatabaseLevelCacheInterface extends QueryCacheInterface {
+
+ /**
+ * Returns how many tasks are pending for refreshing.
+ *
+ * @return how many tasks are pending for refreshing.
+ */
+ int getRefreshPendingQueueSize();
+
+ /**
+ * Returns true if refreshing of entries in database is in progress.
+ *
+ * @return true if refreshing of entries in database is in progress.
+ */
+ boolean refreshIsBusy();
+
+ /**
+ * Returns approximate number of refresh tasks that are currently executed.
+ *
+ * @return approximate number of refresh tasks that are currently executed.
+ */
+ int getRefreshExecutingTasksSize();
+
+ /**
+ * Returns {@link CacheQueryDao} used by the cache.
+ *
+ * @return {@link CacheQueryDao} used by the cache
+ */
+ CacheQueryDao getCacheQueryDao();
+
+ /**
+ * Sets {@link CacheQueryDao}.
+ *
+ * @param cacheQueryDao
+ * new {@link CacheQueryDao} used by the cache
+ */
+ void setCacheQueryDao(CacheQueryDao cacheQueryDao);
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/QueryCacheInterface.java b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/QueryCacheInterface.java
index bb18339908..6c84091a5c 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/QueryCacheInterface.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/QueryCacheInterface.java
@@ -1,80 +1,80 @@
-package lcsb.mapviewer.annotation.cache;
-
-import lcsb.mapviewer.model.cache.CacheType;
-
-import org.w3c.dom.Node;
-
-/**
- * This interface describes general functionality of the cache interface.
- *
- * @author Piotr Gawron
- *
- */
-public interface QueryCacheInterface {
-
- /**
- * Returns xml node from the cache. The entry (xml node in this case) is
- * identified by string and type associated with the entry.
- *
- * @param identifier
- * string identifying node in the database
- * @param type
- * type of the entry
- * @return node from cache for given identifier and type
- */
- Node getXmlNodeByQuery(String identifier, CacheType type);
-
- /**
- * Returns string from the cache. The entry (string in this case) is identified
- * by string and type associated with the entry.
- *
- * @param identifier
- * string identifying node in the database
- * @param type
- * type of the entry
- * @return node from cache for given string identifier and type
- */
- String getStringByQuery(String identifier, CacheType type);
-
- /**
- * Puts new value into cache. The entry is identified with type and identifier.
- *
- * @param identifier
- * string identifying entry in the database
- * @param type
- * type of the entry
- * @param value
- * value to be stored in the cache
- */
- void setCachedQuery(String identifier, CacheType type, Object value);
-
- void setCachedQuery(String identifier, CacheType type, Object value, int validDays);
-
- /**
- * Clears permanently whole cache.
- */
- void clearCache();
-
- /**
- * Removes element from the database.
- *
- * @param identifier
- * string identifying entry in the database
- * @param type
- * type of the entry
- */
- void removeByQuery(String identifier, CacheType type);
-
- /**
- * This method invalidate result, but doesn't remove it (data should be
- * available until resource will be updated from original source). Moreover,
- * value reload method is called.
- *
- * @param identifier
- * string identifying entry in the database
- * @param type
- * type of the entry
- */
- void invalidateByQuery(String identifier, CacheType type);
-
-}
+package lcsb.mapviewer.annotation.cache;
+
+import lcsb.mapviewer.model.cache.CacheType;
+
+import org.w3c.dom.Node;
+
+/**
+ * This interface describes general functionality of the cache interface.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface QueryCacheInterface {
+
+ /**
+ * Returns xml node from the cache. The entry (xml node in this case) is
+ * identified by string and type associated with the entry.
+ *
+ * @param identifier
+ * string identifying node in the database
+ * @param type
+ * type of the entry
+ * @return node from cache for given identifier and type
+ */
+ Node getXmlNodeByQuery(String identifier, CacheType type);
+
+ /**
+ * Returns string from the cache. The entry (string in this case) is identified
+ * by string and type associated with the entry.
+ *
+ * @param identifier
+ * string identifying node in the database
+ * @param type
+ * type of the entry
+ * @return node from cache for given string identifier and type
+ */
+ String getStringByQuery(String identifier, CacheType type);
+
+ /**
+ * Puts new value into cache. The entry is identified with type and identifier.
+ *
+ * @param identifier
+ * string identifying entry in the database
+ * @param type
+ * type of the entry
+ * @param value
+ * value to be stored in the cache
+ */
+ void setCachedQuery(String identifier, CacheType type, Object value);
+
+ void setCachedQuery(String identifier, CacheType type, Object value, int validDays);
+
+ /**
+ * Clears permanently whole cache.
+ */
+ void clearCache();
+
+ /**
+ * Removes element from the database.
+ *
+ * @param identifier
+ * string identifying entry in the database
+ * @param type
+ * type of the entry
+ */
+ void removeByQuery(String identifier, CacheType type);
+
+ /**
+ * This method invalidate result, but doesn't remove it (data should be
+ * available until resource will be updated from original source). Moreover,
+ * value reload method is called.
+ *
+ * @param identifier
+ * string identifying entry in the database
+ * @param type
+ * type of the entry
+ */
+ void invalidateByQuery(String identifier, CacheType type);
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/SourceNotAvailable.java b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/SourceNotAvailable.java
index 506296dadb..29c7bf36fb 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/SourceNotAvailable.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/SourceNotAvailable.java
@@ -1,49 +1,49 @@
-package lcsb.mapviewer.annotation.cache;
-
-/**
- * Exception thrown when source of the data that is stored in database is no
- * longer available.
- *
- * @author Piotr Gawron
- *
- */
-public class SourceNotAvailable extends Exception {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Public constructor with parent exception that was catched.
- *
- * @param e
- * parent exception
- */
- public SourceNotAvailable(Exception e) {
- super(e);
- }
-
- /**
- * Constructor receives some kind of message.
- *
- * @param message
- * message associated with exception
- */
- public SourceNotAvailable(String message) {
- super(message);
- }
-
- /**
- * Public constructor with parent exception that was catched.
- *
- * @param message
- * message associated with exception
- * @param e
- * parent exception
- */
- public SourceNotAvailable(String message, Exception e) {
- super(message, e);
- }
-
-}
+package lcsb.mapviewer.annotation.cache;
+
+/**
+ * Exception thrown when source of the data that is stored in database is no
+ * longer available.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class SourceNotAvailable extends Exception {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Public constructor with parent exception that was catched.
+ *
+ * @param e
+ * parent exception
+ */
+ public SourceNotAvailable(Exception e) {
+ super(e);
+ }
+
+ /**
+ * Constructor receives some kind of message.
+ *
+ * @param message
+ * message associated with exception
+ */
+ public SourceNotAvailable(String message) {
+ super(message);
+ }
+
+ /**
+ * Public constructor with parent exception that was catched.
+ *
+ * @param message
+ * message associated with exception
+ * @param e
+ * parent exception
+ */
+ public SourceNotAvailable(String message, Exception e) {
+ super(message, e);
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/WebPageDownloader.java b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/WebPageDownloader.java
index 5f468f1ad1..05e3f7d406 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/WebPageDownloader.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/WebPageDownloader.java
@@ -1,191 +1,191 @@
-package lcsb.mapviewer.annotation.cache;
-
-import java.io.BufferedReader;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.DataOutputStream;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.concurrent.Callable;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-import java.util.concurrent.Future;
-import java.util.concurrent.TimeUnit;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.annotation.services.WrongResponseCodeIOException;
-
-/**
- * This class helps to download web pages. The pages are downloaded in separate
- * thread, due to the fact that sometimes java socket can hang (related JVM bug:
- * https://bugs.openjdk.java.net/browse/JDK-8075484 ).
- *
- * @author Piotr Gawron
- *
- */
-/**
- * @author Piotr Gawron
- *
- */
-public class WebPageDownloader {
-
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(WebPageDownloader.class);
-
- /**
- * Hard timeout (threads are terminated) of http connection that access data
- * across Internet.
- */
- private static final int HTTP_CONNECTION_TIMEOUT_SEC = 120;
-
- /**
- * How much time should the thread sleep before another try to access the
- * web page that thrown INTERNAL SERVER ERROR http response.
- */
- private static final int HTTP_INTERNAL_ERROR_RECONNECT_SLEEP_TIME = 2000;
-
- /**
- * How many times should the thread retry to connect to the server after
- * receiving INTERNAL SERVER ERROR http response.
- */
- private static final int HTTP_INTERNAL_ERROR_RECONNECT_TIMES = 2;
-
-
-
- /**
- * Returns content of the web page identified by url.
- *
- * @param accessUrl
- * url of a web page
- * @return content of the web page identified by url
- * @throws IOException
- * thrown when there is any problem with accessing webpage
- */
- public String getFromNetwork(String accessUrl) throws IOException {
- return getFromNetwork(accessUrl, "GET", null);
- }
-
-
- /**
- * Returns content of the webpage identified by url. The HTTP query is done
- * using the provided POST if postData is not null.
- *
- *
- * @param accessUrl
- * url of a webpage
- * @param httpRequestMethod
- * type of HTTP request (GET, POST, PUT, PATCH, DELETE, ...)
- * @param data
- * string to be sent in the body of the
- * @return content of the webpage identified by url
- * @throws IOException
- * thrown when there is any problem with accessing webpage
- */
- public String getFromNetwork(String accessUrl, String httpRequestMethod, String data) throws IOException {
-
- /**
- * Tasks that retrieves content from web page
- *
- * @author Piotr Gawron
- *
- */
- class Task implements Callable<String> {
- private volatile String result = null;
-
- @Override
- public String call() throws Exception {
- int tries = 0;
- int code = HttpURLConnection.HTTP_INTERNAL_ERROR;
- HttpURLConnection urlConn = null;
-
- // connect to the server, if HTTP_INTERNAL_ERROR occurred then try to
- // reconnect HTTP_INTERNAL_ERROR_RECONNECT_TIMES times
- while (code == HttpURLConnection.HTTP_INTERNAL_ERROR || code == HttpURLConnection.HTTP_NOT_FOUND) {
- urlConn = openConnection(accessUrl);
- urlConn.addRequestProperty("User-Agent", "minerva-framework");
-
- urlConn.setRequestMethod(httpRequestMethod);
- if (data != null) {
- urlConn.setDoOutput(true);
- DataOutputStream wr = new DataOutputStream(urlConn.getOutputStream());
- wr.writeBytes(data);
- wr.close();
- }
-
- try {
- urlConn.connect();
- code = urlConn.getResponseCode();
- } catch (FileNotFoundException e) {
- code = HttpURLConnection.HTTP_NOT_FOUND;
- } catch (IOException e) {
- code = HttpURLConnection.HTTP_INTERNAL_ERROR;
- }
- tries++;
- if (tries > HTTP_INTERNAL_ERROR_RECONNECT_TIMES) {
- break;
- }
- if (code == HttpURLConnection.HTTP_INTERNAL_ERROR || code == HttpURLConnection.HTTP_NOT_FOUND) {
- logger.debug("Problem with webpage: " + accessUrl);
- logger.debug("Retrying: " + accessUrl);
- try {
- Thread.sleep(HTTP_INTERNAL_ERROR_RECONNECT_SLEEP_TIME);
- } catch (InterruptedException e) {
- }
- }
- }
- try {
- BufferedReader in = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));
- result = IOUtils.toString(in);
- } catch (IOException e) {
- if (e.getClass().equals(IOException.class) || e.getClass().equals(FileNotFoundException.class)) {
- throw new WrongResponseCodeIOException(e, code);
- } else {
- throw e;
- }
- }
- return result;
- }
-
- }
-
- ExecutorService executor = Executors.newSingleThreadExecutor();
- Future<String> future = executor.submit(new Task());
-
- try {
- String result = future.get(HTTP_CONNECTION_TIMEOUT_SEC, TimeUnit.SECONDS);
- executor.shutdownNow();
- return result;
- } catch (Exception e) {
- if (e.getCause() instanceof IOException) {
- throw (IOException) e.getCause();
- }
- throw new IOException("Problem with accessing webpage: " + accessUrl, e);
- }
- }
-
- /**
- * Opens {@link HttpURLConnection connection} to the url given in the
- * argument.
- *
- * @param accessUrl
- * url to the web page
- * @return {@link HttpURLConnection connection} to the url given in the
- * argument
- * @throws MalformedURLException
- * thrown when url is invalid
- * @throws IOException
- * thrown when there is problem with opening connection
- */
- HttpURLConnection openConnection(String accessUrl) throws MalformedURLException, IOException {
- URL url = new URL(accessUrl);
- HttpURLConnection urlConn = (HttpURLConnection) url.openConnection();
- return urlConn;
- }
-
-}
+package lcsb.mapviewer.annotation.cache;
+
+import java.io.BufferedReader;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.DataOutputStream;
+import java.net.HttpURLConnection;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.concurrent.Callable;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
+import java.util.concurrent.TimeUnit;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.annotation.services.WrongResponseCodeIOException;
+
+/**
+ * This class helps to download web pages. The pages are downloaded in separate
+ * thread, due to the fact that sometimes java socket can hang (related JVM bug:
+ * https://bugs.openjdk.java.net/browse/JDK-8075484 ).
+ *
+ * @author Piotr Gawron
+ *
+ */
+/**
+ * @author Piotr Gawron
+ *
+ */
+public class WebPageDownloader {
+
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(WebPageDownloader.class);
+
+ /**
+ * Hard timeout (threads are terminated) of http connection that access data
+ * across Internet.
+ */
+ private static final int HTTP_CONNECTION_TIMEOUT_SEC = 120;
+
+ /**
+ * How much time should the thread sleep before another try to access the
+ * web page that thrown INTERNAL SERVER ERROR http response.
+ */
+ private static final int HTTP_INTERNAL_ERROR_RECONNECT_SLEEP_TIME = 2000;
+
+ /**
+ * How many times should the thread retry to connect to the server after
+ * receiving INTERNAL SERVER ERROR http response.
+ */
+ private static final int HTTP_INTERNAL_ERROR_RECONNECT_TIMES = 2;
+
+
+
+ /**
+ * Returns content of the web page identified by url.
+ *
+ * @param accessUrl
+ * url of a web page
+ * @return content of the web page identified by url
+ * @throws IOException
+ * thrown when there is any problem with accessing webpage
+ */
+ public String getFromNetwork(String accessUrl) throws IOException {
+ return getFromNetwork(accessUrl, "GET", null);
+ }
+
+
+ /**
+ * Returns content of the webpage identified by url. The HTTP query is done
+ * using the provided POST if postData is not null.
+ *
+ *
+ * @param accessUrl
+ * url of a webpage
+ * @param httpRequestMethod
+ * type of HTTP request (GET, POST, PUT, PATCH, DELETE, ...)
+ * @param data
+ * string to be sent in the body of the
+ * @return content of the webpage identified by url
+ * @throws IOException
+ * thrown when there is any problem with accessing webpage
+ */
+ public String getFromNetwork(String accessUrl, String httpRequestMethod, String data) throws IOException {
+
+ /**
+ * Tasks that retrieves content from web page
+ *
+ * @author Piotr Gawron
+ *
+ */
+ class Task implements Callable<String> {
+ private volatile String result = null;
+
+ @Override
+ public String call() throws Exception {
+ int tries = 0;
+ int code = HttpURLConnection.HTTP_INTERNAL_ERROR;
+ HttpURLConnection urlConn = null;
+
+ // connect to the server, if HTTP_INTERNAL_ERROR occurred then try to
+ // reconnect HTTP_INTERNAL_ERROR_RECONNECT_TIMES times
+ while (code == HttpURLConnection.HTTP_INTERNAL_ERROR || code == HttpURLConnection.HTTP_NOT_FOUND) {
+ urlConn = openConnection(accessUrl);
+ urlConn.addRequestProperty("User-Agent", "minerva-framework");
+
+ urlConn.setRequestMethod(httpRequestMethod);
+ if (data != null) {
+ urlConn.setDoOutput(true);
+ DataOutputStream wr = new DataOutputStream(urlConn.getOutputStream());
+ wr.writeBytes(data);
+ wr.close();
+ }
+
+ try {
+ urlConn.connect();
+ code = urlConn.getResponseCode();
+ } catch (FileNotFoundException e) {
+ code = HttpURLConnection.HTTP_NOT_FOUND;
+ } catch (IOException e) {
+ code = HttpURLConnection.HTTP_INTERNAL_ERROR;
+ }
+ tries++;
+ if (tries > HTTP_INTERNAL_ERROR_RECONNECT_TIMES) {
+ break;
+ }
+ if (code == HttpURLConnection.HTTP_INTERNAL_ERROR || code == HttpURLConnection.HTTP_NOT_FOUND) {
+ logger.debug("Problem with webpage: " + accessUrl);
+ logger.debug("Retrying: " + accessUrl);
+ try {
+ Thread.sleep(HTTP_INTERNAL_ERROR_RECONNECT_SLEEP_TIME);
+ } catch (InterruptedException e) {
+ }
+ }
+ }
+ try {
+ BufferedReader in = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));
+ result = IOUtils.toString(in);
+ } catch (IOException e) {
+ if (e.getClass().equals(IOException.class) || e.getClass().equals(FileNotFoundException.class)) {
+ throw new WrongResponseCodeIOException(e, code);
+ } else {
+ throw e;
+ }
+ }
+ return result;
+ }
+
+ }
+
+ ExecutorService executor = Executors.newSingleThreadExecutor();
+ Future<String> future = executor.submit(new Task());
+
+ try {
+ String result = future.get(HTTP_CONNECTION_TIMEOUT_SEC, TimeUnit.SECONDS);
+ executor.shutdownNow();
+ return result;
+ } catch (Exception e) {
+ if (e.getCause() instanceof IOException) {
+ throw (IOException) e.getCause();
+ }
+ throw new IOException("Problem with accessing webpage: " + accessUrl, e);
+ }
+ }
+
+ /**
+ * Opens {@link HttpURLConnection connection} to the url given in the
+ * argument.
+ *
+ * @param accessUrl
+ * url to the web page
+ * @return {@link HttpURLConnection connection} to the url given in the
+ * argument
+ * @throws MalformedURLException
+ * thrown when url is invalid
+ * @throws IOException
+ * thrown when there is problem with opening connection
+ */
+ HttpURLConnection openConnection(String accessUrl) throws MalformedURLException, IOException {
+ URL url = new URL(accessUrl);
+ HttpURLConnection urlConn = (HttpURLConnection) url.openConnection();
+ return urlConn;
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/XmlSerializer.java b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/XmlSerializer.java
index 4f66ee023b..0783e5c99e 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/XmlSerializer.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/XmlSerializer.java
@@ -1,111 +1,111 @@
-package lcsb.mapviewer.annotation.cache;
-
-import java.io.StringWriter;
-
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBException;
-import javax.xml.bind.Marshaller;
-import javax.xml.bind.Unmarshaller;
-
-import org.apache.commons.lang3.SerializationException;
-import org.apache.log4j.Logger;
-import org.w3c.dom.Node;
-
-/**
- * This class allos to serialize and deserialize object of class T into xml
- * {@link String}.
- *
- * @author Piotr Gawron
- *
- * @param <T>
- * type of the object to serialize
- */
-public class XmlSerializer<T> {
-
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(XmlSerializer.class);
-
- /**
- * Class of the object that DAO works on.
- */
- private Class<? extends T> clazz;
-
- /**
- * Java Architecture for XML Binding (JAXB) class that allows transforming T
- * object into xml.
- */
- private Marshaller jaxbMarshaller;
-
- /**
- * Java Architecture for XML Binding (JAXB) class that allows transforming xml
- * describing T into T object.
- */
- private Unmarshaller jaxbUnmarshaller;
-
- /**
- * Default constructor.
- *
- * @param theClass
- * class of the object that DAO will work on
- */
- public XmlSerializer(Class<? extends T> theClass) {
- this.clazz = theClass;
- try {
- JAXBContext jaxbContext;
- jaxbContext = JAXBContext.newInstance(clazz);
- jaxbMarshaller = jaxbContext.createMarshaller();
- jaxbMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
- jaxbUnmarshaller = jaxbContext.createUnmarshaller();
- } catch (JAXBException e) {
- throw new SerializationException(e);
- }
- }
-
- /**
- * Transforms object into xml string.
- *
- * @param object
- * object to transform
- * @return xml string representing object
- */
- public String objectToString(T object) {
- if (object == null) {
- return null;
- }
- StringWriter sw = new StringWriter();
- try {
- jaxbMarshaller.marshal(object, sw);
- } catch (JAXBException e) {
- throw new SerializationException(e);
- } catch (Exception e) {
- logger.error(e, e);
- return null;
- }
- return sw.toString();
- }
-
- /**
- * Creates object from xml node.
- *
- * @param node
- * xml node
- * @return object corresponding to xml node
- */
- @SuppressWarnings("unchecked")
- public T xmlToObject(Node node) {
- if (node == null) {
- return null;
- }
- try {
- return (T) jaxbUnmarshaller.unmarshal(node);
- } catch (JAXBException e) {
- throw new SerializationException(e);
- } catch (Exception e) { // the library can throw NPE sometimes...
- logger.error(e, e);
- return null;
- }
- }
-
-}
+package lcsb.mapviewer.annotation.cache;
+
+import java.io.StringWriter;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Marshaller;
+import javax.xml.bind.Unmarshaller;
+
+import org.apache.commons.lang3.SerializationException;
+import org.apache.log4j.Logger;
+import org.w3c.dom.Node;
+
+/**
+ * This class allos to serialize and deserialize object of class T into xml
+ * {@link String}.
+ *
+ * @author Piotr Gawron
+ *
+ * @param <T>
+ * type of the object to serialize
+ */
+public class XmlSerializer<T> {
+
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(XmlSerializer.class);
+
+ /**
+ * Class of the object that DAO works on.
+ */
+ private Class<? extends T> clazz;
+
+ /**
+ * Java Architecture for XML Binding (JAXB) class that allows transforming T
+ * object into xml.
+ */
+ private Marshaller jaxbMarshaller;
+
+ /**
+ * Java Architecture for XML Binding (JAXB) class that allows transforming xml
+ * describing T into T object.
+ */
+ private Unmarshaller jaxbUnmarshaller;
+
+ /**
+ * Default constructor.
+ *
+ * @param theClass
+ * class of the object that DAO will work on
+ */
+ public XmlSerializer(Class<? extends T> theClass) {
+ this.clazz = theClass;
+ try {
+ JAXBContext jaxbContext;
+ jaxbContext = JAXBContext.newInstance(clazz);
+ jaxbMarshaller = jaxbContext.createMarshaller();
+ jaxbMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
+ jaxbUnmarshaller = jaxbContext.createUnmarshaller();
+ } catch (JAXBException e) {
+ throw new SerializationException(e);
+ }
+ }
+
+ /**
+ * Transforms object into xml string.
+ *
+ * @param object
+ * object to transform
+ * @return xml string representing object
+ */
+ public String objectToString(T object) {
+ if (object == null) {
+ return null;
+ }
+ StringWriter sw = new StringWriter();
+ try {
+ jaxbMarshaller.marshal(object, sw);
+ } catch (JAXBException e) {
+ throw new SerializationException(e);
+ } catch (Exception e) {
+ logger.error(e, e);
+ return null;
+ }
+ return sw.toString();
+ }
+
+ /**
+ * Creates object from xml node.
+ *
+ * @param node
+ * xml node
+ * @return object corresponding to xml node
+ */
+ @SuppressWarnings("unchecked")
+ public T xmlToObject(Node node) {
+ if (node == null) {
+ return null;
+ }
+ try {
+ return (T) jaxbUnmarshaller.unmarshal(node);
+ } catch (JAXBException e) {
+ throw new SerializationException(e);
+ } catch (Exception e) { // the library can throw NPE sometimes...
+ logger.error(e, e);
+ return null;
+ }
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/package-info.java b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/package-info.java
index 7cbd3dd79f..64f1ec2089 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/package-info.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/package-info.java
@@ -1,27 +1,27 @@
-/**
- * This package contains implementation of cache utils. General interface of
- * cache is defined in {@link lcsb.mapviewer.annotation.cache.QueryCacheInterface
- * QueryCacheInterface}. There are three known implementations of this
- * interface:
- * <ul>
- * <li> {@link lcsb.mapviewer.annotation.cache.ApplicationLevelCache
- * ApplicationLevelCache} - allows to cache data within application scope. After
- * application restart everything is lost,</li>
- * <li> {@link lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCache
- * PermanentDatabaseLevelCache} - allows to cache data in the database. It's
- * slower than {@link lcsb.mapviewer.annotation.cache.ApplicationLevelCache
- * ApplicationLevelCache} cache, but the data is available until they are
- * removed from the database,</li>
- * <li> {@link lcsb.mapviewer.annotation.cache.GeneralCache GeneralCache} - it's a mix
- * of above methods. When query to cache is send, first local application cache
- * is looked up and if it's not found there the database cache is checked.</li>
- * </ul>
- * The data stored in cache has
- * {@link lcsb.mapviewer.db.model.reactome.CacheQuery#expires validity date}
- * after which data from cache shouldn't be used. For every data type stored in
- * cache there is {@link lcsb.mapviewer.annotation.cache.CachableInterface
- * CachableInterface} defined. This class is responsible for updating
- * information from original source when expire date is reached.
- */
-package lcsb.mapviewer.annotation.cache;
-
+/**
+ * This package contains implementation of cache utils. General interface of
+ * cache is defined in {@link lcsb.mapviewer.annotation.cache.QueryCacheInterface
+ * QueryCacheInterface}. There are three known implementations of this
+ * interface:
+ * <ul>
+ * <li> {@link lcsb.mapviewer.annotation.cache.ApplicationLevelCache
+ * ApplicationLevelCache} - allows to cache data within application scope. After
+ * application restart everything is lost,</li>
+ * <li> {@link lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCache
+ * PermanentDatabaseLevelCache} - allows to cache data in the database. It's
+ * slower than {@link lcsb.mapviewer.annotation.cache.ApplicationLevelCache
+ * ApplicationLevelCache} cache, but the data is available until they are
+ * removed from the database,</li>
+ * <li> {@link lcsb.mapviewer.annotation.cache.GeneralCache GeneralCache} - it's a mix
+ * of above methods. When query to cache is send, first local application cache
+ * is looked up and if it's not found there the database cache is checked.</li>
+ * </ul>
+ * The data stored in cache has
+ * {@link lcsb.mapviewer.db.model.reactome.CacheQuery#expires validity date}
+ * after which data from cache shouldn't be used. For every data type stored in
+ * cache there is {@link lcsb.mapviewer.annotation.cache.CachableInterface
+ * CachableInterface} defined. This class is responsible for updating
+ * information from original source when expire date is reached.
+ */
+package lcsb.mapviewer.annotation.cache;
+
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/data/Article.java b/annotation/src/main/java/lcsb/mapviewer/annotation/data/Article.java
index 43533ff473..5909001a86 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/Article.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/Article.java
@@ -1,195 +1,195 @@
-package lcsb.mapviewer.annotation.data;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
-
-/**
- * This class represents <a href="http://www.ncbi.nlm.nih.gov/pubmed">pubmed</a>
- * article.
- *
- * @author Piotr Gawron
- *
- */
-@XmlRootElement
-public class Article implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Title of the article.
- */
- private String title;
-
- /**
- * List of authors.
- */
- private List<String> authors = new ArrayList<>();
-
- /**
- * Journal.
- */
- private String journal;
-
- /**
- * Year of issue.
- */
- private Integer year;
-
- /**
- * Url that points to this article.
- */
- private String link;
-
- /**
- * Pubmed identifier of the article.
- */
- private String id;
-
- /**
- * How many citiations were made to this article.
- */
- private int citationCount;
-
- /**
- *
- * @return {@link #title}
- */
- public String getTitle() {
- return title;
- }
-
- /**
- *
- * @param title
- * new {@link #title} value
- */
- @XmlElement
- public void setTitle(String title) {
- this.title = title;
- }
-
- /**
- *
- * @return {@link #authors}
- */
- public List<String> getAuthors() {
- return authors;
- }
-
- /**
- *
- * @param authors
- * new {@link #title} value
- */
- public void setAuthors(List<String> authors) {
- this.authors = authors;
- }
-
- /**
- *
- * @return {@link #journal}
- */
- public String getJournal() {
- return journal;
- }
-
- /**
- *
- * @param journal
- * new {@link #journal} value
- */
- @XmlElement
- public void setJournal(String journal) {
- this.journal = journal;
- }
-
- /**
- *
- * @return {@link #year}
- */
- public Integer getYear() {
- return year;
- }
-
- /**
- *
- * @param year
- * new {@link #year}
- */
- @XmlElement
- public void setYear(Integer year) {
- this.year = year;
- }
-
- /**
- *
- * @return comma separated string with authors
- */
- public String getStringAuthors() {
- String result = "";
- for (String string : authors) {
- if (!result.equalsIgnoreCase("")) {
- result += ", ";
- }
- result += string;
- }
- return result;
- }
-
- /**
- *
- * @return {@link #link}
- */
- public String getLink() {
- return link;
- }
-
- /**
- *
- * @param link
- * new {@link #link}
- */
- public void setLink(String link) {
- this.link = link;
- }
-
- /**
- *
- * @return {@link #id}
- */
- public String getId() {
- return id;
- }
-
- /**
- *
- * @param id
- * new {@link #id} value
- */
- public void setId(String id) {
- this.id = id;
- }
-
- /**
- *
- * @return {@link #citationCount}
- */
- public int getCitationCount() {
- return citationCount;
- }
-
- /**
- *
- * @param citationCount
- * new {@link #citationCount} value
- */
- public void setCitationCount(int citationCount) {
- this.citationCount = citationCount;
- }
-}
+package lcsb.mapviewer.annotation.data;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlRootElement;
+
+/**
+ * This class represents <a href="http://www.ncbi.nlm.nih.gov/pubmed">pubmed</a>
+ * article.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@XmlRootElement
+public class Article implements Serializable {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Title of the article.
+ */
+ private String title;
+
+ /**
+ * List of authors.
+ */
+ private List<String> authors = new ArrayList<>();
+
+ /**
+ * Journal.
+ */
+ private String journal;
+
+ /**
+ * Year of issue.
+ */
+ private Integer year;
+
+ /**
+ * Url that points to this article.
+ */
+ private String link;
+
+ /**
+ * Pubmed identifier of the article.
+ */
+ private String id;
+
+ /**
+ * How many citiations were made to this article.
+ */
+ private int citationCount;
+
+ /**
+ *
+ * @return {@link #title}
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ *
+ * @param title
+ * new {@link #title} value
+ */
+ @XmlElement
+ public void setTitle(String title) {
+ this.title = title;
+ }
+
+ /**
+ *
+ * @return {@link #authors}
+ */
+ public List<String> getAuthors() {
+ return authors;
+ }
+
+ /**
+ *
+ * @param authors
+ * new {@link #title} value
+ */
+ public void setAuthors(List<String> authors) {
+ this.authors = authors;
+ }
+
+ /**
+ *
+ * @return {@link #journal}
+ */
+ public String getJournal() {
+ return journal;
+ }
+
+ /**
+ *
+ * @param journal
+ * new {@link #journal} value
+ */
+ @XmlElement
+ public void setJournal(String journal) {
+ this.journal = journal;
+ }
+
+ /**
+ *
+ * @return {@link #year}
+ */
+ public Integer getYear() {
+ return year;
+ }
+
+ /**
+ *
+ * @param year
+ * new {@link #year}
+ */
+ @XmlElement
+ public void setYear(Integer year) {
+ this.year = year;
+ }
+
+ /**
+ *
+ * @return comma separated string with authors
+ */
+ public String getStringAuthors() {
+ String result = "";
+ for (String string : authors) {
+ if (!result.equalsIgnoreCase("")) {
+ result += ", ";
+ }
+ result += string;
+ }
+ return result;
+ }
+
+ /**
+ *
+ * @return {@link #link}
+ */
+ public String getLink() {
+ return link;
+ }
+
+ /**
+ *
+ * @param link
+ * new {@link #link}
+ */
+ public void setLink(String link) {
+ this.link = link;
+ }
+
+ /**
+ *
+ * @return {@link #id}
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ *
+ * @param id
+ * new {@link #id} value
+ */
+ public void setId(String id) {
+ this.id = id;
+ }
+
+ /**
+ *
+ * @return {@link #citationCount}
+ */
+ public int getCitationCount() {
+ return citationCount;
+ }
+
+ /**
+ *
+ * @param citationCount
+ * new {@link #citationCount} value
+ */
+ public void setCitationCount(int citationCount) {
+ this.citationCount = citationCount;
+ }
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/data/ArticleCitationComparator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/data/ArticleCitationComparator.java
index d826fdfa55..6725ec2b98 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/ArticleCitationComparator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/ArticleCitationComparator.java
@@ -1,19 +1,19 @@
-package lcsb.mapviewer.annotation.data;
-
-import java.util.Comparator;
-
-/**
- * Comparator of {@link Article} class based on the number of
- * {@link Article#citationCount citations}.
- *
- * @author Piotr Gawron
- *
- */
-public class ArticleCitationComparator implements Comparator<Article> {
-
- @Override
- public int compare(Article o1, Article o2) {
- return -((Integer) o1.getCitationCount()).compareTo(o2.getCitationCount());
- }
-
-}
+package lcsb.mapviewer.annotation.data;
+
+import java.util.Comparator;
+
+/**
+ * Comparator of {@link Article} class based on the number of
+ * {@link Article#citationCount citations}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ArticleCitationComparator implements Comparator<Article> {
+
+ @Override
+ public int compare(Article o1, Article o2) {
+ return -((Integer) o1.getCitationCount()).compareTo(o2.getCitationCount());
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/data/Chebi.java b/annotation/src/main/java/lcsb/mapviewer/annotation/data/Chebi.java
index 4990a35b88..66f1f1782b 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/Chebi.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/Chebi.java
@@ -1,247 +1,247 @@
-package lcsb.mapviewer.annotation.data;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.xml.bind.annotation.XmlRootElement;
-
-import org.apache.log4j.Logger;
-
-import uk.ac.ebi.chebi.webapps.chebiWS.model.DataItem;
-import uk.ac.ebi.chebi.webapps.chebiWS.model.Entity;
-import uk.ac.ebi.chebi.webapps.chebiWS.model.OntologyDataItem;
-
-/**
- * This class represents <a href="http://www.ebi.ac.uk/chebi/">chebi</a> object.
- *
- * @author Piotr Gawron
- *
- */
-@XmlRootElement
-public class Chebi implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(Chebi.class);
-
- /**
- * Name of the object.
- */
- private String name;
- /**
- * Chebi identifier.
- */
- private String chebiId;
- /**
- * <a href =
- * "http://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system"
- * >Smiles</a> description.
- */
- private String smiles;
-
- /**
- * <a href = "http://en.wikipedia.org/wiki/International_Chemical_Identifier"
- * >InChI</a> description.
- */
- private String inchi;
-
- /**
- * Key for the
- * <a href = "http://en.wikipedia.org/wiki/International_Chemical_Identifier"
- * >InChI</a> description. It's a hashed value of InChI.
- */
- private String inchiKey;
-
- /**
- * List of synonyms.
- */
- private List<String> synonyms = new ArrayList<>();
-
- /**
- * List of elements that stands above this object in chebi ontology.
- */
- private List<ChebiRelation> incomingChebi = new ArrayList<>();
-
- /**
- * List of elements that stands below this object in chebi ontology.
- */
- private List<ChebiRelation> outgoingChebi = new ArrayList<>();
-
- /**
- * Default constructor.
- */
- public Chebi() {
-
- }
-
- /**
- * Constructor that initilizes object from the data taken from entity acquired
- * from Chebi API.
- *
- * @param entity
- * object received from Chebi API representing chebi object
- */
- public Chebi(Entity entity) {
- this.chebiId = entity.getChebiId();
- this.name = entity.getChebiAsciiName().trim();
- this.smiles = entity.getSmiles();
- this.inchi = entity.getInchi();
- this.inchiKey = entity.getInchiKey();
- for (DataItem di : entity.getSynonyms()) {
- synonyms.add(di.getData());
- }
- for (OntologyDataItem item : entity.getOntologyParents()) {
- ChebiRelation relation = new ChebiRelation(item);
- incomingChebi.add(relation);
- }
- for (OntologyDataItem item : entity.getOntologyChildren()) {
- ChebiRelation relation = new ChebiRelation(item);
- outgoingChebi.add(relation);
- }
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return the chebiId
- * @see #chebiId
- */
- public String getChebiId() {
- return chebiId;
- }
-
- /**
- * @param chebiId
- * the chebiId to set
- * @see #chebiId
- */
- public void setChebiId(String chebiId) {
- this.chebiId = chebiId;
- }
-
- /**
- * @return the smiles
- * @see #smiles
- */
- public String getSmiles() {
- return smiles;
- }
-
- /**
- * @param smiles
- * the smiles to set
- * @see #smiles
- */
- public void setSmiles(String smiles) {
- this.smiles = smiles;
- }
-
- /**
- * @return the inchi
- * @see #inchi
- */
- public String getInchi() {
- return inchi;
- }
-
- /**
- * @param inchi
- * the inchi to set
- * @see #inchi
- */
- public void setInchi(String inchi) {
- this.inchi = inchi;
- }
-
- /**
- * @return the inchiKey
- * @see #inchiKey
- */
- public String getInchiKey() {
- return inchiKey;
- }
-
- /**
- * @param inchiKey
- * the inchiKey to set
- * @see #inchiKey
- */
- public void setInchiKey(String inchiKey) {
- this.inchiKey = inchiKey;
- }
-
- /**
- * @return the synonyms
- * @see #synonyms
- */
- public List<String> getSynonyms() {
- return synonyms;
- }
-
- /**
- * @param synonyms
- * the synonyms to set
- * @see #synonyms
- */
- public void setSynonyms(List<String> synonyms) {
- this.synonyms = synonyms;
- }
-
- /**
- * @return the incomingChebi
- * @see #incomingChebi
- */
- public List<ChebiRelation> getIncomingChebi() {
- return incomingChebi;
- }
-
- /**
- * @param incomingChebi
- * the incomingChebi to set
- * @see #incomingChebi
- */
- public void setIncomingChebi(List<ChebiRelation> incomingChebi) {
- this.incomingChebi = incomingChebi;
- }
-
- /**
- * @return the outgoingChebi
- * @see #outgoingChebi
- */
- public List<ChebiRelation> getOutgoingChebi() {
- return outgoingChebi;
- }
-
- /**
- * @param outgoingChebi
- * the outgoingChebi to set
- * @see #outgoingChebi
- */
- public void setOutgoingChebi(List<ChebiRelation> outgoingChebi) {
- this.outgoingChebi = outgoingChebi;
- }
-
-}
+package lcsb.mapviewer.annotation.data;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.xml.bind.annotation.XmlRootElement;
+
+import org.apache.log4j.Logger;
+
+import uk.ac.ebi.chebi.webapps.chebiWS.model.DataItem;
+import uk.ac.ebi.chebi.webapps.chebiWS.model.Entity;
+import uk.ac.ebi.chebi.webapps.chebiWS.model.OntologyDataItem;
+
+/**
+ * This class represents <a href="http://www.ebi.ac.uk/chebi/">chebi</a> object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@XmlRootElement
+public class Chebi implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(Chebi.class);
+
+ /**
+ * Name of the object.
+ */
+ private String name;
+ /**
+ * Chebi identifier.
+ */
+ private String chebiId;
+ /**
+ * <a href =
+ * "http://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system"
+ * >Smiles</a> description.
+ */
+ private String smiles;
+
+ /**
+ * <a href = "http://en.wikipedia.org/wiki/International_Chemical_Identifier"
+ * >InChI</a> description.
+ */
+ private String inchi;
+
+ /**
+ * Key for the
+ * <a href = "http://en.wikipedia.org/wiki/International_Chemical_Identifier"
+ * >InChI</a> description. It's a hashed value of InChI.
+ */
+ private String inchiKey;
+
+ /**
+ * List of synonyms.
+ */
+ private List<String> synonyms = new ArrayList<>();
+
+ /**
+ * List of elements that stands above this object in chebi ontology.
+ */
+ private List<ChebiRelation> incomingChebi = new ArrayList<>();
+
+ /**
+ * List of elements that stands below this object in chebi ontology.
+ */
+ private List<ChebiRelation> outgoingChebi = new ArrayList<>();
+
+ /**
+ * Default constructor.
+ */
+ public Chebi() {
+
+ }
+
+ /**
+ * Constructor that initilizes object from the data taken from entity acquired
+ * from Chebi API.
+ *
+ * @param entity
+ * object received from Chebi API representing chebi object
+ */
+ public Chebi(Entity entity) {
+ this.chebiId = entity.getChebiId();
+ this.name = entity.getChebiAsciiName().trim();
+ this.smiles = entity.getSmiles();
+ this.inchi = entity.getInchi();
+ this.inchiKey = entity.getInchiKey();
+ for (DataItem di : entity.getSynonyms()) {
+ synonyms.add(di.getData());
+ }
+ for (OntologyDataItem item : entity.getOntologyParents()) {
+ ChebiRelation relation = new ChebiRelation(item);
+ incomingChebi.add(relation);
+ }
+ for (OntologyDataItem item : entity.getOntologyChildren()) {
+ ChebiRelation relation = new ChebiRelation(item);
+ outgoingChebi.add(relation);
+ }
+ }
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * @return the chebiId
+ * @see #chebiId
+ */
+ public String getChebiId() {
+ return chebiId;
+ }
+
+ /**
+ * @param chebiId
+ * the chebiId to set
+ * @see #chebiId
+ */
+ public void setChebiId(String chebiId) {
+ this.chebiId = chebiId;
+ }
+
+ /**
+ * @return the smiles
+ * @see #smiles
+ */
+ public String getSmiles() {
+ return smiles;
+ }
+
+ /**
+ * @param smiles
+ * the smiles to set
+ * @see #smiles
+ */
+ public void setSmiles(String smiles) {
+ this.smiles = smiles;
+ }
+
+ /**
+ * @return the inchi
+ * @see #inchi
+ */
+ public String getInchi() {
+ return inchi;
+ }
+
+ /**
+ * @param inchi
+ * the inchi to set
+ * @see #inchi
+ */
+ public void setInchi(String inchi) {
+ this.inchi = inchi;
+ }
+
+ /**
+ * @return the inchiKey
+ * @see #inchiKey
+ */
+ public String getInchiKey() {
+ return inchiKey;
+ }
+
+ /**
+ * @param inchiKey
+ * the inchiKey to set
+ * @see #inchiKey
+ */
+ public void setInchiKey(String inchiKey) {
+ this.inchiKey = inchiKey;
+ }
+
+ /**
+ * @return the synonyms
+ * @see #synonyms
+ */
+ public List<String> getSynonyms() {
+ return synonyms;
+ }
+
+ /**
+ * @param synonyms
+ * the synonyms to set
+ * @see #synonyms
+ */
+ public void setSynonyms(List<String> synonyms) {
+ this.synonyms = synonyms;
+ }
+
+ /**
+ * @return the incomingChebi
+ * @see #incomingChebi
+ */
+ public List<ChebiRelation> getIncomingChebi() {
+ return incomingChebi;
+ }
+
+ /**
+ * @param incomingChebi
+ * the incomingChebi to set
+ * @see #incomingChebi
+ */
+ public void setIncomingChebi(List<ChebiRelation> incomingChebi) {
+ this.incomingChebi = incomingChebi;
+ }
+
+ /**
+ * @return the outgoingChebi
+ * @see #outgoingChebi
+ */
+ public List<ChebiRelation> getOutgoingChebi() {
+ return outgoingChebi;
+ }
+
+ /**
+ * @param outgoingChebi
+ * the outgoingChebi to set
+ * @see #outgoingChebi
+ */
+ public void setOutgoingChebi(List<ChebiRelation> outgoingChebi) {
+ this.outgoingChebi = outgoingChebi;
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/data/ChebiRelation.java b/annotation/src/main/java/lcsb/mapviewer/annotation/data/ChebiRelation.java
index 8cdc6bd054..c4cce63e7e 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/ChebiRelation.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/ChebiRelation.java
@@ -1,106 +1,106 @@
-package lcsb.mapviewer.annotation.data;
-
-import java.io.Serializable;
-
-import uk.ac.ebi.chebi.webapps.chebiWS.model.OntologyDataItem;
-
-/**
- * Describes relation of the {@link Chebi} object into other elements into chebi
- * ontology.
- *
- * @author Piotr Gawron
- *
- */
-public class ChebiRelation implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Name of the chebi object pointed by this relation.
- */
- private String name;
-
- /**
- * Type of the relation.
- */
- private String type;
-
- /**
- * Chebi identifier of object pointef by this relation.
- */
- private String id;
-
- /**
- * Default constructor.
- */
- public ChebiRelation() {
-
- }
-
- /**
- * Constructor that creates relation from object retrieved by Chebi API.
- *
- * @param item
- * object from Chebi API
- */
- public ChebiRelation(OntologyDataItem item) {
- name = item.getChebiName();
- type = item.getType();
- id = item.getChebiId();
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return the type
- * @see #type
- */
- public String getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(String type) {
- this.type = type;
- }
-
- /**
- * @return the id
- * @see #id
- */
- public String getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(String id) {
- this.id = id;
- }
-
-}
+package lcsb.mapviewer.annotation.data;
+
+import java.io.Serializable;
+
+import uk.ac.ebi.chebi.webapps.chebiWS.model.OntologyDataItem;
+
+/**
+ * Describes relation of the {@link Chebi} object into other elements into chebi
+ * ontology.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ChebiRelation implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Name of the chebi object pointed by this relation.
+ */
+ private String name;
+
+ /**
+ * Type of the relation.
+ */
+ private String type;
+
+ /**
+ * Chebi identifier of object pointef by this relation.
+ */
+ private String id;
+
+ /**
+ * Default constructor.
+ */
+ public ChebiRelation() {
+
+ }
+
+ /**
+ * Constructor that creates relation from object retrieved by Chebi API.
+ *
+ * @param item
+ * object from Chebi API
+ */
+ public ChebiRelation(OntologyDataItem item) {
+ name = item.getChebiName();
+ type = item.getType();
+ id = item.getChebiId();
+ }
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * @return the type
+ * @see #type
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * @param type
+ * the type to set
+ * @see #type
+ */
+ public void setType(String type) {
+ this.type = type;
+ }
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(String id) {
+ this.id = id;
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/data/Chemical.java b/annotation/src/main/java/lcsb/mapviewer/annotation/data/Chemical.java
index 5ec92777b4..a5bb9ba78f 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/Chemical.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/Chemical.java
@@ -1,315 +1,315 @@
-package lcsb.mapviewer.annotation.data;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Comparator;
-import java.util.List;
-
-import javax.xml.bind.annotation.XmlRootElement;
-
-import org.apache.commons.lang3.StringUtils;
-
-import lcsb.mapviewer.common.comparator.StringComparator;
-import lcsb.mapviewer.model.map.MiriamData;
-
-/**
- * Object representing element obtained from Toxigenomic database.
- *
- * @author Ayan Rota
- *
- */
-@XmlRootElement
-public class Chemical implements Serializable, TargettingStructure {
-
- /**
- *
- */
- private static final long serialVersionUID = 3892326511802845188L;
-
- /**
- * Name.
- */
- private String chemicalName;
-
- /**
- * Toxigenomic database chemcial ID (MeSH).
- */
- private MiriamData chemicalId;
-
- /**
- * Toxigenomic database ID (CAS).
- */
- private MiriamData casID;
-
- /**
- * Evidence evidence either marker/mechanism and/or T therapeutic.
- */
- private ChemicalDirectEvidence directEvidence;
-
- /**
- * direct Evidence Publication.
- */
- private List<MiriamData> directEvidencePublication = new ArrayList<>();
-
- /**
- * Genes interacting with the chemical plus publications.
- */
- private List<Target> inferenceNetwork = new ArrayList<>();
-
- /**
- * Inference score.
- */
- private Float inferenceScore;
-
- /**
- * Reference count.
- */
- private Integer refScore;
-
- /**
- * Known synonyms.
- */
- private List<String> synonyms = new ArrayList<>();
-
- /**
- * default constructor.
- */
- public Chemical() {
- super();
- }
-
- /**
- * @param chemicalName
- * name.
- * @param chemicalId
- * id.
- * @param casID
- * cas id.
- * @param directEvidence
- * string value for direct Evidence.
- * @param inferenceNetwork
- * inference network.
- * @param directEvidencePublication
- * publications associated with evidence publications.
- * @param inferenceScore
- * score.
- * @param refScore
- * number of references.
- */
- public Chemical(String chemicalName, MiriamData chemicalId, MiriamData casID, ChemicalDirectEvidence directEvidence, List<Target> inferenceNetwork,
- List<MiriamData> directEvidencePublication, Float inferenceScore, Integer refScore) {
- super();
- this.chemicalName = chemicalName;
- this.chemicalId = chemicalId;
- this.casID = casID;
- this.directEvidence = directEvidence;
- this.inferenceNetwork = inferenceNetwork;
- this.directEvidencePublication = directEvidencePublication;
- this.inferenceScore = inferenceScore;
- this.refScore = refScore;
- }
-
- /**
- * @return the chemicalName
- */
- public String getChemicalName() {
- return chemicalName;
- }
-
- /**
- * @param chemicalName
- * the chemicalName to set
- */
- public void setChemicalName(String chemicalName) {
- this.chemicalName = chemicalName;
- }
-
- /**
- * @return the chemicalId
- */
- public MiriamData getChemicalId() {
- return chemicalId;
- }
-
- /**
- * @param chemicalId
- * the chemicalId to set
- */
- public void setChemicalId(MiriamData chemicalId) {
- this.chemicalId = chemicalId;
- }
-
- /**
- * @return the casType
- */
- public MiriamData getCasID() {
- return casID;
- }
-
- /**
- * @param casID
- * the casType to set
- */
- public void setCasID(MiriamData casID) {
- this.casID = casID;
- }
-
- /**
- * @return the directEvidence
- */
- public ChemicalDirectEvidence getDirectEvidence() {
- return directEvidence;
- }
-
- /**
- * @param directEvidence
- * the directEvidence to set
- */
- public void setDirectEvidence(ChemicalDirectEvidence directEvidence) {
- this.directEvidence = directEvidence;
- }
-
- /**
- * @return the inferenceNetwork
- */
- public List<Target> getInferenceNetwork() {
- return inferenceNetwork;
- }
-
- /**
- * @param inferenceNetwork
- * the inferenceNetwork to set
- */
- public void setInferenceNetwork(List<Target> inferenceNetwork) {
- this.inferenceNetwork = inferenceNetwork;
- }
-
- /**
- * @return the inferenceScore
- */
- public Float getInferenceScore() {
- return inferenceScore;
- }
-
- /**
- * @param inferenceScore
- * the inferenceScore to set
- */
- public void setInferenceScore(Float inferenceScore) {
- this.inferenceScore = inferenceScore;
- }
-
- /**
- * @return the refScore
- */
- public Integer getRefScore() {
- return refScore;
- }
-
- /**
- * @param refScore
- * the refScore to set
- */
- public void setRefScore(Integer refScore) {
- this.refScore = refScore;
- }
-
- /**
- * @return the directEvidencePublication
- */
- public List<MiriamData> getDirectEvidencePublication() {
- return directEvidencePublication;
- }
-
- /**
- * @param directEvidencePublication
- * the directEvidencePublication to set
- */
- public void setDirectEvidencePublication(List<MiriamData> directEvidencePublication) {
- this.directEvidencePublication = directEvidencePublication;
- }
-
- /**
- * @return list of synonyms.
- */
- public List<String> getSynonyms() {
- return synonyms;
- }
-
- /**
- * @return list of synonyms as string.
- */
- public String getSynonymsString() {
- return StringUtils.join(synonyms, ",");
- }
-
- /**
- * @param synonyms
- * list of all names that are synonyms.
- */
- public void setSynonyms(List<String> synonyms) {
- this.synonyms = synonyms;
- }
-
- @Override
- public String toString() {
- StringBuffer result = new StringBuffer();
- result.append("\nname: " + chemicalName + "\nchemicalId:" + chemicalId + "\ncasID:" + casID);
- result.append("\nsynonyms:" + getSynonymsString());
- result.append("\ninferenceScore:" + inferenceScore + "\nrefScore:" + refScore);
- result.append("\ninferenceNetwork: ");
- for (Target item : getInferenceNetwork()) {
- if (item != null) {
- result.append(item.toString());
- }
- }
- result.append("\ndirectEvidence:" + directEvidence + "\ndirectEvidencePublication:\n");
- for (MiriamData publication : directEvidencePublication) {
- result.append("publication DB: " + publication.getDataType() + ", publication Id: " + publication.getResource() + "\n");
- }
-
- return result.toString();
- }
-
- /**
- * Comparator of the objects by their name.
- *
- * @author Piotr Gawron
- *
- */
- public static class NameComparator implements Comparator<Chemical> {
- /**
- * Default string comparator.
- */
- private StringComparator stringComparator = new StringComparator();
-
- @Override
- public int compare(Chemical arg0, Chemical arg1) {
- return stringComparator.compare(arg0.getChemicalName(), arg1.getChemicalName());
- }
-
- }
-
- @Override
- public Collection<MiriamData> getSources() {
- List<MiriamData> sources = new ArrayList<>();
- if (getCasID() != null) {
- sources.add(getCasID());
- }
- if (getChemicalId() != null) {
- sources.add(getChemicalId());
- }
- return sources;
- }
-
- @Override
- public Collection<Target> getTargets() {
- return getInferenceNetwork();
- }
-
- public void addSynonyms(List<String> synonyms) {
- this.synonyms.addAll(synonyms);
- }
-
-}
+package lcsb.mapviewer.annotation.data;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Comparator;
+import java.util.List;
+
+import javax.xml.bind.annotation.XmlRootElement;
+
+import org.apache.commons.lang3.StringUtils;
+
+import lcsb.mapviewer.common.comparator.StringComparator;
+import lcsb.mapviewer.model.map.MiriamData;
+
+/**
+ * Object representing element obtained from Toxigenomic database.
+ *
+ * @author Ayan Rota
+ *
+ */
+@XmlRootElement
+public class Chemical implements Serializable, TargettingStructure {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 3892326511802845188L;
+
+ /**
+ * Name.
+ */
+ private String chemicalName;
+
+ /**
+ * Toxigenomic database chemcial ID (MeSH).
+ */
+ private MiriamData chemicalId;
+
+ /**
+ * Toxigenomic database ID (CAS).
+ */
+ private MiriamData casID;
+
+ /**
+ * Evidence evidence either marker/mechanism and/or T therapeutic.
+ */
+ private ChemicalDirectEvidence directEvidence;
+
+ /**
+ * direct Evidence Publication.
+ */
+ private List<MiriamData> directEvidencePublication = new ArrayList<>();
+
+ /**
+ * Genes interacting with the chemical plus publications.
+ */
+ private List<Target> inferenceNetwork = new ArrayList<>();
+
+ /**
+ * Inference score.
+ */
+ private Float inferenceScore;
+
+ /**
+ * Reference count.
+ */
+ private Integer refScore;
+
+ /**
+ * Known synonyms.
+ */
+ private List<String> synonyms = new ArrayList<>();
+
+ /**
+ * default constructor.
+ */
+ public Chemical() {
+ super();
+ }
+
+ /**
+ * @param chemicalName
+ * name.
+ * @param chemicalId
+ * id.
+ * @param casID
+ * cas id.
+ * @param directEvidence
+ * string value for direct Evidence.
+ * @param inferenceNetwork
+ * inference network.
+ * @param directEvidencePublication
+ * publications associated with evidence publications.
+ * @param inferenceScore
+ * score.
+ * @param refScore
+ * number of references.
+ */
+ public Chemical(String chemicalName, MiriamData chemicalId, MiriamData casID, ChemicalDirectEvidence directEvidence, List<Target> inferenceNetwork,
+ List<MiriamData> directEvidencePublication, Float inferenceScore, Integer refScore) {
+ super();
+ this.chemicalName = chemicalName;
+ this.chemicalId = chemicalId;
+ this.casID = casID;
+ this.directEvidence = directEvidence;
+ this.inferenceNetwork = inferenceNetwork;
+ this.directEvidencePublication = directEvidencePublication;
+ this.inferenceScore = inferenceScore;
+ this.refScore = refScore;
+ }
+
+ /**
+ * @return the chemicalName
+ */
+ public String getChemicalName() {
+ return chemicalName;
+ }
+
+ /**
+ * @param chemicalName
+ * the chemicalName to set
+ */
+ public void setChemicalName(String chemicalName) {
+ this.chemicalName = chemicalName;
+ }
+
+ /**
+ * @return the chemicalId
+ */
+ public MiriamData getChemicalId() {
+ return chemicalId;
+ }
+
+ /**
+ * @param chemicalId
+ * the chemicalId to set
+ */
+ public void setChemicalId(MiriamData chemicalId) {
+ this.chemicalId = chemicalId;
+ }
+
+ /**
+ * @return the casType
+ */
+ public MiriamData getCasID() {
+ return casID;
+ }
+
+ /**
+ * @param casID
+ * the casType to set
+ */
+ public void setCasID(MiriamData casID) {
+ this.casID = casID;
+ }
+
+ /**
+ * @return the directEvidence
+ */
+ public ChemicalDirectEvidence getDirectEvidence() {
+ return directEvidence;
+ }
+
+ /**
+ * @param directEvidence
+ * the directEvidence to set
+ */
+ public void setDirectEvidence(ChemicalDirectEvidence directEvidence) {
+ this.directEvidence = directEvidence;
+ }
+
+ /**
+ * @return the inferenceNetwork
+ */
+ public List<Target> getInferenceNetwork() {
+ return inferenceNetwork;
+ }
+
+ /**
+ * @param inferenceNetwork
+ * the inferenceNetwork to set
+ */
+ public void setInferenceNetwork(List<Target> inferenceNetwork) {
+ this.inferenceNetwork = inferenceNetwork;
+ }
+
+ /**
+ * @return the inferenceScore
+ */
+ public Float getInferenceScore() {
+ return inferenceScore;
+ }
+
+ /**
+ * @param inferenceScore
+ * the inferenceScore to set
+ */
+ public void setInferenceScore(Float inferenceScore) {
+ this.inferenceScore = inferenceScore;
+ }
+
+ /**
+ * @return the refScore
+ */
+ public Integer getRefScore() {
+ return refScore;
+ }
+
+ /**
+ * @param refScore
+ * the refScore to set
+ */
+ public void setRefScore(Integer refScore) {
+ this.refScore = refScore;
+ }
+
+ /**
+ * @return the directEvidencePublication
+ */
+ public List<MiriamData> getDirectEvidencePublication() {
+ return directEvidencePublication;
+ }
+
+ /**
+ * @param directEvidencePublication
+ * the directEvidencePublication to set
+ */
+ public void setDirectEvidencePublication(List<MiriamData> directEvidencePublication) {
+ this.directEvidencePublication = directEvidencePublication;
+ }
+
+ /**
+ * @return list of synonyms.
+ */
+ public List<String> getSynonyms() {
+ return synonyms;
+ }
+
+ /**
+ * @return list of synonyms as string.
+ */
+ public String getSynonymsString() {
+ return StringUtils.join(synonyms, ",");
+ }
+
+ /**
+ * @param synonyms
+ * list of all names that are synonyms.
+ */
+ public void setSynonyms(List<String> synonyms) {
+ this.synonyms = synonyms;
+ }
+
+ @Override
+ public String toString() {
+ StringBuffer result = new StringBuffer();
+ result.append("\nname: " + chemicalName + "\nchemicalId:" + chemicalId + "\ncasID:" + casID);
+ result.append("\nsynonyms:" + getSynonymsString());
+ result.append("\ninferenceScore:" + inferenceScore + "\nrefScore:" + refScore);
+ result.append("\ninferenceNetwork: ");
+ for (Target item : getInferenceNetwork()) {
+ if (item != null) {
+ result.append(item.toString());
+ }
+ }
+ result.append("\ndirectEvidence:" + directEvidence + "\ndirectEvidencePublication:\n");
+ for (MiriamData publication : directEvidencePublication) {
+ result.append("publication DB: " + publication.getDataType() + ", publication Id: " + publication.getResource() + "\n");
+ }
+
+ return result.toString();
+ }
+
+ /**
+ * Comparator of the objects by their name.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ public static class NameComparator implements Comparator<Chemical> {
+ /**
+ * Default string comparator.
+ */
+ private StringComparator stringComparator = new StringComparator();
+
+ @Override
+ public int compare(Chemical arg0, Chemical arg1) {
+ return stringComparator.compare(arg0.getChemicalName(), arg1.getChemicalName());
+ }
+
+ }
+
+ @Override
+ public Collection<MiriamData> getSources() {
+ List<MiriamData> sources = new ArrayList<>();
+ if (getCasID() != null) {
+ sources.add(getCasID());
+ }
+ if (getChemicalId() != null) {
+ sources.add(getChemicalId());
+ }
+ return sources;
+ }
+
+ @Override
+ public Collection<Target> getTargets() {
+ return getInferenceNetwork();
+ }
+
+ public void addSynonyms(List<String> synonyms) {
+ this.synonyms.addAll(synonyms);
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/data/ChemicalDirectEvidence.java b/annotation/src/main/java/lcsb/mapviewer/annotation/data/ChemicalDirectEvidence.java
index 764048f28a..c5e3895247 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/ChemicalDirectEvidence.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/ChemicalDirectEvidence.java
@@ -1,37 +1,37 @@
-package lcsb.mapviewer.annotation.data;
-
-/**
- * Object representing element obtained from Toxigenomic database.
- *
- * @author Ayan Rota
- *
- */
-public enum ChemicalDirectEvidence {
-
- /**
- * Values.
- */
- MARKER("marker/mechanism"), THERAPEUTIC("therapeutic");
-
- /**
- * Value.
- */
- private String value;
-
- /**
- * @param value
- * string to set the value.
- */
- ChemicalDirectEvidence(String value) {
-
- this.value = value;
- }
-
- /**
- * @return the value
- */
- public String getValue() {
- return value;
- }
-
-}
+package lcsb.mapviewer.annotation.data;
+
+/**
+ * Object representing element obtained from Toxigenomic database.
+ *
+ * @author Ayan Rota
+ *
+ */
+public enum ChemicalDirectEvidence {
+
+ /**
+ * Values.
+ */
+ MARKER("marker/mechanism"), THERAPEUTIC("therapeutic");
+
+ /**
+ * Value.
+ */
+ private String value;
+
+ /**
+ * @param value
+ * string to set the value.
+ */
+ ChemicalDirectEvidence(String value) {
+
+ this.value = value;
+ }
+
+ /**
+ * @return the value
+ */
+ public String getValue() {
+ return value;
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/data/Drug.java b/annotation/src/main/java/lcsb/mapviewer/annotation/data/Drug.java
index e8e5844973..ea8576f003 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/Drug.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/Drug.java
@@ -1,336 +1,336 @@
-package lcsb.mapviewer.annotation.data;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Comparator;
-import java.util.List;
-
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.comparator.StringComparator;
-import lcsb.mapviewer.model.map.MiriamData;
-
-/**
- * Desribes information about drug retrieved from external database.
- *
- * @author Piotr Gawron
- *
- */
-@XmlRootElement
-public class Drug implements Serializable, TargettingStructure {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(Drug.class);
-
- /**
- * Source of the data.
- */
- private List<MiriamData> sources = new ArrayList<>();
-
- /**
- * Name of the drug.
- */
- private String name;
-
- /**
- * Description of the drug.
- */
- private String description;
-
- /**
- * Status of blood brain barries for the drug.
- */
- private String bloodBrainBarrier = "N/A";
-
- /**
- * Is the drug approved.
- */
- private Boolean approved;
-
- /**
- * Known brand names.
- */
- private List<String> brandNames = new ArrayList<>();
-
- /**
- * Known targets.
- */
- private List<Target> targets = new ArrayList<>();
-
- /**
- * Known synonyms.
- */
- private List<String> synonyms = new ArrayList<>();
-
- /**
- * Default constructor.
- */
- public Drug() {
-
- }
-
- /**
- * Constructor that initializes object with the same information as parameter.
- *
- * @param drug
- * original drug
- */
- public Drug(Drug drug) {
- if (drug == null) {
- return;
- }
- this.sources.addAll(drug.getSources());
- this.description = drug.description;
- this.brandNames.addAll(drug.getBrandNames());
- this.synonyms.addAll(drug.getSynonyms());
- this.targets.addAll(drug.getTargets());
- this.bloodBrainBarrier = drug.getBloodBrainBarrier();
- this.setApproved(drug.getApproved());
- }
-
- @Override
- public String toString() {
- StringBuilder result = new StringBuilder("");
- for (MiriamData md : sources) {
- result.append("source: " + md.getDataType() + ", drugId: " + md.getResource() + "\n");
- }
- result.append(", name: " + name + "\nDescription:\n" + description + "\nSynonyms:");
- for (String s : synonyms) {
- result.append(s + "|");
- }
- result.append("\nTargets:");
- for (Target t : targets) {
- if (t.getSource() != null) {
- result.append(t.getSource().getResource() + "|" + t.getName() + "|" + t.getGenes());
- } else {
- result.append("N/A |" + t.getName() + "|" + t.getGenes());
- }
- result.append(" (References:");
- for (MiriamData md : t.getReferences()) {
- result.append(md.getResource() + ",");
- }
- result.append(")+\n");
-
- }
- return result.toString();
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return the description
- * @see #description
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * @param description
- * the description to set
- * @see #description
- */
- public void setDescription(String description) {
- this.description = description;
- }
-
- /**
- * @return the bloodBrainBarrier
- * @see #bloodBrainBarrier
- */
- public String getBloodBrainBarrier() {
- return bloodBrainBarrier;
- }
-
- /**
- * @param bloodBrainBarrier
- * the bloodBrainBarrier to set
- * @see #bloodBrainBarrier
- */
- public void setBloodBrainBarrier(String bloodBrainBarrier) {
- this.bloodBrainBarrier = bloodBrainBarrier;
- }
-
- /**
- * @return the brandNames
- * @see #brandNames
- */
- public List<String> getBrandNames() {
- return brandNames;
- }
-
- /**
- * @param brandNames
- * the brandNames to set
- * @see #brandNames
- */
- public void setBrandNames(List<String> brandNames) {
- this.brandNames = brandNames;
- }
-
- /**
- * @return the targets
- * @see #targets
- */
- @XmlElement(name = "target")
- public List<Target> getTargets() {
- return targets;
- }
-
- /**
- * @param targets
- * the targets to set
- * @see #targets
- */
- public void setTargets(List<Target> targets) {
- this.targets = targets;
- }
-
- /**
- * @return the synonyms
- * @see #synonyms
- */
- public List<String> getSynonyms() {
- return synonyms;
- }
-
- /**
- * @param synonyms
- * the synonyms to set
- * @see #synonyms
- */
- public void setSynonyms(List<String> synonyms) {
- this.synonyms = synonyms;
- }
-
- /**
- * Adds brand name into {@link #brandNames}.
- *
- * @param brandName
- * object to add
- */
- public void addBrandName(String brandName) {
- this.brandNames.add(brandName);
- }
-
- /**
- * Adds synonym into {@link #synonyms}.
- *
- * @param synonym
- * object to add
- */
- public void addSynonym(String synonym) {
- if (synonyms.contains(synonym)) {
- logger.warn("Synonym already exists in the drug: " + synonym);
- } else {
- this.synonyms.add(synonym);
- }
- }
-
- /**
- * Adds target into {@link #targets} list.
- *
- * @param target
- * object to add
- */
- public void addTarget(Target target) {
- this.targets.add(target);
- }
-
- /**
- * @param source
- * the source to add
- * @see #sources
- */
- public void addSource(MiriamData source) {
- this.sources.add(source);
- }
-
- /**
- * @return the sources
- * @see #sources
- */
- public List<MiriamData> getSources() {
- return sources;
- }
-
- /**
- * @param sources
- * the sources to set
- * @see #sources
- */
- public void setSources(List<MiriamData> sources) {
- this.sources = sources;
- }
-
- /**
- * Adds targets to the drug.
- *
- * @param targets2
- * list of targets to add
- */
- public void addTargets(List<Target> targets2) {
- this.targets.addAll(targets2);
- }
-
- /**
- * @return the approved
- * @see #approved
- */
- public Boolean getApproved() {
- return approved;
- }
-
- /**
- * @param approved
- * the approved to set
- * @see #approved
- */
- public void setApproved(Boolean approved) {
- this.approved = approved;
- }
-
- /**
- * Comparator of the objects by their name.
- *
- * @author Piotr Gawron
- *
- */
- public static class NameComparator implements Comparator<Drug> {
- /**
- * Default string comparator.
- */
- private StringComparator stringComparator = new StringComparator();
-
- @Override
- public int compare(Drug arg0, Drug arg1) {
- return stringComparator.compare(arg0.getName(), arg1.getName());
- }
-
- }
+package lcsb.mapviewer.annotation.data;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Comparator;
+import java.util.List;
+
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlRootElement;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.comparator.StringComparator;
+import lcsb.mapviewer.model.map.MiriamData;
+
+/**
+ * Desribes information about drug retrieved from external database.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@XmlRootElement
+public class Drug implements Serializable, TargettingStructure {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(Drug.class);
+
+ /**
+ * Source of the data.
+ */
+ private List<MiriamData> sources = new ArrayList<>();
+
+ /**
+ * Name of the drug.
+ */
+ private String name;
+
+ /**
+ * Description of the drug.
+ */
+ private String description;
+
+ /**
+ * Status of blood brain barries for the drug.
+ */
+ private String bloodBrainBarrier = "N/A";
+
+ /**
+ * Is the drug approved.
+ */
+ private Boolean approved;
+
+ /**
+ * Known brand names.
+ */
+ private List<String> brandNames = new ArrayList<>();
+
+ /**
+ * Known targets.
+ */
+ private List<Target> targets = new ArrayList<>();
+
+ /**
+ * Known synonyms.
+ */
+ private List<String> synonyms = new ArrayList<>();
+
+ /**
+ * Default constructor.
+ */
+ public Drug() {
+
+ }
+
+ /**
+ * Constructor that initializes object with the same information as parameter.
+ *
+ * @param drug
+ * original drug
+ */
+ public Drug(Drug drug) {
+ if (drug == null) {
+ return;
+ }
+ this.sources.addAll(drug.getSources());
+ this.description = drug.description;
+ this.brandNames.addAll(drug.getBrandNames());
+ this.synonyms.addAll(drug.getSynonyms());
+ this.targets.addAll(drug.getTargets());
+ this.bloodBrainBarrier = drug.getBloodBrainBarrier();
+ this.setApproved(drug.getApproved());
+ }
+
+ @Override
+ public String toString() {
+ StringBuilder result = new StringBuilder("");
+ for (MiriamData md : sources) {
+ result.append("source: " + md.getDataType() + ", drugId: " + md.getResource() + "\n");
+ }
+ result.append(", name: " + name + "\nDescription:\n" + description + "\nSynonyms:");
+ for (String s : synonyms) {
+ result.append(s + "|");
+ }
+ result.append("\nTargets:");
+ for (Target t : targets) {
+ if (t.getSource() != null) {
+ result.append(t.getSource().getResource() + "|" + t.getName() + "|" + t.getGenes());
+ } else {
+ result.append("N/A |" + t.getName() + "|" + t.getGenes());
+ }
+ result.append(" (References:");
+ for (MiriamData md : t.getReferences()) {
+ result.append(md.getResource() + ",");
+ }
+ result.append(")+\n");
+
+ }
+ return result.toString();
+ }
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * @return the description
+ * @see #description
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * @param description
+ * the description to set
+ * @see #description
+ */
+ public void setDescription(String description) {
+ this.description = description;
+ }
+
+ /**
+ * @return the bloodBrainBarrier
+ * @see #bloodBrainBarrier
+ */
+ public String getBloodBrainBarrier() {
+ return bloodBrainBarrier;
+ }
+
+ /**
+ * @param bloodBrainBarrier
+ * the bloodBrainBarrier to set
+ * @see #bloodBrainBarrier
+ */
+ public void setBloodBrainBarrier(String bloodBrainBarrier) {
+ this.bloodBrainBarrier = bloodBrainBarrier;
+ }
+
+ /**
+ * @return the brandNames
+ * @see #brandNames
+ */
+ public List<String> getBrandNames() {
+ return brandNames;
+ }
+
+ /**
+ * @param brandNames
+ * the brandNames to set
+ * @see #brandNames
+ */
+ public void setBrandNames(List<String> brandNames) {
+ this.brandNames = brandNames;
+ }
+
+ /**
+ * @return the targets
+ * @see #targets
+ */
+ @XmlElement(name = "target")
+ public List<Target> getTargets() {
+ return targets;
+ }
+
+ /**
+ * @param targets
+ * the targets to set
+ * @see #targets
+ */
+ public void setTargets(List<Target> targets) {
+ this.targets = targets;
+ }
+
+ /**
+ * @return the synonyms
+ * @see #synonyms
+ */
+ public List<String> getSynonyms() {
+ return synonyms;
+ }
+
+ /**
+ * @param synonyms
+ * the synonyms to set
+ * @see #synonyms
+ */
+ public void setSynonyms(List<String> synonyms) {
+ this.synonyms = synonyms;
+ }
+
+ /**
+ * Adds brand name into {@link #brandNames}.
+ *
+ * @param brandName
+ * object to add
+ */
+ public void addBrandName(String brandName) {
+ this.brandNames.add(brandName);
+ }
+
+ /**
+ * Adds synonym into {@link #synonyms}.
+ *
+ * @param synonym
+ * object to add
+ */
+ public void addSynonym(String synonym) {
+ if (synonyms.contains(synonym)) {
+ logger.warn("Synonym already exists in the drug: " + synonym);
+ } else {
+ this.synonyms.add(synonym);
+ }
+ }
+
+ /**
+ * Adds target into {@link #targets} list.
+ *
+ * @param target
+ * object to add
+ */
+ public void addTarget(Target target) {
+ this.targets.add(target);
+ }
+
+ /**
+ * @param source
+ * the source to add
+ * @see #sources
+ */
+ public void addSource(MiriamData source) {
+ this.sources.add(source);
+ }
+
+ /**
+ * @return the sources
+ * @see #sources
+ */
+ public List<MiriamData> getSources() {
+ return sources;
+ }
+
+ /**
+ * @param sources
+ * the sources to set
+ * @see #sources
+ */
+ public void setSources(List<MiriamData> sources) {
+ this.sources = sources;
+ }
+
+ /**
+ * Adds targets to the drug.
+ *
+ * @param targets2
+ * list of targets to add
+ */
+ public void addTargets(List<Target> targets2) {
+ this.targets.addAll(targets2);
+ }
+
+ /**
+ * @return the approved
+ * @see #approved
+ */
+ public Boolean getApproved() {
+ return approved;
+ }
+
+ /**
+ * @param approved
+ * the approved to set
+ * @see #approved
+ */
+ public void setApproved(Boolean approved) {
+ this.approved = approved;
+ }
+
+ /**
+ * Comparator of the objects by their name.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ public static class NameComparator implements Comparator<Drug> {
+ /**
+ * Default string comparator.
+ */
+ private StringComparator stringComparator = new StringComparator();
+
+ @Override
+ public int compare(Drug arg0, Drug arg1) {
+ return stringComparator.compare(arg0.getName(), arg1.getName());
+ }
+
+ }
}
\ No newline at end of file
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/data/EntrezData.java b/annotation/src/main/java/lcsb/mapviewer/annotation/data/EntrezData.java
index d8ce8f3883..b826b8c412 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/EntrezData.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/EntrezData.java
@@ -1,152 +1,152 @@
-package lcsb.mapviewer.annotation.data;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.xml.bind.annotation.XmlRootElement;
-
-import lcsb.mapviewer.model.map.MiriamData;
-
-/**
- * Object that stores important information about entrez id used in annotation
- * process.
- *
- * @author Piotr Gawron
- *
- */
-@XmlRootElement
-public class EntrezData implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Symbol of a gene.
- */
- private String symbol = null;
-
- /**
- * Full name of a gene.
- */
- private String fullName = null;
-
- /**
- * Synonyms of a gene.
- */
- private List<String> synonyms = new ArrayList<>();
-
- /**
- * Description of a gene.
- */
- private String description = null;
-
- /**
- * Miriam annotations of a gene.
- */
- private List<MiriamData> miriamData = new ArrayList<>();
-
- /**
- * @return the symbol
- * @see #symbol
- */
- public String getSymbol() {
- return symbol;
- }
-
- /**
- * @param symbol
- * the symbol to set
- * @see #symbol
- */
- public void setSymbol(String symbol) {
- this.symbol = symbol;
- }
-
- /**
- * @return the fullName
- * @see #fullName
- */
- public String getFullName() {
- return fullName;
- }
-
- /**
- * @param fullName
- * the fullName to set
- * @see #fullName
- */
- public void setFullName(String fullName) {
- this.fullName = fullName;
- }
-
- /**
- * @return the synonyms
- * @see #synonyms
- */
- public List<String> getSynonyms() {
- return synonyms;
- }
-
- /**
- * @param synonyms
- * the synonyms to set
- * @see #synonyms
- */
- public void setSynonyms(List<String> synonyms) {
- this.synonyms = synonyms;
- }
-
- /**
- * @return the description
- * @see #description
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * @param description
- * the description to set
- * @see #description
- */
- public void setDescription(String description) {
- this.description = description;
- }
-
- /**
- * @return the miriamData
- * @see #miriamData
- */
- public List<MiriamData> getMiriamData() {
- return miriamData;
- }
-
- /**
- * Adds {@link MiriamData} to the list of annotations.
- *
- * @param miriamData2
- * object to add
- */
- public void addMiriamData(MiriamData miriamData2) {
- this.miriamData.add(miriamData2);
- }
-
- @Override
- public String toString() {
- String result = "Symbol: " + symbol + "\tFull name: " + fullName + "\tSynonyms: " + synonyms + "\tDescription: " + description + "\tMiriam: " + miriamData;
- return result;
- }
-
- /**
- * @param miriamData
- * the miriamData to set
- * @see #miriamData
- */
- public void setMiriamData(List<MiriamData> miriamData) {
- this.miriamData = miriamData;
- }
-
-}
+package lcsb.mapviewer.annotation.data;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.xml.bind.annotation.XmlRootElement;
+
+import lcsb.mapviewer.model.map.MiriamData;
+
+/**
+ * Object that stores important information about entrez id used in annotation
+ * process.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@XmlRootElement
+public class EntrezData implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Symbol of a gene.
+ */
+ private String symbol = null;
+
+ /**
+ * Full name of a gene.
+ */
+ private String fullName = null;
+
+ /**
+ * Synonyms of a gene.
+ */
+ private List<String> synonyms = new ArrayList<>();
+
+ /**
+ * Description of a gene.
+ */
+ private String description = null;
+
+ /**
+ * Miriam annotations of a gene.
+ */
+ private List<MiriamData> miriamData = new ArrayList<>();
+
+ /**
+ * @return the symbol
+ * @see #symbol
+ */
+ public String getSymbol() {
+ return symbol;
+ }
+
+ /**
+ * @param symbol
+ * the symbol to set
+ * @see #symbol
+ */
+ public void setSymbol(String symbol) {
+ this.symbol = symbol;
+ }
+
+ /**
+ * @return the fullName
+ * @see #fullName
+ */
+ public String getFullName() {
+ return fullName;
+ }
+
+ /**
+ * @param fullName
+ * the fullName to set
+ * @see #fullName
+ */
+ public void setFullName(String fullName) {
+ this.fullName = fullName;
+ }
+
+ /**
+ * @return the synonyms
+ * @see #synonyms
+ */
+ public List<String> getSynonyms() {
+ return synonyms;
+ }
+
+ /**
+ * @param synonyms
+ * the synonyms to set
+ * @see #synonyms
+ */
+ public void setSynonyms(List<String> synonyms) {
+ this.synonyms = synonyms;
+ }
+
+ /**
+ * @return the description
+ * @see #description
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * @param description
+ * the description to set
+ * @see #description
+ */
+ public void setDescription(String description) {
+ this.description = description;
+ }
+
+ /**
+ * @return the miriamData
+ * @see #miriamData
+ */
+ public List<MiriamData> getMiriamData() {
+ return miriamData;
+ }
+
+ /**
+ * Adds {@link MiriamData} to the list of annotations.
+ *
+ * @param miriamData2
+ * object to add
+ */
+ public void addMiriamData(MiriamData miriamData2) {
+ this.miriamData.add(miriamData2);
+ }
+
+ @Override
+ public String toString() {
+ String result = "Symbol: " + symbol + "\tFull name: " + fullName + "\tSynonyms: " + synonyms + "\tDescription: " + description + "\tMiriam: " + miriamData;
+ return result;
+ }
+
+ /**
+ * @param miriamData
+ * the miriamData to set
+ * @see #miriamData
+ */
+ public void setMiriamData(List<MiriamData> miriamData) {
+ this.miriamData = miriamData;
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/data/Go.java b/annotation/src/main/java/lcsb/mapviewer/annotation/data/Go.java
index 188df886a6..8031d370f4 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/Go.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/Go.java
@@ -1,86 +1,86 @@
-package lcsb.mapviewer.annotation.data;
-
-import java.io.Serializable;
-
-import javax.xml.bind.annotation.XmlRootElement;
-
-/**
- * Object representing element obtained from Gene Ontoly database.
- *
- * @author Piotr Gawron
- *
- */
-@XmlRootElement
-public class Go implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Human readable name.
- */
- private String commonName;
-
- /**
- * Description of the object.
- */
- private String description;
-
- /**
- * Go identifier.
- */
- private String goTerm;
-
- /**
- * @return the commonName
- * @see #commonName
- */
- public String getCommonName() {
- return commonName;
- }
-
- /**
- * @param commonName
- * the commonName to set
- * @see #commonName
- */
- public void setCommonName(String commonName) {
- this.commonName = commonName;
- }
-
- /**
- * @return the description
- * @see #description
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * @param description
- * the description to set
- * @see #description
- */
- public void setDescription(String description) {
- this.description = description;
- }
-
- /**
- * @return the goTerm
- * @see #goTerm
- */
- public String getGoTerm() {
- return goTerm;
- }
-
- /**
- * @param goTerm
- * the goTerm to set
- * @see #goTerm
- */
- public void setGoTerm(String goTerm) {
- this.goTerm = goTerm;
- }
-
-}
+package lcsb.mapviewer.annotation.data;
+
+import java.io.Serializable;
+
+import javax.xml.bind.annotation.XmlRootElement;
+
+/**
+ * Object representing element obtained from Gene Ontoly database.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@XmlRootElement
+public class Go implements Serializable {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Human readable name.
+ */
+ private String commonName;
+
+ /**
+ * Description of the object.
+ */
+ private String description;
+
+ /**
+ * Go identifier.
+ */
+ private String goTerm;
+
+ /**
+ * @return the commonName
+ * @see #commonName
+ */
+ public String getCommonName() {
+ return commonName;
+ }
+
+ /**
+ * @param commonName
+ * the commonName to set
+ * @see #commonName
+ */
+ public void setCommonName(String commonName) {
+ this.commonName = commonName;
+ }
+
+ /**
+ * @return the description
+ * @see #description
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * @param description
+ * the description to set
+ * @see #description
+ */
+ public void setDescription(String description) {
+ this.description = description;
+ }
+
+ /**
+ * @return the goTerm
+ * @see #goTerm
+ */
+ public String getGoTerm() {
+ return goTerm;
+ }
+
+ /**
+ * @param goTerm
+ * the goTerm to set
+ * @see #goTerm
+ */
+ public void setGoTerm(String goTerm) {
+ this.goTerm = goTerm;
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/data/MeSH.java b/annotation/src/main/java/lcsb/mapviewer/annotation/data/MeSH.java
index 10041a1883..68eae86800 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/MeSH.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/MeSH.java
@@ -1,183 +1,183 @@
-package lcsb.mapviewer.annotation.data;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Set;
-
-import javax.xml.bind.annotation.XmlRootElement;
-
-import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
-
-/**
- * This class represents <a href="http://www.nlm.nih.gov/cgi/mesh//">MeSH</a>
- * object.
- *
- * @author Ayan Rota
- *
- */
-@XmlRootElement
-public class MeSH implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(MeSH.class);
-
- /**
- * short name.
- */
- private String name;
-
- /**
- * MeSH identifier.
- */
- private String meSHId;
-
- /**
- * Detailed description of the MeSH object.
- */
- private String description;
-
- /**
- * List of synonyms.
- */
- private List<String> synonyms = new ArrayList<>();
-
- /**
- * Default constructor.
- */
- public MeSH() {
-
- }
-
- /**
- * @param name
- * short name.
- * @param meSHId
- * database identifier.
- * @param description
- * long description.
- * @param synonyms
- * list of terms used as names for this object.
- */
- public MeSH(String meSHId, String name, String description, List<String> synonyms) {
- super();
- this.name = name;
- this.meSHId = meSHId;
- this.description = description;
- this.synonyms = synonyms;
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return the synonyms
- * @see #synonyms
- */
- public List<String> getSynonyms() {
- return synonyms;
- }
-
- /**
- * @param synonyms
- * the synonyms to set
- * @see #synonyms
- */
- public void setSynonyms(List<String> synonyms) {
- this.synonyms = synonyms;
- }
-
- /**
- * @return database identifier.
- */
- public String getMeSHId() {
- return meSHId;
- }
-
- /**
- * @return description of the object.
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * @param meSHId
- * database identifier
- */
- public void setMeSHId(String meSHId) {
- this.meSHId = meSHId;
- }
-
- /**
- * @param description
- * long description.
- */
- public void setDescription(String description) {
- this.description = description;
- }
-
- @Override
- public String toString() {
- StringBuffer result = new StringBuffer();
- result.append("\nid: " + meSHId);
- result.append("\nname: " + name);
- result.append("\ndescription:" + description);
- result.append("\nsynonyms:" + getSynonymsString());
- return result.toString();
- }
-
- /**
- * @return list of synonyms as string.
- */
- public String getSynonymsString() {
- return StringUtils.join(synonyms, ",");
- }
-
- /**
- * Adds synonym to the synonym list.
- *
- * @param synonym
- * synonym to add
- */
- public void addSynonym(String synonym) {
- synonyms.add(synonym);
- }
-
- /**
- * Adds synonyms to the synonym list.
- *
- * @param synonymsToAdd
- * synonyms to add
- */
- public void addSynonyms(Set<String> synonymsToAdd) {
- for (String synonym : synonymsToAdd) {
- this.synonyms.add(synonym);
- }
-
- }
-
-}
+package lcsb.mapviewer.annotation.data;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
+
+import javax.xml.bind.annotation.XmlRootElement;
+
+import org.apache.commons.lang3.StringUtils;
+import org.apache.log4j.Logger;
+
+/**
+ * This class represents <a href="http://www.nlm.nih.gov/cgi/mesh//">MeSH</a>
+ * object.
+ *
+ * @author Ayan Rota
+ *
+ */
+@XmlRootElement
+public class MeSH implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(MeSH.class);
+
+ /**
+ * short name.
+ */
+ private String name;
+
+ /**
+ * MeSH identifier.
+ */
+ private String meSHId;
+
+ /**
+ * Detailed description of the MeSH object.
+ */
+ private String description;
+
+ /**
+ * List of synonyms.
+ */
+ private List<String> synonyms = new ArrayList<>();
+
+ /**
+ * Default constructor.
+ */
+ public MeSH() {
+
+ }
+
+ /**
+ * @param name
+ * short name.
+ * @param meSHId
+ * database identifier.
+ * @param description
+ * long description.
+ * @param synonyms
+ * list of terms used as names for this object.
+ */
+ public MeSH(String meSHId, String name, String description, List<String> synonyms) {
+ super();
+ this.name = name;
+ this.meSHId = meSHId;
+ this.description = description;
+ this.synonyms = synonyms;
+ }
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * @return the synonyms
+ * @see #synonyms
+ */
+ public List<String> getSynonyms() {
+ return synonyms;
+ }
+
+ /**
+ * @param synonyms
+ * the synonyms to set
+ * @see #synonyms
+ */
+ public void setSynonyms(List<String> synonyms) {
+ this.synonyms = synonyms;
+ }
+
+ /**
+ * @return database identifier.
+ */
+ public String getMeSHId() {
+ return meSHId;
+ }
+
+ /**
+ * @return description of the object.
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * @param meSHId
+ * database identifier
+ */
+ public void setMeSHId(String meSHId) {
+ this.meSHId = meSHId;
+ }
+
+ /**
+ * @param description
+ * long description.
+ */
+ public void setDescription(String description) {
+ this.description = description;
+ }
+
+ @Override
+ public String toString() {
+ StringBuffer result = new StringBuffer();
+ result.append("\nid: " + meSHId);
+ result.append("\nname: " + name);
+ result.append("\ndescription:" + description);
+ result.append("\nsynonyms:" + getSynonymsString());
+ return result.toString();
+ }
+
+ /**
+ * @return list of synonyms as string.
+ */
+ public String getSynonymsString() {
+ return StringUtils.join(synonyms, ",");
+ }
+
+ /**
+ * Adds synonym to the synonym list.
+ *
+ * @param synonym
+ * synonym to add
+ */
+ public void addSynonym(String synonym) {
+ synonyms.add(synonym);
+ }
+
+ /**
+ * Adds synonyms to the synonym list.
+ *
+ * @param synonymsToAdd
+ * synonyms to add
+ */
+ public void addSynonyms(Set<String> synonymsToAdd) {
+ for (String synonym : synonymsToAdd) {
+ this.synonyms.add(synonym);
+ }
+
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/data/MiRNA.java b/annotation/src/main/java/lcsb/mapviewer/annotation/data/MiRNA.java
index f583dc5269..2602a1751a 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/MiRNA.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/MiRNA.java
@@ -1,133 +1,133 @@
-package lcsb.mapviewer.annotation.data;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Comparator;
-import java.util.List;
-
-import javax.xml.bind.annotation.XmlRootElement;
-
-import lcsb.mapviewer.common.comparator.StringComparator;
-import lcsb.mapviewer.model.map.MiriamData;
-
-/**
- * Object representing element obtained from Toxigenomic database.
- *
- * @author Ayan Rota
- *
- */
-@XmlRootElement
-public class MiRNA implements Serializable, TargettingStructure {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * ID coming from MiRBase.
- */
- private String name;
-
- /**
- * Genes interacting with the chemical plus publications.
- */
- private List<Target> targets = new ArrayList<>();
-
- /**
- * default constructor.
- */
- public MiRNA() {
- super();
- }
-
- /**
- * Constructor that takes name of mirna as argument.
- *
- * @param name
- * name of the mirna
- */
- public MiRNA(String name) {
- super();
- this.name = name;
- }
-
- @Override
- public String toString() {
- StringBuffer result = new StringBuffer();
- result.append("\nmiRBaseID: " + name);
- result.append("\ntargetGenes:");
- for (Target target : getTargets()) {
- result.append(target.toString());
- }
-
- return result.toString();
- }
-
- /**
- * @return list of genes plus publications.
- */
- public List<Target> getTargets() {
- return targets;
- }
-
- /**
- * @param targets
- * list of genes plus publications.
- */
- public void setTargets(List<Target> targets) {
- this.targets = targets;
- }
-
- /**
- * @return id form Mirtarbase id.
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * id form MirBase id.
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * Adds target to mirna.
- *
- * @param target
- * target to add.
- */
-
- public void addTarget(Target target) {
- this.targets.add(target);
- }
-
- @Override
- public Collection<MiriamData> getSources() {
- return new ArrayList<>();
- }
-
- /**
- * Comparator of the objects by their name.
- *
- * @author Piotr Gawron
- *
- */
- public static class NameComparator implements Comparator<MiRNA> {
- /**
- * Default string comparator.
- */
- private StringComparator stringComparator = new StringComparator();
-
- @Override
- public int compare(MiRNA arg0, MiRNA arg1) {
- return stringComparator.compare(arg0.getName(), arg1.getName());
- }
-
- }
-
-}
+package lcsb.mapviewer.annotation.data;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Comparator;
+import java.util.List;
+
+import javax.xml.bind.annotation.XmlRootElement;
+
+import lcsb.mapviewer.common.comparator.StringComparator;
+import lcsb.mapviewer.model.map.MiriamData;
+
+/**
+ * Object representing element obtained from Toxigenomic database.
+ *
+ * @author Ayan Rota
+ *
+ */
+@XmlRootElement
+public class MiRNA implements Serializable, TargettingStructure {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * ID coming from MiRBase.
+ */
+ private String name;
+
+ /**
+ * Genes interacting with the chemical plus publications.
+ */
+ private List<Target> targets = new ArrayList<>();
+
+ /**
+ * default constructor.
+ */
+ public MiRNA() {
+ super();
+ }
+
+ /**
+ * Constructor that takes name of mirna as argument.
+ *
+ * @param name
+ * name of the mirna
+ */
+ public MiRNA(String name) {
+ super();
+ this.name = name;
+ }
+
+ @Override
+ public String toString() {
+ StringBuffer result = new StringBuffer();
+ result.append("\nmiRBaseID: " + name);
+ result.append("\ntargetGenes:");
+ for (Target target : getTargets()) {
+ result.append(target.toString());
+ }
+
+ return result.toString();
+ }
+
+ /**
+ * @return list of genes plus publications.
+ */
+ public List<Target> getTargets() {
+ return targets;
+ }
+
+ /**
+ * @param targets
+ * list of genes plus publications.
+ */
+ public void setTargets(List<Target> targets) {
+ this.targets = targets;
+ }
+
+ /**
+ * @return id form Mirtarbase id.
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * id form MirBase id.
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * Adds target to mirna.
+ *
+ * @param target
+ * target to add.
+ */
+
+ public void addTarget(Target target) {
+ this.targets.add(target);
+ }
+
+ @Override
+ public Collection<MiriamData> getSources() {
+ return new ArrayList<>();
+ }
+
+ /**
+ * Comparator of the objects by their name.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ public static class NameComparator implements Comparator<MiRNA> {
+ /**
+ * Default string comparator.
+ */
+ private StringComparator stringComparator = new StringComparator();
+
+ @Override
+ public int compare(MiRNA arg0, MiRNA arg1) {
+ return stringComparator.compare(arg0.getName(), arg1.getName());
+ }
+
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/data/Target.java b/annotation/src/main/java/lcsb/mapviewer/annotation/data/Target.java
index de8c9f6999..6c71b4072e 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/Target.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/Target.java
@@ -1,230 +1,230 @@
-package lcsb.mapviewer.annotation.data;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import javax.xml.bind.annotation.XmlElement;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.MiriamData;
-
-/**
- * Describes element targetted by an element from external database. It could be
- * a {@link Drug} or {@link Chemical} or {@link MiRNA}.
- *
- * @author Piotr Gawron
- *
- */
-public class Target implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- private static transient Logger logger = Logger.getLogger(Target.class);
-
- /**
- * Database from which target was received.
- */
- private MiriamData source;
-
- /**
- * Name of the target.
- */
- private String name;
-
- /**
- * Organism in which target is located.
- */
- private MiriamData organism;
-
- /**
- * List of genes located in a target.
- */
- private List<MiriamData> genes = new ArrayList<>();
-
- /**
- * List of references describing target.
- */
- private List<MiriamData> references = new ArrayList<>();
-
- /**
- * Type of target.
- */
- private TargetType type;
-
- /**
- * Default constructor.
- */
- public Target() {
-
- }
-
- /**
- * Constructor that initializes target with some data.
- *
- * @param source
- * from where the information about target was retrieved
- * @param gene
- * {@link MiriamData} that identifies gene
- * @param references
- * list of references that support this target
- */
- public Target(MiriamData source, MiriamData gene, Collection<MiriamData> references) {
- this.source = source;
- if (gene != null) {
- addGene(gene);
- }
- addReferences(references);
- if (getGenes().size() == 1) {
- setType(TargetType.SINGLE_PROTEIN);
- }
- }
-
- /**
- * @return the type
- * @see #type
- */
- public TargetType getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(TargetType type) {
- this.type = type;
- }
-
- /**
- *
- * @return {@link #references} list
- */
- @XmlElement(name = "pubmed")
- public List<MiriamData> getReferences() {
- return references;
- }
-
- /**
- *
- * @param md
- * new {@link #references} list
- */
- public void addReference(MiriamData md) {
- if (this.references.contains(md)) {
- logger.warn("Target " + getName() + " already has MiriamData: " + md);
- } else {
- this.references.add(md);
- }
- }
-
- /**
- * Adds gene to the gene list.
- *
- * @param gene
- * object to add
- */
- public void addGene(MiriamData gene) {
- if (gene == null) {
- throw new InvalidArgumentException("Cannot add null element");
- }
- this.genes.add(gene);
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return the organism
- * @see #organism
- */
- public MiriamData getOrganism() {
- return organism;
- }
-
- /**
- * @param organism
- * the organism to set
- * @see #organism
- */
- public void setOrganism(MiriamData organism) {
- this.organism = organism;
- }
-
- /**
- * @return the geneCardId
- * @see #genes
- */
- public List<MiriamData> getGenes() {
- return genes;
- }
-
- /**
- * @param genes
- * the genes to set
- * @see #genes
- */
- public void setGenes(List<MiriamData> genes) {
- this.genes = genes;
- }
-
- /**
- * @return the source
- * @see #source
- */
- public MiriamData getSource() {
- return source;
- }
-
- /**
- * @param source
- * the source to set
- * @see #source
- */
- public void setSource(MiriamData source) {
- this.source = source;
- }
-
- /**
- * Adds set of references to the target.
- *
- * @param references
- * objects to add
- *
- * @see #references
- */
- public void addReferences(Collection<MiriamData> references) {
- this.references.addAll(references);
- }
-
- @Override
- public String toString() {
- return "[" + this.getClass().getSimpleName() + "]: " + name + ", source: " + source + ", organism: " + organism
- + "; ";
- }
-
-}
+package lcsb.mapviewer.annotation.data;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import javax.xml.bind.annotation.XmlElement;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.MiriamData;
+
+/**
+ * Describes element targetted by an element from external database. It could be
+ * a {@link Drug} or {@link Chemical} or {@link MiRNA}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class Target implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ private static transient Logger logger = Logger.getLogger(Target.class);
+
+ /**
+ * Database from which target was received.
+ */
+ private MiriamData source;
+
+ /**
+ * Name of the target.
+ */
+ private String name;
+
+ /**
+ * Organism in which target is located.
+ */
+ private MiriamData organism;
+
+ /**
+ * List of genes located in a target.
+ */
+ private List<MiriamData> genes = new ArrayList<>();
+
+ /**
+ * List of references describing target.
+ */
+ private List<MiriamData> references = new ArrayList<>();
+
+ /**
+ * Type of target.
+ */
+ private TargetType type;
+
+ /**
+ * Default constructor.
+ */
+ public Target() {
+
+ }
+
+ /**
+ * Constructor that initializes target with some data.
+ *
+ * @param source
+ * from where the information about target was retrieved
+ * @param gene
+ * {@link MiriamData} that identifies gene
+ * @param references
+ * list of references that support this target
+ */
+ public Target(MiriamData source, MiriamData gene, Collection<MiriamData> references) {
+ this.source = source;
+ if (gene != null) {
+ addGene(gene);
+ }
+ addReferences(references);
+ if (getGenes().size() == 1) {
+ setType(TargetType.SINGLE_PROTEIN);
+ }
+ }
+
+ /**
+ * @return the type
+ * @see #type
+ */
+ public TargetType getType() {
+ return type;
+ }
+
+ /**
+ * @param type
+ * the type to set
+ * @see #type
+ */
+ public void setType(TargetType type) {
+ this.type = type;
+ }
+
+ /**
+ *
+ * @return {@link #references} list
+ */
+ @XmlElement(name = "pubmed")
+ public List<MiriamData> getReferences() {
+ return references;
+ }
+
+ /**
+ *
+ * @param md
+ * new {@link #references} list
+ */
+ public void addReference(MiriamData md) {
+ if (this.references.contains(md)) {
+ logger.warn("Target " + getName() + " already has MiriamData: " + md);
+ } else {
+ this.references.add(md);
+ }
+ }
+
+ /**
+ * Adds gene to the gene list.
+ *
+ * @param gene
+ * object to add
+ */
+ public void addGene(MiriamData gene) {
+ if (gene == null) {
+ throw new InvalidArgumentException("Cannot add null element");
+ }
+ this.genes.add(gene);
+ }
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * @return the organism
+ * @see #organism
+ */
+ public MiriamData getOrganism() {
+ return organism;
+ }
+
+ /**
+ * @param organism
+ * the organism to set
+ * @see #organism
+ */
+ public void setOrganism(MiriamData organism) {
+ this.organism = organism;
+ }
+
+ /**
+ * @return the geneCardId
+ * @see #genes
+ */
+ public List<MiriamData> getGenes() {
+ return genes;
+ }
+
+ /**
+ * @param genes
+ * the genes to set
+ * @see #genes
+ */
+ public void setGenes(List<MiriamData> genes) {
+ this.genes = genes;
+ }
+
+ /**
+ * @return the source
+ * @see #source
+ */
+ public MiriamData getSource() {
+ return source;
+ }
+
+ /**
+ * @param source
+ * the source to set
+ * @see #source
+ */
+ public void setSource(MiriamData source) {
+ this.source = source;
+ }
+
+ /**
+ * Adds set of references to the target.
+ *
+ * @param references
+ * objects to add
+ *
+ * @see #references
+ */
+ public void addReferences(Collection<MiriamData> references) {
+ this.references.addAll(references);
+ }
+
+ @Override
+ public String toString() {
+ return "[" + this.getClass().getSimpleName() + "]: " + name + ", source: " + source + ", organism: " + organism
+ + "; ";
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/data/TargetType.java b/annotation/src/main/java/lcsb/mapviewer/annotation/data/TargetType.java
index 7d2dfa4b08..6b695531bb 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/TargetType.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/TargetType.java
@@ -1,53 +1,53 @@
-package lcsb.mapviewer.annotation.data;
-
-/**
- * Type of the {@link Target}.
- *
- * @author Piotr Gawron
- *
- */
-public enum TargetType {
-
- /**
- * Target is a single protein.
- */
- SINGLE_PROTEIN("Single protein"),
-
- /**
- * Target is a complex.
- */
- COMPLEX_PROTEIN("Complex protein"),
-
- /**
- * Target is a protein family.
- */
- PROTEIN_FAMILY("Protein family"),
-
- /**
- * Target is of other type.
- */
- OTHER("Other");
-
- /**
- * Human readable name.
- */
- private String commonName;
-
- /**
- * Default constructor that creates enum position.
- *
- * @param commonName
- * {@link #commonName}
- */
- TargetType(String commonName) {
- this.commonName = commonName;
- }
-
- /**
- *
- * @return {@link #commonName}
- */
- public String getCommonName() {
- return commonName;
- }
-}
+package lcsb.mapviewer.annotation.data;
+
+/**
+ * Type of the {@link Target}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum TargetType {
+
+ /**
+ * Target is a single protein.
+ */
+ SINGLE_PROTEIN("Single protein"),
+
+ /**
+ * Target is a complex.
+ */
+ COMPLEX_PROTEIN("Complex protein"),
+
+ /**
+ * Target is a protein family.
+ */
+ PROTEIN_FAMILY("Protein family"),
+
+ /**
+ * Target is of other type.
+ */
+ OTHER("Other");
+
+ /**
+ * Human readable name.
+ */
+ private String commonName;
+
+ /**
+ * Default constructor that creates enum position.
+ *
+ * @param commonName
+ * {@link #commonName}
+ */
+ TargetType(String commonName) {
+ this.commonName = commonName;
+ }
+
+ /**
+ *
+ * @return {@link #commonName}
+ */
+ public String getCommonName() {
+ return commonName;
+ }
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/data/package-info.java b/annotation/src/main/java/lcsb/mapviewer/annotation/data/package-info.java
index d90a07e053..1473f561a5 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/package-info.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/package-info.java
@@ -1,5 +1,5 @@
-/**
- * Data structures used by annotation module.
- */
-package lcsb.mapviewer.annotation.data;
-
+/**
+ * Data structures used by annotation module.
+ */
+package lcsb.mapviewer.annotation.data;
+
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
index 17ccdbbe7b..cedc92718e 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java
@@ -1,693 +1,693 @@
-package lcsb.mapviewer.annotation.services;
-
-import java.io.IOException;
-import java.net.URLEncoder;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
-import lcsb.mapviewer.annotation.cache.WebPageDownloader;
-import lcsb.mapviewer.annotation.data.Drug;
-import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.annotation.data.TargetType;
-import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
-import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.UniprotSearchException;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-
-/**
- * Class used for accessing and parsing data from chembl database using
- * <a href="https://www.ebi.ac.uk/chembl/ws">ChEMBL Data Web Services</a>.
- * Parser was initially developed by Janek, but after new API released by ebi it
- * was refactored by Piotr.
- *
- * @author Piotr Gawron
- *
- */
-public class ChEMBLParser extends DrugAnnotation implements IExternalService {
-
- /**
- * Url that access data of drug identified by drug chembl identifier.
- */
- private static final String DRUG_BY_DRUG_ID_API_URL = "https://www.ebi.ac.uk/chembl/api/data/molecule?molecule_chembl_id=";
-
- /**
- * Url that access data about targetting mechanisms for a give drug chembl
- * identifier.
- */
- private static final String TARGET_MECHANISM_BY_DRUG_ID_API_URL = "https://www.ebi.ac.uk/chembl/api/data/mechanism?molecule_chembl_id=";
-
- /**
- * Url that access data about drugs identified by drug target identifier.
- */
- private static final String DRUG_BY_TARGET_ID_API_URL = "https://www.ebi.ac.uk/chembl/api/data/mechanism?target_chembl_id=";
-
- /**
- * Url that access data of drug identified by name.
- */
- private static final String DRUG_NAME_API_URL = "https://www.ebi.ac.uk/chembl/api/data/molecule?pref_name__exact=";
-
- /**
- * Url that access target by identifier.
- */
- private static final String TARGET_API_URL = "https://www.ebi.ac.uk/chembl/api/data/target/";
-
- /**
- * Url that list of all child nodes for chembl ontology term.
- */
- private static final String PARENT_CHILD_API_URL = "https://www.ebi.ac.uk/chembl/api/data/molecule_form/";
-
- /**
- * Suffix that should be added to {@link #PARENT_CHILD_API_URL}.
- */
- private static final String PARENT_CHILD_API_URL_SUFFIX = ".xml";
-
- /**
- * Url used for finding targets containing uniprot identifiers. Important - for
- * now the limit of targets is 1000 so if more targets will be found this link
- * will not provide them.
- */
- private static final String URL_TARGET_FROM_UNIPROT = "https://www.ebi.ac.uk/chembl/api/data/target?limit=1000&target_components__accession=";
-
- /**
- * Prefix used in key for storing data by name.
- */
- static final String NAME_PREFIX = "drug:";
-
- /**
- * Length of the prefix used in key for storing data by name.
- */
- private static final int NAME_PREFIX_LENGTH = NAME_PREFIX.length();
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(ChEMBLParser.class);
-
- /**
- * Service used for annotation of proteins using {@link MiriamType#UNIPROT
- * uniprot}.
- */
- @Autowired
- private UniprotAnnotator uniprotAnnotator;
-
- /**
- * Service used for annotation of proteins (and finding annotation of proteins).
- */
- @Autowired
- private HgncAnnotator hgncAnnotator;
-
- /**
- * Default constructor.
- */
- public ChEMBLParser() {
- super(ChEMBLParser.class);
- }
-
- @Override
- public String refreshCacheQuery(Object query) throws SourceNotAvailable {
- String result = null;
- try {
- if (query instanceof String) {
- String name = (String) query;
- if (name.startsWith(NAME_PREFIX)) {
- name = name.substring(NAME_PREFIX_LENGTH);
- result = getDrugSerializer().objectToString(findDrug(name));
- } else {
- result = super.refreshCacheQuery(query);
- }
- } else {
- result = super.refreshCacheQuery(query);
- }
- } catch (DrugSearchException e) {
- throw new SourceNotAvailable(e);
- }
- return result;
- }
-
- /**
- * Returns target for given chembl identifier.
- *
- * @param md
- * {@link MiriamType#CHEMBL_TARGET chembl identifier} of the target
- * @return target
- * @throws DrugSearchException
- * thrown when there are problems with connection to ChEMBL database
- */
- Target getTargetFromId(MiriamData md) throws DrugSearchException {
- if (!md.getDataType().equals(MiriamType.CHEMBL_TARGET)) {
- throw new InvalidArgumentException(
- "Target must be of a type: " + MiriamType.CHEMBL_TARGET + ". But found: " + md.getDataType());
- }
- try {
- Target target = new Target();
- target.setSource(md);
-
- String accessUrl = TARGET_API_URL + md.getResource();
- String inputLine = getWebPageContent(accessUrl);
-
- Document document = getXmlDocumentFromString(inputLine);
-
- Node response = getNode("target", document.getChildNodes());
-
- NodeList list = response.getChildNodes();
-
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("organism")) {
- // nothing to do here, we use taxonomy id
- } else if (node.getNodeName().equalsIgnoreCase("tax_id")) {
- String value = node.getTextContent();
- MiriamData taxonomy = new MiriamData(MiriamType.TAXONOMY, value);
- String organismName = getTaxonomyBackend().getNameForTaxonomy(taxonomy);
- if (organismName != null) {
- target.setOrganism(taxonomy);
- }
- } else if (node.getNodeName().equalsIgnoreCase("pref_name")) {
- // node with information about name
- target.setName(node.getTextContent());
- } else if (node.getNodeName().equalsIgnoreCase("target_chembl_id")) {
- // identifier of the element
- if (!node.getTextContent().equalsIgnoreCase(md.getResource())) {
- logger.warn("Problem with data returned by API. We asked for target: " + md.getResource()
- + ", but got results for: " + node.getNodeName());
- }
- } else if (node.getNodeName().equalsIgnoreCase("target_type")) {
- // type of target
- String tmp = node.getTextContent();
- if (tmp.equals("SINGLE PROTEIN")) {
- target.setType(TargetType.SINGLE_PROTEIN);
- } else if (tmp.equals("PROTEIN FAMILY")) {
- target.setType(TargetType.PROTEIN_FAMILY);
- } else if (tmp.equals("PROTEIN COMPLEX")) {
- target.setType(TargetType.COMPLEX_PROTEIN);
- } else {
- target.setType(TargetType.OTHER);
- }
- } else if (node.getNodeName().equalsIgnoreCase("target_components")) {
- for (int j = 0; j < node.getChildNodes().getLength(); j++) {
- Node tmpNode = node.getChildNodes().item(j);
- if (tmpNode.getNodeType() == Node.ELEMENT_NODE) {
- MiriamData targetElement = targetComponentToMiriamData(tmpNode);
- if (targetElement != null) {
- target.addGene(targetElement);
- } else {
- logger.warn("Problem with processing target component: " + super.nodeToString(tmpNode));
- }
- }
- }
-
- } else if (node.getNodeName().equalsIgnoreCase("species_group_flag")) {
- // nothing to do here
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("cross_references")) {
- // nothing to do here
- continue;
- } else {
- logger.warn("Unknown node: " + node.getNodeName() + ";" + node.getTextContent());
- }
- }
- }
-
- return target;
- } catch (InvalidXmlSchemaException e) {
- throw new DrugSearchException("Problem with accessing information about target: " + md, e);
- } catch (IOException e) {
- throw new DrugSearchException("Problem with accessing information about target: " + md, e);
- } catch (TaxonomySearchException e) {
- throw new DrugSearchException("Problem with accessing information about target: " + md, e);
- }
- }
-
- /**
- * Parse node of target component to get information about
- * {@link MiriamType#HGNC_SYMBOL} identifier.
- *
- * @param targetComponent
- * xml node to parse
- * @return {@link MiriamData} with {@link MiriamType#HGNC_SYMBOL} identifier
- * that could be extracted from input data
- * @throws DrugSearchException
- * thrown when there is a problem with annotations
- */
- private MiriamData targetComponentToMiriamData(Node targetComponent) throws DrugSearchException {
- MiriamData result = null;
- Node uniprotAccessionId = getNode("accession", targetComponent.getChildNodes());
- if (uniprotAccessionId != null) {
- try {
- result = uniprotAnnotator
- .uniProtToHgnc(new MiriamData(MiriamType.UNIPROT, uniprotAccessionId.getTextContent()));
- result.setAnnotator(null);
- } catch (UniprotSearchException e) {
- throw new DrugSearchException(e);
- }
- }
- return result;
- }
-
- /**
- * REturns list of targes for given drug.
- *
- * @param drugId
- * identifier of a drug for which targets are looked
- * @throws DrugSearchException
- * thrown when there are problems with connection to ChEMBL database
- * @return list of targes for given drug
- */
- List<Target> getTargetsByDrugId(MiriamData drugId) throws DrugSearchException {
- if (!MiriamType.CHEMBL_COMPOUND.equals(drugId.getDataType())) {
- throw new InvalidArgumentException("Only " + MiriamType.CHEMBL_COMPOUND + " are accepted");
- }
- List<Target> targets = new ArrayList<>();
- try {
-
- String page = getWebPageContent(TARGET_MECHANISM_BY_DRUG_ID_API_URL + drugId.getResource());
- Document document = getXmlDocumentFromString(page);
-
- Node response = getNode("response", document);
- Node mechanisms = getNode("mechanisms", response);
- NodeList nodeList = mechanisms.getChildNodes();
- for (int i = 0; i < nodeList.getLength(); i++) {
- Node node = nodeList.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("mechanism")) {
- Node chemblTargetIdNode = getNode("target_chembl_id", node);
- MiriamData targetMiriam = new MiriamData(MiriamType.CHEMBL_TARGET, chemblTargetIdNode.getTextContent());
-
- Target target = getTargetFromId(targetMiriam);
- Node referenceNode = getNode("mechanism_refs", node);
-
- Set<MiriamData> references = parseReferences(referenceNode);
- target.addReferences(references);
- targets.add(target);
- }
- }
- }
- return targets;
- } catch (IOException e) {
- throw new DrugSearchException("Problem with accessing DrugBank database", e);
- } catch (InvalidXmlSchemaException e) {
- throw new DrugSearchException("Problem with parsing DrugBank database response", e);
- }
- }
-
- /**
- * Parse xml node with references.
- *
- * @param referenceNode
- * node with references
- * @return list of references obtained from xml node
- */
- Set<MiriamData> parseReferences(Node referenceNode) {
- Set<MiriamData> result = new HashSet<>();
- if (referenceNode != null) {
- NodeList nodeList = referenceNode.getChildNodes();
- for (int i = 0; i < nodeList.getLength(); i++) {
- Node node = nodeList.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("mechanism")) {
- Node typeNode = super.getNode("ref_type", node);
- if ("PubMed".equalsIgnoreCase(typeNode.getTextContent())) {
- Node idNode = super.getNode("ref_id", node);
- String id = idNode.getTextContent();
- result.add(new MiriamData(MiriamType.PUBMED, id));
- }
- } else {
- logger.warn("Unknown node: " + node.getNodeName());
- }
- }
- }
- }
- return result;
- }
-
- @Override
- public Drug findDrug(String name) throws DrugSearchException {
- name = name.toUpperCase();
-
- String query = NAME_PREFIX + name.toLowerCase().trim();
-
- Drug drug = getDrugSerializer().xmlToObject(getCacheNode(query));
- if (drug != null) {
- return drug;
- }
-
- try {
- name = URLEncoder.encode(name, "UTF-8");
- String accessUrl = DRUG_NAME_API_URL + name;
- String page = getWebPageContent(accessUrl);
-
- Document document = getXmlDocumentFromString(page);
- Node response = getNode("response", document.getChildNodes());
- Node molecules = getNode("molecules", response.getChildNodes());
-
- NodeList list = molecules.getChildNodes();
-
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("molecule")) {
- if (drug == null) {
- drug = parseDrug(node);
- } else {
- logger.warn("More drugs than one found for query: " + query);
- }
- }
- }
- }
-
- if (drug == null) {
- return null;
- }
- setCacheValue(query, getDrugSerializer().objectToString(drug));
- return drug;
- } catch (IOException e) {
- throw new DrugSearchException("Problem with accessing CHEMBL database", e);
- } catch (InvalidXmlSchemaException e) {
- throw new DrugSearchException("Problem with parsing data from CHEMBL database", e);
- }
- }
-
- /**
- * Parse xml node repesenting drug and returns drug with information obtained
- * from there and other places in chembl API.
- *
- * @param node
- * xml node representing drug, sample can be found <a href=
- * "https://www.ebi.ac.uk/chembl/api/data/molecule?molecule_chembl_id=CHEMBL2068724">
- * here</a> (molecule subnode):
- * @return {@link Drug} obtained from xml node
- * @throws DrugSearchException
- * thrown when there is a problem with accessing chembl database
- */
- private Drug parseDrug(Node node) throws DrugSearchException {
- Drug drug = new Drug();
- Node nameNode = getNode("pref_name", node);
- Node phaseNode = getNode("max_phase", node);
- Node idNode = getNode("molecule_chembl_id", node);
-
- drug.setName(nameNode.getTextContent());
- MiriamData drugId = new MiriamData(MiriamType.CHEMBL_COMPOUND, idNode.getTextContent());
- drug.addSource(drugId);
-
- drug.setDescription(null);
- Node synonymsNode = getNode("molecule_synonyms", node);
-
- drug.setSynonyms(parseSynonymsNode(synonymsNode));
- drug.addTargets(getTargetsByDrugId(drugId));
- drug.setApproved("4".equals(phaseNode.getTextContent()));
-
- drug.addTargets(getTargetsForChildElements(drug.getSources().get(0)));
-
- return drug;
- }
-
- /**
- * Get targets for chembl children nodes.
- *
- * @param drugId
- * id of the parent drug
- * @return list of drug targets for children molecules in chembl ontology
- * @throws DrugSearchException
- * thrown when there is a problemw ith processing request
- */
- List<Target> getTargetsForChildElements(MiriamData drugId) throws DrugSearchException {
- List<Target> targets = new ArrayList<>();
- try {
- String id = drugId.getResource();
- String query = PARENT_CHILD_API_URL + id + PARENT_CHILD_API_URL_SUFFIX;
- String page = getWebPageContent(query);
-
- Document document = super.getXmlDocumentFromString(page);
-
- Node response = getNode("response", document);
- Node forms = getNode("molecule_forms", response);
- NodeList list = forms.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("molecule_form")) {
- Node idNode = getNode("molecule_chembl_id", node);
- if (!idNode.getTextContent().equals(id)) {
- targets.addAll(getTargetsByDrugId(new MiriamData(MiriamType.CHEMBL_COMPOUND, idNode.getTextContent())));
- }
- } else {
- logger.warn("Unknown node type: " + node.getNodeName());
- }
- }
- }
- return targets;
- } catch (IOException e) {
- throw new DrugSearchException("Problem with accessing CHEMBL database", e);
- } catch (InvalidXmlSchemaException e) {
- throw new DrugSearchException("Problem with parsing data from CHEMBL database", e);
- }
- }
-
- /**
- * Parse xml node with synonyms.
- *
- * @param synonymsNode
- * xml node with synonyms
- * @return list of synonyms obtained from the input xml
- */
- List<String> parseSynonymsNode(Node synonymsNode) {
- List<String> result = new ArrayList<>();
- NodeList list = synonymsNode.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("synonym")) {
- Node synonymNode = getNode("synonyms", node);
- result.add(synonymNode.getTextContent());
- } else {
- logger.warn("Unknown node: " + node.getNodeName());
- }
- }
- }
- return result;
- }
-
- /**
- * Returns information about drug by chembl drug identifier.
- *
- * @param drugId
- * {@link MiriamType#CHEMBL_COMPOUND chembl drug identifier}
- * @return drug by chembl drug identifier
- * @throws DrugSearchException
- * thrown when there is a problem with accessing data about drug
- */
- Drug getDrugById(MiriamData drugId) throws DrugSearchException {
- if (!MiriamType.CHEMBL_COMPOUND.equals(drugId.getDataType())) {
- throw new InvalidArgumentException("Only " + MiriamType.CHEMBL_COMPOUND + " input data is accepted.");
- }
- try {
- String content = getWebPageContent(DRUG_BY_DRUG_ID_API_URL + drugId.getResource());
- Document document = getXmlDocumentFromString(content);
-
- Node response = getNode("response", document);
- if (response == null) {
- throw new DrugSearchException("Invalid source XML for drug: " + drugId);
- }
- Node moleculesNode = getNode("molecules", response);
- if (moleculesNode == null) {
- throw new DrugSearchException("Invalid source XML for drug: " + drugId);
- }
- Node moleculeNode = getNode("molecule", moleculesNode);
- if (moleculeNode == null) {
- throw new DrugSearchException("Invalid source XML for drug: " + drugId);
- }
- return parseDrug(moleculeNode);
- } catch (IOException e) {
- throw new DrugSearchException("Problem with accessing external database for id: " + drugId, e);
- } catch (InvalidXmlSchemaException e) {
- throw new DrugSearchException("Problem with parsing database result for id: " + drugId, e);
- }
- }
-
- @Override
- public ExternalServiceStatus getServiceStatus() {
- ExternalServiceStatus status = new ExternalServiceStatus("ChEMBL", MiriamType.CHEMBL_COMPOUND.getDbHomepage());
-
- GeneralCacheInterface cacheCopy = getCache();
- this.setCache(null);
-
- try {
- Drug drug = findDrug("Amantadine");
- status.setStatus(ExternalServiceStatusType.OK);
- if (drug == null) {
- status.setStatus(ExternalServiceStatusType.CHANGED);
- } else if (drug.getName().isEmpty()) {
- status.setStatus(ExternalServiceStatusType.CHANGED);
- }
- } catch (Exception e) {
- logger.error(status.getName() + " is down", e);
- status.setStatus(ExternalServiceStatusType.DOWN);
- }
- this.setCache(cacheCopy);
- return status;
- }
-
- @Override
- public List<Drug> getDrugListByTarget(MiriamData target, Collection<MiriamData> organisms)
- throws DrugSearchException {
- List<Drug> result = new ArrayList<>();
- List<MiriamData> uniprotData = new ArrayList<>();
- if (MiriamType.HGNC_SYMBOL.equals(target.getDataType())) {
- try {
- uniprotData = hgncAnnotator.hgncToUniprot(target);
- } catch (AnnotatorException e) {
- throw new DrugSearchException("Cannot transform target into uniprot identifier", e);
- }
- } else if (MiriamType.UNIPROT.equals(target.getDataType())) {
- uniprotData.add(target);
- } else {
- throw new DrugSearchException("Don't know how to process target of " + target.getDataType() + " type.");
- }
- if (uniprotData.size() == 0) {
- return result;
- } else if (uniprotData.size() > 1) {
- logger.warn("Too many uniprot ids. Only first will be taken");
- }
- try {
- String url = URL_TARGET_FROM_UNIPROT + uniprotData.get(0).getResource();
-
- String page = getWebPageContent(url);
- Set<String> drugNames = new HashSet<>();
-
- Document document = getXmlDocumentFromString(page);
-
- Node response = getNode("response", document);
- Node targets = getNode("targets", response);
- NodeList nodeList = targets.getChildNodes();
- for (int i = 0; i < nodeList.getLength(); i++) {
- Node node = nodeList.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("target")) {
- String organismName = getNode("organism", node).getTextContent();
- if (organismMatch(organismName, organisms)) {
- Node chemblTargetIdNode = getNode("target_chembl_id", node);
- MiriamData targetMiriam = new MiriamData(MiriamType.CHEMBL_TARGET, chemblTargetIdNode.getTextContent());
- List<Drug> drugs = getDrugsByChemblTarget(targetMiriam);
- for (Drug drug : drugs) {
- // don't add duplicates
- if (!drugNames.contains(drug.getName())) {
- drugNames.add(drug.getName());
- result.add(drug);
- }
- }
- }
- }
- }
- }
-
- } catch (IOException e) {
- throw new DrugSearchException("Problem with accessing Chembl database", e);
- } catch (InvalidXmlSchemaException e) {
- throw new DrugSearchException("Problem with parsing Chembl response", e);
- }
-
- return result;
-
- }
-
- /**
- * Returns list of drugs found by target identified in the paramter.
- *
- * @param targetMiriam
- * {@link MiriamType#CHEMBL_TARGET chembl target identifier}
- * @return list of drugs found by target identified in the paramter
- * @throws DrugSearchException
- * thrown when there is a problem with accessing chembl database
- */
- List<Drug> getDrugsByChemblTarget(MiriamData targetMiriam) throws DrugSearchException {
- try {
- List<Drug> result = new ArrayList<>();
- String page = getWebPageContent(DRUG_BY_TARGET_ID_API_URL + targetMiriam.getResource());
- Document document = getXmlDocumentFromString(page);
-
- Node response = getNode("response", document);
- Node mechanisms = getNode("mechanisms", response);
- NodeList nodeList = mechanisms.getChildNodes();
- for (int i = 0; i < nodeList.getLength(); i++) {
- Node node = nodeList.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("mechanism")) {
- Node chemblMoleculeIdNode = getNode("molecule_chembl_id", node);
- MiriamData drugId = new MiriamData(MiriamType.CHEMBL_COMPOUND, chemblMoleculeIdNode.getTextContent());
- Drug drug = getDrugById(drugId);
- if (drug != null) {
- result.add(drug);
- }
- }
- }
- }
- return result;
- } catch (IOException e) {
- throw new DrugSearchException("Problem with accessing Chembl database", e);
- } catch (InvalidXmlSchemaException e) {
- throw new DrugSearchException("Problem with parsing Chembl response", e);
- }
-
- }
-
- /**
- * @return the uniprotAnnotator
- * @see #uniprotAnnotator
- */
- public UniprotAnnotator getUniprotAnnotator() {
- return uniprotAnnotator;
- }
-
- /**
- * @param uniprotAnnotator
- * the uniprotAnnotator to set
- * @see #uniprotAnnotator
- */
- public void setUniprotAnnotator(UniprotAnnotator uniprotAnnotator) {
- this.uniprotAnnotator = uniprotAnnotator;
- }
-
- @Override
- protected WebPageDownloader getWebPageDownloader() {
- return super.getWebPageDownloader();
- }
-
- @Override
- protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
- super.setWebPageDownloader(webPageDownloader);
- }
-
- /**
- * @return the hgncAnnotator
- * @see #hgncAnnotator
- */
- public HgncAnnotator getHgncAnnotator() {
- return hgncAnnotator;
- }
-
- /**
- * @param hgncAnnotator
- * the hgncAnnotator to set
- * @see #hgncAnnotator
- */
- public void setHgncAnnotator(HgncAnnotator hgncAnnotator) {
- this.hgncAnnotator = hgncAnnotator;
- }
-
-}
+package lcsb.mapviewer.annotation.services;
+
+import java.io.IOException;
+import java.net.URLEncoder;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.w3c.dom.Document;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.WebPageDownloader;
+import lcsb.mapviewer.annotation.data.Drug;
+import lcsb.mapviewer.annotation.data.Target;
+import lcsb.mapviewer.annotation.data.TargetType;
+import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
+import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
+import lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator;
+import lcsb.mapviewer.annotation.services.annotators.UniprotSearchException;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+
+/**
+ * Class used for accessing and parsing data from chembl database using
+ * <a href="https://www.ebi.ac.uk/chembl/ws">ChEMBL Data Web Services</a>.
+ * Parser was initially developed by Janek, but after new API released by ebi it
+ * was refactored by Piotr.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ChEMBLParser extends DrugAnnotation implements IExternalService {
+
+ /**
+ * Url that access data of drug identified by drug chembl identifier.
+ */
+ private static final String DRUG_BY_DRUG_ID_API_URL = "https://www.ebi.ac.uk/chembl/api/data/molecule?molecule_chembl_id=";
+
+ /**
+ * Url that access data about targetting mechanisms for a give drug chembl
+ * identifier.
+ */
+ private static final String TARGET_MECHANISM_BY_DRUG_ID_API_URL = "https://www.ebi.ac.uk/chembl/api/data/mechanism?molecule_chembl_id=";
+
+ /**
+ * Url that access data about drugs identified by drug target identifier.
+ */
+ private static final String DRUG_BY_TARGET_ID_API_URL = "https://www.ebi.ac.uk/chembl/api/data/mechanism?target_chembl_id=";
+
+ /**
+ * Url that access data of drug identified by name.
+ */
+ private static final String DRUG_NAME_API_URL = "https://www.ebi.ac.uk/chembl/api/data/molecule?pref_name__exact=";
+
+ /**
+ * Url that access target by identifier.
+ */
+ private static final String TARGET_API_URL = "https://www.ebi.ac.uk/chembl/api/data/target/";
+
+ /**
+ * Url that list of all child nodes for chembl ontology term.
+ */
+ private static final String PARENT_CHILD_API_URL = "https://www.ebi.ac.uk/chembl/api/data/molecule_form/";
+
+ /**
+ * Suffix that should be added to {@link #PARENT_CHILD_API_URL}.
+ */
+ private static final String PARENT_CHILD_API_URL_SUFFIX = ".xml";
+
+ /**
+ * Url used for finding targets containing uniprot identifiers. Important - for
+ * now the limit of targets is 1000 so if more targets will be found this link
+ * will not provide them.
+ */
+ private static final String URL_TARGET_FROM_UNIPROT = "https://www.ebi.ac.uk/chembl/api/data/target?limit=1000&target_components__accession=";
+
+ /**
+ * Prefix used in key for storing data by name.
+ */
+ static final String NAME_PREFIX = "drug:";
+
+ /**
+ * Length of the prefix used in key for storing data by name.
+ */
+ private static final int NAME_PREFIX_LENGTH = NAME_PREFIX.length();
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(ChEMBLParser.class);
+
+ /**
+ * Service used for annotation of proteins using {@link MiriamType#UNIPROT
+ * uniprot}.
+ */
+ @Autowired
+ private UniprotAnnotator uniprotAnnotator;
+
+ /**
+ * Service used for annotation of proteins (and finding annotation of proteins).
+ */
+ @Autowired
+ private HgncAnnotator hgncAnnotator;
+
+ /**
+ * Default constructor.
+ */
+ public ChEMBLParser() {
+ super(ChEMBLParser.class);
+ }
+
+ @Override
+ public String refreshCacheQuery(Object query) throws SourceNotAvailable {
+ String result = null;
+ try {
+ if (query instanceof String) {
+ String name = (String) query;
+ if (name.startsWith(NAME_PREFIX)) {
+ name = name.substring(NAME_PREFIX_LENGTH);
+ result = getDrugSerializer().objectToString(findDrug(name));
+ } else {
+ result = super.refreshCacheQuery(query);
+ }
+ } else {
+ result = super.refreshCacheQuery(query);
+ }
+ } catch (DrugSearchException e) {
+ throw new SourceNotAvailable(e);
+ }
+ return result;
+ }
+
+ /**
+ * Returns target for given chembl identifier.
+ *
+ * @param md
+ * {@link MiriamType#CHEMBL_TARGET chembl identifier} of the target
+ * @return target
+ * @throws DrugSearchException
+ * thrown when there are problems with connection to ChEMBL database
+ */
+ Target getTargetFromId(MiriamData md) throws DrugSearchException {
+ if (!md.getDataType().equals(MiriamType.CHEMBL_TARGET)) {
+ throw new InvalidArgumentException(
+ "Target must be of a type: " + MiriamType.CHEMBL_TARGET + ". But found: " + md.getDataType());
+ }
+ try {
+ Target target = new Target();
+ target.setSource(md);
+
+ String accessUrl = TARGET_API_URL + md.getResource();
+ String inputLine = getWebPageContent(accessUrl);
+
+ Document document = getXmlDocumentFromString(inputLine);
+
+ Node response = getNode("target", document.getChildNodes());
+
+ NodeList list = response.getChildNodes();
+
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("organism")) {
+ // nothing to do here, we use taxonomy id
+ } else if (node.getNodeName().equalsIgnoreCase("tax_id")) {
+ String value = node.getTextContent();
+ MiriamData taxonomy = new MiriamData(MiriamType.TAXONOMY, value);
+ String organismName = getTaxonomyBackend().getNameForTaxonomy(taxonomy);
+ if (organismName != null) {
+ target.setOrganism(taxonomy);
+ }
+ } else if (node.getNodeName().equalsIgnoreCase("pref_name")) {
+ // node with information about name
+ target.setName(node.getTextContent());
+ } else if (node.getNodeName().equalsIgnoreCase("target_chembl_id")) {
+ // identifier of the element
+ if (!node.getTextContent().equalsIgnoreCase(md.getResource())) {
+ logger.warn("Problem with data returned by API. We asked for target: " + md.getResource()
+ + ", but got results for: " + node.getNodeName());
+ }
+ } else if (node.getNodeName().equalsIgnoreCase("target_type")) {
+ // type of target
+ String tmp = node.getTextContent();
+ if (tmp.equals("SINGLE PROTEIN")) {
+ target.setType(TargetType.SINGLE_PROTEIN);
+ } else if (tmp.equals("PROTEIN FAMILY")) {
+ target.setType(TargetType.PROTEIN_FAMILY);
+ } else if (tmp.equals("PROTEIN COMPLEX")) {
+ target.setType(TargetType.COMPLEX_PROTEIN);
+ } else {
+ target.setType(TargetType.OTHER);
+ }
+ } else if (node.getNodeName().equalsIgnoreCase("target_components")) {
+ for (int j = 0; j < node.getChildNodes().getLength(); j++) {
+ Node tmpNode = node.getChildNodes().item(j);
+ if (tmpNode.getNodeType() == Node.ELEMENT_NODE) {
+ MiriamData targetElement = targetComponentToMiriamData(tmpNode);
+ if (targetElement != null) {
+ target.addGene(targetElement);
+ } else {
+ logger.warn("Problem with processing target component: " + super.nodeToString(tmpNode));
+ }
+ }
+ }
+
+ } else if (node.getNodeName().equalsIgnoreCase("species_group_flag")) {
+ // nothing to do here
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("cross_references")) {
+ // nothing to do here
+ continue;
+ } else {
+ logger.warn("Unknown node: " + node.getNodeName() + ";" + node.getTextContent());
+ }
+ }
+ }
+
+ return target;
+ } catch (InvalidXmlSchemaException e) {
+ throw new DrugSearchException("Problem with accessing information about target: " + md, e);
+ } catch (IOException e) {
+ throw new DrugSearchException("Problem with accessing information about target: " + md, e);
+ } catch (TaxonomySearchException e) {
+ throw new DrugSearchException("Problem with accessing information about target: " + md, e);
+ }
+ }
+
+ /**
+ * Parse node of target component to get information about
+ * {@link MiriamType#HGNC_SYMBOL} identifier.
+ *
+ * @param targetComponent
+ * xml node to parse
+ * @return {@link MiriamData} with {@link MiriamType#HGNC_SYMBOL} identifier
+ * that could be extracted from input data
+ * @throws DrugSearchException
+ * thrown when there is a problem with annotations
+ */
+ private MiriamData targetComponentToMiriamData(Node targetComponent) throws DrugSearchException {
+ MiriamData result = null;
+ Node uniprotAccessionId = getNode("accession", targetComponent.getChildNodes());
+ if (uniprotAccessionId != null) {
+ try {
+ result = uniprotAnnotator
+ .uniProtToHgnc(new MiriamData(MiriamType.UNIPROT, uniprotAccessionId.getTextContent()));
+ result.setAnnotator(null);
+ } catch (UniprotSearchException e) {
+ throw new DrugSearchException(e);
+ }
+ }
+ return result;
+ }
+
+ /**
+ * REturns list of targes for given drug.
+ *
+ * @param drugId
+ * identifier of a drug for which targets are looked
+ * @throws DrugSearchException
+ * thrown when there are problems with connection to ChEMBL database
+ * @return list of targes for given drug
+ */
+ List<Target> getTargetsByDrugId(MiriamData drugId) throws DrugSearchException {
+ if (!MiriamType.CHEMBL_COMPOUND.equals(drugId.getDataType())) {
+ throw new InvalidArgumentException("Only " + MiriamType.CHEMBL_COMPOUND + " are accepted");
+ }
+ List<Target> targets = new ArrayList<>();
+ try {
+
+ String page = getWebPageContent(TARGET_MECHANISM_BY_DRUG_ID_API_URL + drugId.getResource());
+ Document document = getXmlDocumentFromString(page);
+
+ Node response = getNode("response", document);
+ Node mechanisms = getNode("mechanisms", response);
+ NodeList nodeList = mechanisms.getChildNodes();
+ for (int i = 0; i < nodeList.getLength(); i++) {
+ Node node = nodeList.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("mechanism")) {
+ Node chemblTargetIdNode = getNode("target_chembl_id", node);
+ MiriamData targetMiriam = new MiriamData(MiriamType.CHEMBL_TARGET, chemblTargetIdNode.getTextContent());
+
+ Target target = getTargetFromId(targetMiriam);
+ Node referenceNode = getNode("mechanism_refs", node);
+
+ Set<MiriamData> references = parseReferences(referenceNode);
+ target.addReferences(references);
+ targets.add(target);
+ }
+ }
+ }
+ return targets;
+ } catch (IOException e) {
+ throw new DrugSearchException("Problem with accessing DrugBank database", e);
+ } catch (InvalidXmlSchemaException e) {
+ throw new DrugSearchException("Problem with parsing DrugBank database response", e);
+ }
+ }
+
+ /**
+ * Parse xml node with references.
+ *
+ * @param referenceNode
+ * node with references
+ * @return list of references obtained from xml node
+ */
+ Set<MiriamData> parseReferences(Node referenceNode) {
+ Set<MiriamData> result = new HashSet<>();
+ if (referenceNode != null) {
+ NodeList nodeList = referenceNode.getChildNodes();
+ for (int i = 0; i < nodeList.getLength(); i++) {
+ Node node = nodeList.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("mechanism")) {
+ Node typeNode = super.getNode("ref_type", node);
+ if ("PubMed".equalsIgnoreCase(typeNode.getTextContent())) {
+ Node idNode = super.getNode("ref_id", node);
+ String id = idNode.getTextContent();
+ result.add(new MiriamData(MiriamType.PUBMED, id));
+ }
+ } else {
+ logger.warn("Unknown node: " + node.getNodeName());
+ }
+ }
+ }
+ }
+ return result;
+ }
+
+ @Override
+ public Drug findDrug(String name) throws DrugSearchException {
+ name = name.toUpperCase();
+
+ String query = NAME_PREFIX + name.toLowerCase().trim();
+
+ Drug drug = getDrugSerializer().xmlToObject(getCacheNode(query));
+ if (drug != null) {
+ return drug;
+ }
+
+ try {
+ name = URLEncoder.encode(name, "UTF-8");
+ String accessUrl = DRUG_NAME_API_URL + name;
+ String page = getWebPageContent(accessUrl);
+
+ Document document = getXmlDocumentFromString(page);
+ Node response = getNode("response", document.getChildNodes());
+ Node molecules = getNode("molecules", response.getChildNodes());
+
+ NodeList list = molecules.getChildNodes();
+
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("molecule")) {
+ if (drug == null) {
+ drug = parseDrug(node);
+ } else {
+ logger.warn("More drugs than one found for query: " + query);
+ }
+ }
+ }
+ }
+
+ if (drug == null) {
+ return null;
+ }
+ setCacheValue(query, getDrugSerializer().objectToString(drug));
+ return drug;
+ } catch (IOException e) {
+ throw new DrugSearchException("Problem with accessing CHEMBL database", e);
+ } catch (InvalidXmlSchemaException e) {
+ throw new DrugSearchException("Problem with parsing data from CHEMBL database", e);
+ }
+ }
+
+ /**
+ * Parse xml node repesenting drug and returns drug with information obtained
+ * from there and other places in chembl API.
+ *
+ * @param node
+ * xml node representing drug, sample can be found <a href=
+ * "https://www.ebi.ac.uk/chembl/api/data/molecule?molecule_chembl_id=CHEMBL2068724">
+ * here</a> (molecule subnode):
+ * @return {@link Drug} obtained from xml node
+ * @throws DrugSearchException
+ * thrown when there is a problem with accessing chembl database
+ */
+ private Drug parseDrug(Node node) throws DrugSearchException {
+ Drug drug = new Drug();
+ Node nameNode = getNode("pref_name", node);
+ Node phaseNode = getNode("max_phase", node);
+ Node idNode = getNode("molecule_chembl_id", node);
+
+ drug.setName(nameNode.getTextContent());
+ MiriamData drugId = new MiriamData(MiriamType.CHEMBL_COMPOUND, idNode.getTextContent());
+ drug.addSource(drugId);
+
+ drug.setDescription(null);
+ Node synonymsNode = getNode("molecule_synonyms", node);
+
+ drug.setSynonyms(parseSynonymsNode(synonymsNode));
+ drug.addTargets(getTargetsByDrugId(drugId));
+ drug.setApproved("4".equals(phaseNode.getTextContent()));
+
+ drug.addTargets(getTargetsForChildElements(drug.getSources().get(0)));
+
+ return drug;
+ }
+
+ /**
+ * Get targets for chembl children nodes.
+ *
+ * @param drugId
+ * id of the parent drug
+ * @return list of drug targets for children molecules in chembl ontology
+ * @throws DrugSearchException
+ * thrown when there is a problemw ith processing request
+ */
+ List<Target> getTargetsForChildElements(MiriamData drugId) throws DrugSearchException {
+ List<Target> targets = new ArrayList<>();
+ try {
+ String id = drugId.getResource();
+ String query = PARENT_CHILD_API_URL + id + PARENT_CHILD_API_URL_SUFFIX;
+ String page = getWebPageContent(query);
+
+ Document document = super.getXmlDocumentFromString(page);
+
+ Node response = getNode("response", document);
+ Node forms = getNode("molecule_forms", response);
+ NodeList list = forms.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("molecule_form")) {
+ Node idNode = getNode("molecule_chembl_id", node);
+ if (!idNode.getTextContent().equals(id)) {
+ targets.addAll(getTargetsByDrugId(new MiriamData(MiriamType.CHEMBL_COMPOUND, idNode.getTextContent())));
+ }
+ } else {
+ logger.warn("Unknown node type: " + node.getNodeName());
+ }
+ }
+ }
+ return targets;
+ } catch (IOException e) {
+ throw new DrugSearchException("Problem with accessing CHEMBL database", e);
+ } catch (InvalidXmlSchemaException e) {
+ throw new DrugSearchException("Problem with parsing data from CHEMBL database", e);
+ }
+ }
+
+ /**
+ * Parse xml node with synonyms.
+ *
+ * @param synonymsNode
+ * xml node with synonyms
+ * @return list of synonyms obtained from the input xml
+ */
+ List<String> parseSynonymsNode(Node synonymsNode) {
+ List<String> result = new ArrayList<>();
+ NodeList list = synonymsNode.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("synonym")) {
+ Node synonymNode = getNode("synonyms", node);
+ result.add(synonymNode.getTextContent());
+ } else {
+ logger.warn("Unknown node: " + node.getNodeName());
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Returns information about drug by chembl drug identifier.
+ *
+ * @param drugId
+ * {@link MiriamType#CHEMBL_COMPOUND chembl drug identifier}
+ * @return drug by chembl drug identifier
+ * @throws DrugSearchException
+ * thrown when there is a problem with accessing data about drug
+ */
+ Drug getDrugById(MiriamData drugId) throws DrugSearchException {
+ if (!MiriamType.CHEMBL_COMPOUND.equals(drugId.getDataType())) {
+ throw new InvalidArgumentException("Only " + MiriamType.CHEMBL_COMPOUND + " input data is accepted.");
+ }
+ try {
+ String content = getWebPageContent(DRUG_BY_DRUG_ID_API_URL + drugId.getResource());
+ Document document = getXmlDocumentFromString(content);
+
+ Node response = getNode("response", document);
+ if (response == null) {
+ throw new DrugSearchException("Invalid source XML for drug: " + drugId);
+ }
+ Node moleculesNode = getNode("molecules", response);
+ if (moleculesNode == null) {
+ throw new DrugSearchException("Invalid source XML for drug: " + drugId);
+ }
+ Node moleculeNode = getNode("molecule", moleculesNode);
+ if (moleculeNode == null) {
+ throw new DrugSearchException("Invalid source XML for drug: " + drugId);
+ }
+ return parseDrug(moleculeNode);
+ } catch (IOException e) {
+ throw new DrugSearchException("Problem with accessing external database for id: " + drugId, e);
+ } catch (InvalidXmlSchemaException e) {
+ throw new DrugSearchException("Problem with parsing database result for id: " + drugId, e);
+ }
+ }
+
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ ExternalServiceStatus status = new ExternalServiceStatus("ChEMBL", MiriamType.CHEMBL_COMPOUND.getDbHomepage());
+
+ GeneralCacheInterface cacheCopy = getCache();
+ this.setCache(null);
+
+ try {
+ Drug drug = findDrug("Amantadine");
+ status.setStatus(ExternalServiceStatusType.OK);
+ if (drug == null) {
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ } else if (drug.getName().isEmpty()) {
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ }
+ } catch (Exception e) {
+ logger.error(status.getName() + " is down", e);
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ }
+ this.setCache(cacheCopy);
+ return status;
+ }
+
+ @Override
+ public List<Drug> getDrugListByTarget(MiriamData target, Collection<MiriamData> organisms)
+ throws DrugSearchException {
+ List<Drug> result = new ArrayList<>();
+ List<MiriamData> uniprotData = new ArrayList<>();
+ if (MiriamType.HGNC_SYMBOL.equals(target.getDataType())) {
+ try {
+ uniprotData = hgncAnnotator.hgncToUniprot(target);
+ } catch (AnnotatorException e) {
+ throw new DrugSearchException("Cannot transform target into uniprot identifier", e);
+ }
+ } else if (MiriamType.UNIPROT.equals(target.getDataType())) {
+ uniprotData.add(target);
+ } else {
+ throw new DrugSearchException("Don't know how to process target of " + target.getDataType() + " type.");
+ }
+ if (uniprotData.size() == 0) {
+ return result;
+ } else if (uniprotData.size() > 1) {
+ logger.warn("Too many uniprot ids. Only first will be taken");
+ }
+ try {
+ String url = URL_TARGET_FROM_UNIPROT + uniprotData.get(0).getResource();
+
+ String page = getWebPageContent(url);
+ Set<String> drugNames = new HashSet<>();
+
+ Document document = getXmlDocumentFromString(page);
+
+ Node response = getNode("response", document);
+ Node targets = getNode("targets", response);
+ NodeList nodeList = targets.getChildNodes();
+ for (int i = 0; i < nodeList.getLength(); i++) {
+ Node node = nodeList.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("target")) {
+ String organismName = getNode("organism", node).getTextContent();
+ if (organismMatch(organismName, organisms)) {
+ Node chemblTargetIdNode = getNode("target_chembl_id", node);
+ MiriamData targetMiriam = new MiriamData(MiriamType.CHEMBL_TARGET, chemblTargetIdNode.getTextContent());
+ List<Drug> drugs = getDrugsByChemblTarget(targetMiriam);
+ for (Drug drug : drugs) {
+ // don't add duplicates
+ if (!drugNames.contains(drug.getName())) {
+ drugNames.add(drug.getName());
+ result.add(drug);
+ }
+ }
+ }
+ }
+ }
+ }
+
+ } catch (IOException e) {
+ throw new DrugSearchException("Problem with accessing Chembl database", e);
+ } catch (InvalidXmlSchemaException e) {
+ throw new DrugSearchException("Problem with parsing Chembl response", e);
+ }
+
+ return result;
+
+ }
+
+ /**
+ * Returns list of drugs found by target identified in the paramter.
+ *
+ * @param targetMiriam
+ * {@link MiriamType#CHEMBL_TARGET chembl target identifier}
+ * @return list of drugs found by target identified in the paramter
+ * @throws DrugSearchException
+ * thrown when there is a problem with accessing chembl database
+ */
+ List<Drug> getDrugsByChemblTarget(MiriamData targetMiriam) throws DrugSearchException {
+ try {
+ List<Drug> result = new ArrayList<>();
+ String page = getWebPageContent(DRUG_BY_TARGET_ID_API_URL + targetMiriam.getResource());
+ Document document = getXmlDocumentFromString(page);
+
+ Node response = getNode("response", document);
+ Node mechanisms = getNode("mechanisms", response);
+ NodeList nodeList = mechanisms.getChildNodes();
+ for (int i = 0; i < nodeList.getLength(); i++) {
+ Node node = nodeList.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("mechanism")) {
+ Node chemblMoleculeIdNode = getNode("molecule_chembl_id", node);
+ MiriamData drugId = new MiriamData(MiriamType.CHEMBL_COMPOUND, chemblMoleculeIdNode.getTextContent());
+ Drug drug = getDrugById(drugId);
+ if (drug != null) {
+ result.add(drug);
+ }
+ }
+ }
+ }
+ return result;
+ } catch (IOException e) {
+ throw new DrugSearchException("Problem with accessing Chembl database", e);
+ } catch (InvalidXmlSchemaException e) {
+ throw new DrugSearchException("Problem with parsing Chembl response", e);
+ }
+
+ }
+
+ /**
+ * @return the uniprotAnnotator
+ * @see #uniprotAnnotator
+ */
+ public UniprotAnnotator getUniprotAnnotator() {
+ return uniprotAnnotator;
+ }
+
+ /**
+ * @param uniprotAnnotator
+ * the uniprotAnnotator to set
+ * @see #uniprotAnnotator
+ */
+ public void setUniprotAnnotator(UniprotAnnotator uniprotAnnotator) {
+ this.uniprotAnnotator = uniprotAnnotator;
+ }
+
+ @Override
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
+ }
+
+ @Override
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
+ }
+
+ /**
+ * @return the hgncAnnotator
+ * @see #hgncAnnotator
+ */
+ public HgncAnnotator getHgncAnnotator() {
+ return hgncAnnotator;
+ }
+
+ /**
+ * @param hgncAnnotator
+ * the hgncAnnotator to set
+ * @see #hgncAnnotator
+ */
+ public void setHgncAnnotator(HgncAnnotator hgncAnnotator) {
+ this.hgncAnnotator = hgncAnnotator;
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalParser.java
index ad9344e672..fbaf0862c5 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalParser.java
@@ -1,765 +1,765 @@
-package lcsb.mapviewer.annotation.services;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import org.apache.commons.lang3.SerializationException;
-import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.w3c.dom.Node;
-
-import lcsb.mapviewer.annotation.cache.CachableInterface;
-import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
-import lcsb.mapviewer.annotation.cache.WebPageDownloader;
-import lcsb.mapviewer.annotation.cache.XmlSerializer;
-import lcsb.mapviewer.annotation.data.Chemical;
-import lcsb.mapviewer.annotation.data.ChemicalDirectEvidence;
-import lcsb.mapviewer.annotation.data.MeSH;
-import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
-import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.persist.dao.ProjectDao;
-
-/**
- * This class is a backend to Toxicogenomic Chemical API.
- *
- * @author Ayan Rota
- *
- */
-public class ChemicalParser extends CachableInterface implements IExternalService {
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(ChemicalParser.class);
-
- /**
- * Prefix used for caching elements with chemical identifier as a key.
- */
- static final String CHEMICAL_PREFIX = "chemical:";
-
- /**
- * Prefix used for caching all chemical names in a disease.
- */
- protected static final String DISEASE_CHEMICALS_PREFIX = "DISEASE_CHEMICALS:";
-
- /**
- * Prefix used for caching list of suggested queries for project.
- */
- protected static final String PROJECT_SUGGESTED_QUERY_PREFIX = "PROJECT_CHEMICAL_QUERIES:";
-
- /**
- * Home page of ctd database.
- */
- static final String URL = "https://ctdbase.org/";
-
- /**
- * URL to get a list of chemicals by disease id.
- */
- public static final String DISEASE_URL = "https://ctdbase.org/detail.go?6578706f7274=1&d-1332398-e=5&view=chem&"
- + "type=disease&acc=MESH%3A";
-
- /**
- * URL to get a list of chemicals by gene id.
- */
- public static final String DISEASE_GENE_URL = "https://ctdbase.org/detail.go?slimTerm=all&6578706f7274=1&qid=3464576&"
- + "d-1332398-e=5&view=disease&type=gene&assnType=curated&acc=";
-
- /**
- * Column in results obtained from {@link ChemicalParser#DISEASE_GENE_URL}
- * describing drugs that are related to the gene (gene identifier is provided in
- * the url).
- */
- private static final int DRUG_NAME_COL_IN_GENE_DRUG_LIST = 3;
-
- /**
- * The location of name column in the parsed tab separated chemicals file.
- */
- public static final Integer CHEMICALS_NAME_COL = 0;
-
- /**
- * The location of id column in the parsed tab separated chemicals file.
- */
- public static final Integer CHEMICALS_ID_COL = 1;
-
- /**
- * The location of CAS column in the parsed tab separated chemicals file.
- */
- public static final Integer CHEMICALS_CAS_COL = 2;
-
- /**
- * The location of disease name column in the parsed tab separated chemicals
- * file.
- */
- public static final Integer CHEMICALS_DISEASE_NAME_COL = 3;
-
- /**
- * The location of disease id column in the parsed tab separated chemicals file.
- */
- public static final Integer CHEMICALS_DISEASE_ID_COL = 4;
-
- /**
- * The location of direct column in the parsed tab separated chemicals file.
- */
- public static final Integer CHEMICALS_DIRECT_COL = 5;
-
- /**
- * The location of network of genes column in the parsed tab separated chemicals
- * file.
- */
- public static final Integer CHEMICALS_NETWORK_COL = 6;
-
- /**
- * The location of score column in the parsed tab separated chemicals file.
- */
- public static final Integer CHEMICALS_SCORE_COL = 7;
-
- /**
- * The location of count column in the parsed tab separated chemicals file.
- */
- public static final Integer CHEMICALS_COUNT_COL = 8;
-
- /**
- * The location of pubmed id column in the publications.
- */
- public static final Integer PUBLICATIONS_ID_COL = 0;
-
- /**
- * The location of list of genes column that is associated with this publication
- * for particular chemical.
- */
- public static final Integer PUBLICATIONS_ASSOCIATION_COL = 5;
-
- /**
- * Object that allows to serialize {@link Chemical} elements into xml string and
- * deserialize xml into {@link Chemical} objects.
- */
- private XmlSerializer<Chemical> chemicalSerializer;
-
- /**
- * The status of the db.
- */
- private ExternalServiceStatus status = new ExternalServiceStatus("ctdbase", URL);
-
- /**
- * Object used to perform operations on {@link MiriamType#HGNC hgnc
- * annotations}.
- */
- @Autowired
- private HgncAnnotator hgncAnnotator;
-
- @Autowired
- private ProjectDao projectDao;
-
- @Autowired
- private MeSHParser meshParser;
-
- /**
- *
- */
- public ChemicalParser() {
- super(ChemicalParser.class);
- chemicalSerializer = new XmlSerializer<>(Chemical.class);
- }
-
- @Override
- public ExternalServiceStatus getServiceStatus() {
- GeneralCacheInterface cacheCopy = getCache();
- this.setCache(null);
- status.setStatus(ExternalServiceStatusType.OK);
- try {
- MiriamData diseaseID = new MiriamData(MiriamType.MESH_2012, "D002095");
- MiriamData chemicalID = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "D000395");
- Chemical chemical = getChemicalFromExternalDatabase(diseaseID, chemicalID);
- if (chemical == null || !chemical.getChemicalId().equals(chemicalID)) {
- status.setStatus(ExternalServiceStatusType.CHANGED);
- }
- } catch (Exception e) {
- logger.error("ctdbase service unavailable", e);
- status.setStatus(ExternalServiceStatusType.DOWN);
- }
- this.setCache(cacheCopy);
- return status;
-
- }
-
- /**
- * @param disease
- * the MESH Id for the disease
- * @return list of chemicals id, name pairs
- * @throws ChemicalSearchException
- * thrown when there is problem with accessing ctd database
- */
- public Map<MiriamData, String> getChemicalsForDisease(MiriamData disease) throws ChemicalSearchException {
- if (disease == null || disease.getResource() == null) {
- throw new InvalidArgumentException("disease cannot be null");
- }
-
- // check if we have results in cache
- String chemicalNode = super.getCacheValue(DISEASE_CHEMICALS_PREFIX + disease.getResource());
- if (chemicalNode != null) {
- return deserializeChemicalList(chemicalNode);
- }
-
- Map<MiriamData, String> chemicals = new HashMap<>();
- try {
- String diseaseID = disease.getResource();
- String query = DISEASE_URL + diseaseID;
- String page = getWebPageContent(query);
-
- String[] lines = page.split("\n");
- for (int rowNumber = 1; rowNumber < lines.length; rowNumber++) {
- String[] lineValues = lines[rowNumber].split("\t");
- String diseaseId = lineValues[CHEMICALS_DISEASE_ID_COL];
- diseaseId = MiriamData.getIdFromIdentifier(diseaseId);
- if (diseaseId != null && diseaseID.equals(diseaseId) && lineValues[CHEMICALS_ID_COL] != null) {
- chemicals.put(new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, lineValues[CHEMICALS_ID_COL]),
- lineValues[CHEMICALS_NAME_COL]);
- }
- }
-
- } catch (WrongResponseCodeIOException e) {
- // it means that there are no results for this query
- } catch (IOException e) {
- throw new ChemicalSearchException("ctdbase service unavailable", e);
- }
-
- // put the results into cache
- String cacheResult = serializeChemicalList(chemicals);
- super.setCacheValue(DISEASE_CHEMICALS_PREFIX + disease.getResource(), cacheResult);
-
- return chemicals;
-
- }
-
- /**
- * Serializes list of chemicalId-chemicalName pairs.
- *
- * @param chemicals
- * list of objects to serialize
- * @return serialized string
- */
- public String serializeChemicalList(Map<MiriamData, String> chemicals) {
- StringBuilder cacheResult = new StringBuilder();
- for (MiriamData md : chemicals.keySet()) {
- cacheResult.append(md.getResource() + "\t" + chemicals.get(md) + "\n");
- }
- return cacheResult.toString();
- }
-
- /**
- * Deserializes list of chemicalId-chemicalName pairs.
- *
- * @param chemicalNode
- * string to deserialize
- * @return list of chemicalId-chemicalName pairs
- */
- public Map<MiriamData, String> deserializeChemicalList(String chemicalNode) {
- Map<MiriamData, String> chemicals = new HashMap<>();
-
- String[] lines = chemicalNode.split("\n");
- for (String string : lines) {
- if (string.length() > 0) {
- String[] tmp = string.split("\t");
- String id = tmp[0];
- String name = tmp[1];
- chemicals.put(new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, id), name);
- }
- }
- return chemicals;
- }
-
- /**
- * @param diseaseID
- * The disease id that the chemical IDs belong to.
- * @param chemicalIDs
- * The list of the chemical ID required to be retrieved.
- * @return list of chemicals
- * @throws ChemicalSearchException
- * thrown when there is problem with accessing ctd database
- */
- public List<Chemical> getChemicals(MiriamData diseaseID, Collection<MiriamData> chemicalIDs)
- throws ChemicalSearchException {
- if (diseaseID == null) {
- throw new InvalidArgumentException("disease cannot be null");
- }
- List<Chemical> chemicals = new ArrayList<>();
-
- for (MiriamData chemicalId : chemicalIDs) {
- Chemical chemical = this.getChemicalFromExternalDatabase(diseaseID, chemicalId);
- if (chemical != null) {
- chemicals.add(chemical);
- }
- }
- return chemicals;
- }
-
- /**
- * @param diseaseID
- * Miriam data type for disease id
- * @param chemicalID
- * Miriam data type for chemical id
- * @return formated resource
- */
- public String getIdentifier(MiriamData diseaseID, MiriamData chemicalID) {
- return CHEMICAL_PREFIX + diseaseID.getResource() + ":" + chemicalID.getResource();
- }
-
- @Override
- public Object refreshCacheQuery(Object query) throws SourceNotAvailable {
- try {
- Object result = null;
- if (query instanceof String) {
- String identifier = (String) query;
- if (identifier.startsWith(CHEMICAL_PREFIX)) {
- String[] ids = identifier.split("\\:");
- MiriamData diseaseID = new MiriamData(MiriamType.MESH_2012, ids[1]);
- MiriamData chemicalID = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, ids[2]);
- Chemical chemical = getChemicalFromExternalDatabase(diseaseID, chemicalID);
- if (chemical != null) {
- result = chemicalSerializer.objectToString(chemical);
- } else {
- throw new SourceNotAvailable("Could not find the resource with string \"" + query + "\"");
- }
- } else if (identifier.startsWith(DISEASE_CHEMICALS_PREFIX)) {
- String id = identifier.substring(DISEASE_CHEMICALS_PREFIX.length());
- Map<MiriamData, String> resultObj = getChemicalsForDisease(new MiriamData(MiriamType.MESH_2012, id));
- result = serializeChemicalList(resultObj);
- } else if (identifier.startsWith(PROJECT_SUGGESTED_QUERY_PREFIX)) {
- String[] tmp = identifier.split("\n");
- Integer id = Integer.valueOf(tmp[1]);
- MiriamData diseaseId = new MiriamData(MiriamType.MESH_2012, tmp[2]);
- Project project = projectDao.getById(id);
- if (project == null) {
- throw new SourceNotAvailable("Project with given id doesn't exist: " + id);
- }
- List<String> list = getSuggestedQueryListWithoutCache(project, diseaseId);
- result = StringUtils.join(list, "\n");
- } else {
- result = super.refreshCacheQuery(query);
- }
- } else {
- result = super.refreshCacheQuery(query);
- }
- return result;
- } catch (ChemicalSearchException e) {
- throw new SourceNotAvailable("Problem with accessing ctd database", e);
- }
- }
-
- /**
- * @param diseaseID
- * the Mesh id of the disease.
- * @param chemicalId
- * the chemical id
- * @return list of chemical objects.
- * @throws ChemicalSearchException
- * thrown when there is problem with accessing ctd database
- */
- private Chemical getChemicalFromExternalDatabase(MiriamData diseaseID, MiriamData chemicalId)
- throws ChemicalSearchException {
- Chemical result = null;
- // look for chemical in the cache
- Node chemicalNode = super.getCacheNode(getIdentifier(diseaseID, chemicalId));
- if (chemicalNode != null && chemicalNode.hasChildNodes()) {
- try {
- result = chemicalSerializer.xmlToObject(chemicalNode);
- return result;
- } catch (SerializationException e) {
- logger.error(e, e);
- }
- }
- try {
- String diseaseQuery = DISEASE_URL + diseaseID.getResource();
- String diseasePage = getWebPageContent(diseaseQuery);
- String[] diseaseLines = diseasePage.split("\n");
- for (int rowNumber = 1; rowNumber < diseaseLines.length; rowNumber++) {
- String[] lineValues = diseaseLines[rowNumber].split("\t", -1);
- MiriamData chemID = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, lineValues[CHEMICALS_ID_COL]);
- String diseaseIdentifier = MiriamData.getIdFromIdentifier(lineValues[CHEMICALS_DISEASE_ID_COL]);
- MiriamData currentDiseaseId = new MiriamData(MiriamType.MESH_2012, diseaseIdentifier);
- if (chemicalId.equals(chemID) && diseaseID.equals(currentDiseaseId)) {
- result = getChemicalFromChemicalLine(lineValues, chemID);
- }
- }
- if (result != null) {
- MeSH mesh = meshParser.getMeSH(result.getChemicalId());
- if (mesh!=null) {
- result.addSynonyms(mesh.getSynonyms());
- } else {
- logger.warn("Problematic mesh id: "+result.getChemicalId());
- }
- }
-
- } catch (IOException e) {
- throw new ChemicalSearchException("ctdbase service unavailable", e);
- } catch (AnnotatorException e) {
- throw new ChemicalSearchException("problem with accessing mesh db", e);
- }
-
- // put them in cache
- super.setCacheValue(getIdentifier(diseaseID, chemicalId), chemicalSerializer.objectToString(result));
-
- return result;
- }
-
- /**
- * Method that creates chemical from a tab separated row from ctd database. Data
- * looks like (line wrapping added for clarity):
- *
- * <pre>
- 1. Disease Name Disease ID Direct Evidence Inference Network Inference Score Reference Count
- 2. Drug-Induced Liver Injury MESH:D056486 1-(2-trifluoromethoxyphenyl)-2-nitroethanone|1,4-bis(2-(3,5-dichloropyridyloxy))benzene|
- 2,4-dinitrotoluene|2,6-dinitrotoluene|Acetaminophen|Acetylcysteine|Aflatoxin B1|Azacitidine|Benzo(a)pyrene|Estradiol|Bilirubin|
- bisphenol A|Buthionine Sulfoximine|Carbamazepine|Chlorodiphenyl (54% Chlorine)|Chlorpromazine|Clodronic Acid|cobaltous chloride|
- Copper|Curcumin|Cyclosporine|Deferoxamine|Dexamethasone|Cisplatin|Dieldrin|Dietary Fats|Diethylnitrosamine|epigallocatechin gallate|
- Fenofibrate|Formaldehyde|Genistein|Glutathione|Hydrogen Peroxide|isoliquiritigenin|Lead|Lipopolysaccharides|manganese chloride|
- Medroxyprogesterone Acetate|Metformin|Methotrexate|methylmercuric chloride|N-Methyl-3,4-methylenedioxyamphetamine|morin|Morphine|
- Nanotubes, Carbon|nickel chloride|ochratoxin A|Oxygen|Paclitaxel|perfluoro-n-nonanoic acid|perfluorooctanoic acid|Phenobarbital|
- pirinixic acid|Polyphenols|Polysaccharides|potassium chromate(VI)|propiconazole|Quercetin|resveratrol|rosiglitazone|Rotenone|
- Streptozocin|Tetrachlorodibenzodioxin|titanium dioxide|Tretinoin|usnic acid|Valproic Acid|Vincristine|Zinc|zinc chloride 190.67 634
- * </pre>
- *
- * @param lineValues
- * line split by tab separator
- * @param chemID
- * chemical id
- * @return chemical obtained from input data
- * @throws ChemicalSearchException
- * thrown when there is a problem accessing ctd database
- */
- Chemical getChemicalFromChemicalLine(String[] lineValues, MiriamData chemID) throws ChemicalSearchException {
- String name = lineValues[CHEMICALS_NAME_COL];
- String casIdentifier = lineValues[CHEMICALS_CAS_COL];
- MiriamData casId = null;
- if ((casIdentifier != null) && !casIdentifier.trim().isEmpty()) {
- casId = new MiriamData(MiriamType.CAS, casIdentifier);
- }
-
- String directEvidenceStr = lineValues[CHEMICALS_DIRECT_COL];
- ChemicalDirectEvidence directType = null;
- if (directEvidenceStr.equals(ChemicalDirectEvidence.MARKER.getValue())) {
- directType = ChemicalDirectEvidence.MARKER;
- } else if (directEvidenceStr.equals(ChemicalDirectEvidence.THERAPEUTIC.getValue())) {
- directType = ChemicalDirectEvidence.THERAPEUTIC;
- }
-
- String networkStr = lineValues[CHEMICALS_NETWORK_COL].trim();
- Map<MiriamData, Set<MiriamData>> inferenceNetwork = new HashMap<>();
- List<MiriamData> directEvidencePublication = new ArrayList<>();
- String[] genesIDs = networkStr.split("\\|");
- for (String geneId : genesIDs) {
- if (!geneId.isEmpty()) {
- inferenceNetwork.put(new MiriamData(MiriamType.HGNC_SYMBOL, geneId), new HashSet<>());
- }
- }
-
- Pattern pattern = Pattern.compile("ixnId=([0-9]+)");
- List<MiriamData> invalidHgnc = new ArrayList<>();
- for (MiriamData md : inferenceNetwork.keySet()) {
- try {
- Set<String> idx = new HashSet<>();
- MiriamData entrez = hgncAnnotator.hgncToEntrez(md);
- // if we cannot find entrez this means the name is invalid hgnc and
- // should be removed from our result list (it might be gene name of
- // other species...)
- if (entrez == null) {
- invalidHgnc.add(md);
- } else {
- String query = "https://ctdbase.org/detail.go?type=gene&view=ixn&chemAcc=" + chemID.getResource() + "&acc="
- + entrez.getResource();
- String referencesPage = getWebPageContent(query);
- Matcher matcher = pattern.matcher(referencesPage);
- while (matcher.find()) {
- idx.add(matcher.group(1));
- }
- for (String string : idx) {
- String query2 = "https://ctdbase.org/detail.go?6578706f7274=1&d-1340579-e=5&type=relationship&ixnId="
- + string;
- String referencesPage2 = getWebPageContent(query2);
- String[] lines = referencesPage2.split("\n");
- for (int i = 1; i < lines.length; i++) {
- String[] cols = lines[i].split("\t");
- MiriamData newMiriam = new MiriamData(MiriamType.PUBMED, cols[0]);
- inferenceNetwork.get(md).add(newMiriam);
- }
- }
- }
- } catch (IOException e) {
- throw new ChemicalSearchException(e);
- } catch (AnnotatorException e) {
- throw new ChemicalSearchException("Problem with accessing hgnc db", e);
- }
- }
- for (MiriamData miriamData : invalidHgnc) {
- inferenceNetwork.remove(miriamData);
- }
- Float score = 0f;
- Integer refCount = 0;
- String scoreStr = lineValues[CHEMICALS_SCORE_COL];
- try {
- score = Float.valueOf(scoreStr);
- } catch (NumberFormatException e) {
- logger.error("problem parsing chemcial file from ctd server, invalid value: " + scoreStr, e);
- }
- try {
- refCount = Integer.valueOf(lineValues[CHEMICALS_COUNT_COL]);
- } catch (NumberFormatException e) {
- logger.error(
- "problem parsing chemcial file from ctd server, score, invalid value: " + lineValues[CHEMICALS_COUNT_COL], e);
- }
- List<Target> geneEntries = new ArrayList<>();
-
- for (Map.Entry<MiriamData, Set<MiriamData>> geneEntry : inferenceNetwork.entrySet()) {
- Target target = new Target(null, geneEntry.getKey(), geneEntry.getValue());
- target.setName(geneEntry.getKey().getResource());
- geneEntries.add(target);
- }
- return new Chemical(name, chemID, casId, directType, geneEntries, directEvidencePublication, score, refCount);
- }
-
- /**
- * Returns list of chemicals for given set of target genes related to the
- * disease.
- *
- * @param targets
- * set of target genes
- * @param diseaseMiriam
- * identifier of the disease
- * @return list of chemicals for given set of target genes related to the
- * disease
- * @throws ChemicalSearchException
- * thrown when there is a problem with accessing ctd database
- */
- public List<Chemical> getChemicalListByTarget(Collection<MiriamData> targets, MiriamData diseaseMiriam)
- throws ChemicalSearchException {
- List<Chemical> result = new ArrayList<>();
- Set<MiriamData> entrez = new HashSet<>();
- for (MiriamData target : targets) {
- if (MiriamType.ENTREZ.equals(target.getDataType())) {
- entrez.add(target);
- } else if (MiriamType.HGNC_SYMBOL.equals(target.getDataType())) {
- try {
- MiriamData entrezTarget = hgncAnnotator.hgncToEntrez(target);
- if (entrezTarget != null) {
- entrez.add(entrezTarget);
- } else {
- logger.warn("Cannot find entrez id for " + target);
- }
- } catch (AnnotatorException e) {
- throw new ChemicalSearchException("Problem with accessing hgnc service", e);
- }
- } else {
- throw new InvalidArgumentException(
- "Only " + MiriamType.HGNC_SYMBOL + ", " + MiriamType.ENTREZ + " types is accepted");
- }
- }
- Map<MiriamData, String> chemicalsMap = getChemicalsForDisease(diseaseMiriam);
- Map<String, MiriamData> nameToId = new HashMap<>();
- for (MiriamData miriamData : chemicalsMap.keySet()) {
- nameToId.put(chemicalsMap.get(miriamData), miriamData);
- }
-
- Set<MiriamData> chemicalIds = new HashSet<>();
- chemicalIds.addAll(chemicalsMap.keySet());
-
- Set<MiriamData> geneRelatedChemicals = new HashSet<>();
- for (MiriamData target : entrez) {
- Set<String> geneRelatedChemicalNames = getRelatedChemicalNamesForTarget(diseaseMiriam, target);
- for (String string : geneRelatedChemicalNames) {
- geneRelatedChemicals.add(nameToId.get(string));
- }
- }
- chemicalIds.retainAll(geneRelatedChemicals);
- result = getChemicals(diseaseMiriam, chemicalIds);
-
- return result;
- }
-
- /**
- * Return list of chemical names that interact with a target.
- *
- * @param diseaseMiriam
- * we want to get chemicals in context of the disease
- * @param target
- * target for which we are looking for chemicals
- * @return list of chemical names that interact with a target
- * @throws ChemicalSearchException
- * thrown when there is a problem with accessing external resource
- */
- private Set<String> getRelatedChemicalNamesForTarget(MiriamData diseaseMiriam, MiriamData target)
- throws ChemicalSearchException {
- try {
- Set<String> geneRelatedChemicalNames = new HashSet<>();
- String url = DISEASE_GENE_URL + target.getResource();
- String page = getWebPageContent(url);
- if (!page.contains("<!DOCTYPE html>")) {
- String[] lines = page.split("[\n\r]+");
- for (int i = 1; i < lines.length; i++) {
- String[] line = lines[i].split("\t", -1);
- if (line.length > DRUG_NAME_COL_IN_GENE_DRUG_LIST) {
- if (line[1].equalsIgnoreCase("MESH:" + diseaseMiriam.getResource())) {
- String[] drugNames = line[DRUG_NAME_COL_IN_GENE_DRUG_LIST].split("\\|");
- for (String string : drugNames) {
- geneRelatedChemicalNames.add(string);
- }
- }
- } else {
- logger.warn("Problematic line: " + lines[i]);
- }
- }
- }
- return geneRelatedChemicalNames;
- } catch (IOException e) {
- throw new ChemicalSearchException("Problem with accessing ctd database", e);
- }
- }
-
- /**
- * Returns list of chemicals that interact with a target.
- *
- * @param target
- * target for which we are looking for chemicals
- * @param disease
- * we want to get chemicals in context of the disease
- * @return list of chemicals that interact with a target
- * @throws ChemicalSearchException
- * thrown when there is a problem with accessing chemical database
- */
- public List<Chemical> getChemicalListByTarget(MiriamData target, MiriamData disease) throws ChemicalSearchException {
- List<MiriamData> targets = new ArrayList<>();
- targets.add(target);
- return getChemicalListByTarget(targets, disease);
- }
-
- /**
- * @return the hgncAnnotator
- * @see #hgncAnnotator
- */
- public HgncAnnotator getHgncAnnotator() {
- return hgncAnnotator;
- }
-
- /**
- * @param hgncAnnotator
- * the hgncAnnotator to set
- * @see #hgncAnnotator
- */
- public void setHgncAnnotator(HgncAnnotator hgncAnnotator) {
- this.hgncAnnotator = hgncAnnotator;
- }
-
- @Override
- protected WebPageDownloader getWebPageDownloader() {
- return super.getWebPageDownloader();
- }
-
- @Override
- protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
- super.setWebPageDownloader(webPageDownloader);
- }
-
- public List<String> getSuggestedQueryList(Project project, MiriamData diseaseMiriam) throws ChemicalSearchException {
- if (diseaseMiriam == null) {
- return new ArrayList<>();
- }
- String cacheQuery = PROJECT_SUGGESTED_QUERY_PREFIX + "\n" + project.getId() + "\n" + diseaseMiriam.getResource();
- String cachedData = getCacheValue(cacheQuery);
- List<String> result;
- if (cachedData == null) {
- result = getSuggestedQueryListWithoutCache(project, diseaseMiriam);
- cachedData = StringUtils.join(result, "\n");
- setCacheValue(cacheQuery, cachedData);
- } else {
- result = new ArrayList<>();
- for (String string : cachedData.split("\n")) {
- if (!string.isEmpty()) {
- result.add(string);
- }
- }
- }
- return result;
- }
-
- private List<String> getSuggestedQueryListWithoutCache(Project project, MiriamData diseaseMiriam)
- throws ChemicalSearchException {
- Set<String> resultSet = new HashSet<>();
- Set<MiriamData> targets = new HashSet<>();
- for (ModelData model : project.getModels()) {
- for (Element element : model.getElements()) {
- MiriamData entrez = null;
- MiriamData hgncSymbol = null;
- for (MiriamData miriam : element.getMiriamData()) {
- if (miriam.getDataType().equals(MiriamType.ENTREZ)) {
- entrez = miriam;
- } else if (miriam.getDataType().equals(MiriamType.HGNC_SYMBOL)) {
- hgncSymbol = miriam;
- }
- }
- if (hgncSymbol != null) {
- targets.add(hgncSymbol);
- } else if (entrez != null) {
- targets.add(entrez);
- } else {
- boolean validClass = false;
- for (Class<?> clazz : MiriamType.HGNC_SYMBOL.getValidClass()) {
- if (clazz.isAssignableFrom(element.getClass())) {
- validClass = true;
- }
- }
- if (validClass) {
- MiriamData md = new MiriamData(MiriamType.HGNC_SYMBOL, element.getName());
- try {
- if (hgncAnnotator.isValidHgncMiriam(md)) {
- targets.add(md);
- }
- } catch (AnnotatorException e) {
- logger.error("Problem with accessing HGNC database", e);
- }
- }
- }
- }
- }
- List<Chemical> chemicals = getChemicalListByTarget(targets, diseaseMiriam);
- for (Chemical chemical : chemicals) {
- resultSet.add(chemical.getChemicalName());
- resultSet.addAll(chemical.getSynonyms());
- }
- List<String> result = new ArrayList<>();
- result.addAll(resultSet);
- Collections.sort(result);
- return result;
- }
-
- public List<Chemical> getChemicalsBySynonym(MiriamData diseaseId, String synonym) throws ChemicalSearchException {
- try {
- Collection<MeSH> meshList;
- meshList = meshParser.getMeshBySynonym(synonym);
- List<MiriamData> chemicalIds = new ArrayList<>();
- for (MeSH mesh : meshList) {
- chemicalIds.add(new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, mesh.getMeSHId()));
- }
- return getChemicals(diseaseId, chemicalIds);
- } catch (AnnotatorException e) {
- throw new ChemicalSearchException(e);
- }
- }
-
-}
+package lcsb.mapviewer.annotation.services;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.apache.commons.lang3.SerializationException;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.w3c.dom.Node;
+
+import lcsb.mapviewer.annotation.cache.CachableInterface;
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.WebPageDownloader;
+import lcsb.mapviewer.annotation.cache.XmlSerializer;
+import lcsb.mapviewer.annotation.data.Chemical;
+import lcsb.mapviewer.annotation.data.ChemicalDirectEvidence;
+import lcsb.mapviewer.annotation.data.MeSH;
+import lcsb.mapviewer.annotation.data.Target;
+import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
+import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.persist.dao.ProjectDao;
+
+/**
+ * This class is a backend to Toxicogenomic Chemical API.
+ *
+ * @author Ayan Rota
+ *
+ */
+public class ChemicalParser extends CachableInterface implements IExternalService {
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(ChemicalParser.class);
+
+ /**
+ * Prefix used for caching elements with chemical identifier as a key.
+ */
+ static final String CHEMICAL_PREFIX = "chemical:";
+
+ /**
+ * Prefix used for caching all chemical names in a disease.
+ */
+ protected static final String DISEASE_CHEMICALS_PREFIX = "DISEASE_CHEMICALS:";
+
+ /**
+ * Prefix used for caching list of suggested queries for project.
+ */
+ protected static final String PROJECT_SUGGESTED_QUERY_PREFIX = "PROJECT_CHEMICAL_QUERIES:";
+
+ /**
+ * Home page of ctd database.
+ */
+ static final String URL = "https://ctdbase.org/";
+
+ /**
+ * URL to get a list of chemicals by disease id.
+ */
+ public static final String DISEASE_URL = "https://ctdbase.org/detail.go?6578706f7274=1&d-1332398-e=5&view=chem&"
+ + "type=disease&acc=MESH%3A";
+
+ /**
+ * URL to get a list of chemicals by gene id.
+ */
+ public static final String DISEASE_GENE_URL = "https://ctdbase.org/detail.go?slimTerm=all&6578706f7274=1&qid=3464576&"
+ + "d-1332398-e=5&view=disease&type=gene&assnType=curated&acc=";
+
+ /**
+ * Column in results obtained from {@link ChemicalParser#DISEASE_GENE_URL}
+ * describing drugs that are related to the gene (gene identifier is provided in
+ * the url).
+ */
+ private static final int DRUG_NAME_COL_IN_GENE_DRUG_LIST = 3;
+
+ /**
+ * The location of name column in the parsed tab separated chemicals file.
+ */
+ public static final Integer CHEMICALS_NAME_COL = 0;
+
+ /**
+ * The location of id column in the parsed tab separated chemicals file.
+ */
+ public static final Integer CHEMICALS_ID_COL = 1;
+
+ /**
+ * The location of CAS column in the parsed tab separated chemicals file.
+ */
+ public static final Integer CHEMICALS_CAS_COL = 2;
+
+ /**
+ * The location of disease name column in the parsed tab separated chemicals
+ * file.
+ */
+ public static final Integer CHEMICALS_DISEASE_NAME_COL = 3;
+
+ /**
+ * The location of disease id column in the parsed tab separated chemicals file.
+ */
+ public static final Integer CHEMICALS_DISEASE_ID_COL = 4;
+
+ /**
+ * The location of direct column in the parsed tab separated chemicals file.
+ */
+ public static final Integer CHEMICALS_DIRECT_COL = 5;
+
+ /**
+ * The location of network of genes column in the parsed tab separated chemicals
+ * file.
+ */
+ public static final Integer CHEMICALS_NETWORK_COL = 6;
+
+ /**
+ * The location of score column in the parsed tab separated chemicals file.
+ */
+ public static final Integer CHEMICALS_SCORE_COL = 7;
+
+ /**
+ * The location of count column in the parsed tab separated chemicals file.
+ */
+ public static final Integer CHEMICALS_COUNT_COL = 8;
+
+ /**
+ * The location of pubmed id column in the publications.
+ */
+ public static final Integer PUBLICATIONS_ID_COL = 0;
+
+ /**
+ * The location of list of genes column that is associated with this publication
+ * for particular chemical.
+ */
+ public static final Integer PUBLICATIONS_ASSOCIATION_COL = 5;
+
+ /**
+ * Object that allows to serialize {@link Chemical} elements into xml string and
+ * deserialize xml into {@link Chemical} objects.
+ */
+ private XmlSerializer<Chemical> chemicalSerializer;
+
+ /**
+ * The status of the db.
+ */
+ private ExternalServiceStatus status = new ExternalServiceStatus("ctdbase", URL);
+
+ /**
+ * Object used to perform operations on {@link MiriamType#HGNC hgnc
+ * annotations}.
+ */
+ @Autowired
+ private HgncAnnotator hgncAnnotator;
+
+ @Autowired
+ private ProjectDao projectDao;
+
+ @Autowired
+ private MeSHParser meshParser;
+
+ /**
+ *
+ */
+ public ChemicalParser() {
+ super(ChemicalParser.class);
+ chemicalSerializer = new XmlSerializer<>(Chemical.class);
+ }
+
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ GeneralCacheInterface cacheCopy = getCache();
+ this.setCache(null);
+ status.setStatus(ExternalServiceStatusType.OK);
+ try {
+ MiriamData diseaseID = new MiriamData(MiriamType.MESH_2012, "D002095");
+ MiriamData chemicalID = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "D000395");
+ Chemical chemical = getChemicalFromExternalDatabase(diseaseID, chemicalID);
+ if (chemical == null || !chemical.getChemicalId().equals(chemicalID)) {
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ }
+ } catch (Exception e) {
+ logger.error("ctdbase service unavailable", e);
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ }
+ this.setCache(cacheCopy);
+ return status;
+
+ }
+
+ /**
+ * @param disease
+ * the MESH Id for the disease
+ * @return list of chemicals id, name pairs
+ * @throws ChemicalSearchException
+ * thrown when there is problem with accessing ctd database
+ */
+ public Map<MiriamData, String> getChemicalsForDisease(MiriamData disease) throws ChemicalSearchException {
+ if (disease == null || disease.getResource() == null) {
+ throw new InvalidArgumentException("disease cannot be null");
+ }
+
+ // check if we have results in cache
+ String chemicalNode = super.getCacheValue(DISEASE_CHEMICALS_PREFIX + disease.getResource());
+ if (chemicalNode != null) {
+ return deserializeChemicalList(chemicalNode);
+ }
+
+ Map<MiriamData, String> chemicals = new HashMap<>();
+ try {
+ String diseaseID = disease.getResource();
+ String query = DISEASE_URL + diseaseID;
+ String page = getWebPageContent(query);
+
+ String[] lines = page.split("\n");
+ for (int rowNumber = 1; rowNumber < lines.length; rowNumber++) {
+ String[] lineValues = lines[rowNumber].split("\t");
+ String diseaseId = lineValues[CHEMICALS_DISEASE_ID_COL];
+ diseaseId = MiriamData.getIdFromIdentifier(diseaseId);
+ if (diseaseId != null && diseaseID.equals(diseaseId) && lineValues[CHEMICALS_ID_COL] != null) {
+ chemicals.put(new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, lineValues[CHEMICALS_ID_COL]),
+ lineValues[CHEMICALS_NAME_COL]);
+ }
+ }
+
+ } catch (WrongResponseCodeIOException e) {
+ // it means that there are no results for this query
+ } catch (IOException e) {
+ throw new ChemicalSearchException("ctdbase service unavailable", e);
+ }
+
+ // put the results into cache
+ String cacheResult = serializeChemicalList(chemicals);
+ super.setCacheValue(DISEASE_CHEMICALS_PREFIX + disease.getResource(), cacheResult);
+
+ return chemicals;
+
+ }
+
+ /**
+ * Serializes list of chemicalId-chemicalName pairs.
+ *
+ * @param chemicals
+ * list of objects to serialize
+ * @return serialized string
+ */
+ public String serializeChemicalList(Map<MiriamData, String> chemicals) {
+ StringBuilder cacheResult = new StringBuilder();
+ for (MiriamData md : chemicals.keySet()) {
+ cacheResult.append(md.getResource() + "\t" + chemicals.get(md) + "\n");
+ }
+ return cacheResult.toString();
+ }
+
+ /**
+ * Deserializes list of chemicalId-chemicalName pairs.
+ *
+ * @param chemicalNode
+ * string to deserialize
+ * @return list of chemicalId-chemicalName pairs
+ */
+ public Map<MiriamData, String> deserializeChemicalList(String chemicalNode) {
+ Map<MiriamData, String> chemicals = new HashMap<>();
+
+ String[] lines = chemicalNode.split("\n");
+ for (String string : lines) {
+ if (string.length() > 0) {
+ String[] tmp = string.split("\t");
+ String id = tmp[0];
+ String name = tmp[1];
+ chemicals.put(new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, id), name);
+ }
+ }
+ return chemicals;
+ }
+
+ /**
+ * @param diseaseID
+ * The disease id that the chemical IDs belong to.
+ * @param chemicalIDs
+ * The list of the chemical ID required to be retrieved.
+ * @return list of chemicals
+ * @throws ChemicalSearchException
+ * thrown when there is problem with accessing ctd database
+ */
+ public List<Chemical> getChemicals(MiriamData diseaseID, Collection<MiriamData> chemicalIDs)
+ throws ChemicalSearchException {
+ if (diseaseID == null) {
+ throw new InvalidArgumentException("disease cannot be null");
+ }
+ List<Chemical> chemicals = new ArrayList<>();
+
+ for (MiriamData chemicalId : chemicalIDs) {
+ Chemical chemical = this.getChemicalFromExternalDatabase(diseaseID, chemicalId);
+ if (chemical != null) {
+ chemicals.add(chemical);
+ }
+ }
+ return chemicals;
+ }
+
+ /**
+ * @param diseaseID
+ * Miriam data type for disease id
+ * @param chemicalID
+ * Miriam data type for chemical id
+ * @return formated resource
+ */
+ public String getIdentifier(MiriamData diseaseID, MiriamData chemicalID) {
+ return CHEMICAL_PREFIX + diseaseID.getResource() + ":" + chemicalID.getResource();
+ }
+
+ @Override
+ public Object refreshCacheQuery(Object query) throws SourceNotAvailable {
+ try {
+ Object result = null;
+ if (query instanceof String) {
+ String identifier = (String) query;
+ if (identifier.startsWith(CHEMICAL_PREFIX)) {
+ String[] ids = identifier.split("\\:");
+ MiriamData diseaseID = new MiriamData(MiriamType.MESH_2012, ids[1]);
+ MiriamData chemicalID = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, ids[2]);
+ Chemical chemical = getChemicalFromExternalDatabase(diseaseID, chemicalID);
+ if (chemical != null) {
+ result = chemicalSerializer.objectToString(chemical);
+ } else {
+ throw new SourceNotAvailable("Could not find the resource with string \"" + query + "\"");
+ }
+ } else if (identifier.startsWith(DISEASE_CHEMICALS_PREFIX)) {
+ String id = identifier.substring(DISEASE_CHEMICALS_PREFIX.length());
+ Map<MiriamData, String> resultObj = getChemicalsForDisease(new MiriamData(MiriamType.MESH_2012, id));
+ result = serializeChemicalList(resultObj);
+ } else if (identifier.startsWith(PROJECT_SUGGESTED_QUERY_PREFIX)) {
+ String[] tmp = identifier.split("\n");
+ Integer id = Integer.valueOf(tmp[1]);
+ MiriamData diseaseId = new MiriamData(MiriamType.MESH_2012, tmp[2]);
+ Project project = projectDao.getById(id);
+ if (project == null) {
+ throw new SourceNotAvailable("Project with given id doesn't exist: " + id);
+ }
+ List<String> list = getSuggestedQueryListWithoutCache(project, diseaseId);
+ result = StringUtils.join(list, "\n");
+ } else {
+ result = super.refreshCacheQuery(query);
+ }
+ } else {
+ result = super.refreshCacheQuery(query);
+ }
+ return result;
+ } catch (ChemicalSearchException e) {
+ throw new SourceNotAvailable("Problem with accessing ctd database", e);
+ }
+ }
+
+ /**
+ * @param diseaseID
+ * the Mesh id of the disease.
+ * @param chemicalId
+ * the chemical id
+ * @return list of chemical objects.
+ * @throws ChemicalSearchException
+ * thrown when there is problem with accessing ctd database
+ */
+ private Chemical getChemicalFromExternalDatabase(MiriamData diseaseID, MiriamData chemicalId)
+ throws ChemicalSearchException {
+ Chemical result = null;
+ // look for chemical in the cache
+ Node chemicalNode = super.getCacheNode(getIdentifier(diseaseID, chemicalId));
+ if (chemicalNode != null && chemicalNode.hasChildNodes()) {
+ try {
+ result = chemicalSerializer.xmlToObject(chemicalNode);
+ return result;
+ } catch (SerializationException e) {
+ logger.error(e, e);
+ }
+ }
+ try {
+ String diseaseQuery = DISEASE_URL + diseaseID.getResource();
+ String diseasePage = getWebPageContent(diseaseQuery);
+ String[] diseaseLines = diseasePage.split("\n");
+ for (int rowNumber = 1; rowNumber < diseaseLines.length; rowNumber++) {
+ String[] lineValues = diseaseLines[rowNumber].split("\t", -1);
+ MiriamData chemID = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, lineValues[CHEMICALS_ID_COL]);
+ String diseaseIdentifier = MiriamData.getIdFromIdentifier(lineValues[CHEMICALS_DISEASE_ID_COL]);
+ MiriamData currentDiseaseId = new MiriamData(MiriamType.MESH_2012, diseaseIdentifier);
+ if (chemicalId.equals(chemID) && diseaseID.equals(currentDiseaseId)) {
+ result = getChemicalFromChemicalLine(lineValues, chemID);
+ }
+ }
+ if (result != null) {
+ MeSH mesh = meshParser.getMeSH(result.getChemicalId());
+ if (mesh!=null) {
+ result.addSynonyms(mesh.getSynonyms());
+ } else {
+ logger.warn("Problematic mesh id: "+result.getChemicalId());
+ }
+ }
+
+ } catch (IOException e) {
+ throw new ChemicalSearchException("ctdbase service unavailable", e);
+ } catch (AnnotatorException e) {
+ throw new ChemicalSearchException("problem with accessing mesh db", e);
+ }
+
+ // put them in cache
+ super.setCacheValue(getIdentifier(diseaseID, chemicalId), chemicalSerializer.objectToString(result));
+
+ return result;
+ }
+
+ /**
+ * Method that creates chemical from a tab separated row from ctd database. Data
+ * looks like (line wrapping added for clarity):
+ *
+ * <pre>
+ 1. Disease Name Disease ID Direct Evidence Inference Network Inference Score Reference Count
+ 2. Drug-Induced Liver Injury MESH:D056486 1-(2-trifluoromethoxyphenyl)-2-nitroethanone|1,4-bis(2-(3,5-dichloropyridyloxy))benzene|
+ 2,4-dinitrotoluene|2,6-dinitrotoluene|Acetaminophen|Acetylcysteine|Aflatoxin B1|Azacitidine|Benzo(a)pyrene|Estradiol|Bilirubin|
+ bisphenol A|Buthionine Sulfoximine|Carbamazepine|Chlorodiphenyl (54% Chlorine)|Chlorpromazine|Clodronic Acid|cobaltous chloride|
+ Copper|Curcumin|Cyclosporine|Deferoxamine|Dexamethasone|Cisplatin|Dieldrin|Dietary Fats|Diethylnitrosamine|epigallocatechin gallate|
+ Fenofibrate|Formaldehyde|Genistein|Glutathione|Hydrogen Peroxide|isoliquiritigenin|Lead|Lipopolysaccharides|manganese chloride|
+ Medroxyprogesterone Acetate|Metformin|Methotrexate|methylmercuric chloride|N-Methyl-3,4-methylenedioxyamphetamine|morin|Morphine|
+ Nanotubes, Carbon|nickel chloride|ochratoxin A|Oxygen|Paclitaxel|perfluoro-n-nonanoic acid|perfluorooctanoic acid|Phenobarbital|
+ pirinixic acid|Polyphenols|Polysaccharides|potassium chromate(VI)|propiconazole|Quercetin|resveratrol|rosiglitazone|Rotenone|
+ Streptozocin|Tetrachlorodibenzodioxin|titanium dioxide|Tretinoin|usnic acid|Valproic Acid|Vincristine|Zinc|zinc chloride 190.67 634
+ * </pre>
+ *
+ * @param lineValues
+ * line split by tab separator
+ * @param chemID
+ * chemical id
+ * @return chemical obtained from input data
+ * @throws ChemicalSearchException
+ * thrown when there is a problem accessing ctd database
+ */
+ Chemical getChemicalFromChemicalLine(String[] lineValues, MiriamData chemID) throws ChemicalSearchException {
+ String name = lineValues[CHEMICALS_NAME_COL];
+ String casIdentifier = lineValues[CHEMICALS_CAS_COL];
+ MiriamData casId = null;
+ if ((casIdentifier != null) && !casIdentifier.trim().isEmpty()) {
+ casId = new MiriamData(MiriamType.CAS, casIdentifier);
+ }
+
+ String directEvidenceStr = lineValues[CHEMICALS_DIRECT_COL];
+ ChemicalDirectEvidence directType = null;
+ if (directEvidenceStr.equals(ChemicalDirectEvidence.MARKER.getValue())) {
+ directType = ChemicalDirectEvidence.MARKER;
+ } else if (directEvidenceStr.equals(ChemicalDirectEvidence.THERAPEUTIC.getValue())) {
+ directType = ChemicalDirectEvidence.THERAPEUTIC;
+ }
+
+ String networkStr = lineValues[CHEMICALS_NETWORK_COL].trim();
+ Map<MiriamData, Set<MiriamData>> inferenceNetwork = new HashMap<>();
+ List<MiriamData> directEvidencePublication = new ArrayList<>();
+ String[] genesIDs = networkStr.split("\\|");
+ for (String geneId : genesIDs) {
+ if (!geneId.isEmpty()) {
+ inferenceNetwork.put(new MiriamData(MiriamType.HGNC_SYMBOL, geneId), new HashSet<>());
+ }
+ }
+
+ Pattern pattern = Pattern.compile("ixnId=([0-9]+)");
+ List<MiriamData> invalidHgnc = new ArrayList<>();
+ for (MiriamData md : inferenceNetwork.keySet()) {
+ try {
+ Set<String> idx = new HashSet<>();
+ MiriamData entrez = hgncAnnotator.hgncToEntrez(md);
+ // if we cannot find entrez this means the name is invalid hgnc and
+ // should be removed from our result list (it might be gene name of
+ // other species...)
+ if (entrez == null) {
+ invalidHgnc.add(md);
+ } else {
+ String query = "https://ctdbase.org/detail.go?type=gene&view=ixn&chemAcc=" + chemID.getResource() + "&acc="
+ + entrez.getResource();
+ String referencesPage = getWebPageContent(query);
+ Matcher matcher = pattern.matcher(referencesPage);
+ while (matcher.find()) {
+ idx.add(matcher.group(1));
+ }
+ for (String string : idx) {
+ String query2 = "https://ctdbase.org/detail.go?6578706f7274=1&d-1340579-e=5&type=relationship&ixnId="
+ + string;
+ String referencesPage2 = getWebPageContent(query2);
+ String[] lines = referencesPage2.split("\n");
+ for (int i = 1; i < lines.length; i++) {
+ String[] cols = lines[i].split("\t");
+ MiriamData newMiriam = new MiriamData(MiriamType.PUBMED, cols[0]);
+ inferenceNetwork.get(md).add(newMiriam);
+ }
+ }
+ }
+ } catch (IOException e) {
+ throw new ChemicalSearchException(e);
+ } catch (AnnotatorException e) {
+ throw new ChemicalSearchException("Problem with accessing hgnc db", e);
+ }
+ }
+ for (MiriamData miriamData : invalidHgnc) {
+ inferenceNetwork.remove(miriamData);
+ }
+ Float score = 0f;
+ Integer refCount = 0;
+ String scoreStr = lineValues[CHEMICALS_SCORE_COL];
+ try {
+ score = Float.valueOf(scoreStr);
+ } catch (NumberFormatException e) {
+ logger.error("problem parsing chemcial file from ctd server, invalid value: " + scoreStr, e);
+ }
+ try {
+ refCount = Integer.valueOf(lineValues[CHEMICALS_COUNT_COL]);
+ } catch (NumberFormatException e) {
+ logger.error(
+ "problem parsing chemcial file from ctd server, score, invalid value: " + lineValues[CHEMICALS_COUNT_COL], e);
+ }
+ List<Target> geneEntries = new ArrayList<>();
+
+ for (Map.Entry<MiriamData, Set<MiriamData>> geneEntry : inferenceNetwork.entrySet()) {
+ Target target = new Target(null, geneEntry.getKey(), geneEntry.getValue());
+ target.setName(geneEntry.getKey().getResource());
+ geneEntries.add(target);
+ }
+ return new Chemical(name, chemID, casId, directType, geneEntries, directEvidencePublication, score, refCount);
+ }
+
+ /**
+ * Returns list of chemicals for given set of target genes related to the
+ * disease.
+ *
+ * @param targets
+ * set of target genes
+ * @param diseaseMiriam
+ * identifier of the disease
+ * @return list of chemicals for given set of target genes related to the
+ * disease
+ * @throws ChemicalSearchException
+ * thrown when there is a problem with accessing ctd database
+ */
+ public List<Chemical> getChemicalListByTarget(Collection<MiriamData> targets, MiriamData diseaseMiriam)
+ throws ChemicalSearchException {
+ List<Chemical> result = new ArrayList<>();
+ Set<MiriamData> entrez = new HashSet<>();
+ for (MiriamData target : targets) {
+ if (MiriamType.ENTREZ.equals(target.getDataType())) {
+ entrez.add(target);
+ } else if (MiriamType.HGNC_SYMBOL.equals(target.getDataType())) {
+ try {
+ MiriamData entrezTarget = hgncAnnotator.hgncToEntrez(target);
+ if (entrezTarget != null) {
+ entrez.add(entrezTarget);
+ } else {
+ logger.warn("Cannot find entrez id for " + target);
+ }
+ } catch (AnnotatorException e) {
+ throw new ChemicalSearchException("Problem with accessing hgnc service", e);
+ }
+ } else {
+ throw new InvalidArgumentException(
+ "Only " + MiriamType.HGNC_SYMBOL + ", " + MiriamType.ENTREZ + " types is accepted");
+ }
+ }
+ Map<MiriamData, String> chemicalsMap = getChemicalsForDisease(diseaseMiriam);
+ Map<String, MiriamData> nameToId = new HashMap<>();
+ for (MiriamData miriamData : chemicalsMap.keySet()) {
+ nameToId.put(chemicalsMap.get(miriamData), miriamData);
+ }
+
+ Set<MiriamData> chemicalIds = new HashSet<>();
+ chemicalIds.addAll(chemicalsMap.keySet());
+
+ Set<MiriamData> geneRelatedChemicals = new HashSet<>();
+ for (MiriamData target : entrez) {
+ Set<String> geneRelatedChemicalNames = getRelatedChemicalNamesForTarget(diseaseMiriam, target);
+ for (String string : geneRelatedChemicalNames) {
+ geneRelatedChemicals.add(nameToId.get(string));
+ }
+ }
+ chemicalIds.retainAll(geneRelatedChemicals);
+ result = getChemicals(diseaseMiriam, chemicalIds);
+
+ return result;
+ }
+
+ /**
+ * Return list of chemical names that interact with a target.
+ *
+ * @param diseaseMiriam
+ * we want to get chemicals in context of the disease
+ * @param target
+ * target for which we are looking for chemicals
+ * @return list of chemical names that interact with a target
+ * @throws ChemicalSearchException
+ * thrown when there is a problem with accessing external resource
+ */
+ private Set<String> getRelatedChemicalNamesForTarget(MiriamData diseaseMiriam, MiriamData target)
+ throws ChemicalSearchException {
+ try {
+ Set<String> geneRelatedChemicalNames = new HashSet<>();
+ String url = DISEASE_GENE_URL + target.getResource();
+ String page = getWebPageContent(url);
+ if (!page.contains("<!DOCTYPE html>")) {
+ String[] lines = page.split("[\n\r]+");
+ for (int i = 1; i < lines.length; i++) {
+ String[] line = lines[i].split("\t", -1);
+ if (line.length > DRUG_NAME_COL_IN_GENE_DRUG_LIST) {
+ if (line[1].equalsIgnoreCase("MESH:" + diseaseMiriam.getResource())) {
+ String[] drugNames = line[DRUG_NAME_COL_IN_GENE_DRUG_LIST].split("\\|");
+ for (String string : drugNames) {
+ geneRelatedChemicalNames.add(string);
+ }
+ }
+ } else {
+ logger.warn("Problematic line: " + lines[i]);
+ }
+ }
+ }
+ return geneRelatedChemicalNames;
+ } catch (IOException e) {
+ throw new ChemicalSearchException("Problem with accessing ctd database", e);
+ }
+ }
+
+ /**
+ * Returns list of chemicals that interact with a target.
+ *
+ * @param target
+ * target for which we are looking for chemicals
+ * @param disease
+ * we want to get chemicals in context of the disease
+ * @return list of chemicals that interact with a target
+ * @throws ChemicalSearchException
+ * thrown when there is a problem with accessing chemical database
+ */
+ public List<Chemical> getChemicalListByTarget(MiriamData target, MiriamData disease) throws ChemicalSearchException {
+ List<MiriamData> targets = new ArrayList<>();
+ targets.add(target);
+ return getChemicalListByTarget(targets, disease);
+ }
+
+ /**
+ * @return the hgncAnnotator
+ * @see #hgncAnnotator
+ */
+ public HgncAnnotator getHgncAnnotator() {
+ return hgncAnnotator;
+ }
+
+ /**
+ * @param hgncAnnotator
+ * the hgncAnnotator to set
+ * @see #hgncAnnotator
+ */
+ public void setHgncAnnotator(HgncAnnotator hgncAnnotator) {
+ this.hgncAnnotator = hgncAnnotator;
+ }
+
+ @Override
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
+ }
+
+ @Override
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
+ }
+
+ public List<String> getSuggestedQueryList(Project project, MiriamData diseaseMiriam) throws ChemicalSearchException {
+ if (diseaseMiriam == null) {
+ return new ArrayList<>();
+ }
+ String cacheQuery = PROJECT_SUGGESTED_QUERY_PREFIX + "\n" + project.getId() + "\n" + diseaseMiriam.getResource();
+ String cachedData = getCacheValue(cacheQuery);
+ List<String> result;
+ if (cachedData == null) {
+ result = getSuggestedQueryListWithoutCache(project, diseaseMiriam);
+ cachedData = StringUtils.join(result, "\n");
+ setCacheValue(cacheQuery, cachedData);
+ } else {
+ result = new ArrayList<>();
+ for (String string : cachedData.split("\n")) {
+ if (!string.isEmpty()) {
+ result.add(string);
+ }
+ }
+ }
+ return result;
+ }
+
+ private List<String> getSuggestedQueryListWithoutCache(Project project, MiriamData diseaseMiriam)
+ throws ChemicalSearchException {
+ Set<String> resultSet = new HashSet<>();
+ Set<MiriamData> targets = new HashSet<>();
+ for (ModelData model : project.getModels()) {
+ for (Element element : model.getElements()) {
+ MiriamData entrez = null;
+ MiriamData hgncSymbol = null;
+ for (MiriamData miriam : element.getMiriamData()) {
+ if (miriam.getDataType().equals(MiriamType.ENTREZ)) {
+ entrez = miriam;
+ } else if (miriam.getDataType().equals(MiriamType.HGNC_SYMBOL)) {
+ hgncSymbol = miriam;
+ }
+ }
+ if (hgncSymbol != null) {
+ targets.add(hgncSymbol);
+ } else if (entrez != null) {
+ targets.add(entrez);
+ } else {
+ boolean validClass = false;
+ for (Class<?> clazz : MiriamType.HGNC_SYMBOL.getValidClass()) {
+ if (clazz.isAssignableFrom(element.getClass())) {
+ validClass = true;
+ }
+ }
+ if (validClass) {
+ MiriamData md = new MiriamData(MiriamType.HGNC_SYMBOL, element.getName());
+ try {
+ if (hgncAnnotator.isValidHgncMiriam(md)) {
+ targets.add(md);
+ }
+ } catch (AnnotatorException e) {
+ logger.error("Problem with accessing HGNC database", e);
+ }
+ }
+ }
+ }
+ }
+ List<Chemical> chemicals = getChemicalListByTarget(targets, diseaseMiriam);
+ for (Chemical chemical : chemicals) {
+ resultSet.add(chemical.getChemicalName());
+ resultSet.addAll(chemical.getSynonyms());
+ }
+ List<String> result = new ArrayList<>();
+ result.addAll(resultSet);
+ Collections.sort(result);
+ return result;
+ }
+
+ public List<Chemical> getChemicalsBySynonym(MiriamData diseaseId, String synonym) throws ChemicalSearchException {
+ try {
+ Collection<MeSH> meshList;
+ meshList = meshParser.getMeshBySynonym(synonym);
+ List<MiriamData> chemicalIds = new ArrayList<>();
+ for (MeSH mesh : meshList) {
+ chemicalIds.add(new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, mesh.getMeSHId()));
+ }
+ return getChemicals(diseaseId, chemicalIds);
+ } catch (AnnotatorException e) {
+ throw new ChemicalSearchException(e);
+ }
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalSearchException.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalSearchException.java
index bc6e7d8f50..6c06b5320f 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalSearchException.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalSearchException.java
@@ -1,48 +1,48 @@
-package lcsb.mapviewer.annotation.services;
-
-/**
- * Exception thrown when there was a problem when searching for a chemical.
- *
- * @author Piotr Gawron
- *
- */
-public class ChemicalSearchException extends Exception {
-
- /**
- * Default constructor.
- *
- * @param string
- * exception message
- */
- public ChemicalSearchException(String string) {
- super(string);
- }
-
- /**
- * Default constructor.
- *
- * @param e
- * parent exception
- */
- public ChemicalSearchException(Exception e) {
- super(e);
- }
-
- /**
- * Default constructor.
- *
- * @param message
- * exception message
- * @param e
- * source exception
- */
- public ChemicalSearchException(String message, Exception e) {
- super(message, e);
- }
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
-}
+package lcsb.mapviewer.annotation.services;
+
+/**
+ * Exception thrown when there was a problem when searching for a chemical.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ChemicalSearchException extends Exception {
+
+ /**
+ * Default constructor.
+ *
+ * @param string
+ * exception message
+ */
+ public ChemicalSearchException(String string) {
+ super(string);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param e
+ * parent exception
+ */
+ public ChemicalSearchException(Exception e) {
+ super(e);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * exception message
+ * @param e
+ * source exception
+ */
+ public ChemicalSearchException(String message, Exception e) {
+ super(message, e);
+ }
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugAnnotation.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugAnnotation.java
index 6376921856..8f9146ab17 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugAnnotation.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugAnnotation.java
@@ -1,334 +1,334 @@
-package lcsb.mapviewer.annotation.services;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.annotation.cache.CachableInterface;
-import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
-import lcsb.mapviewer.annotation.cache.XmlSerializer;
-import lcsb.mapviewer.annotation.data.Drug;
-import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
-import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.persist.dao.ProjectDao;
-
-/**
- * Abstract class with some functionalities used by class accessing drug
- * databases.
- *
- * @author Piotr Gawron
- *
- */
-public abstract class DrugAnnotation extends CachableInterface {
-
- /**
- * Prefix used for caching list of suggested queries for project.
- */
- protected static final String PROJECT_SUGGESTED_QUERY_PREFIX = "PROJECT_DRUG_QUERIES:";
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(DrugAnnotation.class);
-
- /**
- * Object that allows to serialize {@link Drug} elements into xml string and
- * deserialize xml into {@link Drug} objects.
- */
- private XmlSerializer<Drug> drugSerializer;
-
- /**
- * Object used to access information about organism taxonomy.
- */
- @Autowired
- private TaxonomyBackend taxonomyBackend;
-
- @Autowired
- private HgncAnnotator hgncAnnotator;
-
- @Autowired
- private ProjectDao projectDao;
-
- /**
- * Default constructor. Initializes structures used for transforming
- * {@link Drug} from/to xml.
- *
- * @param clazz
- * class that identifies this {@link CachableInterface}
- */
- public DrugAnnotation(final Class<? extends DrugAnnotation> clazz) {
- super(clazz);
- drugSerializer = new XmlSerializer<>(Drug.class);
- }
-
- /**
- * Returns a drug for given name.
- *
- * @param name
- * name of the drug
- * @return drug for a given name
- * @throws DrugSearchException
- * thrown when there are problems with finding drug
- */
- public abstract Drug findDrug(String name) throws DrugSearchException;
-
- /**
- * Returns list of drugs that target protein.
- *
- * @param target
- * {@link MiriamData} describing target
- * @param organisms
- * list of organisms to which results should be limited (when no
- * organisms defined filtering will be turned off)
- * @return list of drugs
- * @throws DrugSearchException
- * thrown when there are problems with finding drug
- */
-
- public abstract List<Drug> getDrugListByTarget(MiriamData target, Collection<MiriamData> organisms)
- throws DrugSearchException;
-
- /**
- * Returns list of drugs that target protein.
- *
- * @param target
- * {@link MiriamData} describing target
- * @return list of drugs
- * @throws DrugSearchException
- * thrown when there are problems with finding drug
- */
- public List<Drug> getDrugListByTarget(MiriamData target) throws DrugSearchException {
- return getDrugListByTarget(target, new ArrayList<>());
- }
-
- public String refreshCacheQuery(Object query) throws SourceNotAvailable {
- String result = null;
- try {
- if (query instanceof String) {
- String name = (String) query;
- if (name.startsWith(PROJECT_SUGGESTED_QUERY_PREFIX)) {
- String[] tmp = name.split("\n");
- Integer id = Integer.valueOf(tmp[1]);
- MiriamData diseaseId = new MiriamData(MiriamType.MESH_2012, tmp[2]);
- Project project = projectDao.getById(id);
- if (project == null) {
- throw new SourceNotAvailable("Project with given id doesn't exist: " + id);
- }
- List<String> list = getSuggestedQueryListWithoutCache(project, diseaseId);
- result = StringUtils.join(list, "\n");
-
- } else if (name.startsWith("http")) {
- result = getWebPageContent(name);
- } else {
- throw new InvalidArgumentException("Don't know what to do with string \"" + query + "\"");
- }
- } else {
- throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
- }
- } catch (DrugSearchException e) {
- throw new SourceNotAvailable(e);
- } catch (IOException e) {
- throw new SourceNotAvailable(e);
- }
- return result;
- }
-
- /**
- * Returns list of drugs that target at least one protein from the parameter
- * list.
- *
- * @param targets
- * list of {@link MiriamData} describing targets
- * @param organisms
- * list of organisms to which results should be limited (when no
- * organisms defined filtering will be turned off)
- * @return list of drugs
- * @throws DrugSearchException
- * thrown when there are problems with connection to drug database
- */
- public List<Drug> getDrugListByTargets(Collection<MiriamData> targets, Collection<MiriamData> organisms)
- throws DrugSearchException {
- List<Drug> result = new ArrayList<Drug>();
- Set<String> set = new HashSet<String>();
- Set<MiriamData> searchedResult = new HashSet<MiriamData>();
- for (MiriamData md : targets) {
- if (searchedResult.contains(md)) {
- continue;
- }
- searchedResult.add(md);
- List<Drug> drugs = getDrugListByTarget(md, organisms);
- for (Drug drug : drugs) {
- if (!set.contains(drug.getSources().get(0).getResource())) {
- result.add(drug);
- set.add(drug.getSources().get(0).getResource());
- } else {
- continue;
- }
- }
- }
- return result;
- }
-
- /**
- * Returns list of drugs that target at least one protein from the parameter
- * list.
- *
- * @param targets
- * list of {@link MiriamData} describing targets
- * @return list of drugs
- * @throws DrugSearchException
- * thrown when there are problems with connection to drug database
- */
- public List<Drug> getDrugListByTargets(Collection<MiriamData> targets) throws DrugSearchException {
- return getDrugListByTargets(targets, new ArrayList<>());
- }
-
- /**
- * @return the drugSerializer
- * @see #drugSerializer
- */
- protected XmlSerializer<Drug> getDrugSerializer() {
- return drugSerializer;
- }
-
- /**
- * @param drugSerializer
- * the drugSerializer to set
- * @see #drugSerializer
- */
- protected void setDrugSerializer(XmlSerializer<Drug> drugSerializer) {
- this.drugSerializer = drugSerializer;
- }
-
- /**
- * Checks if organism name matches list of organisms.
- *
- * @param organismName
- * name of the organism (should be something recognizable by
- * {@link MiriamType#TAXONOMY} db).
- * @param organisms
- * list of organisms
- * @return <code>false</code> if organisName couldn't be found in organisms
- * list. If organismName is null or empty or list of organisms is empty
- * true will be returned
- */
- protected boolean organismMatch(String organismName, Collection<MiriamData> organisms) {
- if (organismName == null || organismName.isEmpty() || organisms.size() == 0) {
- return true;
- }
- try {
- MiriamData organism = taxonomyBackend.getByName(organismName);
- return organisms.contains(organism);
- } catch (TaxonomySearchException e) {
- logger.error("Problem with taxonomy search for: " + organismName, e);
- return true;
- }
- }
-
- /**
- * @return the taxonomyBackend
- * @see #taxonomyBackend
- */
- public TaxonomyBackend getTaxonomyBackend() {
- return taxonomyBackend;
- }
-
- /**
- * @param taxonomyBackend
- * the taxonomyBackend to set
- * @see #taxonomyBackend
- */
- public void setTaxonomyBackend(TaxonomyBackend taxonomyBackend) {
- this.taxonomyBackend = taxonomyBackend;
- }
-
- public List<String> getSuggestedQueryList(Project project, MiriamData organism) throws DrugSearchException {
- if (organism == null) {
- return new ArrayList<>();
- }
- String cacheQuery = PROJECT_SUGGESTED_QUERY_PREFIX + "\n" + project.getId() + "\n" + organism.getResource();
- String cachedData = getCacheValue(cacheQuery);
- List<String> result;
- if (cachedData == null) {
- result = getSuggestedQueryListWithoutCache(project, organism);
- cachedData = StringUtils.join(result, "\n");
- setCacheValue(cacheQuery, cachedData);
- } else {
- result = new ArrayList<>();
- for (String string : cachedData.split("\n")) {
- if (!string.isEmpty()) {
- result.add(string);
- }
- }
- }
- return result;
- }
-
- private List<String> getSuggestedQueryListWithoutCache(Project project, MiriamData organism)
- throws DrugSearchException {
- Set<String> resultSet = new HashSet<>();
- Set<MiriamData> targets = new HashSet<>();
- for (ModelData model : project.getModels()) {
- for (Element element : model.getElements()) {
- MiriamData uniprot = null;
- MiriamData hgncSymbol = null;
- for (MiriamData miriam : element.getMiriamData()) {
- if (miriam.getDataType().equals(MiriamType.UNIPROT)) {
- uniprot = miriam;
- } else if (miriam.getDataType().equals(MiriamType.HGNC_SYMBOL)) {
- hgncSymbol = miriam;
- }
- }
- if (hgncSymbol != null) {
- targets.add(hgncSymbol);
- } else if (uniprot != null) {
- targets.add(uniprot);
- } else {
- boolean validClass = false;
- for (Class<?> clazz : MiriamType.HGNC_SYMBOL.getValidClass()) {
- if (clazz.isAssignableFrom(element.getClass())) {
- validClass = true;
- }
- }
- if (validClass) {
- MiriamData md = new MiriamData(MiriamType.HGNC_SYMBOL, element.getName());
- try {
- if (hgncAnnotator.isValidHgncMiriam(md)) {
- targets.add(md);
- }
- } catch (AnnotatorException e) {
- logger.error("Problem with accessing HGNC database", e);
- }
- }
- }
- }
- }
- List<MiriamData> organisms = new ArrayList<>();
- if (organism != null) {
- organisms.add(organism);
- }
- List<Drug> drugs = getDrugListByTargets(targets, organisms);
- for (Drug chemical : drugs) {
- resultSet.add(chemical.getName());
- }
- List<String> result = new ArrayList<>();
- result.addAll(resultSet);
- Collections.sort(result);
- return result;
- }
-
-}
+package lcsb.mapviewer.annotation.services;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.commons.lang3.StringUtils;
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.cache.CachableInterface;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.XmlSerializer;
+import lcsb.mapviewer.annotation.data.Drug;
+import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
+import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.persist.dao.ProjectDao;
+
+/**
+ * Abstract class with some functionalities used by class accessing drug
+ * databases.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public abstract class DrugAnnotation extends CachableInterface {
+
+ /**
+ * Prefix used for caching list of suggested queries for project.
+ */
+ protected static final String PROJECT_SUGGESTED_QUERY_PREFIX = "PROJECT_DRUG_QUERIES:";
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(DrugAnnotation.class);
+
+ /**
+ * Object that allows to serialize {@link Drug} elements into xml string and
+ * deserialize xml into {@link Drug} objects.
+ */
+ private XmlSerializer<Drug> drugSerializer;
+
+ /**
+ * Object used to access information about organism taxonomy.
+ */
+ @Autowired
+ private TaxonomyBackend taxonomyBackend;
+
+ @Autowired
+ private HgncAnnotator hgncAnnotator;
+
+ @Autowired
+ private ProjectDao projectDao;
+
+ /**
+ * Default constructor. Initializes structures used for transforming
+ * {@link Drug} from/to xml.
+ *
+ * @param clazz
+ * class that identifies this {@link CachableInterface}
+ */
+ public DrugAnnotation(final Class<? extends DrugAnnotation> clazz) {
+ super(clazz);
+ drugSerializer = new XmlSerializer<>(Drug.class);
+ }
+
+ /**
+ * Returns a drug for given name.
+ *
+ * @param name
+ * name of the drug
+ * @return drug for a given name
+ * @throws DrugSearchException
+ * thrown when there are problems with finding drug
+ */
+ public abstract Drug findDrug(String name) throws DrugSearchException;
+
+ /**
+ * Returns list of drugs that target protein.
+ *
+ * @param target
+ * {@link MiriamData} describing target
+ * @param organisms
+ * list of organisms to which results should be limited (when no
+ * organisms defined filtering will be turned off)
+ * @return list of drugs
+ * @throws DrugSearchException
+ * thrown when there are problems with finding drug
+ */
+
+ public abstract List<Drug> getDrugListByTarget(MiriamData target, Collection<MiriamData> organisms)
+ throws DrugSearchException;
+
+ /**
+ * Returns list of drugs that target protein.
+ *
+ * @param target
+ * {@link MiriamData} describing target
+ * @return list of drugs
+ * @throws DrugSearchException
+ * thrown when there are problems with finding drug
+ */
+ public List<Drug> getDrugListByTarget(MiriamData target) throws DrugSearchException {
+ return getDrugListByTarget(target, new ArrayList<>());
+ }
+
+ public String refreshCacheQuery(Object query) throws SourceNotAvailable {
+ String result = null;
+ try {
+ if (query instanceof String) {
+ String name = (String) query;
+ if (name.startsWith(PROJECT_SUGGESTED_QUERY_PREFIX)) {
+ String[] tmp = name.split("\n");
+ Integer id = Integer.valueOf(tmp[1]);
+ MiriamData diseaseId = new MiriamData(MiriamType.MESH_2012, tmp[2]);
+ Project project = projectDao.getById(id);
+ if (project == null) {
+ throw new SourceNotAvailable("Project with given id doesn't exist: " + id);
+ }
+ List<String> list = getSuggestedQueryListWithoutCache(project, diseaseId);
+ result = StringUtils.join(list, "\n");
+
+ } else if (name.startsWith("http")) {
+ result = getWebPageContent(name);
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with string \"" + query + "\"");
+ }
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
+ }
+ } catch (DrugSearchException e) {
+ throw new SourceNotAvailable(e);
+ } catch (IOException e) {
+ throw new SourceNotAvailable(e);
+ }
+ return result;
+ }
+
+ /**
+ * Returns list of drugs that target at least one protein from the parameter
+ * list.
+ *
+ * @param targets
+ * list of {@link MiriamData} describing targets
+ * @param organisms
+ * list of organisms to which results should be limited (when no
+ * organisms defined filtering will be turned off)
+ * @return list of drugs
+ * @throws DrugSearchException
+ * thrown when there are problems with connection to drug database
+ */
+ public List<Drug> getDrugListByTargets(Collection<MiriamData> targets, Collection<MiriamData> organisms)
+ throws DrugSearchException {
+ List<Drug> result = new ArrayList<Drug>();
+ Set<String> set = new HashSet<String>();
+ Set<MiriamData> searchedResult = new HashSet<MiriamData>();
+ for (MiriamData md : targets) {
+ if (searchedResult.contains(md)) {
+ continue;
+ }
+ searchedResult.add(md);
+ List<Drug> drugs = getDrugListByTarget(md, organisms);
+ for (Drug drug : drugs) {
+ if (!set.contains(drug.getSources().get(0).getResource())) {
+ result.add(drug);
+ set.add(drug.getSources().get(0).getResource());
+ } else {
+ continue;
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Returns list of drugs that target at least one protein from the parameter
+ * list.
+ *
+ * @param targets
+ * list of {@link MiriamData} describing targets
+ * @return list of drugs
+ * @throws DrugSearchException
+ * thrown when there are problems with connection to drug database
+ */
+ public List<Drug> getDrugListByTargets(Collection<MiriamData> targets) throws DrugSearchException {
+ return getDrugListByTargets(targets, new ArrayList<>());
+ }
+
+ /**
+ * @return the drugSerializer
+ * @see #drugSerializer
+ */
+ protected XmlSerializer<Drug> getDrugSerializer() {
+ return drugSerializer;
+ }
+
+ /**
+ * @param drugSerializer
+ * the drugSerializer to set
+ * @see #drugSerializer
+ */
+ protected void setDrugSerializer(XmlSerializer<Drug> drugSerializer) {
+ this.drugSerializer = drugSerializer;
+ }
+
+ /**
+ * Checks if organism name matches list of organisms.
+ *
+ * @param organismName
+ * name of the organism (should be something recognizable by
+ * {@link MiriamType#TAXONOMY} db).
+ * @param organisms
+ * list of organisms
+ * @return <code>false</code> if organisName couldn't be found in organisms
+ * list. If organismName is null or empty or list of organisms is empty
+ * true will be returned
+ */
+ protected boolean organismMatch(String organismName, Collection<MiriamData> organisms) {
+ if (organismName == null || organismName.isEmpty() || organisms.size() == 0) {
+ return true;
+ }
+ try {
+ MiriamData organism = taxonomyBackend.getByName(organismName);
+ return organisms.contains(organism);
+ } catch (TaxonomySearchException e) {
+ logger.error("Problem with taxonomy search for: " + organismName, e);
+ return true;
+ }
+ }
+
+ /**
+ * @return the taxonomyBackend
+ * @see #taxonomyBackend
+ */
+ public TaxonomyBackend getTaxonomyBackend() {
+ return taxonomyBackend;
+ }
+
+ /**
+ * @param taxonomyBackend
+ * the taxonomyBackend to set
+ * @see #taxonomyBackend
+ */
+ public void setTaxonomyBackend(TaxonomyBackend taxonomyBackend) {
+ this.taxonomyBackend = taxonomyBackend;
+ }
+
+ public List<String> getSuggestedQueryList(Project project, MiriamData organism) throws DrugSearchException {
+ if (organism == null) {
+ return new ArrayList<>();
+ }
+ String cacheQuery = PROJECT_SUGGESTED_QUERY_PREFIX + "\n" + project.getId() + "\n" + organism.getResource();
+ String cachedData = getCacheValue(cacheQuery);
+ List<String> result;
+ if (cachedData == null) {
+ result = getSuggestedQueryListWithoutCache(project, organism);
+ cachedData = StringUtils.join(result, "\n");
+ setCacheValue(cacheQuery, cachedData);
+ } else {
+ result = new ArrayList<>();
+ for (String string : cachedData.split("\n")) {
+ if (!string.isEmpty()) {
+ result.add(string);
+ }
+ }
+ }
+ return result;
+ }
+
+ private List<String> getSuggestedQueryListWithoutCache(Project project, MiriamData organism)
+ throws DrugSearchException {
+ Set<String> resultSet = new HashSet<>();
+ Set<MiriamData> targets = new HashSet<>();
+ for (ModelData model : project.getModels()) {
+ for (Element element : model.getElements()) {
+ MiriamData uniprot = null;
+ MiriamData hgncSymbol = null;
+ for (MiriamData miriam : element.getMiriamData()) {
+ if (miriam.getDataType().equals(MiriamType.UNIPROT)) {
+ uniprot = miriam;
+ } else if (miriam.getDataType().equals(MiriamType.HGNC_SYMBOL)) {
+ hgncSymbol = miriam;
+ }
+ }
+ if (hgncSymbol != null) {
+ targets.add(hgncSymbol);
+ } else if (uniprot != null) {
+ targets.add(uniprot);
+ } else {
+ boolean validClass = false;
+ for (Class<?> clazz : MiriamType.HGNC_SYMBOL.getValidClass()) {
+ if (clazz.isAssignableFrom(element.getClass())) {
+ validClass = true;
+ }
+ }
+ if (validClass) {
+ MiriamData md = new MiriamData(MiriamType.HGNC_SYMBOL, element.getName());
+ try {
+ if (hgncAnnotator.isValidHgncMiriam(md)) {
+ targets.add(md);
+ }
+ } catch (AnnotatorException e) {
+ logger.error("Problem with accessing HGNC database", e);
+ }
+ }
+ }
+ }
+ }
+ List<MiriamData> organisms = new ArrayList<>();
+ if (organism != null) {
+ organisms.add(organism);
+ }
+ List<Drug> drugs = getDrugListByTargets(targets, organisms);
+ for (Drug chemical : drugs) {
+ resultSet.add(chemical.getName());
+ }
+ List<String> result = new ArrayList<>();
+ result.addAll(resultSet);
+ Collections.sort(result);
+ return result;
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugSearchException.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugSearchException.java
index ba889c3ab2..f52c229c3e 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugSearchException.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugSearchException.java
@@ -1,48 +1,48 @@
-package lcsb.mapviewer.annotation.services;
-
-/**
- * Exception thrown when there was a problem when searching for a drug.
- *
- * @author Piotr Gawron
- *
- */
-public class DrugSearchException extends Exception {
-
- /**
- * Default constructor.
- *
- * @param string
- * exception message
- */
- public DrugSearchException(String string) {
- super(string);
- }
-
- /**
- * Default constructor.
- *
- * @param e
- * parent exception
- */
- public DrugSearchException(Exception e) {
- super(e);
- }
-
- /**
- * Default constructor.
- *
- * @param message
- * exception message
- * @param e
- * source exception
- */
- public DrugSearchException(String message, Exception e) {
- super(message, e);
- }
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
-}
+package lcsb.mapviewer.annotation.services;
+
+/**
+ * Exception thrown when there was a problem when searching for a drug.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class DrugSearchException extends Exception {
+
+ /**
+ * Default constructor.
+ *
+ * @param string
+ * exception message
+ */
+ public DrugSearchException(String string) {
+ super(string);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param e
+ * parent exception
+ */
+ public DrugSearchException(Exception e) {
+ super(e);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * exception message
+ * @param e
+ * source exception
+ */
+ public DrugSearchException(String message, Exception e) {
+ super(message, e);
+ }
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java
index fb29370b70..3c680b67ae 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java
@@ -1,773 +1,773 @@
-package lcsb.mapviewer.annotation.services;
-
-import java.io.IOException;
-import java.io.UnsupportedEncodingException;
-import java.net.URLEncoder;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import org.apache.commons.lang3.SerializationException;
-import org.apache.commons.lang3.StringEscapeUtils;
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
-import lcsb.mapviewer.annotation.cache.WebPageDownloader;
-import lcsb.mapviewer.annotation.data.Drug;
-import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.annotation.data.TargetType;
-import lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.UniprotSearchException;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
-
-/**
- * Class used for parsing and accessing data from html interfaces of drugbank
- * database. Parser was developed by Janek. I tried to comment it as best as I
- * could, but...
- *
- * @author Piotr Gawron
- *
- */
-public class DrugbankHTMLParser extends DrugAnnotation implements IExternalService {
-
- /**
- * Maximum available length of the pubmed identifiers.
- */
- private static final int MAX_PUBMED_IDENTIFIER_LENGTH = 9;
-
- /**
- * Prefix used for storing data about drug with name key value.
- */
- static final String DRUG_NAME_PREFIX = "drug:";
-
- /**
- * Service used for annotation of proteins using {@link MiriamType#UNIPROT
- * uniprot}.
- */
- @Autowired
- private UniprotAnnotator uniprotAnnotator;
-
- /**
- * Pattern that extract information about drug name when accessing page about
- * target.
- */
- private final Pattern drugNamePattern = Pattern.compile("(?<=<td><strong>)([\\s\\S]*?)(?=</strong></td>)");
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(DrugbankHTMLParser.class);
-
- /**
- * Url used for finding drug by drug name.
- */
- static final String URLB = "https://www.drugbank.ca/search?searcher=drugs&utf8=%E2%9C%93&button=&filter=false&query=";
-
- /**
- * Url used for retrieving general information about drug.
- */
- static final String URLDRUG = "https://www.drugbank.ca/drugs/";
-
- /**
- * Homepage of drugbank.
- */
- static final String URL = "https://www.drugbank.ca/";
-
- /**
- * Url used for accessing information about target synonyms.
- */
- static final String URLPEP = "https://www.drugbank.ca/biodb/polypeptides/";
-
- /**
- * Url that allows to search for drugs using target hgnc name.
- */
- static final String URL_TARGETS = "https://www.drugbank.ca/search?utf8=%E2%9C%93&searcher=targets&query=";
-
- /**
- * Url that helps finding drug name for given target identifier.
- */
- static final String URL_TARGET_DETAIL = "https://www.drugbank.ca/biodb/bio_entities/";
-
- /**
- * Pattern used to get information about {@link Drug#bloodBrainBarrier blood
- * brain barrier}.
- */
- private Pattern bloodBrainBarrierPattern = Pattern.compile("(?<=<td>)([\\s\\S]*?)(?=</td>)");
-
- /**
- * Pattern that extract information about target identifier when searching for
- * targets with given set of HGNC names.
- */
- private Pattern targetPattern = Pattern.compile("(?<=\"/biodb/bio_entities/)([\\s\\S]*?)(?=\")");
-
- /**
- * Default constructor.
- */
- public DrugbankHTMLParser() {
- super(DrugbankHTMLParser.class);
- }
-
- @Override
- public String refreshCacheQuery(Object query) throws SourceNotAvailable {
- String result = null;
- try {
- if (query instanceof String) {
- String name = (String) query;
- if (name.startsWith(DRUG_NAME_PREFIX)) {
- name = name.substring(DRUG_NAME_PREFIX.length());
- result = getDrugSerializer().objectToString(findDrug(name));
- } else {
- result = super.refreshCacheQuery(query);
- }
- } else {
- result = super.refreshCacheQuery(query);
- }
- } catch (DrugSearchException e) {
- throw new SourceNotAvailable(e);
- }
- return result;
- }
-
- /**
- * Finds the drug identifier in the web page with information about drug.
- *
- * @param webpageContent
- * content of the web page with information about drug
- * @return drugbank identifier
- */
- private String findIdInText(String webpageContent) {
- int i = 0, j = 0;
- i = webpageContent.indexOf("href=\"/drugs/");
- if (i == -1) {
- return null;
- }
- i = i + "href=\"/drugs/".length();
- j = webpageContent.indexOf('"', i);
- return webpageContent.substring(i, j);
- }
-
- /**
- * Finds the drug name in the webpage with information about drug.
- *
- * @param webpageContent
- * content of the webpage with information about drug
- * @return name of the drug
- */
- private String findNameInText(String webpageContent) {
- int i = 0, j = 0;
- i = webpageContent.indexOf("a href=\"/drugs/");
- i = webpageContent.indexOf(">", i);
- i = i + 1;
- j = webpageContent.indexOf('<', i);
- return webpageContent.substring(i, j);
- }
-
- /**
- * Finds the description of the drug on the content of the web page with
- * information about drug.
- *
- * @param webpageContent
- * content of the web page with information about drug
- * @return description of the drug
- */
- String getDescriptionForDrug(String webpageContent) {
- int startIndex = 0, endIndex = 0;
- startIndex = webpageContent.indexOf("Description</dt><dd class=\"col-md-10 col-sm-8\">");
- if (startIndex == -1) {
- return null;
- }
- startIndex = startIndex + "Description</dt><dd class=\"col-md-10 col-sm-8\">".length();
- endIndex = webpageContent.indexOf("</dd", startIndex);
- String description = webpageContent.substring(startIndex, endIndex);
- // find special html characters
- description = StringEscapeUtils.unescapeHtml4(description);
- description = cleanHtml(description);
- if (description.equalsIgnoreCase("Not Available")) {
- description = null;
- }
-
- return description;
- }
-
- /**
- * Returns list of the drug brand names from the web page content.
- *
- * @param page
- * content of the web page with information about drug
- * @return list of the drug brand names
- */
- private List<String> getTargetBrands(String page) {
- List<String> result = new ArrayList<>();
- int i, j, end;
- Boolean finding = true;
- i = page.indexOf("International/Other Brands");
- end = page.indexOf("<dt", i);
- while (finding) {
- i = page.indexOf("separated-list-item\">", i);
- if (i == -1 || i > end) {
- finding = false;
- continue;
- }
- i = i + "separated-list-item\">".length();
- j = page.indexOf("<", i);
- String synonym = StringEscapeUtils.unescapeHtml4(page.substring(i, j));
- synonym = cleanHtml(synonym).trim();
- if (synonym.indexOf("(") > 0) {
- synonym = synonym.substring(0, synonym.indexOf("(")).trim();
- }
- result.add(synonym);
- }
- return result;
- }
-
- /**
- * Returns list of drug synonyms from drugbank database.
- *
- * @param page
- * web page content with drug information
- * @return list of drug synonyms
- */
- private List<String> getDrugSynonyms(String page) {
- List<String> ans = new ArrayList<>();
-
- int i, j, end;
- Boolean finding = true;
- i = page.indexOf("Synonyms");
- end = page.indexOf("Prescription Products", i);
- while (finding) {
- i = page.indexOf("<li>", i);
- if (i == -1 || i > end) {
- finding = false;
- continue;
- }
- i = i + "<li>".length();
- j = page.indexOf("<", i);
- String synonym = StringEscapeUtils.unescapeHtml4(page.substring(i, j));
- ans.add(cleanHtml(synonym));
- }
-
- return ans;
- }
-
- /**
- * Returns references from reference string (obtained from drugbank homepage) .
- *
- * @param descriptionString
- * string containing references obtained from drugbank webpage
- * @return list of references obtained from drugbank {@link String}
- */
- List<MiriamData> getPubmedFromRef(String descriptionString) {
- List<MiriamData> result = new ArrayList<>();
- int currentStartIndex = 0;
- while (true) {
- currentStartIndex = descriptionString.indexOf("/pubmed/", currentStartIndex);
- if (currentStartIndex == -1) {
- break;
- }
- currentStartIndex = currentStartIndex + "/pubmed/".length();
- int endIndex = descriptionString.indexOf('"', currentStartIndex);
- String identifier = descriptionString.substring(currentStartIndex, endIndex);
- String correctedIdentifier = identifier.replaceAll("[^\\d]", "");
- if (!identifier.equals(correctedIdentifier)) {
- if (correctedIdentifier.length() > MAX_PUBMED_IDENTIFIER_LENGTH) {
- correctedIdentifier = correctedIdentifier.substring(0, MAX_PUBMED_IDENTIFIER_LENGTH);
- }
- logger.warn("Problematic pubmed identfier: \"" + identifier + "\". Trying fixing with the result: "
- + correctedIdentifier);
- }
- if (correctedIdentifier.equals("")) {
- break;
- }
- result.add(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, correctedIdentifier));
- }
- return result;
- }
-
- /**
- * Returns targets parsed from page content.
- *
- * @param page
- * webpage content from which data are extracted
- * @throws DrugSearchException
- * thrown when there are problems with connection to DrugBank database
- * @return list of drug {@link Target} parsed from input string
- */
- List<Target> getTargetsForDrug(String page) throws DrugSearchException {
- List<Target> result = new ArrayList<>();
- try {
- int pageStart;
- Target target = new Target();
- target.setType(TargetType.SINGLE_PROTEIN);
-
- pageStart = page.indexOf("bond-list-container targets");
-
- int end = page.indexOf("bond-list-container enzymes");
- if (end < 0) {
- end = page.indexOf("bond-list-container carriers");
- if (end < 0) {
- end = page.indexOf("bond-list-container transporters");
-
- if (end < 0) {
- end = page.indexOf("<tr id=\"comments\">");
- if (end < 0) {
- end = page.length() - 1;
- }
- }
- }
- }
-
- while (pageStart > 0 && pageStart < end) {
- int targetStart = page.indexOf("Details</a>", pageStart);
- if (targetStart < 0) {
- break;
- }
- int nextTargetStart = page.indexOf("Details</a>", targetStart + 1);
- if (nextTargetStart < 0) {
- nextTargetStart = end;
- }
-
- target = parseTarget(page.substring(targetStart, nextTargetStart));
- if (target != null) {
- result.add(target);
- }
- pageStart = nextTargetStart;
-
- }
- } catch (TaxonomySearchException e) {
- throw new DrugSearchException("Problem with finidng information about organism", e);
- } catch (UniprotSearchException e) {
- throw new DrugSearchException("Problem with finidng information about protein", e);
- }
- return result;
- }
-
- /**
- * Parse html info about target into {@link Target} structure.
- *
- * @param htmlPage
- * string with html content
- * @return {@link Target} for given html content
- * @throws UniprotSearchException
- * thrown when there is a problem with accessing uniprot db
- * @throws TaxonomySearchException
- * thrown when there is a problem with accessing taxonomy db
- */
- protected Target parseTarget(String htmlPage) throws UniprotSearchException, TaxonomySearchException {
- int kindIndex = htmlPage.indexOf("Kind</dt><dd class=\"col-md-7 col-sm-6\">");
- kindIndex += "Kind</dt><dd class=\"col-md-7 col-sm-6\">".length();
- int endKindIndex = htmlPage.indexOf("</dd>");
- String type = "";
- if (kindIndex > 0 && endKindIndex > kindIndex) {
- type = htmlPage.substring(kindIndex, endKindIndex);
- }
- if (type.trim().equalsIgnoreCase("Protein")) {
- int uniprotIdStart = htmlPage.indexOf("/biodb/polypeptides/") + "/biodb/polypeptides/".length();
- Target result = new Target();
- result.setType(TargetType.SINGLE_PROTEIN);
-
- // Getting ID && Name
- int uniprotIdEnd = htmlPage.indexOf('"', uniprotIdStart);
- String uniprotId = htmlPage.substring(uniprotIdStart, uniprotIdEnd);
- MiriamData uniprotTarget = new MiriamData(MiriamType.UNIPROT, uniprotId);
- MiriamData hgncTarget = uniprotAnnotator.uniProtToHgnc(uniprotTarget);
- if (hgncTarget != null) {
- hgncTarget.setAnnotator(null);
- result.addGene(hgncTarget);
- } else {
- result.addGene(uniprotTarget);
- }
-
- int nameStart = uniprotIdEnd + 2;
- int nameEnd = htmlPage.indexOf("</", uniprotIdStart);
- String name = StringEscapeUtils.unescapeHtml4(htmlPage.substring(nameStart, nameEnd));
- result.setName(name);
-
- // Getting Organism
- int organismStart = htmlPage.indexOf("Organism</dt><dd class=\"col-md-7 col-sm-6\">", nameEnd)
- + "Organism</dt><dd class=\"col-md-7 col-sm-6\">".length();
- int organismEnd = htmlPage.indexOf("</dd>", organismStart);
- String organismString = htmlPage.substring(organismStart, organismEnd);
- result.setOrganism(getTaxonomyBackend().getByName(organismString));
-
- // Getting References
- int referencesStart = htmlPage.indexOf("<h5>References</h5>", organismEnd);
- if (referencesStart > 0) {
- int referencesEnd = Math.min(htmlPage.indexOf("Details</a>", referencesStart), htmlPage.length());
- if (referencesEnd < 0) {
- referencesEnd = htmlPage.length();
- }
- result.addReferences(getPubmedFromRef(htmlPage.substring(referencesStart, referencesEnd)));
- }
- return result;
- } else {
- logger.warn("Unknown target type: " + type + ". Skipping.");
- return null;
- }
- }
-
- /**
- * Finds information about drug in drugbank database.
- *
- * @param name
- * name of the dug that we are looking for
- * @throws DrugSearchException
- * thrown when there are problems with connection to DrugBank database
- * @return drug with the information obtained from drugbank or <code>null</code>
- * if such data couldn't be found
- */
- private Drug findMoreInformation(String name) throws DrugSearchException {
- Drug result = null;
- try {
- name = URLEncoder.encode(name, "UTF-8");
-
- // minus is to prevent redirection from search that have single result
- String accessUrl = URLB + name + "+-";
-
- String content = getWebPageContent(accessUrl);
-
- String[] lines = content.split("\n");
- for (String inputLine : lines) {
- String tmp = findIdInText(inputLine);
- if (tmp != null) {
- result = new Drug();
- result.addSource(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.DRUGBANK, tmp));
- result.setName(super.cleanHtml(findNameInText(inputLine)));
- break;
- }
- }
-
- if (result != null) {
-
- accessUrl = URLDRUG + result.getSources().get(0).getResource();
-
- String page = getWebPageContent(accessUrl);
-
- result.setDescription(getDescriptionForDrug(page));
-
- result.setSynonyms(getDrugSynonyms(page));
-
- // Getting drug brand names
- result.setBrandNames(getTargetBrands(page));
-
- result.addTargets(getTargetsForDrug(page));
-
- result.setBloodBrainBarrier(getBloodBrainBarrier(page));
-
- result.setApproved(getApproved(page));
-
- if (!nameMatch(result, name)) {
- result = null;
- }
- }
- } catch (IOException e) {
- throw new DrugSearchException(e);
- }
- return result;
- }
-
- /**
- * Check if drug data mateches with the search name.
- *
- * @param drug
- * drug to be checked
- * @param name
- * name of the drug that we were looking for
- * @return true if if drug data matches with the search name
- */
- private boolean nameMatch(Drug drug, String name) {
- Set<String> foundNames = new HashSet<>();
- foundNames.add(drug.getName());
- foundNames.addAll(drug.getSynonyms());
- foundNames.addAll(drug.getBrandNames());
- String lowerCaseName;
- try {
- lowerCaseName = java.net.URLDecoder.decode(name, "UTF-8").toLowerCase().replaceAll("[^A-Za-z0-9]", "");
- } catch (UnsupportedEncodingException e) {
- lowerCaseName = name.toLowerCase().replaceAll("[^A-Za-z0-9]", "");
- }
- for (String string : foundNames) {
- String query = string.toLowerCase().replaceAll("[^A-Za-z0-9]", "");
- if (query.contains(lowerCaseName)) {
- return true;
- }
- }
- return false;
- }
-
- /**
- * Finds blood brain barrier info about drug in the webpage content.
- *
- * @param page
- * webpage content used for parsing
- *
- * @return status of blood brain barrier
- */
- String getBloodBrainBarrier(String page) {
- int index = page.indexOf("<td>Blood Brain Barrier</td>");
- if (index <= 0) {
- return "N/A";
- }
-
- Matcher matcher = bloodBrainBarrierPattern.matcher(page.substring(index));
-
- matcher.find();
- if (!matcher.find()) {
- logger.warn("Invalid html for Blood Brain Barrier...");
- return "N/A";
- }
- String match = matcher.group(1);
- if (match.contains("+")) {
- return "YES";
- } else if (match.contains("-")) {
- return "NO";
- } else {
- logger.warn("Unknown Blood Brain Barrier status: " + match);
- return "N/A";
- }
- }
-
- /**
- * Finds if drug is approved.
- *
- * @param page
- * webpage content used for parsing
- *
- * @return <code>true</code> if drug is approved
- */
- private Boolean getApproved(String page) {
- int index = page.indexOf("<dt class=\"col-md-2 col-sm-4\">Groups</dt>");
- if (index <= 0) {
- return null;
- }
-
- int end = page.indexOf("</dd>", index + 1);
-
- if (end < index) {
- end = page.length();
- }
- String match = page.substring(index, end).toLowerCase();
- if (match.contains("approved")) {
- if (match.contains("investigational") || match.contains("withdrawn") || match.contains("experimental")) {
- logger.warn("Contradicting info about approved status: " + match);
- return null;
- }
- return true;
- } else if (match.contains("investigational") || match.contains("withdrawn") || match.contains("experimental")) {
- return false;
- } else {
- logger.warn("Unknown approved status: " + match);
- return null;
- }
- }
-
- @Override
- public Drug findDrug(String drugName) throws DrugSearchException {
- String query = DRUG_NAME_PREFIX + drugName;
- Drug drug = null;
- try {
- drug = getDrugSerializer().xmlToObject(getCacheNode(query));
- } catch (SerializationException e) {
- logger.error("Problem with deserializing element by query: " + query);
- }
- if (drug != null) {
- return drug;
- }
-
- drug = findMoreInformation(drugName);
-
- try {
- setCacheValue(query, getDrugSerializer().objectToString(drug));
- } catch (SerializationException e) {
- logger.error("Problem with serializing element ");
- }
-
- return drug;
- }
-
- @Override
- public ExternalServiceStatus getServiceStatus() {
- ExternalServiceStatus status = new ExternalServiceStatus("DrugBank", URL);
-
- GeneralCacheInterface cacheCopy = getCache();
- this.setCache(null);
-
- try {
- Drug drug = findDrug("Amantadine");
- status.setStatus(ExternalServiceStatusType.OK);
- if (drug == null) {
- status.setStatus(ExternalServiceStatusType.CHANGED);
- }
- } catch (Exception e) {
- logger.error("DrugBank is down", e);
- status.setStatus(ExternalServiceStatusType.DOWN);
- }
- this.setCache(cacheCopy);
- return status;
- }
-
- @Override
- public List<Drug> getDrugListByTarget(MiriamData targetMiriamData, Collection<MiriamData> organisms)
- throws DrugSearchException {
- List<Drug> result = new ArrayList<>();
- if (targetMiriamData == null) {
- return result;
- }
- if (!(MiriamType.HGNC_SYMBOL.equals(targetMiriamData.getDataType()))) {
- throw new InvalidArgumentException("Only " + MiriamType.HGNC_SYMBOL + " type is accepted");
- }
- String url = URL_TARGETS + targetMiriamData.getResource();
-
- try {
- String page = getWebPageContent(url);
-
- Set<String> drugNames = new HashSet<>();
-
- Matcher matcher = targetPattern.matcher(page);
- while (matcher.find()) {
- String drugbankTargetId = matcher.group(0);
- drugNames.addAll(getDrugNamesForTarget(new MiriamData(MiriamType.DRUGBANK_TARGET_V4, drugbankTargetId),
- targetMiriamData, organisms));
- }
- for (String string : drugNames) {
- Drug drug = findDrug(string);
- if (drug == null) {
- logger.warn("Cannot find drug that should be there: " + string);
- } else {
- boolean targets = false;
- for (Target target : drug.getTargets()) {
- for (MiriamData gene : target.getGenes()) {
- if (gene.equals(targetMiriamData)) {
- targets = true;
- }
- }
- }
- if (targets) {
- result.add(drug);
- } else {
- logger.debug("Skipping drug that doesn't target required target. Drug name: " + drug.getName()
- + "; target: " + targetMiriamData);
- }
- }
- }
-
- return result;
- } catch (IOException e) {
- throw new DrugSearchException("Cannot access drug database", e);
- }
- }
-
- /**
- * Returns list of drugs that target element (target) identified be drugbank
- * identifier.
- *
- * @param drugbankTarget
- * {@link MiriamType#DRUGBANK_TARGET_V4 identifier} of the target
- * @param hgncTarget
- * identifier of the target using {@link MiriamType#HGNC_SYMBOL}, used
- * for verification if the target really points to proper protein/gene
- * @param organisms
- * list of organisms to which results should be limited (when no
- * organisms defined filtering will be turned off)
- * @return list of drugs that target this target
- * @throws DrugSearchException
- * thrown when there are problems with connection to DrugBank database
- */
- private Set<String> getDrugNamesForTarget(MiriamData drugbankTarget, MiriamData hgncTarget,
- Collection<MiriamData> organisms) throws DrugSearchException {
- if (!MiriamType.DRUGBANK_TARGET_V4.equals(drugbankTarget.getDataType())) {
- throw new InvalidArgumentException("drugbankTarget must be of type: " + MiriamType.DRUGBANK_TARGET_V4);
- }
-
- try {
- Set<String> drugNames = new HashSet<>();
- String url = URL_TARGET_DETAIL + drugbankTarget.getResource();
-
- String page = getWebPageContent(url);
-
- int idPosition = page.indexOf("<th>DrugBank ID</th>");
- if (idPosition < 0) {
- throw new DrugSearchException("Problematic web page for target: " + drugbankTarget + "(" + hgncTarget + ")");
- }
-
- int protienLinkPosition = page.indexOf("/polypeptides/");
- // sometimes there might not be an element
- if (protienLinkPosition >= 0) {
- protienLinkPosition = protienLinkPosition + "/polypeptides/".length(); // 20;
- int j = page.indexOf('"', protienLinkPosition);
- String uniprotId = page.substring(protienLinkPosition, j);
- MiriamData uniprotMiriam = new MiriamData(MiriamType.UNIPROT, uniprotId);
- MiriamData hgncMiriam = uniprotAnnotator.uniProtToHgnc(uniprotMiriam);
- if (hgncMiriam != null) hgncMiriam.setAnnotator(null);
- if (hgncMiriam == null || !hgncMiriam.equals(hgncTarget)) {
- logger.debug("Invalid target found. Expected " + hgncTarget + ", but found: " + hgncMiriam + " ("
- + uniprotMiriam + ")");
- return drugNames;
- }
-
- } else {
- logger.warn("Invalid target found. No protein data available.");
- return drugNames;
- }
-
- int organismPosition = page.indexOf("Organism</dt><dd class=\"col-md-10 col-sm-8\">");
- if (organismPosition >= 0) {
- int organismStart = organismPosition + "Organism</dt><dd class=\"col-md-10 col-sm-8\">".length();
- int organismEnd = page.indexOf("<", organismStart + 1);
- String organismName = page.substring(organismStart, organismEnd);
- if (!organismMatch(organismName, organisms)) {
- logger.debug("Organism doesn't match. Found" + organismName + ". Expected: " + organisms);
- return drugNames;
- }
- }
-
- Matcher matcher = drugNamePattern.matcher(page.substring(idPosition));
-
- while (matcher.find()) {
- drugNames.add(matcher.group(1));
- }
-
- return drugNames;
- } catch (IOException e) {
- throw new DrugSearchException("Problem with accessing drugbank db", e);
- } catch (UniprotSearchException e) {
- throw new DrugSearchException("Problem with uniprot annotations", e);
- }
- }
-
- /**
- * @return the uniprotAnnotator
- * @see #uniprotAnnotator
- */
- public UniprotAnnotator getUniprotAnnotator() {
- return uniprotAnnotator;
- }
-
- /**
- * @param uniprotAnnotator
- * the uniprotAnnotator to set
- * @see #uniprotAnnotator
- */
- public void setUniprotAnnotator(UniprotAnnotator uniprotAnnotator) {
- this.uniprotAnnotator = uniprotAnnotator;
- }
-
- @Override
- protected WebPageDownloader getWebPageDownloader() {
- return super.getWebPageDownloader();
- }
-
- @Override
- protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
- super.setWebPageDownloader(webPageDownloader);
- }
-
-}
+package lcsb.mapviewer.annotation.services;
+
+import java.io.IOException;
+import java.io.UnsupportedEncodingException;
+import java.net.URLEncoder;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.apache.commons.lang3.SerializationException;
+import org.apache.commons.lang3.StringEscapeUtils;
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.WebPageDownloader;
+import lcsb.mapviewer.annotation.data.Drug;
+import lcsb.mapviewer.annotation.data.Target;
+import lcsb.mapviewer.annotation.data.TargetType;
+import lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator;
+import lcsb.mapviewer.annotation.services.annotators.UniprotSearchException;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
+
+/**
+ * Class used for parsing and accessing data from html interfaces of drugbank
+ * database. Parser was developed by Janek. I tried to comment it as best as I
+ * could, but...
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class DrugbankHTMLParser extends DrugAnnotation implements IExternalService {
+
+ /**
+ * Maximum available length of the pubmed identifiers.
+ */
+ private static final int MAX_PUBMED_IDENTIFIER_LENGTH = 9;
+
+ /**
+ * Prefix used for storing data about drug with name key value.
+ */
+ static final String DRUG_NAME_PREFIX = "drug:";
+
+ /**
+ * Service used for annotation of proteins using {@link MiriamType#UNIPROT
+ * uniprot}.
+ */
+ @Autowired
+ private UniprotAnnotator uniprotAnnotator;
+
+ /**
+ * Pattern that extract information about drug name when accessing page about
+ * target.
+ */
+ private final Pattern drugNamePattern = Pattern.compile("(?<=<td><strong>)([\\s\\S]*?)(?=</strong></td>)");
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(DrugbankHTMLParser.class);
+
+ /**
+ * Url used for finding drug by drug name.
+ */
+ static final String URLB = "https://www.drugbank.ca/search?searcher=drugs&utf8=%E2%9C%93&button=&filter=false&query=";
+
+ /**
+ * Url used for retrieving general information about drug.
+ */
+ static final String URLDRUG = "https://www.drugbank.ca/drugs/";
+
+ /**
+ * Homepage of drugbank.
+ */
+ static final String URL = "https://www.drugbank.ca/";
+
+ /**
+ * Url used for accessing information about target synonyms.
+ */
+ static final String URLPEP = "https://www.drugbank.ca/biodb/polypeptides/";
+
+ /**
+ * Url that allows to search for drugs using target hgnc name.
+ */
+ static final String URL_TARGETS = "https://www.drugbank.ca/search?utf8=%E2%9C%93&searcher=targets&query=";
+
+ /**
+ * Url that helps finding drug name for given target identifier.
+ */
+ static final String URL_TARGET_DETAIL = "https://www.drugbank.ca/biodb/bio_entities/";
+
+ /**
+ * Pattern used to get information about {@link Drug#bloodBrainBarrier blood
+ * brain barrier}.
+ */
+ private Pattern bloodBrainBarrierPattern = Pattern.compile("(?<=<td>)([\\s\\S]*?)(?=</td>)");
+
+ /**
+ * Pattern that extract information about target identifier when searching for
+ * targets with given set of HGNC names.
+ */
+ private Pattern targetPattern = Pattern.compile("(?<=\"/biodb/bio_entities/)([\\s\\S]*?)(?=\")");
+
+ /**
+ * Default constructor.
+ */
+ public DrugbankHTMLParser() {
+ super(DrugbankHTMLParser.class);
+ }
+
+ @Override
+ public String refreshCacheQuery(Object query) throws SourceNotAvailable {
+ String result = null;
+ try {
+ if (query instanceof String) {
+ String name = (String) query;
+ if (name.startsWith(DRUG_NAME_PREFIX)) {
+ name = name.substring(DRUG_NAME_PREFIX.length());
+ result = getDrugSerializer().objectToString(findDrug(name));
+ } else {
+ result = super.refreshCacheQuery(query);
+ }
+ } else {
+ result = super.refreshCacheQuery(query);
+ }
+ } catch (DrugSearchException e) {
+ throw new SourceNotAvailable(e);
+ }
+ return result;
+ }
+
+ /**
+ * Finds the drug identifier in the web page with information about drug.
+ *
+ * @param webpageContent
+ * content of the web page with information about drug
+ * @return drugbank identifier
+ */
+ private String findIdInText(String webpageContent) {
+ int i = 0, j = 0;
+ i = webpageContent.indexOf("href=\"/drugs/");
+ if (i == -1) {
+ return null;
+ }
+ i = i + "href=\"/drugs/".length();
+ j = webpageContent.indexOf('"', i);
+ return webpageContent.substring(i, j);
+ }
+
+ /**
+ * Finds the drug name in the webpage with information about drug.
+ *
+ * @param webpageContent
+ * content of the webpage with information about drug
+ * @return name of the drug
+ */
+ private String findNameInText(String webpageContent) {
+ int i = 0, j = 0;
+ i = webpageContent.indexOf("a href=\"/drugs/");
+ i = webpageContent.indexOf(">", i);
+ i = i + 1;
+ j = webpageContent.indexOf('<', i);
+ return webpageContent.substring(i, j);
+ }
+
+ /**
+ * Finds the description of the drug on the content of the web page with
+ * information about drug.
+ *
+ * @param webpageContent
+ * content of the web page with information about drug
+ * @return description of the drug
+ */
+ String getDescriptionForDrug(String webpageContent) {
+ int startIndex = 0, endIndex = 0;
+ startIndex = webpageContent.indexOf("Description</dt><dd class=\"col-md-10 col-sm-8\">");
+ if (startIndex == -1) {
+ return null;
+ }
+ startIndex = startIndex + "Description</dt><dd class=\"col-md-10 col-sm-8\">".length();
+ endIndex = webpageContent.indexOf("</dd", startIndex);
+ String description = webpageContent.substring(startIndex, endIndex);
+ // find special html characters
+ description = StringEscapeUtils.unescapeHtml4(description);
+ description = cleanHtml(description);
+ if (description.equalsIgnoreCase("Not Available")) {
+ description = null;
+ }
+
+ return description;
+ }
+
+ /**
+ * Returns list of the drug brand names from the web page content.
+ *
+ * @param page
+ * content of the web page with information about drug
+ * @return list of the drug brand names
+ */
+ private List<String> getTargetBrands(String page) {
+ List<String> result = new ArrayList<>();
+ int i, j, end;
+ Boolean finding = true;
+ i = page.indexOf("International/Other Brands");
+ end = page.indexOf("<dt", i);
+ while (finding) {
+ i = page.indexOf("separated-list-item\">", i);
+ if (i == -1 || i > end) {
+ finding = false;
+ continue;
+ }
+ i = i + "separated-list-item\">".length();
+ j = page.indexOf("<", i);
+ String synonym = StringEscapeUtils.unescapeHtml4(page.substring(i, j));
+ synonym = cleanHtml(synonym).trim();
+ if (synonym.indexOf("(") > 0) {
+ synonym = synonym.substring(0, synonym.indexOf("(")).trim();
+ }
+ result.add(synonym);
+ }
+ return result;
+ }
+
+ /**
+ * Returns list of drug synonyms from drugbank database.
+ *
+ * @param page
+ * web page content with drug information
+ * @return list of drug synonyms
+ */
+ private List<String> getDrugSynonyms(String page) {
+ List<String> ans = new ArrayList<>();
+
+ int i, j, end;
+ Boolean finding = true;
+ i = page.indexOf("Synonyms");
+ end = page.indexOf("Prescription Products", i);
+ while (finding) {
+ i = page.indexOf("<li>", i);
+ if (i == -1 || i > end) {
+ finding = false;
+ continue;
+ }
+ i = i + "<li>".length();
+ j = page.indexOf("<", i);
+ String synonym = StringEscapeUtils.unescapeHtml4(page.substring(i, j));
+ ans.add(cleanHtml(synonym));
+ }
+
+ return ans;
+ }
+
+ /**
+ * Returns references from reference string (obtained from drugbank homepage) .
+ *
+ * @param descriptionString
+ * string containing references obtained from drugbank webpage
+ * @return list of references obtained from drugbank {@link String}
+ */
+ List<MiriamData> getPubmedFromRef(String descriptionString) {
+ List<MiriamData> result = new ArrayList<>();
+ int currentStartIndex = 0;
+ while (true) {
+ currentStartIndex = descriptionString.indexOf("/pubmed/", currentStartIndex);
+ if (currentStartIndex == -1) {
+ break;
+ }
+ currentStartIndex = currentStartIndex + "/pubmed/".length();
+ int endIndex = descriptionString.indexOf('"', currentStartIndex);
+ String identifier = descriptionString.substring(currentStartIndex, endIndex);
+ String correctedIdentifier = identifier.replaceAll("[^\\d]", "");
+ if (!identifier.equals(correctedIdentifier)) {
+ if (correctedIdentifier.length() > MAX_PUBMED_IDENTIFIER_LENGTH) {
+ correctedIdentifier = correctedIdentifier.substring(0, MAX_PUBMED_IDENTIFIER_LENGTH);
+ }
+ logger.warn("Problematic pubmed identfier: \"" + identifier + "\". Trying fixing with the result: "
+ + correctedIdentifier);
+ }
+ if (correctedIdentifier.equals("")) {
+ break;
+ }
+ result.add(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, correctedIdentifier));
+ }
+ return result;
+ }
+
+ /**
+ * Returns targets parsed from page content.
+ *
+ * @param page
+ * webpage content from which data are extracted
+ * @throws DrugSearchException
+ * thrown when there are problems with connection to DrugBank database
+ * @return list of drug {@link Target} parsed from input string
+ */
+ List<Target> getTargetsForDrug(String page) throws DrugSearchException {
+ List<Target> result = new ArrayList<>();
+ try {
+ int pageStart;
+ Target target = new Target();
+ target.setType(TargetType.SINGLE_PROTEIN);
+
+ pageStart = page.indexOf("bond-list-container targets");
+
+ int end = page.indexOf("bond-list-container enzymes");
+ if (end < 0) {
+ end = page.indexOf("bond-list-container carriers");
+ if (end < 0) {
+ end = page.indexOf("bond-list-container transporters");
+
+ if (end < 0) {
+ end = page.indexOf("<tr id=\"comments\">");
+ if (end < 0) {
+ end = page.length() - 1;
+ }
+ }
+ }
+ }
+
+ while (pageStart > 0 && pageStart < end) {
+ int targetStart = page.indexOf("Details</a>", pageStart);
+ if (targetStart < 0) {
+ break;
+ }
+ int nextTargetStart = page.indexOf("Details</a>", targetStart + 1);
+ if (nextTargetStart < 0) {
+ nextTargetStart = end;
+ }
+
+ target = parseTarget(page.substring(targetStart, nextTargetStart));
+ if (target != null) {
+ result.add(target);
+ }
+ pageStart = nextTargetStart;
+
+ }
+ } catch (TaxonomySearchException e) {
+ throw new DrugSearchException("Problem with finidng information about organism", e);
+ } catch (UniprotSearchException e) {
+ throw new DrugSearchException("Problem with finidng information about protein", e);
+ }
+ return result;
+ }
+
+ /**
+ * Parse html info about target into {@link Target} structure.
+ *
+ * @param htmlPage
+ * string with html content
+ * @return {@link Target} for given html content
+ * @throws UniprotSearchException
+ * thrown when there is a problem with accessing uniprot db
+ * @throws TaxonomySearchException
+ * thrown when there is a problem with accessing taxonomy db
+ */
+ protected Target parseTarget(String htmlPage) throws UniprotSearchException, TaxonomySearchException {
+ int kindIndex = htmlPage.indexOf("Kind</dt><dd class=\"col-md-7 col-sm-6\">");
+ kindIndex += "Kind</dt><dd class=\"col-md-7 col-sm-6\">".length();
+ int endKindIndex = htmlPage.indexOf("</dd>");
+ String type = "";
+ if (kindIndex > 0 && endKindIndex > kindIndex) {
+ type = htmlPage.substring(kindIndex, endKindIndex);
+ }
+ if (type.trim().equalsIgnoreCase("Protein")) {
+ int uniprotIdStart = htmlPage.indexOf("/biodb/polypeptides/") + "/biodb/polypeptides/".length();
+ Target result = new Target();
+ result.setType(TargetType.SINGLE_PROTEIN);
+
+ // Getting ID && Name
+ int uniprotIdEnd = htmlPage.indexOf('"', uniprotIdStart);
+ String uniprotId = htmlPage.substring(uniprotIdStart, uniprotIdEnd);
+ MiriamData uniprotTarget = new MiriamData(MiriamType.UNIPROT, uniprotId);
+ MiriamData hgncTarget = uniprotAnnotator.uniProtToHgnc(uniprotTarget);
+ if (hgncTarget != null) {
+ hgncTarget.setAnnotator(null);
+ result.addGene(hgncTarget);
+ } else {
+ result.addGene(uniprotTarget);
+ }
+
+ int nameStart = uniprotIdEnd + 2;
+ int nameEnd = htmlPage.indexOf("</", uniprotIdStart);
+ String name = StringEscapeUtils.unescapeHtml4(htmlPage.substring(nameStart, nameEnd));
+ result.setName(name);
+
+ // Getting Organism
+ int organismStart = htmlPage.indexOf("Organism</dt><dd class=\"col-md-7 col-sm-6\">", nameEnd)
+ + "Organism</dt><dd class=\"col-md-7 col-sm-6\">".length();
+ int organismEnd = htmlPage.indexOf("</dd>", organismStart);
+ String organismString = htmlPage.substring(organismStart, organismEnd);
+ result.setOrganism(getTaxonomyBackend().getByName(organismString));
+
+ // Getting References
+ int referencesStart = htmlPage.indexOf("<h5>References</h5>", organismEnd);
+ if (referencesStart > 0) {
+ int referencesEnd = Math.min(htmlPage.indexOf("Details</a>", referencesStart), htmlPage.length());
+ if (referencesEnd < 0) {
+ referencesEnd = htmlPage.length();
+ }
+ result.addReferences(getPubmedFromRef(htmlPage.substring(referencesStart, referencesEnd)));
+ }
+ return result;
+ } else {
+ logger.warn("Unknown target type: " + type + ". Skipping.");
+ return null;
+ }
+ }
+
+ /**
+ * Finds information about drug in drugbank database.
+ *
+ * @param name
+ * name of the dug that we are looking for
+ * @throws DrugSearchException
+ * thrown when there are problems with connection to DrugBank database
+ * @return drug with the information obtained from drugbank or <code>null</code>
+ * if such data couldn't be found
+ */
+ private Drug findMoreInformation(String name) throws DrugSearchException {
+ Drug result = null;
+ try {
+ name = URLEncoder.encode(name, "UTF-8");
+
+ // minus is to prevent redirection from search that have single result
+ String accessUrl = URLB + name + "+-";
+
+ String content = getWebPageContent(accessUrl);
+
+ String[] lines = content.split("\n");
+ for (String inputLine : lines) {
+ String tmp = findIdInText(inputLine);
+ if (tmp != null) {
+ result = new Drug();
+ result.addSource(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.DRUGBANK, tmp));
+ result.setName(super.cleanHtml(findNameInText(inputLine)));
+ break;
+ }
+ }
+
+ if (result != null) {
+
+ accessUrl = URLDRUG + result.getSources().get(0).getResource();
+
+ String page = getWebPageContent(accessUrl);
+
+ result.setDescription(getDescriptionForDrug(page));
+
+ result.setSynonyms(getDrugSynonyms(page));
+
+ // Getting drug brand names
+ result.setBrandNames(getTargetBrands(page));
+
+ result.addTargets(getTargetsForDrug(page));
+
+ result.setBloodBrainBarrier(getBloodBrainBarrier(page));
+
+ result.setApproved(getApproved(page));
+
+ if (!nameMatch(result, name)) {
+ result = null;
+ }
+ }
+ } catch (IOException e) {
+ throw new DrugSearchException(e);
+ }
+ return result;
+ }
+
+ /**
+ * Check if drug data mateches with the search name.
+ *
+ * @param drug
+ * drug to be checked
+ * @param name
+ * name of the drug that we were looking for
+ * @return true if if drug data matches with the search name
+ */
+ private boolean nameMatch(Drug drug, String name) {
+ Set<String> foundNames = new HashSet<>();
+ foundNames.add(drug.getName());
+ foundNames.addAll(drug.getSynonyms());
+ foundNames.addAll(drug.getBrandNames());
+ String lowerCaseName;
+ try {
+ lowerCaseName = java.net.URLDecoder.decode(name, "UTF-8").toLowerCase().replaceAll("[^A-Za-z0-9]", "");
+ } catch (UnsupportedEncodingException e) {
+ lowerCaseName = name.toLowerCase().replaceAll("[^A-Za-z0-9]", "");
+ }
+ for (String string : foundNames) {
+ String query = string.toLowerCase().replaceAll("[^A-Za-z0-9]", "");
+ if (query.contains(lowerCaseName)) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Finds blood brain barrier info about drug in the webpage content.
+ *
+ * @param page
+ * webpage content used for parsing
+ *
+ * @return status of blood brain barrier
+ */
+ String getBloodBrainBarrier(String page) {
+ int index = page.indexOf("<td>Blood Brain Barrier</td>");
+ if (index <= 0) {
+ return "N/A";
+ }
+
+ Matcher matcher = bloodBrainBarrierPattern.matcher(page.substring(index));
+
+ matcher.find();
+ if (!matcher.find()) {
+ logger.warn("Invalid html for Blood Brain Barrier...");
+ return "N/A";
+ }
+ String match = matcher.group(1);
+ if (match.contains("+")) {
+ return "YES";
+ } else if (match.contains("-")) {
+ return "NO";
+ } else {
+ logger.warn("Unknown Blood Brain Barrier status: " + match);
+ return "N/A";
+ }
+ }
+
+ /**
+ * Finds if drug is approved.
+ *
+ * @param page
+ * webpage content used for parsing
+ *
+ * @return <code>true</code> if drug is approved
+ */
+ private Boolean getApproved(String page) {
+ int index = page.indexOf("<dt class=\"col-md-2 col-sm-4\">Groups</dt>");
+ if (index <= 0) {
+ return null;
+ }
+
+ int end = page.indexOf("</dd>", index + 1);
+
+ if (end < index) {
+ end = page.length();
+ }
+ String match = page.substring(index, end).toLowerCase();
+ if (match.contains("approved")) {
+ if (match.contains("investigational") || match.contains("withdrawn") || match.contains("experimental")) {
+ logger.warn("Contradicting info about approved status: " + match);
+ return null;
+ }
+ return true;
+ } else if (match.contains("investigational") || match.contains("withdrawn") || match.contains("experimental")) {
+ return false;
+ } else {
+ logger.warn("Unknown approved status: " + match);
+ return null;
+ }
+ }
+
+ @Override
+ public Drug findDrug(String drugName) throws DrugSearchException {
+ String query = DRUG_NAME_PREFIX + drugName;
+ Drug drug = null;
+ try {
+ drug = getDrugSerializer().xmlToObject(getCacheNode(query));
+ } catch (SerializationException e) {
+ logger.error("Problem with deserializing element by query: " + query);
+ }
+ if (drug != null) {
+ return drug;
+ }
+
+ drug = findMoreInformation(drugName);
+
+ try {
+ setCacheValue(query, getDrugSerializer().objectToString(drug));
+ } catch (SerializationException e) {
+ logger.error("Problem with serializing element ");
+ }
+
+ return drug;
+ }
+
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ ExternalServiceStatus status = new ExternalServiceStatus("DrugBank", URL);
+
+ GeneralCacheInterface cacheCopy = getCache();
+ this.setCache(null);
+
+ try {
+ Drug drug = findDrug("Amantadine");
+ status.setStatus(ExternalServiceStatusType.OK);
+ if (drug == null) {
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ }
+ } catch (Exception e) {
+ logger.error("DrugBank is down", e);
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ }
+ this.setCache(cacheCopy);
+ return status;
+ }
+
+ @Override
+ public List<Drug> getDrugListByTarget(MiriamData targetMiriamData, Collection<MiriamData> organisms)
+ throws DrugSearchException {
+ List<Drug> result = new ArrayList<>();
+ if (targetMiriamData == null) {
+ return result;
+ }
+ if (!(MiriamType.HGNC_SYMBOL.equals(targetMiriamData.getDataType()))) {
+ throw new InvalidArgumentException("Only " + MiriamType.HGNC_SYMBOL + " type is accepted");
+ }
+ String url = URL_TARGETS + targetMiriamData.getResource();
+
+ try {
+ String page = getWebPageContent(url);
+
+ Set<String> drugNames = new HashSet<>();
+
+ Matcher matcher = targetPattern.matcher(page);
+ while (matcher.find()) {
+ String drugbankTargetId = matcher.group(0);
+ drugNames.addAll(getDrugNamesForTarget(new MiriamData(MiriamType.DRUGBANK_TARGET_V4, drugbankTargetId),
+ targetMiriamData, organisms));
+ }
+ for (String string : drugNames) {
+ Drug drug = findDrug(string);
+ if (drug == null) {
+ logger.warn("Cannot find drug that should be there: " + string);
+ } else {
+ boolean targets = false;
+ for (Target target : drug.getTargets()) {
+ for (MiriamData gene : target.getGenes()) {
+ if (gene.equals(targetMiriamData)) {
+ targets = true;
+ }
+ }
+ }
+ if (targets) {
+ result.add(drug);
+ } else {
+ logger.debug("Skipping drug that doesn't target required target. Drug name: " + drug.getName()
+ + "; target: " + targetMiriamData);
+ }
+ }
+ }
+
+ return result;
+ } catch (IOException e) {
+ throw new DrugSearchException("Cannot access drug database", e);
+ }
+ }
+
+ /**
+ * Returns list of drugs that target element (target) identified be drugbank
+ * identifier.
+ *
+ * @param drugbankTarget
+ * {@link MiriamType#DRUGBANK_TARGET_V4 identifier} of the target
+ * @param hgncTarget
+ * identifier of the target using {@link MiriamType#HGNC_SYMBOL}, used
+ * for verification if the target really points to proper protein/gene
+ * @param organisms
+ * list of organisms to which results should be limited (when no
+ * organisms defined filtering will be turned off)
+ * @return list of drugs that target this target
+ * @throws DrugSearchException
+ * thrown when there are problems with connection to DrugBank database
+ */
+ private Set<String> getDrugNamesForTarget(MiriamData drugbankTarget, MiriamData hgncTarget,
+ Collection<MiriamData> organisms) throws DrugSearchException {
+ if (!MiriamType.DRUGBANK_TARGET_V4.equals(drugbankTarget.getDataType())) {
+ throw new InvalidArgumentException("drugbankTarget must be of type: " + MiriamType.DRUGBANK_TARGET_V4);
+ }
+
+ try {
+ Set<String> drugNames = new HashSet<>();
+ String url = URL_TARGET_DETAIL + drugbankTarget.getResource();
+
+ String page = getWebPageContent(url);
+
+ int idPosition = page.indexOf("<th>DrugBank ID</th>");
+ if (idPosition < 0) {
+ throw new DrugSearchException("Problematic web page for target: " + drugbankTarget + "(" + hgncTarget + ")");
+ }
+
+ int protienLinkPosition = page.indexOf("/polypeptides/");
+ // sometimes there might not be an element
+ if (protienLinkPosition >= 0) {
+ protienLinkPosition = protienLinkPosition + "/polypeptides/".length(); // 20;
+ int j = page.indexOf('"', protienLinkPosition);
+ String uniprotId = page.substring(protienLinkPosition, j);
+ MiriamData uniprotMiriam = new MiriamData(MiriamType.UNIPROT, uniprotId);
+ MiriamData hgncMiriam = uniprotAnnotator.uniProtToHgnc(uniprotMiriam);
+ if (hgncMiriam != null) hgncMiriam.setAnnotator(null);
+ if (hgncMiriam == null || !hgncMiriam.equals(hgncTarget)) {
+ logger.debug("Invalid target found. Expected " + hgncTarget + ", but found: " + hgncMiriam + " ("
+ + uniprotMiriam + ")");
+ return drugNames;
+ }
+
+ } else {
+ logger.warn("Invalid target found. No protein data available.");
+ return drugNames;
+ }
+
+ int organismPosition = page.indexOf("Organism</dt><dd class=\"col-md-10 col-sm-8\">");
+ if (organismPosition >= 0) {
+ int organismStart = organismPosition + "Organism</dt><dd class=\"col-md-10 col-sm-8\">".length();
+ int organismEnd = page.indexOf("<", organismStart + 1);
+ String organismName = page.substring(organismStart, organismEnd);
+ if (!organismMatch(organismName, organisms)) {
+ logger.debug("Organism doesn't match. Found" + organismName + ". Expected: " + organisms);
+ return drugNames;
+ }
+ }
+
+ Matcher matcher = drugNamePattern.matcher(page.substring(idPosition));
+
+ while (matcher.find()) {
+ drugNames.add(matcher.group(1));
+ }
+
+ return drugNames;
+ } catch (IOException e) {
+ throw new DrugSearchException("Problem with accessing drugbank db", e);
+ } catch (UniprotSearchException e) {
+ throw new DrugSearchException("Problem with uniprot annotations", e);
+ }
+ }
+
+ /**
+ * @return the uniprotAnnotator
+ * @see #uniprotAnnotator
+ */
+ public UniprotAnnotator getUniprotAnnotator() {
+ return uniprotAnnotator;
+ }
+
+ /**
+ * @param uniprotAnnotator
+ * the uniprotAnnotator to set
+ * @see #uniprotAnnotator
+ */
+ public void setUniprotAnnotator(UniprotAnnotator uniprotAnnotator) {
+ this.uniprotAnnotator = uniprotAnnotator;
+ }
+
+ @Override
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
+ }
+
+ @Override
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankXMLParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankXMLParser.java
index de7fd5928b..3c46d45801 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankXMLParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankXMLParser.java
@@ -1,404 +1,404 @@
-package lcsb.mapviewer.annotation.services;
-
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.xml.stream.XMLInputFactory;
-import javax.xml.stream.XMLStreamConstants;
-import javax.xml.stream.XMLStreamException;
-import javax.xml.stream.XMLStreamReader;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.annotation.data.Drug;
-import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.annotation.data.TargetType;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
-
-/**
- * Class used for parsing and accessing data from xml drugbank database. Parser
- * was developed by Janek. I tried to comment it as best as I could, but...
- *
- * @author Piotr Gawron
- *
- */
-public class DrugbankXMLParser {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(DrugbankXMLParser.class);
-
- /**
- * ???
- */
- private static final int RELATED_INFORMATION_TAG = 3;
-
- /**
- * Node identifing drug.
- */
- static final String DRUG = "drug";
-
- /**
- * Node identifing drug identifier.
- */
- static final String DID = "drugbank-id";
-
- /**
- * Node identifing drug name.
- */
- static final String NAME = "name";
-
- /**
- * Node identifing drug description.
- */
- static final String DES = "description";
-
- /**
- * Node identifing single synonym.
- */
- static final String SY = "synonym";
-
- /**
- * Node identifing list of synonym.
- */
- static final String SYS = "synonyms";
-
- /**
- * Node identifing single target.
- */
- static final String TAR = "target";
-
- /**
- * Node identifing list of targets.
- */
- static final String TARGETS = "targets";
-
- /**
- * File with the drugbank xml file.
- */
- private String dbFile = null;
-
- /**
- * Object used to access information about organism taxonomy.
- */
- private TaxonomyBackend taxonomyBackend;
-
- /**
- * List of drugs found in the xml file.
- */
- private List<Drug> drugList = null;
-
- /**
- * Default constructor.
- *
- * @param file
- * file where data is stored
- * @param backend
- * {@link #taxonomyBackend}
- */
- public DrugbankXMLParser(String file, TaxonomyBackend backend) {
- this.dbFile = file;
- this.taxonomyBackend = backend;
- }
-
- /**
- * Transforms string representing pubmed identifiers into {@link MiriamData}
- * objects and set them to {@link Target}.
- *
- * @param target
- * where the data should be put
- * @param referencesString
- * string with pubmed identifiers
- */
- void getPubmedFromRef(Target target, String referencesString) {
- int position = 0;
- int length = "/pubmed/".length();
- while ((position = referencesString.indexOf("/pubmed/", position)) > 0) {
- position += length;
- StringBuilder tmp = new StringBuilder("");
- while (position < referencesString.length() && referencesString.charAt(position) >= '0' && referencesString.charAt(position) <= '9') {
- tmp.append(referencesString.charAt(position));
- position++;
- }
- target.addReference(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, tmp.toString()));
- }
- }
-
- /**
- * Adds gene identifiers to the target.
- *
- * @param reader
- * xml reader used for parsing xml
- * @param target
- * where the data should be added
- * @throws XMLStreamException
- * thrown when there is a problem with xml
- */
- public void getGeneCardId(XMLStreamReader reader, Target target) throws XMLStreamException {
- boolean relevant = false;
- int event;
- while (true) {
- event = reader.next();
- if (event == XMLStreamConstants.CHARACTERS) {
- if (reader.getText().trim().equals("GeneCards")) {
- relevant = true;
- } else if (relevant && !reader.getText().trim().equals("")) {
- String identifier = reader.getText().trim();
- target.addGene(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.HGNC_SYMBOL, identifier));
- relevant = false;
- }
- } else if (event == XMLStreamConstants.END_ELEMENT) {
- if (reader.getLocalName().equals("external-identifiers")) {
- break;
- }
- }
- }
- }
-
- /**
- * This function is magic...
- *
- * @param localName
- * ???
- * @param tagContent
- * ???
- * @param tagName
- * ???
- * @param rel
- * ???
- * @param target
- * ???
- * @param drug
- * ???
- * @return ???
- * @throws DrugSearchException
- * thrown when there is a problem with data coming from external
- * databases
- */
- public int targetEndElement(String localName, String tagContent, String tagName, Boolean rel, Target target, Drug drug) throws DrugSearchException {
- if (localName.equals("id")) {
- if (rel) {
- MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.DRUGBANK_TARGET_V4, tagContent);
- target.setSource(md);
- return 0;
- }
- } else if (localName.equals("name")) {
- if (rel) {
- target.setName(tagContent);
- return 0;
- }
- } else if (localName.equals("organism")) {
- if (rel) {
- try {
- target.setOrganism(taxonomyBackend.getByName(tagContent));
- } catch (TaxonomySearchException e) {
- throw new DrugSearchException(e);
- }
- return 0;
- }
-
- } else if (localName.equals("references")) {
- if (rel) {
- return 1;
- }
- } else if (localName.equals(TAR)) {
- if (rel) {
- drug.addTarget(target);
- return 0;
- }
-
- } else if (localName.equals(TARGETS)) {
- return 2;
- } else if (localName.equals(tagName)) {
- return RELATED_INFORMATION_TAG;
- }
- return 0;
- }
-
- /**
- * Adds target to a drug.
- *
- * @param reader
- * xml reader used for parsing xml
- * @param drug
- * where target should be added
- * @throws XMLStreamException
- * thrown when there is a problem with xml
- * @throws DrugSearchException
- * thrown when there is a problem with data coming from external
- * databases
- */
- public void addTargetToDrug(XMLStreamReader reader, Drug drug) throws XMLStreamException, DrugSearchException {
- boolean relatedInformation = true;
- String tagName = null;
- String tagContent = null;
- Target target = null;
- boolean readingReferences = false;
- while (true) {
- int event = reader.next();
-
- if (event == XMLStreamConstants.START_ELEMENT) {
- if (relatedInformation) {
- if (TAR.equals(reader.getLocalName())) {
- target = new Target();
- target.setType(TargetType.SINGLE_PROTEIN);
- } else {
- relatedInformation = false;
- tagName = reader.getLocalName();
- if ("id".equals(tagName) || "name".equals(tagName) || "organism".equals(tagName)) {
- relatedInformation = true;
- }
- if ("references".equals(tagName)) {
- relatedInformation = true;
- readingReferences = true;
- }
- if ("components".equals(tagName)) {
- relatedInformation = true;
- getGeneCardId(reader, target);
- }
- }
- }
- }
- if (event == XMLStreamConstants.CHARACTERS) {
- tagContent = reader.getText().trim();
- if (readingReferences) {
- getPubmedFromRef(target, tagContent);
- }
- }
-
- if (event == XMLStreamConstants.END_ELEMENT) {
- int what = targetEndElement(reader.getLocalName(), tagContent, tagName, relatedInformation, target, drug);
- if (what == 1) {
- readingReferences = false;
- } else if (what == 2) {
- break;
- } else if (what == RELATED_INFORMATION_TAG) {
- relatedInformation = true;
- }
- }
- }
-
- }
-
- /**
- * Checks if tag is important for us or not.
- *
- * @param tagName
- * name of the tag
- * @return true if tag is relevant, <code>false</code> otherwise
- */
- public Boolean tagNameRelated(String tagName) {
- if ("drugs".equals(tagName) || DID.equals(tagName) || NAME.equals(tagName) || DES.equals(tagName) || DES.equals(tagName) || SY.equals(tagName)
- || SYS.equals(tagName)) {
- return true;
- }
- return false;
-
- }
-
- /**
- * Gets drug from xml database.
- *
- * @param drugName
- * name of the drug
- * @return drug from the database
- * @throws DrugSearchException
- * thrown when there is a problem with finding drug
- */
- public Drug findDrug(String drugName) throws DrugSearchException {
- for (Drug drug : getDrugList()) {
- if (drug.getName().equalsIgnoreCase(drugName)) {
- return drug;
- }
- for (String string : drug.getSynonyms()) {
- if (string.equalsIgnoreCase(drugName)) {
- return drug;
- }
- }
- }
- return null;
- }
-
- /**
- * Gets drug list from xml database.
- *
- * @return drug list from the database
- * @throws DrugSearchException
- * thrown when there is problem with finding drug
- */
- public List<Drug> getDrugList() throws DrugSearchException {
- if (drugList != null) {
- return drugList;
- }
- drugList = new ArrayList<Drug>();
- /*************** INIT ******************************/
- try {
- XMLInputFactory f = XMLInputFactory.newInstance();
- FileInputStream temp = new FileInputStream(dbFile);
- XMLStreamReader reader = f.createXMLStreamReader(temp);
-
- Drug drug = null;
- String tagContent = null;
- boolean relevant = true;
- String tagName = null;
- /*************** END OF INIT ***********************/
- while (reader.hasNext()) {
- int event = reader.next();
-
- if (event == XMLStreamConstants.START_ELEMENT) {
- if (relevant) {
- if (DRUG.equals(reader.getLocalName())) {
- drug = new Drug();
- } else {
- relevant = false;
- tagName = reader.getLocalName();
- if (tagNameRelated(tagName)) {
- relevant = true;
- }
- if (TARGETS.equals(tagName)) {
- relevant = true;
- addTargetToDrug(reader, drug);
- }
- }
- }
- } else if (event == XMLStreamConstants.CHARACTERS) {
- tagContent = reader.getText().trim();
- } else if (event == XMLStreamConstants.END_ELEMENT) {
- if (reader.getLocalName().equals(DID)) {
- if (relevant) {
- MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.DRUGBANK, tagContent);
- drug.addSource(md);
- }
- } else if (reader.getLocalName().equals(NAME)) {
- if (relevant) {
- drug.setName(tagContent);
- }
- } else if (reader.getLocalName().equals(DES)) {
- if (relevant && (!"".equals(tagContent.trim()))) {
- drug.setDescription(tagContent);
- }
- } else if (reader.getLocalName().equals(DRUG)) {
- if (relevant) {
- drugList.add(drug);
- }
- } else if (reader.getLocalName().equals(SY)) {
- if (relevant) {
- drug.addSynonym(tagContent);
- }
- } else if (!relevant && tagName.equals(reader.getLocalName())) {
- relevant = true;
- }
- }
- }
-
- } catch (XMLStreamException | FileNotFoundException e) {
- throw new DrugSearchException("Problem with processing input file", e);
- }
- return drugList;
- }
+package lcsb.mapviewer.annotation.services;
+
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamConstants;
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.XMLStreamReader;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.annotation.data.Drug;
+import lcsb.mapviewer.annotation.data.Target;
+import lcsb.mapviewer.annotation.data.TargetType;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
+
+/**
+ * Class used for parsing and accessing data from xml drugbank database. Parser
+ * was developed by Janek. I tried to comment it as best as I could, but...
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class DrugbankXMLParser {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(DrugbankXMLParser.class);
+
+ /**
+ * ???
+ */
+ private static final int RELATED_INFORMATION_TAG = 3;
+
+ /**
+ * Node identifing drug.
+ */
+ static final String DRUG = "drug";
+
+ /**
+ * Node identifing drug identifier.
+ */
+ static final String DID = "drugbank-id";
+
+ /**
+ * Node identifing drug name.
+ */
+ static final String NAME = "name";
+
+ /**
+ * Node identifing drug description.
+ */
+ static final String DES = "description";
+
+ /**
+ * Node identifing single synonym.
+ */
+ static final String SY = "synonym";
+
+ /**
+ * Node identifing list of synonym.
+ */
+ static final String SYS = "synonyms";
+
+ /**
+ * Node identifing single target.
+ */
+ static final String TAR = "target";
+
+ /**
+ * Node identifing list of targets.
+ */
+ static final String TARGETS = "targets";
+
+ /**
+ * File with the drugbank xml file.
+ */
+ private String dbFile = null;
+
+ /**
+ * Object used to access information about organism taxonomy.
+ */
+ private TaxonomyBackend taxonomyBackend;
+
+ /**
+ * List of drugs found in the xml file.
+ */
+ private List<Drug> drugList = null;
+
+ /**
+ * Default constructor.
+ *
+ * @param file
+ * file where data is stored
+ * @param backend
+ * {@link #taxonomyBackend}
+ */
+ public DrugbankXMLParser(String file, TaxonomyBackend backend) {
+ this.dbFile = file;
+ this.taxonomyBackend = backend;
+ }
+
+ /**
+ * Transforms string representing pubmed identifiers into {@link MiriamData}
+ * objects and set them to {@link Target}.
+ *
+ * @param target
+ * where the data should be put
+ * @param referencesString
+ * string with pubmed identifiers
+ */
+ void getPubmedFromRef(Target target, String referencesString) {
+ int position = 0;
+ int length = "/pubmed/".length();
+ while ((position = referencesString.indexOf("/pubmed/", position)) > 0) {
+ position += length;
+ StringBuilder tmp = new StringBuilder("");
+ while (position < referencesString.length() && referencesString.charAt(position) >= '0' && referencesString.charAt(position) <= '9') {
+ tmp.append(referencesString.charAt(position));
+ position++;
+ }
+ target.addReference(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, tmp.toString()));
+ }
+ }
+
+ /**
+ * Adds gene identifiers to the target.
+ *
+ * @param reader
+ * xml reader used for parsing xml
+ * @param target
+ * where the data should be added
+ * @throws XMLStreamException
+ * thrown when there is a problem with xml
+ */
+ public void getGeneCardId(XMLStreamReader reader, Target target) throws XMLStreamException {
+ boolean relevant = false;
+ int event;
+ while (true) {
+ event = reader.next();
+ if (event == XMLStreamConstants.CHARACTERS) {
+ if (reader.getText().trim().equals("GeneCards")) {
+ relevant = true;
+ } else if (relevant && !reader.getText().trim().equals("")) {
+ String identifier = reader.getText().trim();
+ target.addGene(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.HGNC_SYMBOL, identifier));
+ relevant = false;
+ }
+ } else if (event == XMLStreamConstants.END_ELEMENT) {
+ if (reader.getLocalName().equals("external-identifiers")) {
+ break;
+ }
+ }
+ }
+ }
+
+ /**
+ * This function is magic...
+ *
+ * @param localName
+ * ???
+ * @param tagContent
+ * ???
+ * @param tagName
+ * ???
+ * @param rel
+ * ???
+ * @param target
+ * ???
+ * @param drug
+ * ???
+ * @return ???
+ * @throws DrugSearchException
+ * thrown when there is a problem with data coming from external
+ * databases
+ */
+ public int targetEndElement(String localName, String tagContent, String tagName, Boolean rel, Target target, Drug drug) throws DrugSearchException {
+ if (localName.equals("id")) {
+ if (rel) {
+ MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.DRUGBANK_TARGET_V4, tagContent);
+ target.setSource(md);
+ return 0;
+ }
+ } else if (localName.equals("name")) {
+ if (rel) {
+ target.setName(tagContent);
+ return 0;
+ }
+ } else if (localName.equals("organism")) {
+ if (rel) {
+ try {
+ target.setOrganism(taxonomyBackend.getByName(tagContent));
+ } catch (TaxonomySearchException e) {
+ throw new DrugSearchException(e);
+ }
+ return 0;
+ }
+
+ } else if (localName.equals("references")) {
+ if (rel) {
+ return 1;
+ }
+ } else if (localName.equals(TAR)) {
+ if (rel) {
+ drug.addTarget(target);
+ return 0;
+ }
+
+ } else if (localName.equals(TARGETS)) {
+ return 2;
+ } else if (localName.equals(tagName)) {
+ return RELATED_INFORMATION_TAG;
+ }
+ return 0;
+ }
+
+ /**
+ * Adds target to a drug.
+ *
+ * @param reader
+ * xml reader used for parsing xml
+ * @param drug
+ * where target should be added
+ * @throws XMLStreamException
+ * thrown when there is a problem with xml
+ * @throws DrugSearchException
+ * thrown when there is a problem with data coming from external
+ * databases
+ */
+ public void addTargetToDrug(XMLStreamReader reader, Drug drug) throws XMLStreamException, DrugSearchException {
+ boolean relatedInformation = true;
+ String tagName = null;
+ String tagContent = null;
+ Target target = null;
+ boolean readingReferences = false;
+ while (true) {
+ int event = reader.next();
+
+ if (event == XMLStreamConstants.START_ELEMENT) {
+ if (relatedInformation) {
+ if (TAR.equals(reader.getLocalName())) {
+ target = new Target();
+ target.setType(TargetType.SINGLE_PROTEIN);
+ } else {
+ relatedInformation = false;
+ tagName = reader.getLocalName();
+ if ("id".equals(tagName) || "name".equals(tagName) || "organism".equals(tagName)) {
+ relatedInformation = true;
+ }
+ if ("references".equals(tagName)) {
+ relatedInformation = true;
+ readingReferences = true;
+ }
+ if ("components".equals(tagName)) {
+ relatedInformation = true;
+ getGeneCardId(reader, target);
+ }
+ }
+ }
+ }
+ if (event == XMLStreamConstants.CHARACTERS) {
+ tagContent = reader.getText().trim();
+ if (readingReferences) {
+ getPubmedFromRef(target, tagContent);
+ }
+ }
+
+ if (event == XMLStreamConstants.END_ELEMENT) {
+ int what = targetEndElement(reader.getLocalName(), tagContent, tagName, relatedInformation, target, drug);
+ if (what == 1) {
+ readingReferences = false;
+ } else if (what == 2) {
+ break;
+ } else if (what == RELATED_INFORMATION_TAG) {
+ relatedInformation = true;
+ }
+ }
+ }
+
+ }
+
+ /**
+ * Checks if tag is important for us or not.
+ *
+ * @param tagName
+ * name of the tag
+ * @return true if tag is relevant, <code>false</code> otherwise
+ */
+ public Boolean tagNameRelated(String tagName) {
+ if ("drugs".equals(tagName) || DID.equals(tagName) || NAME.equals(tagName) || DES.equals(tagName) || DES.equals(tagName) || SY.equals(tagName)
+ || SYS.equals(tagName)) {
+ return true;
+ }
+ return false;
+
+ }
+
+ /**
+ * Gets drug from xml database.
+ *
+ * @param drugName
+ * name of the drug
+ * @return drug from the database
+ * @throws DrugSearchException
+ * thrown when there is a problem with finding drug
+ */
+ public Drug findDrug(String drugName) throws DrugSearchException {
+ for (Drug drug : getDrugList()) {
+ if (drug.getName().equalsIgnoreCase(drugName)) {
+ return drug;
+ }
+ for (String string : drug.getSynonyms()) {
+ if (string.equalsIgnoreCase(drugName)) {
+ return drug;
+ }
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Gets drug list from xml database.
+ *
+ * @return drug list from the database
+ * @throws DrugSearchException
+ * thrown when there is problem with finding drug
+ */
+ public List<Drug> getDrugList() throws DrugSearchException {
+ if (drugList != null) {
+ return drugList;
+ }
+ drugList = new ArrayList<Drug>();
+ /*************** INIT ******************************/
+ try {
+ XMLInputFactory f = XMLInputFactory.newInstance();
+ FileInputStream temp = new FileInputStream(dbFile);
+ XMLStreamReader reader = f.createXMLStreamReader(temp);
+
+ Drug drug = null;
+ String tagContent = null;
+ boolean relevant = true;
+ String tagName = null;
+ /*************** END OF INIT ***********************/
+ while (reader.hasNext()) {
+ int event = reader.next();
+
+ if (event == XMLStreamConstants.START_ELEMENT) {
+ if (relevant) {
+ if (DRUG.equals(reader.getLocalName())) {
+ drug = new Drug();
+ } else {
+ relevant = false;
+ tagName = reader.getLocalName();
+ if (tagNameRelated(tagName)) {
+ relevant = true;
+ }
+ if (TARGETS.equals(tagName)) {
+ relevant = true;
+ addTargetToDrug(reader, drug);
+ }
+ }
+ }
+ } else if (event == XMLStreamConstants.CHARACTERS) {
+ tagContent = reader.getText().trim();
+ } else if (event == XMLStreamConstants.END_ELEMENT) {
+ if (reader.getLocalName().equals(DID)) {
+ if (relevant) {
+ MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.DRUGBANK, tagContent);
+ drug.addSource(md);
+ }
+ } else if (reader.getLocalName().equals(NAME)) {
+ if (relevant) {
+ drug.setName(tagContent);
+ }
+ } else if (reader.getLocalName().equals(DES)) {
+ if (relevant && (!"".equals(tagContent.trim()))) {
+ drug.setDescription(tagContent);
+ }
+ } else if (reader.getLocalName().equals(DRUG)) {
+ if (relevant) {
+ drugList.add(drug);
+ }
+ } else if (reader.getLocalName().equals(SY)) {
+ if (relevant) {
+ drug.addSynonym(tagContent);
+ }
+ } else if (!relevant && tagName.equals(reader.getLocalName())) {
+ relevant = true;
+ }
+ }
+ }
+
+ } catch (XMLStreamException | FileNotFoundException e) {
+ throw new DrugSearchException("Problem with processing input file", e);
+ }
+ return drugList;
+ }
}
\ No newline at end of file
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ExternalServiceStatus.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ExternalServiceStatus.java
index 15cf7a96d6..dd45fbfd58 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ExternalServiceStatus.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ExternalServiceStatus.java
@@ -1,91 +1,91 @@
-package lcsb.mapviewer.annotation.services;
-
-/**
- * This class represents status of the service that access data from external
- * resources (database, webpage, etc.).
- *
- * @author Piotr Gawron
- *
- */
-public class ExternalServiceStatus {
-
- /**
- * Name of the service.
- */
- private String name;
-
- /**
- * Status of the external resource.
- */
- private ExternalServiceStatusType status;
-
- /**
- * Webpage associated with external resource.
- */
- private String page;
-
- /**
- * Default constructor.
- *
- * @param name
- * name of the service
- * @param page
- * webpage associated with the external resource
- */
- public ExternalServiceStatus(String name, String page) {
- this.setName(name);
- this.setPage(page);
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return the status
- * @see #status
- */
- public ExternalServiceStatusType getStatus() {
- return status;
- }
-
- /**
- * @param status
- * the status to set
- * @see #status
- */
- public void setStatus(ExternalServiceStatusType status) {
- this.status = status;
- }
-
- /**
- * @return the page
- * @see #page
- */
- public String getPage() {
- return page;
- }
-
- /**
- * @param page
- * the page to set
- * @see #page
- */
- public void setPage(String page) {
- this.page = page;
- }
-
-}
+package lcsb.mapviewer.annotation.services;
+
+/**
+ * This class represents status of the service that access data from external
+ * resources (database, webpage, etc.).
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ExternalServiceStatus {
+
+ /**
+ * Name of the service.
+ */
+ private String name;
+
+ /**
+ * Status of the external resource.
+ */
+ private ExternalServiceStatusType status;
+
+ /**
+ * Webpage associated with external resource.
+ */
+ private String page;
+
+ /**
+ * Default constructor.
+ *
+ * @param name
+ * name of the service
+ * @param page
+ * webpage associated with the external resource
+ */
+ public ExternalServiceStatus(String name, String page) {
+ this.setName(name);
+ this.setPage(page);
+ }
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * @return the status
+ * @see #status
+ */
+ public ExternalServiceStatusType getStatus() {
+ return status;
+ }
+
+ /**
+ * @param status
+ * the status to set
+ * @see #status
+ */
+ public void setStatus(ExternalServiceStatusType status) {
+ this.status = status;
+ }
+
+ /**
+ * @return the page
+ * @see #page
+ */
+ public String getPage() {
+ return page;
+ }
+
+ /**
+ * @param page
+ * the page to set
+ * @see #page
+ */
+ public void setPage(String page) {
+ this.page = page;
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ExternalServiceStatusType.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ExternalServiceStatusType.java
index d22f58e0e3..2e3092188b 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ExternalServiceStatusType.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ExternalServiceStatusType.java
@@ -1,65 +1,65 @@
-package lcsb.mapviewer.annotation.services;
-
-/**
- * Status of the external service.
- *
- * @author Piotr Gawron
- *
- */
-public enum ExternalServiceStatusType {
-
- /**
- * Service is ok and access method is ok.
- */
- OK("Ok", 0),
-
- /**
- * Service is down (we don't know anything about access method).
- */
- DOWN("Not available", 1),
-
- /**
- * Service is up, but access method changed.
- */
- CHANGED("Specification changed", 2);
-
- /**
- * Common name of the status.
- */
- private String commonName;
-
- /**
- * Severity level of the status (the higher the worse).
- */
- private int level;
-
- /**
- * Default constructor.
- *
- * @param commonName
- * name of the status
- * @param level
- * severity level of the status
- */
- ExternalServiceStatusType(String commonName, int level) {
- this.commonName = commonName;
- this.level = level;
- }
-
- /**
- * @return the commonName
- * @see #commonName
- */
- public String getCommonName() {
- return commonName;
- }
-
- /**
- * @return the level
- * @see #level
- */
- public int getLevel() {
- return level;
- }
-
-}
+package lcsb.mapviewer.annotation.services;
+
+/**
+ * Status of the external service.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum ExternalServiceStatusType {
+
+ /**
+ * Service is ok and access method is ok.
+ */
+ OK("Ok", 0),
+
+ /**
+ * Service is down (we don't know anything about access method).
+ */
+ DOWN("Not available", 1),
+
+ /**
+ * Service is up, but access method changed.
+ */
+ CHANGED("Specification changed", 2);
+
+ /**
+ * Common name of the status.
+ */
+ private String commonName;
+
+ /**
+ * Severity level of the status (the higher the worse).
+ */
+ private int level;
+
+ /**
+ * Default constructor.
+ *
+ * @param commonName
+ * name of the status
+ * @param level
+ * severity level of the status
+ */
+ ExternalServiceStatusType(String commonName, int level) {
+ this.commonName = commonName;
+ this.level = level;
+ }
+
+ /**
+ * @return the commonName
+ * @see #commonName
+ */
+ public String getCommonName() {
+ return commonName;
+ }
+
+ /**
+ * @return the level
+ * @see #level
+ */
+ public int getLevel() {
+ return level;
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/IExternalService.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/IExternalService.java
index 373b0bb7fd..a6d859ef72 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/IExternalService.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/IExternalService.java
@@ -1,30 +1,30 @@
-package lcsb.mapviewer.annotation.services;
-
-
-/**
- * Interface that should be implemented by all classes that access external
- * resources.
- *
- * @author Piotr Gawron
- *
- */
-public interface IExternalService {
- /**
- * Returns status of the external resource.
- *
- * @return status of the external resource. Three different values are
- * possible:
- * <ul>
- * <li>
- * {@link lcsb.mapviewer.annotation.services.ExternalServiceStatus.Status#OK
- * OK}</li>
- * <li>
- * {@link lcsb.mapviewer.annotation.services.ExternalServiceStatus.Status#DOWN
- * DOWN}</li>
- * <li>
- * {@link lcsb.mapviewer.annotation.services.ExternalServiceStatus.Status#CHANGED
- * CHANGED}</li>
- * </ul>
- */
- ExternalServiceStatus getServiceStatus();
-}
+package lcsb.mapviewer.annotation.services;
+
+
+/**
+ * Interface that should be implemented by all classes that access external
+ * resources.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface IExternalService {
+ /**
+ * Returns status of the external resource.
+ *
+ * @return status of the external resource. Three different values are
+ * possible:
+ * <ul>
+ * <li>
+ * {@link lcsb.mapviewer.annotation.services.ExternalServiceStatus.Status#OK
+ * OK}</li>
+ * <li>
+ * {@link lcsb.mapviewer.annotation.services.ExternalServiceStatus.Status#DOWN
+ * DOWN}</li>
+ * <li>
+ * {@link lcsb.mapviewer.annotation.services.ExternalServiceStatus.Status#CHANGED
+ * CHANGED}</li>
+ * </ul>
+ */
+ ExternalServiceStatus getServiceStatus();
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MeSHParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MeSHParser.java
index 92d1eca9d8..84d2a47962 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MeSHParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MeSHParser.java
@@ -1,330 +1,330 @@
-package lcsb.mapviewer.annotation.services;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.apache.commons.lang3.SerializationException;
-import org.apache.http.HttpStatus;
-import org.apache.log4j.Logger;
-import org.w3c.dom.Node;
-
-import com.google.gson.Gson;
-import com.google.gson.internal.StringMap;
-
-import lcsb.mapviewer.annotation.cache.CachableInterface;
-import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
-import lcsb.mapviewer.annotation.cache.WebPageDownloader;
-import lcsb.mapviewer.annotation.cache.XmlSerializer;
-import lcsb.mapviewer.annotation.data.MeSH;
-import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-
-/**
- * Class used for accessing and parsing data from MeSH database.
- *
- * @author Ayan Rota
- *
- */
-public class MeSHParser extends CachableInterface implements IExternalService {
-
- /**
- * Url used for searching drugs by name.
- */
- private static final String URL_MESH_DATABASE = "https://meshb.nlm.nih.gov/api/record/ui/";
-
- /**
- * Url used for searching mesh terms by synonym.
- */
- private static final String URL_SEARCH_BY_SYNONYM = "https://meshb.nlm.nih.gov/api/search/record?searchInField=termDescriptor&sort=&size=20&searchType=exactMatch&searchMethod=FullWord&q=";
-
- /**
- * Prefix used in the DB to identify the cache entry.
- */
- static final String MESH_PREFIX = "mesh:";
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(MeSHParser.class);
-
- /**
- * Object that allows to serialize {@link MeSH} elements into xml string and
- * deserialize xml into {@link MeSH} objects.
- */
- private XmlSerializer<MeSH> meshSerializer;
-
- /**
- * Default constructor.
- */
- public MeSHParser() {
- super(MeSHParser.class);
- meshSerializer = new XmlSerializer<>(MeSH.class);
- }
-
- @Override
- public String refreshCacheQuery(Object query) throws SourceNotAvailable {
- String result = null;
- try {
- if (query instanceof String) {
- String identifier = (String) query;
- if (identifier.startsWith("http")) {
- result = getWebPageContent(identifier);
- } else if (identifier.startsWith(MESH_PREFIX)) {
- String[] ids = identifier.split("\\:");
- if (ids.length == 2) {
- MiriamData meshID = new MiriamData(MiriamType.MESH_2012, ids[1]);
- MeSH mesh = getMeSHByIdFromDB(meshID);
- result = meshSerializer.objectToString(mesh);
- } else {
- throw new InvalidArgumentException("Problematic query: \"" + query + "\"");
- }
- } else {
- throw new InvalidArgumentException("Don't know what to do with string \"" + query + "\"");
- }
- } else {
- throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
- }
- } catch (IOException e) {
- throw new SourceNotAvailable("Problem with accessing Mesh database", e);
- }
- return result;
- }
-
- /**
- * @param meshID
- * miriam type id.
- * @return returns object.
- * @throws AnnotatorException
- * thrown when there is a problem with accessing mesh database
- */
- public MeSH getMeSH(MiriamData meshID) throws AnnotatorException {
- if (meshID == null || meshID.getResource() == null) {
- throw new InvalidArgumentException("mesh cannot be null ");
- }
-
- MeSH mesh = null;
- // look for Mesh in the cache
- String id = getIdentifier(meshID);
- Node meshNode = super.getCacheNode(id);
- if (meshNode != null && meshNode.hasChildNodes()) {
- try {
- mesh = meshSerializer.xmlToObject(meshNode);
- } catch (SerializationException e) {
- logger.warn("Problem with processing cached info about mesh: " + meshID);
- mesh = null;
- }
- }
- if (mesh == null) {
- try {
- mesh = getMeSHByIdFromDB(meshID);
- } catch (IOException e) {
- throw new AnnotatorException("Problem with accessing MeSH database", e);
- }
- }
- if (mesh != null) {
- super.setCacheValue(id, this.meshSerializer.objectToString(mesh));
- }
-
- return mesh;
- }
-
- /**
- * @param meshID
- * id as miriam data.
- * @return return the object.
- */
- public String getIdentifier(MiriamData meshID) {
- return MESH_PREFIX + meshID.getResource();
- }
-
- /**
- * @param meshID
- * mesh id as Miriam data.
- * @return return as mesh object.
- * @throws IOException
- * thrown when there is problem with accessing web page
- * @throws AnnotatorException
- * thrown when there is a problem with accessing mesh db
- */
- private MeSH getMeSHByIdFromDB(MiriamData meshID) throws IOException {
- try {
- MeSH result = new MeSH();
- String page = getWebPageContent(URL_MESH_DATABASE + meshID.getResource());
-
- Gson gson = new Gson();
-
- Map<?, ?> gsonObject = new HashMap<String, Object>();
- gsonObject = (Map<?, ?>) gson.fromJson(page, gsonObject.getClass());
- Set<String> synonyms = getSynonyms(gsonObject);
- String name = getName(gsonObject);
- String description = getDescription(gsonObject);
- String id = getId(gsonObject);
- synonyms.remove(name);
- result.addSynonyms(synonyms);
- result.setName(name);
- result.setDescription(description);
- result.setMeSHId(id);
-
- return result;
- } catch (WrongResponseCodeIOException e) {
- if (e.getResponseCode() == HttpStatus.SC_NOT_FOUND) {
- return null;
- } else {
- throw e;
- }
- }
- }
-
- /**
- * Extracts name from gson object.
- *
- * @param gsonObject
- * gson to process
- * @return name of {@link MeSH} entry
- */
- private String getName(Map<?, ?> gsonObject) {
- StringMap<?> descriptorTag = (StringMap<?>) gsonObject.get("DescriptorName");
- if (descriptorTag == null) {
- descriptorTag = (StringMap<?>) gsonObject.get("SupplementalRecordName");
- }
- return (String) (((StringMap<?>) descriptorTag.get("String")).get("t"));
- }
-
- /**
- * Extracts Mesh id name from gson object.
- *
- * @param gsonObject
- * gson to process
- * @return id of {@link MeSH} entry
- */
- private String getId(Map<?, ?> gsonObject) {
- StringMap<?> descriptorTag = (StringMap<?>) gsonObject.get("DescriptorUI");
- if (descriptorTag == null) {
- descriptorTag = (StringMap<?>) gsonObject.get("SupplementalRecordUI");
- }
- return (String) descriptorTag.get("t");
- }
-
- /**
- * Extracts Mesh term description from gson object.
- *
- * @param gsonObject
- * gson to process
- * @return description of {@link MeSH} entry
- */
- private String getDescription(Map<?, ?> gsonObject) {
- StringMap<?> concepts = (StringMap<?>) gsonObject.get("_generated");
- return (String) concepts.get("PreferredConceptScopeNote");
- }
-
- /**
- * Extracts list of synonyms from gson object.
- *
- * @param gsonObject
- * gson to process
- * @return synonyms of {@link MeSH} entry
- */
- private Set<String> getSynonyms(Map<?, ?> gsonObject) {
- Set<String> synonyms = new HashSet<>();
- StringMap<?> concepts = (StringMap<?>) gsonObject.get("ConceptList");
- ArrayList<?> conceptList = (ArrayList<?>) concepts.get("Concept");
- for (Object object : conceptList) {
- StringMap<?> concept = (StringMap<?>) object;
- ArrayList<?> termList = (ArrayList<?>) ((StringMap<?>) concept.get("TermList")).get("Term");
- for (Object object2 : termList) {
- StringMap<?> term = (StringMap<?>) object2;
- StringMap<?> synonym = (StringMap<?>) term.get("String");
- synonyms.add((String) synonym.get("t"));
-
- }
- }
- return synonyms;
- }
-
- @Override
- public ExternalServiceStatus getServiceStatus() {
- GeneralCacheInterface cacheCopy = getCache();
- this.setCache(null);
- ExternalServiceStatus status = new ExternalServiceStatus(MiriamType.MESH_2012.getCommonName(),
- MiriamType.MESH_2012.getDbHomepage());
- try {
- status.setStatus(ExternalServiceStatusType.OK);
- MiriamData meshId = new MiriamData(MiriamType.MESH_2012, "D010300");
- MeSH mesh = getMeSH(meshId);
- if (mesh == null || !meshId.getResource().equals(mesh.getMeSHId())) {
- status.setStatus(ExternalServiceStatusType.CHANGED);
- }
- } catch (Exception e) {
- logger.error(e, e);
- status.setStatus(ExternalServiceStatusType.DOWN);
- }
- this.setCache(cacheCopy);
- return status;
- }
-
- /**
- * Checks if the mesh identifier is valid.
- *
- * @param meshId
- * mesh id
- * @return <code>true</code> if it's valid
- * @throws AnnotatorException
- * thrown when there is problem with accessing mesh db
- */
- public boolean isValidMeshId(MiriamData meshId) throws AnnotatorException {
- if (meshId == null) {
- return false;
- }
- return getMeSH(meshId) != null;
- }
-
- @Override
- protected WebPageDownloader getWebPageDownloader() {
- return super.getWebPageDownloader();
- }
-
- @Override
- protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
- super.setWebPageDownloader(webPageDownloader);
- }
-
- public List<MeSH> getMeshBySynonym(String synonym) throws AnnotatorException {
- try {
- List<MeSH> result = new ArrayList<>();
- String page = getWebPageContent(URL_SEARCH_BY_SYNONYM + synonym);
- Gson gson = new Gson();
-
- Map<?, ?> gsonObject = new HashMap<String, Object>();
- gsonObject = (Map<?, ?>) gson.fromJson(page, gsonObject.getClass());
- Set<MiriamData> synonyms = getIdsBySynonymQuery(gsonObject);
- for (MiriamData meshID : synonyms) {
- result.add(getMeSH(meshID));
- }
-
- return result;
- } catch (IOException e) {
- throw new AnnotatorException(e);
- }
- }
-
- private Set<MiriamData> getIdsBySynonymQuery(Map<?, ?> gsonObject) {
- Set<MiriamData> result = new HashSet<>();
- StringMap<?> hits = (StringMap<?>) gsonObject.get("hits");
- ArrayList<?> hitsList = (ArrayList<?>) hits.get("hits");
- for (Object object : hitsList) {
- StringMap<?> hit = (StringMap<?>) object;
- String id = (String) hit.get("_id");
- result.add(new MiriamData(MiriamType.MESH_2012, id));
- }
- return result;
- }
-
-}
+package lcsb.mapviewer.annotation.services;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.commons.lang3.SerializationException;
+import org.apache.http.HttpStatus;
+import org.apache.log4j.Logger;
+import org.w3c.dom.Node;
+
+import com.google.gson.Gson;
+import com.google.gson.internal.StringMap;
+
+import lcsb.mapviewer.annotation.cache.CachableInterface;
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.WebPageDownloader;
+import lcsb.mapviewer.annotation.cache.XmlSerializer;
+import lcsb.mapviewer.annotation.data.MeSH;
+import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+
+/**
+ * Class used for accessing and parsing data from MeSH database.
+ *
+ * @author Ayan Rota
+ *
+ */
+public class MeSHParser extends CachableInterface implements IExternalService {
+
+ /**
+ * Url used for searching drugs by name.
+ */
+ private static final String URL_MESH_DATABASE = "https://meshb.nlm.nih.gov/api/record/ui/";
+
+ /**
+ * Url used for searching mesh terms by synonym.
+ */
+ private static final String URL_SEARCH_BY_SYNONYM = "https://meshb.nlm.nih.gov/api/search/record?searchInField=termDescriptor&sort=&size=20&searchType=exactMatch&searchMethod=FullWord&q=";
+
+ /**
+ * Prefix used in the DB to identify the cache entry.
+ */
+ static final String MESH_PREFIX = "mesh:";
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(MeSHParser.class);
+
+ /**
+ * Object that allows to serialize {@link MeSH} elements into xml string and
+ * deserialize xml into {@link MeSH} objects.
+ */
+ private XmlSerializer<MeSH> meshSerializer;
+
+ /**
+ * Default constructor.
+ */
+ public MeSHParser() {
+ super(MeSHParser.class);
+ meshSerializer = new XmlSerializer<>(MeSH.class);
+ }
+
+ @Override
+ public String refreshCacheQuery(Object query) throws SourceNotAvailable {
+ String result = null;
+ try {
+ if (query instanceof String) {
+ String identifier = (String) query;
+ if (identifier.startsWith("http")) {
+ result = getWebPageContent(identifier);
+ } else if (identifier.startsWith(MESH_PREFIX)) {
+ String[] ids = identifier.split("\\:");
+ if (ids.length == 2) {
+ MiriamData meshID = new MiriamData(MiriamType.MESH_2012, ids[1]);
+ MeSH mesh = getMeSHByIdFromDB(meshID);
+ result = meshSerializer.objectToString(mesh);
+ } else {
+ throw new InvalidArgumentException("Problematic query: \"" + query + "\"");
+ }
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with string \"" + query + "\"");
+ }
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
+ }
+ } catch (IOException e) {
+ throw new SourceNotAvailable("Problem with accessing Mesh database", e);
+ }
+ return result;
+ }
+
+ /**
+ * @param meshID
+ * miriam type id.
+ * @return returns object.
+ * @throws AnnotatorException
+ * thrown when there is a problem with accessing mesh database
+ */
+ public MeSH getMeSH(MiriamData meshID) throws AnnotatorException {
+ if (meshID == null || meshID.getResource() == null) {
+ throw new InvalidArgumentException("mesh cannot be null ");
+ }
+
+ MeSH mesh = null;
+ // look for Mesh in the cache
+ String id = getIdentifier(meshID);
+ Node meshNode = super.getCacheNode(id);
+ if (meshNode != null && meshNode.hasChildNodes()) {
+ try {
+ mesh = meshSerializer.xmlToObject(meshNode);
+ } catch (SerializationException e) {
+ logger.warn("Problem with processing cached info about mesh: " + meshID);
+ mesh = null;
+ }
+ }
+ if (mesh == null) {
+ try {
+ mesh = getMeSHByIdFromDB(meshID);
+ } catch (IOException e) {
+ throw new AnnotatorException("Problem with accessing MeSH database", e);
+ }
+ }
+ if (mesh != null) {
+ super.setCacheValue(id, this.meshSerializer.objectToString(mesh));
+ }
+
+ return mesh;
+ }
+
+ /**
+ * @param meshID
+ * id as miriam data.
+ * @return return the object.
+ */
+ public String getIdentifier(MiriamData meshID) {
+ return MESH_PREFIX + meshID.getResource();
+ }
+
+ /**
+ * @param meshID
+ * mesh id as Miriam data.
+ * @return return as mesh object.
+ * @throws IOException
+ * thrown when there is problem with accessing web page
+ * @throws AnnotatorException
+ * thrown when there is a problem with accessing mesh db
+ */
+ private MeSH getMeSHByIdFromDB(MiriamData meshID) throws IOException {
+ try {
+ MeSH result = new MeSH();
+ String page = getWebPageContent(URL_MESH_DATABASE + meshID.getResource());
+
+ Gson gson = new Gson();
+
+ Map<?, ?> gsonObject = new HashMap<String, Object>();
+ gsonObject = (Map<?, ?>) gson.fromJson(page, gsonObject.getClass());
+ Set<String> synonyms = getSynonyms(gsonObject);
+ String name = getName(gsonObject);
+ String description = getDescription(gsonObject);
+ String id = getId(gsonObject);
+ synonyms.remove(name);
+ result.addSynonyms(synonyms);
+ result.setName(name);
+ result.setDescription(description);
+ result.setMeSHId(id);
+
+ return result;
+ } catch (WrongResponseCodeIOException e) {
+ if (e.getResponseCode() == HttpStatus.SC_NOT_FOUND) {
+ return null;
+ } else {
+ throw e;
+ }
+ }
+ }
+
+ /**
+ * Extracts name from gson object.
+ *
+ * @param gsonObject
+ * gson to process
+ * @return name of {@link MeSH} entry
+ */
+ private String getName(Map<?, ?> gsonObject) {
+ StringMap<?> descriptorTag = (StringMap<?>) gsonObject.get("DescriptorName");
+ if (descriptorTag == null) {
+ descriptorTag = (StringMap<?>) gsonObject.get("SupplementalRecordName");
+ }
+ return (String) (((StringMap<?>) descriptorTag.get("String")).get("t"));
+ }
+
+ /**
+ * Extracts Mesh id name from gson object.
+ *
+ * @param gsonObject
+ * gson to process
+ * @return id of {@link MeSH} entry
+ */
+ private String getId(Map<?, ?> gsonObject) {
+ StringMap<?> descriptorTag = (StringMap<?>) gsonObject.get("DescriptorUI");
+ if (descriptorTag == null) {
+ descriptorTag = (StringMap<?>) gsonObject.get("SupplementalRecordUI");
+ }
+ return (String) descriptorTag.get("t");
+ }
+
+ /**
+ * Extracts Mesh term description from gson object.
+ *
+ * @param gsonObject
+ * gson to process
+ * @return description of {@link MeSH} entry
+ */
+ private String getDescription(Map<?, ?> gsonObject) {
+ StringMap<?> concepts = (StringMap<?>) gsonObject.get("_generated");
+ return (String) concepts.get("PreferredConceptScopeNote");
+ }
+
+ /**
+ * Extracts list of synonyms from gson object.
+ *
+ * @param gsonObject
+ * gson to process
+ * @return synonyms of {@link MeSH} entry
+ */
+ private Set<String> getSynonyms(Map<?, ?> gsonObject) {
+ Set<String> synonyms = new HashSet<>();
+ StringMap<?> concepts = (StringMap<?>) gsonObject.get("ConceptList");
+ ArrayList<?> conceptList = (ArrayList<?>) concepts.get("Concept");
+ for (Object object : conceptList) {
+ StringMap<?> concept = (StringMap<?>) object;
+ ArrayList<?> termList = (ArrayList<?>) ((StringMap<?>) concept.get("TermList")).get("Term");
+ for (Object object2 : termList) {
+ StringMap<?> term = (StringMap<?>) object2;
+ StringMap<?> synonym = (StringMap<?>) term.get("String");
+ synonyms.add((String) synonym.get("t"));
+
+ }
+ }
+ return synonyms;
+ }
+
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ GeneralCacheInterface cacheCopy = getCache();
+ this.setCache(null);
+ ExternalServiceStatus status = new ExternalServiceStatus(MiriamType.MESH_2012.getCommonName(),
+ MiriamType.MESH_2012.getDbHomepage());
+ try {
+ status.setStatus(ExternalServiceStatusType.OK);
+ MiriamData meshId = new MiriamData(MiriamType.MESH_2012, "D010300");
+ MeSH mesh = getMeSH(meshId);
+ if (mesh == null || !meshId.getResource().equals(mesh.getMeSHId())) {
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ }
+ } catch (Exception e) {
+ logger.error(e, e);
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ }
+ this.setCache(cacheCopy);
+ return status;
+ }
+
+ /**
+ * Checks if the mesh identifier is valid.
+ *
+ * @param meshId
+ * mesh id
+ * @return <code>true</code> if it's valid
+ * @throws AnnotatorException
+ * thrown when there is problem with accessing mesh db
+ */
+ public boolean isValidMeshId(MiriamData meshId) throws AnnotatorException {
+ if (meshId == null) {
+ return false;
+ }
+ return getMeSH(meshId) != null;
+ }
+
+ @Override
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
+ }
+
+ @Override
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
+ }
+
+ public List<MeSH> getMeshBySynonym(String synonym) throws AnnotatorException {
+ try {
+ List<MeSH> result = new ArrayList<>();
+ String page = getWebPageContent(URL_SEARCH_BY_SYNONYM + synonym);
+ Gson gson = new Gson();
+
+ Map<?, ?> gsonObject = new HashMap<String, Object>();
+ gsonObject = (Map<?, ?>) gson.fromJson(page, gsonObject.getClass());
+ Set<MiriamData> synonyms = getIdsBySynonymQuery(gsonObject);
+ for (MiriamData meshID : synonyms) {
+ result.add(getMeSH(meshID));
+ }
+
+ return result;
+ } catch (IOException e) {
+ throw new AnnotatorException(e);
+ }
+ }
+
+ private Set<MiriamData> getIdsBySynonymQuery(Map<?, ?> gsonObject) {
+ Set<MiriamData> result = new HashSet<>();
+ StringMap<?> hits = (StringMap<?>) gsonObject.get("hits");
+ ArrayList<?> hitsList = (ArrayList<?>) hits.get("hits");
+ for (Object object : hitsList) {
+ StringMap<?> hit = (StringMap<?>) object;
+ String id = (String) hit.get("_id");
+ result.add(new MiriamData(MiriamType.MESH_2012, id));
+ }
+ return result;
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiRNAParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiRNAParser.java
index c8e1642248..14f4b72d69 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiRNAParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiRNAParser.java
@@ -1,684 +1,684 @@
-package lcsb.mapviewer.annotation.services;
-
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.URISyntaxException;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
-import org.apache.poi.poifs.filesystem.NPOIFSFileSystem;
-import org.apache.poi.ss.usermodel.Cell;
-import org.apache.poi.ss.usermodel.Row;
-import org.apache.poi.ss.usermodel.Sheet;
-import org.apache.poi.ss.usermodel.Workbook;
-import org.apache.poi.ss.usermodel.WorkbookFactory;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.w3c.dom.Node;
-
-import lcsb.mapviewer.annotation.cache.BigFileCache;
-import lcsb.mapviewer.annotation.cache.CachableInterface;
-import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
-import lcsb.mapviewer.annotation.cache.XmlSerializer;
-import lcsb.mapviewer.annotation.data.MiRNA;
-import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.annotation.data.TargetType;
-import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
-import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
-import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.persist.dao.ProjectDao;
-
-/**
- * Class used for accessing and parsing data from MiRNA database.
- *
- * @author Ayan Rota
- *
- */
-public class MiRNAParser extends CachableInterface implements IExternalService {
-
- /**
- * Url used for searching mirna by name.
- */
- private static final String URL_SOURCE_DATABASE = "http://mirtarbase.mbc.nctu.edu.tw/cache/download/6.1/miRTarBase_SE_WR.xls";
-
- /**
- * Cached file with static database about miriam (right now we parse it from
- * excel file).
- */
- private ByteArrayOutputStream sourceInputStream;
-
- /**
- * Prefix used in the DB to identify the cache entry.
- */
- protected static final String MI_RNA_PREFIX = "mirBase:";
-
- protected static final String PROJECT_SUGGESTED_QUERY_PREFIX = "PROJECT_MI_RNA_QUERIES:";
-
- /**
- * Prefix used in the DB to identify the cache entry that will have information
- * about mirna that targets specific target.
- */
- static final String MI_RNA_TARGET_PREFIX = "MIRNA_TARGET:";
-
- /**
- * The location of Mirtarbase id column of Mirtarbase database.
- */
- public static final Integer MIR_TAR_BASE_ID_COL = 0;
-
- /**
- * The location of Mirbase name column of Mirbase database.
- */
- public static final Integer MIR_BASE_NAME_COL = 1;
-
- /**
- * The location of species column.
- */
- public static final Integer SPECIES_COL = 5;
-
- /**
- * The location of target gene HGNC ID column.
- */
- public static final Integer GENE_HGNC_ID_COL = 3;
-
- /**
- * The location of target gene ENTREZ ID column.
- */
- public static final Integer GENE_ENTREZ_ID_COL = 4;
-
- /**
- * The location of publication PEDMED ID column.
- */
- public static final Integer INTERACTION_PEDMED_ID_COL = 8;
-
- /**
- * Size of the buffer when copying files.
- */
- private static final int BUFFER_SIZE = 1024;
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(MiRNAParser.class);
-
- /**
- * Class used to access information about organisms taxonomy.
- */
- @Autowired
- private TaxonomyBackend taxonomyBackend;
-
- @Autowired
- private HgncAnnotator hgncAnnotator;
-
- /**
- * Cache used for storing big files.
- */
- @Autowired
- private BigFileCache bigFileCache;
-
- @Autowired
- private ProjectDao projectDao;
-
- /**
- * Object that allows to serialize {@link MiRNA} elements into xml string and
- * deserialize xml into {@link MiRNA} objects.
- */
- private XmlSerializer<MiRNA> miRnaSerializer;
-
- /**
- * The status of the db.
- */
- private ExternalServiceStatus status = new ExternalServiceStatus("mirTarBase",
- MiriamType.MIR_TAR_BASE_MATURE_SEQUENCE.getDbHomepage());
-
- /**
- * Default constructor.
- */
- public MiRNAParser() {
- super(MiRNAParser.class);
- miRnaSerializer = new XmlSerializer<>(MiRNA.class);
- }
-
- @Override
- public Object refreshCacheQuery(Object query) throws SourceNotAvailable {
- try {
- Object result = null;
- if (query instanceof String) {
- String identifier = (String) query;
- if (identifier.startsWith(MI_RNA_PREFIX)) {
- String[] ids = identifier.split("\\:");
- List<String> miRNAIDs = new ArrayList<>();
- miRNAIDs.add(ids[1]);
- List<MiRNA> list = getMiRnasByNameFromDb(miRNAIDs);
- if (!list.isEmpty()) {
- result = miRnaSerializer.objectToString(list.get(0));
- }
- } else if (identifier.startsWith(MI_RNA_TARGET_PREFIX)) {
- String[] tmp = identifier.substring(MI_RNA_TARGET_PREFIX.length()).split(":");
- MiriamData md = new MiriamData();
- md.setDataType(MiriamType.valueOf(tmp[0]));
- md.setResource(tmp[1]);
- getMiRnaListByTarget(md);
- result = super.getCacheValue(identifier);
- } else if (identifier.startsWith(PROJECT_SUGGESTED_QUERY_PREFIX)) {
- String[] tmp = identifier.split("\n");
- Integer id = Integer.valueOf(tmp[1]);
- Project project = projectDao.getById(id);
- if (project == null) {
- throw new SourceNotAvailable("Project with given id doesn't exist: " + id);
- }
- List<String> list = getSuggestedQueryListWithoutCache(project);
- result = StringUtils.join(list, "\n");
- } else {
- result = super.refreshCacheQuery(query);
- }
- } else {
- result = super.refreshCacheQuery(query);
- }
- return result;
- } catch (MiRNASearchException e) {
- throw new SourceNotAvailable(e);
- }
- }
-
- /**
- * @param names
- * list of rna names to be retrieved.
- * @return list of all object retrieved.
- * @throws MiRNASearchException
- * thrown when there is a problem with accessing mirna database
- */
- public List<MiRNA> getMiRnasByNames(Collection<String> names) throws MiRNASearchException {
- List<MiRNA> miRNAs = new ArrayList<>();
- List<String> idsToRemove = new ArrayList<>();
- MiRNA miRNA = null;
-
- for (String name : names) {
- // look for MiRNA in the cache
- Node miRNANode = super.getCacheNode(MI_RNA_PREFIX + name.toLowerCase());
- if (miRNANode != null && miRNANode.hasChildNodes()) {
- miRNA = miRnaSerializer.xmlToObject(miRNANode);
- miRNAs.add(miRNA);
- idsToRemove.add(name);
- }
- }
- List<String> idsToFind = new ArrayList<>();
- idsToFind.addAll(names);
- for (String toRemove : idsToRemove) {
- idsToFind.remove(toRemove);
- }
- // Not in the cache then get it from external database
- if (!idsToFind.isEmpty()) {
- // logger.debug("MiRNAParser.getMiRNA Start:"+new Date());
- List<MiRNA> fromDBList = this.getMiRnasByNameFromDb(idsToFind);
- for (MiRNA mirna : fromDBList) {
- super.setCacheValue(MI_RNA_PREFIX + mirna.getName().toLowerCase(), miRnaSerializer.objectToString(mirna));
- }
- // logger.debug("MiRNAParser.getMiRNA End:"+new Date());
- // Add them to result
- miRNAs.addAll(fromDBList);
-
- }
- return miRNAs;
- }
-
- /**
- * Returns input stream with a file containing Excel database with mirna data.
- * Original source is located at {@link #URL_SOURCE_DATABASE}.
- *
- * @return input stream with a file containing Excel database with mirna data
- * @throws IOException
- * thrown when there is a problem with accessing mirna data file
- */
- private InputStream getSourceInputStream() throws IOException {
- if (this.sourceInputStream == null) {
- this.sourceInputStream = new ByteArrayOutputStream();
-
- if (!bigFileCache.isCached(URL_SOURCE_DATABASE)) {
- try {
- bigFileCache.downloadFile(URL_SOURCE_DATABASE, false, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- });
- } catch (URISyntaxException e) {
- throw new IOException("Problem with downloading file: " + URL_SOURCE_DATABASE, e);
- }
- }
- String filename = bigFileCache.getAbsolutePathForFile(URL_SOURCE_DATABASE);
- byte[] buffer = new byte[BUFFER_SIZE];
- int len;
- InputStream stream = new FileInputStream(new File(filename));
- try {
- while ((len = stream.read(buffer)) > -1) {
- this.sourceInputStream.write(buffer, 0, len);
- }
- } finally {
- stream.close();
- }
- this.sourceInputStream.flush();
- }
- return new ByteArrayInputStream(sourceInputStream.toByteArray());
- }
-
- /**
- * @param originalNames
- * names of miRNAs
- * @return List of MiRNA
- * @throws MiRNASearchException
- * thrown when there is a problem with accessing mirna database
- */
- protected List<MiRNA> getMiRnasByNameFromDb(List<String> originalNames) throws MiRNASearchException {
- List<String> names = new ArrayList<>();
- for (String string : originalNames) {
- names.add(string.toLowerCase());
- }
-
- Map<String, MiRNA> miRNAs = new HashMap<>();
- List<MiRNA> result = new ArrayList<MiRNA>();
- NPOIFSFileSystem fileInputStream = null;
- try {
- fileInputStream = new NPOIFSFileSystem(getSourceInputStream());
- Workbook workbook = WorkbookFactory.create(fileInputStream);
- Sheet sheet = workbook.getSheetAt(0);
- Iterator<Row> rows = sheet.rowIterator();
- // Skip header
- if (rows.hasNext()) {
- rows.next();
- }
- while (rows.hasNext()) {
- Row row = rows.next();
- Cell targetSpeciesCell = row.getCell(SPECIES_COL, Row.RETURN_BLANK_AS_NULL);
- MiriamData organism = null;
- if (targetSpeciesCell != null) {
- targetSpeciesCell.setCellType(Cell.CELL_TYPE_STRING);
- String value = targetSpeciesCell.getStringCellValue();
- organism = taxonomyBackend.getByName(value);
- }
-
- Cell mirBaseNamecell = row.getCell(MIR_BASE_NAME_COL, Row.RETURN_BLANK_AS_NULL);
- if (mirBaseNamecell == null) {
- continue;
- }
-
- mirBaseNamecell.setCellType(Cell.CELL_TYPE_STRING);
- String name = mirBaseNamecell.getStringCellValue();
- if (name == null || name.trim().isEmpty()) {
- continue;
- }
- if (miRNAs.get(name) == null) {
- miRNAs.put(name, new MiRNA(name));
- }
-
- MiriamData mirTaRBaseId = null;
- Cell mirTaRBaseIdCell = row.getCell(MIR_TAR_BASE_ID_COL, Row.RETURN_BLANK_AS_NULL);
- if (mirTaRBaseIdCell == null) {
- continue;
- } else {
- mirTaRBaseIdCell.setCellType(Cell.CELL_TYPE_STRING);
- String value = mirTaRBaseIdCell.getStringCellValue();
- if (value == null || value.trim().isEmpty()) {
- continue;
- } else {
- mirTaRBaseId = new MiriamData(MiriamType.MIR_TAR_BASE_MATURE_SEQUENCE, value.trim());
- }
- }
-
- Cell hgncCell = row.getCell(GENE_HGNC_ID_COL, Row.RETURN_BLANK_AS_NULL);
- if (hgncCell != null) {
- hgncCell.setCellType(Cell.CELL_TYPE_STRING);
- String geneName = hgncCell.getStringCellValue();
- if (geneName != null && !geneName.trim().isEmpty()) {
- MiriamData gene = null;
- if (TaxonomyBackend.HUMAN_TAXONOMY.equals(organism)) {
- gene = new MiriamData(MiriamType.HGNC_SYMBOL, geneName.trim());
- } else {
- Cell entrezCell = row.getCell(GENE_ENTREZ_ID_COL, Row.RETURN_BLANK_AS_NULL);
- if (entrezCell != null) {
- entrezCell.setCellType(Cell.CELL_TYPE_STRING);
- String entrezVal = entrezCell.getStringCellValue();
- // in case of non human target set the entrez
- gene = new MiriamData(MiriamType.ENTREZ, entrezVal.trim());
- }
- }
- MiRNA rna = miRNAs.get(name);
- Target target = null;
- for (Target t : rna.getTargets()) {
- if (t.getGenes().contains(gene)) {
- if (organism == null && t.getOrganism() == null) {
- target = t;
- } else if (organism != null && organism.equals(t.getOrganism())) {
- target = t;
- }
- }
- }
- if (target == null) {
- target = new Target(mirTaRBaseId, gene, new ArrayList<>());
- target.setType(TargetType.SINGLE_PROTEIN);
- target.setOrganism(organism);
- target.setName(geneName);
- rna.addTarget(target);
- }
- Cell pubmedCell = row.getCell(INTERACTION_PEDMED_ID_COL, Row.RETURN_BLANK_AS_NULL);
- if (pubmedCell != null) {
- pubmedCell.setCellType(Cell.CELL_TYPE_STRING);
- String value = pubmedCell.getStringCellValue();
- if (value != null && !value.trim().isEmpty()) {
- target.addReference(new MiriamData(MiriamType.PUBMED, value));
- }
- }
- }
-
- }
-
- }
- } catch (IOException | TaxonomySearchException e) {
- throw new MiRNASearchException("Problem with reading data about MiRNA", e);
- } finally {
- if (fileInputStream != null) {
- try {
- fileInputStream.close();
- } catch (Exception ex) {
- }
- }
- }
-
- for (String name : miRNAs.keySet()) {
- MiRNA rna = miRNAs.get(name);
- // put them in cache
- super.setCacheValue(MI_RNA_PREFIX + name.toLowerCase(), miRnaSerializer.objectToString(rna));
-
- // add to results if needed
- if (names.contains(name.toLowerCase())) {
- result.add(rna);
- }
- }
- return result;
- }
-
- @Override
- public ExternalServiceStatus getServiceStatus() {
- GeneralCacheInterface cacheCopy = getCache();
- this.setCache(null);
- status.setStatus(ExternalServiceStatusType.OK);
- try {
- List<String> names = new ArrayList<>();
- names.add("hsa-miR-375");
- List<MiRNA> list = this.getMiRnasByNames(names);
- if (list.isEmpty()) {
- status.setStatus(ExternalServiceStatusType.CHANGED);
- } else if (!list.get(0).getName().equals(names.get(0))) {
- status.setStatus(ExternalServiceStatusType.CHANGED);
- }
- } catch (Exception e) {
- logger.error("ctdbase service unavailable", e);
- status.setStatus(ExternalServiceStatusType.DOWN);
- }
- this.setCache(cacheCopy);
- return status;
- }
-
- /**
- * Returns list of MiRNA that targets objects identified by elements given in
- * the parameter.
- *
- * @param targetsMiriam
- * targets that should be targeted by resulting mir rnas
- * @return list of mirnas that target elements identified by paramter
- * @throws MiRNASearchException
- * thrown when there is a problem with accessing mirna database
- */
- public List<MiRNA> getMiRnaListByTargets(Collection<MiriamData> targetsMiriam) throws MiRNASearchException {
- Set<String> mirnaNames = new HashSet<>();
- Set<MiriamData> targets = new HashSet<>();
- for (MiriamData miriamData : targetsMiriam) {
- if (!MiriamType.HGNC_SYMBOL.equals(miriamData.getDataType())
- && !MiriamType.ENTREZ.equals(miriamData.getDataType())) {
- throw new InvalidArgumentException(
- "Only " + MiriamType.HGNC_SYMBOL + " or " + MiriamType.ENTREZ + " objects are accepted");
- } else {
- String miRnaIds = super.getCacheValue(
- MI_RNA_TARGET_PREFIX + miriamData.getDataType() + ":" + miriamData.getResource());
- if (miRnaIds != null) {
- String[] ids = miRnaIds.split("\n");
- for (String string : ids) {
- if (!string.isEmpty()) {
- mirnaNames.add(string);
- }
- }
- } else {
- targets.add(miriamData);
- }
- }
- }
-
- if (targets.size() > 0) {
- NPOIFSFileSystem fileInputStream = null;
- String value = null;
-
- try {
- fileInputStream = new NPOIFSFileSystem(getSourceInputStream());
- Workbook workbook = WorkbookFactory.create(fileInputStream);
- Sheet sheet = workbook.getSheetAt(0);
- Iterator<Row> rows = sheet.rowIterator();
- MiriamData gene = null;
-
- // Skip header
- if (rows.hasNext()) {
- rows.next();
- }
- Map<MiriamData, List<String>> lists = new HashMap<>();
- for (MiriamData md : targets) {
- lists.put(md, new ArrayList<>());
- }
- while (rows.hasNext()) {
- Row row = rows.next();
- Cell cell = row.getCell(SPECIES_COL, Row.RETURN_BLANK_AS_NULL);
- MiriamData organism = null;
- if (cell != null) {
- cell.setCellType(Cell.CELL_TYPE_STRING);
- value = cell.getStringCellValue();
- organism = taxonomyBackend.getByName(value);
- }
-
- cell = row.getCell(MIR_BASE_NAME_COL, Row.RETURN_BLANK_AS_NULL);
- if (cell == null) {
- continue;
- }
-
- cell.setCellType(Cell.CELL_TYPE_STRING);
- value = cell.getStringCellValue();
- if (value == null || value.trim().isEmpty()) {
- continue;
- }
- String mirBaseName = value.trim();
-
- cell = row.getCell(GENE_HGNC_ID_COL, Row.RETURN_BLANK_AS_NULL);
- gene = null;
- if (cell != null) {
- cell.setCellType(Cell.CELL_TYPE_STRING);
- String geneName = cell.getStringCellValue();
- if (geneName != null && !geneName.trim().isEmpty()) {
- if (TaxonomyBackend.HUMAN_TAXONOMY.equals(organism)) {
- gene = new MiriamData(MiriamType.HGNC_SYMBOL, geneName.trim());
- } else {
- Cell entrezCell = row.getCell(GENE_ENTREZ_ID_COL, Row.RETURN_BLANK_AS_NULL);
- if (entrezCell != null) {
- entrezCell.setCellType(Cell.CELL_TYPE_STRING);
- String entrezVal = entrezCell.getStringCellValue();
- // in case of non human target set the entrez
- gene = new MiriamData(MiriamType.ENTREZ, entrezVal.trim());
- }
- }
- if (gene != null) {
- List<String> list = lists.get(gene);
- if (list == null) {
- list = new ArrayList<>();
- lists.put(gene, list);
- }
- list.add(mirBaseName);
- }
- }
- }
- }
- for (MiriamData md : lists.keySet()) {
- StringBuilder serializedStr = new StringBuilder();
- for (String name : lists.get(md)) {
- serializedStr.append(name + "\n");
- }
- super.setCacheValue(MI_RNA_TARGET_PREFIX + md.getDataType() + ":" + md.getResource(),
- serializedStr.toString());
- if (targets.contains(md)) {
- mirnaNames.addAll(lists.get(md));
- }
- }
- } catch (IOException | TaxonomySearchException e) {
- throw new MiRNASearchException("Problem with reading data about MiRNA", e);
- } finally {
- if (fileInputStream != null) {
- try {
- fileInputStream.close();
- } catch (Exception ex) {
- }
- }
- }
- }
- return getMiRnasByNames(mirnaNames);
- }
-
- /**
- * Returns list of MiRNA that targets objects identified by {@link MiriamData}
- * given in the parameter.
- *
- * @param target
- * target that should be targeted by resulting mi rnas
- * @return list of mirnas that target element identified by parameter
- * @throws MiRNASearchException
- * thrown when there is a problem with accessing mirna database
- */
- public List<MiRNA> getMiRnaListByTarget(MiriamData target) throws MiRNASearchException {
- List<MiriamData> list = new ArrayList<>();
- list.add(target);
- return getMiRnaListByTargets(list);
- }
-
- /**
- * @return the miRnaSerializer
- * @see #miRnaSerializer
- */
- protected XmlSerializer<MiRNA> getMiRnaSerializer() {
- return miRnaSerializer;
- }
-
- /**
- * @param miRnaSerializer
- * the miRnaSerializer to set
- * @see #miRnaSerializer
- */
- protected void setMiRnaSerializer(XmlSerializer<MiRNA> miRnaSerializer) {
- this.miRnaSerializer = miRnaSerializer;
- }
-
- /**
- * @return the taxonomyBackend
- * @see #taxonomyBackend
- */
- protected TaxonomyBackend getTaxonomyBackend() {
- return taxonomyBackend;
- }
-
- /**
- * @param taxonomyBackend
- * the taxonomyBackend to set
- * @see #taxonomyBackend
- */
- protected void setTaxonomyBackend(TaxonomyBackend taxonomyBackend) {
- this.taxonomyBackend = taxonomyBackend;
- }
-
- public List<String> getSuggestedQueryList(Project project) throws MiRNASearchException {
- String cacheQuery = PROJECT_SUGGESTED_QUERY_PREFIX + "\n" + project.getId();
- String cachedData = getCacheValue(cacheQuery);
- List<String> result;
- if (cachedData == null) {
- result = getSuggestedQueryListWithoutCache(project);
- cachedData = StringUtils.join(result, "\n");
- setCacheValue(cacheQuery, cachedData);
- } else {
- result = new ArrayList<>();
- for (String string : cachedData.split("\n")) {
- if (!string.isEmpty()) {
- result.add(string);
- }
- }
- }
- return result;
- }
-
- private List<String> getSuggestedQueryListWithoutCache(Project project) throws MiRNASearchException {
- Set<String> resultSet = new HashSet<>();
- Set<MiriamData> targets = new HashSet<>();
- for (ModelData model : project.getModels()) {
- for (Element element : model.getElements()) {
- MiriamData entrez = null;
- MiriamData hgncSymbol = null;
- for (MiriamData miriam : element.getMiriamData()) {
- if (miriam.getDataType().equals(MiriamType.ENTREZ)) {
- entrez = miriam;
- } else if (miriam.getDataType().equals(MiriamType.HGNC_SYMBOL)) {
- hgncSymbol = miriam;
- }
- }
- if (hgncSymbol != null) {
- targets.add(hgncSymbol);
- } else if (entrez != null) {
- targets.add(entrez);
- } else {
- boolean validClass = false;
- for (Class<?> clazz : MiriamType.HGNC_SYMBOL.getValidClass()) {
- if (clazz.isAssignableFrom(element.getClass())) {
- validClass = true;
- }
- }
- if (validClass) {
- MiriamData md = new MiriamData(MiriamType.HGNC_SYMBOL, element.getName());
- try {
- if (hgncAnnotator.isValidHgncMiriam(md)) {
- targets.add(md);
- }
- } catch (AnnotatorException e) {
- logger.error("Problem with accessing HGNC database", e);
- }
- }
- }
- }
- }
- List<MiRNA> miRnas = getMiRnaListByTargets(targets);
- for (MiRNA mirna : miRnas) {
- resultSet.add(mirna.getName());
- }
- List<String> result = new ArrayList<>();
- result.addAll(resultSet);
- Collections.sort(result);
- return result;
- }
-
-}
+package lcsb.mapviewer.annotation.services;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.URISyntaxException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.commons.lang3.StringUtils;
+import org.apache.log4j.Logger;
+import org.apache.poi.poifs.filesystem.NPOIFSFileSystem;
+import org.apache.poi.ss.usermodel.Cell;
+import org.apache.poi.ss.usermodel.Row;
+import org.apache.poi.ss.usermodel.Sheet;
+import org.apache.poi.ss.usermodel.Workbook;
+import org.apache.poi.ss.usermodel.WorkbookFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.w3c.dom.Node;
+
+import lcsb.mapviewer.annotation.cache.BigFileCache;
+import lcsb.mapviewer.annotation.cache.CachableInterface;
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.XmlSerializer;
+import lcsb.mapviewer.annotation.data.MiRNA;
+import lcsb.mapviewer.annotation.data.Target;
+import lcsb.mapviewer.annotation.data.TargetType;
+import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
+import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
+import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.persist.dao.ProjectDao;
+
+/**
+ * Class used for accessing and parsing data from MiRNA database.
+ *
+ * @author Ayan Rota
+ *
+ */
+public class MiRNAParser extends CachableInterface implements IExternalService {
+
+ /**
+ * Url used for searching mirna by name.
+ */
+ private static final String URL_SOURCE_DATABASE = "http://mirtarbase.mbc.nctu.edu.tw/cache/download/6.1/miRTarBase_SE_WR.xls";
+
+ /**
+ * Cached file with static database about miriam (right now we parse it from
+ * excel file).
+ */
+ private ByteArrayOutputStream sourceInputStream;
+
+ /**
+ * Prefix used in the DB to identify the cache entry.
+ */
+ protected static final String MI_RNA_PREFIX = "mirBase:";
+
+ protected static final String PROJECT_SUGGESTED_QUERY_PREFIX = "PROJECT_MI_RNA_QUERIES:";
+
+ /**
+ * Prefix used in the DB to identify the cache entry that will have information
+ * about mirna that targets specific target.
+ */
+ static final String MI_RNA_TARGET_PREFIX = "MIRNA_TARGET:";
+
+ /**
+ * The location of Mirtarbase id column of Mirtarbase database.
+ */
+ public static final Integer MIR_TAR_BASE_ID_COL = 0;
+
+ /**
+ * The location of Mirbase name column of Mirbase database.
+ */
+ public static final Integer MIR_BASE_NAME_COL = 1;
+
+ /**
+ * The location of species column.
+ */
+ public static final Integer SPECIES_COL = 5;
+
+ /**
+ * The location of target gene HGNC ID column.
+ */
+ public static final Integer GENE_HGNC_ID_COL = 3;
+
+ /**
+ * The location of target gene ENTREZ ID column.
+ */
+ public static final Integer GENE_ENTREZ_ID_COL = 4;
+
+ /**
+ * The location of publication PEDMED ID column.
+ */
+ public static final Integer INTERACTION_PEDMED_ID_COL = 8;
+
+ /**
+ * Size of the buffer when copying files.
+ */
+ private static final int BUFFER_SIZE = 1024;
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(MiRNAParser.class);
+
+ /**
+ * Class used to access information about organisms taxonomy.
+ */
+ @Autowired
+ private TaxonomyBackend taxonomyBackend;
+
+ @Autowired
+ private HgncAnnotator hgncAnnotator;
+
+ /**
+ * Cache used for storing big files.
+ */
+ @Autowired
+ private BigFileCache bigFileCache;
+
+ @Autowired
+ private ProjectDao projectDao;
+
+ /**
+ * Object that allows to serialize {@link MiRNA} elements into xml string and
+ * deserialize xml into {@link MiRNA} objects.
+ */
+ private XmlSerializer<MiRNA> miRnaSerializer;
+
+ /**
+ * The status of the db.
+ */
+ private ExternalServiceStatus status = new ExternalServiceStatus("mirTarBase",
+ MiriamType.MIR_TAR_BASE_MATURE_SEQUENCE.getDbHomepage());
+
+ /**
+ * Default constructor.
+ */
+ public MiRNAParser() {
+ super(MiRNAParser.class);
+ miRnaSerializer = new XmlSerializer<>(MiRNA.class);
+ }
+
+ @Override
+ public Object refreshCacheQuery(Object query) throws SourceNotAvailable {
+ try {
+ Object result = null;
+ if (query instanceof String) {
+ String identifier = (String) query;
+ if (identifier.startsWith(MI_RNA_PREFIX)) {
+ String[] ids = identifier.split("\\:");
+ List<String> miRNAIDs = new ArrayList<>();
+ miRNAIDs.add(ids[1]);
+ List<MiRNA> list = getMiRnasByNameFromDb(miRNAIDs);
+ if (!list.isEmpty()) {
+ result = miRnaSerializer.objectToString(list.get(0));
+ }
+ } else if (identifier.startsWith(MI_RNA_TARGET_PREFIX)) {
+ String[] tmp = identifier.substring(MI_RNA_TARGET_PREFIX.length()).split(":");
+ MiriamData md = new MiriamData();
+ md.setDataType(MiriamType.valueOf(tmp[0]));
+ md.setResource(tmp[1]);
+ getMiRnaListByTarget(md);
+ result = super.getCacheValue(identifier);
+ } else if (identifier.startsWith(PROJECT_SUGGESTED_QUERY_PREFIX)) {
+ String[] tmp = identifier.split("\n");
+ Integer id = Integer.valueOf(tmp[1]);
+ Project project = projectDao.getById(id);
+ if (project == null) {
+ throw new SourceNotAvailable("Project with given id doesn't exist: " + id);
+ }
+ List<String> list = getSuggestedQueryListWithoutCache(project);
+ result = StringUtils.join(list, "\n");
+ } else {
+ result = super.refreshCacheQuery(query);
+ }
+ } else {
+ result = super.refreshCacheQuery(query);
+ }
+ return result;
+ } catch (MiRNASearchException e) {
+ throw new SourceNotAvailable(e);
+ }
+ }
+
+ /**
+ * @param names
+ * list of rna names to be retrieved.
+ * @return list of all object retrieved.
+ * @throws MiRNASearchException
+ * thrown when there is a problem with accessing mirna database
+ */
+ public List<MiRNA> getMiRnasByNames(Collection<String> names) throws MiRNASearchException {
+ List<MiRNA> miRNAs = new ArrayList<>();
+ List<String> idsToRemove = new ArrayList<>();
+ MiRNA miRNA = null;
+
+ for (String name : names) {
+ // look for MiRNA in the cache
+ Node miRNANode = super.getCacheNode(MI_RNA_PREFIX + name.toLowerCase());
+ if (miRNANode != null && miRNANode.hasChildNodes()) {
+ miRNA = miRnaSerializer.xmlToObject(miRNANode);
+ miRNAs.add(miRNA);
+ idsToRemove.add(name);
+ }
+ }
+ List<String> idsToFind = new ArrayList<>();
+ idsToFind.addAll(names);
+ for (String toRemove : idsToRemove) {
+ idsToFind.remove(toRemove);
+ }
+ // Not in the cache then get it from external database
+ if (!idsToFind.isEmpty()) {
+ // logger.debug("MiRNAParser.getMiRNA Start:"+new Date());
+ List<MiRNA> fromDBList = this.getMiRnasByNameFromDb(idsToFind);
+ for (MiRNA mirna : fromDBList) {
+ super.setCacheValue(MI_RNA_PREFIX + mirna.getName().toLowerCase(), miRnaSerializer.objectToString(mirna));
+ }
+ // logger.debug("MiRNAParser.getMiRNA End:"+new Date());
+ // Add them to result
+ miRNAs.addAll(fromDBList);
+
+ }
+ return miRNAs;
+ }
+
+ /**
+ * Returns input stream with a file containing Excel database with mirna data.
+ * Original source is located at {@link #URL_SOURCE_DATABASE}.
+ *
+ * @return input stream with a file containing Excel database with mirna data
+ * @throws IOException
+ * thrown when there is a problem with accessing mirna data file
+ */
+ private InputStream getSourceInputStream() throws IOException {
+ if (this.sourceInputStream == null) {
+ this.sourceInputStream = new ByteArrayOutputStream();
+
+ if (!bigFileCache.isCached(URL_SOURCE_DATABASE)) {
+ try {
+ bigFileCache.downloadFile(URL_SOURCE_DATABASE, false, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ });
+ } catch (URISyntaxException e) {
+ throw new IOException("Problem with downloading file: " + URL_SOURCE_DATABASE, e);
+ }
+ }
+ String filename = bigFileCache.getAbsolutePathForFile(URL_SOURCE_DATABASE);
+ byte[] buffer = new byte[BUFFER_SIZE];
+ int len;
+ InputStream stream = new FileInputStream(new File(filename));
+ try {
+ while ((len = stream.read(buffer)) > -1) {
+ this.sourceInputStream.write(buffer, 0, len);
+ }
+ } finally {
+ stream.close();
+ }
+ this.sourceInputStream.flush();
+ }
+ return new ByteArrayInputStream(sourceInputStream.toByteArray());
+ }
+
+ /**
+ * @param originalNames
+ * names of miRNAs
+ * @return List of MiRNA
+ * @throws MiRNASearchException
+ * thrown when there is a problem with accessing mirna database
+ */
+ protected List<MiRNA> getMiRnasByNameFromDb(List<String> originalNames) throws MiRNASearchException {
+ List<String> names = new ArrayList<>();
+ for (String string : originalNames) {
+ names.add(string.toLowerCase());
+ }
+
+ Map<String, MiRNA> miRNAs = new HashMap<>();
+ List<MiRNA> result = new ArrayList<MiRNA>();
+ NPOIFSFileSystem fileInputStream = null;
+ try {
+ fileInputStream = new NPOIFSFileSystem(getSourceInputStream());
+ Workbook workbook = WorkbookFactory.create(fileInputStream);
+ Sheet sheet = workbook.getSheetAt(0);
+ Iterator<Row> rows = sheet.rowIterator();
+ // Skip header
+ if (rows.hasNext()) {
+ rows.next();
+ }
+ while (rows.hasNext()) {
+ Row row = rows.next();
+ Cell targetSpeciesCell = row.getCell(SPECIES_COL, Row.RETURN_BLANK_AS_NULL);
+ MiriamData organism = null;
+ if (targetSpeciesCell != null) {
+ targetSpeciesCell.setCellType(Cell.CELL_TYPE_STRING);
+ String value = targetSpeciesCell.getStringCellValue();
+ organism = taxonomyBackend.getByName(value);
+ }
+
+ Cell mirBaseNamecell = row.getCell(MIR_BASE_NAME_COL, Row.RETURN_BLANK_AS_NULL);
+ if (mirBaseNamecell == null) {
+ continue;
+ }
+
+ mirBaseNamecell.setCellType(Cell.CELL_TYPE_STRING);
+ String name = mirBaseNamecell.getStringCellValue();
+ if (name == null || name.trim().isEmpty()) {
+ continue;
+ }
+ if (miRNAs.get(name) == null) {
+ miRNAs.put(name, new MiRNA(name));
+ }
+
+ MiriamData mirTaRBaseId = null;
+ Cell mirTaRBaseIdCell = row.getCell(MIR_TAR_BASE_ID_COL, Row.RETURN_BLANK_AS_NULL);
+ if (mirTaRBaseIdCell == null) {
+ continue;
+ } else {
+ mirTaRBaseIdCell.setCellType(Cell.CELL_TYPE_STRING);
+ String value = mirTaRBaseIdCell.getStringCellValue();
+ if (value == null || value.trim().isEmpty()) {
+ continue;
+ } else {
+ mirTaRBaseId = new MiriamData(MiriamType.MIR_TAR_BASE_MATURE_SEQUENCE, value.trim());
+ }
+ }
+
+ Cell hgncCell = row.getCell(GENE_HGNC_ID_COL, Row.RETURN_BLANK_AS_NULL);
+ if (hgncCell != null) {
+ hgncCell.setCellType(Cell.CELL_TYPE_STRING);
+ String geneName = hgncCell.getStringCellValue();
+ if (geneName != null && !geneName.trim().isEmpty()) {
+ MiriamData gene = null;
+ if (TaxonomyBackend.HUMAN_TAXONOMY.equals(organism)) {
+ gene = new MiriamData(MiriamType.HGNC_SYMBOL, geneName.trim());
+ } else {
+ Cell entrezCell = row.getCell(GENE_ENTREZ_ID_COL, Row.RETURN_BLANK_AS_NULL);
+ if (entrezCell != null) {
+ entrezCell.setCellType(Cell.CELL_TYPE_STRING);
+ String entrezVal = entrezCell.getStringCellValue();
+ // in case of non human target set the entrez
+ gene = new MiriamData(MiriamType.ENTREZ, entrezVal.trim());
+ }
+ }
+ MiRNA rna = miRNAs.get(name);
+ Target target = null;
+ for (Target t : rna.getTargets()) {
+ if (t.getGenes().contains(gene)) {
+ if (organism == null && t.getOrganism() == null) {
+ target = t;
+ } else if (organism != null && organism.equals(t.getOrganism())) {
+ target = t;
+ }
+ }
+ }
+ if (target == null) {
+ target = new Target(mirTaRBaseId, gene, new ArrayList<>());
+ target.setType(TargetType.SINGLE_PROTEIN);
+ target.setOrganism(organism);
+ target.setName(geneName);
+ rna.addTarget(target);
+ }
+ Cell pubmedCell = row.getCell(INTERACTION_PEDMED_ID_COL, Row.RETURN_BLANK_AS_NULL);
+ if (pubmedCell != null) {
+ pubmedCell.setCellType(Cell.CELL_TYPE_STRING);
+ String value = pubmedCell.getStringCellValue();
+ if (value != null && !value.trim().isEmpty()) {
+ target.addReference(new MiriamData(MiriamType.PUBMED, value));
+ }
+ }
+ }
+
+ }
+
+ }
+ } catch (IOException | TaxonomySearchException e) {
+ throw new MiRNASearchException("Problem with reading data about MiRNA", e);
+ } finally {
+ if (fileInputStream != null) {
+ try {
+ fileInputStream.close();
+ } catch (Exception ex) {
+ }
+ }
+ }
+
+ for (String name : miRNAs.keySet()) {
+ MiRNA rna = miRNAs.get(name);
+ // put them in cache
+ super.setCacheValue(MI_RNA_PREFIX + name.toLowerCase(), miRnaSerializer.objectToString(rna));
+
+ // add to results if needed
+ if (names.contains(name.toLowerCase())) {
+ result.add(rna);
+ }
+ }
+ return result;
+ }
+
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ GeneralCacheInterface cacheCopy = getCache();
+ this.setCache(null);
+ status.setStatus(ExternalServiceStatusType.OK);
+ try {
+ List<String> names = new ArrayList<>();
+ names.add("hsa-miR-375");
+ List<MiRNA> list = this.getMiRnasByNames(names);
+ if (list.isEmpty()) {
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ } else if (!list.get(0).getName().equals(names.get(0))) {
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ }
+ } catch (Exception e) {
+ logger.error("ctdbase service unavailable", e);
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ }
+ this.setCache(cacheCopy);
+ return status;
+ }
+
+ /**
+ * Returns list of MiRNA that targets objects identified by elements given in
+ * the parameter.
+ *
+ * @param targetsMiriam
+ * targets that should be targeted by resulting mir rnas
+ * @return list of mirnas that target elements identified by paramter
+ * @throws MiRNASearchException
+ * thrown when there is a problem with accessing mirna database
+ */
+ public List<MiRNA> getMiRnaListByTargets(Collection<MiriamData> targetsMiriam) throws MiRNASearchException {
+ Set<String> mirnaNames = new HashSet<>();
+ Set<MiriamData> targets = new HashSet<>();
+ for (MiriamData miriamData : targetsMiriam) {
+ if (!MiriamType.HGNC_SYMBOL.equals(miriamData.getDataType())
+ && !MiriamType.ENTREZ.equals(miriamData.getDataType())) {
+ throw new InvalidArgumentException(
+ "Only " + MiriamType.HGNC_SYMBOL + " or " + MiriamType.ENTREZ + " objects are accepted");
+ } else {
+ String miRnaIds = super.getCacheValue(
+ MI_RNA_TARGET_PREFIX + miriamData.getDataType() + ":" + miriamData.getResource());
+ if (miRnaIds != null) {
+ String[] ids = miRnaIds.split("\n");
+ for (String string : ids) {
+ if (!string.isEmpty()) {
+ mirnaNames.add(string);
+ }
+ }
+ } else {
+ targets.add(miriamData);
+ }
+ }
+ }
+
+ if (targets.size() > 0) {
+ NPOIFSFileSystem fileInputStream = null;
+ String value = null;
+
+ try {
+ fileInputStream = new NPOIFSFileSystem(getSourceInputStream());
+ Workbook workbook = WorkbookFactory.create(fileInputStream);
+ Sheet sheet = workbook.getSheetAt(0);
+ Iterator<Row> rows = sheet.rowIterator();
+ MiriamData gene = null;
+
+ // Skip header
+ if (rows.hasNext()) {
+ rows.next();
+ }
+ Map<MiriamData, List<String>> lists = new HashMap<>();
+ for (MiriamData md : targets) {
+ lists.put(md, new ArrayList<>());
+ }
+ while (rows.hasNext()) {
+ Row row = rows.next();
+ Cell cell = row.getCell(SPECIES_COL, Row.RETURN_BLANK_AS_NULL);
+ MiriamData organism = null;
+ if (cell != null) {
+ cell.setCellType(Cell.CELL_TYPE_STRING);
+ value = cell.getStringCellValue();
+ organism = taxonomyBackend.getByName(value);
+ }
+
+ cell = row.getCell(MIR_BASE_NAME_COL, Row.RETURN_BLANK_AS_NULL);
+ if (cell == null) {
+ continue;
+ }
+
+ cell.setCellType(Cell.CELL_TYPE_STRING);
+ value = cell.getStringCellValue();
+ if (value == null || value.trim().isEmpty()) {
+ continue;
+ }
+ String mirBaseName = value.trim();
+
+ cell = row.getCell(GENE_HGNC_ID_COL, Row.RETURN_BLANK_AS_NULL);
+ gene = null;
+ if (cell != null) {
+ cell.setCellType(Cell.CELL_TYPE_STRING);
+ String geneName = cell.getStringCellValue();
+ if (geneName != null && !geneName.trim().isEmpty()) {
+ if (TaxonomyBackend.HUMAN_TAXONOMY.equals(organism)) {
+ gene = new MiriamData(MiriamType.HGNC_SYMBOL, geneName.trim());
+ } else {
+ Cell entrezCell = row.getCell(GENE_ENTREZ_ID_COL, Row.RETURN_BLANK_AS_NULL);
+ if (entrezCell != null) {
+ entrezCell.setCellType(Cell.CELL_TYPE_STRING);
+ String entrezVal = entrezCell.getStringCellValue();
+ // in case of non human target set the entrez
+ gene = new MiriamData(MiriamType.ENTREZ, entrezVal.trim());
+ }
+ }
+ if (gene != null) {
+ List<String> list = lists.get(gene);
+ if (list == null) {
+ list = new ArrayList<>();
+ lists.put(gene, list);
+ }
+ list.add(mirBaseName);
+ }
+ }
+ }
+ }
+ for (MiriamData md : lists.keySet()) {
+ StringBuilder serializedStr = new StringBuilder();
+ for (String name : lists.get(md)) {
+ serializedStr.append(name + "\n");
+ }
+ super.setCacheValue(MI_RNA_TARGET_PREFIX + md.getDataType() + ":" + md.getResource(),
+ serializedStr.toString());
+ if (targets.contains(md)) {
+ mirnaNames.addAll(lists.get(md));
+ }
+ }
+ } catch (IOException | TaxonomySearchException e) {
+ throw new MiRNASearchException("Problem with reading data about MiRNA", e);
+ } finally {
+ if (fileInputStream != null) {
+ try {
+ fileInputStream.close();
+ } catch (Exception ex) {
+ }
+ }
+ }
+ }
+ return getMiRnasByNames(mirnaNames);
+ }
+
+ /**
+ * Returns list of MiRNA that targets objects identified by {@link MiriamData}
+ * given in the parameter.
+ *
+ * @param target
+ * target that should be targeted by resulting mi rnas
+ * @return list of mirnas that target element identified by parameter
+ * @throws MiRNASearchException
+ * thrown when there is a problem with accessing mirna database
+ */
+ public List<MiRNA> getMiRnaListByTarget(MiriamData target) throws MiRNASearchException {
+ List<MiriamData> list = new ArrayList<>();
+ list.add(target);
+ return getMiRnaListByTargets(list);
+ }
+
+ /**
+ * @return the miRnaSerializer
+ * @see #miRnaSerializer
+ */
+ protected XmlSerializer<MiRNA> getMiRnaSerializer() {
+ return miRnaSerializer;
+ }
+
+ /**
+ * @param miRnaSerializer
+ * the miRnaSerializer to set
+ * @see #miRnaSerializer
+ */
+ protected void setMiRnaSerializer(XmlSerializer<MiRNA> miRnaSerializer) {
+ this.miRnaSerializer = miRnaSerializer;
+ }
+
+ /**
+ * @return the taxonomyBackend
+ * @see #taxonomyBackend
+ */
+ protected TaxonomyBackend getTaxonomyBackend() {
+ return taxonomyBackend;
+ }
+
+ /**
+ * @param taxonomyBackend
+ * the taxonomyBackend to set
+ * @see #taxonomyBackend
+ */
+ protected void setTaxonomyBackend(TaxonomyBackend taxonomyBackend) {
+ this.taxonomyBackend = taxonomyBackend;
+ }
+
+ public List<String> getSuggestedQueryList(Project project) throws MiRNASearchException {
+ String cacheQuery = PROJECT_SUGGESTED_QUERY_PREFIX + "\n" + project.getId();
+ String cachedData = getCacheValue(cacheQuery);
+ List<String> result;
+ if (cachedData == null) {
+ result = getSuggestedQueryListWithoutCache(project);
+ cachedData = StringUtils.join(result, "\n");
+ setCacheValue(cacheQuery, cachedData);
+ } else {
+ result = new ArrayList<>();
+ for (String string : cachedData.split("\n")) {
+ if (!string.isEmpty()) {
+ result.add(string);
+ }
+ }
+ }
+ return result;
+ }
+
+ private List<String> getSuggestedQueryListWithoutCache(Project project) throws MiRNASearchException {
+ Set<String> resultSet = new HashSet<>();
+ Set<MiriamData> targets = new HashSet<>();
+ for (ModelData model : project.getModels()) {
+ for (Element element : model.getElements()) {
+ MiriamData entrez = null;
+ MiriamData hgncSymbol = null;
+ for (MiriamData miriam : element.getMiriamData()) {
+ if (miriam.getDataType().equals(MiriamType.ENTREZ)) {
+ entrez = miriam;
+ } else if (miriam.getDataType().equals(MiriamType.HGNC_SYMBOL)) {
+ hgncSymbol = miriam;
+ }
+ }
+ if (hgncSymbol != null) {
+ targets.add(hgncSymbol);
+ } else if (entrez != null) {
+ targets.add(entrez);
+ } else {
+ boolean validClass = false;
+ for (Class<?> clazz : MiriamType.HGNC_SYMBOL.getValidClass()) {
+ if (clazz.isAssignableFrom(element.getClass())) {
+ validClass = true;
+ }
+ }
+ if (validClass) {
+ MiriamData md = new MiriamData(MiriamType.HGNC_SYMBOL, element.getName());
+ try {
+ if (hgncAnnotator.isValidHgncMiriam(md)) {
+ targets.add(md);
+ }
+ } catch (AnnotatorException e) {
+ logger.error("Problem with accessing HGNC database", e);
+ }
+ }
+ }
+ }
+ }
+ List<MiRNA> miRnas = getMiRnaListByTargets(targets);
+ for (MiRNA mirna : miRnas) {
+ resultSet.add(mirna.getName());
+ }
+ List<String> result = new ArrayList<>();
+ result.addAll(resultSet);
+ Collections.sort(result);
+ return result;
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiRNASearchException.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiRNASearchException.java
index eaaa99c929..e63f663df4 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiRNASearchException.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiRNASearchException.java
@@ -1,47 +1,47 @@
-package lcsb.mapviewer.annotation.services;
-
-/**
- * Exception thrown when there was a problem when searching for a mirna.
- *
- * @author Piotr Gawron
- *
- */
-public class MiRNASearchException extends Exception {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- *
- * @param string
- * exception message
- */
- public MiRNASearchException(String string) {
- super(string);
- }
-
- /**
- * Default constructor.
- *
- * @param e
- * parent exception
- */
- public MiRNASearchException(Exception e) {
- super(e);
- }
-
- /**
- * Default constructor.
- *
- * @param message
- * exception message
- * @param e
- * source exception
- */
- public MiRNASearchException(String message, Exception e) {
- super(message, e);
- }
-}
+package lcsb.mapviewer.annotation.services;
+
+/**
+ * Exception thrown when there was a problem when searching for a mirna.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class MiRNASearchException extends Exception {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ *
+ * @param string
+ * exception message
+ */
+ public MiRNASearchException(String string) {
+ super(string);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param e
+ * parent exception
+ */
+ public MiRNASearchException(Exception e) {
+ super(e);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * exception message
+ * @param e
+ * source exception
+ */
+ public MiRNASearchException(String message, Exception e) {
+ super(message, e);
+ }
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnector.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnector.java
index e12b3fea87..00b97432ce 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnector.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnector.java
@@ -1,278 +1,278 @@
-package lcsb.mapviewer.annotation.services;
-
-import java.io.IOException;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-import org.hibernate.AnnotationException;
-
-import com.google.gson.Gson;
-
-import lcsb.mapviewer.annotation.cache.CachableInterface;
-import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
-import lcsb.mapviewer.annotation.cache.WebPageDownloader;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
-import uk.ac.ebi.miriam.lib.MiriamLink;
-
-/**
- * Class responsible for connection to Miriam DB. It allows to update URI of
- * database being used and retrieve urls for miriam uri.
- *
- * @author Piotr Gawron
- *
- */
-public final class MiriamConnector extends CachableInterface implements IExternalService {
-
- /**
- * String used to distinguish cached data for links.
- */
- static final String LINK_DB_PREFIX = "Link: ";
-
- /**
- * String used to distinguish cached data for checking if uri is valid.
- */
- protected static final String VALID_URI_PREFIX = "Validity: ";
-
- /**
- * String describing invalid miriam entries that will be put into db (instead of
- * null).
- */
- private static final String INVALID_LINK = "INVALID";
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(MiriamConnector.class.getName());
-
- /**
- * Miriam Registry API.
- */
- private MiriamLink link;
-
- /**
- * Default class constructor. Prevent initialization.
- */
- public MiriamConnector() {
- super(MiriamConnector.class);
- link = new MiriamLink();
- link.setAddress("https://www.ebi.ac.uk/miriamws/main/MiriamWebServices");
- }
-
- /**
- * Returns url to the web page represented by {@link MiriamData} parameter.
- *
- * @param miriamData
- * miriam data
- * @return url to resource pointed by miriam data
- */
- public String getUrlString(MiriamData miriamData) {
- if (miriamData.getDataType() == null) {
- throw new InvalidArgumentException("Data type cannot be empty.");
- } else if (miriamData.getDataType().getUris().size() == 0) {
- throw new InvalidArgumentException("Url for " + miriamData.getDataType() + " cannot be retreived.");
- }
- String query = LINK_DB_PREFIX + miriamData.getDataType().getUris().get(0) + "\n" + miriamData.getResource();
- String result = getCacheValue(query);
- if (result != null) {
- if (INVALID_LINK.equals(result)) {
- return null;
- }
- return result;
- }
- // hard-coded specific treatment for mesh
- if (MiriamType.MESH_2012.equals(miriamData.getDataType())) {
- result = "http://bioportal.bioontology.org/ontologies/1351?p=terms&conceptid=" + miriamData.getResource();
- } else {
- String uri = miriamData.getDataType().getUris().get(0) + ":" + miriamData.getResource();
- String[] urls = getLink().getLocations(uri);
- if (urls == null) {
- result = null;
- } else if (urls.length > 0) {
- result = urls[0];
- }
- }
- if (result != null) {
- setCacheValue(query, result);
- return result;
- } else {
- logger.warn("Cannot find url for miriam: " + miriamData);
- // if url cannot be found then mark miriam data as invalid for one day
- setCacheValue(query, INVALID_LINK, 1);
- return null;
- }
- }
-
- @Override
- public ExternalServiceStatus getServiceStatus() {
- ExternalServiceStatus status = new ExternalServiceStatus("MIRIAM Registry", "https://www.ebi.ac.uk/miriam/main/");
- GeneralCacheInterface cacheCopy = getCache();
- this.setCache(null);
-
- try {
- String url = getUrlString(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, "3453"));
- status.setStatus(ExternalServiceStatusType.OK);
- if (url == null) {
- status.setStatus(ExternalServiceStatusType.DOWN);
- }
- } catch (Exception e) {
- logger.error(status.getName() + " is down", e);
- status.setStatus(ExternalServiceStatusType.DOWN);
- }
- this.setCache(cacheCopy);
- return status;
- }
-
- /**
- * Check if identifier can be transformed into {@link MiriamData}.
- *
- * @param string
- * identifier in the format NAME:IDENTIFIER. Where NAME is the name
- * from {@link MiriamType#commonName} and IDENTIFIER is resource
- * identifier.
- * @return <code>true</code> if identifier can be transformed into
- * {@link MiriamData}
- */
- public boolean isValidIdentifier(String string) {
- try {
- MiriamType.getMiriamDataFromIdentifier(string);
- return true;
- } catch (InvalidArgumentException e) {
- return false;
- }
- }
-
- @Override
- public String refreshCacheQuery(Object query) throws SourceNotAvailable {
- String result = null;
- if (query instanceof String) {
- String name = (String) query;
- if (name.startsWith(LINK_DB_PREFIX)) {
- String tmp = name.substring(LINK_DB_PREFIX.length());
- String[] rows = tmp.split("\n");
- if (rows.length != 2) {
- throw new InvalidArgumentException("Miriam link query is invalid: " + query);
- }
- MiriamType dataType = MiriamType.getTypeByUri(rows[0]);
- String resource = rows[1];
- result = getUrlString(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, dataType, resource));
- } else if (name.startsWith(VALID_URI_PREFIX)) {
- String tmp = name.substring(VALID_URI_PREFIX.length());
- result = "" + isValid(tmp);
- } else if (name.startsWith("http")) {
- try {
- result = getWebPageContent(name);
- } catch (IOException e) {
- throw new SourceNotAvailable(e);
- }
- } else {
- throw new InvalidArgumentException("Don't know what to do with string \"" + query + "\"");
- }
- } else {
- throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
- }
-
- return result;
- }
-
- /**
- * Checks if uri (like the one defined in {@link MiriamType#uris}) is valid.
- *
- * @param uri
- * uri to check
- * @return <code>true</code> if uri in parameter is valid, <code>false</code>
- * otherwise
- */
- public boolean isValid(String uri) {
- String query = VALID_URI_PREFIX + uri;
- String val = getCacheValue(query);
- if (val != null) {
- return "true".equalsIgnoreCase(val);
- }
-
- boolean result = false;
- String name = getLink().getName(uri);
- if (name == null) {
- result = false;
- } else {
- result = !name.isEmpty();
- }
- setCacheValue(query, "" + result);
- return result;
- }
-
- /**
- * This is alternative version of {@link #getUrlString(MiriamData)} method that
- * is around 30% faster. But it refers to beta version of
- * <a href="https://www.ebi.ac.uk/miriamws/main/rest/">miriam Rest API</a>.
- *
- * @param md
- * miriam data for which access url will be returned
- * @return url to resource pointed by miriam data
- * @throws AnnotationException
- * thrown when there is a problem with accessing miriam REST API
- */
- protected String getUrlString2(MiriamData md) throws AnnotationException {
- try {
- String result = null;
- String queryUri = md.getDataType().getUris().get(0) + ":" + md.getResource();
- String query = "https://www.ebi.ac.uk/miriamws/main/rest/resolve/" + queryUri;
- String page = getWebPageContent(query);
- Gson gson = new Gson();
-
- Map<?, ?> gsonObject = new HashMap<String, Object>();
- gsonObject = (Map<?, ?>) gson.fromJson(page, gsonObject.getClass());
- Object uris = gsonObject.get("uri");
- Map<?, ?> entry = (Map<?, ?>) ((List<?>) uris).get(0);
- result = (String) entry.get("$");
-
- return result;
- } catch (Exception e) {
- throw new AnnotationException("Problem with accessing miriam REST API", e);
- }
- }
-
- /**
- * Returns uri to miriam resource.
- *
- * @param md
- * {@link MiriamData} object for which uri should be returned
- * @return uri to miriam resource
- */
- public String miriamDataToUri(MiriamData md) {
- return md.getDataType().getUris().get(0) + ":" + md.getResource();
- }
-
- @Override
- protected WebPageDownloader getWebPageDownloader() {
- return super.getWebPageDownloader();
- }
-
- @Override
- protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
- super.setWebPageDownloader(webPageDownloader);
- }
-
- /**
- * @return the link
- * @see #link
- */
- MiriamLink getLink() {
- return link;
- }
-
- /**
- * @param link
- * the link to set
- * @see #link
- */
- void setLink(MiriamLink link) {
- this.link = link;
- }
-
-}
+package lcsb.mapviewer.annotation.services;
+
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+import org.hibernate.AnnotationException;
+
+import com.google.gson.Gson;
+
+import lcsb.mapviewer.annotation.cache.CachableInterface;
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.WebPageDownloader;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
+import uk.ac.ebi.miriam.lib.MiriamLink;
+
+/**
+ * Class responsible for connection to Miriam DB. It allows to update URI of
+ * database being used and retrieve urls for miriam uri.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public final class MiriamConnector extends CachableInterface implements IExternalService {
+
+ /**
+ * String used to distinguish cached data for links.
+ */
+ static final String LINK_DB_PREFIX = "Link: ";
+
+ /**
+ * String used to distinguish cached data for checking if uri is valid.
+ */
+ protected static final String VALID_URI_PREFIX = "Validity: ";
+
+ /**
+ * String describing invalid miriam entries that will be put into db (instead of
+ * null).
+ */
+ private static final String INVALID_LINK = "INVALID";
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(MiriamConnector.class.getName());
+
+ /**
+ * Miriam Registry API.
+ */
+ private MiriamLink link;
+
+ /**
+ * Default class constructor. Prevent initialization.
+ */
+ public MiriamConnector() {
+ super(MiriamConnector.class);
+ link = new MiriamLink();
+ link.setAddress("https://www.ebi.ac.uk/miriamws/main/MiriamWebServices");
+ }
+
+ /**
+ * Returns url to the web page represented by {@link MiriamData} parameter.
+ *
+ * @param miriamData
+ * miriam data
+ * @return url to resource pointed by miriam data
+ */
+ public String getUrlString(MiriamData miriamData) {
+ if (miriamData.getDataType() == null) {
+ throw new InvalidArgumentException("Data type cannot be empty.");
+ } else if (miriamData.getDataType().getUris().size() == 0) {
+ throw new InvalidArgumentException("Url for " + miriamData.getDataType() + " cannot be retreived.");
+ }
+ String query = LINK_DB_PREFIX + miriamData.getDataType().getUris().get(0) + "\n" + miriamData.getResource();
+ String result = getCacheValue(query);
+ if (result != null) {
+ if (INVALID_LINK.equals(result)) {
+ return null;
+ }
+ return result;
+ }
+ // hard-coded specific treatment for mesh
+ if (MiriamType.MESH_2012.equals(miriamData.getDataType())) {
+ result = "http://bioportal.bioontology.org/ontologies/1351?p=terms&conceptid=" + miriamData.getResource();
+ } else {
+ String uri = miriamData.getDataType().getUris().get(0) + ":" + miriamData.getResource();
+ String[] urls = getLink().getLocations(uri);
+ if (urls == null) {
+ result = null;
+ } else if (urls.length > 0) {
+ result = urls[0];
+ }
+ }
+ if (result != null) {
+ setCacheValue(query, result);
+ return result;
+ } else {
+ logger.warn("Cannot find url for miriam: " + miriamData);
+ // if url cannot be found then mark miriam data as invalid for one day
+ setCacheValue(query, INVALID_LINK, 1);
+ return null;
+ }
+ }
+
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ ExternalServiceStatus status = new ExternalServiceStatus("MIRIAM Registry", "https://www.ebi.ac.uk/miriam/main/");
+ GeneralCacheInterface cacheCopy = getCache();
+ this.setCache(null);
+
+ try {
+ String url = getUrlString(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, "3453"));
+ status.setStatus(ExternalServiceStatusType.OK);
+ if (url == null) {
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ }
+ } catch (Exception e) {
+ logger.error(status.getName() + " is down", e);
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ }
+ this.setCache(cacheCopy);
+ return status;
+ }
+
+ /**
+ * Check if identifier can be transformed into {@link MiriamData}.
+ *
+ * @param string
+ * identifier in the format NAME:IDENTIFIER. Where NAME is the name
+ * from {@link MiriamType#commonName} and IDENTIFIER is resource
+ * identifier.
+ * @return <code>true</code> if identifier can be transformed into
+ * {@link MiriamData}
+ */
+ public boolean isValidIdentifier(String string) {
+ try {
+ MiriamType.getMiriamDataFromIdentifier(string);
+ return true;
+ } catch (InvalidArgumentException e) {
+ return false;
+ }
+ }
+
+ @Override
+ public String refreshCacheQuery(Object query) throws SourceNotAvailable {
+ String result = null;
+ if (query instanceof String) {
+ String name = (String) query;
+ if (name.startsWith(LINK_DB_PREFIX)) {
+ String tmp = name.substring(LINK_DB_PREFIX.length());
+ String[] rows = tmp.split("\n");
+ if (rows.length != 2) {
+ throw new InvalidArgumentException("Miriam link query is invalid: " + query);
+ }
+ MiriamType dataType = MiriamType.getTypeByUri(rows[0]);
+ String resource = rows[1];
+ result = getUrlString(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, dataType, resource));
+ } else if (name.startsWith(VALID_URI_PREFIX)) {
+ String tmp = name.substring(VALID_URI_PREFIX.length());
+ result = "" + isValid(tmp);
+ } else if (name.startsWith("http")) {
+ try {
+ result = getWebPageContent(name);
+ } catch (IOException e) {
+ throw new SourceNotAvailable(e);
+ }
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with string \"" + query + "\"");
+ }
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
+ }
+
+ return result;
+ }
+
+ /**
+ * Checks if uri (like the one defined in {@link MiriamType#uris}) is valid.
+ *
+ * @param uri
+ * uri to check
+ * @return <code>true</code> if uri in parameter is valid, <code>false</code>
+ * otherwise
+ */
+ public boolean isValid(String uri) {
+ String query = VALID_URI_PREFIX + uri;
+ String val = getCacheValue(query);
+ if (val != null) {
+ return "true".equalsIgnoreCase(val);
+ }
+
+ boolean result = false;
+ String name = getLink().getName(uri);
+ if (name == null) {
+ result = false;
+ } else {
+ result = !name.isEmpty();
+ }
+ setCacheValue(query, "" + result);
+ return result;
+ }
+
+ /**
+ * This is alternative version of {@link #getUrlString(MiriamData)} method that
+ * is around 30% faster. But it refers to beta version of
+ * <a href="https://www.ebi.ac.uk/miriamws/main/rest/">miriam Rest API</a>.
+ *
+ * @param md
+ * miriam data for which access url will be returned
+ * @return url to resource pointed by miriam data
+ * @throws AnnotationException
+ * thrown when there is a problem with accessing miriam REST API
+ */
+ protected String getUrlString2(MiriamData md) throws AnnotationException {
+ try {
+ String result = null;
+ String queryUri = md.getDataType().getUris().get(0) + ":" + md.getResource();
+ String query = "https://www.ebi.ac.uk/miriamws/main/rest/resolve/" + queryUri;
+ String page = getWebPageContent(query);
+ Gson gson = new Gson();
+
+ Map<?, ?> gsonObject = new HashMap<String, Object>();
+ gsonObject = (Map<?, ?>) gson.fromJson(page, gsonObject.getClass());
+ Object uris = gsonObject.get("uri");
+ Map<?, ?> entry = (Map<?, ?>) ((List<?>) uris).get(0);
+ result = (String) entry.get("$");
+
+ return result;
+ } catch (Exception e) {
+ throw new AnnotationException("Problem with accessing miriam REST API", e);
+ }
+ }
+
+ /**
+ * Returns uri to miriam resource.
+ *
+ * @param md
+ * {@link MiriamData} object for which uri should be returned
+ * @return uri to miriam resource
+ */
+ public String miriamDataToUri(MiriamData md) {
+ return md.getDataType().getUris().get(0) + ":" + md.getResource();
+ }
+
+ @Override
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
+ }
+
+ @Override
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
+ }
+
+ /**
+ * @return the link
+ * @see #link
+ */
+ MiriamLink getLink() {
+ return link;
+ }
+
+ /**
+ * @param link
+ * the link to set
+ * @see #link
+ */
+ void setLink(MiriamLink link) {
+ this.link = link;
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingAnnotation.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingAnnotation.java
index d981d5a1ba..1dd95d2302 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingAnnotation.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingAnnotation.java
@@ -1,40 +1,40 @@
-package lcsb.mapviewer.annotation.services;
-
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.modelutils.map.ElementUtils;
-
-/**
- * Defines annotation problem with element when there are no annotations for the
- * element.
- *
- * @author Piotr Gawron
- *
- */
-public class MissingAnnotation implements ProblematicAnnotation {
-
- /**
- * BioEntity improperly annotated.
- */
- private BioEntity bioEntity;
-
- /**
- * Constructor that initializes the data with {@link #bioEntity bioEntity} .
- *
- * @param bioEntity
- * bioEntity that misses annotation
- */
- public MissingAnnotation(BioEntity bioEntity) {
- this.bioEntity = bioEntity;
- }
-
- @Override
- public String getMessage() {
- return new ElementUtils().getElementTag(bioEntity) + "misses annotations.";
- }
-
- @Override
- public String toString() {
- return getMessage();
- }
-
-}
+package lcsb.mapviewer.annotation.services;
+
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
+
+/**
+ * Defines annotation problem with element when there are no annotations for the
+ * element.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class MissingAnnotation implements ProblematicAnnotation {
+
+ /**
+ * BioEntity improperly annotated.
+ */
+ private BioEntity bioEntity;
+
+ /**
+ * Constructor that initializes the data with {@link #bioEntity bioEntity} .
+ *
+ * @param bioEntity
+ * bioEntity that misses annotation
+ */
+ public MissingAnnotation(BioEntity bioEntity) {
+ this.bioEntity = bioEntity;
+ }
+
+ @Override
+ public String getMessage() {
+ return new ElementUtils().getElementTag(bioEntity) + "misses annotations.";
+ }
+
+ @Override
+ public String toString() {
+ return getMessage();
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingRequiredAnnotations.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingRequiredAnnotations.java
index b6a0266de4..bc57929783 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingRequiredAnnotations.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingRequiredAnnotations.java
@@ -1,64 +1,64 @@
-package lcsb.mapviewer.annotation.services;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.modelutils.map.ElementUtils;
-
-/**
- * Defines problem with element annotation when there are some required
- * annotations, but none of them can be found in the element.
- *
- * @author Piotr Gawron
- *
- */
-public class MissingRequiredAnnotations implements ProblematicAnnotation {
-
- /**
- * BioEntity improperly annotated.
- */
- private BioEntity bioEntity;
-
- /**
- * Required miriam type.
- */
- private List<MiriamType> requiredMiriamType = new ArrayList<>();
-
- /**
- * Constructor that initializes the data with {@link #bioEntity bioEntity} and
- * list of improper {@link MiriamData}.
- *
- * @param list
- * list of missing but required {@link MiriamType}
- * @param bioEntity
- * {@link BioEntity}
- */
- public MissingRequiredAnnotations(BioEntity bioEntity, Collection<MiriamType> list) {
- if (list.size() == 0) {
- throw new InvalidArgumentException("List of improper annotations cannot be null");
- }
- this.bioEntity = bioEntity;
- requiredMiriamType.addAll(list);
- }
-
- @Override
- public String getMessage() {
- StringBuilder result = new StringBuilder(new ElementUtils().getElementTag(bioEntity));
- result.append("misses one of the following annotations: ");
- for (MiriamType type : requiredMiriamType) {
- result.append(type.getCommonName() + ", ");
- }
- return result.toString();
- }
-
- @Override
- public String toString() {
- return getMessage();
- }
-
-}
+package lcsb.mapviewer.annotation.services;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
+
+/**
+ * Defines problem with element annotation when there are some required
+ * annotations, but none of them can be found in the element.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class MissingRequiredAnnotations implements ProblematicAnnotation {
+
+ /**
+ * BioEntity improperly annotated.
+ */
+ private BioEntity bioEntity;
+
+ /**
+ * Required miriam type.
+ */
+ private List<MiriamType> requiredMiriamType = new ArrayList<>();
+
+ /**
+ * Constructor that initializes the data with {@link #bioEntity bioEntity} and
+ * list of improper {@link MiriamData}.
+ *
+ * @param list
+ * list of missing but required {@link MiriamType}
+ * @param bioEntity
+ * {@link BioEntity}
+ */
+ public MissingRequiredAnnotations(BioEntity bioEntity, Collection<MiriamType> list) {
+ if (list.size() == 0) {
+ throw new InvalidArgumentException("List of improper annotations cannot be null");
+ }
+ this.bioEntity = bioEntity;
+ requiredMiriamType.addAll(list);
+ }
+
+ @Override
+ public String getMessage() {
+ StringBuilder result = new StringBuilder(new ElementUtils().getElementTag(bioEntity));
+ result.append("misses one of the following annotations: ");
+ for (MiriamType type : requiredMiriamType) {
+ result.append(type.getCommonName() + ", ");
+ }
+ return result.toString();
+ }
+
+ @Override
+ public String toString() {
+ return getMessage();
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ProblematicAnnotation.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ProblematicAnnotation.java
index 8734327cb7..90e41d1cfe 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ProblematicAnnotation.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ProblematicAnnotation.java
@@ -1,17 +1,17 @@
-package lcsb.mapviewer.annotation.services;
-
-/**
- * Interface that describes annotation that is problematic.
- *
- * @author Piotr Gawron
- *
- */
-public interface ProblematicAnnotation {
-
- /**
- * Returns error message.
- *
- * @return problem error message
- */
- String getMessage();
-}
+package lcsb.mapviewer.annotation.services;
+
+/**
+ * Interface that describes annotation that is problematic.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface ProblematicAnnotation {
+
+ /**
+ * Returns error message.
+ *
+ * @return problem error message
+ */
+ String getMessage();
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java
index f62ba7ac96..1bf449dae0 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java
@@ -1,383 +1,383 @@
-package lcsb.mapviewer.annotation.services;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-import javax.xml.xpath.XPath;
-import javax.xml.xpath.XPathConstants;
-import javax.xml.xpath.XPathExpressionException;
-import javax.xml.xpath.XPathFactory;
-
-import org.apache.commons.lang3.SerializationException;
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.w3c.dom.Document;
-import org.w3c.dom.NodeList;
-
-import lcsb.mapviewer.annotation.cache.CachableInterface;
-import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
-import lcsb.mapviewer.annotation.cache.WebPageDownloader;
-import lcsb.mapviewer.annotation.cache.XmlSerializer;
-import lcsb.mapviewer.annotation.data.Article;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-
-/**
- * This class is a backend to publicly available pubmed API in
- * <a href="https://europepmc.org/RestfulWebService">Europe PubMed Central </a>.
- *
- * @author Piotr Gawron
- *
- */
-public class PubmedParser extends CachableInterface implements IExternalService {
-
- /**
- * Pubmed identifier used to check the status of service (functionality from
- * {@link IExternalService}).
- */
- static final int SERVICE_STATUS_PUBMED_ID = 12345;
-
- /**
- * Prefix used for caching elements with pubmed identifier as a key.
- */
- static final String PUBMED_PREFIX = "pubmed: ";
-
- /**
- * Length of {@link #PUBMED_PREFIX} string.
- */
- private static final int PUBMED_PREFIX_LENGTH = PUBMED_PREFIX.length();
-
- /**
- * Version of the remote API that is supported by this connecting class.
- */
- static final String SUPPORTED_VERSION = "5.3.5";
-
- static final String API_URL = "https://www.ebi.ac.uk/europepmc/webservices/rest/";
-
- /**
- * Connector used for accessing data from miriam registry.
- */
- @Autowired
- private MiriamConnector miriamConnector;
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(PubmedParser.class);
-
- /**
- * Object that allows to serialize {@link Article} elements into xml string and
- * deserialize xml into {@link Article} objects.
- */
- private XmlSerializer<Article> articleSerializer;
-
- @Override
- public Object refreshCacheQuery(Object query) throws SourceNotAvailable {
- Object result = null;
- try {
- if (query instanceof String) {
- String name = (String) query;
- if (name.startsWith(PUBMED_PREFIX)) {
- Integer id = Integer.valueOf(name.substring(PUBMED_PREFIX_LENGTH));
- result = articleSerializer.objectToString(getPubmedArticleById(id));
- } else {
- result = super.refreshCacheQuery(query);
- }
- } else {
- result = super.refreshCacheQuery(query);
- }
- } catch (PubmedSearchException e) {
- throw new SourceNotAvailable(e);
- }
-
- return result;
- }
-
- /**
- * Default constructor. Initializes structures used for transforming
- * {@link Article} from/to xml.
- */
- public PubmedParser() {
- super(PubmedParser.class);
- articleSerializer = new XmlSerializer<>(Article.class);
- }
-
- /**
- * Returns article data for given pubmed identifier.
- *
- * @param id
- * pubmed identifier
- * @return article data
- * @throws PubmedSearchException
- * thrown when there is a problem with accessing information about
- * pubmed
- */
- public Article getPubmedArticleById(Integer id) throws PubmedSearchException {
- String queryString = "pubmed: " + id;
- Article result = null;
- try {
- result = articleSerializer.xmlToObject(getCacheNode(queryString));
- } catch (SerializationException e) {
- logger.warn("Problem with deserialization of the string: " + queryString);
- }
- if (result != null && result.getTitle() != null) {
- return result;
- } else {
- logger.debug("Pubmed article (id=" + id + ") not found in cache. Accessing WebService...");
- }
-
- result = new Article();
- try {
- String url = API_URL + "search/resulttype=core&query="
- + java.net.URLEncoder.encode("src:med ext_id:" + id, "UTF-8");
-
- String content = getWebPageContent(url);
-
- Document mainDoc = super.getXmlDocumentFromString(content);
- // Document citationDoc = dBuilder.parse(citationStream);
- mainDoc.getDocumentElement().normalize();
- // citationDoc.getDocumentElement().normalize();
- XPathFactory xPathFactory = XPathFactory.newInstance();
- XPath xpath = xPathFactory.newXPath();
- NodeList nodeList = null;
- // Hit Count
- nodeList = (NodeList) xpath.compile("/responseWrapper/resultList/result/citedByCount").evaluate(mainDoc,
- XPathConstants.NODESET);
- if (nodeList != null && nodeList.getLength() > 0 && nodeList.item(0).getFirstChild() != null) {
- try {
- result.setCitationCount(Integer.valueOf(nodeList.item(0).getFirstChild().getNodeValue()));
- } catch (Exception e) {
- }
- }
- // Title
- nodeList = (NodeList) xpath.compile("/responseWrapper/resultList/result/title").evaluate(mainDoc,
- XPathConstants.NODESET);
- if (nodeList != null && nodeList.getLength() > 0 && nodeList.item(0).getFirstChild() != null) {
- result.setTitle(nodeList.item(0).getFirstChild().getNodeValue());
- }
- // Year
- nodeList = (NodeList) xpath.compile("/responseWrapper/resultList/result/journalInfo/yearOfPublication")
- .evaluate(mainDoc, XPathConstants.NODESET);
- if (nodeList != null && nodeList.getLength() > 0 && nodeList.item(0).getFirstChild() != null) {
- try {
- result.setYear(Integer.valueOf(nodeList.item(0).getFirstChild().getNodeValue()));
- } catch (Exception e) {
- }
- }
- // Journal
- nodeList = (NodeList) xpath.compile("/responseWrapper/resultList/result/journalInfo/journal/title")
- .evaluate(mainDoc, XPathConstants.NODESET);
- if (nodeList != null && nodeList.getLength() > 0 && nodeList.item(0).getFirstChild() != null) {
- result.setJournal(nodeList.item(0).getFirstChild().getNodeValue());
- }
- // Authors
- nodeList = (NodeList) xpath.compile("/responseWrapper/resultList/result/authorString").evaluate(mainDoc,
- XPathConstants.NODESET);
- if (nodeList != null && nodeList.getLength() > 0 && nodeList.item(0).getFirstChild() != null) {
- List<String> authors = new ArrayList<String>();
- String value = nodeList.item(0).getFirstChild().getNodeValue();
- if (value != null && !value.isEmpty()) {
- authors = Arrays.asList(value.split(","));
- }
- result.setAuthors(authors);
- }
- result.setLink(miriamConnector.getUrlString(new MiriamData(MiriamType.PUBMED, id + "")));
- result.setId(id + "");
-
- if (result.getTitle() != null && !result.getTitle().trim().isEmpty()) {
- try {
- setCacheValue(queryString, articleSerializer.objectToString(result));
- } catch (SerializationException e) {
- logger.warn("Problem with serialization of the string: " + queryString);
- }
- } else {
- result = null;
- }
-
- } catch (Exception e) {
- throw new PubmedSearchException(e);
- }
- return result;
- }
-
- /**
- * This method return html \< a\ > tag with link for pubmed id (with some
- * additional information).
- *
- * @param id
- * pubmed identifier
- * @param withTextPrefix
- * should prefix be added to the tag
- * @return link to webpage with pubmed article
- * @throws PubmedSearchException
- * thrown when there is a problem with accessing information about
- * pubmed
- */
- public String getHtmlFullLinkForId(Integer id, boolean withTextPrefix) throws PubmedSearchException {
- String result = "";
- Article article = getPubmedArticleById(id);
- result += "<div style=\"float:left;\" title=\"" + article.getTitle() + ", ";
- result += article.getStringAuthors() + ", ";
- result += article.getYear() + ", ";
- result += article.getJournal() + "\">";
- if (withTextPrefix) {
- result += "pubmed: ";
- }
- result += "<a target=\"_blank\" href = \"" + article.getLink() + "\">" + id + "</a> </div>";
- return result;
- }
-
- /**
- * This method return html \< a\ > tag with link for pubmed id (with some
- * additional information).
- *
- * @param id
- * pubmed identifier
- * @return link to webpage with pubmed article
- * @throws PubmedSearchException
- * thrown when there is a problem with accessing information about
- * pubmed
- */
- public String getHtmlFullLinkForId(Integer id) throws PubmedSearchException {
- return getHtmlFullLinkForId(id, true);
- }
-
- /**
- * Get the summary of the article.
- *
- * @param id
- * pubmed identifier
- * @return summary of the article.
- * @throws PubmedSearchException
- * thrown when there is a problem with accessing information about
- * pubmed
- */
- public String getSummary(Integer id) throws PubmedSearchException {
- Article article = getPubmedArticleById(id);
- if (article == null) {
- return null;
- }
- String result = article.getTitle() + ", " + article.getStringAuthors() + ", " + article.getYear() + ", "
- + article.getJournal();
- return result;
- }
-
- @Override
- public ExternalServiceStatus getServiceStatus() {
- ExternalServiceStatus status = new ExternalServiceStatus("Europe PubMed Central",
- "https://europepmc.org/RestfulWebService");
- GeneralCacheInterface cacheCopy = getCache();
- this.setCache(null);
-
- try {
- Article art = getPubmedArticleById(SERVICE_STATUS_PUBMED_ID);
- if (!getApiVersion().equals(SUPPORTED_VERSION)) {
- logger.debug("New europepmc API version: " + getApiVersion());
- status.setStatus(ExternalServiceStatusType.CHANGED);
- } else if (art == null) {
- status.setStatus(ExternalServiceStatusType.DOWN);
- } else {
- status.setStatus(ExternalServiceStatusType.OK);
- }
- } catch (Exception e) {
- logger.error(status.getName() + " is down", e);
- status.setStatus(ExternalServiceStatusType.DOWN);
- }
- this.setCache(cacheCopy);
- return status;
- }
-
- /**
- * Returns current version of the pmc API.
- *
- * @return version of the api to which this class is connected
- * @throws PubmedSearchException
- * thrown when there is a problem with accessing external databes
- */
- public String getApiVersion() throws PubmedSearchException {
- try {
- String url = API_URL + "search/resulttype=core&query=src%3Amed+ext_id%3A23644949";
-
- String content = getWebPageContent(url);
-
- Document mainDoc = super.getXmlDocumentFromString(content);
- mainDoc.getDocumentElement().normalize();
- XPathFactory xPathFactory = XPathFactory.newInstance();
- XPath xpath = xPathFactory.newXPath();
- NodeList nodeList = (NodeList) xpath.compile("/responseWrapper/version").evaluate(mainDoc,
- XPathConstants.NODESET);
- if (nodeList.getLength() > 0) {
- return nodeList.item(0).getTextContent();
- }
- return null;
- } catch (IOException e) {
- throw new PubmedSearchException("Problem with accessing pubmed db", e);
- } catch (InvalidXmlSchemaException | XPathExpressionException e) {
- throw new PubmedSearchException("Invalid response from pubmed db", e);
- }
- }
-
- /**
- * Get the summary of the article.
- *
- * @param id
- * pubmed identifier
- * @return summary of the article.
- * @throws PubmedSearchException
- * thrown when there is a problem with accessing information about
- * pubmed
- */
- public String getSummary(String id) throws PubmedSearchException {
- return getSummary(Integer.valueOf(id));
- }
-
- /**
- * @return the miriamConnector
- * @see #miriamConnector
- */
- public MiriamConnector getMiriamConnector() {
- return miriamConnector;
- }
-
- /**
- * @param miriamConnector
- * the miriamConnector to set
- * @see #miriamConnector
- */
- public void setMiriamConnector(MiriamConnector miriamConnector) {
- this.miriamConnector = miriamConnector;
- }
-
- /**
- * @return the articleSerializer
- * @see #articleSerializer
- */
- protected XmlSerializer<Article> getArticleSerializer() {
- return articleSerializer;
- }
-
- /**
- * @param articleSerializer
- * the articleSerializer to set
- * @see #articleSerializer
- */
- protected void setArticleSerializer(XmlSerializer<Article> articleSerializer) {
- this.articleSerializer = articleSerializer;
- }
-
- @Override
- protected WebPageDownloader getWebPageDownloader() {
- return super.getWebPageDownloader();
- }
-
- @Override
- protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
- super.setWebPageDownloader(webPageDownloader);
- }
-
-}
+package lcsb.mapviewer.annotation.services;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import javax.xml.xpath.XPath;
+import javax.xml.xpath.XPathConstants;
+import javax.xml.xpath.XPathExpressionException;
+import javax.xml.xpath.XPathFactory;
+
+import org.apache.commons.lang3.SerializationException;
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.w3c.dom.Document;
+import org.w3c.dom.NodeList;
+
+import lcsb.mapviewer.annotation.cache.CachableInterface;
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.WebPageDownloader;
+import lcsb.mapviewer.annotation.cache.XmlSerializer;
+import lcsb.mapviewer.annotation.data.Article;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+
+/**
+ * This class is a backend to publicly available pubmed API in
+ * <a href="https://europepmc.org/RestfulWebService">Europe PubMed Central </a>.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class PubmedParser extends CachableInterface implements IExternalService {
+
+ /**
+ * Pubmed identifier used to check the status of service (functionality from
+ * {@link IExternalService}).
+ */
+ static final int SERVICE_STATUS_PUBMED_ID = 12345;
+
+ /**
+ * Prefix used for caching elements with pubmed identifier as a key.
+ */
+ static final String PUBMED_PREFIX = "pubmed: ";
+
+ /**
+ * Length of {@link #PUBMED_PREFIX} string.
+ */
+ private static final int PUBMED_PREFIX_LENGTH = PUBMED_PREFIX.length();
+
+ /**
+ * Version of the remote API that is supported by this connecting class.
+ */
+ static final String SUPPORTED_VERSION = "5.3.5";
+
+ static final String API_URL = "https://www.ebi.ac.uk/europepmc/webservices/rest/";
+
+ /**
+ * Connector used for accessing data from miriam registry.
+ */
+ @Autowired
+ private MiriamConnector miriamConnector;
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(PubmedParser.class);
+
+ /**
+ * Object that allows to serialize {@link Article} elements into xml string and
+ * deserialize xml into {@link Article} objects.
+ */
+ private XmlSerializer<Article> articleSerializer;
+
+ @Override
+ public Object refreshCacheQuery(Object query) throws SourceNotAvailable {
+ Object result = null;
+ try {
+ if (query instanceof String) {
+ String name = (String) query;
+ if (name.startsWith(PUBMED_PREFIX)) {
+ Integer id = Integer.valueOf(name.substring(PUBMED_PREFIX_LENGTH));
+ result = articleSerializer.objectToString(getPubmedArticleById(id));
+ } else {
+ result = super.refreshCacheQuery(query);
+ }
+ } else {
+ result = super.refreshCacheQuery(query);
+ }
+ } catch (PubmedSearchException e) {
+ throw new SourceNotAvailable(e);
+ }
+
+ return result;
+ }
+
+ /**
+ * Default constructor. Initializes structures used for transforming
+ * {@link Article} from/to xml.
+ */
+ public PubmedParser() {
+ super(PubmedParser.class);
+ articleSerializer = new XmlSerializer<>(Article.class);
+ }
+
+ /**
+ * Returns article data for given pubmed identifier.
+ *
+ * @param id
+ * pubmed identifier
+ * @return article data
+ * @throws PubmedSearchException
+ * thrown when there is a problem with accessing information about
+ * pubmed
+ */
+ public Article getPubmedArticleById(Integer id) throws PubmedSearchException {
+ String queryString = "pubmed: " + id;
+ Article result = null;
+ try {
+ result = articleSerializer.xmlToObject(getCacheNode(queryString));
+ } catch (SerializationException e) {
+ logger.warn("Problem with deserialization of the string: " + queryString);
+ }
+ if (result != null && result.getTitle() != null) {
+ return result;
+ } else {
+ logger.debug("Pubmed article (id=" + id + ") not found in cache. Accessing WebService...");
+ }
+
+ result = new Article();
+ try {
+ String url = API_URL + "search/resulttype=core&query="
+ + java.net.URLEncoder.encode("src:med ext_id:" + id, "UTF-8");
+
+ String content = getWebPageContent(url);
+
+ Document mainDoc = super.getXmlDocumentFromString(content);
+ // Document citationDoc = dBuilder.parse(citationStream);
+ mainDoc.getDocumentElement().normalize();
+ // citationDoc.getDocumentElement().normalize();
+ XPathFactory xPathFactory = XPathFactory.newInstance();
+ XPath xpath = xPathFactory.newXPath();
+ NodeList nodeList = null;
+ // Hit Count
+ nodeList = (NodeList) xpath.compile("/responseWrapper/resultList/result/citedByCount").evaluate(mainDoc,
+ XPathConstants.NODESET);
+ if (nodeList != null && nodeList.getLength() > 0 && nodeList.item(0).getFirstChild() != null) {
+ try {
+ result.setCitationCount(Integer.valueOf(nodeList.item(0).getFirstChild().getNodeValue()));
+ } catch (Exception e) {
+ }
+ }
+ // Title
+ nodeList = (NodeList) xpath.compile("/responseWrapper/resultList/result/title").evaluate(mainDoc,
+ XPathConstants.NODESET);
+ if (nodeList != null && nodeList.getLength() > 0 && nodeList.item(0).getFirstChild() != null) {
+ result.setTitle(nodeList.item(0).getFirstChild().getNodeValue());
+ }
+ // Year
+ nodeList = (NodeList) xpath.compile("/responseWrapper/resultList/result/journalInfo/yearOfPublication")
+ .evaluate(mainDoc, XPathConstants.NODESET);
+ if (nodeList != null && nodeList.getLength() > 0 && nodeList.item(0).getFirstChild() != null) {
+ try {
+ result.setYear(Integer.valueOf(nodeList.item(0).getFirstChild().getNodeValue()));
+ } catch (Exception e) {
+ }
+ }
+ // Journal
+ nodeList = (NodeList) xpath.compile("/responseWrapper/resultList/result/journalInfo/journal/title")
+ .evaluate(mainDoc, XPathConstants.NODESET);
+ if (nodeList != null && nodeList.getLength() > 0 && nodeList.item(0).getFirstChild() != null) {
+ result.setJournal(nodeList.item(0).getFirstChild().getNodeValue());
+ }
+ // Authors
+ nodeList = (NodeList) xpath.compile("/responseWrapper/resultList/result/authorString").evaluate(mainDoc,
+ XPathConstants.NODESET);
+ if (nodeList != null && nodeList.getLength() > 0 && nodeList.item(0).getFirstChild() != null) {
+ List<String> authors = new ArrayList<String>();
+ String value = nodeList.item(0).getFirstChild().getNodeValue();
+ if (value != null && !value.isEmpty()) {
+ authors = Arrays.asList(value.split(","));
+ }
+ result.setAuthors(authors);
+ }
+ result.setLink(miriamConnector.getUrlString(new MiriamData(MiriamType.PUBMED, id + "")));
+ result.setId(id + "");
+
+ if (result.getTitle() != null && !result.getTitle().trim().isEmpty()) {
+ try {
+ setCacheValue(queryString, articleSerializer.objectToString(result));
+ } catch (SerializationException e) {
+ logger.warn("Problem with serialization of the string: " + queryString);
+ }
+ } else {
+ result = null;
+ }
+
+ } catch (Exception e) {
+ throw new PubmedSearchException(e);
+ }
+ return result;
+ }
+
+ /**
+ * This method return html \< a\ > tag with link for pubmed id (with some
+ * additional information).
+ *
+ * @param id
+ * pubmed identifier
+ * @param withTextPrefix
+ * should prefix be added to the tag
+ * @return link to webpage with pubmed article
+ * @throws PubmedSearchException
+ * thrown when there is a problem with accessing information about
+ * pubmed
+ */
+ public String getHtmlFullLinkForId(Integer id, boolean withTextPrefix) throws PubmedSearchException {
+ String result = "";
+ Article article = getPubmedArticleById(id);
+ result += "<div style=\"float:left;\" title=\"" + article.getTitle() + ", ";
+ result += article.getStringAuthors() + ", ";
+ result += article.getYear() + ", ";
+ result += article.getJournal() + "\">";
+ if (withTextPrefix) {
+ result += "pubmed: ";
+ }
+ result += "<a target=\"_blank\" href = \"" + article.getLink() + "\">" + id + "</a> </div>";
+ return result;
+ }
+
+ /**
+ * This method return html \< a\ > tag with link for pubmed id (with some
+ * additional information).
+ *
+ * @param id
+ * pubmed identifier
+ * @return link to webpage with pubmed article
+ * @throws PubmedSearchException
+ * thrown when there is a problem with accessing information about
+ * pubmed
+ */
+ public String getHtmlFullLinkForId(Integer id) throws PubmedSearchException {
+ return getHtmlFullLinkForId(id, true);
+ }
+
+ /**
+ * Get the summary of the article.
+ *
+ * @param id
+ * pubmed identifier
+ * @return summary of the article.
+ * @throws PubmedSearchException
+ * thrown when there is a problem with accessing information about
+ * pubmed
+ */
+ public String getSummary(Integer id) throws PubmedSearchException {
+ Article article = getPubmedArticleById(id);
+ if (article == null) {
+ return null;
+ }
+ String result = article.getTitle() + ", " + article.getStringAuthors() + ", " + article.getYear() + ", "
+ + article.getJournal();
+ return result;
+ }
+
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ ExternalServiceStatus status = new ExternalServiceStatus("Europe PubMed Central",
+ "https://europepmc.org/RestfulWebService");
+ GeneralCacheInterface cacheCopy = getCache();
+ this.setCache(null);
+
+ try {
+ Article art = getPubmedArticleById(SERVICE_STATUS_PUBMED_ID);
+ if (!getApiVersion().equals(SUPPORTED_VERSION)) {
+ logger.debug("New europepmc API version: " + getApiVersion());
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ } else if (art == null) {
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ } else {
+ status.setStatus(ExternalServiceStatusType.OK);
+ }
+ } catch (Exception e) {
+ logger.error(status.getName() + " is down", e);
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ }
+ this.setCache(cacheCopy);
+ return status;
+ }
+
+ /**
+ * Returns current version of the pmc API.
+ *
+ * @return version of the api to which this class is connected
+ * @throws PubmedSearchException
+ * thrown when there is a problem with accessing external databes
+ */
+ public String getApiVersion() throws PubmedSearchException {
+ try {
+ String url = API_URL + "search/resulttype=core&query=src%3Amed+ext_id%3A23644949";
+
+ String content = getWebPageContent(url);
+
+ Document mainDoc = super.getXmlDocumentFromString(content);
+ mainDoc.getDocumentElement().normalize();
+ XPathFactory xPathFactory = XPathFactory.newInstance();
+ XPath xpath = xPathFactory.newXPath();
+ NodeList nodeList = (NodeList) xpath.compile("/responseWrapper/version").evaluate(mainDoc,
+ XPathConstants.NODESET);
+ if (nodeList.getLength() > 0) {
+ return nodeList.item(0).getTextContent();
+ }
+ return null;
+ } catch (IOException e) {
+ throw new PubmedSearchException("Problem with accessing pubmed db", e);
+ } catch (InvalidXmlSchemaException | XPathExpressionException e) {
+ throw new PubmedSearchException("Invalid response from pubmed db", e);
+ }
+ }
+
+ /**
+ * Get the summary of the article.
+ *
+ * @param id
+ * pubmed identifier
+ * @return summary of the article.
+ * @throws PubmedSearchException
+ * thrown when there is a problem with accessing information about
+ * pubmed
+ */
+ public String getSummary(String id) throws PubmedSearchException {
+ return getSummary(Integer.valueOf(id));
+ }
+
+ /**
+ * @return the miriamConnector
+ * @see #miriamConnector
+ */
+ public MiriamConnector getMiriamConnector() {
+ return miriamConnector;
+ }
+
+ /**
+ * @param miriamConnector
+ * the miriamConnector to set
+ * @see #miriamConnector
+ */
+ public void setMiriamConnector(MiriamConnector miriamConnector) {
+ this.miriamConnector = miriamConnector;
+ }
+
+ /**
+ * @return the articleSerializer
+ * @see #articleSerializer
+ */
+ protected XmlSerializer<Article> getArticleSerializer() {
+ return articleSerializer;
+ }
+
+ /**
+ * @param articleSerializer
+ * the articleSerializer to set
+ * @see #articleSerializer
+ */
+ protected void setArticleSerializer(XmlSerializer<Article> articleSerializer) {
+ this.articleSerializer = articleSerializer;
+ }
+
+ @Override
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
+ }
+
+ @Override
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedSearchException.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedSearchException.java
index ce80feb3f0..ae2d8cf115 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedSearchException.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedSearchException.java
@@ -1,38 +1,38 @@
-package lcsb.mapviewer.annotation.services;
-
-/**
- * Exception thrown when there was a problem when searching for a pubmed data.
- *
- * @author Piotr Gawron
- *
- */
-public class PubmedSearchException extends Exception {
-
- /**
- * Default constructor.
- *
- * @param e
- * parent exception
- */
- public PubmedSearchException(Exception e) {
- super(e);
- }
-
- /**
- * Default constructor.
- *
- * @param message
- * exception message
- * @param e
- * source exception
- */
- public PubmedSearchException(String message, Exception e) {
- super(message, e);
- }
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
-}
+package lcsb.mapviewer.annotation.services;
+
+/**
+ * Exception thrown when there was a problem when searching for a pubmed data.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class PubmedSearchException extends Exception {
+
+ /**
+ * Default constructor.
+ *
+ * @param e
+ * parent exception
+ */
+ public PubmedSearchException(Exception e) {
+ super(e);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * exception message
+ * @param e
+ * source exception
+ */
+ public PubmedSearchException(String message, Exception e) {
+ super(message, e);
+ }
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/TaxonomyBackend.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/TaxonomyBackend.java
index 813d91a087..22962ff9eb 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/TaxonomyBackend.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/TaxonomyBackend.java
@@ -1,209 +1,209 @@
-package lcsb.mapviewer.annotation.services;
-
-import java.io.IOException;
-import java.net.URLEncoder;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.annotation.cache.CachableInterface;
-import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
-import lcsb.mapviewer.annotation.cache.WebPageDownloader;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-
-/**
- * This class is a backend to Taxonomy.
- *
- * @author Piotr Gawron
- *
- */
-public class TaxonomyBackend extends CachableInterface implements IExternalService {
-
- /**
- * Constant defining human taxonomy.
- */
- public static final MiriamData HUMAN_TAXONOMY = new MiriamData(MiriamType.TAXONOMY, "9606");
-
- /**
- * Prefix string used for marking the query in database as query by taxonomy
- * term.
- */
- static final String TAXONOMY_CACHE_PREFIX = "TAXONOMY_TERM: ";
-
- /**
- * Prefix string used for marking queries in database as queries returning
- * name by taxonomy id.
- */
- static final String TAXONOMY_NAME_CACHE_PREFIX = "TAXONOMY_NAME_BY_ID: ";
-
- @Override
- public String refreshCacheQuery(Object query) throws SourceNotAvailable {
- String result = null;
- try {
- if (query instanceof String) {
- String name = (String) query;
- if (name.startsWith(TAXONOMY_CACHE_PREFIX)) {
- String term = name.substring(TAXONOMY_CACHE_PREFIX.length());
- MiriamData md = getByName(term);
- if (md != null) {
- result = md.getResource();
- }
- } else if (name.startsWith(TAXONOMY_NAME_CACHE_PREFIX)) {
- String id = name.substring(TAXONOMY_NAME_CACHE_PREFIX.length());
- result = getNameForTaxonomy(new MiriamData(MiriamType.TAXONOMY, id));
- } else if (name.startsWith("http")) {
- result = getWebPageContent(name);
- } else {
- throw new InvalidArgumentException("Don't know what to do with query: " + query);
- }
- } else {
- throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
- }
- } catch (TaxonomySearchException | IOException e) {
- throw new SourceNotAvailable(e);
- }
- return result;
- }
-
- /**
- * Returns {@link MiriamData} representing taxonomy identified by name.
- *
- * @param term
- * name of the organism
- * @return {@link MiriamData} representing taxonomy
- * @throws TaxonomySearchException
- * thrown when there is a problem with accessing taxonomy database
- */
- public MiriamData getByName(String term) throws TaxonomySearchException {
- if (term == null || "".equals(term.trim())) {
- return null;
- }
- String res = getCacheValue(TAXONOMY_CACHE_PREFIX + term);
- if (res != null) {
- return new MiriamData(MiriamType.TAXONOMY, res);
- }
- try {
-
- String queryTerm = term.trim();
- if (queryTerm.indexOf("(") >= 0) {
- queryTerm = queryTerm.substring(0, queryTerm.indexOf("("));
- }
- if (queryTerm.toUpperCase().startsWith("C.")) {
- queryTerm = "Caenorhabditis" + queryTerm.substring(2);
- } else if (queryTerm.toUpperCase().startsWith("D.")) {
- queryTerm = "Drosophila" + queryTerm.substring(2);
- } else if (queryTerm.toUpperCase().startsWith("P.")) {
- queryTerm = "Pristionchus" + queryTerm.substring(2);
- } else if (queryTerm.toUpperCase().startsWith("T.")) {
- queryTerm = "Tribolium" + queryTerm.substring(2);
- } else if (queryTerm.equalsIgnoreCase("Mouse")) {
- queryTerm = "Mus musculus";
- } else if (queryTerm.equalsIgnoreCase("Rat")) {
- queryTerm = "Rattus norvegicus";
- }
- queryTerm = URLEncoder.encode(queryTerm, "UTF-8");
- String url = "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?lvl=0&name=" + queryTerm;
- String page = getWebPageContent(url);
- Pattern idPattern = Pattern.compile("<em>Taxonomy ID: </em>([0-9]+)");
- Matcher matcher = idPattern.matcher(page);
- if (!matcher.find()) {
- logger.warn("Unknown organism: " + term);
- return null;
- } else {
- String name = matcher.group(1);
- setCacheValue(TAXONOMY_CACHE_PREFIX + term, name);
- return new MiriamData(MiriamType.TAXONOMY, name);
- }
- } catch (IOException e) {
- throw new TaxonomySearchException("Problem with accessing taxonomy database", e);
- }
-
- }
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(TaxonomyBackend.class);
-
- /**
- * Default constructor.
- */
- public TaxonomyBackend() {
- super(TaxonomyBackend.class);
- }
-
- @Override
- public ExternalServiceStatus getServiceStatus() {
- ExternalServiceStatus status = new ExternalServiceStatus(MiriamType.TAXONOMY.getCommonName(), MiriamType.TAXONOMY.getDbHomepage());
-
- GeneralCacheInterface cacheCopy = getCache();
- this.setCache(null);
-
- try {
- MiriamData md = getByName("human");
- if (md == null) {
- status.setStatus(ExternalServiceStatusType.CHANGED);
- } else if (md.equals(TaxonomyBackend.HUMAN_TAXONOMY)) {
- status.setStatus(ExternalServiceStatusType.OK);
- } else {
- status.setStatus(ExternalServiceStatusType.CHANGED);
- }
- } catch (Exception e) {
- logger.error(MiriamType.TAXONOMY.getCommonName() + " is down", e);
- status.setStatus(ExternalServiceStatusType.DOWN);
- }
- this.setCache(cacheCopy);
- return status;
- }
-
- /**
- * Returns name for given taxonomy id.
- *
- * @param miriamData
- * object representing taxonomy id
- * @return name for given taxonomy id
- * @throws TaxonomySearchException
- * thrown when there is a problem with accessing external database
- */
- public String getNameForTaxonomy(MiriamData miriamData) throws TaxonomySearchException {
- if (miriamData == null) {
- return null;
- }
- String res = getCacheValue(TAXONOMY_NAME_CACHE_PREFIX + miriamData.getResource());
- if (res != null) {
- return res;
- }
-
- try {
- String url = "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=" + miriamData.getResource();
- String page = getWebPageContent(url);
- Pattern idPattern = Pattern.compile("<title>Taxonomy browser \\(([A-Za-z0-9\\ \\.]+)\\)</title>");
- Matcher matcher = idPattern.matcher(page);
- if (!matcher.find()) {
- logger.warn("Unknown organism: " + miriamData);
- return null;
- } else {
- String name = matcher.group(1);
- setCacheValue(TAXONOMY_NAME_CACHE_PREFIX + miriamData.getResource(), name);
- return name;
- }
- } catch (IOException e) {
- throw new TaxonomySearchException("Problem with accessing taxonomy database", e);
- }
- }
-
- @Override
- protected WebPageDownloader getWebPageDownloader() {
- return super.getWebPageDownloader();
- }
-
- @Override
- protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
- super.setWebPageDownloader(webPageDownloader);
- }
-
-}
+package lcsb.mapviewer.annotation.services;
+
+import java.io.IOException;
+import java.net.URLEncoder;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.annotation.cache.CachableInterface;
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.WebPageDownloader;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+
+/**
+ * This class is a backend to Taxonomy.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class TaxonomyBackend extends CachableInterface implements IExternalService {
+
+ /**
+ * Constant defining human taxonomy.
+ */
+ public static final MiriamData HUMAN_TAXONOMY = new MiriamData(MiriamType.TAXONOMY, "9606");
+
+ /**
+ * Prefix string used for marking the query in database as query by taxonomy
+ * term.
+ */
+ static final String TAXONOMY_CACHE_PREFIX = "TAXONOMY_TERM: ";
+
+ /**
+ * Prefix string used for marking queries in database as queries returning
+ * name by taxonomy id.
+ */
+ static final String TAXONOMY_NAME_CACHE_PREFIX = "TAXONOMY_NAME_BY_ID: ";
+
+ @Override
+ public String refreshCacheQuery(Object query) throws SourceNotAvailable {
+ String result = null;
+ try {
+ if (query instanceof String) {
+ String name = (String) query;
+ if (name.startsWith(TAXONOMY_CACHE_PREFIX)) {
+ String term = name.substring(TAXONOMY_CACHE_PREFIX.length());
+ MiriamData md = getByName(term);
+ if (md != null) {
+ result = md.getResource();
+ }
+ } else if (name.startsWith(TAXONOMY_NAME_CACHE_PREFIX)) {
+ String id = name.substring(TAXONOMY_NAME_CACHE_PREFIX.length());
+ result = getNameForTaxonomy(new MiriamData(MiriamType.TAXONOMY, id));
+ } else if (name.startsWith("http")) {
+ result = getWebPageContent(name);
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with query: " + query);
+ }
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
+ }
+ } catch (TaxonomySearchException | IOException e) {
+ throw new SourceNotAvailable(e);
+ }
+ return result;
+ }
+
+ /**
+ * Returns {@link MiriamData} representing taxonomy identified by name.
+ *
+ * @param term
+ * name of the organism
+ * @return {@link MiriamData} representing taxonomy
+ * @throws TaxonomySearchException
+ * thrown when there is a problem with accessing taxonomy database
+ */
+ public MiriamData getByName(String term) throws TaxonomySearchException {
+ if (term == null || "".equals(term.trim())) {
+ return null;
+ }
+ String res = getCacheValue(TAXONOMY_CACHE_PREFIX + term);
+ if (res != null) {
+ return new MiriamData(MiriamType.TAXONOMY, res);
+ }
+ try {
+
+ String queryTerm = term.trim();
+ if (queryTerm.indexOf("(") >= 0) {
+ queryTerm = queryTerm.substring(0, queryTerm.indexOf("("));
+ }
+ if (queryTerm.toUpperCase().startsWith("C.")) {
+ queryTerm = "Caenorhabditis" + queryTerm.substring(2);
+ } else if (queryTerm.toUpperCase().startsWith("D.")) {
+ queryTerm = "Drosophila" + queryTerm.substring(2);
+ } else if (queryTerm.toUpperCase().startsWith("P.")) {
+ queryTerm = "Pristionchus" + queryTerm.substring(2);
+ } else if (queryTerm.toUpperCase().startsWith("T.")) {
+ queryTerm = "Tribolium" + queryTerm.substring(2);
+ } else if (queryTerm.equalsIgnoreCase("Mouse")) {
+ queryTerm = "Mus musculus";
+ } else if (queryTerm.equalsIgnoreCase("Rat")) {
+ queryTerm = "Rattus norvegicus";
+ }
+ queryTerm = URLEncoder.encode(queryTerm, "UTF-8");
+ String url = "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?lvl=0&name=" + queryTerm;
+ String page = getWebPageContent(url);
+ Pattern idPattern = Pattern.compile("<em>Taxonomy ID: </em>([0-9]+)");
+ Matcher matcher = idPattern.matcher(page);
+ if (!matcher.find()) {
+ logger.warn("Unknown organism: " + term);
+ return null;
+ } else {
+ String name = matcher.group(1);
+ setCacheValue(TAXONOMY_CACHE_PREFIX + term, name);
+ return new MiriamData(MiriamType.TAXONOMY, name);
+ }
+ } catch (IOException e) {
+ throw new TaxonomySearchException("Problem with accessing taxonomy database", e);
+ }
+
+ }
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(TaxonomyBackend.class);
+
+ /**
+ * Default constructor.
+ */
+ public TaxonomyBackend() {
+ super(TaxonomyBackend.class);
+ }
+
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ ExternalServiceStatus status = new ExternalServiceStatus(MiriamType.TAXONOMY.getCommonName(), MiriamType.TAXONOMY.getDbHomepage());
+
+ GeneralCacheInterface cacheCopy = getCache();
+ this.setCache(null);
+
+ try {
+ MiriamData md = getByName("human");
+ if (md == null) {
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ } else if (md.equals(TaxonomyBackend.HUMAN_TAXONOMY)) {
+ status.setStatus(ExternalServiceStatusType.OK);
+ } else {
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ }
+ } catch (Exception e) {
+ logger.error(MiriamType.TAXONOMY.getCommonName() + " is down", e);
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ }
+ this.setCache(cacheCopy);
+ return status;
+ }
+
+ /**
+ * Returns name for given taxonomy id.
+ *
+ * @param miriamData
+ * object representing taxonomy id
+ * @return name for given taxonomy id
+ * @throws TaxonomySearchException
+ * thrown when there is a problem with accessing external database
+ */
+ public String getNameForTaxonomy(MiriamData miriamData) throws TaxonomySearchException {
+ if (miriamData == null) {
+ return null;
+ }
+ String res = getCacheValue(TAXONOMY_NAME_CACHE_PREFIX + miriamData.getResource());
+ if (res != null) {
+ return res;
+ }
+
+ try {
+ String url = "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=" + miriamData.getResource();
+ String page = getWebPageContent(url);
+ Pattern idPattern = Pattern.compile("<title>Taxonomy browser \\(([A-Za-z0-9\\ \\.]+)\\)</title>");
+ Matcher matcher = idPattern.matcher(page);
+ if (!matcher.find()) {
+ logger.warn("Unknown organism: " + miriamData);
+ return null;
+ } else {
+ String name = matcher.group(1);
+ setCacheValue(TAXONOMY_NAME_CACHE_PREFIX + miriamData.getResource(), name);
+ return name;
+ }
+ } catch (IOException e) {
+ throw new TaxonomySearchException("Problem with accessing taxonomy database", e);
+ }
+ }
+
+ @Override
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
+ }
+
+ @Override
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/TaxonomySearchException.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/TaxonomySearchException.java
index e429e11888..ce90c04e61 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/TaxonomySearchException.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/TaxonomySearchException.java
@@ -1,30 +1,30 @@
-package lcsb.mapviewer.annotation.services;
-
-/**
- * Exception that should be thrown when there is a problem with finding
- * information about taxonomy.
- *
- * @author Piotr Gawron
- *
- */
-public class TaxonomySearchException extends Exception {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Constructs a new exception with the specified detail message and cause.
- *
- * @param message
- * the detail message
- * @param cause
- * the cause (A <tt>null</tt> value is permitted, and indicates that
- * the cause is nonexistent or unknown.)
- */
- public TaxonomySearchException(String message, Throwable cause) {
- super(message, cause);
- }
-
-}
+package lcsb.mapviewer.annotation.services;
+
+/**
+ * Exception that should be thrown when there is a problem with finding
+ * information about taxonomy.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class TaxonomySearchException extends Exception {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Constructs a new exception with the specified detail message and cause.
+ *
+ * @param message
+ * the detail message
+ * @param cause
+ * the cause (A <tt>null</tt> value is permitted, and indicates that
+ * the cause is nonexistent or unknown.)
+ */
+ public TaxonomySearchException(String message, Throwable cause) {
+ super(message, cause);
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/WrongResponseCodeIOException.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/WrongResponseCodeIOException.java
index 3811155935..501f7a4807 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/WrongResponseCodeIOException.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/WrongResponseCodeIOException.java
@@ -1,43 +1,43 @@
-package lcsb.mapviewer.annotation.services;
-
-import java.io.IOException;
-
-/**
- * Exception that should be thrown when accessing http url ends up with
- * IOException caused by invalid response code. This exception is for internal
- * use only.
- *
- * @author Piotr Gawron
- *
- */
-public class WrongResponseCodeIOException extends IOException {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- /**
- * Response code returned by the super {@link IOException}.
- */
- private int responseCode;
-
- /**
- * Default constructor.
- *
- * @param exception
- * super exception
- * @param code
- * {@link #responseCode}
- */
- public WrongResponseCodeIOException(IOException exception, int code) {
- super(exception);
- this.responseCode = code;
- }
-
- /**
- * @return the responseCode
- * @see #responseCode
- */
- public int getResponseCode() {
- return responseCode;
- }
-}
+package lcsb.mapviewer.annotation.services;
+
+import java.io.IOException;
+
+/**
+ * Exception that should be thrown when accessing http url ends up with
+ * IOException caused by invalid response code. This exception is for internal
+ * use only.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class WrongResponseCodeIOException extends IOException {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ /**
+ * Response code returned by the super {@link IOException}.
+ */
+ private int responseCode;
+
+ /**
+ * Default constructor.
+ *
+ * @param exception
+ * super exception
+ * @param code
+ * {@link #responseCode}
+ */
+ public WrongResponseCodeIOException(IOException exception, int code) {
+ super(exception);
+ this.responseCode = code;
+ }
+
+ /**
+ * @return the responseCode
+ * @see #responseCode
+ */
+ public int getResponseCode() {
+ return responseCode;
+ }
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorException.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorException.java
index 510e850d99..34ebfe92ee 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorException.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorException.java
@@ -1,48 +1,48 @@
-package lcsb.mapviewer.annotation.services.annotators;
-
-/**
- * Exception thrown when there is a problem with annotator.
- *
- * @author Piotr Gawron
- *
- */
-public class AnnotatorException extends Exception {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- *
- * @param exception
- * original exception
- */
- public AnnotatorException(Exception exception) {
- super(exception);
- }
-
- /**
- * Default constructor.
- *
- * @param message
- * message associated with exception
- * @param exception
- * original exception
- */
- public AnnotatorException(String message, Exception exception) {
- super(message, exception);
- }
-
- /**
- * Default constructor.
- *
- * @param message
- * message associated with exception
- */
- public AnnotatorException(String message) {
- super(message);
- }
-
-}
+package lcsb.mapviewer.annotation.services.annotators;
+
+/**
+ * Exception thrown when there is a problem with annotator.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class AnnotatorException extends Exception {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ *
+ * @param exception
+ * original exception
+ */
+ public AnnotatorException(Exception exception) {
+ super(exception);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * message associated with exception
+ * @param exception
+ * original exception
+ */
+ public AnnotatorException(String message, Exception exception) {
+ super(message, exception);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * message associated with exception
+ */
+ public AnnotatorException(String message) {
+ super(message);
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java
index 0434c77729..4042ea3434 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java
@@ -1,345 +1,345 @@
-package lcsb.mapviewer.annotation.services.annotators;
-
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Scanner;
-
-import org.apache.http.HttpEntity;
-import org.apache.http.client.methods.CloseableHttpResponse;
-import org.apache.http.client.methods.HttpPost;
-import org.apache.http.entity.ContentType;
-import org.apache.http.entity.mime.MultipartEntityBuilder;
-import org.apache.http.impl.client.CloseableHttpClient;
-import org.apache.http.impl.client.HttpClients;
-import org.apache.log4j.Logger;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
-import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
-import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
-import lcsb.mapviewer.annotation.services.IExternalService;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Rna;
-
-/**
- * This class is responsible for connection to Vencata annotation service. The
- * service is available on
- * http://biocompendium.embl.de/map_annotator/REST/GetAnnotation/. This service
- * is RESTful service. To query for an annotation one need to send a POST
- * message with two parameters:<br>
- * Method - this parameter should be set to GetAnnotation <br>
- * File - this parameter should bo connected to a file with a request<br>
- *
- * Request file should looks like the one in testFiles/sampleRequest.xml.<br>
- * As a result the xml file is received. An example of a xml response is in
- * testFiles/sampleResponse.xml
- *
- *
- * @author Piotr Gawron
- *
- */
-public class BiocompendiumAnnotator extends ElementAnnotator implements IExternalService {
-
- /**
- * Address of the restfull API for biocompendium.
- */
- private static final String SERVICE_ADDRESS = "http://biocompendium.embl.de/map_annotator/REST/GetAnnotation/";
-
- /**
- * Standard class logger.
- */
- private final Logger logger = Logger.getLogger(BiocompendiumAnnotator.class);
-
- /**
- * Xml parser used for processing notes into structurized data.
- */
- private RestAnnotationParser rap = new RestAnnotationParser();
-
- /**
- * Default constructor.
- */
- public BiocompendiumAnnotator() {
- super(BiocompendiumAnnotator.class, new Class[] { Protein.class, Gene.class, Rna.class }, true);
- }
-
- @Override
- public String refreshCacheQuery(Object query) throws SourceNotAvailable {
- String result = null;
- try {
- if (query instanceof String) {
- String name = (String) query;
- result = getAnnotation(createMiriamData(MiriamType.HGNC_SYMBOL, name));
- } else {
- throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
- }
- } catch (IOException e) {
- throw new SourceNotAvailable(e);
- }
- return result;
- }
-
- /**
- * Returns String with annotations for species described by {@link MiriamData}
- * with {@link MiriamType#HGNC_SYMBOL} entry.
- *
- * @param md
- * description of the element by {@link MiriamData} with
- * {@link MiriamType#HGNC_SYMBOL} entry
- * @return annotation for species with given name and type from Venkata server
- * @throws IOException
- * thrown when there is a problem with connection to the server
- */
- protected String getAnnotation(MiriamData md) throws IOException {
- if (!MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
- throw new InvalidArgumentException("Only " + MiriamType.HGNC_SYMBOL.getCommonName() + " miriam registry is supported.");
- }
-
- MiriamData miriamData = createMiriamData(md);
- miriamData.setResource(miriamData.getResource().replaceAll("[\n\r]+", " "));
-
- String annotation = getCacheValue(miriamData.getResource());
- if (annotation != null) {
- return annotation;
- }
-
- CloseableHttpClient httpClient = HttpClients.createDefault();
-
- HttpPost httppost = new HttpPost(SERVICE_ADDRESS);
- MultipartEntityBuilder builder = MultipartEntityBuilder.create();
-
- // prepare a query
- String requestXml = dataToString(miriamData);
-
- // save query to a temporary file
- File tmp = File.createTempFile("annotation-plugin", "xml");
- BufferedWriter out = new BufferedWriter(new FileWriter(tmp));
- out.write(requestXml);
- out.close();
-
- builder.addBinaryBody("File", tmp, ContentType.APPLICATION_OCTET_STREAM, tmp.getName());
- HttpEntity multipart = builder.build();
- httppost.setEntity(multipart);
- CloseableHttpResponse response = httpClient.execute(httppost);
-
- HttpEntity entity2 = response.getEntity();
- if (entity2 != null) {
- InputStream instream = entity2.getContent();
- Scanner scanner = new Scanner(instream);
- try {
- Scanner s = scanner.useDelimiter("\\A");
- // get results
- String responseXml = "";
- if (s.hasNext()) {
- responseXml = s.next();
- }
- try {
- annotation = getAnnotationsFromXml(responseXml).get(miriamData.getResource());
- } catch (InvalidXmlSchemaException e) {
- throw new IOException(e);
- }
-
- } finally {
- scanner.close();
- instream.close();
- }
- }
- if (annotation != null) {
- setCacheValue(miriamData.getResource(), annotation);
- }
- return annotation;
- }
-
- /**
- * This method convert a hgnc symbol in miriam data into xml request.
- *
- * @param miriamData
- * - {@link MiriamData} with {@link MiriamType#HGNC_SYMBOL}
- * @return xml string that represent a request to RESTful service
- */
- String dataToString(MiriamData miriamData) {
- if (!MiriamType.HGNC_SYMBOL.equals(miriamData.getDataType())) {
- throw new InvalidArgumentException("Only " + MiriamType.HGNC_SYMBOL.getCommonName() + " miriam registry is supported.");
- }
- String requestXml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n";
- requestXml += "<request>\n";
- requestXml += " <species name=\"" + miriamData.getResource() + "\" type=\"PROTEIN\"/>\n";
- requestXml += "</request>\n";
- return requestXml;
- }
-
- /**
- * This method parse a response xml from annotation service into a map. A key
- * in the map is a name of species and value is a annotation received from the
- * service.
- *
- * @param xml
- * - xml string to be parsed
- * @return a map with information about annotations. A key in the map is a
- * name of species and value is a annotation received from the
- * service.
- * @throws InvalidXmlSchemaException
- * thrown when there is a problem with xml
- */
- Map<String, String> getAnnotationsFromXml(String xml) throws InvalidXmlSchemaException {
- Map<String, String> result = new HashMap<String, String>();
- // if xml is null or empty string then return empty map
- if (xml == null) {
- return result;
- }
- if (xml.isEmpty()) {
- return result;
- }
- // there is a bug in annotation service that create incorrect xml, therefore
- // we need to alter the xml
- xml = correctInvalidXml(xml);
-
- Document doc = getXmlDocumentFromString(xml);
- result = getAnnotationsFromXmlNode(doc);
- return result;
-
- }
-
- /**
- * Transforms xml retrieved from Venkata server into map of annotations. A key
- * in the map is a name of species and value is a annotation received from the
- * service.
- *
- * @param doc
- * - xml node
- * @return a map with information about annotations. A key in the map is a
- * name of species and value is a annotation received from the
- * service.
- */
- private Map<String, String> getAnnotationsFromXmlNode(Node doc) {
- Map<String, String> result = new HashMap<String, String>();
- NodeList root = doc.getChildNodes();
- Node responseNode = getNode("response", root);
- // root node is called "response"
- if (responseNode == null) {
- throw new InvalidArgumentException("Invalid xml returned by annotation service. No response root node");
- }
- NodeList list = responseNode.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- // all nodes in response are species
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("species")) {
- String name = getNodeAttr("name", node).replaceAll("%0A", "\n");
- String annotation = getNodeValue(node);
- if (annotation.contains("Symbol: " + name.split(" ")[0].toUpperCase())) {
- result.put(name, annotation);
- } else {
- logger.warn("Problem with annotation for: " + name);
- result.put(name, "");
- }
- } else {
- throw new InvalidArgumentException("Unknown node in xml response: " + node.getNodeName());
- }
- }
- }
- return result;
- }
-
- /**
- * Corrects invalid xml retrieved from Venkata server.
- *
- * @param xml
- * xml to correct
- * @return corrected xml
- */
- private String correctInvalidXml(String xml) {
- int size = 0;
- int size2 = 0;
- do {
- size = xml.length();
- xml = xml.replaceAll("<species name=\"[^\"]*\" type=\"[^\"]*\">(\\s)*<species", "<species");
- xml = xml.replaceAll("<species name=\"[^\"]*\" type=\"[^\"]*\">(\\s)*</response", "</response");
- size2 = xml.length();
- } while (size != size2);
- return xml;
- }
-
- @Override
- public ExternalServiceStatus getServiceStatus() {
- ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
-
- GeneralCacheInterface cacheCopy = getCache();
- this.setCache(null);
-
- try {
- String annotations = getAnnotation(createMiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
-
- status.setStatus(ExternalServiceStatusType.OK);
- if (annotations == null) {
- status.setStatus(ExternalServiceStatusType.DOWN);
- } else if (!annotations.contains("ymbol")) {
- status.setStatus(ExternalServiceStatusType.CHANGED);
- }
- } catch (Exception e) {
- logger.error(status.getName() + " is down", e);
- status.setStatus(ExternalServiceStatusType.DOWN);
- }
- this.setCache(cacheCopy);
- return status;
- }
-
- @Override
- public void annotateElement(BioEntity element) throws AnnotatorException {
- if (isAnnotatable(element)) {
- try {
- String annotationString = getAnnotation(createMiriamData(MiriamType.HGNC_SYMBOL, element.getName()));
- if (annotationString != null) {
- if (element.getMiriamData().size() == 0) {
- element.addMiriamData(rap.getMiriamData(annotationString));
- }
-
- String annotations = "";
-
- String[] string = annotationString.split("\n");
- boolean remove = false;
- for (String string2 : string) {
- if (string2.startsWith("Symbol:")) {
- remove = true;
- }
- if (remove) {
- annotations += string2 + "\n";
- }
- if (string2.startsWith("Synonyms:")) {
- remove = false;
- }
- }
- annotations = element.getNotes() + "\n" + annotations;
- rap.processNotes(annotations, element);
- }
- } catch (IOException e) {
- throw new AnnotatorException(e);
- }
- }
- }
-
- @Override
- public String getCommonName() {
- return "Biocompendium";
- }
-
- @Override
- public String getUrl() {
- return "http://biocompendium.embl.de/";
- }
-
-}
+package lcsb.mapviewer.annotation.services.annotators;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Scanner;
+
+import org.apache.http.HttpEntity;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpPost;
+import org.apache.http.entity.ContentType;
+import org.apache.http.entity.mime.MultipartEntityBuilder;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClients;
+import org.apache.log4j.Logger;
+import org.w3c.dom.Document;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
+import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
+import lcsb.mapviewer.annotation.services.IExternalService;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+
+/**
+ * This class is responsible for connection to Vencata annotation service. The
+ * service is available on
+ * http://biocompendium.embl.de/map_annotator/REST/GetAnnotation/. This service
+ * is RESTful service. To query for an annotation one need to send a POST
+ * message with two parameters:<br>
+ * Method - this parameter should be set to GetAnnotation <br>
+ * File - this parameter should bo connected to a file with a request<br>
+ *
+ * Request file should looks like the one in testFiles/sampleRequest.xml.<br>
+ * As a result the xml file is received. An example of a xml response is in
+ * testFiles/sampleResponse.xml
+ *
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class BiocompendiumAnnotator extends ElementAnnotator implements IExternalService {
+
+ /**
+ * Address of the restfull API for biocompendium.
+ */
+ private static final String SERVICE_ADDRESS = "http://biocompendium.embl.de/map_annotator/REST/GetAnnotation/";
+
+ /**
+ * Standard class logger.
+ */
+ private final Logger logger = Logger.getLogger(BiocompendiumAnnotator.class);
+
+ /**
+ * Xml parser used for processing notes into structurized data.
+ */
+ private RestAnnotationParser rap = new RestAnnotationParser();
+
+ /**
+ * Default constructor.
+ */
+ public BiocompendiumAnnotator() {
+ super(BiocompendiumAnnotator.class, new Class[] { Protein.class, Gene.class, Rna.class }, true);
+ }
+
+ @Override
+ public String refreshCacheQuery(Object query) throws SourceNotAvailable {
+ String result = null;
+ try {
+ if (query instanceof String) {
+ String name = (String) query;
+ result = getAnnotation(createMiriamData(MiriamType.HGNC_SYMBOL, name));
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
+ }
+ } catch (IOException e) {
+ throw new SourceNotAvailable(e);
+ }
+ return result;
+ }
+
+ /**
+ * Returns String with annotations for species described by {@link MiriamData}
+ * with {@link MiriamType#HGNC_SYMBOL} entry.
+ *
+ * @param md
+ * description of the element by {@link MiriamData} with
+ * {@link MiriamType#HGNC_SYMBOL} entry
+ * @return annotation for species with given name and type from Venkata server
+ * @throws IOException
+ * thrown when there is a problem with connection to the server
+ */
+ protected String getAnnotation(MiriamData md) throws IOException {
+ if (!MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
+ throw new InvalidArgumentException("Only " + MiriamType.HGNC_SYMBOL.getCommonName() + " miriam registry is supported.");
+ }
+
+ MiriamData miriamData = createMiriamData(md);
+ miriamData.setResource(miriamData.getResource().replaceAll("[\n\r]+", " "));
+
+ String annotation = getCacheValue(miriamData.getResource());
+ if (annotation != null) {
+ return annotation;
+ }
+
+ CloseableHttpClient httpClient = HttpClients.createDefault();
+
+ HttpPost httppost = new HttpPost(SERVICE_ADDRESS);
+ MultipartEntityBuilder builder = MultipartEntityBuilder.create();
+
+ // prepare a query
+ String requestXml = dataToString(miriamData);
+
+ // save query to a temporary file
+ File tmp = File.createTempFile("annotation-plugin", "xml");
+ BufferedWriter out = new BufferedWriter(new FileWriter(tmp));
+ out.write(requestXml);
+ out.close();
+
+ builder.addBinaryBody("File", tmp, ContentType.APPLICATION_OCTET_STREAM, tmp.getName());
+ HttpEntity multipart = builder.build();
+ httppost.setEntity(multipart);
+ CloseableHttpResponse response = httpClient.execute(httppost);
+
+ HttpEntity entity2 = response.getEntity();
+ if (entity2 != null) {
+ InputStream instream = entity2.getContent();
+ Scanner scanner = new Scanner(instream);
+ try {
+ Scanner s = scanner.useDelimiter("\\A");
+ // get results
+ String responseXml = "";
+ if (s.hasNext()) {
+ responseXml = s.next();
+ }
+ try {
+ annotation = getAnnotationsFromXml(responseXml).get(miriamData.getResource());
+ } catch (InvalidXmlSchemaException e) {
+ throw new IOException(e);
+ }
+
+ } finally {
+ scanner.close();
+ instream.close();
+ }
+ }
+ if (annotation != null) {
+ setCacheValue(miriamData.getResource(), annotation);
+ }
+ return annotation;
+ }
+
+ /**
+ * This method convert a hgnc symbol in miriam data into xml request.
+ *
+ * @param miriamData
+ * - {@link MiriamData} with {@link MiriamType#HGNC_SYMBOL}
+ * @return xml string that represent a request to RESTful service
+ */
+ String dataToString(MiriamData miriamData) {
+ if (!MiriamType.HGNC_SYMBOL.equals(miriamData.getDataType())) {
+ throw new InvalidArgumentException("Only " + MiriamType.HGNC_SYMBOL.getCommonName() + " miriam registry is supported.");
+ }
+ String requestXml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n";
+ requestXml += "<request>\n";
+ requestXml += " <species name=\"" + miriamData.getResource() + "\" type=\"PROTEIN\"/>\n";
+ requestXml += "</request>\n";
+ return requestXml;
+ }
+
+ /**
+ * This method parse a response xml from annotation service into a map. A key
+ * in the map is a name of species and value is a annotation received from the
+ * service.
+ *
+ * @param xml
+ * - xml string to be parsed
+ * @return a map with information about annotations. A key in the map is a
+ * name of species and value is a annotation received from the
+ * service.
+ * @throws InvalidXmlSchemaException
+ * thrown when there is a problem with xml
+ */
+ Map<String, String> getAnnotationsFromXml(String xml) throws InvalidXmlSchemaException {
+ Map<String, String> result = new HashMap<String, String>();
+ // if xml is null or empty string then return empty map
+ if (xml == null) {
+ return result;
+ }
+ if (xml.isEmpty()) {
+ return result;
+ }
+ // there is a bug in annotation service that create incorrect xml, therefore
+ // we need to alter the xml
+ xml = correctInvalidXml(xml);
+
+ Document doc = getXmlDocumentFromString(xml);
+ result = getAnnotationsFromXmlNode(doc);
+ return result;
+
+ }
+
+ /**
+ * Transforms xml retrieved from Venkata server into map of annotations. A key
+ * in the map is a name of species and value is a annotation received from the
+ * service.
+ *
+ * @param doc
+ * - xml node
+ * @return a map with information about annotations. A key in the map is a
+ * name of species and value is a annotation received from the
+ * service.
+ */
+ private Map<String, String> getAnnotationsFromXmlNode(Node doc) {
+ Map<String, String> result = new HashMap<String, String>();
+ NodeList root = doc.getChildNodes();
+ Node responseNode = getNode("response", root);
+ // root node is called "response"
+ if (responseNode == null) {
+ throw new InvalidArgumentException("Invalid xml returned by annotation service. No response root node");
+ }
+ NodeList list = responseNode.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ // all nodes in response are species
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("species")) {
+ String name = getNodeAttr("name", node).replaceAll("%0A", "\n");
+ String annotation = getNodeValue(node);
+ if (annotation.contains("Symbol: " + name.split(" ")[0].toUpperCase())) {
+ result.put(name, annotation);
+ } else {
+ logger.warn("Problem with annotation for: " + name);
+ result.put(name, "");
+ }
+ } else {
+ throw new InvalidArgumentException("Unknown node in xml response: " + node.getNodeName());
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Corrects invalid xml retrieved from Venkata server.
+ *
+ * @param xml
+ * xml to correct
+ * @return corrected xml
+ */
+ private String correctInvalidXml(String xml) {
+ int size = 0;
+ int size2 = 0;
+ do {
+ size = xml.length();
+ xml = xml.replaceAll("<species name=\"[^\"]*\" type=\"[^\"]*\">(\\s)*<species", "<species");
+ xml = xml.replaceAll("<species name=\"[^\"]*\" type=\"[^\"]*\">(\\s)*</response", "</response");
+ size2 = xml.length();
+ } while (size != size2);
+ return xml;
+ }
+
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
+
+ GeneralCacheInterface cacheCopy = getCache();
+ this.setCache(null);
+
+ try {
+ String annotations = getAnnotation(createMiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
+
+ status.setStatus(ExternalServiceStatusType.OK);
+ if (annotations == null) {
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ } else if (!annotations.contains("ymbol")) {
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ }
+ } catch (Exception e) {
+ logger.error(status.getName() + " is down", e);
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ }
+ this.setCache(cacheCopy);
+ return status;
+ }
+
+ @Override
+ public void annotateElement(BioEntity element) throws AnnotatorException {
+ if (isAnnotatable(element)) {
+ try {
+ String annotationString = getAnnotation(createMiriamData(MiriamType.HGNC_SYMBOL, element.getName()));
+ if (annotationString != null) {
+ if (element.getMiriamData().size() == 0) {
+ element.addMiriamData(rap.getMiriamData(annotationString));
+ }
+
+ String annotations = "";
+
+ String[] string = annotationString.split("\n");
+ boolean remove = false;
+ for (String string2 : string) {
+ if (string2.startsWith("Symbol:")) {
+ remove = true;
+ }
+ if (remove) {
+ annotations += string2 + "\n";
+ }
+ if (string2.startsWith("Synonyms:")) {
+ remove = false;
+ }
+ }
+ annotations = element.getNotes() + "\n" + annotations;
+ rap.processNotes(annotations, element);
+ }
+ } catch (IOException e) {
+ throw new AnnotatorException(e);
+ }
+ }
+ }
+
+ @Override
+ public String getCommonName() {
+ return "Biocompendium";
+ }
+
+ @Override
+ public String getUrl() {
+ return "http://biocompendium.embl.de/";
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiSearchException.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiSearchException.java
index e872bee192..1ca1eb2705 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiSearchException.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiSearchException.java
@@ -1,32 +1,32 @@
-package lcsb.mapviewer.annotation.services.annotators;
-
-import lcsb.mapviewer.annotation.data.Chebi;
-
-/**
- * Exception that should be thrown when there is a problem with finding
- * information about {@link Chebi} elements.
- *
- * @author Piotr Gawron
- *
- */
-public class ChebiSearchException extends Exception {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Constructs a new exception with the specified detail message and cause.
- *
- * @param message
- * the detail message
- * @param cause
- * the cause (A <tt>null</tt> value is permitted, and indicates that
- * the cause is nonexistent or unknown.)
- */
- public ChebiSearchException(String message, Throwable cause) {
- super(message, cause);
- }
-
-}
+package lcsb.mapviewer.annotation.services.annotators;
+
+import lcsb.mapviewer.annotation.data.Chebi;
+
+/**
+ * Exception that should be thrown when there is a problem with finding
+ * information about {@link Chebi} elements.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ChebiSearchException extends Exception {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Constructs a new exception with the specified detail message and cause.
+ *
+ * @param message
+ * the detail message
+ * @param cause
+ * the cause (A <tt>null</tt> value is permitted, and indicates that
+ * the cause is nonexistent or unknown.)
+ */
+ public ChebiSearchException(String message, Throwable cause) {
+ super(message, cause);
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoSearchException.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoSearchException.java
index 2719c69d62..be32c487da 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoSearchException.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoSearchException.java
@@ -1,30 +1,30 @@
-package lcsb.mapviewer.annotation.services.annotators;
-
-/**
- * Exception that should be thrown when there is a problem with finding
- * information about Go elements.
- *
- * @author Piotr Gawron
- *
- */
-public class GoSearchException extends Exception {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Constructs a new exception with the specified detail message and cause.
- *
- * @param message
- * the detail message
- * @param cause
- * the cause (A <tt>null</tt> value is permitted, and indicates that
- * the cause is nonexistent or unknown.)
- */
- public GoSearchException(String message, Throwable cause) {
- super(message, cause);
- }
-
-}
+package lcsb.mapviewer.annotation.services.annotators;
+
+/**
+ * Exception that should be thrown when there is a problem with finding
+ * information about Go elements.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class GoSearchException extends Exception {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Constructs a new exception with the specified detail message and cause.
+ *
+ * @param message
+ * the detail message
+ * @param cause
+ * the cause (A <tt>null</tt> value is permitted, and indicates that
+ * the cause is nonexistent or unknown.)
+ */
+ public GoSearchException(String message, Throwable cause) {
+ super(message, cause);
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java
index 8f94005507..ea9415504e 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java
@@ -1,305 +1,305 @@
-package lcsb.mapviewer.annotation.services.annotators;
-
-import java.io.IOException;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.Set;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
-import lcsb.mapviewer.annotation.cache.WebPageDownloader;
-import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
-import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
-import lcsb.mapviewer.annotation.services.IExternalService;
-import lcsb.mapviewer.annotation.services.WrongResponseCodeIOException;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.modelutils.map.ElementUtils;
-
-/**
- * This is a class that implements a backend to uniprot restfull API.
- *
- * @author Piotr Gawron
- *
- */
-public class UniprotAnnotator extends ElementAnnotator implements IExternalService {
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(UniprotAnnotator.class);
-
- /**
- * Pattern used for finding hgnc symbol from uniprot info page .
- */
- private Pattern uniprotToHgnc = Pattern.compile("GN[\\ ]+Name=([^;\\ ]+)");
-
- /**
- * Pattern used for finding entrez identifier from uniprot info page .
- */
- private Pattern uniprotToEntrez = Pattern.compile("DR[\\ ]+GeneID;\\ ([^;\\ ]+)");
-
- /**
- * Pattern used for finding EC symbol from UniProt info page .
- */
- private Pattern uniprotToEC = Pattern.compile("EC=((\\d+\\.-\\.-\\.-)|(\\d+\\.\\d+\\.-\\.-)|(\\d+\\.\\d+\\.\\d+\\.-)|(\\d+\\.\\d+\\.\\d+\\.\\d+))");
-
-
- /**
- * Class used for some simple operations on {@link BioEntity} elements.
- */
- private ElementUtils elementUtils = new ElementUtils();
-
- /**
- * Default constructor.
- */
- public UniprotAnnotator() {
- super(UniprotAnnotator.class, new Class[] { Protein.class, Gene.class, Rna.class }, false);
- }
-
- @Override
- public ExternalServiceStatus getServiceStatus() {
- ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
-
- GeneralCacheInterface cacheCopy = getCache();
- this.setCache(null);
-
- try {
- MiriamData md = uniProtToHgnc(createMiriamData(MiriamType.UNIPROT, "P37840"));
-
- status.setStatus(ExternalServiceStatusType.OK);
- if (md == null) {
- status.setStatus(ExternalServiceStatusType.DOWN);
- } else if (!md.getResource().equalsIgnoreCase("SNCA")) {
- status.setStatus(ExternalServiceStatusType.CHANGED);
- }
- } catch (Exception e) {
- logger.error(status.getName() + " is down", e);
- status.setStatus(ExternalServiceStatusType.DOWN);
- }
- this.setCache(cacheCopy);
- return status;
- }
-
- @Override
- public void annotateElement(BioEntity object) throws AnnotatorException {
- if (isAnnotatable(object)) {
- String uniprotId = object.getName();
- boolean uniprotFound = false;
- for (MiriamData md : object.getMiriamData()) {
- if (md.getDataType().equals(MiriamType.UNIPROT)) {
- uniprotId = md.getResource();
- uniprotFound = true;
- }
- }
-
- if (uniprotId == null || uniprotId.equals("")) {
- return;
- }
-
- String accessUrl = getUniprotUrl(uniprotId);
- try {
- String pageContent = getWebPageContent(accessUrl);
- // check if we have data over there
- if (!pageContent.contains("<title>Error</title>")) {
- Set<MiriamData> annotations = new HashSet<MiriamData>();
- annotations.addAll(parseHgnc(pageContent));
- annotations.addAll(parseEntrez(pageContent));
- annotations.addAll(parseEC(pageContent));
- if (!uniprotFound) {
- annotations.add(createMiriamData(MiriamType.UNIPROT, uniprotId));
- }
- object.addMiriamData(annotations);
- } else {
- // this means that entry with a given uniprot id doesn't exist
- if (uniprotFound) {
- logger.warn(elementUtils.getElementTag(object) + " Invalid uniprot id: " + uniprotId);
- }
- }
- } catch (WrongResponseCodeIOException exception) {
- logger.warn("Cannot find uniprot data for id: " + uniprotId);
- } catch (IOException exception) {
- throw new AnnotatorException(exception);
- }
- }
- }
-
- /**
- * Returns url to uniprot restfull API about uniprot entry.
- *
- * @param uniprotId
- * uniprot identifier
- * @return url to uniprot restfull API about uniprot entry
- */
- private String getUniprotUrl(String uniprotId) {
- return "https://www.uniprot.org/uniprot/" + uniprotId + ".txt";
- }
-
- /**
- * Parse uniprot webpage to find information about {@link MiriamType#ENTREZ}
- * and returns them.
- *
- * @param pageContent
- * uniprot info page
- * @return set of entrez identifiers found on the webpage
- */
- private Collection<MiriamData> parseEntrez(String pageContent) {
- Collection<MiriamData> result = new HashSet<MiriamData>();
- Matcher m = uniprotToEntrez.matcher(pageContent);
- if (m.find()) {
- result.add(createMiriamData(MiriamType.ENTREZ, m.group(1)));
- }
- return result;
- }
-
- /**
- * Parse uniprot webpage to find information about
- * {@link MiriamType#HGNC_SYMBOL} and returns them.
- *
- * @param pageContent
- * uniprot info page
- * @return set of entrez identifiers found on the webpage
- */
- private Collection<MiriamData> parseHgnc(String pageContent) {
- Collection<MiriamData> result = new HashSet<MiriamData>();
- Matcher m = uniprotToHgnc.matcher(pageContent);
- if (m.find()) {
- result.add(createMiriamData(MiriamType.HGNC_SYMBOL, m.group(1)));
- }
- return result;
- }
-
- /**
- * Parse UniProt webpage to find information about
- * {@link MiriamType#EC}s and returns them.
- *
- * @param pageContent
- * UniProt info page
- * @return EC found on the page
- */
- private Collection<MiriamData> parseEC(String pageContent) {
- Collection<MiriamData> result = new HashSet<MiriamData>();
- Matcher m = uniprotToEC.matcher(pageContent);
- while (m.find()) {
- result.add(createMiriamData(MiriamType.EC, m.group(1)));
- }
- return result;
- }
-
- @Override
- public Object refreshCacheQuery(Object query) throws SourceNotAvailable {
- String name;
- String result = null;
- if (query instanceof String) {
- name = (String) query;
- if (name.startsWith("http")) {
- try {
- result = getWebPageContent(name);
- } catch (IOException e) {
- throw new SourceNotAvailable(e);
- }
- } else {
- throw new InvalidArgumentException("Don't know what to do with query: " + query);
- }
- } else {
- throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
- }
- return result;
- }
-
- /**
- * Transform uniprot identifier into hgnc name.
- *
- * @param uniprot
- * {@link MiriamData} with uniprot identifier
- * @return {@link MiriamData} with hgnc name
- * @throws UniprotSearchException
- * thrown when there is aproblem with accessing external database
- */
- public MiriamData uniProtToHgnc(MiriamData uniprot) throws UniprotSearchException {
- if (uniprot == null) {
- return null;
- }
-
- if (!MiriamType.UNIPROT.equals(uniprot.getDataType())) {
- throw new InvalidArgumentException(MiriamType.UNIPROT + " expected.");
- }
-
- String accessUrl = getUniprotUrl(uniprot.getResource());
- try {
- String pageContent = getWebPageContent(accessUrl);
- Collection<MiriamData> collection = parseHgnc(pageContent);
- if (collection.size() > 0) {
- return collection.iterator().next();
- } else {
- return null;
- }
- } catch (IOException e) {
- throw new UniprotSearchException("Problem with accessing uniprot webpage", e);
- }
-
- }
-
- /**
- * Transform uniprot identifier into EC identifiers.
- *
- * @param uniprot
- * {@link MiriamData} with uniprot identifier
- * @return ArrayList of {@link MiriamData} with EC codes
- * @throws UniprotSearchException
- * thrown when there is a problem with accessing external database
- */
- public Collection<MiriamData> uniProtToEC(MiriamData uniprot) throws UniprotSearchException {
- if (uniprot == null) {
- return null;
- }
-
- if (!MiriamType.UNIPROT.equals(uniprot.getDataType())) {
- throw new InvalidArgumentException(MiriamType.UNIPROT + " expected.");
- }
-
- String accessUrl = getUniprotUrl(uniprot.getResource());
- try {
- String pageContent = getWebPageContent(accessUrl);
- Collection<MiriamData> collection = parseEC(pageContent);
- if (collection.size() > 0) {
- return collection;
- } else {
- return null;
- }
- } catch (IOException e) {
- throw new UniprotSearchException("Problem with accessing uniprot webpage", e);
- }
-
- }
-
- @Override
- public String getCommonName() {
- return MiriamType.UNIPROT.getCommonName();
- }
-
- @Override
- public String getUrl() {
- return MiriamType.UNIPROT.getDbHomepage();
- }
-
- @Override
- protected WebPageDownloader getWebPageDownloader() {
- return super.getWebPageDownloader();
- }
-
- @Override
- protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
- super.setWebPageDownloader(webPageDownloader);
- }
-
-}
+package lcsb.mapviewer.annotation.services.annotators;
+
+import java.io.IOException;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Set;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.WebPageDownloader;
+import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
+import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
+import lcsb.mapviewer.annotation.services.IExternalService;
+import lcsb.mapviewer.annotation.services.WrongResponseCodeIOException;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
+
+/**
+ * This is a class that implements a backend to uniprot restfull API.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class UniprotAnnotator extends ElementAnnotator implements IExternalService {
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(UniprotAnnotator.class);
+
+ /**
+ * Pattern used for finding hgnc symbol from uniprot info page .
+ */
+ private Pattern uniprotToHgnc = Pattern.compile("GN[\\ ]+Name=([^;\\ ]+)");
+
+ /**
+ * Pattern used for finding entrez identifier from uniprot info page .
+ */
+ private Pattern uniprotToEntrez = Pattern.compile("DR[\\ ]+GeneID;\\ ([^;\\ ]+)");
+
+ /**
+ * Pattern used for finding EC symbol from UniProt info page .
+ */
+ private Pattern uniprotToEC = Pattern.compile("EC=((\\d+\\.-\\.-\\.-)|(\\d+\\.\\d+\\.-\\.-)|(\\d+\\.\\d+\\.\\d+\\.-)|(\\d+\\.\\d+\\.\\d+\\.\\d+))");
+
+
+ /**
+ * Class used for some simple operations on {@link BioEntity} elements.
+ */
+ private ElementUtils elementUtils = new ElementUtils();
+
+ /**
+ * Default constructor.
+ */
+ public UniprotAnnotator() {
+ super(UniprotAnnotator.class, new Class[] { Protein.class, Gene.class, Rna.class }, false);
+ }
+
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
+
+ GeneralCacheInterface cacheCopy = getCache();
+ this.setCache(null);
+
+ try {
+ MiriamData md = uniProtToHgnc(createMiriamData(MiriamType.UNIPROT, "P37840"));
+
+ status.setStatus(ExternalServiceStatusType.OK);
+ if (md == null) {
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ } else if (!md.getResource().equalsIgnoreCase("SNCA")) {
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ }
+ } catch (Exception e) {
+ logger.error(status.getName() + " is down", e);
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ }
+ this.setCache(cacheCopy);
+ return status;
+ }
+
+ @Override
+ public void annotateElement(BioEntity object) throws AnnotatorException {
+ if (isAnnotatable(object)) {
+ String uniprotId = object.getName();
+ boolean uniprotFound = false;
+ for (MiriamData md : object.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.UNIPROT)) {
+ uniprotId = md.getResource();
+ uniprotFound = true;
+ }
+ }
+
+ if (uniprotId == null || uniprotId.equals("")) {
+ return;
+ }
+
+ String accessUrl = getUniprotUrl(uniprotId);
+ try {
+ String pageContent = getWebPageContent(accessUrl);
+ // check if we have data over there
+ if (!pageContent.contains("<title>Error</title>")) {
+ Set<MiriamData> annotations = new HashSet<MiriamData>();
+ annotations.addAll(parseHgnc(pageContent));
+ annotations.addAll(parseEntrez(pageContent));
+ annotations.addAll(parseEC(pageContent));
+ if (!uniprotFound) {
+ annotations.add(createMiriamData(MiriamType.UNIPROT, uniprotId));
+ }
+ object.addMiriamData(annotations);
+ } else {
+ // this means that entry with a given uniprot id doesn't exist
+ if (uniprotFound) {
+ logger.warn(elementUtils.getElementTag(object) + " Invalid uniprot id: " + uniprotId);
+ }
+ }
+ } catch (WrongResponseCodeIOException exception) {
+ logger.warn("Cannot find uniprot data for id: " + uniprotId);
+ } catch (IOException exception) {
+ throw new AnnotatorException(exception);
+ }
+ }
+ }
+
+ /**
+ * Returns url to uniprot restfull API about uniprot entry.
+ *
+ * @param uniprotId
+ * uniprot identifier
+ * @return url to uniprot restfull API about uniprot entry
+ */
+ private String getUniprotUrl(String uniprotId) {
+ return "https://www.uniprot.org/uniprot/" + uniprotId + ".txt";
+ }
+
+ /**
+ * Parse uniprot webpage to find information about {@link MiriamType#ENTREZ}
+ * and returns them.
+ *
+ * @param pageContent
+ * uniprot info page
+ * @return set of entrez identifiers found on the webpage
+ */
+ private Collection<MiriamData> parseEntrez(String pageContent) {
+ Collection<MiriamData> result = new HashSet<MiriamData>();
+ Matcher m = uniprotToEntrez.matcher(pageContent);
+ if (m.find()) {
+ result.add(createMiriamData(MiriamType.ENTREZ, m.group(1)));
+ }
+ return result;
+ }
+
+ /**
+ * Parse uniprot webpage to find information about
+ * {@link MiriamType#HGNC_SYMBOL} and returns them.
+ *
+ * @param pageContent
+ * uniprot info page
+ * @return set of entrez identifiers found on the webpage
+ */
+ private Collection<MiriamData> parseHgnc(String pageContent) {
+ Collection<MiriamData> result = new HashSet<MiriamData>();
+ Matcher m = uniprotToHgnc.matcher(pageContent);
+ if (m.find()) {
+ result.add(createMiriamData(MiriamType.HGNC_SYMBOL, m.group(1)));
+ }
+ return result;
+ }
+
+ /**
+ * Parse UniProt webpage to find information about
+ * {@link MiriamType#EC}s and returns them.
+ *
+ * @param pageContent
+ * UniProt info page
+ * @return EC found on the page
+ */
+ private Collection<MiriamData> parseEC(String pageContent) {
+ Collection<MiriamData> result = new HashSet<MiriamData>();
+ Matcher m = uniprotToEC.matcher(pageContent);
+ while (m.find()) {
+ result.add(createMiriamData(MiriamType.EC, m.group(1)));
+ }
+ return result;
+ }
+
+ @Override
+ public Object refreshCacheQuery(Object query) throws SourceNotAvailable {
+ String name;
+ String result = null;
+ if (query instanceof String) {
+ name = (String) query;
+ if (name.startsWith("http")) {
+ try {
+ result = getWebPageContent(name);
+ } catch (IOException e) {
+ throw new SourceNotAvailable(e);
+ }
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with query: " + query);
+ }
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
+ }
+ return result;
+ }
+
+ /**
+ * Transform uniprot identifier into hgnc name.
+ *
+ * @param uniprot
+ * {@link MiriamData} with uniprot identifier
+ * @return {@link MiriamData} with hgnc name
+ * @throws UniprotSearchException
+ * thrown when there is aproblem with accessing external database
+ */
+ public MiriamData uniProtToHgnc(MiriamData uniprot) throws UniprotSearchException {
+ if (uniprot == null) {
+ return null;
+ }
+
+ if (!MiriamType.UNIPROT.equals(uniprot.getDataType())) {
+ throw new InvalidArgumentException(MiriamType.UNIPROT + " expected.");
+ }
+
+ String accessUrl = getUniprotUrl(uniprot.getResource());
+ try {
+ String pageContent = getWebPageContent(accessUrl);
+ Collection<MiriamData> collection = parseHgnc(pageContent);
+ if (collection.size() > 0) {
+ return collection.iterator().next();
+ } else {
+ return null;
+ }
+ } catch (IOException e) {
+ throw new UniprotSearchException("Problem with accessing uniprot webpage", e);
+ }
+
+ }
+
+ /**
+ * Transform uniprot identifier into EC identifiers.
+ *
+ * @param uniprot
+ * {@link MiriamData} with uniprot identifier
+ * @return ArrayList of {@link MiriamData} with EC codes
+ * @throws UniprotSearchException
+ * thrown when there is a problem with accessing external database
+ */
+ public Collection<MiriamData> uniProtToEC(MiriamData uniprot) throws UniprotSearchException {
+ if (uniprot == null) {
+ return null;
+ }
+
+ if (!MiriamType.UNIPROT.equals(uniprot.getDataType())) {
+ throw new InvalidArgumentException(MiriamType.UNIPROT + " expected.");
+ }
+
+ String accessUrl = getUniprotUrl(uniprot.getResource());
+ try {
+ String pageContent = getWebPageContent(accessUrl);
+ Collection<MiriamData> collection = parseEC(pageContent);
+ if (collection.size() > 0) {
+ return collection;
+ } else {
+ return null;
+ }
+ } catch (IOException e) {
+ throw new UniprotSearchException("Problem with accessing uniprot webpage", e);
+ }
+
+ }
+
+ @Override
+ public String getCommonName() {
+ return MiriamType.UNIPROT.getCommonName();
+ }
+
+ @Override
+ public String getUrl() {
+ return MiriamType.UNIPROT.getDbHomepage();
+ }
+
+ @Override
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
+ }
+
+ @Override
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotSearchException.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotSearchException.java
index f3d40ee117..6b12f60e3c 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotSearchException.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotSearchException.java
@@ -1,30 +1,30 @@
-package lcsb.mapviewer.annotation.services.annotators;
-
-/**
- * Exception that should be thrown when there is a problem with finding
- * information about Uniprot.
- *
- * @author Piotr Gawron
- *
- */
-public class UniprotSearchException extends Exception {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Constructs a new exception with the specified detail message and cause.
- *
- * @param message
- * the detail message
- * @param cause
- * the cause (A <tt>null</tt> value is permitted, and indicates that
- * the cause is nonexistent or unknown.)
- */
- public UniprotSearchException(String message, Throwable cause) {
- super(message, cause);
- }
-
-}
+package lcsb.mapviewer.annotation.services.annotators;
+
+/**
+ * Exception that should be thrown when there is a problem with finding
+ * information about Uniprot.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class UniprotSearchException extends Exception {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Constructs a new exception with the specified detail message and cause.
+ *
+ * @param message
+ * the detail message
+ * @param cause
+ * the cause (A <tt>null</tt> value is permitted, and indicates that
+ * the cause is nonexistent or unknown.)
+ */
+ public UniprotSearchException(String message, Throwable cause) {
+ super(message, cause);
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/package-info.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/package-info.java
index ceb28e6260..25b66c7be1 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/package-info.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/package-info.java
@@ -1,9 +1,9 @@
-/**
- * This package contains classes that can annotate
- * {@link lcsb.mapviewer.model.map.BioEntity} objects. General annotation
- * interface is defined in
- * {@link lcsb.mapviewer.annotation.services.annotators.ElementAnnotator} class.
- *
- */
-package lcsb.mapviewer.annotation.services.annotators;
-
+/**
+ * This package contains classes that can annotate
+ * {@link lcsb.mapviewer.model.map.BioEntity} objects. General annotation
+ * interface is defined in
+ * {@link lcsb.mapviewer.annotation.services.annotators.ElementAnnotator} class.
+ *
+ */
+package lcsb.mapviewer.annotation.services.annotators;
+
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/AbstractReferenceGenomeConnector.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/AbstractReferenceGenomeConnector.java
index 4cf8943ccf..385b8c2ae7 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/AbstractReferenceGenomeConnector.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/AbstractReferenceGenomeConnector.java
@@ -1,395 +1,395 @@
-package lcsb.mapviewer.annotation.services.genome;
-
-import java.io.IOException;
-import java.net.URISyntaxException;
-import java.util.concurrent.Callable;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-import java.util.concurrent.Future;
-import java.util.concurrent.ScheduledThreadPoolExecutor;
-import java.util.concurrent.ThreadFactory;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.annotation.cache.BigFileCache;
-import lcsb.mapviewer.annotation.cache.CachableInterface;
-import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.model.map.layout.ReferenceGenome;
-import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
-import lcsb.mapviewer.persist.DbUtils;
-import lcsb.mapviewer.persist.dao.map.layout.ReferenceGenomeDao;
-import lcsb.mapviewer.persist.dao.map.layout.ReferenceGenomeGeneMappingDao;
-
-/**
- * Class containing generic methods for accessing storing and retrieving
- * reference genomes.
- *
- * @author Piotr Gawron
- *
- */
-public abstract class AbstractReferenceGenomeConnector extends CachableInterface implements ReferenceGenomeConnector {
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(AbstractReferenceGenomeConnector.class);
-
- /**
- * Utils that help to manage the sessions in custom multithreaded
- * implementation.
- */
- @Autowired
- private DbUtils dbUtils;
-
- /**
- * Data access object for reference genomes that we have in a database.
- */
- @Autowired
- private ReferenceGenomeDao referenceGenomeDao;
-
- /**
- * Data access object for reference genome mappings that we have in a
- * database.
- */
- @Autowired
- private ReferenceGenomeGeneMappingDao referenceGenomeGeneMappingDao;
-
- /**
- * Interface for storing/accessing big files on teh server (we have local copy
- * if big files on the server).
- */
- @Autowired
- private BigFileCache bigFileCache;
-
- /**
- * Service used for executing tasks in separate thread.
- */
- private ExecutorService asyncExecutorService;
-
- /**
- * Service used for executing tasks immediately.
- */
- private ExecutorService syncExecutorService;
-
- /**
- * Default constructor.
- *
- * @param clazz
- * class that extends this abstract interface
- */
- public AbstractReferenceGenomeConnector(Class<? extends CachableInterface> clazz) {
- super(clazz);
- // the executor is a daemon thread so that it will get killed automatically
- // when the main program exits
- asyncExecutorService = Executors.newScheduledThreadPool(10, new ThreadFactory() {
- @Override
- public Thread newThread(Runnable r) {
- Thread t = new Thread(r);
- t.setDaemon(true);
- return t;
- }
- });
- syncExecutorService = Executors.newScheduledThreadPool(1, new ThreadFactory() {
- @Override
- public Thread newThread(Runnable r) {
- Thread t = new Thread(r);
- t.setDaemon(true);
- return t;
- }
- });
-
- // put in the queue empty task to make sure that everything was initialized
- // (additional managing thread was createed)
- asyncExecutorService.submit(new Callable<Object>() {
- @Override
- public Object call() throws Exception {
- return null;
- }
- });
- syncExecutorService.submit(new Callable<Object>() {
- @Override
- public Object call() throws Exception {
- return null;
- }
- });
- }
-
- /**
- * Task that will be able to fetch mapping genome file with given version from
- * externalserver.
- *
- * @author Piotr Gawron
- *
- */
- private final class DownloadGeneMappingGenomeVersionTask implements Callable<Void> {
-
- /**
- * Url to the file that we want to download.
- *
- */
- private String url;
-
- /**
- * Callback listener that will receive information about download progress.
- *
- */
- private IProgressUpdater updater;
-
- /**
- * Name of the gen genome mapping.
- */
- private String name;
-
- /**
- * Genome where mapping should be added.
- */
- private ReferenceGenome referenceGenome;
-
- /**
- * Default constructor.
- *
- * @param url
- * {@link #url}
- * @param updater
- * {@link #updater}
- * @param referenceGenome
- * {@link #referenceGenome}
- * @param name
- * {@link #name}
- */
- private DownloadGeneMappingGenomeVersionTask(ReferenceGenome referenceGenome, String name, String url, IProgressUpdater updater) {
- this.url = url;
- this.referenceGenome = referenceGenome;
- this.name = name;
- if (updater != null) {
- this.updater = updater;
- } else {
- this.updater = new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- };
- }
- }
-
- @Override
- public Void call() throws Exception {
- getDbUtils().createSessionForCurrentThread();
- try {
- ReferenceGenome referenceGenome = getReferenceGenomeDao().getById(this.referenceGenome.getId());
- for (ReferenceGenomeGeneMapping mapping : referenceGenome.getGeneMapping()) {
- if (mapping.getName().equals(name)) {
- throw new ReferenceGenomeConnectorException("Gene mapping with name: \"" + name + "\" already exists.");
- }
- }
- if (!url.toLowerCase().endsWith("bb")) {
- throw new ReferenceGenomeConnectorException("Only big bed format files are supported but found: \"" + url + "\".");
- }
- ReferenceGenomeGeneMapping mapping = new ReferenceGenomeGeneMapping();
- mapping.setReferenceGenome(referenceGenome);
- mapping.setName(name);
- mapping.setSourceUrl(url);
- referenceGenome.addReferenceGenomeGeneMapping(mapping);
- getReferenceGenomeGeneMappingDao().add(mapping);
- getReferenceGenomeGeneMappingDao().flush();
- getReferenceGenomeDao().commit();
- getBigFileCache().downloadFile(url, false, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- if (updater != null) {
- updater.setProgress(progress);
- }
- // we have to get the object because it's in separate thred
- ReferenceGenomeGeneMapping temp = getReferenceGenomeGeneMappingDao().getById(mapping.getId());
- temp.setDownloadProgress(progress);
- getReferenceGenomeGeneMappingDao().update(temp);
- getReferenceGenomeGeneMappingDao().commit();
- }
- });
- ReferenceGenomeGeneMapping temp = getReferenceGenomeGeneMappingDao().getById(mapping.getId());
- temp.setDownloadProgress(100.0);
- getReferenceGenomeGeneMappingDao().update(temp);
- return null;
- } catch (Exception e) {
- logger.error(e, e);
- throw e;
- } finally {
- getDbUtils().closeSessionForCurrentThread();
- }
- }
-
- }
-
- @Override
- public void downloadGeneMappingGenomeVersion(ReferenceGenome referenceGenome, String name, IProgressUpdater updater, boolean async, String url)
- throws IOException, URISyntaxException, ReferenceGenomeConnectorException {
- Callable<Void> computations = new DownloadGeneMappingGenomeVersionTask(referenceGenome, name, url, updater);
- if (async) {
- getAsyncExecutorService().submit(computations);
- } else {
- Future<Void> task = getSyncExecutorService().submit(computations);
- executeTask(task);
- }
- }
-
- /**
- * @return the dbUtils
- * @see #dbUtils
- */
- public DbUtils getDbUtils() {
- return dbUtils;
- }
-
- /**
- * @param dbUtils
- * the dbUtils to set
- * @see #dbUtils
- */
- public void setDbUtils(DbUtils dbUtils) {
- this.dbUtils = dbUtils;
- }
-
- /**
- * @return the referenceGenomeDao
- * @see #referenceGenomeDao
- */
- public ReferenceGenomeDao getReferenceGenomeDao() {
- return referenceGenomeDao;
- }
-
- /**
- * @param referenceGenomeDao
- * the referenceGenomeDao to set
- * @see #referenceGenomeDao
- */
- public void setReferenceGenomeDao(ReferenceGenomeDao referenceGenomeDao) {
- this.referenceGenomeDao = referenceGenomeDao;
- }
-
- /**
- * @return the referenceGenomeGeneMappingDao
- * @see #referenceGenomeGeneMappingDao
- */
- public ReferenceGenomeGeneMappingDao getReferenceGenomeGeneMappingDao() {
- return referenceGenomeGeneMappingDao;
- }
-
- /**
- * @param referenceGenomeGeneMappingDao
- * the referenceGenomeGeneMappingDao to set
- * @see #referenceGenomeGeneMappingDao
- */
- public void setReferenceGenomeGeneMappingDao(ReferenceGenomeGeneMappingDao referenceGenomeGeneMappingDao) {
- this.referenceGenomeGeneMappingDao = referenceGenomeGeneMappingDao;
- }
-
- /**
- * @return the bigFileCache
- * @see #bigFileCache
- */
- public BigFileCache getBigFileCache() {
- return bigFileCache;
- }
-
- /**
- * @param bigFileCache
- * the bigFileCache to set
- * @see #bigFileCache
- */
- public void setBigFileCache(BigFileCache bigFileCache) {
- this.bigFileCache = bigFileCache;
- }
-
- @Override
- public void removeGeneMapping(ReferenceGenomeGeneMapping mapping2) throws IOException {
- ReferenceGenomeGeneMapping dbMapping = getReferenceGenomeGeneMappingDao().getById(mapping2.getId());
- if (dbMapping == null) {
- logger.warn("Mapping doesn't exist in the DB");
- } else {
- if (getBigFileCache().isCached(dbMapping.getSourceUrl())) {
- getBigFileCache().removeFile(dbMapping.getSourceUrl());
- }
- ReferenceGenome genome = dbMapping.getReferenceGenome();
- genome.getGeneMapping().remove(dbMapping);
- getReferenceGenomeGeneMappingDao().delete(dbMapping);
- }
- }
-
- /**
- * @return the asyncExecutorService
- * @see #asyncExecutorService
- */
- protected ExecutorService getAsyncExecutorService() {
- return asyncExecutorService;
- }
-
- /**
- * @param asyncExecutorService
- * the asyncExecutorService to set
- * @see #asyncExecutorService
- */
- protected void setAsyncExecutorService(ExecutorService asyncExecutorService) {
- this.asyncExecutorService = asyncExecutorService;
- }
-
- /**
- * @return the syncExecutorService
- * @see #syncExecutorService
- */
- protected ExecutorService getSyncExecutorService() {
- return syncExecutorService;
- }
-
- /**
- * @param syncExecutorService
- * the syncExecutorService to set
- * @see #syncExecutorService
- */
- protected void setSyncExecutorService(ExecutorService syncExecutorService) {
- this.syncExecutorService = syncExecutorService;
- }
-
- /**
- * Return number of tasks that are executed or are waiting for execution.
- *
- * @return number of tasks that are executed or are waiting for execution
- */
- public int getDownloadThreadCount() {
- return ((ScheduledThreadPoolExecutor) asyncExecutorService).getQueue().size() + ((ScheduledThreadPoolExecutor) asyncExecutorService).getActiveCount()
- + ((ScheduledThreadPoolExecutor) syncExecutorService).getQueue().size() + ((ScheduledThreadPoolExecutor) syncExecutorService).getActiveCount();
- }
-
- /**
- * Executes download/update task.
- *
- * @param task
- * task to be executed
- * @throws URISyntaxException
- * thrown when task finsihed with {@link URISyntaxException}
- * @throws IOException
- * thrown when task finsihed with {@link IOException}
- * @throws ReferenceGenomeConnectorException
- * thrown when there is a problem with genome connector
- */
- void executeTask(Future<?> task) throws URISyntaxException, IOException, ReferenceGenomeConnectorException {
- try {
- task.get();
- } catch (InterruptedException e) {
- logger.error(e, e);
- } catch (ExecutionException e) {
- if (e.getCause() instanceof URISyntaxException) {
- throw (URISyntaxException) e.getCause();
- } else if (e.getCause() instanceof IOException) {
- throw new IOException((IOException) e.getCause());
- } else if (e.getCause() instanceof ReferenceGenomeConnectorException) {
- throw new ReferenceGenomeConnectorException((ReferenceGenomeConnectorException) e.getCause());
- } else {
- throw new InvalidStateException(e);
- }
- }
- }
-
-}
+package lcsb.mapviewer.annotation.services.genome;
+
+import java.io.IOException;
+import java.net.URISyntaxException;
+import java.util.concurrent.Callable;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
+import java.util.concurrent.ScheduledThreadPoolExecutor;
+import java.util.concurrent.ThreadFactory;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.cache.BigFileCache;
+import lcsb.mapviewer.annotation.cache.CachableInterface;
+import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.model.map.layout.ReferenceGenome;
+import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
+import lcsb.mapviewer.persist.DbUtils;
+import lcsb.mapviewer.persist.dao.map.layout.ReferenceGenomeDao;
+import lcsb.mapviewer.persist.dao.map.layout.ReferenceGenomeGeneMappingDao;
+
+/**
+ * Class containing generic methods for accessing storing and retrieving
+ * reference genomes.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public abstract class AbstractReferenceGenomeConnector extends CachableInterface implements ReferenceGenomeConnector {
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(AbstractReferenceGenomeConnector.class);
+
+ /**
+ * Utils that help to manage the sessions in custom multithreaded
+ * implementation.
+ */
+ @Autowired
+ private DbUtils dbUtils;
+
+ /**
+ * Data access object for reference genomes that we have in a database.
+ */
+ @Autowired
+ private ReferenceGenomeDao referenceGenomeDao;
+
+ /**
+ * Data access object for reference genome mappings that we have in a
+ * database.
+ */
+ @Autowired
+ private ReferenceGenomeGeneMappingDao referenceGenomeGeneMappingDao;
+
+ /**
+ * Interface for storing/accessing big files on teh server (we have local copy
+ * if big files on the server).
+ */
+ @Autowired
+ private BigFileCache bigFileCache;
+
+ /**
+ * Service used for executing tasks in separate thread.
+ */
+ private ExecutorService asyncExecutorService;
+
+ /**
+ * Service used for executing tasks immediately.
+ */
+ private ExecutorService syncExecutorService;
+
+ /**
+ * Default constructor.
+ *
+ * @param clazz
+ * class that extends this abstract interface
+ */
+ public AbstractReferenceGenomeConnector(Class<? extends CachableInterface> clazz) {
+ super(clazz);
+ // the executor is a daemon thread so that it will get killed automatically
+ // when the main program exits
+ asyncExecutorService = Executors.newScheduledThreadPool(10, new ThreadFactory() {
+ @Override
+ public Thread newThread(Runnable r) {
+ Thread t = new Thread(r);
+ t.setDaemon(true);
+ return t;
+ }
+ });
+ syncExecutorService = Executors.newScheduledThreadPool(1, new ThreadFactory() {
+ @Override
+ public Thread newThread(Runnable r) {
+ Thread t = new Thread(r);
+ t.setDaemon(true);
+ return t;
+ }
+ });
+
+ // put in the queue empty task to make sure that everything was initialized
+ // (additional managing thread was createed)
+ asyncExecutorService.submit(new Callable<Object>() {
+ @Override
+ public Object call() throws Exception {
+ return null;
+ }
+ });
+ syncExecutorService.submit(new Callable<Object>() {
+ @Override
+ public Object call() throws Exception {
+ return null;
+ }
+ });
+ }
+
+ /**
+ * Task that will be able to fetch mapping genome file with given version from
+ * externalserver.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ private final class DownloadGeneMappingGenomeVersionTask implements Callable<Void> {
+
+ /**
+ * Url to the file that we want to download.
+ *
+ */
+ private String url;
+
+ /**
+ * Callback listener that will receive information about download progress.
+ *
+ */
+ private IProgressUpdater updater;
+
+ /**
+ * Name of the gen genome mapping.
+ */
+ private String name;
+
+ /**
+ * Genome where mapping should be added.
+ */
+ private ReferenceGenome referenceGenome;
+
+ /**
+ * Default constructor.
+ *
+ * @param url
+ * {@link #url}
+ * @param updater
+ * {@link #updater}
+ * @param referenceGenome
+ * {@link #referenceGenome}
+ * @param name
+ * {@link #name}
+ */
+ private DownloadGeneMappingGenomeVersionTask(ReferenceGenome referenceGenome, String name, String url, IProgressUpdater updater) {
+ this.url = url;
+ this.referenceGenome = referenceGenome;
+ this.name = name;
+ if (updater != null) {
+ this.updater = updater;
+ } else {
+ this.updater = new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ };
+ }
+ }
+
+ @Override
+ public Void call() throws Exception {
+ getDbUtils().createSessionForCurrentThread();
+ try {
+ ReferenceGenome referenceGenome = getReferenceGenomeDao().getById(this.referenceGenome.getId());
+ for (ReferenceGenomeGeneMapping mapping : referenceGenome.getGeneMapping()) {
+ if (mapping.getName().equals(name)) {
+ throw new ReferenceGenomeConnectorException("Gene mapping with name: \"" + name + "\" already exists.");
+ }
+ }
+ if (!url.toLowerCase().endsWith("bb")) {
+ throw new ReferenceGenomeConnectorException("Only big bed format files are supported but found: \"" + url + "\".");
+ }
+ ReferenceGenomeGeneMapping mapping = new ReferenceGenomeGeneMapping();
+ mapping.setReferenceGenome(referenceGenome);
+ mapping.setName(name);
+ mapping.setSourceUrl(url);
+ referenceGenome.addReferenceGenomeGeneMapping(mapping);
+ getReferenceGenomeGeneMappingDao().add(mapping);
+ getReferenceGenomeGeneMappingDao().flush();
+ getReferenceGenomeDao().commit();
+ getBigFileCache().downloadFile(url, false, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ if (updater != null) {
+ updater.setProgress(progress);
+ }
+ // we have to get the object because it's in separate thred
+ ReferenceGenomeGeneMapping temp = getReferenceGenomeGeneMappingDao().getById(mapping.getId());
+ temp.setDownloadProgress(progress);
+ getReferenceGenomeGeneMappingDao().update(temp);
+ getReferenceGenomeGeneMappingDao().commit();
+ }
+ });
+ ReferenceGenomeGeneMapping temp = getReferenceGenomeGeneMappingDao().getById(mapping.getId());
+ temp.setDownloadProgress(100.0);
+ getReferenceGenomeGeneMappingDao().update(temp);
+ return null;
+ } catch (Exception e) {
+ logger.error(e, e);
+ throw e;
+ } finally {
+ getDbUtils().closeSessionForCurrentThread();
+ }
+ }
+
+ }
+
+ @Override
+ public void downloadGeneMappingGenomeVersion(ReferenceGenome referenceGenome, String name, IProgressUpdater updater, boolean async, String url)
+ throws IOException, URISyntaxException, ReferenceGenomeConnectorException {
+ Callable<Void> computations = new DownloadGeneMappingGenomeVersionTask(referenceGenome, name, url, updater);
+ if (async) {
+ getAsyncExecutorService().submit(computations);
+ } else {
+ Future<Void> task = getSyncExecutorService().submit(computations);
+ executeTask(task);
+ }
+ }
+
+ /**
+ * @return the dbUtils
+ * @see #dbUtils
+ */
+ public DbUtils getDbUtils() {
+ return dbUtils;
+ }
+
+ /**
+ * @param dbUtils
+ * the dbUtils to set
+ * @see #dbUtils
+ */
+ public void setDbUtils(DbUtils dbUtils) {
+ this.dbUtils = dbUtils;
+ }
+
+ /**
+ * @return the referenceGenomeDao
+ * @see #referenceGenomeDao
+ */
+ public ReferenceGenomeDao getReferenceGenomeDao() {
+ return referenceGenomeDao;
+ }
+
+ /**
+ * @param referenceGenomeDao
+ * the referenceGenomeDao to set
+ * @see #referenceGenomeDao
+ */
+ public void setReferenceGenomeDao(ReferenceGenomeDao referenceGenomeDao) {
+ this.referenceGenomeDao = referenceGenomeDao;
+ }
+
+ /**
+ * @return the referenceGenomeGeneMappingDao
+ * @see #referenceGenomeGeneMappingDao
+ */
+ public ReferenceGenomeGeneMappingDao getReferenceGenomeGeneMappingDao() {
+ return referenceGenomeGeneMappingDao;
+ }
+
+ /**
+ * @param referenceGenomeGeneMappingDao
+ * the referenceGenomeGeneMappingDao to set
+ * @see #referenceGenomeGeneMappingDao
+ */
+ public void setReferenceGenomeGeneMappingDao(ReferenceGenomeGeneMappingDao referenceGenomeGeneMappingDao) {
+ this.referenceGenomeGeneMappingDao = referenceGenomeGeneMappingDao;
+ }
+
+ /**
+ * @return the bigFileCache
+ * @see #bigFileCache
+ */
+ public BigFileCache getBigFileCache() {
+ return bigFileCache;
+ }
+
+ /**
+ * @param bigFileCache
+ * the bigFileCache to set
+ * @see #bigFileCache
+ */
+ public void setBigFileCache(BigFileCache bigFileCache) {
+ this.bigFileCache = bigFileCache;
+ }
+
+ @Override
+ public void removeGeneMapping(ReferenceGenomeGeneMapping mapping2) throws IOException {
+ ReferenceGenomeGeneMapping dbMapping = getReferenceGenomeGeneMappingDao().getById(mapping2.getId());
+ if (dbMapping == null) {
+ logger.warn("Mapping doesn't exist in the DB");
+ } else {
+ if (getBigFileCache().isCached(dbMapping.getSourceUrl())) {
+ getBigFileCache().removeFile(dbMapping.getSourceUrl());
+ }
+ ReferenceGenome genome = dbMapping.getReferenceGenome();
+ genome.getGeneMapping().remove(dbMapping);
+ getReferenceGenomeGeneMappingDao().delete(dbMapping);
+ }
+ }
+
+ /**
+ * @return the asyncExecutorService
+ * @see #asyncExecutorService
+ */
+ protected ExecutorService getAsyncExecutorService() {
+ return asyncExecutorService;
+ }
+
+ /**
+ * @param asyncExecutorService
+ * the asyncExecutorService to set
+ * @see #asyncExecutorService
+ */
+ protected void setAsyncExecutorService(ExecutorService asyncExecutorService) {
+ this.asyncExecutorService = asyncExecutorService;
+ }
+
+ /**
+ * @return the syncExecutorService
+ * @see #syncExecutorService
+ */
+ protected ExecutorService getSyncExecutorService() {
+ return syncExecutorService;
+ }
+
+ /**
+ * @param syncExecutorService
+ * the syncExecutorService to set
+ * @see #syncExecutorService
+ */
+ protected void setSyncExecutorService(ExecutorService syncExecutorService) {
+ this.syncExecutorService = syncExecutorService;
+ }
+
+ /**
+ * Return number of tasks that are executed or are waiting for execution.
+ *
+ * @return number of tasks that are executed or are waiting for execution
+ */
+ public int getDownloadThreadCount() {
+ return ((ScheduledThreadPoolExecutor) asyncExecutorService).getQueue().size() + ((ScheduledThreadPoolExecutor) asyncExecutorService).getActiveCount()
+ + ((ScheduledThreadPoolExecutor) syncExecutorService).getQueue().size() + ((ScheduledThreadPoolExecutor) syncExecutorService).getActiveCount();
+ }
+
+ /**
+ * Executes download/update task.
+ *
+ * @param task
+ * task to be executed
+ * @throws URISyntaxException
+ * thrown when task finsihed with {@link URISyntaxException}
+ * @throws IOException
+ * thrown when task finsihed with {@link IOException}
+ * @throws ReferenceGenomeConnectorException
+ * thrown when there is a problem with genome connector
+ */
+ void executeTask(Future<?> task) throws URISyntaxException, IOException, ReferenceGenomeConnectorException {
+ try {
+ task.get();
+ } catch (InterruptedException e) {
+ logger.error(e, e);
+ } catch (ExecutionException e) {
+ if (e.getCause() instanceof URISyntaxException) {
+ throw (URISyntaxException) e.getCause();
+ } else if (e.getCause() instanceof IOException) {
+ throw new IOException((IOException) e.getCause());
+ } else if (e.getCause() instanceof ReferenceGenomeConnectorException) {
+ throw new ReferenceGenomeConnectorException((ReferenceGenomeConnectorException) e.getCause());
+ } else {
+ throw new InvalidStateException(e);
+ }
+ }
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/FileNotAvailableException.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/FileNotAvailableException.java
index ceb98b2166..0a11c19a4b 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/FileNotAvailableException.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/FileNotAvailableException.java
@@ -1,48 +1,48 @@
-package lcsb.mapviewer.annotation.services.genome;
-
-/**
- * Exception taht should be thrown when file for specific genome version id not
- * available.
- *
- * @author Piotr Gawron
- *
- */
-public class FileNotAvailableException extends Exception {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- *
- * @param message
- * error message
- */
- public FileNotAvailableException(String message) {
- super(message);
- }
-
- /**
- * Default constructor.
- *
- * @param cause
- * error cause
- */
- public FileNotAvailableException(Throwable cause) {
- super(cause);
- }
-
- /**
- * Default constructor.
- *
- * @param message
- * error message
- * @param cause
- * error cause
- */
- public FileNotAvailableException(String message, Throwable cause) {
- super(message, cause);
- }
-}
+package lcsb.mapviewer.annotation.services.genome;
+
+/**
+ * Exception taht should be thrown when file for specific genome version id not
+ * available.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class FileNotAvailableException extends Exception {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * error message
+ */
+ public FileNotAvailableException(String message) {
+ super(message);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param cause
+ * error cause
+ */
+ public FileNotAvailableException(Throwable cause) {
+ super(cause);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * error message
+ * @param cause
+ * error cause
+ */
+ public FileNotAvailableException(String message, Throwable cause) {
+ super(message, cause);
+ }
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/ReferenceGenomeConnector.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/ReferenceGenomeConnector.java
index 33d279d315..0eeb5101a6 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/ReferenceGenomeConnector.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/ReferenceGenomeConnector.java
@@ -1,158 +1,158 @@
-package lcsb.mapviewer.annotation.services.genome;
-
-import java.io.IOException;
-import java.net.URISyntaxException;
-import java.util.List;
-
-import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.layout.ReferenceGenome;
-import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
-
-/**
- * Interface defining operation on single reference genome type database.
- *
- * @author Piotr Gawron
- *
- */
-public interface ReferenceGenomeConnector {
-
- /**
- * Returns list of downloaded reference genomes. This list should contain list
- * of differente versions of reference genome from this database for given
- * organism.
- *
- * @param organism
- * organism for which list should be obtained
- * @return list of downloaded reference genomes
- */
- List<String> getDownloadedGenomeVersions(MiriamData organism);
-
- /**
- * Returns list of available reference genomes for given organism.
- *
- * @param organism
- * organism for which list should be obtained
- * @return list of available reference genomes
- * @throws ReferenceGenomeConnectorException
- * thrown when there is a problem with accessing external database
- */
- List<String> getAvailableGenomeVersion(MiriamData organism) throws ReferenceGenomeConnectorException;
-
- /**
- * Returns list of reference genome organism available in this database.
- *
- * @return list of reference genome organisms
- * @throws ReferenceGenomeConnectorException
- * thrown when there is a problem with accessing external database
- */
- List<MiriamData> getAvailableOrganisms() throws ReferenceGenomeConnectorException;
-
- /**
- * Downloads reference genome with specified version.
- *
- * @param organism
- * organism for which reference genome should be downloaded
- * @param version
- * version of reference genome
- * @param updater
- * callback funtion that will be called to update information about
- * progress
- * @param async
- * should the download be performed asynchronously
- * @throws FileNotAvailableException
- * thrown when file for given input reference genome is not
- * available
- * @throws IOException
- * thrown when there is a problem with downloading file
- * @throws ReferenceGenomeConnectorException
- * thrown when there is a problem with genome connector
- */
- void downloadGenomeVersion(MiriamData organism, String version, IProgressUpdater updater, boolean async)
- throws FileNotAvailableException, IOException, ReferenceGenomeConnectorException;
-
- /**
- * Downloads reference genome with specified version.
- *
- * @param organism
- * organism for which reference genome should be downloaded
- * @param version
- * version of reference genome
- * @param updater
- * callback funtion that will be called to update information about
- * progress
- * @param async
- * should the download be performed asynchronously
- * @param url
- * url that points to the reference genome
- * @throws IOException
- * thrown when there is a problem with downloading file
- * @throws URISyntaxException
- * thrown when url is invalid
- * @throws ReferenceGenomeConnectorException
- * thrown when there is a problem with genome connector
- */
- void downloadGenomeVersion(MiriamData organism, String version, IProgressUpdater updater, boolean async, String url)
- throws IOException, URISyntaxException, ReferenceGenomeConnectorException;
-
- /**
- * Downloads gene mapping for reference genome.
- *
- * @param referenceGenome
- * reference genome for which gene mapping is downloaded
- * @param updater
- * callback funtion that will be called to update information about
- * progress
- * @param async
- * should the download be performed asynchronously
- * @param name
- * name of the mapping
- * @param url
- * url that points to the reference genome
- * @throws IOException
- * thrown when there is a problem with downloading file
- * @throws URISyntaxException
- * thrown when url is invalid
- * @throws ReferenceGenomeConnectorException
- * thrown when there is problem with accessing external database
- */
- void downloadGeneMappingGenomeVersion(ReferenceGenome referenceGenome, String name, IProgressUpdater updater, boolean async, String url)
- throws IOException, URISyntaxException, ReferenceGenomeConnectorException;
-
- /**
- * Removes reference genome.
- *
- * @param organism
- * organism that defines reference genome
- * @param version
- * version of the reference genome
- * @throws IOException
- * thrown when there is a problem with removing file
- */
- void removeGenomeVersion(MiriamData organism, String version) throws IOException;
-
- /**
- * Returns url to the file that describes reference genome.
- *
- * @param organism
- * organism of reference genome
- * @param version
- * version of the reference genome
- * @return url to the file that describes reference genome
- * @throws FileNotAvailableException
- * thrown when file describing reference genome cannot be found
- */
- String getGenomeVersionFile(MiriamData organism, String version) throws FileNotAvailableException;
-
- /**
- * Removes gene mapping from reference genome.
- *
- * @param mapping
- * mapping to be removed
- * @throws IOException
- * thrown when removing of a file encountered some problems
- */
-
- void removeGeneMapping(ReferenceGenomeGeneMapping mapping) throws IOException;
-
-}
+package lcsb.mapviewer.annotation.services.genome;
+
+import java.io.IOException;
+import java.net.URISyntaxException;
+import java.util.List;
+
+import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.layout.ReferenceGenome;
+import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
+
+/**
+ * Interface defining operation on single reference genome type database.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface ReferenceGenomeConnector {
+
+ /**
+ * Returns list of downloaded reference genomes. This list should contain list
+ * of differente versions of reference genome from this database for given
+ * organism.
+ *
+ * @param organism
+ * organism for which list should be obtained
+ * @return list of downloaded reference genomes
+ */
+ List<String> getDownloadedGenomeVersions(MiriamData organism);
+
+ /**
+ * Returns list of available reference genomes for given organism.
+ *
+ * @param organism
+ * organism for which list should be obtained
+ * @return list of available reference genomes
+ * @throws ReferenceGenomeConnectorException
+ * thrown when there is a problem with accessing external database
+ */
+ List<String> getAvailableGenomeVersion(MiriamData organism) throws ReferenceGenomeConnectorException;
+
+ /**
+ * Returns list of reference genome organism available in this database.
+ *
+ * @return list of reference genome organisms
+ * @throws ReferenceGenomeConnectorException
+ * thrown when there is a problem with accessing external database
+ */
+ List<MiriamData> getAvailableOrganisms() throws ReferenceGenomeConnectorException;
+
+ /**
+ * Downloads reference genome with specified version.
+ *
+ * @param organism
+ * organism for which reference genome should be downloaded
+ * @param version
+ * version of reference genome
+ * @param updater
+ * callback funtion that will be called to update information about
+ * progress
+ * @param async
+ * should the download be performed asynchronously
+ * @throws FileNotAvailableException
+ * thrown when file for given input reference genome is not
+ * available
+ * @throws IOException
+ * thrown when there is a problem with downloading file
+ * @throws ReferenceGenomeConnectorException
+ * thrown when there is a problem with genome connector
+ */
+ void downloadGenomeVersion(MiriamData organism, String version, IProgressUpdater updater, boolean async)
+ throws FileNotAvailableException, IOException, ReferenceGenomeConnectorException;
+
+ /**
+ * Downloads reference genome with specified version.
+ *
+ * @param organism
+ * organism for which reference genome should be downloaded
+ * @param version
+ * version of reference genome
+ * @param updater
+ * callback funtion that will be called to update information about
+ * progress
+ * @param async
+ * should the download be performed asynchronously
+ * @param url
+ * url that points to the reference genome
+ * @throws IOException
+ * thrown when there is a problem with downloading file
+ * @throws URISyntaxException
+ * thrown when url is invalid
+ * @throws ReferenceGenomeConnectorException
+ * thrown when there is a problem with genome connector
+ */
+ void downloadGenomeVersion(MiriamData organism, String version, IProgressUpdater updater, boolean async, String url)
+ throws IOException, URISyntaxException, ReferenceGenomeConnectorException;
+
+ /**
+ * Downloads gene mapping for reference genome.
+ *
+ * @param referenceGenome
+ * reference genome for which gene mapping is downloaded
+ * @param updater
+ * callback funtion that will be called to update information about
+ * progress
+ * @param async
+ * should the download be performed asynchronously
+ * @param name
+ * name of the mapping
+ * @param url
+ * url that points to the reference genome
+ * @throws IOException
+ * thrown when there is a problem with downloading file
+ * @throws URISyntaxException
+ * thrown when url is invalid
+ * @throws ReferenceGenomeConnectorException
+ * thrown when there is problem with accessing external database
+ */
+ void downloadGeneMappingGenomeVersion(ReferenceGenome referenceGenome, String name, IProgressUpdater updater, boolean async, String url)
+ throws IOException, URISyntaxException, ReferenceGenomeConnectorException;
+
+ /**
+ * Removes reference genome.
+ *
+ * @param organism
+ * organism that defines reference genome
+ * @param version
+ * version of the reference genome
+ * @throws IOException
+ * thrown when there is a problem with removing file
+ */
+ void removeGenomeVersion(MiriamData organism, String version) throws IOException;
+
+ /**
+ * Returns url to the file that describes reference genome.
+ *
+ * @param organism
+ * organism of reference genome
+ * @param version
+ * version of the reference genome
+ * @return url to the file that describes reference genome
+ * @throws FileNotAvailableException
+ * thrown when file describing reference genome cannot be found
+ */
+ String getGenomeVersionFile(MiriamData organism, String version) throws FileNotAvailableException;
+
+ /**
+ * Removes gene mapping from reference genome.
+ *
+ * @param mapping
+ * mapping to be removed
+ * @throws IOException
+ * thrown when removing of a file encountered some problems
+ */
+
+ void removeGeneMapping(ReferenceGenomeGeneMapping mapping) throws IOException;
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/ReferenceGenomeConnectorException.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/ReferenceGenomeConnectorException.java
index b6ef25d93f..58253f8b61 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/ReferenceGenomeConnectorException.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/ReferenceGenomeConnectorException.java
@@ -1,50 +1,50 @@
-package lcsb.mapviewer.annotation.services.genome;
-
-/**
- * Thrown when there is aproblem with accessing reference genome database or
- * there are problems with performing some operation on reference genome
- * connection.
- *
- * @author Piotr Gawron
- *
- */
-public class ReferenceGenomeConnectorException extends Exception {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- *
- * @param message
- * message associated with exception
- * @param exception
- * original exception
- */
- public ReferenceGenomeConnectorException(String message, Exception exception) {
- super(message, exception);
- }
-
- /**
- * Default constructor.
- *
- * @param message
- * message associated with exception
- */
- public ReferenceGenomeConnectorException(String message) {
- super(message);
- }
-
- /**
- * Default constructor.
- *
- * @param cause
- * original exception
- */
- public ReferenceGenomeConnectorException(Exception cause) {
- super(cause);
- }
-
-}
+package lcsb.mapviewer.annotation.services.genome;
+
+/**
+ * Thrown when there is aproblem with accessing reference genome database or
+ * there are problems with performing some operation on reference genome
+ * connection.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ReferenceGenomeConnectorException extends Exception {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * message associated with exception
+ * @param exception
+ * original exception
+ */
+ public ReferenceGenomeConnectorException(String message, Exception exception) {
+ super(message, exception);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * message associated with exception
+ */
+ public ReferenceGenomeConnectorException(String message) {
+ super(message);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param cause
+ * original exception
+ */
+ public ReferenceGenomeConnectorException(Exception cause) {
+ super(cause);
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/UcscReferenceGenomeConnector.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/UcscReferenceGenomeConnector.java
index d95d98b5c9..5c891051ef 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/UcscReferenceGenomeConnector.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/UcscReferenceGenomeConnector.java
@@ -1,474 +1,474 @@
-package lcsb.mapviewer.annotation.services.genome;
-
-import java.io.IOException;
-import java.net.URISyntaxException;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-import java.util.concurrent.Callable;
-import java.util.concurrent.Future;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import org.apache.commons.net.ftp.FTP;
-import org.apache.commons.net.ftp.FTPClient;
-import org.apache.commons.net.ftp.FTPFile;
-import org.apache.commons.net.ftp.FTPReply;
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
-import lcsb.mapviewer.annotation.cache.WebPageDownloader;
-import lcsb.mapviewer.annotation.services.TaxonomyBackend;
-import lcsb.mapviewer.annotation.services.TaxonomySearchException;
-import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.ReferenceGenome;
-import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
-import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
-
-/**
- * Implementeation of reference genome connector accessing
- * {@link ReferenceGenomeType#UCSC} database.
- *
- * @author Piotr Gawron
- *
- */
-public class UcscReferenceGenomeConnector extends AbstractReferenceGenomeConnector implements ReferenceGenomeConnector {
-
- /**
- * Server domain name.
- */
- private static final String SERVER = "hgdownload.cse.ucsc.edu";
-
- /**
- * Prefix string used for marking queries in cache database that identifies list
- * of reference genome versions by organism id.
- */
- static final String FILENAME_BY_ORGANISM_VERSION_PREFIX = "ORGANISM_VERSION_FILE:";
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(UcscReferenceGenomeConnector.class);
-
- /**
- * Regex pattern that helps to find out organism names in source file.
- */
- private Pattern organismNamePattern = Pattern.compile("<!--([A-Za-z\\-\\.\\ ]+)Downloads [=]*[\\ ]*-->");
-
- /**
- * Regex pattern that helps to find out reference genome versions.
- */
- private Pattern organismDataUrlPattern = Pattern.compile("\\/goldenPath\\/([A-Za-z0-9\\-\\.]+)\\/bigZips\\/");
-
- /**
- * Access point to taxonomy information.
- */
- @Autowired
- private TaxonomyBackend taxonomyBackend;
-
- /**
- * Default constructor.
- */
- public UcscReferenceGenomeConnector() {
- super(UcscReferenceGenomeConnector.class);
- }
-
- @Override
- public List<String> getDownloadedGenomeVersions(MiriamData organism) {
- List<String> results = new ArrayList<>();
-
- List<ReferenceGenome> genomes = getReferenceGenomeDao().getByType(ReferenceGenomeType.UCSC);
- for (ReferenceGenome referenceGenome : genomes) {
- if (referenceGenome.getOrganism().equals(organism)) {
- results.add(referenceGenome.getVersion());
- }
- }
- return results;
- }
-
- @Override
- public List<String> getAvailableGenomeVersion(MiriamData organism) throws ReferenceGenomeConnectorException {
- Set<String> ids = new HashSet<>();
- try {
- String content = getWebPageContent("http://hgdownload.cse.ucsc.edu/downloads.html");
- Integer start = null;
- Integer end = content.length();
- Matcher matcher = organismNamePattern.matcher(content);
- while (matcher.find()) {
- String name = matcher.group(1).trim();
- if (start != null) {
- end = matcher.start();
- break;
- }
-
- if (name.equalsIgnoreCase("Shared Data")) {
- continue;
- }
- if (name.equalsIgnoreCase("liftOver File")) {
- continue;
- }
- MiriamData taxonomy = taxonomyBackend.getByName(name);
- if (organism.equals(taxonomy)) {
- start = matcher.end();
- }
- }
- // we haven't found a start point for our organism (organism couldn't be
- // found in the list of available organisms)
- if (start != null) {
- String organismContent = content.substring(start, end);
-
- matcher = organismDataUrlPattern.matcher(organismContent);
- while (matcher.find()) {
- String name = matcher.group(1).trim();
- ids.add(name);
- }
- }
-
- } catch (IOException | TaxonomySearchException e) {
- throw new ReferenceGenomeConnectorException("Problem with accessing UCSC database", e);
- }
- List<String> result = new ArrayList<>();
- result.addAll(ids);
- Collections.sort(result, new Comparator<String>() {
- public int compare(String o1, String o2) {
- return extractInt(o2) - extractInt(o1);
- }
-
- });
- return result;
- }
-
- @Override
- public List<MiriamData> getAvailableOrganisms() throws ReferenceGenomeConnectorException {
- try {
- List<MiriamData> result = new ArrayList<>();
- String content = getWebPageContent("http://hgdownload.cse.ucsc.edu/downloads.html");
-
- Matcher matcher = organismNamePattern.matcher(content);
- while (matcher.find()) {
- String name = matcher.group(1).trim();
- if (name.equalsIgnoreCase("Shared Data")) {
- continue;
- }
- if (name.equalsIgnoreCase("liftOver File")) {
- continue;
- }
- MiriamData taxonomy = taxonomyBackend.getByName(name);
- if (taxonomy != null) {
- result.add(taxonomy);
- }
- }
-
- return result;
- } catch (IOException | TaxonomySearchException e) {
- throw new ReferenceGenomeConnectorException("Problem with accessing UCSC database", e);
- }
- }
-
- @Override
- public void downloadGenomeVersion(MiriamData organism, String version, IProgressUpdater updater, boolean async)
- throws FileNotAvailableException, IOException, ReferenceGenomeConnectorException {
- try {
- downloadGenomeVersion(organism, version, updater, async, getGenomeVersionFile(organism, version));
- } catch (URISyntaxException e) {
- throw new InvalidStateException(e);
- }
- }
-
- @Override
- public Object refreshCacheQuery(Object query) throws SourceNotAvailable {
- String result = null;
- try {
- if (query instanceof String) {
- String name = (String) query;
- if (name.startsWith("http")) {
- result = getWebPageContent(name);
- } else if (name.startsWith(FILENAME_BY_ORGANISM_VERSION_PREFIX)) {
- String[] tmp = name.substring(FILENAME_BY_ORGANISM_VERSION_PREFIX.length()).split("\n");
- result = getGenomeVersionFile(new MiriamData(MiriamType.TAXONOMY, tmp[0]), tmp[1]);
- } else {
- throw new InvalidArgumentException("Don't know what to do with string \"" + query + "\"");
- }
- } else {
- throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
- }
- } catch (FileNotAvailableException e) {
- throw new SourceNotAvailable("Cannot find file for the query: " + query, e);
- } catch (IOException e) {
- throw new SourceNotAvailable(e);
- }
- return result;
- }
-
- @Override
- public void removeGenomeVersion(MiriamData organism, String version) throws IOException {
- List<ReferenceGenome> genomes = getReferenceGenomeDao().getByType(ReferenceGenomeType.UCSC);
- for (ReferenceGenome referenceGenome : genomes) {
- if (referenceGenome.getOrganism().equals(organism) && referenceGenome.getVersion().equals(version)) {
- // removing file from big file cache might not be the best idea here
- if (getBigFileCache().isCached(referenceGenome.getSourceUrl())) {
- getBigFileCache().removeFile(referenceGenome.getSourceUrl());
- }
- for (ReferenceGenomeGeneMapping mapping : referenceGenome.getGeneMapping()) {
- if (getBigFileCache().isCached(mapping.getSourceUrl())) {
- getBigFileCache().removeFile(mapping.getSourceUrl());
- }
- }
- getReferenceGenomeDao().delete(referenceGenome);
- }
- }
- }
-
- /**
- * @return the taxonomyBackend
- * @see #taxonomyBackend
- */
- public TaxonomyBackend getTaxonomyBackend() {
- return taxonomyBackend;
- }
-
- /**
- * @param taxonomyBackend
- * the taxonomyBackend to set
- * @see #taxonomyBackend
- */
- public void setTaxonomyBackend(TaxonomyBackend taxonomyBackend) {
- this.taxonomyBackend = taxonomyBackend;
- }
-
- /**
- * Task that will be able to fetch genome file from ftp server.
- *
- * @author Piotr Gawron
- *
- */
- private final class DownloadGenomeVersionTask implements Callable<Void> {
-
- /**
- * Url to the file that we want to download.
- *
- */
- private String url;
-
- /**
- * Callback listener that will receive information about upload progress.
- *
- */
- private IProgressUpdater updater;
-
- /**
- * Organism for which we want to fetch genome.
- */
- private MiriamData organism;
-
- /**
- * Version of the genome.
- */
- private String version;
-
- /**
- * Default constructor.
- *
- * @param url
- * {@link #url}
- * @param updater
- * {@link #updater}
- * @param organism
- * {@link #organism}
- * @param version
- * {@link #version}
- */
- private DownloadGenomeVersionTask(MiriamData organism, String version, String url, IProgressUpdater updater) {
- this.url = url;
- this.organism = organism;
- this.version = version;
- if (updater != null) {
- this.updater = updater;
- } else {
- this.updater = new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- };
- }
- }
-
- @Override
- public Void call() throws Exception {
- getDbUtils().createSessionForCurrentThread();
- try {
- ReferenceGenome referenceGenome = new ReferenceGenome();
- referenceGenome.setOrganism(organism);
- referenceGenome.setType(ReferenceGenomeType.UCSC);
- referenceGenome.setVersion(version);
- referenceGenome.setSourceUrl(url);
- getReferenceGenomeDao().add(referenceGenome);
- getReferenceGenomeDao().flush();
- getReferenceGenomeDao().commit();
- getDbUtils().closeSessionForCurrentThread();
-
- getBigFileCache().downloadFile(url, false, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- if (updater != null) {
- updater.setProgress(progress);
- }
- // we have to get the object because it's in separate thred
- ReferenceGenome temp = getReferenceGenomeDao().getById(referenceGenome.getId());
- temp.setDownloadProgress(progress);
- getReferenceGenomeDao().update(temp);
- getReferenceGenomeDao().commit();
- }
- });
- return null;
- } finally {
- getDbUtils().closeSessionForCurrentThread();
- }
- }
-
- }
-
- @Override
- public void downloadGenomeVersion(MiriamData organism, String version, IProgressUpdater updater, boolean async,
- String customUrl) throws IOException, URISyntaxException, ReferenceGenomeConnectorException {
- Callable<Void> computations = new DownloadGenomeVersionTask(organism, version, customUrl, updater);
- if (async) {
- getAsyncExecutorService().submit(computations);
- } else {
- Future<Void> task = getSyncExecutorService().submit(computations);
- executeTask(task);
- }
- }
-
- /**
- * Returns local path on ftp server to folder with data about given organism and
- * version.
- *
- * @param organism
- * organism of reference genome
- * @param version
- * of reference genome
- * @return local path on ftp server to folder with data about reference genome
- */
- private String getGenomePath(MiriamData organism, String version) {
- return "/goldenPath/" + version + "/bigZips/";
- }
-
- @Override
- public String getGenomeVersionFile(MiriamData organism, String version) throws FileNotAvailableException {
- String filename = super.getCacheValue(
- FILENAME_BY_ORGANISM_VERSION_PREFIX + organism.getResource() + "\n" + version);
- if (filename != null) {
- return filename;
- }
- FTPClient ftp = createFtpClient();
- try {
- ftp.connect(SERVER);
- // After connection attempt, you should check the reply code to verify
- // success.
- int reply = ftp.getReplyCode();
-
- if (!FTPReply.isPositiveCompletion(reply)) {
- throw new FileNotAvailableException(
- "Cannot find file with genome for: " + organism + "; " + version + ". FTP server refused connection.");
- } else {
- ftp.enterLocalPassiveMode();
- ftp.login("anonymous", "");
- ftp.setFileType(FTP.BINARY_FILE_TYPE);
-
- String remotePath = getGenomePath(organism, version);
- FTPFile[] files = ftp.listFiles(remotePath);
- for (FTPFile ftpFile : files) {
- logger.debug(ftpFile.getName());
- if (ftpFile.getName().endsWith(".2bit")) {
- if (filename != null) {
- logger.warn("More than one 2bit file found in a folder: " + remotePath + ". Using first: " + filename);
- } else {
- filename = ftpFile.getName();
- }
- }
- }
- ftp.logout();
- }
- } catch (IOException e) {
- throw new FileNotAvailableException(e);
- } finally {
- if (ftp.isConnected()) {
- try {
- ftp.disconnect();
- } catch (IOException ioe) {
- throw new FileNotAvailableException(
- "Cannot find file with genome for: " + organism + "; " + version + ". Problem with ftp connection.", ioe);
- }
- }
- }
- if (filename == null) {
- throw new FileNotAvailableException("Cannot find file with genome for: " + organism + "; " + version);
- }
- String result = "ftp://" + SERVER + getGenomePath(organism, version) + filename;
- super.setCacheValue(FILENAME_BY_ORGANISM_VERSION_PREFIX + organism.getResource() + "\n" + version, result);
- return result;
- }
-
- /**
- * Creates new instance of {@link FTPClient}.
- *
- * @return new instance of {@link FTPClient}
- */
- FTPClient createFtpClient() {
- FTPClient ftp = new FTPClient();
- return ftp;
- }
-
- /**
- * Extracts int from the version of the genome. The genome version look like
- * follow: xxxx011.
- *
- * @param s
- * genome version where suffix part is integer number that informs
- * about version
- * @return {@link Integer} representing version of the genome from string that
- * describes genome version (it contains also some letters characters}
- */
- int extractInt(String s) {
- int startIndex = 0;
- int endIndex = s.length() - 2;
- for (int i = 0; i < s.length(); i++) {
- startIndex = i;
- if (s.charAt(i) >= '0' && s.charAt(i) <= '9') {
- break;
- }
- }
- for (int i = startIndex; i < s.length(); i++) {
- if (s.charAt(i) < '0' || s.charAt(i) > '9') {
- break;
- }
- endIndex = i;
- }
- endIndex++;
- if (startIndex >= endIndex) {
- return 0;
- } else {
- return Integer.parseInt(s.substring(startIndex, endIndex));
- }
- }
-
- @Override
- protected WebPageDownloader getWebPageDownloader() {
- return super.getWebPageDownloader();
- }
-
- @Override
- protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
- super.setWebPageDownloader(webPageDownloader);
- }
-
-}
+package lcsb.mapviewer.annotation.services.genome;
+
+import java.io.IOException;
+import java.net.URISyntaxException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+import java.util.concurrent.Callable;
+import java.util.concurrent.Future;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.apache.commons.net.ftp.FTP;
+import org.apache.commons.net.ftp.FTPClient;
+import org.apache.commons.net.ftp.FTPFile;
+import org.apache.commons.net.ftp.FTPReply;
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.WebPageDownloader;
+import lcsb.mapviewer.annotation.services.TaxonomyBackend;
+import lcsb.mapviewer.annotation.services.TaxonomySearchException;
+import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.layout.ReferenceGenome;
+import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
+import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
+
+/**
+ * Implementeation of reference genome connector accessing
+ * {@link ReferenceGenomeType#UCSC} database.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class UcscReferenceGenomeConnector extends AbstractReferenceGenomeConnector implements ReferenceGenomeConnector {
+
+ /**
+ * Server domain name.
+ */
+ private static final String SERVER = "hgdownload.cse.ucsc.edu";
+
+ /**
+ * Prefix string used for marking queries in cache database that identifies list
+ * of reference genome versions by organism id.
+ */
+ static final String FILENAME_BY_ORGANISM_VERSION_PREFIX = "ORGANISM_VERSION_FILE:";
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(UcscReferenceGenomeConnector.class);
+
+ /**
+ * Regex pattern that helps to find out organism names in source file.
+ */
+ private Pattern organismNamePattern = Pattern.compile("<!--([A-Za-z\\-\\.\\ ]+)Downloads [=]*[\\ ]*-->");
+
+ /**
+ * Regex pattern that helps to find out reference genome versions.
+ */
+ private Pattern organismDataUrlPattern = Pattern.compile("\\/goldenPath\\/([A-Za-z0-9\\-\\.]+)\\/bigZips\\/");
+
+ /**
+ * Access point to taxonomy information.
+ */
+ @Autowired
+ private TaxonomyBackend taxonomyBackend;
+
+ /**
+ * Default constructor.
+ */
+ public UcscReferenceGenomeConnector() {
+ super(UcscReferenceGenomeConnector.class);
+ }
+
+ @Override
+ public List<String> getDownloadedGenomeVersions(MiriamData organism) {
+ List<String> results = new ArrayList<>();
+
+ List<ReferenceGenome> genomes = getReferenceGenomeDao().getByType(ReferenceGenomeType.UCSC);
+ for (ReferenceGenome referenceGenome : genomes) {
+ if (referenceGenome.getOrganism().equals(organism)) {
+ results.add(referenceGenome.getVersion());
+ }
+ }
+ return results;
+ }
+
+ @Override
+ public List<String> getAvailableGenomeVersion(MiriamData organism) throws ReferenceGenomeConnectorException {
+ Set<String> ids = new HashSet<>();
+ try {
+ String content = getWebPageContent("http://hgdownload.cse.ucsc.edu/downloads.html");
+ Integer start = null;
+ Integer end = content.length();
+ Matcher matcher = organismNamePattern.matcher(content);
+ while (matcher.find()) {
+ String name = matcher.group(1).trim();
+ if (start != null) {
+ end = matcher.start();
+ break;
+ }
+
+ if (name.equalsIgnoreCase("Shared Data")) {
+ continue;
+ }
+ if (name.equalsIgnoreCase("liftOver File")) {
+ continue;
+ }
+ MiriamData taxonomy = taxonomyBackend.getByName(name);
+ if (organism.equals(taxonomy)) {
+ start = matcher.end();
+ }
+ }
+ // we haven't found a start point for our organism (organism couldn't be
+ // found in the list of available organisms)
+ if (start != null) {
+ String organismContent = content.substring(start, end);
+
+ matcher = organismDataUrlPattern.matcher(organismContent);
+ while (matcher.find()) {
+ String name = matcher.group(1).trim();
+ ids.add(name);
+ }
+ }
+
+ } catch (IOException | TaxonomySearchException e) {
+ throw new ReferenceGenomeConnectorException("Problem with accessing UCSC database", e);
+ }
+ List<String> result = new ArrayList<>();
+ result.addAll(ids);
+ Collections.sort(result, new Comparator<String>() {
+ public int compare(String o1, String o2) {
+ return extractInt(o2) - extractInt(o1);
+ }
+
+ });
+ return result;
+ }
+
+ @Override
+ public List<MiriamData> getAvailableOrganisms() throws ReferenceGenomeConnectorException {
+ try {
+ List<MiriamData> result = new ArrayList<>();
+ String content = getWebPageContent("http://hgdownload.cse.ucsc.edu/downloads.html");
+
+ Matcher matcher = organismNamePattern.matcher(content);
+ while (matcher.find()) {
+ String name = matcher.group(1).trim();
+ if (name.equalsIgnoreCase("Shared Data")) {
+ continue;
+ }
+ if (name.equalsIgnoreCase("liftOver File")) {
+ continue;
+ }
+ MiriamData taxonomy = taxonomyBackend.getByName(name);
+ if (taxonomy != null) {
+ result.add(taxonomy);
+ }
+ }
+
+ return result;
+ } catch (IOException | TaxonomySearchException e) {
+ throw new ReferenceGenomeConnectorException("Problem with accessing UCSC database", e);
+ }
+ }
+
+ @Override
+ public void downloadGenomeVersion(MiriamData organism, String version, IProgressUpdater updater, boolean async)
+ throws FileNotAvailableException, IOException, ReferenceGenomeConnectorException {
+ try {
+ downloadGenomeVersion(organism, version, updater, async, getGenomeVersionFile(organism, version));
+ } catch (URISyntaxException e) {
+ throw new InvalidStateException(e);
+ }
+ }
+
+ @Override
+ public Object refreshCacheQuery(Object query) throws SourceNotAvailable {
+ String result = null;
+ try {
+ if (query instanceof String) {
+ String name = (String) query;
+ if (name.startsWith("http")) {
+ result = getWebPageContent(name);
+ } else if (name.startsWith(FILENAME_BY_ORGANISM_VERSION_PREFIX)) {
+ String[] tmp = name.substring(FILENAME_BY_ORGANISM_VERSION_PREFIX.length()).split("\n");
+ result = getGenomeVersionFile(new MiriamData(MiriamType.TAXONOMY, tmp[0]), tmp[1]);
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with string \"" + query + "\"");
+ }
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
+ }
+ } catch (FileNotAvailableException e) {
+ throw new SourceNotAvailable("Cannot find file for the query: " + query, e);
+ } catch (IOException e) {
+ throw new SourceNotAvailable(e);
+ }
+ return result;
+ }
+
+ @Override
+ public void removeGenomeVersion(MiriamData organism, String version) throws IOException {
+ List<ReferenceGenome> genomes = getReferenceGenomeDao().getByType(ReferenceGenomeType.UCSC);
+ for (ReferenceGenome referenceGenome : genomes) {
+ if (referenceGenome.getOrganism().equals(organism) && referenceGenome.getVersion().equals(version)) {
+ // removing file from big file cache might not be the best idea here
+ if (getBigFileCache().isCached(referenceGenome.getSourceUrl())) {
+ getBigFileCache().removeFile(referenceGenome.getSourceUrl());
+ }
+ for (ReferenceGenomeGeneMapping mapping : referenceGenome.getGeneMapping()) {
+ if (getBigFileCache().isCached(mapping.getSourceUrl())) {
+ getBigFileCache().removeFile(mapping.getSourceUrl());
+ }
+ }
+ getReferenceGenomeDao().delete(referenceGenome);
+ }
+ }
+ }
+
+ /**
+ * @return the taxonomyBackend
+ * @see #taxonomyBackend
+ */
+ public TaxonomyBackend getTaxonomyBackend() {
+ return taxonomyBackend;
+ }
+
+ /**
+ * @param taxonomyBackend
+ * the taxonomyBackend to set
+ * @see #taxonomyBackend
+ */
+ public void setTaxonomyBackend(TaxonomyBackend taxonomyBackend) {
+ this.taxonomyBackend = taxonomyBackend;
+ }
+
+ /**
+ * Task that will be able to fetch genome file from ftp server.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ private final class DownloadGenomeVersionTask implements Callable<Void> {
+
+ /**
+ * Url to the file that we want to download.
+ *
+ */
+ private String url;
+
+ /**
+ * Callback listener that will receive information about upload progress.
+ *
+ */
+ private IProgressUpdater updater;
+
+ /**
+ * Organism for which we want to fetch genome.
+ */
+ private MiriamData organism;
+
+ /**
+ * Version of the genome.
+ */
+ private String version;
+
+ /**
+ * Default constructor.
+ *
+ * @param url
+ * {@link #url}
+ * @param updater
+ * {@link #updater}
+ * @param organism
+ * {@link #organism}
+ * @param version
+ * {@link #version}
+ */
+ private DownloadGenomeVersionTask(MiriamData organism, String version, String url, IProgressUpdater updater) {
+ this.url = url;
+ this.organism = organism;
+ this.version = version;
+ if (updater != null) {
+ this.updater = updater;
+ } else {
+ this.updater = new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ };
+ }
+ }
+
+ @Override
+ public Void call() throws Exception {
+ getDbUtils().createSessionForCurrentThread();
+ try {
+ ReferenceGenome referenceGenome = new ReferenceGenome();
+ referenceGenome.setOrganism(organism);
+ referenceGenome.setType(ReferenceGenomeType.UCSC);
+ referenceGenome.setVersion(version);
+ referenceGenome.setSourceUrl(url);
+ getReferenceGenomeDao().add(referenceGenome);
+ getReferenceGenomeDao().flush();
+ getReferenceGenomeDao().commit();
+ getDbUtils().closeSessionForCurrentThread();
+
+ getBigFileCache().downloadFile(url, false, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ if (updater != null) {
+ updater.setProgress(progress);
+ }
+ // we have to get the object because it's in separate thred
+ ReferenceGenome temp = getReferenceGenomeDao().getById(referenceGenome.getId());
+ temp.setDownloadProgress(progress);
+ getReferenceGenomeDao().update(temp);
+ getReferenceGenomeDao().commit();
+ }
+ });
+ return null;
+ } finally {
+ getDbUtils().closeSessionForCurrentThread();
+ }
+ }
+
+ }
+
+ @Override
+ public void downloadGenomeVersion(MiriamData organism, String version, IProgressUpdater updater, boolean async,
+ String customUrl) throws IOException, URISyntaxException, ReferenceGenomeConnectorException {
+ Callable<Void> computations = new DownloadGenomeVersionTask(organism, version, customUrl, updater);
+ if (async) {
+ getAsyncExecutorService().submit(computations);
+ } else {
+ Future<Void> task = getSyncExecutorService().submit(computations);
+ executeTask(task);
+ }
+ }
+
+ /**
+ * Returns local path on ftp server to folder with data about given organism and
+ * version.
+ *
+ * @param organism
+ * organism of reference genome
+ * @param version
+ * of reference genome
+ * @return local path on ftp server to folder with data about reference genome
+ */
+ private String getGenomePath(MiriamData organism, String version) {
+ return "/goldenPath/" + version + "/bigZips/";
+ }
+
+ @Override
+ public String getGenomeVersionFile(MiriamData organism, String version) throws FileNotAvailableException {
+ String filename = super.getCacheValue(
+ FILENAME_BY_ORGANISM_VERSION_PREFIX + organism.getResource() + "\n" + version);
+ if (filename != null) {
+ return filename;
+ }
+ FTPClient ftp = createFtpClient();
+ try {
+ ftp.connect(SERVER);
+ // After connection attempt, you should check the reply code to verify
+ // success.
+ int reply = ftp.getReplyCode();
+
+ if (!FTPReply.isPositiveCompletion(reply)) {
+ throw new FileNotAvailableException(
+ "Cannot find file with genome for: " + organism + "; " + version + ". FTP server refused connection.");
+ } else {
+ ftp.enterLocalPassiveMode();
+ ftp.login("anonymous", "");
+ ftp.setFileType(FTP.BINARY_FILE_TYPE);
+
+ String remotePath = getGenomePath(organism, version);
+ FTPFile[] files = ftp.listFiles(remotePath);
+ for (FTPFile ftpFile : files) {
+ logger.debug(ftpFile.getName());
+ if (ftpFile.getName().endsWith(".2bit")) {
+ if (filename != null) {
+ logger.warn("More than one 2bit file found in a folder: " + remotePath + ". Using first: " + filename);
+ } else {
+ filename = ftpFile.getName();
+ }
+ }
+ }
+ ftp.logout();
+ }
+ } catch (IOException e) {
+ throw new FileNotAvailableException(e);
+ } finally {
+ if (ftp.isConnected()) {
+ try {
+ ftp.disconnect();
+ } catch (IOException ioe) {
+ throw new FileNotAvailableException(
+ "Cannot find file with genome for: " + organism + "; " + version + ". Problem with ftp connection.", ioe);
+ }
+ }
+ }
+ if (filename == null) {
+ throw new FileNotAvailableException("Cannot find file with genome for: " + organism + "; " + version);
+ }
+ String result = "ftp://" + SERVER + getGenomePath(organism, version) + filename;
+ super.setCacheValue(FILENAME_BY_ORGANISM_VERSION_PREFIX + organism.getResource() + "\n" + version, result);
+ return result;
+ }
+
+ /**
+ * Creates new instance of {@link FTPClient}.
+ *
+ * @return new instance of {@link FTPClient}
+ */
+ FTPClient createFtpClient() {
+ FTPClient ftp = new FTPClient();
+ return ftp;
+ }
+
+ /**
+ * Extracts int from the version of the genome. The genome version look like
+ * follow: xxxx011.
+ *
+ * @param s
+ * genome version where suffix part is integer number that informs
+ * about version
+ * @return {@link Integer} representing version of the genome from string that
+ * describes genome version (it contains also some letters characters}
+ */
+ int extractInt(String s) {
+ int startIndex = 0;
+ int endIndex = s.length() - 2;
+ for (int i = 0; i < s.length(); i++) {
+ startIndex = i;
+ if (s.charAt(i) >= '0' && s.charAt(i) <= '9') {
+ break;
+ }
+ }
+ for (int i = startIndex; i < s.length(); i++) {
+ if (s.charAt(i) < '0' || s.charAt(i) > '9') {
+ break;
+ }
+ endIndex = i;
+ }
+ endIndex++;
+ if (startIndex >= endIndex) {
+ return 0;
+ } else {
+ return Integer.parseInt(s.substring(startIndex, endIndex));
+ }
+ }
+
+ @Override
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
+ }
+
+ @Override
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/package-info.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/package-info.java
index e36710236f..8c342028a1 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/package-info.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/package-info.java
@@ -1,4 +1,4 @@
-/**
- * This package contains classes that access reference genome information.
- */
-package lcsb.mapviewer.annotation.services.genome;
+/**
+ * This package contains classes that access reference genome information.
+ */
+package lcsb.mapviewer.annotation.services.genome;
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/package-info.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/package-info.java
index 854d2bd5c2..4ada42b53e 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/package-info.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/package-info.java
@@ -1,6 +1,6 @@
-/**
- * This package contains classes that access different type of annotation data
- * from different type of resources.
- */
-package lcsb.mapviewer.annotation.services;
-
+/**
+ * This package contains classes that access different type of annotation data
+ * from different type of resources.
+ */
+package lcsb.mapviewer.annotation.services;
+
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/AllAnnotationTests.java b/annotation/src/test/java/lcsb/mapviewer/annotation/AllAnnotationTests.java
index f14e65dd4e..4a05c389f6 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/AllAnnotationTests.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/AllAnnotationTests.java
@@ -1,18 +1,18 @@
-package lcsb.mapviewer.annotation;
-
-import lcsb.mapviewer.annotation.cache.AllCacheTests;
-import lcsb.mapviewer.annotation.data.AllDataTests;
-import lcsb.mapviewer.annotation.services.AllServicesTests;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AllCacheTests.class, //
- AllDataTests.class, //
- AllServicesTests.class, //
-})
-
-public class AllAnnotationTests {
-}
+package lcsb.mapviewer.annotation;
+
+import lcsb.mapviewer.annotation.cache.AllCacheTests;
+import lcsb.mapviewer.annotation.data.AllDataTests;
+import lcsb.mapviewer.annotation.services.AllServicesTests;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AllCacheTests.class, //
+ AllDataTests.class, //
+ AllServicesTests.class, //
+})
+
+public class AllAnnotationTests {
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java b/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java
index d62046072c..689b3eba24 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/AnnotationTestFunctions.java
@@ -1,296 +1,296 @@
-package lcsb.mapviewer.annotation;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.Reader;
-import java.io.StringReader;
-import java.io.StringWriter;
-import java.io.UnsupportedEncodingException;
-import java.net.HttpURLConnection;
-import java.net.URL;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.transform.OutputKeys;
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerException;
-import javax.xml.transform.TransformerFactory;
-import javax.xml.transform.dom.DOMSource;
-import javax.xml.transform.stream.StreamResult;
-
-import org.apache.log4j.Logger;
-import org.apache.log4j.spi.LoggingEvent;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.runner.RunWith;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.test.annotation.Rollback;
-import org.springframework.test.context.ContextConfiguration;
-import org.springframework.test.context.junit4.AbstractTransactionalJUnit4SpringContextTests;
-import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
-import org.springframework.transaction.annotation.Transactional;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-import org.xml.sax.InputSource;
-import org.xml.sax.SAXException;
-
-import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
-import lcsb.mapviewer.common.EventStorageLoggerAppender;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.persist.DbUtils;
-import lcsb.mapviewer.persist.dao.cache.CacheTypeDao;
-
-@Transactional(value = "txManager")
-@Rollback(false)
-@ContextConfiguration(locations = { //
- "/applicationContext-annotation.xml", //
- "/applicationContext-persist.xml", //
- "/test-applicationContext.xml", //
- "/test-applicationContext.xml", //
- "/dataSource.xml", //
-})
-@RunWith(SpringJUnit4ClassRunner.class)
-public abstract class AnnotationTestFunctions extends AbstractTransactionalJUnit4SpringContextTests {
-
- @Autowired
- protected PermanentDatabaseLevelCacheInterface cache;
-
- @Autowired
- protected CacheTypeDao cacheTypeDao;
-
- @Autowired
- protected DbUtils dbUtils;
-
- private Logger logger = Logger.getLogger(AnnotationTestFunctions.class);
-
- private EventStorageLoggerAppender appender;
-
- @Before
- public final void _setUp() throws Exception {
- Logger.getRootLogger().removeAppender(appender);
- appender = new EventStorageLoggerAppender(false);
- Logger.getRootLogger().addAppender(appender);
- }
-
- @After
- public final void _tearDown() throws Exception {
- Logger.getRootLogger().removeAppender(appender);
- }
-
- protected List<LoggingEvent> getWarnings() {
- return appender.getWarnings();
- }
-
- protected List<LoggingEvent> getErrors() {
- return appender.getErrors();
- }
-
- protected List<LoggingEvent> getFatals() {
- return appender.getFatals();
- }
-
- protected String readFile(String file) throws IOException {
- StringBuilder stringBuilder = new StringBuilder();
- BufferedReader reader = new BufferedReader(new FileReader(file));
- try {
- String line = null;
- String ls = System.getProperty("line.separator");
-
- while ((line = reader.readLine()) != null) {
- stringBuilder.append(line);
- stringBuilder.append(ls);
- }
- } finally {
- reader.close();
- }
-
- return stringBuilder.toString();
- }
-
- protected Node getNodeFromXmlString(String text) throws InvalidXmlSchemaException, IOException {
- InputSource is = new InputSource();
- is.setCharacterStream(new StringReader(text));
- return getXmlDocumentFromInputSource(is).getChildNodes().item(0);
- }
-
- protected Document getXmlDocumentFromFile(String fileName) throws InvalidXmlSchemaException, IOException {
- File file = new File(fileName);
- InputStream inputStream = new FileInputStream(file);
- Reader reader = null;
- try {
- reader = new InputStreamReader(inputStream, "UTF-8");
- InputSource is = new InputSource(reader);
-
- Document result = getXmlDocumentFromInputSource(is);
- inputStream.close();
- return result;
- } catch (UnsupportedEncodingException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- return null;
- }
-
- protected Document getXmlDocumentFromInputSource(InputSource stream) throws InvalidXmlSchemaException, IOException {
- DocumentBuilder db;
- try {
- db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
- } catch (ParserConfigurationException e) {
- throw new InvalidXmlSchemaException("Problem with xml parser");
- }
- Document doc = null;
- try {
- doc = db.parse(stream);
- } catch (SAXException e) {
- throw new InvalidXmlSchemaException(e);
- }
- return doc;
- }
-
- private static Map<String, Model> models = new HashMap<String, Model>();
-
- protected Model getModelForFile(String fileName, boolean fromCache) throws Exception {
- if (!fromCache) {
- logger.debug("File without cache: " + fileName);
- return new CellDesignerXmlParser().createModel(new ConverterParams().filename(fileName));
- }
- Model result = AnnotationTestFunctions.models.get(fileName);
- if (result == null) {
- logger.debug("File to cache: " + fileName);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- result = parser.createModel(new ConverterParams().filename(fileName).sizeAutoAdjust(false));
- AnnotationTestFunctions.models.put(fileName, result);
- }
- return result;
- }
-
- protected String createTmpFileName() {
- try {
- File f = File.createTempFile("prefix", ".txt");
- String filename = f.getName();
- f.delete();
- return filename;
- } catch (IOException e) {
- e.printStackTrace();
- return null;
- }
- }
-
- protected String nodeToString(Node node) {
- return nodeToString(node, false);
- }
-
- protected String nodeToString(Node node, boolean includeHeadNode) {
- if (node == null)
- return null;
- StringWriter sw = new StringWriter();
- try {
- Transformer t = TransformerFactory.newInstance().newTransformer();
- t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
- t.setOutputProperty(OutputKeys.INDENT, "yes");
- t.setOutputProperty(OutputKeys.METHOD, "xml");
-
- NodeList list = node.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node element = list.item(i);
- t.transform(new DOMSource(element), new StreamResult(sw));
- }
- } catch (TransformerException te) {
- logger.debug("nodeToString Transformer Exception");
- }
- if (includeHeadNode) {
- return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
- }
- return sw.toString();
- }
-
- protected boolean equalFiles(String fileA, String fileB) throws IOException {
- int BLOCK_SIZE = 65536;
- FileInputStream inputStreamA = new FileInputStream(fileA);
- FileInputStream inputStreamB = new FileInputStream(fileB);
- // vary BLOCK_SIZE to suit yourself.
- // it should probably a factor or multiple of the size of a disk
- // sector/cluster.
- // Note that your max heap size may need to be adjused
- // if you have a very big block size or lots of these comparators.
-
- // assume inputStreamA and inputStreamB are streams from your two files.
- byte[] streamABlock = new byte[BLOCK_SIZE];
- byte[] streamBBlock = new byte[BLOCK_SIZE];
- boolean match = true;
- int bytesReadA = 0;
- int bytesReadB = 0;
- do {
- bytesReadA = inputStreamA.read(streamABlock);
- bytesReadB = inputStreamB.read(streamBBlock);
- match = ((bytesReadA == bytesReadB) && Arrays.equals(streamABlock, streamBBlock));
- } while (match && (bytesReadA > -1));
- inputStreamA.close();
- inputStreamB.close();
- return match;
- }
-
- public File createTempDirectory() throws IOException {
- final File temp;
-
- temp = File.createTempFile("temp", Long.toString(System.nanoTime()));
-
- if (!(temp.delete())) {
- throw new IOException("Could not delete temp file: " + temp.getAbsolutePath());
- }
-
- if (!(temp.mkdir())) {
- throw new IOException("Could not create temp directory: " + temp.getAbsolutePath());
- }
-
- return (temp);
- }
-
- protected String getWebpage(String accessUrl) throws IOException {
- String inputLine;
- IOException exception = null;
- for (int i = 0; i < 3; i++) {
- try {
- StringBuilder tmp = new StringBuilder();
- URL url = new URL(accessUrl);
- HttpURLConnection urlConn = (HttpURLConnection) url.openConnection();
- urlConn.setRequestMethod("GET");
- urlConn.connect();
- BufferedReader in = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));
-
- while ((inputLine = in.readLine()) != null) {
- tmp.append(inputLine);
- }
- in.close();
- return tmp.toString();
- } catch (IOException e) {
- exception = e;
- }
- }
- throw exception;
- }
-
- protected void waitForRefreshCacheQueueToEmpty() throws InterruptedException {
- while (cache.refreshIsBusy()) {
- logger.debug("Waiting for refresh queue to empty. " + cache.getRefreshPendingQueueSize() + " pending. "
- + cache.getRefreshExecutingTasksSize() + " tasks are executed.");
- Thread.sleep(300);
- }
- }
-
-}
+package lcsb.mapviewer.annotation;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.io.StringReader;
+import java.io.StringWriter;
+import java.io.UnsupportedEncodingException;
+import java.net.HttpURLConnection;
+import java.net.URL;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.OutputKeys;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerException;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.dom.DOMSource;
+import javax.xml.transform.stream.StreamResult;
+
+import org.apache.log4j.Logger;
+import org.apache.log4j.spi.LoggingEvent;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.runner.RunWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.annotation.Rollback;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.test.context.junit4.AbstractTransactionalJUnit4SpringContextTests;
+import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
+import org.springframework.transaction.annotation.Transactional;
+import org.w3c.dom.Document;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+
+import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
+import lcsb.mapviewer.common.EventStorageLoggerAppender;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.persist.DbUtils;
+import lcsb.mapviewer.persist.dao.cache.CacheTypeDao;
+
+@Transactional(value = "txManager")
+@Rollback(false)
+@ContextConfiguration(locations = { //
+ "/applicationContext-annotation.xml", //
+ "/applicationContext-persist.xml", //
+ "/test-applicationContext.xml", //
+ "/test-applicationContext.xml", //
+ "/dataSource.xml", //
+})
+@RunWith(SpringJUnit4ClassRunner.class)
+public abstract class AnnotationTestFunctions extends AbstractTransactionalJUnit4SpringContextTests {
+
+ @Autowired
+ protected PermanentDatabaseLevelCacheInterface cache;
+
+ @Autowired
+ protected CacheTypeDao cacheTypeDao;
+
+ @Autowired
+ protected DbUtils dbUtils;
+
+ private Logger logger = Logger.getLogger(AnnotationTestFunctions.class);
+
+ private EventStorageLoggerAppender appender;
+
+ @Before
+ public final void _setUp() throws Exception {
+ Logger.getRootLogger().removeAppender(appender);
+ appender = new EventStorageLoggerAppender(false);
+ Logger.getRootLogger().addAppender(appender);
+ }
+
+ @After
+ public final void _tearDown() throws Exception {
+ Logger.getRootLogger().removeAppender(appender);
+ }
+
+ protected List<LoggingEvent> getWarnings() {
+ return appender.getWarnings();
+ }
+
+ protected List<LoggingEvent> getErrors() {
+ return appender.getErrors();
+ }
+
+ protected List<LoggingEvent> getFatals() {
+ return appender.getFatals();
+ }
+
+ protected String readFile(String file) throws IOException {
+ StringBuilder stringBuilder = new StringBuilder();
+ BufferedReader reader = new BufferedReader(new FileReader(file));
+ try {
+ String line = null;
+ String ls = System.getProperty("line.separator");
+
+ while ((line = reader.readLine()) != null) {
+ stringBuilder.append(line);
+ stringBuilder.append(ls);
+ }
+ } finally {
+ reader.close();
+ }
+
+ return stringBuilder.toString();
+ }
+
+ protected Node getNodeFromXmlString(String text) throws InvalidXmlSchemaException, IOException {
+ InputSource is = new InputSource();
+ is.setCharacterStream(new StringReader(text));
+ return getXmlDocumentFromInputSource(is).getChildNodes().item(0);
+ }
+
+ protected Document getXmlDocumentFromFile(String fileName) throws InvalidXmlSchemaException, IOException {
+ File file = new File(fileName);
+ InputStream inputStream = new FileInputStream(file);
+ Reader reader = null;
+ try {
+ reader = new InputStreamReader(inputStream, "UTF-8");
+ InputSource is = new InputSource(reader);
+
+ Document result = getXmlDocumentFromInputSource(is);
+ inputStream.close();
+ return result;
+ } catch (UnsupportedEncodingException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ return null;
+ }
+
+ protected Document getXmlDocumentFromInputSource(InputSource stream) throws InvalidXmlSchemaException, IOException {
+ DocumentBuilder db;
+ try {
+ db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
+ } catch (ParserConfigurationException e) {
+ throw new InvalidXmlSchemaException("Problem with xml parser");
+ }
+ Document doc = null;
+ try {
+ doc = db.parse(stream);
+ } catch (SAXException e) {
+ throw new InvalidXmlSchemaException(e);
+ }
+ return doc;
+ }
+
+ private static Map<String, Model> models = new HashMap<String, Model>();
+
+ protected Model getModelForFile(String fileName, boolean fromCache) throws Exception {
+ if (!fromCache) {
+ logger.debug("File without cache: " + fileName);
+ return new CellDesignerXmlParser().createModel(new ConverterParams().filename(fileName));
+ }
+ Model result = AnnotationTestFunctions.models.get(fileName);
+ if (result == null) {
+ logger.debug("File to cache: " + fileName);
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ result = parser.createModel(new ConverterParams().filename(fileName).sizeAutoAdjust(false));
+ AnnotationTestFunctions.models.put(fileName, result);
+ }
+ return result;
+ }
+
+ protected String createTmpFileName() {
+ try {
+ File f = File.createTempFile("prefix", ".txt");
+ String filename = f.getName();
+ f.delete();
+ return filename;
+ } catch (IOException e) {
+ e.printStackTrace();
+ return null;
+ }
+ }
+
+ protected String nodeToString(Node node) {
+ return nodeToString(node, false);
+ }
+
+ protected String nodeToString(Node node, boolean includeHeadNode) {
+ if (node == null)
+ return null;
+ StringWriter sw = new StringWriter();
+ try {
+ Transformer t = TransformerFactory.newInstance().newTransformer();
+ t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
+ t.setOutputProperty(OutputKeys.INDENT, "yes");
+ t.setOutputProperty(OutputKeys.METHOD, "xml");
+
+ NodeList list = node.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node element = list.item(i);
+ t.transform(new DOMSource(element), new StreamResult(sw));
+ }
+ } catch (TransformerException te) {
+ logger.debug("nodeToString Transformer Exception");
+ }
+ if (includeHeadNode) {
+ return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
+ }
+ return sw.toString();
+ }
+
+ protected boolean equalFiles(String fileA, String fileB) throws IOException {
+ int BLOCK_SIZE = 65536;
+ FileInputStream inputStreamA = new FileInputStream(fileA);
+ FileInputStream inputStreamB = new FileInputStream(fileB);
+ // vary BLOCK_SIZE to suit yourself.
+ // it should probably a factor or multiple of the size of a disk
+ // sector/cluster.
+ // Note that your max heap size may need to be adjused
+ // if you have a very big block size or lots of these comparators.
+
+ // assume inputStreamA and inputStreamB are streams from your two files.
+ byte[] streamABlock = new byte[BLOCK_SIZE];
+ byte[] streamBBlock = new byte[BLOCK_SIZE];
+ boolean match = true;
+ int bytesReadA = 0;
+ int bytesReadB = 0;
+ do {
+ bytesReadA = inputStreamA.read(streamABlock);
+ bytesReadB = inputStreamB.read(streamBBlock);
+ match = ((bytesReadA == bytesReadB) && Arrays.equals(streamABlock, streamBBlock));
+ } while (match && (bytesReadA > -1));
+ inputStreamA.close();
+ inputStreamB.close();
+ return match;
+ }
+
+ public File createTempDirectory() throws IOException {
+ final File temp;
+
+ temp = File.createTempFile("temp", Long.toString(System.nanoTime()));
+
+ if (!(temp.delete())) {
+ throw new IOException("Could not delete temp file: " + temp.getAbsolutePath());
+ }
+
+ if (!(temp.mkdir())) {
+ throw new IOException("Could not create temp directory: " + temp.getAbsolutePath());
+ }
+
+ return (temp);
+ }
+
+ protected String getWebpage(String accessUrl) throws IOException {
+ String inputLine;
+ IOException exception = null;
+ for (int i = 0; i < 3; i++) {
+ try {
+ StringBuilder tmp = new StringBuilder();
+ URL url = new URL(accessUrl);
+ HttpURLConnection urlConn = (HttpURLConnection) url.openConnection();
+ urlConn.setRequestMethod("GET");
+ urlConn.connect();
+ BufferedReader in = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));
+
+ while ((inputLine = in.readLine()) != null) {
+ tmp.append(inputLine);
+ }
+ in.close();
+ return tmp.toString();
+ } catch (IOException e) {
+ exception = e;
+ }
+ }
+ throw exception;
+ }
+
+ protected void waitForRefreshCacheQueueToEmpty() throws InterruptedException {
+ while (cache.refreshIsBusy()) {
+ logger.debug("Waiting for refresh queue to empty. " + cache.getRefreshPendingQueueSize() + " pending. "
+ + cache.getRefreshExecutingTasksSize() + " tasks are executed.");
+ Thread.sleep(300);
+ }
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/AllCacheTests.java b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/AllCacheTests.java
index 85c9607662..6d7c27f99a 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/AllCacheTests.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/AllCacheTests.java
@@ -1,19 +1,19 @@
-package lcsb.mapviewer.annotation.cache;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ ApplicationLevelCacheTest.class, //
- BigFileCacheTest.class, //
- CachableInterfaceTest.class, //
- GeneralCacheTest.class, //
- GeneralCacheWithExclusionTest.class, //
- PermanentDatabaseLevelCacheTest.class, //
- SourceNotAvailableTest.class, //
- WebPageDownloaderTest.class, //
-})
-public class AllCacheTests {
-
-}
+package lcsb.mapviewer.annotation.cache;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ ApplicationLevelCacheTest.class, //
+ BigFileCacheTest.class, //
+ CachableInterfaceTest.class, //
+ GeneralCacheTest.class, //
+ GeneralCacheWithExclusionTest.class, //
+ PermanentDatabaseLevelCacheTest.class, //
+ SourceNotAvailableTest.class, //
+ WebPageDownloaderTest.class, //
+})
+public class AllCacheTests {
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/ApplicationLevelCacheTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/ApplicationLevelCacheTest.java
index 19ea32563b..2a41636316 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/ApplicationLevelCacheTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/ApplicationLevelCacheTest.java
@@ -1,121 +1,121 @@
-package lcsb.mapviewer.annotation.cache;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.w3c.dom.Node;
-
-import lcsb.mapviewer.annotation.AnnotationTestFunctions;
-import lcsb.mapviewer.annotation.services.PubmedParser;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.model.cache.CacheType;
-
-public class ApplicationLevelCacheTest extends AnnotationTestFunctions {
-
- Logger logger = Logger.getLogger(ApplicationLevelCacheTest.class);
-
- boolean status;
-
- @Before
- public void setUp() throws Exception {
- status = Configuration.isApplicationCacheOn();
- }
-
- @After
- public void tearDown() throws Exception {
- Configuration.setApplicationCacheOn(status);
- }
-
- @Test
- public void testApplicationCacheByQuery() {
- try {
- CacheType type = cacheTypeDao.getByClassName(PubmedParser.class.getCanonicalName());
- String xml = "<hello/>";
- String query = "blabla";
- Node sourceNode = getNodeFromXmlString(xml);
- ApplicationLevelCache cache = ApplicationLevelCache.getInstance();
- cache.clearCache();
-
- Node node = cache.getXmlNodeByQuery(query, type);
- assertNull(node);
-
- cache.setCachedQuery(query, type, sourceNode);
- node = cache.getXmlNodeByQuery(query, type);
- assertNotNull(node);
-
- cache.clearCache();
- node = cache.getXmlNodeByQuery(query, type);
- assertNull(node);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
- @Test
- public void testApplicationCacheOff() {
- boolean value = Configuration.isApplicationCacheOn();
-
- try {
- Configuration.setApplicationCacheOn(false);
- assertNull(ApplicationLevelCache.getInstance());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- Configuration.setApplicationCacheOn(value);
- }
- }
-
- @Test
- public void testSetInvalidValue() {
- try {
- ApplicationLevelCache cache = ApplicationLevelCache.getInstance();
- cache.setCachedQuery("bla", null, new Object());
- } catch (CacheException e) {
- assertTrue(e.getMessage().contains("Unknown object type"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testClearCacheWhenMemoryUsageIsHigh() throws Exception {
- Double oldVal = Configuration.getMemorySaturationRatioTriggerClean();
- try {
- CacheType type = new CacheType();
- type.setId(-13);
- ApplicationLevelCache cache = ApplicationLevelCache.getInstance();
- cache.setCachedQuery("bla", type, "test");
-
- assertNotNull(cache.getStringByQuery("bla", type));
- // fill cache with some dumb data
- for (int i = 0; i < ApplicationLevelCache.MIN_CACHED_VALUES_BEFORE_CLEAN; i++) {
- cache.setCachedQuery("bla" + i, type, "test");
- }
- assertNotNull(cache.getStringByQuery("bla", type));
-
- Configuration.setMemorySaturationRatioTriggerClean(0.0);
- cache.performMemoryBalance();
- assertNull(cache.getStringByQuery("bla", type));
-
- } catch (CacheException e) {
- assertTrue(e.getMessage().contains("Unknown object type"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- // restore old value
- Configuration.setMemorySaturationRatioTriggerClean(oldVal);
- }
- }
-
-}
+package lcsb.mapviewer.annotation.cache;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.w3c.dom.Node;
+
+import lcsb.mapviewer.annotation.AnnotationTestFunctions;
+import lcsb.mapviewer.annotation.services.PubmedParser;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.model.cache.CacheType;
+
+public class ApplicationLevelCacheTest extends AnnotationTestFunctions {
+
+ Logger logger = Logger.getLogger(ApplicationLevelCacheTest.class);
+
+ boolean status;
+
+ @Before
+ public void setUp() throws Exception {
+ status = Configuration.isApplicationCacheOn();
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ Configuration.setApplicationCacheOn(status);
+ }
+
+ @Test
+ public void testApplicationCacheByQuery() {
+ try {
+ CacheType type = cacheTypeDao.getByClassName(PubmedParser.class.getCanonicalName());
+ String xml = "<hello/>";
+ String query = "blabla";
+ Node sourceNode = getNodeFromXmlString(xml);
+ ApplicationLevelCache cache = ApplicationLevelCache.getInstance();
+ cache.clearCache();
+
+ Node node = cache.getXmlNodeByQuery(query, type);
+ assertNull(node);
+
+ cache.setCachedQuery(query, type, sourceNode);
+ node = cache.getXmlNodeByQuery(query, type);
+ assertNotNull(node);
+
+ cache.clearCache();
+ node = cache.getXmlNodeByQuery(query, type);
+ assertNull(node);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+ @Test
+ public void testApplicationCacheOff() {
+ boolean value = Configuration.isApplicationCacheOn();
+
+ try {
+ Configuration.setApplicationCacheOn(false);
+ assertNull(ApplicationLevelCache.getInstance());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ Configuration.setApplicationCacheOn(value);
+ }
+ }
+
+ @Test
+ public void testSetInvalidValue() {
+ try {
+ ApplicationLevelCache cache = ApplicationLevelCache.getInstance();
+ cache.setCachedQuery("bla", null, new Object());
+ } catch (CacheException e) {
+ assertTrue(e.getMessage().contains("Unknown object type"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testClearCacheWhenMemoryUsageIsHigh() throws Exception {
+ Double oldVal = Configuration.getMemorySaturationRatioTriggerClean();
+ try {
+ CacheType type = new CacheType();
+ type.setId(-13);
+ ApplicationLevelCache cache = ApplicationLevelCache.getInstance();
+ cache.setCachedQuery("bla", type, "test");
+
+ assertNotNull(cache.getStringByQuery("bla", type));
+ // fill cache with some dumb data
+ for (int i = 0; i < ApplicationLevelCache.MIN_CACHED_VALUES_BEFORE_CLEAN; i++) {
+ cache.setCachedQuery("bla" + i, type, "test");
+ }
+ assertNotNull(cache.getStringByQuery("bla", type));
+
+ Configuration.setMemorySaturationRatioTriggerClean(0.0);
+ cache.performMemoryBalance();
+ assertNull(cache.getStringByQuery("bla", type));
+
+ } catch (CacheException e) {
+ assertTrue(e.getMessage().contains("Unknown object type"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ // restore old value
+ Configuration.setMemorySaturationRatioTriggerClean(oldVal);
+ }
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/BigFileCacheTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/BigFileCacheTest.java
index 3f2e61fb1f..15b3310379 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/BigFileCacheTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/BigFileCacheTest.java
@@ -1,599 +1,599 @@
-package lcsb.mapviewer.annotation.cache;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-import static org.mockito.Matchers.any;
-import static org.mockito.Matchers.anyString;
-import static org.mockito.Mockito.when;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.net.URISyntaxException;
-import java.util.concurrent.Callable;
-import java.util.concurrent.Executors;
-import java.util.concurrent.Future;
-import java.util.concurrent.ThreadFactory;
-
-import org.apache.commons.net.ftp.FTPClient;
-import org.apache.commons.net.ftp.FTPFile;
-import org.apache.commons.net.ftp.FTPReply;
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-import org.mockito.invocation.InvocationOnMock;
-import org.mockito.stubbing.Answer;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.annotation.AnnotationTestFunctions;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.model.cache.BigFileEntry;
-import lcsb.mapviewer.persist.dao.ConfigurationDao;
-import lcsb.mapviewer.persist.dao.cache.BigFileEntryDao;
-
-public class BigFileCacheTest extends AnnotationTestFunctions {
-
- Logger logger = Logger.getLogger(BigFileCacheTest.class);
-
- String ftpUrl = "ftp://ftp.informatik.rwth-aachen.de/pub/Linux/debian-cd/current/i386/bt-cd/MD5SUMS";
-
- String httpUrl = "https://www.google.pl/humans.txt";
-
- @Autowired
- BigFileCache bigFileCache;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testDownloadFile() throws Exception {
- try {
- bigFileCache.downloadFile(ftpUrl, false, null);
- String localFile = bigFileCache.getAbsolutePathForFile(ftpUrl);
- assertTrue(bigFileCache.isCached(ftpUrl));
- assertTrue(bigFileCache.isLocalFileUpToDate(ftpUrl));
- File f = new File(localFile);
- assertTrue(f.exists());
- String content = super.readFile(localFile);
- assertTrue(content.contains("iso"));
-
- // when we try to download file that is already downloaded there should be
- // a warning
- bigFileCache.downloadFile(ftpUrl, false, null);
- assertEquals(1, getWarnings().size());
-
- // however when due to some reason the file will be removed from file
- // system
- f.delete();
- // the file should be downloaded again
- bigFileCache.downloadFile(ftpUrl, false, null);
- // additional warning about it
- assertEquals(2, getWarnings().size());
-
- localFile = bigFileCache.getAbsolutePathForFile(ftpUrl);
- f = new File(localFile);
- assertTrue(f.exists());
-
- // when we are trying to update file that is up to date then we will have
- // a warning about it (but file shouldn't be changed)
- bigFileCache.updateFile(ftpUrl, false);
- assertEquals(3, getWarnings().size());
-
- bigFileCache.removeFile(ftpUrl);
-
- assertNull(bigFileCache.getAbsolutePathForFile(ftpUrl));
-
- assertFalse(f.exists());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDownloadFileWithUnknownProtocol() throws Exception {
- try {
- bigFileCache.downloadFile("wtf://file.com", false, null);
-
- } catch (URISyntaxException e) {
- assertTrue(e.getMessage().contains("Unknown protocol for url"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDownloadAsyncFileFromHttp() throws Exception {
- try {
- bigFileCache.downloadFile(httpUrl, true, null);
- waitForDownload();
- String localFile = bigFileCache.getAbsolutePathForFile(httpUrl);
- assertTrue(bigFileCache.isLocalFileUpToDate(httpUrl));
- File f = new File(localFile);
- assertTrue(f.exists());
- String content = super.readFile(localFile);
- assertTrue(content.contains("Google"));
- bigFileCache.removeFile(httpUrl);
-
- assertNull(bigFileCache.getAbsolutePathForFile(httpUrl));
-
- assertFalse(f.exists());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSavingToInvalidDirectory() throws Exception {
- try {
- String url = httpUrl + "?invalid";
- Configuration.setWebAppDir("/");
- bigFileCache.downloadFile(url, false, null);
- fail("Exception expected");
- } catch (IOException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- Configuration.setWebAppDir("./");
- }
- }
-
- private void waitForDownload() throws InterruptedException {
- while (bigFileCache.getDownloadThreadCount() > 0) {
- logger.debug("Waiting for download to finish");
- Thread.sleep(100);
- }
- }
-
- @Test
- public void testIsLocalHttpFileUpToDateWhenMissing() throws Exception {
- try {
- bigFileCache.isLocalFileUpToDate(httpUrl + "?some_get_param");
- fail("Exception expected");
- } catch (FileNotFoundException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testIsLocalHttpFileUpToDateWhenFileRemovedManually() throws Exception {
- try {
- bigFileCache.downloadFile(httpUrl, false, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- });
- new File(bigFileCache.getAbsolutePathForFile(httpUrl)).delete();
- try {
- bigFileCache.isLocalFileUpToDate(httpUrl);
- fail("Exception expected");
- } catch (FileNotFoundException e) {
- }
- bigFileCache.removeFile(httpUrl);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testIsLocalFtpFileUpToDateWhenMissing() throws Exception {
- try {
- bigFileCache.isLocalFileUpToDate(ftpUrl);
- fail("Exception expected");
- } catch (FileNotFoundException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshCacheQueryWhenFtpConnectionFails() throws Exception {
-
- try {
- bigFileCache.downloadFile(ftpUrl, false, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- });
- assertTrue(bigFileCache.isLocalFileUpToDate(ftpUrl));
-
- FTPClient mockClient = Mockito.mock(FTPClient.class);
- Mockito.doAnswer(new Answer<Integer>() {
-
- @Override
- public Integer answer(InvocationOnMock invocation) throws Throwable {
- return FTPReply.REQUEST_DENIED;
- }
- }).when(mockClient).getReplyCode();
-
- FtpClientFactory factory = Mockito.mock(FtpClientFactory.class);
- when(factory.createFtpClient()).thenReturn(mockClient);
-
- bigFileCache.setFtpClientFactory(factory);
-
- bigFileCache.isLocalFileUpToDate(ftpUrl);
- fail("Exception expected");
- } catch (IOException e) {
- assertTrue(e.getMessage().contains("FTP server refused connection"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- bigFileCache.setFtpClientFactory(new FtpClientFactory());
- bigFileCache.removeFile(ftpUrl);
- }
- }
-
- @Test
- public void testDownloadWhenFtpConnectionFails() throws Exception {
- try {
- FTPClient mockClient = Mockito.mock(FTPClient.class);
- Mockito.doAnswer(new Answer<Integer>() {
- @Override
- public Integer answer(InvocationOnMock invocation) throws Throwable {
- return FTPReply.REQUEST_DENIED;
- }
- }).when(mockClient).getReplyCode();
-
- FtpClientFactory factory = Mockito.mock(FtpClientFactory.class);
- when(factory.createFtpClient()).thenReturn(mockClient);
-
- bigFileCache.setFtpClientFactory(factory);
- bigFileCache.downloadFile(ftpUrl, false, null);
-
- fail("Exception expected");
- } catch (IOException e) {
- assertTrue(e.getMessage().contains("FTP server refused connection"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- bigFileCache.setFtpClientFactory(new FtpClientFactory());
- bigFileCache.removeFile(ftpUrl);
- }
- }
-
- @Test
- public void testDownloadHttpWhenDownloadFails() throws Exception {
- ConfigurationDao configurationDao = bigFileCache.getConfigurationDao();
-
- try {
-
- ConfigurationDao mockDao = Mockito.mock(ConfigurationDao.class);
- when(mockDao.getValueByType(any())).thenThrow(new RuntimeException());
- bigFileCache.setConfigurationDao(mockDao);
- bigFileCache.downloadFile(httpUrl, false, null);
-
- fail("Exception expected");
- } catch (InvalidStateException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- bigFileCache.setConfigurationDao(configurationDao);
- }
- }
-
- @Test
- public void testDownloadedFileRemovedException() throws Exception {
- try {
- String url = ftpUrl;
- bigFileCache.downloadFile(url, false, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- });
- String localFile = bigFileCache.getAbsolutePathForFile(url);
- File f = new File(localFile);
- assertTrue(f.exists());
- f.delete();
-
- try {
- bigFileCache.getAbsolutePathForFile(url);
- fail("Exception expected");
- } catch (FileNotFoundException e) {
-
- }
- try {
- bigFileCache.isLocalFileUpToDate(url);
- fail("Exception expected");
- } catch (FileNotFoundException e) {
-
- }
-
- bigFileCache.removeFile(url);
-
- assertNull(bigFileCache.getAbsolutePathForFile(url));
-
- assertFalse(f.exists());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetPathForFileBeingDownloaded() throws Exception {
- try {
- String url = ftpUrl;
- BigFileCache bigFileCacheUnderTest = new BigFileCache();
- BigFileEntryDao mockDao = Mockito.mock(BigFileEntryDao.class);
- BigFileEntry entry = new BigFileEntry();
- when(mockDao.getByUrl(anyString())).thenReturn(entry);
-
- bigFileCacheUnderTest.setBigFileEntryDao(mockDao);
- try {
- bigFileCacheUnderTest.getAbsolutePathForFile(url);
- fail("Exception expected");
- } catch (FileNotFoundException e) {
- assertTrue(e.getMessage().contains("File is not complete"));
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdateFile() throws Exception {
- try {
- bigFileCache.downloadFile(ftpUrl, false, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- });
- String localFile = bigFileCache.getAbsolutePathForFile(ftpUrl);
- File f = new File(localFile);
- f.delete();
- PrintWriter out = new PrintWriter(localFile);
- out.println("tesxt");
- out.close();
-
- String content = super.readFile(localFile);
- assertFalse(content.contains("iso"));
-
- assertFalse(bigFileCache.isLocalFileUpToDate(ftpUrl));
- bigFileCache.updateFile(ftpUrl, false);
-
- localFile = bigFileCache.getAbsolutePathForFile(ftpUrl);
-
- content = super.readFile(localFile);
- assertTrue(content.contains("iso"));
-
- // now try update asynchronously
- f = new File(localFile);
- f.delete();
- out = new PrintWriter(localFile);
- out.println("tesxt");
- out.close();
-
- assertFalse(bigFileCache.isLocalFileUpToDate(ftpUrl));
- bigFileCache.updateFile(ftpUrl, true);
-
- waitForDownload();
-
- assertTrue(bigFileCache.isLocalFileUpToDate(ftpUrl));
-
- // check when connection fails
- f = new File(localFile);
- f.delete();
- out = new PrintWriter(localFile);
- out.println("tesxt");
- out.close();
-
- FTPClient mockClient = Mockito.mock(FTPClient.class);
- Mockito.doAnswer(new Answer<Integer>() {
-
- // first answer (for checking if the file should be updated)
- @Override
- public Integer answer(InvocationOnMock invocation) throws Throwable {
- return FTPReply.COMMAND_OK;
- }
- }).doAnswer(new Answer<Integer>() {
- // second answer (for downloading)
- @Override
- public Integer answer(InvocationOnMock invocation) throws Throwable {
- return FTPReply.REQUEST_DENIED;
- }
- }).when(mockClient).getReplyCode();
-
- Mockito.doAnswer(new Answer<FTPFile[]>() {
-
- @Override
- public FTPFile[] answer(InvocationOnMock invocation) throws Throwable {
- return new FTPFile[] {};
- }
- }).when(mockClient).listFiles(anyString());
-
- FtpClientFactory factory = Mockito.mock(FtpClientFactory.class);
- when(factory.createFtpClient()).thenReturn(mockClient);
-
- bigFileCache.setFtpClientFactory(factory);
- try {
- bigFileCache.updateFile(ftpUrl, false);
- fail("Exception expected");
- } catch (IOException e) {
- assertTrue(e.getMessage().contains("FTP server refused connection"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- bigFileCache.setFtpClientFactory(new FtpClientFactory());
- }
-
- bigFileCache.removeFile(ftpUrl);
-
- assertNull(bigFileCache.getAbsolutePathForFile(ftpUrl));
-
- assertFalse(f.exists());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetRemoteHttpFileSizeForInvalidUrl() throws Exception {
- try {
- bigFileCache.getRemoteHttpFileSize("invalidurl");
- fail("Exception expected");
- } catch (IOException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRemoveFileThatDoesntExist() throws Exception {
- try {
- bigFileCache.removeFile("unexisting file");
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testIsLocalFileUpToDateForInvalidURI() throws Exception {
- try {
- bigFileCache.isLocalFileUpToDate("unexistingFileProtocol://bla");
- fail("Exception expected");
- } catch (URISyntaxException e) {
- assertTrue(e.getMessage().contains("Unknown protocol"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetDomainName() throws Exception {
- try {
- String domain = bigFileCache.getDomainName("http://www.eskago.pl/radio/eska-rock");
- assertEquals("eskago.pl", domain);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testExecuteProblematicTask() throws Exception {
- try {
- Future<?> task = Executors.newScheduledThreadPool(10, new ThreadFactory() {
- @Override
- public Thread newThread(Runnable r) {
- Thread t = new Thread(r);
- t.setDaemon(true);
- return t;
- }
- }).submit(new Callable<Void>() {
- @Override
- public Void call() throws Exception {
- throw new Exception();
- }
- });
- bigFileCache.executeTask(task);
- fail("Exception expected");
- } catch (InvalidStateException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testExecuteProblematicTask2() throws Exception {
- try {
- Future<?> task = Executors.newScheduledThreadPool(10, new ThreadFactory() {
- @Override
- public Thread newThread(Runnable r) {
- Thread t = new Thread(r);
- t.setDaemon(true);
- return t;
- }
- }).submit(new Callable<Void>() {
- @Override
- public Void call() throws Exception {
- throw new URISyntaxException("", "");
- }
- });
- bigFileCache.executeTask(task);
- fail("Exception expected");
- } catch (URISyntaxException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testExecuteInterruptedTask() throws Exception {
- try {
- Future<?> task = Executors.newScheduledThreadPool(10, new ThreadFactory() {
- @Override
- public Thread newThread(Runnable r) {
- Thread t = new Thread(r);
- t.setDaemon(true);
- return t;
- }
- }).submit(new Callable<Void>() {
- @Override
- public Void call() throws Exception {
- Thread.sleep(100);
- return null;
- }
- });
- Thread t = new Thread(new Runnable() {
- @Override
- public void run() {
- try {
- bigFileCache.executeTask(task);
- } catch (Exception e) {
- logger.fatal(e, e);
- }
- }
- });
-
- t.start();
- // interrupt thread
- t.interrupt();
- t.join();
-
- assertEquals(1, getErrors().size());
- assertEquals(0, getFatals().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.annotation.cache;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import static org.mockito.Matchers.any;
+import static org.mockito.Matchers.anyString;
+import static org.mockito.Mockito.when;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.net.URISyntaxException;
+import java.util.concurrent.Callable;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
+import java.util.concurrent.ThreadFactory;
+
+import org.apache.commons.net.ftp.FTPClient;
+import org.apache.commons.net.ftp.FTPFile;
+import org.apache.commons.net.ftp.FTPReply;
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+import org.mockito.invocation.InvocationOnMock;
+import org.mockito.stubbing.Answer;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.AnnotationTestFunctions;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.model.cache.BigFileEntry;
+import lcsb.mapviewer.persist.dao.ConfigurationDao;
+import lcsb.mapviewer.persist.dao.cache.BigFileEntryDao;
+
+public class BigFileCacheTest extends AnnotationTestFunctions {
+
+ Logger logger = Logger.getLogger(BigFileCacheTest.class);
+
+ String ftpUrl = "ftp://ftp.informatik.rwth-aachen.de/pub/Linux/debian-cd/current/i386/bt-cd/MD5SUMS";
+
+ String httpUrl = "https://www.google.pl/humans.txt";
+
+ @Autowired
+ BigFileCache bigFileCache;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testDownloadFile() throws Exception {
+ try {
+ bigFileCache.downloadFile(ftpUrl, false, null);
+ String localFile = bigFileCache.getAbsolutePathForFile(ftpUrl);
+ assertTrue(bigFileCache.isCached(ftpUrl));
+ assertTrue(bigFileCache.isLocalFileUpToDate(ftpUrl));
+ File f = new File(localFile);
+ assertTrue(f.exists());
+ String content = super.readFile(localFile);
+ assertTrue(content.contains("iso"));
+
+ // when we try to download file that is already downloaded there should be
+ // a warning
+ bigFileCache.downloadFile(ftpUrl, false, null);
+ assertEquals(1, getWarnings().size());
+
+ // however when due to some reason the file will be removed from file
+ // system
+ f.delete();
+ // the file should be downloaded again
+ bigFileCache.downloadFile(ftpUrl, false, null);
+ // additional warning about it
+ assertEquals(2, getWarnings().size());
+
+ localFile = bigFileCache.getAbsolutePathForFile(ftpUrl);
+ f = new File(localFile);
+ assertTrue(f.exists());
+
+ // when we are trying to update file that is up to date then we will have
+ // a warning about it (but file shouldn't be changed)
+ bigFileCache.updateFile(ftpUrl, false);
+ assertEquals(3, getWarnings().size());
+
+ bigFileCache.removeFile(ftpUrl);
+
+ assertNull(bigFileCache.getAbsolutePathForFile(ftpUrl));
+
+ assertFalse(f.exists());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDownloadFileWithUnknownProtocol() throws Exception {
+ try {
+ bigFileCache.downloadFile("wtf://file.com", false, null);
+
+ } catch (URISyntaxException e) {
+ assertTrue(e.getMessage().contains("Unknown protocol for url"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDownloadAsyncFileFromHttp() throws Exception {
+ try {
+ bigFileCache.downloadFile(httpUrl, true, null);
+ waitForDownload();
+ String localFile = bigFileCache.getAbsolutePathForFile(httpUrl);
+ assertTrue(bigFileCache.isLocalFileUpToDate(httpUrl));
+ File f = new File(localFile);
+ assertTrue(f.exists());
+ String content = super.readFile(localFile);
+ assertTrue(content.contains("Google"));
+ bigFileCache.removeFile(httpUrl);
+
+ assertNull(bigFileCache.getAbsolutePathForFile(httpUrl));
+
+ assertFalse(f.exists());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSavingToInvalidDirectory() throws Exception {
+ try {
+ String url = httpUrl + "?invalid";
+ Configuration.setWebAppDir("/");
+ bigFileCache.downloadFile(url, false, null);
+ fail("Exception expected");
+ } catch (IOException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ Configuration.setWebAppDir("./");
+ }
+ }
+
+ private void waitForDownload() throws InterruptedException {
+ while (bigFileCache.getDownloadThreadCount() > 0) {
+ logger.debug("Waiting for download to finish");
+ Thread.sleep(100);
+ }
+ }
+
+ @Test
+ public void testIsLocalHttpFileUpToDateWhenMissing() throws Exception {
+ try {
+ bigFileCache.isLocalFileUpToDate(httpUrl + "?some_get_param");
+ fail("Exception expected");
+ } catch (FileNotFoundException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testIsLocalHttpFileUpToDateWhenFileRemovedManually() throws Exception {
+ try {
+ bigFileCache.downloadFile(httpUrl, false, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ });
+ new File(bigFileCache.getAbsolutePathForFile(httpUrl)).delete();
+ try {
+ bigFileCache.isLocalFileUpToDate(httpUrl);
+ fail("Exception expected");
+ } catch (FileNotFoundException e) {
+ }
+ bigFileCache.removeFile(httpUrl);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testIsLocalFtpFileUpToDateWhenMissing() throws Exception {
+ try {
+ bigFileCache.isLocalFileUpToDate(ftpUrl);
+ fail("Exception expected");
+ } catch (FileNotFoundException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQueryWhenFtpConnectionFails() throws Exception {
+
+ try {
+ bigFileCache.downloadFile(ftpUrl, false, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ });
+ assertTrue(bigFileCache.isLocalFileUpToDate(ftpUrl));
+
+ FTPClient mockClient = Mockito.mock(FTPClient.class);
+ Mockito.doAnswer(new Answer<Integer>() {
+
+ @Override
+ public Integer answer(InvocationOnMock invocation) throws Throwable {
+ return FTPReply.REQUEST_DENIED;
+ }
+ }).when(mockClient).getReplyCode();
+
+ FtpClientFactory factory = Mockito.mock(FtpClientFactory.class);
+ when(factory.createFtpClient()).thenReturn(mockClient);
+
+ bigFileCache.setFtpClientFactory(factory);
+
+ bigFileCache.isLocalFileUpToDate(ftpUrl);
+ fail("Exception expected");
+ } catch (IOException e) {
+ assertTrue(e.getMessage().contains("FTP server refused connection"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ bigFileCache.setFtpClientFactory(new FtpClientFactory());
+ bigFileCache.removeFile(ftpUrl);
+ }
+ }
+
+ @Test
+ public void testDownloadWhenFtpConnectionFails() throws Exception {
+ try {
+ FTPClient mockClient = Mockito.mock(FTPClient.class);
+ Mockito.doAnswer(new Answer<Integer>() {
+ @Override
+ public Integer answer(InvocationOnMock invocation) throws Throwable {
+ return FTPReply.REQUEST_DENIED;
+ }
+ }).when(mockClient).getReplyCode();
+
+ FtpClientFactory factory = Mockito.mock(FtpClientFactory.class);
+ when(factory.createFtpClient()).thenReturn(mockClient);
+
+ bigFileCache.setFtpClientFactory(factory);
+ bigFileCache.downloadFile(ftpUrl, false, null);
+
+ fail("Exception expected");
+ } catch (IOException e) {
+ assertTrue(e.getMessage().contains("FTP server refused connection"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ bigFileCache.setFtpClientFactory(new FtpClientFactory());
+ bigFileCache.removeFile(ftpUrl);
+ }
+ }
+
+ @Test
+ public void testDownloadHttpWhenDownloadFails() throws Exception {
+ ConfigurationDao configurationDao = bigFileCache.getConfigurationDao();
+
+ try {
+
+ ConfigurationDao mockDao = Mockito.mock(ConfigurationDao.class);
+ when(mockDao.getValueByType(any())).thenThrow(new RuntimeException());
+ bigFileCache.setConfigurationDao(mockDao);
+ bigFileCache.downloadFile(httpUrl, false, null);
+
+ fail("Exception expected");
+ } catch (InvalidStateException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ bigFileCache.setConfigurationDao(configurationDao);
+ }
+ }
+
+ @Test
+ public void testDownloadedFileRemovedException() throws Exception {
+ try {
+ String url = ftpUrl;
+ bigFileCache.downloadFile(url, false, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ });
+ String localFile = bigFileCache.getAbsolutePathForFile(url);
+ File f = new File(localFile);
+ assertTrue(f.exists());
+ f.delete();
+
+ try {
+ bigFileCache.getAbsolutePathForFile(url);
+ fail("Exception expected");
+ } catch (FileNotFoundException e) {
+
+ }
+ try {
+ bigFileCache.isLocalFileUpToDate(url);
+ fail("Exception expected");
+ } catch (FileNotFoundException e) {
+
+ }
+
+ bigFileCache.removeFile(url);
+
+ assertNull(bigFileCache.getAbsolutePathForFile(url));
+
+ assertFalse(f.exists());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetPathForFileBeingDownloaded() throws Exception {
+ try {
+ String url = ftpUrl;
+ BigFileCache bigFileCacheUnderTest = new BigFileCache();
+ BigFileEntryDao mockDao = Mockito.mock(BigFileEntryDao.class);
+ BigFileEntry entry = new BigFileEntry();
+ when(mockDao.getByUrl(anyString())).thenReturn(entry);
+
+ bigFileCacheUnderTest.setBigFileEntryDao(mockDao);
+ try {
+ bigFileCacheUnderTest.getAbsolutePathForFile(url);
+ fail("Exception expected");
+ } catch (FileNotFoundException e) {
+ assertTrue(e.getMessage().contains("File is not complete"));
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdateFile() throws Exception {
+ try {
+ bigFileCache.downloadFile(ftpUrl, false, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ });
+ String localFile = bigFileCache.getAbsolutePathForFile(ftpUrl);
+ File f = new File(localFile);
+ f.delete();
+ PrintWriter out = new PrintWriter(localFile);
+ out.println("tesxt");
+ out.close();
+
+ String content = super.readFile(localFile);
+ assertFalse(content.contains("iso"));
+
+ assertFalse(bigFileCache.isLocalFileUpToDate(ftpUrl));
+ bigFileCache.updateFile(ftpUrl, false);
+
+ localFile = bigFileCache.getAbsolutePathForFile(ftpUrl);
+
+ content = super.readFile(localFile);
+ assertTrue(content.contains("iso"));
+
+ // now try update asynchronously
+ f = new File(localFile);
+ f.delete();
+ out = new PrintWriter(localFile);
+ out.println("tesxt");
+ out.close();
+
+ assertFalse(bigFileCache.isLocalFileUpToDate(ftpUrl));
+ bigFileCache.updateFile(ftpUrl, true);
+
+ waitForDownload();
+
+ assertTrue(bigFileCache.isLocalFileUpToDate(ftpUrl));
+
+ // check when connection fails
+ f = new File(localFile);
+ f.delete();
+ out = new PrintWriter(localFile);
+ out.println("tesxt");
+ out.close();
+
+ FTPClient mockClient = Mockito.mock(FTPClient.class);
+ Mockito.doAnswer(new Answer<Integer>() {
+
+ // first answer (for checking if the file should be updated)
+ @Override
+ public Integer answer(InvocationOnMock invocation) throws Throwable {
+ return FTPReply.COMMAND_OK;
+ }
+ }).doAnswer(new Answer<Integer>() {
+ // second answer (for downloading)
+ @Override
+ public Integer answer(InvocationOnMock invocation) throws Throwable {
+ return FTPReply.REQUEST_DENIED;
+ }
+ }).when(mockClient).getReplyCode();
+
+ Mockito.doAnswer(new Answer<FTPFile[]>() {
+
+ @Override
+ public FTPFile[] answer(InvocationOnMock invocation) throws Throwable {
+ return new FTPFile[] {};
+ }
+ }).when(mockClient).listFiles(anyString());
+
+ FtpClientFactory factory = Mockito.mock(FtpClientFactory.class);
+ when(factory.createFtpClient()).thenReturn(mockClient);
+
+ bigFileCache.setFtpClientFactory(factory);
+ try {
+ bigFileCache.updateFile(ftpUrl, false);
+ fail("Exception expected");
+ } catch (IOException e) {
+ assertTrue(e.getMessage().contains("FTP server refused connection"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ bigFileCache.setFtpClientFactory(new FtpClientFactory());
+ }
+
+ bigFileCache.removeFile(ftpUrl);
+
+ assertNull(bigFileCache.getAbsolutePathForFile(ftpUrl));
+
+ assertFalse(f.exists());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetRemoteHttpFileSizeForInvalidUrl() throws Exception {
+ try {
+ bigFileCache.getRemoteHttpFileSize("invalidurl");
+ fail("Exception expected");
+ } catch (IOException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRemoveFileThatDoesntExist() throws Exception {
+ try {
+ bigFileCache.removeFile("unexisting file");
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testIsLocalFileUpToDateForInvalidURI() throws Exception {
+ try {
+ bigFileCache.isLocalFileUpToDate("unexistingFileProtocol://bla");
+ fail("Exception expected");
+ } catch (URISyntaxException e) {
+ assertTrue(e.getMessage().contains("Unknown protocol"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetDomainName() throws Exception {
+ try {
+ String domain = bigFileCache.getDomainName("http://www.eskago.pl/radio/eska-rock");
+ assertEquals("eskago.pl", domain);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testExecuteProblematicTask() throws Exception {
+ try {
+ Future<?> task = Executors.newScheduledThreadPool(10, new ThreadFactory() {
+ @Override
+ public Thread newThread(Runnable r) {
+ Thread t = new Thread(r);
+ t.setDaemon(true);
+ return t;
+ }
+ }).submit(new Callable<Void>() {
+ @Override
+ public Void call() throws Exception {
+ throw new Exception();
+ }
+ });
+ bigFileCache.executeTask(task);
+ fail("Exception expected");
+ } catch (InvalidStateException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testExecuteProblematicTask2() throws Exception {
+ try {
+ Future<?> task = Executors.newScheduledThreadPool(10, new ThreadFactory() {
+ @Override
+ public Thread newThread(Runnable r) {
+ Thread t = new Thread(r);
+ t.setDaemon(true);
+ return t;
+ }
+ }).submit(new Callable<Void>() {
+ @Override
+ public Void call() throws Exception {
+ throw new URISyntaxException("", "");
+ }
+ });
+ bigFileCache.executeTask(task);
+ fail("Exception expected");
+ } catch (URISyntaxException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testExecuteInterruptedTask() throws Exception {
+ try {
+ Future<?> task = Executors.newScheduledThreadPool(10, new ThreadFactory() {
+ @Override
+ public Thread newThread(Runnable r) {
+ Thread t = new Thread(r);
+ t.setDaemon(true);
+ return t;
+ }
+ }).submit(new Callable<Void>() {
+ @Override
+ public Void call() throws Exception {
+ Thread.sleep(100);
+ return null;
+ }
+ });
+ Thread t = new Thread(new Runnable() {
+ @Override
+ public void run() {
+ try {
+ bigFileCache.executeTask(task);
+ } catch (Exception e) {
+ logger.fatal(e, e);
+ }
+ }
+ });
+
+ t.start();
+ // interrupt thread
+ t.interrupt();
+ t.join();
+
+ assertEquals(1, getErrors().size());
+ assertEquals(0, getFatals().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/CachableInterfaceMock.java b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/CachableInterfaceMock.java
index 4e6fa37bcf..f58f0a89cc 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/CachableInterfaceMock.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/CachableInterfaceMock.java
@@ -1,14 +1,14 @@
-package lcsb.mapviewer.annotation.cache;
-
-public class CachableInterfaceMock extends CachableInterface {
-
- public CachableInterfaceMock(Class<? extends CachableInterface> clazz) {
- super(clazz);
- }
-
- @Override
- public Object refreshCacheQuery(Object query) throws SourceNotAvailable {
- return null;
- }
-
-}
+package lcsb.mapviewer.annotation.cache;
+
+public class CachableInterfaceMock extends CachableInterface {
+
+ public CachableInterfaceMock(Class<? extends CachableInterface> clazz) {
+ super(clazz);
+ }
+
+ @Override
+ public Object refreshCacheQuery(Object query) throws SourceNotAvailable {
+ return null;
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/CachableInterfaceTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/CachableInterfaceTest.java
index d7f21ed334..d06de3ee08 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/CachableInterfaceTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/CachableInterfaceTest.java
@@ -1,135 +1,135 @@
-package lcsb.mapviewer.annotation.cache;
-
-import static org.junit.Assert.*;
-import static org.mockito.Matchers.anyString;
-import static org.mockito.Mockito.when;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-import org.w3c.dom.Node;
-
-import lcsb.mapviewer.annotation.AnnotationTestFunctions;
-import lcsb.mapviewer.model.cache.CacheType;
-import lcsb.mapviewer.persist.dao.cache.CacheTypeDao;
-
-
-public class CachableInterfaceTest extends AnnotationTestFunctions {
- Logger logger = Logger.getLogger(CachableInterfaceTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetWebPage() throws Exception {
- try {
- CachableInterfaceMock ci = new CachableInterfaceMock(CachableInterface.class);
- String result = ci.getWebPageContent("http://www.drugbank.ca/biodb/polypeptides/P21728");
- assertNotNull(result);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetWebPage2() throws Exception {
- try {
- CachableInterfaceMock ci = new CachableInterfaceMock(CachableInterface.class);
- String result = ci.getWebPageContent("http://www.drugbank.ca/drugs/DB00091");
- assertNotNull(result);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetWebPageGetCache() throws Exception {
- try {
- CachableInterfaceMock ci = new CachableInterfaceMock(CachableInterface.class);
-
- CacheTypeDao mock = Mockito.mock(CacheTypeDao.class);
- when(mock.getByClassName(anyString())).thenReturn(new CacheType());
- ci.setCacheTypeDao(mock);
- ci.setCache(new GeneralCache());
-
- String cacheKey = "https://www.google.com/";
- String result = ci.getWebPageContent(cacheKey);
- assertNotNull(result);
- String cacheValue = ci.getCacheValue(cacheKey);
- assertTrue(result.equals(cacheValue));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetNode() throws Exception {
- try {
- CachableInterfaceMock ci = new CachableInterfaceMock(CachableInterface.class);
-
- CacheTypeDao mock = Mockito.mock(CacheTypeDao.class);
- when(mock.getByClassName(anyString())).thenReturn(new CacheType());
- ci.setCacheTypeDao(mock);
-
- String xml = "<xml><child/></xml>";
- ci.setCache(new GeneralCache());
- ci.setCacheNode("id", super.getNodeFromXmlString(xml));
-
- Node node = ci.getCacheNode("id");
- assertNotNull(node);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testNewLinesGetWebPage() throws Exception {
- try {
- CachableInterfaceMock ci = new CachableInterfaceMock(CachableInterface.class);
- ci.setCache(null);
- String result = ci.getWebPageContent("http://google.com/");
- assertNotNull(result);
- assertTrue(result.contains("\n"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCleanHtml() throws Exception {
- try {
- CachableInterfaceMock ci = new CachableInterfaceMock(CachableInterface.class);
- String res = ci.cleanHtml("blabla <invalid_tag");
- assertEquals("blabla ",res);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCleanHtml2() throws Exception {
- try {
- CachableInterfaceMock ci = new CachableInterfaceMock(CachableInterface.class);
- String res = ci.cleanHtml("blabla <valid_tag> etc");
- assertEquals("blabla etc",res);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
-}
+package lcsb.mapviewer.annotation.cache;
+
+import static org.junit.Assert.*;
+import static org.mockito.Matchers.anyString;
+import static org.mockito.Mockito.when;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+import org.w3c.dom.Node;
+
+import lcsb.mapviewer.annotation.AnnotationTestFunctions;
+import lcsb.mapviewer.model.cache.CacheType;
+import lcsb.mapviewer.persist.dao.cache.CacheTypeDao;
+
+
+public class CachableInterfaceTest extends AnnotationTestFunctions {
+ Logger logger = Logger.getLogger(CachableInterfaceTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetWebPage() throws Exception {
+ try {
+ CachableInterfaceMock ci = new CachableInterfaceMock(CachableInterface.class);
+ String result = ci.getWebPageContent("http://www.drugbank.ca/biodb/polypeptides/P21728");
+ assertNotNull(result);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetWebPage2() throws Exception {
+ try {
+ CachableInterfaceMock ci = new CachableInterfaceMock(CachableInterface.class);
+ String result = ci.getWebPageContent("http://www.drugbank.ca/drugs/DB00091");
+ assertNotNull(result);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetWebPageGetCache() throws Exception {
+ try {
+ CachableInterfaceMock ci = new CachableInterfaceMock(CachableInterface.class);
+
+ CacheTypeDao mock = Mockito.mock(CacheTypeDao.class);
+ when(mock.getByClassName(anyString())).thenReturn(new CacheType());
+ ci.setCacheTypeDao(mock);
+ ci.setCache(new GeneralCache());
+
+ String cacheKey = "https://www.google.com/";
+ String result = ci.getWebPageContent(cacheKey);
+ assertNotNull(result);
+ String cacheValue = ci.getCacheValue(cacheKey);
+ assertTrue(result.equals(cacheValue));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetNode() throws Exception {
+ try {
+ CachableInterfaceMock ci = new CachableInterfaceMock(CachableInterface.class);
+
+ CacheTypeDao mock = Mockito.mock(CacheTypeDao.class);
+ when(mock.getByClassName(anyString())).thenReturn(new CacheType());
+ ci.setCacheTypeDao(mock);
+
+ String xml = "<xml><child/></xml>";
+ ci.setCache(new GeneralCache());
+ ci.setCacheNode("id", super.getNodeFromXmlString(xml));
+
+ Node node = ci.getCacheNode("id");
+ assertNotNull(node);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testNewLinesGetWebPage() throws Exception {
+ try {
+ CachableInterfaceMock ci = new CachableInterfaceMock(CachableInterface.class);
+ ci.setCache(null);
+ String result = ci.getWebPageContent("http://google.com/");
+ assertNotNull(result);
+ assertTrue(result.contains("\n"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCleanHtml() throws Exception {
+ try {
+ CachableInterfaceMock ci = new CachableInterfaceMock(CachableInterface.class);
+ String res = ci.cleanHtml("blabla <invalid_tag");
+ assertEquals("blabla ",res);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCleanHtml2() throws Exception {
+ try {
+ CachableInterfaceMock ci = new CachableInterfaceMock(CachableInterface.class);
+ String res = ci.cleanHtml("blabla <valid_tag> etc");
+ assertEquals("blabla etc",res);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/GeneralCacheTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/GeneralCacheTest.java
index 1ce7927eaa..8f2a7fe427 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/GeneralCacheTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/GeneralCacheTest.java
@@ -1,137 +1,137 @@
-package lcsb.mapviewer.annotation.cache;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.annotation.AnnotationTestFunctions;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.cache.CacheType;
-
-public class GeneralCacheTest extends AnnotationTestFunctions {
- Logger logger = Logger.getLogger(GeneralCacheTest.class);
-
- GeneralCache cache = new GeneralCache();
-
- @Autowired
- PermanentDatabaseLevelCacheInterface databaseLevelCache;
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- cache.setCache2(databaseLevelCache);
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testClear() {
- QueryCacheInterface origianlCache = cache.getCache2();
- try {
- CacheType type = new CacheType();
- type.setId(-1);
- cache.setCache2(ApplicationLevelCache.getInstance());
- ApplicationLevelCache.getInstance().setCachedQuery("str", type, "val");
- assertNotNull(cache.getStringByQuery("str", type));
- cache.clearCache();
- assertNull(cache.getStringByQuery("str", type));
- } finally {
- cache.setCache2(origianlCache);
- }
- }
-
- @Test
- public void testGetXmlNodeByQueryForInvalidType() {
- try {
- cache.getXmlNodeByQuery("str", null);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Cache type cannot be null"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetCachedQueryForInvalidType() {
- try {
- cache.setCachedQuery("str", null, null);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Cache type cannot be null"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRemoveByQueryForInvalidType() {
- try {
- cache.removeByQuery("str", null);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Cache type cannot be null"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidateByQueryForInvalidType() {
- try {
- cache.invalidateByQuery("str", null);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Cache type cannot be null"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void testGetStringByQueryForInvalidType() {
- try {
- cache.getStringByQuery("str", null);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Cache type cannot be null"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
- @Test
- public void testRemoveByQuery() {
- try {
- CacheType type = new CacheType();
- cache.setCachedQuery("str", type, "val");
- assertNotNull(cache.getStringByQuery("str", type));
- cache.removeByQuery("str", type);
- assertNull(cache.getStringByQuery("str", type));
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Cache type cannot be null"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.annotation.cache;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.AnnotationTestFunctions;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.cache.CacheType;
+
+public class GeneralCacheTest extends AnnotationTestFunctions {
+ Logger logger = Logger.getLogger(GeneralCacheTest.class);
+
+ GeneralCache cache = new GeneralCache();
+
+ @Autowired
+ PermanentDatabaseLevelCacheInterface databaseLevelCache;
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ cache.setCache2(databaseLevelCache);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testClear() {
+ QueryCacheInterface origianlCache = cache.getCache2();
+ try {
+ CacheType type = new CacheType();
+ type.setId(-1);
+ cache.setCache2(ApplicationLevelCache.getInstance());
+ ApplicationLevelCache.getInstance().setCachedQuery("str", type, "val");
+ assertNotNull(cache.getStringByQuery("str", type));
+ cache.clearCache();
+ assertNull(cache.getStringByQuery("str", type));
+ } finally {
+ cache.setCache2(origianlCache);
+ }
+ }
+
+ @Test
+ public void testGetXmlNodeByQueryForInvalidType() {
+ try {
+ cache.getXmlNodeByQuery("str", null);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Cache type cannot be null"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetCachedQueryForInvalidType() {
+ try {
+ cache.setCachedQuery("str", null, null);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Cache type cannot be null"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRemoveByQueryForInvalidType() {
+ try {
+ cache.removeByQuery("str", null);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Cache type cannot be null"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidateByQueryForInvalidType() {
+ try {
+ cache.invalidateByQuery("str", null);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Cache type cannot be null"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void testGetStringByQueryForInvalidType() {
+ try {
+ cache.getStringByQuery("str", null);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Cache type cannot be null"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
+ @Test
+ public void testRemoveByQuery() {
+ try {
+ CacheType type = new CacheType();
+ cache.setCachedQuery("str", type, "val");
+ assertNotNull(cache.getStringByQuery("str", type));
+ cache.removeByQuery("str", type);
+ assertNull(cache.getStringByQuery("str", type));
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Cache type cannot be null"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/GeneralCacheWithExclusionTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/GeneralCacheWithExclusionTest.java
index 81c914488d..6d3aa26c67 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/GeneralCacheWithExclusionTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/GeneralCacheWithExclusionTest.java
@@ -1,133 +1,133 @@
-package lcsb.mapviewer.annotation.cache;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.annotation.AnnotationTestFunctions;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.cache.CacheType;
-
-public class GeneralCacheWithExclusionTest extends AnnotationTestFunctions {
- Logger logger = Logger.getLogger(GeneralCacheWithExclusionTest.class);
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testConstructorWithInvalidParams() {
- try {
- new GeneralCacheWithExclusion(null, 1);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Cache passed as argument cannot be null"));
- }
- }
-
- @Test
- public void testExclusion() throws Exception {
- try {
- CacheType type = new CacheType();
- GeneralCache cache = new GeneralCache();
- cache.setCache2(ApplicationLevelCache.getInstance());
- GeneralCacheWithExclusion cacheWithExclusion = new GeneralCacheWithExclusion(cache, 2);
-
- cacheWithExclusion.setCachedQuery("str", type, super.getNodeFromXmlString("<val/>"));
-
- // after two tries we should get the data that was set
- assertNull(cacheWithExclusion.getXmlNodeByQuery("str", type));
- assertNull(cacheWithExclusion.getXmlNodeByQuery("str", type));
- assertNotNull(cacheWithExclusion.getXmlNodeByQuery("str", type));
-
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Cache passed as argument cannot be null"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testClear() throws Exception {
- try {
- CacheType type = new CacheType();
- GeneralCache cache = new GeneralCache();
- cache.setCache2(ApplicationLevelCache.getInstance());
- GeneralCacheWithExclusion cacheWithExclusion = new GeneralCacheWithExclusion(cache, 0);
-
- cacheWithExclusion.setCachedQuery("str", type, super.getNodeFromXmlString("<val/>"));
-
- assertNotNull(cacheWithExclusion.getXmlNodeByQuery("str", type));
- cacheWithExclusion.clearCache();
-
- assertNull(cacheWithExclusion.getXmlNodeByQuery("str", type));
-
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Cache passed as argument cannot be null"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRemove() throws Exception {
- try {
- CacheType type = new CacheType();
- GeneralCache cache = new GeneralCache();
- cache.setCache2(ApplicationLevelCache.getInstance());
- GeneralCacheWithExclusion cacheWithExclusion = new GeneralCacheWithExclusion(cache, 0);
-
- cacheWithExclusion.setCachedQuery("str", type, super.getNodeFromXmlString("<val/>"));
-
-
- assertNotNull(cacheWithExclusion.getXmlNodeByQuery("str", type));
- cacheWithExclusion.removeByQuery("str", type);
-
- assertNull(cacheWithExclusion.getXmlNodeByQuery("str", type));
-
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Cache passed as argument cannot be null"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidate() throws Exception {
- try {
- CacheType type = new CacheType();
- GeneralCache cache = new GeneralCache();
- cache.setCache2(ApplicationLevelCache.getInstance());
- GeneralCacheWithExclusion cacheWithExclusion = new GeneralCacheWithExclusion(cache, 0);
-
- cacheWithExclusion.setCachedQuery("str", type, super.getNodeFromXmlString("<val/>"));
- cacheWithExclusion.invalidateByQuery("str", type);
-
- assertNull(cacheWithExclusion.getXmlNodeByQuery("str", type));
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Cache passed as argument cannot be null"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.annotation.cache;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.annotation.AnnotationTestFunctions;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.cache.CacheType;
+
+public class GeneralCacheWithExclusionTest extends AnnotationTestFunctions {
+ Logger logger = Logger.getLogger(GeneralCacheWithExclusionTest.class);
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testConstructorWithInvalidParams() {
+ try {
+ new GeneralCacheWithExclusion(null, 1);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Cache passed as argument cannot be null"));
+ }
+ }
+
+ @Test
+ public void testExclusion() throws Exception {
+ try {
+ CacheType type = new CacheType();
+ GeneralCache cache = new GeneralCache();
+ cache.setCache2(ApplicationLevelCache.getInstance());
+ GeneralCacheWithExclusion cacheWithExclusion = new GeneralCacheWithExclusion(cache, 2);
+
+ cacheWithExclusion.setCachedQuery("str", type, super.getNodeFromXmlString("<val/>"));
+
+ // after two tries we should get the data that was set
+ assertNull(cacheWithExclusion.getXmlNodeByQuery("str", type));
+ assertNull(cacheWithExclusion.getXmlNodeByQuery("str", type));
+ assertNotNull(cacheWithExclusion.getXmlNodeByQuery("str", type));
+
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Cache passed as argument cannot be null"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testClear() throws Exception {
+ try {
+ CacheType type = new CacheType();
+ GeneralCache cache = new GeneralCache();
+ cache.setCache2(ApplicationLevelCache.getInstance());
+ GeneralCacheWithExclusion cacheWithExclusion = new GeneralCacheWithExclusion(cache, 0);
+
+ cacheWithExclusion.setCachedQuery("str", type, super.getNodeFromXmlString("<val/>"));
+
+ assertNotNull(cacheWithExclusion.getXmlNodeByQuery("str", type));
+ cacheWithExclusion.clearCache();
+
+ assertNull(cacheWithExclusion.getXmlNodeByQuery("str", type));
+
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Cache passed as argument cannot be null"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRemove() throws Exception {
+ try {
+ CacheType type = new CacheType();
+ GeneralCache cache = new GeneralCache();
+ cache.setCache2(ApplicationLevelCache.getInstance());
+ GeneralCacheWithExclusion cacheWithExclusion = new GeneralCacheWithExclusion(cache, 0);
+
+ cacheWithExclusion.setCachedQuery("str", type, super.getNodeFromXmlString("<val/>"));
+
+
+ assertNotNull(cacheWithExclusion.getXmlNodeByQuery("str", type));
+ cacheWithExclusion.removeByQuery("str", type);
+
+ assertNull(cacheWithExclusion.getXmlNodeByQuery("str", type));
+
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Cache passed as argument cannot be null"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidate() throws Exception {
+ try {
+ CacheType type = new CacheType();
+ GeneralCache cache = new GeneralCache();
+ cache.setCache2(ApplicationLevelCache.getInstance());
+ GeneralCacheWithExclusion cacheWithExclusion = new GeneralCacheWithExclusion(cache, 0);
+
+ cacheWithExclusion.setCachedQuery("str", type, super.getNodeFromXmlString("<val/>"));
+ cacheWithExclusion.invalidateByQuery("str", type);
+
+ assertNull(cacheWithExclusion.getXmlNodeByQuery("str", type));
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Cache passed as argument cannot be null"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/MockCacheInterface.java b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/MockCacheInterface.java
index ff36274cfa..31d47d8a99 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/MockCacheInterface.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/MockCacheInterface.java
@@ -1,33 +1,33 @@
-package lcsb.mapviewer.annotation.cache;
-
-/**
- * Mock implementation of {@link CachableInterface}. It's used for invalid cache
- * elements: {@link lcsb.mapviewer.model.cache.CacheType#INVALID_CACHE}.
- *
- * @author Piotr Gawron
- *
- */
-public final class MockCacheInterface extends CachableInterface {
-
- public static RuntimeException exceptionToThrow = null;
- public static Error errorToThrow;
-
- /**
- * Defsault constructor.
- */
- public MockCacheInterface() {
- super(MockCacheInterface.class);
- }
-
- @Override
- public String refreshCacheQuery(Object query) throws SourceNotAvailable {
- if (exceptionToThrow != null) {
- throw exceptionToThrow;
- }
- if (errorToThrow != null) {
- throw errorToThrow;
- }
- return "<node>[" + query + "] Random: " + Math.random() + "</node>";
- }
-
-}
+package lcsb.mapviewer.annotation.cache;
+
+/**
+ * Mock implementation of {@link CachableInterface}. It's used for invalid cache
+ * elements: {@link lcsb.mapviewer.model.cache.CacheType#INVALID_CACHE}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public final class MockCacheInterface extends CachableInterface {
+
+ public static RuntimeException exceptionToThrow = null;
+ public static Error errorToThrow;
+
+ /**
+ * Defsault constructor.
+ */
+ public MockCacheInterface() {
+ super(MockCacheInterface.class);
+ }
+
+ @Override
+ public String refreshCacheQuery(Object query) throws SourceNotAvailable {
+ if (exceptionToThrow != null) {
+ throw exceptionToThrow;
+ }
+ if (errorToThrow != null) {
+ throw errorToThrow;
+ }
+ return "<node>[" + query + "] Random: " + Math.random() + "</node>";
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCacheTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCacheTest.java
index ffde0cab00..de75cb7662 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCacheTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCacheTest.java
@@ -1,507 +1,507 @@
-package lcsb.mapviewer.annotation.cache;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-import static org.mockito.Mockito.when;
-
-import java.util.Calendar;
-
-import org.apache.commons.lang3.mutable.MutableBoolean;
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-import org.mockito.invocation.InvocationOnMock;
-import org.mockito.stubbing.Answer;
-import org.springframework.test.annotation.Rollback;
-import org.w3c.dom.Node;
-
-import lcsb.mapviewer.annotation.AnnotationTestFunctions;
-import lcsb.mapviewer.annotation.services.PubmedParser;
-import lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.model.cache.CacheQuery;
-import lcsb.mapviewer.model.cache.CacheType;
-import lcsb.mapviewer.persist.dao.cache.CacheQueryDao;
-
-@Rollback(true)
-public class PermanentDatabaseLevelCacheTest extends AnnotationTestFunctions {
-
- Logger logger = Logger.getLogger(PermanentDatabaseLevelCacheTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testByQuery() throws Exception {
- try {
- String xml = "<hello/>";
- String query = "blabla";
-
- String xml2 = "<hello23/>";
-
- CacheType type = cacheTypeDao.getByClassName(PubmedParser.class.getCanonicalName());
-
- Node sourceNode = getNodeFromXmlString(xml);
- Node sourceNode2 = getNodeFromXmlString(xml2);
- cache.removeByQuery(query, type);
-
- Node node = cache.getXmlNodeByQuery(query, type);
- assertNull(node);
-
- cache.setCachedQuery(query, type, sourceNode);
- node = cache.getXmlNodeByQuery(query, type);
- assertNotNull(node);
- assertEquals("hello", node.getNodeName());
-
- cache.setCachedQuery(query, type, sourceNode2);
- node = cache.getXmlNodeByQuery(query, type);
- assertNotNull(node);
- assertEquals("hello23", node.getNodeName());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetInvalidQuery() {
- try {
- String query = "blabla";
- Object object = new Object();
-
- CacheType type = cacheTypeDao.getByClassName(PubmedParser.class.getCanonicalName());
-
- cache.setCachedQuery(query, type, object);
- fail("Exception expected");
-
- } catch (CacheException e) {
- assertTrue(e.getMessage().contains("Unknown object type"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetInvalidXmlNode() {
- try {
- String query = "blabla";
- String object = "hello";
-
- CacheType type = cacheTypeDao.getByClassName(PubmedParser.class.getCanonicalName());
-
- cache.setCachedQuery(query, type, object);
- assertNull(cache.getXmlNodeByQuery(query, type));
-
- assertEquals(2, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test(timeout = 15000)
- public void testRefresh() throws Exception {
- try {
- waitForRefreshCacheQueueToEmpty();
- CacheType invalidType = cacheTypeDao.getByClassName(MockCacheInterface.class.getCanonicalName());
-
- String query = "test query";
- String val = "halo";
- dbUtils.createSessionForCurrentThread();
- cache.setCachedQuery(query, invalidType, val);
- String res = cache.getStringByQuery(query, invalidType);
- dbUtils.closeSessionForCurrentThread();
- assertNotNull(res);
- // for the first time value should be the same (it's not valid but cache
- // wasn't updated)
- assertEquals(val, res);
- // sleep a bit to wait for the second thread
- waitForRefreshCacheQueueToEmpty();
- // for the second time it should change
- dbUtils.createSessionForCurrentThread();
- res = cache.getStringByQuery(query, invalidType);
- dbUtils.closeSessionForCurrentThread();
- assertNotNull(res);
- assertFalse(val.equals(res));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshNode() throws Exception {
- try {
- CacheType invalidType = cacheTypeDao.getByClassName(MockCacheInterface.class.getCanonicalName());
-
- String query = "test query";
- String val = "<node><subnode>halo</subnode></node>";
- Node node = getNodeFromXmlString(val);
- dbUtils.createSessionForCurrentThread();
- cache.setCachedQuery(query, invalidType, node);
- Node res = cache.getXmlNodeByQuery(query, invalidType);
- dbUtils.closeSessionForCurrentThread();
-
- assertNotNull(res);
- // sleep a bit to wait for the second thread
- int counter = dbUtils.getSessionCounter();
- // wait until the other sql session finish
- do {
- Thread.sleep(100);
- counter = dbUtils.getSessionCounter();
- } while (counter > 0);
- Thread.sleep(1000);
- // for the second time it should change
- dbUtils.createSessionForCurrentThread();
- Node res2 = cache.getXmlNodeByQuery(query, invalidType);
- dbUtils.closeSessionForCurrentThread();
- assertNotNull(res2);
-
- String strRes = nodeToString(res);
- String strRes2 = nodeToString(res2);
- assertFalse(strRes.equals(strRes2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidateWhenDbConnectionIsInterrupted() throws Exception {
- CacheQueryDao cacheQueryDao = cache.getCacheQueryDao();
- try {
- CacheType invalidType = cacheTypeDao.getByClassName(MockCacheInterface.class.getCanonicalName());
- String query = "test query";
- CacheQueryDao mockDao = Mockito.mock(CacheQueryDao.class);
- // simulate db connection hanging
- when(mockDao.getByQuery(query, invalidType)).then(new Answer<CacheQuery>() {
- @Override
- public CacheQuery answer(InvocationOnMock invocation) throws Throwable {
- Thread.sleep(100);
- return null;
- }
- });
- cache.setCacheQueryDao(mockDao);
- // run invalidation in separate thread
- Thread t = new Thread(new Runnable() {
- @Override
- public void run() {
- cache.invalidateByQuery(query, invalidType);
- }
- });
-
- t.start();
- // interrupt thread
- t.interrupt();
- t.join();
-
- // check if we have information in the logs about interruption (this is
- // not normal situaion)
- assertEquals(1, getErrors().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- cache.setCacheQueryDao(cacheQueryDao);
- }
- }
-
- @Test
- public void testInvalidateWhenDbConnectionCrash() throws Exception {
- CacheQueryDao cacheQueryDao = cache.getCacheQueryDao();
- try {
- CacheType invalidType = cacheTypeDao.getByClassName(MockCacheInterface.class.getCanonicalName());
- String query = "test query";
- CacheQueryDao mockDao = Mockito.mock(CacheQueryDao.class);
- // simulate db crash
- when(mockDao.getByQuery(query, invalidType)).thenThrow(new InvalidStateException());
- cache.setCacheQueryDao(mockDao);
-
- cache.invalidateByQuery(query, invalidType);
-
- // check if we have information in the logs about interruption (this is
- // not normal situaion)
- assertEquals(1, getErrors().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- cache.setCacheQueryDao(cacheQueryDao);
- }
- }
-
- @Test
- public void testClearCache() throws Exception {
- CacheQueryDao cacheQueryDao = cache.getCacheQueryDao();
- try {
- CacheQueryDao mockDao = Mockito.mock(CacheQueryDao.class);
-
- MutableBoolean cleared = new MutableBoolean(false);
-
- // simulate db crash
- Mockito.doAnswer(new Answer<Void>() {
-
- @Override
- public Void answer(InvocationOnMock invocation) throws Throwable {
- cleared.setValue(true);
- return null;
- }
- }).when(mockDao).clearTable();
- cache.setCacheQueryDao(mockDao);
-
- cache.clearCache();
-
- assertTrue(cleared.getValue());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- cache.setCacheQueryDao(cacheQueryDao);
- }
- }
-
- @Test(timeout = 15000)
- public void testRefreshInvalidType() throws Exception {
- CacheQueryDao cacheQueryDao = cache.getCacheQueryDao();
- try {
- CacheType invalidType = new CacheType();
- String query = "test query";
-
- CacheQueryDao mockDao = Mockito.mock(CacheQueryDao.class);
- // simulate result that is not valid anymore
- when(mockDao.getByQuery(query, invalidType)).thenAnswer(new Answer<CacheQuery>() {
- @Override
- public CacheQuery answer(InvocationOnMock invocation) throws Throwable {
- CacheQuery res = new CacheQuery();
- Calendar expired = Calendar.getInstance();
- expired.add(Calendar.DATE, -1);
- res.setExpires(expired);
- return res;
- }
- });
- cache.setCacheQueryDao(mockDao);
-
- cache.invalidateByQuery(query, invalidType);
-
- while (cache.getRefreshExecutingTasksSize() + cache.getRefreshPendingQueueSize() > 0) {
- Thread.sleep(10);
- }
- assertEquals(1, getFatals().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- cache.setCacheQueryDao(cacheQueryDao);
- }
- }
-
- @Test(timeout = 15000)
- public void testRefreshInvalidType2() throws Exception {
- CacheQueryDao cacheQueryDao = cache.getCacheQueryDao();
- try {
- CacheType invalidType = new CacheType();
- invalidType.setClassName(String.class.getName());
- String query = "test query";
-
- CacheQueryDao mockDao = Mockito.mock(CacheQueryDao.class);
- // simulate result that is not valid anymore
- when(mockDao.getByQuery(query, invalidType)).thenAnswer(new Answer<CacheQuery>() {
- @Override
- public CacheQuery answer(InvocationOnMock invocation) throws Throwable {
- CacheQuery res = new CacheQuery();
- Calendar expired = Calendar.getInstance();
- expired.add(Calendar.DATE, -1);
- res.setExpires(expired);
- return res;
- }
- });
- cache.setCacheQueryDao(mockDao);
-
- cache.invalidateByQuery(query, invalidType);
-
- while (cache.getRefreshExecutingTasksSize() + cache.getRefreshPendingQueueSize() > 0) {
- Thread.sleep(10);
- }
- assertEquals(1, getFatals().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- cache.setCacheQueryDao(cacheQueryDao);
- }
- }
-
- @Test(timeout = 15000)
- public void testRefreshInvalidQuery() throws Exception {
- CacheQueryDao cacheQueryDao = cache.getCacheQueryDao();
- try {
- CacheType type = cacheTypeDao.getByClassName(PubmedParser.class.getCanonicalName());
- String query = "invalid test query";
-
- CacheQueryDao mockDao = Mockito.mock(CacheQueryDao.class);
- // simulate result that is not valid anymore
- when(mockDao.getByQuery(query, type)).thenAnswer(new Answer<CacheQuery>() {
- @Override
- public CacheQuery answer(InvocationOnMock invocation) throws Throwable {
- CacheQuery res = new CacheQuery();
- Calendar expired = Calendar.getInstance();
- expired.add(Calendar.DATE, -1);
- res.setExpires(expired);
- return res;
- }
- });
- cache.setCacheQueryDao(mockDao);
-
- cache.invalidateByQuery(query, type);
-
- while (cache.getRefreshExecutingTasksSize() + cache.getRefreshPendingQueueSize() > 0) {
- Thread.sleep(10);
- }
- assertEquals(1, getErrors().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- cache.setCacheQueryDao(cacheQueryDao);
- }
- }
-
- @Test(timeout = 15000)
- public void testRefreshQueryThatResultsWithNull() throws Exception {
- CacheQueryDao cacheQueryDao = cache.getCacheQueryDao();
- try {
- CacheType type = cacheTypeDao.getByClassName(ChebiAnnotator.class.getCanonicalName());
- String query = ChebiAnnotator.ID_PREFIX + "1234";
-
- CacheQueryDao mockDao = Mockito.mock(CacheQueryDao.class);
- // simulate result that is not valid anymore
- when(mockDao.getByQuery(query, type)).thenAnswer(new Answer<CacheQuery>() {
- @Override
- public CacheQuery answer(InvocationOnMock invocation) throws Throwable {
- CacheQuery res = new CacheQuery();
- Calendar expired = Calendar.getInstance();
- expired.add(Calendar.DATE, -1);
- res.setExpires(expired);
- return res;
- }
- });
- cache.setCacheQueryDao(mockDao);
-
- cache.invalidateByQuery(query, type);
-
- while (cache.getRefreshExecutingTasksSize() + cache.getRefreshPendingQueueSize() > 0) {
- Thread.sleep(10);
- }
- assertEquals(0, getErrors().size());
- assertEquals(0, getFatals().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- cache.setCacheQueryDao(cacheQueryDao);
- }
- }
-
- @Test(timeout = 15000)
- public void testRefreshQueryWithExceptionThrown() throws Exception {
- CacheQueryDao cacheQueryDao = cache.getCacheQueryDao();
- try {
- waitForRefreshCacheQueueToEmpty();
-
- CacheType type = cacheTypeDao.getByClassName(MockCacheInterface.class.getCanonicalName());
- String query = ChebiAnnotator.ID_PREFIX + "1234";
-
- MockCacheInterface.exceptionToThrow = new RuntimeException();
-
- CacheQueryDao mockDao = Mockito.mock(CacheQueryDao.class);
- // simulate result that is not valid anymore
- when(mockDao.getByQuery(query, type)).thenAnswer(new Answer<CacheQuery>() {
- @Override
- public CacheQuery answer(InvocationOnMock invocation) throws Throwable {
- CacheQuery res = new CacheQuery();
- Calendar expired = Calendar.getInstance();
- expired.add(Calendar.DATE, -1);
- res.setExpires(expired);
- return res;
- }
- });
- cache.setCacheQueryDao(mockDao);
-
- cache.invalidateByQuery(query, type);
-
- waitForRefreshCacheQueueToEmpty();
-
- assertEquals(1, getErrors().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- MockCacheInterface.exceptionToThrow = null;
- cache.setCacheQueryDao(cacheQueryDao);
- }
- }
-
- @Test(timeout = 15000)
- public void testRefreshQueryWithErrorThrown() throws Exception {
- CacheQueryDao cacheQueryDao = cache.getCacheQueryDao();
- try {
- CacheType type = cacheTypeDao.getByClassName(MockCacheInterface.class.getCanonicalName());
- String query = ChebiAnnotator.ID_PREFIX + "1234";
-
- MockCacheInterface.errorToThrow = new Error();
-
- CacheQueryDao mockDao = Mockito.mock(CacheQueryDao.class);
- // simulate result that is not valid anymore
- when(mockDao.getByQuery(query, type)).thenAnswer(new Answer<CacheQuery>() {
- @Override
- public CacheQuery answer(InvocationOnMock invocation) throws Throwable {
- CacheQuery res = new CacheQuery();
- Calendar expired = Calendar.getInstance();
- expired.add(Calendar.DATE, -1);
- res.setExpires(expired);
- return res;
- }
- });
- cache.setCacheQueryDao(mockDao);
-
- cache.invalidateByQuery(query, type);
-
- while (cache.getRefreshExecutingTasksSize() + cache.getRefreshPendingQueueSize() > 0) {
- Thread.sleep(10);
- }
- //errors are not caught
- assertEquals(0, getErrors().size());
- assertEquals(0, getFatals().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- MockCacheInterface.errorToThrow = null;
- cache.setCacheQueryDao(cacheQueryDao);
- }
- }
-
-}
+package lcsb.mapviewer.annotation.cache;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import static org.mockito.Mockito.when;
+
+import java.util.Calendar;
+
+import org.apache.commons.lang3.mutable.MutableBoolean;
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+import org.mockito.invocation.InvocationOnMock;
+import org.mockito.stubbing.Answer;
+import org.springframework.test.annotation.Rollback;
+import org.w3c.dom.Node;
+
+import lcsb.mapviewer.annotation.AnnotationTestFunctions;
+import lcsb.mapviewer.annotation.services.PubmedParser;
+import lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.model.cache.CacheQuery;
+import lcsb.mapviewer.model.cache.CacheType;
+import lcsb.mapviewer.persist.dao.cache.CacheQueryDao;
+
+@Rollback(true)
+public class PermanentDatabaseLevelCacheTest extends AnnotationTestFunctions {
+
+ Logger logger = Logger.getLogger(PermanentDatabaseLevelCacheTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testByQuery() throws Exception {
+ try {
+ String xml = "<hello/>";
+ String query = "blabla";
+
+ String xml2 = "<hello23/>";
+
+ CacheType type = cacheTypeDao.getByClassName(PubmedParser.class.getCanonicalName());
+
+ Node sourceNode = getNodeFromXmlString(xml);
+ Node sourceNode2 = getNodeFromXmlString(xml2);
+ cache.removeByQuery(query, type);
+
+ Node node = cache.getXmlNodeByQuery(query, type);
+ assertNull(node);
+
+ cache.setCachedQuery(query, type, sourceNode);
+ node = cache.getXmlNodeByQuery(query, type);
+ assertNotNull(node);
+ assertEquals("hello", node.getNodeName());
+
+ cache.setCachedQuery(query, type, sourceNode2);
+ node = cache.getXmlNodeByQuery(query, type);
+ assertNotNull(node);
+ assertEquals("hello23", node.getNodeName());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetInvalidQuery() {
+ try {
+ String query = "blabla";
+ Object object = new Object();
+
+ CacheType type = cacheTypeDao.getByClassName(PubmedParser.class.getCanonicalName());
+
+ cache.setCachedQuery(query, type, object);
+ fail("Exception expected");
+
+ } catch (CacheException e) {
+ assertTrue(e.getMessage().contains("Unknown object type"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetInvalidXmlNode() {
+ try {
+ String query = "blabla";
+ String object = "hello";
+
+ CacheType type = cacheTypeDao.getByClassName(PubmedParser.class.getCanonicalName());
+
+ cache.setCachedQuery(query, type, object);
+ assertNull(cache.getXmlNodeByQuery(query, type));
+
+ assertEquals(2, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test(timeout = 15000)
+ public void testRefresh() throws Exception {
+ try {
+ waitForRefreshCacheQueueToEmpty();
+ CacheType invalidType = cacheTypeDao.getByClassName(MockCacheInterface.class.getCanonicalName());
+
+ String query = "test query";
+ String val = "halo";
+ dbUtils.createSessionForCurrentThread();
+ cache.setCachedQuery(query, invalidType, val);
+ String res = cache.getStringByQuery(query, invalidType);
+ dbUtils.closeSessionForCurrentThread();
+ assertNotNull(res);
+ // for the first time value should be the same (it's not valid but cache
+ // wasn't updated)
+ assertEquals(val, res);
+ // sleep a bit to wait for the second thread
+ waitForRefreshCacheQueueToEmpty();
+ // for the second time it should change
+ dbUtils.createSessionForCurrentThread();
+ res = cache.getStringByQuery(query, invalidType);
+ dbUtils.closeSessionForCurrentThread();
+ assertNotNull(res);
+ assertFalse(val.equals(res));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshNode() throws Exception {
+ try {
+ CacheType invalidType = cacheTypeDao.getByClassName(MockCacheInterface.class.getCanonicalName());
+
+ String query = "test query";
+ String val = "<node><subnode>halo</subnode></node>";
+ Node node = getNodeFromXmlString(val);
+ dbUtils.createSessionForCurrentThread();
+ cache.setCachedQuery(query, invalidType, node);
+ Node res = cache.getXmlNodeByQuery(query, invalidType);
+ dbUtils.closeSessionForCurrentThread();
+
+ assertNotNull(res);
+ // sleep a bit to wait for the second thread
+ int counter = dbUtils.getSessionCounter();
+ // wait until the other sql session finish
+ do {
+ Thread.sleep(100);
+ counter = dbUtils.getSessionCounter();
+ } while (counter > 0);
+ Thread.sleep(1000);
+ // for the second time it should change
+ dbUtils.createSessionForCurrentThread();
+ Node res2 = cache.getXmlNodeByQuery(query, invalidType);
+ dbUtils.closeSessionForCurrentThread();
+ assertNotNull(res2);
+
+ String strRes = nodeToString(res);
+ String strRes2 = nodeToString(res2);
+ assertFalse(strRes.equals(strRes2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidateWhenDbConnectionIsInterrupted() throws Exception {
+ CacheQueryDao cacheQueryDao = cache.getCacheQueryDao();
+ try {
+ CacheType invalidType = cacheTypeDao.getByClassName(MockCacheInterface.class.getCanonicalName());
+ String query = "test query";
+ CacheQueryDao mockDao = Mockito.mock(CacheQueryDao.class);
+ // simulate db connection hanging
+ when(mockDao.getByQuery(query, invalidType)).then(new Answer<CacheQuery>() {
+ @Override
+ public CacheQuery answer(InvocationOnMock invocation) throws Throwable {
+ Thread.sleep(100);
+ return null;
+ }
+ });
+ cache.setCacheQueryDao(mockDao);
+ // run invalidation in separate thread
+ Thread t = new Thread(new Runnable() {
+ @Override
+ public void run() {
+ cache.invalidateByQuery(query, invalidType);
+ }
+ });
+
+ t.start();
+ // interrupt thread
+ t.interrupt();
+ t.join();
+
+ // check if we have information in the logs about interruption (this is
+ // not normal situaion)
+ assertEquals(1, getErrors().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ cache.setCacheQueryDao(cacheQueryDao);
+ }
+ }
+
+ @Test
+ public void testInvalidateWhenDbConnectionCrash() throws Exception {
+ CacheQueryDao cacheQueryDao = cache.getCacheQueryDao();
+ try {
+ CacheType invalidType = cacheTypeDao.getByClassName(MockCacheInterface.class.getCanonicalName());
+ String query = "test query";
+ CacheQueryDao mockDao = Mockito.mock(CacheQueryDao.class);
+ // simulate db crash
+ when(mockDao.getByQuery(query, invalidType)).thenThrow(new InvalidStateException());
+ cache.setCacheQueryDao(mockDao);
+
+ cache.invalidateByQuery(query, invalidType);
+
+ // check if we have information in the logs about interruption (this is
+ // not normal situaion)
+ assertEquals(1, getErrors().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ cache.setCacheQueryDao(cacheQueryDao);
+ }
+ }
+
+ @Test
+ public void testClearCache() throws Exception {
+ CacheQueryDao cacheQueryDao = cache.getCacheQueryDao();
+ try {
+ CacheQueryDao mockDao = Mockito.mock(CacheQueryDao.class);
+
+ MutableBoolean cleared = new MutableBoolean(false);
+
+ // simulate db crash
+ Mockito.doAnswer(new Answer<Void>() {
+
+ @Override
+ public Void answer(InvocationOnMock invocation) throws Throwable {
+ cleared.setValue(true);
+ return null;
+ }
+ }).when(mockDao).clearTable();
+ cache.setCacheQueryDao(mockDao);
+
+ cache.clearCache();
+
+ assertTrue(cleared.getValue());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ cache.setCacheQueryDao(cacheQueryDao);
+ }
+ }
+
+ @Test(timeout = 15000)
+ public void testRefreshInvalidType() throws Exception {
+ CacheQueryDao cacheQueryDao = cache.getCacheQueryDao();
+ try {
+ CacheType invalidType = new CacheType();
+ String query = "test query";
+
+ CacheQueryDao mockDao = Mockito.mock(CacheQueryDao.class);
+ // simulate result that is not valid anymore
+ when(mockDao.getByQuery(query, invalidType)).thenAnswer(new Answer<CacheQuery>() {
+ @Override
+ public CacheQuery answer(InvocationOnMock invocation) throws Throwable {
+ CacheQuery res = new CacheQuery();
+ Calendar expired = Calendar.getInstance();
+ expired.add(Calendar.DATE, -1);
+ res.setExpires(expired);
+ return res;
+ }
+ });
+ cache.setCacheQueryDao(mockDao);
+
+ cache.invalidateByQuery(query, invalidType);
+
+ while (cache.getRefreshExecutingTasksSize() + cache.getRefreshPendingQueueSize() > 0) {
+ Thread.sleep(10);
+ }
+ assertEquals(1, getFatals().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ cache.setCacheQueryDao(cacheQueryDao);
+ }
+ }
+
+ @Test(timeout = 15000)
+ public void testRefreshInvalidType2() throws Exception {
+ CacheQueryDao cacheQueryDao = cache.getCacheQueryDao();
+ try {
+ CacheType invalidType = new CacheType();
+ invalidType.setClassName(String.class.getName());
+ String query = "test query";
+
+ CacheQueryDao mockDao = Mockito.mock(CacheQueryDao.class);
+ // simulate result that is not valid anymore
+ when(mockDao.getByQuery(query, invalidType)).thenAnswer(new Answer<CacheQuery>() {
+ @Override
+ public CacheQuery answer(InvocationOnMock invocation) throws Throwable {
+ CacheQuery res = new CacheQuery();
+ Calendar expired = Calendar.getInstance();
+ expired.add(Calendar.DATE, -1);
+ res.setExpires(expired);
+ return res;
+ }
+ });
+ cache.setCacheQueryDao(mockDao);
+
+ cache.invalidateByQuery(query, invalidType);
+
+ while (cache.getRefreshExecutingTasksSize() + cache.getRefreshPendingQueueSize() > 0) {
+ Thread.sleep(10);
+ }
+ assertEquals(1, getFatals().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ cache.setCacheQueryDao(cacheQueryDao);
+ }
+ }
+
+ @Test(timeout = 15000)
+ public void testRefreshInvalidQuery() throws Exception {
+ CacheQueryDao cacheQueryDao = cache.getCacheQueryDao();
+ try {
+ CacheType type = cacheTypeDao.getByClassName(PubmedParser.class.getCanonicalName());
+ String query = "invalid test query";
+
+ CacheQueryDao mockDao = Mockito.mock(CacheQueryDao.class);
+ // simulate result that is not valid anymore
+ when(mockDao.getByQuery(query, type)).thenAnswer(new Answer<CacheQuery>() {
+ @Override
+ public CacheQuery answer(InvocationOnMock invocation) throws Throwable {
+ CacheQuery res = new CacheQuery();
+ Calendar expired = Calendar.getInstance();
+ expired.add(Calendar.DATE, -1);
+ res.setExpires(expired);
+ return res;
+ }
+ });
+ cache.setCacheQueryDao(mockDao);
+
+ cache.invalidateByQuery(query, type);
+
+ while (cache.getRefreshExecutingTasksSize() + cache.getRefreshPendingQueueSize() > 0) {
+ Thread.sleep(10);
+ }
+ assertEquals(1, getErrors().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ cache.setCacheQueryDao(cacheQueryDao);
+ }
+ }
+
+ @Test(timeout = 15000)
+ public void testRefreshQueryThatResultsWithNull() throws Exception {
+ CacheQueryDao cacheQueryDao = cache.getCacheQueryDao();
+ try {
+ CacheType type = cacheTypeDao.getByClassName(ChebiAnnotator.class.getCanonicalName());
+ String query = ChebiAnnotator.ID_PREFIX + "1234";
+
+ CacheQueryDao mockDao = Mockito.mock(CacheQueryDao.class);
+ // simulate result that is not valid anymore
+ when(mockDao.getByQuery(query, type)).thenAnswer(new Answer<CacheQuery>() {
+ @Override
+ public CacheQuery answer(InvocationOnMock invocation) throws Throwable {
+ CacheQuery res = new CacheQuery();
+ Calendar expired = Calendar.getInstance();
+ expired.add(Calendar.DATE, -1);
+ res.setExpires(expired);
+ return res;
+ }
+ });
+ cache.setCacheQueryDao(mockDao);
+
+ cache.invalidateByQuery(query, type);
+
+ while (cache.getRefreshExecutingTasksSize() + cache.getRefreshPendingQueueSize() > 0) {
+ Thread.sleep(10);
+ }
+ assertEquals(0, getErrors().size());
+ assertEquals(0, getFatals().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ cache.setCacheQueryDao(cacheQueryDao);
+ }
+ }
+
+ @Test(timeout = 15000)
+ public void testRefreshQueryWithExceptionThrown() throws Exception {
+ CacheQueryDao cacheQueryDao = cache.getCacheQueryDao();
+ try {
+ waitForRefreshCacheQueueToEmpty();
+
+ CacheType type = cacheTypeDao.getByClassName(MockCacheInterface.class.getCanonicalName());
+ String query = ChebiAnnotator.ID_PREFIX + "1234";
+
+ MockCacheInterface.exceptionToThrow = new RuntimeException();
+
+ CacheQueryDao mockDao = Mockito.mock(CacheQueryDao.class);
+ // simulate result that is not valid anymore
+ when(mockDao.getByQuery(query, type)).thenAnswer(new Answer<CacheQuery>() {
+ @Override
+ public CacheQuery answer(InvocationOnMock invocation) throws Throwable {
+ CacheQuery res = new CacheQuery();
+ Calendar expired = Calendar.getInstance();
+ expired.add(Calendar.DATE, -1);
+ res.setExpires(expired);
+ return res;
+ }
+ });
+ cache.setCacheQueryDao(mockDao);
+
+ cache.invalidateByQuery(query, type);
+
+ waitForRefreshCacheQueueToEmpty();
+
+ assertEquals(1, getErrors().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ MockCacheInterface.exceptionToThrow = null;
+ cache.setCacheQueryDao(cacheQueryDao);
+ }
+ }
+
+ @Test(timeout = 15000)
+ public void testRefreshQueryWithErrorThrown() throws Exception {
+ CacheQueryDao cacheQueryDao = cache.getCacheQueryDao();
+ try {
+ CacheType type = cacheTypeDao.getByClassName(MockCacheInterface.class.getCanonicalName());
+ String query = ChebiAnnotator.ID_PREFIX + "1234";
+
+ MockCacheInterface.errorToThrow = new Error();
+
+ CacheQueryDao mockDao = Mockito.mock(CacheQueryDao.class);
+ // simulate result that is not valid anymore
+ when(mockDao.getByQuery(query, type)).thenAnswer(new Answer<CacheQuery>() {
+ @Override
+ public CacheQuery answer(InvocationOnMock invocation) throws Throwable {
+ CacheQuery res = new CacheQuery();
+ Calendar expired = Calendar.getInstance();
+ expired.add(Calendar.DATE, -1);
+ res.setExpires(expired);
+ return res;
+ }
+ });
+ cache.setCacheQueryDao(mockDao);
+
+ cache.invalidateByQuery(query, type);
+
+ while (cache.getRefreshExecutingTasksSize() + cache.getRefreshPendingQueueSize() > 0) {
+ Thread.sleep(10);
+ }
+ //errors are not caught
+ assertEquals(0, getErrors().size());
+ assertEquals(0, getFatals().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ MockCacheInterface.errorToThrow = null;
+ cache.setCacheQueryDao(cacheQueryDao);
+ }
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/SourceNotAvailableTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/SourceNotAvailableTest.java
index 642e83ab5e..ac982ca9ff 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/SourceNotAvailableTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/SourceNotAvailableTest.java
@@ -1,30 +1,30 @@
-package lcsb.mapviewer.annotation.cache;
-
-import static org.junit.Assert.assertTrue;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class SourceNotAvailableTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testConstructor() {
- Exception e = new SourceNotAvailable("meessage");
- assertTrue(e.getMessage().contains("meessage"));
- }
-
-}
+package lcsb.mapviewer.annotation.cache;
+
+import static org.junit.Assert.assertTrue;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class SourceNotAvailableTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testConstructor() {
+ Exception e = new SourceNotAvailable("meessage");
+ assertTrue(e.getMessage().contains("meessage"));
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/WebPageDownloaderTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/WebPageDownloaderTest.java
index 1a1f711b6c..65c6fb5f67 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/cache/WebPageDownloaderTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/cache/WebPageDownloaderTest.java
@@ -1,98 +1,98 @@
-package lcsb.mapviewer.annotation.cache;
-
-import static org.junit.Assert.fail;
-import static org.junit.Assert.assertNotNull;
-
-import java.io.IOException;
-import java.net.HttpURLConnection;
-import java.net.UnknownHostException;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-public class WebPageDownloaderTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testConnectionProblems() {
- WebPageDownloader downloader = new WebPageDownloader() {
- @Override
- public HttpURLConnection openConnection(String url) throws IOException {
- HttpURLConnection result = Mockito.mock(HttpURLConnection.class);
- Mockito.doReturn(HttpURLConnection.HTTP_INTERNAL_ERROR).when(result).getResponseCode();
- Mockito.doThrow(new IOException()).when(result).getInputStream();
- return result;
- }
- };
- try {
- downloader.getFromNetwork("https://www.google.pl/?gws_rd=ssl");
- fail("Exceptio expected");
- } catch (IOException e) {
- }
- }
-
- @Test
- public void testConnectionProblems2() {
- WebPageDownloader downloader = new WebPageDownloader() {
- @Override
- public HttpURLConnection openConnection(String url) throws IOException {
- HttpURLConnection result = Mockito.mock(HttpURLConnection.class);
- Mockito.doReturn(HttpURLConnection.HTTP_OK).when(result).getResponseCode();
- Mockito.doThrow(new UnknownHostException()).when(result).getInputStream();
- return result;
- }
- };
- try {
- downloader.getFromNetwork("https://www.google.pl/?gws_rd=ssl");
- fail("Exceptio expected");
- } catch (IOException e) {
- }
- }
-
- @Test
- public void testSend1() {
- WebPageDownloader downloader = new WebPageDownloader();
- try {
- String result = downloader.getFromNetwork("https://www.google.com/");
- assertNotNull("GET request to Google should return non-null result", result);
- } catch (IOException e) {
- }
- }
-
- @Test
- public void testPost1() {
- WebPageDownloader downloader = new WebPageDownloader();
- try {
- String result = downloader.getFromNetwork("https://www.ebi.ac.uk/pdbe/api/mappings/best_structures/", "POST", "P29373");
- assertNotNull("POST request to Uniprot should return non-null result", result);
- } catch (IOException e) {
- }
-
- }
-
- @Test
- public void testInvalidHttpRequestType() {
- WebPageDownloader downloader = new WebPageDownloader();
- try {
- downloader.getFromNetwork("https://www.ebi.ac.uk/pdbe/api/mappings/best_structures/", "XXX", "P29373");
- fail("Invalid request exception expected");
- } catch (IOException e) {
- }
-
- }
-
-}
+package lcsb.mapviewer.annotation.cache;
+
+import static org.junit.Assert.fail;
+import static org.junit.Assert.assertNotNull;
+
+import java.io.IOException;
+import java.net.HttpURLConnection;
+import java.net.UnknownHostException;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+public class WebPageDownloaderTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testConnectionProblems() {
+ WebPageDownloader downloader = new WebPageDownloader() {
+ @Override
+ public HttpURLConnection openConnection(String url) throws IOException {
+ HttpURLConnection result = Mockito.mock(HttpURLConnection.class);
+ Mockito.doReturn(HttpURLConnection.HTTP_INTERNAL_ERROR).when(result).getResponseCode();
+ Mockito.doThrow(new IOException()).when(result).getInputStream();
+ return result;
+ }
+ };
+ try {
+ downloader.getFromNetwork("https://www.google.pl/?gws_rd=ssl");
+ fail("Exceptio expected");
+ } catch (IOException e) {
+ }
+ }
+
+ @Test
+ public void testConnectionProblems2() {
+ WebPageDownloader downloader = new WebPageDownloader() {
+ @Override
+ public HttpURLConnection openConnection(String url) throws IOException {
+ HttpURLConnection result = Mockito.mock(HttpURLConnection.class);
+ Mockito.doReturn(HttpURLConnection.HTTP_OK).when(result).getResponseCode();
+ Mockito.doThrow(new UnknownHostException()).when(result).getInputStream();
+ return result;
+ }
+ };
+ try {
+ downloader.getFromNetwork("https://www.google.pl/?gws_rd=ssl");
+ fail("Exceptio expected");
+ } catch (IOException e) {
+ }
+ }
+
+ @Test
+ public void testSend1() {
+ WebPageDownloader downloader = new WebPageDownloader();
+ try {
+ String result = downloader.getFromNetwork("https://www.google.com/");
+ assertNotNull("GET request to Google should return non-null result", result);
+ } catch (IOException e) {
+ }
+ }
+
+ @Test
+ public void testPost1() {
+ WebPageDownloader downloader = new WebPageDownloader();
+ try {
+ String result = downloader.getFromNetwork("https://www.ebi.ac.uk/pdbe/api/mappings/best_structures/", "POST", "P29373");
+ assertNotNull("POST request to Uniprot should return non-null result", result);
+ } catch (IOException e) {
+ }
+
+ }
+
+ @Test
+ public void testInvalidHttpRequestType() {
+ WebPageDownloader downloader = new WebPageDownloader();
+ try {
+ downloader.getFromNetwork("https://www.ebi.ac.uk/pdbe/api/mappings/best_structures/", "XXX", "P29373");
+ fail("Invalid request exception expected");
+ } catch (IOException e) {
+ }
+
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/data/AllDataTests.java b/annotation/src/test/java/lcsb/mapviewer/annotation/data/AllDataTests.java
index 6fafd9485a..88f7f1479b 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/data/AllDataTests.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/data/AllDataTests.java
@@ -1,24 +1,24 @@
-package lcsb.mapviewer.annotation.data;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ ArticleCitationComparatorTest.class, //
- ArticleTest.class, //
- ChebiRelationTest.class, //
- ChebiTest.class, //
- ChemicalTest.class, //
- ChemicalDirectEvidenceTest.class, //
- DrugTest.class, //
- EntrezDataTest.class, //
- GoTest.class, //
- MeSHTest.class, //
- MiRNATest.class, //
- TargetTest.class, //
- TargetTypeTest.class,//
-})
-public class AllDataTests {
-
-}
+package lcsb.mapviewer.annotation.data;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ ArticleCitationComparatorTest.class, //
+ ArticleTest.class, //
+ ChebiRelationTest.class, //
+ ChebiTest.class, //
+ ChemicalTest.class, //
+ ChemicalDirectEvidenceTest.class, //
+ DrugTest.class, //
+ EntrezDataTest.class, //
+ GoTest.class, //
+ MeSHTest.class, //
+ MiRNATest.class, //
+ TargetTest.class, //
+ TargetTypeTest.class,//
+})
+public class AllDataTests {
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/data/ArticleCitationComparatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/data/ArticleCitationComparatorTest.java
index f77fcba6e5..7d12657ef9 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/data/ArticleCitationComparatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/data/ArticleCitationComparatorTest.java
@@ -1,47 +1,47 @@
-package lcsb.mapviewer.annotation.data;
-
-import static org.junit.Assert.assertEquals;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ArticleCitationComparatorTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testCompare() {
- Article a1 = new Article();
- a1.setCitationCount(2);
- Article a2 = new Article();
- a2.setCitationCount(10);
- Article a3 = new Article();
- a3.setCitationCount(5);
- List<Article> list = new ArrayList<>();
- list.add(a1);
- list.add(a2);
- list.add(a3);
-
- list.sort(new ArticleCitationComparator());
-
- assertEquals(a2,list.get(0));
- assertEquals(a3,list.get(1));
- assertEquals(a1,list.get(2));
- }
-
-}
+package lcsb.mapviewer.annotation.data;
+
+import static org.junit.Assert.assertEquals;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ArticleCitationComparatorTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testCompare() {
+ Article a1 = new Article();
+ a1.setCitationCount(2);
+ Article a2 = new Article();
+ a2.setCitationCount(10);
+ Article a3 = new Article();
+ a3.setCitationCount(5);
+ List<Article> list = new ArrayList<>();
+ list.add(a1);
+ list.add(a2);
+ list.add(a3);
+
+ list.sort(new ArticleCitationComparator());
+
+ assertEquals(a2,list.get(0));
+ assertEquals(a3,list.get(1));
+ assertEquals(a1,list.get(2));
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/data/ArticleTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/data/ArticleTest.java
index 9301de84e9..0b5bb7a5c0 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/data/ArticleTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/data/ArticleTest.java
@@ -1,27 +1,27 @@
-package lcsb.mapviewer.annotation.data;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ArticleTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new Article());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.annotation.data;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ArticleTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new Article());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/data/ChebiRelationTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/data/ChebiRelationTest.java
index d59e3d3717..c7403c372c 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/data/ChebiRelationTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/data/ChebiRelationTest.java
@@ -1,27 +1,27 @@
-package lcsb.mapviewer.annotation.data;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ChebiRelationTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new ChebiRelation());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.annotation.data;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ChebiRelationTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new ChebiRelation());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/data/ChebiTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/data/ChebiTest.java
index 287f051fd0..12a9762e88 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/data/ChebiTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/data/ChebiTest.java
@@ -1,69 +1,69 @@
-package lcsb.mapviewer.annotation.data;
-
-import static org.junit.Assert.assertEquals;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import uk.ac.ebi.chebi.webapps.chebiWS.model.Entity;
-import uk.ac.ebi.chebi.webapps.chebiWS.model.OntologyDataItem;
-
-public class ChebiTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new Chebi());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- List<ChebiRelation> incomingChebi = new ArrayList<>();
- List<ChebiRelation> outgoingChebi = new ArrayList<>();
- List<String> synonyms = new ArrayList<>();
- Chebi chebi = new Chebi();
- chebi.setIncomingChebi(incomingChebi);
- chebi.setOutgoingChebi(outgoingChebi);
- chebi.setSynonyms(synonyms);
-
- assertEquals(incomingChebi, chebi.getIncomingChebi());
- assertEquals(outgoingChebi, chebi.getOutgoingChebi());
- assertEquals(synonyms, chebi.getSynonyms());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Entity entity = new Entity();
- entity.getOntologyChildren().add(new OntologyDataItem());
- entity.setChebiAsciiName("");
- Chebi chebi = new Chebi(entity);
- assertEquals(1, chebi.getOutgoingChebi().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.annotation.data;
+
+import static org.junit.Assert.assertEquals;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import uk.ac.ebi.chebi.webapps.chebiWS.model.Entity;
+import uk.ac.ebi.chebi.webapps.chebiWS.model.OntologyDataItem;
+
+public class ChebiTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new Chebi());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ List<ChebiRelation> incomingChebi = new ArrayList<>();
+ List<ChebiRelation> outgoingChebi = new ArrayList<>();
+ List<String> synonyms = new ArrayList<>();
+ Chebi chebi = new Chebi();
+ chebi.setIncomingChebi(incomingChebi);
+ chebi.setOutgoingChebi(outgoingChebi);
+ chebi.setSynonyms(synonyms);
+
+ assertEquals(incomingChebi, chebi.getIncomingChebi());
+ assertEquals(outgoingChebi, chebi.getOutgoingChebi());
+ assertEquals(synonyms, chebi.getSynonyms());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Entity entity = new Entity();
+ entity.getOntologyChildren().add(new OntologyDataItem());
+ entity.setChebiAsciiName("");
+ Chebi chebi = new Chebi(entity);
+ assertEquals(1, chebi.getOutgoingChebi().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/data/ChemicalDirectEvidenceTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/data/ChemicalDirectEvidenceTest.java
index 8d409693ce..157d62127c 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/data/ChemicalDirectEvidenceTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/data/ChemicalDirectEvidenceTest.java
@@ -1,31 +1,31 @@
-package lcsb.mapviewer.annotation.data;
-
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ChemicalDirectEvidenceTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testValues() {
- for (ChemicalDirectEvidence value : ChemicalDirectEvidence.values()) {
- assertNotNull(ChemicalDirectEvidence.valueOf(value.toString()));
- }
- }
-
-}
+package lcsb.mapviewer.annotation.data;
+
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ChemicalDirectEvidenceTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testValues() {
+ for (ChemicalDirectEvidence value : ChemicalDirectEvidence.values()) {
+ assertNotNull(ChemicalDirectEvidence.valueOf(value.toString()));
+ }
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/data/ChemicalTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/data/ChemicalTest.java
index 8cde3ee31e..b89bfb937a 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/data/ChemicalTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/data/ChemicalTest.java
@@ -1,67 +1,67 @@
-package lcsb.mapviewer.annotation.data;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.map.MiriamData;
-
-public class ChemicalTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetters() {
- List<Target> inferenceNetwork = new ArrayList<>();
- List<String> synonyms = new ArrayList<>();
- List<MiriamData> directEvidencePublication = new ArrayList<>();
- Chemical chemical = new Chemical();
- chemical.setInferenceNetwork(inferenceNetwork);
- chemical.setDirectEvidencePublication(directEvidencePublication);
- chemical.setSynonyms(synonyms);
-
- assertEquals(inferenceNetwork, chemical.getInferenceNetwork());
- assertEquals(directEvidencePublication, chemical.getDirectEvidencePublication());
- assertEquals(synonyms, chemical.getSynonyms());
-
- }
-
- @Test
- public void testGetSynonymsString() {
- Chemical chemical = new Chemical();
- assertEquals("", chemical.getSynonymsString());
- chemical.getSynonyms().add("12");
- assertEquals("12", chemical.getSynonymsString());
- chemical.getSynonyms().add("qwe");
- assertEquals("12,qwe", chemical.getSynonymsString());
- chemical.getSynonyms().add("zc");
- assertEquals("12,qwe,zc", chemical.getSynonymsString());
- }
-
- @Test
- public void testToString() {
-
- Chemical chemical = new Chemical();
- chemical.getInferenceNetwork().add(new Target());
- chemical.getDirectEvidencePublication().add(new MiriamData());
- assertNotNull(chemical.toString());
- }
-
-}
+package lcsb.mapviewer.annotation.data;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.map.MiriamData;
+
+public class ChemicalTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetters() {
+ List<Target> inferenceNetwork = new ArrayList<>();
+ List<String> synonyms = new ArrayList<>();
+ List<MiriamData> directEvidencePublication = new ArrayList<>();
+ Chemical chemical = new Chemical();
+ chemical.setInferenceNetwork(inferenceNetwork);
+ chemical.setDirectEvidencePublication(directEvidencePublication);
+ chemical.setSynonyms(synonyms);
+
+ assertEquals(inferenceNetwork, chemical.getInferenceNetwork());
+ assertEquals(directEvidencePublication, chemical.getDirectEvidencePublication());
+ assertEquals(synonyms, chemical.getSynonyms());
+
+ }
+
+ @Test
+ public void testGetSynonymsString() {
+ Chemical chemical = new Chemical();
+ assertEquals("", chemical.getSynonymsString());
+ chemical.getSynonyms().add("12");
+ assertEquals("12", chemical.getSynonymsString());
+ chemical.getSynonyms().add("qwe");
+ assertEquals("12,qwe", chemical.getSynonymsString());
+ chemical.getSynonyms().add("zc");
+ assertEquals("12,qwe,zc", chemical.getSynonymsString());
+ }
+
+ @Test
+ public void testToString() {
+
+ Chemical chemical = new Chemical();
+ chemical.getInferenceNetwork().add(new Target());
+ chemical.getDirectEvidencePublication().add(new MiriamData());
+ assertNotNull(chemical.toString());
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/data/DrugTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/data/DrugTest.java
index 13d31788a1..b4afe6785c 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/data/DrugTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/data/DrugTest.java
@@ -1,118 +1,118 @@
-package lcsb.mapviewer.annotation.data;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.annotation.AnnotationTestFunctions;
-import lcsb.mapviewer.annotation.services.TaxonomyBackend;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-
-public class DrugTest extends AnnotationTestFunctions {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new Drug());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Drug d = new Drug();
- d.setDescription("x");
- Drug copy = new Drug(d);
- assertEquals("x", copy.getDescription());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor2() {
- try {
- Drug d = new Drug(null);
- assertNull(d.getName());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToString() {
- try {
- Drug d = new Drug();
- d.addSynonym("Synonym");
- d.addBrandName("bname");
- d.addSource(new MiriamData(MiriamType.DRUGBANK, "xxx"));
- Target target = new Target();
- target.setSource(new MiriamData());
- target.addReference(TaxonomyBackend.HUMAN_TAXONOMY);
- d.addTarget(target);
-
- assertTrue(d.toString().contains("Synonym"));
- assertFalse(d.toString().contains("bname"));
- assertTrue(d.toString().contains("xxx"));
- assertTrue(d.toString().contains(TaxonomyBackend.HUMAN_TAXONOMY.getResource()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddSynonym() {
- try {
- Drug d = new Drug();
- d.addSynonym("Synonym");
- d.addSynonym("Synonym");
-
- assertEquals(1, d.getSynonyms().size());
- assertEquals(1, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- Drug d = new Drug();
- List<Target> targets = new ArrayList<>();
- List<MiriamData> sources = new ArrayList<>();
- d.setTargets(targets);
- d.setSources(sources);
-
- assertEquals(targets, d.getTargets());
- assertEquals(sources, d.getSources());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.annotation.data;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.annotation.AnnotationTestFunctions;
+import lcsb.mapviewer.annotation.services.TaxonomyBackend;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+
+public class DrugTest extends AnnotationTestFunctions {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new Drug());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Drug d = new Drug();
+ d.setDescription("x");
+ Drug copy = new Drug(d);
+ assertEquals("x", copy.getDescription());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor2() {
+ try {
+ Drug d = new Drug(null);
+ assertNull(d.getName());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToString() {
+ try {
+ Drug d = new Drug();
+ d.addSynonym("Synonym");
+ d.addBrandName("bname");
+ d.addSource(new MiriamData(MiriamType.DRUGBANK, "xxx"));
+ Target target = new Target();
+ target.setSource(new MiriamData());
+ target.addReference(TaxonomyBackend.HUMAN_TAXONOMY);
+ d.addTarget(target);
+
+ assertTrue(d.toString().contains("Synonym"));
+ assertFalse(d.toString().contains("bname"));
+ assertTrue(d.toString().contains("xxx"));
+ assertTrue(d.toString().contains(TaxonomyBackend.HUMAN_TAXONOMY.getResource()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddSynonym() {
+ try {
+ Drug d = new Drug();
+ d.addSynonym("Synonym");
+ d.addSynonym("Synonym");
+
+ assertEquals(1, d.getSynonyms().size());
+ assertEquals(1, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ Drug d = new Drug();
+ List<Target> targets = new ArrayList<>();
+ List<MiriamData> sources = new ArrayList<>();
+ d.setTargets(targets);
+ d.setSources(sources);
+
+ assertEquals(targets, d.getTargets());
+ assertEquals(sources, d.getSources());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/data/EntrezDataTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/data/EntrezDataTest.java
index d3a317a19b..8d51c5853d 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/data/EntrezDataTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/data/EntrezDataTest.java
@@ -1,51 +1,51 @@
-package lcsb.mapviewer.annotation.data;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.map.MiriamData;
-
-public class EntrezDataTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetters() {
- List<MiriamData> miriamData = new ArrayList<>();
- EntrezData entrez = new EntrezData();
- entrez.setMiriamData(miriamData);
- assertEquals(miriamData, entrez.getMiriamData());
- }
-
- @Test
- public void testAddMiriamData() {
- EntrezData entrez = new EntrezData();
- entrez.addMiriamData(new MiriamData());
- assertEquals(1, entrez.getMiriamData().size());
- }
-
- @Test
- public void testToString() {
- EntrezData entrez = new EntrezData();
- assertNotNull(entrez.toString());
- }
-
-}
+package lcsb.mapviewer.annotation.data;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.map.MiriamData;
+
+public class EntrezDataTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetters() {
+ List<MiriamData> miriamData = new ArrayList<>();
+ EntrezData entrez = new EntrezData();
+ entrez.setMiriamData(miriamData);
+ assertEquals(miriamData, entrez.getMiriamData());
+ }
+
+ @Test
+ public void testAddMiriamData() {
+ EntrezData entrez = new EntrezData();
+ entrez.addMiriamData(new MiriamData());
+ assertEquals(1, entrez.getMiriamData().size());
+ }
+
+ @Test
+ public void testToString() {
+ EntrezData entrez = new EntrezData();
+ assertNotNull(entrez.toString());
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/data/GoTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/data/GoTest.java
index 9fc76f111c..ba33f5bc6c 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/data/GoTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/data/GoTest.java
@@ -1,28 +1,28 @@
-package lcsb.mapviewer.annotation.data;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class GoTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new Go());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.annotation.data;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class GoTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new Go());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/data/MeSHTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/data/MeSHTest.java
index a73374ab5b..d499ed1b2f 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/data/MeSHTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/data/MeSHTest.java
@@ -1,90 +1,90 @@
-package lcsb.mapviewer.annotation.data;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class MeSHTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new MeSH("is", "name", "desc", new ArrayList<>()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- MeSH mesh = new MeSH();
- List<String> synonyms = new ArrayList<>();
-
- mesh.setSynonyms(synonyms);
-
- assertEquals(synonyms, mesh.getSynonyms());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToString() {
- try {
- MeSH mesh = new MeSH("is", "nam3e", "des3c", new ArrayList<>());
-
- String serial = mesh.toString();
-
- assertTrue(serial.contains("is"));
- assertTrue(serial.contains("nam3e"));
- assertTrue(serial.contains("des3c"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSynonymsToString() {
- try {
- MeSH mesh = new MeSH();
-
- assertEquals("", mesh.getSynonymsString());
-
- mesh.getSynonyms().add("synon");
- assertEquals("synon", mesh.getSynonymsString());
-
- mesh.getSynonyms().add("bla");
- mesh.getSynonyms().add("qwe");
- assertEquals("synon,bla,qwe", mesh.getSynonymsString());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.annotation.data;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class MeSHTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new MeSH("is", "name", "desc", new ArrayList<>()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ MeSH mesh = new MeSH();
+ List<String> synonyms = new ArrayList<>();
+
+ mesh.setSynonyms(synonyms);
+
+ assertEquals(synonyms, mesh.getSynonyms());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToString() {
+ try {
+ MeSH mesh = new MeSH("is", "nam3e", "des3c", new ArrayList<>());
+
+ String serial = mesh.toString();
+
+ assertTrue(serial.contains("is"));
+ assertTrue(serial.contains("nam3e"));
+ assertTrue(serial.contains("des3c"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSynonymsToString() {
+ try {
+ MeSH mesh = new MeSH();
+
+ assertEquals("", mesh.getSynonymsString());
+
+ mesh.getSynonyms().add("synon");
+ assertEquals("synon", mesh.getSynonymsString());
+
+ mesh.getSynonyms().add("bla");
+ mesh.getSynonyms().add("qwe");
+ assertEquals("synon,bla,qwe", mesh.getSynonymsString());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/data/MiRNATest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/data/MiRNATest.java
index 824ef90b87..bff4c92797 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/data/MiRNATest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/data/MiRNATest.java
@@ -1,45 +1,45 @@
-package lcsb.mapviewer.annotation.data;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class MiRNATest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetters() {
- List<Target> inferenceNetwork = new ArrayList<>();
- MiRNA mirna = new MiRNA();
-
- mirna.setTargets(inferenceNetwork);
- assertEquals(inferenceNetwork, mirna.getTargets());
- }
-
- @Test
- public void testToString() {
- MiRNA mirna = new MiRNA();
- mirna.addTarget(new Target());
- String str = mirna.toString();
- assertNotNull(str);
- }
-
-}
+package lcsb.mapviewer.annotation.data;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class MiRNATest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetters() {
+ List<Target> inferenceNetwork = new ArrayList<>();
+ MiRNA mirna = new MiRNA();
+
+ mirna.setTargets(inferenceNetwork);
+ assertEquals(inferenceNetwork, mirna.getTargets());
+ }
+
+ @Test
+ public void testToString() {
+ MiRNA mirna = new MiRNA();
+ mirna.addTarget(new Target());
+ String str = mirna.toString();
+ assertNotNull(str);
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/data/TargetTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/data/TargetTest.java
index 49b41ea930..633ff9d56d 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/data/TargetTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/data/TargetTest.java
@@ -1,65 +1,65 @@
-package lcsb.mapviewer.annotation.data;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.MiriamData;
-
-public class TargetTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new Target());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- List<MiriamData> genes = new ArrayList<>();
- Target target = new Target();
- target.setGenes(genes);
-
- assertEquals(genes, target.getGenes());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddInvalidGene() {
- try {
- Target target = new Target();
- target.addGene(null);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Cannot add null element"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.annotation.data;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.MiriamData;
+
+public class TargetTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new Target());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ List<MiriamData> genes = new ArrayList<>();
+ Target target = new Target();
+ target.setGenes(genes);
+
+ assertEquals(genes, target.getGenes());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddInvalidGene() {
+ try {
+ Target target = new Target();
+ target.addGene(null);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Cannot add null element"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/data/TargetTypeTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/data/TargetTypeTest.java
index 52c5e54406..5cd268ced9 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/data/TargetTypeTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/data/TargetTypeTest.java
@@ -1,32 +1,32 @@
-package lcsb.mapviewer.annotation.data;
-
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class TargetTypeTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testValues() {
- for (TargetType type : TargetType.values()) {
- assertNotNull(type.getCommonName());
- assertNotNull(TargetType.valueOf(type.toString()));
- }
- }
-
-}
+package lcsb.mapviewer.annotation.data;
+
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class TargetTypeTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testValues() {
+ for (TargetType type : TargetType.values()) {
+ assertNotNull(type.getCommonName());
+ assertNotNull(TargetType.valueOf(type.toString()));
+ }
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/AllServicesTests.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/AllServicesTests.java
index 0a71da9f23..1a6650a25e 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/AllServicesTests.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/AllServicesTests.java
@@ -1,34 +1,34 @@
-package lcsb.mapviewer.annotation.services;
-
-import lcsb.mapviewer.annotation.services.annotators.AllAnnotatorTests;
-import lcsb.mapviewer.annotation.services.genome.AllGenomeTests;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AllAnnotatorTests.class, //
- AllGenomeTests.class, //
- ChEMBLParserTest.class, //
- ChemicalParserTest.class, //
- ChemicalSearchExceptionTest.class, //
- DrugAnnotationTest.class, //
- DrugbankHTMLParserTest.class, //
- DrugbankXMLParserTest.class, //
- ExternalServiceStatusTest.class, //
- ExternalServiceStatusTypeTest.class, //
- ImproperAnnotationsTest.class, //
- MeSHParserTest.class, //
- MiriamConnectorTest.class, //
- MiRNASearchExceptionTest.class, //
- MissingAnnotationTest.class, //
- MissingRequiredAnnotationsTest.class, //
- MiRNAParserTest.class, //
- ModelAnnotatorTest.class, //
- PubmedParserTest.class, //
- TaxonomyBackendTest.class,//
-})
-public class AllServicesTests {
-
-}
+package lcsb.mapviewer.annotation.services;
+
+import lcsb.mapviewer.annotation.services.annotators.AllAnnotatorTests;
+import lcsb.mapviewer.annotation.services.genome.AllGenomeTests;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AllAnnotatorTests.class, //
+ AllGenomeTests.class, //
+ ChEMBLParserTest.class, //
+ ChemicalParserTest.class, //
+ ChemicalSearchExceptionTest.class, //
+ DrugAnnotationTest.class, //
+ DrugbankHTMLParserTest.class, //
+ DrugbankXMLParserTest.class, //
+ ExternalServiceStatusTest.class, //
+ ExternalServiceStatusTypeTest.class, //
+ ImproperAnnotationsTest.class, //
+ MeSHParserTest.class, //
+ MiriamConnectorTest.class, //
+ MiRNASearchExceptionTest.class, //
+ MissingAnnotationTest.class, //
+ MissingRequiredAnnotationsTest.class, //
+ MiRNAParserTest.class, //
+ ModelAnnotatorTest.class, //
+ PubmedParserTest.class, //
+ TaxonomyBackendTest.class,//
+})
+public class AllServicesTests {
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
index 934ea70f79..7cc1495a54 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
@@ -1,1257 +1,1257 @@
-package lcsb.mapviewer.annotation.services;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-import static org.mockito.Matchers.any;
-import static org.mockito.Matchers.anyString;
-import static org.mockito.Mockito.when;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.w3c.dom.Node;
-
-import lcsb.mapviewer.annotation.AnnotationTestFunctions;
-import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.GeneralCacheWithExclusion;
-import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
-import lcsb.mapviewer.annotation.cache.WebPageDownloader;
-import lcsb.mapviewer.annotation.cache.XmlSerializer;
-import lcsb.mapviewer.annotation.data.Drug;
-import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.annotation.data.TargetType;
-import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
-import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.UniprotSearchException;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
-
-public class ChEMBLParserTest extends AnnotationTestFunctions {
- Logger logger = Logger.getLogger(ChEMBLParserTest.class);
-
- @Autowired
- private GeneralCacheInterface cache;
-
- @Autowired
- private ChEMBLParser chemblParser;
-
- @Before
- public void setUp() throws Exception {
- chemblParser.setCache(new GeneralCacheWithExclusion(cache, 1));
- }
-
- @After
- public void tearDown() throws Exception {
- chemblParser.setCache(cache);
- }
-
- @Test
- public void test1FindDrug() throws Exception {
- try {
- Drug drug = chemblParser.findDrug("CABOZANTINIB");
-
- assertEquals("CHEMBL2105717", drug.getSources().get(0).getResource());
- assertEquals("CABOZANTINIB", drug.getName());
- assertNull(drug.getDescription());
- assertEquals(2, drug.getTargets().size());
- List<String> lowerCaseSynonyms = new ArrayList<>();
- for (String s : drug.getSynonyms()) {
- lowerCaseSynonyms.add(s.toLowerCase());
- }
- assertTrue(lowerCaseSynonyms.contains("cabozantinib"));
- assertTrue(drug.getApproved());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void test2FindDrug() throws Exception {
- try {
- String n = "DIMETHYL FUMARATE";
- Drug test = chemblParser.findDrug(n);
-
- assertEquals("CHEMBL2107333", test.getSources().get(0).getResource());
- assertEquals("DIMETHYL FUMARATE", test.getName());
- // assertNull(test.getDescription());
- assertEquals(1, test.getTargets().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void test3FindDrug() throws Exception {
- try {
- String n = "LOMITAPIDE";
- Drug test = chemblParser.findDrug(n);
-
- assertEquals("CHEMBL354541", test.getSources().get(0).getResource());
- assertEquals("LOMITAPIDE", test.getName());
- assertNull(test.getDescription());
- assertEquals(1, test.getTargets().size());
-
- for (Target t : test.getTargets()) {
- assertEquals(0, t.getReferences().size());
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void test4FindDrug() throws Exception {
- try {
- String n = "COBICISTAT";
- Drug test = chemblParser.findDrug(n);
-
- assertEquals("CHEMBL2095208", test.getSources().get(0).getResource());
- assertEquals("COBICISTAT", test.getName());
- assertNull(test.getDescription());
- assertEquals(1, test.getTargets().size());
-
- for (Target t : test.getTargets()) {
- assertEquals(0, t.getReferences().size());
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void test5FindDrug() throws Exception {
- try {
- String n = "TALIGLUCERASE ALFA";
- Drug test = chemblParser.findDrug(n);
-
- assertEquals("CHEMBL1964120", test.getSources().get(0).getResource());
- assertEquals("TALIGLUCERASE ALFA", test.getName());
- assertNull(test.getDescription());
- assertEquals(1, test.getTargets().size());
-
- for (Target t : test.getTargets()) {
- assertEquals(0, t.getReferences().size());
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void test6FindDrug() throws Exception {
- try {
- String n = "ABIRATERONE ACETATE";
- Drug test = chemblParser.findDrug(n);
-
- assertEquals("CHEMBL271227", test.getSources().get(0).getResource());
- assertEquals("ABIRATERONE ACETATE", test.getName());
- assertNull(test.getDescription());
- assertEquals(1, test.getTargets().size());
-
- for (Target t : test.getTargets()) {
- assertEquals(0, t.getReferences().size());
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void test7FindDrug() throws Exception {
- try {
- String n = "asdwrgwedas";
- Drug test = chemblParser.findDrug(n);
- assertNull(test);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void test8FindDrug() throws Exception {
- try {
- String n = "aa a32";
- Drug test = chemblParser.findDrug(n);
- assertNull(test);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void test9FindDrug() throws Exception {
- try {
- String name = "PONATINIB";
- Drug test = chemblParser.findDrug(name);
-
- assertEquals("CHEMBL1171837", test.getSources().get(0).getResource());
- assertEquals(name, test.getName());
- assertNull(test.getDescription());
- assertEquals(3, test.getTargets().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void test10FindDrug() throws Exception {
- try {
- String n = "DEXAMETHASONE";
- Drug test = chemblParser.findDrug(n);
-
- assertEquals("CHEMBL384467", test.getSources().get(0).getResource());
- assertEquals("DEXAMETHASONE", test.getName());
- assertNull(test.getDescription());
- assertEquals(1, test.getTargets().size());
-
- for (Target t : test.getTargets()) {
- assertTrue(t.getReferences()
- .contains(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, "16891588")));
- assertTrue(t.getReferences()
- .contains(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, "16956592")));
- assertTrue(t.getReferences()
- .contains(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, "16971495")));
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- /**
- * It is impossible to get references just from target, that's why after
- * getTargetFromId PubMedRef should be empty
- */
- @Test
- public void test1getTargetFromId() throws Exception {
- try {
- Target test = chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "CHEMBL3717"));
-
- assertEquals(test.getSource().getResource(), "CHEMBL3717");
- assertEquals(test.getName(), "Hepatocyte growth factor receptor");
- assertEquals(test.getOrganism().getResource(), "9606");
- assertEquals(TargetType.SINGLE_PROTEIN, test.getType());
- boolean contains = false;
- for (MiriamData md : test.getGenes()) {
- if (md.getResource().equals("MET")) {
- contains = true;
- }
- }
- assertTrue(contains);
- assertEquals(0, test.getReferences().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetTargetFromInvalidId() throws Exception {
- try {
- chemblParser.getTargetFromId(new MiriamData(MiriamType.WIKIPEDIA, "water"));
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetTargetFromIdWhenProblemWithDbConnection() throws Exception {
- WebPageDownloader downloader = chemblParser.getWebPageDownloader();
- try {
- chemblParser.setCache(null);
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("invalid xml");
- chemblParser.setWebPageDownloader(mockDownloader);
- chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "water"));
- fail("Exception expected");
- } catch (DrugSearchException e) {
- assertTrue(e.getMessage().contains("Problem with accessing information about target"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemblParser.setCache(cache);
- chemblParser.setWebPageDownloader(downloader);
- }
-
- }
-
- @Test
- public void testFindDrugWhenProblemWithDbConnection() throws Exception {
- WebPageDownloader downloader = chemblParser.getWebPageDownloader();
- try {
- chemblParser.setCache(null);
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("invalid xml");
- chemblParser.setWebPageDownloader(mockDownloader);
- chemblParser.findDrug("test");
- fail("Exception expected");
- } catch (DrugSearchException e) {
- assertTrue(e.getMessage().contains("Problem with parsing data from CHEMBL database"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemblParser.setCache(cache);
- chemblParser.setWebPageDownloader(downloader);
- }
-
- }
-
- @Test
- public void testGetTargetFromIdWhenProblemWithDbConnection2() throws Exception {
- WebPageDownloader downloader = chemblParser.getWebPageDownloader();
- try {
- chemblParser.setCache(null);
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- chemblParser.setWebPageDownloader(mockDownloader);
- chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "water"));
- fail("Exception expected");
- } catch (DrugSearchException e) {
- assertTrue(e.getMessage().contains("Problem with accessing information about target"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemblParser.setCache(cache);
- chemblParser.setWebPageDownloader(downloader);
- }
-
- }
-
- @Test
- public void testGetTargetFromIdWhenProblemWithUniprot() throws Exception {
- UniprotAnnotator uniprotAnnotator = chemblParser.getUniprotAnnotator();
-
- try {
- UniprotAnnotator mockAnnotator = Mockito.mock(UniprotAnnotator.class);
- when(mockAnnotator.uniProtToHgnc(any())).thenThrow(new UniprotSearchException(null, null));
- chemblParser.setUniprotAnnotator(mockAnnotator);
- chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "CHEMBL3717"));
- fail("Exception expected");
- } catch (DrugSearchException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemblParser.setUniprotAnnotator(uniprotAnnotator);
- }
-
- }
-
- @Test
- public void testGetTargetFromIdWhenProblemWithTaxonomy() throws Exception {
- TaxonomyBackend taxonomyBackend = chemblParser.getTaxonomyBackend();
-
- try {
- TaxonomyBackend mockAnnotator = Mockito.mock(TaxonomyBackend.class);
- when(mockAnnotator.getNameForTaxonomy(any())).thenThrow(new TaxonomySearchException(null, null));
- chemblParser.setTaxonomyBackend(mockAnnotator);
- chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "CHEMBL3717"));
- fail("Exception expected");
- } catch (DrugSearchException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemblParser.setTaxonomyBackend(taxonomyBackend);
- }
-
- }
-
- @Test
- public void testGetTargetFromIdWithProblematicResponse() throws Exception {
- WebPageDownloader downloader = chemblParser.getWebPageDownloader();
- try {
- chemblParser.setCache(null);
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("<target><unk/></target>");
- chemblParser.setWebPageDownloader(mockDownloader);
- chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "water"));
- assertEquals(1, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemblParser.setCache(cache);
- chemblParser.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testGetTargetFromIdWithProblematicResponse2() throws Exception {
- WebPageDownloader downloader = chemblParser.getWebPageDownloader();
- try {
- chemblParser.setCache(null);
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString()))
- .thenReturn("<target><target_components><target_component/></target_components></target>");
- chemblParser.setWebPageDownloader(mockDownloader);
- chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "water"));
- assertEquals(1, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemblParser.setCache(cache);
- chemblParser.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testGetTargetFromIdWithProblematicResponse3() throws Exception {
- WebPageDownloader downloader = chemblParser.getWebPageDownloader();
- try {
- chemblParser.setCache(null);
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString()))
- .thenReturn("<target><target_chembl_id>inv id</target_chembl_id></target>");
- chemblParser.setWebPageDownloader(mockDownloader);
- chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "water"));
- assertEquals(1, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemblParser.setCache(cache);
- chemblParser.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void test2getTargetFromId() throws Exception {
- try {
- Target test = chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "CHEMBL3522"));
-
- assertEquals(test.getSource().getResource(), "CHEMBL3522");
- assertEquals(test.getName(), "Cytochrome P450 17A1");
- assertEquals(test.getOrganism().getResource(), "9606");
- boolean contains = false;
- for (MiriamData md : test.getGenes()) {
- if (md.getResource().equals("CYP17A1")) {
- contains = true;
- }
- }
- assertTrue(contains);
- assertEquals(0, test.getReferences().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void test4getTargetFromId() throws Exception {
- try {
- Target test = chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "CHEMBL2364681"));
-
- assertEquals(test.getSource().getResource(), "CHEMBL2364681");
- assertEquals(test.getName(), "Microsomal triglyceride transfer protein");
- assertEquals(test.getOrganism().getResource(), "9606");
- boolean contains = false;
- boolean contains2 = false;
- for (MiriamData md : test.getGenes()) {
- if (md.getResource().equals("MTTP")) {
- contains = true;
- }
- if (md.getResource().equals("P4HB")) {
- contains2 = true;
- }
- }
- assertTrue(contains);
- assertTrue(contains2);
- assertEquals(0, test.getReferences().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void test5getTargetFromId() throws Exception {
- try {
- Target test = chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "CHEMBL2364176"));
-
- assertEquals(test.getSource().getResource(), "CHEMBL2364176");
- assertEquals(test.getName(), "Glucocerebroside");
- assertEquals(test.getOrganism().getResource(), "9606");
- assertEquals(0, test.getGenes().size());
- assertEquals(0, test.getReferences().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void test6getTargetFromId() throws Exception {
- try {
- Target test = chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "CHEMBL2069156"));
-
- assertEquals(test.getSource().getResource(), "CHEMBL2069156");
- assertEquals(test.getName(), "Kelch-like ECH-associated protein 1");
- assertEquals(test.getOrganism().getResource(), "9606");
- boolean contains = false;
- for (MiriamData md : test.getGenes()) {
- if (md.getResource().equals("KEAP1")) {
- contains = true;
- }
- }
- assertTrue(contains);
- assertEquals(0, test.getReferences().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetTargetsForAmantadine() throws Exception {
- try {
- Drug drug = chemblParser.findDrug("AMANTADINE");
- for (Target target : drug.getTargets()) {
- assertEquals(0, target.getReferences().size());
- }
- assertTrue(drug.getTargets().size() > 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetTargetsWithReferences() throws Exception {
- try {
- Drug drug = chemblParser.findDrug("TRIMETHOPRIM");
- for (Target target : drug.getTargets()) {
- assertEquals(0, target.getReferences().size());
- }
- assertTrue(drug.getTargets().size() > 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindDrugByInvalidHgncTarget() throws Exception {
- try {
- List<Drug> drugs = chemblParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "NR3B"));
- assertNotNull(drugs);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindDrugByHgncWhenHgncCrash() throws Exception {
- HgncAnnotator hgncAnnotator = chemblParser.getHgncAnnotator();
- try {
- HgncAnnotator mockAnnotator = Mockito.mock(HgncAnnotator.class);
- when(mockAnnotator.hgncToUniprot(any())).thenThrow(new AnnotatorException(""));
- chemblParser.setHgncAnnotator(mockAnnotator);
- chemblParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "NR3B"));
- fail("Exception expected");
- } catch (DrugSearchException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemblParser.setHgncAnnotator(hgncAnnotator);
- }
- }
-
- @Test
- public void testFindDrugByHgncTargetWithManyUniprot() throws Exception {
- try {
- List<Drug> drugs = chemblParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "AKAP7"));
- assertNotNull(drugs);
- // we should have a warning that akap7 has more than one uniprot id
- assertEquals(1, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testFindDrugByUniprotTarget() throws Exception {
- try {
- List<Drug> drugs = chemblParser.getDrugListByTarget(new MiriamData(MiriamType.UNIPROT, "O60391"));
- assertTrue(drugs.size() > 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testFindDrugByInvalidTarget() throws Exception {
- try {
- chemblParser.getDrugListByTarget(new MiriamData(MiriamType.MESH_2012, "D010300"));
- } catch (DrugSearchException e) {
- assertTrue(e.getMessage().contains("Don't know how to process target of"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testFindDrugByHgncTarget() throws Exception {
- try {
- List<Drug> drugs = chemblParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "GRIN3B"));
- assertNotNull(drugs);
- assertTrue(drugs.size() > 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testFindDrugByPFKMTarget() throws Exception {
- try {
- // this gene raised some errors at some point
- List<Drug> drugs = chemblParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "PFKM"));
- assertNotNull(drugs);
- assertTrue(drugs.size() >= 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testFindDrugsByHgncTargets() throws Exception {
- try {
- List<Drug> drugs = chemblParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "GRIN3B"));
- List<Drug> drugs2 = chemblParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "GRIN3A"));
- List<MiriamData> hgnc = new ArrayList<MiriamData>();
- hgnc.add(new MiriamData(MiriamType.HGNC_SYMBOL, "GRIN3B"));
- hgnc.add(new MiriamData(MiriamType.HGNC_SYMBOL, "GRIN3A"));
- List<Drug> drugs3 = chemblParser.getDrugListByTargets(hgnc);
- assertNotNull(drugs3);
- assertTrue(drugs.size() + drugs2.size() > drugs3.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testFindDrugByHgncTargetAndFilteredOutByOrganism() throws Exception {
- try {
- List<MiriamData> organisms = new ArrayList<>();
- organisms.add(new MiriamData(MiriamType.TAXONOMY, "-1"));
- List<Drug> drugs = chemblParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "GRIN3B"), organisms);
- assertNotNull(drugs);
- assertEquals("No drugs for this organisms should be found", 0, drugs.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindDrugByHgncTargetAndFilteredByOrganism() throws Exception {
- try {
- List<MiriamData> organisms = new ArrayList<>();
- organisms.add(TaxonomyBackend.HUMAN_TAXONOMY);
- List<Drug> drugs = chemblParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "GRIN3B"), organisms);
- assertNotNull(drugs);
- assertTrue(drugs.size() > 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindDrugsByRepeatingHgncTargets() throws Exception {
- try {
- List<Drug> drugs = chemblParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "GRIN3B"));
- List<MiriamData> hgnc = new ArrayList<MiriamData>();
- hgnc.add(new MiriamData(MiriamType.HGNC_SYMBOL, "GRIN3B"));
- hgnc.add(new MiriamData(MiriamType.HGNC_SYMBOL, "GRIN3B"));
- hgnc.add(new MiriamData(MiriamType.HGNC_SYMBOL, "GRIN3B"));
- List<Drug> drugs3 = chemblParser.getDrugListByTargets(hgnc);
- assertNotNull(drugs3);
- assertEquals(drugs.size(), drugs3.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testCachableInterfaceInvalidateUrl() throws Exception {
- String query = "http://google.lu/";
- String newRes = "hello";
- try {
- waitForRefreshCacheQueueToEmpty();
-
- cache.setCachedQuery(query, chemblParser.getCacheType(), newRes);
- cache.invalidateByQuery(query, chemblParser.getCacheType());
-
- waitForRefreshCacheQueueToEmpty();
-
- String res = cache.getStringByQuery(query, chemblParser.getCacheType());
-
- assertNotNull(res);
-
- assertFalse("Value wasn't refreshed from db", newRes.equals(res));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- // wait max 15 second
- @Test(timeout = 15000)
- public void testCachableInterfaceInvalidateDrug() throws Exception {
- String query = ChEMBLParser.NAME_PREFIX + "TRIMETHOPRIM";
- String newRes = "hello";
- try {
- waitForRefreshCacheQueueToEmpty();
-
- cache.setCachedQuery(query, chemblParser.getCacheType(), newRes);
- cache.invalidateByQuery(query, chemblParser.getCacheType());
-
- waitForRefreshCacheQueueToEmpty();
-
- String res = cache.getStringByQuery(query, chemblParser.getCacheType());
-
- assertNotNull(res);
-
- assertFalse("Value wasn't refreshed from db", newRes.equals(res));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery() throws Exception {
- try {
- chemblParser.refreshCacheQuery("invalid_query");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery2() throws Exception {
- try {
- chemblParser.refreshCacheQuery(new Object());
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshCacheQuery() throws Exception {
- try {
- Object res = chemblParser.refreshCacheQuery("http://google.pl/");
- assertNotNull(res);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshCacheQueryNotAvailable() throws Exception {
- WebPageDownloader downloader = chemblParser.getWebPageDownloader();
- GeneralCacheInterface cache = chemblParser.getCache();
- try {
- // disable cache
- chemblParser.setCache(null);
-
- // simulate problem with downloading
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- chemblParser.setWebPageDownloader(mockDownloader);
- chemblParser.refreshCacheQuery("http://google.pl/");
- fail("Exception expected");
- } catch (SourceNotAvailable e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemblParser.setWebPageDownloader(downloader);
- chemblParser.setCache(cache);
- }
- }
-
- @Test
- public void testGetDrugsByChemblTargetWhenChemblCrash() throws Exception {
- WebPageDownloader downloader = chemblParser.getWebPageDownloader();
- GeneralCacheInterface cache = chemblParser.getCache();
- try {
- // disable cache
- chemblParser.setCache(null);
-
- // simulate problem with downloading
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- chemblParser.setWebPageDownloader(mockDownloader);
- chemblParser.getDrugsByChemblTarget(new MiriamData());
-
- fail("Exception expected");
- } catch (DrugSearchException e) {
- assertEquals("Problem with accessing Chembl database", e.getMessage());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemblParser.setWebPageDownloader(downloader);
- chemblParser.setCache(cache);
- }
- }
-
- @Test
- public void testGetDrugsByChemblTargetWhenChemblCrash2() throws Exception {
- WebPageDownloader downloader = chemblParser.getWebPageDownloader();
- GeneralCacheInterface cache = chemblParser.getCache();
- try {
- // disable cache
- chemblParser.setCache(null);
-
- // simulate problem with downloading
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("");
- chemblParser.setWebPageDownloader(mockDownloader);
- chemblParser.getDrugsByChemblTarget(new MiriamData());
-
- fail("Exception expected");
- } catch (DrugSearchException e) {
- assertEquals("Problem with parsing Chembl response", e.getMessage());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemblParser.setWebPageDownloader(downloader);
- chemblParser.setCache(cache);
- }
- }
-
- @Test
- public void testRefreshCacheQueryWhenChemblDbNotAvailable() throws Exception {
- String query = ChEMBLParser.NAME_PREFIX + "TRIMETHOPRIM";
-
- WebPageDownloader downloader = chemblParser.getWebPageDownloader();
- GeneralCacheInterface cache = chemblParser.getCache();
- try {
- // disable cache
- chemblParser.setCache(null);
-
- // simulate problem with downloading
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- chemblParser.setWebPageDownloader(mockDownloader);
- chemblParser.refreshCacheQuery(query);
- fail("Exception expected");
- } catch (SourceNotAvailable e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemblParser.setWebPageDownloader(downloader);
- chemblParser.setCache(cache);
- }
- }
-
- @Test
- public void testStatus() throws Exception {
- try {
- assertEquals(ExternalServiceStatusType.OK, chemblParser.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSimulateDownStatus() throws Exception {
- WebPageDownloader downloader = chemblParser.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- chemblParser.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.DOWN, chemblParser.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemblParser.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testSimulateChangedStatus() throws Exception {
- WebPageDownloader downloader = chemblParser.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString()))
- .thenReturn("<response><molecules/></response>");
- chemblParser.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.CHANGED, chemblParser.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemblParser.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testSimulateChangedStatus2() throws Exception {
- WebPageDownloader downloader = chemblParser.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
-
- // valid xml but with empty data
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("<response><molecules>"
- + "<molecule><pref_name/><max_phase/><molecule_chembl_id/><molecule_synonyms/></molecule>"
- + "</molecules><mechanisms/><molecule_forms/></response>");
- chemblParser.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.CHANGED, chemblParser.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemblParser.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testGetter() throws Exception {
- ChEMBLParser parser = new ChEMBLParser();
- XmlSerializer<Drug> drugSerializer = new XmlSerializer<>(Drug.class);
- parser.setDrugSerializer(drugSerializer);
- assertEquals(drugSerializer, parser.getDrugSerializer());
- }
-
- @Test
- public void testGetTargetsByInvalidDrugId() throws Exception {
- try {
- chemblParser.getTargetsByDrugId(new MiriamData());
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetTargetsByDrugIdWithExternalDbDown() throws Exception {
- WebPageDownloader downloader = chemblParser.getWebPageDownloader();
- try {
- chemblParser.setCache(null);
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("invalid xml");
- chemblParser.setWebPageDownloader(mockDownloader);
- chemblParser.getTargetsByDrugId(new MiriamData(MiriamType.CHEMBL_COMPOUND, "123"));
- fail("Exception expected");
- } catch (DrugSearchException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemblParser.setWebPageDownloader(downloader);
- chemblParser.setCache(cache);
- }
- }
-
- @Test
- public void testGetTargetsByDrugIdWithExternalDbDown2() throws Exception {
- WebPageDownloader downloader = chemblParser.getWebPageDownloader();
- try {
- chemblParser.setCache(null);
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- chemblParser.setWebPageDownloader(mockDownloader);
- chemblParser.getTargetsByDrugId(new MiriamData(MiriamType.CHEMBL_COMPOUND, "123"));
- fail("Exception expected");
- } catch (DrugSearchException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemblParser.setWebPageDownloader(downloader);
- chemblParser.setCache(cache);
- }
- }
-
- @Test
- public void testFindDrugByUniprotTargetWhenChemblCrash() throws Exception {
- WebPageDownloader downloader = chemblParser.getWebPageDownloader();
- try {
- chemblParser.setCache(null);
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- chemblParser.setWebPageDownloader(mockDownloader);
- chemblParser.getDrugListByTarget(new MiriamData(MiriamType.UNIPROT, "O60391"));
- fail("Exception expected");
- } catch (DrugSearchException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemblParser.setWebPageDownloader(downloader);
- chemblParser.setCache(cache);
- }
-
- }
-
- @Test
- public void testFindDrugByUniprotTargetWhenChemblCrash2() throws Exception {
- WebPageDownloader downloader = chemblParser.getWebPageDownloader();
- try {
- chemblParser.setCache(null);
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("invalid xml");
- chemblParser.setWebPageDownloader(mockDownloader);
- chemblParser.getDrugListByTarget(new MiriamData(MiriamType.UNIPROT, "O60391"));
- fail("Exception expected");
- } catch (DrugSearchException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemblParser.setWebPageDownloader(downloader);
- chemblParser.setCache(cache);
- }
-
- }
-
- @Test
- public void testParseReferences() throws Exception {
- try {
- Node node = super.getXmlDocumentFromFile("testFiles/chembl/references.xml");
- Set<MiriamData> references = chemblParser.parseReferences(node.getFirstChild());
- // we might have more references (if we decide to parse wikipedia, isbn,
- // etc)
- assertTrue(references.size() >= 3);
- assertEquals(1, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testMoreThanOneDrugByName() throws Exception {
- try {
- chemblParser.setCache(new GeneralCacheWithExclusion(cache, 1));
- // we found out that carbidopa drug is doubled in the chembl databse
- chemblParser.findDrug("CARBIDOPA");
- assertEquals(1, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemblParser.setCache(cache);
- }
- }
-
- @Test
- public void testGetDrugByInvalidDrugId() throws Exception {
- try {
- chemblParser.getDrugById(new MiriamData());
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetDrugByDrugIdWhenCehmblCrash() throws Exception {
- WebPageDownloader downloader = chemblParser.getWebPageDownloader();
- try {
- chemblParser.setCache(null);
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("invalid xml");
- chemblParser.setWebPageDownloader(mockDownloader);
- chemblParser.getDrugById(new MiriamData(MiriamType.CHEMBL_COMPOUND, ""));
- fail("Exception expected");
- } catch (DrugSearchException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemblParser.setWebPageDownloader(downloader);
- chemblParser.setCache(cache);
- }
- }
-
- @Test
- public void testGetDrugByDrugIdWhenChemblCrash2() throws Exception {
- WebPageDownloader downloader = chemblParser.getWebPageDownloader();
- try {
- chemblParser.setCache(null);
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- chemblParser.setWebPageDownloader(mockDownloader);
- chemblParser.getDrugById(new MiriamData(MiriamType.CHEMBL_COMPOUND, ""));
- fail("Exception expected");
- } catch (DrugSearchException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemblParser.setWebPageDownloader(downloader);
- chemblParser.setCache(cache);
- }
- }
-
- @Test
- public void testParseSynonymsNode() throws Exception {
- try {
- Node node = super.getNodeFromXmlString(
- "<molecule_synonyms><synonym><synonyms>some synonym</synonyms></synonym><unknode/></molecule_synonyms>");
- List<String> synonyms = chemblParser.parseSynonymsNode(node);
- assertEquals(1, synonyms.size());
- assertEquals(1, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetTargetsForChildElementsWhenChemblCrash() throws Exception {
- WebPageDownloader downloader = chemblParser.getWebPageDownloader();
- try {
- chemblParser.setCache(null);
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- chemblParser.setWebPageDownloader(mockDownloader);
- chemblParser.getTargetsForChildElements(new MiriamData());
- fail("Exception expected");
- } catch (DrugSearchException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemblParser.setWebPageDownloader(downloader);
- chemblParser.setCache(cache);
- }
- }
-
- @Test
- public void testGetTargetsForChildElementsWhenChemblCrash2() throws Exception {
- WebPageDownloader downloader = chemblParser.getWebPageDownloader();
- try {
- chemblParser.setCache(null);
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("invalid xml");
- chemblParser.setWebPageDownloader(mockDownloader);
- chemblParser.getTargetsForChildElements(new MiriamData());
- fail("Exception expected");
- } catch (DrugSearchException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemblParser.setWebPageDownloader(downloader);
- chemblParser.setCache(cache);
- }
- }
-
- @Test
- public void testGetTargetsForChildElementsWhenChemblReturnPartlyInvalidResult() throws Exception {
- WebPageDownloader downloader = chemblParser.getWebPageDownloader();
- try {
- chemblParser.setCache(null);
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString()))
- .thenReturn("<response><molecule_forms><node/></molecule_forms></response>");
- chemblParser.setWebPageDownloader(mockDownloader);
- chemblParser.getTargetsForChildElements(new MiriamData());
- assertEquals(1, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemblParser.setWebPageDownloader(downloader);
- chemblParser.setCache(cache);
- }
- }
-
-}
+package lcsb.mapviewer.annotation.services;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import static org.mockito.Matchers.any;
+import static org.mockito.Matchers.anyString;
+import static org.mockito.Mockito.when;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.w3c.dom.Node;
+
+import lcsb.mapviewer.annotation.AnnotationTestFunctions;
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.GeneralCacheWithExclusion;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.WebPageDownloader;
+import lcsb.mapviewer.annotation.cache.XmlSerializer;
+import lcsb.mapviewer.annotation.data.Drug;
+import lcsb.mapviewer.annotation.data.Target;
+import lcsb.mapviewer.annotation.data.TargetType;
+import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
+import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
+import lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator;
+import lcsb.mapviewer.annotation.services.annotators.UniprotSearchException;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
+
+public class ChEMBLParserTest extends AnnotationTestFunctions {
+ Logger logger = Logger.getLogger(ChEMBLParserTest.class);
+
+ @Autowired
+ private GeneralCacheInterface cache;
+
+ @Autowired
+ private ChEMBLParser chemblParser;
+
+ @Before
+ public void setUp() throws Exception {
+ chemblParser.setCache(new GeneralCacheWithExclusion(cache, 1));
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ chemblParser.setCache(cache);
+ }
+
+ @Test
+ public void test1FindDrug() throws Exception {
+ try {
+ Drug drug = chemblParser.findDrug("CABOZANTINIB");
+
+ assertEquals("CHEMBL2105717", drug.getSources().get(0).getResource());
+ assertEquals("CABOZANTINIB", drug.getName());
+ assertNull(drug.getDescription());
+ assertEquals(2, drug.getTargets().size());
+ List<String> lowerCaseSynonyms = new ArrayList<>();
+ for (String s : drug.getSynonyms()) {
+ lowerCaseSynonyms.add(s.toLowerCase());
+ }
+ assertTrue(lowerCaseSynonyms.contains("cabozantinib"));
+ assertTrue(drug.getApproved());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void test2FindDrug() throws Exception {
+ try {
+ String n = "DIMETHYL FUMARATE";
+ Drug test = chemblParser.findDrug(n);
+
+ assertEquals("CHEMBL2107333", test.getSources().get(0).getResource());
+ assertEquals("DIMETHYL FUMARATE", test.getName());
+ // assertNull(test.getDescription());
+ assertEquals(1, test.getTargets().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void test3FindDrug() throws Exception {
+ try {
+ String n = "LOMITAPIDE";
+ Drug test = chemblParser.findDrug(n);
+
+ assertEquals("CHEMBL354541", test.getSources().get(0).getResource());
+ assertEquals("LOMITAPIDE", test.getName());
+ assertNull(test.getDescription());
+ assertEquals(1, test.getTargets().size());
+
+ for (Target t : test.getTargets()) {
+ assertEquals(0, t.getReferences().size());
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void test4FindDrug() throws Exception {
+ try {
+ String n = "COBICISTAT";
+ Drug test = chemblParser.findDrug(n);
+
+ assertEquals("CHEMBL2095208", test.getSources().get(0).getResource());
+ assertEquals("COBICISTAT", test.getName());
+ assertNull(test.getDescription());
+ assertEquals(1, test.getTargets().size());
+
+ for (Target t : test.getTargets()) {
+ assertEquals(0, t.getReferences().size());
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void test5FindDrug() throws Exception {
+ try {
+ String n = "TALIGLUCERASE ALFA";
+ Drug test = chemblParser.findDrug(n);
+
+ assertEquals("CHEMBL1964120", test.getSources().get(0).getResource());
+ assertEquals("TALIGLUCERASE ALFA", test.getName());
+ assertNull(test.getDescription());
+ assertEquals(1, test.getTargets().size());
+
+ for (Target t : test.getTargets()) {
+ assertEquals(0, t.getReferences().size());
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void test6FindDrug() throws Exception {
+ try {
+ String n = "ABIRATERONE ACETATE";
+ Drug test = chemblParser.findDrug(n);
+
+ assertEquals("CHEMBL271227", test.getSources().get(0).getResource());
+ assertEquals("ABIRATERONE ACETATE", test.getName());
+ assertNull(test.getDescription());
+ assertEquals(1, test.getTargets().size());
+
+ for (Target t : test.getTargets()) {
+ assertEquals(0, t.getReferences().size());
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void test7FindDrug() throws Exception {
+ try {
+ String n = "asdwrgwedas";
+ Drug test = chemblParser.findDrug(n);
+ assertNull(test);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void test8FindDrug() throws Exception {
+ try {
+ String n = "aa a32";
+ Drug test = chemblParser.findDrug(n);
+ assertNull(test);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void test9FindDrug() throws Exception {
+ try {
+ String name = "PONATINIB";
+ Drug test = chemblParser.findDrug(name);
+
+ assertEquals("CHEMBL1171837", test.getSources().get(0).getResource());
+ assertEquals(name, test.getName());
+ assertNull(test.getDescription());
+ assertEquals(3, test.getTargets().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void test10FindDrug() throws Exception {
+ try {
+ String n = "DEXAMETHASONE";
+ Drug test = chemblParser.findDrug(n);
+
+ assertEquals("CHEMBL384467", test.getSources().get(0).getResource());
+ assertEquals("DEXAMETHASONE", test.getName());
+ assertNull(test.getDescription());
+ assertEquals(1, test.getTargets().size());
+
+ for (Target t : test.getTargets()) {
+ assertTrue(t.getReferences()
+ .contains(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, "16891588")));
+ assertTrue(t.getReferences()
+ .contains(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, "16956592")));
+ assertTrue(t.getReferences()
+ .contains(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, "16971495")));
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ /**
+ * It is impossible to get references just from target, that's why after
+ * getTargetFromId PubMedRef should be empty
+ */
+ @Test
+ public void test1getTargetFromId() throws Exception {
+ try {
+ Target test = chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "CHEMBL3717"));
+
+ assertEquals(test.getSource().getResource(), "CHEMBL3717");
+ assertEquals(test.getName(), "Hepatocyte growth factor receptor");
+ assertEquals(test.getOrganism().getResource(), "9606");
+ assertEquals(TargetType.SINGLE_PROTEIN, test.getType());
+ boolean contains = false;
+ for (MiriamData md : test.getGenes()) {
+ if (md.getResource().equals("MET")) {
+ contains = true;
+ }
+ }
+ assertTrue(contains);
+ assertEquals(0, test.getReferences().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetTargetFromInvalidId() throws Exception {
+ try {
+ chemblParser.getTargetFromId(new MiriamData(MiriamType.WIKIPEDIA, "water"));
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetTargetFromIdWhenProblemWithDbConnection() throws Exception {
+ WebPageDownloader downloader = chemblParser.getWebPageDownloader();
+ try {
+ chemblParser.setCache(null);
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("invalid xml");
+ chemblParser.setWebPageDownloader(mockDownloader);
+ chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "water"));
+ fail("Exception expected");
+ } catch (DrugSearchException e) {
+ assertTrue(e.getMessage().contains("Problem with accessing information about target"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemblParser.setCache(cache);
+ chemblParser.setWebPageDownloader(downloader);
+ }
+
+ }
+
+ @Test
+ public void testFindDrugWhenProblemWithDbConnection() throws Exception {
+ WebPageDownloader downloader = chemblParser.getWebPageDownloader();
+ try {
+ chemblParser.setCache(null);
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("invalid xml");
+ chemblParser.setWebPageDownloader(mockDownloader);
+ chemblParser.findDrug("test");
+ fail("Exception expected");
+ } catch (DrugSearchException e) {
+ assertTrue(e.getMessage().contains("Problem with parsing data from CHEMBL database"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemblParser.setCache(cache);
+ chemblParser.setWebPageDownloader(downloader);
+ }
+
+ }
+
+ @Test
+ public void testGetTargetFromIdWhenProblemWithDbConnection2() throws Exception {
+ WebPageDownloader downloader = chemblParser.getWebPageDownloader();
+ try {
+ chemblParser.setCache(null);
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ chemblParser.setWebPageDownloader(mockDownloader);
+ chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "water"));
+ fail("Exception expected");
+ } catch (DrugSearchException e) {
+ assertTrue(e.getMessage().contains("Problem with accessing information about target"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemblParser.setCache(cache);
+ chemblParser.setWebPageDownloader(downloader);
+ }
+
+ }
+
+ @Test
+ public void testGetTargetFromIdWhenProblemWithUniprot() throws Exception {
+ UniprotAnnotator uniprotAnnotator = chemblParser.getUniprotAnnotator();
+
+ try {
+ UniprotAnnotator mockAnnotator = Mockito.mock(UniprotAnnotator.class);
+ when(mockAnnotator.uniProtToHgnc(any())).thenThrow(new UniprotSearchException(null, null));
+ chemblParser.setUniprotAnnotator(mockAnnotator);
+ chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "CHEMBL3717"));
+ fail("Exception expected");
+ } catch (DrugSearchException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemblParser.setUniprotAnnotator(uniprotAnnotator);
+ }
+
+ }
+
+ @Test
+ public void testGetTargetFromIdWhenProblemWithTaxonomy() throws Exception {
+ TaxonomyBackend taxonomyBackend = chemblParser.getTaxonomyBackend();
+
+ try {
+ TaxonomyBackend mockAnnotator = Mockito.mock(TaxonomyBackend.class);
+ when(mockAnnotator.getNameForTaxonomy(any())).thenThrow(new TaxonomySearchException(null, null));
+ chemblParser.setTaxonomyBackend(mockAnnotator);
+ chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "CHEMBL3717"));
+ fail("Exception expected");
+ } catch (DrugSearchException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemblParser.setTaxonomyBackend(taxonomyBackend);
+ }
+
+ }
+
+ @Test
+ public void testGetTargetFromIdWithProblematicResponse() throws Exception {
+ WebPageDownloader downloader = chemblParser.getWebPageDownloader();
+ try {
+ chemblParser.setCache(null);
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("<target><unk/></target>");
+ chemblParser.setWebPageDownloader(mockDownloader);
+ chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "water"));
+ assertEquals(1, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemblParser.setCache(cache);
+ chemblParser.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testGetTargetFromIdWithProblematicResponse2() throws Exception {
+ WebPageDownloader downloader = chemblParser.getWebPageDownloader();
+ try {
+ chemblParser.setCache(null);
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString()))
+ .thenReturn("<target><target_components><target_component/></target_components></target>");
+ chemblParser.setWebPageDownloader(mockDownloader);
+ chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "water"));
+ assertEquals(1, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemblParser.setCache(cache);
+ chemblParser.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testGetTargetFromIdWithProblematicResponse3() throws Exception {
+ WebPageDownloader downloader = chemblParser.getWebPageDownloader();
+ try {
+ chemblParser.setCache(null);
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString()))
+ .thenReturn("<target><target_chembl_id>inv id</target_chembl_id></target>");
+ chemblParser.setWebPageDownloader(mockDownloader);
+ chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "water"));
+ assertEquals(1, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemblParser.setCache(cache);
+ chemblParser.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void test2getTargetFromId() throws Exception {
+ try {
+ Target test = chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "CHEMBL3522"));
+
+ assertEquals(test.getSource().getResource(), "CHEMBL3522");
+ assertEquals(test.getName(), "Cytochrome P450 17A1");
+ assertEquals(test.getOrganism().getResource(), "9606");
+ boolean contains = false;
+ for (MiriamData md : test.getGenes()) {
+ if (md.getResource().equals("CYP17A1")) {
+ contains = true;
+ }
+ }
+ assertTrue(contains);
+ assertEquals(0, test.getReferences().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void test4getTargetFromId() throws Exception {
+ try {
+ Target test = chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "CHEMBL2364681"));
+
+ assertEquals(test.getSource().getResource(), "CHEMBL2364681");
+ assertEquals(test.getName(), "Microsomal triglyceride transfer protein");
+ assertEquals(test.getOrganism().getResource(), "9606");
+ boolean contains = false;
+ boolean contains2 = false;
+ for (MiriamData md : test.getGenes()) {
+ if (md.getResource().equals("MTTP")) {
+ contains = true;
+ }
+ if (md.getResource().equals("P4HB")) {
+ contains2 = true;
+ }
+ }
+ assertTrue(contains);
+ assertTrue(contains2);
+ assertEquals(0, test.getReferences().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void test5getTargetFromId() throws Exception {
+ try {
+ Target test = chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "CHEMBL2364176"));
+
+ assertEquals(test.getSource().getResource(), "CHEMBL2364176");
+ assertEquals(test.getName(), "Glucocerebroside");
+ assertEquals(test.getOrganism().getResource(), "9606");
+ assertEquals(0, test.getGenes().size());
+ assertEquals(0, test.getReferences().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void test6getTargetFromId() throws Exception {
+ try {
+ Target test = chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "CHEMBL2069156"));
+
+ assertEquals(test.getSource().getResource(), "CHEMBL2069156");
+ assertEquals(test.getName(), "Kelch-like ECH-associated protein 1");
+ assertEquals(test.getOrganism().getResource(), "9606");
+ boolean contains = false;
+ for (MiriamData md : test.getGenes()) {
+ if (md.getResource().equals("KEAP1")) {
+ contains = true;
+ }
+ }
+ assertTrue(contains);
+ assertEquals(0, test.getReferences().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetTargetsForAmantadine() throws Exception {
+ try {
+ Drug drug = chemblParser.findDrug("AMANTADINE");
+ for (Target target : drug.getTargets()) {
+ assertEquals(0, target.getReferences().size());
+ }
+ assertTrue(drug.getTargets().size() > 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetTargetsWithReferences() throws Exception {
+ try {
+ Drug drug = chemblParser.findDrug("TRIMETHOPRIM");
+ for (Target target : drug.getTargets()) {
+ assertEquals(0, target.getReferences().size());
+ }
+ assertTrue(drug.getTargets().size() > 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindDrugByInvalidHgncTarget() throws Exception {
+ try {
+ List<Drug> drugs = chemblParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "NR3B"));
+ assertNotNull(drugs);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindDrugByHgncWhenHgncCrash() throws Exception {
+ HgncAnnotator hgncAnnotator = chemblParser.getHgncAnnotator();
+ try {
+ HgncAnnotator mockAnnotator = Mockito.mock(HgncAnnotator.class);
+ when(mockAnnotator.hgncToUniprot(any())).thenThrow(new AnnotatorException(""));
+ chemblParser.setHgncAnnotator(mockAnnotator);
+ chemblParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "NR3B"));
+ fail("Exception expected");
+ } catch (DrugSearchException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemblParser.setHgncAnnotator(hgncAnnotator);
+ }
+ }
+
+ @Test
+ public void testFindDrugByHgncTargetWithManyUniprot() throws Exception {
+ try {
+ List<Drug> drugs = chemblParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "AKAP7"));
+ assertNotNull(drugs);
+ // we should have a warning that akap7 has more than one uniprot id
+ assertEquals(1, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testFindDrugByUniprotTarget() throws Exception {
+ try {
+ List<Drug> drugs = chemblParser.getDrugListByTarget(new MiriamData(MiriamType.UNIPROT, "O60391"));
+ assertTrue(drugs.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testFindDrugByInvalidTarget() throws Exception {
+ try {
+ chemblParser.getDrugListByTarget(new MiriamData(MiriamType.MESH_2012, "D010300"));
+ } catch (DrugSearchException e) {
+ assertTrue(e.getMessage().contains("Don't know how to process target of"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testFindDrugByHgncTarget() throws Exception {
+ try {
+ List<Drug> drugs = chemblParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "GRIN3B"));
+ assertNotNull(drugs);
+ assertTrue(drugs.size() > 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testFindDrugByPFKMTarget() throws Exception {
+ try {
+ // this gene raised some errors at some point
+ List<Drug> drugs = chemblParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "PFKM"));
+ assertNotNull(drugs);
+ assertTrue(drugs.size() >= 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testFindDrugsByHgncTargets() throws Exception {
+ try {
+ List<Drug> drugs = chemblParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "GRIN3B"));
+ List<Drug> drugs2 = chemblParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "GRIN3A"));
+ List<MiriamData> hgnc = new ArrayList<MiriamData>();
+ hgnc.add(new MiriamData(MiriamType.HGNC_SYMBOL, "GRIN3B"));
+ hgnc.add(new MiriamData(MiriamType.HGNC_SYMBOL, "GRIN3A"));
+ List<Drug> drugs3 = chemblParser.getDrugListByTargets(hgnc);
+ assertNotNull(drugs3);
+ assertTrue(drugs.size() + drugs2.size() > drugs3.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testFindDrugByHgncTargetAndFilteredOutByOrganism() throws Exception {
+ try {
+ List<MiriamData> organisms = new ArrayList<>();
+ organisms.add(new MiriamData(MiriamType.TAXONOMY, "-1"));
+ List<Drug> drugs = chemblParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "GRIN3B"), organisms);
+ assertNotNull(drugs);
+ assertEquals("No drugs for this organisms should be found", 0, drugs.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindDrugByHgncTargetAndFilteredByOrganism() throws Exception {
+ try {
+ List<MiriamData> organisms = new ArrayList<>();
+ organisms.add(TaxonomyBackend.HUMAN_TAXONOMY);
+ List<Drug> drugs = chemblParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "GRIN3B"), organisms);
+ assertNotNull(drugs);
+ assertTrue(drugs.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindDrugsByRepeatingHgncTargets() throws Exception {
+ try {
+ List<Drug> drugs = chemblParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "GRIN3B"));
+ List<MiriamData> hgnc = new ArrayList<MiriamData>();
+ hgnc.add(new MiriamData(MiriamType.HGNC_SYMBOL, "GRIN3B"));
+ hgnc.add(new MiriamData(MiriamType.HGNC_SYMBOL, "GRIN3B"));
+ hgnc.add(new MiriamData(MiriamType.HGNC_SYMBOL, "GRIN3B"));
+ List<Drug> drugs3 = chemblParser.getDrugListByTargets(hgnc);
+ assertNotNull(drugs3);
+ assertEquals(drugs.size(), drugs3.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testCachableInterfaceInvalidateUrl() throws Exception {
+ String query = "http://google.lu/";
+ String newRes = "hello";
+ try {
+ waitForRefreshCacheQueueToEmpty();
+
+ cache.setCachedQuery(query, chemblParser.getCacheType(), newRes);
+ cache.invalidateByQuery(query, chemblParser.getCacheType());
+
+ waitForRefreshCacheQueueToEmpty();
+
+ String res = cache.getStringByQuery(query, chemblParser.getCacheType());
+
+ assertNotNull(res);
+
+ assertFalse("Value wasn't refreshed from db", newRes.equals(res));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ // wait max 15 second
+ @Test(timeout = 15000)
+ public void testCachableInterfaceInvalidateDrug() throws Exception {
+ String query = ChEMBLParser.NAME_PREFIX + "TRIMETHOPRIM";
+ String newRes = "hello";
+ try {
+ waitForRefreshCacheQueueToEmpty();
+
+ cache.setCachedQuery(query, chemblParser.getCacheType(), newRes);
+ cache.invalidateByQuery(query, chemblParser.getCacheType());
+
+ waitForRefreshCacheQueueToEmpty();
+
+ String res = cache.getStringByQuery(query, chemblParser.getCacheType());
+
+ assertNotNull(res);
+
+ assertFalse("Value wasn't refreshed from db", newRes.equals(res));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery() throws Exception {
+ try {
+ chemblParser.refreshCacheQuery("invalid_query");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery2() throws Exception {
+ try {
+ chemblParser.refreshCacheQuery(new Object());
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQuery() throws Exception {
+ try {
+ Object res = chemblParser.refreshCacheQuery("http://google.pl/");
+ assertNotNull(res);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQueryNotAvailable() throws Exception {
+ WebPageDownloader downloader = chemblParser.getWebPageDownloader();
+ GeneralCacheInterface cache = chemblParser.getCache();
+ try {
+ // disable cache
+ chemblParser.setCache(null);
+
+ // simulate problem with downloading
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ chemblParser.setWebPageDownloader(mockDownloader);
+ chemblParser.refreshCacheQuery("http://google.pl/");
+ fail("Exception expected");
+ } catch (SourceNotAvailable e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemblParser.setWebPageDownloader(downloader);
+ chemblParser.setCache(cache);
+ }
+ }
+
+ @Test
+ public void testGetDrugsByChemblTargetWhenChemblCrash() throws Exception {
+ WebPageDownloader downloader = chemblParser.getWebPageDownloader();
+ GeneralCacheInterface cache = chemblParser.getCache();
+ try {
+ // disable cache
+ chemblParser.setCache(null);
+
+ // simulate problem with downloading
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ chemblParser.setWebPageDownloader(mockDownloader);
+ chemblParser.getDrugsByChemblTarget(new MiriamData());
+
+ fail("Exception expected");
+ } catch (DrugSearchException e) {
+ assertEquals("Problem with accessing Chembl database", e.getMessage());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemblParser.setWebPageDownloader(downloader);
+ chemblParser.setCache(cache);
+ }
+ }
+
+ @Test
+ public void testGetDrugsByChemblTargetWhenChemblCrash2() throws Exception {
+ WebPageDownloader downloader = chemblParser.getWebPageDownloader();
+ GeneralCacheInterface cache = chemblParser.getCache();
+ try {
+ // disable cache
+ chemblParser.setCache(null);
+
+ // simulate problem with downloading
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("");
+ chemblParser.setWebPageDownloader(mockDownloader);
+ chemblParser.getDrugsByChemblTarget(new MiriamData());
+
+ fail("Exception expected");
+ } catch (DrugSearchException e) {
+ assertEquals("Problem with parsing Chembl response", e.getMessage());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemblParser.setWebPageDownloader(downloader);
+ chemblParser.setCache(cache);
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQueryWhenChemblDbNotAvailable() throws Exception {
+ String query = ChEMBLParser.NAME_PREFIX + "TRIMETHOPRIM";
+
+ WebPageDownloader downloader = chemblParser.getWebPageDownloader();
+ GeneralCacheInterface cache = chemblParser.getCache();
+ try {
+ // disable cache
+ chemblParser.setCache(null);
+
+ // simulate problem with downloading
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ chemblParser.setWebPageDownloader(mockDownloader);
+ chemblParser.refreshCacheQuery(query);
+ fail("Exception expected");
+ } catch (SourceNotAvailable e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemblParser.setWebPageDownloader(downloader);
+ chemblParser.setCache(cache);
+ }
+ }
+
+ @Test
+ public void testStatus() throws Exception {
+ try {
+ assertEquals(ExternalServiceStatusType.OK, chemblParser.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSimulateDownStatus() throws Exception {
+ WebPageDownloader downloader = chemblParser.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ chemblParser.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.DOWN, chemblParser.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemblParser.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testSimulateChangedStatus() throws Exception {
+ WebPageDownloader downloader = chemblParser.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString()))
+ .thenReturn("<response><molecules/></response>");
+ chemblParser.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.CHANGED, chemblParser.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemblParser.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testSimulateChangedStatus2() throws Exception {
+ WebPageDownloader downloader = chemblParser.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+
+ // valid xml but with empty data
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("<response><molecules>"
+ + "<molecule><pref_name/><max_phase/><molecule_chembl_id/><molecule_synonyms/></molecule>"
+ + "</molecules><mechanisms/><molecule_forms/></response>");
+ chemblParser.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.CHANGED, chemblParser.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemblParser.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testGetter() throws Exception {
+ ChEMBLParser parser = new ChEMBLParser();
+ XmlSerializer<Drug> drugSerializer = new XmlSerializer<>(Drug.class);
+ parser.setDrugSerializer(drugSerializer);
+ assertEquals(drugSerializer, parser.getDrugSerializer());
+ }
+
+ @Test
+ public void testGetTargetsByInvalidDrugId() throws Exception {
+ try {
+ chemblParser.getTargetsByDrugId(new MiriamData());
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetTargetsByDrugIdWithExternalDbDown() throws Exception {
+ WebPageDownloader downloader = chemblParser.getWebPageDownloader();
+ try {
+ chemblParser.setCache(null);
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("invalid xml");
+ chemblParser.setWebPageDownloader(mockDownloader);
+ chemblParser.getTargetsByDrugId(new MiriamData(MiriamType.CHEMBL_COMPOUND, "123"));
+ fail("Exception expected");
+ } catch (DrugSearchException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemblParser.setWebPageDownloader(downloader);
+ chemblParser.setCache(cache);
+ }
+ }
+
+ @Test
+ public void testGetTargetsByDrugIdWithExternalDbDown2() throws Exception {
+ WebPageDownloader downloader = chemblParser.getWebPageDownloader();
+ try {
+ chemblParser.setCache(null);
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ chemblParser.setWebPageDownloader(mockDownloader);
+ chemblParser.getTargetsByDrugId(new MiriamData(MiriamType.CHEMBL_COMPOUND, "123"));
+ fail("Exception expected");
+ } catch (DrugSearchException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemblParser.setWebPageDownloader(downloader);
+ chemblParser.setCache(cache);
+ }
+ }
+
+ @Test
+ public void testFindDrugByUniprotTargetWhenChemblCrash() throws Exception {
+ WebPageDownloader downloader = chemblParser.getWebPageDownloader();
+ try {
+ chemblParser.setCache(null);
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ chemblParser.setWebPageDownloader(mockDownloader);
+ chemblParser.getDrugListByTarget(new MiriamData(MiriamType.UNIPROT, "O60391"));
+ fail("Exception expected");
+ } catch (DrugSearchException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemblParser.setWebPageDownloader(downloader);
+ chemblParser.setCache(cache);
+ }
+
+ }
+
+ @Test
+ public void testFindDrugByUniprotTargetWhenChemblCrash2() throws Exception {
+ WebPageDownloader downloader = chemblParser.getWebPageDownloader();
+ try {
+ chemblParser.setCache(null);
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("invalid xml");
+ chemblParser.setWebPageDownloader(mockDownloader);
+ chemblParser.getDrugListByTarget(new MiriamData(MiriamType.UNIPROT, "O60391"));
+ fail("Exception expected");
+ } catch (DrugSearchException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemblParser.setWebPageDownloader(downloader);
+ chemblParser.setCache(cache);
+ }
+
+ }
+
+ @Test
+ public void testParseReferences() throws Exception {
+ try {
+ Node node = super.getXmlDocumentFromFile("testFiles/chembl/references.xml");
+ Set<MiriamData> references = chemblParser.parseReferences(node.getFirstChild());
+ // we might have more references (if we decide to parse wikipedia, isbn,
+ // etc)
+ assertTrue(references.size() >= 3);
+ assertEquals(1, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testMoreThanOneDrugByName() throws Exception {
+ try {
+ chemblParser.setCache(new GeneralCacheWithExclusion(cache, 1));
+ // we found out that carbidopa drug is doubled in the chembl databse
+ chemblParser.findDrug("CARBIDOPA");
+ assertEquals(1, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemblParser.setCache(cache);
+ }
+ }
+
+ @Test
+ public void testGetDrugByInvalidDrugId() throws Exception {
+ try {
+ chemblParser.getDrugById(new MiriamData());
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetDrugByDrugIdWhenCehmblCrash() throws Exception {
+ WebPageDownloader downloader = chemblParser.getWebPageDownloader();
+ try {
+ chemblParser.setCache(null);
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("invalid xml");
+ chemblParser.setWebPageDownloader(mockDownloader);
+ chemblParser.getDrugById(new MiriamData(MiriamType.CHEMBL_COMPOUND, ""));
+ fail("Exception expected");
+ } catch (DrugSearchException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemblParser.setWebPageDownloader(downloader);
+ chemblParser.setCache(cache);
+ }
+ }
+
+ @Test
+ public void testGetDrugByDrugIdWhenChemblCrash2() throws Exception {
+ WebPageDownloader downloader = chemblParser.getWebPageDownloader();
+ try {
+ chemblParser.setCache(null);
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ chemblParser.setWebPageDownloader(mockDownloader);
+ chemblParser.getDrugById(new MiriamData(MiriamType.CHEMBL_COMPOUND, ""));
+ fail("Exception expected");
+ } catch (DrugSearchException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemblParser.setWebPageDownloader(downloader);
+ chemblParser.setCache(cache);
+ }
+ }
+
+ @Test
+ public void testParseSynonymsNode() throws Exception {
+ try {
+ Node node = super.getNodeFromXmlString(
+ "<molecule_synonyms><synonym><synonyms>some synonym</synonyms></synonym><unknode/></molecule_synonyms>");
+ List<String> synonyms = chemblParser.parseSynonymsNode(node);
+ assertEquals(1, synonyms.size());
+ assertEquals(1, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetTargetsForChildElementsWhenChemblCrash() throws Exception {
+ WebPageDownloader downloader = chemblParser.getWebPageDownloader();
+ try {
+ chemblParser.setCache(null);
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ chemblParser.setWebPageDownloader(mockDownloader);
+ chemblParser.getTargetsForChildElements(new MiriamData());
+ fail("Exception expected");
+ } catch (DrugSearchException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemblParser.setWebPageDownloader(downloader);
+ chemblParser.setCache(cache);
+ }
+ }
+
+ @Test
+ public void testGetTargetsForChildElementsWhenChemblCrash2() throws Exception {
+ WebPageDownloader downloader = chemblParser.getWebPageDownloader();
+ try {
+ chemblParser.setCache(null);
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("invalid xml");
+ chemblParser.setWebPageDownloader(mockDownloader);
+ chemblParser.getTargetsForChildElements(new MiriamData());
+ fail("Exception expected");
+ } catch (DrugSearchException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemblParser.setWebPageDownloader(downloader);
+ chemblParser.setCache(cache);
+ }
+ }
+
+ @Test
+ public void testGetTargetsForChildElementsWhenChemblReturnPartlyInvalidResult() throws Exception {
+ WebPageDownloader downloader = chemblParser.getWebPageDownloader();
+ try {
+ chemblParser.setCache(null);
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString()))
+ .thenReturn("<response><molecule_forms><node/></molecule_forms></response>");
+ chemblParser.setWebPageDownloader(mockDownloader);
+ chemblParser.getTargetsForChildElements(new MiriamData());
+ assertEquals(1, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemblParser.setWebPageDownloader(downloader);
+ chemblParser.setCache(cache);
+ }
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalParserTest.java
index d1ddba22fc..cc8a82cc07 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalParserTest.java
@@ -1,665 +1,665 @@
-package lcsb.mapviewer.annotation.services;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-import static org.mockito.Matchers.any;
-import static org.mockito.Matchers.anyString;
-import static org.mockito.Mockito.when;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.commons.lang3.math.NumberUtils;
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.annotation.AnnotationTestFunctions;
-import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.GeneralCacheWithExclusion;
-import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
-import lcsb.mapviewer.annotation.cache.WebPageDownloader;
-import lcsb.mapviewer.annotation.data.Chemical;
-import lcsb.mapviewer.annotation.data.ChemicalDirectEvidence;
-import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
-import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.model.Model;
-
-public class ChemicalParserTest extends AnnotationTestFunctions {
- Logger logger = Logger.getLogger(ChemicalParserTest.class);
-
- final MiriamData parkinsonDiseaseId = new MiriamData(MiriamType.MESH_2012, "D010300");
-
- @Autowired
- private ChemicalParser chemicalParser;
-
- @Autowired
- private GeneralCacheInterface cache;
-
- @Before
- public void setUp() throws Exception {
- chemicalParser.setCache(new GeneralCacheWithExclusion(cache, 1));
- }
-
- @After
- public void tearDown() throws Exception {
- chemicalParser.setCache(cache);
- }
-
- @Test
- public void testCreateChemicalListFromDB() throws Exception {
- GeneralCacheInterface cache = chemicalParser.getCache();
- try {
- // skip first call to cache, so we will have to at least parse the data
- chemicalParser.setCache(new GeneralCacheWithExclusion(cache, 1));
- // Parkinson disease
- Map<MiriamData, String> result = chemicalParser.getChemicalsForDisease(parkinsonDiseaseId);
- assertNotNull(result);
- assertTrue(!result.isEmpty());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemicalParser.setCache(cache);
- }
- }
-
- @Test
- public void testGetChemicalListWhenProblemWithConnection() throws Exception {
- GeneralCacheInterface cache = chemicalParser.getCache();
- WebPageDownloader downloader = chemicalParser.getWebPageDownloader();
- try {
- // skip first call to cache, so we will have to at least parse the data
- chemicalParser.setCache(null);
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- chemicalParser.setWebPageDownloader(mockDownloader);
- // Parkinson disease
- chemicalParser.getChemicalsForDisease(parkinsonDiseaseId);
- } catch (ChemicalSearchException e) {
- assertTrue(e.getMessage().contains("ctdbase service unavailable"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemicalParser.setCache(cache);
- chemicalParser.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testGetChemicalListForInvalidDiseaseId() throws Exception {
- try {
- chemicalParser.getChemicalsForDisease(null);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("disease cannot be null"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateChemicalListFromDBWithInvalidId() throws Exception {
- try {
- // Parkinson disease
- MiriamData diseaseID = new MiriamData(MiriamType.MESH_2012, "D01030012");
- Map<MiriamData, String> result = chemicalParser.getChemicalsForDisease(diseaseID);
- assertNotNull(result);
- assertTrue(result.isEmpty());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindByIDFromChemicalList() throws Exception {
- try {
- // Parkinson disease
- Map<MiriamData, String> listFromDB = chemicalParser.getChemicalsForDisease(parkinsonDiseaseId);
- assertNotNull(listFromDB);
- assertTrue(!listFromDB.isEmpty());
- Map.Entry<MiriamData, String> entry = listFromDB.entrySet().iterator().next();
- assertNotNull(entry);
- // Get the first entry
- String chemicalName1 = entry.getValue();
- assertTrue((chemicalName1 != null) && !chemicalName1.trim().isEmpty());
- chemicalName1 = chemicalName1.trim().toLowerCase();
- MiriamData chemicalId1 = entry.getKey();
- assertTrue(
- (chemicalId1 != null) && (chemicalId1.getResource() != null) && !chemicalId1.getResource().trim().isEmpty());
- // Dopamine with 23 Gens and 60 publication and one marker/mechanism and
- // 60 publications
- MiriamData chemicalId2 = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "D019803");
- // lazabemide with one Gene MAOB and therapeutic and 3 publications
- MiriamData chemicalId3 = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "C059303");
- // caramiphen with no genes and one therapeutic
- MiriamData chemicalId4 = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "C004519");
-
- List<MiriamData> idsList = new ArrayList<MiriamData>();
- idsList.add(chemicalId1);
- idsList.add(chemicalId2);
- idsList.add(chemicalId3);
- idsList.add(chemicalId4);
-
- List<Chemical> chemcials = chemicalParser.getChemicals(parkinsonDiseaseId, idsList);
- for (Chemical chem : chemcials) {
- assertNotNull(chem);
- for (Target t : chem.getInferenceNetwork()) {
- for (MiriamData md : t.getReferences()) {
- assertEquals(MiriamType.PUBMED, md.getDataType());
- assertTrue(NumberUtils.isDigits(md.getResource()));
- }
- }
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetGlutathioneDisulfideData() throws Exception {
- try {
- MiriamData glutathioneDisulfideId = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "D019803");
-
- List<MiriamData> idsList = new ArrayList<>();
- idsList.add(glutathioneDisulfideId);
- List<Chemical> chemicals = chemicalParser.getChemicals(parkinsonDiseaseId, idsList);
-
- assertEquals(1, chemicals.size());
- Chemical glutathioneDisulfide = chemicals.get(0);
-
- assertTrue(glutathioneDisulfide.getSynonyms().size() > 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetChemicalBySynonym() throws Exception {
- try {
- List<Chemical> chemicals = chemicalParser.getChemicalsBySynonym(parkinsonDiseaseId, "MPTP");
-
- assertEquals(1, chemicals.size());
- Chemical mptp = chemicals.get(0);
-
- assertTrue(mptp.getSynonyms().contains("MPTP"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testFindByInvalidIdFromChemicalList() throws Exception {
-
- try {
- // Parkinson disease
- MiriamData chemicalId2 = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "D0198012433");
-
- List<MiriamData> idsList = new ArrayList<MiriamData>();
- idsList.add(chemicalId2);
-
- List<Chemical> chemcials = chemicalParser.getChemicals(parkinsonDiseaseId, idsList);
-
- assertTrue(chemcials.isEmpty());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testFindByInvalidDiseaseIdFromChemicalList() throws Exception {
- try {
- chemicalParser.getChemicals(null, new ArrayList<>());
- fail("Exceptione expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("disease cannot be null"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test(timeout = 30000)
- public void testCachableInterfaceInvalidateChemical() throws Exception {
- try {
-
- Map<MiriamData, String> listFromDB = chemicalParser.getChemicalsForDisease(parkinsonDiseaseId);
- assertNotNull(listFromDB);
- assertTrue(!listFromDB.isEmpty());
- MiriamData chemicalId = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "D015039");
- List<MiriamData> idsList = new ArrayList<MiriamData>();
- idsList.add(chemicalId);
- List<Chemical> chemcials = chemicalParser.getChemicals(parkinsonDiseaseId, idsList);
- assertNotNull(chemcials);
- assertTrue(chemcials.size() > 0);
-
- waitForRefreshCacheQueueToEmpty();
-
- cache.invalidateByQuery(chemicalParser.getIdentifier(parkinsonDiseaseId, chemcials.get(0).getChemicalId()),
- chemicalParser.getCacheType());
-
- waitForRefreshCacheQueueToEmpty();
-
- idsList.clear();
-
- idsList.add(chemcials.get(0).getChemicalId());
-
- List<Chemical> chemcials2 = chemicalParser.getChemicals(parkinsonDiseaseId, idsList);
- assertNotNull(chemcials2);
- assertTrue(chemcials2.size() > 0);
-
- assertFalse("Value wasn't refreshed from db", chemcials.get(0).equals(chemcials2.get(0)));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetByTarget() throws Exception {
- try {
- MiriamData target = new MiriamData(MiriamType.HGNC_SYMBOL, "TNF");
- List<MiriamData> targets = new ArrayList<>();
- targets.add(target);
- List<Chemical> list = chemicalParser.getChemicalListByTarget(targets, parkinsonDiseaseId);
- assertNotNull(list);
- assertFalse(list.isEmpty());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetByInvalidTarget() throws Exception {
- try {
- MiriamData target = new MiriamData(MiriamType.WIKIPEDIA, "TNF");
- List<MiriamData> targets = new ArrayList<>();
- targets.add(target);
- chemicalParser.getChemicalListByTarget(targets, parkinsonDiseaseId);
- fail("Exception expected");
-
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetByUnknownHgnc() throws Exception {
- try {
- // Parkinson disease
- MiriamData target = new MiriamData(MiriamType.HGNC_SYMBOL, "UNK_HGNC");
- chemicalParser.getChemicalListByTarget(target, parkinsonDiseaseId);
- // we have one warning regarding unknown hgnc symbol (we shouldn't throw
- // exception here bcuase these symbols sometimes are some
- // generic gene names)
- assertEquals(1, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetByTargetWhenProblemWithHgncConnection() throws Exception {
- HgncAnnotator annotator = chemicalParser.getHgncAnnotator();
- try {
- HgncAnnotator mockAnnotator = Mockito.mock(HgncAnnotator.class);
- when(mockAnnotator.hgncToEntrez(any())).thenThrow(new AnnotatorException(""));
- chemicalParser.setHgncAnnotator(mockAnnotator);
- // Parkinson disease
- MiriamData target = new MiriamData(MiriamType.HGNC_SYMBOL, "UNK_HGNC");
- List<MiriamData> targets = new ArrayList<>();
- targets.add(target);
- chemicalParser.getChemicalListByTarget(targets, parkinsonDiseaseId);
- fail("Exception expected");
- } catch (ChemicalSearchException e) {
- assertTrue(e.getMessage().contains("Problem with accessing hgnc service"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemicalParser.setHgncAnnotator(annotator);
- }
- }
-
- @Test
- public void testGetByEntrezTarget() throws Exception {
- try {
- // Parkinson disease
- MiriamData target = new MiriamData(MiriamType.ENTREZ, "6647");
- List<MiriamData> targets = new ArrayList<>();
- targets.add(target);
- List<Chemical> list = chemicalParser.getChemicalListByTarget(targets, parkinsonDiseaseId);
- assertTrue(list.size() > 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetByTarget2() throws Exception {
- try {
- // Parkinson disease
- MiriamData target = new MiriamData(MiriamType.HGNC_SYMBOL, "GALM");
- List<MiriamData> targets = new ArrayList<>();
- targets.add(target);
- List<Chemical> list = chemicalParser.getChemicalListByTarget(targets, parkinsonDiseaseId);
- assertNotNull(list);
- assertTrue(list.isEmpty());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshQuery() throws Exception {
- try {
- Object object = chemicalParser.refreshCacheQuery(ChemicalParser.DISEASE_CHEMICALS_PREFIX + "D010300");
- assertNotNull(object);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshQuery2() throws Exception {
- try {
- Object object = chemicalParser.refreshCacheQuery("https://www.google.pl/");
- assertNotNull(object);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetByTargetXXX() throws Exception {
- try {
- // Parkinson disease
- MiriamData target = new MiriamData(MiriamType.HGNC_SYMBOL, "SOD1");
- List<MiriamData> targets = new ArrayList<>();
- targets.add(target);
- List<Chemical> list = chemicalParser.getChemicalListByTarget(targets, parkinsonDiseaseId);
- assertNotNull(list);
- assertTrue(!list.isEmpty());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery() throws Exception {
- try {
- chemicalParser.refreshCacheQuery("invalid_query");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery2() throws Exception {
- try {
- chemicalParser.refreshCacheQuery(new Object());
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshCacheQueryWhenCtdDbNotAvailable() throws Exception {
- MiriamData chemicalId = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "D015039");
-
- String query = chemicalParser.getIdentifier(parkinsonDiseaseId, chemicalId);
-
- WebPageDownloader downloader = chemicalParser.getWebPageDownloader();
- GeneralCacheInterface cache = chemicalParser.getCache();
- try {
- // disable cache
- chemicalParser.setCache(null);
-
- // simulate problem with downloading
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("");
- chemicalParser.setWebPageDownloader(mockDownloader);
- chemicalParser.refreshCacheQuery(query);
- fail("Exception expected");
- } catch (SourceNotAvailable e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemicalParser.setWebPageDownloader(downloader);
- chemicalParser.setCache(cache);
- }
- }
-
- @Test
- public void testStatus() throws Exception {
- try {
- assertEquals(ExternalServiceStatusType.OK, chemicalParser.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSimulateDownStatus() throws Exception {
- WebPageDownloader downloader = chemicalParser.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- chemicalParser.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.DOWN, chemicalParser.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemicalParser.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testSimulateChangedStatus() throws Exception {
- WebPageDownloader downloader = chemicalParser.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("");
- chemicalParser.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.CHANGED, chemicalParser.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemicalParser.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testGetChemicalFromChemicalLineWithInvalidHgnc() throws Exception {
- try {
- String line[] = new String[ChemicalParser.CHEMICALS_COUNT_COL + 1];
- for (int i = 0; i < line.length; i++) {
- line[i] = "";
- }
- line[ChemicalParser.CHEMICALS_DIRECT_COL] = ChemicalDirectEvidence.THERAPEUTIC.getValue();
- line[ChemicalParser.CHEMICALS_NETWORK_COL] = "UNK_HGNC";
- Chemical result = chemicalParser.getChemicalFromChemicalLine(line,
- new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "D015039000"));
- // we have two errors related to parsing inference score and reference
- // count
- assertEquals(2, getErrors().size());
- // there are no genes (we have one that is invalid and should be
- // discarderd)
- assertEquals(0, result.getInferenceNetwork().size());
-
- assertEquals(ChemicalDirectEvidence.THERAPEUTIC, result.getDirectEvidence());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetChemicalFromChemicalLineWithHgncConnectionProblem() throws Exception {
- HgncAnnotator hgncAnnotator = chemicalParser.getHgncAnnotator();
- try {
- String line[] = new String[ChemicalParser.CHEMICALS_COUNT_COL + 1];
- for (int i = 0; i < line.length; i++) {
- line[i] = "";
- }
- line[ChemicalParser.CHEMICALS_DIRECT_COL] = ChemicalDirectEvidence.THERAPEUTIC.getValue();
- line[ChemicalParser.CHEMICALS_NETWORK_COL] = "UNK_HGNC";
- HgncAnnotator mockAnnotator = Mockito.mock(HgncAnnotator.class);
- when(mockAnnotator.hgncToEntrez(any())).thenThrow(new AnnotatorException(""));
- chemicalParser.setHgncAnnotator(mockAnnotator);
- chemicalParser.getChemicalFromChemicalLine(line, new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "D015039000"));
- fail("Exception expected");
- } catch (ChemicalSearchException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemicalParser.setHgncAnnotator(hgncAnnotator);
- }
- }
-
- @Test
- public void testProblemWithPubmeds() throws Exception {
-
- GeneralCacheInterface cache = chemicalParser.getCache();
- WebPageDownloader downloader = chemicalParser.getWebPageDownloader();
- try {
- // Parkinson disease
- MiriamData chemicalID = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "D015039");
-
- List<MiriamData> idsList = new ArrayList<MiriamData>();
- idsList.add(chemicalID);
-
- // remove info about single publication from cache (so we will have to download
- // it)
- chemicalParser.getCache().removeByQuery(
- "https://ctdbase.org/detail.go?6578706f7274=1&d-1340579-e=5&type=relationship&ixnId=4802115",
- chemicalParser.getCacheType());
-
- // disallow to use cache for first query (it will be directly about drug),
- // so parser will have to parse results taking data from cache (or
- // web sites if needed)
- chemicalParser.setCache(new GeneralCacheWithExclusion(chemicalParser.getCache(), 1));
-
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- chemicalParser.setWebPageDownloader(mockDownloader);
- try {
- chemicalParser.getChemicals(parkinsonDiseaseId, idsList);
- fail("Exception expected");
- } catch (ChemicalSearchException e) {
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- chemicalParser.setCache(cache);
- chemicalParser.setWebPageDownloader(downloader);
- }
-
- }
-
- @Test
- public void testGetEmptySuggestedQueryList() throws Exception {
- try {
- Project project = new Project();
- project.setId(-1);
-
- List<String> result = chemicalParser.getSuggestedQueryList(project, parkinsonDiseaseId);
-
- assertEquals(0, result.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetSuggestedQueryList() throws Exception {
- try {
- Project project = new Project();
- Model model = getModelForFile("testFiles/target_chemical/target.xml", false);
- project.addModel(model);
-
- List<String> result = chemicalParser.getSuggestedQueryList(project, parkinsonDiseaseId);
-
- assertTrue(result.size() > 0);
- logger.debug(result);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetSuggestedQueryListForUnknownDiseas() throws Exception {
- try {
- Project project = new Project();
- Model model = getModelForFile("testFiles/target_chemical/target.xml", false);
- project.addModel(model);
-
- List<String> result = chemicalParser.getSuggestedQueryList(project, null);
-
- assertEquals(0, result.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
-}
+package lcsb.mapviewer.annotation.services;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import static org.mockito.Matchers.any;
+import static org.mockito.Matchers.anyString;
+import static org.mockito.Mockito.when;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.commons.lang3.math.NumberUtils;
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.AnnotationTestFunctions;
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.GeneralCacheWithExclusion;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.WebPageDownloader;
+import lcsb.mapviewer.annotation.data.Chemical;
+import lcsb.mapviewer.annotation.data.ChemicalDirectEvidence;
+import lcsb.mapviewer.annotation.data.Target;
+import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
+import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.model.Model;
+
+public class ChemicalParserTest extends AnnotationTestFunctions {
+ Logger logger = Logger.getLogger(ChemicalParserTest.class);
+
+ final MiriamData parkinsonDiseaseId = new MiriamData(MiriamType.MESH_2012, "D010300");
+
+ @Autowired
+ private ChemicalParser chemicalParser;
+
+ @Autowired
+ private GeneralCacheInterface cache;
+
+ @Before
+ public void setUp() throws Exception {
+ chemicalParser.setCache(new GeneralCacheWithExclusion(cache, 1));
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ chemicalParser.setCache(cache);
+ }
+
+ @Test
+ public void testCreateChemicalListFromDB() throws Exception {
+ GeneralCacheInterface cache = chemicalParser.getCache();
+ try {
+ // skip first call to cache, so we will have to at least parse the data
+ chemicalParser.setCache(new GeneralCacheWithExclusion(cache, 1));
+ // Parkinson disease
+ Map<MiriamData, String> result = chemicalParser.getChemicalsForDisease(parkinsonDiseaseId);
+ assertNotNull(result);
+ assertTrue(!result.isEmpty());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemicalParser.setCache(cache);
+ }
+ }
+
+ @Test
+ public void testGetChemicalListWhenProblemWithConnection() throws Exception {
+ GeneralCacheInterface cache = chemicalParser.getCache();
+ WebPageDownloader downloader = chemicalParser.getWebPageDownloader();
+ try {
+ // skip first call to cache, so we will have to at least parse the data
+ chemicalParser.setCache(null);
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ chemicalParser.setWebPageDownloader(mockDownloader);
+ // Parkinson disease
+ chemicalParser.getChemicalsForDisease(parkinsonDiseaseId);
+ } catch (ChemicalSearchException e) {
+ assertTrue(e.getMessage().contains("ctdbase service unavailable"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemicalParser.setCache(cache);
+ chemicalParser.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testGetChemicalListForInvalidDiseaseId() throws Exception {
+ try {
+ chemicalParser.getChemicalsForDisease(null);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("disease cannot be null"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCreateChemicalListFromDBWithInvalidId() throws Exception {
+ try {
+ // Parkinson disease
+ MiriamData diseaseID = new MiriamData(MiriamType.MESH_2012, "D01030012");
+ Map<MiriamData, String> result = chemicalParser.getChemicalsForDisease(diseaseID);
+ assertNotNull(result);
+ assertTrue(result.isEmpty());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindByIDFromChemicalList() throws Exception {
+ try {
+ // Parkinson disease
+ Map<MiriamData, String> listFromDB = chemicalParser.getChemicalsForDisease(parkinsonDiseaseId);
+ assertNotNull(listFromDB);
+ assertTrue(!listFromDB.isEmpty());
+ Map.Entry<MiriamData, String> entry = listFromDB.entrySet().iterator().next();
+ assertNotNull(entry);
+ // Get the first entry
+ String chemicalName1 = entry.getValue();
+ assertTrue((chemicalName1 != null) && !chemicalName1.trim().isEmpty());
+ chemicalName1 = chemicalName1.trim().toLowerCase();
+ MiriamData chemicalId1 = entry.getKey();
+ assertTrue(
+ (chemicalId1 != null) && (chemicalId1.getResource() != null) && !chemicalId1.getResource().trim().isEmpty());
+ // Dopamine with 23 Gens and 60 publication and one marker/mechanism and
+ // 60 publications
+ MiriamData chemicalId2 = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "D019803");
+ // lazabemide with one Gene MAOB and therapeutic and 3 publications
+ MiriamData chemicalId3 = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "C059303");
+ // caramiphen with no genes and one therapeutic
+ MiriamData chemicalId4 = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "C004519");
+
+ List<MiriamData> idsList = new ArrayList<MiriamData>();
+ idsList.add(chemicalId1);
+ idsList.add(chemicalId2);
+ idsList.add(chemicalId3);
+ idsList.add(chemicalId4);
+
+ List<Chemical> chemcials = chemicalParser.getChemicals(parkinsonDiseaseId, idsList);
+ for (Chemical chem : chemcials) {
+ assertNotNull(chem);
+ for (Target t : chem.getInferenceNetwork()) {
+ for (MiriamData md : t.getReferences()) {
+ assertEquals(MiriamType.PUBMED, md.getDataType());
+ assertTrue(NumberUtils.isDigits(md.getResource()));
+ }
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetGlutathioneDisulfideData() throws Exception {
+ try {
+ MiriamData glutathioneDisulfideId = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "D019803");
+
+ List<MiriamData> idsList = new ArrayList<>();
+ idsList.add(glutathioneDisulfideId);
+ List<Chemical> chemicals = chemicalParser.getChemicals(parkinsonDiseaseId, idsList);
+
+ assertEquals(1, chemicals.size());
+ Chemical glutathioneDisulfide = chemicals.get(0);
+
+ assertTrue(glutathioneDisulfide.getSynonyms().size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetChemicalBySynonym() throws Exception {
+ try {
+ List<Chemical> chemicals = chemicalParser.getChemicalsBySynonym(parkinsonDiseaseId, "MPTP");
+
+ assertEquals(1, chemicals.size());
+ Chemical mptp = chemicals.get(0);
+
+ assertTrue(mptp.getSynonyms().contains("MPTP"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testFindByInvalidIdFromChemicalList() throws Exception {
+
+ try {
+ // Parkinson disease
+ MiriamData chemicalId2 = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "D0198012433");
+
+ List<MiriamData> idsList = new ArrayList<MiriamData>();
+ idsList.add(chemicalId2);
+
+ List<Chemical> chemcials = chemicalParser.getChemicals(parkinsonDiseaseId, idsList);
+
+ assertTrue(chemcials.isEmpty());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testFindByInvalidDiseaseIdFromChemicalList() throws Exception {
+ try {
+ chemicalParser.getChemicals(null, new ArrayList<>());
+ fail("Exceptione expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("disease cannot be null"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test(timeout = 30000)
+ public void testCachableInterfaceInvalidateChemical() throws Exception {
+ try {
+
+ Map<MiriamData, String> listFromDB = chemicalParser.getChemicalsForDisease(parkinsonDiseaseId);
+ assertNotNull(listFromDB);
+ assertTrue(!listFromDB.isEmpty());
+ MiriamData chemicalId = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "D015039");
+ List<MiriamData> idsList = new ArrayList<MiriamData>();
+ idsList.add(chemicalId);
+ List<Chemical> chemcials = chemicalParser.getChemicals(parkinsonDiseaseId, idsList);
+ assertNotNull(chemcials);
+ assertTrue(chemcials.size() > 0);
+
+ waitForRefreshCacheQueueToEmpty();
+
+ cache.invalidateByQuery(chemicalParser.getIdentifier(parkinsonDiseaseId, chemcials.get(0).getChemicalId()),
+ chemicalParser.getCacheType());
+
+ waitForRefreshCacheQueueToEmpty();
+
+ idsList.clear();
+
+ idsList.add(chemcials.get(0).getChemicalId());
+
+ List<Chemical> chemcials2 = chemicalParser.getChemicals(parkinsonDiseaseId, idsList);
+ assertNotNull(chemcials2);
+ assertTrue(chemcials2.size() > 0);
+
+ assertFalse("Value wasn't refreshed from db", chemcials.get(0).equals(chemcials2.get(0)));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetByTarget() throws Exception {
+ try {
+ MiriamData target = new MiriamData(MiriamType.HGNC_SYMBOL, "TNF");
+ List<MiriamData> targets = new ArrayList<>();
+ targets.add(target);
+ List<Chemical> list = chemicalParser.getChemicalListByTarget(targets, parkinsonDiseaseId);
+ assertNotNull(list);
+ assertFalse(list.isEmpty());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetByInvalidTarget() throws Exception {
+ try {
+ MiriamData target = new MiriamData(MiriamType.WIKIPEDIA, "TNF");
+ List<MiriamData> targets = new ArrayList<>();
+ targets.add(target);
+ chemicalParser.getChemicalListByTarget(targets, parkinsonDiseaseId);
+ fail("Exception expected");
+
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetByUnknownHgnc() throws Exception {
+ try {
+ // Parkinson disease
+ MiriamData target = new MiriamData(MiriamType.HGNC_SYMBOL, "UNK_HGNC");
+ chemicalParser.getChemicalListByTarget(target, parkinsonDiseaseId);
+ // we have one warning regarding unknown hgnc symbol (we shouldn't throw
+ // exception here bcuase these symbols sometimes are some
+ // generic gene names)
+ assertEquals(1, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetByTargetWhenProblemWithHgncConnection() throws Exception {
+ HgncAnnotator annotator = chemicalParser.getHgncAnnotator();
+ try {
+ HgncAnnotator mockAnnotator = Mockito.mock(HgncAnnotator.class);
+ when(mockAnnotator.hgncToEntrez(any())).thenThrow(new AnnotatorException(""));
+ chemicalParser.setHgncAnnotator(mockAnnotator);
+ // Parkinson disease
+ MiriamData target = new MiriamData(MiriamType.HGNC_SYMBOL, "UNK_HGNC");
+ List<MiriamData> targets = new ArrayList<>();
+ targets.add(target);
+ chemicalParser.getChemicalListByTarget(targets, parkinsonDiseaseId);
+ fail("Exception expected");
+ } catch (ChemicalSearchException e) {
+ assertTrue(e.getMessage().contains("Problem with accessing hgnc service"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemicalParser.setHgncAnnotator(annotator);
+ }
+ }
+
+ @Test
+ public void testGetByEntrezTarget() throws Exception {
+ try {
+ // Parkinson disease
+ MiriamData target = new MiriamData(MiriamType.ENTREZ, "6647");
+ List<MiriamData> targets = new ArrayList<>();
+ targets.add(target);
+ List<Chemical> list = chemicalParser.getChemicalListByTarget(targets, parkinsonDiseaseId);
+ assertTrue(list.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetByTarget2() throws Exception {
+ try {
+ // Parkinson disease
+ MiriamData target = new MiriamData(MiriamType.HGNC_SYMBOL, "GALM");
+ List<MiriamData> targets = new ArrayList<>();
+ targets.add(target);
+ List<Chemical> list = chemicalParser.getChemicalListByTarget(targets, parkinsonDiseaseId);
+ assertNotNull(list);
+ assertTrue(list.isEmpty());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshQuery() throws Exception {
+ try {
+ Object object = chemicalParser.refreshCacheQuery(ChemicalParser.DISEASE_CHEMICALS_PREFIX + "D010300");
+ assertNotNull(object);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshQuery2() throws Exception {
+ try {
+ Object object = chemicalParser.refreshCacheQuery("https://www.google.pl/");
+ assertNotNull(object);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetByTargetXXX() throws Exception {
+ try {
+ // Parkinson disease
+ MiriamData target = new MiriamData(MiriamType.HGNC_SYMBOL, "SOD1");
+ List<MiriamData> targets = new ArrayList<>();
+ targets.add(target);
+ List<Chemical> list = chemicalParser.getChemicalListByTarget(targets, parkinsonDiseaseId);
+ assertNotNull(list);
+ assertTrue(!list.isEmpty());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery() throws Exception {
+ try {
+ chemicalParser.refreshCacheQuery("invalid_query");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery2() throws Exception {
+ try {
+ chemicalParser.refreshCacheQuery(new Object());
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQueryWhenCtdDbNotAvailable() throws Exception {
+ MiriamData chemicalId = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "D015039");
+
+ String query = chemicalParser.getIdentifier(parkinsonDiseaseId, chemicalId);
+
+ WebPageDownloader downloader = chemicalParser.getWebPageDownloader();
+ GeneralCacheInterface cache = chemicalParser.getCache();
+ try {
+ // disable cache
+ chemicalParser.setCache(null);
+
+ // simulate problem with downloading
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("");
+ chemicalParser.setWebPageDownloader(mockDownloader);
+ chemicalParser.refreshCacheQuery(query);
+ fail("Exception expected");
+ } catch (SourceNotAvailable e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemicalParser.setWebPageDownloader(downloader);
+ chemicalParser.setCache(cache);
+ }
+ }
+
+ @Test
+ public void testStatus() throws Exception {
+ try {
+ assertEquals(ExternalServiceStatusType.OK, chemicalParser.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSimulateDownStatus() throws Exception {
+ WebPageDownloader downloader = chemicalParser.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ chemicalParser.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.DOWN, chemicalParser.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemicalParser.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testSimulateChangedStatus() throws Exception {
+ WebPageDownloader downloader = chemicalParser.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("");
+ chemicalParser.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.CHANGED, chemicalParser.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemicalParser.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testGetChemicalFromChemicalLineWithInvalidHgnc() throws Exception {
+ try {
+ String line[] = new String[ChemicalParser.CHEMICALS_COUNT_COL + 1];
+ for (int i = 0; i < line.length; i++) {
+ line[i] = "";
+ }
+ line[ChemicalParser.CHEMICALS_DIRECT_COL] = ChemicalDirectEvidence.THERAPEUTIC.getValue();
+ line[ChemicalParser.CHEMICALS_NETWORK_COL] = "UNK_HGNC";
+ Chemical result = chemicalParser.getChemicalFromChemicalLine(line,
+ new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "D015039000"));
+ // we have two errors related to parsing inference score and reference
+ // count
+ assertEquals(2, getErrors().size());
+ // there are no genes (we have one that is invalid and should be
+ // discarderd)
+ assertEquals(0, result.getInferenceNetwork().size());
+
+ assertEquals(ChemicalDirectEvidence.THERAPEUTIC, result.getDirectEvidence());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetChemicalFromChemicalLineWithHgncConnectionProblem() throws Exception {
+ HgncAnnotator hgncAnnotator = chemicalParser.getHgncAnnotator();
+ try {
+ String line[] = new String[ChemicalParser.CHEMICALS_COUNT_COL + 1];
+ for (int i = 0; i < line.length; i++) {
+ line[i] = "";
+ }
+ line[ChemicalParser.CHEMICALS_DIRECT_COL] = ChemicalDirectEvidence.THERAPEUTIC.getValue();
+ line[ChemicalParser.CHEMICALS_NETWORK_COL] = "UNK_HGNC";
+ HgncAnnotator mockAnnotator = Mockito.mock(HgncAnnotator.class);
+ when(mockAnnotator.hgncToEntrez(any())).thenThrow(new AnnotatorException(""));
+ chemicalParser.setHgncAnnotator(mockAnnotator);
+ chemicalParser.getChemicalFromChemicalLine(line, new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "D015039000"));
+ fail("Exception expected");
+ } catch (ChemicalSearchException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemicalParser.setHgncAnnotator(hgncAnnotator);
+ }
+ }
+
+ @Test
+ public void testProblemWithPubmeds() throws Exception {
+
+ GeneralCacheInterface cache = chemicalParser.getCache();
+ WebPageDownloader downloader = chemicalParser.getWebPageDownloader();
+ try {
+ // Parkinson disease
+ MiriamData chemicalID = new MiriamData(MiriamType.TOXICOGENOMIC_CHEMICAL, "D015039");
+
+ List<MiriamData> idsList = new ArrayList<MiriamData>();
+ idsList.add(chemicalID);
+
+ // remove info about single publication from cache (so we will have to download
+ // it)
+ chemicalParser.getCache().removeByQuery(
+ "https://ctdbase.org/detail.go?6578706f7274=1&d-1340579-e=5&type=relationship&ixnId=4802115",
+ chemicalParser.getCacheType());
+
+ // disallow to use cache for first query (it will be directly about drug),
+ // so parser will have to parse results taking data from cache (or
+ // web sites if needed)
+ chemicalParser.setCache(new GeneralCacheWithExclusion(chemicalParser.getCache(), 1));
+
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ chemicalParser.setWebPageDownloader(mockDownloader);
+ try {
+ chemicalParser.getChemicals(parkinsonDiseaseId, idsList);
+ fail("Exception expected");
+ } catch (ChemicalSearchException e) {
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ chemicalParser.setCache(cache);
+ chemicalParser.setWebPageDownloader(downloader);
+ }
+
+ }
+
+ @Test
+ public void testGetEmptySuggestedQueryList() throws Exception {
+ try {
+ Project project = new Project();
+ project.setId(-1);
+
+ List<String> result = chemicalParser.getSuggestedQueryList(project, parkinsonDiseaseId);
+
+ assertEquals(0, result.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetSuggestedQueryList() throws Exception {
+ try {
+ Project project = new Project();
+ Model model = getModelForFile("testFiles/target_chemical/target.xml", false);
+ project.addModel(model);
+
+ List<String> result = chemicalParser.getSuggestedQueryList(project, parkinsonDiseaseId);
+
+ assertTrue(result.size() > 0);
+ logger.debug(result);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetSuggestedQueryListForUnknownDiseas() throws Exception {
+ try {
+ Project project = new Project();
+ Model model = getModelForFile("testFiles/target_chemical/target.xml", false);
+ project.addModel(model);
+
+ List<String> result = chemicalParser.getSuggestedQueryList(project, null);
+
+ assertEquals(0, result.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalSearchExceptionTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalSearchExceptionTest.java
index d96d0a8d0f..48e93bd829 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalSearchExceptionTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ChemicalSearchExceptionTest.java
@@ -1,30 +1,30 @@
-package lcsb.mapviewer.annotation.services;
-
-import static org.junit.Assert.*;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ChemicalSearchExceptionTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testConstructor() {
- ChemicalSearchException e = new ChemicalSearchException("msg");
- assertEquals("msg", e.getMessage());
- }
-
-}
+package lcsb.mapviewer.annotation.services;
+
+import static org.junit.Assert.*;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ChemicalSearchExceptionTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testConstructor() {
+ ChemicalSearchException e = new ChemicalSearchException("msg");
+ assertEquals("msg", e.getMessage());
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugAnnotationTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugAnnotationTest.java
index d2d8cb49d4..2ac8e9c9c7 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugAnnotationTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugAnnotationTest.java
@@ -1,65 +1,65 @@
-package lcsb.mapviewer.annotation.services;
-
-import static org.junit.Assert.assertEquals;
-
-import java.util.Collection;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.annotation.AnnotationTestFunctions;
-import lcsb.mapviewer.annotation.data.Drug;
-import lcsb.mapviewer.model.map.MiriamData;
-
-public class DrugAnnotationTest extends AnnotationTestFunctions {
- Logger logger = Logger.getLogger(DrugAnnotationTest.class);
-
- @Autowired
- private DrugbankHTMLParser drugBankHTMLParser;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testXmlSerialization() throws Exception {
- try {
- DrugAnnotation drugAnnotation = new DrugAnnotation(DrugAnnotation.class) {
- @Override
- public Drug findDrug(String name) {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public List<Drug> getDrugListByTarget(MiriamData target, Collection<MiriamData> organisms) {
- // TODO Auto-generated method stub
- return null;
- }
-
- };
- Drug drug = drugBankHTMLParser.findDrug("aspirin");
-
- String xml = drugAnnotation.getDrugSerializer().objectToString(drug);
-
- Drug drug2 = drugAnnotation.getDrugSerializer().xmlToObject(getNodeFromXmlString(xml));
-
- assertEquals(drug.getTargets().size(), drug2.getTargets().size());
- assertEquals(drug.getTargets().get(0).getGenes().size(), drug2.getTargets().get(0).getGenes().size());
- assertEquals(drug.getTargets().get(0).getReferences().size(), drug2.getTargets().get(0).getReferences().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.annotation.services;
+
+import static org.junit.Assert.assertEquals;
+
+import java.util.Collection;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.AnnotationTestFunctions;
+import lcsb.mapviewer.annotation.data.Drug;
+import lcsb.mapviewer.model.map.MiriamData;
+
+public class DrugAnnotationTest extends AnnotationTestFunctions {
+ Logger logger = Logger.getLogger(DrugAnnotationTest.class);
+
+ @Autowired
+ private DrugbankHTMLParser drugBankHTMLParser;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testXmlSerialization() throws Exception {
+ try {
+ DrugAnnotation drugAnnotation = new DrugAnnotation(DrugAnnotation.class) {
+ @Override
+ public Drug findDrug(String name) {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public List<Drug> getDrugListByTarget(MiriamData target, Collection<MiriamData> organisms) {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ };
+ Drug drug = drugBankHTMLParser.findDrug("aspirin");
+
+ String xml = drugAnnotation.getDrugSerializer().objectToString(drug);
+
+ Drug drug2 = drugAnnotation.getDrugSerializer().xmlToObject(getNodeFromXmlString(xml));
+
+ assertEquals(drug.getTargets().size(), drug2.getTargets().size());
+ assertEquals(drug.getTargets().get(0).getGenes().size(), drug2.getTargets().get(0).getGenes().size());
+ assertEquals(drug.getTargets().get(0).getReferences().size(), drug2.getTargets().get(0).getReferences().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java
index 3a2da6838a..017020c440 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParserTest.java
@@ -1,832 +1,832 @@
-package lcsb.mapviewer.annotation.services;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-import static org.mockito.Matchers.anyString;
-import static org.mockito.Mockito.when;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.annotation.AnnotationTestFunctions;
-import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.GeneralCacheWithExclusion;
-import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
-import lcsb.mapviewer.annotation.cache.WebPageDownloader;
-import lcsb.mapviewer.annotation.data.Drug;
-import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.model.Model;
-
-public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
- Logger logger = Logger.getLogger(DrugbankHTMLParserTest.class);
-
- @Autowired
- private DrugbankHTMLParser drugBankHTMLParser;
-
- @Autowired
- private GeneralCacheInterface cache;
-
- @Before
- public void setUp() throws Exception {
- drugBankHTMLParser.setCache(new GeneralCacheWithExclusion(cache, 1));
- }
-
- @After
- public void tearDown() throws Exception {
- drugBankHTMLParser.setCache(cache);
- }
-
- @Test
- public void test1FindDrug() throws Exception {
- try {
- Drug test = drugBankHTMLParser.findDrug("Urokinase");
- assertNotNull(test);
- assertEquals(MiriamType.DRUGBANK, test.getSources().get(0).getDataType());
- assertEquals("DB00013", test.getSources().get(0).getResource());
- assertEquals("Urokinase", test.getName());
- assertTrue(test.getBloodBrainBarrier().equalsIgnoreCase("N/A"));
- boolean res = test.getDescription().contains(
- "Low molecular weight form of human urokinase, that consists of an A chain of 2,000 daltons linked by a sulfhydryl bond to a B chain of 30,400 daltons. Recombinant urokinase plasminogen activator");
- assertTrue(res);
- assertEquals(10, test.getTargets().size());
- assertNull(test.getApproved());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void test2FindDrug() throws Exception {
- try {
- Drug test = drugBankHTMLParser.findDrug("diazoxide");
- assertNotNull(test);
- assertEquals("Diazoxide", test.getName());
- assertEquals("DB01119", test.getSources().get(0).getResource());
- assertTrue(test.getBloodBrainBarrier().equalsIgnoreCase("YES"));
- boolean res = test.getDescription().contains(
- "A benzothiadiazine derivative that is a peripheral vasodilator used for hypertensive emergencies. It lacks diuretic effect, apparently because it lacks a sulfonamide group. [PubChem]");
- assertTrue(res);
- assertEquals(6, test.getTargets().size());
- assertTrue(test.getApproved());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testFindRapamycin() throws Exception {
- try {
- // finding synonym
- Drug rapamycinDrug = drugBankHTMLParser.findDrug("Rapamycin");
- assertNotNull(rapamycinDrug);
- assertEquals("Sirolimus", rapamycinDrug.getName());
- assertEquals("DB00877", rapamycinDrug.getSources().get(0).getResource());
- assertTrue(rapamycinDrug.getBloodBrainBarrier().equalsIgnoreCase("NO"));
- boolean res = rapamycinDrug.getDescription().contains("A macrolide compound obtained from Streptomyces");
- assertTrue(res);
- assertEquals(3, rapamycinDrug.getTargets().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindAfegostat() throws Exception {
- try {
- // finding synonym
- Drug rapamycinDrug = drugBankHTMLParser.findDrug("Afegostat");
- assertNotNull(rapamycinDrug);
- assertFalse(rapamycinDrug.getApproved());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void test4FindDrug() throws Exception {
-
- try {
- Drug test = drugBankHTMLParser.findDrug("Methylamine");
- assertNotNull(test);
- assertEquals("Methylamine", test.getName());
- assertEquals("DB01828", test.getSources().get(0).getResource());
- assertEquals(null, test.getDescription());
- assertEquals(1, test.getTargets().size());
-
- List<Target> tmp;
- tmp = test.getTargets();
- for (Target a : tmp) {
- assertEquals("Ammonia channel", a.getName());
- assertEquals(2, a.getReferences().size());
- assertEquals(1, a.getGenes().size());
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void test5FindDrug() throws Exception {
- try {
- Drug amantadineDrug = drugBankHTMLParser.findDrug("Amantadine");
- assertNotNull(amantadineDrug);
- assertEquals("Amantadine", amantadineDrug.getName());
- assertEquals("DB00915", amantadineDrug.getSources().get(0).getResource());
- boolean res = amantadineDrug.getDescription().contains(
- "An antiviral that is used in the prophylactic or symptomatic treatment of influenza A. It is also used as an antiparkinsonian agent, to treat extrapyramidal reactions, and for postherpetic neuralgia. The mechanisms of its effects in movement disorders are not well understood but probably reflect an increase in synthesis and release of dopamine, with perhaps some inhibition of dopamine uptake. [PubChem]");
- assertTrue(res);
- assertEquals(3, amantadineDrug.getTargets().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void test6FindDrug() throws Exception {
- try {
- Drug test = drugBankHTMLParser.findDrug("qwertyuiop");
- assertEquals(null, test);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void test7FindDrug() throws Exception {
- try {
- Drug test = drugBankHTMLParser.findDrug("Aluminum hydroxide");
- assertNotNull(test);
- assertEquals("Aluminum hydroxide", test.getName());
- assertEquals("DB06723", test.getSources().get(0).getResource());
- assertTrue(test.getDescription().contains(
- "Aluminum hydroxide is an inorganic salt used as an antacid. It is a basic compound that acts by neutralizing hydrochloric acid in gastric secretions. Subsequent increases in pH may inhibit the action of pepsin. An increase in bicarbonate ions and prostaglandins may also confer cytoprotective effects."));
- assertEquals(0, test.getTargets().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindDrugAmantadineWithBrandNames() throws Exception {
- try {
- Drug drug = drugBankHTMLParser.findDrug("amantadine");
-
- assertNotNull(drug);
- assertTrue(drug.getBrandNames().contains("PK-Merz"));
- assertTrue(drug.getBrandNames().contains("Symadine"));
- assertTrue(drug.getBrandNames().contains("Symmetrel"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindDrugSelegiline() throws Exception {
- try {
- Drug test = drugBankHTMLParser.findDrug("Selegiline");
- assertNotNull(test);
- assertEquals(2, test.getTargets().size());
- for (String string : new String[] { "MAOA", "MAOB" }) {
- boolean contain = false;
- for (Target target : test.getTargets()) {
- for (MiriamData md : target.getGenes()) {
- if (md.getResource().equals(string)) {
- contain = true;
- }
- }
- }
- assertTrue("Missing traget: " + string, contain);
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindDrugDaidzinWithHtmlCharacters() throws Exception {
- try {
- Drug test = drugBankHTMLParser.findDrug("Daidzin");
- assertNotNull(test);
- for (String str : test.getSynonyms()) {
- assertFalse(str.contains("'"));
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindDrugGliclazideWithHtmlTags() throws Exception {
- try {
- Drug test = drugBankHTMLParser.findDrug("Gliclazide");
- assertNotNull(test);
- assertFalse(test.getDescription().contains("<span"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindDrugSevofluraneWithHtmlTags() throws Exception {
- try {
- Drug test = drugBankHTMLParser.findDrug("sevoflurane");
- assertNotNull(test);
- for (String str : test.getSynonyms()) {
- assertFalse(str.contains("<div"));
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindDrugByHgncTarget() throws Exception {
- try {
- List<Drug> drugs = drugBankHTMLParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "NFKB2"));
- assertNotNull(drugs);
- assertTrue("Only " + drugs.size() + " drugs were found, but at least 8 were expected", drugs.size() >= 8);
-
- drugBankHTMLParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "NFKB2"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindDrugByTFTarget() throws Exception {
- try {
- List<Drug> drugs = drugBankHTMLParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "TF"));
- assertNotNull(drugs);
- for (Drug drug : drugs) {
- assertFalse(drug.getName().equalsIgnoreCase("Iron saccharate"));
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindAluminiumByName() throws Exception {
- try {
- Drug drug = drugBankHTMLParser.findDrug("Aluminium");
- assertTrue(drug.getName().equalsIgnoreCase("Aluminium"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindBIIB054ByName() throws Exception {
- try {
- Drug drug = drugBankHTMLParser.findDrug("BIIB054");
- if (drug != null) {
- // check if are not pointint to BIIB021
- assertFalse(drug.getSources().get(0).getResource().equalsIgnoreCase("DB12359"));
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindDrugByHgncTargetAndFilteredOutByOrganism() throws Exception {
- try {
- List<MiriamData> organisms = new ArrayList<>();
- organisms.add(new MiriamData(MiriamType.TAXONOMY, "-1"));
- List<Drug> drugs = drugBankHTMLParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "NFKB2"),
- organisms);
- assertNotNull(drugs);
- assertEquals("No drugs for this organisms should be found", 0, drugs.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindDrugByHgncTargetAndFilteredByOrganism() throws Exception {
- try {
- List<MiriamData> organisms = new ArrayList<>();
- organisms.add(TaxonomyBackend.HUMAN_TAXONOMY);
- List<Drug> drugs = drugBankHTMLParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "NFKB2"),
- organisms);
- assertNotNull(drugs);
- assertTrue(drugs.size() > 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindDrugByInvalidTarget() throws Exception {
- try {
- drugBankHTMLParser.getDrugListByTarget(new MiriamData(MiriamType.WIKIPEDIA, "h2o"));
- fail("Exception");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("type is accepted"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindDrugByEmptyTarget() throws Exception {
- try {
- List<Drug> drugs = drugBankHTMLParser.getDrugListByTarget(null);
- assertEquals(0, drugs.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testWrongHgncTarget() throws Exception {
- try {
-
- List<Drug> drugs = drugBankHTMLParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "BECN1"));
- assertNotNull(drugs);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindDrugByHgncTargets() throws Exception {
- try {
- List<Drug> drug1 = drugBankHTMLParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "NFKB1"));
- List<Drug> drug2 = drugBankHTMLParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "NFKB2"));
- int size = drug1.size() + drug2.size();
-
- List<MiriamData> list = new ArrayList<MiriamData>();
- list.add(new MiriamData(MiriamType.HGNC_SYMBOL, "NFKB2"));
- list.add(new MiriamData(MiriamType.HGNC_SYMBOL, "NFKB1"));
-
- List<Drug> drugs = drugBankHTMLParser.getDrugListByTargets(list);
- assertNotNull(drugs);
- assertTrue("Merged list should be shorter then sum of the two lists", drugs.size() < size);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test(timeout = 15000)
- public void testCachableInterfaceInvalidateUrl() throws Exception {
- String query = "http://google.lu/";
- String newRes = "hello";
- try {
- waitForRefreshCacheQueueToEmpty();
-
- cache.setCachedQuery(query, drugBankHTMLParser.getCacheType(), newRes);
- cache.invalidateByQuery(query, drugBankHTMLParser.getCacheType());
-
- waitForRefreshCacheQueueToEmpty();
-
- String res = cache.getStringByQuery(query, drugBankHTMLParser.getCacheType());
-
- assertNotNull(res);
-
- assertFalse("Value wasn't refreshed from db", newRes.equals(res));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- // wait max 15 second
- @Test(timeout = 150000)
- public void testCachableInterfaceInvalidateDrug() throws Exception {
-
- String query = "drug:amantadine";
- String newRes = "hello";
- try {
- waitForRefreshCacheQueueToEmpty();
-
- cache.setCachedQuery(query, drugBankHTMLParser.getCacheType(), newRes);
- cache.invalidateByQuery(query, drugBankHTMLParser.getCacheType());
-
- waitForRefreshCacheQueueToEmpty();
-
- String res = cache.getStringByQuery(query, drugBankHTMLParser.getCacheType());
-
- assertNotNull(res);
-
- assertFalse("Value wasn't refreshed from db", newRes.equals(res));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testByTargetsForCCNB1() throws Exception {
- try {
- List<MiriamData> targets = new ArrayList<>();
- MiriamData miriamTarget = new MiriamData(MiriamType.HGNC_SYMBOL, "CCNB1");
- targets.add(miriamTarget);
- List<Drug> drugs = drugBankHTMLParser.getDrugListByTargets(targets);
- for (Drug drug : drugs) {
- boolean found = false;
- for (Target target : drug.getTargets()) {
- for (MiriamData md : target.getGenes()) {
- if (miriamTarget.equals(md)) {
- found = true;
- }
- }
- }
- assertTrue("Drug " + drug.getName() + " doesn't contain expected target", found);
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testFindIbuprofen() throws Exception {
- try {
- Drug drug = drugBankHTMLParser.findDrug("Ibuprofen");
- assertNotNull(drug);
- assertEquals("Ibuprofen", drug.getName());
- assertEquals("DB01050", drug.getSources().get(0).getResource());
- assertNotNull(drug.getDescription());
- assertTrue(drug.getTargets().size() >= 8);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindIronSaccharate() throws Exception {
- try {
- Drug drug = drugBankHTMLParser.findDrug("Iron saccharate");
- assertNotNull(drug);
- MiriamData tfProtein = new MiriamData(MiriamType.HGNC_SYMBOL, "TF");
- for (Target target : drug.getTargets()) {
- for (MiriamData md : target.getGenes()) {
- assertFalse("TF is a carrier, not a target", md.equals(tfProtein));
- }
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindDopamine() throws Exception {
-
- try {
- Drug test = drugBankHTMLParser.findDrug("Dopamine");
- assertNotNull(test);
- for (Target target : test.getTargets()) {
- assertFalse(target.getName().contains("Details"));
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindGadobutrol() throws Exception {
- try {
- Drug gadobutrolDrug = drugBankHTMLParser.findDrug("Gadobutrol");
- assertNotNull(gadobutrolDrug);
- assertTrue(gadobutrolDrug.getBloodBrainBarrier().equalsIgnoreCase("NO"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindDrugWithSpecialCharacters() throws Exception {
-
- try {
- Drug test = drugBankHTMLParser.findDrug("Guanosine-5’-Diphosphate");
- assertNotNull(test);
- assertFalse(test.getName().contains("&"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery() throws Exception {
- try {
- drugBankHTMLParser.refreshCacheQuery("invalid_query");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery2() throws Exception {
- try {
- drugBankHTMLParser.refreshCacheQuery(new Object());
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshCacheQueryNotAvailable() throws Exception {
- WebPageDownloader downloader = drugBankHTMLParser.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- drugBankHTMLParser.setWebPageDownloader(mockDownloader);
- drugBankHTMLParser.refreshCacheQuery("http://google.pl/");
- fail("Exception expected");
- } catch (SourceNotAvailable e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- drugBankHTMLParser.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testRefreshCacheQueryWhenDbNotAvailable() throws Exception {
- WebPageDownloader downloader = drugBankHTMLParser.getWebPageDownloader();
- GeneralCacheInterface cache = drugBankHTMLParser.getCache();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- drugBankHTMLParser.setWebPageDownloader(mockDownloader);
- drugBankHTMLParser.setCache(null);
-
- drugBankHTMLParser.refreshCacheQuery(DrugbankHTMLParser.DRUG_NAME_PREFIX + "aspirin");
- fail("Exception expected");
- } catch (SourceNotAvailable e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- drugBankHTMLParser.setWebPageDownloader(downloader);
- drugBankHTMLParser.setCache(cache);
- }
- }
-
- @Test
- public void testGetPubmedFromRef() throws Exception {
- try {
- String descriptionString = "<a href=\"/pubmed/1234\">link to 1234</a>";
- List<MiriamData> result = drugBankHTMLParser.getPubmedFromRef(descriptionString);
- assertEquals(1, result.size());
- assertEquals(new MiriamData(MiriamType.PUBMED, "1234"), result.get(0));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetPubmedFromRef2() throws Exception {
- try {
- String descriptionString = "<a href=\"/pubmed/12345678901234_\">link to 123456789</a>";
- List<MiriamData> result = drugBankHTMLParser.getPubmedFromRef(descriptionString);
- assertEquals(1, result.size());
- assertEquals(new MiriamData(MiriamType.PUBMED, "123456789"), result.get(0));
- assertEquals(1, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetPubmedFromRef3() throws Exception {
- try {
- String descriptionString = "<a href=\"/pubmed/invalid\">link to invalid</a>";
- List<MiriamData> result = drugBankHTMLParser.getPubmedFromRef(descriptionString);
- assertEquals(0, result.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetDescription() throws Exception {
- try {
- String descriptionString = "untagged description";
- assertNull(drugBankHTMLParser.getDescriptionForDrug(descriptionString));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetTargets() throws Exception {
- try {
- String descriptionString = "invalid content";
- List<Target> targets = drugBankHTMLParser.getTargetsForDrug(descriptionString);
- assertEquals(0, targets.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testStatus() throws Exception {
- try {
- assertEquals(ExternalServiceStatusType.OK, drugBankHTMLParser.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSimulateDownStatus() throws Exception {
- WebPageDownloader downloader = drugBankHTMLParser.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- drugBankHTMLParser.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.DOWN, drugBankHTMLParser.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- drugBankHTMLParser.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testSimulateChangedStatus() throws Exception {
- WebPageDownloader downloader = drugBankHTMLParser.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("");
- drugBankHTMLParser.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.CHANGED, drugBankHTMLParser.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- drugBankHTMLParser.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testGetBBB() throws Exception {
- try {
- assertTrue(
- drugBankHTMLParser.getBloodBrainBarrier("<tr><td>Blood Brain Barrier</td><td>-</td><td>0.7581</td></tr>")
- .equalsIgnoreCase("NO"));
- assertTrue(
- drugBankHTMLParser.getBloodBrainBarrier("<tr><td>Blood Brain Barrier</td><td>+</td><td>0.7581</td></tr>")
- .equalsIgnoreCase("YES"));
- assertTrue(drugBankHTMLParser
- .getBloodBrainBarrier("<tr><td>Blood Brain Barrier</td><td>don't know</td><td>0.7581</td></tr>")
- .equalsIgnoreCase("N/A"));
- assertTrue(drugBankHTMLParser.getBloodBrainBarrier("invalid str").equalsIgnoreCase("N/A"));
- assertTrue(drugBankHTMLParser.getBloodBrainBarrier("<tr><td>Blood Brain Barrier</td>invalid str")
- .equalsIgnoreCase("N/A"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() throws Exception {
- DrugbankHTMLParser parser = new DrugbankHTMLParser();
- UniprotAnnotator uniprotAnnotator = new UniprotAnnotator();
- parser.setUniprotAnnotator(uniprotAnnotator);
- assertEquals(uniprotAnnotator, parser.getUniprotAnnotator());
- }
-
- @Test
- public void parseTarget() throws Exception {
- String content = super.readFile("testFiles/drugbank/target-html-part.html");
- Target target = drugBankHTMLParser.parseTarget(content);
- assertNotNull(target);
- assertEquals(6, target.getReferences().size());
- assertEquals("Matrix protein 2", target.getName());
- }
-
- @Test
- public void testGetEmptySuggestedQueryList() throws Exception {
- try {
- Project project = new Project();
-
- List<String> result = drugBankHTMLParser.getSuggestedQueryList(project, TaxonomyBackend.HUMAN_TAXONOMY);
-
- assertEquals(0, result.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetSuggestedQueryList() throws Exception {
- try {
- Project project = new Project();
- Model model = getModelForFile("testFiles/target_chemical/target.xml", false);
- project.addModel(model);
-
- List<String> result = drugBankHTMLParser.getSuggestedQueryList(project, TaxonomyBackend.HUMAN_TAXONOMY);
-
- assertTrue(result.size() > 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetSuggestedQueryListForUnknownOrganism() throws Exception {
- try {
- Project project = new Project();
- Model model = getModelForFile("testFiles/target_chemical/target.xml", false);
- project.addModel(model);
-
- List<String> result = drugBankHTMLParser.getSuggestedQueryList(project, null);
-
- assertEquals(0, result.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
-}
+package lcsb.mapviewer.annotation.services;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import static org.mockito.Matchers.anyString;
+import static org.mockito.Mockito.when;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.AnnotationTestFunctions;
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.GeneralCacheWithExclusion;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.WebPageDownloader;
+import lcsb.mapviewer.annotation.data.Drug;
+import lcsb.mapviewer.annotation.data.Target;
+import lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.model.Model;
+
+public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
+ Logger logger = Logger.getLogger(DrugbankHTMLParserTest.class);
+
+ @Autowired
+ private DrugbankHTMLParser drugBankHTMLParser;
+
+ @Autowired
+ private GeneralCacheInterface cache;
+
+ @Before
+ public void setUp() throws Exception {
+ drugBankHTMLParser.setCache(new GeneralCacheWithExclusion(cache, 1));
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ drugBankHTMLParser.setCache(cache);
+ }
+
+ @Test
+ public void test1FindDrug() throws Exception {
+ try {
+ Drug test = drugBankHTMLParser.findDrug("Urokinase");
+ assertNotNull(test);
+ assertEquals(MiriamType.DRUGBANK, test.getSources().get(0).getDataType());
+ assertEquals("DB00013", test.getSources().get(0).getResource());
+ assertEquals("Urokinase", test.getName());
+ assertTrue(test.getBloodBrainBarrier().equalsIgnoreCase("N/A"));
+ boolean res = test.getDescription().contains(
+ "Low molecular weight form of human urokinase, that consists of an A chain of 2,000 daltons linked by a sulfhydryl bond to a B chain of 30,400 daltons. Recombinant urokinase plasminogen activator");
+ assertTrue(res);
+ assertEquals(10, test.getTargets().size());
+ assertNull(test.getApproved());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void test2FindDrug() throws Exception {
+ try {
+ Drug test = drugBankHTMLParser.findDrug("diazoxide");
+ assertNotNull(test);
+ assertEquals("Diazoxide", test.getName());
+ assertEquals("DB01119", test.getSources().get(0).getResource());
+ assertTrue(test.getBloodBrainBarrier().equalsIgnoreCase("YES"));
+ boolean res = test.getDescription().contains(
+ "A benzothiadiazine derivative that is a peripheral vasodilator used for hypertensive emergencies. It lacks diuretic effect, apparently because it lacks a sulfonamide group. [PubChem]");
+ assertTrue(res);
+ assertEquals(6, test.getTargets().size());
+ assertTrue(test.getApproved());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testFindRapamycin() throws Exception {
+ try {
+ // finding synonym
+ Drug rapamycinDrug = drugBankHTMLParser.findDrug("Rapamycin");
+ assertNotNull(rapamycinDrug);
+ assertEquals("Sirolimus", rapamycinDrug.getName());
+ assertEquals("DB00877", rapamycinDrug.getSources().get(0).getResource());
+ assertTrue(rapamycinDrug.getBloodBrainBarrier().equalsIgnoreCase("NO"));
+ boolean res = rapamycinDrug.getDescription().contains("A macrolide compound obtained from Streptomyces");
+ assertTrue(res);
+ assertEquals(3, rapamycinDrug.getTargets().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindAfegostat() throws Exception {
+ try {
+ // finding synonym
+ Drug rapamycinDrug = drugBankHTMLParser.findDrug("Afegostat");
+ assertNotNull(rapamycinDrug);
+ assertFalse(rapamycinDrug.getApproved());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void test4FindDrug() throws Exception {
+
+ try {
+ Drug test = drugBankHTMLParser.findDrug("Methylamine");
+ assertNotNull(test);
+ assertEquals("Methylamine", test.getName());
+ assertEquals("DB01828", test.getSources().get(0).getResource());
+ assertEquals(null, test.getDescription());
+ assertEquals(1, test.getTargets().size());
+
+ List<Target> tmp;
+ tmp = test.getTargets();
+ for (Target a : tmp) {
+ assertEquals("Ammonia channel", a.getName());
+ assertEquals(2, a.getReferences().size());
+ assertEquals(1, a.getGenes().size());
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void test5FindDrug() throws Exception {
+ try {
+ Drug amantadineDrug = drugBankHTMLParser.findDrug("Amantadine");
+ assertNotNull(amantadineDrug);
+ assertEquals("Amantadine", amantadineDrug.getName());
+ assertEquals("DB00915", amantadineDrug.getSources().get(0).getResource());
+ boolean res = amantadineDrug.getDescription().contains(
+ "An antiviral that is used in the prophylactic or symptomatic treatment of influenza A. It is also used as an antiparkinsonian agent, to treat extrapyramidal reactions, and for postherpetic neuralgia. The mechanisms of its effects in movement disorders are not well understood but probably reflect an increase in synthesis and release of dopamine, with perhaps some inhibition of dopamine uptake. [PubChem]");
+ assertTrue(res);
+ assertEquals(3, amantadineDrug.getTargets().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void test6FindDrug() throws Exception {
+ try {
+ Drug test = drugBankHTMLParser.findDrug("qwertyuiop");
+ assertEquals(null, test);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void test7FindDrug() throws Exception {
+ try {
+ Drug test = drugBankHTMLParser.findDrug("Aluminum hydroxide");
+ assertNotNull(test);
+ assertEquals("Aluminum hydroxide", test.getName());
+ assertEquals("DB06723", test.getSources().get(0).getResource());
+ assertTrue(test.getDescription().contains(
+ "Aluminum hydroxide is an inorganic salt used as an antacid. It is a basic compound that acts by neutralizing hydrochloric acid in gastric secretions. Subsequent increases in pH may inhibit the action of pepsin. An increase in bicarbonate ions and prostaglandins may also confer cytoprotective effects."));
+ assertEquals(0, test.getTargets().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindDrugAmantadineWithBrandNames() throws Exception {
+ try {
+ Drug drug = drugBankHTMLParser.findDrug("amantadine");
+
+ assertNotNull(drug);
+ assertTrue(drug.getBrandNames().contains("PK-Merz"));
+ assertTrue(drug.getBrandNames().contains("Symadine"));
+ assertTrue(drug.getBrandNames().contains("Symmetrel"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindDrugSelegiline() throws Exception {
+ try {
+ Drug test = drugBankHTMLParser.findDrug("Selegiline");
+ assertNotNull(test);
+ assertEquals(2, test.getTargets().size());
+ for (String string : new String[] { "MAOA", "MAOB" }) {
+ boolean contain = false;
+ for (Target target : test.getTargets()) {
+ for (MiriamData md : target.getGenes()) {
+ if (md.getResource().equals(string)) {
+ contain = true;
+ }
+ }
+ }
+ assertTrue("Missing traget: " + string, contain);
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindDrugDaidzinWithHtmlCharacters() throws Exception {
+ try {
+ Drug test = drugBankHTMLParser.findDrug("Daidzin");
+ assertNotNull(test);
+ for (String str : test.getSynonyms()) {
+ assertFalse(str.contains("'"));
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindDrugGliclazideWithHtmlTags() throws Exception {
+ try {
+ Drug test = drugBankHTMLParser.findDrug("Gliclazide");
+ assertNotNull(test);
+ assertFalse(test.getDescription().contains("<span"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindDrugSevofluraneWithHtmlTags() throws Exception {
+ try {
+ Drug test = drugBankHTMLParser.findDrug("sevoflurane");
+ assertNotNull(test);
+ for (String str : test.getSynonyms()) {
+ assertFalse(str.contains("<div"));
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindDrugByHgncTarget() throws Exception {
+ try {
+ List<Drug> drugs = drugBankHTMLParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "NFKB2"));
+ assertNotNull(drugs);
+ assertTrue("Only " + drugs.size() + " drugs were found, but at least 8 were expected", drugs.size() >= 8);
+
+ drugBankHTMLParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "NFKB2"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindDrugByTFTarget() throws Exception {
+ try {
+ List<Drug> drugs = drugBankHTMLParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "TF"));
+ assertNotNull(drugs);
+ for (Drug drug : drugs) {
+ assertFalse(drug.getName().equalsIgnoreCase("Iron saccharate"));
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindAluminiumByName() throws Exception {
+ try {
+ Drug drug = drugBankHTMLParser.findDrug("Aluminium");
+ assertTrue(drug.getName().equalsIgnoreCase("Aluminium"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindBIIB054ByName() throws Exception {
+ try {
+ Drug drug = drugBankHTMLParser.findDrug("BIIB054");
+ if (drug != null) {
+ // check if are not pointint to BIIB021
+ assertFalse(drug.getSources().get(0).getResource().equalsIgnoreCase("DB12359"));
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindDrugByHgncTargetAndFilteredOutByOrganism() throws Exception {
+ try {
+ List<MiriamData> organisms = new ArrayList<>();
+ organisms.add(new MiriamData(MiriamType.TAXONOMY, "-1"));
+ List<Drug> drugs = drugBankHTMLParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "NFKB2"),
+ organisms);
+ assertNotNull(drugs);
+ assertEquals("No drugs for this organisms should be found", 0, drugs.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindDrugByHgncTargetAndFilteredByOrganism() throws Exception {
+ try {
+ List<MiriamData> organisms = new ArrayList<>();
+ organisms.add(TaxonomyBackend.HUMAN_TAXONOMY);
+ List<Drug> drugs = drugBankHTMLParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "NFKB2"),
+ organisms);
+ assertNotNull(drugs);
+ assertTrue(drugs.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindDrugByInvalidTarget() throws Exception {
+ try {
+ drugBankHTMLParser.getDrugListByTarget(new MiriamData(MiriamType.WIKIPEDIA, "h2o"));
+ fail("Exception");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("type is accepted"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindDrugByEmptyTarget() throws Exception {
+ try {
+ List<Drug> drugs = drugBankHTMLParser.getDrugListByTarget(null);
+ assertEquals(0, drugs.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testWrongHgncTarget() throws Exception {
+ try {
+
+ List<Drug> drugs = drugBankHTMLParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "BECN1"));
+ assertNotNull(drugs);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindDrugByHgncTargets() throws Exception {
+ try {
+ List<Drug> drug1 = drugBankHTMLParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "NFKB1"));
+ List<Drug> drug2 = drugBankHTMLParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "NFKB2"));
+ int size = drug1.size() + drug2.size();
+
+ List<MiriamData> list = new ArrayList<MiriamData>();
+ list.add(new MiriamData(MiriamType.HGNC_SYMBOL, "NFKB2"));
+ list.add(new MiriamData(MiriamType.HGNC_SYMBOL, "NFKB1"));
+
+ List<Drug> drugs = drugBankHTMLParser.getDrugListByTargets(list);
+ assertNotNull(drugs);
+ assertTrue("Merged list should be shorter then sum of the two lists", drugs.size() < size);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test(timeout = 15000)
+ public void testCachableInterfaceInvalidateUrl() throws Exception {
+ String query = "http://google.lu/";
+ String newRes = "hello";
+ try {
+ waitForRefreshCacheQueueToEmpty();
+
+ cache.setCachedQuery(query, drugBankHTMLParser.getCacheType(), newRes);
+ cache.invalidateByQuery(query, drugBankHTMLParser.getCacheType());
+
+ waitForRefreshCacheQueueToEmpty();
+
+ String res = cache.getStringByQuery(query, drugBankHTMLParser.getCacheType());
+
+ assertNotNull(res);
+
+ assertFalse("Value wasn't refreshed from db", newRes.equals(res));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ // wait max 15 second
+ @Test(timeout = 150000)
+ public void testCachableInterfaceInvalidateDrug() throws Exception {
+
+ String query = "drug:amantadine";
+ String newRes = "hello";
+ try {
+ waitForRefreshCacheQueueToEmpty();
+
+ cache.setCachedQuery(query, drugBankHTMLParser.getCacheType(), newRes);
+ cache.invalidateByQuery(query, drugBankHTMLParser.getCacheType());
+
+ waitForRefreshCacheQueueToEmpty();
+
+ String res = cache.getStringByQuery(query, drugBankHTMLParser.getCacheType());
+
+ assertNotNull(res);
+
+ assertFalse("Value wasn't refreshed from db", newRes.equals(res));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testByTargetsForCCNB1() throws Exception {
+ try {
+ List<MiriamData> targets = new ArrayList<>();
+ MiriamData miriamTarget = new MiriamData(MiriamType.HGNC_SYMBOL, "CCNB1");
+ targets.add(miriamTarget);
+ List<Drug> drugs = drugBankHTMLParser.getDrugListByTargets(targets);
+ for (Drug drug : drugs) {
+ boolean found = false;
+ for (Target target : drug.getTargets()) {
+ for (MiriamData md : target.getGenes()) {
+ if (miriamTarget.equals(md)) {
+ found = true;
+ }
+ }
+ }
+ assertTrue("Drug " + drug.getName() + " doesn't contain expected target", found);
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testFindIbuprofen() throws Exception {
+ try {
+ Drug drug = drugBankHTMLParser.findDrug("Ibuprofen");
+ assertNotNull(drug);
+ assertEquals("Ibuprofen", drug.getName());
+ assertEquals("DB01050", drug.getSources().get(0).getResource());
+ assertNotNull(drug.getDescription());
+ assertTrue(drug.getTargets().size() >= 8);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindIronSaccharate() throws Exception {
+ try {
+ Drug drug = drugBankHTMLParser.findDrug("Iron saccharate");
+ assertNotNull(drug);
+ MiriamData tfProtein = new MiriamData(MiriamType.HGNC_SYMBOL, "TF");
+ for (Target target : drug.getTargets()) {
+ for (MiriamData md : target.getGenes()) {
+ assertFalse("TF is a carrier, not a target", md.equals(tfProtein));
+ }
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindDopamine() throws Exception {
+
+ try {
+ Drug test = drugBankHTMLParser.findDrug("Dopamine");
+ assertNotNull(test);
+ for (Target target : test.getTargets()) {
+ assertFalse(target.getName().contains("Details"));
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindGadobutrol() throws Exception {
+ try {
+ Drug gadobutrolDrug = drugBankHTMLParser.findDrug("Gadobutrol");
+ assertNotNull(gadobutrolDrug);
+ assertTrue(gadobutrolDrug.getBloodBrainBarrier().equalsIgnoreCase("NO"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindDrugWithSpecialCharacters() throws Exception {
+
+ try {
+ Drug test = drugBankHTMLParser.findDrug("Guanosine-5’-Diphosphate");
+ assertNotNull(test);
+ assertFalse(test.getName().contains("&"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery() throws Exception {
+ try {
+ drugBankHTMLParser.refreshCacheQuery("invalid_query");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery2() throws Exception {
+ try {
+ drugBankHTMLParser.refreshCacheQuery(new Object());
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQueryNotAvailable() throws Exception {
+ WebPageDownloader downloader = drugBankHTMLParser.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ drugBankHTMLParser.setWebPageDownloader(mockDownloader);
+ drugBankHTMLParser.refreshCacheQuery("http://google.pl/");
+ fail("Exception expected");
+ } catch (SourceNotAvailable e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ drugBankHTMLParser.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQueryWhenDbNotAvailable() throws Exception {
+ WebPageDownloader downloader = drugBankHTMLParser.getWebPageDownloader();
+ GeneralCacheInterface cache = drugBankHTMLParser.getCache();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ drugBankHTMLParser.setWebPageDownloader(mockDownloader);
+ drugBankHTMLParser.setCache(null);
+
+ drugBankHTMLParser.refreshCacheQuery(DrugbankHTMLParser.DRUG_NAME_PREFIX + "aspirin");
+ fail("Exception expected");
+ } catch (SourceNotAvailable e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ drugBankHTMLParser.setWebPageDownloader(downloader);
+ drugBankHTMLParser.setCache(cache);
+ }
+ }
+
+ @Test
+ public void testGetPubmedFromRef() throws Exception {
+ try {
+ String descriptionString = "<a href=\"/pubmed/1234\">link to 1234</a>";
+ List<MiriamData> result = drugBankHTMLParser.getPubmedFromRef(descriptionString);
+ assertEquals(1, result.size());
+ assertEquals(new MiriamData(MiriamType.PUBMED, "1234"), result.get(0));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetPubmedFromRef2() throws Exception {
+ try {
+ String descriptionString = "<a href=\"/pubmed/12345678901234_\">link to 123456789</a>";
+ List<MiriamData> result = drugBankHTMLParser.getPubmedFromRef(descriptionString);
+ assertEquals(1, result.size());
+ assertEquals(new MiriamData(MiriamType.PUBMED, "123456789"), result.get(0));
+ assertEquals(1, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetPubmedFromRef3() throws Exception {
+ try {
+ String descriptionString = "<a href=\"/pubmed/invalid\">link to invalid</a>";
+ List<MiriamData> result = drugBankHTMLParser.getPubmedFromRef(descriptionString);
+ assertEquals(0, result.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetDescription() throws Exception {
+ try {
+ String descriptionString = "untagged description";
+ assertNull(drugBankHTMLParser.getDescriptionForDrug(descriptionString));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetTargets() throws Exception {
+ try {
+ String descriptionString = "invalid content";
+ List<Target> targets = drugBankHTMLParser.getTargetsForDrug(descriptionString);
+ assertEquals(0, targets.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testStatus() throws Exception {
+ try {
+ assertEquals(ExternalServiceStatusType.OK, drugBankHTMLParser.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSimulateDownStatus() throws Exception {
+ WebPageDownloader downloader = drugBankHTMLParser.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ drugBankHTMLParser.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.DOWN, drugBankHTMLParser.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ drugBankHTMLParser.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testSimulateChangedStatus() throws Exception {
+ WebPageDownloader downloader = drugBankHTMLParser.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("");
+ drugBankHTMLParser.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.CHANGED, drugBankHTMLParser.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ drugBankHTMLParser.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testGetBBB() throws Exception {
+ try {
+ assertTrue(
+ drugBankHTMLParser.getBloodBrainBarrier("<tr><td>Blood Brain Barrier</td><td>-</td><td>0.7581</td></tr>")
+ .equalsIgnoreCase("NO"));
+ assertTrue(
+ drugBankHTMLParser.getBloodBrainBarrier("<tr><td>Blood Brain Barrier</td><td>+</td><td>0.7581</td></tr>")
+ .equalsIgnoreCase("YES"));
+ assertTrue(drugBankHTMLParser
+ .getBloodBrainBarrier("<tr><td>Blood Brain Barrier</td><td>don't know</td><td>0.7581</td></tr>")
+ .equalsIgnoreCase("N/A"));
+ assertTrue(drugBankHTMLParser.getBloodBrainBarrier("invalid str").equalsIgnoreCase("N/A"));
+ assertTrue(drugBankHTMLParser.getBloodBrainBarrier("<tr><td>Blood Brain Barrier</td>invalid str")
+ .equalsIgnoreCase("N/A"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() throws Exception {
+ DrugbankHTMLParser parser = new DrugbankHTMLParser();
+ UniprotAnnotator uniprotAnnotator = new UniprotAnnotator();
+ parser.setUniprotAnnotator(uniprotAnnotator);
+ assertEquals(uniprotAnnotator, parser.getUniprotAnnotator());
+ }
+
+ @Test
+ public void parseTarget() throws Exception {
+ String content = super.readFile("testFiles/drugbank/target-html-part.html");
+ Target target = drugBankHTMLParser.parseTarget(content);
+ assertNotNull(target);
+ assertEquals(6, target.getReferences().size());
+ assertEquals("Matrix protein 2", target.getName());
+ }
+
+ @Test
+ public void testGetEmptySuggestedQueryList() throws Exception {
+ try {
+ Project project = new Project();
+
+ List<String> result = drugBankHTMLParser.getSuggestedQueryList(project, TaxonomyBackend.HUMAN_TAXONOMY);
+
+ assertEquals(0, result.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetSuggestedQueryList() throws Exception {
+ try {
+ Project project = new Project();
+ Model model = getModelForFile("testFiles/target_chemical/target.xml", false);
+ project.addModel(model);
+
+ List<String> result = drugBankHTMLParser.getSuggestedQueryList(project, TaxonomyBackend.HUMAN_TAXONOMY);
+
+ assertTrue(result.size() > 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetSuggestedQueryListForUnknownOrganism() throws Exception {
+ try {
+ Project project = new Project();
+ Model model = getModelForFile("testFiles/target_chemical/target.xml", false);
+ project.addModel(model);
+
+ List<String> result = drugBankHTMLParser.getSuggestedQueryList(project, null);
+
+ assertEquals(0, result.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankXMLParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankXMLParserTest.java
index 1d347d5989..7f6c68fa26 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankXMLParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/DrugbankXMLParserTest.java
@@ -1,146 +1,146 @@
-package lcsb.mapviewer.annotation.services;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-import static org.mockito.Matchers.anyString;
-import static org.mockito.Mockito.when;
-
-import org.apache.log4j.Logger;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.annotation.AnnotationTestFunctions;
-import lcsb.mapviewer.annotation.data.Drug;
-import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.model.map.MiriamType;
-
-public class DrugbankXMLParserTest extends AnnotationTestFunctions {
- Logger logger = Logger.getLogger(DrugbankXMLParserTest.class);
-
- String file = "testFiles/target_drugbank/small_drugbank.xml";
-
- @Autowired
- TaxonomyBackend taxonomyBackend;
-
- // this should be improved, but now for performance it's done via static field
- static DrugbankXMLParser read;
-
- @Before
- public void setup() {
- if (read == null) {
- read = new DrugbankXMLParser(file, taxonomyBackend);
- }
- }
-
- @Test
- public void test1FindDrug() throws Exception {
- Drug test = read.findDrug("Urokinase");
- assertEquals(MiriamType.DRUGBANK, test.getSources().get(0).getDataType());
- assertEquals("DB00013", test.getSources().get(0).getResource());
- assertEquals("Urokinase", test.getName());
- assertEquals(
- "Low molecular weight form of human urokinase, that consists of an A chain of 2,000 daltons linked by a sulfhydryl bond to a B chain of 30,400 daltons. Recombinant urokinase plasminogen activator",
- test.getDescription());
- assertEquals(10, test.getTargets().size());
-
- // test.write();
- }
-
- @Test
- public void test2FindDrug() throws Exception {
- Drug test = read.findDrug("diazoxide");
- assertEquals("Diazoxide", test.getName());
- assertEquals("DB01119", test.getSources().get(0).getResource());
- assertEquals(
- "A benzothiadiazine derivative that is a peripheral vasodilator used for hypertensive emergencies. It lacks diuretic effect, apparently because it lacks a sulfonamide group. [PubChem]",
- test.getDescription());
- assertEquals(6, test.getTargets().size());
- }
-
- @Test
- public void test3FindDrug() throws Exception {
- // finding synonym
- Drug test = read.findDrug("Rapamycin");
- assertEquals("Sirolimus", test.getName());
- assertEquals("DB00877", test.getSources().get(0).getResource());
- assertEquals(
- "A macrolide compound obtained from Streptomyces hygroscopicus that acts by selectively blocking the transcriptional activation of cytokines thereby inhibiting cytokine production. It is bioactive only when bound to immunophilins. Sirolimus is a potent immunosuppressant and possesses both antifungal and antineoplastic properties. [PubChem]",
- test.getDescription());
- assertEquals(3, test.getTargets().size());
- }
-
- @Test
- public void test4FindDrug() throws Exception {
- Drug test = read.findDrug("Methylamine");
- assertEquals("Methylamine", test.getName());
- assertEquals("DB01828", test.getSources().get(0).getResource());
- assertEquals(null, test.getDescription());
- assertEquals(1, test.getTargets().size());
-
- for (Target t : test.getTargets()) {
- assertEquals("Ammonia channel", t.getName());
- assertEquals("BE0001338", t.getSource().getResource());
- assertEquals(MiriamType.DRUGBANK_TARGET_V4, t.getSource().getDataType());
- assertEquals(2, t.getReferences().size());
- assertEquals(0, t.getGenes().size());
- }
-
- // test.write();
- }
-
- @Test
- public void test5FindDrug() throws Exception {
- Drug test = read.findDrug("Amantadine");
- assertEquals("Amantadine", test.getName());
- assertEquals("DB00915", test.getSources().get(0).getResource());
- assertEquals(
- "An antiviral that is used in the prophylactic or symptomatic treatment of influenza A. It is also used as an antiparkinsonian agent, to treat extrapyramidal reactions, and for postherpetic neuralgia. The mechanisms of its effects in movement disorders are not well understood but probably reflect an increase in synthesis and release of dopamine, with perhaps some inhibition of dopamine uptake. [PubChem]",
- test.getDescription());
- assertEquals(3, test.getTargets().size());
- }
-
- @Test
- public void test6FindDrug() throws Exception {
-
- Drug test = read.findDrug("qwertyuiop");
- assertEquals(null, test);
- }
-
- @Test
- public void test7FindDrug() throws Exception {
- Drug test = read.findDrug("Aluminum hydroxide");
- assertEquals("Aluminum hydroxide", test.getName());
- assertEquals("DB06723", test.getSources().get(0).getResource());
- assertEquals(
- "Aluminum hydroxide is an inorganic salt used as an antacid. It is a basic compound that acts by neutralizing hydrochloric acid in gastric secretions. Subsequent increases in pH may inhibit the action of pepsin. An increase in bicarbonate ions and prostaglandins may also confer cytoprotective effects.",
- test.getDescription());
- assertEquals(0, test.getTargets().size());
- }
-
- @Test
- public void testFindDrugInInvalidFile() throws Exception {
- try {
- new DrugbankXMLParser("unknown.file.bla", taxonomyBackend).findDrug("unk");
- fail("Exception expected");
-
- } catch (DrugSearchException e) {
- assertTrue(e.getMessage().contains("Problem with processing input file"));
- }
- }
-
- @Test
- public void testFindDrugWithTaxnomyBackendBroken() throws Exception {
- try {
- TaxonomyBackend taxonomyMock = Mockito.mock(TaxonomyBackend.class);
- when(taxonomyMock.getByName(anyString())).thenThrow(new TaxonomySearchException(null, null));
- new DrugbankXMLParser(file, taxonomyMock).findDrug("Amantadine");
- fail("Exception expected");
-
- } catch (DrugSearchException e) {
- assertEquals(TaxonomySearchException.class, e.getCause().getClass());
- }
- }
-}
+package lcsb.mapviewer.annotation.services;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import static org.mockito.Matchers.anyString;
+import static org.mockito.Mockito.when;
+
+import org.apache.log4j.Logger;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.AnnotationTestFunctions;
+import lcsb.mapviewer.annotation.data.Drug;
+import lcsb.mapviewer.annotation.data.Target;
+import lcsb.mapviewer.model.map.MiriamType;
+
+public class DrugbankXMLParserTest extends AnnotationTestFunctions {
+ Logger logger = Logger.getLogger(DrugbankXMLParserTest.class);
+
+ String file = "testFiles/target_drugbank/small_drugbank.xml";
+
+ @Autowired
+ TaxonomyBackend taxonomyBackend;
+
+ // this should be improved, but now for performance it's done via static field
+ static DrugbankXMLParser read;
+
+ @Before
+ public void setup() {
+ if (read == null) {
+ read = new DrugbankXMLParser(file, taxonomyBackend);
+ }
+ }
+
+ @Test
+ public void test1FindDrug() throws Exception {
+ Drug test = read.findDrug("Urokinase");
+ assertEquals(MiriamType.DRUGBANK, test.getSources().get(0).getDataType());
+ assertEquals("DB00013", test.getSources().get(0).getResource());
+ assertEquals("Urokinase", test.getName());
+ assertEquals(
+ "Low molecular weight form of human urokinase, that consists of an A chain of 2,000 daltons linked by a sulfhydryl bond to a B chain of 30,400 daltons. Recombinant urokinase plasminogen activator",
+ test.getDescription());
+ assertEquals(10, test.getTargets().size());
+
+ // test.write();
+ }
+
+ @Test
+ public void test2FindDrug() throws Exception {
+ Drug test = read.findDrug("diazoxide");
+ assertEquals("Diazoxide", test.getName());
+ assertEquals("DB01119", test.getSources().get(0).getResource());
+ assertEquals(
+ "A benzothiadiazine derivative that is a peripheral vasodilator used for hypertensive emergencies. It lacks diuretic effect, apparently because it lacks a sulfonamide group. [PubChem]",
+ test.getDescription());
+ assertEquals(6, test.getTargets().size());
+ }
+
+ @Test
+ public void test3FindDrug() throws Exception {
+ // finding synonym
+ Drug test = read.findDrug("Rapamycin");
+ assertEquals("Sirolimus", test.getName());
+ assertEquals("DB00877", test.getSources().get(0).getResource());
+ assertEquals(
+ "A macrolide compound obtained from Streptomyces hygroscopicus that acts by selectively blocking the transcriptional activation of cytokines thereby inhibiting cytokine production. It is bioactive only when bound to immunophilins. Sirolimus is a potent immunosuppressant and possesses both antifungal and antineoplastic properties. [PubChem]",
+ test.getDescription());
+ assertEquals(3, test.getTargets().size());
+ }
+
+ @Test
+ public void test4FindDrug() throws Exception {
+ Drug test = read.findDrug("Methylamine");
+ assertEquals("Methylamine", test.getName());
+ assertEquals("DB01828", test.getSources().get(0).getResource());
+ assertEquals(null, test.getDescription());
+ assertEquals(1, test.getTargets().size());
+
+ for (Target t : test.getTargets()) {
+ assertEquals("Ammonia channel", t.getName());
+ assertEquals("BE0001338", t.getSource().getResource());
+ assertEquals(MiriamType.DRUGBANK_TARGET_V4, t.getSource().getDataType());
+ assertEquals(2, t.getReferences().size());
+ assertEquals(0, t.getGenes().size());
+ }
+
+ // test.write();
+ }
+
+ @Test
+ public void test5FindDrug() throws Exception {
+ Drug test = read.findDrug("Amantadine");
+ assertEquals("Amantadine", test.getName());
+ assertEquals("DB00915", test.getSources().get(0).getResource());
+ assertEquals(
+ "An antiviral that is used in the prophylactic or symptomatic treatment of influenza A. It is also used as an antiparkinsonian agent, to treat extrapyramidal reactions, and for postherpetic neuralgia. The mechanisms of its effects in movement disorders are not well understood but probably reflect an increase in synthesis and release of dopamine, with perhaps some inhibition of dopamine uptake. [PubChem]",
+ test.getDescription());
+ assertEquals(3, test.getTargets().size());
+ }
+
+ @Test
+ public void test6FindDrug() throws Exception {
+
+ Drug test = read.findDrug("qwertyuiop");
+ assertEquals(null, test);
+ }
+
+ @Test
+ public void test7FindDrug() throws Exception {
+ Drug test = read.findDrug("Aluminum hydroxide");
+ assertEquals("Aluminum hydroxide", test.getName());
+ assertEquals("DB06723", test.getSources().get(0).getResource());
+ assertEquals(
+ "Aluminum hydroxide is an inorganic salt used as an antacid. It is a basic compound that acts by neutralizing hydrochloric acid in gastric secretions. Subsequent increases in pH may inhibit the action of pepsin. An increase in bicarbonate ions and prostaglandins may also confer cytoprotective effects.",
+ test.getDescription());
+ assertEquals(0, test.getTargets().size());
+ }
+
+ @Test
+ public void testFindDrugInInvalidFile() throws Exception {
+ try {
+ new DrugbankXMLParser("unknown.file.bla", taxonomyBackend).findDrug("unk");
+ fail("Exception expected");
+
+ } catch (DrugSearchException e) {
+ assertTrue(e.getMessage().contains("Problem with processing input file"));
+ }
+ }
+
+ @Test
+ public void testFindDrugWithTaxnomyBackendBroken() throws Exception {
+ try {
+ TaxonomyBackend taxonomyMock = Mockito.mock(TaxonomyBackend.class);
+ when(taxonomyMock.getByName(anyString())).thenThrow(new TaxonomySearchException(null, null));
+ new DrugbankXMLParser(file, taxonomyMock).findDrug("Amantadine");
+ fail("Exception expected");
+
+ } catch (DrugSearchException e) {
+ assertEquals(TaxonomySearchException.class, e.getCause().getClass());
+ }
+ }
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ExternalServiceStatusTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ExternalServiceStatusTest.java
index 4d445dc838..7953bf1799 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ExternalServiceStatusTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ExternalServiceStatusTest.java
@@ -1,34 +1,34 @@
-package lcsb.mapviewer.annotation.services;
-
-import static org.junit.Assert.*;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ExternalServiceStatusTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetters() {
- String name = "b";
- String page = "page";
-
- ExternalServiceStatus status = new ExternalServiceStatus(name, page);
- assertEquals(name, status.getName());
- assertEquals(page, status.getPage());
- }
-
-}
+package lcsb.mapviewer.annotation.services;
+
+import static org.junit.Assert.*;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ExternalServiceStatusTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetters() {
+ String name = "b";
+ String page = "page";
+
+ ExternalServiceStatus status = new ExternalServiceStatus(name, page);
+ assertEquals(name, status.getName());
+ assertEquals(page, status.getPage());
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ExternalServiceStatusTypeTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ExternalServiceStatusTypeTest.java
index 471f026614..1eb86e29c9 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ExternalServiceStatusTypeTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ExternalServiceStatusTypeTest.java
@@ -1,33 +1,33 @@
-package lcsb.mapviewer.annotation.services;
-
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ExternalServiceStatusTypeTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testValues() {
- for (ExternalServiceStatusType type : ExternalServiceStatusType.values()) {
- assertNotNull(type.getCommonName());
- assertNotNull(type.getLevel());
- assertNotNull(ExternalServiceStatusType.valueOf(type.toString()));
- }
- }
-
-}
+package lcsb.mapviewer.annotation.services;
+
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ExternalServiceStatusTypeTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testValues() {
+ for (ExternalServiceStatusType type : ExternalServiceStatusType.values()) {
+ assertNotNull(type.getCommonName());
+ assertNotNull(type.getLevel());
+ assertNotNull(ExternalServiceStatusType.valueOf(type.toString()));
+ }
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MeSHParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MeSHParserTest.java
index 007781197a..8fb197d385 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MeSHParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MeSHParserTest.java
@@ -1,347 +1,347 @@
-package lcsb.mapviewer.annotation.services;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-import static org.mockito.Matchers.anyString;
-import static org.mockito.Mockito.when;
-
-import java.io.IOException;
-import java.util.List;
-
-import org.apache.http.HttpStatus;
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.annotation.AnnotationTestFunctions;
-import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.GeneralCacheWithExclusion;
-import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
-import lcsb.mapviewer.annotation.cache.WebPageDownloader;
-import lcsb.mapviewer.annotation.data.MeSH;
-import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-
-public class MeSHParserTest extends AnnotationTestFunctions {
- Logger logger = Logger.getLogger(MeSHParserTest.class);
-
- @Autowired
- MeSHParser meshParser;
-
- @Autowired
- private GeneralCacheInterface cache;
-
- @Before
- public void setUp() throws Exception {
- meshParser.setCache(new GeneralCacheWithExclusion(cache, 1));
- }
-
- @After
- public void tearDown() throws Exception {
- meshParser.setCache(cache);
- }
-
- @Test
- public void testGetMesh() throws Exception {
- try {
- // Parkinson disease
- MiriamData meshID = new MiriamData(MiriamType.MESH_2012, "D004298");
- MeSH mesh = meshParser.getMeSH(meshID);
- assertTrue(mesh != null);
- assertTrue(mesh.getMeSHId() != null);
- assertTrue(mesh.getName() != null);
- assertTrue(mesh.getName().toLowerCase().equals("dopamine"));
- assertTrue(mesh.getDescription() != null);
- assertTrue(mesh.getSynonyms().size() > 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetMeshBySynonym() throws Exception {
- try {
- String synonym = "MPTP";
- List<MeSH> result = meshParser.getMeshBySynonym(synonym);
- assertEquals(1, result.size());
- MeSH mesh = result.get(0);
- assertTrue(mesh.getSynonyms().contains(synonym));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testIsValidMesh() throws Exception {
- try {
- MiriamData meshID = new MiriamData(MiriamType.MESH_2012, "D004298");
- assertTrue(meshParser.isValidMeshId(meshID));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testIsValidMesh3() throws Exception {
- try {
- MiriamData meshID = new MiriamData(MiriamType.MESH_2012, "blablabla");
- assertFalse(meshParser.isValidMeshId(meshID));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testIsValidMesh2() throws Exception {
- try {
- assertFalse(meshParser.isValidMeshId(null));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetInvalidMesh() throws Exception {
- try {
- meshParser.getMeSH(null);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshCacheQuery() throws Exception {
- try {
- Object res = meshParser.refreshCacheQuery("http://google.pl/");
- assertNotNull(res);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetRotenoneMesh() throws Exception {
- try {
- // Rotenone disease -no synonyms
- MiriamData meshID = new MiriamData(MiriamType.MESH_2012, "D012402");
- MeSH mesh = meshParser.getMeSH(meshID);
- assertTrue(mesh != null);
- assertTrue(mesh.getMeSHId() != null);
- assertTrue(mesh.getName() != null);
- assertTrue(mesh.getName().toLowerCase().equals("rotenone"));
- assertTrue(mesh.getDescription() != null);
- assertEquals(0, mesh.getSynonyms().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateChemicalListFromDB3() throws Exception {
- try {
- // One synonyms
- MiriamData meshID = new MiriamData(MiriamType.MESH_2012, "C503102");
- MeSH mesh = meshParser.getMeSH(meshID);
- assertTrue(mesh != null);
- assertTrue(mesh.getMeSHId() != null);
- assertTrue(mesh.getName() != null);
- assertTrue(
- mesh.getName().toLowerCase().contains("1-(3-(2-(1-benzothiophen-5-yl) ethoxy) propyl)-3-azetidinol maleate"));
- assertNull(mesh.getDescription());
- assertEquals(1, mesh.getSynonyms().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetMEshWithNetworkProblems() throws Exception {
- try {
- // Parkinson disease
- MiriamData meshID = new MiriamData(MiriamType.MESH_2012, "D004298");
- MeSHParser parserUnderTest = new MeSHParser();
- WebPageDownloader webPageDownloader = Mockito.mock(WebPageDownloader.class);
- when(webPageDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- parserUnderTest.setWebPageDownloader(webPageDownloader);
-
- parserUnderTest.getMeSH(meshID);
- fail("Exception expected");
- } catch (AnnotatorException e) {
- assertTrue(e.getMessage().contains("Problem with accessing MeSH database"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- /**
- * @throws Exception
- */
- @Test
- public void testExternalDBStatus() throws Exception {
- ExternalServiceStatus status = meshParser.getServiceStatus();
- logger.debug("Status of MeSH DB : " + status.getStatus().name());
- assertTrue(status.getStatus().equals(ExternalServiceStatusType.OK));
- }
-
- @Test
- public void testCachableInterfaceInvalidateChemical() throws Exception {
- try {
- MiriamData meshID = new MiriamData(MiriamType.MESH_2012, "D010300");
- MeSH mesh = meshParser.getMeSH(meshID);
- assertNotNull(mesh);
-
- waitForRefreshCacheQueueToEmpty();
-
- cache.invalidateByQuery(meshParser.getIdentifier(meshID), meshParser.getCacheType());
-
- waitForRefreshCacheQueueToEmpty();
-
- MeSH mesh2 = meshParser.getMeSH(meshID);
- assertNotNull(mesh2);
-
- assertFalse("Value wasn't refreshed from db", mesh.equals(mesh2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCleanHtml() {
- try {
- String withouthHtml = meshParser.cleanHtml(
- "<TD colspan=1>One of the catecholamine <A href=\"/cgi/mesh/2014/MB_cgi?mode=&term=NEUROTRANSMITTERS\">");
- assertFalse(withouthHtml.contains("<"));
- assertFalse(withouthHtml.contains(">"));
- assertTrue(withouthHtml.contains("catecholamine"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testRefreshInvalidCacheQuery() throws Exception {
- try {
- meshParser.refreshCacheQuery("invalid_query");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery2() throws Exception {
- try {
- meshParser.refreshCacheQuery(new Object());
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery3() throws Exception {
- try {
- String query = MeSHParser.MESH_PREFIX + "::::::";
- meshParser.refreshCacheQuery(query);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Problematic query"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshWhenProblemWithSourceDb() throws Exception {
- WebPageDownloader downloader = meshParser.getWebPageDownloader();
- GeneralCacheInterface cache = meshParser.getCache();
- try {
- meshParser.setCache(null);
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- meshParser.setWebPageDownloader(mockDownloader);
-
- MiriamData meshID = new MiriamData(MiriamType.MESH_2012, "D010300");
-
- meshParser.refreshCacheQuery(meshParser.getIdentifier(meshID));
- fail("Exception expected");
- } catch (SourceNotAvailable e) {
- assertTrue(e.getMessage().contains("Problem with accessing Mesh database"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- meshParser.setWebPageDownloader(downloader);
- meshParser.setCache(cache);
- }
- }
-
- @Test
- public void testSimulateDownStatus() throws Exception {
- WebPageDownloader downloader = meshParser.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- meshParser.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.DOWN, meshParser.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- meshParser.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testSimulateChangeStatus() throws Exception {
- WebPageDownloader downloader = meshParser.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString()))
- .thenThrow(new WrongResponseCodeIOException(null, HttpStatus.SC_NOT_FOUND));
- meshParser.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.CHANGED, meshParser.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- meshParser.setWebPageDownloader(downloader);
- }
- }
-
-}
+package lcsb.mapviewer.annotation.services;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import static org.mockito.Matchers.anyString;
+import static org.mockito.Mockito.when;
+
+import java.io.IOException;
+import java.util.List;
+
+import org.apache.http.HttpStatus;
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.AnnotationTestFunctions;
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.GeneralCacheWithExclusion;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.WebPageDownloader;
+import lcsb.mapviewer.annotation.data.MeSH;
+import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+
+public class MeSHParserTest extends AnnotationTestFunctions {
+ Logger logger = Logger.getLogger(MeSHParserTest.class);
+
+ @Autowired
+ MeSHParser meshParser;
+
+ @Autowired
+ private GeneralCacheInterface cache;
+
+ @Before
+ public void setUp() throws Exception {
+ meshParser.setCache(new GeneralCacheWithExclusion(cache, 1));
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ meshParser.setCache(cache);
+ }
+
+ @Test
+ public void testGetMesh() throws Exception {
+ try {
+ // Parkinson disease
+ MiriamData meshID = new MiriamData(MiriamType.MESH_2012, "D004298");
+ MeSH mesh = meshParser.getMeSH(meshID);
+ assertTrue(mesh != null);
+ assertTrue(mesh.getMeSHId() != null);
+ assertTrue(mesh.getName() != null);
+ assertTrue(mesh.getName().toLowerCase().equals("dopamine"));
+ assertTrue(mesh.getDescription() != null);
+ assertTrue(mesh.getSynonyms().size() > 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetMeshBySynonym() throws Exception {
+ try {
+ String synonym = "MPTP";
+ List<MeSH> result = meshParser.getMeshBySynonym(synonym);
+ assertEquals(1, result.size());
+ MeSH mesh = result.get(0);
+ assertTrue(mesh.getSynonyms().contains(synonym));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testIsValidMesh() throws Exception {
+ try {
+ MiriamData meshID = new MiriamData(MiriamType.MESH_2012, "D004298");
+ assertTrue(meshParser.isValidMeshId(meshID));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testIsValidMesh3() throws Exception {
+ try {
+ MiriamData meshID = new MiriamData(MiriamType.MESH_2012, "blablabla");
+ assertFalse(meshParser.isValidMeshId(meshID));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testIsValidMesh2() throws Exception {
+ try {
+ assertFalse(meshParser.isValidMeshId(null));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetInvalidMesh() throws Exception {
+ try {
+ meshParser.getMeSH(null);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQuery() throws Exception {
+ try {
+ Object res = meshParser.refreshCacheQuery("http://google.pl/");
+ assertNotNull(res);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetRotenoneMesh() throws Exception {
+ try {
+ // Rotenone disease -no synonyms
+ MiriamData meshID = new MiriamData(MiriamType.MESH_2012, "D012402");
+ MeSH mesh = meshParser.getMeSH(meshID);
+ assertTrue(mesh != null);
+ assertTrue(mesh.getMeSHId() != null);
+ assertTrue(mesh.getName() != null);
+ assertTrue(mesh.getName().toLowerCase().equals("rotenone"));
+ assertTrue(mesh.getDescription() != null);
+ assertEquals(0, mesh.getSynonyms().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCreateChemicalListFromDB3() throws Exception {
+ try {
+ // One synonyms
+ MiriamData meshID = new MiriamData(MiriamType.MESH_2012, "C503102");
+ MeSH mesh = meshParser.getMeSH(meshID);
+ assertTrue(mesh != null);
+ assertTrue(mesh.getMeSHId() != null);
+ assertTrue(mesh.getName() != null);
+ assertTrue(
+ mesh.getName().toLowerCase().contains("1-(3-(2-(1-benzothiophen-5-yl) ethoxy) propyl)-3-azetidinol maleate"));
+ assertNull(mesh.getDescription());
+ assertEquals(1, mesh.getSynonyms().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetMEshWithNetworkProblems() throws Exception {
+ try {
+ // Parkinson disease
+ MiriamData meshID = new MiriamData(MiriamType.MESH_2012, "D004298");
+ MeSHParser parserUnderTest = new MeSHParser();
+ WebPageDownloader webPageDownloader = Mockito.mock(WebPageDownloader.class);
+ when(webPageDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ parserUnderTest.setWebPageDownloader(webPageDownloader);
+
+ parserUnderTest.getMeSH(meshID);
+ fail("Exception expected");
+ } catch (AnnotatorException e) {
+ assertTrue(e.getMessage().contains("Problem with accessing MeSH database"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ /**
+ * @throws Exception
+ */
+ @Test
+ public void testExternalDBStatus() throws Exception {
+ ExternalServiceStatus status = meshParser.getServiceStatus();
+ logger.debug("Status of MeSH DB : " + status.getStatus().name());
+ assertTrue(status.getStatus().equals(ExternalServiceStatusType.OK));
+ }
+
+ @Test
+ public void testCachableInterfaceInvalidateChemical() throws Exception {
+ try {
+ MiriamData meshID = new MiriamData(MiriamType.MESH_2012, "D010300");
+ MeSH mesh = meshParser.getMeSH(meshID);
+ assertNotNull(mesh);
+
+ waitForRefreshCacheQueueToEmpty();
+
+ cache.invalidateByQuery(meshParser.getIdentifier(meshID), meshParser.getCacheType());
+
+ waitForRefreshCacheQueueToEmpty();
+
+ MeSH mesh2 = meshParser.getMeSH(meshID);
+ assertNotNull(mesh2);
+
+ assertFalse("Value wasn't refreshed from db", mesh.equals(mesh2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCleanHtml() {
+ try {
+ String withouthHtml = meshParser.cleanHtml(
+ "<TD colspan=1>One of the catecholamine <A href=\"/cgi/mesh/2014/MB_cgi?mode=&term=NEUROTRANSMITTERS\">");
+ assertFalse(withouthHtml.contains("<"));
+ assertFalse(withouthHtml.contains(">"));
+ assertTrue(withouthHtml.contains("catecholamine"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery() throws Exception {
+ try {
+ meshParser.refreshCacheQuery("invalid_query");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery2() throws Exception {
+ try {
+ meshParser.refreshCacheQuery(new Object());
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery3() throws Exception {
+ try {
+ String query = MeSHParser.MESH_PREFIX + "::::::";
+ meshParser.refreshCacheQuery(query);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Problematic query"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshWhenProblemWithSourceDb() throws Exception {
+ WebPageDownloader downloader = meshParser.getWebPageDownloader();
+ GeneralCacheInterface cache = meshParser.getCache();
+ try {
+ meshParser.setCache(null);
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ meshParser.setWebPageDownloader(mockDownloader);
+
+ MiriamData meshID = new MiriamData(MiriamType.MESH_2012, "D010300");
+
+ meshParser.refreshCacheQuery(meshParser.getIdentifier(meshID));
+ fail("Exception expected");
+ } catch (SourceNotAvailable e) {
+ assertTrue(e.getMessage().contains("Problem with accessing Mesh database"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ meshParser.setWebPageDownloader(downloader);
+ meshParser.setCache(cache);
+ }
+ }
+
+ @Test
+ public void testSimulateDownStatus() throws Exception {
+ WebPageDownloader downloader = meshParser.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ meshParser.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.DOWN, meshParser.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ meshParser.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testSimulateChangeStatus() throws Exception {
+ WebPageDownloader downloader = meshParser.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString()))
+ .thenThrow(new WrongResponseCodeIOException(null, HttpStatus.SC_NOT_FOUND));
+ meshParser.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.CHANGED, meshParser.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ meshParser.setWebPageDownloader(downloader);
+ }
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiRNAParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiRNAParserTest.java
index a8faadb77a..b6cf175ca0 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiRNAParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiRNAParserTest.java
@@ -1,334 +1,334 @@
-package lcsb.mapviewer.annotation.services;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-import static org.mockito.Matchers.anyString;
-import static org.mockito.Mockito.when;
-
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.annotation.AnnotationTestFunctions;
-import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.GeneralCacheWithExclusion;
-import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
-import lcsb.mapviewer.annotation.data.MiRNA;
-import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.model.Model;
-
-public class MiRNAParserTest extends AnnotationTestFunctions {
- Logger logger = Logger.getLogger(MiRNAParserTest.class);
-
- @Autowired
- MiRNAParser miRNAParser;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void test() throws Exception {
- }
-
- @Test
- public void testExternalDBStatus() throws Exception {
- ExternalServiceStatus status = miRNAParser.getServiceStatus();
- assertTrue(status.getStatus().equals(ExternalServiceStatusType.OK));
- }
-
- @Test
- public void testFindMultipleByIDFromDB() throws Exception {
- try {
- List<String> names = new ArrayList<>();
- names.add("gga-miR-489-3p");
- names.add("rno-miR-9a-5p");
- List<MiRNA> listFromDB = miRNAParser.getMiRnasByNames(names);
- assertTrue(!listFromDB.isEmpty());
- assertEquals(2, listFromDB.size());
- assertEquals(1, listFromDB.get(0).getTargets().size());
- assertEquals(5, listFromDB.get(1).getTargets().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindById() throws Exception {
- try {
- List<String> names = new ArrayList<>();
- names.add("mmu-miR-122-5p");
- List<MiRNA> listFromDB = miRNAParser.getMiRnasByNames(names);
- assertEquals(1, listFromDB.size());
- MiRNA mirna = listFromDB.get(0);
- for (Target target : mirna.getTargets()) {
- assertNotNull(target.getName());
- assertEquals(new MiriamData(MiriamType.TAXONOMY, "10090"), target.getOrganism());
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindWhenProblemWithTaxonomy() throws Exception {
- TaxonomyBackend taxonomyBackend = miRNAParser.getTaxonomyBackend();
- GeneralCacheInterface cache = miRNAParser.getCache();
- try {
- List<String> names = new ArrayList<>();
- names.add("mmu-miR-122-5p");
- miRNAParser.setCache(null);
- TaxonomyBackend backend = Mockito.mock(TaxonomyBackend.class);
- when(backend.getByName(anyString())).thenThrow(new TaxonomySearchException(null, null));
- miRNAParser.setTaxonomyBackend(backend);
- try {
- miRNAParser.getMiRnasByNames(names);
- fail("Exception expected");
- } catch (MiRNASearchException e) {
-
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- miRNAParser.setCache(cache);
- miRNAParser.setTaxonomyBackend(taxonomyBackend);
- }
- }
-
- @Test
- public void testFindById2() throws Exception {
- try {
- List<String> names = new ArrayList<>();
- names.add("hsa-miR-122-5p");
- List<MiRNA> listFromDB = miRNAParser.getMiRnasByNames(names);
- assertEquals(1, listFromDB.size());
- MiRNA mirna = listFromDB.get(0);
- for (Target target : mirna.getTargets()) {
- assertNotNull(target.getName());
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindByTarget() throws Exception {
-
- GeneralCacheInterface cache = miRNAParser.getCache();
- // exclude first cached value
- miRNAParser.setCache(new GeneralCacheWithExclusion(cache, 1));
- try {
- Set<MiriamData> targets = new HashSet<MiriamData>();
- MiriamData hgncTarget = new MiriamData(MiriamType.HGNC_SYMBOL, "PLAG1");
- targets.add(hgncTarget);
- List<MiRNA> listFromDB = miRNAParser.getMiRnaListByTargets(targets);
- assertTrue(listFromDB.size() > 0);
- for (MiRNA miRNA : listFromDB) {
- boolean found = false;
- for (Target targt : miRNA.getTargets()) {
- if (targt.getGenes().contains(hgncTarget)) {
- found = true;
- }
- }
- assertTrue(found);
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- miRNAParser.setCache(cache);
- }
- }
-
- @Test(timeout = 50000)
- public void testCachableInterfaceInvalidateChemical() throws Exception {
- try {
- List<String> listIds = new ArrayList<>();
- listIds.add("gga-miR-489-3p");
- List<MiRNA> list = miRNAParser.getMiRnasByNames(listIds);
- assertTrue(!list.isEmpty());
- assertEquals(1, list.get(0).getTargets().size());
-
- waitForRefreshCacheQueueToEmpty();
-
- cache.invalidateByQuery(MiRNAParser.MI_RNA_PREFIX + list.get(0).getName(), miRNAParser.getCacheType());
-
- waitForRefreshCacheQueueToEmpty();
-
- listIds.clear();
- listIds.add(list.get(0).getName());
-
- List<MiRNA> list2 = miRNAParser.getMiRnasByNames(listIds);
- assertNotNull(list2);
- assertEquals(1, list2.size());
- assertFalse("Value wasn't refreshed from db", list.get(0).equals(list2.get(0)));
- assertTrue(list.get(0).getName().equals(list2.get(0).getName()));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetMiRna() throws Exception {
- try {
- String mirBaseName = "hsa-miR-296-5p";
- List<String> names = new ArrayList<>();
- names.add(mirBaseName);
- List<MiRNA> list = miRNAParser.getMiRnasByNames(names);
- assertTrue(!list.isEmpty());
- MiRNA mirna = list.get(0);
-
- for (Target target : mirna.getTargets()) {
- Set<MiriamData> mds = new HashSet<>();
- mds.addAll(target.getReferences());
- assertEquals("Target contains duplicat references: " + target, mds.size(), target.getReferences().size());
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void invalidMiRNAToString2() throws Exception {
- try {
-
- String str = miRNAParser.getMiRnaSerializer().objectToString(null);
- assertNull(str);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery() throws Exception {
- try {
- miRNAParser.refreshCacheQuery("invalid_query");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery2() throws Exception {
- try {
- miRNAParser.refreshCacheQuery(new Object());
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshCacheQuery() throws Exception {
- try {
- Object result = miRNAParser.refreshCacheQuery(MiRNAParser.MI_RNA_PREFIX + "mmu-miR-122-5p");
- assertNotNull(result);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshCacheQueryWhenProblemWithTaxonomy() throws Exception {
- TaxonomyBackend taxonomyBackend = miRNAParser.getTaxonomyBackend();
- try {
- TaxonomyBackend mockBackend = Mockito.mock(TaxonomyBackend.class);
- when(mockBackend.getByName(anyString())).thenThrow(new TaxonomySearchException(null, null));
- miRNAParser.setTaxonomyBackend(mockBackend);
- miRNAParser.refreshCacheQuery(MiRNAParser.MI_RNA_PREFIX + "mmu-miR-122-5p");
- fail("Exception expected");
- } catch (SourceNotAvailable e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- miRNAParser.setTaxonomyBackend(taxonomyBackend);
- }
- }
-
- @Test
- public void testRefreshCacheQuery2() throws Exception {
- try {
- Object result = miRNAParser
- .refreshCacheQuery(MiRNAParser.MI_RNA_TARGET_PREFIX + MiriamType.HGNC_SYMBOL + ":" + "PLAG1");
- assertNotNull(result);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetEmptySuggestedQueryList() throws Exception {
- try {
- Project project = new Project();
- project.setId(-1);
-
- List<String> result = miRNAParser.getSuggestedQueryList(project);
-
- assertEquals(0, result.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetSuggestedQueryList() throws Exception {
- try {
- Project project = new Project();
- Model model = getModelForFile("testFiles/target_mirna/target.xml", false);
- project.addModel(model);
-
- List<String> result = miRNAParser.getSuggestedQueryList(project);
-
- assertTrue(result.size() > 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
-}
+package lcsb.mapviewer.annotation.services;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import static org.mockito.Matchers.anyString;
+import static org.mockito.Mockito.when;
+
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.AnnotationTestFunctions;
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.GeneralCacheWithExclusion;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.data.MiRNA;
+import lcsb.mapviewer.annotation.data.Target;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.model.Model;
+
+public class MiRNAParserTest extends AnnotationTestFunctions {
+ Logger logger = Logger.getLogger(MiRNAParserTest.class);
+
+ @Autowired
+ MiRNAParser miRNAParser;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void test() throws Exception {
+ }
+
+ @Test
+ public void testExternalDBStatus() throws Exception {
+ ExternalServiceStatus status = miRNAParser.getServiceStatus();
+ assertTrue(status.getStatus().equals(ExternalServiceStatusType.OK));
+ }
+
+ @Test
+ public void testFindMultipleByIDFromDB() throws Exception {
+ try {
+ List<String> names = new ArrayList<>();
+ names.add("gga-miR-489-3p");
+ names.add("rno-miR-9a-5p");
+ List<MiRNA> listFromDB = miRNAParser.getMiRnasByNames(names);
+ assertTrue(!listFromDB.isEmpty());
+ assertEquals(2, listFromDB.size());
+ assertEquals(1, listFromDB.get(0).getTargets().size());
+ assertEquals(5, listFromDB.get(1).getTargets().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindById() throws Exception {
+ try {
+ List<String> names = new ArrayList<>();
+ names.add("mmu-miR-122-5p");
+ List<MiRNA> listFromDB = miRNAParser.getMiRnasByNames(names);
+ assertEquals(1, listFromDB.size());
+ MiRNA mirna = listFromDB.get(0);
+ for (Target target : mirna.getTargets()) {
+ assertNotNull(target.getName());
+ assertEquals(new MiriamData(MiriamType.TAXONOMY, "10090"), target.getOrganism());
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindWhenProblemWithTaxonomy() throws Exception {
+ TaxonomyBackend taxonomyBackend = miRNAParser.getTaxonomyBackend();
+ GeneralCacheInterface cache = miRNAParser.getCache();
+ try {
+ List<String> names = new ArrayList<>();
+ names.add("mmu-miR-122-5p");
+ miRNAParser.setCache(null);
+ TaxonomyBackend backend = Mockito.mock(TaxonomyBackend.class);
+ when(backend.getByName(anyString())).thenThrow(new TaxonomySearchException(null, null));
+ miRNAParser.setTaxonomyBackend(backend);
+ try {
+ miRNAParser.getMiRnasByNames(names);
+ fail("Exception expected");
+ } catch (MiRNASearchException e) {
+
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ miRNAParser.setCache(cache);
+ miRNAParser.setTaxonomyBackend(taxonomyBackend);
+ }
+ }
+
+ @Test
+ public void testFindById2() throws Exception {
+ try {
+ List<String> names = new ArrayList<>();
+ names.add("hsa-miR-122-5p");
+ List<MiRNA> listFromDB = miRNAParser.getMiRnasByNames(names);
+ assertEquals(1, listFromDB.size());
+ MiRNA mirna = listFromDB.get(0);
+ for (Target target : mirna.getTargets()) {
+ assertNotNull(target.getName());
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindByTarget() throws Exception {
+
+ GeneralCacheInterface cache = miRNAParser.getCache();
+ // exclude first cached value
+ miRNAParser.setCache(new GeneralCacheWithExclusion(cache, 1));
+ try {
+ Set<MiriamData> targets = new HashSet<MiriamData>();
+ MiriamData hgncTarget = new MiriamData(MiriamType.HGNC_SYMBOL, "PLAG1");
+ targets.add(hgncTarget);
+ List<MiRNA> listFromDB = miRNAParser.getMiRnaListByTargets(targets);
+ assertTrue(listFromDB.size() > 0);
+ for (MiRNA miRNA : listFromDB) {
+ boolean found = false;
+ for (Target targt : miRNA.getTargets()) {
+ if (targt.getGenes().contains(hgncTarget)) {
+ found = true;
+ }
+ }
+ assertTrue(found);
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ miRNAParser.setCache(cache);
+ }
+ }
+
+ @Test(timeout = 50000)
+ public void testCachableInterfaceInvalidateChemical() throws Exception {
+ try {
+ List<String> listIds = new ArrayList<>();
+ listIds.add("gga-miR-489-3p");
+ List<MiRNA> list = miRNAParser.getMiRnasByNames(listIds);
+ assertTrue(!list.isEmpty());
+ assertEquals(1, list.get(0).getTargets().size());
+
+ waitForRefreshCacheQueueToEmpty();
+
+ cache.invalidateByQuery(MiRNAParser.MI_RNA_PREFIX + list.get(0).getName(), miRNAParser.getCacheType());
+
+ waitForRefreshCacheQueueToEmpty();
+
+ listIds.clear();
+ listIds.add(list.get(0).getName());
+
+ List<MiRNA> list2 = miRNAParser.getMiRnasByNames(listIds);
+ assertNotNull(list2);
+ assertEquals(1, list2.size());
+ assertFalse("Value wasn't refreshed from db", list.get(0).equals(list2.get(0)));
+ assertTrue(list.get(0).getName().equals(list2.get(0).getName()));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetMiRna() throws Exception {
+ try {
+ String mirBaseName = "hsa-miR-296-5p";
+ List<String> names = new ArrayList<>();
+ names.add(mirBaseName);
+ List<MiRNA> list = miRNAParser.getMiRnasByNames(names);
+ assertTrue(!list.isEmpty());
+ MiRNA mirna = list.get(0);
+
+ for (Target target : mirna.getTargets()) {
+ Set<MiriamData> mds = new HashSet<>();
+ mds.addAll(target.getReferences());
+ assertEquals("Target contains duplicat references: " + target, mds.size(), target.getReferences().size());
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void invalidMiRNAToString2() throws Exception {
+ try {
+
+ String str = miRNAParser.getMiRnaSerializer().objectToString(null);
+ assertNull(str);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery() throws Exception {
+ try {
+ miRNAParser.refreshCacheQuery("invalid_query");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery2() throws Exception {
+ try {
+ miRNAParser.refreshCacheQuery(new Object());
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQuery() throws Exception {
+ try {
+ Object result = miRNAParser.refreshCacheQuery(MiRNAParser.MI_RNA_PREFIX + "mmu-miR-122-5p");
+ assertNotNull(result);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQueryWhenProblemWithTaxonomy() throws Exception {
+ TaxonomyBackend taxonomyBackend = miRNAParser.getTaxonomyBackend();
+ try {
+ TaxonomyBackend mockBackend = Mockito.mock(TaxonomyBackend.class);
+ when(mockBackend.getByName(anyString())).thenThrow(new TaxonomySearchException(null, null));
+ miRNAParser.setTaxonomyBackend(mockBackend);
+ miRNAParser.refreshCacheQuery(MiRNAParser.MI_RNA_PREFIX + "mmu-miR-122-5p");
+ fail("Exception expected");
+ } catch (SourceNotAvailable e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ miRNAParser.setTaxonomyBackend(taxonomyBackend);
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQuery2() throws Exception {
+ try {
+ Object result = miRNAParser
+ .refreshCacheQuery(MiRNAParser.MI_RNA_TARGET_PREFIX + MiriamType.HGNC_SYMBOL + ":" + "PLAG1");
+ assertNotNull(result);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetEmptySuggestedQueryList() throws Exception {
+ try {
+ Project project = new Project();
+ project.setId(-1);
+
+ List<String> result = miRNAParser.getSuggestedQueryList(project);
+
+ assertEquals(0, result.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetSuggestedQueryList() throws Exception {
+ try {
+ Project project = new Project();
+ Model model = getModelForFile("testFiles/target_mirna/target.xml", false);
+ project.addModel(model);
+
+ List<String> result = miRNAParser.getSuggestedQueryList(project);
+
+ assertTrue(result.size() > 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiRNASearchExceptionTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiRNASearchExceptionTest.java
index 7aa4e069c5..9e191033dc 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiRNASearchExceptionTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiRNASearchExceptionTest.java
@@ -1,39 +1,39 @@
-package lcsb.mapviewer.annotation.services;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-
-import java.io.IOException;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class MiRNASearchExceptionTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testConstructor1() {
- MiRNASearchException exception = new MiRNASearchException(new IOException());
- assertTrue(exception.getCause().getClass().equals(IOException.class));
- }
-
- @Test
- public void testConstructor2() {
- MiRNASearchException exception = new MiRNASearchException("xsd");
- assertEquals("xsd", exception.getMessage());
- }
-
-}
+package lcsb.mapviewer.annotation.services;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.io.IOException;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class MiRNASearchExceptionTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testConstructor1() {
+ MiRNASearchException exception = new MiRNASearchException(new IOException());
+ assertTrue(exception.getCause().getClass().equals(IOException.class));
+ }
+
+ @Test
+ public void testConstructor2() {
+ MiRNASearchException exception = new MiRNASearchException("xsd");
+ assertEquals("xsd", exception.getMessage());
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiriamConnectorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiriamConnectorTest.java
index b9cdf4c350..dfd08bfe87 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiriamConnectorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiriamConnectorTest.java
@@ -1,372 +1,372 @@
-package lcsb.mapviewer.annotation.services;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-import static org.mockito.Matchers.any;
-import static org.mockito.Matchers.anyString;
-import static org.mockito.Mockito.when;
-
-import java.io.IOException;
-
-import org.apache.log4j.Logger;
-import org.hibernate.AnnotationException;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.annotation.AnnotationTestFunctions;
-import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.GeneralCacheWithExclusion;
-import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
-import lcsb.mapviewer.annotation.cache.WebPageDownloader;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
-import uk.ac.ebi.miriam.lib.MiriamLink;
-
-public class MiriamConnectorTest extends AnnotationTestFunctions {
- Logger logger = Logger.getLogger(MiriamConnectorTest.class);
-
- @Autowired
- MiriamConnector miriamConnector;
-
- GeneralCacheInterface cache;
-
- @Before
- public void setUp() throws Exception {
- cache = miriamConnector.getCache();
- }
-
- @After
- public void tearDown() throws Exception {
- miriamConnector.setCache(cache);
- }
-
- @Test
- public void testGoUri() throws Exception {
- try {
- assertFalse(MiriamType.GO.getUris().size() == 1);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test(timeout = 15000)
- public void testMeshUrl() throws Exception {
- try {
- // exclude first cached value
- miriamConnector.setCache(new GeneralCacheWithExclusion(cache, 1));
- MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.MESH_2012, "D004249");
-
- String pageContent = getWebpage(miriamConnector.getUrlString(md));
- assertTrue(pageContent.contains("DNA Damage"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetUrl() throws Exception {
- try {
- // exclude first cached value
- miriamConnector.setCache(new GeneralCacheWithExclusion(cache, 1));
- MiriamData md = TaxonomyBackend.HUMAN_TAXONOMY;
-
- String url = miriamConnector.getUrlString(md);
- assertNotNull(url);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetUrlForInvalidMiriam() throws Exception {
- try {
- miriamConnector.getUrlString(new MiriamData());
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Data type cannot be empty"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetUrlForInvalidMiriam2() throws Exception {
- try {
- miriamConnector.getUrlString(new MiriamData(MiriamType.UNKNOWN, ""));
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("cannot be retreived"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetUrlForInvalidMiriam3() throws Exception {
- try {
- String url = miriamConnector.getUrlString(new MiriamData(MiriamType.ENTREZ, "abc"));
- assertNull(url);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testIsValidIdentifier() throws Exception {
- try {
- assertTrue(miriamConnector.isValidIdentifier(MiriamType.ENTREZ.getCommonName() + ":" + "1234"));
- assertFalse(miriamConnector.isValidIdentifier("blablabla"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testResolveUrl() throws Exception {
- try {
- // exclude first cached value
- miriamConnector.setCache(new GeneralCacheWithExclusion(cache, 1));
- for (MiriamType mt : MiriamType.values()) {
- if (!MiriamType.UNKNOWN.equals(mt)) {
- assertTrue("Invalid URI for MiriamType: " + mt, miriamConnector.isValid(mt.getUris().get(0)));
- }
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefresh() throws Exception {
- String query = MiriamConnector.VALID_URI_PREFIX + MiriamType.HGNC.getUris().get(0);
- try {
- String res = miriamConnector.refreshCacheQuery(query);
- assertNotNull(res);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefresh2() throws Exception {
- MiriamData md = TaxonomyBackend.HUMAN_TAXONOMY;
- String query = MiriamConnector.LINK_DB_PREFIX + md.getDataType().getUris().get(0) + "\n" + md.getResource();
- try {
- String res = miriamConnector.refreshCacheQuery(query);
- assertNotNull(res);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefresh3() throws Exception {
- try {
- String res = miriamConnector.refreshCacheQuery("https://www.google.pl/");
- assertNotNull(res);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetUrl2() throws Exception {
- try {
- // exclude first cached value
- miriamConnector.setCache(new GeneralCacheWithExclusion(cache, 1));
- MiriamData md = TaxonomyBackend.HUMAN_TAXONOMY;
-
- String url = miriamConnector.getUrlString2(md);
- assertNotNull(url);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetUrlForDoi() throws Exception {
- try {
- // exclude first cached value
- MiriamData md = new MiriamData(MiriamType.DOI, "10.1038/npjsba.2016.20");
-
- String url = miriamConnector.getUrlString(md);
- assertNotNull(url);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testMiriamDataToUri() throws Exception {
- try {
- assertNotNull(miriamConnector.miriamDataToUri(TaxonomyBackend.HUMAN_TAXONOMY));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetUrl2WithInvalidApiResponse() throws Exception {
- WebPageDownloader downloader = miriamConnector.getWebPageDownloader();
- GeneralCacheInterface cache = miriamConnector.getCache();
- try {
- // exclude first cached value
- miriamConnector.setCache(new GeneralCacheWithExclusion(cache, 1));
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- miriamConnector.setWebPageDownloader(mockDownloader);
-
- miriamConnector.getUrlString2(TaxonomyBackend.HUMAN_TAXONOMY);
-
- } catch (AnnotationException e) {
- assertTrue(e.getMessage().contains("Problem with accessing miriam REST API"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- miriamConnector.setWebPageDownloader(downloader);
- miriamConnector.setCache(cache);
- }
- }
-
- @Test
- public void testRefreshCacheQueryNotAvailable() throws Exception {
- WebPageDownloader downloader = miriamConnector.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- miriamConnector.setWebPageDownloader(mockDownloader);
- miriamConnector.refreshCacheQuery("http://google.pl/");
- fail("Exception expected");
- } catch (SourceNotAvailable e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- miriamConnector.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery() throws Exception {
- try {
- miriamConnector.refreshCacheQuery("invalid_query");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery2() throws Exception {
- try {
- miriamConnector.refreshCacheQuery(new Object());
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery3() throws Exception {
- try {
- miriamConnector.refreshCacheQuery(MiriamConnector.LINK_DB_PREFIX);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Miriam link query is invalid"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCheckValidyOfEmptyUri() throws Exception {
- try {
- // user connector without cache
- boolean value = new MiriamConnector().isValid("");
- assertFalse(value);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testStatus() throws Exception {
- try {
- assertEquals(ExternalServiceStatusType.OK, miriamConnector.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSimulateDownStatus() throws Exception {
- MiriamLink link = miriamConnector.getLink();
- try {
- MiriamLink mockDownloader = Mockito.mock(MiriamLink.class);
- when(mockDownloader.getLocations(any())).thenThrow(new InvalidStateException());
- miriamConnector.setLink(mockDownloader);
- assertEquals(ExternalServiceStatusType.DOWN, miriamConnector.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- miriamConnector.setLink(link);
- }
- }
-
- @Test
- public void testSimulateDownStatus2() throws Exception {
- MiriamLink link = miriamConnector.getLink();
- try {
- MiriamLink mockDownloader = Mockito.mock(MiriamLink.class);
- when(mockDownloader.getLocations(any())).thenReturn(null);
- miriamConnector.setLink(mockDownloader);
- assertEquals(ExternalServiceStatusType.DOWN, miriamConnector.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- miriamConnector.setLink(link);
- }
- }
-
-}
+package lcsb.mapviewer.annotation.services;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import static org.mockito.Matchers.any;
+import static org.mockito.Matchers.anyString;
+import static org.mockito.Mockito.when;
+
+import java.io.IOException;
+
+import org.apache.log4j.Logger;
+import org.hibernate.AnnotationException;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.AnnotationTestFunctions;
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.GeneralCacheWithExclusion;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.WebPageDownloader;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
+import uk.ac.ebi.miriam.lib.MiriamLink;
+
+public class MiriamConnectorTest extends AnnotationTestFunctions {
+ Logger logger = Logger.getLogger(MiriamConnectorTest.class);
+
+ @Autowired
+ MiriamConnector miriamConnector;
+
+ GeneralCacheInterface cache;
+
+ @Before
+ public void setUp() throws Exception {
+ cache = miriamConnector.getCache();
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ miriamConnector.setCache(cache);
+ }
+
+ @Test
+ public void testGoUri() throws Exception {
+ try {
+ assertFalse(MiriamType.GO.getUris().size() == 1);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test(timeout = 15000)
+ public void testMeshUrl() throws Exception {
+ try {
+ // exclude first cached value
+ miriamConnector.setCache(new GeneralCacheWithExclusion(cache, 1));
+ MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.MESH_2012, "D004249");
+
+ String pageContent = getWebpage(miriamConnector.getUrlString(md));
+ assertTrue(pageContent.contains("DNA Damage"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetUrl() throws Exception {
+ try {
+ // exclude first cached value
+ miriamConnector.setCache(new GeneralCacheWithExclusion(cache, 1));
+ MiriamData md = TaxonomyBackend.HUMAN_TAXONOMY;
+
+ String url = miriamConnector.getUrlString(md);
+ assertNotNull(url);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetUrlForInvalidMiriam() throws Exception {
+ try {
+ miriamConnector.getUrlString(new MiriamData());
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Data type cannot be empty"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetUrlForInvalidMiriam2() throws Exception {
+ try {
+ miriamConnector.getUrlString(new MiriamData(MiriamType.UNKNOWN, ""));
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("cannot be retreived"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetUrlForInvalidMiriam3() throws Exception {
+ try {
+ String url = miriamConnector.getUrlString(new MiriamData(MiriamType.ENTREZ, "abc"));
+ assertNull(url);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testIsValidIdentifier() throws Exception {
+ try {
+ assertTrue(miriamConnector.isValidIdentifier(MiriamType.ENTREZ.getCommonName() + ":" + "1234"));
+ assertFalse(miriamConnector.isValidIdentifier("blablabla"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testResolveUrl() throws Exception {
+ try {
+ // exclude first cached value
+ miriamConnector.setCache(new GeneralCacheWithExclusion(cache, 1));
+ for (MiriamType mt : MiriamType.values()) {
+ if (!MiriamType.UNKNOWN.equals(mt)) {
+ assertTrue("Invalid URI for MiriamType: " + mt, miriamConnector.isValid(mt.getUris().get(0)));
+ }
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefresh() throws Exception {
+ String query = MiriamConnector.VALID_URI_PREFIX + MiriamType.HGNC.getUris().get(0);
+ try {
+ String res = miriamConnector.refreshCacheQuery(query);
+ assertNotNull(res);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefresh2() throws Exception {
+ MiriamData md = TaxonomyBackend.HUMAN_TAXONOMY;
+ String query = MiriamConnector.LINK_DB_PREFIX + md.getDataType().getUris().get(0) + "\n" + md.getResource();
+ try {
+ String res = miriamConnector.refreshCacheQuery(query);
+ assertNotNull(res);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefresh3() throws Exception {
+ try {
+ String res = miriamConnector.refreshCacheQuery("https://www.google.pl/");
+ assertNotNull(res);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetUrl2() throws Exception {
+ try {
+ // exclude first cached value
+ miriamConnector.setCache(new GeneralCacheWithExclusion(cache, 1));
+ MiriamData md = TaxonomyBackend.HUMAN_TAXONOMY;
+
+ String url = miriamConnector.getUrlString2(md);
+ assertNotNull(url);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetUrlForDoi() throws Exception {
+ try {
+ // exclude first cached value
+ MiriamData md = new MiriamData(MiriamType.DOI, "10.1038/npjsba.2016.20");
+
+ String url = miriamConnector.getUrlString(md);
+ assertNotNull(url);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testMiriamDataToUri() throws Exception {
+ try {
+ assertNotNull(miriamConnector.miriamDataToUri(TaxonomyBackend.HUMAN_TAXONOMY));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetUrl2WithInvalidApiResponse() throws Exception {
+ WebPageDownloader downloader = miriamConnector.getWebPageDownloader();
+ GeneralCacheInterface cache = miriamConnector.getCache();
+ try {
+ // exclude first cached value
+ miriamConnector.setCache(new GeneralCacheWithExclusion(cache, 1));
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ miriamConnector.setWebPageDownloader(mockDownloader);
+
+ miriamConnector.getUrlString2(TaxonomyBackend.HUMAN_TAXONOMY);
+
+ } catch (AnnotationException e) {
+ assertTrue(e.getMessage().contains("Problem with accessing miriam REST API"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ miriamConnector.setWebPageDownloader(downloader);
+ miriamConnector.setCache(cache);
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQueryNotAvailable() throws Exception {
+ WebPageDownloader downloader = miriamConnector.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ miriamConnector.setWebPageDownloader(mockDownloader);
+ miriamConnector.refreshCacheQuery("http://google.pl/");
+ fail("Exception expected");
+ } catch (SourceNotAvailable e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ miriamConnector.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery() throws Exception {
+ try {
+ miriamConnector.refreshCacheQuery("invalid_query");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery2() throws Exception {
+ try {
+ miriamConnector.refreshCacheQuery(new Object());
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery3() throws Exception {
+ try {
+ miriamConnector.refreshCacheQuery(MiriamConnector.LINK_DB_PREFIX);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Miriam link query is invalid"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCheckValidyOfEmptyUri() throws Exception {
+ try {
+ // user connector without cache
+ boolean value = new MiriamConnector().isValid("");
+ assertFalse(value);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testStatus() throws Exception {
+ try {
+ assertEquals(ExternalServiceStatusType.OK, miriamConnector.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSimulateDownStatus() throws Exception {
+ MiriamLink link = miriamConnector.getLink();
+ try {
+ MiriamLink mockDownloader = Mockito.mock(MiriamLink.class);
+ when(mockDownloader.getLocations(any())).thenThrow(new InvalidStateException());
+ miriamConnector.setLink(mockDownloader);
+ assertEquals(ExternalServiceStatusType.DOWN, miriamConnector.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ miriamConnector.setLink(link);
+ }
+ }
+
+ @Test
+ public void testSimulateDownStatus2() throws Exception {
+ MiriamLink link = miriamConnector.getLink();
+ try {
+ MiriamLink mockDownloader = Mockito.mock(MiriamLink.class);
+ when(mockDownloader.getLocations(any())).thenReturn(null);
+ miriamConnector.setLink(mockDownloader);
+ assertEquals(ExternalServiceStatusType.DOWN, miriamConnector.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ miriamConnector.setLink(link);
+ }
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
index 0efd208ec9..ced49d86ec 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
@@ -1,459 +1,459 @@
-package lcsb.mapviewer.annotation.services;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-import static org.mockito.Matchers.any;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.apache.commons.lang3.mutable.MutableDouble;
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.annotation.AnnotationTestFunctions;
-import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
-import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.ReconAnnotator;
-import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
-import lcsb.mapviewer.model.map.model.SubmodelType;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.persist.dao.map.ModelDao;
-
-public class ModelAnnotatorTest extends AnnotationTestFunctions {
- Logger logger = Logger.getLogger(ModelAnnotatorTest.class);
- IProgressUpdater updater = new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- };
-
- @Autowired
- private ModelAnnotator modelAnnotator;
-
- @Autowired
- private ModelDao modelDao;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testAnnotateModel() {
- try {
- Model model = new ModelFullIndexed(null);
-
- model.addReaction(new Reaction());
-
- Species proteinAlias1 = new GenericProtein("a1");
- proteinAlias1.setName("SNCA");
-
- Species proteinAlias2 = new GenericProtein("a2");
- proteinAlias2.setName("PDK1");
- proteinAlias2.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CAS, "c"));
-
- model.addElement(proteinAlias1);
- model.addElement(proteinAlias2);
-
- modelAnnotator.annotateModel(model, updater, null);
-
- assertTrue(model.getElementByElementId("a1").getMiriamData().size() > 0);
- assertTrue(model.getElementByElementId("a2").getMiriamData().size() >= 1);
-
- modelAnnotator.annotateModel(model, updater, null);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
- @Test
- public void testAnnotateModelWithGivenAnnotators() {
- try {
- Model model = new ModelFullIndexed(null);
- GenericProtein species = new GenericProtein("id1");
- species.setName("SNCA");
- model.addElement(species);
-
- GenericProtein species2 = new GenericProtein("id2");
- species2.setName("PDK1");
- species2.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CAS, "c"));
- model.addElement(species2);
- model.addReaction(new Reaction());
-
- Map<Class<?>, List<ElementAnnotator>> annotators = new HashMap<>();
- List<ElementAnnotator> annotatorList = new ArrayList<>();
- annotatorList.addAll(modelAnnotator.getDefaultAnnotators());
- annotators.put(Reaction.class, annotatorList);
- annotators.put(GenericProtein.class, new ArrayList<>());
-
- ReconAnnotator reconMock = Mockito.mock(ReconAnnotator.class);
- Mockito.doThrow(new AnnotatorException("")).when(reconMock).annotateElement(any());
- annotators.get(Reaction.class).add(reconMock);
- modelAnnotator.annotateModel(model, updater, annotators);
-
- // check if our mock threw an exception and if this exception is in logs
- assertEquals(1, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
-
- @Test
- public void testCopyMissingAnnotationsInCD() throws Exception {
- try {
- Model model = getModelForFile("testFiles/annotation/copyingAnnotationModel.xml", true);
-
- modelAnnotator.copyAnnotationFromOtherSpecies(model, updater);
-
- for (Species element : model.getSpeciesList()) {
- if (element.getName().equals("s4"))
- assertEquals(0, element.getMiriamData().size());
- else if (element.getName().equals("hello"))
- assertEquals(1, element.getMiriamData().size());
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDuplicateAnnotations() throws Exception {
- try {
- int counter = 0;
- Model model = getModelForFile("testFiles/annotation/duplicate.xml", false);
-
- Set<String> knowAnnotations = new HashSet<String>();
-
- modelAnnotator.annotateModel(model, updater, null);
- for (MiriamData md : model.getElementByElementId("sa1").getMiriamData()) {
- knowAnnotations.add(md.getDataType() + ":" + md.getRelationType() + ":" + md.getResource());
- }
- counter = 0;
- for (String string : knowAnnotations) {
- if (string.contains("29108")) {
- counter++;
- }
- }
- assertEquals(1, counter);
-
- modelAnnotator.annotateModel(model, updater, null);
-
- knowAnnotations.clear();
- for (MiriamData md : model.getElementByElementId("sa1").getMiriamData()) {
- knowAnnotations.add(md.getDataType() + ":" + md.getRelationType() + ":" + md.getResource());
- }
- counter = 0;
- for (String string : knowAnnotations) {
- if (string.contains("29108")) {
- counter++;
- }
- }
- assertEquals(1, counter);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAnnotationsForSYN() throws Exception {
- try {
- Model model = getModelForFile("testFiles/annotation/emptyAnnotationsSyn1.xml", true);
- Element sa1 = model.getElementByElementId("sa1");
- Element sa2 = model.getElementByElementId("sa2");
-
- assertFalse(sa1.getNotes().contains("Symbol"));
- assertFalse(sa2.getNotes().contains("Symbol"));
- modelAnnotator.annotateModel(model, updater, null);
- assertFalse(sa2.getNotes().contains("Symbol"));
- assertNotNull(sa1.getSymbol());
- assertFalse(sa1.getSymbol().equals(""));
- // modelAnnotator.removeIncorrectAnnotations(model, updater);
- assertNotNull(sa1.getSymbol());
- assertFalse(sa1.getSymbol().equals(""));
- assertFalse(sa1.getNotes().contains("Symbol"));
- assertFalse(sa2.getNotes().contains("Symbol"));
- assertNull(sa2.getSymbol());
-
- for (Species el : model.getSpeciesList()) {
- if (el.getNotes() != null) {
- assertFalse("Invalid notes: " + el.getNotes(), el.getNotes().contains("Symbol"));
- assertFalse("Invalid notes: " + el.getNotes(), el.getNotes().contains("HGNC"));
- }
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindInmproperAnnotations() throws Exception {
- try {
- Model model = getModelForFile("testFiles/annotation/centeredAnchorInModifier.xml", true);
- Collection<? extends ProblematicAnnotation> results = modelAnnotator.findImproperAnnotations(model, new IProgressUpdater() {
-
- @Override
- public void setProgress(double progress) {
- // TODO Auto-generated method stub
-
- }
- }, null);
- assertTrue(results.size() > 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindInmproperAnnotations2() throws Exception {
- try {
- List<MiriamType> list = new ArrayList<>();
- list.add(MiriamType.PUBMED);
- Reaction reaction = new Reaction();
- reaction.addMiriamData(new MiriamData(MiriamType.PUBMED, "12345"));
- List<ImproperAnnotations> result = modelAnnotator.findImproperAnnotations(reaction, list);
- assertEquals(0, result.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindInmproperAnnotations3() throws Exception {
- try {
- List<MiriamType> list = new ArrayList<>();
- list.add(MiriamType.PUBMED);
- Reaction reaction = new Reaction();
- reaction.addMiriamData(new MiriamData(MiriamType.PUBMED, "inv_id"));
- List<ImproperAnnotations> result = modelAnnotator.findImproperAnnotations(reaction, list);
- assertEquals(1, result.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindMissingAnnotations() throws Exception {
- try {
- Model model = getModelForFile("testFiles/annotation/missingAnnotations.xml", false);
- Collection<? extends ProblematicAnnotation> results = modelAnnotator.findMissingAnnotations(model, null);
- assertEquals(7, results.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindMissingAnnotations2() throws Exception {
- try {
- Model model = getModelForFile("testFiles/annotation/missingAnnotations.xml", false);
- Map<Class<? extends BioEntity>, Set<MiriamType>> requestedAnnotations = new HashMap<>();;
- requestedAnnotations.put(GenericProtein.class, new HashSet<>());
- Collection<? extends ProblematicAnnotation> results = modelAnnotator.findMissingAnnotations(model, requestedAnnotations);
- assertEquals(1, results.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAnnotateModelWithDrugMolecule() throws Exception {
- try {
- Model model = super.getModelForFile("testFiles/annotation/problematic.xml", false);
-
- modelAnnotator.annotateModel(model, updater, null);
-
- modelDao.add(model);
-
- modelDao.delete(model);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetDefaultRequired() throws Exception {
- try {
- Map<Class<? extends BioEntity>, Set<MiriamType>> map1 = modelAnnotator.getDefaultRequiredClasses();
- assertNotNull(map1);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetDefaultValid() throws Exception {
- try {
- Map<Class<? extends BioEntity>, Set<MiriamType>> map2 = modelAnnotator.getDefaultValidClasses();
- assertNotNull(map2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testPerformAnnotationAndCheckProgress() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
- Model submodel = new ModelFullIndexed(null);
- Model submodel2 = new ModelFullIndexed(null);
-
- GenericProtein protein = new GenericProtein("el");
-
- model.addSubmodelConnection(new ModelSubmodelConnection(submodel, SubmodelType.UNKNOWN));
- model.addSubmodelConnection(new ModelSubmodelConnection(submodel2, SubmodelType.UNKNOWN));
-
- model.addElement(protein);
- submodel.addElement(protein);
- submodel2.addElement(protein);
-
- final MutableDouble maxProgress = new MutableDouble(0.0);
-
- modelAnnotator.performAnnotations(model, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- maxProgress.setValue(Math.max(progress, maxProgress.getValue()));
- }
- });
- assertTrue(maxProgress.getValue() <= IProgressUpdater.MAX_PROGRESS);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAvailableAnnotators() {
- try {
- List<ElementAnnotator> list = modelAnnotator.getAvailableAnnotators(Protein.class);
- assertTrue(list.size() > 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAvailableAnnotatorNamess() {
- try {
- List<String> list = modelAnnotator.getAvailableAnnotatorNames(Protein.class);
- assertTrue(list.size() > 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAvailableAnnotators2() {
- try {
- List<ElementAnnotator> list = modelAnnotator.getAvailableAnnotators();
- assertTrue(list.size() > 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAvailableDefaultAnnotators() {
- try {
- List<ElementAnnotator> list = modelAnnotator.getAvailableDefaultAnnotators(Protein.class);
- assertTrue(list.size() > 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAvailableDefaultAnnotatorNamess() {
- try {
- List<String> list = modelAnnotator.getAvailableDefaultAnnotatorNames(Protein.class);
- assertTrue(list.size() > 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAnnotatorsFromCommonNames() {
- try {
- List<ElementAnnotator> list = modelAnnotator.getAnnotatorsFromCommonNames(modelAnnotator.getAvailableAnnotatorNames(Protein.class));
- assertTrue(list.size() > 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAnnotatorsFromInvalidName() {
- try {
- String name = "unkName";
- List<String> names = new ArrayList<>();
- names.add(name);
- modelAnnotator.getAnnotatorsFromCommonNames(names);
- fail();
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
-}
+package lcsb.mapviewer.annotation.services;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import static org.mockito.Matchers.any;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.commons.lang3.mutable.MutableDouble;
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.AnnotationTestFunctions;
+import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
+import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
+import lcsb.mapviewer.annotation.services.annotators.ReconAnnotator;
+import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
+import lcsb.mapviewer.model.map.model.SubmodelType;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.persist.dao.map.ModelDao;
+
+public class ModelAnnotatorTest extends AnnotationTestFunctions {
+ Logger logger = Logger.getLogger(ModelAnnotatorTest.class);
+ IProgressUpdater updater = new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ };
+
+ @Autowired
+ private ModelAnnotator modelAnnotator;
+
+ @Autowired
+ private ModelDao modelDao;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testAnnotateModel() {
+ try {
+ Model model = new ModelFullIndexed(null);
+
+ model.addReaction(new Reaction());
+
+ Species proteinAlias1 = new GenericProtein("a1");
+ proteinAlias1.setName("SNCA");
+
+ Species proteinAlias2 = new GenericProtein("a2");
+ proteinAlias2.setName("PDK1");
+ proteinAlias2.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CAS, "c"));
+
+ model.addElement(proteinAlias1);
+ model.addElement(proteinAlias2);
+
+ modelAnnotator.annotateModel(model, updater, null);
+
+ assertTrue(model.getElementByElementId("a1").getMiriamData().size() > 0);
+ assertTrue(model.getElementByElementId("a2").getMiriamData().size() >= 1);
+
+ modelAnnotator.annotateModel(model, updater, null);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+ @Test
+ public void testAnnotateModelWithGivenAnnotators() {
+ try {
+ Model model = new ModelFullIndexed(null);
+ GenericProtein species = new GenericProtein("id1");
+ species.setName("SNCA");
+ model.addElement(species);
+
+ GenericProtein species2 = new GenericProtein("id2");
+ species2.setName("PDK1");
+ species2.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CAS, "c"));
+ model.addElement(species2);
+ model.addReaction(new Reaction());
+
+ Map<Class<?>, List<ElementAnnotator>> annotators = new HashMap<>();
+ List<ElementAnnotator> annotatorList = new ArrayList<>();
+ annotatorList.addAll(modelAnnotator.getDefaultAnnotators());
+ annotators.put(Reaction.class, annotatorList);
+ annotators.put(GenericProtein.class, new ArrayList<>());
+
+ ReconAnnotator reconMock = Mockito.mock(ReconAnnotator.class);
+ Mockito.doThrow(new AnnotatorException("")).when(reconMock).annotateElement(any());
+ annotators.get(Reaction.class).add(reconMock);
+ modelAnnotator.annotateModel(model, updater, annotators);
+
+ // check if our mock threw an exception and if this exception is in logs
+ assertEquals(1, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+
+ @Test
+ public void testCopyMissingAnnotationsInCD() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/annotation/copyingAnnotationModel.xml", true);
+
+ modelAnnotator.copyAnnotationFromOtherSpecies(model, updater);
+
+ for (Species element : model.getSpeciesList()) {
+ if (element.getName().equals("s4"))
+ assertEquals(0, element.getMiriamData().size());
+ else if (element.getName().equals("hello"))
+ assertEquals(1, element.getMiriamData().size());
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDuplicateAnnotations() throws Exception {
+ try {
+ int counter = 0;
+ Model model = getModelForFile("testFiles/annotation/duplicate.xml", false);
+
+ Set<String> knowAnnotations = new HashSet<String>();
+
+ modelAnnotator.annotateModel(model, updater, null);
+ for (MiriamData md : model.getElementByElementId("sa1").getMiriamData()) {
+ knowAnnotations.add(md.getDataType() + ":" + md.getRelationType() + ":" + md.getResource());
+ }
+ counter = 0;
+ for (String string : knowAnnotations) {
+ if (string.contains("29108")) {
+ counter++;
+ }
+ }
+ assertEquals(1, counter);
+
+ modelAnnotator.annotateModel(model, updater, null);
+
+ knowAnnotations.clear();
+ for (MiriamData md : model.getElementByElementId("sa1").getMiriamData()) {
+ knowAnnotations.add(md.getDataType() + ":" + md.getRelationType() + ":" + md.getResource());
+ }
+ counter = 0;
+ for (String string : knowAnnotations) {
+ if (string.contains("29108")) {
+ counter++;
+ }
+ }
+ assertEquals(1, counter);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAnnotationsForSYN() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/annotation/emptyAnnotationsSyn1.xml", true);
+ Element sa1 = model.getElementByElementId("sa1");
+ Element sa2 = model.getElementByElementId("sa2");
+
+ assertFalse(sa1.getNotes().contains("Symbol"));
+ assertFalse(sa2.getNotes().contains("Symbol"));
+ modelAnnotator.annotateModel(model, updater, null);
+ assertFalse(sa2.getNotes().contains("Symbol"));
+ assertNotNull(sa1.getSymbol());
+ assertFalse(sa1.getSymbol().equals(""));
+ // modelAnnotator.removeIncorrectAnnotations(model, updater);
+ assertNotNull(sa1.getSymbol());
+ assertFalse(sa1.getSymbol().equals(""));
+ assertFalse(sa1.getNotes().contains("Symbol"));
+ assertFalse(sa2.getNotes().contains("Symbol"));
+ assertNull(sa2.getSymbol());
+
+ for (Species el : model.getSpeciesList()) {
+ if (el.getNotes() != null) {
+ assertFalse("Invalid notes: " + el.getNotes(), el.getNotes().contains("Symbol"));
+ assertFalse("Invalid notes: " + el.getNotes(), el.getNotes().contains("HGNC"));
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindInmproperAnnotations() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/annotation/centeredAnchorInModifier.xml", true);
+ Collection<? extends ProblematicAnnotation> results = modelAnnotator.findImproperAnnotations(model, new IProgressUpdater() {
+
+ @Override
+ public void setProgress(double progress) {
+ // TODO Auto-generated method stub
+
+ }
+ }, null);
+ assertTrue(results.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindInmproperAnnotations2() throws Exception {
+ try {
+ List<MiriamType> list = new ArrayList<>();
+ list.add(MiriamType.PUBMED);
+ Reaction reaction = new Reaction();
+ reaction.addMiriamData(new MiriamData(MiriamType.PUBMED, "12345"));
+ List<ImproperAnnotations> result = modelAnnotator.findImproperAnnotations(reaction, list);
+ assertEquals(0, result.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindInmproperAnnotations3() throws Exception {
+ try {
+ List<MiriamType> list = new ArrayList<>();
+ list.add(MiriamType.PUBMED);
+ Reaction reaction = new Reaction();
+ reaction.addMiriamData(new MiriamData(MiriamType.PUBMED, "inv_id"));
+ List<ImproperAnnotations> result = modelAnnotator.findImproperAnnotations(reaction, list);
+ assertEquals(1, result.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindMissingAnnotations() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/annotation/missingAnnotations.xml", false);
+ Collection<? extends ProblematicAnnotation> results = modelAnnotator.findMissingAnnotations(model, null);
+ assertEquals(7, results.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindMissingAnnotations2() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/annotation/missingAnnotations.xml", false);
+ Map<Class<? extends BioEntity>, Set<MiriamType>> requestedAnnotations = new HashMap<>();;
+ requestedAnnotations.put(GenericProtein.class, new HashSet<>());
+ Collection<? extends ProblematicAnnotation> results = modelAnnotator.findMissingAnnotations(model, requestedAnnotations);
+ assertEquals(1, results.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotateModelWithDrugMolecule() throws Exception {
+ try {
+ Model model = super.getModelForFile("testFiles/annotation/problematic.xml", false);
+
+ modelAnnotator.annotateModel(model, updater, null);
+
+ modelDao.add(model);
+
+ modelDao.delete(model);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetDefaultRequired() throws Exception {
+ try {
+ Map<Class<? extends BioEntity>, Set<MiriamType>> map1 = modelAnnotator.getDefaultRequiredClasses();
+ assertNotNull(map1);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetDefaultValid() throws Exception {
+ try {
+ Map<Class<? extends BioEntity>, Set<MiriamType>> map2 = modelAnnotator.getDefaultValidClasses();
+ assertNotNull(map2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testPerformAnnotationAndCheckProgress() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+ Model submodel = new ModelFullIndexed(null);
+ Model submodel2 = new ModelFullIndexed(null);
+
+ GenericProtein protein = new GenericProtein("el");
+
+ model.addSubmodelConnection(new ModelSubmodelConnection(submodel, SubmodelType.UNKNOWN));
+ model.addSubmodelConnection(new ModelSubmodelConnection(submodel2, SubmodelType.UNKNOWN));
+
+ model.addElement(protein);
+ submodel.addElement(protein);
+ submodel2.addElement(protein);
+
+ final MutableDouble maxProgress = new MutableDouble(0.0);
+
+ modelAnnotator.performAnnotations(model, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ maxProgress.setValue(Math.max(progress, maxProgress.getValue()));
+ }
+ });
+ assertTrue(maxProgress.getValue() <= IProgressUpdater.MAX_PROGRESS);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAvailableAnnotators() {
+ try {
+ List<ElementAnnotator> list = modelAnnotator.getAvailableAnnotators(Protein.class);
+ assertTrue(list.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAvailableAnnotatorNamess() {
+ try {
+ List<String> list = modelAnnotator.getAvailableAnnotatorNames(Protein.class);
+ assertTrue(list.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAvailableAnnotators2() {
+ try {
+ List<ElementAnnotator> list = modelAnnotator.getAvailableAnnotators();
+ assertTrue(list.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAvailableDefaultAnnotators() {
+ try {
+ List<ElementAnnotator> list = modelAnnotator.getAvailableDefaultAnnotators(Protein.class);
+ assertTrue(list.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAvailableDefaultAnnotatorNamess() {
+ try {
+ List<String> list = modelAnnotator.getAvailableDefaultAnnotatorNames(Protein.class);
+ assertTrue(list.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAnnotatorsFromCommonNames() {
+ try {
+ List<ElementAnnotator> list = modelAnnotator.getAnnotatorsFromCommonNames(modelAnnotator.getAvailableAnnotatorNames(Protein.class));
+ assertTrue(list.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAnnotatorsFromInvalidName() {
+ try {
+ String name = "unkName";
+ List<String> names = new ArrayList<>();
+ names.add(name);
+ modelAnnotator.getAnnotatorsFromCommonNames(names);
+ fail();
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/PubmedParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/PubmedParserTest.java
index bb4b0b68f3..acad513a95 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/PubmedParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/PubmedParserTest.java
@@ -1,425 +1,425 @@
-package lcsb.mapviewer.annotation.services;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-import static org.mockito.Matchers.anyString;
-import static org.mockito.Mockito.when;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.annotation.AnnotationTestFunctions;
-import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
-import lcsb.mapviewer.annotation.cache.WebPageDownloader;
-import lcsb.mapviewer.annotation.cache.XmlSerializer;
-import lcsb.mapviewer.annotation.data.Article;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-
-public class PubmedParserTest extends AnnotationTestFunctions {
- Logger logger = Logger.getLogger(PubmedParserTest.class);
- private boolean status;
- private boolean status2;
- @Autowired
- PubmedParser pubmedParser;
-
- @Autowired
- private GeneralCacheInterface cache;
-
- @Before
- public void setUp() throws Exception {
- status = Configuration.isDbCacheOn();
- status2 = Configuration.isApplicationCacheOn();
- }
-
- @After
- public void tearDown() throws Exception {
- Configuration.setDbCacheOn(status);
- Configuration.setApplicationCacheOn(status2);
- }
-
- @Test
- public void test() {
- try {
- Configuration.setDbCacheOn(false);
- Configuration.setApplicationCacheOn(false);
- Article art = pubmedParser.getPubmedArticleById(9481670);
- assertNotNull(art);
- assertEquals(
- "Adjacent asparagines in the NR2-subunit of the NMDA receptor channel control the voltage-dependent block by extracellular Mg2+.", art.getTitle());
- assertEquals((Integer) 1998, art.getYear());
- assertEquals("The Journal of physiology", art.getJournal());
- assertTrue(art.getStringAuthors().contains("Wollmuth"));
- assertTrue(art.getStringAuthors().contains("Kuner"));
- assertTrue(art.getStringAuthors().contains("Sakmann"));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception " + e.getMessage());
- }
- }
-
- @Test
- public void testCache() {
- try {
- Configuration.setDbCacheOn(true);
- Configuration.setApplicationCacheOn(true);
-
- Article art = pubmedParser.getPubmedArticleById(9481671);
- assertNotNull(art);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception " + e.getMessage());
- }
- }
-
- @Test
- public void testSerialization() {
- try {
-
- Article art = new Article();
- List<String> list = new ArrayList<String>();
- list.add("aaa");
- list.add("bbb");
- art.setTitle("ttt");
- art.setAuthors(list);
- art.setJournal("jjjj");
- art.setYear(123);
-
- String serialString = pubmedParser.getArticleSerializer().objectToString(art);
-
- assertTrue(serialString.contains("aaa"));
- assertTrue(serialString.contains("bbb"));
- assertTrue(serialString.contains("ttt"));
- assertTrue(serialString.contains("jjjj"));
- assertTrue(serialString.contains("123"));
-
- Article art2 = pubmedParser.getArticleSerializer().xmlToObject(getNodeFromXmlString(serialString));
-
- assertEquals(art.getStringAuthors(), art2.getStringAuthors());
- assertEquals(art.getTitle(), art2.getTitle());
- assertEquals(art.getJournal(), art2.getJournal());
- assertEquals(art.getYear(), art2.getYear());
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Exception occurred");
- }
- }
-
- /**
- * This case was problematic with old API used to retrieve data from pubmed
- */
- @Test
- public void testProblematicCase() {
- try {
-
- Article art = pubmedParser.getPubmedArticleById(22363258);
- assertNotNull(art);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception " + e.getMessage());
- }
- }
-
- @Test
- public void testCitationCount() {
- try {
-
- Article art = pubmedParser.getPubmedArticleById(18400456);
- assertNotNull(art);
- assertTrue(art.getCitationCount() >= 53);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception " + e.getMessage());
- }
- }
-
- @Test
- public void testGetSummary() throws Exception {
- try {
- String summary = pubmedParser.getSummary(18400456);
- assertNotNull(summary);
- assertFalse(summary.isEmpty());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetSummary2() throws Exception {
- try {
-
- String summary = pubmedParser.getSummary(23644949);
- assertNull(summary);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetSummary3() throws Exception {
- try {
- String summary = pubmedParser.getSummary("18400456");
- assertNotNull(summary);
- assertFalse(summary.isEmpty());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- // wait max 15 second
- public void testCachableInterface() throws Exception {
- String query = "pubmed: 2112";
- try {
- String newRes = "hello";
- waitForRefreshCacheQueueToEmpty();
-
- cache.setCachedQuery(query, pubmedParser.getCacheType(), newRes);
- cache.invalidateByQuery(query, pubmedParser.getCacheType());
-
- waitForRefreshCacheQueueToEmpty();
-
- String res = cache.getStringByQuery(query, pubmedParser.getCacheType());
-
- assertNotNull(res);
-
- assertFalse("Value wasn't refreshed from db", newRes.equals(res));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery() throws Exception {
- try {
- pubmedParser.refreshCacheQuery("invalid_query");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshWhenExternalNotAvailable() throws Exception {
- WebPageDownloader downloader = pubmedParser.getWebPageDownloader();
- try {
- pubmedParser.setCache(null);
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- pubmedParser.setWebPageDownloader(mockDownloader);
-
- String query = PubmedParser.PUBMED_PREFIX + PubmedParser.SERVICE_STATUS_PUBMED_ID;
-
- pubmedParser.refreshCacheQuery(query);
- fail("Exception expected");
- } catch (SourceNotAvailable e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- pubmedParser.setWebPageDownloader(downloader);
- pubmedParser.setCache(cache);
- }
-
- }
-
- @Test
- public void testRefreshInvalidCacheQuery2() throws Exception {
- try {
- pubmedParser.refreshCacheQuery(new Object());
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetHtmlFullLinkForId() throws Exception {
- try {
- String htmlString = pubmedParser.getHtmlFullLinkForId(1234);
- assertTrue(htmlString.contains("Change in the kinetics of sulphacetamide tissue distribution"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testStatus() throws Exception {
- try {
- assertEquals(ExternalServiceStatusType.OK, pubmedParser.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSimulateDownStatus() throws Exception {
- WebPageDownloader downloader = pubmedParser.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- pubmedParser.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.DOWN, pubmedParser.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- pubmedParser.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testSimulateDownStatus2() throws Exception {
- WebPageDownloader downloader = pubmedParser.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString()))
- .thenReturn("<responseWrapper><version>" + PubmedParser.SUPPORTED_VERSION + "</version></responseWrapper>");
- pubmedParser.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.DOWN, pubmedParser.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- pubmedParser.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testSimulateChangeStatus() throws Exception {
- WebPageDownloader downloader = pubmedParser.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString()))
- .thenReturn("<responseWrapper><version>" + PubmedParser.SUPPORTED_VERSION + "blabla</version></responseWrapper>");
- pubmedParser.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.CHANGED, pubmedParser.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- pubmedParser.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testGetApiVersion() throws Exception {
- try {
- assertNotNull(pubmedParser.getApiVersion());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetApiVersionWhenProblemWithExternalDb() throws Exception {
- WebPageDownloader downloader = pubmedParser.getWebPageDownloader();
- pubmedParser.setCache(null);
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("unknown response");
- pubmedParser.setWebPageDownloader(mockDownloader);
- pubmedParser.getApiVersion();
- fail("Exception expected");
- } catch (PubmedSearchException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- pubmedParser.setCache(cache);
- pubmedParser.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testGetApiVersionWhenProblemWithExternalDb3() throws Exception {
- WebPageDownloader downloader = pubmedParser.getWebPageDownloader();
- pubmedParser.setCache(null);
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("<xml/>");
- pubmedParser.setWebPageDownloader(mockDownloader);
- assertNull(pubmedParser.getApiVersion());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- pubmedParser.setCache(cache);
- pubmedParser.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testGetApiVersionWhenProblemWithExternalDb2() throws Exception {
- WebPageDownloader downloader = pubmedParser.getWebPageDownloader();
- pubmedParser.setCache(null);
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- pubmedParser.setWebPageDownloader(mockDownloader);
- pubmedParser.getApiVersion();
- fail("Exception expected");
- } catch (PubmedSearchException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- pubmedParser.setCache(cache);
- pubmedParser.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testGetters() throws Exception {
- try {
- MiriamConnector mc = new MiriamConnector();
- XmlSerializer<Article> serializer = new XmlSerializer<>(Article.class);
- PubmedParser parser = new PubmedParser();
-
- parser.setMiriamConnector(mc);
- assertEquals(mc, parser.getMiriamConnector());
-
- parser.setArticleSerializer(serializer);
-
- assertEquals(serializer, parser.getArticleSerializer());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.annotation.services;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import static org.mockito.Matchers.anyString;
+import static org.mockito.Mockito.when;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.AnnotationTestFunctions;
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.WebPageDownloader;
+import lcsb.mapviewer.annotation.cache.XmlSerializer;
+import lcsb.mapviewer.annotation.data.Article;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+
+public class PubmedParserTest extends AnnotationTestFunctions {
+ Logger logger = Logger.getLogger(PubmedParserTest.class);
+ private boolean status;
+ private boolean status2;
+ @Autowired
+ PubmedParser pubmedParser;
+
+ @Autowired
+ private GeneralCacheInterface cache;
+
+ @Before
+ public void setUp() throws Exception {
+ status = Configuration.isDbCacheOn();
+ status2 = Configuration.isApplicationCacheOn();
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ Configuration.setDbCacheOn(status);
+ Configuration.setApplicationCacheOn(status2);
+ }
+
+ @Test
+ public void test() {
+ try {
+ Configuration.setDbCacheOn(false);
+ Configuration.setApplicationCacheOn(false);
+ Article art = pubmedParser.getPubmedArticleById(9481670);
+ assertNotNull(art);
+ assertEquals(
+ "Adjacent asparagines in the NR2-subunit of the NMDA receptor channel control the voltage-dependent block by extracellular Mg2+.", art.getTitle());
+ assertEquals((Integer) 1998, art.getYear());
+ assertEquals("The Journal of physiology", art.getJournal());
+ assertTrue(art.getStringAuthors().contains("Wollmuth"));
+ assertTrue(art.getStringAuthors().contains("Kuner"));
+ assertTrue(art.getStringAuthors().contains("Sakmann"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception " + e.getMessage());
+ }
+ }
+
+ @Test
+ public void testCache() {
+ try {
+ Configuration.setDbCacheOn(true);
+ Configuration.setApplicationCacheOn(true);
+
+ Article art = pubmedParser.getPubmedArticleById(9481671);
+ assertNotNull(art);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception " + e.getMessage());
+ }
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+
+ Article art = new Article();
+ List<String> list = new ArrayList<String>();
+ list.add("aaa");
+ list.add("bbb");
+ art.setTitle("ttt");
+ art.setAuthors(list);
+ art.setJournal("jjjj");
+ art.setYear(123);
+
+ String serialString = pubmedParser.getArticleSerializer().objectToString(art);
+
+ assertTrue(serialString.contains("aaa"));
+ assertTrue(serialString.contains("bbb"));
+ assertTrue(serialString.contains("ttt"));
+ assertTrue(serialString.contains("jjjj"));
+ assertTrue(serialString.contains("123"));
+
+ Article art2 = pubmedParser.getArticleSerializer().xmlToObject(getNodeFromXmlString(serialString));
+
+ assertEquals(art.getStringAuthors(), art2.getStringAuthors());
+ assertEquals(art.getTitle(), art2.getTitle());
+ assertEquals(art.getJournal(), art2.getJournal());
+ assertEquals(art.getYear(), art2.getYear());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Exception occurred");
+ }
+ }
+
+ /**
+ * This case was problematic with old API used to retrieve data from pubmed
+ */
+ @Test
+ public void testProblematicCase() {
+ try {
+
+ Article art = pubmedParser.getPubmedArticleById(22363258);
+ assertNotNull(art);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception " + e.getMessage());
+ }
+ }
+
+ @Test
+ public void testCitationCount() {
+ try {
+
+ Article art = pubmedParser.getPubmedArticleById(18400456);
+ assertNotNull(art);
+ assertTrue(art.getCitationCount() >= 53);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception " + e.getMessage());
+ }
+ }
+
+ @Test
+ public void testGetSummary() throws Exception {
+ try {
+ String summary = pubmedParser.getSummary(18400456);
+ assertNotNull(summary);
+ assertFalse(summary.isEmpty());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetSummary2() throws Exception {
+ try {
+
+ String summary = pubmedParser.getSummary(23644949);
+ assertNull(summary);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetSummary3() throws Exception {
+ try {
+ String summary = pubmedParser.getSummary("18400456");
+ assertNotNull(summary);
+ assertFalse(summary.isEmpty());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ // wait max 15 second
+ public void testCachableInterface() throws Exception {
+ String query = "pubmed: 2112";
+ try {
+ String newRes = "hello";
+ waitForRefreshCacheQueueToEmpty();
+
+ cache.setCachedQuery(query, pubmedParser.getCacheType(), newRes);
+ cache.invalidateByQuery(query, pubmedParser.getCacheType());
+
+ waitForRefreshCacheQueueToEmpty();
+
+ String res = cache.getStringByQuery(query, pubmedParser.getCacheType());
+
+ assertNotNull(res);
+
+ assertFalse("Value wasn't refreshed from db", newRes.equals(res));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery() throws Exception {
+ try {
+ pubmedParser.refreshCacheQuery("invalid_query");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshWhenExternalNotAvailable() throws Exception {
+ WebPageDownloader downloader = pubmedParser.getWebPageDownloader();
+ try {
+ pubmedParser.setCache(null);
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ pubmedParser.setWebPageDownloader(mockDownloader);
+
+ String query = PubmedParser.PUBMED_PREFIX + PubmedParser.SERVICE_STATUS_PUBMED_ID;
+
+ pubmedParser.refreshCacheQuery(query);
+ fail("Exception expected");
+ } catch (SourceNotAvailable e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ pubmedParser.setWebPageDownloader(downloader);
+ pubmedParser.setCache(cache);
+ }
+
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery2() throws Exception {
+ try {
+ pubmedParser.refreshCacheQuery(new Object());
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetHtmlFullLinkForId() throws Exception {
+ try {
+ String htmlString = pubmedParser.getHtmlFullLinkForId(1234);
+ assertTrue(htmlString.contains("Change in the kinetics of sulphacetamide tissue distribution"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testStatus() throws Exception {
+ try {
+ assertEquals(ExternalServiceStatusType.OK, pubmedParser.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSimulateDownStatus() throws Exception {
+ WebPageDownloader downloader = pubmedParser.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ pubmedParser.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.DOWN, pubmedParser.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ pubmedParser.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testSimulateDownStatus2() throws Exception {
+ WebPageDownloader downloader = pubmedParser.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString()))
+ .thenReturn("<responseWrapper><version>" + PubmedParser.SUPPORTED_VERSION + "</version></responseWrapper>");
+ pubmedParser.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.DOWN, pubmedParser.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ pubmedParser.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testSimulateChangeStatus() throws Exception {
+ WebPageDownloader downloader = pubmedParser.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString()))
+ .thenReturn("<responseWrapper><version>" + PubmedParser.SUPPORTED_VERSION + "blabla</version></responseWrapper>");
+ pubmedParser.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.CHANGED, pubmedParser.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ pubmedParser.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testGetApiVersion() throws Exception {
+ try {
+ assertNotNull(pubmedParser.getApiVersion());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetApiVersionWhenProblemWithExternalDb() throws Exception {
+ WebPageDownloader downloader = pubmedParser.getWebPageDownloader();
+ pubmedParser.setCache(null);
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("unknown response");
+ pubmedParser.setWebPageDownloader(mockDownloader);
+ pubmedParser.getApiVersion();
+ fail("Exception expected");
+ } catch (PubmedSearchException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ pubmedParser.setCache(cache);
+ pubmedParser.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testGetApiVersionWhenProblemWithExternalDb3() throws Exception {
+ WebPageDownloader downloader = pubmedParser.getWebPageDownloader();
+ pubmedParser.setCache(null);
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("<xml/>");
+ pubmedParser.setWebPageDownloader(mockDownloader);
+ assertNull(pubmedParser.getApiVersion());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ pubmedParser.setCache(cache);
+ pubmedParser.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testGetApiVersionWhenProblemWithExternalDb2() throws Exception {
+ WebPageDownloader downloader = pubmedParser.getWebPageDownloader();
+ pubmedParser.setCache(null);
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ pubmedParser.setWebPageDownloader(mockDownloader);
+ pubmedParser.getApiVersion();
+ fail("Exception expected");
+ } catch (PubmedSearchException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ pubmedParser.setCache(cache);
+ pubmedParser.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testGetters() throws Exception {
+ try {
+ MiriamConnector mc = new MiriamConnector();
+ XmlSerializer<Article> serializer = new XmlSerializer<>(Article.class);
+ PubmedParser parser = new PubmedParser();
+
+ parser.setMiriamConnector(mc);
+ assertEquals(mc, parser.getMiriamConnector());
+
+ parser.setArticleSerializer(serializer);
+
+ assertEquals(serializer, parser.getArticleSerializer());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/TaxonomyBackendTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/TaxonomyBackendTest.java
index a694153509..1feb63abce 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/TaxonomyBackendTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/TaxonomyBackendTest.java
@@ -1,340 +1,340 @@
-package lcsb.mapviewer.annotation.services;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-import static org.mockito.Matchers.anyString;
-import static org.mockito.Mockito.when;
-
-import java.io.IOException;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.annotation.AnnotationTestFunctions;
-import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.GeneralCacheWithExclusion;
-import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
-import lcsb.mapviewer.annotation.cache.WebPageDownloader;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-
-public class TaxonomyBackendTest extends AnnotationTestFunctions {
- Logger logger = Logger.getLogger(TaxonomyBackendTest.class);
-
- @Autowired
- TaxonomyBackend taxonomyBackend;
-
- GeneralCacheInterface cache;
-
- @Before
- public void setUp() throws Exception {
- cache = taxonomyBackend.getCache();
- // exclude two first cached values
- taxonomyBackend.setCache(new GeneralCacheWithExclusion(cache, 2));
- }
-
- @After
- public void tearDown() throws Exception {
- taxonomyBackend.setCache(cache);
- }
-
- @Test
- public void testByName() throws Exception {
- try {
- MiriamData md = taxonomyBackend.getByName("Human");
- assertTrue(md.equals(TaxonomyBackend.HUMAN_TAXONOMY));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testByComplexName() throws Exception {
- try {
- assertNotNull(taxonomyBackend.getByName("Aplysia californica (Sea Hare)"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testByCommonName() throws Exception {
- try {
- assertNotNull(taxonomyBackend.getByName("Rat"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testByEmptyName() throws Exception {
- try {
- assertNull(taxonomyBackend.getByName(null));
- assertNull(taxonomyBackend.getByName(""));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testByAbreviationName() throws Exception {
- try {
- taxonomyBackend.setCache(new GeneralCacheWithExclusion(cache, 1));
- assertNotNull(taxonomyBackend.getByName("C. elegans"));
- taxonomyBackend.setCache(new GeneralCacheWithExclusion(cache, 1));
- assertNotNull(taxonomyBackend.getByName("D. sechellia"));
- taxonomyBackend.setCache(new GeneralCacheWithExclusion(cache, 1));
- assertNotNull(taxonomyBackend.getByName("P. pacificus"));
- taxonomyBackend.setCache(new GeneralCacheWithExclusion(cache, 1));
- assertNotNull(taxonomyBackend.getByName("T. castaneum"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetName() throws Exception {
- try {
- String name = taxonomyBackend.getNameForTaxonomy(new MiriamData(MiriamType.TAXONOMY, "9606"));
- assertTrue(name.contains("Homo sapiens"));
- assertNotNull(taxonomyBackend.getNameForTaxonomy(new MiriamData(MiriamType.TAXONOMY, "9605")));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetNameWhenProblemWithDb() throws Exception {
- WebPageDownloader downloader = taxonomyBackend.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- taxonomyBackend.setWebPageDownloader(mockDownloader);
- taxonomyBackend.setCache(null);
- taxonomyBackend.getNameForTaxonomy(new MiriamData(MiriamType.TAXONOMY, "9606"));
- fail("Exception expected");
- } catch (TaxonomySearchException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- taxonomyBackend.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testGetNameForInvalidTax() throws Exception {
- try {
- String name = taxonomyBackend.getNameForTaxonomy(new MiriamData(MiriamType.TAXONOMY, "-a-"));
- assertNull(name);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetNameForInvalidInputData() throws Exception {
- try {
- String name = taxonomyBackend.getNameForTaxonomy(null);
- assertNull(name);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testByName2() throws Exception {
- try {
- MiriamData md = taxonomyBackend.getByName("homo sapiens");
- assertTrue(md.equals(TaxonomyBackend.HUMAN_TAXONOMY));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testByName3() throws Exception {
- try {
- MiriamData md = taxonomyBackend.getByName("bla bla kiwi");
- assertNull(md);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testByMusMusculusName() throws Exception {
- try {
- MiriamData md = taxonomyBackend.getByName("Mus musculus");
- assertTrue(md.equals(new MiriamData(MiriamType.TAXONOMY, "10090")));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testByMouseName() throws Exception {
- try {
- MiriamData md = taxonomyBackend.getByName("Mouse");
- assertTrue(md.equals(new MiriamData(MiriamType.TAXONOMY, "10090")));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshCacheQuery() throws Exception {
- try {
- String result = taxonomyBackend.refreshCacheQuery(TaxonomyBackend.TAXONOMY_CACHE_PREFIX + "homo sapiens");
- assertNotNull(result);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshCacheQuery2() throws Exception {
- try {
- String result = taxonomyBackend
- .refreshCacheQuery(TaxonomyBackend.TAXONOMY_NAME_CACHE_PREFIX + TaxonomyBackend.HUMAN_TAXONOMY.getResource());
- assertNotNull(result);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshCacheQuery3() throws Exception {
- try {
- String result = taxonomyBackend.refreshCacheQuery("http://google.pl/");
- assertNotNull(result);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery() throws Exception {
- try {
- taxonomyBackend.refreshCacheQuery("unk_query");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery2() throws Exception {
- try {
- taxonomyBackend.refreshCacheQuery(new Object());
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshCacheQueryNotAvailable() throws Exception {
- WebPageDownloader downloader = taxonomyBackend.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- taxonomyBackend.setWebPageDownloader(mockDownloader);
- taxonomyBackend.refreshCacheQuery("http://google.pl/");
- fail("Exception expected");
- } catch (SourceNotAvailable e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- taxonomyBackend.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testStatus() throws Exception {
- try {
- assertEquals(ExternalServiceStatusType.OK, taxonomyBackend.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSimulateDownStatus() throws Exception {
- WebPageDownloader downloader = taxonomyBackend.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- taxonomyBackend.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.DOWN, taxonomyBackend.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- taxonomyBackend.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testSimulateChangedStatus() throws Exception {
- WebPageDownloader downloader = taxonomyBackend.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("");
- taxonomyBackend.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.CHANGED, taxonomyBackend.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- taxonomyBackend.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testSimulateChangedStatus2() throws Exception {
- WebPageDownloader downloader = taxonomyBackend.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("<em>Taxonomy ID: </em>1234");
- taxonomyBackend.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.CHANGED, taxonomyBackend.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- taxonomyBackend.setWebPageDownloader(downloader);
- }
- }
-
-}
+package lcsb.mapviewer.annotation.services;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import static org.mockito.Matchers.anyString;
+import static org.mockito.Mockito.when;
+
+import java.io.IOException;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.AnnotationTestFunctions;
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.GeneralCacheWithExclusion;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.WebPageDownloader;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+
+public class TaxonomyBackendTest extends AnnotationTestFunctions {
+ Logger logger = Logger.getLogger(TaxonomyBackendTest.class);
+
+ @Autowired
+ TaxonomyBackend taxonomyBackend;
+
+ GeneralCacheInterface cache;
+
+ @Before
+ public void setUp() throws Exception {
+ cache = taxonomyBackend.getCache();
+ // exclude two first cached values
+ taxonomyBackend.setCache(new GeneralCacheWithExclusion(cache, 2));
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ taxonomyBackend.setCache(cache);
+ }
+
+ @Test
+ public void testByName() throws Exception {
+ try {
+ MiriamData md = taxonomyBackend.getByName("Human");
+ assertTrue(md.equals(TaxonomyBackend.HUMAN_TAXONOMY));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testByComplexName() throws Exception {
+ try {
+ assertNotNull(taxonomyBackend.getByName("Aplysia californica (Sea Hare)"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testByCommonName() throws Exception {
+ try {
+ assertNotNull(taxonomyBackend.getByName("Rat"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testByEmptyName() throws Exception {
+ try {
+ assertNull(taxonomyBackend.getByName(null));
+ assertNull(taxonomyBackend.getByName(""));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testByAbreviationName() throws Exception {
+ try {
+ taxonomyBackend.setCache(new GeneralCacheWithExclusion(cache, 1));
+ assertNotNull(taxonomyBackend.getByName("C. elegans"));
+ taxonomyBackend.setCache(new GeneralCacheWithExclusion(cache, 1));
+ assertNotNull(taxonomyBackend.getByName("D. sechellia"));
+ taxonomyBackend.setCache(new GeneralCacheWithExclusion(cache, 1));
+ assertNotNull(taxonomyBackend.getByName("P. pacificus"));
+ taxonomyBackend.setCache(new GeneralCacheWithExclusion(cache, 1));
+ assertNotNull(taxonomyBackend.getByName("T. castaneum"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetName() throws Exception {
+ try {
+ String name = taxonomyBackend.getNameForTaxonomy(new MiriamData(MiriamType.TAXONOMY, "9606"));
+ assertTrue(name.contains("Homo sapiens"));
+ assertNotNull(taxonomyBackend.getNameForTaxonomy(new MiriamData(MiriamType.TAXONOMY, "9605")));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetNameWhenProblemWithDb() throws Exception {
+ WebPageDownloader downloader = taxonomyBackend.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ taxonomyBackend.setWebPageDownloader(mockDownloader);
+ taxonomyBackend.setCache(null);
+ taxonomyBackend.getNameForTaxonomy(new MiriamData(MiriamType.TAXONOMY, "9606"));
+ fail("Exception expected");
+ } catch (TaxonomySearchException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ taxonomyBackend.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testGetNameForInvalidTax() throws Exception {
+ try {
+ String name = taxonomyBackend.getNameForTaxonomy(new MiriamData(MiriamType.TAXONOMY, "-a-"));
+ assertNull(name);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetNameForInvalidInputData() throws Exception {
+ try {
+ String name = taxonomyBackend.getNameForTaxonomy(null);
+ assertNull(name);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testByName2() throws Exception {
+ try {
+ MiriamData md = taxonomyBackend.getByName("homo sapiens");
+ assertTrue(md.equals(TaxonomyBackend.HUMAN_TAXONOMY));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testByName3() throws Exception {
+ try {
+ MiriamData md = taxonomyBackend.getByName("bla bla kiwi");
+ assertNull(md);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testByMusMusculusName() throws Exception {
+ try {
+ MiriamData md = taxonomyBackend.getByName("Mus musculus");
+ assertTrue(md.equals(new MiriamData(MiriamType.TAXONOMY, "10090")));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testByMouseName() throws Exception {
+ try {
+ MiriamData md = taxonomyBackend.getByName("Mouse");
+ assertTrue(md.equals(new MiriamData(MiriamType.TAXONOMY, "10090")));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQuery() throws Exception {
+ try {
+ String result = taxonomyBackend.refreshCacheQuery(TaxonomyBackend.TAXONOMY_CACHE_PREFIX + "homo sapiens");
+ assertNotNull(result);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQuery2() throws Exception {
+ try {
+ String result = taxonomyBackend
+ .refreshCacheQuery(TaxonomyBackend.TAXONOMY_NAME_CACHE_PREFIX + TaxonomyBackend.HUMAN_TAXONOMY.getResource());
+ assertNotNull(result);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQuery3() throws Exception {
+ try {
+ String result = taxonomyBackend.refreshCacheQuery("http://google.pl/");
+ assertNotNull(result);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery() throws Exception {
+ try {
+ taxonomyBackend.refreshCacheQuery("unk_query");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery2() throws Exception {
+ try {
+ taxonomyBackend.refreshCacheQuery(new Object());
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQueryNotAvailable() throws Exception {
+ WebPageDownloader downloader = taxonomyBackend.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ taxonomyBackend.setWebPageDownloader(mockDownloader);
+ taxonomyBackend.refreshCacheQuery("http://google.pl/");
+ fail("Exception expected");
+ } catch (SourceNotAvailable e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ taxonomyBackend.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testStatus() throws Exception {
+ try {
+ assertEquals(ExternalServiceStatusType.OK, taxonomyBackend.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSimulateDownStatus() throws Exception {
+ WebPageDownloader downloader = taxonomyBackend.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ taxonomyBackend.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.DOWN, taxonomyBackend.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ taxonomyBackend.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testSimulateChangedStatus() throws Exception {
+ WebPageDownloader downloader = taxonomyBackend.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("");
+ taxonomyBackend.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.CHANGED, taxonomyBackend.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ taxonomyBackend.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testSimulateChangedStatus2() throws Exception {
+ WebPageDownloader downloader = taxonomyBackend.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("<em>Taxonomy ID: </em>1234");
+ taxonomyBackend.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.CHANGED, taxonomyBackend.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ taxonomyBackend.setWebPageDownloader(downloader);
+ }
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AllAnnotatorTests.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AllAnnotatorTests.java
index 5ac4db041c..5db640c506 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AllAnnotatorTests.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AllAnnotatorTests.java
@@ -1,30 +1,30 @@
-package lcsb.mapviewer.annotation.services.annotators;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AnnotatorExceptionTest.class, //
- AnnotatorParamDefTest.class, //
- BrendaAnnotatorTest.class, //
- BiocompendiumAnnotatorTest.class, //
- CazyAnnotatorTest.class, //
- ChebiAnnotatorTest.class, //
- ElementAnnotatorTest.class, //
- EnsemblAnnotatorTest.class, //
- EntrezAnnotatorTest.class, //
- GoAnnotatorTest.class, //
- HgncAnnotatorTest.class, //
- KeggAnnotatorTest.class, //
- MultipleAnnotatorsTest.class, //
- PdbAnnotatorTest.class, //
- ReconAnnotatorTest.class, //
- StitchAnnotatorTest.class, //
- StringAnnotatorTest.class, //
- TairAnnotatorTest.class, //
- UniprotAnnotatorTest.class, //
-})
-public class AllAnnotatorTests {
-
-}
+package lcsb.mapviewer.annotation.services.annotators;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AnnotatorExceptionTest.class, //
+ AnnotatorParamDefTest.class, //
+ BrendaAnnotatorTest.class, //
+ BiocompendiumAnnotatorTest.class, //
+ CazyAnnotatorTest.class, //
+ ChebiAnnotatorTest.class, //
+ ElementAnnotatorTest.class, //
+ EnsemblAnnotatorTest.class, //
+ EntrezAnnotatorTest.class, //
+ GoAnnotatorTest.class, //
+ HgncAnnotatorTest.class, //
+ KeggAnnotatorTest.class, //
+ MultipleAnnotatorsTest.class, //
+ PdbAnnotatorTest.class, //
+ ReconAnnotatorTest.class, //
+ StitchAnnotatorTest.class, //
+ StringAnnotatorTest.class, //
+ TairAnnotatorTest.class, //
+ UniprotAnnotatorTest.class, //
+})
+public class AllAnnotatorTests {
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorExceptionTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorExceptionTest.java
index 629717e148..3001461019 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorExceptionTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorExceptionTest.java
@@ -1,32 +1,32 @@
-package lcsb.mapviewer.annotation.services.annotators;
-
-import static org.junit.Assert.*;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class AnnotatorExceptionTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testConstructor() {
- AnnotatorParamDefinition d = new AnnotatorParamDefinition("name", String.class, "description");
- assertEquals(d.getName(), "name");
- assertEquals(d.getDescription(), "description");
- assertEquals(d.getType(), String.class);
- }
-
-}
+package lcsb.mapviewer.annotation.services.annotators;
+
+import static org.junit.Assert.*;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class AnnotatorExceptionTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testConstructor() {
+ AnnotatorParamDefinition d = new AnnotatorParamDefinition("name", String.class, "description");
+ assertEquals(d.getName(), "name");
+ assertEquals(d.getDescription(), "description");
+ assertEquals(d.getType(), String.class);
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotatorTest.java
index 430c16093f..802ee10b47 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotatorTest.java
@@ -1,361 +1,361 @@
-package lcsb.mapviewer.annotation.services.annotators;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.io.BufferedReader;
-import java.io.FileReader;
-import java.util.ArrayList;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Ignore;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.annotation.AnnotationTestFunctions;
-import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-
-public class BiocompendiumAnnotatorTest extends AnnotationTestFunctions {
- Logger logger = Logger.getLogger(BiocompendiumAnnotatorTest.class);
-
- MiriamData camk4 = new MiriamData(MiriamType.HGNC_SYMBOL, "CAMK4");
- MiriamData slc25a27 = new MiriamData(MiriamType.HGNC_SYMBOL, "SLC25A27");
- MiriamData nsmf = new MiriamData(MiriamType.HGNC_SYMBOL, "NSMF");
- MiriamData mir449a = new MiriamData(MiriamType.HGNC_SYMBOL, "MIR449A");
-
- @Autowired
- private GeneralCacheInterface cache;
-
- @Autowired
- private BiocompendiumAnnotator restService;
-
- @Before
- public void setUp() {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- @Ignore("Bug 32")
- public void testGetAnnotationsForSpecies() throws Exception {
- try {
- String response = restService.getAnnotation(camk4);
- assertNotNull(response);
- assertTrue(response.contains("Symbol: CAMK4"));
-
- response = restService.getAnnotation(slc25a27);
- assertNotNull(response);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() throws Exception {
- try {
- assertNotNull(restService.getCommonName());
- assertNotNull(restService.getUrl());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAnnotationsForInvalidMiriam() throws Exception {
- try {
- restService.getAnnotation(new MiriamData());
- fail("Exception expected");
-
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXml() throws Exception {
- BufferedReader reader;
- try {
- reader = new BufferedReader(new FileReader("testFiles/annotation/sampleResponse.xml"));
- String line = null;
- StringBuilder stringBuilder = new StringBuilder();
- String ls = System.getProperty("line.separator");
-
- while ((line = reader.readLine()) != null) {
- stringBuilder.append(line);
- stringBuilder.append(ls);
- }
- reader.close();
-
- Map<String, String> res = restService.getAnnotationsFromXml(stringBuilder.toString());
-
- assertEquals(2, res.keySet().size());
- String response = res.get("CAMK4");
- assertNotNull(response);
- assertTrue(response.contains("Symbol: CAMK4"));
-
- assertNotNull(res.get("SLC25A27"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test(timeout = 10000)
- @Ignore("Bug 32")
- public void testGetAnnotationsForMiceSpecies() throws Exception {
- ArrayList<String> names = new ArrayList<String>();
-
- names.add("Fmo3");
- names.add("Nqo1");
- names.add("Abcc12");
- names.add("Mgst3");
- names.add("Txnrd1");
- names.add("Cbr3");
- names.add("Hspa1b");
- names.add("Prdx1");
- names.add("Ppard");
- names.add("Tgfb2");
- names.add("Fth1");
- names.add("Prdx6");
- names.add("Nr4a1");
- names.add("Tgfb1");
- names.add("Abcc4");
- names.add("Ager");
- names.add("Gsr");
- names.add("Sod3");
- names.add("Maff");
- names.add("Eif2ak3");
- names.add("Tgfa");
- names.add("Hbegf");
- names.add("Mafg");
- names.add("Adh7");
- names.add("Slc7a11");
- names.add("Epha3");
- names.add("Blvrb");
- // problematic one
- // names.add("Me1");
- names.add("Csnk2a2");
- names.add("Gpx3");
- names.add("Mapk8");
- names.add("Gclm");
- names.add("Epha2");
- names.add("Bdnf");
- // problematic one
- // names.add("ACC2");
- names.add("Ptgr1");
- names.add("Pdgfb");
- names.add("Mapk7");
- names.add("Cbr1");
- names.add("Hsp90aa1");
- names.add("Pgd");
- names.add("Sqstm1");
- names.add("Aldh9a1");
- names.add("Txn");
- names.add("Txnrd3");
- names.add("Srxn1");
- names.add("Gpx2");
- names.add("Npas4");
- names.add("Mapk1");
- names.add("Nrg1");
- names.add("Cbr");
- names.add("Hspa1a");
- names.add("Mgst2");
- names.add("Tgfbr2");
- names.add("Ephx1");
- names.add("Dnajb1");
- names.add("Abcc2");
- names.add("Gclc");
- names.add("Abcc5");
- names.add("Ggt1");
- names.add("Ftl");
- names.add("Egr1");
- names.add("Fgf13");
- // problematic one
- // names.add("Hgf");
- // problematic one
- // names.add("UbcH7");
- names.add("Abcc3");
- names.add("Nfe2l2");
- // problematic one
- // names.add("Hsp70");
- names.add("Hsp90ab1");
-
- try {
- for (int i = 0; i < names.size(); i++) {
- String geneName = names.get(i);
- String annotation = restService.getAnnotation(new MiriamData(MiriamType.HGNC_SYMBOL, geneName));
- assertNotNull("Problem with annotation of mouse gene: " + geneName, annotation);
- assertTrue("Problem with annotation of mouse gene: " + geneName, !annotation.trim().equals(""));
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- @Ignore("Bug 451")
- public void testGetAnnotationsForNSMF() throws Exception {
- try {
- String response = restService.getAnnotation(nsmf);
- assertNotNull(response);
- assertFalse(response.trim().equals(""));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- @Ignore("Bug 451")
- public void testGetAnnotationsForMIR449A() throws Exception {
- try {
- String response = restService.getAnnotation(mir449a);
- assertNotNull(response);
- assertFalse(response.trim().equals(""));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test(timeout = 15000)
- public void testCachableInterfaceInvalidate() throws Exception {
- String query = "GLUD1";
- try {
- String newRes = "hello";
-
- waitForRefreshCacheQueueToEmpty();
-
- cache.setCachedQuery(query, restService.getCacheType(), newRes);
- String res = cache.getStringByQuery(query, restService.getCacheType());
- assertEquals(newRes, res);
- cache.invalidateByQuery(query, restService.getCacheType());
-
- waitForRefreshCacheQueueToEmpty();
-
- res = cache.getStringByQuery(query, restService.getCacheType());
-
- assertNotNull(res);
-
- assertFalse("Value wasn't refreshed from db", newRes.equals(res));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testNameWithNewLine() throws Exception {
- try {
- String response = restService.getAnnotation(new MiriamData(MiriamType.HGNC_SYMBOL, "some\nname"));
- assertNotNull(response);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidValue() throws Exception {
- try {
- restService.refreshCacheQuery(new Object());
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do "));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshValueWhenProblemWithSource() throws Exception {
- try {
- BiocompendiumAnnotator annotatorUnderTest = new BiocompendiumAnnotator() {
- @Override
- Map<String, String> getAnnotationsFromXml(String xml) throws InvalidXmlSchemaException {
- throw new InvalidXmlSchemaException();
- }
- };
- annotatorUnderTest.refreshCacheQuery(camk4.getResource());
- fail("Exception expected");
- } catch (SourceNotAvailable e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetInvalidAnnotations() throws Exception {
- try {
- restService.getAnnotation(new MiriamData(MiriamType.WIKIPEDIA, "world"));
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testInvalidDataToStrubg() throws Exception {
- try {
- restService.dataToString(new MiriamData(MiriamType.WIKIPEDIA, "world"));
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAnnotationsFromInvaldXml() throws Exception {
- try {
- Map<String, String> map = restService.getAnnotationsFromXml("");
- assertEquals(0, map.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAnnotationsFromInvaldXml2() throws Exception {
- try {
- Map<String, String> map = restService.getAnnotationsFromXml(null);
- assertEquals(0, map.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.annotation.services.annotators;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.util.ArrayList;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Ignore;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.AnnotationTestFunctions;
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+
+public class BiocompendiumAnnotatorTest extends AnnotationTestFunctions {
+ Logger logger = Logger.getLogger(BiocompendiumAnnotatorTest.class);
+
+ MiriamData camk4 = new MiriamData(MiriamType.HGNC_SYMBOL, "CAMK4");
+ MiriamData slc25a27 = new MiriamData(MiriamType.HGNC_SYMBOL, "SLC25A27");
+ MiriamData nsmf = new MiriamData(MiriamType.HGNC_SYMBOL, "NSMF");
+ MiriamData mir449a = new MiriamData(MiriamType.HGNC_SYMBOL, "MIR449A");
+
+ @Autowired
+ private GeneralCacheInterface cache;
+
+ @Autowired
+ private BiocompendiumAnnotator restService;
+
+ @Before
+ public void setUp() {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ @Ignore("Bug 32")
+ public void testGetAnnotationsForSpecies() throws Exception {
+ try {
+ String response = restService.getAnnotation(camk4);
+ assertNotNull(response);
+ assertTrue(response.contains("Symbol: CAMK4"));
+
+ response = restService.getAnnotation(slc25a27);
+ assertNotNull(response);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() throws Exception {
+ try {
+ assertNotNull(restService.getCommonName());
+ assertNotNull(restService.getUrl());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAnnotationsForInvalidMiriam() throws Exception {
+ try {
+ restService.getAnnotation(new MiriamData());
+ fail("Exception expected");
+
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXml() throws Exception {
+ BufferedReader reader;
+ try {
+ reader = new BufferedReader(new FileReader("testFiles/annotation/sampleResponse.xml"));
+ String line = null;
+ StringBuilder stringBuilder = new StringBuilder();
+ String ls = System.getProperty("line.separator");
+
+ while ((line = reader.readLine()) != null) {
+ stringBuilder.append(line);
+ stringBuilder.append(ls);
+ }
+ reader.close();
+
+ Map<String, String> res = restService.getAnnotationsFromXml(stringBuilder.toString());
+
+ assertEquals(2, res.keySet().size());
+ String response = res.get("CAMK4");
+ assertNotNull(response);
+ assertTrue(response.contains("Symbol: CAMK4"));
+
+ assertNotNull(res.get("SLC25A27"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test(timeout = 10000)
+ @Ignore("Bug 32")
+ public void testGetAnnotationsForMiceSpecies() throws Exception {
+ ArrayList<String> names = new ArrayList<String>();
+
+ names.add("Fmo3");
+ names.add("Nqo1");
+ names.add("Abcc12");
+ names.add("Mgst3");
+ names.add("Txnrd1");
+ names.add("Cbr3");
+ names.add("Hspa1b");
+ names.add("Prdx1");
+ names.add("Ppard");
+ names.add("Tgfb2");
+ names.add("Fth1");
+ names.add("Prdx6");
+ names.add("Nr4a1");
+ names.add("Tgfb1");
+ names.add("Abcc4");
+ names.add("Ager");
+ names.add("Gsr");
+ names.add("Sod3");
+ names.add("Maff");
+ names.add("Eif2ak3");
+ names.add("Tgfa");
+ names.add("Hbegf");
+ names.add("Mafg");
+ names.add("Adh7");
+ names.add("Slc7a11");
+ names.add("Epha3");
+ names.add("Blvrb");
+ // problematic one
+ // names.add("Me1");
+ names.add("Csnk2a2");
+ names.add("Gpx3");
+ names.add("Mapk8");
+ names.add("Gclm");
+ names.add("Epha2");
+ names.add("Bdnf");
+ // problematic one
+ // names.add("ACC2");
+ names.add("Ptgr1");
+ names.add("Pdgfb");
+ names.add("Mapk7");
+ names.add("Cbr1");
+ names.add("Hsp90aa1");
+ names.add("Pgd");
+ names.add("Sqstm1");
+ names.add("Aldh9a1");
+ names.add("Txn");
+ names.add("Txnrd3");
+ names.add("Srxn1");
+ names.add("Gpx2");
+ names.add("Npas4");
+ names.add("Mapk1");
+ names.add("Nrg1");
+ names.add("Cbr");
+ names.add("Hspa1a");
+ names.add("Mgst2");
+ names.add("Tgfbr2");
+ names.add("Ephx1");
+ names.add("Dnajb1");
+ names.add("Abcc2");
+ names.add("Gclc");
+ names.add("Abcc5");
+ names.add("Ggt1");
+ names.add("Ftl");
+ names.add("Egr1");
+ names.add("Fgf13");
+ // problematic one
+ // names.add("Hgf");
+ // problematic one
+ // names.add("UbcH7");
+ names.add("Abcc3");
+ names.add("Nfe2l2");
+ // problematic one
+ // names.add("Hsp70");
+ names.add("Hsp90ab1");
+
+ try {
+ for (int i = 0; i < names.size(); i++) {
+ String geneName = names.get(i);
+ String annotation = restService.getAnnotation(new MiriamData(MiriamType.HGNC_SYMBOL, geneName));
+ assertNotNull("Problem with annotation of mouse gene: " + geneName, annotation);
+ assertTrue("Problem with annotation of mouse gene: " + geneName, !annotation.trim().equals(""));
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ @Ignore("Bug 451")
+ public void testGetAnnotationsForNSMF() throws Exception {
+ try {
+ String response = restService.getAnnotation(nsmf);
+ assertNotNull(response);
+ assertFalse(response.trim().equals(""));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ @Ignore("Bug 451")
+ public void testGetAnnotationsForMIR449A() throws Exception {
+ try {
+ String response = restService.getAnnotation(mir449a);
+ assertNotNull(response);
+ assertFalse(response.trim().equals(""));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test(timeout = 15000)
+ public void testCachableInterfaceInvalidate() throws Exception {
+ String query = "GLUD1";
+ try {
+ String newRes = "hello";
+
+ waitForRefreshCacheQueueToEmpty();
+
+ cache.setCachedQuery(query, restService.getCacheType(), newRes);
+ String res = cache.getStringByQuery(query, restService.getCacheType());
+ assertEquals(newRes, res);
+ cache.invalidateByQuery(query, restService.getCacheType());
+
+ waitForRefreshCacheQueueToEmpty();
+
+ res = cache.getStringByQuery(query, restService.getCacheType());
+
+ assertNotNull(res);
+
+ assertFalse("Value wasn't refreshed from db", newRes.equals(res));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testNameWithNewLine() throws Exception {
+ try {
+ String response = restService.getAnnotation(new MiriamData(MiriamType.HGNC_SYMBOL, "some\nname"));
+ assertNotNull(response);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidValue() throws Exception {
+ try {
+ restService.refreshCacheQuery(new Object());
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do "));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshValueWhenProblemWithSource() throws Exception {
+ try {
+ BiocompendiumAnnotator annotatorUnderTest = new BiocompendiumAnnotator() {
+ @Override
+ Map<String, String> getAnnotationsFromXml(String xml) throws InvalidXmlSchemaException {
+ throw new InvalidXmlSchemaException();
+ }
+ };
+ annotatorUnderTest.refreshCacheQuery(camk4.getResource());
+ fail("Exception expected");
+ } catch (SourceNotAvailable e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetInvalidAnnotations() throws Exception {
+ try {
+ restService.getAnnotation(new MiriamData(MiriamType.WIKIPEDIA, "world"));
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testInvalidDataToStrubg() throws Exception {
+ try {
+ restService.dataToString(new MiriamData(MiriamType.WIKIPEDIA, "world"));
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAnnotationsFromInvaldXml() throws Exception {
+ try {
+ Map<String, String> map = restService.getAnnotationsFromXml("");
+ assertEquals(0, map.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAnnotationsFromInvaldXml2() throws Exception {
+ try {
+ Map<String, String> map = restService.getAnnotationsFromXml(null);
+ assertEquals(0, map.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/genome/AllGenomeTests.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/genome/AllGenomeTests.java
index 3ee8e7e988..0e7211eec9 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/genome/AllGenomeTests.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/genome/AllGenomeTests.java
@@ -1,11 +1,11 @@
-package lcsb.mapviewer.annotation.services.genome;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ UcscReferenceGenomeConnectorTest.class })
-public class AllGenomeTests {
-
-}
+package lcsb.mapviewer.annotation.services.genome;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ UcscReferenceGenomeConnectorTest.class })
+public class AllGenomeTests {
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/genome/UcscReferenceGenomeConnectorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/genome/UcscReferenceGenomeConnectorTest.java
index 0ae6336559..8edec89f6f 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/genome/UcscReferenceGenomeConnectorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/genome/UcscReferenceGenomeConnectorTest.java
@@ -1,974 +1,974 @@
-package lcsb.mapviewer.annotation.services.genome;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-import static org.mockito.Matchers.any;
-import static org.mockito.Matchers.anyBoolean;
-import static org.mockito.Matchers.anyString;
-import static org.mockito.Mockito.when;
-
-import java.io.IOException;
-import java.net.URISyntaxException;
-import java.util.List;
-import java.util.concurrent.Callable;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Future;
-
-import org.apache.commons.net.ftp.FTPClient;
-import org.apache.commons.net.ftp.FTPFile;
-import org.apache.commons.net.ftp.FTPReply;
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-import org.mockito.invocation.InvocationOnMock;
-import org.mockito.stubbing.Answer;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.annotation.AnnotationTestFunctions;
-import lcsb.mapviewer.annotation.cache.BigFileCache;
-import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
-import lcsb.mapviewer.annotation.cache.WebPageDownloader;
-import lcsb.mapviewer.annotation.services.TaxonomyBackend;
-import lcsb.mapviewer.annotation.services.TaxonomySearchException;
-import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.ReferenceGenome;
-import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
-import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
-import lcsb.mapviewer.persist.dao.map.layout.ReferenceGenomeDao;
-
-public class UcscReferenceGenomeConnectorTest extends AnnotationTestFunctions {
-
- Logger logger = Logger.getLogger(UcscReferenceGenomeConnectorTest.class);
-
- @Autowired
- UcscReferenceGenomeConnector connector;
-
- @Autowired
- ReferenceGenomeDao referenceGenomeDao;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testRefreshCacheQuery() throws Exception {
- try {
- assertNotNull(connector.refreshCacheQuery("http://google.pl/"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAvailableGenomeVersion() throws Exception {
- MiriamData human = new MiriamData(MiriamType.TAXONOMY, "9606");
- try {
- List<String> list = connector.getAvailableGenomeVersion(human);
- logger.debug(list);
- assertTrue(list.size() >= 17);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAvailableGenomeVersionWhenProblemWithTaxonomyServer() throws Exception {
- MiriamData human = new MiriamData(MiriamType.TAXONOMY, "9606");
- TaxonomyBackend taxonomyBackend = connector.getTaxonomyBackend();
- try {
- // simulate problems with taxonomy server
- TaxonomyBackend taxonomyMock = Mockito.mock(TaxonomyBackend.class);
- when(taxonomyMock.getByName(anyString())).thenThrow(new TaxonomySearchException(null, null));
- connector.setTaxonomyBackend(taxonomyMock);
-
- connector.getAvailableGenomeVersion(human);
- fail("Exception expected");
- } catch (ReferenceGenomeConnectorException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- connector.setTaxonomyBackend(taxonomyBackend);
- }
- }
-
- @Test
- public void testGetAvailableGenomeVersionForInvalidTaxonomy() throws Exception {
- MiriamData unknown = new MiriamData(MiriamType.TAXONOMY, "10101010101");
- try {
- List<String> list = connector.getAvailableGenomeVersion(unknown);
- assertEquals(0, list.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAvailableOrganisms() throws Exception {
- try {
- MiriamData human = new MiriamData(MiriamType.TAXONOMY, "9606");
- MiriamData chicken = new MiriamData(MiriamType.TAXONOMY, "9031");
- List<MiriamData> list = connector.getAvailableOrganisms();
- logger.debug(list);
- assertTrue(list.size() > 40);
-
- assertTrue(list.contains(human));
- assertTrue(list.contains(chicken));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAvailableOrganismsWhenUcscWebpageDown() throws Exception {
- WebPageDownloader downloader = connector.getWebPageDownloader();
- GeneralCacheInterface originalCache = connector.getCache();
- try {
- // exclude first cached value
- connector.setCache(null);
-
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- connector.setWebPageDownloader(mockDownloader);
- connector.getAvailableOrganisms();
- fail("Exception expected");
- } catch (ReferenceGenomeConnectorException e) {
- assertTrue(e.getMessage().contains("Problem with accessing UCSC database"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- connector.setWebPageDownloader(downloader);
- connector.setCache(originalCache);
- }
- }
-
- @Test
- public void testDownloadGenomeVersion() throws Exception {
- MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "1570291");
- String version = "eboVir3";
-
- try {
- dbUtils.createSessionForCurrentThread();
- List<String> list = connector.getDownloadedGenomeVersions(yeast);
- if (list.contains(version)) {
- connector.removeGenomeVersion(yeast, version);
- }
- dbUtils.closeSessionForCurrentThread();
- list = connector.getDownloadedGenomeVersions(yeast);
-
- assertFalse(list.contains(version));
-
- connector.downloadGenomeVersion(yeast, version, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, false);
-
- list = connector.getDownloadedGenomeVersions(yeast);
- assertTrue(list.contains(version));
-
- List<ReferenceGenome> genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
- ReferenceGenome genome = null;
- for (ReferenceGenome referenceGenome : genomes) {
- if (referenceGenome.getVersion().equals(version)) {
- genome = referenceGenome;
- }
- }
- assertNotNull(genome);
- connector.downloadGeneMappingGenomeVersion(genome, "test", null, false,
- "http://www.biodalliance.org/datasets/flyThickets.bb");
-
- dbUtils.createSessionForCurrentThread();
- genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
- genome = null;
- for (ReferenceGenome referenceGenome : genomes) {
- if (referenceGenome.getVersion().equals(version)) {
- genome = referenceGenome;
- }
- }
- assertNotNull(genome);
- assertEquals(1, genome.getGeneMapping().size());
- dbUtils.closeSessionForCurrentThread();
-
- try {
- // try to download the same thing for the second time
- connector.downloadGeneMappingGenomeVersion(genome, "test", new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, false, "http://www.biodalliance.org/datasets/flyThickets.bb");
- fail("Exception expected");
- } catch (ReferenceGenomeConnectorException e) {
- assertTrue(e.getMessage().contains("already exists"));
- }
-
- try {
- // try to download something that is not big bed
- connector.downloadGeneMappingGenomeVersion(genome, "test2", new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, false, "http://www.biodalliance.org/datasets/flyThickets.txt");
- fail("Exception expected");
- } catch (ReferenceGenomeConnectorException e) {
- assertTrue(e.getMessage().contains("Only big bed format files are supported"));
- }
-
- // connector.removeGeneMapping(genome.getGeneMapping().get(0));
-
- int warningCount = getWarnings().size();
-
- // try to remove invalid mapping
- connector.removeGeneMapping(new ReferenceGenomeGeneMapping());
-
- assertEquals(warningCount + 1, getWarnings().size());
-
- dbUtils.createSessionForCurrentThread();
- connector.removeGenomeVersion(yeast, version);
- dbUtils.closeSessionForCurrentThread();
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @SuppressWarnings("unchecked")
- @Test
- public void testDownloadGenomeVersionWhenInternalUrlIsInvalid() throws Exception {
- MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "1570291");
- String version = "eboVir3";
-
- ExecutorService originalExecutorService = connector.getSyncExecutorService();
- try {
- ExecutorService executorService = Mockito.mock(ExecutorService.class);
- connector.setSyncExecutorService(executorService);
- Future<?> task = Mockito.mock(Future.class);
- when(task.get()).thenThrow(new ExecutionException(new URISyntaxException("", "")));
- when(executorService.submit(any(Callable.class))).thenReturn(task);
-
- connector.downloadGenomeVersion(yeast, version, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, false);
- fail("Exception expected");
-
- } catch (InvalidStateException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- connector.setSyncExecutorService(originalExecutorService);
- }
- }
-
- @Test
- public void testDownloadGenomeVersionAsync() throws Exception {
- MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "1570291");
- String version = "eboVir3";
-
- BigFileCache bigFileCache = connector.getBigFileCache();
- try {
- dbUtils.createSessionForCurrentThread();
- List<String> list = connector.getDownloadedGenomeVersions(yeast);
- if (list.contains(version)) {
- connector.removeGenomeVersion(yeast, version);
- }
- list = connector.getDownloadedGenomeVersions(yeast);
-
- dbUtils.closeSessionForCurrentThread();
-
- // create a mock for ftp connections (so we speed up tests), the real
- // connection is tested elsewhere
- BigFileCache mockCache = Mockito.mock(BigFileCache.class);
- Mockito.doAnswer(new Answer<Void>() {
-
- @Override
- public Void answer(InvocationOnMock invocation) throws Throwable {
- IProgressUpdater updater = (IProgressUpdater) invocation.getArguments()[2];
- updater.setProgress(100);
- return null;
- }
- }).when(mockCache).downloadFile(anyString(), anyBoolean(), any());
-
- connector.setBigFileCache(mockCache);
-
- assertFalse(list.contains(version));
-
- connector.downloadGenomeVersion(yeast, version, null, true);
-
- waitForDownload();
-
- dbUtils.createSessionForCurrentThread();
- list = connector.getDownloadedGenomeVersions(yeast);
- assertTrue(list.contains(version));
-
- List<ReferenceGenome> genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
- ReferenceGenome genome = null;
- for (ReferenceGenome referenceGenome : genomes) {
- if (referenceGenome.getVersion().equals(version)) {
- genome = referenceGenome;
- }
- }
- dbUtils.closeSessionForCurrentThread();
- assertNotNull(genome);
- connector.downloadGeneMappingGenomeVersion(genome, "test", new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, true, "http://www.biodalliance.org/datasets/flyThickets.bb");
-
- waitForDownload();
-
- genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
- genome = null;
- for (ReferenceGenome referenceGenome : genomes) {
- if (referenceGenome.getVersion().equals(version)) {
- genome = referenceGenome;
- }
- }
- assertNotNull(genome);
- referenceGenomeDao.refresh(genome);
- assertEquals(1, genome.getGeneMapping().size());
-
- try {
- // try to download the same thing for the second time
- connector.downloadGeneMappingGenomeVersion(genome, "test", new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, false, "http://www.biodalliance.org/datasets/flyThickets.bb");
- fail("Exception expected");
- } catch (ReferenceGenomeConnectorException e) {
- assertTrue(e.getMessage().contains("already exists"));
- }
-
- try {
- // try to download something that is not big bed
- connector.downloadGeneMappingGenomeVersion(genome, "test2", new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, false, "http://www.biodalliance.org/datasets/flyThickets.txt");
- fail("Exception expected");
- } catch (ReferenceGenomeConnectorException e) {
- assertTrue(e.getMessage().contains("Only big bed format files are supported"));
- }
-
- connector.removeGeneMapping(genome.getGeneMapping().get(0));
-
- int warningCount = getWarnings().size();
-
- // try to remove invalid mapping
- connector.removeGeneMapping(new ReferenceGenomeGeneMapping());
-
- assertEquals(warningCount + 1, getWarnings().size());
-
- connector.removeGenomeVersion(yeast, version);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- connector.setBigFileCache(bigFileCache);
- }
- }
-
- @Test
- public void testDownloadGenomeVersionAsyncWithException() throws Exception {
- MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "1570291");
- String version = "eboVir3";
-
- BigFileCache bigFileCache = connector.getBigFileCache();
- try {
- dbUtils.createSessionForCurrentThread();
- List<String> list = connector.getDownloadedGenomeVersions(yeast);
- if (list.contains(version)) {
- connector.removeGenomeVersion(yeast, version);
- }
- list = connector.getDownloadedGenomeVersions(yeast);
-
- dbUtils.closeSessionForCurrentThread();
-
- // create a mock for ftp connections (so we speed up tests), the real
- // connection is tested elsewhere
- BigFileCache mockCache = Mockito.mock(BigFileCache.class);
-
- connector.setBigFileCache(mockCache);
-
- assertFalse(list.contains(version));
-
- connector.downloadGenomeVersion(yeast, version, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, true);
-
- waitForDownload();
-
- dbUtils.createSessionForCurrentThread();
- list = connector.getDownloadedGenomeVersions(yeast);
- assertTrue(list.contains(version));
-
- List<ReferenceGenome> genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
- ReferenceGenome genome = null;
- for (ReferenceGenome referenceGenome : genomes) {
- if (referenceGenome.getVersion().equals(version)) {
- genome = referenceGenome;
- }
- }
- dbUtils.closeSessionForCurrentThread();
- assertNotNull(genome);
-
- Mockito.doThrow(new IOException()).when(mockCache).downloadFile(anyString(), anyBoolean(), any());
- assertEquals(0, getErrors().size());
- connector.downloadGeneMappingGenomeVersion(genome, "test", new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, true, "http://www.biodalliance.org/datasets/flyThickets.bb");
-
- waitForDownload();
-
- logger.debug(getErrors());
- // during this downlad we expect exception thrown by downloader
- assertEquals(1, getErrors().size());
-
- Mockito.doThrow(new OutOfMemoryError()).when(mockCache).downloadFile(anyString(), anyBoolean(), any());
- connector.downloadGeneMappingGenomeVersion(genome, "test2", new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, true, "http://www.biodalliance.org/datasets/flyThickets.bb");
-
- waitForDownload();
- // during this downlad we expect error, this shouldn't change list of
- // errors
- assertEquals(1, getErrors().size());
-
- Mockito.doThrow(new URISyntaxException("", "")).when(mockCache).downloadFile(anyString(), anyBoolean(), any());
- connector.downloadGeneMappingGenomeVersion(genome, "test3", new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, true, "http://www.biodalliance.org/datasets/flyThickets.bb");
-
- waitForDownload();
-
- // during this downlad we expect error (exception thrown by downloader)
- assertEquals(2, getErrors().size());
-
- genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
- genome = null;
- for (ReferenceGenome referenceGenome : genomes) {
- if (referenceGenome.getVersion().equals(version)) {
- genome = referenceGenome;
- }
- }
- assertNotNull(genome);
- referenceGenomeDao.refresh(genome);
- assertEquals(3, genome.getGeneMapping().size());
-
- connector.removeGeneMapping(genome.getGeneMapping().get(2));
- connector.removeGeneMapping(genome.getGeneMapping().get(1));
- connector.removeGeneMapping(genome.getGeneMapping().get(0));
- connector.removeGenomeVersion(yeast, version);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- connector.setBigFileCache(bigFileCache);
- }
- }
-
- @Test
- public void testDownloadGenomeVersionWithException() throws Exception {
- MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "1570291");
- String version = "eboVir3";
-
- BigFileCache bigFileCache = connector.getBigFileCache();
- try {
- List<String> list = connector.getDownloadedGenomeVersions(yeast);
- if (list.contains(version)) {
- connector.removeGenomeVersion(yeast, version);
- }
- list = connector.getDownloadedGenomeVersions(yeast);
-
- // create a mock for ftp connections (so we speed up tests), the real
- // connection is tested elsewhere
- BigFileCache mockCache = Mockito.mock(BigFileCache.class);
-
- connector.setBigFileCache(mockCache);
-
- assertFalse(list.contains(version));
-
- connector.downloadGenomeVersion(yeast, version, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, false);
-
- list = connector.getDownloadedGenomeVersions(yeast);
- assertTrue(list.contains(version));
-
- List<ReferenceGenome> genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
- ReferenceGenome genome = null;
- for (ReferenceGenome referenceGenome : genomes) {
- if (referenceGenome.getVersion().equals(version)) {
- genome = referenceGenome;
- }
- }
- assertNotNull(genome);
-
- Mockito.doThrow(new IOException()).when(mockCache).downloadFile(anyString(), anyBoolean(), any());
- assertEquals(0, getErrors().size());
- try {
- connector.downloadGeneMappingGenomeVersion(genome, "test", new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, false, "http://www.biodalliance.org/datasets/flyThickets.bb");
- fail("Exception expected");
- } catch (IOException e) {
-
- }
-
- Mockito.doThrow(new RuntimeException()).when(mockCache).downloadFile(anyString(), anyBoolean(), any());
- try {
- connector.downloadGeneMappingGenomeVersion(genome, "test2", new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, false, "http://www.biodalliance.org/datasets/flyThickets.bb");
-
- fail("Exception expected");
- } catch (InvalidStateException e) {
-
- }
-
- Mockito.doThrow(new URISyntaxException("", "")).when(mockCache).downloadFile(anyString(), anyBoolean(), any());
-
- try {
- connector.downloadGeneMappingGenomeVersion(genome, "test3", new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, false, "http://www.biodalliance.org/datasets/flyThickets.bb");
- fail("Exception expected");
- } catch (URISyntaxException e) {
-
- }
-
- genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
- genome = null;
- for (ReferenceGenome referenceGenome : genomes) {
- if (referenceGenome.getVersion().equals(version)) {
- genome = referenceGenome;
- }
- }
- assertNotNull(genome);
- referenceGenomeDao.refresh(genome);
- assertEquals(3, genome.getGeneMapping().size());
-
- connector.removeGeneMapping(genome.getGeneMapping().get(2));
- connector.removeGeneMapping(genome.getGeneMapping().get(1));
- connector.removeGeneMapping(genome.getGeneMapping().get(0));
- connector.removeGenomeVersion(yeast, version);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- connector.setBigFileCache(bigFileCache);
- }
- }
-
- @Test
- public void testGetGenomeVersionFile() throws Exception {
- MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
- String version = "sacCer3";
- try {
- String url = connector.getGenomeVersionFile(yeast, version);
- assertNotNull(url);
- url.contains("sacCer3.2bit");
- url.contains("ftp");
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetUnknownGenomeVersionFile() {
- MiriamData human = new MiriamData(MiriamType.TAXONOMY, "9606");
- String version = "hg8";
- try {
- connector.getGenomeVersionFile(human, version);
- fail("Exception expected");
- } catch (FileNotAvailableException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalid() throws Exception {
- try {
- connector.refreshCacheQuery("invalid query");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalid2() throws Exception {
- try {
- connector.refreshCacheQuery(new Object());
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefresh() throws Exception {
- try {
- MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
- String version = "sacCer3";
-
- String query = UcscReferenceGenomeConnector.FILENAME_BY_ORGANISM_VERSION_PREFIX + yeast.getResource() + "\n"
- + version;
- Object res = connector.refreshCacheQuery(query);
- assertNotNull(res);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshUnknownFile() throws Exception {
- try {
- MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
- String version = "unkVer";
-
- String query = UcscReferenceGenomeConnector.FILENAME_BY_ORGANISM_VERSION_PREFIX + yeast.getResource() + "\n"
- + version;
- connector.refreshCacheQuery(query);
- } catch (SourceNotAvailable e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() throws Exception {
- try {
- UcscReferenceGenomeConnector connectorUnderTest = new UcscReferenceGenomeConnector();
- connectorUnderTest.setBigFileCache(connector.getBigFileCache());
- connectorUnderTest.setDbUtils(connector.getDbUtils());
- connectorUnderTest.setReferenceGenomeDao(connector.getReferenceGenomeDao());
- connectorUnderTest.setReferenceGenomeGeneMappingDao(connector.getReferenceGenomeGeneMappingDao());
-
- assertEquals(connector.getBigFileCache(), connectorUnderTest.getBigFileCache());
- assertEquals(connector.getDbUtils(), connectorUnderTest.getDbUtils());
- assertEquals(connector.getReferenceGenomeDao(), connectorUnderTest.getReferenceGenomeDao());
- assertEquals(connector.getReferenceGenomeGeneMappingDao(), connectorUnderTest.getReferenceGenomeGeneMappingDao());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGenomeVersionExtractorForInvalidGenome() throws Exception {
- try {
- int version = connector.extractInt("");
- assertEquals(0, version);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGenomeVersionExtractorForInvalidGenome2() throws Exception {
- try {
- int version = connector.extractInt("x");
- assertEquals(0, version);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGenomeVersionExtractorForValid() throws Exception {
- try {
- int version = connector.extractInt("x1");
- assertEquals(1, version);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGenomeVersionExtractorForValid2() throws Exception {
- try {
- int version = connector.extractInt("xy12z");
- assertEquals(12, version);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshCacheQueryNotAvailable() throws Exception {
- WebPageDownloader downloader = connector.getWebPageDownloader();
- GeneralCacheInterface originalCache = connector.getCache();
- try {
- // exclude first cached value
- connector.setCache(null);
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- connector.setWebPageDownloader(mockDownloader);
- connector.refreshCacheQuery("http://google.pl/");
- fail("Exception expected");
- } catch (SourceNotAvailable e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- connector.setWebPageDownloader(downloader);
- connector.setCache(originalCache);
- }
- }
-
- @Test
- public void testRefreshCacheQueryWhenFtpConnectionFails() throws Exception {
- MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
- String version = "sacCer3";
-
- UcscReferenceGenomeConnector connectorUnderTest = new UcscReferenceGenomeConnector() {
- @Override
- FTPClient createFtpClient() {
- FTPClient mockClient = Mockito.mock(FTPClient.class);
- Mockito.doReturn(FTPReply.REQUEST_DENIED).when(mockClient).getReplyCode();
- return mockClient;
- }
- };
-
- try {
- // exclude first cached value
- connectorUnderTest.getGenomeVersionFile(yeast, version);
- fail("Exception expected");
- } catch (FileNotAvailableException e) {
- assertTrue(e.getMessage().contains("FTP server refused connection"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetGenomeVersionFileWhenFtpConnectionFails2() throws Exception {
- MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
- String version = "sacCer3";
-
- UcscReferenceGenomeConnector connectorUnderTest = new UcscReferenceGenomeConnector() {
- @Override
- FTPClient createFtpClient() {
- FTPClient mockClient = Mockito.mock(FTPClient.class);
- try {
- Mockito.doThrow(new IOException()).when(mockClient).connect(anyString());
- Mockito.doReturn(false).when(mockClient).isConnected();
- } catch (Exception e) {
- fail();
- }
- return mockClient;
- }
- };
-
- try {
- // exclude first cached value
- connectorUnderTest.getGenomeVersionFile(yeast, version);
- fail("Exception expected");
- } catch (FileNotAvailableException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetGenomeVersionFileWhenFtpConnectionFails() throws Exception {
- MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
- String version = "sacCer3";
-
- UcscReferenceGenomeConnector connectorUnderTest = new UcscReferenceGenomeConnector() {
- @Override
- FTPClient createFtpClient() {
- FTPClient mockClient = Mockito.mock(FTPClient.class);
- try {
- Mockito.doThrow(new IOException()).when(mockClient).connect(anyString());
- Mockito.doReturn(true).when(mockClient).isConnected();
- } catch (Exception e) {
- fail();
- }
- return mockClient;
- }
- };
-
- try {
- // exclude first cached value
- connectorUnderTest.getGenomeVersionFile(yeast, version);
- fail("Exception expected");
- } catch (FileNotAvailableException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetGenomeVersionFileWhenFtpConnectionFails3() throws Exception {
- MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
- String version = "sacCer3";
-
- UcscReferenceGenomeConnector connectorUnderTest = new UcscReferenceGenomeConnector() {
- @Override
- FTPClient createFtpClient() {
- FTPClient mockClient = Mockito.mock(FTPClient.class);
- try {
- Mockito.doThrow(new IOException()).when(mockClient).connect(anyString());
- Mockito.doReturn(true).when(mockClient).isConnected();
- Mockito.doThrow(new IOException()).when(mockClient).disconnect();
- } catch (Exception e) {
- fail();
- }
- return mockClient;
- }
- };
-
- try {
- // exclude first cached value
- connectorUnderTest.getGenomeVersionFile(yeast, version);
- fail("Exception expected");
- } catch (FileNotAvailableException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetGenomeVersionFileWhenFtpDisconnectConnectionFails() throws Exception {
- MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
- String version = "sacCer3";
-
- UcscReferenceGenomeConnector connectorUnderTest = new UcscReferenceGenomeConnector() {
- @Override
- FTPClient createFtpClient() {
- FTPClient mockClient = Mockito.mock(FTPClient.class);
- try {
- Mockito.doThrow(new IOException()).when(mockClient).disconnect();
- Mockito.doReturn(new FTPFile[] {}).when(mockClient).listFiles(anyString());
- Mockito.doReturn(FTPReply.COMMAND_OK).when(mockClient).getReplyCode();
- Mockito.doReturn(true).when(mockClient).isConnected();
- } catch (Exception e) {
- fail();
- }
- return mockClient;
- }
- };
-
- try {
- // exclude first cached value
- connectorUnderTest.getGenomeVersionFile(yeast, version);
- fail("Exception expected");
- } catch (FileNotAvailableException e) {
- assertTrue(e.getMessage().contains("Problem with ftp connection"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetGenomeVersionFileWithMore2bitFiles() throws Exception {
- MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
- String version = "sacCer3";
-
- UcscReferenceGenomeConnector connectorUnderTest = new UcscReferenceGenomeConnector() {
- @Override
- FTPClient createFtpClient() {
- FTPClient mockClient = Mockito.mock(FTPClient.class);
- try {
- FTPFile file1 = new FTPFile();
- file1.setName("1.2bit");
- FTPFile file2 = new FTPFile();
- file2.setName("2.2bit");
- FTPFile[] files = new FTPFile[] { file1, file2 };
-
- Mockito.doReturn(files).when(mockClient).listFiles(anyString());
- Mockito.doReturn(FTPReply.COMMAND_OK).when(mockClient).getReplyCode();
- } catch (Exception e) {
- fail();
- }
- return mockClient;
- }
- };
-
- try {
- // exclude first cached value
- String url = connectorUnderTest.getGenomeVersionFile(yeast, version);
- assertEquals(1, getWarnings().size());
- assertTrue(url.endsWith("1.2bit"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private void waitForDownload() throws InterruptedException {
- while (connector.getDownloadThreadCount() > 0) {
- logger.debug("Waiting for download to finish");
- Thread.sleep(100);
- }
- }
-}
+package lcsb.mapviewer.annotation.services.genome;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import static org.mockito.Matchers.any;
+import static org.mockito.Matchers.anyBoolean;
+import static org.mockito.Matchers.anyString;
+import static org.mockito.Mockito.when;
+
+import java.io.IOException;
+import java.net.URISyntaxException;
+import java.util.List;
+import java.util.concurrent.Callable;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Future;
+
+import org.apache.commons.net.ftp.FTPClient;
+import org.apache.commons.net.ftp.FTPFile;
+import org.apache.commons.net.ftp.FTPReply;
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+import org.mockito.invocation.InvocationOnMock;
+import org.mockito.stubbing.Answer;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.AnnotationTestFunctions;
+import lcsb.mapviewer.annotation.cache.BigFileCache;
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.WebPageDownloader;
+import lcsb.mapviewer.annotation.services.TaxonomyBackend;
+import lcsb.mapviewer.annotation.services.TaxonomySearchException;
+import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.layout.ReferenceGenome;
+import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
+import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
+import lcsb.mapviewer.persist.dao.map.layout.ReferenceGenomeDao;
+
+public class UcscReferenceGenomeConnectorTest extends AnnotationTestFunctions {
+
+ Logger logger = Logger.getLogger(UcscReferenceGenomeConnectorTest.class);
+
+ @Autowired
+ UcscReferenceGenomeConnector connector;
+
+ @Autowired
+ ReferenceGenomeDao referenceGenomeDao;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testRefreshCacheQuery() throws Exception {
+ try {
+ assertNotNull(connector.refreshCacheQuery("http://google.pl/"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAvailableGenomeVersion() throws Exception {
+ MiriamData human = new MiriamData(MiriamType.TAXONOMY, "9606");
+ try {
+ List<String> list = connector.getAvailableGenomeVersion(human);
+ logger.debug(list);
+ assertTrue(list.size() >= 17);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAvailableGenomeVersionWhenProblemWithTaxonomyServer() throws Exception {
+ MiriamData human = new MiriamData(MiriamType.TAXONOMY, "9606");
+ TaxonomyBackend taxonomyBackend = connector.getTaxonomyBackend();
+ try {
+ // simulate problems with taxonomy server
+ TaxonomyBackend taxonomyMock = Mockito.mock(TaxonomyBackend.class);
+ when(taxonomyMock.getByName(anyString())).thenThrow(new TaxonomySearchException(null, null));
+ connector.setTaxonomyBackend(taxonomyMock);
+
+ connector.getAvailableGenomeVersion(human);
+ fail("Exception expected");
+ } catch (ReferenceGenomeConnectorException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ connector.setTaxonomyBackend(taxonomyBackend);
+ }
+ }
+
+ @Test
+ public void testGetAvailableGenomeVersionForInvalidTaxonomy() throws Exception {
+ MiriamData unknown = new MiriamData(MiriamType.TAXONOMY, "10101010101");
+ try {
+ List<String> list = connector.getAvailableGenomeVersion(unknown);
+ assertEquals(0, list.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAvailableOrganisms() throws Exception {
+ try {
+ MiriamData human = new MiriamData(MiriamType.TAXONOMY, "9606");
+ MiriamData chicken = new MiriamData(MiriamType.TAXONOMY, "9031");
+ List<MiriamData> list = connector.getAvailableOrganisms();
+ logger.debug(list);
+ assertTrue(list.size() > 40);
+
+ assertTrue(list.contains(human));
+ assertTrue(list.contains(chicken));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAvailableOrganismsWhenUcscWebpageDown() throws Exception {
+ WebPageDownloader downloader = connector.getWebPageDownloader();
+ GeneralCacheInterface originalCache = connector.getCache();
+ try {
+ // exclude first cached value
+ connector.setCache(null);
+
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ connector.setWebPageDownloader(mockDownloader);
+ connector.getAvailableOrganisms();
+ fail("Exception expected");
+ } catch (ReferenceGenomeConnectorException e) {
+ assertTrue(e.getMessage().contains("Problem with accessing UCSC database"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ connector.setWebPageDownloader(downloader);
+ connector.setCache(originalCache);
+ }
+ }
+
+ @Test
+ public void testDownloadGenomeVersion() throws Exception {
+ MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "1570291");
+ String version = "eboVir3";
+
+ try {
+ dbUtils.createSessionForCurrentThread();
+ List<String> list = connector.getDownloadedGenomeVersions(yeast);
+ if (list.contains(version)) {
+ connector.removeGenomeVersion(yeast, version);
+ }
+ dbUtils.closeSessionForCurrentThread();
+ list = connector.getDownloadedGenomeVersions(yeast);
+
+ assertFalse(list.contains(version));
+
+ connector.downloadGenomeVersion(yeast, version, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, false);
+
+ list = connector.getDownloadedGenomeVersions(yeast);
+ assertTrue(list.contains(version));
+
+ List<ReferenceGenome> genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
+ ReferenceGenome genome = null;
+ for (ReferenceGenome referenceGenome : genomes) {
+ if (referenceGenome.getVersion().equals(version)) {
+ genome = referenceGenome;
+ }
+ }
+ assertNotNull(genome);
+ connector.downloadGeneMappingGenomeVersion(genome, "test", null, false,
+ "http://www.biodalliance.org/datasets/flyThickets.bb");
+
+ dbUtils.createSessionForCurrentThread();
+ genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
+ genome = null;
+ for (ReferenceGenome referenceGenome : genomes) {
+ if (referenceGenome.getVersion().equals(version)) {
+ genome = referenceGenome;
+ }
+ }
+ assertNotNull(genome);
+ assertEquals(1, genome.getGeneMapping().size());
+ dbUtils.closeSessionForCurrentThread();
+
+ try {
+ // try to download the same thing for the second time
+ connector.downloadGeneMappingGenomeVersion(genome, "test", new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, false, "http://www.biodalliance.org/datasets/flyThickets.bb");
+ fail("Exception expected");
+ } catch (ReferenceGenomeConnectorException e) {
+ assertTrue(e.getMessage().contains("already exists"));
+ }
+
+ try {
+ // try to download something that is not big bed
+ connector.downloadGeneMappingGenomeVersion(genome, "test2", new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, false, "http://www.biodalliance.org/datasets/flyThickets.txt");
+ fail("Exception expected");
+ } catch (ReferenceGenomeConnectorException e) {
+ assertTrue(e.getMessage().contains("Only big bed format files are supported"));
+ }
+
+ // connector.removeGeneMapping(genome.getGeneMapping().get(0));
+
+ int warningCount = getWarnings().size();
+
+ // try to remove invalid mapping
+ connector.removeGeneMapping(new ReferenceGenomeGeneMapping());
+
+ assertEquals(warningCount + 1, getWarnings().size());
+
+ dbUtils.createSessionForCurrentThread();
+ connector.removeGenomeVersion(yeast, version);
+ dbUtils.closeSessionForCurrentThread();
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @SuppressWarnings("unchecked")
+ @Test
+ public void testDownloadGenomeVersionWhenInternalUrlIsInvalid() throws Exception {
+ MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "1570291");
+ String version = "eboVir3";
+
+ ExecutorService originalExecutorService = connector.getSyncExecutorService();
+ try {
+ ExecutorService executorService = Mockito.mock(ExecutorService.class);
+ connector.setSyncExecutorService(executorService);
+ Future<?> task = Mockito.mock(Future.class);
+ when(task.get()).thenThrow(new ExecutionException(new URISyntaxException("", "")));
+ when(executorService.submit(any(Callable.class))).thenReturn(task);
+
+ connector.downloadGenomeVersion(yeast, version, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, false);
+ fail("Exception expected");
+
+ } catch (InvalidStateException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ connector.setSyncExecutorService(originalExecutorService);
+ }
+ }
+
+ @Test
+ public void testDownloadGenomeVersionAsync() throws Exception {
+ MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "1570291");
+ String version = "eboVir3";
+
+ BigFileCache bigFileCache = connector.getBigFileCache();
+ try {
+ dbUtils.createSessionForCurrentThread();
+ List<String> list = connector.getDownloadedGenomeVersions(yeast);
+ if (list.contains(version)) {
+ connector.removeGenomeVersion(yeast, version);
+ }
+ list = connector.getDownloadedGenomeVersions(yeast);
+
+ dbUtils.closeSessionForCurrentThread();
+
+ // create a mock for ftp connections (so we speed up tests), the real
+ // connection is tested elsewhere
+ BigFileCache mockCache = Mockito.mock(BigFileCache.class);
+ Mockito.doAnswer(new Answer<Void>() {
+
+ @Override
+ public Void answer(InvocationOnMock invocation) throws Throwable {
+ IProgressUpdater updater = (IProgressUpdater) invocation.getArguments()[2];
+ updater.setProgress(100);
+ return null;
+ }
+ }).when(mockCache).downloadFile(anyString(), anyBoolean(), any());
+
+ connector.setBigFileCache(mockCache);
+
+ assertFalse(list.contains(version));
+
+ connector.downloadGenomeVersion(yeast, version, null, true);
+
+ waitForDownload();
+
+ dbUtils.createSessionForCurrentThread();
+ list = connector.getDownloadedGenomeVersions(yeast);
+ assertTrue(list.contains(version));
+
+ List<ReferenceGenome> genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
+ ReferenceGenome genome = null;
+ for (ReferenceGenome referenceGenome : genomes) {
+ if (referenceGenome.getVersion().equals(version)) {
+ genome = referenceGenome;
+ }
+ }
+ dbUtils.closeSessionForCurrentThread();
+ assertNotNull(genome);
+ connector.downloadGeneMappingGenomeVersion(genome, "test", new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, true, "http://www.biodalliance.org/datasets/flyThickets.bb");
+
+ waitForDownload();
+
+ genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
+ genome = null;
+ for (ReferenceGenome referenceGenome : genomes) {
+ if (referenceGenome.getVersion().equals(version)) {
+ genome = referenceGenome;
+ }
+ }
+ assertNotNull(genome);
+ referenceGenomeDao.refresh(genome);
+ assertEquals(1, genome.getGeneMapping().size());
+
+ try {
+ // try to download the same thing for the second time
+ connector.downloadGeneMappingGenomeVersion(genome, "test", new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, false, "http://www.biodalliance.org/datasets/flyThickets.bb");
+ fail("Exception expected");
+ } catch (ReferenceGenomeConnectorException e) {
+ assertTrue(e.getMessage().contains("already exists"));
+ }
+
+ try {
+ // try to download something that is not big bed
+ connector.downloadGeneMappingGenomeVersion(genome, "test2", new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, false, "http://www.biodalliance.org/datasets/flyThickets.txt");
+ fail("Exception expected");
+ } catch (ReferenceGenomeConnectorException e) {
+ assertTrue(e.getMessage().contains("Only big bed format files are supported"));
+ }
+
+ connector.removeGeneMapping(genome.getGeneMapping().get(0));
+
+ int warningCount = getWarnings().size();
+
+ // try to remove invalid mapping
+ connector.removeGeneMapping(new ReferenceGenomeGeneMapping());
+
+ assertEquals(warningCount + 1, getWarnings().size());
+
+ connector.removeGenomeVersion(yeast, version);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ connector.setBigFileCache(bigFileCache);
+ }
+ }
+
+ @Test
+ public void testDownloadGenomeVersionAsyncWithException() throws Exception {
+ MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "1570291");
+ String version = "eboVir3";
+
+ BigFileCache bigFileCache = connector.getBigFileCache();
+ try {
+ dbUtils.createSessionForCurrentThread();
+ List<String> list = connector.getDownloadedGenomeVersions(yeast);
+ if (list.contains(version)) {
+ connector.removeGenomeVersion(yeast, version);
+ }
+ list = connector.getDownloadedGenomeVersions(yeast);
+
+ dbUtils.closeSessionForCurrentThread();
+
+ // create a mock for ftp connections (so we speed up tests), the real
+ // connection is tested elsewhere
+ BigFileCache mockCache = Mockito.mock(BigFileCache.class);
+
+ connector.setBigFileCache(mockCache);
+
+ assertFalse(list.contains(version));
+
+ connector.downloadGenomeVersion(yeast, version, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, true);
+
+ waitForDownload();
+
+ dbUtils.createSessionForCurrentThread();
+ list = connector.getDownloadedGenomeVersions(yeast);
+ assertTrue(list.contains(version));
+
+ List<ReferenceGenome> genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
+ ReferenceGenome genome = null;
+ for (ReferenceGenome referenceGenome : genomes) {
+ if (referenceGenome.getVersion().equals(version)) {
+ genome = referenceGenome;
+ }
+ }
+ dbUtils.closeSessionForCurrentThread();
+ assertNotNull(genome);
+
+ Mockito.doThrow(new IOException()).when(mockCache).downloadFile(anyString(), anyBoolean(), any());
+ assertEquals(0, getErrors().size());
+ connector.downloadGeneMappingGenomeVersion(genome, "test", new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, true, "http://www.biodalliance.org/datasets/flyThickets.bb");
+
+ waitForDownload();
+
+ logger.debug(getErrors());
+ // during this downlad we expect exception thrown by downloader
+ assertEquals(1, getErrors().size());
+
+ Mockito.doThrow(new OutOfMemoryError()).when(mockCache).downloadFile(anyString(), anyBoolean(), any());
+ connector.downloadGeneMappingGenomeVersion(genome, "test2", new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, true, "http://www.biodalliance.org/datasets/flyThickets.bb");
+
+ waitForDownload();
+ // during this downlad we expect error, this shouldn't change list of
+ // errors
+ assertEquals(1, getErrors().size());
+
+ Mockito.doThrow(new URISyntaxException("", "")).when(mockCache).downloadFile(anyString(), anyBoolean(), any());
+ connector.downloadGeneMappingGenomeVersion(genome, "test3", new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, true, "http://www.biodalliance.org/datasets/flyThickets.bb");
+
+ waitForDownload();
+
+ // during this downlad we expect error (exception thrown by downloader)
+ assertEquals(2, getErrors().size());
+
+ genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
+ genome = null;
+ for (ReferenceGenome referenceGenome : genomes) {
+ if (referenceGenome.getVersion().equals(version)) {
+ genome = referenceGenome;
+ }
+ }
+ assertNotNull(genome);
+ referenceGenomeDao.refresh(genome);
+ assertEquals(3, genome.getGeneMapping().size());
+
+ connector.removeGeneMapping(genome.getGeneMapping().get(2));
+ connector.removeGeneMapping(genome.getGeneMapping().get(1));
+ connector.removeGeneMapping(genome.getGeneMapping().get(0));
+ connector.removeGenomeVersion(yeast, version);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ connector.setBigFileCache(bigFileCache);
+ }
+ }
+
+ @Test
+ public void testDownloadGenomeVersionWithException() throws Exception {
+ MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "1570291");
+ String version = "eboVir3";
+
+ BigFileCache bigFileCache = connector.getBigFileCache();
+ try {
+ List<String> list = connector.getDownloadedGenomeVersions(yeast);
+ if (list.contains(version)) {
+ connector.removeGenomeVersion(yeast, version);
+ }
+ list = connector.getDownloadedGenomeVersions(yeast);
+
+ // create a mock for ftp connections (so we speed up tests), the real
+ // connection is tested elsewhere
+ BigFileCache mockCache = Mockito.mock(BigFileCache.class);
+
+ connector.setBigFileCache(mockCache);
+
+ assertFalse(list.contains(version));
+
+ connector.downloadGenomeVersion(yeast, version, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, false);
+
+ list = connector.getDownloadedGenomeVersions(yeast);
+ assertTrue(list.contains(version));
+
+ List<ReferenceGenome> genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
+ ReferenceGenome genome = null;
+ for (ReferenceGenome referenceGenome : genomes) {
+ if (referenceGenome.getVersion().equals(version)) {
+ genome = referenceGenome;
+ }
+ }
+ assertNotNull(genome);
+
+ Mockito.doThrow(new IOException()).when(mockCache).downloadFile(anyString(), anyBoolean(), any());
+ assertEquals(0, getErrors().size());
+ try {
+ connector.downloadGeneMappingGenomeVersion(genome, "test", new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, false, "http://www.biodalliance.org/datasets/flyThickets.bb");
+ fail("Exception expected");
+ } catch (IOException e) {
+
+ }
+
+ Mockito.doThrow(new RuntimeException()).when(mockCache).downloadFile(anyString(), anyBoolean(), any());
+ try {
+ connector.downloadGeneMappingGenomeVersion(genome, "test2", new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, false, "http://www.biodalliance.org/datasets/flyThickets.bb");
+
+ fail("Exception expected");
+ } catch (InvalidStateException e) {
+
+ }
+
+ Mockito.doThrow(new URISyntaxException("", "")).when(mockCache).downloadFile(anyString(), anyBoolean(), any());
+
+ try {
+ connector.downloadGeneMappingGenomeVersion(genome, "test3", new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, false, "http://www.biodalliance.org/datasets/flyThickets.bb");
+ fail("Exception expected");
+ } catch (URISyntaxException e) {
+
+ }
+
+ genomes = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC);
+ genome = null;
+ for (ReferenceGenome referenceGenome : genomes) {
+ if (referenceGenome.getVersion().equals(version)) {
+ genome = referenceGenome;
+ }
+ }
+ assertNotNull(genome);
+ referenceGenomeDao.refresh(genome);
+ assertEquals(3, genome.getGeneMapping().size());
+
+ connector.removeGeneMapping(genome.getGeneMapping().get(2));
+ connector.removeGeneMapping(genome.getGeneMapping().get(1));
+ connector.removeGeneMapping(genome.getGeneMapping().get(0));
+ connector.removeGenomeVersion(yeast, version);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ connector.setBigFileCache(bigFileCache);
+ }
+ }
+
+ @Test
+ public void testGetGenomeVersionFile() throws Exception {
+ MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
+ String version = "sacCer3";
+ try {
+ String url = connector.getGenomeVersionFile(yeast, version);
+ assertNotNull(url);
+ url.contains("sacCer3.2bit");
+ url.contains("ftp");
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetUnknownGenomeVersionFile() {
+ MiriamData human = new MiriamData(MiriamType.TAXONOMY, "9606");
+ String version = "hg8";
+ try {
+ connector.getGenomeVersionFile(human, version);
+ fail("Exception expected");
+ } catch (FileNotAvailableException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalid() throws Exception {
+ try {
+ connector.refreshCacheQuery("invalid query");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalid2() throws Exception {
+ try {
+ connector.refreshCacheQuery(new Object());
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefresh() throws Exception {
+ try {
+ MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
+ String version = "sacCer3";
+
+ String query = UcscReferenceGenomeConnector.FILENAME_BY_ORGANISM_VERSION_PREFIX + yeast.getResource() + "\n"
+ + version;
+ Object res = connector.refreshCacheQuery(query);
+ assertNotNull(res);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshUnknownFile() throws Exception {
+ try {
+ MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
+ String version = "unkVer";
+
+ String query = UcscReferenceGenomeConnector.FILENAME_BY_ORGANISM_VERSION_PREFIX + yeast.getResource() + "\n"
+ + version;
+ connector.refreshCacheQuery(query);
+ } catch (SourceNotAvailable e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() throws Exception {
+ try {
+ UcscReferenceGenomeConnector connectorUnderTest = new UcscReferenceGenomeConnector();
+ connectorUnderTest.setBigFileCache(connector.getBigFileCache());
+ connectorUnderTest.setDbUtils(connector.getDbUtils());
+ connectorUnderTest.setReferenceGenomeDao(connector.getReferenceGenomeDao());
+ connectorUnderTest.setReferenceGenomeGeneMappingDao(connector.getReferenceGenomeGeneMappingDao());
+
+ assertEquals(connector.getBigFileCache(), connectorUnderTest.getBigFileCache());
+ assertEquals(connector.getDbUtils(), connectorUnderTest.getDbUtils());
+ assertEquals(connector.getReferenceGenomeDao(), connectorUnderTest.getReferenceGenomeDao());
+ assertEquals(connector.getReferenceGenomeGeneMappingDao(), connectorUnderTest.getReferenceGenomeGeneMappingDao());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGenomeVersionExtractorForInvalidGenome() throws Exception {
+ try {
+ int version = connector.extractInt("");
+ assertEquals(0, version);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGenomeVersionExtractorForInvalidGenome2() throws Exception {
+ try {
+ int version = connector.extractInt("x");
+ assertEquals(0, version);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGenomeVersionExtractorForValid() throws Exception {
+ try {
+ int version = connector.extractInt("x1");
+ assertEquals(1, version);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGenomeVersionExtractorForValid2() throws Exception {
+ try {
+ int version = connector.extractInt("xy12z");
+ assertEquals(12, version);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQueryNotAvailable() throws Exception {
+ WebPageDownloader downloader = connector.getWebPageDownloader();
+ GeneralCacheInterface originalCache = connector.getCache();
+ try {
+ // exclude first cached value
+ connector.setCache(null);
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ connector.setWebPageDownloader(mockDownloader);
+ connector.refreshCacheQuery("http://google.pl/");
+ fail("Exception expected");
+ } catch (SourceNotAvailable e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ connector.setWebPageDownloader(downloader);
+ connector.setCache(originalCache);
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQueryWhenFtpConnectionFails() throws Exception {
+ MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
+ String version = "sacCer3";
+
+ UcscReferenceGenomeConnector connectorUnderTest = new UcscReferenceGenomeConnector() {
+ @Override
+ FTPClient createFtpClient() {
+ FTPClient mockClient = Mockito.mock(FTPClient.class);
+ Mockito.doReturn(FTPReply.REQUEST_DENIED).when(mockClient).getReplyCode();
+ return mockClient;
+ }
+ };
+
+ try {
+ // exclude first cached value
+ connectorUnderTest.getGenomeVersionFile(yeast, version);
+ fail("Exception expected");
+ } catch (FileNotAvailableException e) {
+ assertTrue(e.getMessage().contains("FTP server refused connection"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetGenomeVersionFileWhenFtpConnectionFails2() throws Exception {
+ MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
+ String version = "sacCer3";
+
+ UcscReferenceGenomeConnector connectorUnderTest = new UcscReferenceGenomeConnector() {
+ @Override
+ FTPClient createFtpClient() {
+ FTPClient mockClient = Mockito.mock(FTPClient.class);
+ try {
+ Mockito.doThrow(new IOException()).when(mockClient).connect(anyString());
+ Mockito.doReturn(false).when(mockClient).isConnected();
+ } catch (Exception e) {
+ fail();
+ }
+ return mockClient;
+ }
+ };
+
+ try {
+ // exclude first cached value
+ connectorUnderTest.getGenomeVersionFile(yeast, version);
+ fail("Exception expected");
+ } catch (FileNotAvailableException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetGenomeVersionFileWhenFtpConnectionFails() throws Exception {
+ MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
+ String version = "sacCer3";
+
+ UcscReferenceGenomeConnector connectorUnderTest = new UcscReferenceGenomeConnector() {
+ @Override
+ FTPClient createFtpClient() {
+ FTPClient mockClient = Mockito.mock(FTPClient.class);
+ try {
+ Mockito.doThrow(new IOException()).when(mockClient).connect(anyString());
+ Mockito.doReturn(true).when(mockClient).isConnected();
+ } catch (Exception e) {
+ fail();
+ }
+ return mockClient;
+ }
+ };
+
+ try {
+ // exclude first cached value
+ connectorUnderTest.getGenomeVersionFile(yeast, version);
+ fail("Exception expected");
+ } catch (FileNotAvailableException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetGenomeVersionFileWhenFtpConnectionFails3() throws Exception {
+ MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
+ String version = "sacCer3";
+
+ UcscReferenceGenomeConnector connectorUnderTest = new UcscReferenceGenomeConnector() {
+ @Override
+ FTPClient createFtpClient() {
+ FTPClient mockClient = Mockito.mock(FTPClient.class);
+ try {
+ Mockito.doThrow(new IOException()).when(mockClient).connect(anyString());
+ Mockito.doReturn(true).when(mockClient).isConnected();
+ Mockito.doThrow(new IOException()).when(mockClient).disconnect();
+ } catch (Exception e) {
+ fail();
+ }
+ return mockClient;
+ }
+ };
+
+ try {
+ // exclude first cached value
+ connectorUnderTest.getGenomeVersionFile(yeast, version);
+ fail("Exception expected");
+ } catch (FileNotAvailableException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetGenomeVersionFileWhenFtpDisconnectConnectionFails() throws Exception {
+ MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
+ String version = "sacCer3";
+
+ UcscReferenceGenomeConnector connectorUnderTest = new UcscReferenceGenomeConnector() {
+ @Override
+ FTPClient createFtpClient() {
+ FTPClient mockClient = Mockito.mock(FTPClient.class);
+ try {
+ Mockito.doThrow(new IOException()).when(mockClient).disconnect();
+ Mockito.doReturn(new FTPFile[] {}).when(mockClient).listFiles(anyString());
+ Mockito.doReturn(FTPReply.COMMAND_OK).when(mockClient).getReplyCode();
+ Mockito.doReturn(true).when(mockClient).isConnected();
+ } catch (Exception e) {
+ fail();
+ }
+ return mockClient;
+ }
+ };
+
+ try {
+ // exclude first cached value
+ connectorUnderTest.getGenomeVersionFile(yeast, version);
+ fail("Exception expected");
+ } catch (FileNotAvailableException e) {
+ assertTrue(e.getMessage().contains("Problem with ftp connection"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetGenomeVersionFileWithMore2bitFiles() throws Exception {
+ MiriamData yeast = new MiriamData(MiriamType.TAXONOMY, "4932");
+ String version = "sacCer3";
+
+ UcscReferenceGenomeConnector connectorUnderTest = new UcscReferenceGenomeConnector() {
+ @Override
+ FTPClient createFtpClient() {
+ FTPClient mockClient = Mockito.mock(FTPClient.class);
+ try {
+ FTPFile file1 = new FTPFile();
+ file1.setName("1.2bit");
+ FTPFile file2 = new FTPFile();
+ file2.setName("2.2bit");
+ FTPFile[] files = new FTPFile[] { file1, file2 };
+
+ Mockito.doReturn(files).when(mockClient).listFiles(anyString());
+ Mockito.doReturn(FTPReply.COMMAND_OK).when(mockClient).getReplyCode();
+ } catch (Exception e) {
+ fail();
+ }
+ return mockClient;
+ }
+ };
+
+ try {
+ // exclude first cached value
+ String url = connectorUnderTest.getGenomeVersionFile(yeast, version);
+ assertEquals(1, getWarnings().size());
+ assertTrue(url.endsWith("1.2bit"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private void waitForDownload() throws InterruptedException {
+ while (connector.getDownloadThreadCount() > 0) {
+ logger.debug("Waiting for download to finish");
+ Thread.sleep(100);
+ }
+ }
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/Configuration.java b/commons/src/main/java/lcsb/mapviewer/common/Configuration.java
index 6aafe5c110..73aa6a7a17 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/Configuration.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/Configuration.java
@@ -1,428 +1,428 @@
-package lcsb.mapviewer.common;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileReader;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-/**
- * Basic configuration parameters of the system (these values cannot be modified
- * by the user, user modified values are kept in the db:
- * {@link lcsb.mapviewer.db.model.user.Configuration Configuration} ).
- *
- * @author Piotr Gawron
- *
- */
-public final class Configuration {
-
- /**
- * Default value for {@link #memorySaturationRatioTriggerClean}. It defines at
- * what memory usage level application should release cached objects (to prevent
- * unnecessary out of memory exceptions).
- *
- */
- private static final double DEFAULT_MEMORY_SATURATION_TRIGGER_CLEAN = 0.9;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(Configuration.class);
-
- /**
- * How many elements should be visible in auto-complete lists.
- */
- private static final int DEFAULT_AUTOCOMPLETE_SIZE = 5;
-
- /**
- * What is the minimal zoom level in the Google Maps API. It cannot be set to 0
- * because Google Maps API was designed to visualize map of Earth which is based
- * on torus. Therefore, if we use too small zoom level we will see next to the
- * right edge elements from the left part. When we increase minimal zoom level
- * there will be a gap (huge enough) between the overlapping parts and user will
- * be unaware of that fact.
- */
- public static final int MIN_ZOOM_LEVEL = 2;
-
- /**
- * This constant describes minimum size (in square pixels) of object visible
- * during nesting (it is a soft limit, can be override by depth of the depending
- * tree).
- */
- public static final double MIN_VISIBLE_OBJECT_SIZE = 55000;
-
- /**
- * This constant describes maximum size (in square pixels) of object visible
- * during nesting.
- */
- public static final double MAX_VISIBLE_OBJECT_SIZE = 80000;
-
- /**
- * Address where Parkinson's Disease map is available in the Internet.
- */
- public static final String PUBLICALY_AVAILABLE_PD_MAP = "http://pdmap.uni.lu/MapViewer/?id=pdmap";
-
- /**
- * Where the main web page is located.
- */
- public static final String MAIN_PAGE = "/index.xhtml";
-
- /**
- * Name of the cookie for authentication token.
- */
- public static final String AUTH_TOKEN = "MINERVA_AUTH_TOKEN";
-
- /**
- * Where miriam redirecting web page is located.
- */
- public static final String MIRIAM_PAGE = "miriam.xhtml";
-
- /**
- * Where the login web page is located.
- */
- public static final String LOGIN_PAGE = "/login.xhtml";
-
- /**
- * Spring url for login.
- */
- public static final String SPRING_SECURITY_ACTION = "/login";
-
- /**
- * Spring url for logout.
- */
- public static final String SPRING_SECURITY_LOGOUT = "/j_spring_security_logout";
-
- /**
- * Guest account.
- */
- public static final String ANONYMOUS_LOGIN = "anonymous";
-
- /**
- * Should the application cache be turned on.
- */
- private static boolean applicationCacheOn = true;
-
- /**
- * Should the database cache be turned on.
- */
- private static boolean dbCacheOn = true;
-
- /**
- * This constant defines at what memory usage level application should release
- * cached objects (to prevent unnecessary out of memory exceptions).
- */
- private static Double memorySaturationRatioTriggerClean = DEFAULT_MEMORY_SATURATION_TRIGGER_CLEAN;
-
- /**
- * What is the size of auto-complete elements.
- */
- private static int autocompleteSize = DEFAULT_AUTOCOMPLETE_SIZE;
-
- /**
- * Epsilon used for different types of comparisons.
- */
- public static final double EPSILON = 1e-6;
-
- /**
- * Git version from which framework was built.
- */
- private static String systemBuildVersion = null;
-
- /**
- * Date when the framework was built.
- */
- private static String systemBuildTime = null;
-
- /**
- * Version of the system (used by debian package).
- */
- private static String systemVersion = null;
-
- /**
- * Address that should be allowed to use x-frame.
- */
- private static List<String> xFrametDomain = new ArrayList<>();
-
- /**
- * Directory where tomcat webapp folder is located. Default value is "." because
- * it should be set to proper value when tomcat application is deployed and run.
- */
- private static String webAppDir = "./";
-
- /**
- * Default constructor which prevents instantiation.
- */
- private Configuration() {
-
- }
-
- /**
- * @return the applicationCacheOn
- */
- public static boolean isApplicationCacheOn() {
- return applicationCacheOn;
- }
-
- /**
- * @param applicationCacheOn
- * the applicationCacheOn to set
- */
- public static void setApplicationCacheOn(boolean applicationCacheOn) {
- Configuration.applicationCacheOn = applicationCacheOn;
- }
-
- /**
- * @return the dbCacheOn
- */
- public static boolean isDbCacheOn() {
- return dbCacheOn;
- }
-
- /**
- * @param dbCacheOn
- * the dbCacheOn to set
- */
- public static void setDbCacheOn(boolean dbCacheOn) {
- Configuration.dbCacheOn = dbCacheOn;
- }
-
- /**
- * @return the autocompleteSize
- */
- public static int getAutocompleteSize() {
- return autocompleteSize;
- }
-
- /**
- * @param autocompleteSize
- * the autocompleteSize to set
- */
- public static void setAutocompleteSize(int autocompleteSize) {
- Configuration.autocompleteSize = autocompleteSize;
- }
-
- /**
- * @param baseDir
- * directory where the system is placed
- * @return {@link #systemBuildVersion}
- */
- public static String getSystemBuildVersion(String baseDir) {
- if (systemBuildVersion == null) {
- loadSystemVersion(baseDir);
- }
- return systemBuildVersion;
- }
-
- /**
- * @param baseDir
- * directory where the system is placed
- * @return {@link #systemVersion}
- */
- public static String getSystemVersion(String baseDir) {
- if (systemVersion == null) {
- loadSystemVersion(baseDir);
- }
- return systemVersion;
- }
-
- /**
- * @param baseDir
- * directory where the system is placed
- * @param forceReload
- * if true then forces to reload data from text file
- * @return {@link #systemBuildVersion}
- */
- public static String getSystemBuildVersion(String baseDir, boolean forceReload) {
- if (forceReload) {
- systemBuildVersion = null;
- }
- return getSystemBuildVersion(baseDir);
- }
-
- /**
- * @param baseDir
- * directory where the system is placed
- * @param forceReload
- * if true then forces to reload data from text file
- * @return {@link #systemBuildVersion}
- */
- public static String getSystemVersion(String baseDir, boolean forceReload) {
- if (forceReload) {
- systemVersion = null;
- }
- return getSystemVersion(baseDir);
- }
-
- /**
- * Loads system version (git version, build date) from the file.
- *
- * @param baseDir
- * directory where the system is placed
- */
- protected static void loadSystemVersion(String baseDir) {
- systemBuildVersion = "Unknown";
- systemBuildTime = "Unknown";
- systemVersion = "Unknown";
- File buildVersionFile = null;
- File changelogFile = null;
- if (baseDir == null) {
- buildVersionFile = new File("version.txt");
- changelogFile = new File("CHANGELOG");
- } else {
- buildVersionFile = new File(baseDir + "version.txt");
- changelogFile = new File(baseDir + "CHANGELOG");
- }
- if (buildVersionFile.exists()) {
- loadSystemBuildVersion(buildVersionFile);
- } else {
- logger.error(buildVersionFile.getAbsoluteFile() + " doesn't exist.");
- }
-
- if (changelogFile.exists()) {
- loadSystemVersion(changelogFile);
- } else {
- logger.error(changelogFile.getAbsoluteFile() + " doesn't exist.");
- }
- }
-
- /**
- * Loads system version (git version, build date) from the file.
- *
- * @param file
- * file from which data is loaded
- */
- protected static void loadSystemBuildVersion(File file) {
- try {
- BufferedReader reader = new BufferedReader(new FileReader(file));
- systemBuildVersion = reader.readLine().trim();
- systemBuildTime = reader.readLine().trim();
- reader.close();
- } catch (IOException e) {
- logger.error(e);
- }
- }
-
- /**
- * Loads system version from debian changelog file.
- *
- * @param file
- * debian changelog file
- */
- protected static void loadSystemVersion(File file) {
- try {
- BufferedReader reader = new BufferedReader(new FileReader(file));
- String line = reader.readLine();
-
- int startIndex = line.indexOf("(");
- int endIndex = line.indexOf(")");
-
- if (startIndex >= 0 && endIndex >= 0) {
- systemVersion = line.substring(startIndex + 1, endIndex);
- } else {
- logger.error("Invalid CHANGELOG file. Cannot find system version in line: " + line);
- }
- reader.close();
- } catch (IOException e) {
- logger.error(e);
- }
- }
-
- /**
- * @param baseDir
- * directory where the system is placed
- * @return the systemBuild
- * @see #systemBuildTime
- */
- public static String getSystemBuild(String baseDir) {
- if (systemBuildTime == null) {
- loadSystemVersion(baseDir);
- }
- return systemBuildTime;
- }
-
- /**
- * @param baseDir
- * directory where the system is placed
- * @param forceReload
- * if true then forces to reload data from text file
- * @return the systemBuild
- * @see #systemBuildTime
- */
- public static String getSystemBuild(String baseDir, boolean forceReload) {
- if (forceReload) {
- systemBuildTime = null;
- }
- return getSystemBuild(baseDir);
- }
-
- /**
- * @return the xFrametDomain
- * @see #xFrametDomain
- */
- public static List<String> getxFrameDomain() {
- return xFrametDomain;
- }
-
- /**
- * @param xFrametDomains
- * the xFrametDomain to set
- * @see #xFrametDomain
- */
- public static void setxFrameDomain(List<String> xFrametDomains) {
- Configuration.xFrametDomain = xFrametDomains;
- }
-
- /**
- * @param path
- * the path to webapps to set
- * @see #webAppDir
- */
- public static void setWebAppDir(String path) {
- Configuration.webAppDir = path;
- }
-
- /**
- * @return the {@link #webAppDir}
- */
- public static String getWebAppDir() {
- return Configuration.webAppDir;
- }
-
- /**
- * @return the memorySaturationRatioTriggerClean
- * @see #memorySaturationRatioTriggerClean
- */
- public static Double getMemorySaturationRatioTriggerClean() {
- return memorySaturationRatioTriggerClean;
- }
-
- /**
- * @param memorySaturationRatioTriggerClean
- * the memorySaturationRatioTriggerClean to set
- * @see #memorySaturationRatioTriggerClean
- */
- public static void setMemorySaturationRatioTriggerClean(Double memorySaturationRatioTriggerClean) {
- Configuration.memorySaturationRatioTriggerClean = memorySaturationRatioTriggerClean;
- }
-
- /**
- * Returns information about version of the framework.
- *
- * @param baseDir
- * directory where project was deployed (or information about version
- * is stored)
- * @return information about version of the framework
- */
- public static FrameworkVersion getFrameworkVersion(String baseDir) {
- FrameworkVersion result = new FrameworkVersion();
- loadSystemVersion(baseDir);
- result.setGitVersion(getSystemBuildVersion(baseDir));
- result.setTime(getSystemBuild(baseDir));
- result.setVersion(getSystemVersion(baseDir));
- return result;
- }
-
-}
+package lcsb.mapviewer.common;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Basic configuration parameters of the system (these values cannot be modified
+ * by the user, user modified values are kept in the db:
+ * {@link lcsb.mapviewer.db.model.user.Configuration Configuration} ).
+ *
+ * @author Piotr Gawron
+ *
+ */
+public final class Configuration {
+
+ /**
+ * Default value for {@link #memorySaturationRatioTriggerClean}. It defines at
+ * what memory usage level application should release cached objects (to prevent
+ * unnecessary out of memory exceptions).
+ *
+ */
+ private static final double DEFAULT_MEMORY_SATURATION_TRIGGER_CLEAN = 0.9;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(Configuration.class);
+
+ /**
+ * How many elements should be visible in auto-complete lists.
+ */
+ private static final int DEFAULT_AUTOCOMPLETE_SIZE = 5;
+
+ /**
+ * What is the minimal zoom level in the Google Maps API. It cannot be set to 0
+ * because Google Maps API was designed to visualize map of Earth which is based
+ * on torus. Therefore, if we use too small zoom level we will see next to the
+ * right edge elements from the left part. When we increase minimal zoom level
+ * there will be a gap (huge enough) between the overlapping parts and user will
+ * be unaware of that fact.
+ */
+ public static final int MIN_ZOOM_LEVEL = 2;
+
+ /**
+ * This constant describes minimum size (in square pixels) of object visible
+ * during nesting (it is a soft limit, can be override by depth of the depending
+ * tree).
+ */
+ public static final double MIN_VISIBLE_OBJECT_SIZE = 55000;
+
+ /**
+ * This constant describes maximum size (in square pixels) of object visible
+ * during nesting.
+ */
+ public static final double MAX_VISIBLE_OBJECT_SIZE = 80000;
+
+ /**
+ * Address where Parkinson's Disease map is available in the Internet.
+ */
+ public static final String PUBLICALY_AVAILABLE_PD_MAP = "http://pdmap.uni.lu/MapViewer/?id=pdmap";
+
+ /**
+ * Where the main web page is located.
+ */
+ public static final String MAIN_PAGE = "/index.xhtml";
+
+ /**
+ * Name of the cookie for authentication token.
+ */
+ public static final String AUTH_TOKEN = "MINERVA_AUTH_TOKEN";
+
+ /**
+ * Where miriam redirecting web page is located.
+ */
+ public static final String MIRIAM_PAGE = "miriam.xhtml";
+
+ /**
+ * Where the login web page is located.
+ */
+ public static final String LOGIN_PAGE = "/login.xhtml";
+
+ /**
+ * Spring url for login.
+ */
+ public static final String SPRING_SECURITY_ACTION = "/login";
+
+ /**
+ * Spring url for logout.
+ */
+ public static final String SPRING_SECURITY_LOGOUT = "/j_spring_security_logout";
+
+ /**
+ * Guest account.
+ */
+ public static final String ANONYMOUS_LOGIN = "anonymous";
+
+ /**
+ * Should the application cache be turned on.
+ */
+ private static boolean applicationCacheOn = true;
+
+ /**
+ * Should the database cache be turned on.
+ */
+ private static boolean dbCacheOn = true;
+
+ /**
+ * This constant defines at what memory usage level application should release
+ * cached objects (to prevent unnecessary out of memory exceptions).
+ */
+ private static Double memorySaturationRatioTriggerClean = DEFAULT_MEMORY_SATURATION_TRIGGER_CLEAN;
+
+ /**
+ * What is the size of auto-complete elements.
+ */
+ private static int autocompleteSize = DEFAULT_AUTOCOMPLETE_SIZE;
+
+ /**
+ * Epsilon used for different types of comparisons.
+ */
+ public static final double EPSILON = 1e-6;
+
+ /**
+ * Git version from which framework was built.
+ */
+ private static String systemBuildVersion = null;
+
+ /**
+ * Date when the framework was built.
+ */
+ private static String systemBuildTime = null;
+
+ /**
+ * Version of the system (used by debian package).
+ */
+ private static String systemVersion = null;
+
+ /**
+ * Address that should be allowed to use x-frame.
+ */
+ private static List<String> xFrametDomain = new ArrayList<>();
+
+ /**
+ * Directory where tomcat webapp folder is located. Default value is "." because
+ * it should be set to proper value when tomcat application is deployed and run.
+ */
+ private static String webAppDir = "./";
+
+ /**
+ * Default constructor which prevents instantiation.
+ */
+ private Configuration() {
+
+ }
+
+ /**
+ * @return the applicationCacheOn
+ */
+ public static boolean isApplicationCacheOn() {
+ return applicationCacheOn;
+ }
+
+ /**
+ * @param applicationCacheOn
+ * the applicationCacheOn to set
+ */
+ public static void setApplicationCacheOn(boolean applicationCacheOn) {
+ Configuration.applicationCacheOn = applicationCacheOn;
+ }
+
+ /**
+ * @return the dbCacheOn
+ */
+ public static boolean isDbCacheOn() {
+ return dbCacheOn;
+ }
+
+ /**
+ * @param dbCacheOn
+ * the dbCacheOn to set
+ */
+ public static void setDbCacheOn(boolean dbCacheOn) {
+ Configuration.dbCacheOn = dbCacheOn;
+ }
+
+ /**
+ * @return the autocompleteSize
+ */
+ public static int getAutocompleteSize() {
+ return autocompleteSize;
+ }
+
+ /**
+ * @param autocompleteSize
+ * the autocompleteSize to set
+ */
+ public static void setAutocompleteSize(int autocompleteSize) {
+ Configuration.autocompleteSize = autocompleteSize;
+ }
+
+ /**
+ * @param baseDir
+ * directory where the system is placed
+ * @return {@link #systemBuildVersion}
+ */
+ public static String getSystemBuildVersion(String baseDir) {
+ if (systemBuildVersion == null) {
+ loadSystemVersion(baseDir);
+ }
+ return systemBuildVersion;
+ }
+
+ /**
+ * @param baseDir
+ * directory where the system is placed
+ * @return {@link #systemVersion}
+ */
+ public static String getSystemVersion(String baseDir) {
+ if (systemVersion == null) {
+ loadSystemVersion(baseDir);
+ }
+ return systemVersion;
+ }
+
+ /**
+ * @param baseDir
+ * directory where the system is placed
+ * @param forceReload
+ * if true then forces to reload data from text file
+ * @return {@link #systemBuildVersion}
+ */
+ public static String getSystemBuildVersion(String baseDir, boolean forceReload) {
+ if (forceReload) {
+ systemBuildVersion = null;
+ }
+ return getSystemBuildVersion(baseDir);
+ }
+
+ /**
+ * @param baseDir
+ * directory where the system is placed
+ * @param forceReload
+ * if true then forces to reload data from text file
+ * @return {@link #systemBuildVersion}
+ */
+ public static String getSystemVersion(String baseDir, boolean forceReload) {
+ if (forceReload) {
+ systemVersion = null;
+ }
+ return getSystemVersion(baseDir);
+ }
+
+ /**
+ * Loads system version (git version, build date) from the file.
+ *
+ * @param baseDir
+ * directory where the system is placed
+ */
+ protected static void loadSystemVersion(String baseDir) {
+ systemBuildVersion = "Unknown";
+ systemBuildTime = "Unknown";
+ systemVersion = "Unknown";
+ File buildVersionFile = null;
+ File changelogFile = null;
+ if (baseDir == null) {
+ buildVersionFile = new File("version.txt");
+ changelogFile = new File("CHANGELOG");
+ } else {
+ buildVersionFile = new File(baseDir + "version.txt");
+ changelogFile = new File(baseDir + "CHANGELOG");
+ }
+ if (buildVersionFile.exists()) {
+ loadSystemBuildVersion(buildVersionFile);
+ } else {
+ logger.error(buildVersionFile.getAbsoluteFile() + " doesn't exist.");
+ }
+
+ if (changelogFile.exists()) {
+ loadSystemVersion(changelogFile);
+ } else {
+ logger.error(changelogFile.getAbsoluteFile() + " doesn't exist.");
+ }
+ }
+
+ /**
+ * Loads system version (git version, build date) from the file.
+ *
+ * @param file
+ * file from which data is loaded
+ */
+ protected static void loadSystemBuildVersion(File file) {
+ try {
+ BufferedReader reader = new BufferedReader(new FileReader(file));
+ systemBuildVersion = reader.readLine().trim();
+ systemBuildTime = reader.readLine().trim();
+ reader.close();
+ } catch (IOException e) {
+ logger.error(e);
+ }
+ }
+
+ /**
+ * Loads system version from debian changelog file.
+ *
+ * @param file
+ * debian changelog file
+ */
+ protected static void loadSystemVersion(File file) {
+ try {
+ BufferedReader reader = new BufferedReader(new FileReader(file));
+ String line = reader.readLine();
+
+ int startIndex = line.indexOf("(");
+ int endIndex = line.indexOf(")");
+
+ if (startIndex >= 0 && endIndex >= 0) {
+ systemVersion = line.substring(startIndex + 1, endIndex);
+ } else {
+ logger.error("Invalid CHANGELOG file. Cannot find system version in line: " + line);
+ }
+ reader.close();
+ } catch (IOException e) {
+ logger.error(e);
+ }
+ }
+
+ /**
+ * @param baseDir
+ * directory where the system is placed
+ * @return the systemBuild
+ * @see #systemBuildTime
+ */
+ public static String getSystemBuild(String baseDir) {
+ if (systemBuildTime == null) {
+ loadSystemVersion(baseDir);
+ }
+ return systemBuildTime;
+ }
+
+ /**
+ * @param baseDir
+ * directory where the system is placed
+ * @param forceReload
+ * if true then forces to reload data from text file
+ * @return the systemBuild
+ * @see #systemBuildTime
+ */
+ public static String getSystemBuild(String baseDir, boolean forceReload) {
+ if (forceReload) {
+ systemBuildTime = null;
+ }
+ return getSystemBuild(baseDir);
+ }
+
+ /**
+ * @return the xFrametDomain
+ * @see #xFrametDomain
+ */
+ public static List<String> getxFrameDomain() {
+ return xFrametDomain;
+ }
+
+ /**
+ * @param xFrametDomains
+ * the xFrametDomain to set
+ * @see #xFrametDomain
+ */
+ public static void setxFrameDomain(List<String> xFrametDomains) {
+ Configuration.xFrametDomain = xFrametDomains;
+ }
+
+ /**
+ * @param path
+ * the path to webapps to set
+ * @see #webAppDir
+ */
+ public static void setWebAppDir(String path) {
+ Configuration.webAppDir = path;
+ }
+
+ /**
+ * @return the {@link #webAppDir}
+ */
+ public static String getWebAppDir() {
+ return Configuration.webAppDir;
+ }
+
+ /**
+ * @return the memorySaturationRatioTriggerClean
+ * @see #memorySaturationRatioTriggerClean
+ */
+ public static Double getMemorySaturationRatioTriggerClean() {
+ return memorySaturationRatioTriggerClean;
+ }
+
+ /**
+ * @param memorySaturationRatioTriggerClean
+ * the memorySaturationRatioTriggerClean to set
+ * @see #memorySaturationRatioTriggerClean
+ */
+ public static void setMemorySaturationRatioTriggerClean(Double memorySaturationRatioTriggerClean) {
+ Configuration.memorySaturationRatioTriggerClean = memorySaturationRatioTriggerClean;
+ }
+
+ /**
+ * Returns information about version of the framework.
+ *
+ * @param baseDir
+ * directory where project was deployed (or information about version
+ * is stored)
+ * @return information about version of the framework
+ */
+ public static FrameworkVersion getFrameworkVersion(String baseDir) {
+ FrameworkVersion result = new FrameworkVersion();
+ loadSystemVersion(baseDir);
+ result.setGitVersion(getSystemBuildVersion(baseDir));
+ result.setTime(getSystemBuild(baseDir));
+ result.setVersion(getSystemVersion(baseDir));
+ return result;
+ }
+
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/EventStorageLoggerAppender.java b/commons/src/main/java/lcsb/mapviewer/common/EventStorageLoggerAppender.java
index 94818d2c1d..e51a59c3a8 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/EventStorageLoggerAppender.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/EventStorageLoggerAppender.java
@@ -1,139 +1,139 @@
-package lcsb.mapviewer.common;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Appender;
-import org.apache.log4j.AppenderSkeleton;
-import org.apache.log4j.Level;
-import org.apache.log4j.lf5.LogLevel;
-import org.apache.log4j.spi.LoggingEvent;
-
-/**
- * Custom log4j {@link Appender}. This class is used to store logs in the
- * memory. Such logs should be stored for short period of time. Only logs for
- * the {@link Thread} that created the object will be stored.
- *
- * @author Piotr Gawron
- *
- */
-public class EventStorageLoggerAppender extends AppenderSkeleton {
-
- /**
- * List of {@link LogLevel#DEBUG} logs.
- */
- private List<LoggingEvent> debugEvents = new ArrayList<>();
-
- /**
- * List of {@link LogLevel#INFO} logs.
- */
- private List<LoggingEvent> infoEvents = new ArrayList<>();
-
- /**
- * List of {@link LogLevel#WARN} logs.
- */
- private List<LoggingEvent> warnEvents = new ArrayList<>();
-
- /**
- * List of {@link LogLevel#ERROR} logs.
- */
- private List<LoggingEvent> errorEvents = new ArrayList<>();
-
- /**
- * List of {@link LogLevel#FATAL} logs.
- */
- private List<LoggingEvent> fatalEvents = new ArrayList<>();
-
- /**
- * List of logs with unknown log level.
- */
- private List<LoggingEvent> otherEvents = new ArrayList<>();
-
- /**
- * Identifier of {@link Thread} that created this object.
- */
- private long threadId;
-
- /**
- * Flag that describe if we log only entries for current thread (
- * <code>true</code>) or for all threads (<code>false</code>).
- */
- private boolean currentThreadLogOnly = true;
-
- /**
- * Default constructor.
- */
- public EventStorageLoggerAppender() {
- this(true);
- }
-
- /**
- * Default constructor.
- *
- * @param currentThreadLogOnly
- * if <code>true</code> logs should be taken only from thread that
- * created object, if <code>false</code> all logs will be stored
- */
- public EventStorageLoggerAppender(boolean currentThreadLogOnly) {
- this.threadId = Thread.currentThread().getId();
- this.currentThreadLogOnly = currentThreadLogOnly;
- }
-
- @Override
- protected void append(LoggingEvent event) {
- // store information for all thread only if it is flagged by
- // currentThreadLogOnly, if not only logs from current thread should be
- // stored
- if (!currentThreadLogOnly || threadId == Thread.currentThread().getId()) {
- if (event.getLevel().equals(Level.DEBUG)) {
- debugEvents.add(event);
- } else if (event.getLevel().equals(Level.INFO)) {
- infoEvents.add(event);
- } else if (event.getLevel().equals(Level.WARN)) {
- warnEvents.add(event);
- } else if (event.getLevel().equals(Level.ERROR)) {
- errorEvents.add(event);
- } else if (event.getLevel().equals(Level.FATAL)) {
- fatalEvents.add(event);
- } else {
- otherEvents.add(event);
- }
- }
- }
-
- @Override
- public void close() {
- }
-
- @Override
- public boolean requiresLayout() {
- return false;
- }
-
- /**
- * Returns list of warning logs.
- *
- * @return list of warning logs
- */
- public List<LoggingEvent> getWarnings() {
- return warnEvents;
- }
-
- /**
- * Returns list of error logs.
- *
- * @return list of error logs
- */
- public List<LoggingEvent> getErrors() {
- return errorEvents;
- }
-
- /**
- * Returns list of fatal logs.
- *
- * @return list of fatal logs
- */
- public List<LoggingEvent> getFatals() {
- return fatalEvents;
- }
-}
+package lcsb.mapviewer.common;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Appender;
+import org.apache.log4j.AppenderSkeleton;
+import org.apache.log4j.Level;
+import org.apache.log4j.lf5.LogLevel;
+import org.apache.log4j.spi.LoggingEvent;
+
+/**
+ * Custom log4j {@link Appender}. This class is used to store logs in the
+ * memory. Such logs should be stored for short period of time. Only logs for
+ * the {@link Thread} that created the object will be stored.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class EventStorageLoggerAppender extends AppenderSkeleton {
+
+ /**
+ * List of {@link LogLevel#DEBUG} logs.
+ */
+ private List<LoggingEvent> debugEvents = new ArrayList<>();
+
+ /**
+ * List of {@link LogLevel#INFO} logs.
+ */
+ private List<LoggingEvent> infoEvents = new ArrayList<>();
+
+ /**
+ * List of {@link LogLevel#WARN} logs.
+ */
+ private List<LoggingEvent> warnEvents = new ArrayList<>();
+
+ /**
+ * List of {@link LogLevel#ERROR} logs.
+ */
+ private List<LoggingEvent> errorEvents = new ArrayList<>();
+
+ /**
+ * List of {@link LogLevel#FATAL} logs.
+ */
+ private List<LoggingEvent> fatalEvents = new ArrayList<>();
+
+ /**
+ * List of logs with unknown log level.
+ */
+ private List<LoggingEvent> otherEvents = new ArrayList<>();
+
+ /**
+ * Identifier of {@link Thread} that created this object.
+ */
+ private long threadId;
+
+ /**
+ * Flag that describe if we log only entries for current thread (
+ * <code>true</code>) or for all threads (<code>false</code>).
+ */
+ private boolean currentThreadLogOnly = true;
+
+ /**
+ * Default constructor.
+ */
+ public EventStorageLoggerAppender() {
+ this(true);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param currentThreadLogOnly
+ * if <code>true</code> logs should be taken only from thread that
+ * created object, if <code>false</code> all logs will be stored
+ */
+ public EventStorageLoggerAppender(boolean currentThreadLogOnly) {
+ this.threadId = Thread.currentThread().getId();
+ this.currentThreadLogOnly = currentThreadLogOnly;
+ }
+
+ @Override
+ protected void append(LoggingEvent event) {
+ // store information for all thread only if it is flagged by
+ // currentThreadLogOnly, if not only logs from current thread should be
+ // stored
+ if (!currentThreadLogOnly || threadId == Thread.currentThread().getId()) {
+ if (event.getLevel().equals(Level.DEBUG)) {
+ debugEvents.add(event);
+ } else if (event.getLevel().equals(Level.INFO)) {
+ infoEvents.add(event);
+ } else if (event.getLevel().equals(Level.WARN)) {
+ warnEvents.add(event);
+ } else if (event.getLevel().equals(Level.ERROR)) {
+ errorEvents.add(event);
+ } else if (event.getLevel().equals(Level.FATAL)) {
+ fatalEvents.add(event);
+ } else {
+ otherEvents.add(event);
+ }
+ }
+ }
+
+ @Override
+ public void close() {
+ }
+
+ @Override
+ public boolean requiresLayout() {
+ return false;
+ }
+
+ /**
+ * Returns list of warning logs.
+ *
+ * @return list of warning logs
+ */
+ public List<LoggingEvent> getWarnings() {
+ return warnEvents;
+ }
+
+ /**
+ * Returns list of error logs.
+ *
+ * @return list of error logs
+ */
+ public List<LoggingEvent> getErrors() {
+ return errorEvents;
+ }
+
+ /**
+ * Returns list of fatal logs.
+ *
+ * @return list of fatal logs
+ */
+ public List<LoggingEvent> getFatals() {
+ return fatalEvents;
+ }
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/FrameworkVersion.java b/commons/src/main/java/lcsb/mapviewer/common/FrameworkVersion.java
index b088af39f7..f59648ac18 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/FrameworkVersion.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/FrameworkVersion.java
@@ -1,91 +1,91 @@
-package lcsb.mapviewer.common;
-
-import java.io.Serializable;
-
-/**
- * View representation of the {@link FrameworkVersion}. Contains information
- * about single framework version.
- *
- * @author Piotr Gawron
- *
- */
-public class FrameworkVersion implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Version of the framework.
- */
- private String version;
-
- /**
- * When this version was committed to git.
- */
- private String gitVersion;
-
- /**
- * When the framework was built.
- */
- private String time;
-
- /**
- * Default constructor.
- *
- */
- public FrameworkVersion() {
- }
-
- /**
- * @return the version
- * @see #version
- */
- public String getVersion() {
- return version;
- }
-
- /**
- * @param version
- * the version to set
- * @see #version
- */
- public void setVersion(String version) {
- this.version = version;
- }
-
- /**
- * @return the gitVersion
- * @see #gitVersion
- */
- public String getGitVersion() {
- return gitVersion;
- }
-
- /**
- * @param gitVersion
- * the gitVersion to set
- * @see #gitVersion
- */
- public void setGitVersion(String gitVersion) {
- this.gitVersion = gitVersion;
- }
-
- /**
- * @return the time
- * @see #time
- */
- public String getTime() {
- return time;
- }
-
- /**
- * @param time
- * the time to set
- * @see #time
- */
- public void setTime(String time) {
- this.time = time;
- }
-
-}
+package lcsb.mapviewer.common;
+
+import java.io.Serializable;
+
+/**
+ * View representation of the {@link FrameworkVersion}. Contains information
+ * about single framework version.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class FrameworkVersion implements Serializable {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Version of the framework.
+ */
+ private String version;
+
+ /**
+ * When this version was committed to git.
+ */
+ private String gitVersion;
+
+ /**
+ * When the framework was built.
+ */
+ private String time;
+
+ /**
+ * Default constructor.
+ *
+ */
+ public FrameworkVersion() {
+ }
+
+ /**
+ * @return the version
+ * @see #version
+ */
+ public String getVersion() {
+ return version;
+ }
+
+ /**
+ * @param version
+ * the version to set
+ * @see #version
+ */
+ public void setVersion(String version) {
+ this.version = version;
+ }
+
+ /**
+ * @return the gitVersion
+ * @see #gitVersion
+ */
+ public String getGitVersion() {
+ return gitVersion;
+ }
+
+ /**
+ * @param gitVersion
+ * the gitVersion to set
+ * @see #gitVersion
+ */
+ public void setGitVersion(String gitVersion) {
+ this.gitVersion = gitVersion;
+ }
+
+ /**
+ * @return the time
+ * @see #time
+ */
+ public String getTime() {
+ return time;
+ }
+
+ /**
+ * @param time
+ * the time to set
+ * @see #time
+ */
+ public void setTime(String time) {
+ this.time = time;
+ }
+
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/HttpConnectionMethodType.java b/commons/src/main/java/lcsb/mapviewer/common/HttpConnectionMethodType.java
index 8d5f0c4322..78ed3bbf2c 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/HttpConnectionMethodType.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/HttpConnectionMethodType.java
@@ -1,20 +1,20 @@
-package lcsb.mapviewer.common;
-
-/**
- * Defines type of http connection method.
- *
- * @author Piotr Gawron
- *
- */
-public enum HttpConnectionMethodType {
-
- /**
- * GET method.
- */
- GET, //
-
- /**
- * POST method.
- */
- POST;
-}
+package lcsb.mapviewer.common;
+
+/**
+ * Defines type of http connection method.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum HttpConnectionMethodType {
+
+ /**
+ * GET method.
+ */
+ GET, //
+
+ /**
+ * POST method.
+ */
+ POST;
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/IProgressUpdater.java b/commons/src/main/java/lcsb/mapviewer/common/IProgressUpdater.java
index 7617ae3d36..a74aa0557a 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/IProgressUpdater.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/IProgressUpdater.java
@@ -1,27 +1,27 @@
-package lcsb.mapviewer.common;
-
-/**
- * Progress updater interface. It contains only one function that updates
- * information about process progress (from 0 to 100).
- *
- * @author Piotr Gawron
- *
- */
-public interface IProgressUpdater {
- /**
- * Maximum progress value.
- */
- double MAX_PROGRESS = 100.0;
- /**
- * Defines the minimum progress value change that should be propagated.
- */
- double PROGRESS_BAR_UPDATE_RESOLUTION = 0.5;
-
- /**
- * Set progress status.
- *
- * @param progress
- * progress value (between 0 and 100)
- */
- void setProgress(double progress);
-}
+package lcsb.mapviewer.common;
+
+/**
+ * Progress updater interface. It contains only one function that updates
+ * information about process progress (from 0 to 100).
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface IProgressUpdater {
+ /**
+ * Maximum progress value.
+ */
+ double MAX_PROGRESS = 100.0;
+ /**
+ * Defines the minimum progress value change that should be propagated.
+ */
+ double PROGRESS_BAR_UPDATE_RESOLUTION = 0.5;
+
+ /**
+ * Set progress status.
+ *
+ * @param progress
+ * progress value (between 0 and 100)
+ */
+ void setProgress(double progress);
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/MimeType.java b/commons/src/main/java/lcsb/mapviewer/common/MimeType.java
index ca6960532a..e63d118d52 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/MimeType.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/MimeType.java
@@ -1,86 +1,86 @@
-package lcsb.mapviewer.common;
-
-/**
- * Mime content types of data used in the system. If there is publicly available
- * class with all possible types then we should use it, but I couldn't quickly
- * find it. For the full list see
- * <a href="http://www.iana.org/assignments/media-types/media-types.xhtml">IANA
- * MIME media types list</a>
- *
- * @author Piotr Gawron
- *
- */
-public enum MimeType {
- /**
- * SBML type of file.
- */
- SBML("application/sbml+xml"), //
-
- /**
- * Standard text file.
- */
- TEXT("text/plain"), //
-
- /**
- * Standard XML file.
- */
- XML("application/xml"),
-
- /**
- * <a href="http://www.w3.org/TR/SVG11/mimereg.html">SVG</a> file type.
- */
- SVG("image/svg+xml"),
-
- /**
- * JPG image file type.
- */
- JPG("image/jpeg"),
-
- /**
- * PNG image file type.
- */
- PNG("image/png"),
-
- /**
- * PDF files (see <a href="http://www.rfc-editor.org/rfc/rfc3778.txt"> RFC 3778,
- * The application/pdf Media Type</a>).
- */
- PDF("application/pdf"), //
-
- /**
- * CSS files.
- */
- CSS("text/css"), //
-
- /**
- * JavaScript files.
- */
- JS("text/javascript"),
-
- /**
- * Zip files.
- */
- ZIP("application/zip"); //
-
- /**
- * String representation of the MIME content.
- */
- private String textRepresentation;
-
- /**
- * Default constructor with string definition.
- *
- * @param textRepresentation
- * text representation for MIME type
- */
- MimeType(String textRepresentation) {
- this.textRepresentation = textRepresentation;
- }
-
- /**
- * @return the textRepresentation
- */
- public String getTextRepresentation() {
- return textRepresentation;
- }
-}
+package lcsb.mapviewer.common;
+
+/**
+ * Mime content types of data used in the system. If there is publicly available
+ * class with all possible types then we should use it, but I couldn't quickly
+ * find it. For the full list see
+ * <a href="http://www.iana.org/assignments/media-types/media-types.xhtml">IANA
+ * MIME media types list</a>
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum MimeType {
+ /**
+ * SBML type of file.
+ */
+ SBML("application/sbml+xml"), //
+
+ /**
+ * Standard text file.
+ */
+ TEXT("text/plain"), //
+
+ /**
+ * Standard XML file.
+ */
+ XML("application/xml"),
+
+ /**
+ * <a href="http://www.w3.org/TR/SVG11/mimereg.html">SVG</a> file type.
+ */
+ SVG("image/svg+xml"),
+
+ /**
+ * JPG image file type.
+ */
+ JPG("image/jpeg"),
+
+ /**
+ * PNG image file type.
+ */
+ PNG("image/png"),
+
+ /**
+ * PDF files (see <a href="http://www.rfc-editor.org/rfc/rfc3778.txt"> RFC 3778,
+ * The application/pdf Media Type</a>).
+ */
+ PDF("application/pdf"), //
+
+ /**
+ * CSS files.
+ */
+ CSS("text/css"), //
+
+ /**
+ * JavaScript files.
+ */
+ JS("text/javascript"),
+
+ /**
+ * Zip files.
+ */
+ ZIP("application/zip"); //
+
+ /**
+ * String representation of the MIME content.
+ */
+ private String textRepresentation;
+
+ /**
+ * Default constructor with string definition.
+ *
+ * @param textRepresentation
+ * text representation for MIME type
+ */
+ MimeType(String textRepresentation) {
+ this.textRepresentation = textRepresentation;
+ }
+
+ /**
+ * @return the textRepresentation
+ */
+ public String getTextRepresentation() {
+ return textRepresentation;
+ }
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/ObjectUtils.java b/commons/src/main/java/lcsb/mapviewer/common/ObjectUtils.java
index 145a9790da..b5fd056b5e 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/ObjectUtils.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/ObjectUtils.java
@@ -1,52 +1,52 @@
-package lcsb.mapviewer.common;
-
-import java.lang.reflect.Method;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-
-/**
- * Util class that performs primitive operations on the object.
- *
- * @author Piotr Gawron
- *
- */
-public final class ObjectUtils {
-
- /**
- * Default constructor. Prevents instatiation.
- */
- private ObjectUtils() {
- }
-
- /**
- * Returns object identifier. It assumes that object contains getId method
- * that returns Integer.
- *
- * @param object
- * object for which identifier is looked for
- * @return object identifier
- */
- public static Integer getIdOfObject(Object object) {
- Integer id = (Integer) getParamByGetter(object, "getId");
- return id;
- }
-
- /**
- * Returns object param using string getter function.
- *
- * @param object
- * object from which parameter will be taken
- * @param getterName
- * string with name of the getter function
- * @return object field
- */
- public static Object getParamByGetter(Object object, String getterName) {
- try {
- Method method = object.getClass().getMethod(getterName);
- Object result = method.invoke(object);
- return result;
- } catch (Exception e) {
- throw new InvalidArgumentException(e.getMessage());
- }
- }
-}
+package lcsb.mapviewer.common;
+
+import java.lang.reflect.Method;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+
+/**
+ * Util class that performs primitive operations on the object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public final class ObjectUtils {
+
+ /**
+ * Default constructor. Prevents instatiation.
+ */
+ private ObjectUtils() {
+ }
+
+ /**
+ * Returns object identifier. It assumes that object contains getId method
+ * that returns Integer.
+ *
+ * @param object
+ * object for which identifier is looked for
+ * @return object identifier
+ */
+ public static Integer getIdOfObject(Object object) {
+ Integer id = (Integer) getParamByGetter(object, "getId");
+ return id;
+ }
+
+ /**
+ * Returns object param using string getter function.
+ *
+ * @param object
+ * object from which parameter will be taken
+ * @param getterName
+ * string with name of the getter function
+ * @return object field
+ */
+ public static Object getParamByGetter(Object object, String getterName) {
+ try {
+ Method method = object.getClass().getMethod(getterName);
+ Object result = method.invoke(object);
+ return result;
+ } catch (Exception e) {
+ throw new InvalidArgumentException(e.getMessage());
+ }
+ }
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/Pair.java b/commons/src/main/java/lcsb/mapviewer/common/Pair.java
index 8d8573c0c4..32fb0263a8 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/Pair.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/Pair.java
@@ -1,84 +1,84 @@
-package lcsb.mapviewer.common;
-
-import java.io.Serializable;
-
-/**
- * Represents pair of two objects. It's immutable as long as param classes are
- * immutable.
- *
- * @author Piotr Gawron
- *
- * @param <L>
- * class type of the first object
- * @param <R>
- * class type of the second object
- */
-public class Pair<L, R> implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * First object.
- */
- private final L left;
-
- /**
- * Second object.
- */
- private final R right;
-
- /**
- * Default constructor.
- *
- * @param left
- * {@link #left}
- * @param right
- * {@link #right}
- */
- public Pair(L left, R right) {
- this.left = left;
- this.right = right;
- }
-
- /**
- *
- * @return {@link #left}
- */
- public L getLeft() {
- return left;
- }
-
- /**
- *
- * @return {@link #right}
- */
- public R getRight() {
- return right;
- }
-
- @Override
- public int hashCode() {
- return left.hashCode() ^ right.hashCode();
- }
-
- @Override
- public boolean equals(Object o) {
- if (o == null) {
- return false;
- }
- if (!(o instanceof Pair)) {
- return false;
- }
- Pair<?, ?> pairo = (Pair<?, ?>) o;
- return this.left.equals(pairo.getLeft()) && this.right.equals(pairo.getRight());
- }
-
- @Override
- public String toString() {
- return "Pair: " + getLeft().toString() + ", " + getRight().toString();
- }
-
+package lcsb.mapviewer.common;
+
+import java.io.Serializable;
+
+/**
+ * Represents pair of two objects. It's immutable as long as param classes are
+ * immutable.
+ *
+ * @author Piotr Gawron
+ *
+ * @param <L>
+ * class type of the first object
+ * @param <R>
+ * class type of the second object
+ */
+public class Pair<L, R> implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * First object.
+ */
+ private final L left;
+
+ /**
+ * Second object.
+ */
+ private final R right;
+
+ /**
+ * Default constructor.
+ *
+ * @param left
+ * {@link #left}
+ * @param right
+ * {@link #right}
+ */
+ public Pair(L left, R right) {
+ this.left = left;
+ this.right = right;
+ }
+
+ /**
+ *
+ * @return {@link #left}
+ */
+ public L getLeft() {
+ return left;
+ }
+
+ /**
+ *
+ * @return {@link #right}
+ */
+ public R getRight() {
+ return right;
+ }
+
+ @Override
+ public int hashCode() {
+ return left.hashCode() ^ right.hashCode();
+ }
+
+ @Override
+ public boolean equals(Object o) {
+ if (o == null) {
+ return false;
+ }
+ if (!(o instanceof Pair)) {
+ return false;
+ }
+ Pair<?, ?> pairo = (Pair<?, ?>) o;
+ return this.left.equals(pairo.getLeft()) && this.right.equals(pairo.getRight());
+ }
+
+ @Override
+ public String toString() {
+ return "Pair: " + getLeft().toString() + ", " + getRight().toString();
+ }
+
}
\ No newline at end of file
diff --git a/commons/src/main/java/lcsb/mapviewer/common/SystemClipboard.java b/commons/src/main/java/lcsb/mapviewer/common/SystemClipboard.java
index 16585aa4ef..f69c4c2cb6 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/SystemClipboard.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/SystemClipboard.java
@@ -1,63 +1,63 @@
-package lcsb.mapviewer.common;
-
-import java.awt.Toolkit;
-import java.awt.datatransfer.Clipboard;
-import java.awt.datatransfer.ClipboardOwner;
-import java.awt.datatransfer.DataFlavor;
-import java.awt.datatransfer.StringSelection;
-import java.awt.datatransfer.Transferable;
-
-import org.apache.log4j.Logger;
-
-/**
- * Class allowing access to system clipboard.
- *
- * @author Piotr Gawron
- *
- */
-public class SystemClipboard implements ClipboardOwner {
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(SystemClipboard.class);
-
- @Override
- public void lostOwnership(Clipboard clipboard, Transferable contents) {
- }
-
- /**
- * Place a String on the clipboard, and make this class the owner of the
- * Clipboard's contents.
- *
- * @param aString
- * what we want to put into clipboard
- */
- public void setClipboardContents(String aString) {
- StringSelection stringSelection = new StringSelection(aString);
- Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
- clipboard.setContents(stringSelection, this);
- }
-
- /**
- * Get the String residing on the clipboard.
- *
- * @return any text found on the Clipboard; if none found, return an empty
- * String.
- */
- public String getClipboardContents() {
- String result = null;
- Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
- // odd: the Object param of getContents is not currently used
- Transferable contents = clipboard.getContents(null);
- boolean hasTransferableText = contents.isDataFlavorSupported(DataFlavor.stringFlavor);
- if (hasTransferableText) {
- try {
- result = (String) contents.getTransferData(DataFlavor.stringFlavor);
- } catch (Exception ex) {
- logger.error(ex, ex);
- }
- }
- return result;
- }
-
-}
+package lcsb.mapviewer.common;
+
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.ClipboardOwner;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Class allowing access to system clipboard.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class SystemClipboard implements ClipboardOwner {
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(SystemClipboard.class);
+
+ @Override
+ public void lostOwnership(Clipboard clipboard, Transferable contents) {
+ }
+
+ /**
+ * Place a String on the clipboard, and make this class the owner of the
+ * Clipboard's contents.
+ *
+ * @param aString
+ * what we want to put into clipboard
+ */
+ public void setClipboardContents(String aString) {
+ StringSelection stringSelection = new StringSelection(aString);
+ Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
+ clipboard.setContents(stringSelection, this);
+ }
+
+ /**
+ * Get the String residing on the clipboard.
+ *
+ * @return any text found on the Clipboard; if none found, return an empty
+ * String.
+ */
+ public String getClipboardContents() {
+ String result = null;
+ Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
+ // odd: the Object param of getContents is not currently used
+ Transferable contents = clipboard.getContents(null);
+ boolean hasTransferableText = contents.isDataFlavorSupported(DataFlavor.stringFlavor);
+ if (hasTransferableText) {
+ try {
+ result = (String) contents.getTransferData(DataFlavor.stringFlavor);
+ } catch (Exception ex) {
+ logger.error(ex, ex);
+ }
+ }
+ return result;
+ }
+
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/TextFileUtils.java b/commons/src/main/java/lcsb/mapviewer/common/TextFileUtils.java
index 56823222d6..824ae83c93 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/TextFileUtils.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/TextFileUtils.java
@@ -1,64 +1,64 @@
-package lcsb.mapviewer.common;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.util.HashMap;
-import java.util.Map;
-
-/**
- * Class with util function to operate on text files.
- *
- * @author Piotr Gawron
- *
- */
-public final class TextFileUtils {
-
- /**
- * Name of the param that contains number of columns.
- */
- public static final String COLUMN_COUNT_PARAM = "__COLUMN_COUNT";
-
- /**
- * Default constructor that prevents instatiation.
- */
- private TextFileUtils() {
-
- }
-
- /**
- * Parses input stream to get parameters from header. {@link InputStream}
- * should be a text file. Header parameters are lines at the beginning of the
- * file starting with '#' character.
- *
- * @param is
- * input stream for a file to process
- * @return map with paramteres parsed from input stream
- * @throws IOException
- * thrown when there is a problem with accessing input stream
- */
- public static Map<String, String> getHeaderParametersFromFile(InputStream is) throws IOException {
- Map<String, String> result = new HashMap<String, String>();
- BufferedReader in = new BufferedReader(new InputStreamReader(is));
- String line = null;
- while ((line = in.readLine()) != null) {
- if (line.startsWith("#")) {
- String tmp = line.substring(1);
- if (tmp.indexOf("=") > 0) {
- String key = tmp.substring(0, tmp.indexOf("=")).trim();
- String value = tmp.substring(tmp.indexOf("=") + 1).trim();
- result.put(key, value);
- }
- } else {
- String key = COLUMN_COUNT_PARAM;
- String value = line.split("\t").length + "";
- result.put(key, value);
- break;
- }
- }
- is.close();
- return result;
- }
-
-}
+package lcsb.mapviewer.common;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * Class with util function to operate on text files.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public final class TextFileUtils {
+
+ /**
+ * Name of the param that contains number of columns.
+ */
+ public static final String COLUMN_COUNT_PARAM = "__COLUMN_COUNT";
+
+ /**
+ * Default constructor that prevents instatiation.
+ */
+ private TextFileUtils() {
+
+ }
+
+ /**
+ * Parses input stream to get parameters from header. {@link InputStream}
+ * should be a text file. Header parameters are lines at the beginning of the
+ * file starting with '#' character.
+ *
+ * @param is
+ * input stream for a file to process
+ * @return map with paramteres parsed from input stream
+ * @throws IOException
+ * thrown when there is a problem with accessing input stream
+ */
+ public static Map<String, String> getHeaderParametersFromFile(InputStream is) throws IOException {
+ Map<String, String> result = new HashMap<String, String>();
+ BufferedReader in = new BufferedReader(new InputStreamReader(is));
+ String line = null;
+ while ((line = in.readLine()) != null) {
+ if (line.startsWith("#")) {
+ String tmp = line.substring(1);
+ if (tmp.indexOf("=") > 0) {
+ String key = tmp.substring(0, tmp.indexOf("=")).trim();
+ String value = tmp.substring(tmp.indexOf("=") + 1).trim();
+ result.put(key, value);
+ }
+ } else {
+ String key = COLUMN_COUNT_PARAM;
+ String value = line.split("\t").length + "";
+ result.put(key, value);
+ break;
+ }
+ }
+ is.close();
+ return result;
+ }
+
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java b/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
index 2a7890b879..8ae4384389 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
@@ -1,377 +1,377 @@
-package lcsb.mapviewer.common;
-
-import java.awt.Color;
-import java.io.BufferedReader;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.StringReader;
-import java.io.StringWriter;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.transform.OutputKeys;
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerException;
-import javax.xml.transform.TransformerFactory;
-import javax.xml.transform.dom.DOMSource;
-import javax.xml.transform.stream.StreamResult;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang3.StringEscapeUtils;
-import org.apache.log4j.Logger;
-import org.w3c.dom.Document;
-import org.w3c.dom.NamedNodeMap;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-import org.xml.sax.InputSource;
-import org.xml.sax.SAXException;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-
-/**
- * Abstract class with methods which help in parsing xml using DOM.
- *
- * @author Piotr Gawron
- *
- */
-public class XmlParser {
- /**
- * Base of the hex representation.
- */
- private static final int HEX_BASE = 16;
-
- /**
- * {@link DocumentBuilderFactory} used to create {@link DocumentBuilder} objects
- * that will manipulate xml nodes.
- */
- private static DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(XmlParser.class.getName());
-
- /**
- * DOM document builder used for xml transformations.
- */
- private DocumentBuilder db;
-
- /**
- * Default constructor that prevents from instatiation of the class and
- * initializes fields.
- */
- protected XmlParser() {
- try {
- db = documentBuilderFactory.newDocumentBuilder();
- } catch (ParserConfigurationException e) {
- throw new InvalidStateException("Problem with xml parser");
- }
-
- }
-
- /**
- * Method returns the node of xml nodelist 'nodes' with 'tagName' name. If node
- * could not be found then null is returned.
- *
- * @param tagName
- * name of node to look for
- * @param nodes
- * list of nodes
- * @return node from nodes list with the tagName name, <b>null</b> if such node
- * doesn't exist
- */
- protected Node getNode(final String tagName, final NodeList nodes) {
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase(tagName)) {
- return node;
- }
- }
- }
- return null;
- }
-
- /**
- * Method returns the child node of xml 'parentNode' with 'tagName' name. If
- * node could not be found then null is returned.
- *
- * @param tagName
- * name of node to look for
- * @param parentNode
- * parent node
- * @return node from nodes list with the tagName name, <b>null</b> if such node
- * doesn't exist
- */
- protected Node getNode(final String tagName, final Node parentNode) {
- return getNode(tagName, parentNode.getChildNodes());
- }
-
- /**
- * Method returns list of nodes with 'tagName' name. If node could not be found
- * then empty list is returned.
- *
- * @param tagName
- * name of node to look for
- * @param nodes
- * list of input nodes
- * @return list of nodes with 'tagName' name
- */
- protected List<Node> getNodes(final String tagName, final NodeList nodes) {
- List<Node> result = new ArrayList<Node>();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeName().equalsIgnoreCase(tagName)) {
- result.add(node);
- }
- }
- return result;
- }
-
- /**
- * Method returns the value of node attribute. If attribute could not be found
- * then "" is returned.
- *
- * @param attrName
- * name of the attribute to look for
- * @param node
- * a node
- * @return the value of node attribute, empty string("") if attribute doesn't
- * exist
- */
- protected String getNodeAttr(final String attrName, final Node node) {
- NamedNodeMap attrs = node.getAttributes();
- for (int y = 0; y < attrs.getLength(); y++) {
- Node attr = attrs.item(y);
- if (attr.getNodeName().equalsIgnoreCase(attrName)) {
- return attr.getNodeValue();
- }
- }
- return "";
- }
-
- /**
- * Method returns the text value of node. If text could not be found then "" is
- * returned.
- *
- * @param node
- * a node
- * @return the text value of node or empty string ("") if the text could be
- * found.
- */
- protected String getNodeValue(final Node node) {
- if (node == null) {
- return "";
- }
- NodeList childNodes = node.getChildNodes();
- for (int x = 0; x < childNodes.getLength(); x++) {
- Node data = childNodes.item(x);
- if (data.getNodeType() == Node.TEXT_NODE) {
- return data.getNodeValue();
- }
- }
- return "";
- }
-
- /**
- * Method returns the xml Document from input source given as a parameter.
- *
- * @param stream
- * input stream with xml document
- * @return Document node for the input stream
- * @throws InvalidXmlSchemaException
- * thrown when there is a problem with xml
- */
- protected Document getXmlDocumentFromInputSource(final InputSource stream) throws InvalidXmlSchemaException {
- try {
- synchronized (db) { // DocumentBuilder cannot parse few objects at the
- // same time
- return db.parse(stream);
- }
- } catch (SAXException e) {
- throw new InvalidXmlSchemaException("Problem with xml parser", e);
- } catch (IOException e) {
- throw new InvalidXmlSchemaException("Problem with xml parser", e);
- }
- }
-
- /**
- * Method returns the xml Document from text given as a source.
- *
- * @param text
- * string representing xml document
- * @return Document for the xml document given in the input
- * @throws InvalidXmlSchemaException
- * thrown when there is a problem with xml
- */
- protected Document getXmlDocumentFromString(final String text) throws InvalidXmlSchemaException {
- InputSource is = new InputSource();
- is.setCharacterStream(new StringReader(text));
- try {
- return getXmlDocumentFromInputSource(is);
- } catch (NullPointerException e) {
- logger.error("Problem with input xml: " + text);
- throw new InvalidXmlSchemaException(e);
- }
- }
-
- /**
- * Transforms node into string xml format.
- *
- * @param node
- * node that should be transformed into xml string
- * @return string representation of the xml node
- */
- protected String nodeToString(final Node node) {
- return nodeToString(node, false);
- }
-
- /**
- * Transforms node into string xml format.
- *
- * @param node
- * node that should be transformed into xml string
- * @param includeHeadNode
- * should the top level node exist in the output
- * @return string representation of the xml node
- */
- protected String nodeToString(final Node node, final boolean includeHeadNode) {
- if (node == null) {
- return null;
- }
- StringWriter sw = new StringWriter();
- try {
- Transformer t = TransformerFactory.newInstance().newTransformer();
- t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
- t.setOutputProperty(OutputKeys.INDENT, "yes");
- t.setOutputProperty(OutputKeys.METHOD, "xml");
-
- NodeList list = node.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node element = list.item(i);
- t.transform(new DOMSource(element), new StreamResult(sw));
- }
- } catch (TransformerException te) {
- logger.debug("nodeToString Transformer Exception");
- }
- if (includeHeadNode) {
- return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
- }
- return sw.toString();
- }
-
- /**
- * This method transform color encoded in string (CellDesigner format) into
- * Color.
- *
- * @param color
- * string representing color
- * @return Color object for the fiven string
- */
- protected Color stringToColor(final String color) {
- try {
- String alpha = color.substring(0, 2);
- Color tmp = new Color(hexToInteger(color.substring(2)));
- return new Color(tmp.getRed(), tmp.getGreen(), tmp.getBlue(), hexToInteger(alpha));
- } catch (Exception e) {
- throw new InvalidArgumentException("Invalid color string: " + color);
- }
- }
-
- /**
- * Transforms hex string into Integer.
- *
- * @param hexString
- * string representation in hex base
- * @return Integer value of the hex string
- */
- private Integer hexToInteger(String hexString) {
- return Integer.valueOf(hexString, HEX_BASE);
- }
-
- /**
- * Transforms Color object into string representing this color in RGB.
- *
- * @param color
- * color that should be converted into string
- * @return hex string representation of the color
- */
- protected String colorToString(final Color color) {
- return String.format("%08X", color.getRGB());
- }
-
- /**
- * Method that reads file and transforms it into a string.
- *
- * @param fileName
- * path to a file
- * @return string containing data from the file (default coding is used)
- * @throws IOException
- * thrown when there are some problems with a file
- */
- protected String fileToString(final String fileName) throws IOException {
- BufferedReader reader = new BufferedReader(new FileReader(fileName));
- String line = null;
- StringBuilder stringBuilder = new StringBuilder();
- String ls = System.getProperty("line.separator");
-
- while ((line = reader.readLine()) != null) {
- stringBuilder.append(line);
- stringBuilder.append(ls);
- }
- reader.close();
-
- return stringBuilder.toString();
- }
-
- /**
- * Method that reads all data from inputstream and transform it into a string.
- * UTF-8 coding is used.
- *
- * @param inputStream
- * stream from which we read data
- * @return string representing all data from input stream
- * @throws IOException
- * thrown if there are some problems with input stream
- */
- protected String inputStreamToString(final InputStream inputStream) throws IOException {
- StringWriter writer = new StringWriter();
- IOUtils.copy(inputStream, writer, "UTF-8");
- String result = writer.toString();
- return result;
- }
-
- /**
- * Method that encode string into a string that can be used in xml file.
- *
- * @param string
- * string to be escaped
- * @return escaped string, ready to be used in xml
- */
- protected String escapeXml(final String string) {
- if (string == null) {
- return null;
- }
- // quite expensive
- return StringEscapeUtils.escapeXml(string).replaceAll("\n", " ").replace("\r", " ");
- }
-
- public List<Node> getAllNotNecessirellyDirectChild(String tagName, Node root) {
- List<Node> result = new ArrayList<>();
- for (int x = 0; x < root.getChildNodes().getLength(); x++) {
- Node node = root.getChildNodes().item(x);
- if (node.getNodeName().equalsIgnoreCase(tagName)) {
- result.add(node);
- } else {
- result.addAll(getAllNotNecessirellyDirectChild(tagName, node));
- }
- }
- return result;
- }
-}
+package lcsb.mapviewer.common;
+
+import java.awt.Color;
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.StringReader;
+import java.io.StringWriter;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.OutputKeys;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerException;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.dom.DOMSource;
+import javax.xml.transform.stream.StreamResult;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringEscapeUtils;
+import org.apache.log4j.Logger;
+import org.w3c.dom.Document;
+import org.w3c.dom.NamedNodeMap;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+
+/**
+ * Abstract class with methods which help in parsing xml using DOM.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class XmlParser {
+ /**
+ * Base of the hex representation.
+ */
+ private static final int HEX_BASE = 16;
+
+ /**
+ * {@link DocumentBuilderFactory} used to create {@link DocumentBuilder} objects
+ * that will manipulate xml nodes.
+ */
+ private static DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(XmlParser.class.getName());
+
+ /**
+ * DOM document builder used for xml transformations.
+ */
+ private DocumentBuilder db;
+
+ /**
+ * Default constructor that prevents from instatiation of the class and
+ * initializes fields.
+ */
+ protected XmlParser() {
+ try {
+ db = documentBuilderFactory.newDocumentBuilder();
+ } catch (ParserConfigurationException e) {
+ throw new InvalidStateException("Problem with xml parser");
+ }
+
+ }
+
+ /**
+ * Method returns the node of xml nodelist 'nodes' with 'tagName' name. If node
+ * could not be found then null is returned.
+ *
+ * @param tagName
+ * name of node to look for
+ * @param nodes
+ * list of nodes
+ * @return node from nodes list with the tagName name, <b>null</b> if such node
+ * doesn't exist
+ */
+ protected Node getNode(final String tagName, final NodeList nodes) {
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase(tagName)) {
+ return node;
+ }
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Method returns the child node of xml 'parentNode' with 'tagName' name. If
+ * node could not be found then null is returned.
+ *
+ * @param tagName
+ * name of node to look for
+ * @param parentNode
+ * parent node
+ * @return node from nodes list with the tagName name, <b>null</b> if such node
+ * doesn't exist
+ */
+ protected Node getNode(final String tagName, final Node parentNode) {
+ return getNode(tagName, parentNode.getChildNodes());
+ }
+
+ /**
+ * Method returns list of nodes with 'tagName' name. If node could not be found
+ * then empty list is returned.
+ *
+ * @param tagName
+ * name of node to look for
+ * @param nodes
+ * list of input nodes
+ * @return list of nodes with 'tagName' name
+ */
+ protected List<Node> getNodes(final String tagName, final NodeList nodes) {
+ List<Node> result = new ArrayList<Node>();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeName().equalsIgnoreCase(tagName)) {
+ result.add(node);
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Method returns the value of node attribute. If attribute could not be found
+ * then "" is returned.
+ *
+ * @param attrName
+ * name of the attribute to look for
+ * @param node
+ * a node
+ * @return the value of node attribute, empty string("") if attribute doesn't
+ * exist
+ */
+ protected String getNodeAttr(final String attrName, final Node node) {
+ NamedNodeMap attrs = node.getAttributes();
+ for (int y = 0; y < attrs.getLength(); y++) {
+ Node attr = attrs.item(y);
+ if (attr.getNodeName().equalsIgnoreCase(attrName)) {
+ return attr.getNodeValue();
+ }
+ }
+ return "";
+ }
+
+ /**
+ * Method returns the text value of node. If text could not be found then "" is
+ * returned.
+ *
+ * @param node
+ * a node
+ * @return the text value of node or empty string ("") if the text could be
+ * found.
+ */
+ protected String getNodeValue(final Node node) {
+ if (node == null) {
+ return "";
+ }
+ NodeList childNodes = node.getChildNodes();
+ for (int x = 0; x < childNodes.getLength(); x++) {
+ Node data = childNodes.item(x);
+ if (data.getNodeType() == Node.TEXT_NODE) {
+ return data.getNodeValue();
+ }
+ }
+ return "";
+ }
+
+ /**
+ * Method returns the xml Document from input source given as a parameter.
+ *
+ * @param stream
+ * input stream with xml document
+ * @return Document node for the input stream
+ * @throws InvalidXmlSchemaException
+ * thrown when there is a problem with xml
+ */
+ protected Document getXmlDocumentFromInputSource(final InputSource stream) throws InvalidXmlSchemaException {
+ try {
+ synchronized (db) { // DocumentBuilder cannot parse few objects at the
+ // same time
+ return db.parse(stream);
+ }
+ } catch (SAXException e) {
+ throw new InvalidXmlSchemaException("Problem with xml parser", e);
+ } catch (IOException e) {
+ throw new InvalidXmlSchemaException("Problem with xml parser", e);
+ }
+ }
+
+ /**
+ * Method returns the xml Document from text given as a source.
+ *
+ * @param text
+ * string representing xml document
+ * @return Document for the xml document given in the input
+ * @throws InvalidXmlSchemaException
+ * thrown when there is a problem with xml
+ */
+ protected Document getXmlDocumentFromString(final String text) throws InvalidXmlSchemaException {
+ InputSource is = new InputSource();
+ is.setCharacterStream(new StringReader(text));
+ try {
+ return getXmlDocumentFromInputSource(is);
+ } catch (NullPointerException e) {
+ logger.error("Problem with input xml: " + text);
+ throw new InvalidXmlSchemaException(e);
+ }
+ }
+
+ /**
+ * Transforms node into string xml format.
+ *
+ * @param node
+ * node that should be transformed into xml string
+ * @return string representation of the xml node
+ */
+ protected String nodeToString(final Node node) {
+ return nodeToString(node, false);
+ }
+
+ /**
+ * Transforms node into string xml format.
+ *
+ * @param node
+ * node that should be transformed into xml string
+ * @param includeHeadNode
+ * should the top level node exist in the output
+ * @return string representation of the xml node
+ */
+ protected String nodeToString(final Node node, final boolean includeHeadNode) {
+ if (node == null) {
+ return null;
+ }
+ StringWriter sw = new StringWriter();
+ try {
+ Transformer t = TransformerFactory.newInstance().newTransformer();
+ t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
+ t.setOutputProperty(OutputKeys.INDENT, "yes");
+ t.setOutputProperty(OutputKeys.METHOD, "xml");
+
+ NodeList list = node.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node element = list.item(i);
+ t.transform(new DOMSource(element), new StreamResult(sw));
+ }
+ } catch (TransformerException te) {
+ logger.debug("nodeToString Transformer Exception");
+ }
+ if (includeHeadNode) {
+ return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
+ }
+ return sw.toString();
+ }
+
+ /**
+ * This method transform color encoded in string (CellDesigner format) into
+ * Color.
+ *
+ * @param color
+ * string representing color
+ * @return Color object for the fiven string
+ */
+ protected Color stringToColor(final String color) {
+ try {
+ String alpha = color.substring(0, 2);
+ Color tmp = new Color(hexToInteger(color.substring(2)));
+ return new Color(tmp.getRed(), tmp.getGreen(), tmp.getBlue(), hexToInteger(alpha));
+ } catch (Exception e) {
+ throw new InvalidArgumentException("Invalid color string: " + color);
+ }
+ }
+
+ /**
+ * Transforms hex string into Integer.
+ *
+ * @param hexString
+ * string representation in hex base
+ * @return Integer value of the hex string
+ */
+ private Integer hexToInteger(String hexString) {
+ return Integer.valueOf(hexString, HEX_BASE);
+ }
+
+ /**
+ * Transforms Color object into string representing this color in RGB.
+ *
+ * @param color
+ * color that should be converted into string
+ * @return hex string representation of the color
+ */
+ protected String colorToString(final Color color) {
+ return String.format("%08X", color.getRGB());
+ }
+
+ /**
+ * Method that reads file and transforms it into a string.
+ *
+ * @param fileName
+ * path to a file
+ * @return string containing data from the file (default coding is used)
+ * @throws IOException
+ * thrown when there are some problems with a file
+ */
+ protected String fileToString(final String fileName) throws IOException {
+ BufferedReader reader = new BufferedReader(new FileReader(fileName));
+ String line = null;
+ StringBuilder stringBuilder = new StringBuilder();
+ String ls = System.getProperty("line.separator");
+
+ while ((line = reader.readLine()) != null) {
+ stringBuilder.append(line);
+ stringBuilder.append(ls);
+ }
+ reader.close();
+
+ return stringBuilder.toString();
+ }
+
+ /**
+ * Method that reads all data from inputstream and transform it into a string.
+ * UTF-8 coding is used.
+ *
+ * @param inputStream
+ * stream from which we read data
+ * @return string representing all data from input stream
+ * @throws IOException
+ * thrown if there are some problems with input stream
+ */
+ protected String inputStreamToString(final InputStream inputStream) throws IOException {
+ StringWriter writer = new StringWriter();
+ IOUtils.copy(inputStream, writer, "UTF-8");
+ String result = writer.toString();
+ return result;
+ }
+
+ /**
+ * Method that encode string into a string that can be used in xml file.
+ *
+ * @param string
+ * string to be escaped
+ * @return escaped string, ready to be used in xml
+ */
+ protected String escapeXml(final String string) {
+ if (string == null) {
+ return null;
+ }
+ // quite expensive
+ return StringEscapeUtils.escapeXml(string).replaceAll("\n", " ").replace("\r", " ");
+ }
+
+ public List<Node> getAllNotNecessirellyDirectChild(String tagName, Node root) {
+ List<Node> result = new ArrayList<>();
+ for (int x = 0; x < root.getChildNodes().getLength(); x++) {
+ Node node = root.getChildNodes().item(x);
+ if (node.getNodeName().equalsIgnoreCase(tagName)) {
+ result.add(node);
+ } else {
+ result.addAll(getAllNotNecessirellyDirectChild(tagName, node));
+ }
+ }
+ return result;
+ }
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/comparator/BooleanComparator.java b/commons/src/main/java/lcsb/mapviewer/common/comparator/BooleanComparator.java
index 55b6281f92..c7f3bd733c 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/comparator/BooleanComparator.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/comparator/BooleanComparator.java
@@ -1,27 +1,27 @@
-package lcsb.mapviewer.common.comparator;
-
-import java.util.Comparator;
-
-/**
- * Comparator implemented for {@link Boolean} class.
- *
- * @author Piotr Gawron
- *
- */
-public class BooleanComparator implements Comparator<Boolean> {
-
- @Override
- public int compare(Boolean arg0, Boolean arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
- return arg0.compareTo(arg1);
- }
-
-}
+package lcsb.mapviewer.common.comparator;
+
+import java.util.Comparator;
+
+/**
+ * Comparator implemented for {@link Boolean} class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class BooleanComparator implements Comparator<Boolean> {
+
+ @Override
+ public int compare(Boolean arg0, Boolean arg1) {
+ if (arg0 == null) {
+ if (arg1 == null) {
+ return 0;
+ } else {
+ return 1;
+ }
+ } else if (arg1 == null) {
+ return -1;
+ }
+ return arg0.compareTo(arg1);
+ }
+
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/comparator/ColorComparator.java b/commons/src/main/java/lcsb/mapviewer/common/comparator/ColorComparator.java
index f109abd046..efaf121466 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/comparator/ColorComparator.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/comparator/ColorComparator.java
@@ -1,29 +1,29 @@
-package lcsb.mapviewer.common.comparator;
-
-import java.awt.Color;
-import java.util.Comparator;
-
-/**
- * Comparator implementation for {@link Color} class.
- *
- * @author Piotr Gawron
- *
- */
-public class ColorComparator implements Comparator<Color> {
-
- @Override
- public int compare(Color arg0, Color arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
-
- } else if (arg1 == null) {
- return -1;
- }
- return ((Integer) arg0.getRGB()).compareTo(arg1.getRGB());
- }
-
-}
+package lcsb.mapviewer.common.comparator;
+
+import java.awt.Color;
+import java.util.Comparator;
+
+/**
+ * Comparator implementation for {@link Color} class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ColorComparator implements Comparator<Color> {
+
+ @Override
+ public int compare(Color arg0, Color arg1) {
+ if (arg0 == null) {
+ if (arg1 == null) {
+ return 0;
+ } else {
+ return 1;
+ }
+
+ } else if (arg1 == null) {
+ return -1;
+ }
+ return ((Integer) arg0.getRGB()).compareTo(arg1.getRGB());
+ }
+
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/comparator/DoubleComparator.java b/commons/src/main/java/lcsb/mapviewer/common/comparator/DoubleComparator.java
index f25e5690f7..a1320b5f13 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/comparator/DoubleComparator.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/comparator/DoubleComparator.java
@@ -1,56 +1,56 @@
-package lcsb.mapviewer.common.comparator;
-
-import java.util.Comparator;
-
-import lcsb.mapviewer.common.Configuration;
-
-/**
- * Comparator used for {@link Double} class.
- *
- * @author Piotr Gawron
- *
- */
-public class DoubleComparator implements Comparator<Double> {
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Default constructor.
- */
- public DoubleComparator() {
- this(Configuration.EPSILON);
- }
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public DoubleComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- @Override
- public int compare(Double arg0, Double arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
-
- } else if (arg1 == null) {
- return -1;
- }
- if (Math.abs(arg0 - arg1) < epsilon) {
- return 0;
- } else {
- return arg0.compareTo(arg1);
- }
- }
-
-}
+package lcsb.mapviewer.common.comparator;
+
+import java.util.Comparator;
+
+import lcsb.mapviewer.common.Configuration;
+
+/**
+ * Comparator used for {@link Double} class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class DoubleComparator implements Comparator<Double> {
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Default constructor.
+ */
+ public DoubleComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public DoubleComparator(double epsilon) {
+ this.epsilon = epsilon;
+ }
+
+ @Override
+ public int compare(Double arg0, Double arg1) {
+ if (arg0 == null) {
+ if (arg1 == null) {
+ return 0;
+ } else {
+ return 1;
+ }
+
+ } else if (arg1 == null) {
+ return -1;
+ }
+ if (Math.abs(arg0 - arg1) < epsilon) {
+ return 0;
+ } else {
+ return arg0.compareTo(arg1);
+ }
+ }
+
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/comparator/EnumComparator.java b/commons/src/main/java/lcsb/mapviewer/common/comparator/EnumComparator.java
index 8da925497e..8157cfb562 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/comparator/EnumComparator.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/comparator/EnumComparator.java
@@ -1,29 +1,29 @@
-package lcsb.mapviewer.common.comparator;
-
-import java.awt.Color;
-import java.util.Comparator;
-
-/**
- * Comparator implementation for {@link Color} class.
- *
- * @author Piotr Gawron
- *
- */
-public class EnumComparator implements Comparator<Enum<?>> {
-
- @Override
- public int compare(Enum arg0, Enum arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
-
- } else if (arg1 == null) {
- return -1;
- }
- return arg0.compareTo(arg1);
- }
-
-}
+package lcsb.mapviewer.common.comparator;
+
+import java.awt.Color;
+import java.util.Comparator;
+
+/**
+ * Comparator implementation for {@link Color} class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class EnumComparator implements Comparator<Enum<?>> {
+
+ @Override
+ public int compare(Enum arg0, Enum arg1) {
+ if (arg0 == null) {
+ if (arg1 == null) {
+ return 0;
+ } else {
+ return 1;
+ }
+
+ } else if (arg1 == null) {
+ return -1;
+ }
+ return arg0.compareTo(arg1);
+ }
+
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/comparator/IntegerComparator.java b/commons/src/main/java/lcsb/mapviewer/common/comparator/IntegerComparator.java
index 6730bc258f..5ae981421a 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/comparator/IntegerComparator.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/comparator/IntegerComparator.java
@@ -1,27 +1,27 @@
-package lcsb.mapviewer.common.comparator;
-
-import java.util.Comparator;
-
-/**
- * Comparator implemented for {@link Integer} class.
- *
- * @author Piotr Gawron
- *
- */
-public class IntegerComparator implements Comparator<Integer> {
-
- @Override
- public int compare(Integer arg0, Integer arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
- return arg0.compareTo(arg1);
- }
-
-}
+package lcsb.mapviewer.common.comparator;
+
+import java.util.Comparator;
+
+/**
+ * Comparator implemented for {@link Integer} class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class IntegerComparator implements Comparator<Integer> {
+
+ @Override
+ public int compare(Integer arg0, Integer arg1) {
+ if (arg0 == null) {
+ if (arg1 == null) {
+ return 0;
+ } else {
+ return 1;
+ }
+ } else if (arg1 == null) {
+ return -1;
+ }
+ return arg0.compareTo(arg1);
+ }
+
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/comparator/PointComparator.java b/commons/src/main/java/lcsb/mapviewer/common/comparator/PointComparator.java
index c66c9db86e..4283684288 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/comparator/PointComparator.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/comparator/PointComparator.java
@@ -1,58 +1,58 @@
-package lcsb.mapviewer.common.comparator;
-
-import java.awt.geom.Point2D;
-import java.util.Comparator;
-
-import lcsb.mapviewer.common.Configuration;
-
-/**
- * Comparator used for {@link Point2D} class.
- *
- * @author Piotr Gawron
- *
- */
-public class PointComparator implements Comparator<Point2D> {
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public PointComparator(double epsilon) {
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public PointComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public int compare(Point2D arg0, Point2D arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
-
- } else if (arg1 == null) {
- return -1;
- }
- if (Math.abs(arg0.distance(arg1)) < epsilon) {
- return 0;
- } else {
- // this could be modified to assure monotonousness of comparison
- return -1;
- }
- }
-
-}
+package lcsb.mapviewer.common.comparator;
+
+import java.awt.geom.Point2D;
+import java.util.Comparator;
+
+import lcsb.mapviewer.common.Configuration;
+
+/**
+ * Comparator used for {@link Point2D} class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class PointComparator implements Comparator<Point2D> {
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public PointComparator(double epsilon) {
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public PointComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ public int compare(Point2D arg0, Point2D arg1) {
+ if (arg0 == null) {
+ if (arg1 == null) {
+ return 0;
+ } else {
+ return 1;
+ }
+
+ } else if (arg1 == null) {
+ return -1;
+ }
+ if (Math.abs(arg0.distance(arg1)) < epsilon) {
+ return 0;
+ } else {
+ // this could be modified to assure monotonousness of comparison
+ return -1;
+ }
+ }
+
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/comparator/SetComparator.java b/commons/src/main/java/lcsb/mapviewer/common/comparator/SetComparator.java
index 0ebaa4b86a..bc3658717b 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/comparator/SetComparator.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/comparator/SetComparator.java
@@ -1,66 +1,66 @@
-package lcsb.mapviewer.common.comparator;
-
-import java.util.Comparator;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-
-/**
- * Comparator used for comparing sets of strings.
- *
- * @author Piotr Gawron
- *
- */
-public class SetComparator<T> implements Comparator<Set<T>> {
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(SetComparator.class);
-
- private Comparator<T> objectComparator;
-
- public SetComparator(Comparator<T> objectComparator) {
- this.objectComparator = objectComparator;
- }
-
- @Override
- public int compare(Set<T> arg0, Set<T> arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- for (T objectInList1 : arg1) {
- boolean found = false;
- for (T objectInList0 : arg0) {
- if (objectComparator.compare(objectInList0, objectInList1) == 0) {
- found = true;
- }
- }
- if (!found) {
- logger.debug("Cannot find object " + objectInList1 + " in set: " + arg0);
- return 1;
- }
- }
-
- for (T objectInList0 : arg0) {
- boolean found = false;
- for (T objectInList1 : arg1) {
- if (objectComparator.compare(objectInList0, objectInList1) == 0) {
- found = true;
- }
- }
- if (!found) {
- logger.debug("Cannot find object " + objectInList0 + " in set: " + arg1);
- return 1;
- }
- }
- return 0;
- }
-
-}
+package lcsb.mapviewer.common.comparator;
+
+import java.util.Comparator;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Comparator used for comparing sets of strings.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class SetComparator<T> implements Comparator<Set<T>> {
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(SetComparator.class);
+
+ private Comparator<T> objectComparator;
+
+ public SetComparator(Comparator<T> objectComparator) {
+ this.objectComparator = objectComparator;
+ }
+
+ @Override
+ public int compare(Set<T> arg0, Set<T> arg1) {
+ if (arg0 == null) {
+ if (arg1 == null) {
+ return 0;
+ } else {
+ return 1;
+ }
+ } else if (arg1 == null) {
+ return -1;
+ }
+
+ for (T objectInList1 : arg1) {
+ boolean found = false;
+ for (T objectInList0 : arg0) {
+ if (objectComparator.compare(objectInList0, objectInList1) == 0) {
+ found = true;
+ }
+ }
+ if (!found) {
+ logger.debug("Cannot find object " + objectInList1 + " in set: " + arg0);
+ return 1;
+ }
+ }
+
+ for (T objectInList0 : arg0) {
+ boolean found = false;
+ for (T objectInList1 : arg1) {
+ if (objectComparator.compare(objectInList0, objectInList1) == 0) {
+ found = true;
+ }
+ }
+ if (!found) {
+ logger.debug("Cannot find object " + objectInList0 + " in set: " + arg1);
+ return 1;
+ }
+ }
+ return 0;
+ }
+
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/comparator/StringComparator.java b/commons/src/main/java/lcsb/mapviewer/common/comparator/StringComparator.java
index f6a69398ba..183e49593e 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/comparator/StringComparator.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/comparator/StringComparator.java
@@ -1,56 +1,56 @@
-package lcsb.mapviewer.common.comparator;
-
-import java.util.Comparator;
-
-import org.apache.log4j.Logger;
-
-/**
- * Comparator used for {@link String} class. It's null safe (it allows to
- * compare strings that are null).
- *
- * @author Piotr Gawron
- *
- */
-public class StringComparator implements Comparator<String> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(StringComparator.class);
-
- @Override
- public int compare(String arg0, String arg1) {
- return compare(arg0, arg1, false);
- }
-
- /**
- * Allows to compare two strings ignoring whitespace difference.
- *
- * @param arg0
- * first string to compare
- * @param arg1
- * second string to compare
- * @param ignoreWhiteSpaceDifference
- * should the difference in whitespace be ignored
- * @return 0 when strings are identical, -1/1 when they are different
- */
- public int compare(String arg0, String arg1, boolean ignoreWhiteSpaceDifference) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (ignoreWhiteSpaceDifference) {
- String str1 = arg0.replaceAll("[\n\r\t\\ ]+", "\n");
- String str2 = arg1.replaceAll("[\n\r\t\\ ]+", "\n");
- return str1.trim().compareTo(str2.trim());
- }
- return arg0.trim().compareTo(arg1.trim());
- }
-
-}
+package lcsb.mapviewer.common.comparator;
+
+import java.util.Comparator;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Comparator used for {@link String} class. It's null safe (it allows to
+ * compare strings that are null).
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class StringComparator implements Comparator<String> {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(StringComparator.class);
+
+ @Override
+ public int compare(String arg0, String arg1) {
+ return compare(arg0, arg1, false);
+ }
+
+ /**
+ * Allows to compare two strings ignoring whitespace difference.
+ *
+ * @param arg0
+ * first string to compare
+ * @param arg1
+ * second string to compare
+ * @param ignoreWhiteSpaceDifference
+ * should the difference in whitespace be ignored
+ * @return 0 when strings are identical, -1/1 when they are different
+ */
+ public int compare(String arg0, String arg1, boolean ignoreWhiteSpaceDifference) {
+ if (arg0 == null) {
+ if (arg1 == null) {
+ return 0;
+ } else {
+ return 1;
+ }
+ } else if (arg1 == null) {
+ return -1;
+ }
+
+ if (ignoreWhiteSpaceDifference) {
+ String str1 = arg0.replaceAll("[\n\r\t\\ ]+", "\n");
+ String str2 = arg1.replaceAll("[\n\r\t\\ ]+", "\n");
+ return str1.trim().compareTo(str2.trim());
+ }
+ return arg0.trim().compareTo(arg1.trim());
+ }
+
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/comparator/StringListComparator.java b/commons/src/main/java/lcsb/mapviewer/common/comparator/StringListComparator.java
index 69815109e7..92ccd809e3 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/comparator/StringListComparator.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/comparator/StringListComparator.java
@@ -1,56 +1,56 @@
-package lcsb.mapviewer.common.comparator;
-
-import java.util.Comparator;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-/**
- * Comparator used for list of strings.
- *
- * @author Piotr Gawron
- *
- */
-public class StringListComparator implements Comparator<List<String>> {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(StringListComparator.class);
-
- /**
- * String comparator used for comparing strings.
- */
- private StringComparator stringComparator = new StringComparator();
- /**
- * Integer comparator used for comparing integers.
- */
- private IntegerComparator integerComparator = new IntegerComparator();
-
- @Override
- public int compare(List<String> arg0, List<String> arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (arg0.size() != arg1.size()) {
- logger.debug("String lists have different size: " + arg0.size() + ", " + arg1.size());
- return integerComparator.compare(arg0.size(), arg1.size());
- }
-
- for (int i = 0; i < arg0.size(); i++) {
- if (stringComparator.compare(arg0.get(i), arg1.get(i)) != 0) {
- logger.debug("Strings in list different: \"" + arg0.get(i) + "\", \"" + arg1.get(i) + "\"");
- return stringComparator.compare(arg0.get(i), arg1.get(i));
- }
- }
-
- return 0;
- }
-
-}
+package lcsb.mapviewer.common.comparator;
+
+import java.util.Comparator;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Comparator used for list of strings.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class StringListComparator implements Comparator<List<String>> {
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(StringListComparator.class);
+
+ /**
+ * String comparator used for comparing strings.
+ */
+ private StringComparator stringComparator = new StringComparator();
+ /**
+ * Integer comparator used for comparing integers.
+ */
+ private IntegerComparator integerComparator = new IntegerComparator();
+
+ @Override
+ public int compare(List<String> arg0, List<String> arg1) {
+ if (arg0 == null) {
+ if (arg1 == null) {
+ return 0;
+ } else {
+ return 1;
+ }
+ } else if (arg1 == null) {
+ return -1;
+ }
+
+ if (arg0.size() != arg1.size()) {
+ logger.debug("String lists have different size: " + arg0.size() + ", " + arg1.size());
+ return integerComparator.compare(arg0.size(), arg1.size());
+ }
+
+ for (int i = 0; i < arg0.size(); i++) {
+ if (stringComparator.compare(arg0.get(i), arg1.get(i)) != 0) {
+ logger.debug("Strings in list different: \"" + arg0.get(i) + "\", \"" + arg1.get(i) + "\"");
+ return stringComparator.compare(arg0.get(i), arg1.get(i));
+ }
+ }
+
+ return 0;
+ }
+
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/comparator/package-info.java b/commons/src/main/java/lcsb/mapviewer/common/comparator/package-info.java
index c2d45d21fc..7303e6069b 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/comparator/package-info.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/comparator/package-info.java
@@ -1,5 +1,5 @@
-/**
- * Package with comparators for common classes.
- */
-package lcsb.mapviewer.common.comparator;
-
+/**
+ * Package with comparators for common classes.
+ */
+package lcsb.mapviewer.common.comparator;
+
diff --git a/commons/src/main/java/lcsb/mapviewer/common/exception/InvalidArgumentException.java b/commons/src/main/java/lcsb/mapviewer/common/exception/InvalidArgumentException.java
index 634543e07f..cc38a4c8f2 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/exception/InvalidArgumentException.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/exception/InvalidArgumentException.java
@@ -1,56 +1,56 @@
-package lcsb.mapviewer.common.exception;
-
-/**
- * Exception to be thrown when one of the argument is invalid.
- *
- * @author Piotr Gawron
- *
- */
-public class InvalidArgumentException extends RuntimeException {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor - initializes instance variable to unknown.
- */
-
- public InvalidArgumentException() {
- super(); // call superclass constructor
- }
-
- /**
- * Public constructor with parent exception that was catched.
- *
- * @param e
- * parent exception
- */
-
- public InvalidArgumentException(final String e) {
- super(e);
- }
-
- /**
- * Public constructor with parent exception that was catched.
- *
- * @param e
- * parent exception
- */
- public InvalidArgumentException(final Exception e) {
- super(e);
- }
-
- /**
- * Public constructor with parent exception that was catched.
- *
- * @param message
- * exception message
- * @param e
- * parent exception
- */
- public InvalidArgumentException(final String message, final Exception e) {
- super(message, e);
- }
-
-}
+package lcsb.mapviewer.common.exception;
+
+/**
+ * Exception to be thrown when one of the argument is invalid.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class InvalidArgumentException extends RuntimeException {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor - initializes instance variable to unknown.
+ */
+
+ public InvalidArgumentException() {
+ super(); // call superclass constructor
+ }
+
+ /**
+ * Public constructor with parent exception that was catched.
+ *
+ * @param e
+ * parent exception
+ */
+
+ public InvalidArgumentException(final String e) {
+ super(e);
+ }
+
+ /**
+ * Public constructor with parent exception that was catched.
+ *
+ * @param e
+ * parent exception
+ */
+ public InvalidArgumentException(final Exception e) {
+ super(e);
+ }
+
+ /**
+ * Public constructor with parent exception that was catched.
+ *
+ * @param message
+ * exception message
+ * @param e
+ * parent exception
+ */
+ public InvalidArgumentException(final String message, final Exception e) {
+ super(message, e);
+ }
+
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/exception/InvalidClassException.java b/commons/src/main/java/lcsb/mapviewer/common/exception/InvalidClassException.java
index df46ac2024..c09f00529a 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/exception/InvalidClassException.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/exception/InvalidClassException.java
@@ -1,38 +1,38 @@
-package lcsb.mapviewer.common.exception;
-
-/**
- * Exception thrown when the class of the object is invalid.
- *
- * @author Piotr Gawron
- *
- */
-public class InvalidClassException extends RuntimeException {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor with message passed in the argument.
- *
- * @param string
- * message of this exception
- */
- public InvalidClassException(String string) {
- super(string);
- }
-
- /**
- * Default constructor with message passed in the argument and super
- * exception.
- *
- * @param string
- * message of this exception
- * @param e
- * exception catched and passed to this object
- */
- public InvalidClassException(String string, Exception e) {
- super(string, e);
- }
-}
+package lcsb.mapviewer.common.exception;
+
+/**
+ * Exception thrown when the class of the object is invalid.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class InvalidClassException extends RuntimeException {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor with message passed in the argument.
+ *
+ * @param string
+ * message of this exception
+ */
+ public InvalidClassException(String string) {
+ super(string);
+ }
+
+ /**
+ * Default constructor with message passed in the argument and super
+ * exception.
+ *
+ * @param string
+ * message of this exception
+ * @param e
+ * exception catched and passed to this object
+ */
+ public InvalidClassException(String string, Exception e) {
+ super(string, e);
+ }
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/exception/InvalidStateException.java b/commons/src/main/java/lcsb/mapviewer/common/exception/InvalidStateException.java
index f5fbe6b732..6c1405dfba 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/exception/InvalidStateException.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/exception/InvalidStateException.java
@@ -1,56 +1,56 @@
-package lcsb.mapviewer.common.exception;
-
-/**
- * Exception that should be thrown when application/class/method entered to
- * invalid state.
- *
- * @author Piotr Gawron
- *
- */
-public class InvalidStateException extends RuntimeException {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public InvalidStateException() {
- super();
- }
-
- /**
- * Default constructor with message passed in the argument.
- *
- * @param string
- * message of this exception
- */
- public InvalidStateException(String string) {
- super(string);
- }
-
- /**
- * Public constructor with parent exception that was catched.
- *
- * @param e
- * parent exception
- */
- public InvalidStateException(Exception e) {
- super(e);
- }
-
- /**
- * Public constructor with parent exception that was catched.
- *
- * @param string
- * message of this exception
- * @param e
- * parent exception
- */
- public InvalidStateException(String string, Exception e) {
- super(string, e);
- }
-
-}
+package lcsb.mapviewer.common.exception;
+
+/**
+ * Exception that should be thrown when application/class/method entered to
+ * invalid state.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class InvalidStateException extends RuntimeException {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public InvalidStateException() {
+ super();
+ }
+
+ /**
+ * Default constructor with message passed in the argument.
+ *
+ * @param string
+ * message of this exception
+ */
+ public InvalidStateException(String string) {
+ super(string);
+ }
+
+ /**
+ * Public constructor with parent exception that was catched.
+ *
+ * @param e
+ * parent exception
+ */
+ public InvalidStateException(Exception e) {
+ super(e);
+ }
+
+ /**
+ * Public constructor with parent exception that was catched.
+ *
+ * @param string
+ * message of this exception
+ * @param e
+ * parent exception
+ */
+ public InvalidStateException(String string, Exception e) {
+ super(string, e);
+ }
+
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/exception/InvalidXmlSchemaException.java b/commons/src/main/java/lcsb/mapviewer/common/exception/InvalidXmlSchemaException.java
index caf9f481f7..42194290a3 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/exception/InvalidXmlSchemaException.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/exception/InvalidXmlSchemaException.java
@@ -1,56 +1,56 @@
-package lcsb.mapviewer.common.exception;
-
-/**
- * Exception that shold be thrown when the xml schema is invalid.
- *
- * @author Piotr Gawron
- *
- */
-public class InvalidXmlSchemaException extends Exception {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor - initializes instance variable to unknown.
- */
-
- public InvalidXmlSchemaException() {
- super(); // call superclass constructor
- }
-
- /**
- * Constructor receives some kind of message.
- *
- * @param err
- * message associated with exception
- */
-
- public InvalidXmlSchemaException(final String err) {
- super(err);
- }
-
- /**
- * Constructor receives some kind of message and parent exception.
- *
- * @param err
- * message associated with exception
- * @param throwable
- * parent exception
- */
- public InvalidXmlSchemaException(final String err, final Throwable throwable) {
- super(err, throwable);
- }
-
- /**
- * Public constructor with parent exception that was catched.
- *
- * @param e
- * parent exception
- */
-
- public InvalidXmlSchemaException(final Exception e) {
- super(e);
- }
-}
+package lcsb.mapviewer.common.exception;
+
+/**
+ * Exception that shold be thrown when the xml schema is invalid.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class InvalidXmlSchemaException extends Exception {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor - initializes instance variable to unknown.
+ */
+
+ public InvalidXmlSchemaException() {
+ super(); // call superclass constructor
+ }
+
+ /**
+ * Constructor receives some kind of message.
+ *
+ * @param err
+ * message associated with exception
+ */
+
+ public InvalidXmlSchemaException(final String err) {
+ super(err);
+ }
+
+ /**
+ * Constructor receives some kind of message and parent exception.
+ *
+ * @param err
+ * message associated with exception
+ * @param throwable
+ * parent exception
+ */
+ public InvalidXmlSchemaException(final String err, final Throwable throwable) {
+ super(err, throwable);
+ }
+
+ /**
+ * Public constructor with parent exception that was catched.
+ *
+ * @param e
+ * parent exception
+ */
+
+ public InvalidXmlSchemaException(final Exception e) {
+ super(e);
+ }
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/exception/NotImplementedException.java b/commons/src/main/java/lcsb/mapviewer/common/exception/NotImplementedException.java
index 0c9d160f90..816128136c 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/exception/NotImplementedException.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/exception/NotImplementedException.java
@@ -1,35 +1,35 @@
-package lcsb.mapviewer.common.exception;
-
-/**
- * Exception that should be thrown when application/class/method entered to the
- * part of code that wasn't implemented (for instance the class is not abstract,
- * but method should be considered abstrac...).
- *
- * @author Piotr Gawron
- *
- */
-public class NotImplementedException extends RuntimeException {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public NotImplementedException() {
- super();
- }
-
- /**
- * Default constructor with message passed in the argument.
- *
- * @param string
- * message of this exception
- */
- public NotImplementedException(String string) {
- super(string);
- }
-
-}
+package lcsb.mapviewer.common.exception;
+
+/**
+ * Exception that should be thrown when application/class/method entered to the
+ * part of code that wasn't implemented (for instance the class is not abstract,
+ * but method should be considered abstrac...).
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class NotImplementedException extends RuntimeException {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public NotImplementedException() {
+ super();
+ }
+
+ /**
+ * Default constructor with message passed in the argument.
+ *
+ * @param string
+ * message of this exception
+ */
+ public NotImplementedException(String string) {
+ super(string);
+ }
+
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/exception/package-info.java b/commons/src/main/java/lcsb/mapviewer/common/exception/package-info.java
index 1482d19fc4..fb2c61871f 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/exception/package-info.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/exception/package-info.java
@@ -1,5 +1,5 @@
-/**
- * Common exceptions thrown by the system.
- */
-package lcsb.mapviewer.common.exception;
-
+/**
+ * Common exceptions thrown by the system.
+ */
+package lcsb.mapviewer.common.exception;
+
diff --git a/commons/src/main/java/lcsb/mapviewer/common/geometry/ColorParser.java b/commons/src/main/java/lcsb/mapviewer/common/geometry/ColorParser.java
index 76ee7ad305..7e240ab6e5 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/geometry/ColorParser.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/geometry/ColorParser.java
@@ -1,77 +1,77 @@
-package lcsb.mapviewer.common.geometry;
-
-import java.awt.Color;
-import java.util.HashMap;
-import java.util.Map;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-
-/**
- * Parser clas to extract {@link Color} objects from {@link String}.
- *
- * @author Piotr Gawron
- *
- */
-public class ColorParser {
-
- /**
- * Base of the hex representation.
- */
- private static final int HEX_BASE = 16;
-
- /**
- * Length of the string describing color in RGB: "#RRGGBB".
- */
- private static final int COLOR_STRING_LENGTH = 7;
-
- /**
- * Where starts description of red color in string representing color.
- */
- private static final int COLOR_SUBSTRING_START_RED = 1;
-
- /**
- * Where starts description of green color in string representing color.
- */
- private static final int COLOR_SUBSTRING_START_GREEN = 3;
-
- /**
- * Where starts description of blue color in string representing color.
- */
- private static final int COLOR_SUBSTRING_START_BLUE = 5;
-
- /**
- * Extracts {@link Color} from input {@link String}.
- *
- * @param string
- * text to process
- * @return {@link Color} obtained from input text
- */
- public Color parse(String string) {
- if (string.charAt(0) != '#') {
- string = "#" + string;
- }
- if (string.length() != COLOR_STRING_LENGTH) {
- throw new InvalidArgumentException(
- "Invalid color value: " + string + ". Correct format: #xxxxxx (where x is a hex value)");
- } else {
- return new Color(
- Integer.valueOf(string.substring(COLOR_SUBSTRING_START_RED, COLOR_SUBSTRING_START_GREEN), HEX_BASE), //
- Integer.valueOf(string.substring(COLOR_SUBSTRING_START_GREEN, COLOR_SUBSTRING_START_BLUE), HEX_BASE), //
- Integer.valueOf(string.substring(COLOR_SUBSTRING_START_BLUE, COLOR_STRING_LENGTH), HEX_BASE));
- }
- }
-
- /**
- * Converts color into list of attributes.
- *
- * @param color
- * color to convert
- * @return map with list of color attributes
- */
- public Map<String, Object> colorToMap(Color color) {
- Map<String, Object> result = new HashMap<>();
- result.put("alpha", color.getAlpha());
- result.put("rgb", color.getRGB());
- return result;
- }
-}
+package lcsb.mapviewer.common.geometry;
+
+import java.awt.Color;
+import java.util.HashMap;
+import java.util.Map;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+
+/**
+ * Parser clas to extract {@link Color} objects from {@link String}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ColorParser {
+
+ /**
+ * Base of the hex representation.
+ */
+ private static final int HEX_BASE = 16;
+
+ /**
+ * Length of the string describing color in RGB: "#RRGGBB".
+ */
+ private static final int COLOR_STRING_LENGTH = 7;
+
+ /**
+ * Where starts description of red color in string representing color.
+ */
+ private static final int COLOR_SUBSTRING_START_RED = 1;
+
+ /**
+ * Where starts description of green color in string representing color.
+ */
+ private static final int COLOR_SUBSTRING_START_GREEN = 3;
+
+ /**
+ * Where starts description of blue color in string representing color.
+ */
+ private static final int COLOR_SUBSTRING_START_BLUE = 5;
+
+ /**
+ * Extracts {@link Color} from input {@link String}.
+ *
+ * @param string
+ * text to process
+ * @return {@link Color} obtained from input text
+ */
+ public Color parse(String string) {
+ if (string.charAt(0) != '#') {
+ string = "#" + string;
+ }
+ if (string.length() != COLOR_STRING_LENGTH) {
+ throw new InvalidArgumentException(
+ "Invalid color value: " + string + ". Correct format: #xxxxxx (where x is a hex value)");
+ } else {
+ return new Color(
+ Integer.valueOf(string.substring(COLOR_SUBSTRING_START_RED, COLOR_SUBSTRING_START_GREEN), HEX_BASE), //
+ Integer.valueOf(string.substring(COLOR_SUBSTRING_START_GREEN, COLOR_SUBSTRING_START_BLUE), HEX_BASE), //
+ Integer.valueOf(string.substring(COLOR_SUBSTRING_START_BLUE, COLOR_STRING_LENGTH), HEX_BASE));
+ }
+ }
+
+ /**
+ * Converts color into list of attributes.
+ *
+ * @param color
+ * color to convert
+ * @return map with list of color attributes
+ */
+ public Map<String, Object> colorToMap(Color color) {
+ Map<String, Object> result = new HashMap<>();
+ result.put("alpha", color.getAlpha());
+ result.put("rgb", color.getRGB());
+ return result;
+ }
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/geometry/CompositeStroke.java b/commons/src/main/java/lcsb/mapviewer/common/geometry/CompositeStroke.java
index 1fbd1c61ef..df71302607 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/geometry/CompositeStroke.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/geometry/CompositeStroke.java
@@ -1,41 +1,41 @@
-package lcsb.mapviewer.common.geometry;
-
-import java.awt.Shape;
-import java.awt.Stroke;
-
-/**
- * This class represent {@link Stroke} that consist of two nested {@link Stroke
- * strokes}. In this way we can create a double line. More information can be
- * found <a href="http://www.jhlabs.com/java/java2d/strokes/">here</a>.
- *
- * @author Piotr Gawron
- *
- */
-public class CompositeStroke implements Stroke {
-
- /**
- * Outside stroke.
- */
- private Stroke stroke1;
-
- /**
- * Inside stroke used as a border of outside stroke.
- */
- private Stroke stroke2;
-
- /**
- * DEfault constructor.
- *
- * @param stroke1 {@link #stroke1}
- * @param stroke2 {@link #stroke2}
- */
- public CompositeStroke(Stroke stroke1, Stroke stroke2) {
- this.stroke1 = stroke1;
- this.stroke2 = stroke2;
- }
-
- @Override
- public Shape createStrokedShape(Shape shape) {
- return stroke2.createStrokedShape(stroke1.createStrokedShape(shape));
- }
-}
+package lcsb.mapviewer.common.geometry;
+
+import java.awt.Shape;
+import java.awt.Stroke;
+
+/**
+ * This class represent {@link Stroke} that consist of two nested {@link Stroke
+ * strokes}. In this way we can create a double line. More information can be
+ * found <a href="http://www.jhlabs.com/java/java2d/strokes/">here</a>.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CompositeStroke implements Stroke {
+
+ /**
+ * Outside stroke.
+ */
+ private Stroke stroke1;
+
+ /**
+ * Inside stroke used as a border of outside stroke.
+ */
+ private Stroke stroke2;
+
+ /**
+ * DEfault constructor.
+ *
+ * @param stroke1 {@link #stroke1}
+ * @param stroke2 {@link #stroke2}
+ */
+ public CompositeStroke(Stroke stroke1, Stroke stroke2) {
+ this.stroke1 = stroke1;
+ this.stroke2 = stroke2;
+ }
+
+ @Override
+ public Shape createStrokedShape(Shape shape) {
+ return stroke2.createStrokedShape(stroke1.createStrokedShape(shape));
+ }
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/geometry/DoubleDimension.java b/commons/src/main/java/lcsb/mapviewer/common/geometry/DoubleDimension.java
index 945c474a55..9c1fdce748 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/geometry/DoubleDimension.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/geometry/DoubleDimension.java
@@ -1,36 +1,36 @@
-package lcsb.mapviewer.common.geometry;
-
-import java.awt.geom.Dimension2D;
-
-public class DoubleDimension extends Dimension2D {
-
- private double width;
- private double height;
-
- public DoubleDimension(double width, double height) {
- this.width = width;
- this.height = height;
- }
-
- @Override
- public double getWidth() {
- return width;
- }
-
- @Override
- public double getHeight() {
- return height;
- }
-
- @Override
- public void setSize(double width, double height) {
- this.width = width;
- this.height = height;
- }
-
- @Override
- public String toString() {
- return "DoubleDimension[" + width + "," + height + "]";
- }
-
-}
+package lcsb.mapviewer.common.geometry;
+
+import java.awt.geom.Dimension2D;
+
+public class DoubleDimension extends Dimension2D {
+
+ private double width;
+ private double height;
+
+ public DoubleDimension(double width, double height) {
+ this.width = width;
+ this.height = height;
+ }
+
+ @Override
+ public double getWidth() {
+ return width;
+ }
+
+ @Override
+ public double getHeight() {
+ return height;
+ }
+
+ @Override
+ public void setSize(double width, double height) {
+ this.width = width;
+ this.height = height;
+ }
+
+ @Override
+ public String toString() {
+ return "DoubleDimension[" + width + "," + height + "]";
+ }
+
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/geometry/EllipseTransformation.java b/commons/src/main/java/lcsb/mapviewer/common/geometry/EllipseTransformation.java
index 882ad8b9ae..03e0c3cb58 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/geometry/EllipseTransformation.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/geometry/EllipseTransformation.java
@@ -1,153 +1,153 @@
-package lcsb.mapviewer.common.geometry;
-
-import java.awt.geom.Ellipse2D;
-import java.awt.geom.Point2D;
-
-import lcsb.mapviewer.common.Configuration;
-
-import org.apache.log4j.Logger;
-
-/**
- * This class contains basic operators on ellipse used by converters.
- *
- * @author Piotr Gawron
- *
- */
-public class EllipseTransformation {
- /**
- * PI value.
- */
- private static final double PI = Math.PI;
- /**
- * PI/2 value.
- */
- private static final double PI_1_2 = Math.PI / 2;
- /**
- * 3/2 PI value.
- */
- private static final double PI_3_2 = PI_1_2 * 3;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(EllipseTransformation.class.getName());
-
- /**
- * Method returns a cross point between ellipse and a line (from center point
- * with angle between the line and X axis).
- *
- * @param ellipse
- * ellipse object on which we want to find point
- * @param angle
- * angle in degrees
- * @return point on the ellipse that connect center of the ellipse with the
- * line that cross X axis by angle
- */
- public Point2D getPointOnEllipseByDegree(final Ellipse2D ellipse, final double angle) {
- return getPointOnEllipseByRadian(ellipse, Math.toRadians(angle));
- }
-
- /**
- * Method returns a cross point between ellipse and a line (from center point
- * with angle between the line and X axis).
- *
- * @param x
- * x coordinate of the ellipse
- * @param y
- * y coordinate of the ellipse
- * @param width
- * width of the ellipse
- * @param height
- * height of the ellipse
- * @param angle
- * angle in degrees
- * @return point on the ellipse that connect center of the ellipse with the
- * line that cross X axis by angle
- */
- public Point2D getPointOnEllipseByDegree(final double x, final double y, final double width, final double height, final double angle) {
- return getPointOnEllipseByRadian(x, y, width, height, Math.toRadians(angle));
- }
-
- /**
- * Method returns a cross point between ellipse and a line (from center point
- * with angle between the line and X axis).
- *
- * @param x
- * x coordinate of the ellipse
- * @param y
- * y coordinate of the ellipse
- * @param width
- * width of the ellipse
- * @param height
- * height of the ellipse
- * @param angle
- * angle in radians
- * @return point on the ellipse that connect center of the ellipse with the
- * line that cross X axis by angle
- */
- public Point2D getPointOnEllipseByRadian(final double x, final double y, final double width, final double height, final double angle) {
- double boundedAngle = angle;
-
- while (boundedAngle < 0) {
- boundedAngle += 2 * Math.PI;
- }
- while (boundedAngle > (2 * Math.PI - Configuration.EPSILON)) {
- boundedAngle -= 2 * Math.PI;
- }
- Point2D result = new Point2D.Double();
-
- double a = width / 2;
- double b = height / 2;
-
- double resX = 0;
- double resY = 0;
- // special cases (atan is infinity)
- if (Math.abs(boundedAngle - 0) < Configuration.EPSILON) {
- resX = -a;
- resY = 0;
- } else if (Math.abs(boundedAngle - PI) < Configuration.EPSILON) {
- resX = a;
- resY = 0;
- } else if (Math.abs(boundedAngle - PI_1_2) < Configuration.EPSILON) {
- resX = 0;
- resY = -b;
- } else if (Math.abs(boundedAngle - PI_3_2) < Configuration.EPSILON) {
- resX = 0;
- resY = b;
- } else {
- double tan = Math.tan(boundedAngle);
-
- resX = a * b / Math.sqrt(b * b + a * a * tan * tan);
- resY = resX * tan;
- if (boundedAngle <= PI_1_2 || boundedAngle > PI_3_2) {
- resX = -resX;
- resY = -resY;
- }
- }
-
- resX += x + a;
- resY += y + b;
-
- result.setLocation(resX, resY);
- return result;
- }
-
- /**
- * Method returns a cross point between ellipse and a line (from center point
- * with angle between the line and X axis).
- *
- * @param ellipse
- * ellipse object on which we want to find point
- * @param angle
- * angle in radians
- * @return point on the ellipse that connect center of the ellipse with the
- * line that cross X axis by angle
- */
- public Point2D getPointOnEllipseByRadian(final Ellipse2D ellipse, final double angle) {
- double width = ellipse.getWidth();
- double height = ellipse.getHeight();
-
- return getPointOnEllipseByRadian(ellipse.getX(), ellipse.getY(), width, height, angle);
- }
-}
+package lcsb.mapviewer.common.geometry;
+
+import java.awt.geom.Ellipse2D;
+import java.awt.geom.Point2D;
+
+import lcsb.mapviewer.common.Configuration;
+
+import org.apache.log4j.Logger;
+
+/**
+ * This class contains basic operators on ellipse used by converters.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class EllipseTransformation {
+ /**
+ * PI value.
+ */
+ private static final double PI = Math.PI;
+ /**
+ * PI/2 value.
+ */
+ private static final double PI_1_2 = Math.PI / 2;
+ /**
+ * 3/2 PI value.
+ */
+ private static final double PI_3_2 = PI_1_2 * 3;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(EllipseTransformation.class.getName());
+
+ /**
+ * Method returns a cross point between ellipse and a line (from center point
+ * with angle between the line and X axis).
+ *
+ * @param ellipse
+ * ellipse object on which we want to find point
+ * @param angle
+ * angle in degrees
+ * @return point on the ellipse that connect center of the ellipse with the
+ * line that cross X axis by angle
+ */
+ public Point2D getPointOnEllipseByDegree(final Ellipse2D ellipse, final double angle) {
+ return getPointOnEllipseByRadian(ellipse, Math.toRadians(angle));
+ }
+
+ /**
+ * Method returns a cross point between ellipse and a line (from center point
+ * with angle between the line and X axis).
+ *
+ * @param x
+ * x coordinate of the ellipse
+ * @param y
+ * y coordinate of the ellipse
+ * @param width
+ * width of the ellipse
+ * @param height
+ * height of the ellipse
+ * @param angle
+ * angle in degrees
+ * @return point on the ellipse that connect center of the ellipse with the
+ * line that cross X axis by angle
+ */
+ public Point2D getPointOnEllipseByDegree(final double x, final double y, final double width, final double height, final double angle) {
+ return getPointOnEllipseByRadian(x, y, width, height, Math.toRadians(angle));
+ }
+
+ /**
+ * Method returns a cross point between ellipse and a line (from center point
+ * with angle between the line and X axis).
+ *
+ * @param x
+ * x coordinate of the ellipse
+ * @param y
+ * y coordinate of the ellipse
+ * @param width
+ * width of the ellipse
+ * @param height
+ * height of the ellipse
+ * @param angle
+ * angle in radians
+ * @return point on the ellipse that connect center of the ellipse with the
+ * line that cross X axis by angle
+ */
+ public Point2D getPointOnEllipseByRadian(final double x, final double y, final double width, final double height, final double angle) {
+ double boundedAngle = angle;
+
+ while (boundedAngle < 0) {
+ boundedAngle += 2 * Math.PI;
+ }
+ while (boundedAngle > (2 * Math.PI - Configuration.EPSILON)) {
+ boundedAngle -= 2 * Math.PI;
+ }
+ Point2D result = new Point2D.Double();
+
+ double a = width / 2;
+ double b = height / 2;
+
+ double resX = 0;
+ double resY = 0;
+ // special cases (atan is infinity)
+ if (Math.abs(boundedAngle - 0) < Configuration.EPSILON) {
+ resX = -a;
+ resY = 0;
+ } else if (Math.abs(boundedAngle - PI) < Configuration.EPSILON) {
+ resX = a;
+ resY = 0;
+ } else if (Math.abs(boundedAngle - PI_1_2) < Configuration.EPSILON) {
+ resX = 0;
+ resY = -b;
+ } else if (Math.abs(boundedAngle - PI_3_2) < Configuration.EPSILON) {
+ resX = 0;
+ resY = b;
+ } else {
+ double tan = Math.tan(boundedAngle);
+
+ resX = a * b / Math.sqrt(b * b + a * a * tan * tan);
+ resY = resX * tan;
+ if (boundedAngle <= PI_1_2 || boundedAngle > PI_3_2) {
+ resX = -resX;
+ resY = -resY;
+ }
+ }
+
+ resX += x + a;
+ resY += y + b;
+
+ result.setLocation(resX, resY);
+ return result;
+ }
+
+ /**
+ * Method returns a cross point between ellipse and a line (from center point
+ * with angle between the line and X axis).
+ *
+ * @param ellipse
+ * ellipse object on which we want to find point
+ * @param angle
+ * angle in radians
+ * @return point on the ellipse that connect center of the ellipse with the
+ * line that cross X axis by angle
+ */
+ public Point2D getPointOnEllipseByRadian(final Ellipse2D ellipse, final double angle) {
+ double width = ellipse.getWidth();
+ double height = ellipse.getHeight();
+
+ return getPointOnEllipseByRadian(ellipse.getX(), ellipse.getY(), width, height, angle);
+ }
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/geometry/PointTransformation.java b/commons/src/main/java/lcsb/mapviewer/common/geometry/PointTransformation.java
index e307b58cb0..6472057afc 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/geometry/PointTransformation.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/geometry/PointTransformation.java
@@ -1,62 +1,62 @@
-package lcsb.mapviewer.common.geometry;
-
-import java.awt.geom.Point2D;
-
-import org.apache.log4j.Logger;
-
-/**
- * Class for basic point transformations.
- *
- * @author Piotr Gawron
- *
- */
-public class PointTransformation {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(PointTransformation.class.getName());
-
- /**
- * Rotates point around center using the angle.
- *
- * @param point
- * object that we want to rotate
- * @param angle
- * angle by which we want to rotate
- * @param center
- * central point around which we rotate the object
- * @return the same object rotated by the apropriate angle
- */
- public Point2D rotatePoint(final Point2D point, final double angle, final Point2D center) {
- double s = Math.sin(angle);
- double c = Math.cos(angle);
-
- // translate point back to origin:
-
- point.setLocation(point.getX() - center.getX(), point.getY() - center.getY());
-
- // rotate point
- double xnew = point.getX() * c - point.getY() * s;
- double ynew = point.getX() * s + point.getY() * c;
-
- // translate point back:
- point.setLocation(xnew + center.getX(), ynew + center.getY());
- return point;
- }
-
- /**
- * Checks if a point given in the parameter is valid (can be used for
- * drawing). The point is considered as valid if coordinates are finite (NaN
- * and Infinity are invalid - they cannot be drawn).
- *
- * @param point
- * point to check
- * @return <code>true</code> if coordinates are normal real numbers,
- * <code>false</code> otherwise (NaN, infinity)
- */
- public boolean isValidPoint(Point2D point) {
- return Double.isFinite(point.getX()) && Double.isFinite(point.getY());
- }
-
-}
+package lcsb.mapviewer.common.geometry;
+
+import java.awt.geom.Point2D;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Class for basic point transformations.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class PointTransformation {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(PointTransformation.class.getName());
+
+ /**
+ * Rotates point around center using the angle.
+ *
+ * @param point
+ * object that we want to rotate
+ * @param angle
+ * angle by which we want to rotate
+ * @param center
+ * central point around which we rotate the object
+ * @return the same object rotated by the apropriate angle
+ */
+ public Point2D rotatePoint(final Point2D point, final double angle, final Point2D center) {
+ double s = Math.sin(angle);
+ double c = Math.cos(angle);
+
+ // translate point back to origin:
+
+ point.setLocation(point.getX() - center.getX(), point.getY() - center.getY());
+
+ // rotate point
+ double xnew = point.getX() * c - point.getY() * s;
+ double ynew = point.getX() * s + point.getY() * c;
+
+ // translate point back:
+ point.setLocation(xnew + center.getX(), ynew + center.getY());
+ return point;
+ }
+
+ /**
+ * Checks if a point given in the parameter is valid (can be used for
+ * drawing). The point is considered as valid if coordinates are finite (NaN
+ * and Infinity are invalid - they cannot be drawn).
+ *
+ * @param point
+ * point to check
+ * @return <code>true</code> if coordinates are normal real numbers,
+ * <code>false</code> otherwise (NaN, infinity)
+ */
+ public boolean isValidPoint(Point2D point) {
+ return Double.isFinite(point.getX()) && Double.isFinite(point.getY());
+ }
+
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/geometry/TextAlignment.java b/commons/src/main/java/lcsb/mapviewer/common/geometry/TextAlignment.java
index 6b81396465..d4bfcdc62c 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/geometry/TextAlignment.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/geometry/TextAlignment.java
@@ -1,25 +1,25 @@
-package lcsb.mapviewer.common.geometry;
-
-/**
- * Enum defining type of alignment to be used.
- *
- * @author Piotr Gawron
- *
- */
-public enum TextAlignment {
-
- /**
- * Text should be aligned to left.
- */
- LEFT,
-
- /**
- * Text should be aligned to right.
- */
- RIGHT,
-
- /**
- * Text should be centered.
- */
- CENTER;
-}
+package lcsb.mapviewer.common.geometry;
+
+/**
+ * Enum defining type of alignment to be used.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum TextAlignment {
+
+ /**
+ * Text should be aligned to left.
+ */
+ LEFT,
+
+ /**
+ * Text should be aligned to right.
+ */
+ RIGHT,
+
+ /**
+ * Text should be centered.
+ */
+ CENTER;
+}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/geometry/package-info.java b/commons/src/main/java/lcsb/mapviewer/common/geometry/package-info.java
index 1151bf5aae..333ba68b32 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/geometry/package-info.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/geometry/package-info.java
@@ -1,12 +1,12 @@
-/**
- * Provides classes (with functionality not implemented in jre) that allows to
- * manipulate on the common geometry objects, like:
- * <ul>
- * <li>lines,</li>
- * <li>ellipses,</li>
- * <li>points,</li>
- * </ul>
- * .
- */
-package lcsb.mapviewer.common.geometry;
-
+/**
+ * Provides classes (with functionality not implemented in jre) that allows to
+ * manipulate on the common geometry objects, like:
+ * <ul>
+ * <li>lines,</li>
+ * <li>ellipses,</li>
+ * <li>points,</li>
+ * </ul>
+ * .
+ */
+package lcsb.mapviewer.common.geometry;
+
diff --git a/commons/src/main/java/lcsb/mapviewer/common/package-info.java b/commons/src/main/java/lcsb/mapviewer/common/package-info.java
index 55b5860687..fd4528e939 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/package-info.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/package-info.java
@@ -1,5 +1,5 @@
-/**
- * Common objects for the whole project that aren't related to the project.
- */
-package lcsb.mapviewer.common;
-
+/**
+ * Common objects for the whole project that aren't related to the project.
+ */
+package lcsb.mapviewer.common;
+
diff --git a/commons/src/test/java/lcsb/mapviewer/common/AllCommonTests.java b/commons/src/test/java/lcsb/mapviewer/common/AllCommonTests.java
index 561bc13f4a..8c28d00230 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/AllCommonTests.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/AllCommonTests.java
@@ -1,27 +1,27 @@
-package lcsb.mapviewer.common;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-import lcsb.mapviewer.common.comparator.AllComparatorTests;
-import lcsb.mapviewer.common.exception.AllExceptionTests;
-import lcsb.mapviewer.common.geometry.AllGeometryTests;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AllComparatorTests.class, //
- AllExceptionTests.class, //
- AllGeometryTests.class, //
- ConfigurationTest.class, //
- EventStorageLoggerAppenderTest.class, //
- HttpConnectionMethodTypeTest.class, //
- MimeTypeTest.class, //
- ObjectUtilsTest.class, //
- PairTest.class, //
- SystemClipboardTest.class, //
- TextFileUtilsTest.class, //
- XmlParserTest.class, //
-})
-public class AllCommonTests {
-
-}
+package lcsb.mapviewer.common;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+import lcsb.mapviewer.common.comparator.AllComparatorTests;
+import lcsb.mapviewer.common.exception.AllExceptionTests;
+import lcsb.mapviewer.common.geometry.AllGeometryTests;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AllComparatorTests.class, //
+ AllExceptionTests.class, //
+ AllGeometryTests.class, //
+ ConfigurationTest.class, //
+ EventStorageLoggerAppenderTest.class, //
+ HttpConnectionMethodTypeTest.class, //
+ MimeTypeTest.class, //
+ ObjectUtilsTest.class, //
+ PairTest.class, //
+ SystemClipboardTest.class, //
+ TextFileUtilsTest.class, //
+ XmlParserTest.class, //
+})
+public class AllCommonTests {
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/CommonTestFunctions.java b/commons/src/test/java/lcsb/mapviewer/common/CommonTestFunctions.java
index f002f8cad2..d702ff7dfe 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/CommonTestFunctions.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/CommonTestFunctions.java
@@ -1,36 +1,36 @@
-package lcsb.mapviewer.common;
-
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.apache.log4j.spi.LoggingEvent;
-import org.junit.After;
-import org.junit.Before;
-
-import lcsb.mapviewer.common.EventStorageLoggerAppender;
-
-public class CommonTestFunctions {
-
- private EventStorageLoggerAppender appender;
-
- @Before
- public final void _setUp() throws Exception {
- Logger.getRootLogger().removeAppender(appender);
- appender = new EventStorageLoggerAppender();
- Logger.getRootLogger().addAppender(appender);
- }
-
- @After
- public final void _tearDown() throws Exception {
- Logger.getRootLogger().removeAppender(appender);
- }
-
- protected List<LoggingEvent> getWarnings() {
- return appender.getWarnings();
- }
-
- protected List<LoggingEvent> getErrors() {
- return appender.getErrors();
- }
-
-}
+package lcsb.mapviewer.common;
+
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.apache.log4j.spi.LoggingEvent;
+import org.junit.After;
+import org.junit.Before;
+
+import lcsb.mapviewer.common.EventStorageLoggerAppender;
+
+public class CommonTestFunctions {
+
+ private EventStorageLoggerAppender appender;
+
+ @Before
+ public final void _setUp() throws Exception {
+ Logger.getRootLogger().removeAppender(appender);
+ appender = new EventStorageLoggerAppender();
+ Logger.getRootLogger().addAppender(appender);
+ }
+
+ @After
+ public final void _tearDown() throws Exception {
+ Logger.getRootLogger().removeAppender(appender);
+ }
+
+ protected List<LoggingEvent> getWarnings() {
+ return appender.getWarnings();
+ }
+
+ protected List<LoggingEvent> getErrors() {
+ return appender.getErrors();
+ }
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/ConfigurationTest.java b/commons/src/test/java/lcsb/mapviewer/common/ConfigurationTest.java
index 14b510510c..a1e6ba03e7 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/ConfigurationTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/ConfigurationTest.java
@@ -1,127 +1,127 @@
-package lcsb.mapviewer.common;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-
-import java.io.File;
-import java.lang.reflect.Constructor;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ConfigurationTest extends CommonTestFunctions{
-
- Logger logger = Logger.getLogger(ConfigurationTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetters() {
- Configuration.setApplicationCacheOn(false);
- assertFalse(Configuration.isApplicationCacheOn());
- Configuration.setAutocompleteSize(1);
- assertEquals(1, Configuration.getAutocompleteSize());
- Configuration.setDbCacheOn(false);
- assertFalse(Configuration.isDbCacheOn());
- }
-
- @Test
- public void testLoadSystemBuildVersion() {
- Configuration.loadSystemVersion((String) null);
- assertEquals("Unknown", Configuration.getSystemBuildVersion(null));
- assertEquals("Unknown", Configuration.getSystemBuild(null));
- assertEquals("Unknown", Configuration.getSystemVersion(null));
- }
-
- @Test
- public void testLoadSystemBuildVersion2() {
- Configuration.loadSystemVersion((String) null);
- Configuration.loadSystemVersion(new File("unknown.xxx"));
- assertEquals("Unknown", Configuration.getSystemBuildVersion(null));
- assertEquals("Unknown", Configuration.getSystemBuild(null));
- assertEquals("Unknown", Configuration.getSystemVersion(null));
- }
-
- @Test
- public void testGetSystemBuildVersion() {
- assertEquals("100", Configuration.getSystemBuildVersion("testFiles/version/", true));
- assertEquals("100", Configuration.getSystemBuildVersion(null, false));
- assertEquals("101", Configuration.getSystemVersion("testFiles/version/", true));
- }
-
- @Test
- public void testGetSystemBuild() {
- assertEquals("102", Configuration.getSystemBuild("testFiles/version/", true));
- assertEquals("102", Configuration.getSystemBuild(null, false));
- }
-
- @Test
- public void testXGetSystemVersion() {
- List<String> frame = new ArrayList<>();
- frame.add("test");
- Configuration.setxFrameDomain(frame);
- assertEquals(frame, Configuration.getxFrameDomain());
- }
-
- @Test
- public void testWebAppDir() {
- String dir = "test2";
- Configuration.setWebAppDir(dir);
- assertEquals(dir, Configuration.getWebAppDir());
- }
-
-
- @Test
- public void testLoadInvalidSystemBuildVersion() {
- Configuration.loadSystemBuildVersion(new File("invalid_path"));
- assertEquals(1, super.getErrors().size());
- }
-
- @Test
- public void testLoadInvalidSystemVersion() {
- Configuration.loadSystemVersion(new File("testFiles/version/INVALID_CHANGELOG"));
- assertEquals(1, super.getErrors().size());
- }
-
- @Test
- public void testGetFrameworkVersion() {
- FrameworkVersion version = Configuration.getFrameworkVersion(null);
- assertEquals("Unknown", version.getGitVersion());
- assertEquals("Unknown", version.getTime());
- assertEquals("Unknown", version.getVersion());
- }
-
- @Test
- public void testGetMemorySaturationRatioTriggerClean() {
- double newRatio = 33;
- double oldRatio = Configuration.getMemorySaturationRatioTriggerClean();
- try {
- Configuration.setMemorySaturationRatioTriggerClean(newRatio);
- assertEquals(newRatio, Configuration.getMemorySaturationRatioTriggerClean(), Configuration.EPSILON);
- } finally {
- Configuration.setMemorySaturationRatioTriggerClean(oldRatio);
- }
- }
-
- @Test
- public void testPrivateConstructor() throws Exception {
- try {
- Constructor<?> constr = Configuration.class.getDeclaredConstructor(new Class<?>[] {});
- constr.setAccessible(true);
- assertNotNull(constr.newInstance(new Object[] {}));
- } catch (Exception e) {
- throw e;
- }
- }
-}
+package lcsb.mapviewer.common;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+
+import java.io.File;
+import java.lang.reflect.Constructor;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ConfigurationTest extends CommonTestFunctions{
+
+ Logger logger = Logger.getLogger(ConfigurationTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetters() {
+ Configuration.setApplicationCacheOn(false);
+ assertFalse(Configuration.isApplicationCacheOn());
+ Configuration.setAutocompleteSize(1);
+ assertEquals(1, Configuration.getAutocompleteSize());
+ Configuration.setDbCacheOn(false);
+ assertFalse(Configuration.isDbCacheOn());
+ }
+
+ @Test
+ public void testLoadSystemBuildVersion() {
+ Configuration.loadSystemVersion((String) null);
+ assertEquals("Unknown", Configuration.getSystemBuildVersion(null));
+ assertEquals("Unknown", Configuration.getSystemBuild(null));
+ assertEquals("Unknown", Configuration.getSystemVersion(null));
+ }
+
+ @Test
+ public void testLoadSystemBuildVersion2() {
+ Configuration.loadSystemVersion((String) null);
+ Configuration.loadSystemVersion(new File("unknown.xxx"));
+ assertEquals("Unknown", Configuration.getSystemBuildVersion(null));
+ assertEquals("Unknown", Configuration.getSystemBuild(null));
+ assertEquals("Unknown", Configuration.getSystemVersion(null));
+ }
+
+ @Test
+ public void testGetSystemBuildVersion() {
+ assertEquals("100", Configuration.getSystemBuildVersion("testFiles/version/", true));
+ assertEquals("100", Configuration.getSystemBuildVersion(null, false));
+ assertEquals("101", Configuration.getSystemVersion("testFiles/version/", true));
+ }
+
+ @Test
+ public void testGetSystemBuild() {
+ assertEquals("102", Configuration.getSystemBuild("testFiles/version/", true));
+ assertEquals("102", Configuration.getSystemBuild(null, false));
+ }
+
+ @Test
+ public void testXGetSystemVersion() {
+ List<String> frame = new ArrayList<>();
+ frame.add("test");
+ Configuration.setxFrameDomain(frame);
+ assertEquals(frame, Configuration.getxFrameDomain());
+ }
+
+ @Test
+ public void testWebAppDir() {
+ String dir = "test2";
+ Configuration.setWebAppDir(dir);
+ assertEquals(dir, Configuration.getWebAppDir());
+ }
+
+
+ @Test
+ public void testLoadInvalidSystemBuildVersion() {
+ Configuration.loadSystemBuildVersion(new File("invalid_path"));
+ assertEquals(1, super.getErrors().size());
+ }
+
+ @Test
+ public void testLoadInvalidSystemVersion() {
+ Configuration.loadSystemVersion(new File("testFiles/version/INVALID_CHANGELOG"));
+ assertEquals(1, super.getErrors().size());
+ }
+
+ @Test
+ public void testGetFrameworkVersion() {
+ FrameworkVersion version = Configuration.getFrameworkVersion(null);
+ assertEquals("Unknown", version.getGitVersion());
+ assertEquals("Unknown", version.getTime());
+ assertEquals("Unknown", version.getVersion());
+ }
+
+ @Test
+ public void testGetMemorySaturationRatioTriggerClean() {
+ double newRatio = 33;
+ double oldRatio = Configuration.getMemorySaturationRatioTriggerClean();
+ try {
+ Configuration.setMemorySaturationRatioTriggerClean(newRatio);
+ assertEquals(newRatio, Configuration.getMemorySaturationRatioTriggerClean(), Configuration.EPSILON);
+ } finally {
+ Configuration.setMemorySaturationRatioTriggerClean(oldRatio);
+ }
+ }
+
+ @Test
+ public void testPrivateConstructor() throws Exception {
+ try {
+ Constructor<?> constr = Configuration.class.getDeclaredConstructor(new Class<?>[] {});
+ constr.setAccessible(true);
+ assertNotNull(constr.newInstance(new Object[] {}));
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/EventStorageLoggerAppenderTest.java b/commons/src/test/java/lcsb/mapviewer/common/EventStorageLoggerAppenderTest.java
index 8d09a890f9..d03f01a0fc 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/EventStorageLoggerAppenderTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/EventStorageLoggerAppenderTest.java
@@ -1,61 +1,61 @@
-package lcsb.mapviewer.common;
-
-import static org.junit.Assert.assertEquals;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class EventStorageLoggerAppenderTest {
- Logger logger = Logger.getLogger(EventStorageLoggerAppenderTest.class);
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testLogCatching() {
- try {
- EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
- logger.addAppender(appender);
- logger.warn("test");
- logger.debug("1");
- logger.error("2");
- logger.info("3");
- logger.fatal("4");
- logger.trace("5");
- assertEquals(1, appender.getWarnings().size());
- assertEquals(1, appender.getFatals().size());
- assertEquals(1, appender.getErrors().size());
- logger.removeAppender(appender);
- logger.warn("test");
- assertEquals(1, appender.getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
- appender.requiresLayout();
- appender.close();
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.common;
+
+import static org.junit.Assert.assertEquals;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class EventStorageLoggerAppenderTest {
+ Logger logger = Logger.getLogger(EventStorageLoggerAppenderTest.class);
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testLogCatching() {
+ try {
+ EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
+ logger.addAppender(appender);
+ logger.warn("test");
+ logger.debug("1");
+ logger.error("2");
+ logger.info("3");
+ logger.fatal("4");
+ logger.trace("5");
+ assertEquals(1, appender.getWarnings().size());
+ assertEquals(1, appender.getFatals().size());
+ assertEquals(1, appender.getErrors().size());
+ logger.removeAppender(appender);
+ logger.warn("test");
+ assertEquals(1, appender.getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
+ appender.requiresLayout();
+ appender.close();
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/HttpConnectionMethodTypeTest.java b/commons/src/test/java/lcsb/mapviewer/common/HttpConnectionMethodTypeTest.java
index 9789b766e9..2723073007 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/HttpConnectionMethodTypeTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/HttpConnectionMethodTypeTest.java
@@ -1,29 +1,29 @@
-package lcsb.mapviewer.common;
-
-import static org.junit.Assert.*;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class HttpConnectionMethodTypeTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testValidValues() {
- for (HttpConnectionMethodType type : HttpConnectionMethodType.values()) {
- assertNotNull(type);
-
- // for coverage tests
- HttpConnectionMethodType.valueOf(type.toString());
- }
- }
-
-}
+package lcsb.mapviewer.common;
+
+import static org.junit.Assert.*;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class HttpConnectionMethodTypeTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testValidValues() {
+ for (HttpConnectionMethodType type : HttpConnectionMethodType.values()) {
+ assertNotNull(type);
+
+ // for coverage tests
+ HttpConnectionMethodType.valueOf(type.toString());
+ }
+ }
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/MimeTypeTest.java b/commons/src/test/java/lcsb/mapviewer/common/MimeTypeTest.java
index 9087471b07..50189c2ae3 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/MimeTypeTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/MimeTypeTest.java
@@ -1,32 +1,32 @@
-package lcsb.mapviewer.common;
-
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class MimeTypeTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testValidValues() {
- for (MimeType type : MimeType.values()) {
- assertNotNull(type);
- assertNotNull(type.getTextRepresentation());
- assertFalse(type.getTextRepresentation().isEmpty());
-
- //for coverage tests
- MimeType.valueOf(type.toString());
- }
- }
-
-}
+package lcsb.mapviewer.common;
+
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class MimeTypeTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testValidValues() {
+ for (MimeType type : MimeType.values()) {
+ assertNotNull(type);
+ assertNotNull(type.getTextRepresentation());
+ assertFalse(type.getTextRepresentation().isEmpty());
+
+ //for coverage tests
+ MimeType.valueOf(type.toString());
+ }
+ }
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/ObjectUtilsTest.java b/commons/src/test/java/lcsb/mapviewer/common/ObjectUtilsTest.java
index 71ee157432..ff8b79effc 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/ObjectUtilsTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/ObjectUtilsTest.java
@@ -1,58 +1,58 @@
-package lcsb.mapviewer.common;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import java.lang.reflect.Constructor;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-
-public class ObjectUtilsTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetIdOfObject() {
- Object obj = new Object() {
- @SuppressWarnings("unused")
- public int getId() {
- return 107;
- }
- };
- assertEquals((Integer) 107, ObjectUtils.getIdOfObject(obj));
- }
-
- @Test
- public void testGetIdOfObjectWithoutId() {
- Object obj = new Object();
- try {
- ObjectUtils.getIdOfObject(obj);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- }
- }
-
- @Test
- public void testPrivateConstructor() throws Exception {
- try {
- Constructor<?> constr = ObjectUtils.class.getDeclaredConstructor(new Class<?>[] {});
- constr.setAccessible(true);
- assertNotNull(constr.newInstance(new Object[] {}));
- } catch (Exception e) {
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.common;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import java.lang.reflect.Constructor;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+
+public class ObjectUtilsTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetIdOfObject() {
+ Object obj = new Object() {
+ @SuppressWarnings("unused")
+ public int getId() {
+ return 107;
+ }
+ };
+ assertEquals((Integer) 107, ObjectUtils.getIdOfObject(obj));
+ }
+
+ @Test
+ public void testGetIdOfObjectWithoutId() {
+ Object obj = new Object();
+ try {
+ ObjectUtils.getIdOfObject(obj);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ }
+ }
+
+ @Test
+ public void testPrivateConstructor() throws Exception {
+ try {
+ Constructor<?> constr = ObjectUtils.class.getDeclaredConstructor(new Class<?>[] {});
+ constr.setAccessible(true);
+ assertNotNull(constr.newInstance(new Object[] {}));
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/PairTest.java b/commons/src/test/java/lcsb/mapviewer/common/PairTest.java
index 286787b3f2..33178d5e6a 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/PairTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/PairTest.java
@@ -1,70 +1,70 @@
-package lcsb.mapviewer.common;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class PairTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testConstructor() {
- Pair<String, Integer> pair = new Pair<String, Integer>("test str", 12);
- assertEquals("test str", pair.getLeft());
- assertEquals((Integer) 12, pair.getRight());
- }
-
- @Test
- public void testEquals() {
- Pair<String, Integer> pair = new Pair<String, Integer>("test str", 12);
- Pair<String, Integer> pair2 = new Pair<String, Integer>("test str", 12);
- Pair<String, String> pair3 = new Pair<String, String>("test str", "str");
- Pair<String, Integer> pair4 = new Pair<String, Integer>("test str", 124);
- Pair<String, Integer> pair5 = new Pair<String, Integer>("test str1", 12);
- assertTrue(pair.equals(pair2));
- assertFalse(pair.equals(pair3));
- assertFalse(pair.equals(pair4));
- assertFalse(pair.equals(pair5));
-
- assertTrue(pair2.equals(pair));
- assertFalse(pair3.equals(pair));
- assertFalse(pair4.equals(pair));
- assertFalse(pair5.equals(pair));
- assertFalse(pair4.equals(new Object()));
- }
-
- @Test
- public void testHashCode() {
- Pair<String, Integer> pair = new Pair<String, Integer>("test str", 12);
- Pair<String, Integer> pair2 = new Pair<String, Integer>("test str", 12);
- Pair<String, Integer> pair3 = new Pair<String, Integer>("test str", 124);
- assertEquals(pair.hashCode(), pair2.hashCode());
- assertTrue(pair.hashCode() != pair3.hashCode());
- }
-
- @Test
- public void testNullEquals() {
- Pair<String, Integer> pair = new Pair<String, Integer>("test str", 12);
- Pair<String, Integer> pair2 = null;
- assertFalse(pair.equals(pair2));
- }
-
- @Test
- public void testToString() {
- Pair<String, Integer> pair = new Pair<String, Integer>("test str", 12);
- assertTrue(pair.toString().contains(pair.getLeft().toString()));
- assertTrue(pair.toString().contains(pair.getRight().toString()));
- }
-
-}
+package lcsb.mapviewer.common;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class PairTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testConstructor() {
+ Pair<String, Integer> pair = new Pair<String, Integer>("test str", 12);
+ assertEquals("test str", pair.getLeft());
+ assertEquals((Integer) 12, pair.getRight());
+ }
+
+ @Test
+ public void testEquals() {
+ Pair<String, Integer> pair = new Pair<String, Integer>("test str", 12);
+ Pair<String, Integer> pair2 = new Pair<String, Integer>("test str", 12);
+ Pair<String, String> pair3 = new Pair<String, String>("test str", "str");
+ Pair<String, Integer> pair4 = new Pair<String, Integer>("test str", 124);
+ Pair<String, Integer> pair5 = new Pair<String, Integer>("test str1", 12);
+ assertTrue(pair.equals(pair2));
+ assertFalse(pair.equals(pair3));
+ assertFalse(pair.equals(pair4));
+ assertFalse(pair.equals(pair5));
+
+ assertTrue(pair2.equals(pair));
+ assertFalse(pair3.equals(pair));
+ assertFalse(pair4.equals(pair));
+ assertFalse(pair5.equals(pair));
+ assertFalse(pair4.equals(new Object()));
+ }
+
+ @Test
+ public void testHashCode() {
+ Pair<String, Integer> pair = new Pair<String, Integer>("test str", 12);
+ Pair<String, Integer> pair2 = new Pair<String, Integer>("test str", 12);
+ Pair<String, Integer> pair3 = new Pair<String, Integer>("test str", 124);
+ assertEquals(pair.hashCode(), pair2.hashCode());
+ assertTrue(pair.hashCode() != pair3.hashCode());
+ }
+
+ @Test
+ public void testNullEquals() {
+ Pair<String, Integer> pair = new Pair<String, Integer>("test str", 12);
+ Pair<String, Integer> pair2 = null;
+ assertFalse(pair.equals(pair2));
+ }
+
+ @Test
+ public void testToString() {
+ Pair<String, Integer> pair = new Pair<String, Integer>("test str", 12);
+ assertTrue(pair.toString().contains(pair.getLeft().toString()));
+ assertTrue(pair.toString().contains(pair.getRight().toString()));
+ }
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/SystemClipboardTest.java b/commons/src/test/java/lcsb/mapviewer/common/SystemClipboardTest.java
index 604262c4cf..88ba17059b 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/SystemClipboardTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/SystemClipboardTest.java
@@ -1,98 +1,98 @@
-package lcsb.mapviewer.common;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
-
-import java.awt.Toolkit;
-import java.awt.datatransfer.Clipboard;
-import java.awt.datatransfer.DataFlavor;
-import java.awt.datatransfer.Transferable;
-import java.awt.datatransfer.UnsupportedFlavorException;
-import java.io.IOException;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class SystemClipboardTest {
- Logger logger = Logger.getLogger(SystemClipboardTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testClipboard() throws Exception {
- try {
- SystemClipboard sc = new SystemClipboard();
- sc.setClipboardContents("TEST");
-
- SystemClipboard sc2 = new SystemClipboard();
- assertEquals("TEST",sc2.getClipboardContents());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidClipboard() throws Exception {
- try {
- SystemClipboard sc2 = new SystemClipboard();
-
- Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
- clipboard.setContents(new Transferable() {
-
- @Override
- public boolean isDataFlavorSupported(DataFlavor flavor) {
- return true;
- }
-
- @Override
- public DataFlavor[] getTransferDataFlavors() {
- return null;
- }
-
- @Override
- public Object getTransferData(DataFlavor flavor) throws UnsupportedFlavorException, IOException {
- throw new UnsupportedFlavorException(flavor);
- }
- }, sc2);
-
- assertEquals(null,sc2.getClipboardContents());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testLostOwnership() throws Exception {
- try {
- SystemClipboard sc = new SystemClipboard();
- sc.lostOwnership(null, null);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testEmpty() throws Exception {
- try {
- SystemClipboard sc2 = new SystemClipboard();
- sc2.setClipboardContents(null);
- assertNull(sc2.getClipboardContents());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
-}
+package lcsb.mapviewer.common;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.Transferable;
+import java.awt.datatransfer.UnsupportedFlavorException;
+import java.io.IOException;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class SystemClipboardTest {
+ Logger logger = Logger.getLogger(SystemClipboardTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testClipboard() throws Exception {
+ try {
+ SystemClipboard sc = new SystemClipboard();
+ sc.setClipboardContents("TEST");
+
+ SystemClipboard sc2 = new SystemClipboard();
+ assertEquals("TEST",sc2.getClipboardContents());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidClipboard() throws Exception {
+ try {
+ SystemClipboard sc2 = new SystemClipboard();
+
+ Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
+ clipboard.setContents(new Transferable() {
+
+ @Override
+ public boolean isDataFlavorSupported(DataFlavor flavor) {
+ return true;
+ }
+
+ @Override
+ public DataFlavor[] getTransferDataFlavors() {
+ return null;
+ }
+
+ @Override
+ public Object getTransferData(DataFlavor flavor) throws UnsupportedFlavorException, IOException {
+ throw new UnsupportedFlavorException(flavor);
+ }
+ }, sc2);
+
+ assertEquals(null,sc2.getClipboardContents());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testLostOwnership() throws Exception {
+ try {
+ SystemClipboard sc = new SystemClipboard();
+ sc.lostOwnership(null, null);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testEmpty() throws Exception {
+ try {
+ SystemClipboard sc2 = new SystemClipboard();
+ sc2.setClipboardContents(null);
+ assertNull(sc2.getClipboardContents());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/TextFileUtilsTest.java b/commons/src/test/java/lcsb/mapviewer/common/TextFileUtilsTest.java
index 9eafbad9a8..f7e8851f8c 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/TextFileUtilsTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/TextFileUtilsTest.java
@@ -1,78 +1,78 @@
-package lcsb.mapviewer.common;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-
-import java.io.ByteArrayInputStream;
-import java.io.FileInputStream;
-import java.io.InputStream;
-import java.lang.reflect.Constructor;
-import java.nio.charset.StandardCharsets;
-import java.util.Map;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class TextFileUtilsTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetHeaderParametersFromFile() throws Exception {
- try {
- String fileContent = "#header\n" + //
- "#param1=value1\n" + //
- "#\n" + //
- "no header\n" + //
- "#param2=value\n";
-
- Map<String, String> params = TextFileUtils.getHeaderParametersFromFile(new ByteArrayInputStream(fileContent.getBytes(StandardCharsets.UTF_8)));
- assertTrue(params.keySet().size() >= 1);
- assertNull(params.get("param2"));
- assertEquals("value1", params.get("param1"));
- assertNull(params.get("header"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseHeader() throws Exception {
- try {
- InputStream is = new FileInputStream("testFiles/fileHeader.txt");
- Map<String, String> map = TextFileUtils.getHeaderParametersFromFile(is);
-
- assertEquals("1.0", map.get("VERSION"));
- assertEquals("example name", map.get("NAME"));
- assertEquals("layout description", map.get("DESCRIPTION"));
- assertEquals("", map.get("MISSING"));
- assertEquals("A=B", map.get("TRICKY"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testPrivateConstructor() throws Exception {
- try {
- Constructor<?> constr = TextFileUtils.class.getDeclaredConstructor(new Class<?>[] {});
- constr.setAccessible(true);
- assertNotNull(constr.newInstance(new Object[] {}));
- } catch (Exception e) {
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.common;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+
+import java.io.ByteArrayInputStream;
+import java.io.FileInputStream;
+import java.io.InputStream;
+import java.lang.reflect.Constructor;
+import java.nio.charset.StandardCharsets;
+import java.util.Map;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class TextFileUtilsTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetHeaderParametersFromFile() throws Exception {
+ try {
+ String fileContent = "#header\n" + //
+ "#param1=value1\n" + //
+ "#\n" + //
+ "no header\n" + //
+ "#param2=value\n";
+
+ Map<String, String> params = TextFileUtils.getHeaderParametersFromFile(new ByteArrayInputStream(fileContent.getBytes(StandardCharsets.UTF_8)));
+ assertTrue(params.keySet().size() >= 1);
+ assertNull(params.get("param2"));
+ assertEquals("value1", params.get("param1"));
+ assertNull(params.get("header"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseHeader() throws Exception {
+ try {
+ InputStream is = new FileInputStream("testFiles/fileHeader.txt");
+ Map<String, String> map = TextFileUtils.getHeaderParametersFromFile(is);
+
+ assertEquals("1.0", map.get("VERSION"));
+ assertEquals("example name", map.get("NAME"));
+ assertEquals("layout description", map.get("DESCRIPTION"));
+ assertEquals("", map.get("MISSING"));
+ assertEquals("A=B", map.get("TRICKY"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testPrivateConstructor() throws Exception {
+ try {
+ Constructor<?> constr = TextFileUtils.class.getDeclaredConstructor(new Class<?>[] {});
+ constr.setAccessible(true);
+ assertNotNull(constr.newInstance(new Object[] {}));
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/XmlParserTest.java b/commons/src/test/java/lcsb/mapviewer/common/XmlParserTest.java
index 5e2188cfd4..a2bd25fb39 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/XmlParserTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/XmlParserTest.java
@@ -1,474 +1,474 @@
-package lcsb.mapviewer.common;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.awt.Color;
-import java.io.ByteArrayInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.lang.reflect.Field;
-import java.nio.charset.StandardCharsets;
-import java.util.List;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
-
-import org.apache.log4j.Logger;
-import org.apache.xerces.dom.DocumentImpl;
-import org.apache.xerces.dom.ElementImpl;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.w3c.dom.Document;
-import org.w3c.dom.Element;
-import org.w3c.dom.NamedNodeMap;
-import org.w3c.dom.Node;
-import org.xml.sax.InputSource;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-
-public class XmlParserTest {
- Logger logger = Logger.getLogger(XmlParserTest.class);
-
- XmlParser parser = new XmlParser();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testColorParsing() {
- try {
- String strColor = "ffcbcd09";
-
- Color c = parser.stringToColor(strColor);
- String resultString = parser.colorToString(c);
- assertTrue("Different string representation: " + strColor + " - " + resultString, strColor.equalsIgnoreCase(resultString));
-
- Color c2 = parser.stringToColor(resultString);
-
- assertEquals(c.getRed(), c2.getRed());
- assertEquals(c.getGreen(), c2.getGreen());
- assertEquals(c.getBlue(), c2.getBlue());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidColorParsing() {
- try {
- String strColor = "hello world";
-
- parser.stringToColor(strColor);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testColorParsingWithAlpha() {
- try {
- String strColor = "fecbcd09";
-
- Color c = parser.stringToColor(strColor);
- String resultString = parser.colorToString(c);
- assertTrue("Different string representation: " + strColor + " - " + resultString, strColor.equalsIgnoreCase(resultString));
-
- Color c2 = parser.stringToColor(resultString);
-
- assertEquals(c.getRed(), c2.getRed());
- assertEquals(c.getGreen(), c2.getGreen());
- assertEquals(c.getBlue(), c2.getBlue());
- assertEquals(c.getAlpha(), c2.getAlpha());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetXmlDocumentFromString() throws Exception {
- try {
- Document validDoc = parser.getXmlDocumentFromString("<node>test</node>");
- assertNotNull(validDoc);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testNodeToString() throws Exception {
- try {
- String xml = "<test_node>test_x</test_node>";
- Document validDoc = parser.getXmlDocumentFromString(xml);
- String str = parser.nodeToString(validDoc);
- assertEquals(xml.trim(), str.trim());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testEmptyNodeToString() throws Exception {
- try {
- String str = parser.nodeToString(null);
- assertNull(str);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testNodeToStringWithHeader() throws Exception {
- try {
- String xml = "<test_node>test_x</test_node>";
- Document validDoc = parser.getXmlDocumentFromString(xml);
- String str = parser.nodeToString(validDoc, true);
- assertTrue(str.contains(xml));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidNodeToString() throws Exception {
- try {
- final DocumentImpl xmlDoc = new DocumentImpl();
-
- Element root = xmlDoc.createElement("booking");
-
- class Tmp extends ElementImpl {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- public Tmp() {
- this.ownerDocument = xmlDoc;
- }
-
- @Override
- public NamedNodeMap getAttributes() {
- return null;
- }
-
- }
- ;
- Element el = new Tmp();
- root.appendChild(el);
- assertNotNull(parser.nodeToString(root, true));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetXmlDocumentFromInvalidString() throws Exception {
- try {
- parser.getXmlDocumentFromString("<node>test<node>");
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetXmlDocumentFromInvalidInputStream() throws Exception {
- try {
- parser.getXmlDocumentFromInputSource(new InputSource());
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testEscapeXml() throws Exception {
- try {
- String str = parser.escapeXml("<xml>node</xml>");
- assertFalse(str.contains("<"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testEscapeNullXml() throws Exception {
- try {
- String str = parser.escapeXml(null);
- assertNull(str);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testFileToString() throws Exception {
- try {
- String str = parser.fileToString("testFiles/test.txt");
- assertTrue(str.contains("test"));
- assertTrue(str.contains("file"));
- assertTrue(str.contains("with some content"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testInputStreamToString() throws Exception {
- try {
- InputStream stream = new ByteArrayInputStream("stream string".getBytes(StandardCharsets.UTF_8));
- String str = parser.inputStreamToString(stream);
- assertEquals("stream string", str);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetNodeValue() throws Exception {
- try {
- Document document = parser.getXmlDocumentFromString("<node>content</node>");
- Node node = parser.getNode("node", document);
- String str = parser.getNodeValue(node);
- assertEquals("content", str);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetNodeValue2() throws Exception {
- try {
- String str = parser.getNodeValue(null);
- assertEquals("", str);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetNodeValue3() throws Exception {
- try {
- Document document = parser.getXmlDocumentFromString("<node></node>");
- Node node = parser.getNode("node", document);
- String str = parser.getNodeValue(node);
- assertEquals("", str);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetNodeValue4() throws Exception {
- try {
- Document document = parser.getXmlDocumentFromString("<node><subnode/></node>");
- Node node = parser.getNode("node", document);
- String str = parser.getNodeValue(node);
- assertEquals("", str);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testInputStreamToStringThrowsException() throws Exception {
- try {
- parser.inputStreamToString(new InputStream() {
- @Override
- public int read() throws IOException {
- throw new IOException();
- }
- });
- fail("Exception expected");
- } catch (IOException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testFileToStringThrowsException() throws Exception {
- try {
- parser.fileToString("testFiles/unknown file.txt");
- fail("Exception expected");
- } catch (IOException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetNodeAttr() throws Exception {
- try {
- Document document = parser.getXmlDocumentFromString("<node attr=\"val\">content</node>");
- Node node = parser.getNode("node", document);
- String str = parser.getNodeAttr("attr", node);
- assertEquals("val", str);
- str = parser.getNodeAttr("attr2", node);
- assertEquals("", str);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetNodes() throws Exception {
- try {
- Document document = parser.getXmlDocumentFromString("<node><subnode>content1</subnode><subnode>content2</subnode><other/></node>");
- Node node = parser.getNode("node", document);
- List<Node> nodes = parser.getNodes("subnode", node.getChildNodes());
- assertEquals(2, nodes.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetNode() throws Exception {
- try {
- Document document = parser.getXmlDocumentFromString("<node><subnode>content1</subnode><subnode>content2</subnode><other/></node>");
- Node node = parser.getNode("node", document);
- Node child = parser.getNode("other", node.getChildNodes());
- assertNotNull(child);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetNode2() throws Exception {
- try {
- Document document = parser.getXmlDocumentFromString("<node attr=\"x\"><subnode>content1</subnode><subnode>content2</subnode><other/></node>");
- Node node = parser.getNode("node", document);
- Node child = parser.getNode("other2", node.getChildNodes());
- assertNull(child);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetNode3() throws Exception {
- try {
- Document document = parser.getXmlDocumentFromString("<node attr=\"x\">xxx</node>");
- Node node = parser.getNode("node", document);
- Node child = parser.getNode("other2", node.getChildNodes());
- assertNull(child);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testExceptionInConstructor() throws Exception {
- DocumentBuilderFactory factory = null;
- Field privateStringField = XmlParser.class.getDeclaredField("documentBuilderFactory");
- try {
-
- privateStringField.setAccessible(true);
-
- factory = (DocumentBuilderFactory) privateStringField.get(parser);
- privateStringField.set(parser, new DocumentBuilderFactory() {
-
- @Override
- public void setFeature(String name, boolean value) throws ParserConfigurationException {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void setAttribute(String name, Object value) throws IllegalArgumentException {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public DocumentBuilder newDocumentBuilder() throws ParserConfigurationException {
- throw new ParserConfigurationException();
- }
-
- @Override
- public boolean getFeature(String name) throws ParserConfigurationException {
- // TODO Auto-generated method stub
- return false;
- }
-
- @Override
- public Object getAttribute(String name) throws IllegalArgumentException {
- // TODO Auto-generated method stub
- return null;
- }
- });
- new XmlParser();
- fail("Exception expected");
- } catch (InvalidStateException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- privateStringField.set(parser, factory);
- }
- }
-
-}
+package lcsb.mapviewer.common;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.awt.Color;
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.lang.reflect.Field;
+import java.nio.charset.StandardCharsets;
+import java.util.List;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.apache.log4j.Logger;
+import org.apache.xerces.dom.DocumentImpl;
+import org.apache.xerces.dom.ElementImpl;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.w3c.dom.NamedNodeMap;
+import org.w3c.dom.Node;
+import org.xml.sax.InputSource;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+
+public class XmlParserTest {
+ Logger logger = Logger.getLogger(XmlParserTest.class);
+
+ XmlParser parser = new XmlParser();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testColorParsing() {
+ try {
+ String strColor = "ffcbcd09";
+
+ Color c = parser.stringToColor(strColor);
+ String resultString = parser.colorToString(c);
+ assertTrue("Different string representation: " + strColor + " - " + resultString, strColor.equalsIgnoreCase(resultString));
+
+ Color c2 = parser.stringToColor(resultString);
+
+ assertEquals(c.getRed(), c2.getRed());
+ assertEquals(c.getGreen(), c2.getGreen());
+ assertEquals(c.getBlue(), c2.getBlue());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidColorParsing() {
+ try {
+ String strColor = "hello world";
+
+ parser.stringToColor(strColor);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testColorParsingWithAlpha() {
+ try {
+ String strColor = "fecbcd09";
+
+ Color c = parser.stringToColor(strColor);
+ String resultString = parser.colorToString(c);
+ assertTrue("Different string representation: " + strColor + " - " + resultString, strColor.equalsIgnoreCase(resultString));
+
+ Color c2 = parser.stringToColor(resultString);
+
+ assertEquals(c.getRed(), c2.getRed());
+ assertEquals(c.getGreen(), c2.getGreen());
+ assertEquals(c.getBlue(), c2.getBlue());
+ assertEquals(c.getAlpha(), c2.getAlpha());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetXmlDocumentFromString() throws Exception {
+ try {
+ Document validDoc = parser.getXmlDocumentFromString("<node>test</node>");
+ assertNotNull(validDoc);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testNodeToString() throws Exception {
+ try {
+ String xml = "<test_node>test_x</test_node>";
+ Document validDoc = parser.getXmlDocumentFromString(xml);
+ String str = parser.nodeToString(validDoc);
+ assertEquals(xml.trim(), str.trim());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testEmptyNodeToString() throws Exception {
+ try {
+ String str = parser.nodeToString(null);
+ assertNull(str);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testNodeToStringWithHeader() throws Exception {
+ try {
+ String xml = "<test_node>test_x</test_node>";
+ Document validDoc = parser.getXmlDocumentFromString(xml);
+ String str = parser.nodeToString(validDoc, true);
+ assertTrue(str.contains(xml));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidNodeToString() throws Exception {
+ try {
+ final DocumentImpl xmlDoc = new DocumentImpl();
+
+ Element root = xmlDoc.createElement("booking");
+
+ class Tmp extends ElementImpl {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ public Tmp() {
+ this.ownerDocument = xmlDoc;
+ }
+
+ @Override
+ public NamedNodeMap getAttributes() {
+ return null;
+ }
+
+ }
+ ;
+ Element el = new Tmp();
+ root.appendChild(el);
+ assertNotNull(parser.nodeToString(root, true));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetXmlDocumentFromInvalidString() throws Exception {
+ try {
+ parser.getXmlDocumentFromString("<node>test<node>");
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetXmlDocumentFromInvalidInputStream() throws Exception {
+ try {
+ parser.getXmlDocumentFromInputSource(new InputSource());
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testEscapeXml() throws Exception {
+ try {
+ String str = parser.escapeXml("<xml>node</xml>");
+ assertFalse(str.contains("<"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testEscapeNullXml() throws Exception {
+ try {
+ String str = parser.escapeXml(null);
+ assertNull(str);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testFileToString() throws Exception {
+ try {
+ String str = parser.fileToString("testFiles/test.txt");
+ assertTrue(str.contains("test"));
+ assertTrue(str.contains("file"));
+ assertTrue(str.contains("with some content"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testInputStreamToString() throws Exception {
+ try {
+ InputStream stream = new ByteArrayInputStream("stream string".getBytes(StandardCharsets.UTF_8));
+ String str = parser.inputStreamToString(stream);
+ assertEquals("stream string", str);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetNodeValue() throws Exception {
+ try {
+ Document document = parser.getXmlDocumentFromString("<node>content</node>");
+ Node node = parser.getNode("node", document);
+ String str = parser.getNodeValue(node);
+ assertEquals("content", str);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetNodeValue2() throws Exception {
+ try {
+ String str = parser.getNodeValue(null);
+ assertEquals("", str);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetNodeValue3() throws Exception {
+ try {
+ Document document = parser.getXmlDocumentFromString("<node></node>");
+ Node node = parser.getNode("node", document);
+ String str = parser.getNodeValue(node);
+ assertEquals("", str);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetNodeValue4() throws Exception {
+ try {
+ Document document = parser.getXmlDocumentFromString("<node><subnode/></node>");
+ Node node = parser.getNode("node", document);
+ String str = parser.getNodeValue(node);
+ assertEquals("", str);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testInputStreamToStringThrowsException() throws Exception {
+ try {
+ parser.inputStreamToString(new InputStream() {
+ @Override
+ public int read() throws IOException {
+ throw new IOException();
+ }
+ });
+ fail("Exception expected");
+ } catch (IOException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testFileToStringThrowsException() throws Exception {
+ try {
+ parser.fileToString("testFiles/unknown file.txt");
+ fail("Exception expected");
+ } catch (IOException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetNodeAttr() throws Exception {
+ try {
+ Document document = parser.getXmlDocumentFromString("<node attr=\"val\">content</node>");
+ Node node = parser.getNode("node", document);
+ String str = parser.getNodeAttr("attr", node);
+ assertEquals("val", str);
+ str = parser.getNodeAttr("attr2", node);
+ assertEquals("", str);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetNodes() throws Exception {
+ try {
+ Document document = parser.getXmlDocumentFromString("<node><subnode>content1</subnode><subnode>content2</subnode><other/></node>");
+ Node node = parser.getNode("node", document);
+ List<Node> nodes = parser.getNodes("subnode", node.getChildNodes());
+ assertEquals(2, nodes.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetNode() throws Exception {
+ try {
+ Document document = parser.getXmlDocumentFromString("<node><subnode>content1</subnode><subnode>content2</subnode><other/></node>");
+ Node node = parser.getNode("node", document);
+ Node child = parser.getNode("other", node.getChildNodes());
+ assertNotNull(child);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetNode2() throws Exception {
+ try {
+ Document document = parser.getXmlDocumentFromString("<node attr=\"x\"><subnode>content1</subnode><subnode>content2</subnode><other/></node>");
+ Node node = parser.getNode("node", document);
+ Node child = parser.getNode("other2", node.getChildNodes());
+ assertNull(child);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetNode3() throws Exception {
+ try {
+ Document document = parser.getXmlDocumentFromString("<node attr=\"x\">xxx</node>");
+ Node node = parser.getNode("node", document);
+ Node child = parser.getNode("other2", node.getChildNodes());
+ assertNull(child);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testExceptionInConstructor() throws Exception {
+ DocumentBuilderFactory factory = null;
+ Field privateStringField = XmlParser.class.getDeclaredField("documentBuilderFactory");
+ try {
+
+ privateStringField.setAccessible(true);
+
+ factory = (DocumentBuilderFactory) privateStringField.get(parser);
+ privateStringField.set(parser, new DocumentBuilderFactory() {
+
+ @Override
+ public void setFeature(String name, boolean value) throws ParserConfigurationException {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void setAttribute(String name, Object value) throws IllegalArgumentException {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public DocumentBuilder newDocumentBuilder() throws ParserConfigurationException {
+ throw new ParserConfigurationException();
+ }
+
+ @Override
+ public boolean getFeature(String name) throws ParserConfigurationException {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public Object getAttribute(String name) throws IllegalArgumentException {
+ // TODO Auto-generated method stub
+ return null;
+ }
+ });
+ new XmlParser();
+ fail("Exception expected");
+ } catch (InvalidStateException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ privateStringField.set(parser, factory);
+ }
+ }
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/comparator/AllComparatorTests.java b/commons/src/test/java/lcsb/mapviewer/common/comparator/AllComparatorTests.java
index a82e7c0355..3922a2b20b 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/comparator/AllComparatorTests.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/comparator/AllComparatorTests.java
@@ -1,21 +1,21 @@
-package lcsb.mapviewer.common.comparator;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ BooleanComparatorTest.class, //
- ColorComparatorTest.class, //
- DoubleComparatorTest.class, //
- EnumComparatorTest.class, //
- IntegerComparatorTest.class, //
- PointComparatorTest.class, //
- StringComparatorTest.class, //
- StringListComparatorTest.class, //
- StringSetComparatorTest.class, //
- SetComparatorTest.class,//
-})
-public class AllComparatorTests {
-
-}
+package lcsb.mapviewer.common.comparator;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ BooleanComparatorTest.class, //
+ ColorComparatorTest.class, //
+ DoubleComparatorTest.class, //
+ EnumComparatorTest.class, //
+ IntegerComparatorTest.class, //
+ PointComparatorTest.class, //
+ StringComparatorTest.class, //
+ StringListComparatorTest.class, //
+ StringSetComparatorTest.class, //
+ SetComparatorTest.class,//
+})
+public class AllComparatorTests {
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/comparator/BooleanComparatorTest.java b/commons/src/test/java/lcsb/mapviewer/common/comparator/BooleanComparatorTest.java
index 87d0984b9d..d8329fcc9c 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/comparator/BooleanComparatorTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/comparator/BooleanComparatorTest.java
@@ -1,36 +1,36 @@
-package lcsb.mapviewer.common.comparator;
-
-import static org.junit.Assert.*;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class BooleanComparatorTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testNotNullComparison() {
- BooleanComparator comp = new BooleanComparator();
- assertTrue(comp.compare(new Boolean(true), new Boolean(true)) == 0);
- assertTrue(comp.compare(new Boolean(false), new Boolean(false)) == 0);
- assertFalse(comp.compare(new Boolean(false), new Boolean(true)) == 0);
- assertFalse(comp.compare(new Boolean(true), new Boolean(false)) == 0);
- }
-
- @Test
- public void testNullComparison() {
- BooleanComparator comp = new BooleanComparator();
- assertTrue(comp.compare(null, null) == 0);
- assertFalse(comp.compare(new Boolean(false), null) == 0);
- assertFalse(comp.compare(null, new Boolean(false)) == 0);
- }
-
-}
+package lcsb.mapviewer.common.comparator;
+
+import static org.junit.Assert.*;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class BooleanComparatorTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testNotNullComparison() {
+ BooleanComparator comp = new BooleanComparator();
+ assertTrue(comp.compare(new Boolean(true), new Boolean(true)) == 0);
+ assertTrue(comp.compare(new Boolean(false), new Boolean(false)) == 0);
+ assertFalse(comp.compare(new Boolean(false), new Boolean(true)) == 0);
+ assertFalse(comp.compare(new Boolean(true), new Boolean(false)) == 0);
+ }
+
+ @Test
+ public void testNullComparison() {
+ BooleanComparator comp = new BooleanComparator();
+ assertTrue(comp.compare(null, null) == 0);
+ assertFalse(comp.compare(new Boolean(false), null) == 0);
+ assertFalse(comp.compare(null, new Boolean(false)) == 0);
+ }
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/comparator/ColorComparatorTest.java b/commons/src/test/java/lcsb/mapviewer/common/comparator/ColorComparatorTest.java
index 5d82f57c79..febdaff65a 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/comparator/ColorComparatorTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/comparator/ColorComparatorTest.java
@@ -1,38 +1,38 @@
-package lcsb.mapviewer.common.comparator;
-
-import static org.junit.Assert.*;
-
-import java.awt.Color;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ColorComparatorTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testNotNullComparison() {
- ColorComparator comp = new ColorComparator();
- assertTrue(comp.compare(Color.BLACK, Color.BLACK) == 0);
- assertTrue(comp.compare(Color.RED, Color.RED) == 0);
- assertFalse(comp.compare(Color.RED, Color.BLACK) == 0);
- assertFalse(comp.compare(Color.BLACK, Color.RED) == 0);
- }
-
- @Test
- public void testNullComparison() {
- ColorComparator comp = new ColorComparator();
- assertTrue(comp.compare(null, null) == 0);
- assertFalse(comp.compare(Color.RED, null) == 0);
- assertFalse(comp.compare(null, Color.RED) == 0);
- }
-
-}
+package lcsb.mapviewer.common.comparator;
+
+import static org.junit.Assert.*;
+
+import java.awt.Color;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ColorComparatorTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testNotNullComparison() {
+ ColorComparator comp = new ColorComparator();
+ assertTrue(comp.compare(Color.BLACK, Color.BLACK) == 0);
+ assertTrue(comp.compare(Color.RED, Color.RED) == 0);
+ assertFalse(comp.compare(Color.RED, Color.BLACK) == 0);
+ assertFalse(comp.compare(Color.BLACK, Color.RED) == 0);
+ }
+
+ @Test
+ public void testNullComparison() {
+ ColorComparator comp = new ColorComparator();
+ assertTrue(comp.compare(null, null) == 0);
+ assertFalse(comp.compare(Color.RED, null) == 0);
+ assertFalse(comp.compare(null, Color.RED) == 0);
+ }
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/comparator/DoubleComparatorTest.java b/commons/src/test/java/lcsb/mapviewer/common/comparator/DoubleComparatorTest.java
index a1f9da671b..91243e054d 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/comparator/DoubleComparatorTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/comparator/DoubleComparatorTest.java
@@ -1,44 +1,44 @@
-package lcsb.mapviewer.common.comparator;
-
-import static org.junit.Assert.*;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class DoubleComparatorTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testNotNullComparison() {
- DoubleComparator comp = new DoubleComparator();
- assertTrue(comp.compare(new Double(5.01), new Double(5.01)) == 0);
- assertTrue(comp.compare(new Double(2.73), new Double(2.73)) == 0);
- assertFalse(comp.compare(new Double(2.73), new Double(5.01)) == 0);
- assertFalse(comp.compare(new Double(5.01), new Double(2.73)) == 0);
- }
-
- @Test
- public void testEpsilonComp() {
- DoubleComparator comp = new DoubleComparator(10);
- assertTrue(comp.compare(new Double(5.01), new Double(1.01)) == 0);
- assertFalse(comp.compare(new Double(2.73), new Double(-105.01)) == 0);
- assertTrue(comp.compare(new Double(5.01), new Double(-2.73)) == 0);
- }
-
- @Test
- public void testNullComparison() {
- DoubleComparator comp = new DoubleComparator();
- assertTrue(comp.compare(null, null) == 0);
- assertFalse(comp.compare(new Double(2.73), null) == 0);
- assertFalse(comp.compare(null, new Double(2.73)) == 0);
- }
-
-}
+package lcsb.mapviewer.common.comparator;
+
+import static org.junit.Assert.*;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class DoubleComparatorTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testNotNullComparison() {
+ DoubleComparator comp = new DoubleComparator();
+ assertTrue(comp.compare(new Double(5.01), new Double(5.01)) == 0);
+ assertTrue(comp.compare(new Double(2.73), new Double(2.73)) == 0);
+ assertFalse(comp.compare(new Double(2.73), new Double(5.01)) == 0);
+ assertFalse(comp.compare(new Double(5.01), new Double(2.73)) == 0);
+ }
+
+ @Test
+ public void testEpsilonComp() {
+ DoubleComparator comp = new DoubleComparator(10);
+ assertTrue(comp.compare(new Double(5.01), new Double(1.01)) == 0);
+ assertFalse(comp.compare(new Double(2.73), new Double(-105.01)) == 0);
+ assertTrue(comp.compare(new Double(5.01), new Double(-2.73)) == 0);
+ }
+
+ @Test
+ public void testNullComparison() {
+ DoubleComparator comp = new DoubleComparator();
+ assertTrue(comp.compare(null, null) == 0);
+ assertFalse(comp.compare(new Double(2.73), null) == 0);
+ assertFalse(comp.compare(null, new Double(2.73)) == 0);
+ }
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/comparator/IntegerComparatorTest.java b/commons/src/test/java/lcsb/mapviewer/common/comparator/IntegerComparatorTest.java
index e396de6274..65b7ab4653 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/comparator/IntegerComparatorTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/comparator/IntegerComparatorTest.java
@@ -1,35 +1,35 @@
-package lcsb.mapviewer.common.comparator;
-
-import static org.junit.Assert.*;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class IntegerComparatorTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testNotNullComparison() {
- IntegerComparator comp = new IntegerComparator();
- assertTrue(comp.compare(new Integer(13), new Integer(13)) == 0);
- assertTrue(comp.compare(new Integer(-59), new Integer(-59)) == 0);
- assertFalse(comp.compare(new Integer(-59), new Integer(13)) == 0);
- assertFalse(comp.compare(new Integer(13), new Integer(-59)) == 0);
- }
-
- @Test
- public void testNullComparison() {
- IntegerComparator comp = new IntegerComparator();
- assertTrue(comp.compare(null, null) == 0);
- assertFalse(comp.compare(new Integer(-59), null) == 0);
- assertFalse(comp.compare(null, new Integer(-59)) == 0);
- }
-}
+package lcsb.mapviewer.common.comparator;
+
+import static org.junit.Assert.*;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class IntegerComparatorTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testNotNullComparison() {
+ IntegerComparator comp = new IntegerComparator();
+ assertTrue(comp.compare(new Integer(13), new Integer(13)) == 0);
+ assertTrue(comp.compare(new Integer(-59), new Integer(-59)) == 0);
+ assertFalse(comp.compare(new Integer(-59), new Integer(13)) == 0);
+ assertFalse(comp.compare(new Integer(13), new Integer(-59)) == 0);
+ }
+
+ @Test
+ public void testNullComparison() {
+ IntegerComparator comp = new IntegerComparator();
+ assertTrue(comp.compare(null, null) == 0);
+ assertFalse(comp.compare(new Integer(-59), null) == 0);
+ assertFalse(comp.compare(null, new Integer(-59)) == 0);
+ }
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/comparator/PointComparatorTest.java b/commons/src/test/java/lcsb/mapviewer/common/comparator/PointComparatorTest.java
index 49ff29d5af..0d2097325e 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/comparator/PointComparatorTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/comparator/PointComparatorTest.java
@@ -1,47 +1,47 @@
-package lcsb.mapviewer.common.comparator;
-
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.geom.Point2D;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class PointComparatorTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testNotNullComparison() {
- PointComparator comp = new PointComparator();
- assertTrue(comp.compare(new Point2D.Double(106, 5.01), new Point2D.Double(106, 5.01)) == 0);
- assertTrue(comp.compare(new Point2D.Double(106, 2.73), new Point2D.Double(106, 2.73)) == 0);
- assertFalse(comp.compare(new Point2D.Double(106, 2.73), new Point2D.Double(106, 5.01)) == 0);
- assertFalse(comp.compare(new Point2D.Double(106, 5.01), new Point2D.Double(106, 2.73)) == 0);
- }
-
- @Test
- public void testEpsilonComp() {
- PointComparator comp = new PointComparator(10);
- assertTrue(comp.compare(new Point2D.Double(106, 5.01), new Point2D.Double(106, 1.01)) == 0);
- assertFalse(comp.compare(new Point2D.Double(106, 2.73), new Point2D.Double(106, -105.01)) == 0);
- assertTrue(comp.compare(new Point2D.Double(106, 5.01), new Point2D.Double(106, -2.73)) == 0);
- }
-
- @Test
- public void testNullComparison() {
- PointComparator comp = new PointComparator();
- assertTrue(comp.compare(null, null) == 0);
- assertFalse(comp.compare(new Point2D.Double(106, 2.73), null) == 0);
- assertFalse(comp.compare(null, new Point2D.Double(106, 2.73)) == 0);
- }
-
-}
+package lcsb.mapviewer.common.comparator;
+
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import java.awt.geom.Point2D;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class PointComparatorTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testNotNullComparison() {
+ PointComparator comp = new PointComparator();
+ assertTrue(comp.compare(new Point2D.Double(106, 5.01), new Point2D.Double(106, 5.01)) == 0);
+ assertTrue(comp.compare(new Point2D.Double(106, 2.73), new Point2D.Double(106, 2.73)) == 0);
+ assertFalse(comp.compare(new Point2D.Double(106, 2.73), new Point2D.Double(106, 5.01)) == 0);
+ assertFalse(comp.compare(new Point2D.Double(106, 5.01), new Point2D.Double(106, 2.73)) == 0);
+ }
+
+ @Test
+ public void testEpsilonComp() {
+ PointComparator comp = new PointComparator(10);
+ assertTrue(comp.compare(new Point2D.Double(106, 5.01), new Point2D.Double(106, 1.01)) == 0);
+ assertFalse(comp.compare(new Point2D.Double(106, 2.73), new Point2D.Double(106, -105.01)) == 0);
+ assertTrue(comp.compare(new Point2D.Double(106, 5.01), new Point2D.Double(106, -2.73)) == 0);
+ }
+
+ @Test
+ public void testNullComparison() {
+ PointComparator comp = new PointComparator();
+ assertTrue(comp.compare(null, null) == 0);
+ assertFalse(comp.compare(new Point2D.Double(106, 2.73), null) == 0);
+ assertFalse(comp.compare(null, new Point2D.Double(106, 2.73)) == 0);
+ }
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/comparator/StringComparatorTest.java b/commons/src/test/java/lcsb/mapviewer/common/comparator/StringComparatorTest.java
index 6e09a53cd4..88b635ee56 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/comparator/StringComparatorTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/comparator/StringComparatorTest.java
@@ -1,44 +1,44 @@
-package lcsb.mapviewer.common.comparator;
-
-import static org.junit.Assert.*;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class StringComparatorTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testNotNullComparison() {
- StringComparator comp = new StringComparator();
- assertTrue(comp.compare("test1", "test1") == 0);
- assertTrue(comp.compare("xxx3", "xxx3") == 0);
- assertFalse(comp.compare("xxx3", "test1") == 0);
- assertFalse(comp.compare("test1", "xxx3") == 0);
- }
-
- @Test
- public void testComparisonWithoutWhitespace() {
- StringComparator comp = new StringComparator();
- assertTrue(comp.compare("test1 32", "test1 32",true) == 0);
- assertTrue(comp.compare("test1\t32", "test1 \n32",true) == 0);
- assertFalse(comp.compare("test132", "test1 32",true) == 0);
- }
-
- @Test
- public void testNullComparison() {
- StringComparator comp = new StringComparator();
- assertTrue(comp.compare(null, null) == 0);
- assertFalse(comp.compare("xxx3", null) == 0);
- assertFalse(comp.compare(null, "xxx3") == 0);
- }
-
-}
+package lcsb.mapviewer.common.comparator;
+
+import static org.junit.Assert.*;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class StringComparatorTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testNotNullComparison() {
+ StringComparator comp = new StringComparator();
+ assertTrue(comp.compare("test1", "test1") == 0);
+ assertTrue(comp.compare("xxx3", "xxx3") == 0);
+ assertFalse(comp.compare("xxx3", "test1") == 0);
+ assertFalse(comp.compare("test1", "xxx3") == 0);
+ }
+
+ @Test
+ public void testComparisonWithoutWhitespace() {
+ StringComparator comp = new StringComparator();
+ assertTrue(comp.compare("test1 32", "test1 32",true) == 0);
+ assertTrue(comp.compare("test1\t32", "test1 \n32",true) == 0);
+ assertFalse(comp.compare("test132", "test1 32",true) == 0);
+ }
+
+ @Test
+ public void testNullComparison() {
+ StringComparator comp = new StringComparator();
+ assertTrue(comp.compare(null, null) == 0);
+ assertFalse(comp.compare("xxx3", null) == 0);
+ assertFalse(comp.compare(null, "xxx3") == 0);
+ }
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/comparator/StringListComparatorTest.java b/commons/src/test/java/lcsb/mapviewer/common/comparator/StringListComparatorTest.java
index 65771f6028..e22dbc1cb5 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/comparator/StringListComparatorTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/comparator/StringListComparatorTest.java
@@ -1,56 +1,56 @@
-package lcsb.mapviewer.common.comparator;
-
-import static org.junit.Assert.*;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class StringListComparatorTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
-
- @Test
- public void testNotNullComparisonEqualLength() {
- List<String> list1 = new ArrayList<>();
- List<String> list2 = new ArrayList<>();
- List<String> list3 = new ArrayList<>();
- list1.add("str1");
- list2.add("str2");
- list3.add("str1");
- StringListComparator comp = new StringListComparator();
- assertTrue(comp.compare(list1, list3) == 0);
- assertFalse(comp.compare(list1, list2) == 0);
- assertFalse(comp.compare(list2, list3) == 0);
- }
-
- @Test
- public void testNotNullComparisonDiffLength() {
- List<String> list1 = new ArrayList<>();
- List<String> list2 = new ArrayList<>();
- list1.add("str1");
- list2.add("str2");
- list2.add("str1");
- StringListComparator comp = new StringListComparator();
- assertFalse(comp.compare(list1, list2) == 0);
- }
-
- @Test
- public void testNullComparison() {
- StringListComparator comp = new StringListComparator();
- assertTrue(comp.compare(null, null) == 0);
- assertFalse(comp.compare(new ArrayList<>(), null) == 0);
- assertFalse(comp.compare(null, new ArrayList<>()) == 0);
- }
-
-}
+package lcsb.mapviewer.common.comparator;
+
+import static org.junit.Assert.*;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class StringListComparatorTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+
+ @Test
+ public void testNotNullComparisonEqualLength() {
+ List<String> list1 = new ArrayList<>();
+ List<String> list2 = new ArrayList<>();
+ List<String> list3 = new ArrayList<>();
+ list1.add("str1");
+ list2.add("str2");
+ list3.add("str1");
+ StringListComparator comp = new StringListComparator();
+ assertTrue(comp.compare(list1, list3) == 0);
+ assertFalse(comp.compare(list1, list2) == 0);
+ assertFalse(comp.compare(list2, list3) == 0);
+ }
+
+ @Test
+ public void testNotNullComparisonDiffLength() {
+ List<String> list1 = new ArrayList<>();
+ List<String> list2 = new ArrayList<>();
+ list1.add("str1");
+ list2.add("str2");
+ list2.add("str1");
+ StringListComparator comp = new StringListComparator();
+ assertFalse(comp.compare(list1, list2) == 0);
+ }
+
+ @Test
+ public void testNullComparison() {
+ StringListComparator comp = new StringListComparator();
+ assertTrue(comp.compare(null, null) == 0);
+ assertFalse(comp.compare(new ArrayList<>(), null) == 0);
+ assertFalse(comp.compare(null, new ArrayList<>()) == 0);
+ }
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/comparator/StringSetComparatorTest.java b/commons/src/test/java/lcsb/mapviewer/common/comparator/StringSetComparatorTest.java
index ceab74d187..d74ca665e1 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/comparator/StringSetComparatorTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/comparator/StringSetComparatorTest.java
@@ -1,61 +1,61 @@
-package lcsb.mapviewer.common.comparator;
-
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-
-import java.util.HashSet;
-import java.util.Set;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class StringSetComparatorTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testNotNullComparisonEqualLength() {
- Set<String> list1 = new HashSet<>();
- Set<String> list2 = new HashSet<>();
- Set<String> list3 = new HashSet<>();
- list1.add("str1");
- list1.add("x");
- list2.add("str2");
- list2.add("x");
- list3.add("x");
- list3.add("str1");
- StringSetComparator comp = new StringSetComparator();
- assertTrue(comp.compare(list1, list3) == 0);
- assertFalse(comp.compare(list1, list2) == 0);
- assertFalse(comp.compare(list2, list3) == 0);
- }
-
- @Test
- public void testNotNullComparisonDiffLength() {
- Set<String> list1 = new HashSet<>();
- Set<String> list2 = new HashSet<>();
- list1.add("str1");
- list2.add("str2");
- list2.add("str1");
- StringSetComparator comp = new StringSetComparator();
- assertFalse(comp.compare(list1, list2) == 0);
- assertFalse(comp.compare(list2, list1) == 0);
- }
-
- @Test
- public void testNullComparison() {
- StringSetComparator comp = new StringSetComparator();
- assertTrue(comp.compare(null, null) == 0);
- assertFalse(comp.compare(new HashSet<>(), null) == 0);
- assertFalse(comp.compare(null, new HashSet<>()) == 0);
- }
-
-
-}
+package lcsb.mapviewer.common.comparator;
+
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class StringSetComparatorTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testNotNullComparisonEqualLength() {
+ Set<String> list1 = new HashSet<>();
+ Set<String> list2 = new HashSet<>();
+ Set<String> list3 = new HashSet<>();
+ list1.add("str1");
+ list1.add("x");
+ list2.add("str2");
+ list2.add("x");
+ list3.add("x");
+ list3.add("str1");
+ StringSetComparator comp = new StringSetComparator();
+ assertTrue(comp.compare(list1, list3) == 0);
+ assertFalse(comp.compare(list1, list2) == 0);
+ assertFalse(comp.compare(list2, list3) == 0);
+ }
+
+ @Test
+ public void testNotNullComparisonDiffLength() {
+ Set<String> list1 = new HashSet<>();
+ Set<String> list2 = new HashSet<>();
+ list1.add("str1");
+ list2.add("str2");
+ list2.add("str1");
+ StringSetComparator comp = new StringSetComparator();
+ assertFalse(comp.compare(list1, list2) == 0);
+ assertFalse(comp.compare(list2, list1) == 0);
+ }
+
+ @Test
+ public void testNullComparison() {
+ StringSetComparator comp = new StringSetComparator();
+ assertTrue(comp.compare(null, null) == 0);
+ assertFalse(comp.compare(new HashSet<>(), null) == 0);
+ assertFalse(comp.compare(null, new HashSet<>()) == 0);
+ }
+
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/exception/AllExceptionTests.java b/commons/src/test/java/lcsb/mapviewer/common/exception/AllExceptionTests.java
index 78b1c8ebaf..c97eba1515 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/exception/AllExceptionTests.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/exception/AllExceptionTests.java
@@ -1,12 +1,12 @@
-package lcsb.mapviewer.common.exception;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ InvalidArgumentExceptionTest.class, InvalidClassExceptionTest.class, InvalidStateExceptionTest.class, InvalidXmlSchemaExceptionTest.class,
- NotImplementedExceptionTest.class })
-public class AllExceptionTests {
-
-}
+package lcsb.mapviewer.common.exception;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ InvalidArgumentExceptionTest.class, InvalidClassExceptionTest.class, InvalidStateExceptionTest.class, InvalidXmlSchemaExceptionTest.class,
+ NotImplementedExceptionTest.class })
+public class AllExceptionTests {
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/exception/InvalidArgumentExceptionTest.java b/commons/src/test/java/lcsb/mapviewer/common/exception/InvalidArgumentExceptionTest.java
index 70043e17e1..4f29bfe219 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/exception/InvalidArgumentExceptionTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/exception/InvalidArgumentExceptionTest.java
@@ -1,39 +1,39 @@
-package lcsb.mapviewer.common.exception;
-
-import static org.junit.Assert.*;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class InvalidArgumentExceptionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testConstructor1() {
- assertNotNull(new InvalidArgumentException());
- }
-
- @Test
- public void testConstructor2() {
- assertNotNull(new InvalidArgumentException("str"));
- }
-
- @Test
- public void testConstructor3() {
- assertNotNull(new InvalidArgumentException(new Exception()));
- }
-
- @Test
- public void testConstructor4() {
- assertNotNull(new InvalidArgumentException("dsr", new Exception()));
- }
-
-}
+package lcsb.mapviewer.common.exception;
+
+import static org.junit.Assert.*;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class InvalidArgumentExceptionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testConstructor1() {
+ assertNotNull(new InvalidArgumentException());
+ }
+
+ @Test
+ public void testConstructor2() {
+ assertNotNull(new InvalidArgumentException("str"));
+ }
+
+ @Test
+ public void testConstructor3() {
+ assertNotNull(new InvalidArgumentException(new Exception()));
+ }
+
+ @Test
+ public void testConstructor4() {
+ assertNotNull(new InvalidArgumentException("dsr", new Exception()));
+ }
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/exception/InvalidClassExceptionTest.java b/commons/src/test/java/lcsb/mapviewer/common/exception/InvalidClassExceptionTest.java
index 2b6bee2582..4dcb0c5896 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/exception/InvalidClassExceptionTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/exception/InvalidClassExceptionTest.java
@@ -1,29 +1,29 @@
-package lcsb.mapviewer.common.exception;
-
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class InvalidClassExceptionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testConstructor1() {
- assertNotNull(new InvalidClassException("str"));
- }
-
- @Test
- public void testConstructor2() {
- assertNotNull(new InvalidClassException("dsr", new Exception()));
- }
-
-}
+package lcsb.mapviewer.common.exception;
+
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class InvalidClassExceptionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testConstructor1() {
+ assertNotNull(new InvalidClassException("str"));
+ }
+
+ @Test
+ public void testConstructor2() {
+ assertNotNull(new InvalidClassException("dsr", new Exception()));
+ }
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/exception/InvalidStateExceptionTest.java b/commons/src/test/java/lcsb/mapviewer/common/exception/InvalidStateExceptionTest.java
index 4b5eaf6d5b..4ff04ade68 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/exception/InvalidStateExceptionTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/exception/InvalidStateExceptionTest.java
@@ -1,39 +1,39 @@
-package lcsb.mapviewer.common.exception;
-
-import static org.junit.Assert.*;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class InvalidStateExceptionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testConstructor1() {
- assertNotNull(new InvalidStateException());
- }
-
- @Test
- public void testConstructor2() {
- assertNotNull(new InvalidStateException("str"));
- }
-
- @Test
- public void testConstructor3() {
- assertNotNull(new InvalidStateException(new Exception()));
- }
-
- @Test
- public void testConstructor4() {
- assertNotNull(new InvalidStateException("dsr", new Exception()));
- }
-
-}
+package lcsb.mapviewer.common.exception;
+
+import static org.junit.Assert.*;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class InvalidStateExceptionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testConstructor1() {
+ assertNotNull(new InvalidStateException());
+ }
+
+ @Test
+ public void testConstructor2() {
+ assertNotNull(new InvalidStateException("str"));
+ }
+
+ @Test
+ public void testConstructor3() {
+ assertNotNull(new InvalidStateException(new Exception()));
+ }
+
+ @Test
+ public void testConstructor4() {
+ assertNotNull(new InvalidStateException("dsr", new Exception()));
+ }
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/exception/InvalidXmlSchemaExceptionTest.java b/commons/src/test/java/lcsb/mapviewer/common/exception/InvalidXmlSchemaExceptionTest.java
index 4548e61f40..95ae7bbc05 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/exception/InvalidXmlSchemaExceptionTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/exception/InvalidXmlSchemaExceptionTest.java
@@ -1,39 +1,39 @@
-package lcsb.mapviewer.common.exception;
-
-import static org.junit.Assert.*;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class InvalidXmlSchemaExceptionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testConstructor1() {
- assertNotNull(new InvalidXmlSchemaException());
- }
-
- @Test
- public void testConstructor2() {
- assertNotNull(new InvalidXmlSchemaException("str"));
- }
-
- @Test
- public void testConstructor3() {
- assertNotNull(new InvalidXmlSchemaException(new Exception()));
- }
-
- @Test
- public void testConstructor4() {
- assertNotNull(new InvalidXmlSchemaException("dsr", new Exception()));
- }
-
-}
+package lcsb.mapviewer.common.exception;
+
+import static org.junit.Assert.*;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class InvalidXmlSchemaExceptionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testConstructor1() {
+ assertNotNull(new InvalidXmlSchemaException());
+ }
+
+ @Test
+ public void testConstructor2() {
+ assertNotNull(new InvalidXmlSchemaException("str"));
+ }
+
+ @Test
+ public void testConstructor3() {
+ assertNotNull(new InvalidXmlSchemaException(new Exception()));
+ }
+
+ @Test
+ public void testConstructor4() {
+ assertNotNull(new InvalidXmlSchemaException("dsr", new Exception()));
+ }
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/exception/NotImplementedExceptionTest.java b/commons/src/test/java/lcsb/mapviewer/common/exception/NotImplementedExceptionTest.java
index 2aeabe5eee..17d933b020 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/exception/NotImplementedExceptionTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/exception/NotImplementedExceptionTest.java
@@ -1,29 +1,29 @@
-package lcsb.mapviewer.common.exception;
-
-import static org.junit.Assert.*;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class NotImplementedExceptionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testConstructor1() {
- assertNotNull(new NotImplementedException());
- }
-
- @Test
- public void testConstructor2() {
- assertNotNull(new NotImplementedException("str"));
- }
-
-}
+package lcsb.mapviewer.common.exception;
+
+import static org.junit.Assert.*;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class NotImplementedExceptionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testConstructor1() {
+ assertNotNull(new NotImplementedException());
+ }
+
+ @Test
+ public void testConstructor2() {
+ assertNotNull(new NotImplementedException("str"));
+ }
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/geometry/AllGeometryTests.java b/commons/src/test/java/lcsb/mapviewer/common/geometry/AllGeometryTests.java
index a6fe609f2e..2ea3ba8a69 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/geometry/AllGeometryTests.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/geometry/AllGeometryTests.java
@@ -1,17 +1,17 @@
-package lcsb.mapviewer.common.geometry;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ ColorParserTest.class, //
- CompositeStrokeTest.class, //
- EllipseTransformationTest.class, //
- LineTransformationTest.class, //
- PointTransformationTest.class, //
- TextAlignmentTest.class,//
-})
-public class AllGeometryTests {
-
-}
+package lcsb.mapviewer.common.geometry;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ ColorParserTest.class, //
+ CompositeStrokeTest.class, //
+ EllipseTransformationTest.class, //
+ LineTransformationTest.class, //
+ PointTransformationTest.class, //
+ TextAlignmentTest.class,//
+})
+public class AllGeometryTests {
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/geometry/ColorParserTest.java b/commons/src/test/java/lcsb/mapviewer/common/geometry/ColorParserTest.java
index 6fde224cd5..5f7f8a3e18 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/geometry/ColorParserTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/geometry/ColorParserTest.java
@@ -1,68 +1,68 @@
-package lcsb.mapviewer.common.geometry;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.fail;
-
-import java.awt.Color;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-
-public class ColorParserTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
-
- @Test
- public void testSetInvalidColor() throws Exception {
- try {
- ColorParser parser = new ColorParser();
- parser.parse("qwe");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetInvalidColor2() throws Exception {
- try {
- ColorParser parser = new ColorParser();
- parser.parse("fffffff");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetColor() throws Exception {
- try {
- ColorParser parser = new ColorParser();
- Color color = parser.parse("#ffffff");
- assertEquals(Color.WHITE, color);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.common.geometry;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.fail;
+
+import java.awt.Color;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+
+public class ColorParserTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+
+ @Test
+ public void testSetInvalidColor() throws Exception {
+ try {
+ ColorParser parser = new ColorParser();
+ parser.parse("qwe");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetInvalidColor2() throws Exception {
+ try {
+ ColorParser parser = new ColorParser();
+ parser.parse("fffffff");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetColor() throws Exception {
+ try {
+ ColorParser parser = new ColorParser();
+ Color color = parser.parse("#ffffff");
+ assertEquals(Color.WHITE, color);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/geometry/CompositeStrokeTest.java b/commons/src/test/java/lcsb/mapviewer/common/geometry/CompositeStrokeTest.java
index 95be640aff..a4251214cd 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/geometry/CompositeStrokeTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/geometry/CompositeStrokeTest.java
@@ -1,26 +1,26 @@
-package lcsb.mapviewer.common.geometry;
-
-import java.awt.BasicStroke;
-import java.awt.geom.Line2D;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class CompositeStrokeTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void test() {
- CompositeStroke cs = new CompositeStroke(new BasicStroke(10f), new BasicStroke(0.5f));
- cs.createStrokedShape(new Line2D.Double(0.1, 0.1, 0.1, 0.1));
- }
-
-}
+package lcsb.mapviewer.common.geometry;
+
+import java.awt.BasicStroke;
+import java.awt.geom.Line2D;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class CompositeStrokeTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void test() {
+ CompositeStroke cs = new CompositeStroke(new BasicStroke(10f), new BasicStroke(0.5f));
+ cs.createStrokedShape(new Line2D.Double(0.1, 0.1, 0.1, 0.1));
+ }
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/geometry/EllipseTransformationTest.java b/commons/src/test/java/lcsb/mapviewer/common/geometry/EllipseTransformationTest.java
index a87a4ae920..eeeca94a54 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/geometry/EllipseTransformationTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/geometry/EllipseTransformationTest.java
@@ -1,82 +1,82 @@
-package lcsb.mapviewer.common.geometry;
-
-import static org.junit.Assert.*;
-
-import java.awt.geom.Ellipse2D;
-import java.awt.geom.Point2D;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Configuration;
-
-public class EllipseTransformationTest {
- Logger logger = Logger.getLogger(EllipseTransformationTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testPointOnEllipse() {
- EllipseTransformation et = new EllipseTransformation();
- Point2D point = et.getPointOnEllipseByDegree(0, 0, 200, 200, 0);
- assertTrue(point.distance(0, 100) <= Configuration.EPSILON);
- }
-
- @Test
- public void testPointOnEllipse2() {
- EllipseTransformation et = new EllipseTransformation();
- Point2D point = et.getPointOnEllipseByDegree(0, 0, 200, 200, 90);
- assertTrue(point.distance(100, 0) <= Configuration.EPSILON);
- }
-
- @Test
- public void testPointOnEllipse3() {
- EllipseTransformation et = new EllipseTransformation();
- Point2D point = et.getPointOnEllipseByDegree(0, 0, 200, 200, 180);
- assertTrue(point.distance(200, 100) <= Configuration.EPSILON);
- }
-
- @Test
- public void testPointOnEllipse4() {
- EllipseTransformation et = new EllipseTransformation();
- Point2D point = et.getPointOnEllipseByDegree(0, 0, 200, 200, 270);
- assertTrue(point.distance(100, 200) <= Configuration.EPSILON);
- }
-
- @Test
- public void testPointOnEllipse5() {
- EllipseTransformation et = new EllipseTransformation();
- Point2D point = et.getPointOnEllipseByDegree(0, 0, 200, 200, 360);
- assertTrue(point.distance(0, 100) <= Configuration.EPSILON);
- }
-
- @Test
- public void testPointOnEllipse6() {
- EllipseTransformation et = new EllipseTransformation();
- Point2D point = et.getPointOnEllipseByDegree(0, 0, 200, 200, 300);
- assertNotNull(point);
- }
-
- @Test
- public void testPointOnEllipse7() {
- EllipseTransformation et = new EllipseTransformation();
- Point2D point = et.getPointOnEllipseByDegree(0, 0, 200, 200, -360);
- assertTrue(point.distance(0, 100) <= Configuration.EPSILON);
- }
-
- @Test
- public void testPointOnEllipse8() {
- EllipseTransformation et = new EllipseTransformation();
- Point2D point = et.getPointOnEllipseByDegree(new Ellipse2D.Double(0, 0, 200, 200), -360);
- assertTrue(point.distance(0, 100) <= Configuration.EPSILON);
- }
-
-}
+package lcsb.mapviewer.common.geometry;
+
+import static org.junit.Assert.*;
+
+import java.awt.geom.Ellipse2D;
+import java.awt.geom.Point2D;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+
+public class EllipseTransformationTest {
+ Logger logger = Logger.getLogger(EllipseTransformationTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testPointOnEllipse() {
+ EllipseTransformation et = new EllipseTransformation();
+ Point2D point = et.getPointOnEllipseByDegree(0, 0, 200, 200, 0);
+ assertTrue(point.distance(0, 100) <= Configuration.EPSILON);
+ }
+
+ @Test
+ public void testPointOnEllipse2() {
+ EllipseTransformation et = new EllipseTransformation();
+ Point2D point = et.getPointOnEllipseByDegree(0, 0, 200, 200, 90);
+ assertTrue(point.distance(100, 0) <= Configuration.EPSILON);
+ }
+
+ @Test
+ public void testPointOnEllipse3() {
+ EllipseTransformation et = new EllipseTransformation();
+ Point2D point = et.getPointOnEllipseByDegree(0, 0, 200, 200, 180);
+ assertTrue(point.distance(200, 100) <= Configuration.EPSILON);
+ }
+
+ @Test
+ public void testPointOnEllipse4() {
+ EllipseTransformation et = new EllipseTransformation();
+ Point2D point = et.getPointOnEllipseByDegree(0, 0, 200, 200, 270);
+ assertTrue(point.distance(100, 200) <= Configuration.EPSILON);
+ }
+
+ @Test
+ public void testPointOnEllipse5() {
+ EllipseTransformation et = new EllipseTransformation();
+ Point2D point = et.getPointOnEllipseByDegree(0, 0, 200, 200, 360);
+ assertTrue(point.distance(0, 100) <= Configuration.EPSILON);
+ }
+
+ @Test
+ public void testPointOnEllipse6() {
+ EllipseTransformation et = new EllipseTransformation();
+ Point2D point = et.getPointOnEllipseByDegree(0, 0, 200, 200, 300);
+ assertNotNull(point);
+ }
+
+ @Test
+ public void testPointOnEllipse7() {
+ EllipseTransformation et = new EllipseTransformation();
+ Point2D point = et.getPointOnEllipseByDegree(0, 0, 200, 200, -360);
+ assertTrue(point.distance(0, 100) <= Configuration.EPSILON);
+ }
+
+ @Test
+ public void testPointOnEllipse8() {
+ EllipseTransformation et = new EllipseTransformation();
+ Point2D point = et.getPointOnEllipseByDegree(new Ellipse2D.Double(0, 0, 200, 200), -360);
+ assertTrue(point.distance(0, 100) <= Configuration.EPSILON);
+ }
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/geometry/LineTransformationTest.java b/commons/src/test/java/lcsb/mapviewer/common/geometry/LineTransformationTest.java
index 433c975b4f..078abe6591 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/geometry/LineTransformationTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/geometry/LineTransformationTest.java
@@ -1,214 +1,214 @@
-package lcsb.mapviewer.common.geometry;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-
-import java.awt.Shape;
-import java.awt.geom.AffineTransform;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.Line2D;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
-import java.awt.geom.RoundRectangle2D;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Configuration;
-
-public class LineTransformationTest {
- static Logger logger = Logger.getLogger(LineTransformationTest.class);
- static double EPSILON = Configuration.EPSILON;
- LineTransformation lineTransformation = new LineTransformation();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testIntersection() {
- Shape s = new RoundRectangle2D.Double(0.0, 0.0, 100.0, 100.0, 10.0, 10.0);
- Line2D line = new Line2D.Double(50, 50, 50, 200);
- Point2D p = lineTransformation.getIntersectionWithPathIterator(line, s.getPathIterator(new AffineTransform()));
- Point2D intPoint = new Point2D.Double(50, 100);
- double dist = p.distance(intPoint);
- assertEquals("Invalid intersection point: " + p, 0, dist, EPSILON);
- }
-
- @Test
- public void testIntersectionWithBezierCurve() {
- double x = 0;
- double y = 0;
- double w = 100;
- double h = 200;
- GeneralPath path = new GeneralPath();
-
- path.moveTo((float) (x + 0.25 * w), (float) (y + 0.25 * h));
- path.quadTo((float) (x + 0.05 * w), (float) (y + 0.25 * h), x, (float) (y + 0.5 * h));
- path.curveTo(x, (float) (y + 0.66 * h), (float) (x + 0.18 * w), (float) (y + 0.9 * h), (float) (x + 0.31 * w), (float) (y + 0.8 * h));
- path.curveTo((float) (x + 0.4 * w), (y + h), (float) (x + 0.7 * w), (y + h), (float) (x + 0.8 * w), (float) (y + 0.8 * h));
- path.curveTo((x + w), (float) (y + 0.8 * h), (x + w), (float) (y + 0.6 * h), (float) (x + 0.875 * w), (float) (y + 0.5 * h));
- path.curveTo((x + w), (float) (y + 0.3 * h), (float) (x + 0.8 * w), (float) (y + 0.1 * h), (float) (x + 0.625 * w), (float) (y + 0.2 * h));
- path.curveTo((float) (x + 0.5 * w), (float) (y + 0.05 * h), (float) (x + 0.3 * w), (float) (y + 0.05 * h), (float) (x + 0.25 * w), (float) (y + 0.25 * h));
- path.closePath();
-
- Line2D line = new Line2D.Double(50, 50, 50, 300);
- Point2D p = lineTransformation.getIntersectionWithPathIterator(line, path.getPathIterator(new AffineTransform()));
- assertNotNull(p);
- }
-
- @Test
- public void testIntersectionToInvalidPath() {
- Line2D line = new Line2D.Double(50, 50, 50, 200);
- Point2D p = lineTransformation.getIntersectionWithPathIterator(line, null);
- assertNull(p);
-
- Shape s = new Rectangle2D.Double(0.0, 0.0, 10.0, 0.0);
- p = lineTransformation.getIntersectionWithPathIterator(line, s.getPathIterator(new AffineTransform()));
- assertNull(p);
-
- p = lineTransformation.getIntersectionWithPathIterator(line, new PathIterator() {
-
- @Override
- public void next() {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public boolean isDone() {
- return true;
- }
-
- @Override
- public int getWindingRule() {
- // TODO Auto-generated method stub
- return 0;
- }
-
- @Override
- public int currentSegment(double[] coords) {
- // TODO Auto-generated method stub
- return 0;
- }
-
- @Override
- public int currentSegment(float[] coords) {
- // TODO Auto-generated method stub
- return 0;
- }
- });
- assertNull(p);
- }
-
- @Test
- public void testDistance() {
- assertNotNull(lineTransformation);
- Point2D p1 = new Point2D.Double(2, 2);
- Point2D p2 = new Point2D.Double(3, 3);
- Point2D p3 = new Point2D.Double(4, 4);
-
- double dist = lineTransformation.distBetweenPointAndLineSegment(p1, p2, p3);
- double d = Math.sqrt(2);
- assertEquals(dist, d, EPSILON);
-
- p3 = new Point2D.Double(3, 4);
- dist = lineTransformation.distBetweenPointAndLineSegment(p1, p2, p3);
- assertEquals(dist, 1, EPSILON);
-
- p3 = new Point2D.Double(3, 3);
- dist = lineTransformation.distBetweenPointAndLineSegment(p1, p2, p3);
- assertEquals(dist, 0, EPSILON);
-
- p3 = new Point2D.Double(2.5, 2.5);
- dist = lineTransformation.distBetweenPointAndLineSegment(p1, p2, p3);
- assertEquals(dist, 0, EPSILON);
-
- p3 = new Point2D.Double(2, 2);
- dist = lineTransformation.distBetweenPointAndLineSegment(p1, p2, p3);
- assertEquals(dist, 0, EPSILON);
-
- p3 = new Point2D.Double(2, 0);
- dist = lineTransformation.distBetweenPointAndLineSegment(p1, p2, p3);
- assertEquals(dist, 2, EPSILON);
-
- p3 = new Point2D.Double(3, 2);
- dist = lineTransformation.distBetweenPointAndLineSegment(p1, p2, p3);
- d = Math.sqrt(0.5);
- assertEquals(dist, d, EPSILON);
-
- }
-
- @Test
- public void testDistanceToEmptyLine() {
- Point2D p1 = new Point2D.Double(2, 2);
- Point2D p2 = new Point2D.Double(3, 3);
- double dist = lineTransformation.distBetweenPointAndLineSegment(p1, p1, p2);
- assertEquals(p1.distance(p2), dist, EPSILON);
-
- // the same with line
- Line2D line = new Line2D.Double(p1, p1);
- dist = lineTransformation.distBetweenPointAndLineSegment(line, p2);
- assertEquals(p1.distance(p2), dist, EPSILON);
- }
-
- @Test
- public void testClosestPointOnSegmentLineToPointOnEmptyLine() {
- Point2D p1 = new Point2D.Double(2, 2);
- Point2D p2 = new Point2D.Double(3, 3);
- Point2D p3 = lineTransformation.closestPointOnSegmentLineToPoint(p1, p1, p2);
- assertEquals(p3, p1);
-
- // the same with line
- Line2D line = new Line2D.Double(p1, p1);
- p3 = lineTransformation.closestPointOnSegmentLineToPoint(line, p2);
- assertEquals(p3, p1);
-
- }
-
- @Test
- public void testClosestPoint() {
- assertNotNull(lineTransformation);
- Point2D p1 = new Point2D.Double(2, 2);
- Point2D p2 = new Point2D.Double(3, 3);
- Point2D p3 = new Point2D.Double(4, 4);
-
- Point2D res = lineTransformation.closestPointOnSegmentLineToPoint(p1, p2, p3);
- double d = Math.sqrt(2);
- assertEquals(res.distance(p3), d, EPSILON);
-
- p3 = new Point2D.Double(3, 4);
- res = lineTransformation.closestPointOnSegmentLineToPoint(p1, p2, p3);
- assertEquals(res.distance(p3), 1, EPSILON);
-
- p3 = new Point2D.Double(3, 3);
- res = lineTransformation.closestPointOnSegmentLineToPoint(p1, p2, p3);
- assertEquals(res.distance(p3), 0, EPSILON);
-
- p3 = new Point2D.Double(2.5, 2.5);
- res = lineTransformation.closestPointOnSegmentLineToPoint(p1, p2, p3);
- assertEquals(res.distance(p3), 0, EPSILON);
-
- p3 = new Point2D.Double(2, 2);
- res = lineTransformation.closestPointOnSegmentLineToPoint(p1, p2, p3);
- assertEquals(res.distance(p3), 0, EPSILON);
-
- p3 = new Point2D.Double(2, 0);
- res = lineTransformation.closestPointOnSegmentLineToPoint(p1, p2, p3);
- assertEquals(res.distance(p3), 2, EPSILON);
-
- p3 = new Point2D.Double(3, 2);
- res = lineTransformation.closestPointOnSegmentLineToPoint(p1, p2, p3);
- d = Math.sqrt(0.5);
- assertEquals(res.distance(p3), d, EPSILON);
-
- }
-}
+package lcsb.mapviewer.common.geometry;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+
+import java.awt.Shape;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.Line2D;
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+import java.awt.geom.RoundRectangle2D;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+
+public class LineTransformationTest {
+ static Logger logger = Logger.getLogger(LineTransformationTest.class);
+ static double EPSILON = Configuration.EPSILON;
+ LineTransformation lineTransformation = new LineTransformation();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testIntersection() {
+ Shape s = new RoundRectangle2D.Double(0.0, 0.0, 100.0, 100.0, 10.0, 10.0);
+ Line2D line = new Line2D.Double(50, 50, 50, 200);
+ Point2D p = lineTransformation.getIntersectionWithPathIterator(line, s.getPathIterator(new AffineTransform()));
+ Point2D intPoint = new Point2D.Double(50, 100);
+ double dist = p.distance(intPoint);
+ assertEquals("Invalid intersection point: " + p, 0, dist, EPSILON);
+ }
+
+ @Test
+ public void testIntersectionWithBezierCurve() {
+ double x = 0;
+ double y = 0;
+ double w = 100;
+ double h = 200;
+ GeneralPath path = new GeneralPath();
+
+ path.moveTo((float) (x + 0.25 * w), (float) (y + 0.25 * h));
+ path.quadTo((float) (x + 0.05 * w), (float) (y + 0.25 * h), x, (float) (y + 0.5 * h));
+ path.curveTo(x, (float) (y + 0.66 * h), (float) (x + 0.18 * w), (float) (y + 0.9 * h), (float) (x + 0.31 * w), (float) (y + 0.8 * h));
+ path.curveTo((float) (x + 0.4 * w), (y + h), (float) (x + 0.7 * w), (y + h), (float) (x + 0.8 * w), (float) (y + 0.8 * h));
+ path.curveTo((x + w), (float) (y + 0.8 * h), (x + w), (float) (y + 0.6 * h), (float) (x + 0.875 * w), (float) (y + 0.5 * h));
+ path.curveTo((x + w), (float) (y + 0.3 * h), (float) (x + 0.8 * w), (float) (y + 0.1 * h), (float) (x + 0.625 * w), (float) (y + 0.2 * h));
+ path.curveTo((float) (x + 0.5 * w), (float) (y + 0.05 * h), (float) (x + 0.3 * w), (float) (y + 0.05 * h), (float) (x + 0.25 * w), (float) (y + 0.25 * h));
+ path.closePath();
+
+ Line2D line = new Line2D.Double(50, 50, 50, 300);
+ Point2D p = lineTransformation.getIntersectionWithPathIterator(line, path.getPathIterator(new AffineTransform()));
+ assertNotNull(p);
+ }
+
+ @Test
+ public void testIntersectionToInvalidPath() {
+ Line2D line = new Line2D.Double(50, 50, 50, 200);
+ Point2D p = lineTransformation.getIntersectionWithPathIterator(line, null);
+ assertNull(p);
+
+ Shape s = new Rectangle2D.Double(0.0, 0.0, 10.0, 0.0);
+ p = lineTransformation.getIntersectionWithPathIterator(line, s.getPathIterator(new AffineTransform()));
+ assertNull(p);
+
+ p = lineTransformation.getIntersectionWithPathIterator(line, new PathIterator() {
+
+ @Override
+ public void next() {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public boolean isDone() {
+ return true;
+ }
+
+ @Override
+ public int getWindingRule() {
+ // TODO Auto-generated method stub
+ return 0;
+ }
+
+ @Override
+ public int currentSegment(double[] coords) {
+ // TODO Auto-generated method stub
+ return 0;
+ }
+
+ @Override
+ public int currentSegment(float[] coords) {
+ // TODO Auto-generated method stub
+ return 0;
+ }
+ });
+ assertNull(p);
+ }
+
+ @Test
+ public void testDistance() {
+ assertNotNull(lineTransformation);
+ Point2D p1 = new Point2D.Double(2, 2);
+ Point2D p2 = new Point2D.Double(3, 3);
+ Point2D p3 = new Point2D.Double(4, 4);
+
+ double dist = lineTransformation.distBetweenPointAndLineSegment(p1, p2, p3);
+ double d = Math.sqrt(2);
+ assertEquals(dist, d, EPSILON);
+
+ p3 = new Point2D.Double(3, 4);
+ dist = lineTransformation.distBetweenPointAndLineSegment(p1, p2, p3);
+ assertEquals(dist, 1, EPSILON);
+
+ p3 = new Point2D.Double(3, 3);
+ dist = lineTransformation.distBetweenPointAndLineSegment(p1, p2, p3);
+ assertEquals(dist, 0, EPSILON);
+
+ p3 = new Point2D.Double(2.5, 2.5);
+ dist = lineTransformation.distBetweenPointAndLineSegment(p1, p2, p3);
+ assertEquals(dist, 0, EPSILON);
+
+ p3 = new Point2D.Double(2, 2);
+ dist = lineTransformation.distBetweenPointAndLineSegment(p1, p2, p3);
+ assertEquals(dist, 0, EPSILON);
+
+ p3 = new Point2D.Double(2, 0);
+ dist = lineTransformation.distBetweenPointAndLineSegment(p1, p2, p3);
+ assertEquals(dist, 2, EPSILON);
+
+ p3 = new Point2D.Double(3, 2);
+ dist = lineTransformation.distBetweenPointAndLineSegment(p1, p2, p3);
+ d = Math.sqrt(0.5);
+ assertEquals(dist, d, EPSILON);
+
+ }
+
+ @Test
+ public void testDistanceToEmptyLine() {
+ Point2D p1 = new Point2D.Double(2, 2);
+ Point2D p2 = new Point2D.Double(3, 3);
+ double dist = lineTransformation.distBetweenPointAndLineSegment(p1, p1, p2);
+ assertEquals(p1.distance(p2), dist, EPSILON);
+
+ // the same with line
+ Line2D line = new Line2D.Double(p1, p1);
+ dist = lineTransformation.distBetweenPointAndLineSegment(line, p2);
+ assertEquals(p1.distance(p2), dist, EPSILON);
+ }
+
+ @Test
+ public void testClosestPointOnSegmentLineToPointOnEmptyLine() {
+ Point2D p1 = new Point2D.Double(2, 2);
+ Point2D p2 = new Point2D.Double(3, 3);
+ Point2D p3 = lineTransformation.closestPointOnSegmentLineToPoint(p1, p1, p2);
+ assertEquals(p3, p1);
+
+ // the same with line
+ Line2D line = new Line2D.Double(p1, p1);
+ p3 = lineTransformation.closestPointOnSegmentLineToPoint(line, p2);
+ assertEquals(p3, p1);
+
+ }
+
+ @Test
+ public void testClosestPoint() {
+ assertNotNull(lineTransformation);
+ Point2D p1 = new Point2D.Double(2, 2);
+ Point2D p2 = new Point2D.Double(3, 3);
+ Point2D p3 = new Point2D.Double(4, 4);
+
+ Point2D res = lineTransformation.closestPointOnSegmentLineToPoint(p1, p2, p3);
+ double d = Math.sqrt(2);
+ assertEquals(res.distance(p3), d, EPSILON);
+
+ p3 = new Point2D.Double(3, 4);
+ res = lineTransformation.closestPointOnSegmentLineToPoint(p1, p2, p3);
+ assertEquals(res.distance(p3), 1, EPSILON);
+
+ p3 = new Point2D.Double(3, 3);
+ res = lineTransformation.closestPointOnSegmentLineToPoint(p1, p2, p3);
+ assertEquals(res.distance(p3), 0, EPSILON);
+
+ p3 = new Point2D.Double(2.5, 2.5);
+ res = lineTransformation.closestPointOnSegmentLineToPoint(p1, p2, p3);
+ assertEquals(res.distance(p3), 0, EPSILON);
+
+ p3 = new Point2D.Double(2, 2);
+ res = lineTransformation.closestPointOnSegmentLineToPoint(p1, p2, p3);
+ assertEquals(res.distance(p3), 0, EPSILON);
+
+ p3 = new Point2D.Double(2, 0);
+ res = lineTransformation.closestPointOnSegmentLineToPoint(p1, p2, p3);
+ assertEquals(res.distance(p3), 2, EPSILON);
+
+ p3 = new Point2D.Double(3, 2);
+ res = lineTransformation.closestPointOnSegmentLineToPoint(p1, p2, p3);
+ d = Math.sqrt(0.5);
+ assertEquals(res.distance(p3), d, EPSILON);
+
+ }
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/geometry/PointTransformationTest.java b/commons/src/test/java/lcsb/mapviewer/common/geometry/PointTransformationTest.java
index 2bd903a735..1868f38ed3 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/geometry/PointTransformationTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/geometry/PointTransformationTest.java
@@ -1,44 +1,44 @@
-package lcsb.mapviewer.common.geometry;
-
-import static org.junit.Assert.*;
-
-import java.awt.geom.Point2D;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Configuration;
-
-public class PointTransformationTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testRotate() {
- PointTransformation pt = new PointTransformation();
- Point2D p1 = new Point2D.Double(1, 0);
- Point2D p2 = new Point2D.Double(2, 0);
- Point2D p3 = new Point2D.Double(3, 0);
- Point2D res = pt.rotatePoint(p1, Math.PI, p2);
- assertEquals(0.0, p3.distance(res), Configuration.EPSILON);
- }
-
- @Test
- public void testIsValid() {
- PointTransformation pt = new PointTransformation();
- Point2D p1 = new Point2D.Double(1, 0);
- Point2D p2 = new Point2D.Double(1, Double.NEGATIVE_INFINITY);
- Point2D p3 = new Point2D.Double(Double.NEGATIVE_INFINITY, 2);
- assertTrue(pt.isValidPoint(p1));
- assertFalse(pt.isValidPoint(p2));
- assertFalse(pt.isValidPoint(p3));
- }
-
-}
+package lcsb.mapviewer.common.geometry;
+
+import static org.junit.Assert.*;
+
+import java.awt.geom.Point2D;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+
+public class PointTransformationTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testRotate() {
+ PointTransformation pt = new PointTransformation();
+ Point2D p1 = new Point2D.Double(1, 0);
+ Point2D p2 = new Point2D.Double(2, 0);
+ Point2D p3 = new Point2D.Double(3, 0);
+ Point2D res = pt.rotatePoint(p1, Math.PI, p2);
+ assertEquals(0.0, p3.distance(res), Configuration.EPSILON);
+ }
+
+ @Test
+ public void testIsValid() {
+ PointTransformation pt = new PointTransformation();
+ Point2D p1 = new Point2D.Double(1, 0);
+ Point2D p2 = new Point2D.Double(1, Double.NEGATIVE_INFINITY);
+ Point2D p3 = new Point2D.Double(Double.NEGATIVE_INFINITY, 2);
+ assertTrue(pt.isValidPoint(p1));
+ assertFalse(pt.isValidPoint(p2));
+ assertFalse(pt.isValidPoint(p3));
+ }
+
+}
diff --git a/commons/src/test/java/lcsb/mapviewer/common/geometry/TextAlignmentTest.java b/commons/src/test/java/lcsb/mapviewer/common/geometry/TextAlignmentTest.java
index 8c62a6db83..b14349b8ef 100644
--- a/commons/src/test/java/lcsb/mapviewer/common/geometry/TextAlignmentTest.java
+++ b/commons/src/test/java/lcsb/mapviewer/common/geometry/TextAlignmentTest.java
@@ -1,29 +1,29 @@
-package lcsb.mapviewer.common.geometry;
-
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class TextAlignmentTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testValidValues() {
- for (TextAlignment type : TextAlignment.values()) {
- assertNotNull(type);
-
- // for coverage tests
- TextAlignment.valueOf(type.toString());
- }
- }
-
-}
+package lcsb.mapviewer.common.geometry;
+
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class TextAlignmentTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testValidValues() {
+ for (TextAlignment type : TextAlignment.values()) {
+ assertNotNull(type);
+
+ // for coverage tests
+ TextAlignment.valueOf(type.toString());
+ }
+ }
+
+}
diff --git a/console/src/main/java/lcsb/mapviewer/run/ImageToCellDesignerBackground.java b/console/src/main/java/lcsb/mapviewer/run/ImageToCellDesignerBackground.java
index 32eccad2d9..4cc73e75a8 100644
--- a/console/src/main/java/lcsb/mapviewer/run/ImageToCellDesignerBackground.java
+++ b/console/src/main/java/lcsb/mapviewer/run/ImageToCellDesignerBackground.java
@@ -1,135 +1,135 @@
-package lcsb.mapviewer.run;
-
-import java.awt.geom.Point2D;
-import java.io.BufferedReader;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.PrintWriter;
-
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.persist.ApplicationContextLoader;
-
-import org.apache.log4j.Logger;
-
-/**
- * This class creates celldesigner file from file with lines. The file is put as
- * an layer "image".
- *
- * @author Piotr Gawron
- *
- */
-public final class ImageToCellDesignerBackground {
- /**
- * MArgin of the image.
- */
- private static final double MARGIN = 100;
- /**
- * Scale of the image.
- */
- private static final double SCALE = 8;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ImageToCellDesignerBackground.class.getName());
-
- /**
- * Static main method used to run this stand alone code.
- *
- * @param args
- * command line arguments
- */
- public static void main(String[] args) {
- ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
- ImageToCellDesignerBackground main = new ImageToCellDesignerBackground();
- ApplicationContextLoader.injectDependencies(main);
- main.run();
- }
-
- /**
- * Default constructor.
- */
- private ImageToCellDesignerBackground() {
-
- }
-
- /**
- * Generate CD file with image.
- */
- private void run() {
- BufferedReader br = null;
- try {
- String fileName = "testFiles/simple_brain_coords.txt";
-
- br = new BufferedReader(new FileReader(fileName));
- StringBuilder sb = new StringBuilder();
- String line = br.readLine();
-
- String id = null;
- Point2D point = null;
- Model model = new ModelFullIndexed(null);
- Layer layer = new Layer();
- layer.setLayerId("1");
- layer.setName("image");
- layer.setVisible(true);
- line = br.readLine();
- double maxX = 0;
- double maxY = 0;
- while (line != null) {
- String[] tmp = line.split(" ");
- String newId = tmp[0];
- double x = SCALE * Double.parseDouble(tmp[1]);
- double y = SCALE * Double.parseDouble(tmp[2]);
-
- maxX = Math.max(maxX, x);
- maxY = Math.max(maxY, y);
- Point2D newPoint = new Point2D.Double(x, y);
- if (newId.equals(id)) {
- layer.addLayerLine(new PolylineData(point, newPoint));
- }
- point = newPoint;
- id = newId;
-
- sb.append(line);
- sb.append(System.lineSeparator());
- line = br.readLine();
- }
- for (PolylineData pd : layer.getLines()) {
- double x = MARGIN + pd.getBeginPoint().getX();
- double y = MARGIN + maxY - pd.getBeginPoint().getY();
- pd.setStartPoint(new Point2D.Double(x, y));
-
- x = MARGIN + pd.getEndPoint().getX();
- y = MARGIN + maxY - pd.getEndPoint().getY();
- pd.setEndPoint(new Point2D.Double(x, y));
- }
- model.addLayer(layer);
- model.setWidth(maxX + 2 * MARGIN);
- model.setHeight(maxY + 2 * MARGIN);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model);
-
- PrintWriter writer = new PrintWriter("tmp.xml", "UTF-8");
- writer.println(xml);
- logger.debug(xml);
- writer.close();
-
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- } finally {
- if (br != null) {
- try {
- br.close();
- } catch (IOException e) {
- logger.error(e.getMessage(), e);
- }
- }
- }
- }
-
-}
+package lcsb.mapviewer.run;
+
+import java.awt.geom.Point2D;
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.PrintWriter;
+
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.persist.ApplicationContextLoader;
+
+import org.apache.log4j.Logger;
+
+/**
+ * This class creates celldesigner file from file with lines. The file is put as
+ * an layer "image".
+ *
+ * @author Piotr Gawron
+ *
+ */
+public final class ImageToCellDesignerBackground {
+ /**
+ * MArgin of the image.
+ */
+ private static final double MARGIN = 100;
+ /**
+ * Scale of the image.
+ */
+ private static final double SCALE = 8;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ImageToCellDesignerBackground.class.getName());
+
+ /**
+ * Static main method used to run this stand alone code.
+ *
+ * @param args
+ * command line arguments
+ */
+ public static void main(String[] args) {
+ ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
+ ImageToCellDesignerBackground main = new ImageToCellDesignerBackground();
+ ApplicationContextLoader.injectDependencies(main);
+ main.run();
+ }
+
+ /**
+ * Default constructor.
+ */
+ private ImageToCellDesignerBackground() {
+
+ }
+
+ /**
+ * Generate CD file with image.
+ */
+ private void run() {
+ BufferedReader br = null;
+ try {
+ String fileName = "testFiles/simple_brain_coords.txt";
+
+ br = new BufferedReader(new FileReader(fileName));
+ StringBuilder sb = new StringBuilder();
+ String line = br.readLine();
+
+ String id = null;
+ Point2D point = null;
+ Model model = new ModelFullIndexed(null);
+ Layer layer = new Layer();
+ layer.setLayerId("1");
+ layer.setName("image");
+ layer.setVisible(true);
+ line = br.readLine();
+ double maxX = 0;
+ double maxY = 0;
+ while (line != null) {
+ String[] tmp = line.split(" ");
+ String newId = tmp[0];
+ double x = SCALE * Double.parseDouble(tmp[1]);
+ double y = SCALE * Double.parseDouble(tmp[2]);
+
+ maxX = Math.max(maxX, x);
+ maxY = Math.max(maxY, y);
+ Point2D newPoint = new Point2D.Double(x, y);
+ if (newId.equals(id)) {
+ layer.addLayerLine(new PolylineData(point, newPoint));
+ }
+ point = newPoint;
+ id = newId;
+
+ sb.append(line);
+ sb.append(System.lineSeparator());
+ line = br.readLine();
+ }
+ for (PolylineData pd : layer.getLines()) {
+ double x = MARGIN + pd.getBeginPoint().getX();
+ double y = MARGIN + maxY - pd.getBeginPoint().getY();
+ pd.setStartPoint(new Point2D.Double(x, y));
+
+ x = MARGIN + pd.getEndPoint().getX();
+ y = MARGIN + maxY - pd.getEndPoint().getY();
+ pd.setEndPoint(new Point2D.Double(x, y));
+ }
+ model.addLayer(layer);
+ model.setWidth(maxX + 2 * MARGIN);
+ model.setHeight(maxY + 2 * MARGIN);
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model);
+
+ PrintWriter writer = new PrintWriter("tmp.xml", "UTF-8");
+ writer.println(xml);
+ logger.debug(xml);
+ writer.close();
+
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ } finally {
+ if (br != null) {
+ try {
+ br.close();
+ } catch (IOException e) {
+ logger.error(e.getMessage(), e);
+ }
+ }
+ }
+ }
+
+}
diff --git a/console/src/main/java/lcsb/mapviewer/run/LegendGenerator.java b/console/src/main/java/lcsb/mapviewer/run/LegendGenerator.java
index bccf00ae75..0416bda730 100644
--- a/console/src/main/java/lcsb/mapviewer/run/LegendGenerator.java
+++ b/console/src/main/java/lcsb/mapviewer/run/LegendGenerator.java
@@ -1,170 +1,170 @@
-package lcsb.mapviewer.run;
-
-import java.awt.Desktop;
-import java.io.File;
-import java.io.IOException;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.commands.CopyCommand;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.InvalidInputDataExecption;
-import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
-import lcsb.mapviewer.converter.graphics.DrawingException;
-import lcsb.mapviewer.converter.graphics.PngImageGenerator;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.model.Model;
-
-/**
- * This class is responsible for creation of legend.PNG from CellDesigner file.
- *
- * @author Piotr Gawron
- *
- */
-public class LegendGenerator {
-
- /**
- * This enum contains predefined legend images as CellDEsigner files.
- *
- * @author Piotr Gawron
- *
- */
- private enum LegendObject {
- // /**
- // * First legend element.
- // */
- // LEGEND_A("testFiles/legend/legend_5_2.xml", "legend_a.png", 50, 0, 600,
- // 480),
- // /**
- // * Second legend element.
- // */
- // LEGEND_B("testFiles/legend/legend_4_3.xml", "legend_b.png", 920, 0, 600,
- // 480),
- // /**
- // * Third legend element.
- // */
- // LEGEND_C("testFiles/legend/legend_4_4.xml", "legend_c.png", 500, 0, 600,
- // 480),
- /**
- * Fourth legend element.
- */
- LEGEND_D("C:/Users/piotr.gawron/Desktop/test.xml", "legend_d.png", 0, 0, 1280, 480);
-
- /**
- * File with the legend data in CellDEsigner format.
- */
- private String inputFile = null;
- /**
- * Where the legend should be saved.
- */
- private String outputFile = null;
- /**
- * X coordinate where the image in input file starts.
- */
- private int startX = 0;
- /**
- * Y coordinate where the image in input file starts.
- */
- private int startY = 0;
- /**
- * Width of the legend image.
- */
- private Integer width = null;
- /**
- * Height of the legend image.
- */
- private Integer height = null;
-
- /**
- * Default constructor.
- *
- * @param input
- * {@link #inputFile}
- * @param output
- * {@link #outputFile}
- * @param startX
- * {@link #startX}
- * @param startY
- * {@link #startY}
- * @param width
- * {@link #width}
- * @param height
- * {@link #height}
- */
- LegendObject(String input, String output, int startX, int startY, int width, int height) {
- this.inputFile = input;
- this.outputFile = output;
- this.startX = startX;
- this.startY = startY;
- this.width = width;
- this.height = height;
- }
- }
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(LegendGenerator.class.getName());
-
- /**
- * What zoom factor should be used to generate legend files.
- */
- private static final double ZOOM_FACTOR = 1.4;
-
- /**
- * Static main method used to run this stand alone code.
- *
- * @param args
- * command line arguments
- */
- public static void main(String[] args) {
- try {
- new LegendGenerator().run();
-
- } catch (Exception e) {
- e.printStackTrace();
- logger.error("Unknown exception: " + e.getMessage());
- }
- }
-
- /**
- * Creates all legend images.
- *
- * @throws IOException
- * thrown when there are some general problems with files
- * @throws DrawingException
- * thrown when there was a problem with drawing one of the maps
- * @throws InvalidInputDataExecption
- */
- public void run() throws Exception {
- for (LegendObject lo : LegendObject.values()) {
- createLegend(lo);
- }
- }
-
- /**
- * Creates single legend file.
- *
- * @param lo
- * type of the legend file to create
- * @throws IOException
- * thrown when there are some general problems with input/output
- * file
- * @throws DrawingException
- * thrown when there was a problem with drawing a legend
- * @throws InvalidInputDataExecption
- * thrown when xml file is invalid
- */
- private void createLegend(LegendObject lo) throws Exception {
- Model model = new CellDesignerXmlParser().createModel(new ConverterParams().filename(lo.inputFile));
-
- // and save it to leged.png
- String fileName = lo.outputFile;
-
- Model copy = new CopyCommand(model).execute();
- PngImageGenerator generator = new PngImageGenerator(
- new Params().scale(ZOOM_FACTOR).x(lo.startX).y(lo.startY).width(lo.width).height(lo.height).model(copy).level(2).nested(true));
- generator.saveToFile(fileName);
- Desktop.getDesktop().open(new File(fileName));
- }
-}
+package lcsb.mapviewer.run;
+
+import java.awt.Desktop;
+import java.io.File;
+import java.io.IOException;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.CopyCommand;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
+import lcsb.mapviewer.converter.graphics.DrawingException;
+import lcsb.mapviewer.converter.graphics.PngImageGenerator;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+
+/**
+ * This class is responsible for creation of legend.PNG from CellDesigner file.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class LegendGenerator {
+
+ /**
+ * This enum contains predefined legend images as CellDEsigner files.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ private enum LegendObject {
+ // /**
+ // * First legend element.
+ // */
+ // LEGEND_A("testFiles/legend/legend_5_2.xml", "legend_a.png", 50, 0, 600,
+ // 480),
+ // /**
+ // * Second legend element.
+ // */
+ // LEGEND_B("testFiles/legend/legend_4_3.xml", "legend_b.png", 920, 0, 600,
+ // 480),
+ // /**
+ // * Third legend element.
+ // */
+ // LEGEND_C("testFiles/legend/legend_4_4.xml", "legend_c.png", 500, 0, 600,
+ // 480),
+ /**
+ * Fourth legend element.
+ */
+ LEGEND_D("C:/Users/piotr.gawron/Desktop/test.xml", "legend_d.png", 0, 0, 1280, 480);
+
+ /**
+ * File with the legend data in CellDEsigner format.
+ */
+ private String inputFile = null;
+ /**
+ * Where the legend should be saved.
+ */
+ private String outputFile = null;
+ /**
+ * X coordinate where the image in input file starts.
+ */
+ private int startX = 0;
+ /**
+ * Y coordinate where the image in input file starts.
+ */
+ private int startY = 0;
+ /**
+ * Width of the legend image.
+ */
+ private Integer width = null;
+ /**
+ * Height of the legend image.
+ */
+ private Integer height = null;
+
+ /**
+ * Default constructor.
+ *
+ * @param input
+ * {@link #inputFile}
+ * @param output
+ * {@link #outputFile}
+ * @param startX
+ * {@link #startX}
+ * @param startY
+ * {@link #startY}
+ * @param width
+ * {@link #width}
+ * @param height
+ * {@link #height}
+ */
+ LegendObject(String input, String output, int startX, int startY, int width, int height) {
+ this.inputFile = input;
+ this.outputFile = output;
+ this.startX = startX;
+ this.startY = startY;
+ this.width = width;
+ this.height = height;
+ }
+ }
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(LegendGenerator.class.getName());
+
+ /**
+ * What zoom factor should be used to generate legend files.
+ */
+ private static final double ZOOM_FACTOR = 1.4;
+
+ /**
+ * Static main method used to run this stand alone code.
+ *
+ * @param args
+ * command line arguments
+ */
+ public static void main(String[] args) {
+ try {
+ new LegendGenerator().run();
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ logger.error("Unknown exception: " + e.getMessage());
+ }
+ }
+
+ /**
+ * Creates all legend images.
+ *
+ * @throws IOException
+ * thrown when there are some general problems with files
+ * @throws DrawingException
+ * thrown when there was a problem with drawing one of the maps
+ * @throws InvalidInputDataExecption
+ */
+ public void run() throws Exception {
+ for (LegendObject lo : LegendObject.values()) {
+ createLegend(lo);
+ }
+ }
+
+ /**
+ * Creates single legend file.
+ *
+ * @param lo
+ * type of the legend file to create
+ * @throws IOException
+ * thrown when there are some general problems with input/output
+ * file
+ * @throws DrawingException
+ * thrown when there was a problem with drawing a legend
+ * @throws InvalidInputDataExecption
+ * thrown when xml file is invalid
+ */
+ private void createLegend(LegendObject lo) throws Exception {
+ Model model = new CellDesignerXmlParser().createModel(new ConverterParams().filename(lo.inputFile));
+
+ // and save it to leged.png
+ String fileName = lo.outputFile;
+
+ Model copy = new CopyCommand(model).execute();
+ PngImageGenerator generator = new PngImageGenerator(
+ new Params().scale(ZOOM_FACTOR).x(lo.startX).y(lo.startY).width(lo.width).height(lo.height).model(copy).level(2).nested(true));
+ generator.saveToFile(fileName);
+ Desktop.getDesktop().open(new File(fileName));
+ }
+}
diff --git a/console/src/main/java/lcsb/mapviewer/run/PdMapAnnotations.java b/console/src/main/java/lcsb/mapviewer/run/PdMapAnnotations.java
index 3f159553cd..dec5792fe1 100644
--- a/console/src/main/java/lcsb/mapviewer/run/PdMapAnnotations.java
+++ b/console/src/main/java/lcsb/mapviewer/run/PdMapAnnotations.java
@@ -1,82 +1,82 @@
-package lcsb.mapviewer.run;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * Class with some PD map specific information.
- *
- * @author Piotr Gawron
- *
- */
-public final class PdMapAnnotations {
-
- /**
- * Default class constructor. Prevent initialization.
- */
- private PdMapAnnotations() {
-
- }
-
- /**
- * Returns url to pdmap with reaction selected on it.
- *
- * @param reaction
- * reaction to be selected
- * @return url to the reaction in pd map
- */
- public static String getLinkForReaction(Reaction reaction) {
- return Configuration.PUBLICALY_AVAILABLE_PD_MAP + "&search=reaction:" + reaction.getIdReaction();
- }
-
- /**
- * Returns filename of the last available version of pd project from testFiles
- * directory.
- *
- * @return filename of the last available version of pd project
- * @throws FileNotFoundException
- * thrown when file cannot be found
- */
- public static String getLastPdFilename() throws FileNotFoundException {
- String result = null;
- File folder = new File("testFiles/pd_full/");
- File[] listOfFiles = folder.listFiles();
-
- for (int i = 0; i < listOfFiles.length; i++) {
-
- if (listOfFiles[i].isFile() && listOfFiles[i].getAbsolutePath().toLowerCase().endsWith("xml")) {
- if (result == null) {
- result = listOfFiles[i].getAbsolutePath();
- } else {
- if (result.compareTo(listOfFiles[i].getAbsolutePath()) < 0) {
- result = listOfFiles[i].getAbsolutePath();
- }
- }
- }
- }
- if (result == null) {
- throw new FileNotFoundException();
- } else {
- return result;
- }
- }
-
- /**
- * Returns version of the last pd file project.
- *
- * @return version of the last pd file project
- */
- public static String getLastPdVersion() {
- String result = null;
- try {
- String[] tokens = getLastPdFilename().split("[\\/\\\\]");
- result = tokens[tokens.length - 1].replace(".xml", "");
- } catch (FileNotFoundException e) {
- return null;
- }
- return result;
- }
-}
+package lcsb.mapviewer.run;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * Class with some PD map specific information.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public final class PdMapAnnotations {
+
+ /**
+ * Default class constructor. Prevent initialization.
+ */
+ private PdMapAnnotations() {
+
+ }
+
+ /**
+ * Returns url to pdmap with reaction selected on it.
+ *
+ * @param reaction
+ * reaction to be selected
+ * @return url to the reaction in pd map
+ */
+ public static String getLinkForReaction(Reaction reaction) {
+ return Configuration.PUBLICALY_AVAILABLE_PD_MAP + "&search=reaction:" + reaction.getIdReaction();
+ }
+
+ /**
+ * Returns filename of the last available version of pd project from testFiles
+ * directory.
+ *
+ * @return filename of the last available version of pd project
+ * @throws FileNotFoundException
+ * thrown when file cannot be found
+ */
+ public static String getLastPdFilename() throws FileNotFoundException {
+ String result = null;
+ File folder = new File("testFiles/pd_full/");
+ File[] listOfFiles = folder.listFiles();
+
+ for (int i = 0; i < listOfFiles.length; i++) {
+
+ if (listOfFiles[i].isFile() && listOfFiles[i].getAbsolutePath().toLowerCase().endsWith("xml")) {
+ if (result == null) {
+ result = listOfFiles[i].getAbsolutePath();
+ } else {
+ if (result.compareTo(listOfFiles[i].getAbsolutePath()) < 0) {
+ result = listOfFiles[i].getAbsolutePath();
+ }
+ }
+ }
+ }
+ if (result == null) {
+ throw new FileNotFoundException();
+ } else {
+ return result;
+ }
+ }
+
+ /**
+ * Returns version of the last pd file project.
+ *
+ * @return version of the last pd file project
+ */
+ public static String getLastPdVersion() {
+ String result = null;
+ try {
+ String[] tokens = getLastPdFilename().split("[\\/\\\\]");
+ result = tokens[tokens.length - 1].replace(".xml", "");
+ } catch (FileNotFoundException e) {
+ return null;
+ }
+ return result;
+ }
+}
diff --git a/console/src/main/java/lcsb/mapviewer/run/ReactomeComparison.java b/console/src/main/java/lcsb/mapviewer/run/ReactomeComparison.java
index 48ae8ea11c..ad0da2b687 100644
--- a/console/src/main/java/lcsb/mapviewer/run/ReactomeComparison.java
+++ b/console/src/main/java/lcsb/mapviewer/run/ReactomeComparison.java
@@ -1,407 +1,407 @@
-package lcsb.mapviewer.run;
-
-import static org.junit.Assert.fail;
-
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.io.UnsupportedEncodingException;
-import java.text.DecimalFormat;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-import org.apache.log4j.PropertyConfigurator;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
-import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.persist.ApplicationContextLoader;
-import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
-import lcsb.mapviewer.reactome.model.ReactomeReactionlikeEvent;
-import lcsb.mapviewer.reactome.utils.ComparatorException;
-import lcsb.mapviewer.reactome.utils.DataFormatter;
-import lcsb.mapviewer.reactome.utils.DataSourceUpdater;
-import lcsb.mapviewer.reactome.utils.ReactionComparator;
-import lcsb.mapviewer.reactome.utils.ReactomeQueryUtil;
-import lcsb.mapviewer.reactome.utils.comparators.MatchResult;
-import lcsb.mapviewer.reactome.utils.comparators.MatchResult.MatchStatus;
-
-/**
- * This class generates report of comparison between data on PD-map and
- * reactome.
- *
- * @author Piotr Gawron
- *
- */
-
-public class ReactomeComparison {
- /**
- * Number of nanoseconds in second :).
- */
- private static final double NANOSECONDS_IN_SECOND = 1000000000.0;
-
- /**
- * Local model used for comparison.
- */
- private Model model;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ReactomeComparison.class);
-
- /**
- * Comparator of reactions between our model and reactome.
- */
- @Autowired
- private ReactionComparator reactionComparator;
-
- /**
- * Class used for accessing reactome data.
- */
- @Autowired
- private DataSourceUpdater rc;
-
- /**
- * Util class used for manipulating information in reactome objects.
- */
- @Autowired
- private ReactomeQueryUtil rcu;
-
- /**
- * Formatter used for reaction comparison.
- */
- @Autowired
- private DataFormatter dataFormatter;
-
- /**
- * Static main method used to run this stand alone code.
- *
- * @param args
- * command line arguments
- */
- public static void main(String[] args) {
- long startTime = System.nanoTime();
- PropertyConfigurator.configure("src/main/webapp/WEB-INF/resources/log4j.properties");
- ReactomeComparison main = new ReactomeComparison();
- ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
- ApplicationContextLoader.injectDependencies(main);
- main.run();
- long endTime = System.nanoTime();
-
- long duration = endTime - startTime;
- double sec = duration / NANOSECONDS_IN_SECOND;
- System.out.println("Duration: " + new DecimalFormat("#.###").format(sec) + "s");
- }
-
- /**
- * Executes comparison between model and reactome representation.
- */
- public void run() {
- try {
- model = new CellDesignerXmlParser().createModel(new ConverterParams().filename(PdMapAnnotations.getLastPdFilename()));
-
- Set<String> list = new HashSet<String>();
-
- for (Species element : model.getSpeciesList()) {
- list.add(element.getName());
- }
- logger.debug("Species: " + list.size());
-
- List<String> ids = new ArrayList<String>();
- for (Reaction reaction : model.getReactions()) {
- ids.add(reaction.getIdReaction());
- }
- Collections.sort(ids);
- List<MatchResult> results = new ArrayList<MatchResult>();
-
- printHeader();
- int i = 0;
- for (String string : ids) {
- Reaction reaction = model.getReactionByReactionId(string);
- logger.info("Reaction: " + string + "; " + (i++) + "/" + ids.size());
- if (rcu.getReactomeIdentifierForReaction(reaction) != null) {
- MatchResult result = checkReaction(string);
- if (result != null) {
- results.add(result);
- printResult(result);
- }
- } else {
- ReactomeReactionlikeEvent reactomReaction = rcu.getSimilarReaction(reaction);
- if (reactomReaction != null) {
- MatchResult matchResult = new MatchResult();
- matchResult.setStatus(MatchStatus.SIMILAR_REACTION_FOUND);
- matchResult.setLocalReaction(reaction);
- matchResult.setReactomeReaction(reactomReaction);
- results.add(matchResult);
- printResult(matchResult);
-
- }
- }
- }
- printFooter(results);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
-
- }
-
- /**
- * Prints report footer.
- *
- * @param results
- * results used in the report
- */
- private void printFooter(List<MatchResult> results) {
- writer.println("</table>");
-
- int ok = 0;
- int mismatch = 0;
- int severe = 0;
- int similar = 0;
- for (MatchResult matchResult : results) {
- if (matchResult.getStatus() == MatchStatus.OK) {
- ok++;
- } else if (matchResult.getStatus() == MatchStatus.MISMATCH) {
- mismatch++;
- } else if (matchResult.getStatus() == MatchStatus.SIMILAR_REACTION_FOUND) {
- similar++;
- } else {
- severe++;
- }
- }
- writer.println("<p>Reactions checked: " + (results.size()) + "</p>");
- writer.println("<p>OK: " + ok + "</p>");
- writer.println("<p>MISMATCH: " + mismatch + "</p>");
- writer.println("<p>SEVERE PROBLEMS: " + severe + "</p>");
- writer.println("<p>SIMILAR: " + similar + "</p>");
-
- writer.println("</body></html>");
- writer.close();
-
- }
-
- /**
- * Object to which the report is written.
- */
- private PrintWriter writer;
-
- /**
- * Creates report stream and prints header of the report.
- *
- * @throws FileNotFoundException
- * if there is a problem with creating report file
- * @throws UnsupportedEncodingException
- * thrown when there are problems with encoding
- */
- private void printHeader() throws FileNotFoundException, UnsupportedEncodingException {
- writer = new PrintWriter("out/report/report.html", "UTF-8");
- writer.println("<html><head></head><body>");
- writer.println("<table cellspacing=\"0\">");
-
- String resultString = "<tr>";
- resultString += "<td" + style + ">Reaction</td>";
- resultString += "<td" + style + ">REACTOME ID</td>";
- resultString += "<td" + style + ">Status</td>";
- resultString += "<td" + style + ">Similarity</td>";
- resultString += "<td" + style + ">Unknown reaction input</td>";
- resultString += "<td" + style + ">Unknown reaction modifier</td>";
- resultString += "<td" + style + ">Unknown reaction output</td>";
- resultString += "<td" + style + ">Unknown reactome input</td>";
- resultString += "<td" + style + ">Unknown reactome modifier</td>";
- resultString += "<td" + style + ">Unknown reactome output</td>";
- resultString += "</tr>";
- writer.println(resultString);
-
- }
-
- /**
- * Formatter of decimal numbers.
- */
- private DecimalFormat df = new DecimalFormat("#.##");
-
- /**
- * Style used by report cells.
- */
- private String style = " style=\"border-width:1;border-style:solid;border-color:#000000;\" ";
-
- /**
- * Prints result row.
- *
- * @param result
- * result to be printed
- * @throws AnnotatorException
- * thrown when there is a problem accessing external annotation
- * service
- */
- private void printResult(MatchResult result) throws AnnotatorException {
- String color = "#000000";
- String status = "";
- String error = "";
- switch (result.getStatus()) {
- case OK:
- color = "#52D017";
- status = "OK";
- error = "<td colspan=\"6\" " + style + "></td>";
- return;
- case SIMILAR_REACTION_FOUND:
- color = "#5757E0";
- status = "SIMILAR";
- error = "<td colspan=\"6\" " + style + "></td>";
- return;
- case MISMATCH:
- color = "#FFFF00";
- status = "MISMATCH";
- error += "<td" + style + ">" + dataFormatter.getInvalidLocalInputString(result) + " </td>";
- error += "<td" + style + ">" + dataFormatter.getInvalidLocalModifierString(result) + " </td>";
- error += "<td" + style + ">" + dataFormatter.getInvalidLocalOutputString(result) + " </td>";
- error += "<td" + style + ">" + dataFormatter.getInvalidReactomeInputString(result) + " </td>";
- error += "<td" + style + ">" + dataFormatter.getInvalidReactomeModifierString(result) + " </td>";
- error += "<td" + style + ">" + dataFormatter.getInvalidReactomeOutputString(result) + " </td>";
- break;
- case INVALID_REACTOME_ID:
- color = "#FF0000";
- status = "REACTOME id does not point to reaction";
- error = "<td colspan=\"6\" " + style + "></td>";
- return;
- case INVALID_REACTION_WITH_PHEONTYPE:
- color = "#FF0000";
- status = "Impossible to map reaction to reactome - reaction contains Phenotype";
- error = "<td colspan=\"6\" " + style + "></td>";
- return;
- default:
- return;
- }
- String resultString = "<tr bgcolor = \"" + color + "\">";
- String reactionId = result.getLocalReaction().getIdReaction();
- String reactomId = null;
- reactomId = rcu.getReactomeIdentifierForReaction(result.getLocalReaction());
-
- resultString += "<td" + style + "><a target=\"_blank\" href=\"" + PdMapAnnotations.getLinkForReaction(result.getLocalReaction()) + "\">" + reactionId
- + "</a> ";
- resultString += "<a target=\"_blank\" href=\"" + rcu.getReactomeUrlForStableIdentifier(reactomId) + "\">" + reactomId + "</a></td>";
-
- if (result.getReactomeReaction() != null) {
- reactomId = result.getReactomeReaction().getStableIdentifier().getIdentifier() + "."
- + result.getReactomeReaction().getStableIdentifier().getIdentifierVersion();
- } else {
- reactomId = rcu.getReactomeIdentifierForReaction(result.getLocalReaction());
- }
-
- resultString += "<td" + style + "><a target=\"_blank\" href=\"" + rcu.getReactomeUrlForStableIdentifier(reactomId) + "\">" + reactomId + "</a></td>";
- resultString += "<td" + style + ">" + status + "</td>";
- resultString += "<td" + style + ">" + df.format(result.getScore() * IProgressUpdater.MAX_PROGRESS) + "%</td>";
- resultString += error;
- resultString += "</tr>";
- writer.println(resultString);
- System.out.println(resultString);
- }
-
- /**
- * Compares our model reaction to reactome representation.
- *
- * @param id
- * identifier of our reaction
- * @return result of reaction comparison
- * @throws IOException
- * thrown whene there are problems accessing reactome reaction
- * @throws ComparatorException
- * thrown when there is a problem with comparison {@link Reaction}
- * with Reactome object
- *
- */
- private MatchResult checkReaction(String id) throws IOException, ComparatorException {
- return checkReaction(model.getReactionByReactionId(id));
- }
-
- /**
- * Compares our model reaction to reactome representation.
- *
- * @param reaction
- * our reaction
- * @return result of reaction comparison
- * @throws IOException
- * thrown whene there are problems accessing reactome reaction
- * @throws ComparatorException
- * thrown when there is a problem with comparison {@link Reaction}
- * with Reactome object
- */
- private MatchResult checkReaction(Reaction reaction) throws IOException, ComparatorException {
- String stableIdentifier = rcu.getReactomeIdentifierForReaction(reaction);
- if (stableIdentifier != null) {
- String identifier = stableIdentifier.split("\\.")[0];
- String version = stableIdentifier.split("\\.")[1];
-
- ReactomeDatabaseObject object = rc.getFullObjectForStableIdentifier(identifier, version);
- if (object != null && object instanceof ReactomeReactionlikeEvent) {
- return reactionComparator.compareReactions(reaction, (ReactomeReactionlikeEvent) object);
-
- } else {
- MatchResult result = new MatchResult();
- result.setLocalReaction(reaction);
- result.setStatus(MatchStatus.INVALID_REACTOME_ID);
- return result;
- }
- }
- return null;
- }
-
- /**
- * @return the reactionComparator
- */
- public ReactionComparator getReactionComparator() {
- return reactionComparator;
- }
-
- /**
- * @param reactionComparator
- * the reactionComparator to set
- */
- public void setReactionComparator(ReactionComparator reactionComparator) {
- this.reactionComparator = reactionComparator;
- }
-
- /**
- * @return the dataFormatter
- */
- public DataFormatter getDataFormatter() {
- return dataFormatter;
- }
-
- /**
- * @param dataFormatter
- * the dataFormatter to set
- */
- public void setDataFormatter(DataFormatter dataFormatter) {
- this.dataFormatter = dataFormatter;
- }
-
- /**
- * @return the rc
- * @see #rc
- */
- public DataSourceUpdater getRc() {
- return rc;
- }
-
- /**
- * @param rc
- * the rc to set
- * @see #rc
- */
- public void setRc(DataSourceUpdater rc) {
- this.rc = rc;
- }
-
-}
+package lcsb.mapviewer.run;
+
+import static org.junit.Assert.fail;
+
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.io.UnsupportedEncodingException;
+import java.text.DecimalFormat;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.apache.log4j.PropertyConfigurator;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
+import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.persist.ApplicationContextLoader;
+import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
+import lcsb.mapviewer.reactome.model.ReactomeReactionlikeEvent;
+import lcsb.mapviewer.reactome.utils.ComparatorException;
+import lcsb.mapviewer.reactome.utils.DataFormatter;
+import lcsb.mapviewer.reactome.utils.DataSourceUpdater;
+import lcsb.mapviewer.reactome.utils.ReactionComparator;
+import lcsb.mapviewer.reactome.utils.ReactomeQueryUtil;
+import lcsb.mapviewer.reactome.utils.comparators.MatchResult;
+import lcsb.mapviewer.reactome.utils.comparators.MatchResult.MatchStatus;
+
+/**
+ * This class generates report of comparison between data on PD-map and
+ * reactome.
+ *
+ * @author Piotr Gawron
+ *
+ */
+
+public class ReactomeComparison {
+ /**
+ * Number of nanoseconds in second :).
+ */
+ private static final double NANOSECONDS_IN_SECOND = 1000000000.0;
+
+ /**
+ * Local model used for comparison.
+ */
+ private Model model;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ReactomeComparison.class);
+
+ /**
+ * Comparator of reactions between our model and reactome.
+ */
+ @Autowired
+ private ReactionComparator reactionComparator;
+
+ /**
+ * Class used for accessing reactome data.
+ */
+ @Autowired
+ private DataSourceUpdater rc;
+
+ /**
+ * Util class used for manipulating information in reactome objects.
+ */
+ @Autowired
+ private ReactomeQueryUtil rcu;
+
+ /**
+ * Formatter used for reaction comparison.
+ */
+ @Autowired
+ private DataFormatter dataFormatter;
+
+ /**
+ * Static main method used to run this stand alone code.
+ *
+ * @param args
+ * command line arguments
+ */
+ public static void main(String[] args) {
+ long startTime = System.nanoTime();
+ PropertyConfigurator.configure("src/main/webapp/WEB-INF/resources/log4j.properties");
+ ReactomeComparison main = new ReactomeComparison();
+ ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
+ ApplicationContextLoader.injectDependencies(main);
+ main.run();
+ long endTime = System.nanoTime();
+
+ long duration = endTime - startTime;
+ double sec = duration / NANOSECONDS_IN_SECOND;
+ System.out.println("Duration: " + new DecimalFormat("#.###").format(sec) + "s");
+ }
+
+ /**
+ * Executes comparison between model and reactome representation.
+ */
+ public void run() {
+ try {
+ model = new CellDesignerXmlParser().createModel(new ConverterParams().filename(PdMapAnnotations.getLastPdFilename()));
+
+ Set<String> list = new HashSet<String>();
+
+ for (Species element : model.getSpeciesList()) {
+ list.add(element.getName());
+ }
+ logger.debug("Species: " + list.size());
+
+ List<String> ids = new ArrayList<String>();
+ for (Reaction reaction : model.getReactions()) {
+ ids.add(reaction.getIdReaction());
+ }
+ Collections.sort(ids);
+ List<MatchResult> results = new ArrayList<MatchResult>();
+
+ printHeader();
+ int i = 0;
+ for (String string : ids) {
+ Reaction reaction = model.getReactionByReactionId(string);
+ logger.info("Reaction: " + string + "; " + (i++) + "/" + ids.size());
+ if (rcu.getReactomeIdentifierForReaction(reaction) != null) {
+ MatchResult result = checkReaction(string);
+ if (result != null) {
+ results.add(result);
+ printResult(result);
+ }
+ } else {
+ ReactomeReactionlikeEvent reactomReaction = rcu.getSimilarReaction(reaction);
+ if (reactomReaction != null) {
+ MatchResult matchResult = new MatchResult();
+ matchResult.setStatus(MatchStatus.SIMILAR_REACTION_FOUND);
+ matchResult.setLocalReaction(reaction);
+ matchResult.setReactomeReaction(reactomReaction);
+ results.add(matchResult);
+ printResult(matchResult);
+
+ }
+ }
+ }
+ printFooter(results);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+
+ }
+
+ /**
+ * Prints report footer.
+ *
+ * @param results
+ * results used in the report
+ */
+ private void printFooter(List<MatchResult> results) {
+ writer.println("</table>");
+
+ int ok = 0;
+ int mismatch = 0;
+ int severe = 0;
+ int similar = 0;
+ for (MatchResult matchResult : results) {
+ if (matchResult.getStatus() == MatchStatus.OK) {
+ ok++;
+ } else if (matchResult.getStatus() == MatchStatus.MISMATCH) {
+ mismatch++;
+ } else if (matchResult.getStatus() == MatchStatus.SIMILAR_REACTION_FOUND) {
+ similar++;
+ } else {
+ severe++;
+ }
+ }
+ writer.println("<p>Reactions checked: " + (results.size()) + "</p>");
+ writer.println("<p>OK: " + ok + "</p>");
+ writer.println("<p>MISMATCH: " + mismatch + "</p>");
+ writer.println("<p>SEVERE PROBLEMS: " + severe + "</p>");
+ writer.println("<p>SIMILAR: " + similar + "</p>");
+
+ writer.println("</body></html>");
+ writer.close();
+
+ }
+
+ /**
+ * Object to which the report is written.
+ */
+ private PrintWriter writer;
+
+ /**
+ * Creates report stream and prints header of the report.
+ *
+ * @throws FileNotFoundException
+ * if there is a problem with creating report file
+ * @throws UnsupportedEncodingException
+ * thrown when there are problems with encoding
+ */
+ private void printHeader() throws FileNotFoundException, UnsupportedEncodingException {
+ writer = new PrintWriter("out/report/report.html", "UTF-8");
+ writer.println("<html><head></head><body>");
+ writer.println("<table cellspacing=\"0\">");
+
+ String resultString = "<tr>";
+ resultString += "<td" + style + ">Reaction</td>";
+ resultString += "<td" + style + ">REACTOME ID</td>";
+ resultString += "<td" + style + ">Status</td>";
+ resultString += "<td" + style + ">Similarity</td>";
+ resultString += "<td" + style + ">Unknown reaction input</td>";
+ resultString += "<td" + style + ">Unknown reaction modifier</td>";
+ resultString += "<td" + style + ">Unknown reaction output</td>";
+ resultString += "<td" + style + ">Unknown reactome input</td>";
+ resultString += "<td" + style + ">Unknown reactome modifier</td>";
+ resultString += "<td" + style + ">Unknown reactome output</td>";
+ resultString += "</tr>";
+ writer.println(resultString);
+
+ }
+
+ /**
+ * Formatter of decimal numbers.
+ */
+ private DecimalFormat df = new DecimalFormat("#.##");
+
+ /**
+ * Style used by report cells.
+ */
+ private String style = " style=\"border-width:1;border-style:solid;border-color:#000000;\" ";
+
+ /**
+ * Prints result row.
+ *
+ * @param result
+ * result to be printed
+ * @throws AnnotatorException
+ * thrown when there is a problem accessing external annotation
+ * service
+ */
+ private void printResult(MatchResult result) throws AnnotatorException {
+ String color = "#000000";
+ String status = "";
+ String error = "";
+ switch (result.getStatus()) {
+ case OK:
+ color = "#52D017";
+ status = "OK";
+ error = "<td colspan=\"6\" " + style + "></td>";
+ return;
+ case SIMILAR_REACTION_FOUND:
+ color = "#5757E0";
+ status = "SIMILAR";
+ error = "<td colspan=\"6\" " + style + "></td>";
+ return;
+ case MISMATCH:
+ color = "#FFFF00";
+ status = "MISMATCH";
+ error += "<td" + style + ">" + dataFormatter.getInvalidLocalInputString(result) + " </td>";
+ error += "<td" + style + ">" + dataFormatter.getInvalidLocalModifierString(result) + " </td>";
+ error += "<td" + style + ">" + dataFormatter.getInvalidLocalOutputString(result) + " </td>";
+ error += "<td" + style + ">" + dataFormatter.getInvalidReactomeInputString(result) + " </td>";
+ error += "<td" + style + ">" + dataFormatter.getInvalidReactomeModifierString(result) + " </td>";
+ error += "<td" + style + ">" + dataFormatter.getInvalidReactomeOutputString(result) + " </td>";
+ break;
+ case INVALID_REACTOME_ID:
+ color = "#FF0000";
+ status = "REACTOME id does not point to reaction";
+ error = "<td colspan=\"6\" " + style + "></td>";
+ return;
+ case INVALID_REACTION_WITH_PHEONTYPE:
+ color = "#FF0000";
+ status = "Impossible to map reaction to reactome - reaction contains Phenotype";
+ error = "<td colspan=\"6\" " + style + "></td>";
+ return;
+ default:
+ return;
+ }
+ String resultString = "<tr bgcolor = \"" + color + "\">";
+ String reactionId = result.getLocalReaction().getIdReaction();
+ String reactomId = null;
+ reactomId = rcu.getReactomeIdentifierForReaction(result.getLocalReaction());
+
+ resultString += "<td" + style + "><a target=\"_blank\" href=\"" + PdMapAnnotations.getLinkForReaction(result.getLocalReaction()) + "\">" + reactionId
+ + "</a> ";
+ resultString += "<a target=\"_blank\" href=\"" + rcu.getReactomeUrlForStableIdentifier(reactomId) + "\">" + reactomId + "</a></td>";
+
+ if (result.getReactomeReaction() != null) {
+ reactomId = result.getReactomeReaction().getStableIdentifier().getIdentifier() + "."
+ + result.getReactomeReaction().getStableIdentifier().getIdentifierVersion();
+ } else {
+ reactomId = rcu.getReactomeIdentifierForReaction(result.getLocalReaction());
+ }
+
+ resultString += "<td" + style + "><a target=\"_blank\" href=\"" + rcu.getReactomeUrlForStableIdentifier(reactomId) + "\">" + reactomId + "</a></td>";
+ resultString += "<td" + style + ">" + status + "</td>";
+ resultString += "<td" + style + ">" + df.format(result.getScore() * IProgressUpdater.MAX_PROGRESS) + "%</td>";
+ resultString += error;
+ resultString += "</tr>";
+ writer.println(resultString);
+ System.out.println(resultString);
+ }
+
+ /**
+ * Compares our model reaction to reactome representation.
+ *
+ * @param id
+ * identifier of our reaction
+ * @return result of reaction comparison
+ * @throws IOException
+ * thrown whene there are problems accessing reactome reaction
+ * @throws ComparatorException
+ * thrown when there is a problem with comparison {@link Reaction}
+ * with Reactome object
+ *
+ */
+ private MatchResult checkReaction(String id) throws IOException, ComparatorException {
+ return checkReaction(model.getReactionByReactionId(id));
+ }
+
+ /**
+ * Compares our model reaction to reactome representation.
+ *
+ * @param reaction
+ * our reaction
+ * @return result of reaction comparison
+ * @throws IOException
+ * thrown whene there are problems accessing reactome reaction
+ * @throws ComparatorException
+ * thrown when there is a problem with comparison {@link Reaction}
+ * with Reactome object
+ */
+ private MatchResult checkReaction(Reaction reaction) throws IOException, ComparatorException {
+ String stableIdentifier = rcu.getReactomeIdentifierForReaction(reaction);
+ if (stableIdentifier != null) {
+ String identifier = stableIdentifier.split("\\.")[0];
+ String version = stableIdentifier.split("\\.")[1];
+
+ ReactomeDatabaseObject object = rc.getFullObjectForStableIdentifier(identifier, version);
+ if (object != null && object instanceof ReactomeReactionlikeEvent) {
+ return reactionComparator.compareReactions(reaction, (ReactomeReactionlikeEvent) object);
+
+ } else {
+ MatchResult result = new MatchResult();
+ result.setLocalReaction(reaction);
+ result.setStatus(MatchStatus.INVALID_REACTOME_ID);
+ return result;
+ }
+ }
+ return null;
+ }
+
+ /**
+ * @return the reactionComparator
+ */
+ public ReactionComparator getReactionComparator() {
+ return reactionComparator;
+ }
+
+ /**
+ * @param reactionComparator
+ * the reactionComparator to set
+ */
+ public void setReactionComparator(ReactionComparator reactionComparator) {
+ this.reactionComparator = reactionComparator;
+ }
+
+ /**
+ * @return the dataFormatter
+ */
+ public DataFormatter getDataFormatter() {
+ return dataFormatter;
+ }
+
+ /**
+ * @param dataFormatter
+ * the dataFormatter to set
+ */
+ public void setDataFormatter(DataFormatter dataFormatter) {
+ this.dataFormatter = dataFormatter;
+ }
+
+ /**
+ * @return the rc
+ * @see #rc
+ */
+ public DataSourceUpdater getRc() {
+ return rc;
+ }
+
+ /**
+ * @param rc
+ * the rc to set
+ * @see #rc
+ */
+ public void setRc(DataSourceUpdater rc) {
+ this.rc = rc;
+ }
+
+}
diff --git a/console/src/main/java/lcsb/mapviewer/run/ReactomeExport.java b/console/src/main/java/lcsb/mapviewer/run/ReactomeExport.java
index 79d565bd1e..ef19b3a0c6 100644
--- a/console/src/main/java/lcsb/mapviewer/run/ReactomeExport.java
+++ b/console/src/main/java/lcsb/mapviewer/run/ReactomeExport.java
@@ -1,609 +1,609 @@
-package lcsb.mapviewer.run;
-
-import java.awt.Rectangle;
-import java.awt.geom.Point2D;
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-import org.apache.log4j.PropertyConfigurator;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.AbstractNode;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.reaction.NodeOperator;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.ReactionNode;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Ion;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.persist.ApplicationContextLoader;
-import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
-import lcsb.mapviewer.reactome.utils.DataSourceUpdater;
-import lcsb.mapviewer.reactome.utils.ReactomeQueryUtil;
-
-/**
- * This class create a data that could be used by visualized in reactome
- * visualization framework. It was developed only for test purpose and has no
- * real value.
- */
-public class ReactomeExport {
- /**
- * Size of the map to vizualize.
- */
- private static final int DEFAULT_SIZE = 30000;
- /**
- * Bounds of the map to vizualize.
- */
- private static Rectangle bound = new Rectangle(0, 0, DEFAULT_SIZE, DEFAULT_SIZE);
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ReactomeExport.class.getName());
-
- /**
- * Class used for accessing reactome data.
- */
- @Autowired
- private DataSourceUpdater rc;
-
- /**
- * Util class used for manipulating information in reactome objects.
- */
- @Autowired
- private ReactomeQueryUtil rcu;
-
- /**
- * Static main method used to run this stand alone code.
- *
- * @param args
- * command line arguments
- */
- public static void main(String[] args) {
- PropertyConfigurator.configure("src/main/webapp/WEB-INF/resources/log4j.properties");
- ReactomeExport main = new ReactomeExport();
- ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
- ApplicationContextLoader.injectDependencies(main);
- main.run();
-
- }
-
- /**
- * String containing the result of export.
- */
- private String result = "";
-
- /**
- * Adds text to the output.
- *
- * @param str
- * text to add
- */
- private void print(String str) {
- result += str;
- }
-
- /**
- * Identifier counter used for generating identifiers in the reactome
- * visualization model.
- */
- private int id = 0;
-
- /**
- * Map between aliases in our model and identifiers that will be used in the
- * reactome vizualization model.
- */
- private Map<Element, Integer> tempIds = new HashMap<Element, Integer>();
-
- /**
- * Creates reactome identifier for alias.
- *
- * @param alias
- * object for which identifier is created
- * @return identifier of the alias
- */
- public int addElement(Element alias) {
- int result = -1;
- if (tempIds.containsKey(alias)) {
- result = tempIds.get(alias);
- } else {
- tempIds.put(alias, ++id);
- result = id;
-
- if (alias instanceof Complex) {
- for (Element a : ((Complex) alias).getElements()) {
- addElement(a);
- }
- } else if (alias instanceof Compartment) {
- for (Element a : ((Compartment) alias).getElements()) {
- addElement(a);
- }
- }
- }
-
- return result;
- }
-
- /**
- * Creates file with reactome vizualization.
- */
- private void run() {
- CellDesignerXmlParser p = new CellDesignerXmlParser();
- try {
- Model model = p.createModel(new ConverterParams().filename(PdMapAnnotations.getLastPdFilename()));
- print("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
- print("<Process reactomeId=\"0\">\n");
- print("<Properties>\n");
- print("<displayName>PD map</displayName>\n");
- print("</Properties>\n");
- printAliases(model);
- printReactions(model);
- print("</Process>\n");
-
- PrintWriter writer = new PrintWriter("out/report/reactome-viewer.xml", "UTF-8");
- writer.print(result);
- writer.close();
-
- } catch (Exception e) {
- logger.error(e.getMessage());
- e.printStackTrace();
- }
-
- }
-
- /**
- * Creates representation of the aliases in the reactome visualization model.
- *
- * @param model
- * our model to be visualized
- * @throws IOException
- * thrown when there are problems accessing reactome database
- */
- private void printAliases(Model model) throws IOException {
- print("<Nodes>\n");
- List<Element> aliases = new ArrayList<Element>();
- aliases.addAll(model.getElements());
- Collections.sort(aliases, Element.SIZE_COMPARATOR);
- for (Element alias : aliases) {
- if (!aliasFeasible(alias)) {
- continue;
- }
- int currId = addElement(alias);
- Map<String, String> parameters = new HashMap<>();
- Map<String, String> attributes = new HashMap<>();
-
- attributes.put("id", currId + "");
- attributes.put("position", (int) alias.getCenterX() + " " + (int) alias.getCenterY());
- attributes
- .put("bounds", alias.getX().intValue() + " " + alias.getY().intValue() + " " + alias.getWidth().intValue() + " " + alias.getHeight().intValue());
- attributes.put("textPosition", (int) alias.getCenterX() + " " + (int) alias.getCenterY());
- attributes.put("reactomeId", "0");
-
- Set<Integer> components = new HashSet<Integer>();
- String type = "";
- if (alias instanceof Species) {
- String stableIdentifier = rcu.getReactomeIdentifierForSpecies(alias);
- if (stableIdentifier != null) {
- ReactomeDatabaseObject obj = rc.getFullObjectForStableIdentifier(stableIdentifier);
- if (obj != null && obj.getDbId() != null) {
- attributes.put("reactomeId", obj.getDbId() + "");
- }
- }
- parameters.put("displayName", alias.getName());
- if (alias instanceof Complex) {
- for (Element a : ((Complex) alias).getElements()) {
- components.add(addElement(a));
- }
- }
- }
- if (alias instanceof Compartment) {
- parameters.put("displayName", alias.getName());
- for (Element a : ((Compartment) alias).getElements()) {
- components.add(addElement(a));
- }
- }
-
- if (alias instanceof Complex) {
- type = "org.gk.render.RenderableComplex";
- attributes.put("hideComponents", "true");
- attributes.put("textPosition", (int) alias.getCenterX() + " " + (int) (alias.getY() + alias.getHeight()));
- } else if (alias instanceof SimpleMolecule) {
- type = "org.gk.render.RenderableChemical";
- } else if (alias instanceof Ion) {
- type = "org.gk.render.RenderableChemical";
- } else if (alias instanceof Protein) {
- type = "org.gk.render.RenderableProtein";
- } else if (alias instanceof Species) {
- type = "org.gk.render.RenderableEntity";
- } else if (alias instanceof Compartment) {
- type = "org.gk.render.RenderableCompartment";
- } else {
- logger.debug("Ignoring: " + parameters.get("displayName") + "(" + alias.getClass() + ")");
- continue;
- }
- print("<" + type);
- for (String string : attributes.keySet()) {
- print(" " + string + "=\"" + attributes.get(string) + "\"");
- }
- print(">");
- for (String key : parameters.keySet()) {
- print("<" + key + ">" + parameters.get(key) + "</" + key + ">");
- }
-
- if (components.size() != 0) {
- print("\n <Components>\n");
- for (Integer i : components) {
- print(" <Component id=\"" + i + "\"/>\n");
- }
- print(" </Components>\n");
- }
- print("</" + type + ">\n");
-
- }
- print("</Nodes>\n");
- }
-
- /**
- * Creates reactions in reactome visuazliation model from our model.
- *
- * @param model
- * model to be visualized
- * @throws IOException
- * thrown when there are problems with accessing reactome database
- */
- private void printReactions(Model model) throws IOException {
- print("<Edges>\n");
- for (Reaction reaction : model.getReactions()) {
- if (!isReactionFeasible(reaction)) {
- continue;
- }
- int currId = ++id;
- Map<String, String> parameters = new HashMap<String, String>();
- Map<Integer, String> inputs = new HashMap<Integer, String>();
- Map<Integer, String> outputs = new HashMap<Integer, String>();
- Map<Integer, String> catalysts = new HashMap<Integer, String>();
-
- Map<String, String> attributes = new HashMap<String, String>();
-
- attributes.put("id", currId + "");
- attributes.put("position", (int) reaction.getCenterPoint().getX() + " " + (int) reaction.getCenterPoint().getY());
- attributes.put("points", getReactionMiddlePoints(reaction));
- attributes.put("lineWidth", "1.0");
- attributes.put("reactomeId", "0");
-
- parameters.put("displayName", reaction.getIdReaction());
-
- String stableIdentifier = rcu.getReactomeIdentifierForReaction(reaction);
- if (stableIdentifier != null) {
- ReactomeDatabaseObject obj = rc.getFullObjectForStableIdentifier(stableIdentifier);
- if (obj != null && obj.getDbId() != null) {
- attributes.put("reactomeId", obj.getDbId() + "");
- }
- }
-
- for (ReactionNode node : reaction.getReactionNodes()) {
- Integer id = tempIds.get(node.getElement());
- if (node instanceof Reactant) {
- inputs.put(id, getInputString((Reactant) node));
- } else if (node instanceof Product) {
- outputs.put(id, getOutputString((Product) node));
- } else if (node instanceof Modifier) {
- catalysts.put(id, getModifierString((Modifier) node));
- }
- }
-
- String type = "org.gk.render.RenderableReaction";
-
- print("<" + type);
- for (String string : attributes.keySet()) {
- print(" " + string + "=\"" + attributes.get(string) + "\"");
- }
- print(">\n");
- print(" <Properties>\n");
- for (String key : parameters.keySet()) {
- print(" <" + key + ">" + parameters.get(key) + "</" + key + ">\n");
- }
- print(" </Properties>\n");
-
- if (inputs.size() != 0) {
- print(" <Inputs>\n");
- for (Integer i : inputs.keySet()) {
- print(" <Input id=\"" + i + "\" points=\"" + inputs.get(i) + "\"/>\n");
- }
- print(" </Inputs>\n");
- }
- if (outputs.size() != 0) {
- print(" <Outputs>\n");
- for (Integer i : outputs.keySet()) {
- print(" <Output id=\"" + i + "\" points=\"" + outputs.get(i) + "\"/>\n");
- }
- print(" </Outputs>\n");
- }
- if (catalysts.size() != 0) {
- print(" <Catalysts>\n");
- for (Integer i : catalysts.keySet()) {
- print(" <Catalyst id=\"" + i + "\" points=\"" + catalysts.get(i) + "\"/>\n");
- }
- print(" </Catalysts>\n");
- }
- print("</" + type + ">\n");
-
- }
-
- print("</Edges>\n");
- }
-
- /**
- * Returns string representing modifier.
- *
- * @param node
- * modifier in our model
- * @return string representing modifier that can be used in reactome
- * visualization
- */
- private String getModifierString(ReactionNode node) {
- String result = null;
- List<Point2D> points = node.getLine().getPoints();
- for (int i = 0; i < points.size() - 1; i++) {
- if (result == null) {
- result = "";
- } else {
- result += ", ";
- }
- Point2D point = points.get(i);
- result += (int) point.getX() + " " + (int) point.getY();
- }
- return result;
- }
-
- /**
- * Returns string representing product.
- *
- * @param node
- * product in our model
- * @return string representing product that can be used in reactome
- * visualization
- */
- private String getOutputString(ReactionNode node) {
- for (NodeOperator tmpNode : node.getReaction().getOperators()) {
- if (tmpNode.isProductOperator()) {
- String result = null;
- List<Point2D> points = node.getLine().getPoints();
- for (int i = points.size() - 1; i >= 0; i--) {
- if (result == null) {
- result = "";
- } else {
- result += ", ";
- }
- Point2D point = points.get(i);
- result += (int) point.getX() + " " + (int) point.getY();
- }
- return result;
- }
- }
- Point2D point = node.getLine().getEndPoint();
- String result = (int) point.getX() + " " + (int) point.getY();
- return result;
- }
-
- /**
- * Returns string representing reactant.
- *
- * @param node
- * reactant in our model
- * @return string representing reactant that can be used in reactome
- * visualization
- */
- private String getInputString(ReactionNode node) {
- for (NodeOperator tmpNode : node.getReaction().getOperators()) {
- if (tmpNode.isReactantOperator()) {
- String result = null;
- List<Point2D> points = node.getLine().getPoints();
- for (int i = 0; i < points.size(); i++) {
- if (result == null) {
- result = "";
- } else {
- result += ", ";
- }
- Point2D point = points.get(i);
- result += (int) point.getX() + " " + (int) point.getY();
- }
- return result;
- }
- }
- Point2D point = node.getLine().getPoints().get(0);
- String result = (int) point.getX() + " " + (int) point.getY();
- return result;
- }
-
- /**
- * Check if reaction can be easily transformed into reactome vizualization
- * tool.
- *
- * @param reaction
- * reaction to be checked
- * @return <code>true</code> if reaction can be easily transformed,
- * <code>false</code> otherwise
- */
- private boolean isReactionFeasible(Reaction reaction) {
- for (ReactionNode node : reaction.getReactionNodes()) {
- if (!aliasFeasible(node.getElement())) {
- return false;
- }
- }
- int counter = 0;
- for (NodeOperator node : reaction.getOperators()) {
- if (node.isProductOperator()) {
- counter++;
- }
- if (counter > 1) {
- logger.debug("To many operators in the input: " + reaction.getIdReaction());
- return false;
- }
- }
- counter = 0;
- for (NodeOperator node : reaction.getOperators()) {
- if (node.isReactantOperator()) {
- counter++;
- }
- if (counter > 1) {
- logger.debug("To many operators in the output: " + reaction.getIdReaction());
- return false;
- }
- }
- counter = 0;
- for (NodeOperator node : reaction.getOperators()) {
- if (node.isModifierOperator()) {
- logger.debug("To complicated catalyst: " + reaction.getIdReaction());
- return false;
- }
- }
- return true;
- }
-
- /**
- * Returns string representing reaction line.
- *
- * @param reaction
- * reaction to be transformed
- * @return string representing reaction line
- */
- private String getReactionMiddlePoints(Reaction reaction) {
- String result = null;
- NodeOperator node = null;
- for (NodeOperator n : reaction.getOperators()) {
- if (n.isReactantOperator()) {
- node = n;
- }
- }
- if (node != null) {
- for (Point2D point : node.getLine().getPoints()) {
- if (result == null) {
- result = (int) point.getX() + " " + (int) point.getY();
- } else {
- result += ", " + (int) point.getX() + " " + (int) point.getY();
- }
- }
- } else {
- AbstractNode tmp = null;
- for (AbstractNode reactionNode : reaction.getNodes()) {
- if (reactionNode instanceof Reactant) {
- tmp = reactionNode;
- }
- }
- List<Point2D> points = tmp.getLine().getPoints();
- for (int i = 0; i < points.size(); i++) {
- Point2D point = points.get(i);
- if (result == null) {
- result = (int) point.getX() + " " + (int) point.getY();
- } else {
- result += ", " + (int) point.getX() + " " + (int) point.getY();
- }
- }
- }
-
- node = null;
- for (NodeOperator n : reaction.getOperators()) {
- if (n.isProductOperator()) {
- node = n;
- }
- }
- if (node != null) {
- List<Point2D> points = node.getLine().getPoints();
- for (int i = points.size() - 1; i >= 0; i--) {
- Point2D point = points.get(i);
- if (result == null) {
- result = (int) point.getX() + " " + (int) point.getY();
- } else {
- result += ", " + (int) point.getX() + " " + (int) point.getY();
- }
- }
- } else {
- AbstractNode tmp = null;
- for (AbstractNode reactionNode : reaction.getNodes()) {
- if (reactionNode instanceof Product) {
- tmp = reactionNode;
- }
- }
- List<Point2D> points = tmp.getLine().getPoints();
- for (int i = 0; i < points.size(); i++) {
- Point2D point = points.get(i);
- if (result == null) {
- result = (int) point.getX() + " " + (int) point.getY();
- } else {
- result += ", " + (int) point.getX() + " " + (int) point.getY();
- }
- }
- }
-
- return result;
- }
-
- /**
- * Checks if alias can be put into reactome vizualization.
- *
- * @param alias
- * alias to check
- * @return <code>true</code> if alias can be put into reactome vizualization,
- * <code>false</code> otherwise
- */
- public boolean aliasFeasible(Element alias) {
- Point2D point = new Point2D.Double(alias.getX(), alias.getY());
- Point2D point2 = new Point2D.Double(alias.getX() + alias.getWidth(), alias.getY() + alias.getHeight());
- if (bound.contains(point) && bound.contains(point2)) {
- return true;
- }
- return false;
- }
-
- /**
- * @return the rc
- * @see #rc
- */
- public DataSourceUpdater getRc() {
- return rc;
- }
-
- /**
- * @param rc
- * the rc to set
- * @see #rc
- */
- public void setRc(DataSourceUpdater rc) {
- this.rc = rc;
- }
-
- /**
- * @return the rcu
- * @see #rcu
- */
- public ReactomeQueryUtil getRcu() {
- return rcu;
- }
-
- /**
- * @param rcu
- * the rcu to set
- * @see #rcu
- */
- public void setRcu(ReactomeQueryUtil rcu) {
- this.rcu = rcu;
- }
-
-}
+package lcsb.mapviewer.run;
+
+import java.awt.Rectangle;
+import java.awt.geom.Point2D;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.apache.log4j.PropertyConfigurator;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.AbstractNode;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.reaction.NodeOperator;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.persist.ApplicationContextLoader;
+import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
+import lcsb.mapviewer.reactome.utils.DataSourceUpdater;
+import lcsb.mapviewer.reactome.utils.ReactomeQueryUtil;
+
+/**
+ * This class create a data that could be used by visualized in reactome
+ * visualization framework. It was developed only for test purpose and has no
+ * real value.
+ */
+public class ReactomeExport {
+ /**
+ * Size of the map to vizualize.
+ */
+ private static final int DEFAULT_SIZE = 30000;
+ /**
+ * Bounds of the map to vizualize.
+ */
+ private static Rectangle bound = new Rectangle(0, 0, DEFAULT_SIZE, DEFAULT_SIZE);
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ReactomeExport.class.getName());
+
+ /**
+ * Class used for accessing reactome data.
+ */
+ @Autowired
+ private DataSourceUpdater rc;
+
+ /**
+ * Util class used for manipulating information in reactome objects.
+ */
+ @Autowired
+ private ReactomeQueryUtil rcu;
+
+ /**
+ * Static main method used to run this stand alone code.
+ *
+ * @param args
+ * command line arguments
+ */
+ public static void main(String[] args) {
+ PropertyConfigurator.configure("src/main/webapp/WEB-INF/resources/log4j.properties");
+ ReactomeExport main = new ReactomeExport();
+ ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
+ ApplicationContextLoader.injectDependencies(main);
+ main.run();
+
+ }
+
+ /**
+ * String containing the result of export.
+ */
+ private String result = "";
+
+ /**
+ * Adds text to the output.
+ *
+ * @param str
+ * text to add
+ */
+ private void print(String str) {
+ result += str;
+ }
+
+ /**
+ * Identifier counter used for generating identifiers in the reactome
+ * visualization model.
+ */
+ private int id = 0;
+
+ /**
+ * Map between aliases in our model and identifiers that will be used in the
+ * reactome vizualization model.
+ */
+ private Map<Element, Integer> tempIds = new HashMap<Element, Integer>();
+
+ /**
+ * Creates reactome identifier for alias.
+ *
+ * @param alias
+ * object for which identifier is created
+ * @return identifier of the alias
+ */
+ public int addElement(Element alias) {
+ int result = -1;
+ if (tempIds.containsKey(alias)) {
+ result = tempIds.get(alias);
+ } else {
+ tempIds.put(alias, ++id);
+ result = id;
+
+ if (alias instanceof Complex) {
+ for (Element a : ((Complex) alias).getElements()) {
+ addElement(a);
+ }
+ } else if (alias instanceof Compartment) {
+ for (Element a : ((Compartment) alias).getElements()) {
+ addElement(a);
+ }
+ }
+ }
+
+ return result;
+ }
+
+ /**
+ * Creates file with reactome vizualization.
+ */
+ private void run() {
+ CellDesignerXmlParser p = new CellDesignerXmlParser();
+ try {
+ Model model = p.createModel(new ConverterParams().filename(PdMapAnnotations.getLastPdFilename()));
+ print("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
+ print("<Process reactomeId=\"0\">\n");
+ print("<Properties>\n");
+ print("<displayName>PD map</displayName>\n");
+ print("</Properties>\n");
+ printAliases(model);
+ printReactions(model);
+ print("</Process>\n");
+
+ PrintWriter writer = new PrintWriter("out/report/reactome-viewer.xml", "UTF-8");
+ writer.print(result);
+ writer.close();
+
+ } catch (Exception e) {
+ logger.error(e.getMessage());
+ e.printStackTrace();
+ }
+
+ }
+
+ /**
+ * Creates representation of the aliases in the reactome visualization model.
+ *
+ * @param model
+ * our model to be visualized
+ * @throws IOException
+ * thrown when there are problems accessing reactome database
+ */
+ private void printAliases(Model model) throws IOException {
+ print("<Nodes>\n");
+ List<Element> aliases = new ArrayList<Element>();
+ aliases.addAll(model.getElements());
+ Collections.sort(aliases, Element.SIZE_COMPARATOR);
+ for (Element alias : aliases) {
+ if (!aliasFeasible(alias)) {
+ continue;
+ }
+ int currId = addElement(alias);
+ Map<String, String> parameters = new HashMap<>();
+ Map<String, String> attributes = new HashMap<>();
+
+ attributes.put("id", currId + "");
+ attributes.put("position", (int) alias.getCenterX() + " " + (int) alias.getCenterY());
+ attributes
+ .put("bounds", alias.getX().intValue() + " " + alias.getY().intValue() + " " + alias.getWidth().intValue() + " " + alias.getHeight().intValue());
+ attributes.put("textPosition", (int) alias.getCenterX() + " " + (int) alias.getCenterY());
+ attributes.put("reactomeId", "0");
+
+ Set<Integer> components = new HashSet<Integer>();
+ String type = "";
+ if (alias instanceof Species) {
+ String stableIdentifier = rcu.getReactomeIdentifierForSpecies(alias);
+ if (stableIdentifier != null) {
+ ReactomeDatabaseObject obj = rc.getFullObjectForStableIdentifier(stableIdentifier);
+ if (obj != null && obj.getDbId() != null) {
+ attributes.put("reactomeId", obj.getDbId() + "");
+ }
+ }
+ parameters.put("displayName", alias.getName());
+ if (alias instanceof Complex) {
+ for (Element a : ((Complex) alias).getElements()) {
+ components.add(addElement(a));
+ }
+ }
+ }
+ if (alias instanceof Compartment) {
+ parameters.put("displayName", alias.getName());
+ for (Element a : ((Compartment) alias).getElements()) {
+ components.add(addElement(a));
+ }
+ }
+
+ if (alias instanceof Complex) {
+ type = "org.gk.render.RenderableComplex";
+ attributes.put("hideComponents", "true");
+ attributes.put("textPosition", (int) alias.getCenterX() + " " + (int) (alias.getY() + alias.getHeight()));
+ } else if (alias instanceof SimpleMolecule) {
+ type = "org.gk.render.RenderableChemical";
+ } else if (alias instanceof Ion) {
+ type = "org.gk.render.RenderableChemical";
+ } else if (alias instanceof Protein) {
+ type = "org.gk.render.RenderableProtein";
+ } else if (alias instanceof Species) {
+ type = "org.gk.render.RenderableEntity";
+ } else if (alias instanceof Compartment) {
+ type = "org.gk.render.RenderableCompartment";
+ } else {
+ logger.debug("Ignoring: " + parameters.get("displayName") + "(" + alias.getClass() + ")");
+ continue;
+ }
+ print("<" + type);
+ for (String string : attributes.keySet()) {
+ print(" " + string + "=\"" + attributes.get(string) + "\"");
+ }
+ print(">");
+ for (String key : parameters.keySet()) {
+ print("<" + key + ">" + parameters.get(key) + "</" + key + ">");
+ }
+
+ if (components.size() != 0) {
+ print("\n <Components>\n");
+ for (Integer i : components) {
+ print(" <Component id=\"" + i + "\"/>\n");
+ }
+ print(" </Components>\n");
+ }
+ print("</" + type + ">\n");
+
+ }
+ print("</Nodes>\n");
+ }
+
+ /**
+ * Creates reactions in reactome visuazliation model from our model.
+ *
+ * @param model
+ * model to be visualized
+ * @throws IOException
+ * thrown when there are problems with accessing reactome database
+ */
+ private void printReactions(Model model) throws IOException {
+ print("<Edges>\n");
+ for (Reaction reaction : model.getReactions()) {
+ if (!isReactionFeasible(reaction)) {
+ continue;
+ }
+ int currId = ++id;
+ Map<String, String> parameters = new HashMap<String, String>();
+ Map<Integer, String> inputs = new HashMap<Integer, String>();
+ Map<Integer, String> outputs = new HashMap<Integer, String>();
+ Map<Integer, String> catalysts = new HashMap<Integer, String>();
+
+ Map<String, String> attributes = new HashMap<String, String>();
+
+ attributes.put("id", currId + "");
+ attributes.put("position", (int) reaction.getCenterPoint().getX() + " " + (int) reaction.getCenterPoint().getY());
+ attributes.put("points", getReactionMiddlePoints(reaction));
+ attributes.put("lineWidth", "1.0");
+ attributes.put("reactomeId", "0");
+
+ parameters.put("displayName", reaction.getIdReaction());
+
+ String stableIdentifier = rcu.getReactomeIdentifierForReaction(reaction);
+ if (stableIdentifier != null) {
+ ReactomeDatabaseObject obj = rc.getFullObjectForStableIdentifier(stableIdentifier);
+ if (obj != null && obj.getDbId() != null) {
+ attributes.put("reactomeId", obj.getDbId() + "");
+ }
+ }
+
+ for (ReactionNode node : reaction.getReactionNodes()) {
+ Integer id = tempIds.get(node.getElement());
+ if (node instanceof Reactant) {
+ inputs.put(id, getInputString((Reactant) node));
+ } else if (node instanceof Product) {
+ outputs.put(id, getOutputString((Product) node));
+ } else if (node instanceof Modifier) {
+ catalysts.put(id, getModifierString((Modifier) node));
+ }
+ }
+
+ String type = "org.gk.render.RenderableReaction";
+
+ print("<" + type);
+ for (String string : attributes.keySet()) {
+ print(" " + string + "=\"" + attributes.get(string) + "\"");
+ }
+ print(">\n");
+ print(" <Properties>\n");
+ for (String key : parameters.keySet()) {
+ print(" <" + key + ">" + parameters.get(key) + "</" + key + ">\n");
+ }
+ print(" </Properties>\n");
+
+ if (inputs.size() != 0) {
+ print(" <Inputs>\n");
+ for (Integer i : inputs.keySet()) {
+ print(" <Input id=\"" + i + "\" points=\"" + inputs.get(i) + "\"/>\n");
+ }
+ print(" </Inputs>\n");
+ }
+ if (outputs.size() != 0) {
+ print(" <Outputs>\n");
+ for (Integer i : outputs.keySet()) {
+ print(" <Output id=\"" + i + "\" points=\"" + outputs.get(i) + "\"/>\n");
+ }
+ print(" </Outputs>\n");
+ }
+ if (catalysts.size() != 0) {
+ print(" <Catalysts>\n");
+ for (Integer i : catalysts.keySet()) {
+ print(" <Catalyst id=\"" + i + "\" points=\"" + catalysts.get(i) + "\"/>\n");
+ }
+ print(" </Catalysts>\n");
+ }
+ print("</" + type + ">\n");
+
+ }
+
+ print("</Edges>\n");
+ }
+
+ /**
+ * Returns string representing modifier.
+ *
+ * @param node
+ * modifier in our model
+ * @return string representing modifier that can be used in reactome
+ * visualization
+ */
+ private String getModifierString(ReactionNode node) {
+ String result = null;
+ List<Point2D> points = node.getLine().getPoints();
+ for (int i = 0; i < points.size() - 1; i++) {
+ if (result == null) {
+ result = "";
+ } else {
+ result += ", ";
+ }
+ Point2D point = points.get(i);
+ result += (int) point.getX() + " " + (int) point.getY();
+ }
+ return result;
+ }
+
+ /**
+ * Returns string representing product.
+ *
+ * @param node
+ * product in our model
+ * @return string representing product that can be used in reactome
+ * visualization
+ */
+ private String getOutputString(ReactionNode node) {
+ for (NodeOperator tmpNode : node.getReaction().getOperators()) {
+ if (tmpNode.isProductOperator()) {
+ String result = null;
+ List<Point2D> points = node.getLine().getPoints();
+ for (int i = points.size() - 1; i >= 0; i--) {
+ if (result == null) {
+ result = "";
+ } else {
+ result += ", ";
+ }
+ Point2D point = points.get(i);
+ result += (int) point.getX() + " " + (int) point.getY();
+ }
+ return result;
+ }
+ }
+ Point2D point = node.getLine().getEndPoint();
+ String result = (int) point.getX() + " " + (int) point.getY();
+ return result;
+ }
+
+ /**
+ * Returns string representing reactant.
+ *
+ * @param node
+ * reactant in our model
+ * @return string representing reactant that can be used in reactome
+ * visualization
+ */
+ private String getInputString(ReactionNode node) {
+ for (NodeOperator tmpNode : node.getReaction().getOperators()) {
+ if (tmpNode.isReactantOperator()) {
+ String result = null;
+ List<Point2D> points = node.getLine().getPoints();
+ for (int i = 0; i < points.size(); i++) {
+ if (result == null) {
+ result = "";
+ } else {
+ result += ", ";
+ }
+ Point2D point = points.get(i);
+ result += (int) point.getX() + " " + (int) point.getY();
+ }
+ return result;
+ }
+ }
+ Point2D point = node.getLine().getPoints().get(0);
+ String result = (int) point.getX() + " " + (int) point.getY();
+ return result;
+ }
+
+ /**
+ * Check if reaction can be easily transformed into reactome vizualization
+ * tool.
+ *
+ * @param reaction
+ * reaction to be checked
+ * @return <code>true</code> if reaction can be easily transformed,
+ * <code>false</code> otherwise
+ */
+ private boolean isReactionFeasible(Reaction reaction) {
+ for (ReactionNode node : reaction.getReactionNodes()) {
+ if (!aliasFeasible(node.getElement())) {
+ return false;
+ }
+ }
+ int counter = 0;
+ for (NodeOperator node : reaction.getOperators()) {
+ if (node.isProductOperator()) {
+ counter++;
+ }
+ if (counter > 1) {
+ logger.debug("To many operators in the input: " + reaction.getIdReaction());
+ return false;
+ }
+ }
+ counter = 0;
+ for (NodeOperator node : reaction.getOperators()) {
+ if (node.isReactantOperator()) {
+ counter++;
+ }
+ if (counter > 1) {
+ logger.debug("To many operators in the output: " + reaction.getIdReaction());
+ return false;
+ }
+ }
+ counter = 0;
+ for (NodeOperator node : reaction.getOperators()) {
+ if (node.isModifierOperator()) {
+ logger.debug("To complicated catalyst: " + reaction.getIdReaction());
+ return false;
+ }
+ }
+ return true;
+ }
+
+ /**
+ * Returns string representing reaction line.
+ *
+ * @param reaction
+ * reaction to be transformed
+ * @return string representing reaction line
+ */
+ private String getReactionMiddlePoints(Reaction reaction) {
+ String result = null;
+ NodeOperator node = null;
+ for (NodeOperator n : reaction.getOperators()) {
+ if (n.isReactantOperator()) {
+ node = n;
+ }
+ }
+ if (node != null) {
+ for (Point2D point : node.getLine().getPoints()) {
+ if (result == null) {
+ result = (int) point.getX() + " " + (int) point.getY();
+ } else {
+ result += ", " + (int) point.getX() + " " + (int) point.getY();
+ }
+ }
+ } else {
+ AbstractNode tmp = null;
+ for (AbstractNode reactionNode : reaction.getNodes()) {
+ if (reactionNode instanceof Reactant) {
+ tmp = reactionNode;
+ }
+ }
+ List<Point2D> points = tmp.getLine().getPoints();
+ for (int i = 0; i < points.size(); i++) {
+ Point2D point = points.get(i);
+ if (result == null) {
+ result = (int) point.getX() + " " + (int) point.getY();
+ } else {
+ result += ", " + (int) point.getX() + " " + (int) point.getY();
+ }
+ }
+ }
+
+ node = null;
+ for (NodeOperator n : reaction.getOperators()) {
+ if (n.isProductOperator()) {
+ node = n;
+ }
+ }
+ if (node != null) {
+ List<Point2D> points = node.getLine().getPoints();
+ for (int i = points.size() - 1; i >= 0; i--) {
+ Point2D point = points.get(i);
+ if (result == null) {
+ result = (int) point.getX() + " " + (int) point.getY();
+ } else {
+ result += ", " + (int) point.getX() + " " + (int) point.getY();
+ }
+ }
+ } else {
+ AbstractNode tmp = null;
+ for (AbstractNode reactionNode : reaction.getNodes()) {
+ if (reactionNode instanceof Product) {
+ tmp = reactionNode;
+ }
+ }
+ List<Point2D> points = tmp.getLine().getPoints();
+ for (int i = 0; i < points.size(); i++) {
+ Point2D point = points.get(i);
+ if (result == null) {
+ result = (int) point.getX() + " " + (int) point.getY();
+ } else {
+ result += ", " + (int) point.getX() + " " + (int) point.getY();
+ }
+ }
+ }
+
+ return result;
+ }
+
+ /**
+ * Checks if alias can be put into reactome vizualization.
+ *
+ * @param alias
+ * alias to check
+ * @return <code>true</code> if alias can be put into reactome vizualization,
+ * <code>false</code> otherwise
+ */
+ public boolean aliasFeasible(Element alias) {
+ Point2D point = new Point2D.Double(alias.getX(), alias.getY());
+ Point2D point2 = new Point2D.Double(alias.getX() + alias.getWidth(), alias.getY() + alias.getHeight());
+ if (bound.contains(point) && bound.contains(point2)) {
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * @return the rc
+ * @see #rc
+ */
+ public DataSourceUpdater getRc() {
+ return rc;
+ }
+
+ /**
+ * @param rc
+ * the rc to set
+ * @see #rc
+ */
+ public void setRc(DataSourceUpdater rc) {
+ this.rc = rc;
+ }
+
+ /**
+ * @return the rcu
+ * @see #rcu
+ */
+ public ReactomeQueryUtil getRcu() {
+ return rcu;
+ }
+
+ /**
+ * @param rcu
+ * the rcu to set
+ * @see #rcu
+ */
+ public void setRcu(ReactomeQueryUtil rcu) {
+ this.rcu = rcu;
+ }
+
+}
diff --git a/console/src/main/java/lcsb/mapviewer/run/Statistics.java b/console/src/main/java/lcsb/mapviewer/run/Statistics.java
index 600a4ba8a0..d812241e9e 100644
--- a/console/src/main/java/lcsb/mapviewer/run/Statistics.java
+++ b/console/src/main/java/lcsb/mapviewer/run/Statistics.java
@@ -1,388 +1,388 @@
-package lcsb.mapviewer.run;
-
-import java.text.DecimalFormat;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.annotation.data.Article;
-import lcsb.mapviewer.annotation.services.ModelAnnotator;
-import lcsb.mapviewer.annotation.services.ProblematicAnnotation;
-import lcsb.mapviewer.annotation.services.PubmedParser;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.persist.ApplicationContextLoader;
-import lcsb.mapviewer.persist.DbUtils;
-
-/**
- * Class used for analyzing the CellDEsigner model and generating some statistic
- * about it.
- *
- * @author Piotr Gawron
- *
- */
-public class Statistics {
- /**
- * Number of nanoseconds in second.
- */
- private static final double NANOSECONDS_IN_SECOND = 1000000000.0;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(Statistics.class.getName());
-
- /**
- * Module that allows to annotate maps.
- */
- @Autowired
- private ModelAnnotator modelAnnotator;
-
- /**
- * Local backend to the pubmed data.
- */
- @Autowired
- private PubmedParser pubmedBackend;
-
- /**
- * Utils that help to manage the sessions in custom multithreaded
- * implementation.
- */
- @Autowired
- private DbUtils dbUtils;
-
- /**
- * Static main method used to run this stand alone code.
- *
- * @param args
- * command line arguments
- */
- public static void main(String[] args) {
- try {
- String[] modelFileNames = new String[] { "testFiles/pd_full/PD_160714_2/PD_160714_2.xml", //
- "testFiles/pd_full/PD_160714_2/submaps/PARK2_substrates.xml", //
- "testFiles/pd_full/PD_160714_2/submaps/Ubiquitin_proteasome_system.xml", //
- "testFiles/pd_full/PD_160714_2/submaps/Fatty_acid_and_ketone_body_metabolism.xml", //
- };
-
- long startTime = System.nanoTime();
-
- Statistics main = new Statistics();
- ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
- ApplicationContextLoader.injectDependencies(main);
-
- main.run(modelFileNames);
- long endTime = System.nanoTime();
-
- long duration = endTime - startTime;
- double sec = duration / NANOSECONDS_IN_SECOND;
- System.out.println("Duration: " + new DecimalFormat("#.###").format(sec) + "s");
- } catch (Exception e) {
- e.printStackTrace();
- }
-
- }
-
- /**
- * Generate statistics.
- *
- * @param fileNames
- * filenames for the models used for statistic generation
- */
- public void run(String[] fileNames) {
- dbUtils.createSessionForCurrentThread();
- List<Model> models = new ArrayList<>();
- try {
- // String modelName = PdMapAnnotations.getLastPdFilename();
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- for (String name : fileNames) {
- Model model = parser.createModel(new ConverterParams().filename(name));
- models.add(model);
- }
-
- IProgressUpdater updater = new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- logger.debug("Progress: " + progress);
- }
- };
- for (Model model : models) {
- modelAnnotator.performAnnotations(model, updater);
- }
- // modelAnnotator.removeIncorrectAnnotations(model, updater);
-
- printStatistics(models);
-
- // printAnnotationInformation(model);
- //
- // PrintWriter writer = new PrintWriter("tmp.html", "UTF-8");
- // writer.println(createPubmedExportString(model));
- // writer.close();
- } catch (Exception e) {
- logger.error(e.getMessage());
- e.printStackTrace();
- }
-
- dbUtils.closeSessionForCurrentThread();
- }
-
- /**
- * Prints statistics for the model.
- *
- * @param models
- * models under analysis
- */
- protected void printStatistics(List<Model> models) {
- int reactionNumber = 0;
- for (Model model2 : models) {
- reactionNumber += model2.getReactions().size();
- }
- print("Reactions: ");
- print(" number: " + reactionNumber);
- Map<String, Set<String>> ids = new HashMap<String, Set<String>>();
- int pubmedReactions = 0;
- for (Model model : models) {
- for (Reaction reaction : model.getReactions()) {
- for (MiriamData md : reaction.getMiriamData()) {
- String type = md.getDataType().getCommonName();
- Set<String> set = ids.get(type);
- if (set == null) {
- set = new HashSet<String>();
- ids.put(type, set);
- }
- set.add(md.getResource());
- }
- if (reaction.getMiriamData().size() == 1) {
- if (reaction.getMiriamData().iterator().next().getDataType().equals(MiriamType.PUBMED)) {
- pubmedReactions++;
- }
- }
- }
- }
-
- for (String string : ids.keySet()) {
- print(" " + string + ": " + ids.get(string).size());
- }
- print(" pubmed reactions: " + pubmedReactions);
-
- ids.clear();
- print("-----------------------------");
- print("Elements: ");
- Set<String> names = new HashSet<>();
- Map<String, Set<String>> typeNames = new HashMap<>();
-
- for (Model model : models) {
- for (Element element : model.getElements()) {
- if (element instanceof Species) {
- names.add(element.getName());
- Set<String> tmp = typeNames.get(element.getClass().getName());
- if (tmp == null) {
- tmp = new HashSet<String>();
- typeNames.put(element.getClass().getName(), tmp);
- }
- tmp.add(element.getName());
- for (MiriamData md : element.getMiriamData()) {
- String type = md.getDataType().getCommonName();
- Set<String> set = ids.get(type);
- if (set == null) {
- set = new HashSet<String>();
- ids.put(type, set);
- }
- set.add(md.getResource());
- }
- }
- }
- }
- print(" distinct names: " + names.size());
-
- for (String string : ids.keySet()) {
- print(" " + string + ": " + ids.get(string).size());
- }
-
- print("-----------------------------");
- print(" distinct elements types: ");
- for (String string : typeNames.keySet()) {
- print(" " + string + ": " + typeNames.get(string).size());
- }
-
- Set<String> set = new HashSet<String>();
- for (Model model : models) {
- for (Compartment comp : model.getCompartments()) {
- set.add(comp.getName());
- }
- }
- print(" compartments: " + set.size());
- }
-
- /**
- * Prints information about inproper annotations.
- *
- * @param model
- * model under analysis
- */
- protected void printAnnotationInformation(Model model) {
- print("-----------------------------");
- print("Improper annotations:");
- Collection<? extends ProblematicAnnotation> improper = modelAnnotator.findImproperAnnotations(model, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, null);
- for (ProblematicAnnotation improperAnnotation : improper) {
- print(improperAnnotation.toString());
- }
- print("-----------------------------");
- print("Missing annotations:");
- Collection<ProblematicAnnotation> missing = modelAnnotator.findMissingAnnotations(model, null);
- for (ProblematicAnnotation improperAnnotation : missing) {
- print(improperAnnotation.toString());
- }
- print("-----------------------------");
- print("Complex annotations:");
- for (Element element : model.getElements()) {
- if (element instanceof Complex && element.getMiriamData().size() > 0) {
- print(element.getClass().getSimpleName() + ";\t\tname=" + element.getName() + ";\t\tid=" + element.getElementId());
- }
- }
- print("-----------------------------");
- print("Pubmed annotated elements:");
- // Collection<? extends ProblematicAnnotation> pubmes =
- // modelAnnotator.findPubmedAnnotatedElements(model);
- // for (ProblematicAnnotation improperAnnotation : pubmes) {
- //
- // if (improperAnnotation.getObject() != null) {
- // AnnotatedObject element = improperAnnotation.getObject();
- // String ids = "";
- // for (MiriamData md : improperAnnotation.getMd()) {
- // ids += md.getResource() + ", ";
- // }
- // print(element.getClass().getSimpleName() + ";\t\tname=" +
- // element.getName() + ";\t\tid=" + element.getElementId() + ";\t\tpubmed= "
- // + ids);
- // }
- // }
- }
-
- /**
- * Prints line of the report.
- *
- * @param string
- * text to print
- */
- void print(String string) {
- System.out.println(string);
- }
-
- /**
- * @return the modelAnnotator
- */
- public ModelAnnotator getModelAnnotator() {
- return modelAnnotator;
- }
-
- /**
- * @param modelAnnotator
- * the modelAnnotator to set
- */
- public void setModelAnnotator(ModelAnnotator modelAnnotator) {
- this.modelAnnotator = modelAnnotator;
- }
-
- /**
- * Create tab separated string with information about pubmed articles used in
- * the map.
- *
- * @param model
- * analyzed model
- * @return tab separated string with information about pubmed articles
- * @throws Exception
- * thrown when there is a problem with pubmed
- */
- protected String createPubmedExportString(Model model) throws Exception {
- Map<String, List<String>> links = new HashMap<String, List<String>>();
- for (Element element : model.getElements()) {
- for (MiriamData md : element.getMiriamData()) {
- if (MiriamType.PUBMED.equals(md.getDataType())) {
- List<String> list = links.get(md.getResource());
- if (list == null) {
- list = new ArrayList<String>();
- links.put(md.getResource(), list);
- }
- String address = "<a href =\"" + Configuration.PUBLICALY_AVAILABLE_PD_MAP + "&search=species:" + element.getElementId() + "\">" + element.getName()
- + "</a>";
- list.add(address);
- }
- }
- }
-
- for (Reaction reaction : model.getReactions()) {
- for (MiriamData md : reaction.getMiriamData()) {
- if (MiriamType.PUBMED.equals(md.getDataType())) {
- List<String> list = links.get(md.getResource());
- if (list == null) {
- list = new ArrayList<String>();
- links.put(md.getResource(), list);
- }
- String address = "<a href =\"" + PdMapAnnotations.getLinkForReaction(reaction) + "\">Reaction: " + reaction.getIdReaction() + "</a>";
- list.add(address);
- }
- }
- }
-
- StringBuilder result = new StringBuilder();
-
- result.append("<html><head/><body><table>");
- for (String string : links.keySet()) {
- Article article = pubmedBackend.getPubmedArticleById(Integer.valueOf(string));
- result.append("<tr><td><a href =\"" + article.getLink() + "\">" + string + "</a></td>");
- result.append("<td>" + article.getTitle() + "</td>");
- result.append("<td>" + article.getStringAuthors() + "</td>");
- result.append("<td>" + article.getJournal() + "</td>");
- result.append("<td>" + article.getYear() + "</td>");
- for (String str : links.get(string)) {
- result.append("<td>");
- result.append(str);
- result.append("</td>");
- }
- result.append("</tr>\n");
- }
- result.append("</table></body></html>");
-
- return result.toString();
- }
-
- /**
- * @return the pubmedBackend
- * @see #pubmedBackend
- */
- public PubmedParser getPubmedBackend() {
- return pubmedBackend;
- }
-
- /**
- * @param pubmedBackend
- * the pubmedBackend to set
- * @see #pubmedBackend
- */
- public void setPubmedBackend(PubmedParser pubmedBackend) {
- this.pubmedBackend = pubmedBackend;
- }
-
-}
+package lcsb.mapviewer.run;
+
+import java.text.DecimalFormat;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.data.Article;
+import lcsb.mapviewer.annotation.services.ModelAnnotator;
+import lcsb.mapviewer.annotation.services.ProblematicAnnotation;
+import lcsb.mapviewer.annotation.services.PubmedParser;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.persist.ApplicationContextLoader;
+import lcsb.mapviewer.persist.DbUtils;
+
+/**
+ * Class used for analyzing the CellDEsigner model and generating some statistic
+ * about it.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class Statistics {
+ /**
+ * Number of nanoseconds in second.
+ */
+ private static final double NANOSECONDS_IN_SECOND = 1000000000.0;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(Statistics.class.getName());
+
+ /**
+ * Module that allows to annotate maps.
+ */
+ @Autowired
+ private ModelAnnotator modelAnnotator;
+
+ /**
+ * Local backend to the pubmed data.
+ */
+ @Autowired
+ private PubmedParser pubmedBackend;
+
+ /**
+ * Utils that help to manage the sessions in custom multithreaded
+ * implementation.
+ */
+ @Autowired
+ private DbUtils dbUtils;
+
+ /**
+ * Static main method used to run this stand alone code.
+ *
+ * @param args
+ * command line arguments
+ */
+ public static void main(String[] args) {
+ try {
+ String[] modelFileNames = new String[] { "testFiles/pd_full/PD_160714_2/PD_160714_2.xml", //
+ "testFiles/pd_full/PD_160714_2/submaps/PARK2_substrates.xml", //
+ "testFiles/pd_full/PD_160714_2/submaps/Ubiquitin_proteasome_system.xml", //
+ "testFiles/pd_full/PD_160714_2/submaps/Fatty_acid_and_ketone_body_metabolism.xml", //
+ };
+
+ long startTime = System.nanoTime();
+
+ Statistics main = new Statistics();
+ ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
+ ApplicationContextLoader.injectDependencies(main);
+
+ main.run(modelFileNames);
+ long endTime = System.nanoTime();
+
+ long duration = endTime - startTime;
+ double sec = duration / NANOSECONDS_IN_SECOND;
+ System.out.println("Duration: " + new DecimalFormat("#.###").format(sec) + "s");
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ }
+
+ /**
+ * Generate statistics.
+ *
+ * @param fileNames
+ * filenames for the models used for statistic generation
+ */
+ public void run(String[] fileNames) {
+ dbUtils.createSessionForCurrentThread();
+ List<Model> models = new ArrayList<>();
+ try {
+ // String modelName = PdMapAnnotations.getLastPdFilename();
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ for (String name : fileNames) {
+ Model model = parser.createModel(new ConverterParams().filename(name));
+ models.add(model);
+ }
+
+ IProgressUpdater updater = new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ logger.debug("Progress: " + progress);
+ }
+ };
+ for (Model model : models) {
+ modelAnnotator.performAnnotations(model, updater);
+ }
+ // modelAnnotator.removeIncorrectAnnotations(model, updater);
+
+ printStatistics(models);
+
+ // printAnnotationInformation(model);
+ //
+ // PrintWriter writer = new PrintWriter("tmp.html", "UTF-8");
+ // writer.println(createPubmedExportString(model));
+ // writer.close();
+ } catch (Exception e) {
+ logger.error(e.getMessage());
+ e.printStackTrace();
+ }
+
+ dbUtils.closeSessionForCurrentThread();
+ }
+
+ /**
+ * Prints statistics for the model.
+ *
+ * @param models
+ * models under analysis
+ */
+ protected void printStatistics(List<Model> models) {
+ int reactionNumber = 0;
+ for (Model model2 : models) {
+ reactionNumber += model2.getReactions().size();
+ }
+ print("Reactions: ");
+ print(" number: " + reactionNumber);
+ Map<String, Set<String>> ids = new HashMap<String, Set<String>>();
+ int pubmedReactions = 0;
+ for (Model model : models) {
+ for (Reaction reaction : model.getReactions()) {
+ for (MiriamData md : reaction.getMiriamData()) {
+ String type = md.getDataType().getCommonName();
+ Set<String> set = ids.get(type);
+ if (set == null) {
+ set = new HashSet<String>();
+ ids.put(type, set);
+ }
+ set.add(md.getResource());
+ }
+ if (reaction.getMiriamData().size() == 1) {
+ if (reaction.getMiriamData().iterator().next().getDataType().equals(MiriamType.PUBMED)) {
+ pubmedReactions++;
+ }
+ }
+ }
+ }
+
+ for (String string : ids.keySet()) {
+ print(" " + string + ": " + ids.get(string).size());
+ }
+ print(" pubmed reactions: " + pubmedReactions);
+
+ ids.clear();
+ print("-----------------------------");
+ print("Elements: ");
+ Set<String> names = new HashSet<>();
+ Map<String, Set<String>> typeNames = new HashMap<>();
+
+ for (Model model : models) {
+ for (Element element : model.getElements()) {
+ if (element instanceof Species) {
+ names.add(element.getName());
+ Set<String> tmp = typeNames.get(element.getClass().getName());
+ if (tmp == null) {
+ tmp = new HashSet<String>();
+ typeNames.put(element.getClass().getName(), tmp);
+ }
+ tmp.add(element.getName());
+ for (MiriamData md : element.getMiriamData()) {
+ String type = md.getDataType().getCommonName();
+ Set<String> set = ids.get(type);
+ if (set == null) {
+ set = new HashSet<String>();
+ ids.put(type, set);
+ }
+ set.add(md.getResource());
+ }
+ }
+ }
+ }
+ print(" distinct names: " + names.size());
+
+ for (String string : ids.keySet()) {
+ print(" " + string + ": " + ids.get(string).size());
+ }
+
+ print("-----------------------------");
+ print(" distinct elements types: ");
+ for (String string : typeNames.keySet()) {
+ print(" " + string + ": " + typeNames.get(string).size());
+ }
+
+ Set<String> set = new HashSet<String>();
+ for (Model model : models) {
+ for (Compartment comp : model.getCompartments()) {
+ set.add(comp.getName());
+ }
+ }
+ print(" compartments: " + set.size());
+ }
+
+ /**
+ * Prints information about inproper annotations.
+ *
+ * @param model
+ * model under analysis
+ */
+ protected void printAnnotationInformation(Model model) {
+ print("-----------------------------");
+ print("Improper annotations:");
+ Collection<? extends ProblematicAnnotation> improper = modelAnnotator.findImproperAnnotations(model, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, null);
+ for (ProblematicAnnotation improperAnnotation : improper) {
+ print(improperAnnotation.toString());
+ }
+ print("-----------------------------");
+ print("Missing annotations:");
+ Collection<ProblematicAnnotation> missing = modelAnnotator.findMissingAnnotations(model, null);
+ for (ProblematicAnnotation improperAnnotation : missing) {
+ print(improperAnnotation.toString());
+ }
+ print("-----------------------------");
+ print("Complex annotations:");
+ for (Element element : model.getElements()) {
+ if (element instanceof Complex && element.getMiriamData().size() > 0) {
+ print(element.getClass().getSimpleName() + ";\t\tname=" + element.getName() + ";\t\tid=" + element.getElementId());
+ }
+ }
+ print("-----------------------------");
+ print("Pubmed annotated elements:");
+ // Collection<? extends ProblematicAnnotation> pubmes =
+ // modelAnnotator.findPubmedAnnotatedElements(model);
+ // for (ProblematicAnnotation improperAnnotation : pubmes) {
+ //
+ // if (improperAnnotation.getObject() != null) {
+ // AnnotatedObject element = improperAnnotation.getObject();
+ // String ids = "";
+ // for (MiriamData md : improperAnnotation.getMd()) {
+ // ids += md.getResource() + ", ";
+ // }
+ // print(element.getClass().getSimpleName() + ";\t\tname=" +
+ // element.getName() + ";\t\tid=" + element.getElementId() + ";\t\tpubmed= "
+ // + ids);
+ // }
+ // }
+ }
+
+ /**
+ * Prints line of the report.
+ *
+ * @param string
+ * text to print
+ */
+ void print(String string) {
+ System.out.println(string);
+ }
+
+ /**
+ * @return the modelAnnotator
+ */
+ public ModelAnnotator getModelAnnotator() {
+ return modelAnnotator;
+ }
+
+ /**
+ * @param modelAnnotator
+ * the modelAnnotator to set
+ */
+ public void setModelAnnotator(ModelAnnotator modelAnnotator) {
+ this.modelAnnotator = modelAnnotator;
+ }
+
+ /**
+ * Create tab separated string with information about pubmed articles used in
+ * the map.
+ *
+ * @param model
+ * analyzed model
+ * @return tab separated string with information about pubmed articles
+ * @throws Exception
+ * thrown when there is a problem with pubmed
+ */
+ protected String createPubmedExportString(Model model) throws Exception {
+ Map<String, List<String>> links = new HashMap<String, List<String>>();
+ for (Element element : model.getElements()) {
+ for (MiriamData md : element.getMiriamData()) {
+ if (MiriamType.PUBMED.equals(md.getDataType())) {
+ List<String> list = links.get(md.getResource());
+ if (list == null) {
+ list = new ArrayList<String>();
+ links.put(md.getResource(), list);
+ }
+ String address = "<a href =\"" + Configuration.PUBLICALY_AVAILABLE_PD_MAP + "&search=species:" + element.getElementId() + "\">" + element.getName()
+ + "</a>";
+ list.add(address);
+ }
+ }
+ }
+
+ for (Reaction reaction : model.getReactions()) {
+ for (MiriamData md : reaction.getMiriamData()) {
+ if (MiriamType.PUBMED.equals(md.getDataType())) {
+ List<String> list = links.get(md.getResource());
+ if (list == null) {
+ list = new ArrayList<String>();
+ links.put(md.getResource(), list);
+ }
+ String address = "<a href =\"" + PdMapAnnotations.getLinkForReaction(reaction) + "\">Reaction: " + reaction.getIdReaction() + "</a>";
+ list.add(address);
+ }
+ }
+ }
+
+ StringBuilder result = new StringBuilder();
+
+ result.append("<html><head/><body><table>");
+ for (String string : links.keySet()) {
+ Article article = pubmedBackend.getPubmedArticleById(Integer.valueOf(string));
+ result.append("<tr><td><a href =\"" + article.getLink() + "\">" + string + "</a></td>");
+ result.append("<td>" + article.getTitle() + "</td>");
+ result.append("<td>" + article.getStringAuthors() + "</td>");
+ result.append("<td>" + article.getJournal() + "</td>");
+ result.append("<td>" + article.getYear() + "</td>");
+ for (String str : links.get(string)) {
+ result.append("<td>");
+ result.append(str);
+ result.append("</td>");
+ }
+ result.append("</tr>\n");
+ }
+ result.append("</table></body></html>");
+
+ return result.toString();
+ }
+
+ /**
+ * @return the pubmedBackend
+ * @see #pubmedBackend
+ */
+ public PubmedParser getPubmedBackend() {
+ return pubmedBackend;
+ }
+
+ /**
+ * @param pubmedBackend
+ * the pubmedBackend to set
+ * @see #pubmedBackend
+ */
+ public void setPubmedBackend(PubmedParser pubmedBackend) {
+ this.pubmedBackend = pubmedBackend;
+ }
+
+}
diff --git a/console/src/main/java/lcsb/mapviewer/run/UnknownReactionInReactome.java b/console/src/main/java/lcsb/mapviewer/run/UnknownReactionInReactome.java
index a528f95489..3f0e61f966 100644
--- a/console/src/main/java/lcsb/mapviewer/run/UnknownReactionInReactome.java
+++ b/console/src/main/java/lcsb/mapviewer/run/UnknownReactionInReactome.java
@@ -1,299 +1,299 @@
-package lcsb.mapviewer.run;
-
-import java.io.FileNotFoundException;
-import java.io.PrintWriter;
-import java.io.UnsupportedEncodingException;
-import java.text.DecimalFormat;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-import org.apache.log4j.PropertyConfigurator;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.annotation.services.PubmedParser;
-import lcsb.mapviewer.commands.CreateHierarchyCommand;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.graphics.MapGenerator;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.ReactionNode;
-import lcsb.mapviewer.persist.ApplicationContextLoader;
-import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
-import lcsb.mapviewer.reactome.utils.DataFormatter;
-import lcsb.mapviewer.reactome.utils.ReactomeQueryUtil;
-import lcsb.mapviewer.reactome.utils.comparators.MatchResult;
-
-/**
- * This class prepare report of data that are not included in reactome and maybe
- * should be added.
- *
- * @author Piotr Gawron
- *
- */
-public class UnknownReactionInReactome {
- /**
- * Number of nanoseconds in a second.
- */
- private static final double NANOSECONDS_IN_SECOND = 1000000000.0;
-
- /**
- * Model used for generating raport.
- */
- private Model model;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(UnknownReactionInReactome.class);
-
- /**
- * Util class used for manipulating information in reactome objects.
- */
- @Autowired
- private ReactomeQueryUtil rcu;
-
- /**
- * Formatter used for reaction comparison.
- */
- @Autowired
- private DataFormatter dataFormatter;
-
- /**
- * Class used for accessing data in pubmed database.
- */
- @Autowired
- private PubmedParser pubmedParser;
-
- /**
- * Static main method used to run this stand alone code.
- *
- * @param args
- * command line arguments
- */
- public static void main(String[] args) {
- long startTime = System.nanoTime();
- PropertyConfigurator.configure("src/main/webapp/WEB-INF/resources/log4j.properties");
- UnknownReactionInReactome main = new UnknownReactionInReactome();
- ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
- ApplicationContextLoader.injectDependencies(main);
- main.run();
- long endTime = System.nanoTime();
-
- long duration = endTime - startTime;
- double sec = duration / NANOSECONDS_IN_SECOND;
- System.out.println("Duration: " + new DecimalFormat("#.###").format(sec) + "s");
- }
-
- /**
- * Executes comparison between model and reactome to generate report.
- */
- public void run() {
- try {
- MapGenerator mg = new MapGenerator();
- model = new CellDesignerXmlParser().createModel(new ConverterParams().filename(PdMapAnnotations.getLastPdFilename()));
- new CreateHierarchyCommand(model, mg.computeZoomLevels(model), mg.computeZoomFactor(model)).execute();
- List<String> ids = new ArrayList<String>();
- for (Reaction reaction : model.getReactions()) {
- if (rcu.getReactomeIdentifierForReaction(reaction) == null) {
- ids.add(reaction.getIdReaction());
- }
- }
- Collections.sort(ids);
- printHeader();
- List<MatchResult> results = new ArrayList<MatchResult>();
- for (String string : ids) {
- boolean unknown = true;
- boolean pubmed = false;
- Reaction reaction = model.getReactionByReactionId(string);
- for (MiriamData md : reaction.getMiriamData()) {
- if (md.getDataType().equals(MiriamType.PUBMED)) {
- pubmed = true;
- ReactomeDatabaseObject obj = rcu.getLiteratureReferenceByPubMedId(Integer.parseInt(md.getResource()));
- if (obj != null) {
- unknown = false;
- }
- }
- }
- if (pubmed && unknown) {
- MatchResult matchResult = new MatchResult();
- matchResult.setLocalReaction(reaction);
- for (ReactionNode node : reaction.getReactants()) {
- matchResult.addInvalidLocalInput(node.getElement());
- }
- for (ReactionNode node : reaction.getProducts()) {
- matchResult.addInvalidLocalOutput(node.getElement());
- }
- for (ReactionNode node : reaction.getModifiers()) {
- matchResult.addInvalidLocalModifier(node.getElement());
- }
- results.add(matchResult);
- printResult(matchResult);
- }
- }
- printFooter(results);
-
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- }
-
- }
-
- /**
- * Prints report footer.
- *
- * @param results
- * results used in the report
- */
- private void printFooter(List<MatchResult> results) {
-
- writer.println("</table>");
- writer.println("Reactions: " + results.size());
- writer.println("</body></html>");
-
- writer.close();
- }
-
- /**
- * Object to which the report is written.
- */
- private PrintWriter writer;
-
- /**
- * Creates report stream and prints header of the report.
- *
- * @throws FileNotFoundException
- * if there is a problem with creating report file
- * @throws UnsupportedEncodingException
- * thrown when there are problems with encoding
- */
- private void printHeader() throws FileNotFoundException, UnsupportedEncodingException {
- writer = new PrintWriter("out/report/report-export.html", "UTF-8");
- writer.println("<html><head></head><body>");
- writer.println("<table cellspacing=\"0\"");
-
- String resultString = "<tr>";
- resultString += "<td" + style + ">Reaction</td>";
- resultString += "<td" + style + ">Pubmed ids</td>";
- resultString += "<td" + style + ">Ontologies</td>";
- resultString += "<td" + style + ">Input</td>";
- resultString += "<td" + style + ">Modifier</td>";
- resultString += "<td" + style + ">Output</td>";
- resultString += "</tr>";
- writer.println(resultString);
-
- }
-
- /**
- * Style used by report cells.
- */
- private String style = " style=\"border-width:1;border-style:solid;border-color:#000000;\" ";
-
- /**
- * Prints result row.
- *
- * @param result
- * result to be printed
- * @throws Exception
- * thrown when there is a problem with printing
- */
- private void printResult(MatchResult result) throws Exception {
-
- Set<String> ontologies = new HashSet<String>();
-
- for (Compartment alias : model.getCompartments()) {
- for (ReactionNode node : result.getLocalReaction().getReactionNodes()) {
- if (alias.contains(node.getElement())) {
- ontologies.add(alias.getName());
- break;
- }
- }
- }
-
- String color = "#FFFFFF";
- String resultString = "<tr bgcolor = \"" + color + "\">";
- String reactionId = result.getLocalReaction().getIdReaction();
- resultString += "<td" + style + "><a target=\"_blank\" href=\"" + PdMapAnnotations.getLinkForReaction(result.getLocalReaction()) + "\">" + reactionId
- + "</a></td>";
-
- String pubmed = "";
- for (MiriamData md : result.getLocalReaction().getMiriamData()) {
- if (md.getDataType().equals(MiriamType.PUBMED)) {
- pubmed += pubmedParser.getHtmlFullLinkForId(Integer.valueOf(md.getResource()), false) + "<br/>";
- }
- }
-
- resultString += "<td" + style + ">" + pubmed + "</td>";
-
- String ont = "";
- for (String string : ontologies) {
- if (!ont.equals("")) {
- ont += "<hr/>";
- }
- ont += string;
- }
- resultString += "<td" + style + ">" + ont + "</td>";
-
- resultString += "<td" + style + ">" + dataFormatter.getInvalidLocalInputString(result) + " </td>";
- resultString += "<td" + style + ">" + dataFormatter.getInvalidLocalModifierString(result) + " </td>";
- resultString += "<td" + style + ">" + dataFormatter.getInvalidLocalOutputString(result) + " </td>";
- resultString += "</tr>";
- writer.println(resultString);
- System.out.println(resultString);
- }
-
- /**
- * @return the dataFormatter
- */
- public DataFormatter getDataFormatter() {
- return dataFormatter;
- }
-
- /**
- * @param dataFormatter
- * the dataFormatter to set
- */
- public void setDataFormatter(DataFormatter dataFormatter) {
- this.dataFormatter = dataFormatter;
- }
-
- /**
- * @return the pubmedParser
- */
- public PubmedParser getPubmedParser() {
- return pubmedParser;
- }
-
- /**
- * @param pubmedParser
- * the pubmedParser to set
- */
- public void setPubmedParser(PubmedParser pubmedParser) {
- this.pubmedParser = pubmedParser;
- }
-
- /**
- * @return the rcu
- * @see #rcu
- */
- public ReactomeQueryUtil getRcu() {
- return rcu;
- }
-
- /**
- * @param rcu
- * the rcu to set
- * @see #rcu
- */
- public void setRcu(ReactomeQueryUtil rcu) {
- this.rcu = rcu;
- }
-
-}
+package lcsb.mapviewer.run;
+
+import java.io.FileNotFoundException;
+import java.io.PrintWriter;
+import java.io.UnsupportedEncodingException;
+import java.text.DecimalFormat;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.apache.log4j.PropertyConfigurator;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.services.PubmedParser;
+import lcsb.mapviewer.commands.CreateHierarchyCommand;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.graphics.MapGenerator;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.persist.ApplicationContextLoader;
+import lcsb.mapviewer.reactome.model.ReactomeDatabaseObject;
+import lcsb.mapviewer.reactome.utils.DataFormatter;
+import lcsb.mapviewer.reactome.utils.ReactomeQueryUtil;
+import lcsb.mapviewer.reactome.utils.comparators.MatchResult;
+
+/**
+ * This class prepare report of data that are not included in reactome and maybe
+ * should be added.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class UnknownReactionInReactome {
+ /**
+ * Number of nanoseconds in a second.
+ */
+ private static final double NANOSECONDS_IN_SECOND = 1000000000.0;
+
+ /**
+ * Model used for generating raport.
+ */
+ private Model model;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(UnknownReactionInReactome.class);
+
+ /**
+ * Util class used for manipulating information in reactome objects.
+ */
+ @Autowired
+ private ReactomeQueryUtil rcu;
+
+ /**
+ * Formatter used for reaction comparison.
+ */
+ @Autowired
+ private DataFormatter dataFormatter;
+
+ /**
+ * Class used for accessing data in pubmed database.
+ */
+ @Autowired
+ private PubmedParser pubmedParser;
+
+ /**
+ * Static main method used to run this stand alone code.
+ *
+ * @param args
+ * command line arguments
+ */
+ public static void main(String[] args) {
+ long startTime = System.nanoTime();
+ PropertyConfigurator.configure("src/main/webapp/WEB-INF/resources/log4j.properties");
+ UnknownReactionInReactome main = new UnknownReactionInReactome();
+ ApplicationContextLoader.loadApplicationContext("consoleApplicationContext.xml");
+ ApplicationContextLoader.injectDependencies(main);
+ main.run();
+ long endTime = System.nanoTime();
+
+ long duration = endTime - startTime;
+ double sec = duration / NANOSECONDS_IN_SECOND;
+ System.out.println("Duration: " + new DecimalFormat("#.###").format(sec) + "s");
+ }
+
+ /**
+ * Executes comparison between model and reactome to generate report.
+ */
+ public void run() {
+ try {
+ MapGenerator mg = new MapGenerator();
+ model = new CellDesignerXmlParser().createModel(new ConverterParams().filename(PdMapAnnotations.getLastPdFilename()));
+ new CreateHierarchyCommand(model, mg.computeZoomLevels(model), mg.computeZoomFactor(model)).execute();
+ List<String> ids = new ArrayList<String>();
+ for (Reaction reaction : model.getReactions()) {
+ if (rcu.getReactomeIdentifierForReaction(reaction) == null) {
+ ids.add(reaction.getIdReaction());
+ }
+ }
+ Collections.sort(ids);
+ printHeader();
+ List<MatchResult> results = new ArrayList<MatchResult>();
+ for (String string : ids) {
+ boolean unknown = true;
+ boolean pubmed = false;
+ Reaction reaction = model.getReactionByReactionId(string);
+ for (MiriamData md : reaction.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.PUBMED)) {
+ pubmed = true;
+ ReactomeDatabaseObject obj = rcu.getLiteratureReferenceByPubMedId(Integer.parseInt(md.getResource()));
+ if (obj != null) {
+ unknown = false;
+ }
+ }
+ }
+ if (pubmed && unknown) {
+ MatchResult matchResult = new MatchResult();
+ matchResult.setLocalReaction(reaction);
+ for (ReactionNode node : reaction.getReactants()) {
+ matchResult.addInvalidLocalInput(node.getElement());
+ }
+ for (ReactionNode node : reaction.getProducts()) {
+ matchResult.addInvalidLocalOutput(node.getElement());
+ }
+ for (ReactionNode node : reaction.getModifiers()) {
+ matchResult.addInvalidLocalModifier(node.getElement());
+ }
+ results.add(matchResult);
+ printResult(matchResult);
+ }
+ }
+ printFooter(results);
+
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ }
+
+ }
+
+ /**
+ * Prints report footer.
+ *
+ * @param results
+ * results used in the report
+ */
+ private void printFooter(List<MatchResult> results) {
+
+ writer.println("</table>");
+ writer.println("Reactions: " + results.size());
+ writer.println("</body></html>");
+
+ writer.close();
+ }
+
+ /**
+ * Object to which the report is written.
+ */
+ private PrintWriter writer;
+
+ /**
+ * Creates report stream and prints header of the report.
+ *
+ * @throws FileNotFoundException
+ * if there is a problem with creating report file
+ * @throws UnsupportedEncodingException
+ * thrown when there are problems with encoding
+ */
+ private void printHeader() throws FileNotFoundException, UnsupportedEncodingException {
+ writer = new PrintWriter("out/report/report-export.html", "UTF-8");
+ writer.println("<html><head></head><body>");
+ writer.println("<table cellspacing=\"0\"");
+
+ String resultString = "<tr>";
+ resultString += "<td" + style + ">Reaction</td>";
+ resultString += "<td" + style + ">Pubmed ids</td>";
+ resultString += "<td" + style + ">Ontologies</td>";
+ resultString += "<td" + style + ">Input</td>";
+ resultString += "<td" + style + ">Modifier</td>";
+ resultString += "<td" + style + ">Output</td>";
+ resultString += "</tr>";
+ writer.println(resultString);
+
+ }
+
+ /**
+ * Style used by report cells.
+ */
+ private String style = " style=\"border-width:1;border-style:solid;border-color:#000000;\" ";
+
+ /**
+ * Prints result row.
+ *
+ * @param result
+ * result to be printed
+ * @throws Exception
+ * thrown when there is a problem with printing
+ */
+ private void printResult(MatchResult result) throws Exception {
+
+ Set<String> ontologies = new HashSet<String>();
+
+ for (Compartment alias : model.getCompartments()) {
+ for (ReactionNode node : result.getLocalReaction().getReactionNodes()) {
+ if (alias.contains(node.getElement())) {
+ ontologies.add(alias.getName());
+ break;
+ }
+ }
+ }
+
+ String color = "#FFFFFF";
+ String resultString = "<tr bgcolor = \"" + color + "\">";
+ String reactionId = result.getLocalReaction().getIdReaction();
+ resultString += "<td" + style + "><a target=\"_blank\" href=\"" + PdMapAnnotations.getLinkForReaction(result.getLocalReaction()) + "\">" + reactionId
+ + "</a></td>";
+
+ String pubmed = "";
+ for (MiriamData md : result.getLocalReaction().getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.PUBMED)) {
+ pubmed += pubmedParser.getHtmlFullLinkForId(Integer.valueOf(md.getResource()), false) + "<br/>";
+ }
+ }
+
+ resultString += "<td" + style + ">" + pubmed + "</td>";
+
+ String ont = "";
+ for (String string : ontologies) {
+ if (!ont.equals("")) {
+ ont += "<hr/>";
+ }
+ ont += string;
+ }
+ resultString += "<td" + style + ">" + ont + "</td>";
+
+ resultString += "<td" + style + ">" + dataFormatter.getInvalidLocalInputString(result) + " </td>";
+ resultString += "<td" + style + ">" + dataFormatter.getInvalidLocalModifierString(result) + " </td>";
+ resultString += "<td" + style + ">" + dataFormatter.getInvalidLocalOutputString(result) + " </td>";
+ resultString += "</tr>";
+ writer.println(resultString);
+ System.out.println(resultString);
+ }
+
+ /**
+ * @return the dataFormatter
+ */
+ public DataFormatter getDataFormatter() {
+ return dataFormatter;
+ }
+
+ /**
+ * @param dataFormatter
+ * the dataFormatter to set
+ */
+ public void setDataFormatter(DataFormatter dataFormatter) {
+ this.dataFormatter = dataFormatter;
+ }
+
+ /**
+ * @return the pubmedParser
+ */
+ public PubmedParser getPubmedParser() {
+ return pubmedParser;
+ }
+
+ /**
+ * @param pubmedParser
+ * the pubmedParser to set
+ */
+ public void setPubmedParser(PubmedParser pubmedParser) {
+ this.pubmedParser = pubmedParser;
+ }
+
+ /**
+ * @return the rcu
+ * @see #rcu
+ */
+ public ReactomeQueryUtil getRcu() {
+ return rcu;
+ }
+
+ /**
+ * @param rcu
+ * the rcu to set
+ * @see #rcu
+ */
+ public void setRcu(ReactomeQueryUtil rcu) {
+ this.rcu = rcu;
+ }
+
+}
diff --git a/console/src/main/java/lcsb/mapviewer/run/VibineSnippet.java b/console/src/main/java/lcsb/mapviewer/run/VibineSnippet.java
index dd2aee9685..5aaf8a299a 100644
--- a/console/src/main/java/lcsb/mapviewer/run/VibineSnippet.java
+++ b/console/src/main/java/lcsb/mapviewer/run/VibineSnippet.java
@@ -1,105 +1,105 @@
-package lcsb.mapviewer.run;
-
-import java.io.FileNotFoundException;
-import java.text.DecimalFormat;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.ReactionNode;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * This class is a snippet for Vibine collaboration project. It shows how to
- * access our internal data structures and source files.
- *
- * @author Piotr Gawron
- *
- */
-public class VibineSnippet {
-
- /**
- * Number of nanoseconds in second.
- */
- private static final double NANOSECONDS_IN_SECOND = 1000000000.0;
-
- /**
- * CellDesigner file on with some data that is used in this snippet (it's PD
- * map from June 2015).
- */
- private static final String INPUT_FILE = "testFiles/pd_full/PD_150625_3.xml";
-
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(VibineSnippet.class);
-
- /**
- * Main entry point to the program.
- *
- * @param args
- * parameters with which the program was run
- */
- public static void main(String[] args) {
- VibineSnippet main = new VibineSnippet();
- long startTime = System.nanoTime();
-
- try {
- main.run();
- } catch (Exception e) {
- main.logger.error(e, e);
- } finally {
- long endTime = System.nanoTime();
- long duration = endTime - startTime;
- double sec = duration / NANOSECONDS_IN_SECOND;
- System.out.println("Duration: " + new DecimalFormat("#.###").format(sec) + "s");
- }
- }
-
- /**
- * This method transform {@link #inputOptions input data}.
- *
- * @throws FileNotFoundException
- *
- * @throws Exception
- * thrown when the there is a problem...
- */
- private void run() throws Exception {
- logger.debug("Opening file: " + INPUT_FILE);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- Model model = parser.createModel(new ConverterParams().filename(INPUT_FILE));
-
- logger.debug("File processed.");
-
- logger.debug("-------------------------------");
- logger.debug("Number of elements: " + model.getElements().size());
-
- logger.debug("Number of reactions: " + model.getReactions().size());
-
- logger.debug("-------------------------------");
- String speciesId = "sa7208";
- String reactionId = "re332";
-
- Species species = model.getElementByElementId(speciesId);
-
- logger.debug("Element with id: " + speciesId);
- logger.debug("Element type: " + species.getClass());
- logger.debug("Element name: " + species.getName());
-
- logger.debug("-------------------------------");
- Reaction reaction = model.getReactionByReactionId(reactionId);
-
- logger.debug("Reaction with id: " + reactionId);
- logger.debug("Reaction has " + reaction.getReactionNodes().size() + " members.");
- for (ReactionNode node : reaction.getReactionNodes()) {
- logger.debug(
- node.getClass().getSimpleName() + "; points to " + node.getElement().getClass().getSimpleName() + "[" + node.getElement().getElementId() + "]");
- }
- logger.debug("-------------------------------");
- }
-
-}
+package lcsb.mapviewer.run;
+
+import java.io.FileNotFoundException;
+import java.text.DecimalFormat;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This class is a snippet for Vibine collaboration project. It shows how to
+ * access our internal data structures and source files.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class VibineSnippet {
+
+ /**
+ * Number of nanoseconds in second.
+ */
+ private static final double NANOSECONDS_IN_SECOND = 1000000000.0;
+
+ /**
+ * CellDesigner file on with some data that is used in this snippet (it's PD
+ * map from June 2015).
+ */
+ private static final String INPUT_FILE = "testFiles/pd_full/PD_150625_3.xml";
+
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(VibineSnippet.class);
+
+ /**
+ * Main entry point to the program.
+ *
+ * @param args
+ * parameters with which the program was run
+ */
+ public static void main(String[] args) {
+ VibineSnippet main = new VibineSnippet();
+ long startTime = System.nanoTime();
+
+ try {
+ main.run();
+ } catch (Exception e) {
+ main.logger.error(e, e);
+ } finally {
+ long endTime = System.nanoTime();
+ long duration = endTime - startTime;
+ double sec = duration / NANOSECONDS_IN_SECOND;
+ System.out.println("Duration: " + new DecimalFormat("#.###").format(sec) + "s");
+ }
+ }
+
+ /**
+ * This method transform {@link #inputOptions input data}.
+ *
+ * @throws FileNotFoundException
+ *
+ * @throws Exception
+ * thrown when the there is a problem...
+ */
+ private void run() throws Exception {
+ logger.debug("Opening file: " + INPUT_FILE);
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ Model model = parser.createModel(new ConverterParams().filename(INPUT_FILE));
+
+ logger.debug("File processed.");
+
+ logger.debug("-------------------------------");
+ logger.debug("Number of elements: " + model.getElements().size());
+
+ logger.debug("Number of reactions: " + model.getReactions().size());
+
+ logger.debug("-------------------------------");
+ String speciesId = "sa7208";
+ String reactionId = "re332";
+
+ Species species = model.getElementByElementId(speciesId);
+
+ logger.debug("Element with id: " + speciesId);
+ logger.debug("Element type: " + species.getClass());
+ logger.debug("Element name: " + species.getName());
+
+ logger.debug("-------------------------------");
+ Reaction reaction = model.getReactionByReactionId(reactionId);
+
+ logger.debug("Reaction with id: " + reactionId);
+ logger.debug("Reaction has " + reaction.getReactionNodes().size() + " members.");
+ for (ReactionNode node : reaction.getReactionNodes()) {
+ logger.debug(
+ node.getClass().getSimpleName() + "; points to " + node.getElement().getClass().getSimpleName() + "[" + node.getElement().getElementId() + "]");
+ }
+ logger.debug("-------------------------------");
+ }
+
+}
diff --git a/console/src/main/java/lcsb/mapviewer/run/package-info.java b/console/src/main/java/lcsb/mapviewer/run/package-info.java
index bfe3f70ad5..545660f7d8 100644
--- a/console/src/main/java/lcsb/mapviewer/run/package-info.java
+++ b/console/src/main/java/lcsb/mapviewer/run/package-info.java
@@ -1,10 +1,10 @@
-/**
- * Provides some clases that can be run from command line and perform some operations on the data:<ul>
- * <li>extract information,</li>
- * <li>add information,</li>
- * <li>remove data,</li>
- * <li>validate data.</li>
- * </ul>
- */
-package lcsb.mapviewer.run;
-
+/**
+ * Provides some clases that can be run from command line and perform some operations on the data:<ul>
+ * <li>extract information,</li>
+ * <li>add information,</li>
+ * <li>remove data,</li>
+ * <li>validate data.</li>
+ * </ul>
+ */
+package lcsb.mapviewer.run;
+
diff --git a/console/src/test/java/lcsb/mapviewer/run/PdMapAnnotationsTest.java b/console/src/test/java/lcsb/mapviewer/run/PdMapAnnotationsTest.java
index 3c0f4bfef1..587c930333 100644
--- a/console/src/test/java/lcsb/mapviewer/run/PdMapAnnotationsTest.java
+++ b/console/src/test/java/lcsb/mapviewer/run/PdMapAnnotationsTest.java
@@ -1,40 +1,40 @@
-package lcsb.mapviewer.run;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.io.File;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.run.PdMapAnnotations;
-
-public class PdMapAnnotationsTest {
- Logger logger = Logger.getLogger(PdMapAnnotationsTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void test() {
- try {
- String fileName = PdMapAnnotations.getLastPdFilename();
- assertNotNull(fileName);
- File file = new File(fileName);
- assertTrue(file.exists());
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception occurred");
- }
- }
-
-}
+package lcsb.mapviewer.run;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.io.File;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.run.PdMapAnnotations;
+
+public class PdMapAnnotationsTest {
+ Logger logger = Logger.getLogger(PdMapAnnotationsTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void test() {
+ try {
+ String fileName = PdMapAnnotations.getLastPdFilename();
+ assertNotNull(fileName);
+ File file = new File(fileName);
+ assertTrue(file.exists());
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception occurred");
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollection.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollection.java
index 477a446ee6..00ea8ca911 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollection.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollection.java
@@ -1,241 +1,241 @@
-package lcsb.mapviewer.converter.model.celldesigner;
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.field.AbstractSiteModification;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-
-/**
- * This structure contains information about {@link CellDesignerElement
- * CellDesigner elements} parsed from the file. The information about this
- * elements is used in different places in the parsing process.
- */
-public class CellDesignerElementCollection {
-
- /**
- * Element by element identifier (it's CellDesigner identifier).
- */
- private Map<String, CellDesignerElement<?>> elementById = new HashMap<>();
-
- /**
- * Returns element by given identifier.
- *
- * @param speciesId
- * element identifier
- * @return element by given identifier
- *
- * @param <T>
- * type of returned object
- */
- @SuppressWarnings("unchecked")
- public <T extends CellDesignerElement<?>> T getElementByElementId(String speciesId) {
- return (T) elementById.get(speciesId);
- }
-
- /**
- *
- */
- private Map<String, String> sbmlIdByElement = new HashMap<>();
-
- /**
- * Returns element identifier that should be used for model element when
- * creating cell designer xml file.
- *
- * @param modelElement
- * model element for which we want to obtain identifier
- * @return identifier of cell designer element that will be exported
- */
- public String getElementId(Element modelElement) {
- if ("default".equals(modelElement.getElementId())) {
- return modelElement.getElementId();
- } else {
- String sbmlId = getSbmlId(modelElement, true);
- if (sbmlIdByElement.get(sbmlId) == null) {
- String id = "s_id_" + modelElement.getElementId();
- if (sbmlIdByElement.values().contains(id)) {
- throw new InvalidArgumentException("id duplicates");
- }
- sbmlIdByElement.put(sbmlId, id);
- }
- return sbmlIdByElement.get(sbmlId);
-
- }
- }
-
- /**
- * Creates a String that identifies element as distinct SBML entity.
- *
- * @param modelElement
- * element that we want to identify
- * @param useComplex
- * should we use identifier of a complex. This should be used by
- * default (because if the complex is different then element should
- * have different identifier). However, when element asks complex for
- * id, complex will try to resolve ids of children (because this is
- * what defines complex identity), and in such situation it should
- * disable resolving complex, because there will by infinity cyclic
- * calls and stack overflow error will be thrown.
- * @return unique String for SBML entity
- */
- private String getSbmlId(Element modelElement, boolean useComplex) {
- String compartmenName = "default";
- if (modelElement.getCompartment() != null) {
- compartmenName = modelElement.getCompartment().getName();
- }
-
- String modifications = "";
- List<ModificationResidue> regions = new ArrayList<>();
- if (modelElement instanceof AntisenseRna) {
- AntisenseRna asAntisenseRna = ((AntisenseRna) modelElement);
- regions.addAll(asAntisenseRna.getRegions());
- } else if (modelElement instanceof Gene) {
- Gene asGene = ((Gene) modelElement);
- regions.addAll(asGene.getModificationResidues());
- } else if (modelElement instanceof Protein) {
- Protein asProtein = ((Protein) modelElement);
- modifications = asProtein.getStructuralState();
- regions.addAll(asProtein.getModificationResidues());
- } else if (modelElement instanceof Rna) {
- Rna asRna = ((Rna) modelElement);
- regions.addAll(asRna.getRegions());
- } else if (modelElement instanceof Complex) {
- Complex asComplex = ((Complex) modelElement);
- modifications = asComplex.getStructuralState();
- }
- for (ModificationResidue region : regions) {
- if (region instanceof AbstractSiteModification) {
- modifications += ((AbstractSiteModification) region).getState();
- }
- }
-
- String complexId = "";
- String homodimer = "";
- if (modelElement instanceof Species) {
- homodimer = ((Species) modelElement).getHomodimer() + "";
- if (((Species) modelElement).getComplex() != null) {
- if (useComplex) {
- if (!isCyclicNesting(((Species) modelElement).getComplex())) {
- complexId = getElementId(((Species) modelElement).getComplex());
- } else {
- throw new InvalidArgumentException(
- "Cycling nested structure found in element: " + modelElement.getElementId());
- }
- } else {
- complexId = ((Species) modelElement).getComplex().getName();
- }
- }
- }
- String childrenId = "";
- if (modelElement instanceof Complex) {
- Complex asComplex = (Complex) modelElement;
- List<String> childIds = new ArrayList<>();
- for (Species child : asComplex.getAllChildren()) {
- childIds.add(getSbmlId(child, false));
- }
- Collections.sort(childIds);
- for (String string : childIds) {
- childrenId += string + "\n";
- }
- }
-
- // identifier that distinguish elements in SBML depends only on type,
- // name, compartment, modifications, homodimer, state, complex where it's
- // located,
- // children of the complex
- String sbmlId = compartmenName + "\n" + modelElement.getName() + "\n" + modelElement.getStringType() + "\n"
- + modifications + "\n" + complexId + "\n" + homodimer + "\n" + childrenId;
-
- return sbmlId;
- }
-
- /**
- * Checks if complex parenting is cyclic.
- *
- * @param complex
- * complex for which data is checked
- * @return true if parent of the complex is also a (grand)child of this complex,
- * false otherwise
- */
- private boolean isCyclicNesting(Complex complex) {
- Set<Complex> foundComplexes = new HashSet<>();
- while (complex != null) {
- if (foundComplexes.contains(complex)) {
- return true;
- }
- foundComplexes.add(complex);
- complex = complex.getComplex();
- }
- return false;
- }
-
- /**
- * Adds cell designer structures.
- *
- * @param elements
- * list of objects to add
- */
- public void addElements(List<? extends CellDesignerElement<?>> elements) {
- for (CellDesignerElement<?> element : elements) {
- addElement(element);
- }
- }
-
- /**
- * Adds cell designer object.
- *
- * @param element
- * object to add
- */
- public void addElement(CellDesignerElement<?> element) {
- addElement(element, element.getElementId());
- }
-
- /**
- * Adds CellDesigner element with custom id (instead the one obtained from
- * CellDesigner structure).
- *
- * @param element
- * element to be add
- * @param id
- * id that should be used for identifying element
- */
- public void addElement(CellDesignerElement<?> element, String id) {
- if (elementById.get(id) != null) {
- throw new InvalidArgumentException("[" + element.getClass().getSimpleName() + " " + element.getElementId() + "]\t"
- + "Element with given id alread exists. ID: " + id);
- }
- elementById.put(id, element);
- }
-
- /**
- * Adds CellDesigner structure in a way that it would be accessed via identifier
- * for model structure. Method used only for unit test.
- *
- * @param modelElement
- * model element that will create identifier
- * @param element
- * element to be added
- */
- public void addModelElement(Element modelElement, CellDesignerElement<?> element) {
- addElement(element, getElementId(modelElement));
- if (getElementByElementId(element.getElementId()) == null) {
- addElement(element);
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.AbstractSiteModification;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+
+/**
+ * This structure contains information about {@link CellDesignerElement
+ * CellDesigner elements} parsed from the file. The information about this
+ * elements is used in different places in the parsing process.
+ */
+public class CellDesignerElementCollection {
+
+ /**
+ * Element by element identifier (it's CellDesigner identifier).
+ */
+ private Map<String, CellDesignerElement<?>> elementById = new HashMap<>();
+
+ /**
+ * Returns element by given identifier.
+ *
+ * @param speciesId
+ * element identifier
+ * @return element by given identifier
+ *
+ * @param <T>
+ * type of returned object
+ */
+ @SuppressWarnings("unchecked")
+ public <T extends CellDesignerElement<?>> T getElementByElementId(String speciesId) {
+ return (T) elementById.get(speciesId);
+ }
+
+ /**
+ *
+ */
+ private Map<String, String> sbmlIdByElement = new HashMap<>();
+
+ /**
+ * Returns element identifier that should be used for model element when
+ * creating cell designer xml file.
+ *
+ * @param modelElement
+ * model element for which we want to obtain identifier
+ * @return identifier of cell designer element that will be exported
+ */
+ public String getElementId(Element modelElement) {
+ if ("default".equals(modelElement.getElementId())) {
+ return modelElement.getElementId();
+ } else {
+ String sbmlId = getSbmlId(modelElement, true);
+ if (sbmlIdByElement.get(sbmlId) == null) {
+ String id = "s_id_" + modelElement.getElementId();
+ if (sbmlIdByElement.values().contains(id)) {
+ throw new InvalidArgumentException("id duplicates");
+ }
+ sbmlIdByElement.put(sbmlId, id);
+ }
+ return sbmlIdByElement.get(sbmlId);
+
+ }
+ }
+
+ /**
+ * Creates a String that identifies element as distinct SBML entity.
+ *
+ * @param modelElement
+ * element that we want to identify
+ * @param useComplex
+ * should we use identifier of a complex. This should be used by
+ * default (because if the complex is different then element should
+ * have different identifier). However, when element asks complex for
+ * id, complex will try to resolve ids of children (because this is
+ * what defines complex identity), and in such situation it should
+ * disable resolving complex, because there will by infinity cyclic
+ * calls and stack overflow error will be thrown.
+ * @return unique String for SBML entity
+ */
+ private String getSbmlId(Element modelElement, boolean useComplex) {
+ String compartmenName = "default";
+ if (modelElement.getCompartment() != null) {
+ compartmenName = modelElement.getCompartment().getName();
+ }
+
+ String modifications = "";
+ List<ModificationResidue> regions = new ArrayList<>();
+ if (modelElement instanceof AntisenseRna) {
+ AntisenseRna asAntisenseRna = ((AntisenseRna) modelElement);
+ regions.addAll(asAntisenseRna.getRegions());
+ } else if (modelElement instanceof Gene) {
+ Gene asGene = ((Gene) modelElement);
+ regions.addAll(asGene.getModificationResidues());
+ } else if (modelElement instanceof Protein) {
+ Protein asProtein = ((Protein) modelElement);
+ modifications = asProtein.getStructuralState();
+ regions.addAll(asProtein.getModificationResidues());
+ } else if (modelElement instanceof Rna) {
+ Rna asRna = ((Rna) modelElement);
+ regions.addAll(asRna.getRegions());
+ } else if (modelElement instanceof Complex) {
+ Complex asComplex = ((Complex) modelElement);
+ modifications = asComplex.getStructuralState();
+ }
+ for (ModificationResidue region : regions) {
+ if (region instanceof AbstractSiteModification) {
+ modifications += ((AbstractSiteModification) region).getState();
+ }
+ }
+
+ String complexId = "";
+ String homodimer = "";
+ if (modelElement instanceof Species) {
+ homodimer = ((Species) modelElement).getHomodimer() + "";
+ if (((Species) modelElement).getComplex() != null) {
+ if (useComplex) {
+ if (!isCyclicNesting(((Species) modelElement).getComplex())) {
+ complexId = getElementId(((Species) modelElement).getComplex());
+ } else {
+ throw new InvalidArgumentException(
+ "Cycling nested structure found in element: " + modelElement.getElementId());
+ }
+ } else {
+ complexId = ((Species) modelElement).getComplex().getName();
+ }
+ }
+ }
+ String childrenId = "";
+ if (modelElement instanceof Complex) {
+ Complex asComplex = (Complex) modelElement;
+ List<String> childIds = new ArrayList<>();
+ for (Species child : asComplex.getAllChildren()) {
+ childIds.add(getSbmlId(child, false));
+ }
+ Collections.sort(childIds);
+ for (String string : childIds) {
+ childrenId += string + "\n";
+ }
+ }
+
+ // identifier that distinguish elements in SBML depends only on type,
+ // name, compartment, modifications, homodimer, state, complex where it's
+ // located,
+ // children of the complex
+ String sbmlId = compartmenName + "\n" + modelElement.getName() + "\n" + modelElement.getStringType() + "\n"
+ + modifications + "\n" + complexId + "\n" + homodimer + "\n" + childrenId;
+
+ return sbmlId;
+ }
+
+ /**
+ * Checks if complex parenting is cyclic.
+ *
+ * @param complex
+ * complex for which data is checked
+ * @return true if parent of the complex is also a (grand)child of this complex,
+ * false otherwise
+ */
+ private boolean isCyclicNesting(Complex complex) {
+ Set<Complex> foundComplexes = new HashSet<>();
+ while (complex != null) {
+ if (foundComplexes.contains(complex)) {
+ return true;
+ }
+ foundComplexes.add(complex);
+ complex = complex.getComplex();
+ }
+ return false;
+ }
+
+ /**
+ * Adds cell designer structures.
+ *
+ * @param elements
+ * list of objects to add
+ */
+ public void addElements(List<? extends CellDesignerElement<?>> elements) {
+ for (CellDesignerElement<?> element : elements) {
+ addElement(element);
+ }
+ }
+
+ /**
+ * Adds cell designer object.
+ *
+ * @param element
+ * object to add
+ */
+ public void addElement(CellDesignerElement<?> element) {
+ addElement(element, element.getElementId());
+ }
+
+ /**
+ * Adds CellDesigner element with custom id (instead the one obtained from
+ * CellDesigner structure).
+ *
+ * @param element
+ * element to be add
+ * @param id
+ * id that should be used for identifying element
+ */
+ public void addElement(CellDesignerElement<?> element, String id) {
+ if (elementById.get(id) != null) {
+ throw new InvalidArgumentException("[" + element.getClass().getSimpleName() + " " + element.getElementId() + "]\t"
+ + "Element with given id alread exists. ID: " + id);
+ }
+ elementById.put(id, element);
+ }
+
+ /**
+ * Adds CellDesigner structure in a way that it would be accessed via identifier
+ * for model structure. Method used only for unit test.
+ *
+ * @param modelElement
+ * model element that will create identifier
+ * @param element
+ * element to be added
+ */
+ public void addModelElement(Element modelElement, CellDesignerElement<?> element) {
+ addElement(element, getElementId(modelElement));
+ if (getElementByElementId(element.getElementId()) == null) {
+ addElement(element);
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerParserException.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerParserException.java
index beaf497336..3009ac1a3a 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerParserException.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerParserException.java
@@ -1,57 +1,57 @@
-package lcsb.mapviewer.converter.model.celldesigner;
-
-/**
- * Exception that shold be thrown when the parser encouter problem with
- * cellDesigner file.
- *
- * @author Piotr Gawron
- *
- */
-public abstract class CellDesignerParserException extends Exception {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor - initializes instance variable to unknown.
- */
-
- public CellDesignerParserException() {
- super(); // call superclass constructor
- }
-
- /**
- * Constructor receives some kind of message.
- *
- * @param err
- * message associated with exception
- */
-
- public CellDesignerParserException(final String err) {
- super(err);
- }
-
- /**
- * Constructor receives some kind of message and parent exception.
- *
- * @param err
- * message associated with exception
- * @param throwable
- * parent exception
- */
- public CellDesignerParserException(final String err, final Throwable throwable) {
- super(err, throwable);
- }
-
- /**
- * Public constructor with parent exception that was catched.
- *
- * @param e
- * parent exception
- */
-
- public CellDesignerParserException(final Throwable e) {
- super(e);
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner;
+
+/**
+ * Exception that shold be thrown when the parser encouter problem with
+ * cellDesigner file.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public abstract class CellDesignerParserException extends Exception {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor - initializes instance variable to unknown.
+ */
+
+ public CellDesignerParserException() {
+ super(); // call superclass constructor
+ }
+
+ /**
+ * Constructor receives some kind of message.
+ *
+ * @param err
+ * message associated with exception
+ */
+
+ public CellDesignerParserException(final String err) {
+ super(err);
+ }
+
+ /**
+ * Constructor receives some kind of message and parent exception.
+ *
+ * @param err
+ * message associated with exception
+ * @param throwable
+ * parent exception
+ */
+ public CellDesignerParserException(final String err, final Throwable throwable) {
+ super(err, throwable);
+ }
+
+ /**
+ * Public constructor with parent exception that was catched.
+ *
+ * @param e
+ * parent exception
+ */
+
+ public CellDesignerParserException(final Throwable e) {
+ super(e);
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
index 8ab5a64b64..dcea803793 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
@@ -1,709 +1,709 @@
-package lcsb.mapviewer.converter.model.celldesigner;
-
-import java.awt.geom.Line2D;
-import java.awt.geom.Rectangle2D;
-import java.io.ByteArrayInputStream;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.commons.io.FilenameUtils;
-import org.apache.commons.lang3.StringEscapeUtils;
-import org.apache.log4j.Logger;
-import org.apache.log4j.spi.LoggingEvent;
-import org.apache.xerces.parsers.DOMParser;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import lcsb.mapviewer.common.EventStorageLoggerAppender;
-import lcsb.mapviewer.common.MimeType;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.XmlParser;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.IConverter;
-import lcsb.mapviewer.converter.InvalidInputDataExecption;
-import lcsb.mapviewer.converter.model.celldesigner.alias.AliasCollectionXmlParser;
-import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
-import lcsb.mapviewer.converter.model.celldesigner.compartment.CompartmentCollectionXmlParser;
-import lcsb.mapviewer.converter.model.celldesigner.function.FunctionCollectionXmlParser;
-import lcsb.mapviewer.converter.model.celldesigner.parameter.ParameterCollectionXmlParser;
-import lcsb.mapviewer.converter.model.celldesigner.reaction.ReactionCollectionXmlParser;
-import lcsb.mapviewer.converter.model.celldesigner.species.InternalModelSpeciesData;
-import lcsb.mapviewer.converter.model.celldesigner.species.SpeciesCollectionXmlParser;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
-import lcsb.mapviewer.converter.model.celldesigner.unit.UnitCollectionXmlParser;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.InconsistentModelException;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.layout.graphics.LayerOval;
-import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
-import lcsb.mapviewer.model.map.layout.graphics.LayerText;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * This class is a parser for CellDesigner files. There are two typical use
- * cases:
- * <ul>
- * <li>CellDesigner xml -> our model. To perform this action
- * {@link #createModel(Params)} method should be called.</li>
- * <li>our model -> CellDesigner xml. To perform this action
- * {@link #toXml(Model)} method should be called.</li>
- * </ul>
- * <p/>
- * CellDEsigner format is the extension of <a href="http://sbml.org">SBML</a>.
- * More information about this format could be found <a href=
- * "http://www.celldesigner.org/documents/CellDesigner4ExtensionTagSpecificationE.pdf"
- * >here</a>.
- *
- * @author Piotr Gawron
- *
- */
-public class CellDesignerXmlParser extends XmlParser implements IConverter {
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(CellDesignerXmlParser.class.getName());
-
- /**
- * CellDesigner parser for layers.
- */
- private LayerXmlParser layerParser = new LayerXmlParser();
-
- /**
- * CellDesigner parser for compartments collections.
- */
- private CompartmentCollectionXmlParser compartmentCollectionXmlParser;
-
- /**
- * CellDesigner parser for species collections.
- */
- private SpeciesCollectionXmlParser speciesSbmlParser;
-
- /**
- * CellDesigner parser for alias collections.
- */
- private AliasCollectionXmlParser aliasCollectionParser;
-
- /**
- * Annotation parser.
- */
- private RestAnnotationParser rap = new RestAnnotationParser();
-
- @Override
- public Model createModel(ConverterParams params) throws InvalidInputDataExecption {
- CellDesignerElementCollection elements = new CellDesignerElementCollection();
- FunctionCollectionXmlParser functionParser = new FunctionCollectionXmlParser();
- UnitCollectionXmlParser unitParser = new UnitCollectionXmlParser();
-
- Model model = new ModelFullIndexed(null);
-
- if (params.getFilename() != null) {
- model.setName(FilenameUtils.getBaseName(params.getFilename()));
- }
- speciesSbmlParser = new SpeciesCollectionXmlParser(elements);
- aliasCollectionParser = new AliasCollectionXmlParser(elements, model);
- compartmentCollectionXmlParser = new CompartmentCollectionXmlParser(elements);
-
- ParameterCollectionXmlParser parameterParser = new ParameterCollectionXmlParser(model);
-
- DOMParser parser = new DOMParser();
- try {
- parser.parse(params.getSource());
- } catch (IOException e) {
- throw new InvalidInputDataExecption("IO Problem with a file: " + params.getSource().getSystemId(), e);
- }
- Document doc = parser.getDocument();
- try {
-
- // Get the document's root XML node
- NodeList root = doc.getChildNodes();
-
- // Navigate down the hierarchy to get to the CEO node
- Node sbmlNode = getNode("SBML", root);
- if (sbmlNode == null) {
- throw new InvalidInputDataExecption("No SBML node");
- }
-
- Node modelNode = getNode("model", sbmlNode.getChildNodes());
- if (modelNode == null) {
- throw new InvalidInputDataExecption("No model node in SBML");
- }
- // we ignore metaid - it's useless and obstruct data model
- // model.setMetaId(getNodeAttr("metaId", modelNode));
- model.setIdModel(getNodeAttr("id", modelNode));
-
- Node compartmentNode = getNode("listOfCompartments", modelNode.getChildNodes());
- if (compartmentNode != null) {
- List<CellDesignerCompartment> compartments = compartmentCollectionXmlParser
- .parseXmlCompartmentCollection(compartmentNode);
- elements.addElements(compartments);
- }
-
- InternalModelSpeciesData modelData = new InternalModelSpeciesData();
-
- Node speciesNode = getNode("listOfSpecies", modelNode.getChildNodes());
- if (speciesNode != null) {
- List<Pair<String, ? extends CellDesignerSpecies<?>>> species = speciesSbmlParser
- .parseSbmlSpeciesCollection(speciesNode);
- modelData.updateSpecies(species);
- }
- Node reactionsNode = null;
- Node functionsNode = null;
- Node unitsNode = null;
- Node parametersNode = null;
-
- NodeList nodes = modelNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("annotation")) {
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("listOfSpecies")) {
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("listOfReactions")) {
- reactionsNode = node;
- } else if (node.getNodeName().equalsIgnoreCase("listOfCompartments")) {
- // we already parsed compartments
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("notes")) {
- String notes = rap.getNotes(node);
- if (notes != null) {
- notes = StringEscapeUtils.unescapeHtml4(notes);
- }
- model.setNotes(notes);
- } else if (node.getNodeName().equalsIgnoreCase("listOfUnitDefinitions")) {
- unitsNode = node;
- } else if (node.getNodeName().equalsIgnoreCase("listOfFunctionDefinitions")) {
- functionsNode = node;
- } else if (node.getNodeName().equalsIgnoreCase("listOfParameters")) {
- parametersNode = node;
- } else {
- throw new InvalidInputDataExecption("Unknown element of model: " + node.getNodeName());
- }
- }
- }
-
- if (unitsNode != null) {
- model.addUnits(unitParser.parseXmlUnitCollection(unitsNode));
- }
-
- if (parametersNode != null) {
- model.addParameters(parameterParser.parseXmlParameterCollection(parametersNode));
- }
-
- Node annotationNode = getNode("annotation", modelNode.getChildNodes());
- if (annotationNode == null) {
- throw new InvalidInputDataExecption("No annotation node in SBML/model");
- }
-
- parseAnnotation(model, annotationNode, modelData, elements);
-
- if (speciesNode != null) {
- List<Pair<String, ? extends CellDesignerSpecies<?>>> species = speciesSbmlParser
- .parseSbmlSpeciesCollection(speciesNode);
- modelData.updateSpecies(species);
- }
- if (functionsNode != null) {
- model.addFunctions(functionParser.parseXmlFunctionCollection(functionsNode));
- }
-
- if (reactionsNode != null) {
- ReactionCollectionXmlParser reactionCollectionXmlParser = new ReactionCollectionXmlParser(model, elements,
- params.isSbgnFormat());
- List<Reaction> reactions = reactionCollectionXmlParser.parseXmlReactionCollection(reactionsNode);
- model.addReactions(reactions);
- }
-
- if (params.isSizeAutoAdjust()) {
- Rectangle2D bound = getModelBound(model);
- double width = bound.getWidth() + 2 * (Math.max(0, bound.getX()));
- double height = bound.getHeight() + 2 * (Math.max(0, bound.getY()));
-
- model.setWidth(width);
- model.setHeight(height);
- }
- } catch (InvalidXmlSchemaException e) {
- throw new InvalidInputDataExecption(e);
- } catch (CellDesignerParserException e) {
- throw new InvalidInputDataExecption(e);
- }
-
- return model;
- }
-
- /**
- * Computes bound of the model.
- *
- * @param model
- * object for which computaion is done
- * @return bound of the model
- */
- Rectangle2D getModelBound(Model model) {
- double maxX = 0;
- double maxY = 0;
- double minX = model.getWidth();
- double minY = model.getHeight();
- for (Element alias : model.getElements()) {
- maxX = Math.max(maxX, alias.getWidth() + alias.getX());
- maxY = Math.max(maxY, alias.getHeight() + alias.getY());
-
- minX = Math.min(minX, alias.getX());
- minY = Math.min(minY, alias.getY());
-
- }
-
- for (Reaction reaction : model.getReactions()) {
- for (Line2D line : reaction.getLines()) {
- maxX = Math.max(maxX, line.getX1());
- maxX = Math.max(maxX, line.getX2());
- maxY = Math.max(maxY, line.getY1());
- maxY = Math.max(maxY, line.getY2());
-
- minX = Math.min(minX, line.getX1());
- minX = Math.min(minX, line.getX2());
- minY = Math.min(minY, line.getY1());
- minY = Math.min(minY, line.getY2());
- }
- }
-
- for (Layer layer : model.getLayers()) {
- for (PolylineData lline : layer.getLines()) {
- for (Line2D line : lline.getLines()) {
- maxX = Math.max(maxX, line.getX1());
- maxX = Math.max(maxX, line.getX2());
- maxY = Math.max(maxY, line.getY1());
- maxY = Math.max(maxY, line.getY2());
-
- minX = Math.min(minX, line.getX1());
- minX = Math.min(minX, line.getX2());
- minY = Math.min(minY, line.getY1());
- minY = Math.min(minY, line.getY2());
- }
- }
- for (LayerRect rect : layer.getRectangles()) {
- maxX = Math.max(maxX, rect.getX());
- maxX = Math.max(maxX, rect.getX() + rect.getWidth());
- maxY = Math.max(maxY, rect.getY());
- maxY = Math.max(maxY, rect.getY() + rect.getHeight());
-
- minX = Math.min(minX, rect.getX());
- minX = Math.min(minX, rect.getX() + rect.getWidth());
- minY = Math.min(minY, rect.getY());
- minY = Math.min(minY, rect.getY() + rect.getHeight());
- }
- for (LayerOval oval : layer.getOvals()) {
- maxX = Math.max(maxX, oval.getX());
- maxX = Math.max(maxX, oval.getX() + oval.getWidth());
- maxY = Math.max(maxY, oval.getY());
- maxY = Math.max(maxY, oval.getY() + oval.getHeight());
-
- minX = Math.min(minX, oval.getX());
- minX = Math.min(minX, oval.getX() + oval.getWidth());
- minY = Math.min(minY, oval.getY());
- minY = Math.min(minY, oval.getY() + oval.getHeight());
- }
- for (LayerText text : layer.getTexts()) {
- maxX = Math.max(maxX, text.getX());
- maxX = Math.max(maxX, text.getX() + text.getWidth());
- maxY = Math.max(maxY, text.getY());
- maxY = Math.max(maxY, text.getY() + text.getHeight());
-
- minX = Math.min(minX, text.getX());
- minX = Math.min(minX, text.getX() + text.getWidth());
- minY = Math.min(minY, text.getY());
- minY = Math.min(minY, text.getY() + text.getHeight());
- }
- }
-
- Rectangle2D result = new Rectangle2D.Double(minX, minY, maxX - minX, maxY - minY);
- return result;
- }
-
- /**
- * Parse annotation part of CellDesigner xml.
- *
- * @param model
- * model that is parsed (and will be updated)
- * @param modelData
- * object containing information about species during CellDesigner
- * parsing
- * @param elements
- * collection of {@link CellDesignerElement cell designer elements}
- * parsed from xml
- * @param annotationNode
- * xml node to parse
- * @throws InvalidXmlSchemaException
- * thrown when xmlString is invalid
- */
- private void parseAnnotation(Model model, Node annotationNode, InternalModelSpeciesData modelData,
- CellDesignerElementCollection elements) throws InvalidXmlSchemaException {
- SpeciesCollectionXmlParser parser = new SpeciesCollectionXmlParser(elements);
-
- Node extensionNode = getNode("celldesigner:extension", annotationNode.getChildNodes());
- if (extensionNode == null) {
- throw new InvalidXmlSchemaException("No celldesigner:extension node in SBML/model/annotation");
- }
-
- NodeList nodes = extensionNode.getChildNodes();
- Node includedSpecies = null;
- Node listofSpeciesAlias = null;
- Node listOfComplexSpeciesAlias = null;
- Node listOfComparmentAlias = null;
- Node listOfProteins = null;
- Node listOfGenes = null;
- Node listOfRnas = null;
- Node listOfGroups = null;
- Node listOfAntisenseRnas = null;
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:modelVersion")) {
- // we ignore map version (there is no use for us)
- // model.setVersion(getNodeValue(node));
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:modelDisplay")) {
- model.setWidth(getNodeAttr("sizeX", node));
- model.setHeight(getNodeAttr("sizeY", node));
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfSpeciesAliases")) {
- listofSpeciesAlias = node;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfComplexSpeciesAliases")) {
- listOfComplexSpeciesAlias = node;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfProteins")) {
- listOfProteins = node;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfGenes")) {
- listOfGenes = node;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfRNAs")) {
- listOfRnas = node;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfAntisenseRNAs")) {
- listOfAntisenseRnas = node;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfIncludedSpecies")) {
- includedSpecies = node;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfCompartmentAliases")) {
- listOfComparmentAlias = node;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfLayers")) {
- model.addLayers(layerParser.parseLayers(node));
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfGroups")) {
- listOfGroups = node;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfBlockDiagrams")) {
- layerParser.parseBlocks(model, node);
- } else {
- throw new InvalidXmlSchemaException("Unknown element of annotation: " + node.getNodeName());
- }
- }
- }
-
- if (listOfComparmentAlias != null) {
- List<Compartment> aliases = aliasCollectionParser.parseXmlCompartmentAliasCollection(listOfComparmentAlias);
- for (Element alias : aliases) {
- rap.processNotes(alias);
- model.addElement(alias);
- }
- }
-
- if (includedSpecies != null) {
- List<Pair<String, ? extends CellDesignerSpecies<?>>> species = parser
- .parseIncludedSpeciesCollection(includedSpecies);
- modelData.updateSpecies(species);
- }
-
- if (listOfProteins != null) {
- List<Pair<String, ? extends CellDesignerSpecies<?>>> species = parser.parseXmlProteinCollection(listOfProteins);
- modelData.updateSpecies(species);
- }
- if (listOfGenes != null) {
- List<Pair<String, ? extends CellDesignerSpecies<?>>> species = parser.parseXmlGeneCollection(listOfGenes);
- modelData.updateSpecies(species);
- }
- if (listOfRnas != null) {
- List<Pair<String, ? extends CellDesignerSpecies<?>>> species = parser.parseXmlRnaCollection(listOfRnas);
- modelData.updateSpecies(species);
- }
- if (listOfAntisenseRnas != null) {
- List<Pair<String, ? extends CellDesignerSpecies<?>>> species = parser
- .parseXmlAntisenseRnaCollection(listOfAntisenseRnas);
- modelData.updateSpecies(species);
- }
-
- for (CellDesignerSpecies<?> species : modelData.getAll()) {
- if (!species.getElementId().equals("")) {
- elements.addElement(species);
- } else {
- logger.warn("Species (class: " + species.getClass().getName() + ", name: " + species.getName()
- + ") exists in CD file, but is never instantiated. It's CellDesigner file problem.");
- }
- }
-
- if (listOfComplexSpeciesAlias != null) {
- List<Complex> aliases = aliasCollectionParser.parseXmlComplexAliasCollection(listOfComplexSpeciesAlias);
- for (Element alias : aliases) {
- rap.processNotes(alias);
- model.addElement(alias);
- }
- }
-
- if (listofSpeciesAlias != null) {
- List<Species> aliases = aliasCollectionParser.parseXmlSpeciesAliasCollection(listofSpeciesAlias);
- for (Element alias : aliases) {
- rap.processNotes(alias);
- model.addElement(alias);
- }
- }
-
- if (includedSpecies != null) {
- parseAnnotationAliasesConnections(model, getNode("celldesigner:listOfSpeciesAliases", nodes));
- parseAnnotationComplexAliasesConnections(model, getNode("celldesigner:listOfComplexSpeciesAliases", nodes));
- }
-
- if (listOfGroups != null) {
- layerParser.parseGroups(model, listOfGroups);
- }
-
- }
-
- /**
- * Parses celldesigner:listOfComplexSpeciesAliases node for annotation part of
- * the CellDEsigner format.
- *
- * @param model
- * model that is parsed
- * @param aliasNode
- * node to parse
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- void parseAnnotationComplexAliasesConnections(Model model, Node aliasNode) throws InvalidXmlSchemaException {
- NodeList nodes = aliasNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:complexSpeciesAlias")) {
- String aliasId = getNodeAttr("id", node);
- String complexId = getNodeAttr("complexSpeciesAlias", node);
- Complex alias = model.getElementByElementId(aliasId);
- if (alias == null) {
- throw new InvalidXmlSchemaException("Alias does not exist " + aliasId);
- }
- Complex parentComplex = model.getElementByElementId(complexId);
- if (parentComplex != null) {
- parentComplex.addSpecies(alias);
- alias.setComplex(parentComplex);
- }
- } else {
- throw new InvalidXmlSchemaException(
- "Unknown element of celldesigner:listOfComplexSpeciesAliases: " + node.getNodeName());
- }
- }
- }
-
- }
-
- /**
- * Parses celldesigner:listOfSpeciesAliases node for annotation part of the
- * CellDesigner format.
- *
- * @param model
- * model that is parsed
- * @param aliasNode
- * node to parse
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- void parseAnnotationAliasesConnections(Model model, Node aliasNode) throws InvalidXmlSchemaException {
- NodeList nodes = aliasNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:speciesAlias")) {
- String aliasId = getNodeAttr("id", node);
- String complexId = getNodeAttr("complexSpeciesAlias", node);
- Element alias = model.getElementByElementId(aliasId);
- if (alias == null) {
- throw new InvalidXmlSchemaException("Alias does not exist " + aliasId);
- } else if (alias instanceof Species) {
- Species species = ((Species) alias);
- Complex complex = model.getElementByElementId(complexId);
- if (complex != null) {
- species.setComplex(complex);
- complex.addSpecies(species);
- }
- }
- } else {
- throw new InvalidXmlSchemaException(
- "Unknown element of celldesigner:listOfSpeciesAliases: " + node.getNodeName());
- }
- }
- }
- }
-
- /**
- * Transforms model into CellDesigner xml.
- *
- * @param model
- * model that should be transformed
- * @return CellDesigner xml string for the model
- * @throws InconsistentModelException
- * thrown when then model is invalid
- * @throws InconsistentModelException
- */
- public String toXml(Model model) throws InconsistentModelException {
- EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
- try {
- Logger.getRootLogger().addAppender(appender);
- CellDesignerElementCollection elements = new CellDesignerElementCollection();
-
- SpeciesCollectionXmlParser speciesCollectionXmlParser = new SpeciesCollectionXmlParser(elements);
- ReactionCollectionXmlParser reactionCollectionXmlParser = new ReactionCollectionXmlParser(model, elements, false);
- UnitCollectionXmlParser unitCollectionXmlParser = new UnitCollectionXmlParser();
- FunctionCollectionXmlParser functionCollectionXmlParser = new FunctionCollectionXmlParser();
- ParameterCollectionXmlParser parameterCollectionXmlParser = new ParameterCollectionXmlParser(model);
-
- aliasCollectionParser = new AliasCollectionXmlParser(elements, model);
-
- StringBuilder result = new StringBuilder();
- result.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
- result.append("<sbml xmlns=\"http://www.sbml.org/sbml/level2/version4\" "
- + "xmlns:celldesigner=\"http://www.sbml.org/2001/ns/celldesigner\" level=\"2\" version=\"4\">\n");
- // metaid is a string cell designer id, usually it's model id and as far as
- // we can tell it's not used at all
- result.append("<model metaid=\"" + model.getIdModel() + "\" id=\"" + model.getIdModel() + "\">\n");
-
- result.append(unitCollectionXmlParser.toXml(model.getUnits()));
- result.append(functionCollectionXmlParser.toXml(model.getFunctions()));
- result.append(parameterCollectionXmlParser.toXml(model.getParameters()));
- result.append(annotationToXml(model, elements));
-
- compartmentCollectionXmlParser = new CompartmentCollectionXmlParser(elements);
-
- result.append(compartmentCollectionXmlParser.toXml(model.getCompartments()));
-
- result.append(speciesCollectionXmlParser.speciesCollectionToSbmlString(model.getSpeciesList()));
-
- result.append(reactionCollectionXmlParser.reactionCollectionToXmlString(model.getReactions()));
- if (model.getNotes() != null || !appender.getWarnings().isEmpty()) {
- result.append("<notes>");
- if (model.getNotes() != null) {
- result.append(escapeXml(model.getNotes()));
- }
- for (LoggingEvent event : appender.getWarnings()) {
- if (event.getMessage() instanceof String) {
- result.append("\n" + ((String) event.getMessage()));
- }
- }
- result.append("</notes>");
- }
-
- result.append("</model>");
- result.append("</sbml>");
- return result.toString();
- } finally {
- Logger.getRootLogger().removeAppender(appender);
- }
- }
-
- /**
- * Generates xml node that should be in annotation part of the model.
- *
- * @param model
- * model to transform
- * @param elements
- * collection of {@link CellDesignerElement cell designer elements}
- * parsed from xml
- * @return annotation xml string for the model
- */
- private String annotationToXml(Model model, CellDesignerElementCollection elements) {
- SpeciesCollectionXmlParser speciesCollectionXmlParser = new SpeciesCollectionXmlParser(elements);
-
- StringBuilder result = new StringBuilder();
- result.append("<annotation>\n");
- result.append("<celldesigner:extension>\n");
- result.append("<celldesigner:modelVersion>4.0</celldesigner:modelVersion>\n");
- result.append("<celldesigner:modelDisplay sizeX=\"" + model.getWidth().intValue() + "\" sizeY=\""
- + model.getHeight().intValue() + "\"/>\n");
-
- result.append(speciesCollectionXmlParser.speciesCollectionToXmlIncludedString(model.getSpeciesList()));
-
- result.append(aliasCollectionParser.compartmentAliasCollectionToXmlString(model.getCompartments()));
- result.append(aliasCollectionParser.complexAliasCollectionToXmlString(model.getComplexList()));
- result.append(aliasCollectionParser.speciesAliasCollectionToXmlString(model.getNotComplexSpeciesList()));
-
- List<Protein> proteins = new ArrayList<>();
- List<Gene> genes = new ArrayList<>();
- List<Rna> rnas = new ArrayList<>();
- List<AntisenseRna> antisenseRnas = new ArrayList<>();
- for (Element element : model.getElements()) {
- if (element instanceof Protein) {
- proteins.add((Protein) element);
- } else if (element instanceof Gene) {
- genes.add((Gene) element);
- } else if (element instanceof AntisenseRna) {
- antisenseRnas.add((AntisenseRna) element);
- } else if (element instanceof Rna) {
- rnas.add((Rna) element);
- }
- }
-
- result.append(speciesCollectionXmlParser.proteinCollectionToXmlString(proteins));
- result.append(speciesCollectionXmlParser.geneCollectionToXmlString(genes));
- result.append(speciesCollectionXmlParser.rnaCollectionToXmlString(rnas));
- result.append(speciesCollectionXmlParser.antisenseRnaCollectionToXmlString(antisenseRnas));
- result.append(layerParser.layerCollectionToXml(model.getLayers()));
-
- result.append("</celldesigner:extension>\n");
- result.append("</annotation>\n");
- return result.toString();
- }
-
- @Override
- public InputStream exportModelToInputStream(Model model) throws InconsistentModelException {
- String exportedString = toXml(model);
- InputStream inputStream = new ByteArrayInputStream(exportedString.getBytes());
- return inputStream;
- }
-
- @Override
- public File exportModelToFile(Model model, String filePath) throws InconsistentModelException, IOException {
- File file = new File(filePath);
- String exportedString = toXml(model);
- FileWriter fileWriter = new FileWriter(file);
- fileWriter.write(exportedString);
- fileWriter.flush();
- fileWriter.close();
-
- return file;
- }
-
- @Override
- public String getCommonName() {
- return "CellDesigner SBML";
- }
-
- @Override
- public MimeType getMimeType() {
- return MimeType.SBML;
- }
-
- @Override
- public String getFileExtension() {
- return "xml";
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner;
+
+import java.awt.geom.Line2D;
+import java.awt.geom.Rectangle2D;
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.io.FilenameUtils;
+import org.apache.commons.lang3.StringEscapeUtils;
+import org.apache.log4j.Logger;
+import org.apache.log4j.spi.LoggingEvent;
+import org.apache.xerces.parsers.DOMParser;
+import org.w3c.dom.Document;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import lcsb.mapviewer.common.EventStorageLoggerAppender;
+import lcsb.mapviewer.common.MimeType;
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.model.celldesigner.alias.AliasCollectionXmlParser;
+import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
+import lcsb.mapviewer.converter.model.celldesigner.compartment.CompartmentCollectionXmlParser;
+import lcsb.mapviewer.converter.model.celldesigner.function.FunctionCollectionXmlParser;
+import lcsb.mapviewer.converter.model.celldesigner.parameter.ParameterCollectionXmlParser;
+import lcsb.mapviewer.converter.model.celldesigner.reaction.ReactionCollectionXmlParser;
+import lcsb.mapviewer.converter.model.celldesigner.species.InternalModelSpeciesData;
+import lcsb.mapviewer.converter.model.celldesigner.species.SpeciesCollectionXmlParser;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.unit.UnitCollectionXmlParser;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.layout.graphics.LayerOval;
+import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
+import lcsb.mapviewer.model.map.layout.graphics.LayerText;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This class is a parser for CellDesigner files. There are two typical use
+ * cases:
+ * <ul>
+ * <li>CellDesigner xml -> our model. To perform this action
+ * {@link #createModel(Params)} method should be called.</li>
+ * <li>our model -> CellDesigner xml. To perform this action
+ * {@link #toXml(Model)} method should be called.</li>
+ * </ul>
+ * <p/>
+ * CellDEsigner format is the extension of <a href="http://sbml.org">SBML</a>.
+ * More information about this format could be found <a href=
+ * "http://www.celldesigner.org/documents/CellDesigner4ExtensionTagSpecificationE.pdf"
+ * >here</a>.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CellDesignerXmlParser extends XmlParser implements IConverter {
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(CellDesignerXmlParser.class.getName());
+
+ /**
+ * CellDesigner parser for layers.
+ */
+ private LayerXmlParser layerParser = new LayerXmlParser();
+
+ /**
+ * CellDesigner parser for compartments collections.
+ */
+ private CompartmentCollectionXmlParser compartmentCollectionXmlParser;
+
+ /**
+ * CellDesigner parser for species collections.
+ */
+ private SpeciesCollectionXmlParser speciesSbmlParser;
+
+ /**
+ * CellDesigner parser for alias collections.
+ */
+ private AliasCollectionXmlParser aliasCollectionParser;
+
+ /**
+ * Annotation parser.
+ */
+ private RestAnnotationParser rap = new RestAnnotationParser();
+
+ @Override
+ public Model createModel(ConverterParams params) throws InvalidInputDataExecption {
+ CellDesignerElementCollection elements = new CellDesignerElementCollection();
+ FunctionCollectionXmlParser functionParser = new FunctionCollectionXmlParser();
+ UnitCollectionXmlParser unitParser = new UnitCollectionXmlParser();
+
+ Model model = new ModelFullIndexed(null);
+
+ if (params.getFilename() != null) {
+ model.setName(FilenameUtils.getBaseName(params.getFilename()));
+ }
+ speciesSbmlParser = new SpeciesCollectionXmlParser(elements);
+ aliasCollectionParser = new AliasCollectionXmlParser(elements, model);
+ compartmentCollectionXmlParser = new CompartmentCollectionXmlParser(elements);
+
+ ParameterCollectionXmlParser parameterParser = new ParameterCollectionXmlParser(model);
+
+ DOMParser parser = new DOMParser();
+ try {
+ parser.parse(params.getSource());
+ } catch (IOException e) {
+ throw new InvalidInputDataExecption("IO Problem with a file: " + params.getSource().getSystemId(), e);
+ }
+ Document doc = parser.getDocument();
+ try {
+
+ // Get the document's root XML node
+ NodeList root = doc.getChildNodes();
+
+ // Navigate down the hierarchy to get to the CEO node
+ Node sbmlNode = getNode("SBML", root);
+ if (sbmlNode == null) {
+ throw new InvalidInputDataExecption("No SBML node");
+ }
+
+ Node modelNode = getNode("model", sbmlNode.getChildNodes());
+ if (modelNode == null) {
+ throw new InvalidInputDataExecption("No model node in SBML");
+ }
+ // we ignore metaid - it's useless and obstruct data model
+ // model.setMetaId(getNodeAttr("metaId", modelNode));
+ model.setIdModel(getNodeAttr("id", modelNode));
+
+ Node compartmentNode = getNode("listOfCompartments", modelNode.getChildNodes());
+ if (compartmentNode != null) {
+ List<CellDesignerCompartment> compartments = compartmentCollectionXmlParser
+ .parseXmlCompartmentCollection(compartmentNode);
+ elements.addElements(compartments);
+ }
+
+ InternalModelSpeciesData modelData = new InternalModelSpeciesData();
+
+ Node speciesNode = getNode("listOfSpecies", modelNode.getChildNodes());
+ if (speciesNode != null) {
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> species = speciesSbmlParser
+ .parseSbmlSpeciesCollection(speciesNode);
+ modelData.updateSpecies(species);
+ }
+ Node reactionsNode = null;
+ Node functionsNode = null;
+ Node unitsNode = null;
+ Node parametersNode = null;
+
+ NodeList nodes = modelNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("annotation")) {
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("listOfSpecies")) {
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("listOfReactions")) {
+ reactionsNode = node;
+ } else if (node.getNodeName().equalsIgnoreCase("listOfCompartments")) {
+ // we already parsed compartments
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("notes")) {
+ String notes = rap.getNotes(node);
+ if (notes != null) {
+ notes = StringEscapeUtils.unescapeHtml4(notes);
+ }
+ model.setNotes(notes);
+ } else if (node.getNodeName().equalsIgnoreCase("listOfUnitDefinitions")) {
+ unitsNode = node;
+ } else if (node.getNodeName().equalsIgnoreCase("listOfFunctionDefinitions")) {
+ functionsNode = node;
+ } else if (node.getNodeName().equalsIgnoreCase("listOfParameters")) {
+ parametersNode = node;
+ } else {
+ throw new InvalidInputDataExecption("Unknown element of model: " + node.getNodeName());
+ }
+ }
+ }
+
+ if (unitsNode != null) {
+ model.addUnits(unitParser.parseXmlUnitCollection(unitsNode));
+ }
+
+ if (parametersNode != null) {
+ model.addParameters(parameterParser.parseXmlParameterCollection(parametersNode));
+ }
+
+ Node annotationNode = getNode("annotation", modelNode.getChildNodes());
+ if (annotationNode == null) {
+ throw new InvalidInputDataExecption("No annotation node in SBML/model");
+ }
+
+ parseAnnotation(model, annotationNode, modelData, elements);
+
+ if (speciesNode != null) {
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> species = speciesSbmlParser
+ .parseSbmlSpeciesCollection(speciesNode);
+ modelData.updateSpecies(species);
+ }
+ if (functionsNode != null) {
+ model.addFunctions(functionParser.parseXmlFunctionCollection(functionsNode));
+ }
+
+ if (reactionsNode != null) {
+ ReactionCollectionXmlParser reactionCollectionXmlParser = new ReactionCollectionXmlParser(model, elements,
+ params.isSbgnFormat());
+ List<Reaction> reactions = reactionCollectionXmlParser.parseXmlReactionCollection(reactionsNode);
+ model.addReactions(reactions);
+ }
+
+ if (params.isSizeAutoAdjust()) {
+ Rectangle2D bound = getModelBound(model);
+ double width = bound.getWidth() + 2 * (Math.max(0, bound.getX()));
+ double height = bound.getHeight() + 2 * (Math.max(0, bound.getY()));
+
+ model.setWidth(width);
+ model.setHeight(height);
+ }
+ } catch (InvalidXmlSchemaException e) {
+ throw new InvalidInputDataExecption(e);
+ } catch (CellDesignerParserException e) {
+ throw new InvalidInputDataExecption(e);
+ }
+
+ return model;
+ }
+
+ /**
+ * Computes bound of the model.
+ *
+ * @param model
+ * object for which computaion is done
+ * @return bound of the model
+ */
+ Rectangle2D getModelBound(Model model) {
+ double maxX = 0;
+ double maxY = 0;
+ double minX = model.getWidth();
+ double minY = model.getHeight();
+ for (Element alias : model.getElements()) {
+ maxX = Math.max(maxX, alias.getWidth() + alias.getX());
+ maxY = Math.max(maxY, alias.getHeight() + alias.getY());
+
+ minX = Math.min(minX, alias.getX());
+ minY = Math.min(minY, alias.getY());
+
+ }
+
+ for (Reaction reaction : model.getReactions()) {
+ for (Line2D line : reaction.getLines()) {
+ maxX = Math.max(maxX, line.getX1());
+ maxX = Math.max(maxX, line.getX2());
+ maxY = Math.max(maxY, line.getY1());
+ maxY = Math.max(maxY, line.getY2());
+
+ minX = Math.min(minX, line.getX1());
+ minX = Math.min(minX, line.getX2());
+ minY = Math.min(minY, line.getY1());
+ minY = Math.min(minY, line.getY2());
+ }
+ }
+
+ for (Layer layer : model.getLayers()) {
+ for (PolylineData lline : layer.getLines()) {
+ for (Line2D line : lline.getLines()) {
+ maxX = Math.max(maxX, line.getX1());
+ maxX = Math.max(maxX, line.getX2());
+ maxY = Math.max(maxY, line.getY1());
+ maxY = Math.max(maxY, line.getY2());
+
+ minX = Math.min(minX, line.getX1());
+ minX = Math.min(minX, line.getX2());
+ minY = Math.min(minY, line.getY1());
+ minY = Math.min(minY, line.getY2());
+ }
+ }
+ for (LayerRect rect : layer.getRectangles()) {
+ maxX = Math.max(maxX, rect.getX());
+ maxX = Math.max(maxX, rect.getX() + rect.getWidth());
+ maxY = Math.max(maxY, rect.getY());
+ maxY = Math.max(maxY, rect.getY() + rect.getHeight());
+
+ minX = Math.min(minX, rect.getX());
+ minX = Math.min(minX, rect.getX() + rect.getWidth());
+ minY = Math.min(minY, rect.getY());
+ minY = Math.min(minY, rect.getY() + rect.getHeight());
+ }
+ for (LayerOval oval : layer.getOvals()) {
+ maxX = Math.max(maxX, oval.getX());
+ maxX = Math.max(maxX, oval.getX() + oval.getWidth());
+ maxY = Math.max(maxY, oval.getY());
+ maxY = Math.max(maxY, oval.getY() + oval.getHeight());
+
+ minX = Math.min(minX, oval.getX());
+ minX = Math.min(minX, oval.getX() + oval.getWidth());
+ minY = Math.min(minY, oval.getY());
+ minY = Math.min(minY, oval.getY() + oval.getHeight());
+ }
+ for (LayerText text : layer.getTexts()) {
+ maxX = Math.max(maxX, text.getX());
+ maxX = Math.max(maxX, text.getX() + text.getWidth());
+ maxY = Math.max(maxY, text.getY());
+ maxY = Math.max(maxY, text.getY() + text.getHeight());
+
+ minX = Math.min(minX, text.getX());
+ minX = Math.min(minX, text.getX() + text.getWidth());
+ minY = Math.min(minY, text.getY());
+ minY = Math.min(minY, text.getY() + text.getHeight());
+ }
+ }
+
+ Rectangle2D result = new Rectangle2D.Double(minX, minY, maxX - minX, maxY - minY);
+ return result;
+ }
+
+ /**
+ * Parse annotation part of CellDesigner xml.
+ *
+ * @param model
+ * model that is parsed (and will be updated)
+ * @param modelData
+ * object containing information about species during CellDesigner
+ * parsing
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
+ * @param annotationNode
+ * xml node to parse
+ * @throws InvalidXmlSchemaException
+ * thrown when xmlString is invalid
+ */
+ private void parseAnnotation(Model model, Node annotationNode, InternalModelSpeciesData modelData,
+ CellDesignerElementCollection elements) throws InvalidXmlSchemaException {
+ SpeciesCollectionXmlParser parser = new SpeciesCollectionXmlParser(elements);
+
+ Node extensionNode = getNode("celldesigner:extension", annotationNode.getChildNodes());
+ if (extensionNode == null) {
+ throw new InvalidXmlSchemaException("No celldesigner:extension node in SBML/model/annotation");
+ }
+
+ NodeList nodes = extensionNode.getChildNodes();
+ Node includedSpecies = null;
+ Node listofSpeciesAlias = null;
+ Node listOfComplexSpeciesAlias = null;
+ Node listOfComparmentAlias = null;
+ Node listOfProteins = null;
+ Node listOfGenes = null;
+ Node listOfRnas = null;
+ Node listOfGroups = null;
+ Node listOfAntisenseRnas = null;
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:modelVersion")) {
+ // we ignore map version (there is no use for us)
+ // model.setVersion(getNodeValue(node));
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:modelDisplay")) {
+ model.setWidth(getNodeAttr("sizeX", node));
+ model.setHeight(getNodeAttr("sizeY", node));
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfSpeciesAliases")) {
+ listofSpeciesAlias = node;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfComplexSpeciesAliases")) {
+ listOfComplexSpeciesAlias = node;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfProteins")) {
+ listOfProteins = node;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfGenes")) {
+ listOfGenes = node;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfRNAs")) {
+ listOfRnas = node;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfAntisenseRNAs")) {
+ listOfAntisenseRnas = node;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfIncludedSpecies")) {
+ includedSpecies = node;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfCompartmentAliases")) {
+ listOfComparmentAlias = node;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfLayers")) {
+ model.addLayers(layerParser.parseLayers(node));
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfGroups")) {
+ listOfGroups = node;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfBlockDiagrams")) {
+ layerParser.parseBlocks(model, node);
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of annotation: " + node.getNodeName());
+ }
+ }
+ }
+
+ if (listOfComparmentAlias != null) {
+ List<Compartment> aliases = aliasCollectionParser.parseXmlCompartmentAliasCollection(listOfComparmentAlias);
+ for (Element alias : aliases) {
+ rap.processNotes(alias);
+ model.addElement(alias);
+ }
+ }
+
+ if (includedSpecies != null) {
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> species = parser
+ .parseIncludedSpeciesCollection(includedSpecies);
+ modelData.updateSpecies(species);
+ }
+
+ if (listOfProteins != null) {
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> species = parser.parseXmlProteinCollection(listOfProteins);
+ modelData.updateSpecies(species);
+ }
+ if (listOfGenes != null) {
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> species = parser.parseXmlGeneCollection(listOfGenes);
+ modelData.updateSpecies(species);
+ }
+ if (listOfRnas != null) {
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> species = parser.parseXmlRnaCollection(listOfRnas);
+ modelData.updateSpecies(species);
+ }
+ if (listOfAntisenseRnas != null) {
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> species = parser
+ .parseXmlAntisenseRnaCollection(listOfAntisenseRnas);
+ modelData.updateSpecies(species);
+ }
+
+ for (CellDesignerSpecies<?> species : modelData.getAll()) {
+ if (!species.getElementId().equals("")) {
+ elements.addElement(species);
+ } else {
+ logger.warn("Species (class: " + species.getClass().getName() + ", name: " + species.getName()
+ + ") exists in CD file, but is never instantiated. It's CellDesigner file problem.");
+ }
+ }
+
+ if (listOfComplexSpeciesAlias != null) {
+ List<Complex> aliases = aliasCollectionParser.parseXmlComplexAliasCollection(listOfComplexSpeciesAlias);
+ for (Element alias : aliases) {
+ rap.processNotes(alias);
+ model.addElement(alias);
+ }
+ }
+
+ if (listofSpeciesAlias != null) {
+ List<Species> aliases = aliasCollectionParser.parseXmlSpeciesAliasCollection(listofSpeciesAlias);
+ for (Element alias : aliases) {
+ rap.processNotes(alias);
+ model.addElement(alias);
+ }
+ }
+
+ if (includedSpecies != null) {
+ parseAnnotationAliasesConnections(model, getNode("celldesigner:listOfSpeciesAliases", nodes));
+ parseAnnotationComplexAliasesConnections(model, getNode("celldesigner:listOfComplexSpeciesAliases", nodes));
+ }
+
+ if (listOfGroups != null) {
+ layerParser.parseGroups(model, listOfGroups);
+ }
+
+ }
+
+ /**
+ * Parses celldesigner:listOfComplexSpeciesAliases node for annotation part of
+ * the CellDEsigner format.
+ *
+ * @param model
+ * model that is parsed
+ * @param aliasNode
+ * node to parse
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ void parseAnnotationComplexAliasesConnections(Model model, Node aliasNode) throws InvalidXmlSchemaException {
+ NodeList nodes = aliasNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:complexSpeciesAlias")) {
+ String aliasId = getNodeAttr("id", node);
+ String complexId = getNodeAttr("complexSpeciesAlias", node);
+ Complex alias = model.getElementByElementId(aliasId);
+ if (alias == null) {
+ throw new InvalidXmlSchemaException("Alias does not exist " + aliasId);
+ }
+ Complex parentComplex = model.getElementByElementId(complexId);
+ if (parentComplex != null) {
+ parentComplex.addSpecies(alias);
+ alias.setComplex(parentComplex);
+ }
+ } else {
+ throw new InvalidXmlSchemaException(
+ "Unknown element of celldesigner:listOfComplexSpeciesAliases: " + node.getNodeName());
+ }
+ }
+ }
+
+ }
+
+ /**
+ * Parses celldesigner:listOfSpeciesAliases node for annotation part of the
+ * CellDesigner format.
+ *
+ * @param model
+ * model that is parsed
+ * @param aliasNode
+ * node to parse
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ void parseAnnotationAliasesConnections(Model model, Node aliasNode) throws InvalidXmlSchemaException {
+ NodeList nodes = aliasNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:speciesAlias")) {
+ String aliasId = getNodeAttr("id", node);
+ String complexId = getNodeAttr("complexSpeciesAlias", node);
+ Element alias = model.getElementByElementId(aliasId);
+ if (alias == null) {
+ throw new InvalidXmlSchemaException("Alias does not exist " + aliasId);
+ } else if (alias instanceof Species) {
+ Species species = ((Species) alias);
+ Complex complex = model.getElementByElementId(complexId);
+ if (complex != null) {
+ species.setComplex(complex);
+ complex.addSpecies(species);
+ }
+ }
+ } else {
+ throw new InvalidXmlSchemaException(
+ "Unknown element of celldesigner:listOfSpeciesAliases: " + node.getNodeName());
+ }
+ }
+ }
+ }
+
+ /**
+ * Transforms model into CellDesigner xml.
+ *
+ * @param model
+ * model that should be transformed
+ * @return CellDesigner xml string for the model
+ * @throws InconsistentModelException
+ * thrown when then model is invalid
+ * @throws InconsistentModelException
+ */
+ public String toXml(Model model) throws InconsistentModelException {
+ EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
+ try {
+ Logger.getRootLogger().addAppender(appender);
+ CellDesignerElementCollection elements = new CellDesignerElementCollection();
+
+ SpeciesCollectionXmlParser speciesCollectionXmlParser = new SpeciesCollectionXmlParser(elements);
+ ReactionCollectionXmlParser reactionCollectionXmlParser = new ReactionCollectionXmlParser(model, elements, false);
+ UnitCollectionXmlParser unitCollectionXmlParser = new UnitCollectionXmlParser();
+ FunctionCollectionXmlParser functionCollectionXmlParser = new FunctionCollectionXmlParser();
+ ParameterCollectionXmlParser parameterCollectionXmlParser = new ParameterCollectionXmlParser(model);
+
+ aliasCollectionParser = new AliasCollectionXmlParser(elements, model);
+
+ StringBuilder result = new StringBuilder();
+ result.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
+ result.append("<sbml xmlns=\"http://www.sbml.org/sbml/level2/version4\" "
+ + "xmlns:celldesigner=\"http://www.sbml.org/2001/ns/celldesigner\" level=\"2\" version=\"4\">\n");
+ // metaid is a string cell designer id, usually it's model id and as far as
+ // we can tell it's not used at all
+ result.append("<model metaid=\"" + model.getIdModel() + "\" id=\"" + model.getIdModel() + "\">\n");
+
+ result.append(unitCollectionXmlParser.toXml(model.getUnits()));
+ result.append(functionCollectionXmlParser.toXml(model.getFunctions()));
+ result.append(parameterCollectionXmlParser.toXml(model.getParameters()));
+ result.append(annotationToXml(model, elements));
+
+ compartmentCollectionXmlParser = new CompartmentCollectionXmlParser(elements);
+
+ result.append(compartmentCollectionXmlParser.toXml(model.getCompartments()));
+
+ result.append(speciesCollectionXmlParser.speciesCollectionToSbmlString(model.getSpeciesList()));
+
+ result.append(reactionCollectionXmlParser.reactionCollectionToXmlString(model.getReactions()));
+ if (model.getNotes() != null || !appender.getWarnings().isEmpty()) {
+ result.append("<notes>");
+ if (model.getNotes() != null) {
+ result.append(escapeXml(model.getNotes()));
+ }
+ for (LoggingEvent event : appender.getWarnings()) {
+ if (event.getMessage() instanceof String) {
+ result.append("\n" + ((String) event.getMessage()));
+ }
+ }
+ result.append("</notes>");
+ }
+
+ result.append("</model>");
+ result.append("</sbml>");
+ return result.toString();
+ } finally {
+ Logger.getRootLogger().removeAppender(appender);
+ }
+ }
+
+ /**
+ * Generates xml node that should be in annotation part of the model.
+ *
+ * @param model
+ * model to transform
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
+ * @return annotation xml string for the model
+ */
+ private String annotationToXml(Model model, CellDesignerElementCollection elements) {
+ SpeciesCollectionXmlParser speciesCollectionXmlParser = new SpeciesCollectionXmlParser(elements);
+
+ StringBuilder result = new StringBuilder();
+ result.append("<annotation>\n");
+ result.append("<celldesigner:extension>\n");
+ result.append("<celldesigner:modelVersion>4.0</celldesigner:modelVersion>\n");
+ result.append("<celldesigner:modelDisplay sizeX=\"" + model.getWidth().intValue() + "\" sizeY=\""
+ + model.getHeight().intValue() + "\"/>\n");
+
+ result.append(speciesCollectionXmlParser.speciesCollectionToXmlIncludedString(model.getSpeciesList()));
+
+ result.append(aliasCollectionParser.compartmentAliasCollectionToXmlString(model.getCompartments()));
+ result.append(aliasCollectionParser.complexAliasCollectionToXmlString(model.getComplexList()));
+ result.append(aliasCollectionParser.speciesAliasCollectionToXmlString(model.getNotComplexSpeciesList()));
+
+ List<Protein> proteins = new ArrayList<>();
+ List<Gene> genes = new ArrayList<>();
+ List<Rna> rnas = new ArrayList<>();
+ List<AntisenseRna> antisenseRnas = new ArrayList<>();
+ for (Element element : model.getElements()) {
+ if (element instanceof Protein) {
+ proteins.add((Protein) element);
+ } else if (element instanceof Gene) {
+ genes.add((Gene) element);
+ } else if (element instanceof AntisenseRna) {
+ antisenseRnas.add((AntisenseRna) element);
+ } else if (element instanceof Rna) {
+ rnas.add((Rna) element);
+ }
+ }
+
+ result.append(speciesCollectionXmlParser.proteinCollectionToXmlString(proteins));
+ result.append(speciesCollectionXmlParser.geneCollectionToXmlString(genes));
+ result.append(speciesCollectionXmlParser.rnaCollectionToXmlString(rnas));
+ result.append(speciesCollectionXmlParser.antisenseRnaCollectionToXmlString(antisenseRnas));
+ result.append(layerParser.layerCollectionToXml(model.getLayers()));
+
+ result.append("</celldesigner:extension>\n");
+ result.append("</annotation>\n");
+ return result.toString();
+ }
+
+ @Override
+ public InputStream exportModelToInputStream(Model model) throws InconsistentModelException {
+ String exportedString = toXml(model);
+ InputStream inputStream = new ByteArrayInputStream(exportedString.getBytes());
+ return inputStream;
+ }
+
+ @Override
+ public File exportModelToFile(Model model, String filePath) throws InconsistentModelException, IOException {
+ File file = new File(filePath);
+ String exportedString = toXml(model);
+ FileWriter fileWriter = new FileWriter(file);
+ fileWriter.write(exportedString);
+ fileWriter.flush();
+ fileWriter.close();
+
+ return file;
+ }
+
+ @Override
+ public String getCommonName() {
+ return "CellDesigner SBML";
+ }
+
+ @Override
+ public MimeType getMimeType() {
+ return MimeType.SBML;
+ }
+
+ @Override
+ public String getFileExtension() {
+ return "xml";
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CommonXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CommonXmlParser.java
index a334aac73e..5955ca31d2 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CommonXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CommonXmlParser.java
@@ -1,106 +1,106 @@
-package lcsb.mapviewer.converter.model.celldesigner;
-
-import java.awt.Color;
-import java.awt.Dimension;
-import java.awt.geom.Point2D;
-
-import lcsb.mapviewer.common.XmlParser;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.SingleLine;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.View;
-
-import org.w3c.dom.Node;
-
-/**
- * Class with parsers for common CellDesigner objects.
- *
- * @author Piotr Gawron
- *
- */
-public class CommonXmlParser extends XmlParser {
- /**
- * Parse xml representation of position into Poin2D object.
- *
- * @param node
- * xml node to parse
- * @return Point2D object
- */
- public Point2D getPosition(Node node) {
- double x = Double.parseDouble(getNodeAttr("x", node));
- double y = Double.parseDouble(getNodeAttr("y", node));
- return new Point2D.Double(x, y);
-
- }
-
- /**
- * Parse xml representation of dimension.
- *
- * @param node
- * xml node to parse
- * @return dimension (with width and height fields)
- */
- public Dimension getDimension(Node node) {
- double width = Double.parseDouble(getNodeAttr("width", node));
- double height = Double.parseDouble(getNodeAttr("height", node));
- Dimension result = new Dimension();
- result.setSize(width, height);
- return result;
- }
-
- /**
- * Parse xml representation of CellDesigner SingleLine.
- *
- * @param node
- * xml node to parse
- * @return sinle line object (with width field)
- */
- public SingleLine getSingleLine(Node node) {
- SingleLine result = new SingleLine();
- result.setWidth(Double.parseDouble(getNodeAttr("width", node)));
- return result;
- }
-
- /**
- * Parse xml representation of CellDesigner color.
- *
- * @param node
- * xml node to parse
- * @return Color value stored in xml
- */
- public Color getColor(Node node) {
- String color = getNodeAttr("color", node);
- return stringToColor(color);
- }
-
- /**
- * Parse xml representation of CellDesigner view.
- *
- * @param node
- * xml node to parse
- * @return view parsed from xml
- * @see View
- */
- public View getView(Node node) {
- View result = new View();
- Node tmpNode = getNode("celldesigner:innerPosition", node.getChildNodes());
- if (tmpNode != null) {
- result.setInnerPosition(getPosition(tmpNode));
- }
-
- tmpNode = getNode("celldesigner:boxSize", node.getChildNodes());
- if (tmpNode != null) {
- result.setBoxSize(getDimension(tmpNode));
- }
-
- tmpNode = getNode("celldesigner:singleLine", node.getChildNodes());
- if (tmpNode != null) {
- result.setSingleLine(getSingleLine(tmpNode));
- }
-
- tmpNode = getNode("celldesigner:paint", node.getChildNodes());
- if (tmpNode != null) {
- result.setColor(getColor(tmpNode));
- }
- return result;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.geom.Point2D;
+
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.SingleLine;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.View;
+
+import org.w3c.dom.Node;
+
+/**
+ * Class with parsers for common CellDesigner objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CommonXmlParser extends XmlParser {
+ /**
+ * Parse xml representation of position into Poin2D object.
+ *
+ * @param node
+ * xml node to parse
+ * @return Point2D object
+ */
+ public Point2D getPosition(Node node) {
+ double x = Double.parseDouble(getNodeAttr("x", node));
+ double y = Double.parseDouble(getNodeAttr("y", node));
+ return new Point2D.Double(x, y);
+
+ }
+
+ /**
+ * Parse xml representation of dimension.
+ *
+ * @param node
+ * xml node to parse
+ * @return dimension (with width and height fields)
+ */
+ public Dimension getDimension(Node node) {
+ double width = Double.parseDouble(getNodeAttr("width", node));
+ double height = Double.parseDouble(getNodeAttr("height", node));
+ Dimension result = new Dimension();
+ result.setSize(width, height);
+ return result;
+ }
+
+ /**
+ * Parse xml representation of CellDesigner SingleLine.
+ *
+ * @param node
+ * xml node to parse
+ * @return sinle line object (with width field)
+ */
+ public SingleLine getSingleLine(Node node) {
+ SingleLine result = new SingleLine();
+ result.setWidth(Double.parseDouble(getNodeAttr("width", node)));
+ return result;
+ }
+
+ /**
+ * Parse xml representation of CellDesigner color.
+ *
+ * @param node
+ * xml node to parse
+ * @return Color value stored in xml
+ */
+ public Color getColor(Node node) {
+ String color = getNodeAttr("color", node);
+ return stringToColor(color);
+ }
+
+ /**
+ * Parse xml representation of CellDesigner view.
+ *
+ * @param node
+ * xml node to parse
+ * @return view parsed from xml
+ * @see View
+ */
+ public View getView(Node node) {
+ View result = new View();
+ Node tmpNode = getNode("celldesigner:innerPosition", node.getChildNodes());
+ if (tmpNode != null) {
+ result.setInnerPosition(getPosition(tmpNode));
+ }
+
+ tmpNode = getNode("celldesigner:boxSize", node.getChildNodes());
+ if (tmpNode != null) {
+ result.setBoxSize(getDimension(tmpNode));
+ }
+
+ tmpNode = getNode("celldesigner:singleLine", node.getChildNodes());
+ if (tmpNode != null) {
+ result.setSingleLine(getSingleLine(tmpNode));
+ }
+
+ tmpNode = getNode("celldesigner:paint", node.getChildNodes());
+ if (tmpNode != null) {
+ result.setColor(getColor(tmpNode));
+ }
+ return result;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/InvalidGroupException.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/InvalidGroupException.java
index ab3f278c60..5ddddf5576 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/InvalidGroupException.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/InvalidGroupException.java
@@ -1,59 +1,59 @@
-package lcsb.mapviewer.converter.model.celldesigner;
-
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-
-/**
- * Exception that shold be thrown when the group in xml schema is invalid.
- *
- * @author Piotr Gawron
- *
- */
-public class InvalidGroupException extends InvalidXmlSchemaException {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor - initializes instance variable to unknown.
- */
-
- public InvalidGroupException() {
- super(); // call superclass constructor
- }
-
- /**
- * Constructor receives some kind of message.
- *
- * @param err
- * message associated with exception
- */
-
- public InvalidGroupException(final String err) {
- super(err);
- }
-
- /**
- * Constructor receives some kind of message and parent exception.
- *
- * @param err
- * message associated with exception
- * @param throwable
- * parent exception
- */
- public InvalidGroupException(final String err, final Throwable throwable) {
- super(err, throwable);
- }
-
- /**
- * Public constructor with parent exception that was catched.
- *
- * @param e
- * parent exception
- */
-
- public InvalidGroupException(final Exception e) {
- super(e);
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner;
+
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+
+/**
+ * Exception that shold be thrown when the group in xml schema is invalid.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class InvalidGroupException extends InvalidXmlSchemaException {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor - initializes instance variable to unknown.
+ */
+
+ public InvalidGroupException() {
+ super(); // call superclass constructor
+ }
+
+ /**
+ * Constructor receives some kind of message.
+ *
+ * @param err
+ * message associated with exception
+ */
+
+ public InvalidGroupException(final String err) {
+ super(err);
+ }
+
+ /**
+ * Constructor receives some kind of message and parent exception.
+ *
+ * @param err
+ * message associated with exception
+ * @param throwable
+ * parent exception
+ */
+ public InvalidGroupException(final String err, final Throwable throwable) {
+ super(err, throwable);
+ }
+
+ /**
+ * Public constructor with parent exception that was catched.
+ *
+ * @param e
+ * parent exception
+ */
+
+ public InvalidGroupException(final Exception e) {
+ super(e);
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParser.java
index 51b36f8732..8cf5bbe5ea 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParser.java
@@ -1,535 +1,535 @@
-package lcsb.mapviewer.converter.model.celldesigner;
-
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import lcsb.mapviewer.common.XmlParser;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.model.graphics.ArrowType;
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.BlockDiagram;
-import lcsb.mapviewer.model.map.layout.ElementGroup;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.layout.graphics.LayerOval;
-import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
-import lcsb.mapviewer.model.map.layout.graphics.LayerText;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * Parser used for parsing CellDesigner xml to get {@link Layer} object.
- *
- * @author Piotr Gawron
- *
- */
-public class LayerXmlParser extends XmlParser {
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(LayerXmlParser.class.getName());
-
- /**
- * Parser for common CellDesigner structures.
- */
- private CommonXmlParser commonParser = new CommonXmlParser();
-
- /**
- * PArses CellDesigner xml node with collection of layers into collection of
- * Layers.
- *
- * @param layersNode
- * xml node
- * @return collection of layers
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- public Collection<Layer> parseLayers(Node layersNode) throws InvalidXmlSchemaException {
- List<Layer> result = new ArrayList<Layer>();
- NodeList nodes = layersNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:layer")) {
- Layer layer = getLayer(node);
- result.add(layer);
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfLayers: " + node.getNodeName());
- }
- }
- }
- return result;
- }
-
- /**
- * Transforms collection of layers into CellDesigner xml node.
- *
- * @param layers
- * collection of layers
- * @return xml node representing layers collection
- */
- public String layerCollectionToXml(Collection<Layer> layers) {
- StringBuilder result = new StringBuilder();
- result.append("<celldesigner:listOfLayers>");
- for (Layer layer : layers) {
- result.append(layerToXml(layer));
- }
- result.append("</celldesigner:listOfLayers>\n");
- return result.toString();
- }
-
- /**
- * Parses collection of block diagrams and adds them into the model.
- *
- * @param model
- * model where the data is stored.
- * @param xmlNode
- * xml node
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- public void parseBlocks(Model model, Node xmlNode) throws InvalidXmlSchemaException {
- NodeList nodes = xmlNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:blockDiagram")) {
- model.addBlockDiagream(getBlockDiagram(node, model));
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfBlockDiagrams: " + node.getNodeName());
- }
- }
- }
- }
-
- /**
- * Parses block diagrams from CellDesigner xml. Important! It's not yet
- * implemented.
- *
- * @param node
- * xml node to parse
- * @param model
- * model where data is stored
- * @return parsed block diagram
- */
- private BlockDiagram getBlockDiagram(Node node, Model model) {
- logger.warn("BlockDiagrams are not implemented");
- return null;
- }
-
- /**
- * Parses CellDesigner node with collection of Alias Group and adds the groups
- * into this model.
- *
- * @param model
- * model where the data is stored
- * @param xmlNode
- * xml node
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- public void parseGroups(Model model, Node xmlNode) throws InvalidXmlSchemaException {
- NodeList nodes = xmlNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:group")) {
- model.addElementGroup(getAliasGroup(node, model));
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfGroups: " + node.getNodeName());
- }
- }
- }
- }
-
- /**
- * Parses xml node for alias group.
- *
- * @param groupNode
- * xml node
- * @param model
- * model where the data is stored
- * @return parsed alias group
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- ElementGroup getAliasGroup(Node groupNode, Model model) throws InvalidXmlSchemaException {
- ElementGroup result = new ElementGroup();
- String id = getNodeAttr("id", groupNode);
- result.setIdGroup(id);
- String members = getNodeAttr("members", groupNode);
-
- String[] list = members.split(",");
- for (String string : list) {
- Element alias = model.getElementByElementId(string);
- if (alias == null) {
- throw new InvalidGroupException("Group \"" + id + "\" contains alias with id: \"" + string + "\", but such alias doesn't exist in the model.");
- }
- result.addElement(alias);
- }
-
- NodeList nodes = groupNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:group: " + node.getNodeName());
- }
- }
-
- return result;
- }
-
- /**
- * Parses CellDesigner xml node for single layer.
- *
- * @param layerNode
- * xml node
- * @return Layer that corresponds to CellDesigner xml node.
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- Layer getLayer(Node layerNode) throws InvalidXmlSchemaException {
- Layer layer = new Layer();
- layer.setLayerId(getNodeAttr("id", layerNode));
- layer.setName(getNodeAttr("name", layerNode));
- layer.setLocked(getNodeAttr("locked", layerNode));
- layer.setVisible(getNodeAttr("visible", layerNode));
- NodeList list = layerNode.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equals("celldesigner:listOfTexts")) {
- NodeList residueList = node.getChildNodes();
- for (int j = 0; j < residueList.getLength(); j++) {
- Node textNode = residueList.item(j);
- if (textNode.getNodeType() == Node.ELEMENT_NODE) {
- if (textNode.getNodeName().equalsIgnoreCase("celldesigner:layerSpeciesAlias")) {
- layer.addLayerText(getLayerText(textNode));
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfTexts " + textNode.getNodeName());
- }
- }
- }
- } else if (node.getNodeName().equals("celldesigner:listOfSquares")) {
- NodeList residueList = node.getChildNodes();
- for (int j = 0; j < residueList.getLength(); j++) {
- Node textNode = residueList.item(j);
- if (textNode.getNodeType() == Node.ELEMENT_NODE) {
- if (textNode.getNodeName().equalsIgnoreCase("celldesigner:layerCompartmentAlias")) {
- if (getNodeAttr("type", textNode).equalsIgnoreCase("SQUARE")) {
- layer.addLayerRect(getLayerRect(textNode));
- } else if (getNodeAttr("type", textNode).equalsIgnoreCase("OVAL")) {
- layer.addLayerOval(getLayerOval(textNode));
- } else {
- throw new InvalidXmlSchemaException("Unknown celldesigner:layerCompartmentAlias type: " + getNodeAttr("type", textNode));
- }
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfSquares " + textNode.getNodeName());
- }
- }
- }
- } else if (node.getNodeName().equals("celldesigner:listOfFreeLines")) {
- NodeList residueList = node.getChildNodes();
- for (int j = 0; j < residueList.getLength(); j++) {
- Node textNode = residueList.item(j);
- if (textNode.getNodeType() == Node.ELEMENT_NODE) {
- if (textNode.getNodeName().equalsIgnoreCase("celldesigner:layerFreeLine")) {
- layer.addLayerLine(getLayerLine(textNode));
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfFreeLines " + textNode.getNodeName());
- }
- }
- }
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:layer " + node.getNodeName());
- }
- }
- }
-
- return layer;
- }
-
- /**
- * Creates CellDesigner xml for a layer.
- *
- * @param layer
- * object to be transformed into xml
- * @return CellDesigner xml representation for the layer
- */
- String layerToXml(Layer layer) {
- StringBuilder result = new StringBuilder();
- result.append("<celldesigner:layer id =\"" + layer.getLayerId() + "\" ");
- result.append(" name =\"" + layer.getName() + "\" ");
- result.append(" locked =\"" + layer.isLocked() + "\" ");
- result.append(" visible =\"" + layer.isVisible() + "\">\n");
-
- result.append("<celldesigner:listOfTexts>\n");
- for (LayerText layerText : layer.getTexts()) {
- result.append(layerTextToXml(layerText));
- }
- result.append("</celldesigner:listOfTexts>\n");
-
- result.append("<celldesigner:listOfSquares>\n");
- for (LayerRect layerRect : layer.getRectangles()) {
- result.append(layerRectToXml(layerRect));
- }
- for (LayerOval layerOval : layer.getOvals()) {
- result.append(layerOvalToXml(layerOval));
- }
- result.append("</celldesigner:listOfSquares>\n");
-
- result.append("<celldesigner:listOfFreeLines>\n");
- for (PolylineData layerLine : layer.getLines()) {
- result.append(layerLineToXml(layerLine));
- }
- result.append("</celldesigner:listOfFreeLines>\n");
-
- result.append("</celldesigner:layer>\n");
- return result.toString();
- }
-
- /**
- * Parses CellDesigner xml node into LayerRect object.
- *
- * @param textNode
- * CellDesigner xml node for layer text object.
- * @return LayerRect instance representing the cml node
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- LayerRect getLayerRect(Node textNode) throws InvalidXmlSchemaException {
- LayerRect result = new LayerRect();
- NodeList nodes = textNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:paint")) {
- result.setColor(commonParser.getColor(node));
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:bounds")) {
- result.setX(getNodeAttr("x", node));
- result.setY(getNodeAttr("y", node));
- result.setWidth(getNodeAttr("w", node));
- result.setHeight(getNodeAttr("h", node));
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:ispaint")) {
- // ???
- continue;
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:layerCompartmentAlias: " + node.getNodeName());
- }
- }
- }
- return result;
- }
-
- /**
- * Transforms LayerRect object into CellDesigner xml node.
- *
- * @param layer
- * object to be transformed into xml
- * @return CellDesigner xml node for LayerRect
- */
- String layerRectToXml(LayerRect layer) {
- StringBuilder result = new StringBuilder();
- result.append("<celldesigner:layerCompartmentAlias type=\"Square\">");
- result.append("<celldesigner:paint color=\"" + colorToString(layer.getColor()) + "\"/>");
- result.append("<celldesigner:bounds x=\"" + layer.getX() + "\" ");
- result.append(" y=\"" + layer.getY() + "\" ");
- result.append(" w=\"" + layer.getWidth() + "\" ");
- result.append(" h=\"" + layer.getHeight() + "\"/>");
- result.append("</celldesigner:layerCompartmentAlias>");
- return result.toString();
- }
-
- /**
- * Parses CellDesigner xml node into LayerLine object.
- *
- * @param lineNode
- * CellDesigner xml node for layer text object.
- * @return LayerLine instance representing the cml node
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- PolylineData getLayerLine(Node lineNode) throws InvalidXmlSchemaException {
- PolylineData ld = new PolylineData();
-
- if (getNodeAttr("isDotted", lineNode).equalsIgnoreCase("true")) {
- ld.getEndAtd().setArrowLineType(LineType.DOTTED);
- }
- if (getNodeAttr("isArrow", lineNode).equalsIgnoreCase("true")) {
- ld.getEndAtd().setArrowType(ArrowType.FULL);
- }
- NodeList nodes = lineNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:bounds")) {
- double sx = Double.parseDouble(getNodeAttr("sx", node));
- double sy = Double.parseDouble(getNodeAttr("sy", node));
- double ex = Double.parseDouble(getNodeAttr("ex", node));
- double ey = Double.parseDouble(getNodeAttr("ey", node));
- Point2D startPoint = new Point2D.Double(sx, sy);
- Point2D endPoint = new Point2D.Double(ex, ey);
- ld.addPoint(startPoint);
- ld.addPoint(endPoint);
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:line")) {
- ld.setColor(stringToColor(getNodeAttr("color", node)));
- ld.setWidth(getNodeAttr("width", node));
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:layerFreeLine: " + node.getNodeName());
- }
- }
- }
- return ld;
- }
-
- /**
- * Transforms LayerLine object into CellDesigner xml node.
- *
- * @param layer
- * object to be transformed into xml
- * @return CellDesigner xml node for LayerLine
- */
- String layerLineToXml(PolylineData layer) {
- StringBuilder result = new StringBuilder();
- result.append("<celldesigner:layerFreeLine ");
- result.append(" isDotted=\"" + layer.getEndAtd().getArrowLineType().equals(LineType.DOTTED) + "\" ");
- result.append(" isArrow=\"" + layer.getEndAtd().getArrowType().equals(ArrowType.FULL) + "\" >");
-
- result.append("<celldesigner:bounds sx=\"" + layer.getBeginPoint().getX() + "\" ");
- result.append(" sy=\"" + layer.getBeginPoint().getY() + "\" ");
- result.append(" ex=\"" + layer.getEndPoint().getX() + "\" ");
- result.append(" ey=\"" + layer.getEndPoint().getY() + "\" />");
- result.append("<celldesigner:line ");
- result.append(" width=\"" + layer.getWidth() + "\" ");
- result.append(" color=\"" + colorToString(layer.getColor()) + "\"/>");
- result.append("</celldesigner:layerFreeLine>\n");
- return result.toString();
- }
-
- /**
- * Parses CellDesigner xml node into LayerOval object.
- *
- * @param textNode
- * CellDesigner xml node for layer text object.
- * @return LayerOval instance representing the cml node
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- LayerOval getLayerOval(Node textNode) throws InvalidXmlSchemaException {
- LayerOval result = new LayerOval();
- NodeList nodes = textNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:paint")) {
- result.setColor(commonParser.getColor(node));
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:bounds")) {
- result.setX(getNodeAttr("x", node));
- result.setY(getNodeAttr("y", node));
- result.setWidth(getNodeAttr("w", node));
- result.setHeight(getNodeAttr("h", node));
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:ispaint")) {
- // ???
- continue;
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:layerCompartmentAlias: " + node.getNodeName());
- }
- }
- }
- return result;
- }
-
- /**
- * Transforms LayerOval object into CellDesigner xml node.
- *
- * @param layer
- * object to be transformed into xml
- * @return CellDesigner xml node for LayerOval
- */
- String layerOvalToXml(LayerOval layer) {
- StringBuilder result = new StringBuilder();
- result.append("<celldesigner:layerCompartmentAlias type=\"Oval\">");
- result.append("<celldesigner:paint color=\"" + colorToString(layer.getColor()) + "\"/>");
- result.append("<celldesigner:bounds x=\"" + layer.getX() + "\" ");
- result.append(" y=\"" + layer.getY() + "\" ");
- result.append(" w=\"" + layer.getWidth() + "\" ");
- result.append(" h=\"" + layer.getHeight() + "\"/>");
- result.append("</celldesigner:layerCompartmentAlias>");
- return result.toString();
- }
-
- /**
- * Parses CellDesigner xml node into LayerText object.
- *
- * @param textNode
- * CellDesigner xml node for layer text object.
- * @return LayerText instance representing the cml node
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- LayerText getLayerText(Node textNode) throws InvalidXmlSchemaException {
- LayerText result = new LayerText();
- NodeList nodes = textNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:layerNotes")) {
- result.setNotes(getNodeValue(node).trim());
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:paint")) {
- result.setColor(commonParser.getColor(node));
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:bounds")) {
- result.setX(getNodeAttr("x", node));
- result.setY(getNodeAttr("y", node));
- result.setWidth(getNodeAttr("w", node));
- result.setHeight(getNodeAttr("h", node));
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:font")) {
- result.setFontSize(getNodeAttr("size", node));
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:layerSpeciesAlias: " + node.getNodeName());
- }
- }
- }
- return result;
-
- }
-
- /**
- * Transforms LayerText object into CellDesigner xml node.
- *
- * @param layer
- * object to be transformed into xml
- * @return CellDesigner xml node for LayerText
- */
- String layerTextToXml(LayerText layer) {
- StringBuilder result = new StringBuilder();
- result.append("<celldesigner:layerSpeciesAlias>");
- result.append("<celldesigner:layerNotes>\n");
- result.append(super.escapeXml(layer.getNotes()));
- result.append("\n</celldesigner:layerNotes>");
- result.append("<celldesigner:paint color=\"" + colorToString(layer.getColor()) + "\"/>");
- result.append("<celldesigner:bounds x=\"" + layer.getX() + "\" ");
- result.append(" y=\"" + layer.getY() + "\" ");
- result.append(" w=\"" + layer.getWidth() + "\" ");
- result.append(" h=\"" + layer.getHeight() + "\"/>");
- result.append("<celldesigner:font size=\"" + layer.getFontSize() + "\"/>");
- result.append("</celldesigner:layerSpeciesAlias>\n");
- return result.toString();
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.model.graphics.ArrowType;
+import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.layout.BlockDiagram;
+import lcsb.mapviewer.model.map.layout.ElementGroup;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.layout.graphics.LayerOval;
+import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
+import lcsb.mapviewer.model.map.layout.graphics.LayerText;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * Parser used for parsing CellDesigner xml to get {@link Layer} object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class LayerXmlParser extends XmlParser {
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(LayerXmlParser.class.getName());
+
+ /**
+ * Parser for common CellDesigner structures.
+ */
+ private CommonXmlParser commonParser = new CommonXmlParser();
+
+ /**
+ * PArses CellDesigner xml node with collection of layers into collection of
+ * Layers.
+ *
+ * @param layersNode
+ * xml node
+ * @return collection of layers
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ public Collection<Layer> parseLayers(Node layersNode) throws InvalidXmlSchemaException {
+ List<Layer> result = new ArrayList<Layer>();
+ NodeList nodes = layersNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:layer")) {
+ Layer layer = getLayer(node);
+ result.add(layer);
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfLayers: " + node.getNodeName());
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Transforms collection of layers into CellDesigner xml node.
+ *
+ * @param layers
+ * collection of layers
+ * @return xml node representing layers collection
+ */
+ public String layerCollectionToXml(Collection<Layer> layers) {
+ StringBuilder result = new StringBuilder();
+ result.append("<celldesigner:listOfLayers>");
+ for (Layer layer : layers) {
+ result.append(layerToXml(layer));
+ }
+ result.append("</celldesigner:listOfLayers>\n");
+ return result.toString();
+ }
+
+ /**
+ * Parses collection of block diagrams and adds them into the model.
+ *
+ * @param model
+ * model where the data is stored.
+ * @param xmlNode
+ * xml node
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ public void parseBlocks(Model model, Node xmlNode) throws InvalidXmlSchemaException {
+ NodeList nodes = xmlNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:blockDiagram")) {
+ model.addBlockDiagream(getBlockDiagram(node, model));
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfBlockDiagrams: " + node.getNodeName());
+ }
+ }
+ }
+ }
+
+ /**
+ * Parses block diagrams from CellDesigner xml. Important! It's not yet
+ * implemented.
+ *
+ * @param node
+ * xml node to parse
+ * @param model
+ * model where data is stored
+ * @return parsed block diagram
+ */
+ private BlockDiagram getBlockDiagram(Node node, Model model) {
+ logger.warn("BlockDiagrams are not implemented");
+ return null;
+ }
+
+ /**
+ * Parses CellDesigner node with collection of Alias Group and adds the groups
+ * into this model.
+ *
+ * @param model
+ * model where the data is stored
+ * @param xmlNode
+ * xml node
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ public void parseGroups(Model model, Node xmlNode) throws InvalidXmlSchemaException {
+ NodeList nodes = xmlNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:group")) {
+ model.addElementGroup(getAliasGroup(node, model));
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfGroups: " + node.getNodeName());
+ }
+ }
+ }
+ }
+
+ /**
+ * Parses xml node for alias group.
+ *
+ * @param groupNode
+ * xml node
+ * @param model
+ * model where the data is stored
+ * @return parsed alias group
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ ElementGroup getAliasGroup(Node groupNode, Model model) throws InvalidXmlSchemaException {
+ ElementGroup result = new ElementGroup();
+ String id = getNodeAttr("id", groupNode);
+ result.setIdGroup(id);
+ String members = getNodeAttr("members", groupNode);
+
+ String[] list = members.split(",");
+ for (String string : list) {
+ Element alias = model.getElementByElementId(string);
+ if (alias == null) {
+ throw new InvalidGroupException("Group \"" + id + "\" contains alias with id: \"" + string + "\", but such alias doesn't exist in the model.");
+ }
+ result.addElement(alias);
+ }
+
+ NodeList nodes = groupNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:group: " + node.getNodeName());
+ }
+ }
+
+ return result;
+ }
+
+ /**
+ * Parses CellDesigner xml node for single layer.
+ *
+ * @param layerNode
+ * xml node
+ * @return Layer that corresponds to CellDesigner xml node.
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ Layer getLayer(Node layerNode) throws InvalidXmlSchemaException {
+ Layer layer = new Layer();
+ layer.setLayerId(getNodeAttr("id", layerNode));
+ layer.setName(getNodeAttr("name", layerNode));
+ layer.setLocked(getNodeAttr("locked", layerNode));
+ layer.setVisible(getNodeAttr("visible", layerNode));
+ NodeList list = layerNode.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equals("celldesigner:listOfTexts")) {
+ NodeList residueList = node.getChildNodes();
+ for (int j = 0; j < residueList.getLength(); j++) {
+ Node textNode = residueList.item(j);
+ if (textNode.getNodeType() == Node.ELEMENT_NODE) {
+ if (textNode.getNodeName().equalsIgnoreCase("celldesigner:layerSpeciesAlias")) {
+ layer.addLayerText(getLayerText(textNode));
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfTexts " + textNode.getNodeName());
+ }
+ }
+ }
+ } else if (node.getNodeName().equals("celldesigner:listOfSquares")) {
+ NodeList residueList = node.getChildNodes();
+ for (int j = 0; j < residueList.getLength(); j++) {
+ Node textNode = residueList.item(j);
+ if (textNode.getNodeType() == Node.ELEMENT_NODE) {
+ if (textNode.getNodeName().equalsIgnoreCase("celldesigner:layerCompartmentAlias")) {
+ if (getNodeAttr("type", textNode).equalsIgnoreCase("SQUARE")) {
+ layer.addLayerRect(getLayerRect(textNode));
+ } else if (getNodeAttr("type", textNode).equalsIgnoreCase("OVAL")) {
+ layer.addLayerOval(getLayerOval(textNode));
+ } else {
+ throw new InvalidXmlSchemaException("Unknown celldesigner:layerCompartmentAlias type: " + getNodeAttr("type", textNode));
+ }
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfSquares " + textNode.getNodeName());
+ }
+ }
+ }
+ } else if (node.getNodeName().equals("celldesigner:listOfFreeLines")) {
+ NodeList residueList = node.getChildNodes();
+ for (int j = 0; j < residueList.getLength(); j++) {
+ Node textNode = residueList.item(j);
+ if (textNode.getNodeType() == Node.ELEMENT_NODE) {
+ if (textNode.getNodeName().equalsIgnoreCase("celldesigner:layerFreeLine")) {
+ layer.addLayerLine(getLayerLine(textNode));
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfFreeLines " + textNode.getNodeName());
+ }
+ }
+ }
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:layer " + node.getNodeName());
+ }
+ }
+ }
+
+ return layer;
+ }
+
+ /**
+ * Creates CellDesigner xml for a layer.
+ *
+ * @param layer
+ * object to be transformed into xml
+ * @return CellDesigner xml representation for the layer
+ */
+ String layerToXml(Layer layer) {
+ StringBuilder result = new StringBuilder();
+ result.append("<celldesigner:layer id =\"" + layer.getLayerId() + "\" ");
+ result.append(" name =\"" + layer.getName() + "\" ");
+ result.append(" locked =\"" + layer.isLocked() + "\" ");
+ result.append(" visible =\"" + layer.isVisible() + "\">\n");
+
+ result.append("<celldesigner:listOfTexts>\n");
+ for (LayerText layerText : layer.getTexts()) {
+ result.append(layerTextToXml(layerText));
+ }
+ result.append("</celldesigner:listOfTexts>\n");
+
+ result.append("<celldesigner:listOfSquares>\n");
+ for (LayerRect layerRect : layer.getRectangles()) {
+ result.append(layerRectToXml(layerRect));
+ }
+ for (LayerOval layerOval : layer.getOvals()) {
+ result.append(layerOvalToXml(layerOval));
+ }
+ result.append("</celldesigner:listOfSquares>\n");
+
+ result.append("<celldesigner:listOfFreeLines>\n");
+ for (PolylineData layerLine : layer.getLines()) {
+ result.append(layerLineToXml(layerLine));
+ }
+ result.append("</celldesigner:listOfFreeLines>\n");
+
+ result.append("</celldesigner:layer>\n");
+ return result.toString();
+ }
+
+ /**
+ * Parses CellDesigner xml node into LayerRect object.
+ *
+ * @param textNode
+ * CellDesigner xml node for layer text object.
+ * @return LayerRect instance representing the cml node
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ LayerRect getLayerRect(Node textNode) throws InvalidXmlSchemaException {
+ LayerRect result = new LayerRect();
+ NodeList nodes = textNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:paint")) {
+ result.setColor(commonParser.getColor(node));
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:bounds")) {
+ result.setX(getNodeAttr("x", node));
+ result.setY(getNodeAttr("y", node));
+ result.setWidth(getNodeAttr("w", node));
+ result.setHeight(getNodeAttr("h", node));
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:ispaint")) {
+ // ???
+ continue;
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:layerCompartmentAlias: " + node.getNodeName());
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Transforms LayerRect object into CellDesigner xml node.
+ *
+ * @param layer
+ * object to be transformed into xml
+ * @return CellDesigner xml node for LayerRect
+ */
+ String layerRectToXml(LayerRect layer) {
+ StringBuilder result = new StringBuilder();
+ result.append("<celldesigner:layerCompartmentAlias type=\"Square\">");
+ result.append("<celldesigner:paint color=\"" + colorToString(layer.getColor()) + "\"/>");
+ result.append("<celldesigner:bounds x=\"" + layer.getX() + "\" ");
+ result.append(" y=\"" + layer.getY() + "\" ");
+ result.append(" w=\"" + layer.getWidth() + "\" ");
+ result.append(" h=\"" + layer.getHeight() + "\"/>");
+ result.append("</celldesigner:layerCompartmentAlias>");
+ return result.toString();
+ }
+
+ /**
+ * Parses CellDesigner xml node into LayerLine object.
+ *
+ * @param lineNode
+ * CellDesigner xml node for layer text object.
+ * @return LayerLine instance representing the cml node
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ PolylineData getLayerLine(Node lineNode) throws InvalidXmlSchemaException {
+ PolylineData ld = new PolylineData();
+
+ if (getNodeAttr("isDotted", lineNode).equalsIgnoreCase("true")) {
+ ld.getEndAtd().setArrowLineType(LineType.DOTTED);
+ }
+ if (getNodeAttr("isArrow", lineNode).equalsIgnoreCase("true")) {
+ ld.getEndAtd().setArrowType(ArrowType.FULL);
+ }
+ NodeList nodes = lineNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:bounds")) {
+ double sx = Double.parseDouble(getNodeAttr("sx", node));
+ double sy = Double.parseDouble(getNodeAttr("sy", node));
+ double ex = Double.parseDouble(getNodeAttr("ex", node));
+ double ey = Double.parseDouble(getNodeAttr("ey", node));
+ Point2D startPoint = new Point2D.Double(sx, sy);
+ Point2D endPoint = new Point2D.Double(ex, ey);
+ ld.addPoint(startPoint);
+ ld.addPoint(endPoint);
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:line")) {
+ ld.setColor(stringToColor(getNodeAttr("color", node)));
+ ld.setWidth(getNodeAttr("width", node));
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:layerFreeLine: " + node.getNodeName());
+ }
+ }
+ }
+ return ld;
+ }
+
+ /**
+ * Transforms LayerLine object into CellDesigner xml node.
+ *
+ * @param layer
+ * object to be transformed into xml
+ * @return CellDesigner xml node for LayerLine
+ */
+ String layerLineToXml(PolylineData layer) {
+ StringBuilder result = new StringBuilder();
+ result.append("<celldesigner:layerFreeLine ");
+ result.append(" isDotted=\"" + layer.getEndAtd().getArrowLineType().equals(LineType.DOTTED) + "\" ");
+ result.append(" isArrow=\"" + layer.getEndAtd().getArrowType().equals(ArrowType.FULL) + "\" >");
+
+ result.append("<celldesigner:bounds sx=\"" + layer.getBeginPoint().getX() + "\" ");
+ result.append(" sy=\"" + layer.getBeginPoint().getY() + "\" ");
+ result.append(" ex=\"" + layer.getEndPoint().getX() + "\" ");
+ result.append(" ey=\"" + layer.getEndPoint().getY() + "\" />");
+ result.append("<celldesigner:line ");
+ result.append(" width=\"" + layer.getWidth() + "\" ");
+ result.append(" color=\"" + colorToString(layer.getColor()) + "\"/>");
+ result.append("</celldesigner:layerFreeLine>\n");
+ return result.toString();
+ }
+
+ /**
+ * Parses CellDesigner xml node into LayerOval object.
+ *
+ * @param textNode
+ * CellDesigner xml node for layer text object.
+ * @return LayerOval instance representing the cml node
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ LayerOval getLayerOval(Node textNode) throws InvalidXmlSchemaException {
+ LayerOval result = new LayerOval();
+ NodeList nodes = textNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:paint")) {
+ result.setColor(commonParser.getColor(node));
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:bounds")) {
+ result.setX(getNodeAttr("x", node));
+ result.setY(getNodeAttr("y", node));
+ result.setWidth(getNodeAttr("w", node));
+ result.setHeight(getNodeAttr("h", node));
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:ispaint")) {
+ // ???
+ continue;
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:layerCompartmentAlias: " + node.getNodeName());
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Transforms LayerOval object into CellDesigner xml node.
+ *
+ * @param layer
+ * object to be transformed into xml
+ * @return CellDesigner xml node for LayerOval
+ */
+ String layerOvalToXml(LayerOval layer) {
+ StringBuilder result = new StringBuilder();
+ result.append("<celldesigner:layerCompartmentAlias type=\"Oval\">");
+ result.append("<celldesigner:paint color=\"" + colorToString(layer.getColor()) + "\"/>");
+ result.append("<celldesigner:bounds x=\"" + layer.getX() + "\" ");
+ result.append(" y=\"" + layer.getY() + "\" ");
+ result.append(" w=\"" + layer.getWidth() + "\" ");
+ result.append(" h=\"" + layer.getHeight() + "\"/>");
+ result.append("</celldesigner:layerCompartmentAlias>");
+ return result.toString();
+ }
+
+ /**
+ * Parses CellDesigner xml node into LayerText object.
+ *
+ * @param textNode
+ * CellDesigner xml node for layer text object.
+ * @return LayerText instance representing the cml node
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ LayerText getLayerText(Node textNode) throws InvalidXmlSchemaException {
+ LayerText result = new LayerText();
+ NodeList nodes = textNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:layerNotes")) {
+ result.setNotes(getNodeValue(node).trim());
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:paint")) {
+ result.setColor(commonParser.getColor(node));
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:bounds")) {
+ result.setX(getNodeAttr("x", node));
+ result.setY(getNodeAttr("y", node));
+ result.setWidth(getNodeAttr("w", node));
+ result.setHeight(getNodeAttr("h", node));
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:font")) {
+ result.setFontSize(getNodeAttr("size", node));
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:layerSpeciesAlias: " + node.getNodeName());
+ }
+ }
+ }
+ return result;
+
+ }
+
+ /**
+ * Transforms LayerText object into CellDesigner xml node.
+ *
+ * @param layer
+ * object to be transformed into xml
+ * @return CellDesigner xml node for LayerText
+ */
+ String layerTextToXml(LayerText layer) {
+ StringBuilder result = new StringBuilder();
+ result.append("<celldesigner:layerSpeciesAlias>");
+ result.append("<celldesigner:layerNotes>\n");
+ result.append(super.escapeXml(layer.getNotes()));
+ result.append("\n</celldesigner:layerNotes>");
+ result.append("<celldesigner:paint color=\"" + colorToString(layer.getColor()) + "\"/>");
+ result.append("<celldesigner:bounds x=\"" + layer.getX() + "\" ");
+ result.append(" y=\"" + layer.getY() + "\" ");
+ result.append(" w=\"" + layer.getWidth() + "\" ");
+ result.append(" h=\"" + layer.getHeight() + "\"/>");
+ result.append("<celldesigner:font size=\"" + layer.getFontSize() + "\"/>");
+ result.append("</celldesigner:layerSpeciesAlias>\n");
+ return result.toString();
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AbstractAliasXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AbstractAliasXmlParser.java
index a4a9319242..c112f6bd8c 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AbstractAliasXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AbstractAliasXmlParser.java
@@ -1,87 +1,87 @@
-package lcsb.mapviewer.converter.model.celldesigner.alias;
-
-import org.apache.log4j.Logger;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import lcsb.mapviewer.common.XmlParser;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.model.celldesigner.CommonXmlParser;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * Generic abstract interface for parsing CellDesigner xml nodes with species
- * definition.
- *
- * @author Piotr Gawron
- *
- * @param <T>
- * type of the object to parse
- */
-public abstract class AbstractAliasXmlParser<T extends Element> extends XmlParser {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(AbstractAliasXmlParser.class.getName());
-
- /**
- * Set of common functions used in parsing cell designer xml.
- */
- private CommonXmlParser commonParser = new CommonXmlParser();
-
- /**
- * Parse object from the xml node.
- *
- * @param node
- * xml node to parse
- *
- * @return parsed object
- * @throws InvalidXmlSchemaException
- * thrown when xmlString is invalid
- */
- abstract T parseXmlAlias(Node node) throws InvalidXmlSchemaException;
-
- /**
- * Parse object from the xml string.
- *
- * @param xmlString
- * xml string
- * @return parsed object
- * @throws InvalidXmlSchemaException
- * thrown when xmlString is invalid
- */
- public T parseXmlAlias(String xmlString) throws InvalidXmlSchemaException {
- Document doc = getXmlDocumentFromString(xmlString);
- NodeList root = doc.getChildNodes();
- return parseXmlAlias(root.item(0));
-
- }
-
- /**
- * Method that transform object into CellDesigner xml.
- *
- * @param alias
- * object to be transformed
- * @return CellDesigner xml representation of the alias
- */
- abstract String toXml(T alias);
-
- /**
- * @return the commonParser
- */
- CommonXmlParser getCommonParser() {
- return commonParser;
- }
-
- /**
- * @param commonParser
- * the commonParser to set
- */
- void setCommonParser(CommonXmlParser commonParser) {
- this.commonParser = commonParser;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.alias;
+
+import org.apache.log4j.Logger;
+import org.w3c.dom.Document;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.model.celldesigner.CommonXmlParser;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * Generic abstract interface for parsing CellDesigner xml nodes with species
+ * definition.
+ *
+ * @author Piotr Gawron
+ *
+ * @param <T>
+ * type of the object to parse
+ */
+public abstract class AbstractAliasXmlParser<T extends Element> extends XmlParser {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(AbstractAliasXmlParser.class.getName());
+
+ /**
+ * Set of common functions used in parsing cell designer xml.
+ */
+ private CommonXmlParser commonParser = new CommonXmlParser();
+
+ /**
+ * Parse object from the xml node.
+ *
+ * @param node
+ * xml node to parse
+ *
+ * @return parsed object
+ * @throws InvalidXmlSchemaException
+ * thrown when xmlString is invalid
+ */
+ abstract T parseXmlAlias(Node node) throws InvalidXmlSchemaException;
+
+ /**
+ * Parse object from the xml string.
+ *
+ * @param xmlString
+ * xml string
+ * @return parsed object
+ * @throws InvalidXmlSchemaException
+ * thrown when xmlString is invalid
+ */
+ public T parseXmlAlias(String xmlString) throws InvalidXmlSchemaException {
+ Document doc = getXmlDocumentFromString(xmlString);
+ NodeList root = doc.getChildNodes();
+ return parseXmlAlias(root.item(0));
+
+ }
+
+ /**
+ * Method that transform object into CellDesigner xml.
+ *
+ * @param alias
+ * object to be transformed
+ * @return CellDesigner xml representation of the alias
+ */
+ abstract String toXml(T alias);
+
+ /**
+ * @return the commonParser
+ */
+ CommonXmlParser getCommonParser() {
+ return commonParser;
+ }
+
+ /**
+ * @param commonParser
+ * the commonParser to set
+ */
+ void setCommonParser(CommonXmlParser commonParser) {
+ this.commonParser = commonParser;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParser.java
index e80d09ae7a..51cc31b58b 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParser.java
@@ -1,241 +1,241 @@
-package lcsb.mapviewer.converter.model.celldesigner.alias;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import lcsb.mapviewer.common.XmlParser;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * This class contains function to parse CellDesigner xml nodes containing
- * collection of aliases. It also contains functionality to do reverse operation
- * - transform set of aliases into xml node.
- *
- * @author Piotr Gawron
- *
- */
-public class AliasCollectionXmlParser extends XmlParser {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(AliasCollectionXmlParser.class.getName());
-
- /**
- * Single SpeciesAlias parser for CellDesigner node.
- */
- private SpeciesAliasXmlParser speciesAliasParser = null;
-
- /**
- * Single ComplexAlias parser for CellDesigner node.
- */
- private ComplexAliasXmlParser complexAliasParser = null;
-
- /**
- * Single CompartmentAlias parser for CellDesigner node.
- */
- private CompartmentAliasXmlParser compartmentAliasParser = null;
-
- /**
- * Annotation parser.
- */
- private RestAnnotationParser rap = new RestAnnotationParser();
-
- /**
- * Default parser. As an parameter model object for which parsing is done is
- * required. This is due to the fact that CellDesigner model is very tangled
- * and very often data are distributed in many different places and in other
- * places they are missing...
- *
- * @param model
- * map model for which parsing is performed
- * @param elements
- * collection of {@link CellDesignerElement cell designer elements}
- * parsed from xml
- */
- public AliasCollectionXmlParser(CellDesignerElementCollection elements, Model model) {
- speciesAliasParser = new SpeciesAliasXmlParser(elements, model);
- complexAliasParser = new ComplexAliasXmlParser(elements, model);
- compartmentAliasParser = new CompartmentAliasXmlParser(elements, model);
- }
-
- /**
- * Parses xml node containing list of species aliases into collection of
- * SpeciesAlias.
- *
- * @param aliasListNode
- * xml node to be parsed
- * @return collection of SpeciesAlias obtained from xml node
- * @throws InvalidXmlSchemaException
- * thrown when there is a problem with xml
- */
- public List<Species> parseXmlSpeciesAliasCollection(Node aliasListNode) throws InvalidXmlSchemaException {
- List<Species> result = new ArrayList<Species>();
- NodeList nodes = aliasListNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:speciesAlias")) {
- Species alias = speciesAliasParser.parseXmlAlias(node);
- rap.processNotes(alias);
- result.add(alias);
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfSpeciesAliases: " + node.getNodeName());
- }
- }
- }
- return result;
- }
-
- /**
- * Creates xml string representing collection of SpeciesAlias.
- *
- * @param collection
- * collection of SpeciesAlias
- * @return xml string representing collection of SpeciesAlias
- */
- public String speciesAliasCollectionToXmlString(Collection<Species> collection) {
- StringBuilder sb = new StringBuilder("<celldesigner:listOfSpeciesAliases>\n");
- for (Species alias : collection) {
- sb.append(speciesAliasParser.toXml(alias));
- }
- sb.append("</celldesigner:listOfSpeciesAliases>\n");
- return sb.toString();
- }
-
- /**
- * Parses xml node containing list of complex aliases into collection of
- * ComplexAlias.
- *
- * @param aliasListNode
- * xml node to be parsed
- * @return collection of ComplexAlias obtained from xml node
- * @throws InvalidXmlSchemaException
- * thrown when xmlString is invalid
- */
- public List<Complex> parseXmlComplexAliasCollection(Node aliasListNode) throws InvalidXmlSchemaException {
- List<Complex> result = new ArrayList<Complex>();
- NodeList nodes = aliasListNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:complexSpeciesAlias")) {
- Complex alias = complexAliasParser.parseXmlAlias(node);
- result.add(alias);
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfComplexSpeciesAliases: " + node.getNodeName());
- }
- }
- }
- for (Complex complexAlias : result) {
- complexAliasParser.addReference(complexAlias);
- }
- return result;
- }
-
- /**
- * Creates xml string representing collection of ComplexAlias.
- *
- * @param collection
- * collection of ComplexAlias
- * @return xml string representing collection of ComplexAlias
- */
- public String complexAliasCollectionToXmlString(Collection<Complex> collection) {
- StringBuilder sb = new StringBuilder("<celldesigner:listOfComplexSpeciesAliases>\n");
- for (Complex alias : collection) {
- sb.append(complexAliasParser.toXml(alias));
- }
- sb.append("</celldesigner:listOfComplexSpeciesAliases>\n");
- return sb.toString();
- }
-
- /**
- * Parses xml node containing list of compartment aliases into collection of
- * CompartmentAlias.
- *
- * @param aliasListNode
- * xml node to be parsed
- * @return collection of CompartmentAlias obtained from xml node
- * @throws InvalidXmlSchemaException
- * thrown when xmlString is invalid
- */
- public List<Compartment> parseXmlCompartmentAliasCollection(Node aliasListNode) throws InvalidXmlSchemaException {
- List<Compartment> result = new ArrayList<>();
- NodeList nodes = aliasListNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:compartmentAlias")) {
- Compartment alias = compartmentAliasParser.parseXmlAlias(node);
- result.add(alias);
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfCompartmentAliases: " + node.getNodeName());
- }
- }
- }
- assignParents(result);
-
- return result;
- }
-
- /**
- * Assing compartment parents for list of compartments.
- *
- * @param compartments
- * compartments that are looking for parents
- */
- private void assignParents(List<Compartment> compartments) {
- Compartment nullParent = new Compartment("null");
- nullParent.setWidth(Double.MAX_VALUE);
- nullParent.setHeight(Double.MAX_VALUE);
- nullParent.setX(0.0);
- nullParent.setY(0.0);
- for (Compartment child : compartments) {
- Compartment parent = nullParent;
- for (Compartment potentialParent : compartments) {
- if (potentialParent.contains(child)) {
- if (parent.getSize() > potentialParent.getSize()) {
- parent = potentialParent;
- }
- }
- }
- if (parent != nullParent) {
- child.setCompartment(parent);
- parent.addElement(child);
- }
- }
- }
-
- /**
- * Creates xml string representing collection of CompartmentAlias.
- *
- * @param collection
- * collection of CompartmentAlias
- * @return xml string representing collection of CompartmentAlias
- */
- public String compartmentAliasCollectionToXmlString(Collection<Compartment> collection) {
- StringBuilder sb = new StringBuilder("<celldesigner:listOfCompartmentAliases>\n");
- for (Compartment compartment : collection) {
- // artifitial compartment aliases cannot be exported
- if (!(compartment instanceof PathwayCompartment)) {
- sb.append(compartmentAliasParser.toXml(compartment));
- }
- }
- sb.append("</celldesigner:listOfCompartmentAliases>\n");
- return sb.toString();
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.alias;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This class contains function to parse CellDesigner xml nodes containing
+ * collection of aliases. It also contains functionality to do reverse operation
+ * - transform set of aliases into xml node.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class AliasCollectionXmlParser extends XmlParser {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(AliasCollectionXmlParser.class.getName());
+
+ /**
+ * Single SpeciesAlias parser for CellDesigner node.
+ */
+ private SpeciesAliasXmlParser speciesAliasParser = null;
+
+ /**
+ * Single ComplexAlias parser for CellDesigner node.
+ */
+ private ComplexAliasXmlParser complexAliasParser = null;
+
+ /**
+ * Single CompartmentAlias parser for CellDesigner node.
+ */
+ private CompartmentAliasXmlParser compartmentAliasParser = null;
+
+ /**
+ * Annotation parser.
+ */
+ private RestAnnotationParser rap = new RestAnnotationParser();
+
+ /**
+ * Default parser. As an parameter model object for which parsing is done is
+ * required. This is due to the fact that CellDesigner model is very tangled
+ * and very often data are distributed in many different places and in other
+ * places they are missing...
+ *
+ * @param model
+ * map model for which parsing is performed
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
+ */
+ public AliasCollectionXmlParser(CellDesignerElementCollection elements, Model model) {
+ speciesAliasParser = new SpeciesAliasXmlParser(elements, model);
+ complexAliasParser = new ComplexAliasXmlParser(elements, model);
+ compartmentAliasParser = new CompartmentAliasXmlParser(elements, model);
+ }
+
+ /**
+ * Parses xml node containing list of species aliases into collection of
+ * SpeciesAlias.
+ *
+ * @param aliasListNode
+ * xml node to be parsed
+ * @return collection of SpeciesAlias obtained from xml node
+ * @throws InvalidXmlSchemaException
+ * thrown when there is a problem with xml
+ */
+ public List<Species> parseXmlSpeciesAliasCollection(Node aliasListNode) throws InvalidXmlSchemaException {
+ List<Species> result = new ArrayList<Species>();
+ NodeList nodes = aliasListNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:speciesAlias")) {
+ Species alias = speciesAliasParser.parseXmlAlias(node);
+ rap.processNotes(alias);
+ result.add(alias);
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfSpeciesAliases: " + node.getNodeName());
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Creates xml string representing collection of SpeciesAlias.
+ *
+ * @param collection
+ * collection of SpeciesAlias
+ * @return xml string representing collection of SpeciesAlias
+ */
+ public String speciesAliasCollectionToXmlString(Collection<Species> collection) {
+ StringBuilder sb = new StringBuilder("<celldesigner:listOfSpeciesAliases>\n");
+ for (Species alias : collection) {
+ sb.append(speciesAliasParser.toXml(alias));
+ }
+ sb.append("</celldesigner:listOfSpeciesAliases>\n");
+ return sb.toString();
+ }
+
+ /**
+ * Parses xml node containing list of complex aliases into collection of
+ * ComplexAlias.
+ *
+ * @param aliasListNode
+ * xml node to be parsed
+ * @return collection of ComplexAlias obtained from xml node
+ * @throws InvalidXmlSchemaException
+ * thrown when xmlString is invalid
+ */
+ public List<Complex> parseXmlComplexAliasCollection(Node aliasListNode) throws InvalidXmlSchemaException {
+ List<Complex> result = new ArrayList<Complex>();
+ NodeList nodes = aliasListNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:complexSpeciesAlias")) {
+ Complex alias = complexAliasParser.parseXmlAlias(node);
+ result.add(alias);
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfComplexSpeciesAliases: " + node.getNodeName());
+ }
+ }
+ }
+ for (Complex complexAlias : result) {
+ complexAliasParser.addReference(complexAlias);
+ }
+ return result;
+ }
+
+ /**
+ * Creates xml string representing collection of ComplexAlias.
+ *
+ * @param collection
+ * collection of ComplexAlias
+ * @return xml string representing collection of ComplexAlias
+ */
+ public String complexAliasCollectionToXmlString(Collection<Complex> collection) {
+ StringBuilder sb = new StringBuilder("<celldesigner:listOfComplexSpeciesAliases>\n");
+ for (Complex alias : collection) {
+ sb.append(complexAliasParser.toXml(alias));
+ }
+ sb.append("</celldesigner:listOfComplexSpeciesAliases>\n");
+ return sb.toString();
+ }
+
+ /**
+ * Parses xml node containing list of compartment aliases into collection of
+ * CompartmentAlias.
+ *
+ * @param aliasListNode
+ * xml node to be parsed
+ * @return collection of CompartmentAlias obtained from xml node
+ * @throws InvalidXmlSchemaException
+ * thrown when xmlString is invalid
+ */
+ public List<Compartment> parseXmlCompartmentAliasCollection(Node aliasListNode) throws InvalidXmlSchemaException {
+ List<Compartment> result = new ArrayList<>();
+ NodeList nodes = aliasListNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:compartmentAlias")) {
+ Compartment alias = compartmentAliasParser.parseXmlAlias(node);
+ result.add(alias);
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfCompartmentAliases: " + node.getNodeName());
+ }
+ }
+ }
+ assignParents(result);
+
+ return result;
+ }
+
+ /**
+ * Assing compartment parents for list of compartments.
+ *
+ * @param compartments
+ * compartments that are looking for parents
+ */
+ private void assignParents(List<Compartment> compartments) {
+ Compartment nullParent = new Compartment("null");
+ nullParent.setWidth(Double.MAX_VALUE);
+ nullParent.setHeight(Double.MAX_VALUE);
+ nullParent.setX(0.0);
+ nullParent.setY(0.0);
+ for (Compartment child : compartments) {
+ Compartment parent = nullParent;
+ for (Compartment potentialParent : compartments) {
+ if (potentialParent.contains(child)) {
+ if (parent.getSize() > potentialParent.getSize()) {
+ parent = potentialParent;
+ }
+ }
+ }
+ if (parent != nullParent) {
+ child.setCompartment(parent);
+ parent.addElement(child);
+ }
+ }
+ }
+
+ /**
+ * Creates xml string representing collection of CompartmentAlias.
+ *
+ * @param collection
+ * collection of CompartmentAlias
+ * @return xml string representing collection of CompartmentAlias
+ */
+ public String compartmentAliasCollectionToXmlString(Collection<Compartment> collection) {
+ StringBuilder sb = new StringBuilder("<celldesigner:listOfCompartmentAliases>\n");
+ for (Compartment compartment : collection) {
+ // artifitial compartment aliases cannot be exported
+ if (!(compartment instanceof PathwayCompartment)) {
+ sb.append(compartmentAliasParser.toXml(compartment));
+ }
+ }
+ sb.append("</celldesigner:listOfCompartmentAliases>\n");
+ return sb.toString();
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParser.java
index bb923a34ce..15afeae9ec 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParser.java
@@ -1,190 +1,190 @@
-package lcsb.mapviewer.converter.model.celldesigner.alias;
-
-import org.apache.log4j.Logger;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
-import lcsb.mapviewer.model.map.compartment.BottomSquareCompartment;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.compartment.LeftSquareCompartment;
-import lcsb.mapviewer.model.map.compartment.OvalCompartment;
-import lcsb.mapviewer.model.map.compartment.RightSquareCompartment;
-import lcsb.mapviewer.model.map.compartment.SquareCompartment;
-import lcsb.mapviewer.model.map.compartment.TopSquareCompartment;
-import lcsb.mapviewer.model.map.model.Model;
-
-/**
- * Parser for CellDesigner xml for compartment aliases.
- *
- * @author Piotr Gawron
- *
- */
-public class CompartmentAliasXmlParser extends AbstractAliasXmlParser<Compartment> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(CompartmentAliasXmlParser.class.getName());
-
- /**
- * Model for which we are parsing aliases.
- */
- private Model model = null;
-
- /**
- * Collection of {@link CellDesignerElement cell designer elements} parsed from
- * xml.
- */
- private CellDesignerElementCollection elements;
-
- /**
- * Default constructor.
- *
- * @param elements
- * collection of {@link CellDesignerElement cell designer elements}
- * parsed from xml
- * @param model
- * model for which this parser will be used
- */
- public CompartmentAliasXmlParser(CellDesignerElementCollection elements, Model model) {
- this.model = model;
- this.elements = elements;
- }
-
- @Override
- Compartment parseXmlAlias(Node aliasNode) throws InvalidXmlSchemaException {
-
- String compartmentId = getNodeAttr("compartment", aliasNode);
- CellDesignerCompartment compartment = elements.getElementByElementId(compartmentId);
- if (compartment == null) {
- throw new InvalidXmlSchemaException("Compartment does not exist in a model: " + compartmentId);
- }
- String aliasId = getNodeAttr("id", aliasNode);
- Compartment result = compartment.createModelElement(aliasId);
- elements.addElement(compartment, aliasId);
-
- NodeList nodes = aliasNode.getChildNodes();
- for (int i = 0; i < nodes.getLength(); i++) {
- Node node = nodes.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:class")) {
- String type = getNodeValue(node);
- if (type.equalsIgnoreCase("SQUARE")) {
- result = new SquareCompartment(result);
- } else if (type.equalsIgnoreCase("SQUARE_CLOSEUP_NORTH")) {
- result = new BottomSquareCompartment(result, model);
- } else if (type.equalsIgnoreCase("SQUARE_CLOSEUP_SOUTH")) {
- result = new TopSquareCompartment(result, model);
- } else if (type.equalsIgnoreCase("SQUARE_CLOSEUP_WEST")) {
- result = new RightSquareCompartment(result, model);
- } else if (type.equalsIgnoreCase("SQUARE_CLOSEUP_EAST")) {
- result = new LeftSquareCompartment(result, model);
- } else if (type.equalsIgnoreCase("OVAL")) {
- result = new OvalCompartment(result);
- } else {
- throw new InvalidXmlSchemaException("Unknown compartment type: " + type);
- }
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:bounds")) {
- result.setX(getNodeAttr("x", node));
- result.setY(getNodeAttr("y", node));
- result.setWidth(getNodeAttr("w", node));
- result.setHeight(getNodeAttr("h", node));
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:doubleLine")) {
- result.setLineThickness(getNodeAttr("thickness", node));
- result.setLineOuterWidth(getNodeAttr("outerWidth", node));
- result.setLineInnerWidth(getNodeAttr("innerWidth", node));
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:paint")) {
- result.setColor(getCommonParser().getColor(node));
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:info")) {
- // not handled
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:point")) {
- if (result instanceof BottomSquareCompartment) {
- result.setY(getNodeAttr("y", node));
- } else if (result instanceof LeftSquareCompartment) {
- result.setX(getNodeAttr("x", node));
- } else if (result instanceof RightSquareCompartment) {
- result.setX(getNodeAttr("x", node));
- result.setWidth(result.getWidth() - result.getX());
- } else if (result instanceof TopSquareCompartment) {
- result.setY(getNodeAttr("y", node));
- } else {
- throw new InvalidXmlSchemaException(
- "Don't know what to do with celldesigner:point for class: " + result.getClass());
- }
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:namePoint")) {
- result.setNamePoint(getCommonParser().getPosition(node));
- } else {
- throw new InvalidXmlSchemaException(
- "Unknown element of celldesigner:compartmentAlias: " + node.getNodeName());
- }
- }
- }
- return result;
- }
-
- @Override
- public String toXml(Compartment compartment) {
- StringBuilder sb = new StringBuilder("");
-
- sb.append("<celldesigner:compartmentAlias ");
- sb.append("id=\"" + compartment.getElementId() + "\" ");
- sb.append("compartment=\"" + elements.getElementId(compartment) + "\">\n");
-
- boolean bounds = true;
-
- if (compartment.getClass().getName().equals(SquareCompartment.class.getName())) {
- sb.append("<celldesigner:class>SQUARE</celldesigner:class>\n");
- } else if (compartment.getClass().getName().equals(OvalCompartment.class.getName())) {
- sb.append("<celldesigner:class>OVAL</celldesigner:class>\n");
- } else if (compartment.getClass().getName().equals(BottomSquareCompartment.class.getName())) {
- sb.append("<celldesigner:class>SQUARE_CLOSEUP_NORTH</celldesigner:class>\n");
- bounds = false;
- sb.append("<celldesigner:point x=\"10\" y=\"" + compartment.getY() + "\"/>");
- } else if (compartment.getClass().getName().equals(TopSquareCompartment.class.getName())) {
- sb.append("<celldesigner:class>SQUARE_CLOSEUP_SOUTH</celldesigner:class>\n");
- bounds = false;
- sb.append("<celldesigner:point x=\"10\" y=\"" + compartment.getY() + "\"/>");
- } else if (compartment.getClass().getName().equals(LeftSquareCompartment.class.getName())) {
- sb.append("<celldesigner:class>SQUARE_CLOSEUP_EAST</celldesigner:class>\n");
- bounds = false;
- sb.append("<celldesigner:point x=\"" + compartment.getWidth() + "\" y=\"10\"/>");
- } else if (compartment.getClass().getName().equals(RightSquareCompartment.class.getName())) {
- sb.append("<celldesigner:class>SQUARE_CLOSEUP_WEST</celldesigner:class>\n");
- bounds = false;
- sb.append("<celldesigner:point x=\"" + compartment.getX() + "\" y=\"10\"/>");
- } else {
- throw new NotImplementedException("Unknown compartment class: " + compartment.getClass());
- }
- if (bounds) {
- sb.append("<celldesigner:bounds ");
- sb.append("x=\"" + compartment.getX() + "\" ");
- sb.append("y=\"" + compartment.getY() + "\" ");
- sb.append("w=\"" + compartment.getWidth() + "\" ");
- sb.append("h=\"" + compartment.getHeight() + "\"/>\n");
- }
-
- sb.append("<celldesigner:namePoint ");
- sb.append("x=\"" + compartment.getNamePoint().getX() + "\" ");
- sb.append("y=\"" + compartment.getNamePoint().getY() + "\"/>\n");
-
- sb.append("<celldesigner:doubleLine ");
- sb.append("thickness=\"" + compartment.getThickness() + "\" ");
- sb.append("outerWidth=\"" + compartment.getOuterWidth() + "\" ");
- sb.append("innerWidth=\"" + compartment.getInnerWidth() + "\"/>\n");
-
- sb.append("<celldesigner:paint ");
- sb.append("color=\"" + colorToString(compartment.getColor()) + "\" scheme=\"Color\"/>\n");
-
- sb.append("</celldesigner:compartmentAlias>\n");
-
- return sb.toString();
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.alias;
+
+import org.apache.log4j.Logger;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
+import lcsb.mapviewer.model.map.compartment.BottomSquareCompartment;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.LeftSquareCompartment;
+import lcsb.mapviewer.model.map.compartment.OvalCompartment;
+import lcsb.mapviewer.model.map.compartment.RightSquareCompartment;
+import lcsb.mapviewer.model.map.compartment.SquareCompartment;
+import lcsb.mapviewer.model.map.compartment.TopSquareCompartment;
+import lcsb.mapviewer.model.map.model.Model;
+
+/**
+ * Parser for CellDesigner xml for compartment aliases.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CompartmentAliasXmlParser extends AbstractAliasXmlParser<Compartment> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(CompartmentAliasXmlParser.class.getName());
+
+ /**
+ * Model for which we are parsing aliases.
+ */
+ private Model model = null;
+
+ /**
+ * Collection of {@link CellDesignerElement cell designer elements} parsed from
+ * xml.
+ */
+ private CellDesignerElementCollection elements;
+
+ /**
+ * Default constructor.
+ *
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
+ * @param model
+ * model for which this parser will be used
+ */
+ public CompartmentAliasXmlParser(CellDesignerElementCollection elements, Model model) {
+ this.model = model;
+ this.elements = elements;
+ }
+
+ @Override
+ Compartment parseXmlAlias(Node aliasNode) throws InvalidXmlSchemaException {
+
+ String compartmentId = getNodeAttr("compartment", aliasNode);
+ CellDesignerCompartment compartment = elements.getElementByElementId(compartmentId);
+ if (compartment == null) {
+ throw new InvalidXmlSchemaException("Compartment does not exist in a model: " + compartmentId);
+ }
+ String aliasId = getNodeAttr("id", aliasNode);
+ Compartment result = compartment.createModelElement(aliasId);
+ elements.addElement(compartment, aliasId);
+
+ NodeList nodes = aliasNode.getChildNodes();
+ for (int i = 0; i < nodes.getLength(); i++) {
+ Node node = nodes.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:class")) {
+ String type = getNodeValue(node);
+ if (type.equalsIgnoreCase("SQUARE")) {
+ result = new SquareCompartment(result);
+ } else if (type.equalsIgnoreCase("SQUARE_CLOSEUP_NORTH")) {
+ result = new BottomSquareCompartment(result, model);
+ } else if (type.equalsIgnoreCase("SQUARE_CLOSEUP_SOUTH")) {
+ result = new TopSquareCompartment(result, model);
+ } else if (type.equalsIgnoreCase("SQUARE_CLOSEUP_WEST")) {
+ result = new RightSquareCompartment(result, model);
+ } else if (type.equalsIgnoreCase("SQUARE_CLOSEUP_EAST")) {
+ result = new LeftSquareCompartment(result, model);
+ } else if (type.equalsIgnoreCase("OVAL")) {
+ result = new OvalCompartment(result);
+ } else {
+ throw new InvalidXmlSchemaException("Unknown compartment type: " + type);
+ }
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:bounds")) {
+ result.setX(getNodeAttr("x", node));
+ result.setY(getNodeAttr("y", node));
+ result.setWidth(getNodeAttr("w", node));
+ result.setHeight(getNodeAttr("h", node));
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:doubleLine")) {
+ result.setLineThickness(getNodeAttr("thickness", node));
+ result.setLineOuterWidth(getNodeAttr("outerWidth", node));
+ result.setLineInnerWidth(getNodeAttr("innerWidth", node));
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:paint")) {
+ result.setColor(getCommonParser().getColor(node));
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:info")) {
+ // not handled
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:point")) {
+ if (result instanceof BottomSquareCompartment) {
+ result.setY(getNodeAttr("y", node));
+ } else if (result instanceof LeftSquareCompartment) {
+ result.setX(getNodeAttr("x", node));
+ } else if (result instanceof RightSquareCompartment) {
+ result.setX(getNodeAttr("x", node));
+ result.setWidth(result.getWidth() - result.getX());
+ } else if (result instanceof TopSquareCompartment) {
+ result.setY(getNodeAttr("y", node));
+ } else {
+ throw new InvalidXmlSchemaException(
+ "Don't know what to do with celldesigner:point for class: " + result.getClass());
+ }
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:namePoint")) {
+ result.setNamePoint(getCommonParser().getPosition(node));
+ } else {
+ throw new InvalidXmlSchemaException(
+ "Unknown element of celldesigner:compartmentAlias: " + node.getNodeName());
+ }
+ }
+ }
+ return result;
+ }
+
+ @Override
+ public String toXml(Compartment compartment) {
+ StringBuilder sb = new StringBuilder("");
+
+ sb.append("<celldesigner:compartmentAlias ");
+ sb.append("id=\"" + compartment.getElementId() + "\" ");
+ sb.append("compartment=\"" + elements.getElementId(compartment) + "\">\n");
+
+ boolean bounds = true;
+
+ if (compartment.getClass().getName().equals(SquareCompartment.class.getName())) {
+ sb.append("<celldesigner:class>SQUARE</celldesigner:class>\n");
+ } else if (compartment.getClass().getName().equals(OvalCompartment.class.getName())) {
+ sb.append("<celldesigner:class>OVAL</celldesigner:class>\n");
+ } else if (compartment.getClass().getName().equals(BottomSquareCompartment.class.getName())) {
+ sb.append("<celldesigner:class>SQUARE_CLOSEUP_NORTH</celldesigner:class>\n");
+ bounds = false;
+ sb.append("<celldesigner:point x=\"10\" y=\"" + compartment.getY() + "\"/>");
+ } else if (compartment.getClass().getName().equals(TopSquareCompartment.class.getName())) {
+ sb.append("<celldesigner:class>SQUARE_CLOSEUP_SOUTH</celldesigner:class>\n");
+ bounds = false;
+ sb.append("<celldesigner:point x=\"10\" y=\"" + compartment.getY() + "\"/>");
+ } else if (compartment.getClass().getName().equals(LeftSquareCompartment.class.getName())) {
+ sb.append("<celldesigner:class>SQUARE_CLOSEUP_EAST</celldesigner:class>\n");
+ bounds = false;
+ sb.append("<celldesigner:point x=\"" + compartment.getWidth() + "\" y=\"10\"/>");
+ } else if (compartment.getClass().getName().equals(RightSquareCompartment.class.getName())) {
+ sb.append("<celldesigner:class>SQUARE_CLOSEUP_WEST</celldesigner:class>\n");
+ bounds = false;
+ sb.append("<celldesigner:point x=\"" + compartment.getX() + "\" y=\"10\"/>");
+ } else {
+ throw new NotImplementedException("Unknown compartment class: " + compartment.getClass());
+ }
+ if (bounds) {
+ sb.append("<celldesigner:bounds ");
+ sb.append("x=\"" + compartment.getX() + "\" ");
+ sb.append("y=\"" + compartment.getY() + "\" ");
+ sb.append("w=\"" + compartment.getWidth() + "\" ");
+ sb.append("h=\"" + compartment.getHeight() + "\"/>\n");
+ }
+
+ sb.append("<celldesigner:namePoint ");
+ sb.append("x=\"" + compartment.getNamePoint().getX() + "\" ");
+ sb.append("y=\"" + compartment.getNamePoint().getY() + "\"/>\n");
+
+ sb.append("<celldesigner:doubleLine ");
+ sb.append("thickness=\"" + compartment.getThickness() + "\" ");
+ sb.append("outerWidth=\"" + compartment.getOuterWidth() + "\" ");
+ sb.append("innerWidth=\"" + compartment.getInnerWidth() + "\"/>\n");
+
+ sb.append("<celldesigner:paint ");
+ sb.append("color=\"" + colorToString(compartment.getColor()) + "\" scheme=\"Color\"/>\n");
+
+ sb.append("</celldesigner:compartmentAlias>\n");
+
+ return sb.toString();
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParser.java
index 3e3b7bc662..3c2596bf1a 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParser.java
@@ -1,287 +1,287 @@
-package lcsb.mapviewer.converter.model.celldesigner.alias;
-
-import java.util.HashMap;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.View;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * Parser of CellDesigner xml used for parsing complex aliases. Important: Only
- * one instance per model should be used.
- *
- * @author Piotr Gawron
- *
- * @see Complex
- */
-public class ComplexAliasXmlParser extends AbstractAliasXmlParser<Complex> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(ComplexAliasXmlParser.class.getName());
-
- /**
- * Because of the CellDesigner xml model we have to store information about
- * all processed Complexes. This infomrmation later on is used for connecting
- * complexes in hierarchical view.
- */
- private Map<String, Complex> complexAliasesMapById = new HashMap<String, Complex>();
-
- /**
- * Because of the CellDesigner xml model we have to store information about
- * parents of all Complexes. This infomrmation later on is used for connecting
- * complexes in hierarchical view. We cannot do it immediatelly because some
- * complexes doesn't exist yet.
- */
- private Map<String, String> parents = new HashMap<String, String>();
-
- /**
- * Model for which we are parsing aliases.
- */
- private Model model = null;
-
- /**
- * Collection of {@link CellDesignerElement cell designer elements} parsed
- * from xml.
- */
- private CellDesignerElementCollection elements;
-
- /**
- * Default constructor with model object for which we parse data.
- *
- * @param model
- * model for which we parse elements
- * @param elements
- * collection of {@link CellDesignerElement cell designer elements}
- * parsed from xml
- */
- public ComplexAliasXmlParser(CellDesignerElementCollection elements, Model model) {
- this.model = model;
- this.elements = elements;
- }
-
- @Override
- Complex parseXmlAlias(Node aliasNode) throws InvalidXmlSchemaException {
-
- String aliasId = getNodeAttr("id", aliasNode);
-
- String speciesId = getNodeAttr("species", aliasNode);
- CellDesignerComplexSpecies species = (CellDesignerComplexSpecies) elements.getElementByElementId(speciesId);
- if (species == null) {
- throw new InvalidXmlSchemaException("No species with id=\"" + speciesId + "\" for complex alias \"" + aliasId + "\"");
- }
- Complex result = species.createModelElement(aliasId);
- elements.addElement(species, aliasId);
-
- String state = "usual";
- NodeList nodes = aliasNode.getChildNodes();
- View usualView = null;
- View briefView = null;
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:activity")) {
- result.setActivity(getNodeValue(node).equalsIgnoreCase("active"));
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:bounds")) {
- result.setX(getNodeAttr("X", node));
- result.setY(getNodeAttr("Y", node));
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:font")) {
- result.setFontSize(getNodeAttr("size", node));
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:view")) {
- state = getNodeAttr("state", node);
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:usualView")) {
- usualView = getCommonParser().getView(node);
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:briefView")) {
- briefView = getCommonParser().getView(node);
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:backupView")) {
- // not handled
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:info")) {
- processAliasState(node, result);
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:backupSize")) {
- // not handled
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:structuralState")) {
- // not handled
- continue;
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:speciesAlias: " + node.getNodeName());
- }
- }
- }
-
- View view = null;
- if (state.equalsIgnoreCase("usual")) {
- view = usualView;
- } else if (state.equalsIgnoreCase("brief")) {
- view = briefView;
- } else if (state.equalsIgnoreCase("complexparentbrief")) {
- view = briefView;
- }
-
- if (view != null) {
- // inner position defines the position in compartment or complexAlias
- // result.moveBy(view.innerPosition);
- result.setWidth(view.getBoxSize().width);
- result.setHeight(view.getBoxSize().height);
- result.setLineWidth(view.getSingleLine().getWidth());
- result.setColor(view.getColor());
- } else if (!state.equalsIgnoreCase("complexnoborder")) {
- throw new InvalidXmlSchemaException("No view (" + state + ") in ComplexAlias for " + result.getElementId());
- }
- result.setState(state);
- String compartmentAliasId = getNodeAttr("compartmentAlias", aliasNode);
- if (!compartmentAliasId.isEmpty()) {
- Compartment ca = model.getElementByElementId(compartmentAliasId);
- if (ca == null) {
- throw new InvalidXmlSchemaException("CompartmentAlias does not exist: " + compartmentAliasId);
- } else {
- result.setCompartment(ca);
- ca.addElement(result);
- }
- }
- String complexSpeciesAliasId = getNodeAttr("complexSpeciesAlias", aliasNode);
- if (!complexSpeciesAliasId.equals("")) {
- parents.put(result.getElementId(), complexSpeciesAliasId);
- }
- complexAliasesMapById.put(result.getElementId(), result);
- return result;
- }
-
- /**
- * Process node with information about alias state and puts data into alias.
- *
- * @param node
- * node where information about alias state is stored
- * @param alias
- * alias object to be modified if necessary
- */
- private void processAliasState(Node node, Species alias) {
- String state = getNodeAttr("state", node);
- if ("open".equalsIgnoreCase(state)) {
- String prefix = getNodeAttr("prefix", node);
- String label = getNodeAttr("label", node);
- alias.setStatePrefix(prefix);
- alias.setStateLabel(label);
- } else if ("empty".equalsIgnoreCase(state)) {
- return;
- } else if (state == null || state.isEmpty()) {
- return;
- } else {
- throw new NotImplementedException("[Alias: " + alias.getElementId() + "] Unkown alias state: " + state);
- }
-
- }
-
- /**
- * Adds parent reference for the complexAlias.
- *
- * @param alias
- * alias for which we want to add parent information
- */
- public void addReference(Complex alias) {
- String parentId = parents.get(alias.getElementId());
- if (parentId != null) {
- Complex ca = complexAliasesMapById.get(parentId);
- if (ca == null) {
- throw new InvalidArgumentException("Parent complex alias does not exist: " + parentId + " for alias: " + alias.getElementId());
- } else {
- alias.setComplex(ca);
- ca.addSpecies(alias);
- }
- }
- }
-
- @Override
- public String toXml(Complex alias) {
- Compartment ca = null;
- // we have to exclude artifitial compartment aliases, becuase they aren't
- // exported to CellDesigner file
- if (alias.getCompartment() != null && !(alias.getCompartment() instanceof PathwayCompartment)) {
- ca = alias.getCompartment();
- } else if (alias.getComplex() == null) {
- ModelData modelData = alias.getModelData();
- if (modelData != null) {
- for (Compartment cAlias : modelData.getModel().getCompartments()) {
- if (!(cAlias instanceof PathwayCompartment) && cAlias.cross(alias)) {
- if (ca == null) {
- ca = cAlias;
- } else if (ca.getSize() > cAlias.getSize()) {
- ca = cAlias;
- }
- }
- }
- }
- }
-
- Complex complexAlias = alias.getComplex();
-
- String compartmentAliasId = null;
- if (ca != null) {
- compartmentAliasId = ca.getElementId();
- }
- StringBuilder sb = new StringBuilder("");
- sb.append("<celldesigner:complexSpeciesAlias ");
- sb.append("id=\"" + alias.getElementId() + "\" ");
- sb.append("species=\"" + elements.getElementId(alias) + "\" ");
- if (compartmentAliasId != null) {
- sb.append("compartmentAlias=\"" + compartmentAliasId + "\" ");
- }
- if (complexAlias != null) {
- sb.append("complexSpeciesAlias=\"" + complexAlias.getElementId() + "\"");
- }
- sb.append(">\n");
-
- if (alias.getActivity() != null) {
- if (alias.getActivity()) {
- sb.append("<celldesigner:activity>active</celldesigner:activity>\n");
- } else {
- sb.append("<celldesigner:activity>inactive</celldesigner:activity>\n");
- }
- }
-
- sb.append("<celldesigner:bounds ");
- sb.append("x=\"" + alias.getX() + "\" ");
- sb.append("y=\"" + alias.getY() + "\" ");
- sb.append("w=\"" + alias.getWidth() + "\" ");
- sb.append("h=\"" + alias.getHeight() + "\" ");
- sb.append("/>\n");
-
- sb.append("<celldesigner:font size=\"" + alias.getFontSize() + "\"/>");
-
- sb.append("<celldesigner:view state=\"usual\"/>\n");
- sb.append("<celldesigner:usualView>");
- sb.append("<celldesigner:innerPosition x=\"" + alias.getX() + "\" y=\"" + alias.getY() + "\"/>");
- sb.append("<celldesigner:boxSize width=\"" + alias.getWidth() + "\" height=\"" + alias.getHeight() + "\"/>");
- sb.append("<celldesigner:singleLine width=\"" + alias.getLineWidth() + "\"/>");
- sb.append("<celldesigner:paint color=\"" + colorToString(alias.getColor()) + "\" scheme=\"Color\"/>");
- sb.append("</celldesigner:usualView>\n");
- sb.append("<celldesigner:briefView>");
- sb.append("<celldesigner:innerPosition x=\"" + alias.getX() + "\" y=\"" + alias.getY() + "\"/>");
- sb.append("<celldesigner:boxSize width=\"" + alias.getWidth() + "\" height=\"" + alias.getHeight() + "\"/>");
- sb.append("<celldesigner:singleLine width=\"" + alias.getWidth() + "\"/>");
- sb.append("<celldesigner:paint color=\"" + colorToString(alias.getColor()) + "\" scheme=\"Color\"/>");
- sb.append("</celldesigner:briefView>\n");
-
- sb.append("</celldesigner:complexSpeciesAlias>\n");
- return sb.toString();
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.alias;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.View;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * Parser of CellDesigner xml used for parsing complex aliases. Important: Only
+ * one instance per model should be used.
+ *
+ * @author Piotr Gawron
+ *
+ * @see Complex
+ */
+public class ComplexAliasXmlParser extends AbstractAliasXmlParser<Complex> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(ComplexAliasXmlParser.class.getName());
+
+ /**
+ * Because of the CellDesigner xml model we have to store information about
+ * all processed Complexes. This infomrmation later on is used for connecting
+ * complexes in hierarchical view.
+ */
+ private Map<String, Complex> complexAliasesMapById = new HashMap<String, Complex>();
+
+ /**
+ * Because of the CellDesigner xml model we have to store information about
+ * parents of all Complexes. This infomrmation later on is used for connecting
+ * complexes in hierarchical view. We cannot do it immediatelly because some
+ * complexes doesn't exist yet.
+ */
+ private Map<String, String> parents = new HashMap<String, String>();
+
+ /**
+ * Model for which we are parsing aliases.
+ */
+ private Model model = null;
+
+ /**
+ * Collection of {@link CellDesignerElement cell designer elements} parsed
+ * from xml.
+ */
+ private CellDesignerElementCollection elements;
+
+ /**
+ * Default constructor with model object for which we parse data.
+ *
+ * @param model
+ * model for which we parse elements
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
+ */
+ public ComplexAliasXmlParser(CellDesignerElementCollection elements, Model model) {
+ this.model = model;
+ this.elements = elements;
+ }
+
+ @Override
+ Complex parseXmlAlias(Node aliasNode) throws InvalidXmlSchemaException {
+
+ String aliasId = getNodeAttr("id", aliasNode);
+
+ String speciesId = getNodeAttr("species", aliasNode);
+ CellDesignerComplexSpecies species = (CellDesignerComplexSpecies) elements.getElementByElementId(speciesId);
+ if (species == null) {
+ throw new InvalidXmlSchemaException("No species with id=\"" + speciesId + "\" for complex alias \"" + aliasId + "\"");
+ }
+ Complex result = species.createModelElement(aliasId);
+ elements.addElement(species, aliasId);
+
+ String state = "usual";
+ NodeList nodes = aliasNode.getChildNodes();
+ View usualView = null;
+ View briefView = null;
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:activity")) {
+ result.setActivity(getNodeValue(node).equalsIgnoreCase("active"));
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:bounds")) {
+ result.setX(getNodeAttr("X", node));
+ result.setY(getNodeAttr("Y", node));
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:font")) {
+ result.setFontSize(getNodeAttr("size", node));
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:view")) {
+ state = getNodeAttr("state", node);
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:usualView")) {
+ usualView = getCommonParser().getView(node);
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:briefView")) {
+ briefView = getCommonParser().getView(node);
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:backupView")) {
+ // not handled
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:info")) {
+ processAliasState(node, result);
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:backupSize")) {
+ // not handled
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:structuralState")) {
+ // not handled
+ continue;
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:speciesAlias: " + node.getNodeName());
+ }
+ }
+ }
+
+ View view = null;
+ if (state.equalsIgnoreCase("usual")) {
+ view = usualView;
+ } else if (state.equalsIgnoreCase("brief")) {
+ view = briefView;
+ } else if (state.equalsIgnoreCase("complexparentbrief")) {
+ view = briefView;
+ }
+
+ if (view != null) {
+ // inner position defines the position in compartment or complexAlias
+ // result.moveBy(view.innerPosition);
+ result.setWidth(view.getBoxSize().width);
+ result.setHeight(view.getBoxSize().height);
+ result.setLineWidth(view.getSingleLine().getWidth());
+ result.setColor(view.getColor());
+ } else if (!state.equalsIgnoreCase("complexnoborder")) {
+ throw new InvalidXmlSchemaException("No view (" + state + ") in ComplexAlias for " + result.getElementId());
+ }
+ result.setState(state);
+ String compartmentAliasId = getNodeAttr("compartmentAlias", aliasNode);
+ if (!compartmentAliasId.isEmpty()) {
+ Compartment ca = model.getElementByElementId(compartmentAliasId);
+ if (ca == null) {
+ throw new InvalidXmlSchemaException("CompartmentAlias does not exist: " + compartmentAliasId);
+ } else {
+ result.setCompartment(ca);
+ ca.addElement(result);
+ }
+ }
+ String complexSpeciesAliasId = getNodeAttr("complexSpeciesAlias", aliasNode);
+ if (!complexSpeciesAliasId.equals("")) {
+ parents.put(result.getElementId(), complexSpeciesAliasId);
+ }
+ complexAliasesMapById.put(result.getElementId(), result);
+ return result;
+ }
+
+ /**
+ * Process node with information about alias state and puts data into alias.
+ *
+ * @param node
+ * node where information about alias state is stored
+ * @param alias
+ * alias object to be modified if necessary
+ */
+ private void processAliasState(Node node, Species alias) {
+ String state = getNodeAttr("state", node);
+ if ("open".equalsIgnoreCase(state)) {
+ String prefix = getNodeAttr("prefix", node);
+ String label = getNodeAttr("label", node);
+ alias.setStatePrefix(prefix);
+ alias.setStateLabel(label);
+ } else if ("empty".equalsIgnoreCase(state)) {
+ return;
+ } else if (state == null || state.isEmpty()) {
+ return;
+ } else {
+ throw new NotImplementedException("[Alias: " + alias.getElementId() + "] Unkown alias state: " + state);
+ }
+
+ }
+
+ /**
+ * Adds parent reference for the complexAlias.
+ *
+ * @param alias
+ * alias for which we want to add parent information
+ */
+ public void addReference(Complex alias) {
+ String parentId = parents.get(alias.getElementId());
+ if (parentId != null) {
+ Complex ca = complexAliasesMapById.get(parentId);
+ if (ca == null) {
+ throw new InvalidArgumentException("Parent complex alias does not exist: " + parentId + " for alias: " + alias.getElementId());
+ } else {
+ alias.setComplex(ca);
+ ca.addSpecies(alias);
+ }
+ }
+ }
+
+ @Override
+ public String toXml(Complex alias) {
+ Compartment ca = null;
+ // we have to exclude artifitial compartment aliases, becuase they aren't
+ // exported to CellDesigner file
+ if (alias.getCompartment() != null && !(alias.getCompartment() instanceof PathwayCompartment)) {
+ ca = alias.getCompartment();
+ } else if (alias.getComplex() == null) {
+ ModelData modelData = alias.getModelData();
+ if (modelData != null) {
+ for (Compartment cAlias : modelData.getModel().getCompartments()) {
+ if (!(cAlias instanceof PathwayCompartment) && cAlias.cross(alias)) {
+ if (ca == null) {
+ ca = cAlias;
+ } else if (ca.getSize() > cAlias.getSize()) {
+ ca = cAlias;
+ }
+ }
+ }
+ }
+ }
+
+ Complex complexAlias = alias.getComplex();
+
+ String compartmentAliasId = null;
+ if (ca != null) {
+ compartmentAliasId = ca.getElementId();
+ }
+ StringBuilder sb = new StringBuilder("");
+ sb.append("<celldesigner:complexSpeciesAlias ");
+ sb.append("id=\"" + alias.getElementId() + "\" ");
+ sb.append("species=\"" + elements.getElementId(alias) + "\" ");
+ if (compartmentAliasId != null) {
+ sb.append("compartmentAlias=\"" + compartmentAliasId + "\" ");
+ }
+ if (complexAlias != null) {
+ sb.append("complexSpeciesAlias=\"" + complexAlias.getElementId() + "\"");
+ }
+ sb.append(">\n");
+
+ if (alias.getActivity() != null) {
+ if (alias.getActivity()) {
+ sb.append("<celldesigner:activity>active</celldesigner:activity>\n");
+ } else {
+ sb.append("<celldesigner:activity>inactive</celldesigner:activity>\n");
+ }
+ }
+
+ sb.append("<celldesigner:bounds ");
+ sb.append("x=\"" + alias.getX() + "\" ");
+ sb.append("y=\"" + alias.getY() + "\" ");
+ sb.append("w=\"" + alias.getWidth() + "\" ");
+ sb.append("h=\"" + alias.getHeight() + "\" ");
+ sb.append("/>\n");
+
+ sb.append("<celldesigner:font size=\"" + alias.getFontSize() + "\"/>");
+
+ sb.append("<celldesigner:view state=\"usual\"/>\n");
+ sb.append("<celldesigner:usualView>");
+ sb.append("<celldesigner:innerPosition x=\"" + alias.getX() + "\" y=\"" + alias.getY() + "\"/>");
+ sb.append("<celldesigner:boxSize width=\"" + alias.getWidth() + "\" height=\"" + alias.getHeight() + "\"/>");
+ sb.append("<celldesigner:singleLine width=\"" + alias.getLineWidth() + "\"/>");
+ sb.append("<celldesigner:paint color=\"" + colorToString(alias.getColor()) + "\" scheme=\"Color\"/>");
+ sb.append("</celldesigner:usualView>\n");
+ sb.append("<celldesigner:briefView>");
+ sb.append("<celldesigner:innerPosition x=\"" + alias.getX() + "\" y=\"" + alias.getY() + "\"/>");
+ sb.append("<celldesigner:boxSize width=\"" + alias.getWidth() + "\" height=\"" + alias.getHeight() + "\"/>");
+ sb.append("<celldesigner:singleLine width=\"" + alias.getWidth() + "\"/>");
+ sb.append("<celldesigner:paint color=\"" + colorToString(alias.getColor()) + "\" scheme=\"Color\"/>");
+ sb.append("</celldesigner:briefView>\n");
+
+ sb.append("</celldesigner:complexSpeciesAlias>\n");
+ return sb.toString();
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/package-info.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/package-info.java
index dcc787516f..4790cb66ee 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/package-info.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/package-info.java
@@ -1,6 +1,6 @@
-/**
- * This package contains converters for CellDesigner xml nodes representing
- * aliases.
- */
-package lcsb.mapviewer.converter.model.celldesigner.alias;
-
+/**
+ * This package contains converters for CellDesigner xml nodes representing
+ * aliases.
+ */
+package lcsb.mapviewer.converter.model.celldesigner.alias;
+
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/package-info.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/package-info.java
index 4124bcd42a..d69c31ead7 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/package-info.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/package-info.java
@@ -1,5 +1,5 @@
-/**
- * Contains parser for annotation nodes.
- */
-package lcsb.mapviewer.converter.model.celldesigner.annotation;
-
+/**
+ * Contains parser for annotation nodes.
+ */
+package lcsb.mapviewer.converter.model.celldesigner.annotation;
+
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParser.java
index 71c850dd42..6057b82fe7 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParser.java
@@ -1,108 +1,108 @@
-package lcsb.mapviewer.converter.model.celldesigner.compartment;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.XmlParser;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
-
-/**
- * CellDEsigner xml parser for collection of compartments.
- *
- * @author Piotr Gawron
- *
- */
-public class CompartmentCollectionXmlParser extends XmlParser {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(CompartmentCollectionXmlParser.class.getName());
-
- /**
- * CellDesigner xml parser for single compartment.
- */
- private CompartmentXmlParser compartmentParser;
-
- /**
- * Collection of {@link CellDesignerElement cell designer elements} parsed
- * from xml.
- */
- private CellDesignerElementCollection elements;
-
- /**
- * Default constructor.
- *
- * @param elements
- * collection of {@link CellDesignerElement cell designer elements}
- * parsed from xml
- */
- public CompartmentCollectionXmlParser(CellDesignerElementCollection elements) {
- this.elements = elements;
- compartmentParser = new CompartmentXmlParser(elements);
- }
-
- /**
- * Parse CellDEsigner xml node with collection of compartments.
- *
- * @param compartmentsNode
- * xml node to parse
- * @return list of compartments obtained from xml node
- * @throws InvalidXmlSchemaException
- * thrown when there is a problem with xml
- */
- public List<CellDesignerCompartment> parseXmlCompartmentCollection(Node compartmentsNode) throws InvalidXmlSchemaException {
- List<CellDesignerCompartment> result = new ArrayList<CellDesignerCompartment>();
- NodeList nodes = compartmentsNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("compartment")) {
- Pair<String, CellDesignerCompartment> compartmentPair = compartmentParser.parseXmlElement(node);
- result.add(compartmentPair.getRight());
- } else {
- throw new InvalidXmlSchemaException("Unknown element of model/listOfCompartments: " + node.getNodeName());
- }
- }
- }
- return result;
- }
-
- /**
- * Creates CellDesigner xml string from set of compartments.
- *
- * @param collection
- * collection of compartments to be transformed into xml
- * @return xml representation of the compartments
- */
- public String toXml(Collection<Compartment> collection) {
- StringBuilder result = new StringBuilder();
- result.append("<listOfCompartments>\n");
- Set<String> addedIds = new HashSet<>();
- for (Compartment compartment : collection) {
- String sbmlId = elements.getElementId(compartment);
- if (!addedIds.contains(sbmlId) && !(compartment instanceof PathwayCompartment)) {
- addedIds.add(sbmlId);
- result.append(compartmentParser.toXml(compartment));
- }
- }
- Compartment defaultCompartment = new Compartment("default");
- result.append(compartmentParser.toXml(defaultCompartment));
- result.append("</listOfCompartments>\n");
- return result.toString();
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.compartment;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
+
+/**
+ * CellDEsigner xml parser for collection of compartments.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CompartmentCollectionXmlParser extends XmlParser {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(CompartmentCollectionXmlParser.class.getName());
+
+ /**
+ * CellDesigner xml parser for single compartment.
+ */
+ private CompartmentXmlParser compartmentParser;
+
+ /**
+ * Collection of {@link CellDesignerElement cell designer elements} parsed
+ * from xml.
+ */
+ private CellDesignerElementCollection elements;
+
+ /**
+ * Default constructor.
+ *
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
+ */
+ public CompartmentCollectionXmlParser(CellDesignerElementCollection elements) {
+ this.elements = elements;
+ compartmentParser = new CompartmentXmlParser(elements);
+ }
+
+ /**
+ * Parse CellDEsigner xml node with collection of compartments.
+ *
+ * @param compartmentsNode
+ * xml node to parse
+ * @return list of compartments obtained from xml node
+ * @throws InvalidXmlSchemaException
+ * thrown when there is a problem with xml
+ */
+ public List<CellDesignerCompartment> parseXmlCompartmentCollection(Node compartmentsNode) throws InvalidXmlSchemaException {
+ List<CellDesignerCompartment> result = new ArrayList<CellDesignerCompartment>();
+ NodeList nodes = compartmentsNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("compartment")) {
+ Pair<String, CellDesignerCompartment> compartmentPair = compartmentParser.parseXmlElement(node);
+ result.add(compartmentPair.getRight());
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of model/listOfCompartments: " + node.getNodeName());
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Creates CellDesigner xml string from set of compartments.
+ *
+ * @param collection
+ * collection of compartments to be transformed into xml
+ * @return xml representation of the compartments
+ */
+ public String toXml(Collection<Compartment> collection) {
+ StringBuilder result = new StringBuilder();
+ result.append("<listOfCompartments>\n");
+ Set<String> addedIds = new HashSet<>();
+ for (Compartment compartment : collection) {
+ String sbmlId = elements.getElementId(compartment);
+ if (!addedIds.contains(sbmlId) && !(compartment instanceof PathwayCompartment)) {
+ addedIds.add(sbmlId);
+ result.append(compartmentParser.toXml(compartment));
+ }
+ }
+ Compartment defaultCompartment = new Compartment("default");
+ result.append(compartmentParser.toXml(defaultCompartment));
+ result.append("</listOfCompartments>\n");
+ return result.toString();
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParser.java
index cb1ce612b8..b284a5ab92 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParser.java
@@ -1,171 +1,171 @@
-package lcsb.mapviewer.converter.model.celldesigner.compartment;
-
-import org.apache.log4j.Logger;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
-import lcsb.mapviewer.converter.model.celldesigner.species.AbstractElementXmlParser;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
-
-/**
- * Parser of CellDesginer xml nodes for compartment elements.
- *
- * @author Piotr Gawron
- *
- */
-public class CompartmentXmlParser extends AbstractElementXmlParser<CellDesignerCompartment, Compartment> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(CompartmentXmlParser.class.getName());
-
- /**
- * Parser used to retrieve Miriam data for the element.
- */
- private XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser();
-
- /**
- * Collection of {@link CellDesignerElement cell designer elements} parsed
- * from xml.
- */
- private CellDesignerElementCollection elements;
-
- /**
- * Xml parser used for processing notes into structurized data.
- */
- private RestAnnotationParser rap = new RestAnnotationParser();
-
- /**
- * Default constructor.
- *
- * @param elements
- * collection of {@link CellDesignerElement cell designer elements}
- * parsed from xml
- */
- public CompartmentXmlParser(CellDesignerElementCollection elements) {
- this.elements = elements;
- }
-
- @Override
- public Pair<String, CellDesignerCompartment> parseXmlElement(Node compartmentNode) throws InvalidXmlSchemaException {
- CellDesignerCompartment compartment = new CellDesignerCompartment();
- // we ignore metaid - it's useless and obstruct data model
- // compartment.setMetaId(getNodeAttr("metaid", compartmentNode));
- compartment.setElementId(getNodeAttr("id", compartmentNode));
- compartment.setName(decodeName(getNodeAttr("name", compartmentNode)));
- NodeList nodes = compartmentNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("annotation")) {
- parseAnnotationNode(compartment, node);
- } else if (node.getNodeName().equalsIgnoreCase("notes")) {
- compartment.setNotes(rap.getNotes(node));
- } else {
- throw new InvalidXmlSchemaException("Unknown element of Compartment: " + node.getNodeName());
- }
- }
- }
- return new Pair<String, CellDesignerCompartment>(compartment.getElementId(), compartment);
- }
-
- /**
- * Process annotation part of the xml node.
- *
- * @param compartment
- * object that we create
- * @param xmlNode
- * annotation xml node
- * @throws InvalidXmlSchemaException
- * thrown when there is a problem with xml
- */
- private void parseAnnotationNode(CellDesignerCompartment compartment, Node xmlNode) throws InvalidXmlSchemaException {
- NodeList annotationNodes = xmlNode.getChildNodes();
- for (int y = 0; y < annotationNodes.getLength(); y++) {
- Node annotationNode = annotationNodes.item(y);
- if (annotationNode.getNodeType() == Node.ELEMENT_NODE) {
- if (annotationNode.getNodeName().equalsIgnoreCase("rdf:RDF")) {
- compartment.addMiriamData(xmlAnnotationParser.parseRdfNode(annotationNode));
- } else if (annotationNode.getNodeName().equalsIgnoreCase("celldesigner:extension")) {
- parseExtensionNode(compartment, annotationNode);
- } else {
- throw new InvalidXmlSchemaException("Unknown element of Compartment/annotation: " + annotationNode.getNodeName());
- }
- }
- }
- }
-
- /**
- * Process extension part of the xml node.
- *
- * @param compartment
- * object that we create
- * @param xmlNode
- * annotation xml node
- * @throws InvalidXmlSchemaException
- * thrown when xmlNode is invalid
- */
- private void parseExtensionNode(CellDesignerCompartment compartment, Node xmlNode) throws InvalidXmlSchemaException {
- NodeList annotationNodes = xmlNode.getChildNodes();
- for (int y = 0; y < annotationNodes.getLength(); y++) {
- Node annotationNode = annotationNodes.item(y);
- if (annotationNode.getNodeType() == Node.ELEMENT_NODE) {
- if (annotationNode.getNodeName().equalsIgnoreCase("celldesigner:name")) {
- // ignore it (we already have this name)
- continue;
- } else {
- throw new InvalidXmlSchemaException("Unknown element of Compartment/annotation/extension: " + annotationNode.getNodeName());
- }
- }
- }
- }
-
- @Override
- public String toXml(Compartment compartment) {
- StringBuilder sb = new StringBuilder("");
- sb.append("<compartment ");
- sb.append("metaid=\"" + elements.getElementId(compartment) + "\" ");
- sb.append("id=\"" + elements.getElementId(compartment) + "\" ");
- sb.append("name=\"" + encodeName(compartment.getName()) + "\" ");
- sb.append("size=\"1\" ");
- sb.append("units=\"volume\" ");
- String parentName = "default";
-
- if (compartment.getCompartment() != null && !(compartment.getCompartment() instanceof PathwayCompartment)) {
- parentName = elements.getElementId(compartment.getCompartment());
- }
-
- // default is the top level compartment
- if (!compartment.getElementId().equals("default")) {
- sb.append("outside=\"" + parentName + "\" ");
- }
- sb.append(">\n");
- sb.append("<annotation>\n");
- sb.append("<celldesigner:extension>\n");
- sb.append("<celldesigner:name>" + encodeName(compartment.getName()) + "</celldesigner:name>\n");
- sb.append("</celldesigner:extension>\n");
- sb.append(xmlAnnotationParser.dataSetToXmlString(compartment.getMiriamData()));
- sb.append("</annotation>\n");
- sb.append("<notes>");
- sb.append("<html xmlns=\"http://www.w3.org/1999/xhtml\"><head><title/></head><body>");
- RestAnnotationParser rap = new RestAnnotationParser();
- sb.append(rap.createAnnotationString(compartment));
- if (compartment.getNotes() != null) {
- sb.append(compartment.getNotes());
- }
- sb.append("</body></html>");
- sb.append("</notes>\n");
- sb.append("</compartment>\n");
- return sb.toString();
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.compartment;
+
+import org.apache.log4j.Logger;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
+import lcsb.mapviewer.converter.model.celldesigner.species.AbstractElementXmlParser;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
+
+/**
+ * Parser of CellDesginer xml nodes for compartment elements.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CompartmentXmlParser extends AbstractElementXmlParser<CellDesignerCompartment, Compartment> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(CompartmentXmlParser.class.getName());
+
+ /**
+ * Parser used to retrieve Miriam data for the element.
+ */
+ private XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser();
+
+ /**
+ * Collection of {@link CellDesignerElement cell designer elements} parsed
+ * from xml.
+ */
+ private CellDesignerElementCollection elements;
+
+ /**
+ * Xml parser used for processing notes into structurized data.
+ */
+ private RestAnnotationParser rap = new RestAnnotationParser();
+
+ /**
+ * Default constructor.
+ *
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
+ */
+ public CompartmentXmlParser(CellDesignerElementCollection elements) {
+ this.elements = elements;
+ }
+
+ @Override
+ public Pair<String, CellDesignerCompartment> parseXmlElement(Node compartmentNode) throws InvalidXmlSchemaException {
+ CellDesignerCompartment compartment = new CellDesignerCompartment();
+ // we ignore metaid - it's useless and obstruct data model
+ // compartment.setMetaId(getNodeAttr("metaid", compartmentNode));
+ compartment.setElementId(getNodeAttr("id", compartmentNode));
+ compartment.setName(decodeName(getNodeAttr("name", compartmentNode)));
+ NodeList nodes = compartmentNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("annotation")) {
+ parseAnnotationNode(compartment, node);
+ } else if (node.getNodeName().equalsIgnoreCase("notes")) {
+ compartment.setNotes(rap.getNotes(node));
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of Compartment: " + node.getNodeName());
+ }
+ }
+ }
+ return new Pair<String, CellDesignerCompartment>(compartment.getElementId(), compartment);
+ }
+
+ /**
+ * Process annotation part of the xml node.
+ *
+ * @param compartment
+ * object that we create
+ * @param xmlNode
+ * annotation xml node
+ * @throws InvalidXmlSchemaException
+ * thrown when there is a problem with xml
+ */
+ private void parseAnnotationNode(CellDesignerCompartment compartment, Node xmlNode) throws InvalidXmlSchemaException {
+ NodeList annotationNodes = xmlNode.getChildNodes();
+ for (int y = 0; y < annotationNodes.getLength(); y++) {
+ Node annotationNode = annotationNodes.item(y);
+ if (annotationNode.getNodeType() == Node.ELEMENT_NODE) {
+ if (annotationNode.getNodeName().equalsIgnoreCase("rdf:RDF")) {
+ compartment.addMiriamData(xmlAnnotationParser.parseRdfNode(annotationNode));
+ } else if (annotationNode.getNodeName().equalsIgnoreCase("celldesigner:extension")) {
+ parseExtensionNode(compartment, annotationNode);
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of Compartment/annotation: " + annotationNode.getNodeName());
+ }
+ }
+ }
+ }
+
+ /**
+ * Process extension part of the xml node.
+ *
+ * @param compartment
+ * object that we create
+ * @param xmlNode
+ * annotation xml node
+ * @throws InvalidXmlSchemaException
+ * thrown when xmlNode is invalid
+ */
+ private void parseExtensionNode(CellDesignerCompartment compartment, Node xmlNode) throws InvalidXmlSchemaException {
+ NodeList annotationNodes = xmlNode.getChildNodes();
+ for (int y = 0; y < annotationNodes.getLength(); y++) {
+ Node annotationNode = annotationNodes.item(y);
+ if (annotationNode.getNodeType() == Node.ELEMENT_NODE) {
+ if (annotationNode.getNodeName().equalsIgnoreCase("celldesigner:name")) {
+ // ignore it (we already have this name)
+ continue;
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of Compartment/annotation/extension: " + annotationNode.getNodeName());
+ }
+ }
+ }
+ }
+
+ @Override
+ public String toXml(Compartment compartment) {
+ StringBuilder sb = new StringBuilder("");
+ sb.append("<compartment ");
+ sb.append("metaid=\"" + elements.getElementId(compartment) + "\" ");
+ sb.append("id=\"" + elements.getElementId(compartment) + "\" ");
+ sb.append("name=\"" + encodeName(compartment.getName()) + "\" ");
+ sb.append("size=\"1\" ");
+ sb.append("units=\"volume\" ");
+ String parentName = "default";
+
+ if (compartment.getCompartment() != null && !(compartment.getCompartment() instanceof PathwayCompartment)) {
+ parentName = elements.getElementId(compartment.getCompartment());
+ }
+
+ // default is the top level compartment
+ if (!compartment.getElementId().equals("default")) {
+ sb.append("outside=\"" + parentName + "\" ");
+ }
+ sb.append(">\n");
+ sb.append("<annotation>\n");
+ sb.append("<celldesigner:extension>\n");
+ sb.append("<celldesigner:name>" + encodeName(compartment.getName()) + "</celldesigner:name>\n");
+ sb.append("</celldesigner:extension>\n");
+ sb.append(xmlAnnotationParser.dataSetToXmlString(compartment.getMiriamData()));
+ sb.append("</annotation>\n");
+ sb.append("<notes>");
+ sb.append("<html xmlns=\"http://www.w3.org/1999/xhtml\"><head><title/></head><body>");
+ RestAnnotationParser rap = new RestAnnotationParser();
+ sb.append(rap.createAnnotationString(compartment));
+ if (compartment.getNotes() != null) {
+ sb.append(compartment.getNotes());
+ }
+ sb.append("</body></html>");
+ sb.append("</notes>\n");
+ sb.append("</compartment>\n");
+ return sb.toString();
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/package-info.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/package-info.java
index 5bcc2667e1..8d5a65ecbb 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/package-info.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/package-info.java
@@ -1,6 +1,6 @@
-/**
- * This package contains converters for CellDesigner xml nodes representing
- * compartments.
- */
-package lcsb.mapviewer.converter.model.celldesigner.compartment;
-
+/**
+ * This package contains converters for CellDesigner xml nodes representing
+ * compartments.
+ */
+package lcsb.mapviewer.converter.model.celldesigner.compartment;
+
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ComplexCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ComplexCellDesignerAliasConverter.java
index 9ce0d41feb..f3de602426 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ComplexCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ComplexCellDesignerAliasConverter.java
@@ -1,70 +1,70 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import java.awt.geom.AffineTransform;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Complex;
-
-/**
- * Class that provides CellDesigner specific graphical information for
- * ComplexAlias. It's used for conversion from xml to normal x,y coordinates.
- *
- * @author Piotr Gawron
- *
- */
-public class ComplexCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Complex> {
-
- /**
- * Default constructor.
- *
- * @param sbgn
- * Should the converter use sbgn standard
- */
- protected ComplexCellDesignerAliasConverter(boolean sbgn) {
- super(sbgn);
- }
-
- /**
- * How big is the triangle trimmed part of the complex.
- */
- private static final int TRIMMED_CORNER_SIZE = 5;
-
- @Override
- public Point2D getPointCoordinates(Complex alias, CellDesignerAnchor anchor) {
- if (invalidAnchorPosition(alias, anchor)) {
- return alias.getCenter();
- }
- return getRectangleTransformation().getPointOnRectangleByAnchor(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), anchor);
- }
-
- @Override
- public PathIterator getBoundPathIterator(Complex alias) {
- return getAliasPath(alias).getPathIterator(new AffineTransform());
- }
-
- /**
- * Returns the border of complex alias.
- *
- * @param alias
- * exact object for which we want to get a border
- * @return border of the alias
- */
- private GeneralPath getAliasPath(Element alias) {
- GeneralPath path = new GeneralPath(GeneralPath.WIND_EVEN_ODD);
- path.moveTo(alias.getX() + TRIMMED_CORNER_SIZE, alias.getY());
- path.lineTo(alias.getX() + alias.getWidth() - TRIMMED_CORNER_SIZE, alias.getY());
- path.lineTo(alias.getX() + alias.getWidth(), alias.getY() + TRIMMED_CORNER_SIZE);
- path.lineTo(alias.getX() + alias.getWidth(), alias.getY() + alias.getHeight() - TRIMMED_CORNER_SIZE);
- path.lineTo(alias.getX() + alias.getWidth() - TRIMMED_CORNER_SIZE, alias.getY() + alias.getHeight());
- path.lineTo(alias.getX() + TRIMMED_CORNER_SIZE, alias.getY() + alias.getHeight());
- path.lineTo(alias.getX(), alias.getY() + alias.getHeight() - TRIMMED_CORNER_SIZE);
- path.lineTo(alias.getX(), alias.getY() + TRIMMED_CORNER_SIZE);
- path.closePath();
- return path;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import java.awt.geom.AffineTransform;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
+
+/**
+ * Class that provides CellDesigner specific graphical information for
+ * ComplexAlias. It's used for conversion from xml to normal x,y coordinates.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ComplexCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Complex> {
+
+ /**
+ * Default constructor.
+ *
+ * @param sbgn
+ * Should the converter use sbgn standard
+ */
+ protected ComplexCellDesignerAliasConverter(boolean sbgn) {
+ super(sbgn);
+ }
+
+ /**
+ * How big is the triangle trimmed part of the complex.
+ */
+ private static final int TRIMMED_CORNER_SIZE = 5;
+
+ @Override
+ public Point2D getPointCoordinates(Complex alias, CellDesignerAnchor anchor) {
+ if (invalidAnchorPosition(alias, anchor)) {
+ return alias.getCenter();
+ }
+ return getRectangleTransformation().getPointOnRectangleByAnchor(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), anchor);
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(Complex alias) {
+ return getAliasPath(alias).getPathIterator(new AffineTransform());
+ }
+
+ /**
+ * Returns the border of complex alias.
+ *
+ * @param alias
+ * exact object for which we want to get a border
+ * @return border of the alias
+ */
+ private GeneralPath getAliasPath(Element alias) {
+ GeneralPath path = new GeneralPath(GeneralPath.WIND_EVEN_ODD);
+ path.moveTo(alias.getX() + TRIMMED_CORNER_SIZE, alias.getY());
+ path.lineTo(alias.getX() + alias.getWidth() - TRIMMED_CORNER_SIZE, alias.getY());
+ path.lineTo(alias.getX() + alias.getWidth(), alias.getY() + TRIMMED_CORNER_SIZE);
+ path.lineTo(alias.getX() + alias.getWidth(), alias.getY() + alias.getHeight() - TRIMMED_CORNER_SIZE);
+ path.lineTo(alias.getX() + alias.getWidth() - TRIMMED_CORNER_SIZE, alias.getY() + alias.getHeight());
+ path.lineTo(alias.getX() + TRIMMED_CORNER_SIZE, alias.getY() + alias.getHeight());
+ path.lineTo(alias.getX(), alias.getY() + alias.getHeight() - TRIMMED_CORNER_SIZE);
+ path.lineTo(alias.getX(), alias.getY() + TRIMMED_CORNER_SIZE);
+ path.closePath();
+ return path;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/DegradedCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/DegradedCellDesignerAliasConverter.java
index 0e808eaa8b..3c3a031e06 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/DegradedCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/DegradedCellDesignerAliasConverter.java
@@ -1,107 +1,107 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * Class that provides CellDesigner specific graphical information for Degraded
- * elements. It's used for conversion from xml to normal x,y coordinates.
- *
- * @author Piotr Gawron
- *
- */
-public class DegradedCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
-
- /**
- * Default constructor.
- *
- * @param sbgn
- * Should the converter use sbgn standard
- */
- protected DegradedCellDesignerAliasConverter(boolean sbgn) {
- super(sbgn);
- }
-
- /**
- * Part of height of the line used to cross degraded circle that goes behind
- * this circle.
- */
- private static final int DEGRADED_MARGIN = 7;
-
- @Override
- public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
- double diameter = getDiameter(alias);
- double x = getXCoord(alias, diameter);
- double y = getYCoord(alias);
- if (invalidAnchorPosition(alias, anchor)) {
- return alias.getCenter();
- }
-
- return getEllipseTransformation().getPointOnEllipseByAnchor(x, y, diameter, diameter, anchor);
- }
-
- /**
- * Returns transformed y coordinate for the degraded alias.
- *
- * @param alias
- * object alias to to which we are looking for y coordinate
- * @return y coordinate of the alias
- */
- private double getYCoord(Element alias) {
- double y = alias.getY() + DEGRADED_MARGIN;
- return y;
- }
-
- /**
- * Returns transformed x coordinate for the degraded alias.
- *
- * @param alias
- * object alias to to which we are looking for x coordinate
- * @param diameter
- * diameter of cross line used in this alias
- * @return x coordinate of the alias
- */
- private double getXCoord(Element alias, double diameter) {
- double x = alias.getX() + (alias.getWidth() - diameter) / 2;
- return x;
- }
-
- /**
- * Computes diameter of cross line for the degraded alias.
- *
- * @param alias
- * object alias to to which we are looking for diameter.
- * @return diameter of the cross line
- */
- private double getDiameter(Element alias) {
- double diameter = Math.min(alias.getWidth(), alias.getHeight()) - 2 * DEGRADED_MARGIN;
- if (diameter < 0) {
- diameter = 0;
- }
- return diameter;
- }
-
- @Override
- public Point2D getAnchorPointCoordinates(Species alias, double angle) {
- if (alias.getWidth() == 0 && alias.getHeight() == 0) {
- return alias.getCenter();
- }
- double diameter = getDiameter(alias);
- double x = getXCoord(alias, diameter);
- double y = getYCoord(alias);
- Point2D result = getEllipseTransformation().getPointOnEllipseByRadian(x, y, diameter, diameter, angle);
- return result;
-
- }
-
- @Override
- public PathIterator getBoundPathIterator(Species alias) {
- throw new NotImplementedException("This class doesn't have bound");
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * Class that provides CellDesigner specific graphical information for Degraded
+ * elements. It's used for conversion from xml to normal x,y coordinates.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class DegradedCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
+
+ /**
+ * Default constructor.
+ *
+ * @param sbgn
+ * Should the converter use sbgn standard
+ */
+ protected DegradedCellDesignerAliasConverter(boolean sbgn) {
+ super(sbgn);
+ }
+
+ /**
+ * Part of height of the line used to cross degraded circle that goes behind
+ * this circle.
+ */
+ private static final int DEGRADED_MARGIN = 7;
+
+ @Override
+ public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
+ double diameter = getDiameter(alias);
+ double x = getXCoord(alias, diameter);
+ double y = getYCoord(alias);
+ if (invalidAnchorPosition(alias, anchor)) {
+ return alias.getCenter();
+ }
+
+ return getEllipseTransformation().getPointOnEllipseByAnchor(x, y, diameter, diameter, anchor);
+ }
+
+ /**
+ * Returns transformed y coordinate for the degraded alias.
+ *
+ * @param alias
+ * object alias to to which we are looking for y coordinate
+ * @return y coordinate of the alias
+ */
+ private double getYCoord(Element alias) {
+ double y = alias.getY() + DEGRADED_MARGIN;
+ return y;
+ }
+
+ /**
+ * Returns transformed x coordinate for the degraded alias.
+ *
+ * @param alias
+ * object alias to to which we are looking for x coordinate
+ * @param diameter
+ * diameter of cross line used in this alias
+ * @return x coordinate of the alias
+ */
+ private double getXCoord(Element alias, double diameter) {
+ double x = alias.getX() + (alias.getWidth() - diameter) / 2;
+ return x;
+ }
+
+ /**
+ * Computes diameter of cross line for the degraded alias.
+ *
+ * @param alias
+ * object alias to to which we are looking for diameter.
+ * @return diameter of the cross line
+ */
+ private double getDiameter(Element alias) {
+ double diameter = Math.min(alias.getWidth(), alias.getHeight()) - 2 * DEGRADED_MARGIN;
+ if (diameter < 0) {
+ diameter = 0;
+ }
+ return diameter;
+ }
+
+ @Override
+ public Point2D getAnchorPointCoordinates(Species alias, double angle) {
+ if (alias.getWidth() == 0 && alias.getHeight() == 0) {
+ return alias.getCenter();
+ }
+ double diameter = getDiameter(alias);
+ double x = getXCoord(alias, diameter);
+ double y = getYCoord(alias);
+ Point2D result = getEllipseTransformation().getPointOnEllipseByRadian(x, y, diameter, diameter, angle);
+ return result;
+
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(Species alias) {
+ throw new NotImplementedException("This class doesn't have bound");
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/DrugCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/DrugCellDesignerAliasConverter.java
index b6bf21ff24..837c81674f 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/DrugCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/DrugCellDesignerAliasConverter.java
@@ -1,92 +1,92 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import java.awt.Shape;
-import java.awt.geom.AffineTransform;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-import java.awt.geom.RoundRectangle2D;
-import java.util.ArrayList;
-
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * Class that provides CellDesigner specific graphical information for Drug.
- * It's used for conversion from xml to normal x,y coordinates.
- *
- * @author Piotr Gawron
- *
- */
-public class DrugCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
-
- /**
- * Default constructor.
- *
- * @param sbgn
- * Should the converter use sbgn standard
- */
- protected DrugCellDesignerAliasConverter(boolean sbgn) {
- super(sbgn);
- }
-
- /**
- * How big should be the arc in rectangle for drug representation.
- */
- private static final int RECTANGLE_CORNER_ARC_SIZE = 40;
-
- @Override
- public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
- if (invalidAnchorPosition(alias, anchor)) {
- return alias.getCenter();
- }
- ArrayList<Point2D> list = getDrugPoints(alias);
-
- return getPolygonTransformation().getPointOnPolygonByAnchor(list, anchor);
- }
-
- @Override
- protected PathIterator getBoundPathIterator(Species alias) {
- return getDrugShape(alias).getPathIterator(new AffineTransform());
- }
-
- /**
- * Returns shape of the Drug as a list of points.
- *
- * @param alias
- * alias for which we are looking for a border
- * @return list of points defining border of the given alias
- */
- protected ArrayList<Point2D> getDrugPoints(Species alias) {
- ArrayList<Point2D> list = new ArrayList<Point2D>();
-
- double x = alias.getX();
- double y = alias.getY();
- double width = alias.getWidth();
- double height = alias.getHeight();
-
- // CHECKSTYLE:OFF
- list.add(new Point2D.Double(x, y + height / 2));
- list.add(new Point2D.Double(x + width / 12, y));
- list.add(new Point2D.Double(x + width / 2, y));
- list.add(new Point2D.Double(x + width * 11 / 12, y));
- list.add(new Point2D.Double(x + width, y + height / 2));
- list.add(new Point2D.Double(x + width * 11 / 12, y + height));
- list.add(new Point2D.Double(x + width / 2, y + height));
- list.add(new Point2D.Double(x + width / 12, y + height));
- // CHECKSTYLE:ON
- return list;
- }
-
- /**
- * Returns shape of the Drug.
- *
- * @param alias
- * alias for which we are looking for a border
- * @return Shape object defining given alias
- */
- private Shape getDrugShape(Element alias) {
- return new RoundRectangle2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), RECTANGLE_CORNER_ARC_SIZE, RECTANGLE_CORNER_ARC_SIZE);
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import java.awt.Shape;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+import java.awt.geom.RoundRectangle2D;
+import java.util.ArrayList;
+
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * Class that provides CellDesigner specific graphical information for Drug.
+ * It's used for conversion from xml to normal x,y coordinates.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class DrugCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
+
+ /**
+ * Default constructor.
+ *
+ * @param sbgn
+ * Should the converter use sbgn standard
+ */
+ protected DrugCellDesignerAliasConverter(boolean sbgn) {
+ super(sbgn);
+ }
+
+ /**
+ * How big should be the arc in rectangle for drug representation.
+ */
+ private static final int RECTANGLE_CORNER_ARC_SIZE = 40;
+
+ @Override
+ public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
+ if (invalidAnchorPosition(alias, anchor)) {
+ return alias.getCenter();
+ }
+ ArrayList<Point2D> list = getDrugPoints(alias);
+
+ return getPolygonTransformation().getPointOnPolygonByAnchor(list, anchor);
+ }
+
+ @Override
+ protected PathIterator getBoundPathIterator(Species alias) {
+ return getDrugShape(alias).getPathIterator(new AffineTransform());
+ }
+
+ /**
+ * Returns shape of the Drug as a list of points.
+ *
+ * @param alias
+ * alias for which we are looking for a border
+ * @return list of points defining border of the given alias
+ */
+ protected ArrayList<Point2D> getDrugPoints(Species alias) {
+ ArrayList<Point2D> list = new ArrayList<Point2D>();
+
+ double x = alias.getX();
+ double y = alias.getY();
+ double width = alias.getWidth();
+ double height = alias.getHeight();
+
+ // CHECKSTYLE:OFF
+ list.add(new Point2D.Double(x, y + height / 2));
+ list.add(new Point2D.Double(x + width / 12, y));
+ list.add(new Point2D.Double(x + width / 2, y));
+ list.add(new Point2D.Double(x + width * 11 / 12, y));
+ list.add(new Point2D.Double(x + width, y + height / 2));
+ list.add(new Point2D.Double(x + width * 11 / 12, y + height));
+ list.add(new Point2D.Double(x + width / 2, y + height));
+ list.add(new Point2D.Double(x + width / 12, y + height));
+ // CHECKSTYLE:ON
+ return list;
+ }
+
+ /**
+ * Returns shape of the Drug.
+ *
+ * @param alias
+ * alias for which we are looking for a border
+ * @return Shape object defining given alias
+ */
+ private Shape getDrugShape(Element alias) {
+ return new RoundRectangle2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), RECTANGLE_CORNER_ARC_SIZE, RECTANGLE_CORNER_ARC_SIZE);
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/IonCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/IonCellDesignerAliasConverter.java
index 5b8e000b50..8b8a8b779f 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/IonCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/IonCellDesignerAliasConverter.java
@@ -1,119 +1,119 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Ion;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * Class that provides CellDesigner specific graphical information for Ion. It's
- * used for conversion from xml to normal x,y coordinates.
- *
- * @author Piotr Gawron
- *
- */
-public class IonCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Ion> {
-
- Logger logger = Logger.getLogger(IonCellDesignerAliasConverter.class);
-
- /**
- * Default constructor.
- *
- * @param sbgn
- * Should the converter use SBGN standard
- */
- protected IonCellDesignerAliasConverter(boolean sbgn) {
- super(sbgn);
- }
-
- @Override
- public Point2D getPointCoordinates(Ion alias, CellDesignerAnchor anchor) {
- double diameter = getDiameter(alias);
- double x = getXCoord(alias, diameter);
- double y = getYCoord(alias);
- if (invalidAnchorPosition(alias, anchor)) {
- return alias.getCenter();
- }
-
- return getEllipseTransformation().getPointOnEllipseByAnchor(x, y, diameter, diameter, anchor);
- }
-
- /**
- * Returns transformed y coordinate for the ion alias.
- *
- * @param alias
- * object alias to to which we are looking for y coordinate
- * @return y coordinate of the alias
- */
- private double getYCoord(Element alias) {
- double y = alias.getY();
- return y;
- }
-
- /**
- * Returns transformed x coordinate for the ion alias.
- *
- * @param alias
- * object alias to to which we are looking for x coordinate
- * @param diameter
- * diameter of the circle representing alias
- * @return x coordinate of the alias
- */
- private double getXCoord(Element alias, double diameter) {
- double x = alias.getX() + (alias.getWidth() - diameter) / 2;
- return x;
- }
-
- /**
- * Returns diameter of the ion alias.
- *
- * @param alias
- * object alias to to which we are looking for diameter.
- * @return diameter of the alias
- */
- private double getDiameter(Element alias) {
- double diameter = Math.min(alias.getWidth(), alias.getHeight());
- if (diameter < 0) {
- diameter = 0;
- }
- return diameter;
- }
-
- @Override
- public Point2D getAnchorPointCoordinates(Ion alias, double angle) {
- if (alias.getWidth() == 0 && alias.getHeight() == 0) {
- return alias.getCenter();
- }
- double diameter = getDiameter(alias);
- double x = getXCoord(alias, diameter);
- double y = getYCoord(alias);
- Point2D result = getEllipseTransformation().getPointOnEllipseByRadian(x, y, diameter, diameter, angle);
- return result;
-
- }
-
- @Override
- protected PathIterator getBoundPathIterator(Ion alias) {
- throw new NotImplementedException("This class doesn't have bound");
- }
-
- @Override
- public Point2D getPointCoordinatesOnBorder(Ion ion, final double angle) {
- if (ion.getWidth() == 0 && ion.getHeight() == 0) {
- logger.warn("Looking for coordinates for the alias with 0 size");
- return ion.getCenter();
- }
- double diameter = getDiameter(ion);
- double x = getXCoord(ion, diameter);
- double y = getYCoord(ion);
- Point2D result = getEllipseTransformation().getPointOnEllipseByRadian(x, y, diameter, diameter, angle);
- return result;
-
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * Class that provides CellDesigner specific graphical information for Ion. It's
+ * used for conversion from xml to normal x,y coordinates.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class IonCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Ion> {
+
+ Logger logger = Logger.getLogger(IonCellDesignerAliasConverter.class);
+
+ /**
+ * Default constructor.
+ *
+ * @param sbgn
+ * Should the converter use SBGN standard
+ */
+ protected IonCellDesignerAliasConverter(boolean sbgn) {
+ super(sbgn);
+ }
+
+ @Override
+ public Point2D getPointCoordinates(Ion alias, CellDesignerAnchor anchor) {
+ double diameter = getDiameter(alias);
+ double x = getXCoord(alias, diameter);
+ double y = getYCoord(alias);
+ if (invalidAnchorPosition(alias, anchor)) {
+ return alias.getCenter();
+ }
+
+ return getEllipseTransformation().getPointOnEllipseByAnchor(x, y, diameter, diameter, anchor);
+ }
+
+ /**
+ * Returns transformed y coordinate for the ion alias.
+ *
+ * @param alias
+ * object alias to to which we are looking for y coordinate
+ * @return y coordinate of the alias
+ */
+ private double getYCoord(Element alias) {
+ double y = alias.getY();
+ return y;
+ }
+
+ /**
+ * Returns transformed x coordinate for the ion alias.
+ *
+ * @param alias
+ * object alias to to which we are looking for x coordinate
+ * @param diameter
+ * diameter of the circle representing alias
+ * @return x coordinate of the alias
+ */
+ private double getXCoord(Element alias, double diameter) {
+ double x = alias.getX() + (alias.getWidth() - diameter) / 2;
+ return x;
+ }
+
+ /**
+ * Returns diameter of the ion alias.
+ *
+ * @param alias
+ * object alias to to which we are looking for diameter.
+ * @return diameter of the alias
+ */
+ private double getDiameter(Element alias) {
+ double diameter = Math.min(alias.getWidth(), alias.getHeight());
+ if (diameter < 0) {
+ diameter = 0;
+ }
+ return diameter;
+ }
+
+ @Override
+ public Point2D getAnchorPointCoordinates(Ion alias, double angle) {
+ if (alias.getWidth() == 0 && alias.getHeight() == 0) {
+ return alias.getCenter();
+ }
+ double diameter = getDiameter(alias);
+ double x = getXCoord(alias, diameter);
+ double y = getYCoord(alias);
+ Point2D result = getEllipseTransformation().getPointOnEllipseByRadian(x, y, diameter, diameter, angle);
+ return result;
+
+ }
+
+ @Override
+ protected PathIterator getBoundPathIterator(Ion alias) {
+ throw new NotImplementedException("This class doesn't have bound");
+ }
+
+ @Override
+ public Point2D getPointCoordinatesOnBorder(Ion ion, final double angle) {
+ if (ion.getWidth() == 0 && ion.getHeight() == 0) {
+ logger.warn("Looking for coordinates for the alias with 0 size");
+ return ion.getCenter();
+ }
+ double diameter = getDiameter(ion);
+ double x = getXCoord(ion, diameter);
+ double y = getYCoord(ion);
+ Point2D result = getEllipseTransformation().getPointOnEllipseByRadian(x, y, diameter, diameter, angle);
+ return result;
+
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/PhenotypeCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/PhenotypeCellDesignerAliasConverter.java
index 1c1ab361e4..c09fbbb901 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/PhenotypeCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/PhenotypeCellDesignerAliasConverter.java
@@ -1,94 +1,94 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import java.awt.geom.AffineTransform;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * Class that provides CellDesigner specific graphical information for
- * Phenotype. It's used for conversion from xml to normal x,y coordinates.
- *
- * @author Piotr Gawron
- *
- */
-public class PhenotypeCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
-
- /**
- * Default constructor.
- *
- * @param sbgn
- * Should the converter use sbgn standard
- */
- protected PhenotypeCellDesignerAliasConverter(boolean sbgn) {
- super(sbgn);
- }
-
- @Override
- public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
- if (invalidAnchorPosition(alias, anchor)) {
- return alias.getCenter();
- }
- return getPolygonTransformation().getPointOnPolygonByAnchor(getPointsForAlias(alias), anchor);
- }
-
- /**
- * Returns shape of the Phenotype as a list of points.
- *
- * @param alias
- * alias for which we are looking for a border
- * @return list of points defining border of the given alias
- */
- private ArrayList<Point2D> getPointsForAlias(Element alias) {
- ArrayList<Point2D> list = new ArrayList<Point2D>();
-
- double x = alias.getX();
- double y = alias.getY();
- double width = alias.getWidth();
- double height = alias.getHeight();
-
- // CHECKSTYLE:OFF
- list.add(new Point2D.Double(x, y + height / 2));
- list.add(new Point2D.Double(x + width / 6, y));
- list.add(new Point2D.Double(x + width / 2, y));
- list.add(new Point2D.Double(x + width * 5 / 6, y));
- list.add(new Point2D.Double(x + width, y + height / 2));
- list.add(new Point2D.Double(x + width * 5 / 6, y + height));
- list.add(new Point2D.Double(x + width / 2, y + height));
- list.add(new Point2D.Double(x + width / 6, y + height));
- // CHECKSTYLE:ON
- return list;
- }
-
- @Override
- public PathIterator getBoundPathIterator(Species alias) {
- return getPhenotypePath(alias).getPathIterator(new AffineTransform());
- }
-
- /**
- * Returns shape of the Phenotype as a GeneralPath object.
- *
- * @param alias
- * alias for which we are looking for a border
- * @return GeneralPath object defining border of the given alias
- */
- private GeneralPath getPhenotypePath(Element alias) {
- // CHECKSTYLE:OFF
- GeneralPath path = new GeneralPath(GeneralPath.WIND_EVEN_ODD, 6);
- path.moveTo(alias.getX() + alias.getWidth() / 6, alias.getY());
- path.lineTo(alias.getX() + alias.getWidth() * 5 / 6, alias.getY());
- path.lineTo(alias.getX() + alias.getWidth(), alias.getY() + alias.getHeight() / 2);
- path.lineTo(alias.getX() + alias.getWidth() * 5 / 6, alias.getY() + alias.getHeight());
- path.lineTo(alias.getX() + alias.getWidth() / 6, alias.getY() + alias.getHeight());
- path.lineTo(alias.getX(), alias.getY() + alias.getHeight() / 2);
- // CHECKSTYLE:ON
- path.closePath();
- return path;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import java.awt.geom.AffineTransform;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * Class that provides CellDesigner specific graphical information for
+ * Phenotype. It's used for conversion from xml to normal x,y coordinates.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class PhenotypeCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Species> {
+
+ /**
+ * Default constructor.
+ *
+ * @param sbgn
+ * Should the converter use sbgn standard
+ */
+ protected PhenotypeCellDesignerAliasConverter(boolean sbgn) {
+ super(sbgn);
+ }
+
+ @Override
+ public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
+ if (invalidAnchorPosition(alias, anchor)) {
+ return alias.getCenter();
+ }
+ return getPolygonTransformation().getPointOnPolygonByAnchor(getPointsForAlias(alias), anchor);
+ }
+
+ /**
+ * Returns shape of the Phenotype as a list of points.
+ *
+ * @param alias
+ * alias for which we are looking for a border
+ * @return list of points defining border of the given alias
+ */
+ private ArrayList<Point2D> getPointsForAlias(Element alias) {
+ ArrayList<Point2D> list = new ArrayList<Point2D>();
+
+ double x = alias.getX();
+ double y = alias.getY();
+ double width = alias.getWidth();
+ double height = alias.getHeight();
+
+ // CHECKSTYLE:OFF
+ list.add(new Point2D.Double(x, y + height / 2));
+ list.add(new Point2D.Double(x + width / 6, y));
+ list.add(new Point2D.Double(x + width / 2, y));
+ list.add(new Point2D.Double(x + width * 5 / 6, y));
+ list.add(new Point2D.Double(x + width, y + height / 2));
+ list.add(new Point2D.Double(x + width * 5 / 6, y + height));
+ list.add(new Point2D.Double(x + width / 2, y + height));
+ list.add(new Point2D.Double(x + width / 6, y + height));
+ // CHECKSTYLE:ON
+ return list;
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(Species alias) {
+ return getPhenotypePath(alias).getPathIterator(new AffineTransform());
+ }
+
+ /**
+ * Returns shape of the Phenotype as a GeneralPath object.
+ *
+ * @param alias
+ * alias for which we are looking for a border
+ * @return GeneralPath object defining border of the given alias
+ */
+ private GeneralPath getPhenotypePath(Element alias) {
+ // CHECKSTYLE:OFF
+ GeneralPath path = new GeneralPath(GeneralPath.WIND_EVEN_ODD, 6);
+ path.moveTo(alias.getX() + alias.getWidth() / 6, alias.getY());
+ path.lineTo(alias.getX() + alias.getWidth() * 5 / 6, alias.getY());
+ path.lineTo(alias.getX() + alias.getWidth(), alias.getY() + alias.getHeight() / 2);
+ path.lineTo(alias.getX() + alias.getWidth() * 5 / 6, alias.getY() + alias.getHeight());
+ path.lineTo(alias.getX() + alias.getWidth() / 6, alias.getY() + alias.getHeight());
+ path.lineTo(alias.getX(), alias.getY() + alias.getHeight() / 2);
+ // CHECKSTYLE:ON
+ path.closePath();
+ return path;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinCellDesignerAliasConverter.java
index 6dc397bf9e..fe5d4724dd 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinCellDesignerAliasConverter.java
@@ -1,231 +1,231 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import java.awt.Shape;
-import java.awt.geom.AffineTransform;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-import java.awt.geom.RoundRectangle2D;
-import java.util.ArrayList;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.IonChannelProtein;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.ReceptorProtein;
-import lcsb.mapviewer.model.map.species.TruncatedProtein;
-import lcsb.mapviewer.modelutils.map.ElementUtils;
-
-/**
- * Class that provides CellDesigner specific graphical information for Protein.
- * It's used for conversion from xml to normal x,y coordinates.
- *
- * @author Piotr Gawron
- *
- */
-public class ProteinCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Protein> {
-
- /**
- * Default constructor.
- *
- * @param sbgn
- * Should the converter use sbgn standard
- */
- protected ProteinCellDesignerAliasConverter(boolean sbgn) {
- super(sbgn);
- }
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(ProteinCellDesignerAliasConverter.class);
-
- /**
- * How big should be the arc in rectangle for generic protein representation.
- */
- private static final int GENERIC_PROTEIN_RECTANGLE_CORNER_ARC_SIZE = 10;
-
- /**
- * Helps in providing human readable identifiers of elements for logging.
- */
- private ElementUtils eu = new ElementUtils();
-
- @Override
- public Point2D getPointCoordinates(Protein alias, CellDesignerAnchor anchor) {
- Point2D result = null;
- if (invalidAnchorPosition(alias, anchor)) {
- result = alias.getCenter();
- } else {
- int homodir = alias.getHomodimer();
-
- alias.setWidth(alias.getWidth() - AbstractCellDesignerAliasConverter.HOMODIMER_OFFSET * (homodir - 1));
- alias.setHeight(alias.getHeight() - AbstractCellDesignerAliasConverter.HOMODIMER_OFFSET * (homodir - 1));
-
- if (alias instanceof GenericProtein) {
- result = getRectangleTransformation().getPointOnRectangleByAnchor(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), anchor);
- } else if (alias instanceof ReceptorProtein) {
- ArrayList<Point2D> points = getReceptorPoints(alias);
- result = getPolygonTransformation().getPointOnPolygonByAnchor(points, anchor);
- } else if (alias instanceof IonChannelProtein) {
- result = getRectangleTransformation().getPointOnRectangleByAnchor(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), anchor);
- } else if (alias instanceof TruncatedProtein) {
- ArrayList<Point2D> points = getTruncatedPoints(alias);
- result = getPolygonTransformation().getPointOnPolygonByAnchor(points, anchor);
- } else {
- throw new NotImplementedException(eu.getElementTag(alias) + "Unknown type: " + alias.getClass());
- }
-
- alias.setWidth(alias.getWidth() + AbstractCellDesignerAliasConverter.HOMODIMER_OFFSET * (homodir - 1));
- alias.setHeight(alias.getHeight() + AbstractCellDesignerAliasConverter.HOMODIMER_OFFSET * (homodir - 1));
- }
- return result;
- }
-
- @Override
- public PathIterator getBoundPathIterator(Protein alias) {
- if (alias instanceof GenericProtein) {
- return getGenericShape(alias).getPathIterator(new AffineTransform());
- } else if (alias instanceof ReceptorProtein) {
- return getReceptorShape(alias).getPathIterator(new AffineTransform());
- } else if (alias instanceof IonChannelProtein) {
- return getGenericShape(alias).getPathIterator(new AffineTransform());
- } else if (alias instanceof TruncatedProtein) {
- return getTruncatedShape(alias).getPathIterator(new AffineTransform());
- } else {
- throw new NotImplementedException(eu.getElementTag(alias) + "Not implemented protein converter for type: " + alias.getClass());
- }
- }
-
- /**
- * Returns shape of generic protein.
- *
- * @param alias
- * alias for which we are looking for a border
- * @return Shape object defining given alias
- */
- private Shape getGenericShape(Element alias) {
- return new RoundRectangle2D.Double(
- alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), GENERIC_PROTEIN_RECTANGLE_CORNER_ARC_SIZE, GENERIC_PROTEIN_RECTANGLE_CORNER_ARC_SIZE);
- }
-
- /**
- * Returns shape of the Truncated protein as a list of points.
- *
- * @param alias
- * alias for which we are looking for a border
- * @return list of points defining border of the given alias
- */
- private ArrayList<Point2D> getTruncatedPoints(Element alias) {
- double x = alias.getX();
- double y = alias.getY();
- double width = alias.getWidth();
- double height = alias.getHeight();
- ArrayList<Point2D> points = new ArrayList<Point2D>();
- // CHECKSTYLE:OFF
- points.add(new Point2D.Double(x, y + height / 2));
- points.add(new Point2D.Double(x, y + height / 4));
- points.add(new Point2D.Double(x, y));
- points.add(new Point2D.Double(x + width / 4, y));
- points.add(new Point2D.Double(x + width / 2, y));
- points.add(new Point2D.Double(x + width * 3 / 4, y));
- points.add(new Point2D.Double(x + width, y));
- points.add(new Point2D.Double(x + width, y + height * 3 / 10));
- points.add(new Point2D.Double(x + width, y + height * 3 / 5));
- points.add(new Point2D.Double(x + width * 4 / 5, y + height * 2 / 5));
- points.add(new Point2D.Double(x + width * 4 / 5, y + height * 7 / 10));
- points.add(new Point2D.Double(x + width * 4 / 5, y + height));
- points.add(new Point2D.Double(x + width / 2, y + height));
- points.add(new Point2D.Double(x + width / 4, y + height));
- points.add(new Point2D.Double(x, y + height));
- points.add(new Point2D.Double(x, y + height * 3 / 4));
-
- // CHECKSTYLE:ON
-
- return points;
- }
-
- /**
- * Returns shape of receptor protein.
- *
- * @param alias
- * alias for which we are looking for a border
- * @return Shape object defining given alias
- */
- protected Shape getReceptorShape(Element alias) {
- Shape shape;
- GeneralPath path = new GeneralPath(GeneralPath.WIND_EVEN_ODD);
- ArrayList<Point2D> points = getReceptorPoints(alias);
- path.moveTo(points.get(0).getX(), points.get(0).getY());
- for (int i = 1; i < points.size(); i++) {
- path.lineTo(points.get(i).getX(), points.get(i).getY());
- }
- path.closePath();
- shape = path;
- return shape;
- }
-
- /**
- * Returns shape of truncated protein.
- *
- * @param alias
- * alias for which we are looking for a border
- * @return Shape object defining given alias
- */
- protected Shape getTruncatedShape(Element alias) {
- Shape shape;
- GeneralPath path = new GeneralPath();
-
- // CHECKSTYLE:OFF
- path.moveTo(alias.getX() + 10, alias.getY());
- path.lineTo(alias.getX() + alias.getWidth(), alias.getY());
- path.lineTo(alias.getX() + alias.getWidth(), alias.getY() + alias.getHeight() * 3 / 5);
- path.lineTo(alias.getX() + alias.getWidth() * 4 / 5, alias.getY() + alias.getHeight() * 2 / 5);
- path.lineTo(alias.getX() + alias.getWidth() * 4 / 5, alias.getY() + alias.getHeight());
- path.lineTo(alias.getX() + 10, alias.getY() + alias.getHeight());
- path.curveTo(
- alias.getX() + 5, alias.getY() + alias.getHeight() - 2, alias.getX() + 2, alias.getY() + alias.getHeight() - 5, alias.getX(),
- alias.getY() + alias.getHeight() - 10);
- path.lineTo(alias.getX(), alias.getY() + 10);
- path.curveTo(alias.getX() + 2, alias.getY() + 5, alias.getX() + 5, alias.getY() + 2, alias.getX() + 10, alias.getY());
-
- // CHECKSTYLE:ON
-
- path.closePath();
- shape = path;
- return shape;
- }
-
- /**
- * Returns shape of receptor protein as a list of points.
- *
- * @param alias
- * alias for which we are looking for a border
- * @return list of points defining border of the given alias
- */
- private ArrayList<Point2D> getReceptorPoints(Element alias) {
- double x = alias.getX();
- double y = alias.getY();
- double width = alias.getWidth();
- double height = alias.getHeight();
- ArrayList<Point2D> points = new ArrayList<Point2D>();
-
- // CHECKSTYLE:OFF
- points.add(new Point2D.Double(x, y + height * 2 / 5));
- points.add(new Point2D.Double(x, y));
- points.add(new Point2D.Double(x + width / 2, y + height / 5));
- points.add(new Point2D.Double(x + width, y));
- points.add(new Point2D.Double(x + width, y + height * 2 / 5));
- points.add(new Point2D.Double(x + width, y + height * 4 / 5));
- points.add(new Point2D.Double(x + width / 2, y + height));
- points.add(new Point2D.Double(x, y + height * 4 / 5));
- // CHECKSTYLE:ON
-
- return points;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import java.awt.Shape;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+import java.awt.geom.RoundRectangle2D;
+import java.util.ArrayList;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.IonChannelProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.ReceptorProtein;
+import lcsb.mapviewer.model.map.species.TruncatedProtein;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
+
+/**
+ * Class that provides CellDesigner specific graphical information for Protein.
+ * It's used for conversion from xml to normal x,y coordinates.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ProteinCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<Protein> {
+
+ /**
+ * Default constructor.
+ *
+ * @param sbgn
+ * Should the converter use sbgn standard
+ */
+ protected ProteinCellDesignerAliasConverter(boolean sbgn) {
+ super(sbgn);
+ }
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(ProteinCellDesignerAliasConverter.class);
+
+ /**
+ * How big should be the arc in rectangle for generic protein representation.
+ */
+ private static final int GENERIC_PROTEIN_RECTANGLE_CORNER_ARC_SIZE = 10;
+
+ /**
+ * Helps in providing human readable identifiers of elements for logging.
+ */
+ private ElementUtils eu = new ElementUtils();
+
+ @Override
+ public Point2D getPointCoordinates(Protein alias, CellDesignerAnchor anchor) {
+ Point2D result = null;
+ if (invalidAnchorPosition(alias, anchor)) {
+ result = alias.getCenter();
+ } else {
+ int homodir = alias.getHomodimer();
+
+ alias.setWidth(alias.getWidth() - AbstractCellDesignerAliasConverter.HOMODIMER_OFFSET * (homodir - 1));
+ alias.setHeight(alias.getHeight() - AbstractCellDesignerAliasConverter.HOMODIMER_OFFSET * (homodir - 1));
+
+ if (alias instanceof GenericProtein) {
+ result = getRectangleTransformation().getPointOnRectangleByAnchor(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), anchor);
+ } else if (alias instanceof ReceptorProtein) {
+ ArrayList<Point2D> points = getReceptorPoints(alias);
+ result = getPolygonTransformation().getPointOnPolygonByAnchor(points, anchor);
+ } else if (alias instanceof IonChannelProtein) {
+ result = getRectangleTransformation().getPointOnRectangleByAnchor(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), anchor);
+ } else if (alias instanceof TruncatedProtein) {
+ ArrayList<Point2D> points = getTruncatedPoints(alias);
+ result = getPolygonTransformation().getPointOnPolygonByAnchor(points, anchor);
+ } else {
+ throw new NotImplementedException(eu.getElementTag(alias) + "Unknown type: " + alias.getClass());
+ }
+
+ alias.setWidth(alias.getWidth() + AbstractCellDesignerAliasConverter.HOMODIMER_OFFSET * (homodir - 1));
+ alias.setHeight(alias.getHeight() + AbstractCellDesignerAliasConverter.HOMODIMER_OFFSET * (homodir - 1));
+ }
+ return result;
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(Protein alias) {
+ if (alias instanceof GenericProtein) {
+ return getGenericShape(alias).getPathIterator(new AffineTransform());
+ } else if (alias instanceof ReceptorProtein) {
+ return getReceptorShape(alias).getPathIterator(new AffineTransform());
+ } else if (alias instanceof IonChannelProtein) {
+ return getGenericShape(alias).getPathIterator(new AffineTransform());
+ } else if (alias instanceof TruncatedProtein) {
+ return getTruncatedShape(alias).getPathIterator(new AffineTransform());
+ } else {
+ throw new NotImplementedException(eu.getElementTag(alias) + "Not implemented protein converter for type: " + alias.getClass());
+ }
+ }
+
+ /**
+ * Returns shape of generic protein.
+ *
+ * @param alias
+ * alias for which we are looking for a border
+ * @return Shape object defining given alias
+ */
+ private Shape getGenericShape(Element alias) {
+ return new RoundRectangle2D.Double(
+ alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight(), GENERIC_PROTEIN_RECTANGLE_CORNER_ARC_SIZE, GENERIC_PROTEIN_RECTANGLE_CORNER_ARC_SIZE);
+ }
+
+ /**
+ * Returns shape of the Truncated protein as a list of points.
+ *
+ * @param alias
+ * alias for which we are looking for a border
+ * @return list of points defining border of the given alias
+ */
+ private ArrayList<Point2D> getTruncatedPoints(Element alias) {
+ double x = alias.getX();
+ double y = alias.getY();
+ double width = alias.getWidth();
+ double height = alias.getHeight();
+ ArrayList<Point2D> points = new ArrayList<Point2D>();
+ // CHECKSTYLE:OFF
+ points.add(new Point2D.Double(x, y + height / 2));
+ points.add(new Point2D.Double(x, y + height / 4));
+ points.add(new Point2D.Double(x, y));
+ points.add(new Point2D.Double(x + width / 4, y));
+ points.add(new Point2D.Double(x + width / 2, y));
+ points.add(new Point2D.Double(x + width * 3 / 4, y));
+ points.add(new Point2D.Double(x + width, y));
+ points.add(new Point2D.Double(x + width, y + height * 3 / 10));
+ points.add(new Point2D.Double(x + width, y + height * 3 / 5));
+ points.add(new Point2D.Double(x + width * 4 / 5, y + height * 2 / 5));
+ points.add(new Point2D.Double(x + width * 4 / 5, y + height * 7 / 10));
+ points.add(new Point2D.Double(x + width * 4 / 5, y + height));
+ points.add(new Point2D.Double(x + width / 2, y + height));
+ points.add(new Point2D.Double(x + width / 4, y + height));
+ points.add(new Point2D.Double(x, y + height));
+ points.add(new Point2D.Double(x, y + height * 3 / 4));
+
+ // CHECKSTYLE:ON
+
+ return points;
+ }
+
+ /**
+ * Returns shape of receptor protein.
+ *
+ * @param alias
+ * alias for which we are looking for a border
+ * @return Shape object defining given alias
+ */
+ protected Shape getReceptorShape(Element alias) {
+ Shape shape;
+ GeneralPath path = new GeneralPath(GeneralPath.WIND_EVEN_ODD);
+ ArrayList<Point2D> points = getReceptorPoints(alias);
+ path.moveTo(points.get(0).getX(), points.get(0).getY());
+ for (int i = 1; i < points.size(); i++) {
+ path.lineTo(points.get(i).getX(), points.get(i).getY());
+ }
+ path.closePath();
+ shape = path;
+ return shape;
+ }
+
+ /**
+ * Returns shape of truncated protein.
+ *
+ * @param alias
+ * alias for which we are looking for a border
+ * @return Shape object defining given alias
+ */
+ protected Shape getTruncatedShape(Element alias) {
+ Shape shape;
+ GeneralPath path = new GeneralPath();
+
+ // CHECKSTYLE:OFF
+ path.moveTo(alias.getX() + 10, alias.getY());
+ path.lineTo(alias.getX() + alias.getWidth(), alias.getY());
+ path.lineTo(alias.getX() + alias.getWidth(), alias.getY() + alias.getHeight() * 3 / 5);
+ path.lineTo(alias.getX() + alias.getWidth() * 4 / 5, alias.getY() + alias.getHeight() * 2 / 5);
+ path.lineTo(alias.getX() + alias.getWidth() * 4 / 5, alias.getY() + alias.getHeight());
+ path.lineTo(alias.getX() + 10, alias.getY() + alias.getHeight());
+ path.curveTo(
+ alias.getX() + 5, alias.getY() + alias.getHeight() - 2, alias.getX() + 2, alias.getY() + alias.getHeight() - 5, alias.getX(),
+ alias.getY() + alias.getHeight() - 10);
+ path.lineTo(alias.getX(), alias.getY() + 10);
+ path.curveTo(alias.getX() + 2, alias.getY() + 5, alias.getX() + 5, alias.getY() + 2, alias.getX() + 10, alias.getY());
+
+ // CHECKSTYLE:ON
+
+ path.closePath();
+ shape = path;
+ return shape;
+ }
+
+ /**
+ * Returns shape of receptor protein as a list of points.
+ *
+ * @param alias
+ * alias for which we are looking for a border
+ * @return list of points defining border of the given alias
+ */
+ private ArrayList<Point2D> getReceptorPoints(Element alias) {
+ double x = alias.getX();
+ double y = alias.getY();
+ double width = alias.getWidth();
+ double height = alias.getHeight();
+ ArrayList<Point2D> points = new ArrayList<Point2D>();
+
+ // CHECKSTYLE:OFF
+ points.add(new Point2D.Double(x, y + height * 2 / 5));
+ points.add(new Point2D.Double(x, y));
+ points.add(new Point2D.Double(x + width / 2, y + height / 5));
+ points.add(new Point2D.Double(x + width, y));
+ points.add(new Point2D.Double(x + width, y + height * 2 / 5));
+ points.add(new Point2D.Double(x + width, y + height * 4 / 5));
+ points.add(new Point2D.Double(x + width / 2, y + height));
+ points.add(new Point2D.Double(x, y + height * 4 / 5));
+ // CHECKSTYLE:ON
+
+ return points;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ReactionCellDesignerConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ReactionCellDesignerConverter.java
index 7598f7d255..64592dd9c0 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ReactionCellDesignerConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ReactionCellDesignerConverter.java
@@ -1,23 +1,23 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-/**
- * Class that provides CellDesigner specific graphical information for Reaction.
- * It's used for conversion from xml to normal x,y coordinates.
- *
- * @author Piotr Gawron
- *
- */
-public final class ReactionCellDesignerConverter {
- /**
- * What is the size of rectangle that is drawn in center point of the
- * reaction.
- */
- public static final double RECT_SIZE = 10;
-
- /**
- * Default constructor that prevents instatiation.
- */
- protected ReactionCellDesignerConverter() {
-
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+/**
+ * Class that provides CellDesigner specific graphical information for Reaction.
+ * It's used for conversion from xml to normal x,y coordinates.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public final class ReactionCellDesignerConverter {
+ /**
+ * What is the size of rectangle that is drawn in center point of the
+ * reaction.
+ */
+ public static final double RECT_SIZE = 10;
+
+ /**
+ * Default constructor that prevents instatiation.
+ */
+ protected ReactionCellDesignerConverter() {
+
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/SimpleMoleculeCellDesignerAliasConverter.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/SimpleMoleculeCellDesignerAliasConverter.java
index 20a2e974e2..4f5e3a7bb3 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/SimpleMoleculeCellDesignerAliasConverter.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/SimpleMoleculeCellDesignerAliasConverter.java
@@ -1,84 +1,84 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
-
-/**
- * Class that provides CellDesigner specific graphical information for
- * SimpleMolecule. It's used for conversion from xml to normal x,y coordinates.
- *
- * @author Piotr Gawron
- *
- */
-public class SimpleMoleculeCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<SimpleMolecule> {
-
- Logger logger = Logger.getLogger(SimpleMoleculeCellDesignerAliasConverter.class);
-
- /**
- * Default constructor.
- *
- * @param sbgn
- * Should the converter use sbgn standard
- */
- protected SimpleMoleculeCellDesignerAliasConverter(boolean sbgn) {
- super(sbgn);
- }
-
- @Override
- public Point2D getPointCoordinates(SimpleMolecule alias, CellDesignerAnchor anchor) {
- double x = alias.getX();
- double y = alias.getY();
- double width = Math.max(alias.getWidth(), 1);
- double height = Math.max(alias.getHeight(), 1);
- if (invalidAnchorPosition(alias, anchor)) {
- return alias.getCenter();
- }
- if (isSbgn()) {
- return getEllipseTransformation().getPointOnEllipseByAnchor(x + (width - height) / 2, y, height, height, anchor);
- }
- return getEllipseTransformation().getPointOnEllipseByAnchor(x, y, width, height, anchor);
- }
-
- @Override
- public Point2D getAnchorPointCoordinates(SimpleMolecule alias, double angle) {
- if (alias.getWidth().equals(0.0) && alias.getHeight().equals(0.0)) {
- return alias.getCenter();
- }
- Point2D result;
- if (!isSbgn()) {
- result = getEllipseTransformation().getPointOnEllipseByRadian(alias.getX(), alias.getY(), alias.getWidth(),
- alias.getHeight(), angle);
- } else {
- result = getEllipseTransformation().getPointOnEllipseByRadian(
- alias.getX() + (alias.getWidth() - alias.getHeight()) / 2, alias.getY(), alias.getHeight(), alias.getHeight(),
- angle);
- }
- return result;
-
- }
-
- @Override
- public PathIterator getBoundPathIterator(SimpleMolecule alias) {
- throw new NotImplementedException("This class doesn't provide boundPath");
- }
-
- @Override
- public Point2D getPointCoordinatesOnBorder(final SimpleMolecule simpleMolecule, final double angle) {
- if (simpleMolecule.getWidth() == 0 && simpleMolecule.getHeight() == 0) {
- logger.warn("Looking for coordinates on border of alias of size 0");
- return simpleMolecule.getCenter();
- }
- Point2D result;
- result = getEllipseTransformation().getPointOnEllipseByRadian(simpleMolecule.getX(), simpleMolecule.getY(),
- simpleMolecule.getWidth(), simpleMolecule.getHeight(), angle);
- return result;
-
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+
+/**
+ * Class that provides CellDesigner specific graphical information for
+ * SimpleMolecule. It's used for conversion from xml to normal x,y coordinates.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class SimpleMoleculeCellDesignerAliasConverter extends AbstractCellDesignerAliasConverter<SimpleMolecule> {
+
+ Logger logger = Logger.getLogger(SimpleMoleculeCellDesignerAliasConverter.class);
+
+ /**
+ * Default constructor.
+ *
+ * @param sbgn
+ * Should the converter use sbgn standard
+ */
+ protected SimpleMoleculeCellDesignerAliasConverter(boolean sbgn) {
+ super(sbgn);
+ }
+
+ @Override
+ public Point2D getPointCoordinates(SimpleMolecule alias, CellDesignerAnchor anchor) {
+ double x = alias.getX();
+ double y = alias.getY();
+ double width = Math.max(alias.getWidth(), 1);
+ double height = Math.max(alias.getHeight(), 1);
+ if (invalidAnchorPosition(alias, anchor)) {
+ return alias.getCenter();
+ }
+ if (isSbgn()) {
+ return getEllipseTransformation().getPointOnEllipseByAnchor(x + (width - height) / 2, y, height, height, anchor);
+ }
+ return getEllipseTransformation().getPointOnEllipseByAnchor(x, y, width, height, anchor);
+ }
+
+ @Override
+ public Point2D getAnchorPointCoordinates(SimpleMolecule alias, double angle) {
+ if (alias.getWidth().equals(0.0) && alias.getHeight().equals(0.0)) {
+ return alias.getCenter();
+ }
+ Point2D result;
+ if (!isSbgn()) {
+ result = getEllipseTransformation().getPointOnEllipseByRadian(alias.getX(), alias.getY(), alias.getWidth(),
+ alias.getHeight(), angle);
+ } else {
+ result = getEllipseTransformation().getPointOnEllipseByRadian(
+ alias.getX() + (alias.getWidth() - alias.getHeight()) / 2, alias.getY(), alias.getHeight(), alias.getHeight(),
+ angle);
+ }
+ return result;
+
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(SimpleMolecule alias) {
+ throw new NotImplementedException("This class doesn't provide boundPath");
+ }
+
+ @Override
+ public Point2D getPointCoordinatesOnBorder(final SimpleMolecule simpleMolecule, final double angle) {
+ if (simpleMolecule.getWidth() == 0 && simpleMolecule.getHeight() == 0) {
+ logger.warn("Looking for coordinates on border of alias of size 0");
+ return simpleMolecule.getCenter();
+ }
+ Point2D result;
+ result = getEllipseTransformation().getPointOnEllipseByRadian(simpleMolecule.getX(), simpleMolecule.getY(),
+ simpleMolecule.getWidth(), simpleMolecule.getHeight(), angle);
+ return result;
+
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerAnchor.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerAnchor.java
index 5f5cc426d4..6e84905d3d 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerAnchor.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerAnchor.java
@@ -1,145 +1,145 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
-
-/**
- * List of all possible anchor values in CellDesigner. It starts in the east
- * anchor (center; max to the right point). Next anchors are listed in clockwise
- * order.
- *
- * @author Piotr Gawron
- *
- */
-public enum CellDesignerAnchor {
-
- /**
- * East direction.
- */
- E("E", 0.0), //
-
- /**
- * East southeast direction.
- */
- ESE("ESE", 22.5), //
-
- /**
- * Southeast direction.
- */
- SE("SE", 45.0), //
-
- /**
- * South southeast direction.
- */
- SSE("SSE", 67.5), //
-
- /**
- * South direction.
- */
- S("S", 90.0), //
-
- /**
- * South southwest direction.
- */
- SSW("SSW", 112.5), //
-
- /**
- * Southwest direction.
- */
- SW("SW", 135.0), //
-
- /**
- * West southwest direction.
- */
- WSW("WSW", 157.5), //
-
- /**
- * West direction.
- */
- W("W", 180.0), //
-
- /**
- * West northwest direction.
- */
- WNW("WNW", 202.5), //
-
- /**
- * Northwest direction.
- */
- NW("NW", 225.0), //
-
- /**
- * North northwest direction.
- */
- NNW("NNW", 247.5), //
-
- /**
- * North direction.
- */
- N("N", 270.0), //
-
- /**
- * North northeast direction.
- */
- NNE("NNE", 292.5), //
-
- /**
- * Northeast direction.
- */
- NE("NE", 315.0), //
-
- /**
- * East northeast direction.
- */
- ENE("ENE", 337.5), //
-
- /**
- * Unknown direction.
- */
- INACTIVE("INACTIVE", null); // UNDOCUMENTED
-
- /**
- * We have this number of different valid anchors in CellDesigner.
- */
- static final int DIFFERENT_ANCHORS = 16;
-
- /**
- * Name of the anchor.
- */
- private String name;
-
- /**
- * Angle (in radians) on the border where the ancor is localized.
- */
- private Double angle;
-
- /**
- * Default constructor with name and angle value.
- *
- * @param name
- * name of the anchor
- * @param angleDegrees
- * angle (in degrees) on the border where the ancor is localized
- */
- CellDesignerAnchor(String name, Double angleDegrees) {
- this.name = name;
- if (angleDegrees == null) {
- this.angle = null;
- } else {
- this.angle = Math.toRadians(angleDegrees);
- }
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @return the angle
- * @see #angle
- */
- public Double getAngle() {
- return angle;
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
+
+/**
+ * List of all possible anchor values in CellDesigner. It starts in the east
+ * anchor (center; max to the right point). Next anchors are listed in clockwise
+ * order.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum CellDesignerAnchor {
+
+ /**
+ * East direction.
+ */
+ E("E", 0.0), //
+
+ /**
+ * East southeast direction.
+ */
+ ESE("ESE", 22.5), //
+
+ /**
+ * Southeast direction.
+ */
+ SE("SE", 45.0), //
+
+ /**
+ * South southeast direction.
+ */
+ SSE("SSE", 67.5), //
+
+ /**
+ * South direction.
+ */
+ S("S", 90.0), //
+
+ /**
+ * South southwest direction.
+ */
+ SSW("SSW", 112.5), //
+
+ /**
+ * Southwest direction.
+ */
+ SW("SW", 135.0), //
+
+ /**
+ * West southwest direction.
+ */
+ WSW("WSW", 157.5), //
+
+ /**
+ * West direction.
+ */
+ W("W", 180.0), //
+
+ /**
+ * West northwest direction.
+ */
+ WNW("WNW", 202.5), //
+
+ /**
+ * Northwest direction.
+ */
+ NW("NW", 225.0), //
+
+ /**
+ * North northwest direction.
+ */
+ NNW("NNW", 247.5), //
+
+ /**
+ * North direction.
+ */
+ N("N", 270.0), //
+
+ /**
+ * North northeast direction.
+ */
+ NNE("NNE", 292.5), //
+
+ /**
+ * Northeast direction.
+ */
+ NE("NE", 315.0), //
+
+ /**
+ * East northeast direction.
+ */
+ ENE("ENE", 337.5), //
+
+ /**
+ * Unknown direction.
+ */
+ INACTIVE("INACTIVE", null); // UNDOCUMENTED
+
+ /**
+ * We have this number of different valid anchors in CellDesigner.
+ */
+ static final int DIFFERENT_ANCHORS = 16;
+
+ /**
+ * Name of the anchor.
+ */
+ private String name;
+
+ /**
+ * Angle (in radians) on the border where the ancor is localized.
+ */
+ private Double angle;
+
+ /**
+ * Default constructor with name and angle value.
+ *
+ * @param name
+ * name of the anchor
+ * @param angleDegrees
+ * angle (in degrees) on the border where the ancor is localized
+ */
+ CellDesignerAnchor(String name, Double angleDegrees) {
+ this.name = name;
+ if (angleDegrees == null) {
+ this.angle = null;
+ } else {
+ this.angle = Math.toRadians(angleDegrees);
+ }
+ }
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @return the angle
+ * @see #angle
+ */
+ public Double getAngle() {
+ return angle;
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerEllipseTransformation.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerEllipseTransformation.java
index 5e560391d8..13b748f5c3 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerEllipseTransformation.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerEllipseTransformation.java
@@ -1,48 +1,48 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
-
-import java.awt.geom.Point2D;
-
-import lcsb.mapviewer.common.geometry.EllipseTransformation;
-
-import org.apache.log4j.Logger;
-
-/**
- * This class contains basic operators on ellipse used by CellDesigner
- * converters.
- *
- * @author Piotr Gawron
- *
- */
-public class CellDesignerEllipseTransformation extends EllipseTransformation {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(CellDesignerEllipseTransformation.class.getName());
-
- /**
- * Method returns a cross point between ellipse and a line (from center point
- * to the anchor point).
- *
- * @param x
- * x coordinate of the ellipse
- * @param y
- * y coordinate of the ellipse
- * @param width
- * width of the ellipse
- * @param height
- * height of the ellipse
- * @param anchor
- * anchor on ellipse where we look for the point
- * @return coordinates on the ellipse described by the anchor point
- */
- public Point2D getPointOnEllipseByAnchor(double x, double y, double width, double height, CellDesignerAnchor anchor) {
-
- if (anchor == null || anchor.getAngle() == null) {
- return new Point2D.Double(x + width / 2, y + height / 2);
- } else {
- double angle = anchor.getAngle();
- return new Point2D.Double(x + width / 2 + Math.cos(angle) * width / 2, y + height / 2 + Math.sin(angle) * height / 2);
- }
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
+
+import java.awt.geom.Point2D;
+
+import lcsb.mapviewer.common.geometry.EllipseTransformation;
+
+import org.apache.log4j.Logger;
+
+/**
+ * This class contains basic operators on ellipse used by CellDesigner
+ * converters.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CellDesignerEllipseTransformation extends EllipseTransformation {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(CellDesignerEllipseTransformation.class.getName());
+
+ /**
+ * Method returns a cross point between ellipse and a line (from center point
+ * to the anchor point).
+ *
+ * @param x
+ * x coordinate of the ellipse
+ * @param y
+ * y coordinate of the ellipse
+ * @param width
+ * width of the ellipse
+ * @param height
+ * height of the ellipse
+ * @param anchor
+ * anchor on ellipse where we look for the point
+ * @return coordinates on the ellipse described by the anchor point
+ */
+ public Point2D getPointOnEllipseByAnchor(double x, double y, double width, double height, CellDesignerAnchor anchor) {
+
+ if (anchor == null || anchor.getAngle() == null) {
+ return new Point2D.Double(x + width / 2, y + height / 2);
+ } else {
+ double angle = anchor.getAngle();
+ return new Point2D.Double(x + width / 2 + Math.cos(angle) * width / 2, y + height / 2 + Math.sin(angle) * height / 2);
+ }
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerLineTransformation.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerLineTransformation.java
index adee72bf94..0e7e2c69c4 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerLineTransformation.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerLineTransformation.java
@@ -1,135 +1,135 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
-
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.List;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.geometry.LineTransformation;
-import lcsb.mapviewer.common.geometry.PointTransformation;
-import lcsb.mapviewer.model.graphics.PolylineData;
-
-import org.apache.log4j.Logger;
-
-/**
- * Class with basic operations on lines with special functions for CellDesigner
- * format.
- *
- * @author Piotr Gawron
- *
- */
-public class CellDesignerLineTransformation extends LineTransformation {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(CellDesignerLineTransformation.class.getName());
-
- /**
- * Class used for transformations on {@link Point2D} class.
- */
- private static PointTransformation pt = new PointTransformation();
-
- /**
- * Transform data in CellDesigner format into typical x,y coordinates for all
- * points.
- *
- * CellDesigner format stores coordinates of a line in a different base. In
- * this base we have two points that define a base: vector between these
- * points is 1 unit in first coordinate, and orthogonal vector to the one
- * mentioned before is 1 unit in the second coordinate. Moreover, these two
- * points defining base belong to this line.
- *
- *
- * @param startPoint
- * first point defining CellDesigner base
- * @param endPoint
- * second point defining CellDesigner base
- * @param midPoints
- * points defining line
- * @return line in standard x,y format
- */
- public List<Point2D> getLinePointsFromPoints(final Point2D startPoint, final Point2D endPoint, final List<Point2D> midPoints) {
- if (!pt.isValidPoint(startPoint)) {
- throw new InvalidArgumentException("Invalid start point: " + startPoint);
- }
- if (!pt.isValidPoint(endPoint)) {
- throw new InvalidArgumentException("Invalid end point: " + endPoint);
- }
- List<Point2D> result = new ArrayList<Point2D>();
-
- double dx1 = endPoint.getX() - startPoint.getX();
- double dy1 = endPoint.getY() - startPoint.getY();
-
- double dx2 = -dy1;
- double dy2 = dx1;
-
- result.add(startPoint);
-
- if (midPoints != null) {
- for (Point2D p : midPoints) {
- if (!pt.isValidPoint(p)) {
- throw new InvalidArgumentException("Invalid point: " + p);
- }
- double x = startPoint.getX() + dx1 * p.getX() + dx2 * p.getY();
- double y = startPoint.getY() + dy1 * p.getX() + dy2 * p.getY();
- result.add(new Point2D.Double(x, y));
- }
- }
-
- result.add(endPoint);
- return result;
-
- }
-
- /**
- * Transform line of typical xy coordinates into coordinates used by
- * celldesigner.
- *
- * CellDesigner format stores coordinates of a line in a different base. In
- * this base we have two points that define a base: vector between these
- * points is 1 unit in first coordinate, and orthogonal vector to the one
- * mentioned before is 1 unit in the second coordinate. These two points are
- * the first and the last.
- *
- * @param line
- * line to be transformed into CellDesigner format
- * @return points of the line in CellDesigner format (without the first and
- * the last)
- */
- public List<Point2D> getPointsFromLine(final PolylineData line) {
- if (line == null) {
- throw new InvalidArgumentException("Line cannot be null.");
- }
- if (line.getPoints().size() < 2) {
- throw new InvalidArgumentException("Invalid line passed as an argument.");
- }
-
- double ax = line.getBeginPoint().getX();
- double ay = line.getBeginPoint().getY();
-
- double bx = line.getEndPoint().getX();
- double by = line.getEndPoint().getY();
-
- double dx = bx - ax;
- double dy = by - ay;
-
- List<Point2D> result = new ArrayList<Point2D>();
-
- if (dy * dy + dx * dx == 0) {
- throw new InvalidArgumentException("First and last point in the line must differ but found: " + line.getBeginPoint() + ", " + line.getEndPoint());
- }
-
- for (int i = 1; i < line.getPoints().size() - 1; i++) {
- double ox = line.getPoints().get(i).getX();
- double oy = line.getPoints().get(i).getY();
-
- double py = (dy * (ax - ox) + dx * (oy - ay)) / (dy * dy + dx * dx);
- double px = (dx * (ox - ax) + dy * (oy - ay)) / (dx * dx + dy * dy);
- result.add(new Point2D.Double(px, py));
- }
-
- return result;
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.List;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.geometry.LineTransformation;
+import lcsb.mapviewer.common.geometry.PointTransformation;
+import lcsb.mapviewer.model.graphics.PolylineData;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Class with basic operations on lines with special functions for CellDesigner
+ * format.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CellDesignerLineTransformation extends LineTransformation {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(CellDesignerLineTransformation.class.getName());
+
+ /**
+ * Class used for transformations on {@link Point2D} class.
+ */
+ private static PointTransformation pt = new PointTransformation();
+
+ /**
+ * Transform data in CellDesigner format into typical x,y coordinates for all
+ * points.
+ *
+ * CellDesigner format stores coordinates of a line in a different base. In
+ * this base we have two points that define a base: vector between these
+ * points is 1 unit in first coordinate, and orthogonal vector to the one
+ * mentioned before is 1 unit in the second coordinate. Moreover, these two
+ * points defining base belong to this line.
+ *
+ *
+ * @param startPoint
+ * first point defining CellDesigner base
+ * @param endPoint
+ * second point defining CellDesigner base
+ * @param midPoints
+ * points defining line
+ * @return line in standard x,y format
+ */
+ public List<Point2D> getLinePointsFromPoints(final Point2D startPoint, final Point2D endPoint, final List<Point2D> midPoints) {
+ if (!pt.isValidPoint(startPoint)) {
+ throw new InvalidArgumentException("Invalid start point: " + startPoint);
+ }
+ if (!pt.isValidPoint(endPoint)) {
+ throw new InvalidArgumentException("Invalid end point: " + endPoint);
+ }
+ List<Point2D> result = new ArrayList<Point2D>();
+
+ double dx1 = endPoint.getX() - startPoint.getX();
+ double dy1 = endPoint.getY() - startPoint.getY();
+
+ double dx2 = -dy1;
+ double dy2 = dx1;
+
+ result.add(startPoint);
+
+ if (midPoints != null) {
+ for (Point2D p : midPoints) {
+ if (!pt.isValidPoint(p)) {
+ throw new InvalidArgumentException("Invalid point: " + p);
+ }
+ double x = startPoint.getX() + dx1 * p.getX() + dx2 * p.getY();
+ double y = startPoint.getY() + dy1 * p.getX() + dy2 * p.getY();
+ result.add(new Point2D.Double(x, y));
+ }
+ }
+
+ result.add(endPoint);
+ return result;
+
+ }
+
+ /**
+ * Transform line of typical xy coordinates into coordinates used by
+ * celldesigner.
+ *
+ * CellDesigner format stores coordinates of a line in a different base. In
+ * this base we have two points that define a base: vector between these
+ * points is 1 unit in first coordinate, and orthogonal vector to the one
+ * mentioned before is 1 unit in the second coordinate. These two points are
+ * the first and the last.
+ *
+ * @param line
+ * line to be transformed into CellDesigner format
+ * @return points of the line in CellDesigner format (without the first and
+ * the last)
+ */
+ public List<Point2D> getPointsFromLine(final PolylineData line) {
+ if (line == null) {
+ throw new InvalidArgumentException("Line cannot be null.");
+ }
+ if (line.getPoints().size() < 2) {
+ throw new InvalidArgumentException("Invalid line passed as an argument.");
+ }
+
+ double ax = line.getBeginPoint().getX();
+ double ay = line.getBeginPoint().getY();
+
+ double bx = line.getEndPoint().getX();
+ double by = line.getEndPoint().getY();
+
+ double dx = bx - ax;
+ double dy = by - ay;
+
+ List<Point2D> result = new ArrayList<Point2D>();
+
+ if (dy * dy + dx * dx == 0) {
+ throw new InvalidArgumentException("First and last point in the line must differ but found: " + line.getBeginPoint() + ", " + line.getEndPoint());
+ }
+
+ for (int i = 1; i < line.getPoints().size() - 1; i++) {
+ double ox = line.getPoints().get(i).getX();
+ double oy = line.getPoints().get(i).getY();
+
+ double py = (dy * (ax - ox) + dx * (oy - ay)) / (dy * dy + dx * dx);
+ double px = (dx * (ox - ax) + dy * (oy - ay)) / (dx * dx + dy * dy);
+ result.add(new Point2D.Double(px, py));
+ }
+
+ return result;
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerPointTransformation.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerPointTransformation.java
index 856d37bb6c..4fb062a8dc 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerPointTransformation.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerPointTransformation.java
@@ -1,90 +1,90 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
-
-import java.awt.geom.Point2D;
-
-import lcsb.mapviewer.common.geometry.PointTransformation;
-
-import org.apache.log4j.Logger;
-
-/**
- * Class for basic point transformations.
- *
- * @author Piotr Gawron
- *
- */
-public class CellDesignerPointTransformation extends PointTransformation {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(CellDesignerPointTransformation.class.getName());
-
- /**
- * This method transform coordinates of pointP in celldesginer format (base:
- * pointA, pointB, pointC) into normal x,y coordinates.
- *
- * In CellDesigner some points are in different base consisted from three
- * points. In this base vector between pointA and pointC is 1 unit on X axis
- * (in normal world); and vector between pointB and pointC is 1 unit on Y
- * axis.
- *
- * @param pointA
- * central point of CellDesigner base
- * @param pointB
- * first point of CellDesigner base
- * @param pointC
- * second point of CellDesigner base
- * @param pointP
- * point to be transformed into normal coordinates
- * @return standard x,y coordinate
- */
- public Point2D getCoordinatesInNormalBase(final Point2D pointA, final Point2D pointB, final Point2D pointC, final Point2D pointP) {
- double dx1 = pointA.getX() - pointC.getX();
- double dy1 = pointA.getY() - pointC.getY();
-
- double dx2 = pointB.getX() - pointC.getX();
- double dy2 = pointB.getY() - pointC.getY();
-
- double x = pointC.getX() + dx1 * pointP.getX() + dx2 * pointP.getY();
- double y = pointC.getY() + dy1 * pointP.getX() + dy2 * pointP.getY();
-
- Point2D pointO = new Point2D.Double(x, y);
-
- return pointO;
- }
-
- /**
- * This method transform coordinates of pointP in x,y coordinates into
- * celldesginer format (base: pointA, pointB, pointC)
- *
- * In CellDesigner some points are in different base consisted from three
- * points. In this base vector between pointA and pointC is 1 unit on X axis
- * (in normal world); and vector between pointB and pointC is 1 unit on Y
- * axis.
- *
- * @param pointA
- * central point of CellDesigner base
- * @param pointB
- * first point of CellDesigner base
- * @param pointC
- * second point of CellDesigner base
- * @param pointO
- * point to be transformed
- * @return point in CellDesigner base
- */
- public Point2D getCoordinatesInCellDesignerBase(final Point2D pointA, final Point2D pointB, final Point2D pointC, final Point2D pointO) {
- double dx1 = pointA.getX() - pointC.getX();
- double dy1 = pointA.getY() - pointC.getY();
-
- double dx2 = pointB.getX() - pointC.getX();
- double dy2 = pointB.getY() - pointC.getY();
-
- double y = (dy1 * (pointO.getX() - pointC.getX()) + dx1 * (pointC.getY() - pointO.getY())) / (dx2 * dy1 - dx1 * dy2);
- double x = (dy2 * (pointC.getX() - pointO.getX()) + dx2 * (pointO.getY() - pointC.getY())) / (dx2 * dy1 - dx1 * dy2);
-
- Point2D pointP = new Point2D.Double(x, y);
-
- return pointP;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
+
+import java.awt.geom.Point2D;
+
+import lcsb.mapviewer.common.geometry.PointTransformation;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Class for basic point transformations.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CellDesignerPointTransformation extends PointTransformation {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(CellDesignerPointTransformation.class.getName());
+
+ /**
+ * This method transform coordinates of pointP in celldesginer format (base:
+ * pointA, pointB, pointC) into normal x,y coordinates.
+ *
+ * In CellDesigner some points are in different base consisted from three
+ * points. In this base vector between pointA and pointC is 1 unit on X axis
+ * (in normal world); and vector between pointB and pointC is 1 unit on Y
+ * axis.
+ *
+ * @param pointA
+ * central point of CellDesigner base
+ * @param pointB
+ * first point of CellDesigner base
+ * @param pointC
+ * second point of CellDesigner base
+ * @param pointP
+ * point to be transformed into normal coordinates
+ * @return standard x,y coordinate
+ */
+ public Point2D getCoordinatesInNormalBase(final Point2D pointA, final Point2D pointB, final Point2D pointC, final Point2D pointP) {
+ double dx1 = pointA.getX() - pointC.getX();
+ double dy1 = pointA.getY() - pointC.getY();
+
+ double dx2 = pointB.getX() - pointC.getX();
+ double dy2 = pointB.getY() - pointC.getY();
+
+ double x = pointC.getX() + dx1 * pointP.getX() + dx2 * pointP.getY();
+ double y = pointC.getY() + dy1 * pointP.getX() + dy2 * pointP.getY();
+
+ Point2D pointO = new Point2D.Double(x, y);
+
+ return pointO;
+ }
+
+ /**
+ * This method transform coordinates of pointP in x,y coordinates into
+ * celldesginer format (base: pointA, pointB, pointC)
+ *
+ * In CellDesigner some points are in different base consisted from three
+ * points. In this base vector between pointA and pointC is 1 unit on X axis
+ * (in normal world); and vector between pointB and pointC is 1 unit on Y
+ * axis.
+ *
+ * @param pointA
+ * central point of CellDesigner base
+ * @param pointB
+ * first point of CellDesigner base
+ * @param pointC
+ * second point of CellDesigner base
+ * @param pointO
+ * point to be transformed
+ * @return point in CellDesigner base
+ */
+ public Point2D getCoordinatesInCellDesignerBase(final Point2D pointA, final Point2D pointB, final Point2D pointC, final Point2D pointO) {
+ double dx1 = pointA.getX() - pointC.getX();
+ double dy1 = pointA.getY() - pointC.getY();
+
+ double dx2 = pointB.getX() - pointC.getX();
+ double dy2 = pointB.getY() - pointC.getY();
+
+ double y = (dy1 * (pointO.getX() - pointC.getX()) + dx1 * (pointC.getY() - pointO.getY())) / (dx2 * dy1 - dx1 * dy2);
+ double x = (dy2 * (pointC.getX() - pointO.getX()) + dx2 * (pointO.getY() - pointC.getY())) / (dx2 * dy1 - dx1 * dy2);
+
+ Point2D pointP = new Point2D.Double(x, y);
+
+ return pointP;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerPolygonTransformation.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerPolygonTransformation.java
index d59e780389..7236486ea5 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerPolygonTransformation.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerPolygonTransformation.java
@@ -1,110 +1,110 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
-
-import java.awt.geom.Point2D;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-
-/**
- * Class with basic operations on polygons.
- *
- * @author Piotr Gawron
- *
- */
-public class CellDesignerPolygonTransformation {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(CellDesignerPolygonTransformation.class.getName());
-
- /**
- * Returns a middle point between two points (using Euclidean distance).
- *
- * @param pointA
- * first coordinate
- * @param pointB
- * second coordinate
- * @return central point between pointA and pointB
- */
- private Point2D getMidPoint(Point2D pointA, Point2D pointB) {
- return new Point2D.Double((pointA.getX() + pointB.getX()) / 2, (pointA.getY() + pointB.getY()) / 2);
- }
-
- /**
- * Returns a point on polygon for the anchor given as a parameter.
- *
- * @param points
- * list of points which describes polygon. By default polygon can
- * contain only 8 or 16 points (all CellDesigner elements can be
- * drawn as such coordinates).
- * @param anchor
- * direction in which we look for coordinates
- * @return coordinates on the polygon described by the anchor point
- */
- public Point2D getPointOnPolygonByAnchor(List<Point2D> points, CellDesignerAnchor anchor) {
- if (points.size() == CellDesignerAnchor.DIFFERENT_ANCHORS / 2) {
- return getPointOn8NodesPolygonByAnchor(points, anchor);
- } else if (points.size() == CellDesignerAnchor.DIFFERENT_ANCHORS) {
- return getPointOn16NodesPolygonByAnchor(points, anchor);
- } else {
- throw new InvalidArgumentException("Invalid number of points: " + points.size());
- }
- }
-
- /**
- * Creates a copy of a point given as a parameter.
- *
- * @param point
- * object to copy
- * @return copy of the point parameter
- */
- private Point2D copyPoint(Point2D point) {
- return new Point2D.Double(point.getX(), point.getY());
- }
-
- /**
- * This method returns a point on the border defined by the list of 8 points
- * for a given anchor.
- *
- * @param points
- * list of 8 points that define a polygon
- * @param anchor
- * direction in which we are looking for a point
- * @return point on the border
- */
- private Point2D getPointOn8NodesPolygonByAnchor(List<Point2D> points, CellDesignerAnchor anchor) {
- if (anchor == null || anchor.getAngle() == null) {
- throw new InvalidArgumentException("Invalid anchor: " + anchor);
- } else {
- int position = (anchor.ordinal() + CellDesignerAnchor.DIFFERENT_ANCHORS / 2) % CellDesignerAnchor.DIFFERENT_ANCHORS;
- if (position % 2 == 0) {
- return copyPoint(points.get(position / 2));
- } else {
- return getMidPoint(points.get(position / 2), points.get((position / 2 + 1) % (CellDesignerAnchor.DIFFERENT_ANCHORS / 2)));
- }
- }
- }
-
- /**
- * This method returns a point on the border defined by the list of 16 points
- * for a given anchor.
- *
- * @param points
- * list of 16 points that define a polygon
- * @param anchor
- * direction in which we are looking for a point
- * @return point on the border
- */
- private Point2D getPointOn16NodesPolygonByAnchor(List<Point2D> points, CellDesignerAnchor anchor) {
- if (anchor == null || anchor.getAngle() == null) {
- throw new InvalidArgumentException("Invalid anchor: " + anchor);
- } else {
- int position = (anchor.ordinal() + CellDesignerAnchor.DIFFERENT_ANCHORS / 2) % CellDesignerAnchor.DIFFERENT_ANCHORS;
- return copyPoint(points.get(position));
- }
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
+
+import java.awt.geom.Point2D;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+
+/**
+ * Class with basic operations on polygons.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CellDesignerPolygonTransformation {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(CellDesignerPolygonTransformation.class.getName());
+
+ /**
+ * Returns a middle point between two points (using Euclidean distance).
+ *
+ * @param pointA
+ * first coordinate
+ * @param pointB
+ * second coordinate
+ * @return central point between pointA and pointB
+ */
+ private Point2D getMidPoint(Point2D pointA, Point2D pointB) {
+ return new Point2D.Double((pointA.getX() + pointB.getX()) / 2, (pointA.getY() + pointB.getY()) / 2);
+ }
+
+ /**
+ * Returns a point on polygon for the anchor given as a parameter.
+ *
+ * @param points
+ * list of points which describes polygon. By default polygon can
+ * contain only 8 or 16 points (all CellDesigner elements can be
+ * drawn as such coordinates).
+ * @param anchor
+ * direction in which we look for coordinates
+ * @return coordinates on the polygon described by the anchor point
+ */
+ public Point2D getPointOnPolygonByAnchor(List<Point2D> points, CellDesignerAnchor anchor) {
+ if (points.size() == CellDesignerAnchor.DIFFERENT_ANCHORS / 2) {
+ return getPointOn8NodesPolygonByAnchor(points, anchor);
+ } else if (points.size() == CellDesignerAnchor.DIFFERENT_ANCHORS) {
+ return getPointOn16NodesPolygonByAnchor(points, anchor);
+ } else {
+ throw new InvalidArgumentException("Invalid number of points: " + points.size());
+ }
+ }
+
+ /**
+ * Creates a copy of a point given as a parameter.
+ *
+ * @param point
+ * object to copy
+ * @return copy of the point parameter
+ */
+ private Point2D copyPoint(Point2D point) {
+ return new Point2D.Double(point.getX(), point.getY());
+ }
+
+ /**
+ * This method returns a point on the border defined by the list of 8 points
+ * for a given anchor.
+ *
+ * @param points
+ * list of 8 points that define a polygon
+ * @param anchor
+ * direction in which we are looking for a point
+ * @return point on the border
+ */
+ private Point2D getPointOn8NodesPolygonByAnchor(List<Point2D> points, CellDesignerAnchor anchor) {
+ if (anchor == null || anchor.getAngle() == null) {
+ throw new InvalidArgumentException("Invalid anchor: " + anchor);
+ } else {
+ int position = (anchor.ordinal() + CellDesignerAnchor.DIFFERENT_ANCHORS / 2) % CellDesignerAnchor.DIFFERENT_ANCHORS;
+ if (position % 2 == 0) {
+ return copyPoint(points.get(position / 2));
+ } else {
+ return getMidPoint(points.get(position / 2), points.get((position / 2 + 1) % (CellDesignerAnchor.DIFFERENT_ANCHORS / 2)));
+ }
+ }
+ }
+
+ /**
+ * This method returns a point on the border defined by the list of 16 points
+ * for a given anchor.
+ *
+ * @param points
+ * list of 16 points that define a polygon
+ * @param anchor
+ * direction in which we are looking for a point
+ * @return point on the border
+ */
+ private Point2D getPointOn16NodesPolygonByAnchor(List<Point2D> points, CellDesignerAnchor anchor) {
+ if (anchor == null || anchor.getAngle() == null) {
+ throw new InvalidArgumentException("Invalid anchor: " + anchor);
+ } else {
+ int position = (anchor.ordinal() + CellDesignerAnchor.DIFFERENT_ANCHORS / 2) % CellDesignerAnchor.DIFFERENT_ANCHORS;
+ return copyPoint(points.get(position));
+ }
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerRectangleTransformation.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerRectangleTransformation.java
index e6204f62a5..e19456989b 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerRectangleTransformation.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerRectangleTransformation.java
@@ -1,58 +1,58 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
-
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-
-import org.apache.log4j.Logger;
-
-/**
- * Class with basic operations on rectangles.
- *
- * @author Piotr Gawron
- *
- */
-public class CellDesignerRectangleTransformation {
-
- /**
- * Object used for transformation on the polygons.
- */
- private CellDesignerPolygonTransformation polygonTransformation = new CellDesignerPolygonTransformation();
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(CellDesignerRectangleTransformation.class.getName());
-
- /**
- * Returns a point on a rectangle for anchor.
- *
- * @param x
- * x coordinate of the rectangle
- * @param y
- * y coordinate of the rectangle
- * @param width
- * width of the rectangle
- * @param height
- * height of the rectangle
- * @param anchor
- * point where we are looking for the point
- * @return coordinates on the rectangle in direction described by anchor
- */
- public Point2D getPointOnRectangleByAnchor(double x, double y, double width, double height, CellDesignerAnchor anchor) {
- if (anchor == null || anchor.getAngle() == null) {
- return new Point2D.Double(x + width / 2, y + height / 2);
- }
- ArrayList<Point2D> list = new ArrayList<Point2D>();
- list.add(new Point2D.Double(x, y + height / 2));
- list.add(new Point2D.Double(x, y));
- list.add(new Point2D.Double(x + width / 2, y));
- list.add(new Point2D.Double(x + width, y));
- list.add(new Point2D.Double(x + width, y + height / 2));
- list.add(new Point2D.Double(x + width, y + height));
- list.add(new Point2D.Double(x + width / 2, y + height));
- list.add(new Point2D.Double(x, y + height));
- return polygonTransformation.getPointOnPolygonByAnchor(list, anchor);
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Class with basic operations on rectangles.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CellDesignerRectangleTransformation {
+
+ /**
+ * Object used for transformation on the polygons.
+ */
+ private CellDesignerPolygonTransformation polygonTransformation = new CellDesignerPolygonTransformation();
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(CellDesignerRectangleTransformation.class.getName());
+
+ /**
+ * Returns a point on a rectangle for anchor.
+ *
+ * @param x
+ * x coordinate of the rectangle
+ * @param y
+ * y coordinate of the rectangle
+ * @param width
+ * width of the rectangle
+ * @param height
+ * height of the rectangle
+ * @param anchor
+ * point where we are looking for the point
+ * @return coordinates on the rectangle in direction described by anchor
+ */
+ public Point2D getPointOnRectangleByAnchor(double x, double y, double width, double height, CellDesignerAnchor anchor) {
+ if (anchor == null || anchor.getAngle() == null) {
+ return new Point2D.Double(x + width / 2, y + height / 2);
+ }
+ ArrayList<Point2D> list = new ArrayList<Point2D>();
+ list.add(new Point2D.Double(x, y + height / 2));
+ list.add(new Point2D.Double(x, y));
+ list.add(new Point2D.Double(x + width / 2, y));
+ list.add(new Point2D.Double(x + width, y));
+ list.add(new Point2D.Double(x + width, y + height / 2));
+ list.add(new Point2D.Double(x + width, y + height));
+ list.add(new Point2D.Double(x + width / 2, y + height));
+ list.add(new Point2D.Double(x, y + height));
+ return polygonTransformation.getPointOnPolygonByAnchor(list, anchor);
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/PolylineDataFactory.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/PolylineDataFactory.java
index 64483cb31c..7eb77cb7f7 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/PolylineDataFactory.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/PolylineDataFactory.java
@@ -1,61 +1,61 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
-
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.List;
-
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints;
-import lcsb.mapviewer.model.graphics.PolylineData;
-
-/**
- * Facory util that creates {@link PolylineData} objects from CellDesigner
- * structure.
- *
- * @author Piotr Gawron
- *
- */
-public final class PolylineDataFactory {
-
- /**
- * Default constructore that prevent instantiation.
- */
- private PolylineDataFactory() {
- }
-
- /**
- * Creates {@link PolylineData} object from two CellDesigner base points and
- * list of points (in CellDesigner formet).
- *
- * @param baseA
- * first base point
- * @param baseB
- * second base point
- * @param points
- * intermediate points in CellDesigner format
- * @return {@link PolylineData} object representing input data
- */
- public static PolylineData createPolylineDataFromEditPoints(Point2D baseA, Point2D baseB, List<Point2D> points) {
- List<Point2D> pointsList = new CellDesignerLineTransformation().getLinePointsFromPoints(baseA, baseB, points);
- return new PolylineData(pointsList);
- }
-
- /**
- * Creates {@link PolylineData} object from two CellDesigner base points and
- * list of points (in CellDesigner formet).
- *
- * @param baseA
- * first base point
- * @param baseB
- * second base point
- * @param points
- * structure with intermediate points in CellDesigner format
- * @return {@link PolylineData} object representing input data
- */
- public static PolylineData createPolylineDataFromEditPoints(Point2D baseA, Point2D baseB, EditPoints points) {
- if (points != null) {
- return createPolylineDataFromEditPoints(baseA, baseB, points.getPoints());
- } else {
- return createPolylineDataFromEditPoints(baseA, baseB, new ArrayList<Point2D>());
- }
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.List;
+
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints;
+import lcsb.mapviewer.model.graphics.PolylineData;
+
+/**
+ * Facory util that creates {@link PolylineData} objects from CellDesigner
+ * structure.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public final class PolylineDataFactory {
+
+ /**
+ * Default constructore that prevent instantiation.
+ */
+ private PolylineDataFactory() {
+ }
+
+ /**
+ * Creates {@link PolylineData} object from two CellDesigner base points and
+ * list of points (in CellDesigner formet).
+ *
+ * @param baseA
+ * first base point
+ * @param baseB
+ * second base point
+ * @param points
+ * intermediate points in CellDesigner format
+ * @return {@link PolylineData} object representing input data
+ */
+ public static PolylineData createPolylineDataFromEditPoints(Point2D baseA, Point2D baseB, List<Point2D> points) {
+ List<Point2D> pointsList = new CellDesignerLineTransformation().getLinePointsFromPoints(baseA, baseB, points);
+ return new PolylineData(pointsList);
+ }
+
+ /**
+ * Creates {@link PolylineData} object from two CellDesigner base points and
+ * list of points (in CellDesigner formet).
+ *
+ * @param baseA
+ * first base point
+ * @param baseB
+ * second base point
+ * @param points
+ * structure with intermediate points in CellDesigner format
+ * @return {@link PolylineData} object representing input data
+ */
+ public static PolylineData createPolylineDataFromEditPoints(Point2D baseA, Point2D baseB, EditPoints points) {
+ if (points != null) {
+ return createPolylineDataFromEditPoints(baseA, baseB, points.getPoints());
+ } else {
+ return createPolylineDataFromEditPoints(baseA, baseB, new ArrayList<Point2D>());
+ }
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/package-info.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/package-info.java
index 53215dc750..b164954ded 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/package-info.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/package-info.java
@@ -1,6 +1,6 @@
-/**
- * Provides classes that helps to transform geometry structures in CellDesigner
- * into more intuitive structures.
- */
-package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
-
+/**
+ * Provides classes that helps to transform geometry structures in CellDesigner
+ * into more intuitive structures.
+ */
+package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
+
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/package-info.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/package-info.java
index b595b6e5c2..7ac605eb0d 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/package-info.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/package-info.java
@@ -1,6 +1,6 @@
-/**
- * Provides classes that transform geometry information from CellDesigner
- * objects into normal x,y coordinates in our model.
- */
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
+/**
+ * Provides classes that transform geometry information from CellDesigner
+ * objects into normal x,y coordinates in our model.
+ */
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/package-info.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/package-info.java
index e29dde072b..89e84c422f 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/package-info.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/package-info.java
@@ -1,8 +1,8 @@
-/**
- * This package contains converter from CellDesigner xml fromat into our Model.
- * Take a look at the class
- * {@link lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser
- * CellDesignerXmlParser} to see how it works.
- */
-package lcsb.mapviewer.converter.model.celldesigner;
-
+/**
+ * This package contains converter from CellDesigner xml fromat into our Model.
+ * Take a look at the class
+ * {@link lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser
+ * CellDesignerXmlParser} to see how it works.
+ */
+package lcsb.mapviewer.converter.model.celldesigner;
+
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParser.java
index cb8166ffe7..2f06de27b1 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParser.java
@@ -1,113 +1,113 @@
-package lcsb.mapviewer.converter.model.celldesigner.reaction;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import lcsb.mapviewer.common.XmlParser;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.ConverterException;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerParserException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
-import lcsb.mapviewer.model.map.InconsistentModelException;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * Parser used for extracting collections of reaction from CellDesigner xml.
- *
- * @author Piotr Gawron
- *
- */
-public class ReactionCollectionXmlParser extends XmlParser {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(ReactionCollectionXmlParser.class.getName());
-
- /**
- * Model for which parsing (or transformation to xml) is being done.
- */
- private Model model = null;
-
- /**
- * Object used for parsing single reaction.
- */
- private ReactionXmlParser xmlStructureFactory;
-
- /**
- * Default constructor. Model is required because some nodes require access to
- * other parts of the model.
- *
- * @param sbgn
- * should sbgn standard be used
- * @param elements
- * collection of {@link CellDesignerElement cell designer elements}
- * parsed from xml
- * @param model
- * model that is parsed/transformed into xml
- */
- public ReactionCollectionXmlParser(Model model, CellDesignerElementCollection elements, boolean sbgn) {
- this.model = model;
- xmlStructureFactory = new ReactionXmlParser(elements, sbgn);
- }
-
- /**
- * Parse CellDesigner xml node with set of reactions into list of
- * {@link Reaction}.
- *
- * @param reactionsNode
- * xml node
- * @return list of reaction taken from xml node
- * @throws CellDesignerParserException
- * thrown when there is a problem with xml node
- * @throws InvalidXmlSchemaException
- * thrown when reactionsNode is invalid xml
- */
- public List<Reaction> parseXmlReactionCollection(Node reactionsNode) throws CellDesignerParserException, InvalidXmlSchemaException {
- List<Reaction> result = new ArrayList<Reaction>();
- NodeList nodes = reactionsNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("reaction")) {
- Reaction reaction = xmlStructureFactory.getReaction(node, model);
- result.add(reaction);
- } else {
- throw new InvalidXmlSchemaException("Unknown element of model/listOfReactions: " + node.getNodeName());
- }
- }
- }
-
- return result;
- }
-
- /**
- * Transforms set of reactions into CellDesigner xml string.
- *
- * @param collection
- * set of reactions
- * @return CellDesigner xml string representing set of reactions
- * @throws ConverterException
- */
- public String reactionCollectionToXmlString(Collection<Reaction> collection) throws InconsistentModelException {
- String result = "";
- result += "<listOfReactions>\n";
- for (Reaction reaction : collection) {
- try {
- result += xmlStructureFactory.toXml(reaction);
- } catch (SelfReactionException e) {
- logger.warn("Reaction omitted: " + e.getMessage());
- }
- }
- result += "</listOfReactions>\n";
- return result;
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.reaction;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerParserException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * Parser used for extracting collections of reaction from CellDesigner xml.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ReactionCollectionXmlParser extends XmlParser {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(ReactionCollectionXmlParser.class.getName());
+
+ /**
+ * Model for which parsing (or transformation to xml) is being done.
+ */
+ private Model model = null;
+
+ /**
+ * Object used for parsing single reaction.
+ */
+ private ReactionXmlParser xmlStructureFactory;
+
+ /**
+ * Default constructor. Model is required because some nodes require access to
+ * other parts of the model.
+ *
+ * @param sbgn
+ * should sbgn standard be used
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
+ * @param model
+ * model that is parsed/transformed into xml
+ */
+ public ReactionCollectionXmlParser(Model model, CellDesignerElementCollection elements, boolean sbgn) {
+ this.model = model;
+ xmlStructureFactory = new ReactionXmlParser(elements, sbgn);
+ }
+
+ /**
+ * Parse CellDesigner xml node with set of reactions into list of
+ * {@link Reaction}.
+ *
+ * @param reactionsNode
+ * xml node
+ * @return list of reaction taken from xml node
+ * @throws CellDesignerParserException
+ * thrown when there is a problem with xml node
+ * @throws InvalidXmlSchemaException
+ * thrown when reactionsNode is invalid xml
+ */
+ public List<Reaction> parseXmlReactionCollection(Node reactionsNode) throws CellDesignerParserException, InvalidXmlSchemaException {
+ List<Reaction> result = new ArrayList<Reaction>();
+ NodeList nodes = reactionsNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("reaction")) {
+ Reaction reaction = xmlStructureFactory.getReaction(node, model);
+ result.add(reaction);
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of model/listOfReactions: " + node.getNodeName());
+ }
+ }
+ }
+
+ return result;
+ }
+
+ /**
+ * Transforms set of reactions into CellDesigner xml string.
+ *
+ * @param collection
+ * set of reactions
+ * @return CellDesigner xml string representing set of reactions
+ * @throws ConverterException
+ */
+ public String reactionCollectionToXmlString(Collection<Reaction> collection) throws InconsistentModelException {
+ String result = "";
+ result += "<listOfReactions>\n";
+ for (Reaction reaction : collection) {
+ try {
+ result += xmlStructureFactory.toXml(reaction);
+ } catch (SelfReactionException e) {
+ logger.warn("Reaction omitted: " + e.getMessage());
+ }
+ }
+ result += "</listOfReactions>\n";
+ return result;
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
index 1552eea16f..7cdc91e067 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
@@ -1,1760 +1,1760 @@
-package lcsb.mapviewer.converter.model.celldesigner.reaction;
-
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.LinkedHashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import lcsb.mapviewer.common.XmlParser;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesignerConverter;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerPointTransformation;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.PolylineDataFactory;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.ConnectScheme;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.LineProperties;
-import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
-import lcsb.mapviewer.converter.model.celldesigner.types.ModifierTypeUtils;
-import lcsb.mapviewer.converter.model.celldesigner.types.OperatorType;
-import lcsb.mapviewer.converter.model.celldesigner.types.OperatorTypeUtils;
-import lcsb.mapviewer.model.graphics.ArrowType;
-import lcsb.mapviewer.model.graphics.ArrowTypeData;
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.AbstractNode;
-import lcsb.mapviewer.model.map.reaction.AndOperator;
-import lcsb.mapviewer.model.map.reaction.AssociationOperator;
-import lcsb.mapviewer.model.map.reaction.DissociationOperator;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.reaction.NandOperator;
-import lcsb.mapviewer.model.map.reaction.NodeOperator;
-import lcsb.mapviewer.model.map.reaction.OrOperator;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.ReactionNode;
-import lcsb.mapviewer.model.map.reaction.SplitOperator;
-import lcsb.mapviewer.model.map.reaction.TruncationOperator;
-import lcsb.mapviewer.model.map.reaction.UnknownOperator;
-import lcsb.mapviewer.model.map.reaction.type.BooleanLogicGateReaction;
-import lcsb.mapviewer.model.map.reaction.type.DissociationReaction;
-import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
-import lcsb.mapviewer.model.map.reaction.type.SimpleReactionInterface;
-import lcsb.mapviewer.model.map.reaction.type.TruncationReaction;
-import lcsb.mapviewer.model.map.reaction.type.TwoProductReactionInterface;
-import lcsb.mapviewer.model.map.reaction.type.TwoReactantReactionInterface;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * This is a part of {@link ReactionXmlParser} class functionality that allows
- * to read reaction from CellDesigner xml node.
- *
- * @author Piotr Gawron
- *
- */
-public class ReactionFromXml extends XmlParser {
-
- /**
- * Reactant lines in cell designer ends in the 2/5 of the center line.
- */
- private static final double REACTANT_END_RATIO = 0.4;
-
- /**
- * Product lines in cell designer starts in the 3/5 of the center line.
- */
- private static final double PRODUCT_START_RATIO = 0.6;
-
- /**
- * Stores information about {@link CellDesignerAnchor} for a node.
- */
- private Map<ReactionNode, CellDesignerAnchor> anchorsByNodes = new HashMap<>();
-
- /**
- * Stores information about operator type that should be used for a modifier
- * node.
- */
- private Map<ReactionNode, String> typeByModifier = new HashMap<>();
-
- /**
- * Stores information to which point on the central rectangle modifier should be
- * connected.
- */
- private Map<ReactionNode, String> lineTypeByModifier = new HashMap<>();
-
- /**
- * Stores information about list of points that create line describing modifier.
- */
- private Map<ReactionNode, List<Point2D>> pointsByModifier = new HashMap<>();
-
- /**
- * Helps to determine if the key Modifier should be treats as part of
- * NodeOperator (value in the map).
- */
- private Map<Modifier, Modifier> modifierParentOperator = new HashMap<>();
-
- /**
- * Identifies central line segment in {@link TwoProductReactionInterface} and
- * {@link TwoReactantReactionInterface} reactions.
- */
- private Map<ReactionNode, Integer> indexByComplexReaction = new HashMap<>();
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(ReactionXmlParser.class.getName());
-
- /**
- * Xml parser used for processing notes into structured data.
- */
- private RestAnnotationParser rap = new RestAnnotationParser();
-
- /**
- * Helper object used for manipulation on the point coordinates in CellDesigner
- * format.
- */
- private CellDesignerPointTransformation pointTransformation = new CellDesignerPointTransformation();
-
- /**
- * Should SBGN standard be used.
- */
- private boolean sbgn;
-
- CellDesignerElementCollection elements;
-
- /**
- * Default constructor.
- *
- * @param sbgn
- * Should the converter use SBGN standard
- */
- public ReactionFromXml(CellDesignerElementCollection elements, boolean sbgn) {
- this.elements = elements;
- this.sbgn = sbgn;
- }
-
- /**
- * Returns {@link Reaction} object from CellDesigner xml node.
- *
- * @param reactionNode
- * xml node
- * @param model
- * model where the reaction is placed
- * @return reaction from xml node
- * @throws ReactionParserException
- * thrown when the xml is invalid
- * @throws InvalidXmlSchemaException
- * thrown when reactionNode is invalid xml
- */
- public Reaction getReaction(Node reactionNode, Model model) throws ReactionParserException {
- Reaction result = new Reaction();
- // we ignore metaid - it's useless and obstruct data model
- // result.setMetaId(getNodeAttr("metaid", reactionNode));
- result.setIdReaction(getNodeAttr("id", reactionNode));
- result.setName(getNodeAttr("name", reactionNode));
- // by default this value is true...
- result.setReversible(!(getNodeAttr("reversible", reactionNode).equalsIgnoreCase("false")));
-
- NodeList nodes = reactionNode.getChildNodes();
- Node annotationNode = null;
- Node kineticsNode = null;
- Node reactantsNode = null;
- Node productsNode = null;
- Node modifiersNode = null;
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("annotation")) {
- annotationNode = node;
- } else if (node.getNodeName().equalsIgnoreCase("listOfReactants")) {
- reactantsNode = node;
- } else if (node.getNodeName().equalsIgnoreCase("listOfProducts")) {
- productsNode = node;
- } else if (node.getNodeName().equalsIgnoreCase("listOfModifiers")) {
- modifiersNode = node;
- } else if (node.getNodeName().equalsIgnoreCase("notes")) {
- rap.processNotes(rap.getNotes(node), result);
- } else if (node.getNodeName().equalsIgnoreCase("kineticLaw")) {
- kineticsNode = node;
- } else {
- throw new ReactionParserException("Unknown element of reaction: " + node.getNodeName(), result);
- }
- }
- }
- if (annotationNode != null) {
- result = parseReactionAnnotation(annotationNode, result, model);
- } else {
- throw new ReactionParserException("No annotation node in reaction", result);
- }
- Map<String, Element> elements = getSpeciesIdToElementMappingFromAnnotationNode(annotationNode, model);
- if (kineticsNode != null) {
- KineticsXmlParser kineticsParser = new KineticsXmlParser(model);
- try {
- result.setKinetics(kineticsParser.parseKinetics(kineticsNode, elements));
- } catch (InvalidXmlSchemaException e) {
- throw new ReactionParserException(result, e);
- }
- }
- assignStochiometry(result.getReactants(), reactantsNode, elements);
- assignStochiometry(result.getProducts(), productsNode, elements);
- assignStochiometry(result.getModifiers(), modifiersNode, elements);
-
- return result;
- }
-
- private void assignStochiometry(Collection<? extends ReactionNode> reactionNodes, Node nodes,
- Map<String, Element> speciesIdToElement) {
- if (nodes != null) {
- for (Node child : super.getNodes("speciesReference", nodes.getChildNodes())) {
- String param = super.getNodeAttr("stoichiometry", child);
- if (param != null && !param.isEmpty()) {
- Double stoichometry = Double.parseDouble(param);
- String speciesId = super.getNodeAttr("species", child);
- Element e = speciesIdToElement.get(speciesId);
- boolean assigned = false;
- for (ReactionNode reactionNode : reactionNodes) {
- if (reactionNode.getElement().equals(e)) {
- assigned = true;
- reactionNode.setStoichiometry(stoichometry);
- }
- }
- if (!assigned) {
- throw new InvalidStateException("Cannot assign stoichiometry for element: " + speciesId);
- }
- }
- }
- }
- }
-
- private Map<String, Element> getSpeciesIdToElementMappingFromAnnotationNode(Node annotationNode, Model model) {
- Map<String, Element> result = new HashMap<>();
-
- List<Node> elementNodes = new ArrayList<>();
- elementNodes.addAll(super.getAllNotNecessirellyDirectChild("celldesigner:baseReactant", annotationNode));
- elementNodes.addAll(super.getAllNotNecessirellyDirectChild("celldesigner:baseProduct", annotationNode));
- elementNodes.addAll(super.getAllNotNecessirellyDirectChild("celldesigner:linkTarget", annotationNode));
-
- for (Node node : elementNodes) {
- String speciesId = super.getNodeAttr("species", node);
- String aliasId = super.getNodeAttr("alias", node);
- addElementMapping(model, result, speciesId, aliasId);
- }
-
- for (Node node : super.getAllNotNecessirellyDirectChild("celldesigner:reactantLink", annotationNode)) {
- String speciesId = super.getNodeAttr("reactant", node);
- String aliasId = super.getNodeAttr("alias", node);
- addElementMapping(model, result, speciesId, aliasId);
- }
-
- for (Node node : super.getAllNotNecessirellyDirectChild("celldesigner:productLink", annotationNode)) {
- String speciesId = super.getNodeAttr("product", node);
- String aliasId = super.getNodeAttr("alias", node);
- addElementMapping(model, result, speciesId, aliasId);
- }
- for (Node node : super.getAllNotNecessirellyDirectChild("celldesigner:modification", annotationNode)) {
- String speciesId = super.getNodeAttr("modifiers", node);
- String aliasId = super.getNodeAttr("aliases", node);
- addElementMapping(model, result, speciesId, aliasId);
- }
-
- return result;
- }
-
- private void addElementMapping(Model model, Map<String, Element> result, String speciesId, String aliasId) {
- String[] aliasIds = aliasId.split(",");
- String[] speciesIds = speciesId.split(",");
- for (int i = 0; i < aliasIds.length; i++) {
-
- Element element = model.getElementByElementId(aliasIds[i]);
- result.put(speciesIds[i], element);
- addCompartmentMapping(result, element);
- }
- }
-
- private void addCompartmentMapping(Map<String, Element> result, Element element) {
- Compartment compartment = element.getCompartment();
- if (compartment != null) {
- // in kinetics we can have reference to compartment (so we need to find SBML
- // compartment id)
- String compartmentId = elements.getElementByElementId(compartment.getElementId()).getElementId();
- result.put(compartmentId, compartment);
- }
- }
-
- /**
- * Parses reaction annotation node and update reaction.
- *
- * @param annotationNode
- * xml node
- * @param result
- * reaction to update
- * @param model
- * model where reaction is placed
- * @return updated reaction
- * @throws ReactionParserException
- * thrown when the xml is invalid
- * @throws InvalidXmlSchemaException
- * thrown when annotationNode is invalid xml
- */
- private Reaction parseReactionAnnotation(Node annotationNode, Reaction result, Model model)
- throws ReactionParserException {
- NodeList nodes = annotationNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:extension")) {
- result = parseReactionExtension(result, node, model);
- } else if (node.getNodeName().equalsIgnoreCase("rdf:RDF")) {
- try {
- XmlAnnotationParser xmlParser = new XmlAnnotationParser();
- result.addMiriamData(xmlParser.parseRdfNode(nodes));
- } catch (InvalidXmlSchemaException e) {
- throw new ReactionParserException("Problem with parsing RDF", result, e);
- }
- } else {
- throw new ReactionParserException("Unknown element of reaction/annotation: " + node.getNodeName(), result);
- }
- }
- }
- return result;
- }
-
- /**
- * Parses CellDesigner extension to sbml reaction node and updates reaction.
- *
- * @param result
- * reaction to update
- * @param node
- * xml node
- * @param model
- * model where reaction is placed
- * @return updated reaction
- * @throws ReactionParserException
- * thrown when the xml is invalid and reason is more specific
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- *
- */
- private Reaction parseReactionExtension(Reaction result, Node node, Model model) throws ReactionParserException {
- NodeList extensionNodes = node.getChildNodes();
- LineProperties line = null;
- ConnectScheme connectScheme = null;
- EditPoints points = null;
- Node reactantsLinkNode = null;
- Node productsLinkNode = null;
- Node modifiersLinkNode = null;
- Node gateMembers = null;
- String type = null;
- for (int y = 0; y < extensionNodes.getLength(); y++) {
- Node nodeReaction = extensionNodes.item(y);
- if (nodeReaction.getNodeType() == Node.ELEMENT_NODE) {
- if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:reactionType")) {
- type = getNodeValue(nodeReaction);
- } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:baseReactants")) {
- NodeList reactantsNodes = nodeReaction.getChildNodes();
- for (int z = 0; z < reactantsNodes.getLength(); z++) {
- Node reactantNode = reactantsNodes.item(z);
- if (reactantNode.getNodeType() == Node.ELEMENT_NODE) {
- if (reactantNode.getNodeName().equalsIgnoreCase("celldesigner:baseReactant")) {
- parseBaseReactant(result, reactantNode, model);
- } else {
- throw new ReactionParserException(
- "Unknown element of celldesigner:baseReactants: " + node.getNodeName(), result);
- }
- }
- }
- } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:baseProducts")) {
- NodeList reactantsNodes = nodeReaction.getChildNodes();
- for (int z = 0; z < reactantsNodes.getLength(); z++) {
- Node reactantNode = reactantsNodes.item(z);
- if (reactantNode.getNodeType() == Node.ELEMENT_NODE) {
- if (reactantNode.getNodeName().equalsIgnoreCase("celldesigner:baseProduct")) {
- parseBaseProduct(model, result, reactantNode);
- } else {
- throw new ReactionParserException("Unknown element of celldesigner:baseProducts: " + node.getNodeName(),
- result);
- }
- }
- }
- } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:line")) {
- line = getLineProperties(nodeReaction);
- } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:connectScheme")) {
- try {
- connectScheme = parseConnectScheme(nodeReaction);
- } catch (InvalidXmlSchemaException e) {
- throw new ReactionParserException(result, e);
- }
- } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:listOfReactantLinks")) {
- reactantsLinkNode = nodeReaction;
- } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:listOfProductLinks")) {
- productsLinkNode = nodeReaction;
- } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:listOfModification")) {
- modifiersLinkNode = nodeReaction;
- } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:editPoints")) {
- points = parseEditPoints(nodeReaction);
- } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:name")) {
- result.setName(getNodeValue(nodeReaction));
- } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:listOfGateMember")) {
- gateMembers = nodeReaction;
- } else {
- throw new ReactionParserException(
- "Unknown element of reaction/celldesigner:extension: " + nodeReaction.getNodeName(), result);
- }
- }
- }
- if (gateMembers != null) {
- try {
- points = gateMembersToPoints(gateMembers);
- } catch (InvalidXmlSchemaException e) {
- throw new ReactionParserException(result, e);
- }
- }
- result = createProperTypeReaction(type, result);
- if (connectScheme == null) {
- throw new ReactionParserException("No connectScheme node", result);
- }
- if (points == null) {
- points = new EditPoints();
- }
- if (result instanceof SimpleReactionInterface) {
- createLinesForSimpleReaction(result, points, connectScheme);
- } else if (result instanceof TwoReactantReactionInterface) {
- createLinesForTwoReactantReaction(result, points, gateMembers != null);
- createOperatorsForTwoReactantReaction(result, gateMembers);
-
- } else if (result instanceof TwoProductReactionInterface) {
- createLinesForTwoProductReaction(result, points);
- createOperatorsForTwoProductReaction(result);
- } else {
- throw new ReactionParserException(
- "Problem with parsing lines. Unknown reaction: " + type + "; " + result.getClass().getName(), result);
- }
- if (reactantsLinkNode != null) {
- parseReactantLinks(result, reactantsLinkNode, model);
- }
- if (productsLinkNode != null) {
- parseProductLinks(result, productsLinkNode, model);
- }
-
- // create operators
- createOperators(result);
-
- // now try to create modifiers (we must have set fixed layout data for the
- // core of the reaction)
- if (modifiersLinkNode != null) {
- parseReactionModification(result, modifiersLinkNode, model);
- }
- for (int i = 0; i < result.getModifiers().size(); i++) {
- Modifier modifier = result.getModifiers().get(i);
- if (modifier.getElement() == null) {
- List<Modifier> modifiers = new ArrayList<Modifier>();
- modifiers.add(modifier);
- for (Modifier modifier2 : result.getModifiers()) {
- if (modifierParentOperator.get(modifier2) == modifier) {
- modifiers.add(modifier2);
- }
- }
- computeLineForModification(result, modifiers);
- createOperatorFromModifiers(result, modifiers);
- result.removeModifier(modifier);
- i--;
- } else if (modifier.getLine() == null) {
- createLineForModifier(result, modifier);
- }
- }
-
- if (line != null) {
- for (AbstractNode rNode : result.getNodes()) {
- rNode.getLine().setWidth(line.getWidth());
- rNode.getLine().setColor(line.getColor());
- }
- }
- if (result.isReversible()) {
- for (Reactant reactant : result.getReactants()) {
- reactant.getLine().getBeginAtd().setArrowType(result.getProducts().get(0).getLine().getEndAtd().getArrowType());
- }
- }
-
- return result;
- }
-
- /**
- * Creates reaction with a new type.
- *
- * @param type
- * CellDesigner type of a reaction
- * @param result
- * initial data
- * @return reaction with a new type
- * @throws ReactionParserException
- */
- Reaction createProperTypeReaction(String type, Reaction result) throws ReactionParserException {
- ReactionLineData rdl = ReactionLineData.getByCellDesignerString(type);
- if (rdl == null) {
- throw new ReactionParserException("Unknown CellDesigner class type: " + type + ".", result);
- }
- return rdl.createReaction(result);
- }
-
- /**
- * Creates CellDesigner {@link EditPoints} structure for gate members node.
- *
- * @param gateMembers
- * xml node
- * @return {@link EditPoints} structure representing line information for the
- * xml node
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- private EditPoints gateMembersToPoints(Node gateMembers) throws InvalidXmlSchemaException {
- Node lastMember = null;
- EditPoints result = new EditPoints();
- Integer num0 = null;
- Integer num1 = null;
- Integer num2 = null;
- for (int i = 0; i < gateMembers.getChildNodes().getLength(); i++) {
- Node child = gateMembers.getChildNodes().item(i);
- if (child.getNodeType() == Node.ELEMENT_NODE) {
-
- if (child.getNodeName().equalsIgnoreCase("celldesigner:GateMember")) {
- String type = getNodeAttr("type", child);
- if (type.startsWith(ReactionLineData.BOOLEAN_LOGIC_GATE.getCellDesignerString())) {
- lastMember = child;
- } else {
- String pointsString = getNodeAttr("editPoints", child);
- List<Point2D> points = parseEditPointsString(pointsString);
- if (num0 == null) {
- num0 = points.size();
- } else if (num1 == null) {
- num1 = points.size();
- } else {
- throw new InvalidXmlSchemaException("Too many gate members");
- }
- result.getPoints().addAll(points);
- }
- } else {
- throw new InvalidXmlSchemaException("Unknown node type: " + child.getNodeName());
- }
- }
- }
- if (lastMember == null) {
- throw new InvalidXmlSchemaException("Missing gate member connecting members");
- } else {
- String pointsString = getNodeAttr("editPoints", lastMember);
- List<Point2D> points = parseEditPointsString(pointsString);
- num2 = points.size() - 1;
- result.getPoints().addAll(points);
- }
- result.setNum0(num0);
- result.setNum1(num1);
- result.setNum2(num2);
- return result;
- }
-
- /**
- * Creates line information for the modifier.
- *
- * @param reaction
- * reaction where modifier is placed
- * @param modifier
- * modifier to update
- */
- private void createLineForModifier(Reaction reaction, Modifier modifier) {
- Element element = modifier.getElement();
- CellDesignerAliasConverter converter = new CellDesignerAliasConverter(element, sbgn);
- Point2D startPoint = converter.getPointCoordinates(element, anchorsByNodes.get(modifier));
- ModifierTypeUtils modifierTypeUtils = new ModifierTypeUtils();
-
- Point2D p = modifierTypeUtils.getAnchorPointOnReactionRect(modifier.getReaction(),
- lineTypeByModifier.get(modifier));
- PolylineData line = PolylineDataFactory.createPolylineDataFromEditPoints(startPoint, p,
- pointsByModifier.get(modifier));
-
- startPoint = converter.getAnchorPointCoordinates(element, anchorsByNodes.get(modifier), line);
- line.setStartPoint(startPoint);
- modifier.setLine(line);
- modifierTypeUtils.updateLineEndPoint(modifier);
- }
-
- /**
- * Creates operators for CellDesigner reaction that belongs to
- * {@link TwoProductReactionInterface}.
- *
- * @param result
- * reaction to be updated
- * @throws ReactionParserException
- * thrown when there is a problem with creating operators (input data
- * is invalid)
- */
- private void createOperatorsForTwoProductReaction(Reaction result) throws ReactionParserException {
- int inputs = 0;
- NodeOperator operator = null;
- if (result.getClass() == DissociationReaction.class) {
- operator = new DissociationOperator();
- } else if (result.getClass() == TruncationReaction.class) {
- operator = new TruncationOperator();
- } else {
- throw new ReactionParserException("Invalid reaction type", result);
- }
- for (AbstractNode node : result.getNodes()) {
- if (node.getClass() == Product.class) {
- operator.addOutput(node);
- } else if (node.getClass() == Reactant.class) {
- inputs++;
- if (inputs > 1) {
- throw new ReactionParserException("Reaction has more than one reactant", result);
- }
- }
- }
- if (operator.getOutputs().size() > 2) {
- throw new ReactionParserException("Too many products: " + operator.getOutputs().size(), result);
- }
-
- // and now we have to modify lines
-
- Reactant reactant = result.getReactants().get(0);
- Integer index = indexByComplexReaction.get(reactant);
-
- Point2D p1, p2;
-
- p1 = reactant.getLine().getPoints().get(index);
- p2 = reactant.getLine().getPoints().get(index + 1);
-
- p1 = new Point2D.Double(p1.getX(), p1.getY());
- p2 = new Point2D.Double(p2.getX(), p2.getY());
-
- Point2D p = new Point2D.Double((p2.getX() + p1.getX()) / 2, (p2.getY() + p1.getY()) / 2);
- operator.setLine(reactant.getLine().getSubline(0, index + 1));
- operator.getLine().addPoint(p);
-
- p = new Point2D.Double((p2.getX() + p1.getX()) / 2, (p2.getY() + p1.getY()) / 2);
-
- reactant.setLine(reactant.getLine().getSubline(index + 1, reactant.getLine().getPoints().size()).reverse());
- reactant.getLine().getPoints().add(p);
-
- reactant.getLine().trimEnd(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
- operator.getLine().trimEnd(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
-
- result.addNode(operator);
- }
-
- /**
- * Creates general input/output operators for the model.
- *
- * @param result
- * reaction to be updated
- */
- private void createOperators(Reaction result) {
- // central line points
- Point2D p1 = result.getReactants().get(0).getLine().getPoints()
- .get(result.getReactants().get(0).getLine().getPoints().size() - 2);
- Point2D p2 = result.getProducts().get(0).getLine().getPoints().get(1);
- Point2D tmp = result.getProducts().get(0).getLine().getPoints().get(0);
- Point2D productSplitOperatorBeginPoint = new Point2D.Double(tmp.getX(), tmp.getY());
-
- // where the line from reactants ends
- tmp = result.getReactants().get(0).getLine().getPoints()
- .get(result.getReactants().get(0).getLine().getPoints().size() - 1);
- Point2D reactantAndOperatorEndPoint = new Point2D.Double(tmp.getX(), tmp.getY());
-
- Set<AbstractNode> toExclude = new HashSet<AbstractNode>();
- Set<AbstractNode> toInclude = new HashSet<AbstractNode>();
- for (NodeOperator operator : result.getOperators()) {
- toExclude.addAll(operator.getInputs());
- if (operator.isReactantOperator()) {
- toInclude.add(operator);
- // if we have operator in input then central line changes
- p1 = operator.getLine().getPoints().get(operator.getLine().getPoints().size() - 2);
- tmp = operator.getLine().getPoints().get(operator.getLine().getPoints().size() - 1);
- reactantAndOperatorEndPoint = new Point2D.Double(tmp.getX(), tmp.getY());
- }
- if (operator.isProductOperator()) {
- // if we have operator in output then central line changes
- p2 = operator.getLine().getPoints().get(operator.getLine().getPoints().size() - 2);
- tmp = operator.getLine().getPoints().get(operator.getLine().getPoints().size() - 1);
- productSplitOperatorBeginPoint = new Point2D.Double(tmp.getX(), tmp.getY());
- }
- }
-
- double dx = p2.getX() - p1.getX();
- double dy = p2.getY() - p1.getY();
-
- Point2D reactantAndOperatorBeginPoint = new Point2D.Double(p1.getX() + dx * REACTANT_END_RATIO,
- p1.getY() + dy * REACTANT_END_RATIO);
-
- PolylineData ld = new PolylineData(reactantAndOperatorBeginPoint, reactantAndOperatorEndPoint);
-
- LineType lineType = null;
- Set<AbstractNode> nodes = new LinkedHashSet<AbstractNode>();
- for (Reactant reactant : result.getReactants()) {
- if (!toExclude.contains(reactant)) {
- nodes.add(reactant);
- if (lineType == null) {
- lineType = reactant.getLine().getType();
- }
- }
- }
- nodes.addAll(toInclude);
- nodes.removeAll(toExclude);
-
- // add an operator only when the number of input nodes is greater than one
- if (nodes.size() > 1) {
- AndOperator inputOperator = new AndOperator();
- inputOperator.setLine(ld);
- inputOperator.addInputs(nodes);
- for (Reactant reactant : result.getReactants()) {
- if (!toExclude.contains(reactant)) {
- reactant.getLine().getEndPoint().setLocation(reactantAndOperatorBeginPoint.getX(),
- reactantAndOperatorBeginPoint.getY());
- }
- }
- if (lineType != null) {
- inputOperator.getLine().setType(lineType);
- }
- result.addNode(inputOperator);
- }
-
- // and now we try to handle with output operators
-
- toExclude = new HashSet<AbstractNode>();
- toInclude = new HashSet<AbstractNode>();
- for (NodeOperator nOperator : result.getOperators()) {
- toExclude.addAll(nOperator.getOutputs());
- if (nOperator.isProductOperator()) {
- toInclude.add(nOperator);
- }
- }
-
- Point2D productSplitOperatorEndPoint = new Point2D.Double(p1.getX() + dx * PRODUCT_START_RATIO,
- p1.getY() + dy * PRODUCT_START_RATIO);
-
- ld = new PolylineData(productSplitOperatorEndPoint, productSplitOperatorBeginPoint);
-
- lineType = null;
- nodes = new LinkedHashSet<AbstractNode>();
- for (Product product : result.getProducts()) {
- if (!toExclude.contains(product)) {
- nodes.add(product);
- if (lineType == null) {
- lineType = product.getLine().getType();
- }
- }
- }
- nodes.addAll(toInclude);
- nodes.removeAll(toExclude);
- if (nodes.size() > 1) {
- SplitOperator outputOperator = new SplitOperator();
- outputOperator.setLine(ld);
- outputOperator.addOutputs(nodes);
- for (Product product : result.getProducts()) {
- if (!toExclude.contains(product)) {
- // outputOperator.addOutput(product);
- product.getLine().getPoints().get(0).setLocation(productSplitOperatorEndPoint.getX(),
- productSplitOperatorEndPoint.getY());
- }
- }
- if (lineType != null) {
- outputOperator.getLine().setType(lineType);
- }
- result.addNode(outputOperator);
- }
- }
-
- /**
- * Creates operators in modifiers.
- *
- * @param reaction
- * reaction to update
- * @param modifiers
- * list of modifiers that must be put into operators
- */
- private void createOperatorFromModifiers(Reaction reaction, List<Modifier> modifiers) {
- OperatorTypeUtils otu = new OperatorTypeUtils();
- String type = typeByModifier.get(modifiers.get(0));
- NodeOperator operator = otu.createModifierForStringType(type);
-
- operator.setLine(modifiers.get(0).getLine());
-
- for (int i = 1; i < modifiers.size(); i++) {
- operator.addInput(modifiers.get(i));
- }
-
- ModifierTypeUtils modifierTypeUtils = new ModifierTypeUtils();
- modifierTypeUtils.updateLineEndPoint(operator);
- reaction.addNode(operator);
- }
-
- /**
- * Creates operators for CellDesigner reaction that belongs to
- * {@link TwoReactantReactionInterface}.
- *
- * @param result
- * reaction to be updated
- * @param gateMembers
- * node representing line information for the operator
- * @throws ReactionParserException
- * thrown when the xml is invalid
- */
- private void createOperatorsForTwoReactantReaction(Reaction result, Node gateMembers) throws ReactionParserException {
- NodeOperator andOperator = null;
- if (result instanceof HeterodimerAssociationReaction) {
- andOperator = new AssociationOperator();
- } else if (result instanceof BooleanLogicGateReaction) {
- andOperator = new AndOperator();
- } else {
- throw new ReactionParserException("Unknown class type with two reactants", result);
- }
- int outputs = 0;
- for (AbstractNode node : result.getNodes()) {
- if (node.getClass() == Reactant.class) {
- andOperator.addInput(node);
- } else if (node.getClass() == Product.class) {
- outputs++;
- if (outputs > 1) {
- throw new ReactionParserException("Reaction has more than one product", result);
- }
- }
- }
- if (andOperator.getInputs().size() > 2) {
- throw new ReactionParserException("Too many reactants.", result);
- }
-
- // and now we have to modify lines
-
- Product product = result.getProducts().get(0);
- Integer index = indexByComplexReaction.get(product);
- if (index != null) {
- Point2D p1, p2;
-
- p1 = product.getLine().getPoints().get(index);
- p2 = product.getLine().getPoints().get(index + 1);
-
- p1 = new Point2D.Double(p1.getX(), p1.getY());
- p2 = new Point2D.Double(p2.getX(), p2.getY());
-
- Point2D p = new Point2D.Double((p2.getX() + p1.getX()) / 2, (p2.getY() + p1.getY()) / 2);
- andOperator.setLine(product.getLine().getSubline(0, index + 1));
- andOperator.getLine().addPoint(p);
- andOperator.getLine().trimEnd(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
-
- p = new Point2D.Double((p2.getX() + p1.getX()) / 2, (p2.getY() + p1.getY()) / 2);
-
- product.setLine(product.getLine().getSubline(index, product.getLine().getPoints().size()));
- product.getLine().getPoints().set(0, p);
- product.getLine().trimBegin(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
-
- product.getLine().getEndAtd().setArrowType(ArrowType.FULL);
-
- result.addNode(andOperator);
- } else {
- NodeOperator operator = null;
- Set<String> undefinedTypes = new HashSet<String>();
- for (int i = 0; i < gateMembers.getChildNodes().getLength(); i++) {
- Node child = gateMembers.getChildNodes().item(i);
- if (child.getNodeType() == Node.ELEMENT_NODE) {
-
- if (child.getNodeName().equalsIgnoreCase("celldesigner:GateMember")) {
- String type = getNodeAttr("type", child);
-
- if (type.equalsIgnoreCase(OperatorType.AND_OPERATOR_STRING.getStringName())) {
- operator = new AndOperator();
- } else if (type.equalsIgnoreCase(OperatorType.OR_OPERATOR_STRING.getStringName())) {
- operator = new OrOperator();
- } else if (type.equalsIgnoreCase(OperatorType.NAND_OPERATOR_STRING.getStringName())) {
- operator = new NandOperator();
- } else if (type.equalsIgnoreCase(OperatorType.UNKNOWN_OPERATOR_STRING.getStringName())) {
- operator = new UnknownOperator();
- } else {
- undefinedTypes.add(type);
- }
- }
- }
- }
- if (operator == null) {
- String types = "";
- for (String string : undefinedTypes) {
- types += string + ", ";
- }
- throw new ReactionParserException(
- "Couldn't find type of BOOLEAN_LOGIC_GATE. Unknown types identified: " + types, result);
- }
-
- operator.addInputs(andOperator.getInputs());
- operator.addOutput(product);
-
- // empty line
- PolylineData line = new PolylineData();
- line.addPoint(product.getLine().getBeginPoint());
- line.addPoint(product.getLine().getBeginPoint());
-
- operator.setLine(line);
- result.addNode(operator);
- }
-
- }
-
- /**
- * Creates lines for reaction that belongs to
- * {@link TwoProductReactionInterface}.
- *
- * @param reaction
- * reaction to update
- * @param points
- * information about points
- */
- private void createLinesForTwoProductReaction(Reaction reaction, EditPoints points) {
- Point2D p = points.getPoints().get(points.size() - 1);
- Product product1 = reaction.getProducts().get(0);
- Product product2 = reaction.getProducts().get(1);
- Reactant reactant = reaction.getReactants().get(0);
-
- CellDesignerAliasConverter reactantConverter = new CellDesignerAliasConverter(reactant.getElement(), sbgn);
- CellDesignerAliasConverter product1Converter = new CellDesignerAliasConverter(product1.getElement(), sbgn);
- CellDesignerAliasConverter product2Converter = new CellDesignerAliasConverter(product2.getElement(), sbgn);
-
- Point2D p1 = reactantConverter.getPointCoordinates(reactant.getElement(), anchorsByNodes.get(reactant));
- Point2D p2 = product1Converter.getPointCoordinates(product1.getElement(), anchorsByNodes.get(product1));
- Point2D p3 = product2Converter.getPointCoordinates(product2.getElement(), anchorsByNodes.get(product2));
-
- Point2D centerPoint = pointTransformation.getCoordinatesInNormalBase(product1.getElement().getCenter(),
- product2.getElement().getCenter(), reactant.getElement().getCenter(), p);
-
- int startId0 = 0;
- int num0 = points.getNum0();
- int startId1 = num0;
- int num1 = num0 + points.getNum1();
- int startId2 = num1;
- int num2 = num1 + points.getNum2();
-
- ArrayList<Point2D> linePoints1 = new ArrayList<Point2D>(points.getPoints().subList(startId0, num0));
- ArrayList<Point2D> linePoints2 = new ArrayList<Point2D>(points.getPoints().subList(startId1, num1));
- ArrayList<Point2D> linePoints3 = new ArrayList<Point2D>(points.getPoints().subList(startId2, num2));
-
- PolylineData product1Line = PolylineDataFactory.createPolylineDataFromEditPoints(centerPoint, p2, linePoints2);
- PolylineData product2Line = PolylineDataFactory.createPolylineDataFromEditPoints(centerPoint, p3, linePoints3);
-
- PolylineData reactantLine = PolylineDataFactory.createPolylineDataFromEditPoints(centerPoint, p1, linePoints1);
-
- p1 = product2Converter.getAnchorPointCoordinates(product2.getElement(), anchorsByNodes.get(product2),
- product2Line.reverse());
- product2Line.setEndPoint(p1);
-
- p1 = product1Converter.getAnchorPointCoordinates(product1.getElement(), anchorsByNodes.get(product1),
- product1Line.reverse());
- product1Line.setEndPoint(p1);
-
- p1 = reactantConverter.getAnchorPointCoordinates(reactant.getElement(), anchorsByNodes.get(reactant),
- reactantLine.reverse());
- reactantLine.setEndPoint(p1);
-
- product2Line.getEndAtd().setArrowType(ArrowType.FULL);
- product1Line.getEndAtd().setArrowType(ArrowType.FULL);
- product1.setLine(product1Line);
- product2.setLine(product2Line);
- reactant.setLine(reactantLine);
-
- indexByComplexReaction.put(reactant, points.getIndex());
-
- }
-
- /**
- * Creates lines for reaction that belongs to
- * {@link TwoReactantReactionInterface}.
- *
- * @param reaction
- * reaction to update
- * @param points
- * information about points
- * @param hasGateMemebers
- * does the reaction has gate members
- * @throws ReactionParserException
- * thrown when data for reaction is invalid
- */
- private void createLinesForTwoReactantReaction(Reaction reaction, EditPoints points, boolean hasGateMemebers)
- throws ReactionParserException {
- Point2D p = points.getPoints().get(points.size() - 1);
- Product product = reaction.getProducts().get(0);
- Reactant reactant1 = reaction.getReactants().get(0);
- Reactant reactant2 = reaction.getReactants().get(1);
- CellDesignerAliasConverter productConverter = new CellDesignerAliasConverter(product.getElement(), sbgn);
- CellDesignerAliasConverter reactantConverter1 = new CellDesignerAliasConverter(reactant1.getElement(), sbgn);
- CellDesignerAliasConverter reactantConverter2 = new CellDesignerAliasConverter(reactant2.getElement(), sbgn);
- Point2D p1 = reactantConverter1.getPointCoordinates(reactant1.getElement(), anchorsByNodes.get(reactant1));
- Point2D p2 = reactantConverter2.getPointCoordinates(reactant2.getElement(), anchorsByNodes.get(reactant2));
- Point2D p3 = productConverter.getPointCoordinates(product.getElement(), anchorsByNodes.get(product));
-
- Element alias1 = reactant1.getElement();
- Element alias2 = reactant2.getElement();
- Element alias3 = product.getElement();
-
- Point2D pointA = alias2.getCenter();
- Point2D pointC = alias1.getCenter();
- Point2D pointB = alias3.getCenter();
- Point2D pointP = p;
- Point2D centerPoint = null;
- if (!hasGateMemebers) {
- centerPoint = pointTransformation.getCoordinatesInNormalBase(pointA, pointB, pointC, pointP);
- } else {
- centerPoint = pointP;
- }
-
- int startId0 = 0;
- int num0 = points.getNum0();
- int startId1 = num0;
- int num1 = num0 + points.getNum1();
- int startId2 = num1;
- int num2 = num1 + points.getNum2();
-
- List<Point2D> linePoints1 = new ArrayList<Point2D>(points.getPoints().subList(startId0, num0));
- List<Point2D> linePoints2 = new ArrayList<Point2D>(points.getPoints().subList(startId1, num1));
- List<Point2D> linePoints3 = new ArrayList<Point2D>(points.getPoints().subList(startId2, num2));
-
- PolylineData reactant1Line = null;
- PolylineData reactant2Line = null;
- if (!hasGateMemebers) {
- reactant1Line = PolylineDataFactory.createPolylineDataFromEditPoints(centerPoint, p1, linePoints1);
- reactant2Line = PolylineDataFactory.createPolylineDataFromEditPoints(centerPoint, p2, linePoints2);
- } else {
- reactant1Line = PolylineDataFactory.createPolylineDataFromEditPoints(p1, centerPoint, linePoints1);
- reactant1Line = reactant1Line.reverse();
-
- reactant2Line = PolylineDataFactory.createPolylineDataFromEditPoints(p2, centerPoint, linePoints2);
- reactant2Line = reactant2Line.reverse();
- }
-
- PolylineData productLine = PolylineDataFactory.createPolylineDataFromEditPoints(centerPoint, p3, linePoints3);
-
- p1 = reactantConverter1.getAnchorPointCoordinates(reactant1.getElement(), anchorsByNodes.get(reactant1),
- reactant1Line.reverse());
- reactant1Line.setEndPoint(p1);
- reactant1Line = reactant1Line.reverse();
-
- p1 = reactantConverter2.getAnchorPointCoordinates(reactant2.getElement(), anchorsByNodes.get(reactant2),
- reactant2Line.reverse());
- reactant2Line.setEndPoint(p1);
- reactant2Line = reactant2Line.reverse();
-
- p1 = productConverter.getAnchorPointCoordinates(product.getElement(), anchorsByNodes.get(product),
- productLine.reverse());
- productLine.setEndPoint(p1);
- if (hasGateMemebers) {
- productLine.getEndAtd().setArrowType(ArrowType.OPEN);
- }
-
- product.setLine(productLine);
- reactant1.setLine(reactant1Line);
- reactant2.setLine(reactant2Line);
-
- indexByComplexReaction.put(product, points.getIndex());
- }
-
- /**
- * Creates lines for reaction that belongs to {@link SimpleReactionInterface}
- * (only one standard product and one standard reactant).
- *
- * @param reaction
- * reaction to update
- * @param editPoints
- * information about points
- * @param scheme
- * some additional information about the line
- */
- private void createLinesForSimpleReaction(Reaction reaction, EditPoints editPoints, ConnectScheme scheme) {
- Product product = reaction.getProducts().get(0);
- Reactant reactant = reaction.getReactants().get(0);
- CellDesignerAliasConverter productConverter = new CellDesignerAliasConverter(product.getElement(), sbgn);
- CellDesignerAliasConverter reactantConverter = new CellDesignerAliasConverter(reactant.getElement(), sbgn);
-
- Point2D endPoint = productConverter.getPointCoordinates(product.getElement(), anchorsByNodes.get(product));
- Point2D startPoint = reactantConverter.getPointCoordinates(reactant.getElement(), anchorsByNodes.get(reactant));
-
- PolylineData ld = PolylineDataFactory.createPolylineDataFromEditPoints(startPoint, endPoint,
- editPoints.getPoints());
-
- // first place where the index of rectangle is kept
- Integer index = editPoints.getIndex();
-
- // second place where index of rectangle is kept
- if (index == null) {
- index = scheme.getConnectIndex();
- if (index != null) {
- // but...
- // direction of the index is reversed...
- index = ld.getPoints().size() - index - 2;
- }
- }
- // but sometimes there is no information about index...
- if (index == null) {
- index = 0;
- }
- startPoint = reactantConverter.getAnchorPointCoordinates(reactant.getElement(), anchorsByNodes.get(reactant), ld);
- endPoint = productConverter.getAnchorPointCoordinates(product.getElement(), anchorsByNodes.get(product),
- ld.reverse());
- ld.getPoints().set(0, startPoint);
- ld.getPoints().set(ld.getPoints().size() - 1, endPoint);
-
- PolylineData line = new PolylineData(ld);
-
- PolylineData reactantLine = line.getSubline(0, ld.getPoints().size() - index - 1);
- PolylineData productLine = line.getSubline(ld.getPoints().size() - index - 2, ld.getPoints().size());
-
- Point2D p1 = ld.getPoints().get(ld.getPoints().size() - index - 2);
- Point2D p2 = ld.getPoints().get(ld.getPoints().size() - index - 1);
- Point2D p = new Point2D.Double((p2.getX() + p1.getX()) / 2, (p2.getY() + p1.getY()) / 2);
- reactantLine.getPoints().add(p);
- reactantLine.trimEnd(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
-
- p = new Point2D.Double((p2.getX() + p1.getX()) / 2, (p2.getY() + p1.getY()) / 2);
- productLine.getPoints().set(0, p);
- productLine.trimBegin(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
-
- productLine.getEndAtd().setArrowType(ArrowType.FULL);
-
- reactant.setLine(reactantLine);
- product.setLine(productLine);
-
- ReactionLineData rld = ReactionLineData.getByReactionType(reaction.getClass());
- reactantLine.setType(rld.getLineType());
- productLine.setType(rld.getLineType());
- productLine.getEndAtd().setArrowType(rld.getProductArrowType());
- productLine.trimEnd(rld.getProductLineTrim());
- }
-
- /**
- * Prepares {@link EditPoints} structure from xml node.
- *
- * @param rootNode
- * xml node
- * @return {@link EditPoints} object containing CellDesigner line data
- */
- private EditPoints parseEditPoints(Node rootNode) {
- EditPoints result = new EditPoints();
- String num0 = getNodeAttr("num0", rootNode);
- String num1 = getNodeAttr("num1", rootNode);
- String num2 = getNodeAttr("num2", rootNode);
- if (!num0.equals("")) {
- result.setNum0(Integer.parseInt(num0));
- }
- if (!num1.equals("")) {
- result.setNum1(Integer.parseInt(num1));
- }
- if (!num2.equals("")) {
- result.setNum2(Integer.parseInt(num2));
- }
- String index = getNodeAttr("tShapeIndex", rootNode);
- if (!index.equals("")) {
- result.setIndex(Integer.parseInt(index));
- }
-
- String pointsString = getNodeValue(rootNode);
- result.setPoints(parseEditPointsString(pointsString));
- return result;
- }
-
- /**
- * Parses CellDesigner point by point string.
- *
- * @param pointsString
- * String containing points
- * @return list of points
- */
- ArrayList<Point2D> parseEditPointsString(String pointsString) {
- ArrayList<Point2D> points2 = new ArrayList<Point2D>();
- if (pointsString.isEmpty()) {
- return points2;
- }
- String[] points = pointsString.trim().split(" ");
- for (String string : points) {
- String[] p = string.split(",");
- if (p.length != 2) {
- throw new InvalidArgumentException("Invalid editPoint string: " + string);
- } else {
- double posX = Double.parseDouble(p[0]);
- double posY = Double.parseDouble(p[1]);
- Point2D point = new Point2D.Double(posX, posY);
- if (!pointTransformation.isValidPoint(point)) {
- throw new InvalidArgumentException(
- "Invalid point parsed from input string: " + string + ". Result point: " + point);
- }
- points2.add(point);
- }
- }
- return points2;
- }
-
- /**
- * Parses xml node with reactantLink nodes and creates reactants in the
- * reaction.
- *
- * @param result
- * reaction to be updated
- * @param rootNode
- * xml node to parse
- * @param model
- * model where reaction is placed
- * @throws ReactionParserException
- * thrown when the xml is invalid
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- private void parseReactantLinks(Reaction result, Node rootNode, Model model) throws ReactionParserException {
- NodeList list = rootNode.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:reactantLink")) {
- Reactant newReactant = getReactantLink(node, model, result);
- result.addReactant(newReactant);
- } else {
- throw new ReactionParserException(
- "Unknown element of celldesigner:listOfReactantLinks: " + node.getNodeName(), result);
- }
- }
- }
- }
-
- /**
- * Parses xml node for reactanLink and creates reactant from it.
- *
- * @param rootNode
- * xml node to parse
- * @param model
- * model where reaction is placed
- * @param reaction
- * reaction that is being parsed
- * @return reactant obtained from xml node
- * @throws ReactionParserException
- * thrown when the xml is invalid and reason is more specific
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- private Reactant getReactantLink(Node rootNode, Model model, Reaction reaction) throws ReactionParserException {
- String aliasId = getNodeAttr("alias", rootNode);
- Species al = (Species) model.getElementByElementId(aliasId);
- if (al == null) {
- throw new ReactionParserException("Alias doesn't exist (id: " + aliasId + ")", reaction);
- }
-
- Reactant result = new Reactant(al);
- CellDesignerAnchor anchor = null;
- EditPoints points = null;
-
- NodeList nodes = rootNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:connectScheme")) {
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:linkAnchor")) {
- anchor = CellDesignerAnchor.valueOf(getNodeAttr("position", node).toUpperCase());
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:line")) {
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:editPoints")) {
- points = parseEditPoints(node);
- } else {
- throw new ReactionParserException("Unknown element of celldesigner:reactantLink: " + node.getNodeName(),
- reaction);
- }
- }
- }
-
- CellDesignerAliasConverter reactantConverter = new CellDesignerAliasConverter(al, sbgn);
- Point2D additionalPoint = reactantConverter.getPointCoordinates(al, anchor);
- ArrowTypeData atd = new ArrowTypeData();
- atd.setArrowType(ArrowType.NONE);
-
- Point2D endPoint;
-
- Line2D centerLine = reaction.getCenterLine();
-
- double dx = centerLine.getX2() - centerLine.getX1();
- double dy = centerLine.getY2() - centerLine.getY1();
- double coef = REACTANT_END_RATIO;
- endPoint = new Point2D.Double(centerLine.getX1() + dx * coef, centerLine.getY1() + dy * coef);
-
- PolylineData polyline = PolylineDataFactory.createPolylineDataFromEditPoints(additionalPoint, endPoint, points);
-
- additionalPoint = reactantConverter.getAnchorPointCoordinates(al, anchor, polyline);
- polyline.setStartPoint(additionalPoint);
- result.setLine(polyline);
-
- return result;
- }
-
- /**
- * Parses xml node with productLink nodes and creates products in the reaction.
- *
- * @param result
- * reaction to be updated
- * @param rootNode
- * xml node to parse
- * @param model
- * model where reaction is placed
- * @throws ReactionParserException
- * thrown when the xml is invalid
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- private void parseProductLinks(Reaction result, Node rootNode, Model model) throws ReactionParserException {
- NodeList list = rootNode.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:productLink")) {
- Product link = getProductLink(node, model, result);
- result.addProduct(link);
- } else {
- throw new ReactionParserException("Unknown element of celldesigner:listOfProductLinks: " + node.getNodeName(),
- result);
- }
- }
- }
- }
-
- /**
- * Parses xml node for productLink and creates product from it.
- *
- * @param rootNode
- * xml node to parse
- * @param model
- * model where reaction is placed
- * @param reaction
- * reaction that is being parsed
- * @return product obtained from xml node
- * @throws ReactionParserException
- * thrown when the xml is invalid
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- private Product getProductLink(Node rootNode, Model model, Reaction reaction) throws ReactionParserException {
- String aliasId = getNodeAttr("alias", rootNode);
- Species al = (Species) model.getElementByElementId(aliasId);
- if (al == null) {
- throw new ReactionParserException("Alias doesn't exist (id: " + aliasId + ")", reaction);
- }
-
- Product result = new Product(al);
-
- CellDesignerAnchor anchor = null;
- EditPoints points = null;
-
- NodeList nodes = rootNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:connectScheme")) {
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:linkAnchor")) {
- anchor = CellDesignerAnchor.valueOf(getNodeAttr("position", node).toUpperCase());
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:line")) {
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:editPoints")) {
- points = parseEditPoints(node);
- } else {
- throw new ReactionParserException("Unknown element of celldesigner:reactantLink: " + node.getNodeName(),
- reaction);
- }
- }
- }
-
- CellDesignerAliasConverter reactantConverter = new CellDesignerAliasConverter(al, sbgn);
- Point2D additionalPoint = reactantConverter.getPointCoordinates(al, anchor);
- ArrowTypeData atd = new ArrowTypeData();
- atd.setArrowType(ArrowType.NONE);
-
- Point2D endPoint;
-
- // central line points
- Point2D p1 = reaction.getReactants().get(0).getLine().getPoints()
- .get(reaction.getReactants().get(0).getLine().getPoints().size() - 2);
- Point2D p2 = reaction.getProducts().get(0).getLine().getPoints().get(1);
-
- Set<AbstractNode> toExclude = new HashSet<AbstractNode>();
- Set<AbstractNode> toInclude = new HashSet<AbstractNode>();
- for (NodeOperator operator : reaction.getOperators()) {
- toExclude.addAll(operator.getInputs());
- if (operator.isReactantOperator()) {
- toInclude.add(operator);
- // if we have operator in input then central line changes
- p1 = operator.getLine().getPoints().get(operator.getLine().getPoints().size() - 2);
- }
- if (operator.isProductOperator()) {
- // if we have operator in output then central line changes
- p2 = operator.getLine().getPoints().get(operator.getLine().getPoints().size() - 2);
- }
- }
-
- double dx = p2.getX() - p1.getX();
- double dy = p2.getY() - p1.getY();
- double coef = PRODUCT_START_RATIO;
- endPoint = new Point2D.Double(p1.getX() + dx * coef, p1.getY() + dy * coef);
-
- PolylineData polyline = PolylineDataFactory.createPolylineDataFromEditPoints(endPoint, additionalPoint, points);
- additionalPoint = reactantConverter.getAnchorPointCoordinates(al, anchor, polyline.reverse());
- polyline.setEndPoint(additionalPoint);
-
- polyline.getEndAtd().setArrowType(ArrowType.FULL);
- result.setLine(polyline);
- return result;
- }
-
- /**
- * Creates {@link LineProperties} object from the node.
- *
- * @param node
- * xml node to parse
- * @return {@link LineProperties} object
- */
- private LineProperties getLineProperties(Node node) {
- LineProperties line = new LineProperties();
- String tmp = getNodeAttr("width", node);
- line.setWidth(Double.parseDouble(tmp));
- tmp = getNodeAttr("color", node);
- line.setColor(stringToColor(tmp));
- line.setType(getNodeAttr("type", node));
- return line;
- }
-
- /**
- * PArse reaction modifiactions and add them into reaction.
- *
- * @param result
- * reaction currently processed
- * @param rootNode
- * xml node to parse
- * @param model
- * model where reaction is placed
- * @throws ReactionParserException
- * thrown when the xml is invalid, and reason is more specific
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- private void parseReactionModification(Reaction result, Node rootNode, Model model) throws ReactionParserException {
- NodeList nodes = rootNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:modification")) {
- parseModificationReaction(result, node, model);
- } else {
- throw new ReactionParserException("Unknown element of celldesigner:listOfModification: " + node.getNodeName(),
- result);
- }
- }
- }
- }
-
- /**
- * PArses modification node and adds this modification to reaction.
- *
- * @param reaction
- * reaction currently processed
- * @param rootNode
- * xml node
- * @param model
- * model where reaction is placed
- * @throws ReactionParserException
- * thrown when node cannot be parsed properly
- */
- private void parseModificationReaction(Reaction reaction, Node rootNode, Model model) throws ReactionParserException {
- ModifierTypeUtils modifierTypeUtils = new ModifierTypeUtils();
- String type = getNodeAttr("type", rootNode);
- String modificationType = getNodeAttr("modificationType", rootNode);
- String aliasId = getNodeAttr("aliases", rootNode);
- String lineConnectionType = getNodeAttr("targetLineIndex", rootNode);
- String points = getNodeAttr("editPoints", rootNode);
-
- List<Species> aliasList = new ArrayList<Species>();
-
- String[] list = aliasId.split(",");
- for (String string : list) {
- Species al = (Species) model.getElementByElementId(string);
- if (al != null) {
- aliasList.add(al);
- } else {
- throw new ReactionParserException("Unknown alias: " + string, reaction);
- }
- }
- Modifier result = null;
- if (aliasList.size() > 1) {
- result = new Modifier(null);
- reaction.addModifier(result);
- for (int i = 0; i < aliasList.size(); i++) {
- Modifier mod = modifierTypeUtils.createModifierForStringType(modificationType, aliasList.get(i));
- modifierParentOperator.put(mod, result);
- reaction.addModifier(mod);
- }
- } else {
- ModifierType mType = modifierTypeUtils.getModifierTypeForStringType(type);
- if (mType == null) {
- String errorInfo = "[" + reaction.getClass().getSimpleName() + "\t" + reaction.getIdReaction()
- + "]\tUnknown modifier type: " + type;
- if (ReactionLineData.getByCellDesignerString(type) != null) {
- errorInfo += ".\tThis type can be applied to reaction type only, not modifier.";
- }
- throw new UnknownModifierClassException(errorInfo, type, reaction.getIdReaction());
- }
- for (Modifier modifier : reaction.getModifiers()) {
- if (modifier.getElement() == aliasList.get(0) && modifier.getClass() == mType.getClazz()) {
- result = modifier;
- }
- }
- if (result == null) {
- result = modifierTypeUtils.createModifierForStringType(type, aliasList.get(0));
- reaction.addModifier(result);
- }
- }
- pointsByModifier.put(result, parseEditPointsString(points));
- typeByModifier.put(result, type);
- lineTypeByModifier.put(result, lineConnectionType);
-
- NodeList nodes = rootNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:connectScheme")) {
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:line")) {
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:linkTarget")) {
- try {
- CellDesignerAnchor anchor = getAnchorFromLinkTarget(node);
- anchorsByNodes.put(result, anchor);
- } catch (InvalidXmlSchemaException e) {
- throw new ReactionParserException(reaction, e);
- }
- } else {
- throw new ReactionParserException("Unknown element of celldesigner:listOfModification: " + node.getNodeName(),
- reaction);
- }
- }
-
- }
-
- }
-
- /**
- * Creates lines for modifiers.
- *
- * @param reaction
- * reaction where modifiers are placed
- * @param modifiers
- * list of modifiers for which lines should be generated
- */
- private void computeLineForModification(Reaction reaction, List<Modifier> modifiers) {
- ModifierTypeUtils modifierTypeUtils = new ModifierTypeUtils();
- Point2D p = modifierTypeUtils.getAnchorPointOnReactionRect(reaction, lineTypeByModifier.get(modifiers.get(0)));
-
- Point2D startPoint;
- List<Point2D> subPoints;
- // in case we have more then one alias in modification then we need to
- // define the start point as a different one then one on the alias
- Modifier modifier = modifiers.get(0);
- List<Point2D> points = pointsByModifier.get(modifier);
- startPoint = points.get(points.size() - 1);
- subPoints = points.subList(0, points.size() - 1);
- PolylineData line = PolylineDataFactory.createPolylineDataFromEditPoints(startPoint, p, subPoints);
- modifier.setLine(line);
-
- Point2D endPoint = startPoint;
-
- for (int i = 1; i < modifiers.size(); i++) {
- Modifier param = modifiers.get(i);
- CellDesignerAliasConverter reactantConverter = new CellDesignerAliasConverter(param.getElement(), sbgn);
- startPoint = reactantConverter.getPointCoordinates(param.getElement(), anchorsByNodes.get(param));
-
- PolylineData polyline = PolylineDataFactory.createPolylineDataFromEditPoints(startPoint, endPoint,
- pointsByModifier.get(param));
-
- startPoint = reactantConverter.getAnchorPointCoordinates(param.getElement(), anchorsByNodes.get(param), polyline);
- polyline.setStartPoint(startPoint);
- param.setLine(polyline);
- }
- }
-
- /**
- * Returns {@link CellDesignerAnchor} point from linkAnchor xml node.
- *
- * @param rootNode
- * xml node
- * @return {@link CellDesignerAnchor} object representing anchor point
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- private CellDesignerAnchor getAnchorFromLinkTarget(Node rootNode) throws InvalidXmlSchemaException {
- CellDesignerAnchor result = null;
-
- NodeList nodes = rootNode.getChildNodes();
- for (int z = 0; z < nodes.getLength(); z++) {
- Node node = nodes.item(z);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:linkAnchor")) {
- result = CellDesignerAnchor.valueOf(getNodeAttr("position", node).toUpperCase());
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:connectScheme: " + node.getNodeName());
- }
- }
- }
- return result;
- }
-
- /**
- * Creates {@link ConnectScheme} object from xml node.
- *
- * @param nodeReaction
- * xml node to parse
- * @return {@link ConnectScheme} object for given xml
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- private ConnectScheme parseConnectScheme(Node nodeReaction) throws InvalidXmlSchemaException {
- ConnectScheme result = new ConnectScheme();
- result.setConnectPolicy(getNodeAttr("connectPolicy", nodeReaction));
- result.setConnectIndex(getNodeAttr("rectangleIndex", nodeReaction));
- NodeList reactantsNodes = nodeReaction.getChildNodes();
- for (int z = 0; z < reactantsNodes.getLength(); z++) {
- Node reactantNode = reactantsNodes.item(z);
- if (reactantNode.getNodeType() == Node.ELEMENT_NODE) {
- if (reactantNode.getNodeName().equalsIgnoreCase("celldesigner:listOfLineDirection")) {
- result.setLineDirections(getlineDirectionMapForReactions(reactantNode));
- } else {
- throw new InvalidXmlSchemaException(
- "Unknown element of celldesigner:connectScheme: " + nodeReaction.getNodeName());
- }
- }
- }
- return result;
- }
-
- /**
- * Parse lineDirectionMap. This structure is nowhere used.
- *
- * @param reactantNode
- * xml node
- * @return map with directions for every line
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- private Map<String, String> getlineDirectionMapForReactions(Node reactantNode) throws InvalidXmlSchemaException {
- Map<String, String> result = new HashMap<String, String>();
- NodeList nodes = reactantNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:lineDirection")) {
- String index = getNodeAttr("index", node);
- String value = getNodeAttr("value", node);
- result.put(index, value);
- } else {
- throw new InvalidXmlSchemaException(
- "Unknown element of reaction/celldesigner:baseReactant: " + node.getNodeName());
- }
- }
- }
- return result;
- }
-
- /**
- * PArses baseReactant node from CellDEsigenr xml node and adds it into
- * reaction.
- *
- * @param result
- * reaction that is processed
- * @param reactantNode
- * xml node to parse
- * @param model
- * model where reaction is placed
- * @throws ReactionParserException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- private void parseBaseReactant(Reaction result, Node reactantNode, Model model) throws ReactionParserException {
- String aliasId = getNodeAttr("alias", reactantNode);
- Species alias = model.getElementByElementId(aliasId);
- if (alias == null) {
- throw new ReactionParserException("Alias with id=" + aliasId + " doesn't exist.", result);
- }
- Reactant reactant = new Reactant(alias);
- result.addReactant(reactant);
- NodeList nodes = reactantNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:linkAnchor")) {
- anchorsByNodes.put(reactant, CellDesignerAnchor.valueOf(getNodeAttr("position", node)));
- } else {
- throw new ReactionParserException(
- "Unknown element of reaction/celldesigner:baseReactant: " + node.getNodeName(), result);
- }
- }
-
- }
- }
-
- /**
- * Parses baseProduct node from CellDEsigenr xml node and adds it into reaction.
- *
- * @param result
- * reaction that is processed
- * @param reactantNode
- * xml node to parse
- * @param model
- * model where reaction is placed
- * @throws ReactionParserException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- private void parseBaseProduct(Model model, Reaction result, Node reactantNode) throws ReactionParserException {
- String aliasId = getNodeAttr("alias", reactantNode);
- Species alias = (Species) model.getElementByElementId(aliasId);
- if (alias == null) {
- throw new ReactionParserException("Alias with id=" + aliasId + " doesn't exist.", result);
- }
- Product product = new Product(alias);
- result.addProduct(product);
- NodeList nodes = reactantNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:linkAnchor")) {
- anchorsByNodes.put(product, CellDesignerAnchor.valueOf(getNodeAttr("position", node)));
- } else {
- throw new ReactionParserException(
- "Unknown element of reaction/celldesigner:baseProduct: " + node.getNodeName(), result);
- }
- }
- }
-
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.reaction;
+
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesignerConverter;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerPointTransformation;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.PolylineDataFactory;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.ConnectScheme;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.LineProperties;
+import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
+import lcsb.mapviewer.converter.model.celldesigner.types.ModifierTypeUtils;
+import lcsb.mapviewer.converter.model.celldesigner.types.OperatorType;
+import lcsb.mapviewer.converter.model.celldesigner.types.OperatorTypeUtils;
+import lcsb.mapviewer.model.graphics.ArrowType;
+import lcsb.mapviewer.model.graphics.ArrowTypeData;
+import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.AbstractNode;
+import lcsb.mapviewer.model.map.reaction.AndOperator;
+import lcsb.mapviewer.model.map.reaction.AssociationOperator;
+import lcsb.mapviewer.model.map.reaction.DissociationOperator;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.reaction.NandOperator;
+import lcsb.mapviewer.model.map.reaction.NodeOperator;
+import lcsb.mapviewer.model.map.reaction.OrOperator;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.reaction.SplitOperator;
+import lcsb.mapviewer.model.map.reaction.TruncationOperator;
+import lcsb.mapviewer.model.map.reaction.UnknownOperator;
+import lcsb.mapviewer.model.map.reaction.type.BooleanLogicGateReaction;
+import lcsb.mapviewer.model.map.reaction.type.DissociationReaction;
+import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
+import lcsb.mapviewer.model.map.reaction.type.SimpleReactionInterface;
+import lcsb.mapviewer.model.map.reaction.type.TruncationReaction;
+import lcsb.mapviewer.model.map.reaction.type.TwoProductReactionInterface;
+import lcsb.mapviewer.model.map.reaction.type.TwoReactantReactionInterface;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This is a part of {@link ReactionXmlParser} class functionality that allows
+ * to read reaction from CellDesigner xml node.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ReactionFromXml extends XmlParser {
+
+ /**
+ * Reactant lines in cell designer ends in the 2/5 of the center line.
+ */
+ private static final double REACTANT_END_RATIO = 0.4;
+
+ /**
+ * Product lines in cell designer starts in the 3/5 of the center line.
+ */
+ private static final double PRODUCT_START_RATIO = 0.6;
+
+ /**
+ * Stores information about {@link CellDesignerAnchor} for a node.
+ */
+ private Map<ReactionNode, CellDesignerAnchor> anchorsByNodes = new HashMap<>();
+
+ /**
+ * Stores information about operator type that should be used for a modifier
+ * node.
+ */
+ private Map<ReactionNode, String> typeByModifier = new HashMap<>();
+
+ /**
+ * Stores information to which point on the central rectangle modifier should be
+ * connected.
+ */
+ private Map<ReactionNode, String> lineTypeByModifier = new HashMap<>();
+
+ /**
+ * Stores information about list of points that create line describing modifier.
+ */
+ private Map<ReactionNode, List<Point2D>> pointsByModifier = new HashMap<>();
+
+ /**
+ * Helps to determine if the key Modifier should be treats as part of
+ * NodeOperator (value in the map).
+ */
+ private Map<Modifier, Modifier> modifierParentOperator = new HashMap<>();
+
+ /**
+ * Identifies central line segment in {@link TwoProductReactionInterface} and
+ * {@link TwoReactantReactionInterface} reactions.
+ */
+ private Map<ReactionNode, Integer> indexByComplexReaction = new HashMap<>();
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(ReactionXmlParser.class.getName());
+
+ /**
+ * Xml parser used for processing notes into structured data.
+ */
+ private RestAnnotationParser rap = new RestAnnotationParser();
+
+ /**
+ * Helper object used for manipulation on the point coordinates in CellDesigner
+ * format.
+ */
+ private CellDesignerPointTransformation pointTransformation = new CellDesignerPointTransformation();
+
+ /**
+ * Should SBGN standard be used.
+ */
+ private boolean sbgn;
+
+ CellDesignerElementCollection elements;
+
+ /**
+ * Default constructor.
+ *
+ * @param sbgn
+ * Should the converter use SBGN standard
+ */
+ public ReactionFromXml(CellDesignerElementCollection elements, boolean sbgn) {
+ this.elements = elements;
+ this.sbgn = sbgn;
+ }
+
+ /**
+ * Returns {@link Reaction} object from CellDesigner xml node.
+ *
+ * @param reactionNode
+ * xml node
+ * @param model
+ * model where the reaction is placed
+ * @return reaction from xml node
+ * @throws ReactionParserException
+ * thrown when the xml is invalid
+ * @throws InvalidXmlSchemaException
+ * thrown when reactionNode is invalid xml
+ */
+ public Reaction getReaction(Node reactionNode, Model model) throws ReactionParserException {
+ Reaction result = new Reaction();
+ // we ignore metaid - it's useless and obstruct data model
+ // result.setMetaId(getNodeAttr("metaid", reactionNode));
+ result.setIdReaction(getNodeAttr("id", reactionNode));
+ result.setName(getNodeAttr("name", reactionNode));
+ // by default this value is true...
+ result.setReversible(!(getNodeAttr("reversible", reactionNode).equalsIgnoreCase("false")));
+
+ NodeList nodes = reactionNode.getChildNodes();
+ Node annotationNode = null;
+ Node kineticsNode = null;
+ Node reactantsNode = null;
+ Node productsNode = null;
+ Node modifiersNode = null;
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("annotation")) {
+ annotationNode = node;
+ } else if (node.getNodeName().equalsIgnoreCase("listOfReactants")) {
+ reactantsNode = node;
+ } else if (node.getNodeName().equalsIgnoreCase("listOfProducts")) {
+ productsNode = node;
+ } else if (node.getNodeName().equalsIgnoreCase("listOfModifiers")) {
+ modifiersNode = node;
+ } else if (node.getNodeName().equalsIgnoreCase("notes")) {
+ rap.processNotes(rap.getNotes(node), result);
+ } else if (node.getNodeName().equalsIgnoreCase("kineticLaw")) {
+ kineticsNode = node;
+ } else {
+ throw new ReactionParserException("Unknown element of reaction: " + node.getNodeName(), result);
+ }
+ }
+ }
+ if (annotationNode != null) {
+ result = parseReactionAnnotation(annotationNode, result, model);
+ } else {
+ throw new ReactionParserException("No annotation node in reaction", result);
+ }
+ Map<String, Element> elements = getSpeciesIdToElementMappingFromAnnotationNode(annotationNode, model);
+ if (kineticsNode != null) {
+ KineticsXmlParser kineticsParser = new KineticsXmlParser(model);
+ try {
+ result.setKinetics(kineticsParser.parseKinetics(kineticsNode, elements));
+ } catch (InvalidXmlSchemaException e) {
+ throw new ReactionParserException(result, e);
+ }
+ }
+ assignStochiometry(result.getReactants(), reactantsNode, elements);
+ assignStochiometry(result.getProducts(), productsNode, elements);
+ assignStochiometry(result.getModifiers(), modifiersNode, elements);
+
+ return result;
+ }
+
+ private void assignStochiometry(Collection<? extends ReactionNode> reactionNodes, Node nodes,
+ Map<String, Element> speciesIdToElement) {
+ if (nodes != null) {
+ for (Node child : super.getNodes("speciesReference", nodes.getChildNodes())) {
+ String param = super.getNodeAttr("stoichiometry", child);
+ if (param != null && !param.isEmpty()) {
+ Double stoichometry = Double.parseDouble(param);
+ String speciesId = super.getNodeAttr("species", child);
+ Element e = speciesIdToElement.get(speciesId);
+ boolean assigned = false;
+ for (ReactionNode reactionNode : reactionNodes) {
+ if (reactionNode.getElement().equals(e)) {
+ assigned = true;
+ reactionNode.setStoichiometry(stoichometry);
+ }
+ }
+ if (!assigned) {
+ throw new InvalidStateException("Cannot assign stoichiometry for element: " + speciesId);
+ }
+ }
+ }
+ }
+ }
+
+ private Map<String, Element> getSpeciesIdToElementMappingFromAnnotationNode(Node annotationNode, Model model) {
+ Map<String, Element> result = new HashMap<>();
+
+ List<Node> elementNodes = new ArrayList<>();
+ elementNodes.addAll(super.getAllNotNecessirellyDirectChild("celldesigner:baseReactant", annotationNode));
+ elementNodes.addAll(super.getAllNotNecessirellyDirectChild("celldesigner:baseProduct", annotationNode));
+ elementNodes.addAll(super.getAllNotNecessirellyDirectChild("celldesigner:linkTarget", annotationNode));
+
+ for (Node node : elementNodes) {
+ String speciesId = super.getNodeAttr("species", node);
+ String aliasId = super.getNodeAttr("alias", node);
+ addElementMapping(model, result, speciesId, aliasId);
+ }
+
+ for (Node node : super.getAllNotNecessirellyDirectChild("celldesigner:reactantLink", annotationNode)) {
+ String speciesId = super.getNodeAttr("reactant", node);
+ String aliasId = super.getNodeAttr("alias", node);
+ addElementMapping(model, result, speciesId, aliasId);
+ }
+
+ for (Node node : super.getAllNotNecessirellyDirectChild("celldesigner:productLink", annotationNode)) {
+ String speciesId = super.getNodeAttr("product", node);
+ String aliasId = super.getNodeAttr("alias", node);
+ addElementMapping(model, result, speciesId, aliasId);
+ }
+ for (Node node : super.getAllNotNecessirellyDirectChild("celldesigner:modification", annotationNode)) {
+ String speciesId = super.getNodeAttr("modifiers", node);
+ String aliasId = super.getNodeAttr("aliases", node);
+ addElementMapping(model, result, speciesId, aliasId);
+ }
+
+ return result;
+ }
+
+ private void addElementMapping(Model model, Map<String, Element> result, String speciesId, String aliasId) {
+ String[] aliasIds = aliasId.split(",");
+ String[] speciesIds = speciesId.split(",");
+ for (int i = 0; i < aliasIds.length; i++) {
+
+ Element element = model.getElementByElementId(aliasIds[i]);
+ result.put(speciesIds[i], element);
+ addCompartmentMapping(result, element);
+ }
+ }
+
+ private void addCompartmentMapping(Map<String, Element> result, Element element) {
+ Compartment compartment = element.getCompartment();
+ if (compartment != null) {
+ // in kinetics we can have reference to compartment (so we need to find SBML
+ // compartment id)
+ String compartmentId = elements.getElementByElementId(compartment.getElementId()).getElementId();
+ result.put(compartmentId, compartment);
+ }
+ }
+
+ /**
+ * Parses reaction annotation node and update reaction.
+ *
+ * @param annotationNode
+ * xml node
+ * @param result
+ * reaction to update
+ * @param model
+ * model where reaction is placed
+ * @return updated reaction
+ * @throws ReactionParserException
+ * thrown when the xml is invalid
+ * @throws InvalidXmlSchemaException
+ * thrown when annotationNode is invalid xml
+ */
+ private Reaction parseReactionAnnotation(Node annotationNode, Reaction result, Model model)
+ throws ReactionParserException {
+ NodeList nodes = annotationNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:extension")) {
+ result = parseReactionExtension(result, node, model);
+ } else if (node.getNodeName().equalsIgnoreCase("rdf:RDF")) {
+ try {
+ XmlAnnotationParser xmlParser = new XmlAnnotationParser();
+ result.addMiriamData(xmlParser.parseRdfNode(nodes));
+ } catch (InvalidXmlSchemaException e) {
+ throw new ReactionParserException("Problem with parsing RDF", result, e);
+ }
+ } else {
+ throw new ReactionParserException("Unknown element of reaction/annotation: " + node.getNodeName(), result);
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Parses CellDesigner extension to sbml reaction node and updates reaction.
+ *
+ * @param result
+ * reaction to update
+ * @param node
+ * xml node
+ * @param model
+ * model where reaction is placed
+ * @return updated reaction
+ * @throws ReactionParserException
+ * thrown when the xml is invalid and reason is more specific
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ *
+ */
+ private Reaction parseReactionExtension(Reaction result, Node node, Model model) throws ReactionParserException {
+ NodeList extensionNodes = node.getChildNodes();
+ LineProperties line = null;
+ ConnectScheme connectScheme = null;
+ EditPoints points = null;
+ Node reactantsLinkNode = null;
+ Node productsLinkNode = null;
+ Node modifiersLinkNode = null;
+ Node gateMembers = null;
+ String type = null;
+ for (int y = 0; y < extensionNodes.getLength(); y++) {
+ Node nodeReaction = extensionNodes.item(y);
+ if (nodeReaction.getNodeType() == Node.ELEMENT_NODE) {
+ if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:reactionType")) {
+ type = getNodeValue(nodeReaction);
+ } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:baseReactants")) {
+ NodeList reactantsNodes = nodeReaction.getChildNodes();
+ for (int z = 0; z < reactantsNodes.getLength(); z++) {
+ Node reactantNode = reactantsNodes.item(z);
+ if (reactantNode.getNodeType() == Node.ELEMENT_NODE) {
+ if (reactantNode.getNodeName().equalsIgnoreCase("celldesigner:baseReactant")) {
+ parseBaseReactant(result, reactantNode, model);
+ } else {
+ throw new ReactionParserException(
+ "Unknown element of celldesigner:baseReactants: " + node.getNodeName(), result);
+ }
+ }
+ }
+ } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:baseProducts")) {
+ NodeList reactantsNodes = nodeReaction.getChildNodes();
+ for (int z = 0; z < reactantsNodes.getLength(); z++) {
+ Node reactantNode = reactantsNodes.item(z);
+ if (reactantNode.getNodeType() == Node.ELEMENT_NODE) {
+ if (reactantNode.getNodeName().equalsIgnoreCase("celldesigner:baseProduct")) {
+ parseBaseProduct(model, result, reactantNode);
+ } else {
+ throw new ReactionParserException("Unknown element of celldesigner:baseProducts: " + node.getNodeName(),
+ result);
+ }
+ }
+ }
+ } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:line")) {
+ line = getLineProperties(nodeReaction);
+ } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:connectScheme")) {
+ try {
+ connectScheme = parseConnectScheme(nodeReaction);
+ } catch (InvalidXmlSchemaException e) {
+ throw new ReactionParserException(result, e);
+ }
+ } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:listOfReactantLinks")) {
+ reactantsLinkNode = nodeReaction;
+ } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:listOfProductLinks")) {
+ productsLinkNode = nodeReaction;
+ } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:listOfModification")) {
+ modifiersLinkNode = nodeReaction;
+ } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:editPoints")) {
+ points = parseEditPoints(nodeReaction);
+ } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:name")) {
+ result.setName(getNodeValue(nodeReaction));
+ } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:listOfGateMember")) {
+ gateMembers = nodeReaction;
+ } else {
+ throw new ReactionParserException(
+ "Unknown element of reaction/celldesigner:extension: " + nodeReaction.getNodeName(), result);
+ }
+ }
+ }
+ if (gateMembers != null) {
+ try {
+ points = gateMembersToPoints(gateMembers);
+ } catch (InvalidXmlSchemaException e) {
+ throw new ReactionParserException(result, e);
+ }
+ }
+ result = createProperTypeReaction(type, result);
+ if (connectScheme == null) {
+ throw new ReactionParserException("No connectScheme node", result);
+ }
+ if (points == null) {
+ points = new EditPoints();
+ }
+ if (result instanceof SimpleReactionInterface) {
+ createLinesForSimpleReaction(result, points, connectScheme);
+ } else if (result instanceof TwoReactantReactionInterface) {
+ createLinesForTwoReactantReaction(result, points, gateMembers != null);
+ createOperatorsForTwoReactantReaction(result, gateMembers);
+
+ } else if (result instanceof TwoProductReactionInterface) {
+ createLinesForTwoProductReaction(result, points);
+ createOperatorsForTwoProductReaction(result);
+ } else {
+ throw new ReactionParserException(
+ "Problem with parsing lines. Unknown reaction: " + type + "; " + result.getClass().getName(), result);
+ }
+ if (reactantsLinkNode != null) {
+ parseReactantLinks(result, reactantsLinkNode, model);
+ }
+ if (productsLinkNode != null) {
+ parseProductLinks(result, productsLinkNode, model);
+ }
+
+ // create operators
+ createOperators(result);
+
+ // now try to create modifiers (we must have set fixed layout data for the
+ // core of the reaction)
+ if (modifiersLinkNode != null) {
+ parseReactionModification(result, modifiersLinkNode, model);
+ }
+ for (int i = 0; i < result.getModifiers().size(); i++) {
+ Modifier modifier = result.getModifiers().get(i);
+ if (modifier.getElement() == null) {
+ List<Modifier> modifiers = new ArrayList<Modifier>();
+ modifiers.add(modifier);
+ for (Modifier modifier2 : result.getModifiers()) {
+ if (modifierParentOperator.get(modifier2) == modifier) {
+ modifiers.add(modifier2);
+ }
+ }
+ computeLineForModification(result, modifiers);
+ createOperatorFromModifiers(result, modifiers);
+ result.removeModifier(modifier);
+ i--;
+ } else if (modifier.getLine() == null) {
+ createLineForModifier(result, modifier);
+ }
+ }
+
+ if (line != null) {
+ for (AbstractNode rNode : result.getNodes()) {
+ rNode.getLine().setWidth(line.getWidth());
+ rNode.getLine().setColor(line.getColor());
+ }
+ }
+ if (result.isReversible()) {
+ for (Reactant reactant : result.getReactants()) {
+ reactant.getLine().getBeginAtd().setArrowType(result.getProducts().get(0).getLine().getEndAtd().getArrowType());
+ }
+ }
+
+ return result;
+ }
+
+ /**
+ * Creates reaction with a new type.
+ *
+ * @param type
+ * CellDesigner type of a reaction
+ * @param result
+ * initial data
+ * @return reaction with a new type
+ * @throws ReactionParserException
+ */
+ Reaction createProperTypeReaction(String type, Reaction result) throws ReactionParserException {
+ ReactionLineData rdl = ReactionLineData.getByCellDesignerString(type);
+ if (rdl == null) {
+ throw new ReactionParserException("Unknown CellDesigner class type: " + type + ".", result);
+ }
+ return rdl.createReaction(result);
+ }
+
+ /**
+ * Creates CellDesigner {@link EditPoints} structure for gate members node.
+ *
+ * @param gateMembers
+ * xml node
+ * @return {@link EditPoints} structure representing line information for the
+ * xml node
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ private EditPoints gateMembersToPoints(Node gateMembers) throws InvalidXmlSchemaException {
+ Node lastMember = null;
+ EditPoints result = new EditPoints();
+ Integer num0 = null;
+ Integer num1 = null;
+ Integer num2 = null;
+ for (int i = 0; i < gateMembers.getChildNodes().getLength(); i++) {
+ Node child = gateMembers.getChildNodes().item(i);
+ if (child.getNodeType() == Node.ELEMENT_NODE) {
+
+ if (child.getNodeName().equalsIgnoreCase("celldesigner:GateMember")) {
+ String type = getNodeAttr("type", child);
+ if (type.startsWith(ReactionLineData.BOOLEAN_LOGIC_GATE.getCellDesignerString())) {
+ lastMember = child;
+ } else {
+ String pointsString = getNodeAttr("editPoints", child);
+ List<Point2D> points = parseEditPointsString(pointsString);
+ if (num0 == null) {
+ num0 = points.size();
+ } else if (num1 == null) {
+ num1 = points.size();
+ } else {
+ throw new InvalidXmlSchemaException("Too many gate members");
+ }
+ result.getPoints().addAll(points);
+ }
+ } else {
+ throw new InvalidXmlSchemaException("Unknown node type: " + child.getNodeName());
+ }
+ }
+ }
+ if (lastMember == null) {
+ throw new InvalidXmlSchemaException("Missing gate member connecting members");
+ } else {
+ String pointsString = getNodeAttr("editPoints", lastMember);
+ List<Point2D> points = parseEditPointsString(pointsString);
+ num2 = points.size() - 1;
+ result.getPoints().addAll(points);
+ }
+ result.setNum0(num0);
+ result.setNum1(num1);
+ result.setNum2(num2);
+ return result;
+ }
+
+ /**
+ * Creates line information for the modifier.
+ *
+ * @param reaction
+ * reaction where modifier is placed
+ * @param modifier
+ * modifier to update
+ */
+ private void createLineForModifier(Reaction reaction, Modifier modifier) {
+ Element element = modifier.getElement();
+ CellDesignerAliasConverter converter = new CellDesignerAliasConverter(element, sbgn);
+ Point2D startPoint = converter.getPointCoordinates(element, anchorsByNodes.get(modifier));
+ ModifierTypeUtils modifierTypeUtils = new ModifierTypeUtils();
+
+ Point2D p = modifierTypeUtils.getAnchorPointOnReactionRect(modifier.getReaction(),
+ lineTypeByModifier.get(modifier));
+ PolylineData line = PolylineDataFactory.createPolylineDataFromEditPoints(startPoint, p,
+ pointsByModifier.get(modifier));
+
+ startPoint = converter.getAnchorPointCoordinates(element, anchorsByNodes.get(modifier), line);
+ line.setStartPoint(startPoint);
+ modifier.setLine(line);
+ modifierTypeUtils.updateLineEndPoint(modifier);
+ }
+
+ /**
+ * Creates operators for CellDesigner reaction that belongs to
+ * {@link TwoProductReactionInterface}.
+ *
+ * @param result
+ * reaction to be updated
+ * @throws ReactionParserException
+ * thrown when there is a problem with creating operators (input data
+ * is invalid)
+ */
+ private void createOperatorsForTwoProductReaction(Reaction result) throws ReactionParserException {
+ int inputs = 0;
+ NodeOperator operator = null;
+ if (result.getClass() == DissociationReaction.class) {
+ operator = new DissociationOperator();
+ } else if (result.getClass() == TruncationReaction.class) {
+ operator = new TruncationOperator();
+ } else {
+ throw new ReactionParserException("Invalid reaction type", result);
+ }
+ for (AbstractNode node : result.getNodes()) {
+ if (node.getClass() == Product.class) {
+ operator.addOutput(node);
+ } else if (node.getClass() == Reactant.class) {
+ inputs++;
+ if (inputs > 1) {
+ throw new ReactionParserException("Reaction has more than one reactant", result);
+ }
+ }
+ }
+ if (operator.getOutputs().size() > 2) {
+ throw new ReactionParserException("Too many products: " + operator.getOutputs().size(), result);
+ }
+
+ // and now we have to modify lines
+
+ Reactant reactant = result.getReactants().get(0);
+ Integer index = indexByComplexReaction.get(reactant);
+
+ Point2D p1, p2;
+
+ p1 = reactant.getLine().getPoints().get(index);
+ p2 = reactant.getLine().getPoints().get(index + 1);
+
+ p1 = new Point2D.Double(p1.getX(), p1.getY());
+ p2 = new Point2D.Double(p2.getX(), p2.getY());
+
+ Point2D p = new Point2D.Double((p2.getX() + p1.getX()) / 2, (p2.getY() + p1.getY()) / 2);
+ operator.setLine(reactant.getLine().getSubline(0, index + 1));
+ operator.getLine().addPoint(p);
+
+ p = new Point2D.Double((p2.getX() + p1.getX()) / 2, (p2.getY() + p1.getY()) / 2);
+
+ reactant.setLine(reactant.getLine().getSubline(index + 1, reactant.getLine().getPoints().size()).reverse());
+ reactant.getLine().getPoints().add(p);
+
+ reactant.getLine().trimEnd(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
+ operator.getLine().trimEnd(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
+
+ result.addNode(operator);
+ }
+
+ /**
+ * Creates general input/output operators for the model.
+ *
+ * @param result
+ * reaction to be updated
+ */
+ private void createOperators(Reaction result) {
+ // central line points
+ Point2D p1 = result.getReactants().get(0).getLine().getPoints()
+ .get(result.getReactants().get(0).getLine().getPoints().size() - 2);
+ Point2D p2 = result.getProducts().get(0).getLine().getPoints().get(1);
+ Point2D tmp = result.getProducts().get(0).getLine().getPoints().get(0);
+ Point2D productSplitOperatorBeginPoint = new Point2D.Double(tmp.getX(), tmp.getY());
+
+ // where the line from reactants ends
+ tmp = result.getReactants().get(0).getLine().getPoints()
+ .get(result.getReactants().get(0).getLine().getPoints().size() - 1);
+ Point2D reactantAndOperatorEndPoint = new Point2D.Double(tmp.getX(), tmp.getY());
+
+ Set<AbstractNode> toExclude = new HashSet<AbstractNode>();
+ Set<AbstractNode> toInclude = new HashSet<AbstractNode>();
+ for (NodeOperator operator : result.getOperators()) {
+ toExclude.addAll(operator.getInputs());
+ if (operator.isReactantOperator()) {
+ toInclude.add(operator);
+ // if we have operator in input then central line changes
+ p1 = operator.getLine().getPoints().get(operator.getLine().getPoints().size() - 2);
+ tmp = operator.getLine().getPoints().get(operator.getLine().getPoints().size() - 1);
+ reactantAndOperatorEndPoint = new Point2D.Double(tmp.getX(), tmp.getY());
+ }
+ if (operator.isProductOperator()) {
+ // if we have operator in output then central line changes
+ p2 = operator.getLine().getPoints().get(operator.getLine().getPoints().size() - 2);
+ tmp = operator.getLine().getPoints().get(operator.getLine().getPoints().size() - 1);
+ productSplitOperatorBeginPoint = new Point2D.Double(tmp.getX(), tmp.getY());
+ }
+ }
+
+ double dx = p2.getX() - p1.getX();
+ double dy = p2.getY() - p1.getY();
+
+ Point2D reactantAndOperatorBeginPoint = new Point2D.Double(p1.getX() + dx * REACTANT_END_RATIO,
+ p1.getY() + dy * REACTANT_END_RATIO);
+
+ PolylineData ld = new PolylineData(reactantAndOperatorBeginPoint, reactantAndOperatorEndPoint);
+
+ LineType lineType = null;
+ Set<AbstractNode> nodes = new LinkedHashSet<AbstractNode>();
+ for (Reactant reactant : result.getReactants()) {
+ if (!toExclude.contains(reactant)) {
+ nodes.add(reactant);
+ if (lineType == null) {
+ lineType = reactant.getLine().getType();
+ }
+ }
+ }
+ nodes.addAll(toInclude);
+ nodes.removeAll(toExclude);
+
+ // add an operator only when the number of input nodes is greater than one
+ if (nodes.size() > 1) {
+ AndOperator inputOperator = new AndOperator();
+ inputOperator.setLine(ld);
+ inputOperator.addInputs(nodes);
+ for (Reactant reactant : result.getReactants()) {
+ if (!toExclude.contains(reactant)) {
+ reactant.getLine().getEndPoint().setLocation(reactantAndOperatorBeginPoint.getX(),
+ reactantAndOperatorBeginPoint.getY());
+ }
+ }
+ if (lineType != null) {
+ inputOperator.getLine().setType(lineType);
+ }
+ result.addNode(inputOperator);
+ }
+
+ // and now we try to handle with output operators
+
+ toExclude = new HashSet<AbstractNode>();
+ toInclude = new HashSet<AbstractNode>();
+ for (NodeOperator nOperator : result.getOperators()) {
+ toExclude.addAll(nOperator.getOutputs());
+ if (nOperator.isProductOperator()) {
+ toInclude.add(nOperator);
+ }
+ }
+
+ Point2D productSplitOperatorEndPoint = new Point2D.Double(p1.getX() + dx * PRODUCT_START_RATIO,
+ p1.getY() + dy * PRODUCT_START_RATIO);
+
+ ld = new PolylineData(productSplitOperatorEndPoint, productSplitOperatorBeginPoint);
+
+ lineType = null;
+ nodes = new LinkedHashSet<AbstractNode>();
+ for (Product product : result.getProducts()) {
+ if (!toExclude.contains(product)) {
+ nodes.add(product);
+ if (lineType == null) {
+ lineType = product.getLine().getType();
+ }
+ }
+ }
+ nodes.addAll(toInclude);
+ nodes.removeAll(toExclude);
+ if (nodes.size() > 1) {
+ SplitOperator outputOperator = new SplitOperator();
+ outputOperator.setLine(ld);
+ outputOperator.addOutputs(nodes);
+ for (Product product : result.getProducts()) {
+ if (!toExclude.contains(product)) {
+ // outputOperator.addOutput(product);
+ product.getLine().getPoints().get(0).setLocation(productSplitOperatorEndPoint.getX(),
+ productSplitOperatorEndPoint.getY());
+ }
+ }
+ if (lineType != null) {
+ outputOperator.getLine().setType(lineType);
+ }
+ result.addNode(outputOperator);
+ }
+ }
+
+ /**
+ * Creates operators in modifiers.
+ *
+ * @param reaction
+ * reaction to update
+ * @param modifiers
+ * list of modifiers that must be put into operators
+ */
+ private void createOperatorFromModifiers(Reaction reaction, List<Modifier> modifiers) {
+ OperatorTypeUtils otu = new OperatorTypeUtils();
+ String type = typeByModifier.get(modifiers.get(0));
+ NodeOperator operator = otu.createModifierForStringType(type);
+
+ operator.setLine(modifiers.get(0).getLine());
+
+ for (int i = 1; i < modifiers.size(); i++) {
+ operator.addInput(modifiers.get(i));
+ }
+
+ ModifierTypeUtils modifierTypeUtils = new ModifierTypeUtils();
+ modifierTypeUtils.updateLineEndPoint(operator);
+ reaction.addNode(operator);
+ }
+
+ /**
+ * Creates operators for CellDesigner reaction that belongs to
+ * {@link TwoReactantReactionInterface}.
+ *
+ * @param result
+ * reaction to be updated
+ * @param gateMembers
+ * node representing line information for the operator
+ * @throws ReactionParserException
+ * thrown when the xml is invalid
+ */
+ private void createOperatorsForTwoReactantReaction(Reaction result, Node gateMembers) throws ReactionParserException {
+ NodeOperator andOperator = null;
+ if (result instanceof HeterodimerAssociationReaction) {
+ andOperator = new AssociationOperator();
+ } else if (result instanceof BooleanLogicGateReaction) {
+ andOperator = new AndOperator();
+ } else {
+ throw new ReactionParserException("Unknown class type with two reactants", result);
+ }
+ int outputs = 0;
+ for (AbstractNode node : result.getNodes()) {
+ if (node.getClass() == Reactant.class) {
+ andOperator.addInput(node);
+ } else if (node.getClass() == Product.class) {
+ outputs++;
+ if (outputs > 1) {
+ throw new ReactionParserException("Reaction has more than one product", result);
+ }
+ }
+ }
+ if (andOperator.getInputs().size() > 2) {
+ throw new ReactionParserException("Too many reactants.", result);
+ }
+
+ // and now we have to modify lines
+
+ Product product = result.getProducts().get(0);
+ Integer index = indexByComplexReaction.get(product);
+ if (index != null) {
+ Point2D p1, p2;
+
+ p1 = product.getLine().getPoints().get(index);
+ p2 = product.getLine().getPoints().get(index + 1);
+
+ p1 = new Point2D.Double(p1.getX(), p1.getY());
+ p2 = new Point2D.Double(p2.getX(), p2.getY());
+
+ Point2D p = new Point2D.Double((p2.getX() + p1.getX()) / 2, (p2.getY() + p1.getY()) / 2);
+ andOperator.setLine(product.getLine().getSubline(0, index + 1));
+ andOperator.getLine().addPoint(p);
+ andOperator.getLine().trimEnd(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
+
+ p = new Point2D.Double((p2.getX() + p1.getX()) / 2, (p2.getY() + p1.getY()) / 2);
+
+ product.setLine(product.getLine().getSubline(index, product.getLine().getPoints().size()));
+ product.getLine().getPoints().set(0, p);
+ product.getLine().trimBegin(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
+
+ product.getLine().getEndAtd().setArrowType(ArrowType.FULL);
+
+ result.addNode(andOperator);
+ } else {
+ NodeOperator operator = null;
+ Set<String> undefinedTypes = new HashSet<String>();
+ for (int i = 0; i < gateMembers.getChildNodes().getLength(); i++) {
+ Node child = gateMembers.getChildNodes().item(i);
+ if (child.getNodeType() == Node.ELEMENT_NODE) {
+
+ if (child.getNodeName().equalsIgnoreCase("celldesigner:GateMember")) {
+ String type = getNodeAttr("type", child);
+
+ if (type.equalsIgnoreCase(OperatorType.AND_OPERATOR_STRING.getStringName())) {
+ operator = new AndOperator();
+ } else if (type.equalsIgnoreCase(OperatorType.OR_OPERATOR_STRING.getStringName())) {
+ operator = new OrOperator();
+ } else if (type.equalsIgnoreCase(OperatorType.NAND_OPERATOR_STRING.getStringName())) {
+ operator = new NandOperator();
+ } else if (type.equalsIgnoreCase(OperatorType.UNKNOWN_OPERATOR_STRING.getStringName())) {
+ operator = new UnknownOperator();
+ } else {
+ undefinedTypes.add(type);
+ }
+ }
+ }
+ }
+ if (operator == null) {
+ String types = "";
+ for (String string : undefinedTypes) {
+ types += string + ", ";
+ }
+ throw new ReactionParserException(
+ "Couldn't find type of BOOLEAN_LOGIC_GATE. Unknown types identified: " + types, result);
+ }
+
+ operator.addInputs(andOperator.getInputs());
+ operator.addOutput(product);
+
+ // empty line
+ PolylineData line = new PolylineData();
+ line.addPoint(product.getLine().getBeginPoint());
+ line.addPoint(product.getLine().getBeginPoint());
+
+ operator.setLine(line);
+ result.addNode(operator);
+ }
+
+ }
+
+ /**
+ * Creates lines for reaction that belongs to
+ * {@link TwoProductReactionInterface}.
+ *
+ * @param reaction
+ * reaction to update
+ * @param points
+ * information about points
+ */
+ private void createLinesForTwoProductReaction(Reaction reaction, EditPoints points) {
+ Point2D p = points.getPoints().get(points.size() - 1);
+ Product product1 = reaction.getProducts().get(0);
+ Product product2 = reaction.getProducts().get(1);
+ Reactant reactant = reaction.getReactants().get(0);
+
+ CellDesignerAliasConverter reactantConverter = new CellDesignerAliasConverter(reactant.getElement(), sbgn);
+ CellDesignerAliasConverter product1Converter = new CellDesignerAliasConverter(product1.getElement(), sbgn);
+ CellDesignerAliasConverter product2Converter = new CellDesignerAliasConverter(product2.getElement(), sbgn);
+
+ Point2D p1 = reactantConverter.getPointCoordinates(reactant.getElement(), anchorsByNodes.get(reactant));
+ Point2D p2 = product1Converter.getPointCoordinates(product1.getElement(), anchorsByNodes.get(product1));
+ Point2D p3 = product2Converter.getPointCoordinates(product2.getElement(), anchorsByNodes.get(product2));
+
+ Point2D centerPoint = pointTransformation.getCoordinatesInNormalBase(product1.getElement().getCenter(),
+ product2.getElement().getCenter(), reactant.getElement().getCenter(), p);
+
+ int startId0 = 0;
+ int num0 = points.getNum0();
+ int startId1 = num0;
+ int num1 = num0 + points.getNum1();
+ int startId2 = num1;
+ int num2 = num1 + points.getNum2();
+
+ ArrayList<Point2D> linePoints1 = new ArrayList<Point2D>(points.getPoints().subList(startId0, num0));
+ ArrayList<Point2D> linePoints2 = new ArrayList<Point2D>(points.getPoints().subList(startId1, num1));
+ ArrayList<Point2D> linePoints3 = new ArrayList<Point2D>(points.getPoints().subList(startId2, num2));
+
+ PolylineData product1Line = PolylineDataFactory.createPolylineDataFromEditPoints(centerPoint, p2, linePoints2);
+ PolylineData product2Line = PolylineDataFactory.createPolylineDataFromEditPoints(centerPoint, p3, linePoints3);
+
+ PolylineData reactantLine = PolylineDataFactory.createPolylineDataFromEditPoints(centerPoint, p1, linePoints1);
+
+ p1 = product2Converter.getAnchorPointCoordinates(product2.getElement(), anchorsByNodes.get(product2),
+ product2Line.reverse());
+ product2Line.setEndPoint(p1);
+
+ p1 = product1Converter.getAnchorPointCoordinates(product1.getElement(), anchorsByNodes.get(product1),
+ product1Line.reverse());
+ product1Line.setEndPoint(p1);
+
+ p1 = reactantConverter.getAnchorPointCoordinates(reactant.getElement(), anchorsByNodes.get(reactant),
+ reactantLine.reverse());
+ reactantLine.setEndPoint(p1);
+
+ product2Line.getEndAtd().setArrowType(ArrowType.FULL);
+ product1Line.getEndAtd().setArrowType(ArrowType.FULL);
+ product1.setLine(product1Line);
+ product2.setLine(product2Line);
+ reactant.setLine(reactantLine);
+
+ indexByComplexReaction.put(reactant, points.getIndex());
+
+ }
+
+ /**
+ * Creates lines for reaction that belongs to
+ * {@link TwoReactantReactionInterface}.
+ *
+ * @param reaction
+ * reaction to update
+ * @param points
+ * information about points
+ * @param hasGateMemebers
+ * does the reaction has gate members
+ * @throws ReactionParserException
+ * thrown when data for reaction is invalid
+ */
+ private void createLinesForTwoReactantReaction(Reaction reaction, EditPoints points, boolean hasGateMemebers)
+ throws ReactionParserException {
+ Point2D p = points.getPoints().get(points.size() - 1);
+ Product product = reaction.getProducts().get(0);
+ Reactant reactant1 = reaction.getReactants().get(0);
+ Reactant reactant2 = reaction.getReactants().get(1);
+ CellDesignerAliasConverter productConverter = new CellDesignerAliasConverter(product.getElement(), sbgn);
+ CellDesignerAliasConverter reactantConverter1 = new CellDesignerAliasConverter(reactant1.getElement(), sbgn);
+ CellDesignerAliasConverter reactantConverter2 = new CellDesignerAliasConverter(reactant2.getElement(), sbgn);
+ Point2D p1 = reactantConverter1.getPointCoordinates(reactant1.getElement(), anchorsByNodes.get(reactant1));
+ Point2D p2 = reactantConverter2.getPointCoordinates(reactant2.getElement(), anchorsByNodes.get(reactant2));
+ Point2D p3 = productConverter.getPointCoordinates(product.getElement(), anchorsByNodes.get(product));
+
+ Element alias1 = reactant1.getElement();
+ Element alias2 = reactant2.getElement();
+ Element alias3 = product.getElement();
+
+ Point2D pointA = alias2.getCenter();
+ Point2D pointC = alias1.getCenter();
+ Point2D pointB = alias3.getCenter();
+ Point2D pointP = p;
+ Point2D centerPoint = null;
+ if (!hasGateMemebers) {
+ centerPoint = pointTransformation.getCoordinatesInNormalBase(pointA, pointB, pointC, pointP);
+ } else {
+ centerPoint = pointP;
+ }
+
+ int startId0 = 0;
+ int num0 = points.getNum0();
+ int startId1 = num0;
+ int num1 = num0 + points.getNum1();
+ int startId2 = num1;
+ int num2 = num1 + points.getNum2();
+
+ List<Point2D> linePoints1 = new ArrayList<Point2D>(points.getPoints().subList(startId0, num0));
+ List<Point2D> linePoints2 = new ArrayList<Point2D>(points.getPoints().subList(startId1, num1));
+ List<Point2D> linePoints3 = new ArrayList<Point2D>(points.getPoints().subList(startId2, num2));
+
+ PolylineData reactant1Line = null;
+ PolylineData reactant2Line = null;
+ if (!hasGateMemebers) {
+ reactant1Line = PolylineDataFactory.createPolylineDataFromEditPoints(centerPoint, p1, linePoints1);
+ reactant2Line = PolylineDataFactory.createPolylineDataFromEditPoints(centerPoint, p2, linePoints2);
+ } else {
+ reactant1Line = PolylineDataFactory.createPolylineDataFromEditPoints(p1, centerPoint, linePoints1);
+ reactant1Line = reactant1Line.reverse();
+
+ reactant2Line = PolylineDataFactory.createPolylineDataFromEditPoints(p2, centerPoint, linePoints2);
+ reactant2Line = reactant2Line.reverse();
+ }
+
+ PolylineData productLine = PolylineDataFactory.createPolylineDataFromEditPoints(centerPoint, p3, linePoints3);
+
+ p1 = reactantConverter1.getAnchorPointCoordinates(reactant1.getElement(), anchorsByNodes.get(reactant1),
+ reactant1Line.reverse());
+ reactant1Line.setEndPoint(p1);
+ reactant1Line = reactant1Line.reverse();
+
+ p1 = reactantConverter2.getAnchorPointCoordinates(reactant2.getElement(), anchorsByNodes.get(reactant2),
+ reactant2Line.reverse());
+ reactant2Line.setEndPoint(p1);
+ reactant2Line = reactant2Line.reverse();
+
+ p1 = productConverter.getAnchorPointCoordinates(product.getElement(), anchorsByNodes.get(product),
+ productLine.reverse());
+ productLine.setEndPoint(p1);
+ if (hasGateMemebers) {
+ productLine.getEndAtd().setArrowType(ArrowType.OPEN);
+ }
+
+ product.setLine(productLine);
+ reactant1.setLine(reactant1Line);
+ reactant2.setLine(reactant2Line);
+
+ indexByComplexReaction.put(product, points.getIndex());
+ }
+
+ /**
+ * Creates lines for reaction that belongs to {@link SimpleReactionInterface}
+ * (only one standard product and one standard reactant).
+ *
+ * @param reaction
+ * reaction to update
+ * @param editPoints
+ * information about points
+ * @param scheme
+ * some additional information about the line
+ */
+ private void createLinesForSimpleReaction(Reaction reaction, EditPoints editPoints, ConnectScheme scheme) {
+ Product product = reaction.getProducts().get(0);
+ Reactant reactant = reaction.getReactants().get(0);
+ CellDesignerAliasConverter productConverter = new CellDesignerAliasConverter(product.getElement(), sbgn);
+ CellDesignerAliasConverter reactantConverter = new CellDesignerAliasConverter(reactant.getElement(), sbgn);
+
+ Point2D endPoint = productConverter.getPointCoordinates(product.getElement(), anchorsByNodes.get(product));
+ Point2D startPoint = reactantConverter.getPointCoordinates(reactant.getElement(), anchorsByNodes.get(reactant));
+
+ PolylineData ld = PolylineDataFactory.createPolylineDataFromEditPoints(startPoint, endPoint,
+ editPoints.getPoints());
+
+ // first place where the index of rectangle is kept
+ Integer index = editPoints.getIndex();
+
+ // second place where index of rectangle is kept
+ if (index == null) {
+ index = scheme.getConnectIndex();
+ if (index != null) {
+ // but...
+ // direction of the index is reversed...
+ index = ld.getPoints().size() - index - 2;
+ }
+ }
+ // but sometimes there is no information about index...
+ if (index == null) {
+ index = 0;
+ }
+ startPoint = reactantConverter.getAnchorPointCoordinates(reactant.getElement(), anchorsByNodes.get(reactant), ld);
+ endPoint = productConverter.getAnchorPointCoordinates(product.getElement(), anchorsByNodes.get(product),
+ ld.reverse());
+ ld.getPoints().set(0, startPoint);
+ ld.getPoints().set(ld.getPoints().size() - 1, endPoint);
+
+ PolylineData line = new PolylineData(ld);
+
+ PolylineData reactantLine = line.getSubline(0, ld.getPoints().size() - index - 1);
+ PolylineData productLine = line.getSubline(ld.getPoints().size() - index - 2, ld.getPoints().size());
+
+ Point2D p1 = ld.getPoints().get(ld.getPoints().size() - index - 2);
+ Point2D p2 = ld.getPoints().get(ld.getPoints().size() - index - 1);
+ Point2D p = new Point2D.Double((p2.getX() + p1.getX()) / 2, (p2.getY() + p1.getY()) / 2);
+ reactantLine.getPoints().add(p);
+ reactantLine.trimEnd(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
+
+ p = new Point2D.Double((p2.getX() + p1.getX()) / 2, (p2.getY() + p1.getY()) / 2);
+ productLine.getPoints().set(0, p);
+ productLine.trimBegin(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
+
+ productLine.getEndAtd().setArrowType(ArrowType.FULL);
+
+ reactant.setLine(reactantLine);
+ product.setLine(productLine);
+
+ ReactionLineData rld = ReactionLineData.getByReactionType(reaction.getClass());
+ reactantLine.setType(rld.getLineType());
+ productLine.setType(rld.getLineType());
+ productLine.getEndAtd().setArrowType(rld.getProductArrowType());
+ productLine.trimEnd(rld.getProductLineTrim());
+ }
+
+ /**
+ * Prepares {@link EditPoints} structure from xml node.
+ *
+ * @param rootNode
+ * xml node
+ * @return {@link EditPoints} object containing CellDesigner line data
+ */
+ private EditPoints parseEditPoints(Node rootNode) {
+ EditPoints result = new EditPoints();
+ String num0 = getNodeAttr("num0", rootNode);
+ String num1 = getNodeAttr("num1", rootNode);
+ String num2 = getNodeAttr("num2", rootNode);
+ if (!num0.equals("")) {
+ result.setNum0(Integer.parseInt(num0));
+ }
+ if (!num1.equals("")) {
+ result.setNum1(Integer.parseInt(num1));
+ }
+ if (!num2.equals("")) {
+ result.setNum2(Integer.parseInt(num2));
+ }
+ String index = getNodeAttr("tShapeIndex", rootNode);
+ if (!index.equals("")) {
+ result.setIndex(Integer.parseInt(index));
+ }
+
+ String pointsString = getNodeValue(rootNode);
+ result.setPoints(parseEditPointsString(pointsString));
+ return result;
+ }
+
+ /**
+ * Parses CellDesigner point by point string.
+ *
+ * @param pointsString
+ * String containing points
+ * @return list of points
+ */
+ ArrayList<Point2D> parseEditPointsString(String pointsString) {
+ ArrayList<Point2D> points2 = new ArrayList<Point2D>();
+ if (pointsString.isEmpty()) {
+ return points2;
+ }
+ String[] points = pointsString.trim().split(" ");
+ for (String string : points) {
+ String[] p = string.split(",");
+ if (p.length != 2) {
+ throw new InvalidArgumentException("Invalid editPoint string: " + string);
+ } else {
+ double posX = Double.parseDouble(p[0]);
+ double posY = Double.parseDouble(p[1]);
+ Point2D point = new Point2D.Double(posX, posY);
+ if (!pointTransformation.isValidPoint(point)) {
+ throw new InvalidArgumentException(
+ "Invalid point parsed from input string: " + string + ". Result point: " + point);
+ }
+ points2.add(point);
+ }
+ }
+ return points2;
+ }
+
+ /**
+ * Parses xml node with reactantLink nodes and creates reactants in the
+ * reaction.
+ *
+ * @param result
+ * reaction to be updated
+ * @param rootNode
+ * xml node to parse
+ * @param model
+ * model where reaction is placed
+ * @throws ReactionParserException
+ * thrown when the xml is invalid
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ private void parseReactantLinks(Reaction result, Node rootNode, Model model) throws ReactionParserException {
+ NodeList list = rootNode.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:reactantLink")) {
+ Reactant newReactant = getReactantLink(node, model, result);
+ result.addReactant(newReactant);
+ } else {
+ throw new ReactionParserException(
+ "Unknown element of celldesigner:listOfReactantLinks: " + node.getNodeName(), result);
+ }
+ }
+ }
+ }
+
+ /**
+ * Parses xml node for reactanLink and creates reactant from it.
+ *
+ * @param rootNode
+ * xml node to parse
+ * @param model
+ * model where reaction is placed
+ * @param reaction
+ * reaction that is being parsed
+ * @return reactant obtained from xml node
+ * @throws ReactionParserException
+ * thrown when the xml is invalid and reason is more specific
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ private Reactant getReactantLink(Node rootNode, Model model, Reaction reaction) throws ReactionParserException {
+ String aliasId = getNodeAttr("alias", rootNode);
+ Species al = (Species) model.getElementByElementId(aliasId);
+ if (al == null) {
+ throw new ReactionParserException("Alias doesn't exist (id: " + aliasId + ")", reaction);
+ }
+
+ Reactant result = new Reactant(al);
+ CellDesignerAnchor anchor = null;
+ EditPoints points = null;
+
+ NodeList nodes = rootNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:connectScheme")) {
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:linkAnchor")) {
+ anchor = CellDesignerAnchor.valueOf(getNodeAttr("position", node).toUpperCase());
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:line")) {
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:editPoints")) {
+ points = parseEditPoints(node);
+ } else {
+ throw new ReactionParserException("Unknown element of celldesigner:reactantLink: " + node.getNodeName(),
+ reaction);
+ }
+ }
+ }
+
+ CellDesignerAliasConverter reactantConverter = new CellDesignerAliasConverter(al, sbgn);
+ Point2D additionalPoint = reactantConverter.getPointCoordinates(al, anchor);
+ ArrowTypeData atd = new ArrowTypeData();
+ atd.setArrowType(ArrowType.NONE);
+
+ Point2D endPoint;
+
+ Line2D centerLine = reaction.getCenterLine();
+
+ double dx = centerLine.getX2() - centerLine.getX1();
+ double dy = centerLine.getY2() - centerLine.getY1();
+ double coef = REACTANT_END_RATIO;
+ endPoint = new Point2D.Double(centerLine.getX1() + dx * coef, centerLine.getY1() + dy * coef);
+
+ PolylineData polyline = PolylineDataFactory.createPolylineDataFromEditPoints(additionalPoint, endPoint, points);
+
+ additionalPoint = reactantConverter.getAnchorPointCoordinates(al, anchor, polyline);
+ polyline.setStartPoint(additionalPoint);
+ result.setLine(polyline);
+
+ return result;
+ }
+
+ /**
+ * Parses xml node with productLink nodes and creates products in the reaction.
+ *
+ * @param result
+ * reaction to be updated
+ * @param rootNode
+ * xml node to parse
+ * @param model
+ * model where reaction is placed
+ * @throws ReactionParserException
+ * thrown when the xml is invalid
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ private void parseProductLinks(Reaction result, Node rootNode, Model model) throws ReactionParserException {
+ NodeList list = rootNode.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:productLink")) {
+ Product link = getProductLink(node, model, result);
+ result.addProduct(link);
+ } else {
+ throw new ReactionParserException("Unknown element of celldesigner:listOfProductLinks: " + node.getNodeName(),
+ result);
+ }
+ }
+ }
+ }
+
+ /**
+ * Parses xml node for productLink and creates product from it.
+ *
+ * @param rootNode
+ * xml node to parse
+ * @param model
+ * model where reaction is placed
+ * @param reaction
+ * reaction that is being parsed
+ * @return product obtained from xml node
+ * @throws ReactionParserException
+ * thrown when the xml is invalid
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ private Product getProductLink(Node rootNode, Model model, Reaction reaction) throws ReactionParserException {
+ String aliasId = getNodeAttr("alias", rootNode);
+ Species al = (Species) model.getElementByElementId(aliasId);
+ if (al == null) {
+ throw new ReactionParserException("Alias doesn't exist (id: " + aliasId + ")", reaction);
+ }
+
+ Product result = new Product(al);
+
+ CellDesignerAnchor anchor = null;
+ EditPoints points = null;
+
+ NodeList nodes = rootNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:connectScheme")) {
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:linkAnchor")) {
+ anchor = CellDesignerAnchor.valueOf(getNodeAttr("position", node).toUpperCase());
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:line")) {
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:editPoints")) {
+ points = parseEditPoints(node);
+ } else {
+ throw new ReactionParserException("Unknown element of celldesigner:reactantLink: " + node.getNodeName(),
+ reaction);
+ }
+ }
+ }
+
+ CellDesignerAliasConverter reactantConverter = new CellDesignerAliasConverter(al, sbgn);
+ Point2D additionalPoint = reactantConverter.getPointCoordinates(al, anchor);
+ ArrowTypeData atd = new ArrowTypeData();
+ atd.setArrowType(ArrowType.NONE);
+
+ Point2D endPoint;
+
+ // central line points
+ Point2D p1 = reaction.getReactants().get(0).getLine().getPoints()
+ .get(reaction.getReactants().get(0).getLine().getPoints().size() - 2);
+ Point2D p2 = reaction.getProducts().get(0).getLine().getPoints().get(1);
+
+ Set<AbstractNode> toExclude = new HashSet<AbstractNode>();
+ Set<AbstractNode> toInclude = new HashSet<AbstractNode>();
+ for (NodeOperator operator : reaction.getOperators()) {
+ toExclude.addAll(operator.getInputs());
+ if (operator.isReactantOperator()) {
+ toInclude.add(operator);
+ // if we have operator in input then central line changes
+ p1 = operator.getLine().getPoints().get(operator.getLine().getPoints().size() - 2);
+ }
+ if (operator.isProductOperator()) {
+ // if we have operator in output then central line changes
+ p2 = operator.getLine().getPoints().get(operator.getLine().getPoints().size() - 2);
+ }
+ }
+
+ double dx = p2.getX() - p1.getX();
+ double dy = p2.getY() - p1.getY();
+ double coef = PRODUCT_START_RATIO;
+ endPoint = new Point2D.Double(p1.getX() + dx * coef, p1.getY() + dy * coef);
+
+ PolylineData polyline = PolylineDataFactory.createPolylineDataFromEditPoints(endPoint, additionalPoint, points);
+ additionalPoint = reactantConverter.getAnchorPointCoordinates(al, anchor, polyline.reverse());
+ polyline.setEndPoint(additionalPoint);
+
+ polyline.getEndAtd().setArrowType(ArrowType.FULL);
+ result.setLine(polyline);
+ return result;
+ }
+
+ /**
+ * Creates {@link LineProperties} object from the node.
+ *
+ * @param node
+ * xml node to parse
+ * @return {@link LineProperties} object
+ */
+ private LineProperties getLineProperties(Node node) {
+ LineProperties line = new LineProperties();
+ String tmp = getNodeAttr("width", node);
+ line.setWidth(Double.parseDouble(tmp));
+ tmp = getNodeAttr("color", node);
+ line.setColor(stringToColor(tmp));
+ line.setType(getNodeAttr("type", node));
+ return line;
+ }
+
+ /**
+ * PArse reaction modifiactions and add them into reaction.
+ *
+ * @param result
+ * reaction currently processed
+ * @param rootNode
+ * xml node to parse
+ * @param model
+ * model where reaction is placed
+ * @throws ReactionParserException
+ * thrown when the xml is invalid, and reason is more specific
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ private void parseReactionModification(Reaction result, Node rootNode, Model model) throws ReactionParserException {
+ NodeList nodes = rootNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:modification")) {
+ parseModificationReaction(result, node, model);
+ } else {
+ throw new ReactionParserException("Unknown element of celldesigner:listOfModification: " + node.getNodeName(),
+ result);
+ }
+ }
+ }
+ }
+
+ /**
+ * PArses modification node and adds this modification to reaction.
+ *
+ * @param reaction
+ * reaction currently processed
+ * @param rootNode
+ * xml node
+ * @param model
+ * model where reaction is placed
+ * @throws ReactionParserException
+ * thrown when node cannot be parsed properly
+ */
+ private void parseModificationReaction(Reaction reaction, Node rootNode, Model model) throws ReactionParserException {
+ ModifierTypeUtils modifierTypeUtils = new ModifierTypeUtils();
+ String type = getNodeAttr("type", rootNode);
+ String modificationType = getNodeAttr("modificationType", rootNode);
+ String aliasId = getNodeAttr("aliases", rootNode);
+ String lineConnectionType = getNodeAttr("targetLineIndex", rootNode);
+ String points = getNodeAttr("editPoints", rootNode);
+
+ List<Species> aliasList = new ArrayList<Species>();
+
+ String[] list = aliasId.split(",");
+ for (String string : list) {
+ Species al = (Species) model.getElementByElementId(string);
+ if (al != null) {
+ aliasList.add(al);
+ } else {
+ throw new ReactionParserException("Unknown alias: " + string, reaction);
+ }
+ }
+ Modifier result = null;
+ if (aliasList.size() > 1) {
+ result = new Modifier(null);
+ reaction.addModifier(result);
+ for (int i = 0; i < aliasList.size(); i++) {
+ Modifier mod = modifierTypeUtils.createModifierForStringType(modificationType, aliasList.get(i));
+ modifierParentOperator.put(mod, result);
+ reaction.addModifier(mod);
+ }
+ } else {
+ ModifierType mType = modifierTypeUtils.getModifierTypeForStringType(type);
+ if (mType == null) {
+ String errorInfo = "[" + reaction.getClass().getSimpleName() + "\t" + reaction.getIdReaction()
+ + "]\tUnknown modifier type: " + type;
+ if (ReactionLineData.getByCellDesignerString(type) != null) {
+ errorInfo += ".\tThis type can be applied to reaction type only, not modifier.";
+ }
+ throw new UnknownModifierClassException(errorInfo, type, reaction.getIdReaction());
+ }
+ for (Modifier modifier : reaction.getModifiers()) {
+ if (modifier.getElement() == aliasList.get(0) && modifier.getClass() == mType.getClazz()) {
+ result = modifier;
+ }
+ }
+ if (result == null) {
+ result = modifierTypeUtils.createModifierForStringType(type, aliasList.get(0));
+ reaction.addModifier(result);
+ }
+ }
+ pointsByModifier.put(result, parseEditPointsString(points));
+ typeByModifier.put(result, type);
+ lineTypeByModifier.put(result, lineConnectionType);
+
+ NodeList nodes = rootNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:connectScheme")) {
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:line")) {
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:linkTarget")) {
+ try {
+ CellDesignerAnchor anchor = getAnchorFromLinkTarget(node);
+ anchorsByNodes.put(result, anchor);
+ } catch (InvalidXmlSchemaException e) {
+ throw new ReactionParserException(reaction, e);
+ }
+ } else {
+ throw new ReactionParserException("Unknown element of celldesigner:listOfModification: " + node.getNodeName(),
+ reaction);
+ }
+ }
+
+ }
+
+ }
+
+ /**
+ * Creates lines for modifiers.
+ *
+ * @param reaction
+ * reaction where modifiers are placed
+ * @param modifiers
+ * list of modifiers for which lines should be generated
+ */
+ private void computeLineForModification(Reaction reaction, List<Modifier> modifiers) {
+ ModifierTypeUtils modifierTypeUtils = new ModifierTypeUtils();
+ Point2D p = modifierTypeUtils.getAnchorPointOnReactionRect(reaction, lineTypeByModifier.get(modifiers.get(0)));
+
+ Point2D startPoint;
+ List<Point2D> subPoints;
+ // in case we have more then one alias in modification then we need to
+ // define the start point as a different one then one on the alias
+ Modifier modifier = modifiers.get(0);
+ List<Point2D> points = pointsByModifier.get(modifier);
+ startPoint = points.get(points.size() - 1);
+ subPoints = points.subList(0, points.size() - 1);
+ PolylineData line = PolylineDataFactory.createPolylineDataFromEditPoints(startPoint, p, subPoints);
+ modifier.setLine(line);
+
+ Point2D endPoint = startPoint;
+
+ for (int i = 1; i < modifiers.size(); i++) {
+ Modifier param = modifiers.get(i);
+ CellDesignerAliasConverter reactantConverter = new CellDesignerAliasConverter(param.getElement(), sbgn);
+ startPoint = reactantConverter.getPointCoordinates(param.getElement(), anchorsByNodes.get(param));
+
+ PolylineData polyline = PolylineDataFactory.createPolylineDataFromEditPoints(startPoint, endPoint,
+ pointsByModifier.get(param));
+
+ startPoint = reactantConverter.getAnchorPointCoordinates(param.getElement(), anchorsByNodes.get(param), polyline);
+ polyline.setStartPoint(startPoint);
+ param.setLine(polyline);
+ }
+ }
+
+ /**
+ * Returns {@link CellDesignerAnchor} point from linkAnchor xml node.
+ *
+ * @param rootNode
+ * xml node
+ * @return {@link CellDesignerAnchor} object representing anchor point
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ private CellDesignerAnchor getAnchorFromLinkTarget(Node rootNode) throws InvalidXmlSchemaException {
+ CellDesignerAnchor result = null;
+
+ NodeList nodes = rootNode.getChildNodes();
+ for (int z = 0; z < nodes.getLength(); z++) {
+ Node node = nodes.item(z);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:linkAnchor")) {
+ result = CellDesignerAnchor.valueOf(getNodeAttr("position", node).toUpperCase());
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:connectScheme: " + node.getNodeName());
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Creates {@link ConnectScheme} object from xml node.
+ *
+ * @param nodeReaction
+ * xml node to parse
+ * @return {@link ConnectScheme} object for given xml
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ private ConnectScheme parseConnectScheme(Node nodeReaction) throws InvalidXmlSchemaException {
+ ConnectScheme result = new ConnectScheme();
+ result.setConnectPolicy(getNodeAttr("connectPolicy", nodeReaction));
+ result.setConnectIndex(getNodeAttr("rectangleIndex", nodeReaction));
+ NodeList reactantsNodes = nodeReaction.getChildNodes();
+ for (int z = 0; z < reactantsNodes.getLength(); z++) {
+ Node reactantNode = reactantsNodes.item(z);
+ if (reactantNode.getNodeType() == Node.ELEMENT_NODE) {
+ if (reactantNode.getNodeName().equalsIgnoreCase("celldesigner:listOfLineDirection")) {
+ result.setLineDirections(getlineDirectionMapForReactions(reactantNode));
+ } else {
+ throw new InvalidXmlSchemaException(
+ "Unknown element of celldesigner:connectScheme: " + nodeReaction.getNodeName());
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Parse lineDirectionMap. This structure is nowhere used.
+ *
+ * @param reactantNode
+ * xml node
+ * @return map with directions for every line
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ private Map<String, String> getlineDirectionMapForReactions(Node reactantNode) throws InvalidXmlSchemaException {
+ Map<String, String> result = new HashMap<String, String>();
+ NodeList nodes = reactantNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:lineDirection")) {
+ String index = getNodeAttr("index", node);
+ String value = getNodeAttr("value", node);
+ result.put(index, value);
+ } else {
+ throw new InvalidXmlSchemaException(
+ "Unknown element of reaction/celldesigner:baseReactant: " + node.getNodeName());
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * PArses baseReactant node from CellDEsigenr xml node and adds it into
+ * reaction.
+ *
+ * @param result
+ * reaction that is processed
+ * @param reactantNode
+ * xml node to parse
+ * @param model
+ * model where reaction is placed
+ * @throws ReactionParserException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ private void parseBaseReactant(Reaction result, Node reactantNode, Model model) throws ReactionParserException {
+ String aliasId = getNodeAttr("alias", reactantNode);
+ Species alias = model.getElementByElementId(aliasId);
+ if (alias == null) {
+ throw new ReactionParserException("Alias with id=" + aliasId + " doesn't exist.", result);
+ }
+ Reactant reactant = new Reactant(alias);
+ result.addReactant(reactant);
+ NodeList nodes = reactantNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:linkAnchor")) {
+ anchorsByNodes.put(reactant, CellDesignerAnchor.valueOf(getNodeAttr("position", node)));
+ } else {
+ throw new ReactionParserException(
+ "Unknown element of reaction/celldesigner:baseReactant: " + node.getNodeName(), result);
+ }
+ }
+
+ }
+ }
+
+ /**
+ * Parses baseProduct node from CellDEsigenr xml node and adds it into reaction.
+ *
+ * @param result
+ * reaction that is processed
+ * @param reactantNode
+ * xml node to parse
+ * @param model
+ * model where reaction is placed
+ * @throws ReactionParserException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ private void parseBaseProduct(Model model, Reaction result, Node reactantNode) throws ReactionParserException {
+ String aliasId = getNodeAttr("alias", reactantNode);
+ Species alias = (Species) model.getElementByElementId(aliasId);
+ if (alias == null) {
+ throw new ReactionParserException("Alias with id=" + aliasId + " doesn't exist.", result);
+ }
+ Product product = new Product(alias);
+ result.addProduct(product);
+ NodeList nodes = reactantNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:linkAnchor")) {
+ anchorsByNodes.put(product, CellDesignerAnchor.valueOf(getNodeAttr("position", node)));
+ } else {
+ throw new ReactionParserException(
+ "Unknown element of reaction/celldesigner:baseProduct: " + node.getNodeName(), result);
+ }
+ }
+ }
+
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionLineData.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionLineData.java
index 638c44995c..7c37fcba83 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionLineData.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionLineData.java
@@ -1,412 +1,412 @@
-package lcsb.mapviewer.converter.model.celldesigner.reaction;
-
-import java.util.HashMap;
-import java.util.Map;
-
-import lcsb.mapviewer.model.graphics.ArrowType;
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.type.BooleanLogicGateReaction;
-import lcsb.mapviewer.model.map.reaction.type.CatalysisReaction;
-import lcsb.mapviewer.model.map.reaction.type.DissociationReaction;
-import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
-import lcsb.mapviewer.model.map.reaction.type.InhibitionReaction;
-import lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction;
-import lcsb.mapviewer.model.map.reaction.type.ModulationReaction;
-import lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction;
-import lcsb.mapviewer.model.map.reaction.type.PhysicalStimulationReaction;
-import lcsb.mapviewer.model.map.reaction.type.PositiveInfluenceReaction;
-import lcsb.mapviewer.model.map.reaction.type.ReducedModulationReaction;
-import lcsb.mapviewer.model.map.reaction.type.ReducedPhysicalStimulationReaction;
-import lcsb.mapviewer.model.map.reaction.type.ReducedTriggerReaction;
-import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
-import lcsb.mapviewer.model.map.reaction.type.TranscriptionReaction;
-import lcsb.mapviewer.model.map.reaction.type.TranslationReaction;
-import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
-import lcsb.mapviewer.model.map.reaction.type.TriggerReaction;
-import lcsb.mapviewer.model.map.reaction.type.TruncationReaction;
-import lcsb.mapviewer.model.map.reaction.type.UnknownCatalysisReaction;
-import lcsb.mapviewer.model.map.reaction.type.UnknownInhibitionReaction;
-import lcsb.mapviewer.model.map.reaction.type.UnknownNegativeInfluenceReaction;
-import lcsb.mapviewer.model.map.reaction.type.UnknownPositiveInfluenceReaction;
-import lcsb.mapviewer.model.map.reaction.type.UnknownReducedModulationReaction;
-import lcsb.mapviewer.model.map.reaction.type.UnknownReducedPhysicalStimulationReaction;
-import lcsb.mapviewer.model.map.reaction.type.UnknownReducedTriggerReaction;
-import lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction;
-
-/**
- * This class represent graphical information about lines/arrows that are
- * related to CellDesigner {@link Reaction} type.
- *
- * @author Piotr Gawron
- *
- */
-public enum ReactionLineData {
-
- /**
- * Information about arrows/lines for {@link BooleanLogicGateReaction} class.
- */
- BOOLEAN_LOGIC_GATE(BooleanLogicGateReaction.class, "BOOLEAN_LOGIC_GATE"),
-
- /**
- * Information about arrows/lines for {@link CatalysisReaction} class.
- */
- CATALYSIS(CatalysisReaction.class, "CATALYSIS", LineType.SOLID, ArrowType.CIRCLE),
-
- /**
- * Information about arrows/lines for {@link DissociationReaction} class.
- */
- DISSOCIATION(DissociationReaction.class, "DISSOCIATION"),
-
- /**
- * Information about arrows/lines for {@link HeterodimerAssociationReaction}
- * class.
- */
- HETERODIMER_ASSOCIATION(HeterodimerAssociationReaction.class, "HETERODIMER_ASSOCIATION"),
-
- /**
- * Information about arrows/lines for {@link InhibitionReaction} class.
- */
- INHIBITION(InhibitionReaction.class, "INHIBITION", LineType.SOLID, ArrowType.CROSSBAR),
-
- /**
- * Information about arrows/lines for {@link KnownTransitionOmittedReaction}
- * class.
- */
- KNOWN_TRANSITION_OMITTED(KnownTransitionOmittedReaction.class, "KNOWN_TRANSITION_OMITTED"),
-
- /**
- * Information about arrows/lines for {@link ModulationReaction} class.
- */
- MODULATION(ModulationReaction.class, "MODULATION", LineType.SOLID, ArrowType.DIAMOND),
-
- /**
- * Information about arrows/lines for {@link NegativeInfluenceReaction} class.
- */
- NEGATIVE_INFLUENCE(NegativeInfluenceReaction.class, "NEGATIVE_INFLUENCE", LineType.SOLID, ArrowType.CROSSBAR, 3),
-
- /**
- * Information about arrows/lines for {@link PhysicalStimulationReaction} class.
- */
- PHYSICAL_STIMULATION(PhysicalStimulationReaction.class, "PHYSICAL_STIMULATION", LineType.SOLID, ArrowType.BLANK),
-
- /**
- * Information about arrows/lines for {@link PositiveInfluenceReaction} class.
- */
- POSITIVE_INFLUENCE(PositiveInfluenceReaction.class, "POSITIVE_INFLUENCE", LineType.SOLID, ArrowType.OPEN),
-
- /**
- * Information about arrows/lines for {@link ReducedModulationReaction} class.
- */
- REDUCED_MODULATION(ReducedModulationReaction.class, "REDUCED_MODULATION", LineType.SOLID, ArrowType.DIAMOND),
-
- /**
- * Information about arrows/lines for {@link ReducedPhysicalStimulationReaction}
- * class.
- */
- REDUCED_PHYSICAL_STIMULATION(ReducedPhysicalStimulationReaction.class, "REDUCED_PHYSICAL_STIMULATION", LineType.SOLID,
- ArrowType.BLANK),
-
- /**
- * Information about arrows/lines for {@link ReducedTriggerReaction} class.
- */
- REDUCED_TRIGGER(ReducedTriggerReaction.class, "REDUCED_TRIGGER", LineType.SOLID, ArrowType.BLANK_CROSSBAR),
-
- /**
- * Information about arrows/lines for {@link StateTransitionReaction} class.
- */
- STATE_TRANSITION(StateTransitionReaction.class, "STATE_TRANSITION"),
-
- /**
- * Information about arrows/lines for {@link TranscriptionReaction} class.
- */
- TRANSCRIPTION(TranscriptionReaction.class, "TRANSCRIPTION", LineType.DASH_DOT_DOT),
-
- /**
- * Information about arrows/lines for {@link TranslationReaction} class.
- */
- TRANSLATION(TranslationReaction.class, "TRANSLATION", LineType.DASH_DOT),
-
- /**
- * Information about arrows/lines for {@link TransportReaction} class.
- */
- TRANSPORT(TransportReaction.class, "TRANSPORT", LineType.SOLID, ArrowType.FULL_CROSSBAR),
-
- /**
- * Information about arrows/lines for {@link TriggerReaction} class.
- */
- TRIGGER(TriggerReaction.class, "TRIGGER", LineType.SOLID, ArrowType.BLANK_CROSSBAR),
-
- /**
- * Information about arrows/lines for {@link TruncationReaction} class.
- */
- TRUNCATION(TruncationReaction.class, "TRUNCATION"),
-
- /**
- * Information about arrows/lines for {@link UnknownCatalysisReaction} class.
- */
- UNKNOWN_CATALYSIS(UnknownCatalysisReaction.class, "UNKNOWN_CATALYSIS", LineType.DASHED, ArrowType.CIRCLE),
-
- /**
- * Information about arrows/lines for {@link UnknownInhibitionReaction} class.
- */
- UNKNOWN_INHIBITION(UnknownInhibitionReaction.class, "UNKNOWN_INHIBITION", LineType.DASHED, ArrowType.CROSSBAR),
-
- /**
- * Information about arrows/lines for {@link UnknownNegativeInfluenceReaction}
- * class.
- */
- UNKNOWN_NEGATIVE_INFLUENCE(UnknownNegativeInfluenceReaction.class, "UNKNOWN_NEGATIVE_INFLUENCE", LineType.DASHED,
- ArrowType.CROSSBAR, 3),
-
- /**
- * Information about arrows/lines for {@link UnknownPositiveInfluenceReaction}
- * class.
- */
- UNKNOWN_POSITIVE_INFLUENCE(UnknownPositiveInfluenceReaction.class, "UNKNOWN_POSITIVE_INFLUENCE", LineType.DASHED,
- ArrowType.OPEN),
-
- /**
- * Information about arrows/lines for {@link UnknownReducedModulationReaction}
- * class.
- */
- UNKNOWN_REDUCED_MODEULATION(UnknownReducedModulationReaction.class, "UNKNOWN_REDUCED_MODULATION", LineType.DASHED,
- ArrowType.DIAMOND),
-
- /**
- * Information about arrows/lines for
- * {@link UnknownReducedPhysicalStimulationReaction} class.
- */
- UNKNOWN_REDUCED_PHYSICAL_STIMULATION(UnknownReducedPhysicalStimulationReaction.class,
- "UNKNOWN_REDUCED_PHYSICAL_STIMULATION", LineType.DASHED, //
- ArrowType.BLANK),
-
- /**
- * Information about arrows/lines for {@link UnknownReducedTriggerReaction}
- * class.
- */
- UNKNOWN_REDUCED_TRIGGER(UnknownReducedTriggerReaction.class, "UNKNOWN_REDUCED_TRIGGER", LineType.DASHED,
- ArrowType.BLANK_CROSSBAR),
-
- /**
- * Information about arrows/lines for {@link UnknownTransitionReaction} class.
- */
- UNKNOWN_TRANSITION(UnknownTransitionReaction.class, "UNKNOWN_TRANSITION");
-
- /**
- * {@link Reaction} class for which the data is stored.
- */
- private Class<? extends Reaction> reactionClass;
-
- /**
- * Type of arrow that should be used by products.
- */
- private ArrowType productArrowType;
-
- /**
- * Line types that should be used by the reaction.
- */
- private LineType lineType;
-
- /**
- * How much product line should be trimmed at the end.
- */
- private double productLineTrim;
-
- /**
- * String used by CellDesigner to represent reaction.
- */
- private String cellDesignerString;
-
- /**
- *
- * @param clazz
- * {@link #reactionClass}
- * @param cellDesignerString
- * {@link #cellDesignerString}
- */
- ReactionLineData(Class<? extends Reaction> clazz, String cellDesignerString) {
- this(clazz, cellDesignerString, LineType.SOLID);
-
- }
-
- /**
- *
- * @param clazz
- * {@link #reactionClass}
- * @param cellDesignerString
- * {@link #cellDesignerString}
- * @param lineType
- * {@link #lineType}
- */
- ReactionLineData(Class<? extends Reaction> clazz, String cellDesignerString, LineType lineType) {
- this(clazz, cellDesignerString, lineType, ArrowType.FULL);
- }
-
- /**
- *
- * @param clazz
- * {@link #reactionClass}
- * @param cellDesignerString
- * {@link #cellDesignerString}
- * @param lineType
- * {@link #lineType}
- * @param productArrowType
- * {@link #productArrowType}
- */
- ReactionLineData(Class<? extends Reaction> clazz, String cellDesignerString, LineType lineType,
- ArrowType productArrowType) {
- this(clazz, cellDesignerString, lineType, productArrowType, 0.0);
- }
-
- /**
- *
- * @param clazz
- * {@link #reactionClass}
- * @param cellDesignerString
- * {@link #cellDesignerString}
- * @param lineType
- * {@link #lineType}
- * @param productArrowType
- * {@link #productArrowType}
- * @param productLineTrim
- * {@link #productLineTrim}
- */
- ReactionLineData(Class<? extends Reaction> clazz, String cellDesignerString, LineType lineType,
- ArrowType productArrowType, double productLineTrim) {
- this.reactionClass = clazz;
- this.lineType = lineType;
- this.productArrowType = productArrowType;
- this.productLineTrim = productLineTrim;
- this.cellDesignerString = cellDesignerString;
- }
-
- /**
- * @return the reactionClass
- * @see #reactionClass
- */
- public Class<? extends Reaction> getReactionClass() {
- return reactionClass;
- }
-
- /**
- * @return the productArrowType
- * @see #productArrowType
- */
- public ArrowType getProductArrowType() {
- return productArrowType;
- }
-
- /**
- * @return the lineType
- * @see #lineType
- */
- public LineType getLineType() {
- return lineType;
- }
-
- /**
- * @return the productLineTrim
- * @see #productLineTrim
- */
- public double getProductLineTrim() {
- return productLineTrim;
- }
-
- /**
- * Map used for reverse lookup between {@link Reaction} types and
- * {@link ReactionLineData}.
- */
- private static Map<Class<? extends Reaction>, ReactionLineData> map = null;
-
- /**
- * Map used for reverse lookup between {@link #cellDesignerString} types and
- * {@link ReactionLineData}.
- */
- private static Map<String, ReactionLineData> cellDesignerMap = null;
-
- /**
- * Method that finds {@link ReactionLineData} or given {@link Reaction} type.
- *
- * @param clazz
- * type for which {@link ReactionLineData} will be returned
- * @return {@link ReactionLineData} or given {@link Reaction} type
- */
- public static ReactionLineData getByReactionType(Class<? extends Reaction> clazz) {
- if (map == null) {
- map = new HashMap<Class<? extends Reaction>, ReactionLineData>();
- for (ReactionLineData rld : values()) {
- map.put(rld.getReactionClass(), rld);
- }
- }
- return map.get(clazz);
- }
-
- /**
- * @return the cellDesignerString
- * @see #cellDesignerString
- */
- public String getCellDesignerString() {
- return cellDesignerString;
- }
-
- /**
- * Returns {@link ReactionLineData} identified by CellDEsigner string that
- * identifies this Reaction type.
- *
- * @param type
- * {@link #cellDesignerString}
- * @return {@link ReactionLineData} identified by CellDEsigner string that
- * identifies this Reaction type
- */
- public static ReactionLineData getByCellDesignerString(String type) {
- if (cellDesignerMap == null) {
- cellDesignerMap = new HashMap<String, ReactionLineData>();
- for (ReactionLineData rld : values()) {
- cellDesignerMap.put(rld.getCellDesignerString(), rld);
- }
- }
- return cellDesignerMap.get(type);
- }
-
- /**
- * Creates instance of {@link Reaction} represented by this enum and copies the
- * data from result parameter.
- *
- * @param result
- * original data
- * @return instance of {@link Reaction} represented by this enum and copies the
- * data from result parameter
- * @throws ReactionParserException
- */
- public Reaction createReaction(Reaction result) throws ReactionParserException {
- try {
- return reactionClass.getConstructor(Reaction.class).newInstance(result);
- } catch (Exception e) {
- throw new ReactionParserException("Problem with creation the new instance of reaction. ", result, e);
- }
- }
-
- /**
- * Returns {@link ReactionLineData} that can be aplpied for lines with given
- * line type and arrow type. If there are more then one possibility, one of them
- * will be returned (nothing is guaranteed).
- *
- * @param lineType
- * type of the line for which are looking for {@link ReactionLineData}
- * @param productArrowType
- * type of the arrow for which are looking for {@link ReactionLineData}
- * @return {@link ReactionLineData} that can be aplpied for lines with given
- * line type and arrow type. If there are more then one possibility, one
- * of them will be returned (nothing is guaranteed)
- */
- public static ReactionLineData getByLineType(LineType lineType, ArrowType productArrowType) {
- for (ReactionLineData rld : values()) {
- if (rld.getLineType().equals(lineType) && rld.getProductArrowType().equals(productArrowType)) {
- return rld;
- }
- }
- return null;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.reaction;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import lcsb.mapviewer.model.graphics.ArrowType;
+import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.type.BooleanLogicGateReaction;
+import lcsb.mapviewer.model.map.reaction.type.CatalysisReaction;
+import lcsb.mapviewer.model.map.reaction.type.DissociationReaction;
+import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
+import lcsb.mapviewer.model.map.reaction.type.InhibitionReaction;
+import lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction;
+import lcsb.mapviewer.model.map.reaction.type.ModulationReaction;
+import lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction;
+import lcsb.mapviewer.model.map.reaction.type.PhysicalStimulationReaction;
+import lcsb.mapviewer.model.map.reaction.type.PositiveInfluenceReaction;
+import lcsb.mapviewer.model.map.reaction.type.ReducedModulationReaction;
+import lcsb.mapviewer.model.map.reaction.type.ReducedPhysicalStimulationReaction;
+import lcsb.mapviewer.model.map.reaction.type.ReducedTriggerReaction;
+import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
+import lcsb.mapviewer.model.map.reaction.type.TranscriptionReaction;
+import lcsb.mapviewer.model.map.reaction.type.TranslationReaction;
+import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
+import lcsb.mapviewer.model.map.reaction.type.TriggerReaction;
+import lcsb.mapviewer.model.map.reaction.type.TruncationReaction;
+import lcsb.mapviewer.model.map.reaction.type.UnknownCatalysisReaction;
+import lcsb.mapviewer.model.map.reaction.type.UnknownInhibitionReaction;
+import lcsb.mapviewer.model.map.reaction.type.UnknownNegativeInfluenceReaction;
+import lcsb.mapviewer.model.map.reaction.type.UnknownPositiveInfluenceReaction;
+import lcsb.mapviewer.model.map.reaction.type.UnknownReducedModulationReaction;
+import lcsb.mapviewer.model.map.reaction.type.UnknownReducedPhysicalStimulationReaction;
+import lcsb.mapviewer.model.map.reaction.type.UnknownReducedTriggerReaction;
+import lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction;
+
+/**
+ * This class represent graphical information about lines/arrows that are
+ * related to CellDesigner {@link Reaction} type.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum ReactionLineData {
+
+ /**
+ * Information about arrows/lines for {@link BooleanLogicGateReaction} class.
+ */
+ BOOLEAN_LOGIC_GATE(BooleanLogicGateReaction.class, "BOOLEAN_LOGIC_GATE"),
+
+ /**
+ * Information about arrows/lines for {@link CatalysisReaction} class.
+ */
+ CATALYSIS(CatalysisReaction.class, "CATALYSIS", LineType.SOLID, ArrowType.CIRCLE),
+
+ /**
+ * Information about arrows/lines for {@link DissociationReaction} class.
+ */
+ DISSOCIATION(DissociationReaction.class, "DISSOCIATION"),
+
+ /**
+ * Information about arrows/lines for {@link HeterodimerAssociationReaction}
+ * class.
+ */
+ HETERODIMER_ASSOCIATION(HeterodimerAssociationReaction.class, "HETERODIMER_ASSOCIATION"),
+
+ /**
+ * Information about arrows/lines for {@link InhibitionReaction} class.
+ */
+ INHIBITION(InhibitionReaction.class, "INHIBITION", LineType.SOLID, ArrowType.CROSSBAR),
+
+ /**
+ * Information about arrows/lines for {@link KnownTransitionOmittedReaction}
+ * class.
+ */
+ KNOWN_TRANSITION_OMITTED(KnownTransitionOmittedReaction.class, "KNOWN_TRANSITION_OMITTED"),
+
+ /**
+ * Information about arrows/lines for {@link ModulationReaction} class.
+ */
+ MODULATION(ModulationReaction.class, "MODULATION", LineType.SOLID, ArrowType.DIAMOND),
+
+ /**
+ * Information about arrows/lines for {@link NegativeInfluenceReaction} class.
+ */
+ NEGATIVE_INFLUENCE(NegativeInfluenceReaction.class, "NEGATIVE_INFLUENCE", LineType.SOLID, ArrowType.CROSSBAR, 3),
+
+ /**
+ * Information about arrows/lines for {@link PhysicalStimulationReaction} class.
+ */
+ PHYSICAL_STIMULATION(PhysicalStimulationReaction.class, "PHYSICAL_STIMULATION", LineType.SOLID, ArrowType.BLANK),
+
+ /**
+ * Information about arrows/lines for {@link PositiveInfluenceReaction} class.
+ */
+ POSITIVE_INFLUENCE(PositiveInfluenceReaction.class, "POSITIVE_INFLUENCE", LineType.SOLID, ArrowType.OPEN),
+
+ /**
+ * Information about arrows/lines for {@link ReducedModulationReaction} class.
+ */
+ REDUCED_MODULATION(ReducedModulationReaction.class, "REDUCED_MODULATION", LineType.SOLID, ArrowType.DIAMOND),
+
+ /**
+ * Information about arrows/lines for {@link ReducedPhysicalStimulationReaction}
+ * class.
+ */
+ REDUCED_PHYSICAL_STIMULATION(ReducedPhysicalStimulationReaction.class, "REDUCED_PHYSICAL_STIMULATION", LineType.SOLID,
+ ArrowType.BLANK),
+
+ /**
+ * Information about arrows/lines for {@link ReducedTriggerReaction} class.
+ */
+ REDUCED_TRIGGER(ReducedTriggerReaction.class, "REDUCED_TRIGGER", LineType.SOLID, ArrowType.BLANK_CROSSBAR),
+
+ /**
+ * Information about arrows/lines for {@link StateTransitionReaction} class.
+ */
+ STATE_TRANSITION(StateTransitionReaction.class, "STATE_TRANSITION"),
+
+ /**
+ * Information about arrows/lines for {@link TranscriptionReaction} class.
+ */
+ TRANSCRIPTION(TranscriptionReaction.class, "TRANSCRIPTION", LineType.DASH_DOT_DOT),
+
+ /**
+ * Information about arrows/lines for {@link TranslationReaction} class.
+ */
+ TRANSLATION(TranslationReaction.class, "TRANSLATION", LineType.DASH_DOT),
+
+ /**
+ * Information about arrows/lines for {@link TransportReaction} class.
+ */
+ TRANSPORT(TransportReaction.class, "TRANSPORT", LineType.SOLID, ArrowType.FULL_CROSSBAR),
+
+ /**
+ * Information about arrows/lines for {@link TriggerReaction} class.
+ */
+ TRIGGER(TriggerReaction.class, "TRIGGER", LineType.SOLID, ArrowType.BLANK_CROSSBAR),
+
+ /**
+ * Information about arrows/lines for {@link TruncationReaction} class.
+ */
+ TRUNCATION(TruncationReaction.class, "TRUNCATION"),
+
+ /**
+ * Information about arrows/lines for {@link UnknownCatalysisReaction} class.
+ */
+ UNKNOWN_CATALYSIS(UnknownCatalysisReaction.class, "UNKNOWN_CATALYSIS", LineType.DASHED, ArrowType.CIRCLE),
+
+ /**
+ * Information about arrows/lines for {@link UnknownInhibitionReaction} class.
+ */
+ UNKNOWN_INHIBITION(UnknownInhibitionReaction.class, "UNKNOWN_INHIBITION", LineType.DASHED, ArrowType.CROSSBAR),
+
+ /**
+ * Information about arrows/lines for {@link UnknownNegativeInfluenceReaction}
+ * class.
+ */
+ UNKNOWN_NEGATIVE_INFLUENCE(UnknownNegativeInfluenceReaction.class, "UNKNOWN_NEGATIVE_INFLUENCE", LineType.DASHED,
+ ArrowType.CROSSBAR, 3),
+
+ /**
+ * Information about arrows/lines for {@link UnknownPositiveInfluenceReaction}
+ * class.
+ */
+ UNKNOWN_POSITIVE_INFLUENCE(UnknownPositiveInfluenceReaction.class, "UNKNOWN_POSITIVE_INFLUENCE", LineType.DASHED,
+ ArrowType.OPEN),
+
+ /**
+ * Information about arrows/lines for {@link UnknownReducedModulationReaction}
+ * class.
+ */
+ UNKNOWN_REDUCED_MODEULATION(UnknownReducedModulationReaction.class, "UNKNOWN_REDUCED_MODULATION", LineType.DASHED,
+ ArrowType.DIAMOND),
+
+ /**
+ * Information about arrows/lines for
+ * {@link UnknownReducedPhysicalStimulationReaction} class.
+ */
+ UNKNOWN_REDUCED_PHYSICAL_STIMULATION(UnknownReducedPhysicalStimulationReaction.class,
+ "UNKNOWN_REDUCED_PHYSICAL_STIMULATION", LineType.DASHED, //
+ ArrowType.BLANK),
+
+ /**
+ * Information about arrows/lines for {@link UnknownReducedTriggerReaction}
+ * class.
+ */
+ UNKNOWN_REDUCED_TRIGGER(UnknownReducedTriggerReaction.class, "UNKNOWN_REDUCED_TRIGGER", LineType.DASHED,
+ ArrowType.BLANK_CROSSBAR),
+
+ /**
+ * Information about arrows/lines for {@link UnknownTransitionReaction} class.
+ */
+ UNKNOWN_TRANSITION(UnknownTransitionReaction.class, "UNKNOWN_TRANSITION");
+
+ /**
+ * {@link Reaction} class for which the data is stored.
+ */
+ private Class<? extends Reaction> reactionClass;
+
+ /**
+ * Type of arrow that should be used by products.
+ */
+ private ArrowType productArrowType;
+
+ /**
+ * Line types that should be used by the reaction.
+ */
+ private LineType lineType;
+
+ /**
+ * How much product line should be trimmed at the end.
+ */
+ private double productLineTrim;
+
+ /**
+ * String used by CellDesigner to represent reaction.
+ */
+ private String cellDesignerString;
+
+ /**
+ *
+ * @param clazz
+ * {@link #reactionClass}
+ * @param cellDesignerString
+ * {@link #cellDesignerString}
+ */
+ ReactionLineData(Class<? extends Reaction> clazz, String cellDesignerString) {
+ this(clazz, cellDesignerString, LineType.SOLID);
+
+ }
+
+ /**
+ *
+ * @param clazz
+ * {@link #reactionClass}
+ * @param cellDesignerString
+ * {@link #cellDesignerString}
+ * @param lineType
+ * {@link #lineType}
+ */
+ ReactionLineData(Class<? extends Reaction> clazz, String cellDesignerString, LineType lineType) {
+ this(clazz, cellDesignerString, lineType, ArrowType.FULL);
+ }
+
+ /**
+ *
+ * @param clazz
+ * {@link #reactionClass}
+ * @param cellDesignerString
+ * {@link #cellDesignerString}
+ * @param lineType
+ * {@link #lineType}
+ * @param productArrowType
+ * {@link #productArrowType}
+ */
+ ReactionLineData(Class<? extends Reaction> clazz, String cellDesignerString, LineType lineType,
+ ArrowType productArrowType) {
+ this(clazz, cellDesignerString, lineType, productArrowType, 0.0);
+ }
+
+ /**
+ *
+ * @param clazz
+ * {@link #reactionClass}
+ * @param cellDesignerString
+ * {@link #cellDesignerString}
+ * @param lineType
+ * {@link #lineType}
+ * @param productArrowType
+ * {@link #productArrowType}
+ * @param productLineTrim
+ * {@link #productLineTrim}
+ */
+ ReactionLineData(Class<? extends Reaction> clazz, String cellDesignerString, LineType lineType,
+ ArrowType productArrowType, double productLineTrim) {
+ this.reactionClass = clazz;
+ this.lineType = lineType;
+ this.productArrowType = productArrowType;
+ this.productLineTrim = productLineTrim;
+ this.cellDesignerString = cellDesignerString;
+ }
+
+ /**
+ * @return the reactionClass
+ * @see #reactionClass
+ */
+ public Class<? extends Reaction> getReactionClass() {
+ return reactionClass;
+ }
+
+ /**
+ * @return the productArrowType
+ * @see #productArrowType
+ */
+ public ArrowType getProductArrowType() {
+ return productArrowType;
+ }
+
+ /**
+ * @return the lineType
+ * @see #lineType
+ */
+ public LineType getLineType() {
+ return lineType;
+ }
+
+ /**
+ * @return the productLineTrim
+ * @see #productLineTrim
+ */
+ public double getProductLineTrim() {
+ return productLineTrim;
+ }
+
+ /**
+ * Map used for reverse lookup between {@link Reaction} types and
+ * {@link ReactionLineData}.
+ */
+ private static Map<Class<? extends Reaction>, ReactionLineData> map = null;
+
+ /**
+ * Map used for reverse lookup between {@link #cellDesignerString} types and
+ * {@link ReactionLineData}.
+ */
+ private static Map<String, ReactionLineData> cellDesignerMap = null;
+
+ /**
+ * Method that finds {@link ReactionLineData} or given {@link Reaction} type.
+ *
+ * @param clazz
+ * type for which {@link ReactionLineData} will be returned
+ * @return {@link ReactionLineData} or given {@link Reaction} type
+ */
+ public static ReactionLineData getByReactionType(Class<? extends Reaction> clazz) {
+ if (map == null) {
+ map = new HashMap<Class<? extends Reaction>, ReactionLineData>();
+ for (ReactionLineData rld : values()) {
+ map.put(rld.getReactionClass(), rld);
+ }
+ }
+ return map.get(clazz);
+ }
+
+ /**
+ * @return the cellDesignerString
+ * @see #cellDesignerString
+ */
+ public String getCellDesignerString() {
+ return cellDesignerString;
+ }
+
+ /**
+ * Returns {@link ReactionLineData} identified by CellDEsigner string that
+ * identifies this Reaction type.
+ *
+ * @param type
+ * {@link #cellDesignerString}
+ * @return {@link ReactionLineData} identified by CellDEsigner string that
+ * identifies this Reaction type
+ */
+ public static ReactionLineData getByCellDesignerString(String type) {
+ if (cellDesignerMap == null) {
+ cellDesignerMap = new HashMap<String, ReactionLineData>();
+ for (ReactionLineData rld : values()) {
+ cellDesignerMap.put(rld.getCellDesignerString(), rld);
+ }
+ }
+ return cellDesignerMap.get(type);
+ }
+
+ /**
+ * Creates instance of {@link Reaction} represented by this enum and copies the
+ * data from result parameter.
+ *
+ * @param result
+ * original data
+ * @return instance of {@link Reaction} represented by this enum and copies the
+ * data from result parameter
+ * @throws ReactionParserException
+ */
+ public Reaction createReaction(Reaction result) throws ReactionParserException {
+ try {
+ return reactionClass.getConstructor(Reaction.class).newInstance(result);
+ } catch (Exception e) {
+ throw new ReactionParserException("Problem with creation the new instance of reaction. ", result, e);
+ }
+ }
+
+ /**
+ * Returns {@link ReactionLineData} that can be aplpied for lines with given
+ * line type and arrow type. If there are more then one possibility, one of them
+ * will be returned (nothing is guaranteed).
+ *
+ * @param lineType
+ * type of the line for which are looking for {@link ReactionLineData}
+ * @param productArrowType
+ * type of the arrow for which are looking for {@link ReactionLineData}
+ * @return {@link ReactionLineData} that can be aplpied for lines with given
+ * line type and arrow type. If there are more then one possibility, one
+ * of them will be returned (nothing is guaranteed)
+ */
+ public static ReactionLineData getByLineType(LineType lineType, ArrowType productArrowType) {
+ for (ReactionLineData rld : values()) {
+ if (rld.getLineType().equals(lineType) && rld.getProductArrowType().equals(productArrowType)) {
+ return rld;
+ }
+ }
+ return null;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserException.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserException.java
index f0458b832e..86ed00cd4c 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserException.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserException.java
@@ -1,102 +1,102 @@
-package lcsb.mapviewer.converter.model.celldesigner.reaction;
-
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerParserException;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * Exception thrown when problem with parsing
- * {@link lcsb.mapviewer.model.map.reaction.Reaction} is encountered.
- *
- * @author Piotr Gawron
- *
- */
-public class ReactionParserException extends CellDesignerParserException {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Identifier of reaction that was a reason for this exception.
- */
- private String reactionId;
-
- /**
- * Default constructor.
- *
- * @param message
- * message thrown
- * @param reactionId
- * {@link #reactionId}
- */
- public ReactionParserException(String message, String reactionId) {
- super(message);
- this.reactionId = reactionId;
- }
-
- /**
- * Default constructor.
- *
- * @param message
- * message thrown
- * @param reaction
- * {@link #reactionId}
- */
- public ReactionParserException(String message, Reaction reaction) {
- super(message);
- if (reaction != null) {
- setReactionId(reaction.getIdReaction());
- }
- }
-
- /**
- * Default constructor.
- *
- * @param message
- * message thrown
- * @param reaction
- * {@link #reactionId}
- * @param e
- * super exception
- */
- public ReactionParserException(String message, Reaction reaction, Exception e) {
- super(message, e);
- if (reaction != null) {
- setReactionId(reaction.getIdReaction());
- }
- }
-
- /**
- * Default constructor.
- *
- * @param reaction
- * {@link #reactionId}
- * @param e
- * super exception
- */
- public ReactionParserException(Reaction reaction, Throwable e) {
- super(e);
- if (reaction != null) {
- setReactionId(reaction.getIdReaction());
- }
- }
-
- /**
- * @return the reactionId
- * @see #reactionId
- */
- public String getReactionId() {
- return reactionId;
- }
-
- /**
- * @param reactionId
- * the reactionId to set
- * @see #reactionId
- */
- public void setReactionId(String reactionId) {
- this.reactionId = reactionId;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.reaction;
+
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerParserException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * Exception thrown when problem with parsing
+ * {@link lcsb.mapviewer.model.map.reaction.Reaction} is encountered.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ReactionParserException extends CellDesignerParserException {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Identifier of reaction that was a reason for this exception.
+ */
+ private String reactionId;
+
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * message thrown
+ * @param reactionId
+ * {@link #reactionId}
+ */
+ public ReactionParserException(String message, String reactionId) {
+ super(message);
+ this.reactionId = reactionId;
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * message thrown
+ * @param reaction
+ * {@link #reactionId}
+ */
+ public ReactionParserException(String message, Reaction reaction) {
+ super(message);
+ if (reaction != null) {
+ setReactionId(reaction.getIdReaction());
+ }
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * message thrown
+ * @param reaction
+ * {@link #reactionId}
+ * @param e
+ * super exception
+ */
+ public ReactionParserException(String message, Reaction reaction, Exception e) {
+ super(message, e);
+ if (reaction != null) {
+ setReactionId(reaction.getIdReaction());
+ }
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param reaction
+ * {@link #reactionId}
+ * @param e
+ * super exception
+ */
+ public ReactionParserException(Reaction reaction, Throwable e) {
+ super(e);
+ if (reaction != null) {
+ setReactionId(reaction.getIdReaction());
+ }
+ }
+
+ /**
+ * @return the reactionId
+ * @see #reactionId
+ */
+ public String getReactionId() {
+ return reactionId;
+ }
+
+ /**
+ * @param reactionId
+ * the reactionId to set
+ * @see #reactionId
+ */
+ public void setReactionId(String reactionId) {
+ this.reactionId = reactionId;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java
index 7058ed10ec..04dfa0ab8a 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java
@@ -1,1107 +1,1107 @@
-package lcsb.mapviewer.converter.model.celldesigner.reaction;
-
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.XmlParser;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.ConverterException;
-import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerLineTransformation;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerPointTransformation;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
-import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
-import lcsb.mapviewer.converter.model.celldesigner.types.ModifierTypeUtils;
-import lcsb.mapviewer.converter.model.celldesigner.types.OperatorType;
-import lcsb.mapviewer.converter.model.celldesigner.types.OperatorTypeUtils;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.InconsistentModelException;
-import lcsb.mapviewer.model.map.reaction.AbstractNode;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.reaction.NodeOperator;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.type.SimpleReactionInterface;
-import lcsb.mapviewer.model.map.reaction.type.TwoProductReactionInterface;
-import lcsb.mapviewer.model.map.reaction.type.TwoReactantReactionInterface;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.modelutils.map.ElementUtils;
-
-/**
- * This is a part of {@link ReactionXmlParser} class functionality that allows
- * to export reaction into CellDesigner xml node.
- *
- * @author Piotr Gawron
- *
- */
-public class ReactionToXml extends XmlParser {
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ReactionToXml.class);
-
- /**
- * Helper object used for manipulation on the point coorinates in CellDesigner
- * format.
- */
- private CellDesignerPointTransformation pointTransformation = new CellDesignerPointTransformation();
-
- /**
- * Helper object used for manipulation on the line structures in CellDesigner
- * format.
- */
- private CellDesignerLineTransformation lineTransformation = new CellDesignerLineTransformation();
-
- /**
- * Collection of {@link CellDesignerElement cell designer elements} parsed from
- * xml.
- */
- private CellDesignerElementCollection elements;
-
- /**
- * Helps in providing human readable identifiers of elements for logging.
- */
- private ElementUtils eu = new ElementUtils();
-
- /**
- * Defines if SBGN standard should be used.
- */
- private boolean sbgn;
-
- /**
- * Default constructor. Model is required because some nodes require access to
- * other parts of the model.
- *
- * @param sbgn
- * Should the converter use SBGN standard
- * @param elements
- * collection of {@link CellDesignerElement cell designer elements}
- * parsed from xml
- */
- public ReactionToXml(CellDesignerElementCollection elements, boolean sbgn) {
- this.elements = elements;
- this.sbgn = sbgn;
- }
-
- /**
- * Transform reaction into CellDesigner xml representation.
- *
- * @param reaction
- * reaction to transform
- * @return xml representation of reaction
- * @throws ConverterException
- */
- public String toXml(Reaction reaction) throws InconsistentModelException {
- if (reaction.getReactants().get(0).getElement().equals(reaction.getProducts().get(0).getElement())) {
- throw new SelfReactionException("Reaction " + reaction.getElementId() + " is a self reference for element "
- + reaction.getProducts().get(0).getElement().getElementId());
- }
- StringBuilder sb = new StringBuilder();
- sb.append("<reaction ");
- sb.append("metaid=\"" + reaction.getIdReaction() + "\" ");
- sb.append("id=\"" + reaction.getIdReaction() + "\" ");
- sb.append("name=\"" + reaction.getName() + "\" ");
- sb.append("reversible=\"" + reaction.isReversible() + "\" ");
- sb.append(">\n");
- if (reaction.getNotes() != null && !reaction.getNotes().equals("")) {
- sb.append("<notes>");
-
- sb.append("<html xmlns=\"http://www.w3.org/1999/xhtml\"><head><title/></head><body>");
- sb.append(reaction.getNotes());
- sb.append("</body></html>");
-
- sb.append("</notes>");
-
- }
-
- sb.append(getAnnotationXmlStringForReaction(reaction));
- sb.append(getListOfReactantsXmlStringForReaction(reaction));
- sb.append(getListOfProductsXmlStringForReaction(reaction));
- sb.append(getSbmlListOfModificationsXmlStringForReaction(reaction));
- sb.append(getKineticsLawXml(reaction));
-
- sb.append("</reaction>\n");
- return sb.toString();
- }
-
- private String getKineticsLawXml(Reaction reaction) throws InconsistentModelException {
- if (reaction.getKinetics() != null) {
- KineticsXmlParser xmlParser = new KineticsXmlParser(reaction.getModel());
- return xmlParser.toXml(reaction.getKinetics(), elements);
- } else {
- return "";
- }
- }
-
- /**
- * Returns xml node with list of modification.
- *
- * @param reaction
- * reaction for which list is generated
- * @return xml node with list of modification
- */
- private String getListOfModificationsXmlStringForReaction(Reaction reaction) {
- StringBuilder sb = new StringBuilder();
- sb.append("<celldesigner:listOfModification>\n");
-
- // to preserve order of modifier we have to make it a little complicated
-
- Map<Modifier, NodeOperator> operators = new HashMap<Modifier, NodeOperator>();
- Set<NodeOperator> usedOperators = new HashSet<NodeOperator>();
-
- for (NodeOperator node : reaction.getOperators()) {
- if (node.isModifierOperator()) {
- for (AbstractNode modNode : node.getInputs()) {
- Modifier modifier = (Modifier) modNode;
- operators.put(modifier, node);
- if (node.getLine().getBeginPoint().distance(modifier.getLine().getEndPoint()) > Configuration.EPSILON) {
- logger.warn("Modifier should end in the same point as operator starts, but: "
- + node.getLine().getBeginPoint() + ", " + modifier.getLine().getEndPoint());
- }
- }
- }
- }
- for (Modifier modifier : reaction.getModifiers()) {
- NodeOperator node = operators.get(modifier);
- if (node != null) {
- if (!usedOperators.contains(node)) {
- usedOperators.add(node);
- sb.append(getModifierXmlString(node));
- }
- }
- sb.append(getModifierXmlString(modifier, node));
- }
- sb.append("</celldesigner:listOfModification>\n");
- return sb.toString();
- }
-
- /**
- * Returns sbml node with list of modifications.
- *
- * @param reaction
- * reaction for which list is generated
- * @return sbml node with list of modifications
- */
- private String getSbmlListOfModificationsXmlStringForReaction(Reaction reaction) {
- if (reaction.getModifiers().size() == 0) {
- return "";
- }
- StringBuilder sb = new StringBuilder();
- sb.append("<listOfModifiers>\n");
- for (Modifier modifier : reaction.getModifiers()) {
- sb.append(getModifierReferenceXmlString(modifier));
- }
- sb.append("</listOfModifiers>\n");
- return sb.toString();
- }
-
- /**
- * Creates modifierSpeciesReference sbml node for given modifer.
- *
- * @param modifier
- * modifier to be transaformed
- * @return modifierSpeciesReference sbml node for given modifer
- */
- private String getModifierReferenceXmlString(Modifier modifier) {
- StringBuilder sb = new StringBuilder();
- Species element = (Species) modifier.getElement();
-
- Set<Element> parents = new HashSet<>();
-
- // we need top parent species
- while (element.getComplex() != null) {
- element = element.getComplex();
- if (parents.contains(element)) {
- throw new InvalidArgumentException(eu.getElementTag(element) + " Complex information is cyclic");
- }
- parents.add(element);
- }
-
- sb.append("<modifierSpeciesReference ");
- sb.append("metaid=\"" + elements.getElementId(element) + "\" ");
-
- sb.append("species=\"" + elements.getElementId(element) + "\">\n");
- sb.append("<annotation>\n");
- sb.append("<celldesigner:extension>\n");
- sb.append("<celldesigner:alias>" + modifier.getElement().getElementId() + "</celldesigner:alias>\n");
- sb.append("</celldesigner:extension>\n");
- sb.append("</annotation>\n");
- sb.append("</modifierSpeciesReference>\n");
-
- return sb.toString();
- }
-
- /**
- * Creates xml node for given modifer operator.
- *
- * @param modifierOperator
- * modifier operator to be transaformed
- * @return xml node for given modifer operator
- */
- private String getModifierXmlString(NodeOperator modifierOperator) {
- StringBuilder sb = new StringBuilder();
- OperatorTypeUtils otu = new OperatorTypeUtils();
- ModifierTypeUtils mtu = new ModifierTypeUtils();
- ModifierType modifierType = mtu.getModifierTypeForOperator(modifierOperator);
- sb.append("<celldesigner:modification ");
- String type = otu.getStringTypeByOperator(modifierOperator);
- sb.append(" type=\"" + type + "\" ");
- sb.append(" modificationType=\"" + modifierType.getStringName() + "\" ");
- String modifiers = "";
- String aliases = "";
- for (AbstractNode modifier : modifierOperator.getInputs()) {
- if (modifier instanceof Modifier) {
- Modifier mod = (Modifier) modifier;
- if (modifiers.equals("")) {
- modifiers = elements.getElementId(mod.getElement());
- aliases = mod.getElement().getElementId();
- } else {
- modifiers += "," + elements.getElementId(mod.getElement());
- aliases += "," + mod.getElement().getElementId();
- }
-
- }
- }
- sb.append(" modifiers=\"" + modifiers + "\" ");
- sb.append(" aliases=\"" + aliases + "\" ");
- sb.append(" targetLineIndex=\"" + mtu.getTargetLineIndexByModifier(modifierOperator) + "\" ");
- PolylineData line = new PolylineData(modifierOperator.getLine());
-
- line.trimEnd(-modifierType.getTrimLength());
-
- // TODO
- // check the order (reverse or not, begin or end point)
- line = line.reverse();
- List<Point2D> points = lineTransformation.getPointsFromLine(line);
- sb.append(" editPoints=\"");
- for (int i = 1; i < points.size() - 1; i++) {
- sb.append(points.get(i).getX() + "," + points.get(i).getY() + " ");
- }
- sb.append(line.getEndPoint().getX() + "," + line.getEndPoint().getY());
- sb.append("\"");
-
- sb.append(">\n");
- PolylineData[] lines = new PolylineData[] { modifierOperator.getLine() };
- sb.append(getConnectSchemeXmlStringForLines(lines));
-
- sb.append("<celldesigner:line ");
- sb.append("width=\"" + modifierOperator.getLine().getWidth() + "\" ");
- sb.append("color=\"" + colorToString(modifierOperator.getLine().getColor()) + "\" ");
- sb.append("type=\"Straight\" ");
- sb.append("/>\n");
-
- sb.append("</celldesigner:modification>\n");
- return sb.toString();
- }
-
- /**
- * Creates xml node for given modifer.
- *
- * @param modifier
- * modifier to be transaformed
- * @param gate
- * operator to which modifier is connected (if any)
- * @return xml node for given modifer
- */
- private String getModifierXmlString(Modifier modifier, NodeOperator gate) {
- StringBuilder sb = new StringBuilder();
- ModifierTypeUtils modifierTypeUtils = new ModifierTypeUtils();
- sb.append("<celldesigner:modification ");
- String type = modifierTypeUtils.getStringTypeByModifier(modifier);
- sb.append(" type=\"" + type + "\" ");
- sb.append(" modifiers=\"" + elements.getElementId(modifier.getElement()) + "\" ");
- sb.append(" aliases=\"" + modifier.getElement().getElementId() + "\" ");
- sb.append(" targetLineIndex=\"" + modifierTypeUtils.getTargetLineIndexByModifier(modifier) + "\" ");
- PolylineData line = new PolylineData(modifier.getLine());
-
- line.trimEnd(-modifierTypeUtils.getModifierTypeForClazz(modifier.getClass()).getTrimLength());
- if (gate != null) {
- line.setEndPoint(gate.getLine().getBeginPoint());
- CellDesignerAliasConverter converter = new CellDesignerAliasConverter(modifier.getElement(), sbgn);
- CellDesignerAnchor anchor = converter.getAnchorForCoordinates(modifier.getElement(), line.getBeginPoint());
- Point2D start = converter.getPointCoordinates(modifier.getElement(), anchor);
- line.setStartPoint(start);
- }
-
- List<Point2D> points = lineTransformation.getPointsFromLine(line);
- if (points.size() > 0) {
-
- boolean first = true;
- sb.append(" editPoints=\"");
-
- for (Point2D point : points) {
- if (first) {
- first = false;
- } else {
- sb.append(" ");
- }
- sb.append(point.getX() + "," + point.getY());
- }
- sb.append("\"");
- }
-
- sb.append(">\n");
- PolylineData[] lines = new PolylineData[] { modifier.getLine() };
- sb.append(getConnectSchemeXmlStringForLines(lines));
- sb.append(getLinkTargetXmlString(modifier));
-
- sb.append("<celldesigner:line ");
- sb.append("width=\"" + modifier.getLine().getWidth() + "\" ");
- sb.append("color=\"" + colorToString(modifier.getLine().getColor()) + "\" ");
- sb.append("type=\"Straight\" ");
- sb.append("/>\n");
-
- sb.append("</celldesigner:modification>\n");
- return sb.toString();
- }
-
- /**
- * Gets target link string for given modifier.
- *
- * @param modifier
- * modifier to be transformed
- * @return anchor xml node representing modifier connection to reaction
- */
- private String getLinkTargetXmlString(Modifier modifier) {
- StringBuilder sb = new StringBuilder();
- sb.append("<celldesigner:linkTarget species=\"" + elements.getElementId(modifier.getElement()) + "\" alias=\""
- + modifier.getElement().getElementId() + "\">\n");
- sb.append(getAnchorXml(modifier.getElement(), modifier.getLine().getBeginPoint()));
- sb.append("</celldesigner:linkTarget>\n");
-
- return sb.toString();
- }
-
- /**
- * Creates sbml node for list of products.
- *
- * @param reaction
- * reaction from which products are taken
- * @return sbml node representing lsit of products
- */
- private String getListOfProductsXmlStringForReaction(Reaction reaction) {
- StringBuilder sb = new StringBuilder();
- sb.append("<listOfProducts>\n");
- for (Product product : reaction.getProducts()) {
- // metaid is missing, maybe it will work ;)
-
- Species element = (Species) product.getElement();
-
- Set<Element> parents = new HashSet<>();
-
- // we need top parent species
- while (element.getComplex() != null) {
- element = element.getComplex();
- if (parents.contains(element)) {
- throw new InvalidArgumentException(eu.getElementTag(element) + " Complex information is cyclic");
- }
- parents.add(element);
- }
-
- sb.append("<speciesReference species=\"" + elements.getElementId(element) + "\" ");
- if (product.getStoichiometry() != null) {
- sb.append(" stoichiometry=\"" + product.getStoichiometry() + "\" ");
- }
- sb.append(">\n");
-
- sb.append("<annotation>\n");
- sb.append("<celldesigner:extension>\n");
- sb.append("<celldesigner:alias>" + product.getElement().getElementId() + "</celldesigner:alias>\n");
- sb.append("</celldesigner:extension>\n");
- sb.append("</annotation>\n");
- sb.append("</speciesReference>\n");
- }
- sb.append("</listOfProducts>\n");
- return sb.toString();
- }
-
- /**
- * Creates sbml node for list of reactants.
- *
- * @param reaction
- * reaction from which products are taken
- * @return sbml node representing list of reactants
- */
- private String getListOfReactantsXmlStringForReaction(Reaction reaction) {
- StringBuilder sb = new StringBuilder();
- sb.append("<listOfReactants>\n");
- for (Reactant reactant : reaction.getReactants()) {
- // metaid is missing, maybe it will work ;)
- Species species = (Species) reactant.getElement();
-
- Set<Element> parents = new HashSet<>();
-
- // we need top parent species
- while (species.getComplex() != null) {
- species = species.getComplex();
- if (parents.contains(species)) {
- throw new InvalidArgumentException(eu.getElementTag(species) + " Complex information is cyclic");
- }
- parents.add(species);
- }
-
- sb.append("<speciesReference species=\"" + elements.getElementId(species) + "\" ");
- if (reactant.getStoichiometry() != null) {
- sb.append(" stoichiometry=\"" + reactant.getStoichiometry() + "\" ");
- }
- sb.append(">\n");
- sb.append("<annotation>\n");
- sb.append("<celldesigner:extension>\n");
- sb.append("<celldesigner:alias>" + reactant.getElement().getElementId() + "</celldesigner:alias>\n");
- sb.append("</celldesigner:extension>\n");
- sb.append("</annotation>\n");
- sb.append("</speciesReference>\n");
- }
- sb.append("</listOfReactants>\n");
- return sb.toString();
- }
-
- /**
- * Creates annotation xml node for reaction.
- *
- * @param reaction
- * reaction to be processed
- * @return xml node representing annotation part
- */
- private String getAnnotationXmlStringForReaction(Reaction reaction) {
- ReactionLineData rdl = ReactionLineData.getByReactionType(reaction.getClass());
- if (rdl == null) {
- throw new InvalidArgumentException("Unknown reaction type: " + reaction.getClass());
- }
- String reactionClassString = rdl.getCellDesignerString();
- StringBuilder sb = new StringBuilder();
- sb.append("<annotation>\n");
- sb.append("<celldesigner:extension>\n");
- sb.append("<celldesigner:reactionType>" + reactionClassString + "</celldesigner:reactionType>");
- sb.append(getBaseReactantsXmlStringForReaction(reaction));
- sb.append(getBaseProductsXmlStringForReaction(reaction));
- sb.append(getListOfReactantLinksXmlStringForReaction(reaction));
- sb.append(getListOfProductLinksXmlStringForReaction(reaction));
- sb.append(getConnectSchemeXmlStringForReaction(reaction));
- sb.append(getEditPointsXmlStringForReaction(reaction));
- sb.append(getListOfModificationsXmlStringForReaction(reaction));
- sb.append(getListOfGateMembersXmlStringForReaction(reaction));
-
- sb.append("<celldesigner:line ");
- sb.append("width=\"" + reaction.getReactants().get(0).getLine().getWidth() + "\" ");
- sb.append("color=\"" + colorToString(reaction.getReactants().get(0).getLine().getColor()) + "\" ");
- sb.append("type=\"Straight\" ");
- sb.append("/>\n");
-
- XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser();
- sb.append("</celldesigner:extension>\n");
- sb.append(xmlAnnotationParser.dataSetToXmlString(reaction.getMiriamData()));
- sb.append("</annotation>\n");
- return sb.toString();
- }
-
- /**
- * Returns xml node with a list of gate members for reaction. For now only
- * {@link TwoReactantReactionInterface} is supported.
- *
- * @param reaction
- * reaction for which the cml will be returned
- * @return xml string with list of gate members for reaction
- */
- private StringBuilder getListOfGateMembersXmlStringForReaction(Reaction reaction) {
- StringBuilder result = new StringBuilder();
- if (reaction instanceof TwoReactantReactionInterface) {
- Reactant reactant1 = reaction.getReactants().get(0);
- Reactant reactant2 = reaction.getReactants().get(1);
- Product product = reaction.getProducts().get(0);
- NodeOperator operator = reaction.getOperators().get(0);
- OperatorType type = OperatorType.getTypeByClass(operator.getClass());
-
- // if type is not defined then we are working on something that doesn't
- // use gates
- if (type != null) {
- result.append("<celldesigner:listOfGateMember>\n");
- ReactionLineData lineData = ReactionLineData.getByLineType(reaction.getProducts().get(0).getLine().getType(),
- reaction.getProducts().get(0).getLine().getEndAtd().getArrowType());
- Element alias1 = reactant1.getElement();
- Element alias2 = reactant2.getElement();
-
- // product line
- result.append("<celldesigner:GateMember type=\"" + type.getStringName() + "\"");
- result.append(" aliases=\"" + alias1.getElementId() + "," + alias2.getElementId() + "\"");
- result.append(" modificationType=\"" + lineData.getCellDesignerString() + "\"");
-
- CellDesignerLineTransformation clt = new CellDesignerLineTransformation();
- List<Point2D> points = clt.getPointsFromLine(product.getLine());
-
- result.append(" editPoints=\"");
- for (int i = 0; i < points.size(); i++) {
- result.append(points.get(i).getX() + "," + points.get(i).getY() + " ");
- }
- result.append(product.getLine().getBeginPoint().getX() + "," + product.getLine().getBeginPoint().getY() + " ");
- result.append("\">\n");
-
- result.append("<celldesigner:connectScheme connectPolicy=\"direct\">\n");
- result.append("<celldesigner:listOfLineDirection>\n");
- for (int i = 0; i < product.getLine().getPoints().size() - 1; i++) {
- result.append("<celldesigner:lineDirection index=\"" + i + "\" value=\"unknown\"/>\n");
- }
- result.append("</celldesigner:listOfLineDirection>\n");
- result.append("</celldesigner:connectScheme>\n");
-
- result.append("</celldesigner:GateMember>\n");
-
- // reactant 1 line
-
- result.append("<celldesigner:GateMember type=\"" + lineData.getCellDesignerString() + "\"");
- result.append(" aliases=\"" + alias1.getElementId() + "\"");
-
- points = clt.getPointsFromLine(reactant1.getLine());
-
- result.append(" editPoints=\"");
- for (int i = 0; i < points.size(); i++) {
- result.append(points.get(i).getX() + "," + points.get(i).getY() + " ");
- }
- result.append("\">\n");
-
- result.append("<celldesigner:connectScheme connectPolicy=\"direct\">\n");
- result.append("<celldesigner:listOfLineDirection>\n");
- for (int i = 0; i < reactant1.getLine().getPoints().size() - 1; i++) {
- result.append("<celldesigner:lineDirection index=\"" + i + "\" value=\"unknown\"/>\n");
- }
- result.append("</celldesigner:listOfLineDirection>\n");
- result.append("</celldesigner:connectScheme>\n");
-
- result.append("</celldesigner:GateMember>\n");
-
- // reactant 2 line
-
- result.append("<celldesigner:GateMember type=\"" + lineData.getCellDesignerString() + "\"");
- result.append(" aliases=\"" + alias2.getElementId() + "\"");
-
- points = clt.getPointsFromLine(reactant2.getLine());
-
- result.append(" editPoints=\"");
- for (int i = 0; i < points.size(); i++) {
- result.append(points.get(i).getX() + "," + points.get(i).getY() + " ");
- }
- result.append("\">\n");
-
- result.append("<celldesigner:connectScheme connectPolicy=\"direct\">\n");
- result.append("<celldesigner:listOfLineDirection>\n");
- for (int i = 0; i < reactant2.getLine().getPoints().size() - 1; i++) {
- result.append("<celldesigner:lineDirection index=\"" + i + "\" value=\"unknown\"/>\n");
- }
- result.append("</celldesigner:listOfLineDirection>\n");
- result.append("</celldesigner:connectScheme>\n");
-
- result.append("</celldesigner:GateMember>\n");
-
- result.append("</celldesigner:listOfGateMember>\n");
- }
- }
- return result;
- }
-
- /**
- * Creates xml node (listOfProductLinks) with list of products.
- *
- * @param reaction
- * reaction for which list of products is created
- * @return xml node (listOfProductLinks) with list of products
- */
- private String getListOfProductLinksXmlStringForReaction(Reaction reaction) {
- StringBuilder sb = new StringBuilder();
- sb.append("<celldesigner:listOfProductLinks>\n");
- int firstElement = 1;
- if (reaction instanceof TwoProductReactionInterface) {
- firstElement = 2;
- }
- for (int i = firstElement; i < reaction.getProducts().size(); i++) {
- sb.append(getProductLinkXmlString(reaction.getProducts().get(i)));
- }
- sb.append("</celldesigner:listOfProductLinks>\n");
- return sb.toString();
- }
-
- /**
- * Creates xml node (listOfReactantLinks) with list of reactants.
- *
- * @param reaction
- * reaction for which list of reactants is created
- * @return xml node (listOfReactantLinks) with list of reactants
- */
- private String getListOfReactantLinksXmlStringForReaction(Reaction reaction) {
- StringBuilder sb = new StringBuilder();
- sb.append("<celldesigner:listOfReactantLinks>\n");
- int firstElement = 1;
- if (reaction instanceof TwoReactantReactionInterface) {
- firstElement = 2;
- }
- for (int i = firstElement; i < reaction.getReactants().size(); i++) {
- sb.append(getReactantLinkXmlString(reaction.getReactants().get(i)));
- }
- sb.append("</celldesigner:listOfReactantLinks>\n");
- return sb.toString();
- }
-
- /**
- * Creates rectantLink xml node for reactant.
- *
- * @param reactant
- * reactant to be transformed
- * @return xml node describing reactantLink
- */
- private String getReactantLinkXmlString(Reactant reactant) {
- Element alias = reactant.getElement();
- StringBuilder sb = new StringBuilder();
- sb.append("<celldesigner:reactantLink ");
- sb.append("reactant=\"" + elements.getElementId(alias) + "\" ");
- sb.append("alias=\"" + alias.getElementId() + "\" ");
- // targetLineIndex is missing (maybe it's unimportant :))
- sb.append(">\n");
-
- sb.append(getAnchorXml(alias, reactant.getLine().getBeginPoint()));
-
- sb.append("<celldesigner:connectScheme connectPolicy=\"direct\">\n");
- sb.append("<celldesigner:listOfLineDirection>\n");
- for (int i = 0; i < reactant.getLine().getPoints().size() - 1; i++) {
- sb.append("<celldesigner:lineDirection index=\"" + i + "\" value=\"unknown\"/>\n");
- }
- sb.append("</celldesigner:listOfLineDirection>\n");
- sb.append("</celldesigner:connectScheme>\n");
-
- // TODO
- sb.append(getEditPointsXmlStringForLine(new PolylineData[] { reactant.getLine() }, 0));
- sb.append("<celldesigner:line ");
- sb.append("width=\"" + reactant.getLine().getWidth() + "\" ");
- sb.append("color=\"" + colorToString(reactant.getLine().getColor()) + "\" ");
- sb.append("type=\"Straight\" ");
- sb.append("/>\n");
- sb.append("</celldesigner:reactantLink>");
- return sb.toString();
- }
-
- /**
- * Creates productLink xml node for product.
- *
- * @param product
- * product to be transformed
- * @return xml node describing productLink
- */
- private String getProductLinkXmlString(Product product) {
- Element alias = product.getElement();
- PolylineData[] lines = new PolylineData[] { product.getLine() };
-
- StringBuilder sb = new StringBuilder();
- sb.append("<celldesigner:productLink ");
- sb.append("product=\"" + elements.getElementId(alias) + "\" ");
- sb.append("alias=\"" + alias.getElementId() + "\" ");
- // targetLineIndex is missing (maybe it's unimportant :))
- sb.append(">\n");
-
- sb.append(getAnchorXml(alias, product.getLine().getEndPoint()));
-
- sb.append(getConnectSchemeXmlStringForLines(lines));
-
- // TODO
- sb.append(getEditPointsXmlStringForLine(lines, 0));
- sb.append("<celldesigner:line ");
- sb.append("width=\"" + product.getLine().getWidth() + "\" ");
- sb.append("color=\"" + colorToString(product.getLine().getColor()) + "\" ");
- sb.append("type=\"Straight\" ");
- sb.append("/>\n");
- sb.append("</celldesigner:productLink>");
- return sb.toString();
- }
-
- /**
- * Creates valid xml node with connectScheme for the set of lines.
- *
- * @param lines
- * list of lines to be included in connectScheme. As far as I remember
- * only one or three lines could be provided.
- * @return xml node with connectScheme
- */
- String getConnectSchemeXmlStringForLines(PolylineData[] lines) {
- StringBuilder sb = new StringBuilder();
- sb.append("<celldesigner:connectScheme ");
- sb.append("connectPolicy=\"direct\" ");
- // where on the line reactangle is positioned (it's not necessary so we skip
- // it)
- // if (rectangleIndex != null) {
- // sb.append("rectangleIndex=\"" + rectangleIndex + "\" ");
- // }
- sb.append(">\n");
- sb.append("<celldesigner:listOfLineDirection>\n");
- int armId = 0;
- for (PolylineData line : lines) {
- String arm = "";
- if (lines.length > 1) {
- arm = " arm\"" + armId + "\" ";
- armId++;
- }
- for (int i = 0; i < line.getPoints().size() - 1; i++) {
- sb.append("<celldesigner:lineDirection " + arm + " index=\"" + i + "\" value=\"unknown\"/>\n");
- }
- }
- sb.append("</celldesigner:listOfLineDirection>\n");
- sb.append("</celldesigner:connectScheme>\n");
- return sb.toString();
- }
-
- /**
- * Creates
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints}
- * structure representing lines in CellDesigner.
- *
- * @param lines
- * lines to be transformed into single
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints}
- * structure
- * @param centerIndex
- * where the central line is positioned
- * @return xml node
- */
- private String getEditPointsXmlStringForLine(PolylineData[] lines, Integer centerIndex) {
- return getEditPointsXmlStringForLine(lines, null, centerIndex);
- }
-
- /**
- * Creates
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints}
- * structure representing lines in CellDesigner.
- *
- * @param lines
- * lines to be transformed into single
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints}
- * structure
- * @param centerPoint
- * central point whene list of lines is greater than 1
- * @param centerIndex
- * where the central line is positioned
- * @return xml node
- */
- private String getEditPointsXmlStringForLine(PolylineData[] lines, Point2D centerPoint, Integer centerIndex) {
- StringBuilder sb = new StringBuilder();
-
- sb.append("<celldesigner:editPoints ");
- if (lines.length > 1) {
- for (int i = 0; i < lines.length; i++) {
- sb.append(" num" + i + "=\"" + (lines[i].getPoints().size() - 2) + "\" ");
- }
- if (centerIndex != null) {
- sb.append(" tShapeIndex=\"" + centerIndex + "\"");
- }
- }
- sb.append(">");
-
- boolean first = true;
- for (PolylineData pd : lines) {
- List<Point2D> points = lineTransformation.getPointsFromLine(pd);
-
- for (Point2D point : points) {
- if (first) {
- first = false;
- } else {
- sb.append(" ");
- }
- sb.append(point.getX() + "," + point.getY());
- }
- }
- if (centerPoint != null) {
- sb.append(" " + centerPoint.getX() + "," + centerPoint.getY());
- }
- sb.append("</celldesigner:editPoints>\n");
-
- // when we don't have any points then we cannot create editPoints node (CD
- // throws null pointer exception)
- if (first && centerPoint == null) {
- return "";
- }
- return sb.toString();
- }
-
- /**
- * Returns xml node representing
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints}
- * structure.
- *
- * @param reaction
- * reaction for which xml node is generated
- * @return xml node representing
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints}
- * structure
- */
- String getEditPointsXmlStringForReaction(Reaction reaction) {
- if (reaction instanceof SimpleReactionInterface) {
- Product product = reaction.getProducts().get(0);
- Reactant reactant = reaction.getReactants().get(0);
- List<Point2D> points = new ArrayList<Point2D>();
- for (int i = 0; i < reactant.getLine().getPoints().size() - 1; i++) {
- points.add(reactant.getLine().getPoints().get(i));
- }
- for (int i = 1; i < product.getLine().getPoints().size(); i++) {
- points.add(product.getLine().getPoints().get(i));
- }
-
- PolylineData pd = new PolylineData(points);
- // TODO
- return getEditPointsXmlStringForLine(new PolylineData[] { pd }, reactant.getLine().getPoints().size() - 1);
- } else if (reaction instanceof TwoReactantReactionInterface) {
- Reactant reactant1 = reaction.getReactants().get(0);
- Reactant reactant2 = reaction.getReactants().get(1);
- PolylineData line1 = reactant1.getLine();
- PolylineData line2 = reactant2.getLine();
- List<Point2D> points = new ArrayList<Point2D>();
- for (NodeOperator operator : reaction.getOperators()) {
- if (operator.isReactantOperator()) {
- boolean process = true;
- for (AbstractNode node : operator.getInputs()) {
- if (!(node instanceof Reactant)) {
- process = false;
- }
- }
- if (process) {
- for (int i = 0; i < operator.getLine().getPoints().size() - 1; i++) {
- points.add(operator.getLine().getPoints().get(i));
- }
- }
- }
- }
- Product product = reaction.getProducts().get(0);
- for (int i = 1; i < product.getLine().getPoints().size(); i++) {
- points.add(product.getLine().getPoints().get(i));
- }
-
- Point2D endPoint = points.get(points.size() - 1);
- CellDesignerAliasConverter converter = new CellDesignerAliasConverter(product.getElement(), sbgn);
- CellDesignerAnchor anchor = converter.getAnchorForCoordinates(product.getElement(), endPoint);
- if (anchor == null) { // when we have no anchor, then end point is set
- // to
- // the center of alias
- points.set(points.size() - 1, product.getElement().getCenter());
- }
-
- PolylineData line3 = new PolylineData(points);
-
- Point2D pointC = reactant1.getElement().getCenter();
- Point2D pointA = reactant2.getElement().getCenter();
- Point2D pointB = product.getElement().getCenter();
-
- Point2D pointO = line3.getBeginPoint();
-
- Point2D centerPoint = pointTransformation.getCoordinatesInCellDesignerBase(pointA, pointB, pointC, pointO);
-
- return getEditPointsXmlStringForLine(
- new PolylineData[] { line1.reverse(), line2.reverse(), line3.reverse().reverse() }, centerPoint,
- line3.getPoints().size() - product.getLine().getPoints().size());
-
- } else if (reaction instanceof TwoProductReactionInterface) {
- List<Point2D> points = new ArrayList<Point2D>();
- Reactant reactant = reaction.getReactants().get(0);
- Product product1 = reaction.getProducts().get(0);
- Product product2 = reaction.getProducts().get(1);
- for (int i = 0; i < reactant.getLine().getPoints().size() - 1; i++) {
- points.add(reactant.getLine().getPoints().get(i));
- }
-
- Point2D startPoint = points.get(0);
- CellDesignerAliasConverter converter = new CellDesignerAliasConverter(reactant.getElement(), sbgn);
- CellDesignerAnchor anchor = converter.getAnchorForCoordinates(reactant.getElement(), startPoint);
- if (anchor == null) { // when we have no anchor, then end point is set
- // to
- // the center of alias
- points.set(points.size() - 1, reactant.getElement().getCenter());
- }
- int index = points.size();
- for (NodeOperator operator : reaction.getOperators()) {
- if (operator.isProductOperator()) {
- boolean process = true;
- for (AbstractNode node : operator.getOutputs()) {
- if (!(node instanceof Product)) {
- process = false;
- }
- }
- if (process) {
- for (int i = operator.getLine().getPoints().size() - 2; i >= 0; i--) {
- points.add(operator.getLine().getPoints().get(i));
- }
- }
- }
- }
- index = points.size() - index - 1;
-
- PolylineData line1 = new PolylineData(points);
-
- PolylineData line2 = product1.getLine();
- PolylineData line3 = product2.getLine();
-
- Point2D pointA = product1.getElement().getCenter();
- Point2D pointB = product2.getElement().getCenter();
- Point2D pointC = reactant.getElement().getCenter();
-
- Point2D pointO = line2.getBeginPoint();
-
- Point2D centerPoint = pointTransformation.getCoordinatesInCellDesignerBase(pointA, pointB, pointC, pointO);
-
- return getEditPointsXmlStringForLine(new PolylineData[] { line1.reverse(), line2, line3 }, centerPoint, index);
- } else {
- throw new InvalidArgumentException("Unhandled reaction type: " + reaction.getClass());
- }
- }
-
- /**
- * Creates valid xml node with connectScheme for the reaction.
- *
- * @param reaction
- * reaction for which the connectSchema is going to be created
- * @return xml node with connectScheme
- */
- String getConnectSchemeXmlStringForReaction(Reaction reaction) {
- StringBuilder sb = new StringBuilder();
- sb.append("<celldesigner:connectScheme ");
- sb.append("connectPolicy=\"direct\" ");
- int rectangleIndex = -1;
- if (reaction instanceof SimpleReactionInterface) {
- rectangleIndex = reaction.getReactants().get(0).getLine().getPoints().size() - 2;
- sb.append("rectangleIndex=\"" + rectangleIndex + "\" ");
- }
- sb.append(">\n");
- sb.append("<celldesigner:listOfLineDirection>\n");
- if (reaction instanceof SimpleReactionInterface) {
- int size = reaction.getReactants().get(0).getLine().getPoints().size()
- + reaction.getProducts().get(0).getLine().getPoints().size() - 2 - 1;
- for (int i = 0; i < size; i++) {
- sb.append("<celldesigner:lineDirection index=\"" + i + "\" value=\"unknown\"/>\n");
- }
- } else if (reaction instanceof TwoProductReactionInterface || reaction instanceof TwoReactantReactionInterface) {
- String string = getEditPointsXmlStringForReaction(reaction);
- Pattern p0 = Pattern.compile("num0=\"([0-9]+)");
- Pattern p1 = Pattern.compile("num1=\"([0-9]+)");
- Pattern p2 = Pattern.compile("num2=\"([0-9]+)");
- Matcher m0 = p0.matcher(string);
- Matcher m1 = p1.matcher(string);
- Matcher m2 = p2.matcher(string);
- int num0 = 0;
- int num1 = 0;
- int num2 = 0;
-
- if (m0.find() && m1.find() && m2.find()) {
- num0 = Integer.parseInt(m0.group(1));
- num1 = Integer.parseInt(m1.group(1));
- num2 = Integer.parseInt(m2.group(1));
- } else {
- throw new InvalidArgumentException("Invalid editPoints string" + string);
- }
-
- for (int i = 0; i <= num0; i++) {
- sb.append("<celldesigner:lineDirection arm=\"0\" index=\"" + i + "\" value=\"unknown\"/>\n");
- }
- for (int i = 0; i <= num1; i++) {
- sb.append("<celldesigner:lineDirection arm=\"1\" index=\"" + i + "\" value=\"unknown\"/>\n");
- }
- for (int i = 0; i <= num2; i++) {
- sb.append("<celldesigner:lineDirection arm=\"2\" index=\"" + i + "\" value=\"unknown\"/>\n");
- }
- } else {
- throw new InvalidArgumentException("Unknown reaction type: " + reaction.getClass());
-
- }
- sb.append("</celldesigner:listOfLineDirection>\n");
- sb.append("</celldesigner:connectScheme>\n");
- return sb.toString();
- }
-
- /**
- * Returns xml node with list of base products.
- *
- * @param reaction
- * reaction for which the node is created
- * @return xml node with list of base products
- */
- private String getBaseProductsXmlStringForReaction(Reaction reaction) {
- List<Product> products = new ArrayList<Product>();
- products.add(reaction.getProducts().get(0));
- if (reaction instanceof TwoProductReactionInterface) {
- products.add(reaction.getProducts().get(1));
- }
-
- StringBuilder sb = new StringBuilder();
- sb.append("<celldesigner:baseProducts>\n");
- for (Product product : products) {
- Element alias = product.getElement();
- sb.append("<celldesigner:baseProduct ");
- sb.append("species=\"" + elements.getElementId(product.getElement()) + "\" ");
- sb.append("alias=\"" + product.getElement().getElementId() + "\" ");
- sb.append(">\n");
- sb.append(getAnchorXml(alias, product.getLine().getEndPoint()));
-
- sb.append("</celldesigner:baseProduct>\n");
- }
- sb.append("</celldesigner:baseProducts>\n");
- return sb.toString();
- }
-
- /**
- * Returns xml node with list of base reactants.
- *
- * @param reaction
- * reaction for which the node is created
- * @return xml node with list of base reactants
- */
- private String getBaseReactantsXmlStringForReaction(Reaction reaction) {
- List<Reactant> reactants = new ArrayList<Reactant>();
- reactants.add(reaction.getReactants().get(0));
- if (reaction instanceof TwoReactantReactionInterface) {
- reactants.add(reaction.getReactants().get(1));
- }
-
- StringBuilder sb = new StringBuilder();
- sb.append("<celldesigner:baseReactants>\n");
- for (Reactant reactant : reactants) {
- Element alias = reactant.getElement();
- sb.append("<celldesigner:baseReactant ");
- sb.append("species=\"" + elements.getElementId(reactant.getElement()) + "\" ");
- sb.append("alias=\"" + reactant.getElement().getElementId() + "\" ");
- sb.append(">\n");
- sb.append(getAnchorXml(alias, reactant.getLine().getBeginPoint()));
-
- sb.append("</celldesigner:baseReactant>\n");
- }
- sb.append("</celldesigner:baseReactants>\n");
- return sb.toString();
- }
-
- /**
- * Returns xml node that describes anchor point.
- *
- * @param alias
- * alias on which we are looking for anchor
- * @param point
- * point on the alias that should be aligned to the closest anchor
- * point
- * @return xml node with anchor point
- */
- private String getAnchorXml(Element alias, Point2D point) {
- CellDesignerAliasConverter converter = new CellDesignerAliasConverter(alias, sbgn);
- CellDesignerAnchor anchor = converter.getAnchorForCoordinates(alias, point);
- if (anchor != null) {
- return "<celldesigner:linkAnchor position=\"" + anchor + "\"/>\n";
- } else {
- return "";
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.reaction;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerLineTransformation;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerPointTransformation;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
+import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
+import lcsb.mapviewer.converter.model.celldesigner.types.ModifierTypeUtils;
+import lcsb.mapviewer.converter.model.celldesigner.types.OperatorType;
+import lcsb.mapviewer.converter.model.celldesigner.types.OperatorTypeUtils;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.reaction.AbstractNode;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.reaction.NodeOperator;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.type.SimpleReactionInterface;
+import lcsb.mapviewer.model.map.reaction.type.TwoProductReactionInterface;
+import lcsb.mapviewer.model.map.reaction.type.TwoReactantReactionInterface;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
+
+/**
+ * This is a part of {@link ReactionXmlParser} class functionality that allows
+ * to export reaction into CellDesigner xml node.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ReactionToXml extends XmlParser {
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ReactionToXml.class);
+
+ /**
+ * Helper object used for manipulation on the point coorinates in CellDesigner
+ * format.
+ */
+ private CellDesignerPointTransformation pointTransformation = new CellDesignerPointTransformation();
+
+ /**
+ * Helper object used for manipulation on the line structures in CellDesigner
+ * format.
+ */
+ private CellDesignerLineTransformation lineTransformation = new CellDesignerLineTransformation();
+
+ /**
+ * Collection of {@link CellDesignerElement cell designer elements} parsed from
+ * xml.
+ */
+ private CellDesignerElementCollection elements;
+
+ /**
+ * Helps in providing human readable identifiers of elements for logging.
+ */
+ private ElementUtils eu = new ElementUtils();
+
+ /**
+ * Defines if SBGN standard should be used.
+ */
+ private boolean sbgn;
+
+ /**
+ * Default constructor. Model is required because some nodes require access to
+ * other parts of the model.
+ *
+ * @param sbgn
+ * Should the converter use SBGN standard
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
+ */
+ public ReactionToXml(CellDesignerElementCollection elements, boolean sbgn) {
+ this.elements = elements;
+ this.sbgn = sbgn;
+ }
+
+ /**
+ * Transform reaction into CellDesigner xml representation.
+ *
+ * @param reaction
+ * reaction to transform
+ * @return xml representation of reaction
+ * @throws ConverterException
+ */
+ public String toXml(Reaction reaction) throws InconsistentModelException {
+ if (reaction.getReactants().get(0).getElement().equals(reaction.getProducts().get(0).getElement())) {
+ throw new SelfReactionException("Reaction " + reaction.getElementId() + " is a self reference for element "
+ + reaction.getProducts().get(0).getElement().getElementId());
+ }
+ StringBuilder sb = new StringBuilder();
+ sb.append("<reaction ");
+ sb.append("metaid=\"" + reaction.getIdReaction() + "\" ");
+ sb.append("id=\"" + reaction.getIdReaction() + "\" ");
+ sb.append("name=\"" + reaction.getName() + "\" ");
+ sb.append("reversible=\"" + reaction.isReversible() + "\" ");
+ sb.append(">\n");
+ if (reaction.getNotes() != null && !reaction.getNotes().equals("")) {
+ sb.append("<notes>");
+
+ sb.append("<html xmlns=\"http://www.w3.org/1999/xhtml\"><head><title/></head><body>");
+ sb.append(reaction.getNotes());
+ sb.append("</body></html>");
+
+ sb.append("</notes>");
+
+ }
+
+ sb.append(getAnnotationXmlStringForReaction(reaction));
+ sb.append(getListOfReactantsXmlStringForReaction(reaction));
+ sb.append(getListOfProductsXmlStringForReaction(reaction));
+ sb.append(getSbmlListOfModificationsXmlStringForReaction(reaction));
+ sb.append(getKineticsLawXml(reaction));
+
+ sb.append("</reaction>\n");
+ return sb.toString();
+ }
+
+ private String getKineticsLawXml(Reaction reaction) throws InconsistentModelException {
+ if (reaction.getKinetics() != null) {
+ KineticsXmlParser xmlParser = new KineticsXmlParser(reaction.getModel());
+ return xmlParser.toXml(reaction.getKinetics(), elements);
+ } else {
+ return "";
+ }
+ }
+
+ /**
+ * Returns xml node with list of modification.
+ *
+ * @param reaction
+ * reaction for which list is generated
+ * @return xml node with list of modification
+ */
+ private String getListOfModificationsXmlStringForReaction(Reaction reaction) {
+ StringBuilder sb = new StringBuilder();
+ sb.append("<celldesigner:listOfModification>\n");
+
+ // to preserve order of modifier we have to make it a little complicated
+
+ Map<Modifier, NodeOperator> operators = new HashMap<Modifier, NodeOperator>();
+ Set<NodeOperator> usedOperators = new HashSet<NodeOperator>();
+
+ for (NodeOperator node : reaction.getOperators()) {
+ if (node.isModifierOperator()) {
+ for (AbstractNode modNode : node.getInputs()) {
+ Modifier modifier = (Modifier) modNode;
+ operators.put(modifier, node);
+ if (node.getLine().getBeginPoint().distance(modifier.getLine().getEndPoint()) > Configuration.EPSILON) {
+ logger.warn("Modifier should end in the same point as operator starts, but: "
+ + node.getLine().getBeginPoint() + ", " + modifier.getLine().getEndPoint());
+ }
+ }
+ }
+ }
+ for (Modifier modifier : reaction.getModifiers()) {
+ NodeOperator node = operators.get(modifier);
+ if (node != null) {
+ if (!usedOperators.contains(node)) {
+ usedOperators.add(node);
+ sb.append(getModifierXmlString(node));
+ }
+ }
+ sb.append(getModifierXmlString(modifier, node));
+ }
+ sb.append("</celldesigner:listOfModification>\n");
+ return sb.toString();
+ }
+
+ /**
+ * Returns sbml node with list of modifications.
+ *
+ * @param reaction
+ * reaction for which list is generated
+ * @return sbml node with list of modifications
+ */
+ private String getSbmlListOfModificationsXmlStringForReaction(Reaction reaction) {
+ if (reaction.getModifiers().size() == 0) {
+ return "";
+ }
+ StringBuilder sb = new StringBuilder();
+ sb.append("<listOfModifiers>\n");
+ for (Modifier modifier : reaction.getModifiers()) {
+ sb.append(getModifierReferenceXmlString(modifier));
+ }
+ sb.append("</listOfModifiers>\n");
+ return sb.toString();
+ }
+
+ /**
+ * Creates modifierSpeciesReference sbml node for given modifer.
+ *
+ * @param modifier
+ * modifier to be transaformed
+ * @return modifierSpeciesReference sbml node for given modifer
+ */
+ private String getModifierReferenceXmlString(Modifier modifier) {
+ StringBuilder sb = new StringBuilder();
+ Species element = (Species) modifier.getElement();
+
+ Set<Element> parents = new HashSet<>();
+
+ // we need top parent species
+ while (element.getComplex() != null) {
+ element = element.getComplex();
+ if (parents.contains(element)) {
+ throw new InvalidArgumentException(eu.getElementTag(element) + " Complex information is cyclic");
+ }
+ parents.add(element);
+ }
+
+ sb.append("<modifierSpeciesReference ");
+ sb.append("metaid=\"" + elements.getElementId(element) + "\" ");
+
+ sb.append("species=\"" + elements.getElementId(element) + "\">\n");
+ sb.append("<annotation>\n");
+ sb.append("<celldesigner:extension>\n");
+ sb.append("<celldesigner:alias>" + modifier.getElement().getElementId() + "</celldesigner:alias>\n");
+ sb.append("</celldesigner:extension>\n");
+ sb.append("</annotation>\n");
+ sb.append("</modifierSpeciesReference>\n");
+
+ return sb.toString();
+ }
+
+ /**
+ * Creates xml node for given modifer operator.
+ *
+ * @param modifierOperator
+ * modifier operator to be transaformed
+ * @return xml node for given modifer operator
+ */
+ private String getModifierXmlString(NodeOperator modifierOperator) {
+ StringBuilder sb = new StringBuilder();
+ OperatorTypeUtils otu = new OperatorTypeUtils();
+ ModifierTypeUtils mtu = new ModifierTypeUtils();
+ ModifierType modifierType = mtu.getModifierTypeForOperator(modifierOperator);
+ sb.append("<celldesigner:modification ");
+ String type = otu.getStringTypeByOperator(modifierOperator);
+ sb.append(" type=\"" + type + "\" ");
+ sb.append(" modificationType=\"" + modifierType.getStringName() + "\" ");
+ String modifiers = "";
+ String aliases = "";
+ for (AbstractNode modifier : modifierOperator.getInputs()) {
+ if (modifier instanceof Modifier) {
+ Modifier mod = (Modifier) modifier;
+ if (modifiers.equals("")) {
+ modifiers = elements.getElementId(mod.getElement());
+ aliases = mod.getElement().getElementId();
+ } else {
+ modifiers += "," + elements.getElementId(mod.getElement());
+ aliases += "," + mod.getElement().getElementId();
+ }
+
+ }
+ }
+ sb.append(" modifiers=\"" + modifiers + "\" ");
+ sb.append(" aliases=\"" + aliases + "\" ");
+ sb.append(" targetLineIndex=\"" + mtu.getTargetLineIndexByModifier(modifierOperator) + "\" ");
+ PolylineData line = new PolylineData(modifierOperator.getLine());
+
+ line.trimEnd(-modifierType.getTrimLength());
+
+ // TODO
+ // check the order (reverse or not, begin or end point)
+ line = line.reverse();
+ List<Point2D> points = lineTransformation.getPointsFromLine(line);
+ sb.append(" editPoints=\"");
+ for (int i = 1; i < points.size() - 1; i++) {
+ sb.append(points.get(i).getX() + "," + points.get(i).getY() + " ");
+ }
+ sb.append(line.getEndPoint().getX() + "," + line.getEndPoint().getY());
+ sb.append("\"");
+
+ sb.append(">\n");
+ PolylineData[] lines = new PolylineData[] { modifierOperator.getLine() };
+ sb.append(getConnectSchemeXmlStringForLines(lines));
+
+ sb.append("<celldesigner:line ");
+ sb.append("width=\"" + modifierOperator.getLine().getWidth() + "\" ");
+ sb.append("color=\"" + colorToString(modifierOperator.getLine().getColor()) + "\" ");
+ sb.append("type=\"Straight\" ");
+ sb.append("/>\n");
+
+ sb.append("</celldesigner:modification>\n");
+ return sb.toString();
+ }
+
+ /**
+ * Creates xml node for given modifer.
+ *
+ * @param modifier
+ * modifier to be transaformed
+ * @param gate
+ * operator to which modifier is connected (if any)
+ * @return xml node for given modifer
+ */
+ private String getModifierXmlString(Modifier modifier, NodeOperator gate) {
+ StringBuilder sb = new StringBuilder();
+ ModifierTypeUtils modifierTypeUtils = new ModifierTypeUtils();
+ sb.append("<celldesigner:modification ");
+ String type = modifierTypeUtils.getStringTypeByModifier(modifier);
+ sb.append(" type=\"" + type + "\" ");
+ sb.append(" modifiers=\"" + elements.getElementId(modifier.getElement()) + "\" ");
+ sb.append(" aliases=\"" + modifier.getElement().getElementId() + "\" ");
+ sb.append(" targetLineIndex=\"" + modifierTypeUtils.getTargetLineIndexByModifier(modifier) + "\" ");
+ PolylineData line = new PolylineData(modifier.getLine());
+
+ line.trimEnd(-modifierTypeUtils.getModifierTypeForClazz(modifier.getClass()).getTrimLength());
+ if (gate != null) {
+ line.setEndPoint(gate.getLine().getBeginPoint());
+ CellDesignerAliasConverter converter = new CellDesignerAliasConverter(modifier.getElement(), sbgn);
+ CellDesignerAnchor anchor = converter.getAnchorForCoordinates(modifier.getElement(), line.getBeginPoint());
+ Point2D start = converter.getPointCoordinates(modifier.getElement(), anchor);
+ line.setStartPoint(start);
+ }
+
+ List<Point2D> points = lineTransformation.getPointsFromLine(line);
+ if (points.size() > 0) {
+
+ boolean first = true;
+ sb.append(" editPoints=\"");
+
+ for (Point2D point : points) {
+ if (first) {
+ first = false;
+ } else {
+ sb.append(" ");
+ }
+ sb.append(point.getX() + "," + point.getY());
+ }
+ sb.append("\"");
+ }
+
+ sb.append(">\n");
+ PolylineData[] lines = new PolylineData[] { modifier.getLine() };
+ sb.append(getConnectSchemeXmlStringForLines(lines));
+ sb.append(getLinkTargetXmlString(modifier));
+
+ sb.append("<celldesigner:line ");
+ sb.append("width=\"" + modifier.getLine().getWidth() + "\" ");
+ sb.append("color=\"" + colorToString(modifier.getLine().getColor()) + "\" ");
+ sb.append("type=\"Straight\" ");
+ sb.append("/>\n");
+
+ sb.append("</celldesigner:modification>\n");
+ return sb.toString();
+ }
+
+ /**
+ * Gets target link string for given modifier.
+ *
+ * @param modifier
+ * modifier to be transformed
+ * @return anchor xml node representing modifier connection to reaction
+ */
+ private String getLinkTargetXmlString(Modifier modifier) {
+ StringBuilder sb = new StringBuilder();
+ sb.append("<celldesigner:linkTarget species=\"" + elements.getElementId(modifier.getElement()) + "\" alias=\""
+ + modifier.getElement().getElementId() + "\">\n");
+ sb.append(getAnchorXml(modifier.getElement(), modifier.getLine().getBeginPoint()));
+ sb.append("</celldesigner:linkTarget>\n");
+
+ return sb.toString();
+ }
+
+ /**
+ * Creates sbml node for list of products.
+ *
+ * @param reaction
+ * reaction from which products are taken
+ * @return sbml node representing lsit of products
+ */
+ private String getListOfProductsXmlStringForReaction(Reaction reaction) {
+ StringBuilder sb = new StringBuilder();
+ sb.append("<listOfProducts>\n");
+ for (Product product : reaction.getProducts()) {
+ // metaid is missing, maybe it will work ;)
+
+ Species element = (Species) product.getElement();
+
+ Set<Element> parents = new HashSet<>();
+
+ // we need top parent species
+ while (element.getComplex() != null) {
+ element = element.getComplex();
+ if (parents.contains(element)) {
+ throw new InvalidArgumentException(eu.getElementTag(element) + " Complex information is cyclic");
+ }
+ parents.add(element);
+ }
+
+ sb.append("<speciesReference species=\"" + elements.getElementId(element) + "\" ");
+ if (product.getStoichiometry() != null) {
+ sb.append(" stoichiometry=\"" + product.getStoichiometry() + "\" ");
+ }
+ sb.append(">\n");
+
+ sb.append("<annotation>\n");
+ sb.append("<celldesigner:extension>\n");
+ sb.append("<celldesigner:alias>" + product.getElement().getElementId() + "</celldesigner:alias>\n");
+ sb.append("</celldesigner:extension>\n");
+ sb.append("</annotation>\n");
+ sb.append("</speciesReference>\n");
+ }
+ sb.append("</listOfProducts>\n");
+ return sb.toString();
+ }
+
+ /**
+ * Creates sbml node for list of reactants.
+ *
+ * @param reaction
+ * reaction from which products are taken
+ * @return sbml node representing list of reactants
+ */
+ private String getListOfReactantsXmlStringForReaction(Reaction reaction) {
+ StringBuilder sb = new StringBuilder();
+ sb.append("<listOfReactants>\n");
+ for (Reactant reactant : reaction.getReactants()) {
+ // metaid is missing, maybe it will work ;)
+ Species species = (Species) reactant.getElement();
+
+ Set<Element> parents = new HashSet<>();
+
+ // we need top parent species
+ while (species.getComplex() != null) {
+ species = species.getComplex();
+ if (parents.contains(species)) {
+ throw new InvalidArgumentException(eu.getElementTag(species) + " Complex information is cyclic");
+ }
+ parents.add(species);
+ }
+
+ sb.append("<speciesReference species=\"" + elements.getElementId(species) + "\" ");
+ if (reactant.getStoichiometry() != null) {
+ sb.append(" stoichiometry=\"" + reactant.getStoichiometry() + "\" ");
+ }
+ sb.append(">\n");
+ sb.append("<annotation>\n");
+ sb.append("<celldesigner:extension>\n");
+ sb.append("<celldesigner:alias>" + reactant.getElement().getElementId() + "</celldesigner:alias>\n");
+ sb.append("</celldesigner:extension>\n");
+ sb.append("</annotation>\n");
+ sb.append("</speciesReference>\n");
+ }
+ sb.append("</listOfReactants>\n");
+ return sb.toString();
+ }
+
+ /**
+ * Creates annotation xml node for reaction.
+ *
+ * @param reaction
+ * reaction to be processed
+ * @return xml node representing annotation part
+ */
+ private String getAnnotationXmlStringForReaction(Reaction reaction) {
+ ReactionLineData rdl = ReactionLineData.getByReactionType(reaction.getClass());
+ if (rdl == null) {
+ throw new InvalidArgumentException("Unknown reaction type: " + reaction.getClass());
+ }
+ String reactionClassString = rdl.getCellDesignerString();
+ StringBuilder sb = new StringBuilder();
+ sb.append("<annotation>\n");
+ sb.append("<celldesigner:extension>\n");
+ sb.append("<celldesigner:reactionType>" + reactionClassString + "</celldesigner:reactionType>");
+ sb.append(getBaseReactantsXmlStringForReaction(reaction));
+ sb.append(getBaseProductsXmlStringForReaction(reaction));
+ sb.append(getListOfReactantLinksXmlStringForReaction(reaction));
+ sb.append(getListOfProductLinksXmlStringForReaction(reaction));
+ sb.append(getConnectSchemeXmlStringForReaction(reaction));
+ sb.append(getEditPointsXmlStringForReaction(reaction));
+ sb.append(getListOfModificationsXmlStringForReaction(reaction));
+ sb.append(getListOfGateMembersXmlStringForReaction(reaction));
+
+ sb.append("<celldesigner:line ");
+ sb.append("width=\"" + reaction.getReactants().get(0).getLine().getWidth() + "\" ");
+ sb.append("color=\"" + colorToString(reaction.getReactants().get(0).getLine().getColor()) + "\" ");
+ sb.append("type=\"Straight\" ");
+ sb.append("/>\n");
+
+ XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser();
+ sb.append("</celldesigner:extension>\n");
+ sb.append(xmlAnnotationParser.dataSetToXmlString(reaction.getMiriamData()));
+ sb.append("</annotation>\n");
+ return sb.toString();
+ }
+
+ /**
+ * Returns xml node with a list of gate members for reaction. For now only
+ * {@link TwoReactantReactionInterface} is supported.
+ *
+ * @param reaction
+ * reaction for which the cml will be returned
+ * @return xml string with list of gate members for reaction
+ */
+ private StringBuilder getListOfGateMembersXmlStringForReaction(Reaction reaction) {
+ StringBuilder result = new StringBuilder();
+ if (reaction instanceof TwoReactantReactionInterface) {
+ Reactant reactant1 = reaction.getReactants().get(0);
+ Reactant reactant2 = reaction.getReactants().get(1);
+ Product product = reaction.getProducts().get(0);
+ NodeOperator operator = reaction.getOperators().get(0);
+ OperatorType type = OperatorType.getTypeByClass(operator.getClass());
+
+ // if type is not defined then we are working on something that doesn't
+ // use gates
+ if (type != null) {
+ result.append("<celldesigner:listOfGateMember>\n");
+ ReactionLineData lineData = ReactionLineData.getByLineType(reaction.getProducts().get(0).getLine().getType(),
+ reaction.getProducts().get(0).getLine().getEndAtd().getArrowType());
+ Element alias1 = reactant1.getElement();
+ Element alias2 = reactant2.getElement();
+
+ // product line
+ result.append("<celldesigner:GateMember type=\"" + type.getStringName() + "\"");
+ result.append(" aliases=\"" + alias1.getElementId() + "," + alias2.getElementId() + "\"");
+ result.append(" modificationType=\"" + lineData.getCellDesignerString() + "\"");
+
+ CellDesignerLineTransformation clt = new CellDesignerLineTransformation();
+ List<Point2D> points = clt.getPointsFromLine(product.getLine());
+
+ result.append(" editPoints=\"");
+ for (int i = 0; i < points.size(); i++) {
+ result.append(points.get(i).getX() + "," + points.get(i).getY() + " ");
+ }
+ result.append(product.getLine().getBeginPoint().getX() + "," + product.getLine().getBeginPoint().getY() + " ");
+ result.append("\">\n");
+
+ result.append("<celldesigner:connectScheme connectPolicy=\"direct\">\n");
+ result.append("<celldesigner:listOfLineDirection>\n");
+ for (int i = 0; i < product.getLine().getPoints().size() - 1; i++) {
+ result.append("<celldesigner:lineDirection index=\"" + i + "\" value=\"unknown\"/>\n");
+ }
+ result.append("</celldesigner:listOfLineDirection>\n");
+ result.append("</celldesigner:connectScheme>\n");
+
+ result.append("</celldesigner:GateMember>\n");
+
+ // reactant 1 line
+
+ result.append("<celldesigner:GateMember type=\"" + lineData.getCellDesignerString() + "\"");
+ result.append(" aliases=\"" + alias1.getElementId() + "\"");
+
+ points = clt.getPointsFromLine(reactant1.getLine());
+
+ result.append(" editPoints=\"");
+ for (int i = 0; i < points.size(); i++) {
+ result.append(points.get(i).getX() + "," + points.get(i).getY() + " ");
+ }
+ result.append("\">\n");
+
+ result.append("<celldesigner:connectScheme connectPolicy=\"direct\">\n");
+ result.append("<celldesigner:listOfLineDirection>\n");
+ for (int i = 0; i < reactant1.getLine().getPoints().size() - 1; i++) {
+ result.append("<celldesigner:lineDirection index=\"" + i + "\" value=\"unknown\"/>\n");
+ }
+ result.append("</celldesigner:listOfLineDirection>\n");
+ result.append("</celldesigner:connectScheme>\n");
+
+ result.append("</celldesigner:GateMember>\n");
+
+ // reactant 2 line
+
+ result.append("<celldesigner:GateMember type=\"" + lineData.getCellDesignerString() + "\"");
+ result.append(" aliases=\"" + alias2.getElementId() + "\"");
+
+ points = clt.getPointsFromLine(reactant2.getLine());
+
+ result.append(" editPoints=\"");
+ for (int i = 0; i < points.size(); i++) {
+ result.append(points.get(i).getX() + "," + points.get(i).getY() + " ");
+ }
+ result.append("\">\n");
+
+ result.append("<celldesigner:connectScheme connectPolicy=\"direct\">\n");
+ result.append("<celldesigner:listOfLineDirection>\n");
+ for (int i = 0; i < reactant2.getLine().getPoints().size() - 1; i++) {
+ result.append("<celldesigner:lineDirection index=\"" + i + "\" value=\"unknown\"/>\n");
+ }
+ result.append("</celldesigner:listOfLineDirection>\n");
+ result.append("</celldesigner:connectScheme>\n");
+
+ result.append("</celldesigner:GateMember>\n");
+
+ result.append("</celldesigner:listOfGateMember>\n");
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Creates xml node (listOfProductLinks) with list of products.
+ *
+ * @param reaction
+ * reaction for which list of products is created
+ * @return xml node (listOfProductLinks) with list of products
+ */
+ private String getListOfProductLinksXmlStringForReaction(Reaction reaction) {
+ StringBuilder sb = new StringBuilder();
+ sb.append("<celldesigner:listOfProductLinks>\n");
+ int firstElement = 1;
+ if (reaction instanceof TwoProductReactionInterface) {
+ firstElement = 2;
+ }
+ for (int i = firstElement; i < reaction.getProducts().size(); i++) {
+ sb.append(getProductLinkXmlString(reaction.getProducts().get(i)));
+ }
+ sb.append("</celldesigner:listOfProductLinks>\n");
+ return sb.toString();
+ }
+
+ /**
+ * Creates xml node (listOfReactantLinks) with list of reactants.
+ *
+ * @param reaction
+ * reaction for which list of reactants is created
+ * @return xml node (listOfReactantLinks) with list of reactants
+ */
+ private String getListOfReactantLinksXmlStringForReaction(Reaction reaction) {
+ StringBuilder sb = new StringBuilder();
+ sb.append("<celldesigner:listOfReactantLinks>\n");
+ int firstElement = 1;
+ if (reaction instanceof TwoReactantReactionInterface) {
+ firstElement = 2;
+ }
+ for (int i = firstElement; i < reaction.getReactants().size(); i++) {
+ sb.append(getReactantLinkXmlString(reaction.getReactants().get(i)));
+ }
+ sb.append("</celldesigner:listOfReactantLinks>\n");
+ return sb.toString();
+ }
+
+ /**
+ * Creates rectantLink xml node for reactant.
+ *
+ * @param reactant
+ * reactant to be transformed
+ * @return xml node describing reactantLink
+ */
+ private String getReactantLinkXmlString(Reactant reactant) {
+ Element alias = reactant.getElement();
+ StringBuilder sb = new StringBuilder();
+ sb.append("<celldesigner:reactantLink ");
+ sb.append("reactant=\"" + elements.getElementId(alias) + "\" ");
+ sb.append("alias=\"" + alias.getElementId() + "\" ");
+ // targetLineIndex is missing (maybe it's unimportant :))
+ sb.append(">\n");
+
+ sb.append(getAnchorXml(alias, reactant.getLine().getBeginPoint()));
+
+ sb.append("<celldesigner:connectScheme connectPolicy=\"direct\">\n");
+ sb.append("<celldesigner:listOfLineDirection>\n");
+ for (int i = 0; i < reactant.getLine().getPoints().size() - 1; i++) {
+ sb.append("<celldesigner:lineDirection index=\"" + i + "\" value=\"unknown\"/>\n");
+ }
+ sb.append("</celldesigner:listOfLineDirection>\n");
+ sb.append("</celldesigner:connectScheme>\n");
+
+ // TODO
+ sb.append(getEditPointsXmlStringForLine(new PolylineData[] { reactant.getLine() }, 0));
+ sb.append("<celldesigner:line ");
+ sb.append("width=\"" + reactant.getLine().getWidth() + "\" ");
+ sb.append("color=\"" + colorToString(reactant.getLine().getColor()) + "\" ");
+ sb.append("type=\"Straight\" ");
+ sb.append("/>\n");
+ sb.append("</celldesigner:reactantLink>");
+ return sb.toString();
+ }
+
+ /**
+ * Creates productLink xml node for product.
+ *
+ * @param product
+ * product to be transformed
+ * @return xml node describing productLink
+ */
+ private String getProductLinkXmlString(Product product) {
+ Element alias = product.getElement();
+ PolylineData[] lines = new PolylineData[] { product.getLine() };
+
+ StringBuilder sb = new StringBuilder();
+ sb.append("<celldesigner:productLink ");
+ sb.append("product=\"" + elements.getElementId(alias) + "\" ");
+ sb.append("alias=\"" + alias.getElementId() + "\" ");
+ // targetLineIndex is missing (maybe it's unimportant :))
+ sb.append(">\n");
+
+ sb.append(getAnchorXml(alias, product.getLine().getEndPoint()));
+
+ sb.append(getConnectSchemeXmlStringForLines(lines));
+
+ // TODO
+ sb.append(getEditPointsXmlStringForLine(lines, 0));
+ sb.append("<celldesigner:line ");
+ sb.append("width=\"" + product.getLine().getWidth() + "\" ");
+ sb.append("color=\"" + colorToString(product.getLine().getColor()) + "\" ");
+ sb.append("type=\"Straight\" ");
+ sb.append("/>\n");
+ sb.append("</celldesigner:productLink>");
+ return sb.toString();
+ }
+
+ /**
+ * Creates valid xml node with connectScheme for the set of lines.
+ *
+ * @param lines
+ * list of lines to be included in connectScheme. As far as I remember
+ * only one or three lines could be provided.
+ * @return xml node with connectScheme
+ */
+ String getConnectSchemeXmlStringForLines(PolylineData[] lines) {
+ StringBuilder sb = new StringBuilder();
+ sb.append("<celldesigner:connectScheme ");
+ sb.append("connectPolicy=\"direct\" ");
+ // where on the line reactangle is positioned (it's not necessary so we skip
+ // it)
+ // if (rectangleIndex != null) {
+ // sb.append("rectangleIndex=\"" + rectangleIndex + "\" ");
+ // }
+ sb.append(">\n");
+ sb.append("<celldesigner:listOfLineDirection>\n");
+ int armId = 0;
+ for (PolylineData line : lines) {
+ String arm = "";
+ if (lines.length > 1) {
+ arm = " arm\"" + armId + "\" ";
+ armId++;
+ }
+ for (int i = 0; i < line.getPoints().size() - 1; i++) {
+ sb.append("<celldesigner:lineDirection " + arm + " index=\"" + i + "\" value=\"unknown\"/>\n");
+ }
+ }
+ sb.append("</celldesigner:listOfLineDirection>\n");
+ sb.append("</celldesigner:connectScheme>\n");
+ return sb.toString();
+ }
+
+ /**
+ * Creates
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints}
+ * structure representing lines in CellDesigner.
+ *
+ * @param lines
+ * lines to be transformed into single
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints}
+ * structure
+ * @param centerIndex
+ * where the central line is positioned
+ * @return xml node
+ */
+ private String getEditPointsXmlStringForLine(PolylineData[] lines, Integer centerIndex) {
+ return getEditPointsXmlStringForLine(lines, null, centerIndex);
+ }
+
+ /**
+ * Creates
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints}
+ * structure representing lines in CellDesigner.
+ *
+ * @param lines
+ * lines to be transformed into single
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints}
+ * structure
+ * @param centerPoint
+ * central point whene list of lines is greater than 1
+ * @param centerIndex
+ * where the central line is positioned
+ * @return xml node
+ */
+ private String getEditPointsXmlStringForLine(PolylineData[] lines, Point2D centerPoint, Integer centerIndex) {
+ StringBuilder sb = new StringBuilder();
+
+ sb.append("<celldesigner:editPoints ");
+ if (lines.length > 1) {
+ for (int i = 0; i < lines.length; i++) {
+ sb.append(" num" + i + "=\"" + (lines[i].getPoints().size() - 2) + "\" ");
+ }
+ if (centerIndex != null) {
+ sb.append(" tShapeIndex=\"" + centerIndex + "\"");
+ }
+ }
+ sb.append(">");
+
+ boolean first = true;
+ for (PolylineData pd : lines) {
+ List<Point2D> points = lineTransformation.getPointsFromLine(pd);
+
+ for (Point2D point : points) {
+ if (first) {
+ first = false;
+ } else {
+ sb.append(" ");
+ }
+ sb.append(point.getX() + "," + point.getY());
+ }
+ }
+ if (centerPoint != null) {
+ sb.append(" " + centerPoint.getX() + "," + centerPoint.getY());
+ }
+ sb.append("</celldesigner:editPoints>\n");
+
+ // when we don't have any points then we cannot create editPoints node (CD
+ // throws null pointer exception)
+ if (first && centerPoint == null) {
+ return "";
+ }
+ return sb.toString();
+ }
+
+ /**
+ * Returns xml node representing
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints}
+ * structure.
+ *
+ * @param reaction
+ * reaction for which xml node is generated
+ * @return xml node representing
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints}
+ * structure
+ */
+ String getEditPointsXmlStringForReaction(Reaction reaction) {
+ if (reaction instanceof SimpleReactionInterface) {
+ Product product = reaction.getProducts().get(0);
+ Reactant reactant = reaction.getReactants().get(0);
+ List<Point2D> points = new ArrayList<Point2D>();
+ for (int i = 0; i < reactant.getLine().getPoints().size() - 1; i++) {
+ points.add(reactant.getLine().getPoints().get(i));
+ }
+ for (int i = 1; i < product.getLine().getPoints().size(); i++) {
+ points.add(product.getLine().getPoints().get(i));
+ }
+
+ PolylineData pd = new PolylineData(points);
+ // TODO
+ return getEditPointsXmlStringForLine(new PolylineData[] { pd }, reactant.getLine().getPoints().size() - 1);
+ } else if (reaction instanceof TwoReactantReactionInterface) {
+ Reactant reactant1 = reaction.getReactants().get(0);
+ Reactant reactant2 = reaction.getReactants().get(1);
+ PolylineData line1 = reactant1.getLine();
+ PolylineData line2 = reactant2.getLine();
+ List<Point2D> points = new ArrayList<Point2D>();
+ for (NodeOperator operator : reaction.getOperators()) {
+ if (operator.isReactantOperator()) {
+ boolean process = true;
+ for (AbstractNode node : operator.getInputs()) {
+ if (!(node instanceof Reactant)) {
+ process = false;
+ }
+ }
+ if (process) {
+ for (int i = 0; i < operator.getLine().getPoints().size() - 1; i++) {
+ points.add(operator.getLine().getPoints().get(i));
+ }
+ }
+ }
+ }
+ Product product = reaction.getProducts().get(0);
+ for (int i = 1; i < product.getLine().getPoints().size(); i++) {
+ points.add(product.getLine().getPoints().get(i));
+ }
+
+ Point2D endPoint = points.get(points.size() - 1);
+ CellDesignerAliasConverter converter = new CellDesignerAliasConverter(product.getElement(), sbgn);
+ CellDesignerAnchor anchor = converter.getAnchorForCoordinates(product.getElement(), endPoint);
+ if (anchor == null) { // when we have no anchor, then end point is set
+ // to
+ // the center of alias
+ points.set(points.size() - 1, product.getElement().getCenter());
+ }
+
+ PolylineData line3 = new PolylineData(points);
+
+ Point2D pointC = reactant1.getElement().getCenter();
+ Point2D pointA = reactant2.getElement().getCenter();
+ Point2D pointB = product.getElement().getCenter();
+
+ Point2D pointO = line3.getBeginPoint();
+
+ Point2D centerPoint = pointTransformation.getCoordinatesInCellDesignerBase(pointA, pointB, pointC, pointO);
+
+ return getEditPointsXmlStringForLine(
+ new PolylineData[] { line1.reverse(), line2.reverse(), line3.reverse().reverse() }, centerPoint,
+ line3.getPoints().size() - product.getLine().getPoints().size());
+
+ } else if (reaction instanceof TwoProductReactionInterface) {
+ List<Point2D> points = new ArrayList<Point2D>();
+ Reactant reactant = reaction.getReactants().get(0);
+ Product product1 = reaction.getProducts().get(0);
+ Product product2 = reaction.getProducts().get(1);
+ for (int i = 0; i < reactant.getLine().getPoints().size() - 1; i++) {
+ points.add(reactant.getLine().getPoints().get(i));
+ }
+
+ Point2D startPoint = points.get(0);
+ CellDesignerAliasConverter converter = new CellDesignerAliasConverter(reactant.getElement(), sbgn);
+ CellDesignerAnchor anchor = converter.getAnchorForCoordinates(reactant.getElement(), startPoint);
+ if (anchor == null) { // when we have no anchor, then end point is set
+ // to
+ // the center of alias
+ points.set(points.size() - 1, reactant.getElement().getCenter());
+ }
+ int index = points.size();
+ for (NodeOperator operator : reaction.getOperators()) {
+ if (operator.isProductOperator()) {
+ boolean process = true;
+ for (AbstractNode node : operator.getOutputs()) {
+ if (!(node instanceof Product)) {
+ process = false;
+ }
+ }
+ if (process) {
+ for (int i = operator.getLine().getPoints().size() - 2; i >= 0; i--) {
+ points.add(operator.getLine().getPoints().get(i));
+ }
+ }
+ }
+ }
+ index = points.size() - index - 1;
+
+ PolylineData line1 = new PolylineData(points);
+
+ PolylineData line2 = product1.getLine();
+ PolylineData line3 = product2.getLine();
+
+ Point2D pointA = product1.getElement().getCenter();
+ Point2D pointB = product2.getElement().getCenter();
+ Point2D pointC = reactant.getElement().getCenter();
+
+ Point2D pointO = line2.getBeginPoint();
+
+ Point2D centerPoint = pointTransformation.getCoordinatesInCellDesignerBase(pointA, pointB, pointC, pointO);
+
+ return getEditPointsXmlStringForLine(new PolylineData[] { line1.reverse(), line2, line3 }, centerPoint, index);
+ } else {
+ throw new InvalidArgumentException("Unhandled reaction type: " + reaction.getClass());
+ }
+ }
+
+ /**
+ * Creates valid xml node with connectScheme for the reaction.
+ *
+ * @param reaction
+ * reaction for which the connectSchema is going to be created
+ * @return xml node with connectScheme
+ */
+ String getConnectSchemeXmlStringForReaction(Reaction reaction) {
+ StringBuilder sb = new StringBuilder();
+ sb.append("<celldesigner:connectScheme ");
+ sb.append("connectPolicy=\"direct\" ");
+ int rectangleIndex = -1;
+ if (reaction instanceof SimpleReactionInterface) {
+ rectangleIndex = reaction.getReactants().get(0).getLine().getPoints().size() - 2;
+ sb.append("rectangleIndex=\"" + rectangleIndex + "\" ");
+ }
+ sb.append(">\n");
+ sb.append("<celldesigner:listOfLineDirection>\n");
+ if (reaction instanceof SimpleReactionInterface) {
+ int size = reaction.getReactants().get(0).getLine().getPoints().size()
+ + reaction.getProducts().get(0).getLine().getPoints().size() - 2 - 1;
+ for (int i = 0; i < size; i++) {
+ sb.append("<celldesigner:lineDirection index=\"" + i + "\" value=\"unknown\"/>\n");
+ }
+ } else if (reaction instanceof TwoProductReactionInterface || reaction instanceof TwoReactantReactionInterface) {
+ String string = getEditPointsXmlStringForReaction(reaction);
+ Pattern p0 = Pattern.compile("num0=\"([0-9]+)");
+ Pattern p1 = Pattern.compile("num1=\"([0-9]+)");
+ Pattern p2 = Pattern.compile("num2=\"([0-9]+)");
+ Matcher m0 = p0.matcher(string);
+ Matcher m1 = p1.matcher(string);
+ Matcher m2 = p2.matcher(string);
+ int num0 = 0;
+ int num1 = 0;
+ int num2 = 0;
+
+ if (m0.find() && m1.find() && m2.find()) {
+ num0 = Integer.parseInt(m0.group(1));
+ num1 = Integer.parseInt(m1.group(1));
+ num2 = Integer.parseInt(m2.group(1));
+ } else {
+ throw new InvalidArgumentException("Invalid editPoints string" + string);
+ }
+
+ for (int i = 0; i <= num0; i++) {
+ sb.append("<celldesigner:lineDirection arm=\"0\" index=\"" + i + "\" value=\"unknown\"/>\n");
+ }
+ for (int i = 0; i <= num1; i++) {
+ sb.append("<celldesigner:lineDirection arm=\"1\" index=\"" + i + "\" value=\"unknown\"/>\n");
+ }
+ for (int i = 0; i <= num2; i++) {
+ sb.append("<celldesigner:lineDirection arm=\"2\" index=\"" + i + "\" value=\"unknown\"/>\n");
+ }
+ } else {
+ throw new InvalidArgumentException("Unknown reaction type: " + reaction.getClass());
+
+ }
+ sb.append("</celldesigner:listOfLineDirection>\n");
+ sb.append("</celldesigner:connectScheme>\n");
+ return sb.toString();
+ }
+
+ /**
+ * Returns xml node with list of base products.
+ *
+ * @param reaction
+ * reaction for which the node is created
+ * @return xml node with list of base products
+ */
+ private String getBaseProductsXmlStringForReaction(Reaction reaction) {
+ List<Product> products = new ArrayList<Product>();
+ products.add(reaction.getProducts().get(0));
+ if (reaction instanceof TwoProductReactionInterface) {
+ products.add(reaction.getProducts().get(1));
+ }
+
+ StringBuilder sb = new StringBuilder();
+ sb.append("<celldesigner:baseProducts>\n");
+ for (Product product : products) {
+ Element alias = product.getElement();
+ sb.append("<celldesigner:baseProduct ");
+ sb.append("species=\"" + elements.getElementId(product.getElement()) + "\" ");
+ sb.append("alias=\"" + product.getElement().getElementId() + "\" ");
+ sb.append(">\n");
+ sb.append(getAnchorXml(alias, product.getLine().getEndPoint()));
+
+ sb.append("</celldesigner:baseProduct>\n");
+ }
+ sb.append("</celldesigner:baseProducts>\n");
+ return sb.toString();
+ }
+
+ /**
+ * Returns xml node with list of base reactants.
+ *
+ * @param reaction
+ * reaction for which the node is created
+ * @return xml node with list of base reactants
+ */
+ private String getBaseReactantsXmlStringForReaction(Reaction reaction) {
+ List<Reactant> reactants = new ArrayList<Reactant>();
+ reactants.add(reaction.getReactants().get(0));
+ if (reaction instanceof TwoReactantReactionInterface) {
+ reactants.add(reaction.getReactants().get(1));
+ }
+
+ StringBuilder sb = new StringBuilder();
+ sb.append("<celldesigner:baseReactants>\n");
+ for (Reactant reactant : reactants) {
+ Element alias = reactant.getElement();
+ sb.append("<celldesigner:baseReactant ");
+ sb.append("species=\"" + elements.getElementId(reactant.getElement()) + "\" ");
+ sb.append("alias=\"" + reactant.getElement().getElementId() + "\" ");
+ sb.append(">\n");
+ sb.append(getAnchorXml(alias, reactant.getLine().getBeginPoint()));
+
+ sb.append("</celldesigner:baseReactant>\n");
+ }
+ sb.append("</celldesigner:baseReactants>\n");
+ return sb.toString();
+ }
+
+ /**
+ * Returns xml node that describes anchor point.
+ *
+ * @param alias
+ * alias on which we are looking for anchor
+ * @param point
+ * point on the alias that should be aligned to the closest anchor
+ * point
+ * @return xml node with anchor point
+ */
+ private String getAnchorXml(Element alias, Point2D point) {
+ CellDesignerAliasConverter converter = new CellDesignerAliasConverter(alias, sbgn);
+ CellDesignerAnchor anchor = converter.getAnchorForCoordinates(alias, point);
+ if (anchor != null) {
+ return "<celldesigner:linkAnchor position=\"" + anchor + "\"/>\n";
+ } else {
+ return "";
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionXmlParser.java
index 96d37edc31..d5ee3684e0 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionXmlParser.java
@@ -1,76 +1,76 @@
-package lcsb.mapviewer.converter.model.celldesigner.reaction;
-
-import org.w3c.dom.Node;
-
-import lcsb.mapviewer.common.XmlParser;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.ConverterException;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
-import lcsb.mapviewer.model.map.InconsistentModelException;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * Parser used to transform CellDesigner xml node into Reaction. It allows also
- * to transform {@link Reaction} into CellDesigner node.
- *
- * @author Piotr Gawron
- *
- */
-public class ReactionXmlParser extends XmlParser {
-
- /**
- * Class that allows to export data into CellDesigner xml node.
- */
- private ReactionToXml reactionToXml;
-
- /**
- * Class that allows to import data from CellDesigner xml node.
- */
- private ReactionFromXml reactionFromXml;
-
- /**
- * Default constructor. Model is required because some nodes require access to
- * other parts of the model.
- *
- * @param sbgn
- * Should SBGN standard be used
- * @param elements
- * collection of {@link CellDesignerElement cell designer elements}
- * parsed from xml
- */
- public ReactionXmlParser(CellDesignerElementCollection elements, boolean sbgn) {
- reactionToXml = new ReactionToXml(elements, sbgn);
- reactionFromXml = new ReactionFromXml(elements, sbgn);
- }
-
- /**
- * Returns {@link Reaction} object from CellDesigner xml node.
- *
- * @param node
- * xml node
- * @param model
- * model where the reaction is placed
- * @return reaction from xml node
- * @throws ReactionParserException
- * thrown when the xml is invalid
- * @throws InvalidXmlSchemaException
- * thrown when node is invalid xml
- */
- public Reaction getReaction(Node node, Model model) throws ReactionParserException, InvalidXmlSchemaException {
- return reactionFromXml.getReaction(node, model);
- }
-
- /**
- * Transform reaction into CellDesigner xml representation.
- *
- * @param reaction
- * reaction to transform
- * @return xml representation of reaction
- * @throws ConverterException
- */
- public String toXml(Reaction reaction) throws InconsistentModelException {
- return reactionToXml.toXml(reaction);
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.reaction;
+
+import org.w3c.dom.Node;
+
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * Parser used to transform CellDesigner xml node into Reaction. It allows also
+ * to transform {@link Reaction} into CellDesigner node.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ReactionXmlParser extends XmlParser {
+
+ /**
+ * Class that allows to export data into CellDesigner xml node.
+ */
+ private ReactionToXml reactionToXml;
+
+ /**
+ * Class that allows to import data from CellDesigner xml node.
+ */
+ private ReactionFromXml reactionFromXml;
+
+ /**
+ * Default constructor. Model is required because some nodes require access to
+ * other parts of the model.
+ *
+ * @param sbgn
+ * Should SBGN standard be used
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
+ */
+ public ReactionXmlParser(CellDesignerElementCollection elements, boolean sbgn) {
+ reactionToXml = new ReactionToXml(elements, sbgn);
+ reactionFromXml = new ReactionFromXml(elements, sbgn);
+ }
+
+ /**
+ * Returns {@link Reaction} object from CellDesigner xml node.
+ *
+ * @param node
+ * xml node
+ * @param model
+ * model where the reaction is placed
+ * @return reaction from xml node
+ * @throws ReactionParserException
+ * thrown when the xml is invalid
+ * @throws InvalidXmlSchemaException
+ * thrown when node is invalid xml
+ */
+ public Reaction getReaction(Node node, Model model) throws ReactionParserException, InvalidXmlSchemaException {
+ return reactionFromXml.getReaction(node, model);
+ }
+
+ /**
+ * Transform reaction into CellDesigner xml representation.
+ *
+ * @param reaction
+ * reaction to transform
+ * @return xml representation of reaction
+ * @throws ConverterException
+ */
+ public String toXml(Reaction reaction) throws InconsistentModelException {
+ return reactionToXml.toXml(reaction);
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/SelfReactionException.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/SelfReactionException.java
index b85d6f5537..f7b13b93e3 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/SelfReactionException.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/SelfReactionException.java
@@ -1,31 +1,31 @@
-package lcsb.mapviewer.converter.model.celldesigner.reaction;
-
-import lcsb.mapviewer.model.map.InconsistentModelException;
-
-/**
- * Exception thrown when CellDesigner exporter tries to export reaction that
- * uses the same element as product and reactant.
- *
- * @author Piotr Gawron
- *
- */
-public class SelfReactionException extends InconsistentModelException {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor with a message passed in the argument.
- *
- * @param message
- * text message of this exception
- */
- public SelfReactionException(String message) {
- super(message);
- }
-
- public SelfReactionException(Exception e) {
- super(e);
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.reaction;
+
+import lcsb.mapviewer.model.map.InconsistentModelException;
+
+/**
+ * Exception thrown when CellDesigner exporter tries to export reaction that
+ * uses the same element as product and reactant.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class SelfReactionException extends InconsistentModelException {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor with a message passed in the argument.
+ *
+ * @param message
+ * text message of this exception
+ */
+ public SelfReactionException(String message) {
+ super(message);
+ }
+
+ public SelfReactionException(Exception e) {
+ super(e);
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/UnknownModifierClassException.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/UnknownModifierClassException.java
index 62e920940d..160c69da42 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/UnknownModifierClassException.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/UnknownModifierClassException.java
@@ -1,54 +1,54 @@
-package lcsb.mapviewer.converter.model.celldesigner.reaction;
-
-/**
- * Exception thrown when unknown
- * {@link lcsb.mapviewer.model.map.reaction.Modifier} class found.
- *
- * @author Piotr Gawron
- *
- */
-public class UnknownModifierClassException extends ReactionParserException {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Type of reaction that was a reason for this exception.
- */
- private String modificationType;
-
- /**
- * Default constructor.
- *
- * @param message
- * message thrown
- * @param type
- * {@link #modificationType}
- * @param reactionId
- * {@link #reactionId}
- */
- public UnknownModifierClassException(String message, String type, String reactionId) {
- super(message, reactionId);
- this.modificationType = type;
- }
-
- /**
- * @return the modificationType
- * @see #modificationType
- */
- public String getModificationType() {
- return modificationType;
- }
-
- /**
- * @param modificationType
- * the modificationType to set
- * @see #modificationType
- */
- public void setModificationType(String modificationType) {
- this.modificationType = modificationType;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.reaction;
+
+/**
+ * Exception thrown when unknown
+ * {@link lcsb.mapviewer.model.map.reaction.Modifier} class found.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class UnknownModifierClassException extends ReactionParserException {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Type of reaction that was a reason for this exception.
+ */
+ private String modificationType;
+
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * message thrown
+ * @param type
+ * {@link #modificationType}
+ * @param reactionId
+ * {@link #reactionId}
+ */
+ public UnknownModifierClassException(String message, String type, String reactionId) {
+ super(message, reactionId);
+ this.modificationType = type;
+ }
+
+ /**
+ * @return the modificationType
+ * @see #modificationType
+ */
+ public String getModificationType() {
+ return modificationType;
+ }
+
+ /**
+ * @param modificationType
+ * the modificationType to set
+ * @see #modificationType
+ */
+ public void setModificationType(String modificationType) {
+ this.modificationType = modificationType;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/package-info.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/package-info.java
index 0a91a8dc26..3a0bc37998 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/package-info.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/package-info.java
@@ -1,6 +1,6 @@
-/**
- * This package contains parsers used for parsing CellDesiger xml for
- * {@link lcsb.mapviewer.db.model.map.reaction.Reaction Reaction}.
- */
-package lcsb.mapviewer.converter.model.celldesigner.reaction;
-
+/**
+ * This package contains parsers used for parsing CellDesiger xml for
+ * {@link lcsb.mapviewer.db.model.map.reaction.Reaction Reaction}.
+ */
+package lcsb.mapviewer.converter.model.celldesigner.reaction;
+
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/InternalModelSpeciesData.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/InternalModelSpeciesData.java
index fe20ad5b43..74548a88b6 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/InternalModelSpeciesData.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/InternalModelSpeciesData.java
@@ -1,214 +1,214 @@
-package lcsb.mapviewer.converter.model.celldesigner.species;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRna;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerDegraded;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerDrug;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGene;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerIon;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerPhenotype;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSimpleMolecule;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerUnknown;
-
-/**
- * This class contains information about all species in model that are relevant
- * during parsing via CellDesigner parser.
- *
- * @author Piotr Gawron
- *
- */
-public class InternalModelSpeciesData {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(InternalModelSpeciesData.class);
-
- /**
- * Collection of proteins. Used only by the CellDesigner parser.
- */
- private SpeciesCollection<CellDesignerProtein<?>> proteins;
-
- /**
- * Collection of genes. Used only by the CellDesigner parser.
- */
- private SpeciesCollection<CellDesignerGene> genes;
-
- /**
- * Collection of genes. Used only by the CellDesigner parser.
- */
- private SpeciesCollection<CellDesignerRna> rnas;
-
- /**
- * Collection of antisense rnas. Used only by the CellDesigner parser.
- */
- private SpeciesCollection<CellDesignerAntisenseRna> antisenseRnas;
-
- /**
- * Collection of phenotypes. Used only by the CellDesigner parser.
- */
- private SpeciesCollection<CellDesignerPhenotype> phenotypes;
-
- /**
- * Collection of ions. Used only by the CellDesigner parser.
- */
- private SpeciesCollection<CellDesignerIon> ions;
-
- /**
- * Collection of simple molecules. Used only by the CellDesigner parser.
- */
- private SpeciesCollection<CellDesignerSimpleMolecule> simpleMolecules;
-
- /**
- * Collection of drugs. Used only by the CellDesigner parser.
- */
- private SpeciesCollection<CellDesignerDrug> drugs;
-
- /**
- * Collection of unknowns. Used only by the CellDesigner parser.
- */
- private SpeciesCollection<CellDesignerUnknown> unknowns;
-
- /**
- * Collection of degraded elements. Used only by the CellDesigner parser.
- */
- private SpeciesCollection<CellDesignerDegraded> degradeds;
-
- /**
- * Collection of complexes.
- */
- private List<CellDesignerComplexSpecies> complexes = new ArrayList<>();
-
- /**
- * Default constructor.
- */
- public InternalModelSpeciesData() {
- proteins = new SpeciesCollection<>();
- genes = new SpeciesCollection<>();
- rnas = new SpeciesCollection<>();
- antisenseRnas = new SpeciesCollection<>();
- phenotypes = new SpeciesCollection<>();
- ions = new SpeciesCollection<>();
- simpleMolecules = new SpeciesCollection<>();
- drugs = new SpeciesCollection<>();
- unknowns = new SpeciesCollection<>();
- degradeds = new SpeciesCollection<>();
- }
-
- /**
- *
- * @return {@link #proteins}
- */
- public Collection<CellDesignerProtein<?>> getProteins() {
- return proteins.getAll();
- }
-
- /**
- *
- * @return {@link #genes}
- */
- public Collection<CellDesignerGene> getGenes() {
- return genes.getAll();
- }
-
- /**
- *
- * @return {@link #rnas}
- */
- public Collection<CellDesignerRna> getRnas() {
- return rnas.getAll();
- }
-
- /**
- *
- * @return {@link #antisenseRnas}
- */
- public Collection<CellDesignerAntisenseRna> getAntisenseRnas() {
- return antisenseRnas.getAll();
- }
-
- /**
- * Updates information about species in the dataset.
- *
- * @param collection
- * set of species to be updated, first element in pair defines
- * celldesigner identifier, second is the species
- */
- public void updateSpecies(Collection<Pair<String, ? extends CellDesignerSpecies<?>>> collection) {
- for (Pair<String, ? extends CellDesignerSpecies<?>> species : collection) {
- updateSpecies(species.getRight(), species.getLeft());
- }
- }
-
- /**
- * Updates information about species in the dataset (identified by
- * celldesigner specific identifier).
- *
- * @param sp
- * species to be updated
- * @param identifier
- * celldesigner identifier
- */
- public void updateSpecies(CellDesignerSpecies<?> sp, String identifier) {
- if (sp instanceof CellDesignerGene) {
- genes.updateSpeciesByLocalId((CellDesignerGene) sp, identifier);
- } else if (sp instanceof CellDesignerProtein) {
- proteins.updateSpeciesByLocalId((CellDesignerProtein<?>) sp, identifier);
- } else if (sp instanceof CellDesignerRna) {
- rnas.updateSpeciesByLocalId((CellDesignerRna) sp, identifier);
- } else if (sp instanceof CellDesignerAntisenseRna) {
- antisenseRnas.updateSpeciesByLocalId((CellDesignerAntisenseRna) sp, identifier);
- } else if (sp instanceof CellDesignerDegraded) {
- degradeds.updateSpeciesByLocalId((CellDesignerDegraded) sp, identifier);
- } else if (sp instanceof CellDesignerUnknown) {
- unknowns.updateSpeciesByLocalId((CellDesignerUnknown) sp, identifier);
- } else if (sp instanceof CellDesignerDrug) {
- drugs.updateSpeciesByLocalId((CellDesignerDrug) sp, identifier);
- } else if (sp instanceof CellDesignerSimpleMolecule) {
- simpleMolecules.updateSpeciesByLocalId((CellDesignerSimpleMolecule) sp, identifier);
- } else if (sp instanceof CellDesignerIon) {
- ions.updateSpeciesByLocalId((CellDesignerIon) sp, identifier);
- } else if (sp instanceof CellDesignerPhenotype) {
- phenotypes.updateSpeciesByLocalId((CellDesignerPhenotype) sp, identifier);
- } else if (sp instanceof CellDesignerComplexSpecies) {
- complexes.add((CellDesignerComplexSpecies) sp);
- } else {
- throw new InvalidArgumentException("Unknown species type: " + sp.getClass().getName());
- }
- }
-
- /**
- * Returns list of all species in dataset.
- *
- * @return list of all species in dataset
- */
- public Collection<CellDesignerSpecies<?>> getAll() {
- List<CellDesignerSpecies<?>> result = new ArrayList<>();
-
- result.addAll(genes.getAll());
- result.addAll(rnas.getAll());
- result.addAll(antisenseRnas.getAll());
- result.addAll(phenotypes.getAll());
- result.addAll(ions.getAll());
- result.addAll(simpleMolecules.getAll());
- result.addAll(drugs.getAll());
- result.addAll(unknowns.getAll());
- result.addAll(degradeds.getAll());
- result.addAll(proteins.getAll());
- result.addAll(complexes);
-
- return result;
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.species;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerDegraded;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerDrug;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGene;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerIon;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerPhenotype;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSimpleMolecule;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerUnknown;
+
+/**
+ * This class contains information about all species in model that are relevant
+ * during parsing via CellDesigner parser.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class InternalModelSpeciesData {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(InternalModelSpeciesData.class);
+
+ /**
+ * Collection of proteins. Used only by the CellDesigner parser.
+ */
+ private SpeciesCollection<CellDesignerProtein<?>> proteins;
+
+ /**
+ * Collection of genes. Used only by the CellDesigner parser.
+ */
+ private SpeciesCollection<CellDesignerGene> genes;
+
+ /**
+ * Collection of genes. Used only by the CellDesigner parser.
+ */
+ private SpeciesCollection<CellDesignerRna> rnas;
+
+ /**
+ * Collection of antisense rnas. Used only by the CellDesigner parser.
+ */
+ private SpeciesCollection<CellDesignerAntisenseRna> antisenseRnas;
+
+ /**
+ * Collection of phenotypes. Used only by the CellDesigner parser.
+ */
+ private SpeciesCollection<CellDesignerPhenotype> phenotypes;
+
+ /**
+ * Collection of ions. Used only by the CellDesigner parser.
+ */
+ private SpeciesCollection<CellDesignerIon> ions;
+
+ /**
+ * Collection of simple molecules. Used only by the CellDesigner parser.
+ */
+ private SpeciesCollection<CellDesignerSimpleMolecule> simpleMolecules;
+
+ /**
+ * Collection of drugs. Used only by the CellDesigner parser.
+ */
+ private SpeciesCollection<CellDesignerDrug> drugs;
+
+ /**
+ * Collection of unknowns. Used only by the CellDesigner parser.
+ */
+ private SpeciesCollection<CellDesignerUnknown> unknowns;
+
+ /**
+ * Collection of degraded elements. Used only by the CellDesigner parser.
+ */
+ private SpeciesCollection<CellDesignerDegraded> degradeds;
+
+ /**
+ * Collection of complexes.
+ */
+ private List<CellDesignerComplexSpecies> complexes = new ArrayList<>();
+
+ /**
+ * Default constructor.
+ */
+ public InternalModelSpeciesData() {
+ proteins = new SpeciesCollection<>();
+ genes = new SpeciesCollection<>();
+ rnas = new SpeciesCollection<>();
+ antisenseRnas = new SpeciesCollection<>();
+ phenotypes = new SpeciesCollection<>();
+ ions = new SpeciesCollection<>();
+ simpleMolecules = new SpeciesCollection<>();
+ drugs = new SpeciesCollection<>();
+ unknowns = new SpeciesCollection<>();
+ degradeds = new SpeciesCollection<>();
+ }
+
+ /**
+ *
+ * @return {@link #proteins}
+ */
+ public Collection<CellDesignerProtein<?>> getProteins() {
+ return proteins.getAll();
+ }
+
+ /**
+ *
+ * @return {@link #genes}
+ */
+ public Collection<CellDesignerGene> getGenes() {
+ return genes.getAll();
+ }
+
+ /**
+ *
+ * @return {@link #rnas}
+ */
+ public Collection<CellDesignerRna> getRnas() {
+ return rnas.getAll();
+ }
+
+ /**
+ *
+ * @return {@link #antisenseRnas}
+ */
+ public Collection<CellDesignerAntisenseRna> getAntisenseRnas() {
+ return antisenseRnas.getAll();
+ }
+
+ /**
+ * Updates information about species in the dataset.
+ *
+ * @param collection
+ * set of species to be updated, first element in pair defines
+ * celldesigner identifier, second is the species
+ */
+ public void updateSpecies(Collection<Pair<String, ? extends CellDesignerSpecies<?>>> collection) {
+ for (Pair<String, ? extends CellDesignerSpecies<?>> species : collection) {
+ updateSpecies(species.getRight(), species.getLeft());
+ }
+ }
+
+ /**
+ * Updates information about species in the dataset (identified by
+ * celldesigner specific identifier).
+ *
+ * @param sp
+ * species to be updated
+ * @param identifier
+ * celldesigner identifier
+ */
+ public void updateSpecies(CellDesignerSpecies<?> sp, String identifier) {
+ if (sp instanceof CellDesignerGene) {
+ genes.updateSpeciesByLocalId((CellDesignerGene) sp, identifier);
+ } else if (sp instanceof CellDesignerProtein) {
+ proteins.updateSpeciesByLocalId((CellDesignerProtein<?>) sp, identifier);
+ } else if (sp instanceof CellDesignerRna) {
+ rnas.updateSpeciesByLocalId((CellDesignerRna) sp, identifier);
+ } else if (sp instanceof CellDesignerAntisenseRna) {
+ antisenseRnas.updateSpeciesByLocalId((CellDesignerAntisenseRna) sp, identifier);
+ } else if (sp instanceof CellDesignerDegraded) {
+ degradeds.updateSpeciesByLocalId((CellDesignerDegraded) sp, identifier);
+ } else if (sp instanceof CellDesignerUnknown) {
+ unknowns.updateSpeciesByLocalId((CellDesignerUnknown) sp, identifier);
+ } else if (sp instanceof CellDesignerDrug) {
+ drugs.updateSpeciesByLocalId((CellDesignerDrug) sp, identifier);
+ } else if (sp instanceof CellDesignerSimpleMolecule) {
+ simpleMolecules.updateSpeciesByLocalId((CellDesignerSimpleMolecule) sp, identifier);
+ } else if (sp instanceof CellDesignerIon) {
+ ions.updateSpeciesByLocalId((CellDesignerIon) sp, identifier);
+ } else if (sp instanceof CellDesignerPhenotype) {
+ phenotypes.updateSpeciesByLocalId((CellDesignerPhenotype) sp, identifier);
+ } else if (sp instanceof CellDesignerComplexSpecies) {
+ complexes.add((CellDesignerComplexSpecies) sp);
+ } else {
+ throw new InvalidArgumentException("Unknown species type: " + sp.getClass().getName());
+ }
+ }
+
+ /**
+ * Returns list of all species in dataset.
+ *
+ * @return list of all species in dataset
+ */
+ public Collection<CellDesignerSpecies<?>> getAll() {
+ List<CellDesignerSpecies<?>> result = new ArrayList<>();
+
+ result.addAll(genes.getAll());
+ result.addAll(rnas.getAll());
+ result.addAll(antisenseRnas.getAll());
+ result.addAll(phenotypes.getAll());
+ result.addAll(ions.getAll());
+ result.addAll(simpleMolecules.getAll());
+ result.addAll(drugs.getAll());
+ result.addAll(unknowns.getAll());
+ result.addAll(degradeds.getAll());
+ result.addAll(proteins.getAll());
+ result.addAll(complexes);
+
+ return result;
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinMapping.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinMapping.java
index 09ed6d9405..49de3bfaf8 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinMapping.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinMapping.java
@@ -1,155 +1,155 @@
-package lcsb.mapviewer.converter.model.celldesigner.species;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGenericProtein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerIonChannelProtein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerReceptorProtein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerTruncatedProtein;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.IonChannelProtein;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.ReceptorProtein;
-import lcsb.mapviewer.model.map.species.TruncatedProtein;
-
-/**
- * This enum contains information about mapping between CellDesigner xml nodes
- * and classes that extend {@link CellDesignerProtein}.
- *
- * @author Piotr Gawron
- *
- */
-public enum ProteinMapping {
-
- /**
- * {@link GenericProtein}.
- */
- GENERIC_PROTEIN(GenericProtein.class, CellDesignerGenericProtein.class, "GENERIC"),
-
- /**
- * {@link IonChannelProtein}.
- */
- ION_CHANNEL_PROTEIN(IonChannelProtein.class, CellDesignerIonChannelProtein.class, "ION_CHANNEL"),
-
- /**
- * {@link ReceptorProtein}.
- */
- RECEPTOR_PROTEIN(ReceptorProtein.class, CellDesignerReceptorProtein.class, "RECEPTOR"),
-
- /**
- * {@link TruncatedProtein}.
- */
- TRUNCATED_PROTEIN(TruncatedProtein.class, CellDesignerTruncatedProtein.class, "TRUNCATED");
-
- /**
- * CellDesigner xml node type.
- */
- private String cellDesignerString;
-
- /**
- * Model class that should be used to represent cell designer node.
- */
- private Class<? extends Protein> clazz;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(ProteinMapping.class);
-
- /**
- * {@link CellDesignerProtein Celldesigner structure} used to represent the
- * node.
- */
- private Class<? extends CellDesignerProtein<?>> cellDesignerClazz;
-
- /**
- * Default constructor.
- *
- * @param cellDesignerClazz
- * {@link #clazz}
- * @param modelClazz
- * {@link #clazz class} in model corresponding to celldesigner object
- * @param cellDesignerString
- * {@link #cellDesignerString}
- */
- ProteinMapping(Class<? extends Protein> modelClazz, Class<? extends CellDesignerProtein<?>> cellDesignerClazz, String cellDesignerString) {
- this.cellDesignerString = cellDesignerString;
- this.clazz = modelClazz;
- this.cellDesignerClazz = cellDesignerClazz;
- }
-
- /**
- * @return the cellDesignerName
- * @see #cellDesignerString
- */
- public String getCellDesignerString() {
- return cellDesignerString;
- }
-
- /**
- * @return the clazz
- * @see #clazz
- */
- public Class<? extends Protein> getClazz() {
- return clazz;
- }
-
- /**
- * Returns celldesigner class type that represents xml node.
- *
- * @return celldesigner class type that represents xml node
- */
- public Class<? extends CellDesignerProtein<?>> getCellDesignerClazz() {
- return cellDesignerClazz;
- }
-
- /**
- * Returns {@link ProteinMapping} for given CellDesigner xml node name.
- *
- * @param string
- * CellDesigner xml node name
- * @return {@link ProteinMapping} for given CellDesigner xml node name
- */
- public static ProteinMapping getMappingByString(String string) {
- for (ProteinMapping mapping : ProteinMapping.values()) {
- if (mapping.getCellDesignerString().equals(string)) {
- return mapping;
- }
- }
- return null;
- }
-
- /**
- * Returns {@link ProteinMapping} for given {@link CellDesignerProtein} class.
- *
- * @param searchClazz
- * {@link CellDesignerProtein} class
- * @return {@link ProteinMapping} for given {@link CellDesignerProtein} class
- */
- public static ProteinMapping getMappingByClass(Class<? extends Protein> searchClazz) {
- for (ProteinMapping mapping : ProteinMapping.values()) {
- if (mapping.getClazz().isAssignableFrom(searchClazz)) {
- return mapping;
- }
- }
- return null;
- }
-
- /**
- * Creates instance of {@link CellDesignerProtein} specific for this
- * {@link ProteinMapping}.
- *
- * @return new instance of {@link CellDesignerProtein} specific for this
- * {@link ProteinMapping}.
- */
- public CellDesignerProtein<?> createProtein() {
- try {
- return cellDesignerClazz.getConstructor().newInstance();
- } catch (Exception e) {
- throw new InvalidStateException(e);
- }
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.species;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGenericProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerIonChannelProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerReceptorProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerTruncatedProtein;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.IonChannelProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.ReceptorProtein;
+import lcsb.mapviewer.model.map.species.TruncatedProtein;
+
+/**
+ * This enum contains information about mapping between CellDesigner xml nodes
+ * and classes that extend {@link CellDesignerProtein}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum ProteinMapping {
+
+ /**
+ * {@link GenericProtein}.
+ */
+ GENERIC_PROTEIN(GenericProtein.class, CellDesignerGenericProtein.class, "GENERIC"),
+
+ /**
+ * {@link IonChannelProtein}.
+ */
+ ION_CHANNEL_PROTEIN(IonChannelProtein.class, CellDesignerIonChannelProtein.class, "ION_CHANNEL"),
+
+ /**
+ * {@link ReceptorProtein}.
+ */
+ RECEPTOR_PROTEIN(ReceptorProtein.class, CellDesignerReceptorProtein.class, "RECEPTOR"),
+
+ /**
+ * {@link TruncatedProtein}.
+ */
+ TRUNCATED_PROTEIN(TruncatedProtein.class, CellDesignerTruncatedProtein.class, "TRUNCATED");
+
+ /**
+ * CellDesigner xml node type.
+ */
+ private String cellDesignerString;
+
+ /**
+ * Model class that should be used to represent cell designer node.
+ */
+ private Class<? extends Protein> clazz;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(ProteinMapping.class);
+
+ /**
+ * {@link CellDesignerProtein Celldesigner structure} used to represent the
+ * node.
+ */
+ private Class<? extends CellDesignerProtein<?>> cellDesignerClazz;
+
+ /**
+ * Default constructor.
+ *
+ * @param cellDesignerClazz
+ * {@link #clazz}
+ * @param modelClazz
+ * {@link #clazz class} in model corresponding to celldesigner object
+ * @param cellDesignerString
+ * {@link #cellDesignerString}
+ */
+ ProteinMapping(Class<? extends Protein> modelClazz, Class<? extends CellDesignerProtein<?>> cellDesignerClazz, String cellDesignerString) {
+ this.cellDesignerString = cellDesignerString;
+ this.clazz = modelClazz;
+ this.cellDesignerClazz = cellDesignerClazz;
+ }
+
+ /**
+ * @return the cellDesignerName
+ * @see #cellDesignerString
+ */
+ public String getCellDesignerString() {
+ return cellDesignerString;
+ }
+
+ /**
+ * @return the clazz
+ * @see #clazz
+ */
+ public Class<? extends Protein> getClazz() {
+ return clazz;
+ }
+
+ /**
+ * Returns celldesigner class type that represents xml node.
+ *
+ * @return celldesigner class type that represents xml node
+ */
+ public Class<? extends CellDesignerProtein<?>> getCellDesignerClazz() {
+ return cellDesignerClazz;
+ }
+
+ /**
+ * Returns {@link ProteinMapping} for given CellDesigner xml node name.
+ *
+ * @param string
+ * CellDesigner xml node name
+ * @return {@link ProteinMapping} for given CellDesigner xml node name
+ */
+ public static ProteinMapping getMappingByString(String string) {
+ for (ProteinMapping mapping : ProteinMapping.values()) {
+ if (mapping.getCellDesignerString().equals(string)) {
+ return mapping;
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Returns {@link ProteinMapping} for given {@link CellDesignerProtein} class.
+ *
+ * @param searchClazz
+ * {@link CellDesignerProtein} class
+ * @return {@link ProteinMapping} for given {@link CellDesignerProtein} class
+ */
+ public static ProteinMapping getMappingByClass(Class<? extends Protein> searchClazz) {
+ for (ProteinMapping mapping : ProteinMapping.values()) {
+ if (mapping.getClazz().isAssignableFrom(searchClazz)) {
+ return mapping;
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Creates instance of {@link CellDesignerProtein} specific for this
+ * {@link ProteinMapping}.
+ *
+ * @return new instance of {@link CellDesignerProtein} specific for this
+ * {@link ProteinMapping}.
+ */
+ public CellDesignerProtein<?> createProtein() {
+ try {
+ return cellDesignerClazz.getConstructor().newInstance();
+ } catch (Exception e) {
+ throw new InvalidStateException(e);
+ }
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollection.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollection.java
index 8741c3038d..83ff2439c7 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollection.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollection.java
@@ -1,173 +1,173 @@
-package lcsb.mapviewer.converter.model.celldesigner.species;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
-
-/**
- * This collection performs some magic, so please try no to understand it :). It
- * is required by the CellDEsigner xml schema. It helps to update and clone
- * properly species elements during parsing CellDesigner map, because definition
- * of species is split between three different places in the xml and in every
- * place almost any subset of information about species can appear. However some
- * of these information should appear in more than one copy of the element...
- *
- * @author Piotr Gawron
- *
- * @param <C>
- * class of the species
- */
-public class SpeciesCollection<C extends CellDesignerSpecies<?>> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(SpeciesCollection.class.getName());
-
- /**
- * List of all elements added to this collection.
- */
- private ArrayList<C> allElements;
-
- /**
- * Map of species identified by specific identifier of the species (like
- * {@link lcsb.mapviewer.db.model.map.species.CellDesignerProtein#proteinId
- * Protein#proteinId}.
- */
- private Map<String, ArrayList<C>> speciesListByLocalId;
-
- /**
- * Default Constructor. Initializes collection. Checks if method signature is
- * proper.
- *
- */
- public SpeciesCollection() {
- allElements = new ArrayList<C>();
- speciesListByLocalId = new HashMap<String, ArrayList<C>>();
- }
-
- /**
- * Adds element to collection.
- *
- * @param localId
- * celldesigner identifier
- * @param element
- * object to add
- */
- public void add(C element, String localId) {
- ArrayList<C> list = speciesListByLocalId.get(localId);
- if (list == null) {
- list = new ArrayList<C>();
- speciesListByLocalId.put(localId, list);
- }
- list.add(element);
- allElements.add(element);
- }
-
- /**
- * Returns list of species identifierd by local species specific identifier.
- *
- * @param localId
- * identifier of this species will be used to return the list
- * @return list of species identifierd by local species specific identifier
- */
- public ArrayList<C> getSpeciesListByLocalId(String localId) {
- return speciesListByLocalId.get(localId);
- }
-
- /**
- * This method is magic :). It updates information in every element in the
- * collection when the information should be propagated. And add species to
- * the collection when necessary.
- *
- * @param sp
- * data from this species should be propagated to other species
- * @param identifier
- * celldesigner identifier that determine which elements should be
- * modified
- */
- public void updateSpeciesByLocalId(C sp, String identifier) {
- C result = null;
-
- ArrayList<C> list = getSpeciesListByLocalId(identifier);
- if (list == null || list.size() == 0) {
- result = sp;
- add(sp, identifier);
- } else {
- ArrayList<C> toRemove = new ArrayList<C>();
- ArrayList<C> toAdd = new ArrayList<C>();
- for (C c : list) {
- // propagate the data only when idSpecies is not set or the idSpecies is
- // equlas to the one from which we updating data
- if (c.getElementId().equals("") || c.getElementId().equals(sp.getElementId())) {
- c.update(sp);
- if (c.getClass() != sp.getClass() && c.getClass().isAssignableFrom(sp.getClass())) {
- toRemove.add(c);
- C newInstance = createNewInstance(sp.getClass(), c);
- toAdd.add(newInstance);
- result = newInstance;
- } else {
- result = c;
- }
- } else if (sp.getElementId().equals("")) {
- c.update(sp);
- if (c.getClass() != sp.getClass() && c.getClass().isAssignableFrom(sp.getClass())) {
- toRemove.add(c);
- C newInstance = createNewInstance(sp.getClass(), c);
- toAdd.add(newInstance);
- result = newInstance;
- } else {
- result = c;
- }
- }
- }
- list.removeAll(toRemove);
- list.addAll(toAdd);
- allElements.removeAll(toRemove);
- allElements.addAll(toAdd);
-
- // if we haven't found any object to update then probably we have to add
- // species to the collection
- if (result == null) {
- result = sp;
- add(result, identifier);
- }
- }
- }
-
- /**
- * Creates a new instance of the object defined by clazz parameter and
- * initialized by c parameter.
- *
- * @param clazz
- * class of the object
- * @param c
- * original object and param of the constructor
- * @return new instance of the object
- */
- @SuppressWarnings({ "rawtypes", "unchecked" })
- protected C createNewInstance(Class clazz, C c) {
- try {
- return (C) clazz.getConstructor(CellDesignerSpecies.class).newInstance(c);
- } catch (Exception e) {
- throw new InvalidStateException("Problem with creating object", e);
- }
- }
-
- /**
- * Returns all elements from collection.
- *
- * @return collection with all elements
- */
- public Collection<C> getAll() {
- return allElements;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.species;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+
+/**
+ * This collection performs some magic, so please try no to understand it :). It
+ * is required by the CellDEsigner xml schema. It helps to update and clone
+ * properly species elements during parsing CellDesigner map, because definition
+ * of species is split between three different places in the xml and in every
+ * place almost any subset of information about species can appear. However some
+ * of these information should appear in more than one copy of the element...
+ *
+ * @author Piotr Gawron
+ *
+ * @param <C>
+ * class of the species
+ */
+public class SpeciesCollection<C extends CellDesignerSpecies<?>> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(SpeciesCollection.class.getName());
+
+ /**
+ * List of all elements added to this collection.
+ */
+ private ArrayList<C> allElements;
+
+ /**
+ * Map of species identified by specific identifier of the species (like
+ * {@link lcsb.mapviewer.db.model.map.species.CellDesignerProtein#proteinId
+ * Protein#proteinId}.
+ */
+ private Map<String, ArrayList<C>> speciesListByLocalId;
+
+ /**
+ * Default Constructor. Initializes collection. Checks if method signature is
+ * proper.
+ *
+ */
+ public SpeciesCollection() {
+ allElements = new ArrayList<C>();
+ speciesListByLocalId = new HashMap<String, ArrayList<C>>();
+ }
+
+ /**
+ * Adds element to collection.
+ *
+ * @param localId
+ * celldesigner identifier
+ * @param element
+ * object to add
+ */
+ public void add(C element, String localId) {
+ ArrayList<C> list = speciesListByLocalId.get(localId);
+ if (list == null) {
+ list = new ArrayList<C>();
+ speciesListByLocalId.put(localId, list);
+ }
+ list.add(element);
+ allElements.add(element);
+ }
+
+ /**
+ * Returns list of species identifierd by local species specific identifier.
+ *
+ * @param localId
+ * identifier of this species will be used to return the list
+ * @return list of species identifierd by local species specific identifier
+ */
+ public ArrayList<C> getSpeciesListByLocalId(String localId) {
+ return speciesListByLocalId.get(localId);
+ }
+
+ /**
+ * This method is magic :). It updates information in every element in the
+ * collection when the information should be propagated. And add species to
+ * the collection when necessary.
+ *
+ * @param sp
+ * data from this species should be propagated to other species
+ * @param identifier
+ * celldesigner identifier that determine which elements should be
+ * modified
+ */
+ public void updateSpeciesByLocalId(C sp, String identifier) {
+ C result = null;
+
+ ArrayList<C> list = getSpeciesListByLocalId(identifier);
+ if (list == null || list.size() == 0) {
+ result = sp;
+ add(sp, identifier);
+ } else {
+ ArrayList<C> toRemove = new ArrayList<C>();
+ ArrayList<C> toAdd = new ArrayList<C>();
+ for (C c : list) {
+ // propagate the data only when idSpecies is not set or the idSpecies is
+ // equlas to the one from which we updating data
+ if (c.getElementId().equals("") || c.getElementId().equals(sp.getElementId())) {
+ c.update(sp);
+ if (c.getClass() != sp.getClass() && c.getClass().isAssignableFrom(sp.getClass())) {
+ toRemove.add(c);
+ C newInstance = createNewInstance(sp.getClass(), c);
+ toAdd.add(newInstance);
+ result = newInstance;
+ } else {
+ result = c;
+ }
+ } else if (sp.getElementId().equals("")) {
+ c.update(sp);
+ if (c.getClass() != sp.getClass() && c.getClass().isAssignableFrom(sp.getClass())) {
+ toRemove.add(c);
+ C newInstance = createNewInstance(sp.getClass(), c);
+ toAdd.add(newInstance);
+ result = newInstance;
+ } else {
+ result = c;
+ }
+ }
+ }
+ list.removeAll(toRemove);
+ list.addAll(toAdd);
+ allElements.removeAll(toRemove);
+ allElements.addAll(toAdd);
+
+ // if we haven't found any object to update then probably we have to add
+ // species to the collection
+ if (result == null) {
+ result = sp;
+ add(result, identifier);
+ }
+ }
+ }
+
+ /**
+ * Creates a new instance of the object defined by clazz parameter and
+ * initialized by c parameter.
+ *
+ * @param clazz
+ * class of the object
+ * @param c
+ * original object and param of the constructor
+ * @return new instance of the object
+ */
+ @SuppressWarnings({ "rawtypes", "unchecked" })
+ protected C createNewInstance(Class clazz, C c) {
+ try {
+ return (C) clazz.getConstructor(CellDesignerSpecies.class).newInstance(c);
+ } catch (Exception e) {
+ throw new InvalidStateException("Problem with creating object", e);
+ }
+ }
+
+ /**
+ * Returns all elements from collection.
+ *
+ * @return collection with all elements
+ */
+ public Collection<C> getAll() {
+ return allElements;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/package-info.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/package-info.java
index 7b15345c0e..6f59a20abe 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/package-info.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/package-info.java
@@ -1,6 +1,6 @@
-/**
- * This package contains parsers used for parsing CellDesiger xml for
- * {@link lcsb.mapviewer.db.model.map.species.CellDesignerSpecies Species}.
- */
-package lcsb.mapviewer.converter.model.celldesigner.species;
-
+/**
+ * This package contains parsers used for parsing CellDesiger xml for
+ * {@link lcsb.mapviewer.db.model.map.species.CellDesignerSpecies Species}.
+ */
+package lcsb.mapviewer.converter.model.celldesigner.species;
+
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerChemical.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerChemical.java
index dab97cf4b6..0146ba0bbd 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerChemical.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerChemical.java
@@ -1,125 +1,125 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import lcsb.mapviewer.model.map.species.Chemical;
-
-/**
- * Class representing CellDesigner {@link Chemical}.
- *
- * @param <T>
- * model class tha corresponds to this cell designer structure
- *
- * @author Piotr Gawron
- *
- */
-public abstract class CellDesignerChemical<T extends Chemical> extends CellDesignerSpecies<T> {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * <a href=
- * "http://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system"
- * >Smiles</a> parameter for the chemical.
- */
- private String smiles;
-
- /**
- * <a href= "http://en.wikipedia.org/wiki/International_Chemical_Identifier" >
- * InChI</a> parameter for the chemical.
- */
-
- private String inChI;
-
- /**
- * <a href=
- * "http://en.wikipedia.org/wiki/International_Chemical_Identifier#InChIKey" >
- * InChIKey</a> parameter for the chemical.
- */
-
- private String inChIKey;
-
- /**
- * Creates a chemical from the species given in the parameter.
- *
- * @param species
- * original species from which this chemical will be created
- */
- public CellDesignerChemical(CellDesignerSpecies<?> species) {
- super(species);
- if (species instanceof CellDesignerChemical) {
- CellDesignerChemical<?> chemical = (CellDesignerChemical<?>) species;
- this.smiles = chemical.smiles;
- this.inChI = chemical.inChI;
- this.inChIKey = chemical.inChIKey;
- }
- }
-
- /**
- * Default constructor.
- */
- public CellDesignerChemical() {
- super();
- }
-
- /**
- * @return the smiles
- * @see #smiles
- */
- public String getSmiles() {
- return smiles;
- }
-
- /**
- * @param smiles
- * the smiles to set
- * @see #smiles
- */
- public void setSmiles(String smiles) {
- this.smiles = smiles;
- }
-
- /**
- * @return the inChI
- * @see #inChI
- */
- public String getInChI() {
- return inChI;
- }
-
- /**
- * @param inChI
- * the inChI to set
- * @see #inChI
- */
- public void setInChI(String inChI) {
- this.inChI = inChI;
- }
-
- /**
- * @return the inChIKey
- * @see #inChIKey
- */
- public String getInChIKey() {
- return inChIKey;
- }
-
- /**
- * @param inChIKey
- * the inChIKey to set
- * @see #inChIKey
- */
- public void setInChIKey(String inChIKey) {
- this.inChIKey = inChIKey;
- }
-
- @Override
- protected void setModelObjectFields(T result) {
- super.setModelObjectFields(result);
- result.setInChI(inChI);
- result.setInChIKey(inChIKey);
- result.setSmiles(smiles);
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import lcsb.mapviewer.model.map.species.Chemical;
+
+/**
+ * Class representing CellDesigner {@link Chemical}.
+ *
+ * @param <T>
+ * model class tha corresponds to this cell designer structure
+ *
+ * @author Piotr Gawron
+ *
+ */
+public abstract class CellDesignerChemical<T extends Chemical> extends CellDesignerSpecies<T> {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * <a href=
+ * "http://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system"
+ * >Smiles</a> parameter for the chemical.
+ */
+ private String smiles;
+
+ /**
+ * <a href= "http://en.wikipedia.org/wiki/International_Chemical_Identifier" >
+ * InChI</a> parameter for the chemical.
+ */
+
+ private String inChI;
+
+ /**
+ * <a href=
+ * "http://en.wikipedia.org/wiki/International_Chemical_Identifier#InChIKey" >
+ * InChIKey</a> parameter for the chemical.
+ */
+
+ private String inChIKey;
+
+ /**
+ * Creates a chemical from the species given in the parameter.
+ *
+ * @param species
+ * original species from which this chemical will be created
+ */
+ public CellDesignerChemical(CellDesignerSpecies<?> species) {
+ super(species);
+ if (species instanceof CellDesignerChemical) {
+ CellDesignerChemical<?> chemical = (CellDesignerChemical<?>) species;
+ this.smiles = chemical.smiles;
+ this.inChI = chemical.inChI;
+ this.inChIKey = chemical.inChIKey;
+ }
+ }
+
+ /**
+ * Default constructor.
+ */
+ public CellDesignerChemical() {
+ super();
+ }
+
+ /**
+ * @return the smiles
+ * @see #smiles
+ */
+ public String getSmiles() {
+ return smiles;
+ }
+
+ /**
+ * @param smiles
+ * the smiles to set
+ * @see #smiles
+ */
+ public void setSmiles(String smiles) {
+ this.smiles = smiles;
+ }
+
+ /**
+ * @return the inChI
+ * @see #inChI
+ */
+ public String getInChI() {
+ return inChI;
+ }
+
+ /**
+ * @param inChI
+ * the inChI to set
+ * @see #inChI
+ */
+ public void setInChI(String inChI) {
+ this.inChI = inChI;
+ }
+
+ /**
+ * @return the inChIKey
+ * @see #inChIKey
+ */
+ public String getInChIKey() {
+ return inChIKey;
+ }
+
+ /**
+ * @param inChIKey
+ * the inChIKey to set
+ * @see #inChIKey
+ */
+ public void setInChIKey(String inChIKey) {
+ this.inChIKey = inChIKey;
+ }
+
+ @Override
+ protected void setModelObjectFields(T result) {
+ super.setModelObjectFields(result);
+ result.setInChI(inChI);
+ result.setInChIKey(inChIKey);
+ result.setSmiles(smiles);
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerComplexSpecies.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerComplexSpecies.java
index 89f996caa8..a5ce21f7a1 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerComplexSpecies.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerComplexSpecies.java
@@ -1,170 +1,170 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import java.util.HashSet;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Complex;
-
-/**
- * Class representing CellDesigner {@link Complex}.
- *
- * @author Piotr Gawron
- *
- */
-public class CellDesignerComplexSpecies extends CellDesignerSpecies<Complex> {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(CellDesignerComplexSpecies.class.getName());
-
- /**
- * Elements that exists in this complex.
- */
- private Set<CellDesignerElement<?>> elements = new HashSet<>();
-
- /**
- * State of the complex species.
- */
- private String structuralState = null;
-
- /**
- * Default constructor.
- */
- public CellDesignerComplexSpecies() {
- super();
- }
-
- /**
- * Constructor that initiale the complex with the data from the object passed
- * as an argument.
- *
- * @param original
- * object used for initializing data
- */
- public CellDesignerComplexSpecies(CellDesignerSpecies<?> original) {
- super(original);
- if (original instanceof CellDesignerComplexSpecies) {
- CellDesignerComplexSpecies complex = (CellDesignerComplexSpecies) original;
- structuralState = complex.getStructuralState();
- for (CellDesignerElement<?> element : complex.getElements()) {
- addElement(element.copy());
- }
- }
- }
-
- /**
- * Constructor with species id.
- *
- * @param complexId
- * {@link CellDesignerSpecies#idSpecies}
- */
- public CellDesignerComplexSpecies(String complexId) {
- super(complexId);
- }
-
- @Override
- public CellDesignerComplexSpecies copy() {
- if (this.getClass() == CellDesignerComplexSpecies.class) {
- return new CellDesignerComplexSpecies(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- /**
- * Adds element to the complex.
- *
- * @param element
- * object to add
- */
- public void addElement(CellDesignerElement<?> element) {
- if (element instanceof CellDesignerSpecies) {
- for (CellDesignerElement<?> el : elements) {
- if (el instanceof CellDesignerSpecies) {
- if (el.getElementId().equals(element.getElementId())) {
- throw new InvalidArgumentException("Cannot add two species with the same id: " + el.getElementId());
- }
- }
- }
- }
- this.elements.add(element);
- }
-
- /**
- * Returns list of all elements in the complex. Also subelements are included.
- *
- * @return list of all elements in the complex.
- */
- public Set<CellDesignerSpecies<?>> getAllSimpleChildren() {
- Set<CellDesignerSpecies<?>> result = new HashSet<>();
- for (CellDesignerElement<?> element : getElements()) {
- if (element instanceof CellDesignerComplexSpecies) {
- result.addAll(((CellDesignerComplexSpecies) element).getAllSimpleChildren());
- } else if (element instanceof CellDesignerSpecies) {
- result.add((CellDesignerSpecies<?>) element);
- }
- }
- return result;
- }
-
- /**
- * @return the structuralState
- * @see #structuralState
- */
- public String getStructuralState() {
- return structuralState;
- }
-
- /**
- * @param structuralState
- * the structuralState to set
- * @see #structuralState
- */
- public void setStructuralState(String structuralState) {
- if (this.structuralState != null && !this.structuralState.equals("") && !this.structuralState.equals(structuralState)) {
- logger.warn("replacing structural state, Old: " + this.structuralState + " into new: " + structuralState);
- }
- this.structuralState = structuralState;
- }
-
- /**
- * @return the elements
- * @see #elements
- */
- public Set<CellDesignerElement<?>> getElements() {
- return elements;
- }
-
- /**
- * @param elements
- * the elements to set
- * @see #elements
- */
- public void setElements(Set<CellDesignerElement<?>> elements) {
- this.elements = elements;
- }
-
- @Override
- public Complex createModelElement(String aliasId) {
- Complex result = new Complex(aliasId);
- super.setModelObjectFields(result);
-
- if (elements.size() > 0) {
- throw new NotImplementedException();
- }
- result.setStructuralState(structuralState);
-
- return result;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Complex;
+
+/**
+ * Class representing CellDesigner {@link Complex}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CellDesignerComplexSpecies extends CellDesignerSpecies<Complex> {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(CellDesignerComplexSpecies.class.getName());
+
+ /**
+ * Elements that exists in this complex.
+ */
+ private Set<CellDesignerElement<?>> elements = new HashSet<>();
+
+ /**
+ * State of the complex species.
+ */
+ private String structuralState = null;
+
+ /**
+ * Default constructor.
+ */
+ public CellDesignerComplexSpecies() {
+ super();
+ }
+
+ /**
+ * Constructor that initiale the complex with the data from the object passed
+ * as an argument.
+ *
+ * @param original
+ * object used for initializing data
+ */
+ public CellDesignerComplexSpecies(CellDesignerSpecies<?> original) {
+ super(original);
+ if (original instanceof CellDesignerComplexSpecies) {
+ CellDesignerComplexSpecies complex = (CellDesignerComplexSpecies) original;
+ structuralState = complex.getStructuralState();
+ for (CellDesignerElement<?> element : complex.getElements()) {
+ addElement(element.copy());
+ }
+ }
+ }
+
+ /**
+ * Constructor with species id.
+ *
+ * @param complexId
+ * {@link CellDesignerSpecies#idSpecies}
+ */
+ public CellDesignerComplexSpecies(String complexId) {
+ super(complexId);
+ }
+
+ @Override
+ public CellDesignerComplexSpecies copy() {
+ if (this.getClass() == CellDesignerComplexSpecies.class) {
+ return new CellDesignerComplexSpecies(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ /**
+ * Adds element to the complex.
+ *
+ * @param element
+ * object to add
+ */
+ public void addElement(CellDesignerElement<?> element) {
+ if (element instanceof CellDesignerSpecies) {
+ for (CellDesignerElement<?> el : elements) {
+ if (el instanceof CellDesignerSpecies) {
+ if (el.getElementId().equals(element.getElementId())) {
+ throw new InvalidArgumentException("Cannot add two species with the same id: " + el.getElementId());
+ }
+ }
+ }
+ }
+ this.elements.add(element);
+ }
+
+ /**
+ * Returns list of all elements in the complex. Also subelements are included.
+ *
+ * @return list of all elements in the complex.
+ */
+ public Set<CellDesignerSpecies<?>> getAllSimpleChildren() {
+ Set<CellDesignerSpecies<?>> result = new HashSet<>();
+ for (CellDesignerElement<?> element : getElements()) {
+ if (element instanceof CellDesignerComplexSpecies) {
+ result.addAll(((CellDesignerComplexSpecies) element).getAllSimpleChildren());
+ } else if (element instanceof CellDesignerSpecies) {
+ result.add((CellDesignerSpecies<?>) element);
+ }
+ }
+ return result;
+ }
+
+ /**
+ * @return the structuralState
+ * @see #structuralState
+ */
+ public String getStructuralState() {
+ return structuralState;
+ }
+
+ /**
+ * @param structuralState
+ * the structuralState to set
+ * @see #structuralState
+ */
+ public void setStructuralState(String structuralState) {
+ if (this.structuralState != null && !this.structuralState.equals("") && !this.structuralState.equals(structuralState)) {
+ logger.warn("replacing structural state, Old: " + this.structuralState + " into new: " + structuralState);
+ }
+ this.structuralState = structuralState;
+ }
+
+ /**
+ * @return the elements
+ * @see #elements
+ */
+ public Set<CellDesignerElement<?>> getElements() {
+ return elements;
+ }
+
+ /**
+ * @param elements
+ * the elements to set
+ * @see #elements
+ */
+ public void setElements(Set<CellDesignerElement<?>> elements) {
+ this.elements = elements;
+ }
+
+ @Override
+ public Complex createModelElement(String aliasId) {
+ Complex result = new Complex(aliasId);
+ super.setModelObjectFields(result);
+
+ if (elements.size() > 0) {
+ throw new NotImplementedException();
+ }
+ result.setStructuralState(structuralState);
+
+ return result;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerDegraded.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerDegraded.java
index 7ef30e6d43..1bde95f6c9 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerDegraded.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerDegraded.java
@@ -1,51 +1,51 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Degraded;
-
-/**
- * Class representing CellDesigner {@link Degraded}.
- *
- * @author Piotr Gawron
- *
- */
-public class CellDesignerDegraded extends CellDesignerSpecies<Degraded> {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Constructor that copies the data from species given in the argument.
- *
- * @param species
- * parent species from which we want to copy data
- */
- public CellDesignerDegraded(CellDesignerSpecies<?> species) {
- super(species);
- }
-
- /**
- * Default constructor.
- */
- public CellDesignerDegraded() {
- }
-
- @Override
- public CellDesignerDegraded copy() {
- if (this.getClass() == CellDesignerDegraded.class) {
- return new CellDesignerDegraded(super.copy());
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- @Override
- public Degraded createModelElement(String aliasId) {
- Degraded result = new Degraded(aliasId);
- super.setModelObjectFields(result);
- return result;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Degraded;
+
+/**
+ * Class representing CellDesigner {@link Degraded}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CellDesignerDegraded extends CellDesignerSpecies<Degraded> {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Constructor that copies the data from species given in the argument.
+ *
+ * @param species
+ * parent species from which we want to copy data
+ */
+ public CellDesignerDegraded(CellDesignerSpecies<?> species) {
+ super(species);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public CellDesignerDegraded() {
+ }
+
+ @Override
+ public CellDesignerDegraded copy() {
+ if (this.getClass() == CellDesignerDegraded.class) {
+ return new CellDesignerDegraded(super.copy());
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ @Override
+ public Degraded createModelElement(String aliasId) {
+ Degraded result = new Degraded(aliasId);
+ super.setModelObjectFields(result);
+ return result;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerDrug.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerDrug.java
index df5daabb48..290938153d 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerDrug.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerDrug.java
@@ -1,51 +1,51 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Drug;
-
-/**
- * Class representing CellDesigner {@link Drug}.
- *
- * @author Piotr Gawron
- *
- */
-public class CellDesignerDrug extends CellDesignerSpecies<Drug> {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Constructor that copies the data from species given in the argument.
- *
- * @param species
- * parent species from which we want to copy data
- */
- public CellDesignerDrug(CellDesignerSpecies<?> species) {
- super(species);
- }
-
- /**
- * Default constructor.
- */
- public CellDesignerDrug() {
- }
-
- @Override
- public CellDesignerDrug copy() {
- if (this.getClass() == CellDesignerDrug.class) {
- return new CellDesignerDrug(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- @Override
- public Drug createModelElement(String aliasId) {
- Drug result = new Drug(aliasId);
- super.setModelObjectFields(result);
- return result;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Drug;
+
+/**
+ * Class representing CellDesigner {@link Drug}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CellDesignerDrug extends CellDesignerSpecies<Drug> {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Constructor that copies the data from species given in the argument.
+ *
+ * @param species
+ * parent species from which we want to copy data
+ */
+ public CellDesignerDrug(CellDesignerSpecies<?> species) {
+ super(species);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public CellDesignerDrug() {
+ }
+
+ @Override
+ public CellDesignerDrug copy() {
+ if (this.getClass() == CellDesignerDrug.class) {
+ return new CellDesignerDrug(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ @Override
+ public Drug createModelElement(String aliasId) {
+ Drug result = new Drug(aliasId);
+ super.setModelObjectFields(result);
+ return result;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGene.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGene.java
index 7e485de816..247887c598 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGene.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGene.java
@@ -1,122 +1,122 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * Class representing CellDesigner {@link Gene}.
- *
- * @author Piotr Gawron
- *
- */
-public class CellDesignerGene extends CellDesignerSpecies<Gene> {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * List of modifications for the Gene.
- */
- private List<CellDesignerModificationResidue> modificationResidues = new ArrayList<>();
-
- /**
- * Constructor that initializes gene with the data passed in the argument.
- *
- * @param species
- * original species used for data initialization
- */
- public CellDesignerGene(CellDesignerSpecies<?> species) {
- super(species);
- if (species instanceof CellDesignerGene) {
- CellDesignerGene gene = (CellDesignerGene) species;
- for (CellDesignerModificationResidue mr : gene.getModificationResidues()) {
- addModificationResidue(new CellDesignerModificationResidue(mr));
- }
- }
- }
-
- @Override
- public void update(CellDesignerSpecies<?> species) {
- super.update(species);
- if (species instanceof CellDesignerGene) {
- CellDesignerGene gene = (CellDesignerGene) species;
-
- for (CellDesignerModificationResidue mr : gene.getModificationResidues()) {
- addModificationResidue(mr);
- }
- }
- }
-
- /**
- * Default constructor.
- */
- public CellDesignerGene() {
- super();
- }
-
- @Override
- public CellDesignerGene copy() {
- if (this.getClass() == CellDesignerGene.class) {
- return new CellDesignerGene(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- /**
- * Adds modification to the gene.
- *
- * @param modificationResidue
- * modification to add
- */
- public void addModificationResidue(CellDesignerModificationResidue modificationResidue) {
- for (CellDesignerModificationResidue mr : modificationResidues) {
- if (mr.getIdModificationResidue().equals(modificationResidue.getIdModificationResidue())) {
- mr.update(modificationResidue);
- return;
- }
- }
- modificationResidues.add(modificationResidue);
- modificationResidue.setSpecies(this);
-
- }
-
- /**
- * @return the modificationResidues
- * @see #modificationResidues
- */
- public List<CellDesignerModificationResidue> getModificationResidues() {
- return modificationResidues;
- }
-
- /**
- * @param modificationResidues
- * the modificationResidues to set
- * @see #modificationResidues
- */
- public void setModificationResidues(List<CellDesignerModificationResidue> modificationResidues) {
- this.modificationResidues = modificationResidues;
- }
-
- @Override
- public Gene createModelElement(String aliasId) {
- Gene result = new Gene(aliasId);
- super.setModelObjectFields(result);
- return result;
- }
-
- @Override
- public void updateModelElementAfterLayoutAdded(Species element) {
- for (CellDesignerModificationResidue region : modificationResidues) {
- ((Gene) element).addModificationResidue(region.createModificationResidue(element));
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * Class representing CellDesigner {@link Gene}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CellDesignerGene extends CellDesignerSpecies<Gene> {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * List of modifications for the Gene.
+ */
+ private List<CellDesignerModificationResidue> modificationResidues = new ArrayList<>();
+
+ /**
+ * Constructor that initializes gene with the data passed in the argument.
+ *
+ * @param species
+ * original species used for data initialization
+ */
+ public CellDesignerGene(CellDesignerSpecies<?> species) {
+ super(species);
+ if (species instanceof CellDesignerGene) {
+ CellDesignerGene gene = (CellDesignerGene) species;
+ for (CellDesignerModificationResidue mr : gene.getModificationResidues()) {
+ addModificationResidue(new CellDesignerModificationResidue(mr));
+ }
+ }
+ }
+
+ @Override
+ public void update(CellDesignerSpecies<?> species) {
+ super.update(species);
+ if (species instanceof CellDesignerGene) {
+ CellDesignerGene gene = (CellDesignerGene) species;
+
+ for (CellDesignerModificationResidue mr : gene.getModificationResidues()) {
+ addModificationResidue(mr);
+ }
+ }
+ }
+
+ /**
+ * Default constructor.
+ */
+ public CellDesignerGene() {
+ super();
+ }
+
+ @Override
+ public CellDesignerGene copy() {
+ if (this.getClass() == CellDesignerGene.class) {
+ return new CellDesignerGene(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ /**
+ * Adds modification to the gene.
+ *
+ * @param modificationResidue
+ * modification to add
+ */
+ public void addModificationResidue(CellDesignerModificationResidue modificationResidue) {
+ for (CellDesignerModificationResidue mr : modificationResidues) {
+ if (mr.getIdModificationResidue().equals(modificationResidue.getIdModificationResidue())) {
+ mr.update(modificationResidue);
+ return;
+ }
+ }
+ modificationResidues.add(modificationResidue);
+ modificationResidue.setSpecies(this);
+
+ }
+
+ /**
+ * @return the modificationResidues
+ * @see #modificationResidues
+ */
+ public List<CellDesignerModificationResidue> getModificationResidues() {
+ return modificationResidues;
+ }
+
+ /**
+ * @param modificationResidues
+ * the modificationResidues to set
+ * @see #modificationResidues
+ */
+ public void setModificationResidues(List<CellDesignerModificationResidue> modificationResidues) {
+ this.modificationResidues = modificationResidues;
+ }
+
+ @Override
+ public Gene createModelElement(String aliasId) {
+ Gene result = new Gene(aliasId);
+ super.setModelObjectFields(result);
+ return result;
+ }
+
+ @Override
+ public void updateModelElementAfterLayoutAdded(Species element) {
+ for (CellDesignerModificationResidue region : modificationResidues) {
+ ((Gene) element).addModificationResidue(region.createModificationResidue(element));
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGenericProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGenericProtein.java
index a7625eefba..28dec49afe 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGenericProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGenericProtein.java
@@ -1,71 +1,71 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-
-/**
- * Class representing CellDesigner {@link GenericProtein}.
- *
- * @author Piotr Gawron
- *
- */
-public class CellDesignerGenericProtein extends CellDesignerProtein<GenericProtein> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private transient Logger logger = Logger.getLogger(CellDesignerGenericProtein.class);
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public CellDesignerGenericProtein() {
- super();
- }
-
- /**
- * Constructor that creates a copy of species.
- *
- * @param species
- * original species
- */
- public CellDesignerGenericProtein(CellDesignerSpecies<?> species) {
- super(species);
- }
-
- /**
- * Default constructor.
- *
- * @param id
- * identifier of the protein
- */
- public CellDesignerGenericProtein(String id) {
- setElementId(id);
- setName(id);
- }
-
- @Override
- public CellDesignerGenericProtein copy() {
- if (this.getClass().equals(CellDesignerGenericProtein.class)) {
- return new CellDesignerGenericProtein(this);
- } else {
- throw new NotImplementedException("Copy method for " + this.getClass() + " class not implemented");
- }
- }
-
- @Override
- public GenericProtein createModelElement(String aliasId) {
- GenericProtein result = new GenericProtein(aliasId);
- super.setModelObjectFields(result);
-
- return result;
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+
+/**
+ * Class representing CellDesigner {@link GenericProtein}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CellDesignerGenericProtein extends CellDesignerProtein<GenericProtein> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private transient Logger logger = Logger.getLogger(CellDesignerGenericProtein.class);
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public CellDesignerGenericProtein() {
+ super();
+ }
+
+ /**
+ * Constructor that creates a copy of species.
+ *
+ * @param species
+ * original species
+ */
+ public CellDesignerGenericProtein(CellDesignerSpecies<?> species) {
+ super(species);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param id
+ * identifier of the protein
+ */
+ public CellDesignerGenericProtein(String id) {
+ setElementId(id);
+ setName(id);
+ }
+
+ @Override
+ public CellDesignerGenericProtein copy() {
+ if (this.getClass().equals(CellDesignerGenericProtein.class)) {
+ return new CellDesignerGenericProtein(this);
+ } else {
+ throw new NotImplementedException("Copy method for " + this.getClass() + " class not implemented");
+ }
+ }
+
+ @Override
+ public GenericProtein createModelElement(String aliasId) {
+ GenericProtein result = new GenericProtein(aliasId);
+ super.setModelObjectFields(result);
+
+ return result;
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerIonChannelProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerIonChannelProtein.java
index 2a1da5d743..bd9cc31b09 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerIonChannelProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerIonChannelProtein.java
@@ -1,52 +1,52 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.IonChannelProtein;
-
-/**
- * Class representing CellDesigner {@link IonChannelProtein}.
- *
- * @author Piotr Gawron
- *
- */
-public class CellDesignerIonChannelProtein extends CellDesignerProtein<IonChannelProtein> {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public CellDesignerIonChannelProtein() {
- super();
- }
-
- /**
- * Constructor that creates a copy of species.
- *
- * @param species
- * original species
- */
- public CellDesignerIonChannelProtein(CellDesignerSpecies<?> species) {
- super(species);
- }
-
- @Override
- public CellDesignerIonChannelProtein copy() {
- if (this.getClass().equals(CellDesignerIonChannelProtein.class)) {
- return new CellDesignerIonChannelProtein(this);
- } else {
- throw new NotImplementedException("Copy method for " + this.getClass() + " class not implemented");
- }
- }
-
- @Override
- public IonChannelProtein createModelElement(String aliasId) {
- IonChannelProtein result = new IonChannelProtein(aliasId);
- super.setModelObjectFields(result);
- return result;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.IonChannelProtein;
+
+/**
+ * Class representing CellDesigner {@link IonChannelProtein}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CellDesignerIonChannelProtein extends CellDesignerProtein<IonChannelProtein> {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public CellDesignerIonChannelProtein() {
+ super();
+ }
+
+ /**
+ * Constructor that creates a copy of species.
+ *
+ * @param species
+ * original species
+ */
+ public CellDesignerIonChannelProtein(CellDesignerSpecies<?> species) {
+ super(species);
+ }
+
+ @Override
+ public CellDesignerIonChannelProtein copy() {
+ if (this.getClass().equals(CellDesignerIonChannelProtein.class)) {
+ return new CellDesignerIonChannelProtein(this);
+ } else {
+ throw new NotImplementedException("Copy method for " + this.getClass() + " class not implemented");
+ }
+ }
+
+ @Override
+ public IonChannelProtein createModelElement(String aliasId) {
+ IonChannelProtein result = new IonChannelProtein(aliasId);
+ super.setModelObjectFields(result);
+ return result;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerPhenotype.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerPhenotype.java
index 8ee7a94bce..6611cc4c50 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerPhenotype.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerPhenotype.java
@@ -1,52 +1,52 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Phenotype;
-
-/**
- * Class representing CellDesigner {@link Phenotype} object.
- *
- * @author Piotr Gawron
- *
- */
-public class CellDesignerPhenotype extends CellDesignerSpecies<Phenotype> {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Constructor that initializes phenotype with the data passed in the
- * argument.
- *
- * @param species
- * original species used for data initialization
- */
- public CellDesignerPhenotype(CellDesignerSpecies<?> species) {
- super(species);
- }
-
- /**
- * Default constructor.
- */
- public CellDesignerPhenotype() {
- }
-
- @Override
- public CellDesignerPhenotype copy() {
- if (this.getClass() == CellDesignerPhenotype.class) {
- return new CellDesignerPhenotype(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- @Override
- public Phenotype createModelElement(String aliasId) {
- Phenotype result = new Phenotype(aliasId);
- super.setModelObjectFields(result);
- return result;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Phenotype;
+
+/**
+ * Class representing CellDesigner {@link Phenotype} object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CellDesignerPhenotype extends CellDesignerSpecies<Phenotype> {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Constructor that initializes phenotype with the data passed in the
+ * argument.
+ *
+ * @param species
+ * original species used for data initialization
+ */
+ public CellDesignerPhenotype(CellDesignerSpecies<?> species) {
+ super(species);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public CellDesignerPhenotype() {
+ }
+
+ @Override
+ public CellDesignerPhenotype copy() {
+ if (this.getClass() == CellDesignerPhenotype.class) {
+ return new CellDesignerPhenotype(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ @Override
+ public Phenotype createModelElement(String aliasId) {
+ Phenotype result = new Phenotype(aliasId);
+ super.setModelObjectFields(result);
+ return result;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerReceptorProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerReceptorProtein.java
index f838567d0b..6779848bf1 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerReceptorProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerReceptorProtein.java
@@ -1,52 +1,52 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.ReceptorProtein;
-
-/**
- * Class representing CellDesigner {@link ReceptorProtein}.
- *
- * @author Piotr Gawron
- *
- */
-public class CellDesignerReceptorProtein extends CellDesignerProtein<ReceptorProtein> {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public CellDesignerReceptorProtein() {
- super();
- }
-
- /**
- * Constructor that creates a copy of species.
- *
- * @param species
- * original species
- */
- public CellDesignerReceptorProtein(CellDesignerSpecies<?> species) {
- super(species);
- }
-
- @Override
- public CellDesignerReceptorProtein copy() {
- if (this.getClass().equals(CellDesignerReceptorProtein.class)) {
- return new CellDesignerReceptorProtein(this);
- } else {
- throw new NotImplementedException("Copy method for " + this.getClass() + " class not implemented");
- }
- }
-
- @Override
- public ReceptorProtein createModelElement(String aliasId) {
- ReceptorProtein result = new ReceptorProtein(aliasId);
- super.setModelObjectFields(result);
- return result;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.ReceptorProtein;
+
+/**
+ * Class representing CellDesigner {@link ReceptorProtein}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CellDesignerReceptorProtein extends CellDesignerProtein<ReceptorProtein> {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public CellDesignerReceptorProtein() {
+ super();
+ }
+
+ /**
+ * Constructor that creates a copy of species.
+ *
+ * @param species
+ * original species
+ */
+ public CellDesignerReceptorProtein(CellDesignerSpecies<?> species) {
+ super(species);
+ }
+
+ @Override
+ public CellDesignerReceptorProtein copy() {
+ if (this.getClass().equals(CellDesignerReceptorProtein.class)) {
+ return new CellDesignerReceptorProtein(this);
+ } else {
+ throw new NotImplementedException("Copy method for " + this.getClass() + " class not implemented");
+ }
+ }
+
+ @Override
+ public ReceptorProtein createModelElement(String aliasId) {
+ ReceptorProtein result = new ReceptorProtein(aliasId);
+ super.setModelObjectFields(result);
+ return result;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSimpleMolecule.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSimpleMolecule.java
index cdbf286113..40b0f240c5 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSimpleMolecule.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSimpleMolecule.java
@@ -1,59 +1,59 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
-
-/**
- * Class representing CellDesigner {@link SimpleMolecule}.
- *
- * @author Piotr Gawron
- *
- */
-public class CellDesignerSimpleMolecule extends CellDesignerChemical<SimpleMolecule> {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(CellDesignerSimpleMolecule.class.getName());
-
- /**
- * Constructor that initializes molecule with the data passed in the argument.
- *
- * @param species
- * original species used for data initialization
- */
- public CellDesignerSimpleMolecule(CellDesignerSpecies<?> species) {
- super(species);
- }
-
- /**
- * Default constructor.
- */
- public CellDesignerSimpleMolecule() {
- }
-
- @Override
- public CellDesignerSimpleMolecule copy() {
- if (this.getClass() == CellDesignerSimpleMolecule.class) {
- return new CellDesignerSimpleMolecule(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- @Override
- public SimpleMolecule createModelElement(String aliasId) {
- SimpleMolecule result = new SimpleMolecule(aliasId);
- super.setModelObjectFields(result);
- return result;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+
+/**
+ * Class representing CellDesigner {@link SimpleMolecule}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CellDesignerSimpleMolecule extends CellDesignerChemical<SimpleMolecule> {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(CellDesignerSimpleMolecule.class.getName());
+
+ /**
+ * Constructor that initializes molecule with the data passed in the argument.
+ *
+ * @param species
+ * original species used for data initialization
+ */
+ public CellDesignerSimpleMolecule(CellDesignerSpecies<?> species) {
+ super(species);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public CellDesignerSimpleMolecule() {
+ }
+
+ @Override
+ public CellDesignerSimpleMolecule copy() {
+ if (this.getClass() == CellDesignerSimpleMolecule.class) {
+ return new CellDesignerSimpleMolecule(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ @Override
+ public SimpleMolecule createModelElement(String aliasId) {
+ SimpleMolecule result = new SimpleMolecule(aliasId);
+ super.setModelObjectFields(result);
+ return result;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSpecies.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSpecies.java
index 189df358e9..9decf2eaf8 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSpecies.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSpecies.java
@@ -1,547 +1,547 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
-
-/**
- * Generic CellDesigner element.
- *
- * @param <T>
- * model class that corresponds to this cell designer structure
- * @author Piotr Gawron
- *
- */
-public class CellDesignerSpecies<T extends Species> extends CellDesignerElement<T> {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(CellDesignerSpecies.class.getName());
-
- /**
- * Identifier of the species. It must be unique within the model.
- */
- private String idSpecies;
-
- /**
- * Initial amount of species.
- */
- private Double initialAmount = null;
-
- /**
- * Charge of the species.
- */
- private Integer charge = null;
-
- /**
- * Initial concentration of species.
- */
- private Double initialConcentration = null;
-
- /**
- * Is only substance units allowed.
- */
- private Boolean onlySubstanceUnits = null;
-
- /**
- * How many dimers are in this species.
- */
- private int homodimer = 1;
-
- /**
- * Position on the compartment.
- */
- private PositionToCompartment positionToCompartment = null;
-
- /**
- * Is species hypothetical.
- */
- private Boolean hypothetical = null;
-
- private SbmlUnitType substanceUnits;
-
- private Boolean boundaryCondition;
-
- private Boolean constant;
-
- /**
- * Set hypothetical flag from text input.
- *
- * @param text
- * string with true/false value that determines hypothetical state.
- * @see #hypothetical
- */
- public void setHypothetical(String text) {
- hypothetical = text.equals("true");
- }
-
- /**
- * Constructor that copies the data from species given in the argument.
- *
- * @param species
- * parent species from which we want to copy data
- */
- public CellDesignerSpecies(CellDesignerSpecies<?> species) {
- super(species);
- this.hypothetical = species.hypothetical;
- this.idSpecies = species.idSpecies;
- this.positionToCompartment = species.positionToCompartment;
- this.initialAmount = species.initialAmount;
- this.charge = species.charge;
- this.initialConcentration = species.initialConcentration;
- this.onlySubstanceUnits = species.onlySubstanceUnits;
- this.homodimer = species.homodimer;
- this.constant = species.constant;
- this.substanceUnits = species.substanceUnits;
- this.boundaryCondition = species.boundaryCondition;
- }
-
- /**
- * Default constructor.
- */
- public CellDesignerSpecies() {
- super();
- idSpecies = "";
- }
-
- /**
- * Default constructor with species identifier as a parameter.
- *
- * @param id
- * species identifier
- */
- public CellDesignerSpecies(String id) {
- this();
- this.idSpecies = id;
- this.setName(id);
- }
-
- @Override
- public CellDesignerSpecies<T> copy() {
- CellDesignerSpecies<T> result = new CellDesignerSpecies<T>(this);
-
- result.idSpecies = idSpecies;
- result.setNotes(getNotes());
- result.setHypothetical(hypothetical);
- // correct this
-
- result.setParent(getParent());
-
- return result;
- }
-
- /**
- * Updates species with the value from the species given in the parameter.
- *
- * @param species
- * object from which we are updating information
- */
- public void update(CellDesignerSpecies<?> species) {
- if (getName() == null || getName().equals("")) {
- setName(species.getName());
- } else if (!getName().trim().equals(species.getName().trim())) {
- String id = species.getElementId();
- if (id == null || id.equals("")) {
- id = getElementId();
- }
- logger.warn(
- "Two different names in species with id =" + id + ": \"" + species.getName() + "\", \"" + getName() + "\"");
- setName(species.getName());
- }
- if (idSpecies == null || idSpecies.equals("")) {
- setElementId(species.getElementId());
- }
- for (MiriamData md : species.getMiriamData()) {
- if (!getMiriamData().contains(md)) {
- addMiriamData(new MiriamData(md));
- }
- }
- if (this.getNotes() == null || this.getNotes().trim().equals("")) {
- setNotes(species.getNotes());
- } else if (species.getNotes() != null && !species.getNotes().trim().equals("")
- && !this.getNotes().equals(species.getNotes())) {
- String string1 = this.getNotes();
-
- String string2 = species.getNotes();
-
- string1 = string1.trim();
- string2 = string2.trim();
- if (string2.toLowerCase().contains(string1.toLowerCase())) {
- setNotes(species.getNotes());
- } else if (!string1.toLowerCase().contains(string2.toLowerCase())) {
- // insert new information
- setNotes(string2 + getNotes());
- }
- }
-
- if (getParent() == null) {
- setParent(species.getParent());
- }
-
- if (species.getHypothetical() != null) {
- setHypothetical(species.getHypothetical());
- }
-
- if (getSymbol() != null && !getSymbol().equals("")) {
- if (species.getSymbol() != null && !species.getSymbol().equals("")) {
- if (!species.getSymbol().equals(getSymbol())) {
- logger.warn("Different symbol names: " + species.getSymbol() + ", " + getSymbol() + ". Ignoring...");
- }
- }
- } else {
- setSymbol(species.getSymbol());
- }
-
- if (getFullName() != null && !getFullName().equals("")) {
- if (species.getFullName() != null && !species.getFullName().equals("")) {
- if (!species.getFullName().equals(getFullName())) {
- logger.warn("Different symbol names: " + species.getFullName() + ", " + getFullName() + ". Ignoring...");
- }
- }
- } else {
- setFullName(species.getFullName());
- }
-
- for (String string : species.getSynonyms()) {
- if (!getSynonyms().contains(string)) {
- getSynonyms().add(string);
- }
- }
-
- for (String string : species.getFormerSymbols()) {
- if (!getFormerSymbols().contains(string)) {
- getFormerSymbols().add(string);
- }
- }
- if (species.getHomodimer() != 1) {
- setHomodimer(species.getHomodimer());
- }
- if (species.getOnlySubstanceUnits() != null) {
- setOnlySubstanceUnits(species.getOnlySubstanceUnits());
- }
- if (species.getInitialAmount() != null) {
- setInitialAmount(species.getInitialAmount());
- }
- if (species.getInitialConcentration() != null) {
- setInitialConcentration(species.getInitialConcentration());
- }
- if (species.isConstant() != null) {
- setConstant(species.isConstant());
- }
- if (species.isBoundaryCondition() != null) {
- setBoundaryCondition(species.isBoundaryCondition());
- }
- }
-
- /**
- * Sets initial amount from text.
- *
- * @param text
- * initial amount in string format
- * @see #initialAmount
- */
-
- public void setInitialAmount(String text) {
- if (text != null && !text.trim().equals("")) {
- try {
- initialAmount = Double.parseDouble(text);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid species amount: " + text, e);
- }
- } else {
- initialAmount = null;
- }
-
- }
-
- /**
- * Sets charge from text.
- *
- * @param text
- * charge in string format
- * @see #charge
- */
- public void setCharge(String text) {
- if (text != null && !text.trim().equals("")) {
- try {
- charge = Integer.parseInt(text);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid species charge: " + text, e);
- }
- } else {
- charge = null;
- }
-
- }
-
- /**
- * Sets OnlySubstanceUnits amount from text.
- *
- * @param text
- * OnlySubstanceUnits in string format
- * @see #onlySubstanceUnits
- */
- public void setOnlySubstanceUnits(String text) {
- onlySubstanceUnits = textToBoolean(text, "Invalid species value for only substance unit boolean: " + text);
- }
-
- /**
- * Sets initial concentration amount from text.
- *
- * @param text
- * initial concentration in string format
- * @see #initialConcentration
- */
- public void setInitialConcentration(String text) {
- if (text != null && !text.trim().equals("")) {
- try {
- initialConcentration = Double.parseDouble(text);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid species initial concentration: " + text, e);
- }
- } else {
- initialConcentration = null;
- }
- }
-
- /**
- * Is species hypothetical or not.
- *
- * @return <code>true</code> if species is hypothetical, <code>false</code>
- * otherwise
- */
- public boolean isHypothetical() {
- if (hypothetical == null) {
- return false;
- }
- return hypothetical;
- }
-
- @Override
- public String getElementId() {
- return this.idSpecies;
- }
-
- @Override
- public void setElementId(String id) {
- if (this.idSpecies.equals(id) || this.idSpecies.equals("")) {
- this.idSpecies = id;
- } else if (!id.equals("")) {
- throw new InvalidArgumentException(
- "Cannot change identifier of the species in the runtime. OLD: " + this.idSpecies + ", NEW: " + id);
- } else {
- this.idSpecies = id;
- }
- }
-
- /**
- * @return the initialAmount
- * @see #initialAmount
- */
- public Double getInitialAmount() {
- return initialAmount;
- }
-
- /**
- * @param initialAmount
- * the initialAmount to set
- * @see #initialAmount
- */
- public void setInitialAmount(Double initialAmount) {
- this.initialAmount = initialAmount;
- }
-
- /**
- * @return the charge
- * @see #charge
- */
- public Integer getCharge() {
- return charge;
- }
-
- /**
- * @param charge
- * the charge to set
- * @see #charge
- */
- public void setCharge(Integer charge) {
- this.charge = charge;
- }
-
- /**
- * @return the onlySubstanceUnits
- * @see #onlySubstanceUnits
- */
- public Boolean getOnlySubstanceUnits() {
- return onlySubstanceUnits;
- }
-
- /**
- * @param onlySubstanceUnits
- * the onlySubstanceUnits to set
- * @see #onlySubstanceUnits
- */
- public void setOnlySubstanceUnits(Boolean onlySubstanceUnits) {
- this.onlySubstanceUnits = onlySubstanceUnits;
- }
-
- /**
- * @return the initialConcentration
- * @see #initialConcentration
- */
- public Double getInitialConcentration() {
- return initialConcentration;
- }
-
- /**
- * @param initialConcentration
- * the initialConcentration to set
- * @see #initialConcentration
- */
- public void setInitialConcentration(Double initialConcentration) {
- this.initialConcentration = initialConcentration;
- }
-
- /**
- * @return the hypothetical
- * @see #hypothetical
- */
- public Boolean getHypothetical() {
- return hypothetical;
- }
-
- /**
- * @param hypothetical
- * the hypothetical to set
- * @see #hypothetical
- */
- public void setHypothetical(Boolean hypothetical) {
- this.hypothetical = hypothetical;
- }
-
- /**
- * @return the onlySubstanceUnits
- * @see #onlySubstanceUnits
- */
- public Boolean hasOnlySubstanceUnits() {
- return onlySubstanceUnits;
- }
-
- /**
- * @return the positionToCompartment
- * @see #positionToCompartment
- */
- public PositionToCompartment getPositionToCompartment() {
- return positionToCompartment;
- }
-
- /**
- * @param positionToCompartment
- * the positionToCompartment to set
- * @see #positionToCompartment
- */
- public void setPositionToCompartment(PositionToCompartment positionToCompartment) {
- this.positionToCompartment = positionToCompartment;
- }
-
- /**
- * @return the homodimer
- * @see #homodimer
- */
- public int getHomodimer() {
- return homodimer;
- }
-
- /**
- * @param homodimer
- * the homodimer to set
- * @see #homodimer
- */
- public void setHomodimer(int homodimer) {
- this.homodimer = homodimer;
- }
-
- @Override
- public T createModelElement(String aliasId) {
- throw new NotImplementedException("" + this.getClass());
- }
-
- @Override
- protected void setModelObjectFields(T result) {
- super.setModelObjectFields(result);
- result.setInitialAmount(initialAmount);
- result.setCharge(charge);
- result.setInitialConcentration(initialConcentration);
- result.setOnlySubstanceUnits(onlySubstanceUnits);
- result.setConstant(constant);
- result.setBoundaryCondition(boundaryCondition);
- result.setSubstanceUnits(substanceUnits);
- result.setHomodimer(homodimer);
- result.setPositionToCompartment(positionToCompartment);
- result.setHypothetical(hypothetical);
- }
-
- public void setSubstanceUnits(SbmlUnitType substanceUnits) {
- this.substanceUnits = substanceUnits;
- }
-
- public SbmlUnitType getSubstanceUnit() {
- return this.substanceUnits;
- }
-
- public Boolean isBoundaryCondition() {
- return boundaryCondition;
- }
-
- public Boolean isConstant() {
- return constant;
- }
-
- public void setBoundaryCondition(String text) {
- boundaryCondition = textToBoolean(text, "Invalid species value for only substance unit boolean: " + text);
- }
-
- private Boolean textToBoolean(String text, String errorMessage) {
- Boolean result;
- if (text != null && !text.trim().equals("")) {
- if (text.equalsIgnoreCase("TRUE")) {
- result = true;
- } else if (text.equalsIgnoreCase("FALSE")) {
- result = false;
- } else {
- throw new InvalidArgumentException(errorMessage);
- }
- } else {
- result = null;
- }
- return result;
- }
-
- public void setConstant(String text) {
- constant = textToBoolean(text, "Invalid species value for only constant boolean: " + text);
- }
-
- public void setBoundaryCondition(Boolean boundaryCondition) {
- this.boundaryCondition = boundaryCondition;
- }
-
- public void setConstant(Boolean constant) {
- this.constant = constant;
- }
-
- @Override
- public void updateModelElementAfterLayoutAdded(Species element) {
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
+
+/**
+ * Generic CellDesigner element.
+ *
+ * @param <T>
+ * model class that corresponds to this cell designer structure
+ * @author Piotr Gawron
+ *
+ */
+public class CellDesignerSpecies<T extends Species> extends CellDesignerElement<T> {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(CellDesignerSpecies.class.getName());
+
+ /**
+ * Identifier of the species. It must be unique within the model.
+ */
+ private String idSpecies;
+
+ /**
+ * Initial amount of species.
+ */
+ private Double initialAmount = null;
+
+ /**
+ * Charge of the species.
+ */
+ private Integer charge = null;
+
+ /**
+ * Initial concentration of species.
+ */
+ private Double initialConcentration = null;
+
+ /**
+ * Is only substance units allowed.
+ */
+ private Boolean onlySubstanceUnits = null;
+
+ /**
+ * How many dimers are in this species.
+ */
+ private int homodimer = 1;
+
+ /**
+ * Position on the compartment.
+ */
+ private PositionToCompartment positionToCompartment = null;
+
+ /**
+ * Is species hypothetical.
+ */
+ private Boolean hypothetical = null;
+
+ private SbmlUnitType substanceUnits;
+
+ private Boolean boundaryCondition;
+
+ private Boolean constant;
+
+ /**
+ * Set hypothetical flag from text input.
+ *
+ * @param text
+ * string with true/false value that determines hypothetical state.
+ * @see #hypothetical
+ */
+ public void setHypothetical(String text) {
+ hypothetical = text.equals("true");
+ }
+
+ /**
+ * Constructor that copies the data from species given in the argument.
+ *
+ * @param species
+ * parent species from which we want to copy data
+ */
+ public CellDesignerSpecies(CellDesignerSpecies<?> species) {
+ super(species);
+ this.hypothetical = species.hypothetical;
+ this.idSpecies = species.idSpecies;
+ this.positionToCompartment = species.positionToCompartment;
+ this.initialAmount = species.initialAmount;
+ this.charge = species.charge;
+ this.initialConcentration = species.initialConcentration;
+ this.onlySubstanceUnits = species.onlySubstanceUnits;
+ this.homodimer = species.homodimer;
+ this.constant = species.constant;
+ this.substanceUnits = species.substanceUnits;
+ this.boundaryCondition = species.boundaryCondition;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public CellDesignerSpecies() {
+ super();
+ idSpecies = "";
+ }
+
+ /**
+ * Default constructor with species identifier as a parameter.
+ *
+ * @param id
+ * species identifier
+ */
+ public CellDesignerSpecies(String id) {
+ this();
+ this.idSpecies = id;
+ this.setName(id);
+ }
+
+ @Override
+ public CellDesignerSpecies<T> copy() {
+ CellDesignerSpecies<T> result = new CellDesignerSpecies<T>(this);
+
+ result.idSpecies = idSpecies;
+ result.setNotes(getNotes());
+ result.setHypothetical(hypothetical);
+ // correct this
+
+ result.setParent(getParent());
+
+ return result;
+ }
+
+ /**
+ * Updates species with the value from the species given in the parameter.
+ *
+ * @param species
+ * object from which we are updating information
+ */
+ public void update(CellDesignerSpecies<?> species) {
+ if (getName() == null || getName().equals("")) {
+ setName(species.getName());
+ } else if (!getName().trim().equals(species.getName().trim())) {
+ String id = species.getElementId();
+ if (id == null || id.equals("")) {
+ id = getElementId();
+ }
+ logger.warn(
+ "Two different names in species with id =" + id + ": \"" + species.getName() + "\", \"" + getName() + "\"");
+ setName(species.getName());
+ }
+ if (idSpecies == null || idSpecies.equals("")) {
+ setElementId(species.getElementId());
+ }
+ for (MiriamData md : species.getMiriamData()) {
+ if (!getMiriamData().contains(md)) {
+ addMiriamData(new MiriamData(md));
+ }
+ }
+ if (this.getNotes() == null || this.getNotes().trim().equals("")) {
+ setNotes(species.getNotes());
+ } else if (species.getNotes() != null && !species.getNotes().trim().equals("")
+ && !this.getNotes().equals(species.getNotes())) {
+ String string1 = this.getNotes();
+
+ String string2 = species.getNotes();
+
+ string1 = string1.trim();
+ string2 = string2.trim();
+ if (string2.toLowerCase().contains(string1.toLowerCase())) {
+ setNotes(species.getNotes());
+ } else if (!string1.toLowerCase().contains(string2.toLowerCase())) {
+ // insert new information
+ setNotes(string2 + getNotes());
+ }
+ }
+
+ if (getParent() == null) {
+ setParent(species.getParent());
+ }
+
+ if (species.getHypothetical() != null) {
+ setHypothetical(species.getHypothetical());
+ }
+
+ if (getSymbol() != null && !getSymbol().equals("")) {
+ if (species.getSymbol() != null && !species.getSymbol().equals("")) {
+ if (!species.getSymbol().equals(getSymbol())) {
+ logger.warn("Different symbol names: " + species.getSymbol() + ", " + getSymbol() + ". Ignoring...");
+ }
+ }
+ } else {
+ setSymbol(species.getSymbol());
+ }
+
+ if (getFullName() != null && !getFullName().equals("")) {
+ if (species.getFullName() != null && !species.getFullName().equals("")) {
+ if (!species.getFullName().equals(getFullName())) {
+ logger.warn("Different symbol names: " + species.getFullName() + ", " + getFullName() + ". Ignoring...");
+ }
+ }
+ } else {
+ setFullName(species.getFullName());
+ }
+
+ for (String string : species.getSynonyms()) {
+ if (!getSynonyms().contains(string)) {
+ getSynonyms().add(string);
+ }
+ }
+
+ for (String string : species.getFormerSymbols()) {
+ if (!getFormerSymbols().contains(string)) {
+ getFormerSymbols().add(string);
+ }
+ }
+ if (species.getHomodimer() != 1) {
+ setHomodimer(species.getHomodimer());
+ }
+ if (species.getOnlySubstanceUnits() != null) {
+ setOnlySubstanceUnits(species.getOnlySubstanceUnits());
+ }
+ if (species.getInitialAmount() != null) {
+ setInitialAmount(species.getInitialAmount());
+ }
+ if (species.getInitialConcentration() != null) {
+ setInitialConcentration(species.getInitialConcentration());
+ }
+ if (species.isConstant() != null) {
+ setConstant(species.isConstant());
+ }
+ if (species.isBoundaryCondition() != null) {
+ setBoundaryCondition(species.isBoundaryCondition());
+ }
+ }
+
+ /**
+ * Sets initial amount from text.
+ *
+ * @param text
+ * initial amount in string format
+ * @see #initialAmount
+ */
+
+ public void setInitialAmount(String text) {
+ if (text != null && !text.trim().equals("")) {
+ try {
+ initialAmount = Double.parseDouble(text);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid species amount: " + text, e);
+ }
+ } else {
+ initialAmount = null;
+ }
+
+ }
+
+ /**
+ * Sets charge from text.
+ *
+ * @param text
+ * charge in string format
+ * @see #charge
+ */
+ public void setCharge(String text) {
+ if (text != null && !text.trim().equals("")) {
+ try {
+ charge = Integer.parseInt(text);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid species charge: " + text, e);
+ }
+ } else {
+ charge = null;
+ }
+
+ }
+
+ /**
+ * Sets OnlySubstanceUnits amount from text.
+ *
+ * @param text
+ * OnlySubstanceUnits in string format
+ * @see #onlySubstanceUnits
+ */
+ public void setOnlySubstanceUnits(String text) {
+ onlySubstanceUnits = textToBoolean(text, "Invalid species value for only substance unit boolean: " + text);
+ }
+
+ /**
+ * Sets initial concentration amount from text.
+ *
+ * @param text
+ * initial concentration in string format
+ * @see #initialConcentration
+ */
+ public void setInitialConcentration(String text) {
+ if (text != null && !text.trim().equals("")) {
+ try {
+ initialConcentration = Double.parseDouble(text);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid species initial concentration: " + text, e);
+ }
+ } else {
+ initialConcentration = null;
+ }
+ }
+
+ /**
+ * Is species hypothetical or not.
+ *
+ * @return <code>true</code> if species is hypothetical, <code>false</code>
+ * otherwise
+ */
+ public boolean isHypothetical() {
+ if (hypothetical == null) {
+ return false;
+ }
+ return hypothetical;
+ }
+
+ @Override
+ public String getElementId() {
+ return this.idSpecies;
+ }
+
+ @Override
+ public void setElementId(String id) {
+ if (this.idSpecies.equals(id) || this.idSpecies.equals("")) {
+ this.idSpecies = id;
+ } else if (!id.equals("")) {
+ throw new InvalidArgumentException(
+ "Cannot change identifier of the species in the runtime. OLD: " + this.idSpecies + ", NEW: " + id);
+ } else {
+ this.idSpecies = id;
+ }
+ }
+
+ /**
+ * @return the initialAmount
+ * @see #initialAmount
+ */
+ public Double getInitialAmount() {
+ return initialAmount;
+ }
+
+ /**
+ * @param initialAmount
+ * the initialAmount to set
+ * @see #initialAmount
+ */
+ public void setInitialAmount(Double initialAmount) {
+ this.initialAmount = initialAmount;
+ }
+
+ /**
+ * @return the charge
+ * @see #charge
+ */
+ public Integer getCharge() {
+ return charge;
+ }
+
+ /**
+ * @param charge
+ * the charge to set
+ * @see #charge
+ */
+ public void setCharge(Integer charge) {
+ this.charge = charge;
+ }
+
+ /**
+ * @return the onlySubstanceUnits
+ * @see #onlySubstanceUnits
+ */
+ public Boolean getOnlySubstanceUnits() {
+ return onlySubstanceUnits;
+ }
+
+ /**
+ * @param onlySubstanceUnits
+ * the onlySubstanceUnits to set
+ * @see #onlySubstanceUnits
+ */
+ public void setOnlySubstanceUnits(Boolean onlySubstanceUnits) {
+ this.onlySubstanceUnits = onlySubstanceUnits;
+ }
+
+ /**
+ * @return the initialConcentration
+ * @see #initialConcentration
+ */
+ public Double getInitialConcentration() {
+ return initialConcentration;
+ }
+
+ /**
+ * @param initialConcentration
+ * the initialConcentration to set
+ * @see #initialConcentration
+ */
+ public void setInitialConcentration(Double initialConcentration) {
+ this.initialConcentration = initialConcentration;
+ }
+
+ /**
+ * @return the hypothetical
+ * @see #hypothetical
+ */
+ public Boolean getHypothetical() {
+ return hypothetical;
+ }
+
+ /**
+ * @param hypothetical
+ * the hypothetical to set
+ * @see #hypothetical
+ */
+ public void setHypothetical(Boolean hypothetical) {
+ this.hypothetical = hypothetical;
+ }
+
+ /**
+ * @return the onlySubstanceUnits
+ * @see #onlySubstanceUnits
+ */
+ public Boolean hasOnlySubstanceUnits() {
+ return onlySubstanceUnits;
+ }
+
+ /**
+ * @return the positionToCompartment
+ * @see #positionToCompartment
+ */
+ public PositionToCompartment getPositionToCompartment() {
+ return positionToCompartment;
+ }
+
+ /**
+ * @param positionToCompartment
+ * the positionToCompartment to set
+ * @see #positionToCompartment
+ */
+ public void setPositionToCompartment(PositionToCompartment positionToCompartment) {
+ this.positionToCompartment = positionToCompartment;
+ }
+
+ /**
+ * @return the homodimer
+ * @see #homodimer
+ */
+ public int getHomodimer() {
+ return homodimer;
+ }
+
+ /**
+ * @param homodimer
+ * the homodimer to set
+ * @see #homodimer
+ */
+ public void setHomodimer(int homodimer) {
+ this.homodimer = homodimer;
+ }
+
+ @Override
+ public T createModelElement(String aliasId) {
+ throw new NotImplementedException("" + this.getClass());
+ }
+
+ @Override
+ protected void setModelObjectFields(T result) {
+ super.setModelObjectFields(result);
+ result.setInitialAmount(initialAmount);
+ result.setCharge(charge);
+ result.setInitialConcentration(initialConcentration);
+ result.setOnlySubstanceUnits(onlySubstanceUnits);
+ result.setConstant(constant);
+ result.setBoundaryCondition(boundaryCondition);
+ result.setSubstanceUnits(substanceUnits);
+ result.setHomodimer(homodimer);
+ result.setPositionToCompartment(positionToCompartment);
+ result.setHypothetical(hypothetical);
+ }
+
+ public void setSubstanceUnits(SbmlUnitType substanceUnits) {
+ this.substanceUnits = substanceUnits;
+ }
+
+ public SbmlUnitType getSubstanceUnit() {
+ return this.substanceUnits;
+ }
+
+ public Boolean isBoundaryCondition() {
+ return boundaryCondition;
+ }
+
+ public Boolean isConstant() {
+ return constant;
+ }
+
+ public void setBoundaryCondition(String text) {
+ boundaryCondition = textToBoolean(text, "Invalid species value for only substance unit boolean: " + text);
+ }
+
+ private Boolean textToBoolean(String text, String errorMessage) {
+ Boolean result;
+ if (text != null && !text.trim().equals("")) {
+ if (text.equalsIgnoreCase("TRUE")) {
+ result = true;
+ } else if (text.equalsIgnoreCase("FALSE")) {
+ result = false;
+ } else {
+ throw new InvalidArgumentException(errorMessage);
+ }
+ } else {
+ result = null;
+ }
+ return result;
+ }
+
+ public void setConstant(String text) {
+ constant = textToBoolean(text, "Invalid species value for only constant boolean: " + text);
+ }
+
+ public void setBoundaryCondition(Boolean boundaryCondition) {
+ this.boundaryCondition = boundaryCondition;
+ }
+
+ public void setConstant(Boolean constant) {
+ this.constant = constant;
+ }
+
+ @Override
+ public void updateModelElementAfterLayoutAdded(Species element) {
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerTruncatedProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerTruncatedProtein.java
index f3484fcbd4..aec05429b1 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerTruncatedProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerTruncatedProtein.java
@@ -1,53 +1,53 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.TruncatedProtein;
-
-/**
- * Class representing CellDesigner {@link TruncatedProtein}.
- *
- * @author Piotr Gawron
- *
- */
-public class CellDesignerTruncatedProtein extends CellDesignerProtein<TruncatedProtein> {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public CellDesignerTruncatedProtein() {
- super();
- }
-
- /**
- * Constructor that creates a copy of species.
- *
- * @param species
- * original species
- */
- public CellDesignerTruncatedProtein(CellDesignerSpecies<?> species) {
- super(species);
- }
-
- @Override
- public CellDesignerTruncatedProtein copy() {
- if (this.getClass().equals(CellDesignerTruncatedProtein.class)) {
- return new CellDesignerTruncatedProtein(this);
- } else {
- throw new NotImplementedException("Copy method for " + this.getClass() + " class not implemented");
- }
- }
-
- @Override
- public TruncatedProtein createModelElement(String aliasId) {
- TruncatedProtein result = new TruncatedProtein(aliasId);
- super.setModelObjectFields(result);
-
- return result;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.TruncatedProtein;
+
+/**
+ * Class representing CellDesigner {@link TruncatedProtein}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CellDesignerTruncatedProtein extends CellDesignerProtein<TruncatedProtein> {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public CellDesignerTruncatedProtein() {
+ super();
+ }
+
+ /**
+ * Constructor that creates a copy of species.
+ *
+ * @param species
+ * original species
+ */
+ public CellDesignerTruncatedProtein(CellDesignerSpecies<?> species) {
+ super(species);
+ }
+
+ @Override
+ public CellDesignerTruncatedProtein copy() {
+ if (this.getClass().equals(CellDesignerTruncatedProtein.class)) {
+ return new CellDesignerTruncatedProtein(this);
+ } else {
+ throw new NotImplementedException("Copy method for " + this.getClass() + " class not implemented");
+ }
+ }
+
+ @Override
+ public TruncatedProtein createModelElement(String aliasId) {
+ TruncatedProtein result = new TruncatedProtein(aliasId);
+ super.setModelObjectFields(result);
+
+ return result;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerUnknown.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerUnknown.java
index 5253b209d0..c6d0326199 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerUnknown.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerUnknown.java
@@ -1,50 +1,50 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Unknown;
-
-/**
- * Class representing CellDesigner {@link Unknown} element.
- *
- * @author Piotr Gawron
- *
- */
-public class CellDesignerUnknown extends CellDesignerSpecies<Unknown> {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Constructor that initializes unknown with the data passed in the argument.
- *
- * @param species
- * original species used for data initialization
- */
- public CellDesignerUnknown(CellDesignerSpecies<?> species) {
- super(species);
- }
-
- /**
- * Default constructor.
- */
- public CellDesignerUnknown() {
- }
-
- @Override
- public CellDesignerUnknown copy() {
- if (this.getClass() == CellDesignerUnknown.class) {
- return new CellDesignerUnknown(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- @Override
- public Unknown createModelElement(String aliasId) {
- Unknown result = new Unknown(aliasId);
- super.setModelObjectFields(result);
- return result;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Unknown;
+
+/**
+ * Class representing CellDesigner {@link Unknown} element.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CellDesignerUnknown extends CellDesignerSpecies<Unknown> {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Constructor that initializes unknown with the data passed in the argument.
+ *
+ * @param species
+ * original species used for data initialization
+ */
+ public CellDesignerUnknown(CellDesignerSpecies<?> species) {
+ super(species);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public CellDesignerUnknown() {
+ }
+
+ @Override
+ public CellDesignerUnknown copy() {
+ if (this.getClass() == CellDesignerUnknown.class) {
+ return new CellDesignerUnknown(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ @Override
+ public Unknown createModelElement(String aliasId) {
+ Unknown result = new Unknown(aliasId);
+ super.setModelObjectFields(result);
+ return result;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/ConnectScheme.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/ConnectScheme.java
index b301451164..0f1596600e 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/ConnectScheme.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/ConnectScheme.java
@@ -1,112 +1,112 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
-
-import java.util.HashMap;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-
-/**
- * CellDEsigner structure used for storing some line information.
- *
- * @author Piotr Gawron
- *
- */
-public class ConnectScheme {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(ConnectScheme.class.getName());
-
- /**
- * Not used in our model... No ide what it means.
- */
- private String connectPolicy;
-
- /**
- * Defines where the central point is placed.
- */
- private Integer connectIndex;
-
- /**
- * Not used in our model... No ide what it means.
- */
- private Map<String, String> lineDirections;
-
- /**
- * Default constructor.
- */
- public ConnectScheme() {
- connectPolicy = "";
- connectIndex = null;
- lineDirections = new HashMap<String, String>();
- }
-
- /**
- *
- * @param directions
- * the directions to set
- * @see #directions
- */
- public void setLineDirections(Map<String, String> directions) {
- lineDirections = directions;
- }
-
- /**
- *
- * @param text
- * the connectIndex to set in String format
- * @see #connectIndex
- */
- public void setConnectIndex(String text) {
- if (text == null || "".equals(text)) {
- connectIndex = null;
- } else {
- setConnectIndex(Integer.parseInt(text));
- }
-
- }
-
- /**
- * @return the connectPolicy
- * @see #connectPolicy
- */
- public String getConnectPolicy() {
- return connectPolicy;
- }
-
- /**
- * @param connectPolicy
- * the connectPolicy to set
- * @see #connectPolicy
- */
- public void setConnectPolicy(String connectPolicy) {
- this.connectPolicy = connectPolicy;
- }
-
- /**
- * @return the connectIndex
- * @see #connectIndex
- */
- public Integer getConnectIndex() {
- return connectIndex;
- }
-
- /**
- * @param connectIndex
- * the connectIndex to set
- * @see #connectIndex
- */
- public void setConnectIndex(Integer connectIndex) {
- this.connectIndex = connectIndex;
- }
-
- /**
- * @return the lineDirections
- * @see #lineDirections
- */
- public Map<String, String> getLineDirections() {
- return lineDirections;
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+
+/**
+ * CellDEsigner structure used for storing some line information.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ConnectScheme {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(ConnectScheme.class.getName());
+
+ /**
+ * Not used in our model... No ide what it means.
+ */
+ private String connectPolicy;
+
+ /**
+ * Defines where the central point is placed.
+ */
+ private Integer connectIndex;
+
+ /**
+ * Not used in our model... No ide what it means.
+ */
+ private Map<String, String> lineDirections;
+
+ /**
+ * Default constructor.
+ */
+ public ConnectScheme() {
+ connectPolicy = "";
+ connectIndex = null;
+ lineDirections = new HashMap<String, String>();
+ }
+
+ /**
+ *
+ * @param directions
+ * the directions to set
+ * @see #directions
+ */
+ public void setLineDirections(Map<String, String> directions) {
+ lineDirections = directions;
+ }
+
+ /**
+ *
+ * @param text
+ * the connectIndex to set in String format
+ * @see #connectIndex
+ */
+ public void setConnectIndex(String text) {
+ if (text == null || "".equals(text)) {
+ connectIndex = null;
+ } else {
+ setConnectIndex(Integer.parseInt(text));
+ }
+
+ }
+
+ /**
+ * @return the connectPolicy
+ * @see #connectPolicy
+ */
+ public String getConnectPolicy() {
+ return connectPolicy;
+ }
+
+ /**
+ * @param connectPolicy
+ * the connectPolicy to set
+ * @see #connectPolicy
+ */
+ public void setConnectPolicy(String connectPolicy) {
+ this.connectPolicy = connectPolicy;
+ }
+
+ /**
+ * @return the connectIndex
+ * @see #connectIndex
+ */
+ public Integer getConnectIndex() {
+ return connectIndex;
+ }
+
+ /**
+ * @param connectIndex
+ * the connectIndex to set
+ * @see #connectIndex
+ */
+ public void setConnectIndex(Integer connectIndex) {
+ this.connectIndex = connectIndex;
+ }
+
+ /**
+ * @return the lineDirections
+ * @see #lineDirections
+ */
+ public Map<String, String> getLineDirections() {
+ return lineDirections;
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/EditPoints.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/EditPoints.java
index a207ce0239..18347406a3 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/EditPoints.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/EditPoints.java
@@ -1,174 +1,174 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
-
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.List;
-
-/**
- * CellDesigner structure for storing information about base lines in the
- * reaction.
- *
- * @author Piotr Gawron
- *
- */
-public class EditPoints {
-
- /**
- * List of internal points in CellDesigner format. Usually it means that edge
- * values represents base in which the interanal points are stored. However,
- * it doesn't have to be true in all case. For more detail analysie usage of
- * this class in the parser.
- *
- * @see lcsb.mapviewer.converter.model.celldesigner.geometry.helper.PolylineDataFactory#createPolylineDataFromEditPoints(Point2D,
- * Point2D, EditPoints)
- */
- private List<Point2D> points;
-
- /**
- * This value in reactions with three base reactants+products (reactions that
- * implements
- * {@link lcsb.mapviewer.db.model.map.reaction.type.TwoReactantReactionInterface
- * TwoReactantReactionInterface} or
- * {@link lcsb.mapviewer.db.model.map.reaction.type.TwoProductReactionInterface
- * TwoProductReactionInterface}) define where starts the first line in this
- * strange line description. See also usage of this field in CellDesigner
- * parser.
- */
-
- private int num0;
-
- /**
- * This value in reactions with three base reactants+products (reactions that
- * implements
- * {@link lcsb.mapviewer.db.model.map.reaction.type.TwoReactantReactionInterface
- * TwoReactantReactionInterface} or
- * {@link lcsb.mapviewer.db.model.map.reaction.type.TwoProductReactionInterface
- * TwoProductReactionInterface}) define where starts the second line in this
- * strange line description. See also usage of this field in CellDesigner
- * parser.
- */
- private int num1;
-
- /**
- * This value in reactions with three base reactants+products (reactions that
- * implements
- * {@link lcsb.mapviewer.db.model.map.reaction.type.TwoReactantReactionInterface
- * TwoReactantReactionInterface} or
- * {@link lcsb.mapviewer.db.model.map.reaction.type.TwoProductReactionInterface
- * TwoProductReactionInterface}) define where starts the third line in this
- * strange line description. See also usage of this field in CellDesigner
- * parser.
- */
- private int num2;
-
- /**
- * This value defines in which segment center of the reaction is put.
- */
- private Integer index;
-
- /**
- * Default constructor.
- */
- public EditPoints() {
- points = new ArrayList<Point2D>();
- num0 = 0;
- num1 = 0;
- num2 = 0;
- index = null;
- }
-
- /**
- * @return the points
- * @see #points
- */
- public List<Point2D> getPoints() {
- return points;
- }
-
- /**
- * @param points
- * the points to set
- * @see #points
- */
- public void setPoints(List<Point2D> points) {
- this.points = points;
- }
-
- /**
- * @return the num0
- * @see #num0
- */
- public int getNum0() {
- return num0;
- }
-
- /**
- * @param num0
- * the num0 to set
- * @see #num0
- */
- public void setNum0(int num0) {
- this.num0 = num0;
- }
-
- /**
- * @return the num1
- * @see #num1
- */
- public int getNum1() {
- return num1;
- }
-
- /**
- * @param num1
- * the num1 to set
- * @see #num1
- */
- public void setNum1(int num1) {
- this.num1 = num1;
- }
-
- /**
- * @return the num2
- * @see #num2
- */
- public int getNum2() {
- return num2;
- }
-
- /**
- * @param num2
- * the num2 to set
- * @see #num2
- */
- public void setNum2(int num2) {
- this.num2 = num2;
- }
-
- /**
- * @return the index
- * @see #index
- */
- public Integer getIndex() {
- return index;
- }
-
- /**
- * @param index
- * the index to set
- * @see #index
- */
- public void setIndex(Integer index) {
- this.index = index;
- }
-
- /**
- * Returns number of points in the line.
- *
- * @return number of points in the line
- */
- public int size() {
- return points.size();
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * CellDesigner structure for storing information about base lines in the
+ * reaction.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class EditPoints {
+
+ /**
+ * List of internal points in CellDesigner format. Usually it means that edge
+ * values represents base in which the interanal points are stored. However,
+ * it doesn't have to be true in all case. For more detail analysie usage of
+ * this class in the parser.
+ *
+ * @see lcsb.mapviewer.converter.model.celldesigner.geometry.helper.PolylineDataFactory#createPolylineDataFromEditPoints(Point2D,
+ * Point2D, EditPoints)
+ */
+ private List<Point2D> points;
+
+ /**
+ * This value in reactions with three base reactants+products (reactions that
+ * implements
+ * {@link lcsb.mapviewer.db.model.map.reaction.type.TwoReactantReactionInterface
+ * TwoReactantReactionInterface} or
+ * {@link lcsb.mapviewer.db.model.map.reaction.type.TwoProductReactionInterface
+ * TwoProductReactionInterface}) define where starts the first line in this
+ * strange line description. See also usage of this field in CellDesigner
+ * parser.
+ */
+
+ private int num0;
+
+ /**
+ * This value in reactions with three base reactants+products (reactions that
+ * implements
+ * {@link lcsb.mapviewer.db.model.map.reaction.type.TwoReactantReactionInterface
+ * TwoReactantReactionInterface} or
+ * {@link lcsb.mapviewer.db.model.map.reaction.type.TwoProductReactionInterface
+ * TwoProductReactionInterface}) define where starts the second line in this
+ * strange line description. See also usage of this field in CellDesigner
+ * parser.
+ */
+ private int num1;
+
+ /**
+ * This value in reactions with three base reactants+products (reactions that
+ * implements
+ * {@link lcsb.mapviewer.db.model.map.reaction.type.TwoReactantReactionInterface
+ * TwoReactantReactionInterface} or
+ * {@link lcsb.mapviewer.db.model.map.reaction.type.TwoProductReactionInterface
+ * TwoProductReactionInterface}) define where starts the third line in this
+ * strange line description. See also usage of this field in CellDesigner
+ * parser.
+ */
+ private int num2;
+
+ /**
+ * This value defines in which segment center of the reaction is put.
+ */
+ private Integer index;
+
+ /**
+ * Default constructor.
+ */
+ public EditPoints() {
+ points = new ArrayList<Point2D>();
+ num0 = 0;
+ num1 = 0;
+ num2 = 0;
+ index = null;
+ }
+
+ /**
+ * @return the points
+ * @see #points
+ */
+ public List<Point2D> getPoints() {
+ return points;
+ }
+
+ /**
+ * @param points
+ * the points to set
+ * @see #points
+ */
+ public void setPoints(List<Point2D> points) {
+ this.points = points;
+ }
+
+ /**
+ * @return the num0
+ * @see #num0
+ */
+ public int getNum0() {
+ return num0;
+ }
+
+ /**
+ * @param num0
+ * the num0 to set
+ * @see #num0
+ */
+ public void setNum0(int num0) {
+ this.num0 = num0;
+ }
+
+ /**
+ * @return the num1
+ * @see #num1
+ */
+ public int getNum1() {
+ return num1;
+ }
+
+ /**
+ * @param num1
+ * the num1 to set
+ * @see #num1
+ */
+ public void setNum1(int num1) {
+ this.num1 = num1;
+ }
+
+ /**
+ * @return the num2
+ * @see #num2
+ */
+ public int getNum2() {
+ return num2;
+ }
+
+ /**
+ * @param num2
+ * the num2 to set
+ * @see #num2
+ */
+ public void setNum2(int num2) {
+ this.num2 = num2;
+ }
+
+ /**
+ * @return the index
+ * @see #index
+ */
+ public Integer getIndex() {
+ return index;
+ }
+
+ /**
+ * @param index
+ * the index to set
+ * @see #index
+ */
+ public void setIndex(Integer index) {
+ this.index = index;
+ }
+
+ /**
+ * Returns number of points in the line.
+ *
+ * @return number of points in the line
+ */
+ public int size() {
+ return points.size();
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/LineProperties.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/LineProperties.java
index c8c4203e2b..99b103be11 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/LineProperties.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/LineProperties.java
@@ -1,89 +1,89 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
-
-import java.awt.Color;
-
-/**
- * Structure used in CellDEsigner model to store information about line
- * properties.
- *
- * @author Piotr Gawron
- *
- */
-public class LineProperties {
-
- /**
- * Width of the line.
- */
- private double width;
-
- /**
- * Color of the line.
- */
- private Color color;
-
- /**
- * Line type (no idea what is the format).
- */
- private String type;
-
- /**
- * Default constructor.
- */
- public LineProperties() {
- width = 1;
- color = Color.BLACK;
- type = "";
- }
-
- /**
- * @return the width
- * @see #width
- */
- public double getWidth() {
- return width;
- }
-
- /**
- * @param width
- * the width to set
- * @see #width
- */
- public void setWidth(double width) {
- this.width = width;
- }
-
- /**
- * @return the color
- * @see #color
- */
- public Color getColor() {
- return color;
- }
-
- /**
- * @param color
- * the color to set
- * @see #color
- */
- public void setColor(Color color) {
- this.color = color;
- }
-
- /**
- * @return the type
- * @see #type
- */
- public String getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(String type) {
- this.type = type;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
+
+import java.awt.Color;
+
+/**
+ * Structure used in CellDEsigner model to store information about line
+ * properties.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class LineProperties {
+
+ /**
+ * Width of the line.
+ */
+ private double width;
+
+ /**
+ * Color of the line.
+ */
+ private Color color;
+
+ /**
+ * Line type (no idea what is the format).
+ */
+ private String type;
+
+ /**
+ * Default constructor.
+ */
+ public LineProperties() {
+ width = 1;
+ color = Color.BLACK;
+ type = "";
+ }
+
+ /**
+ * @return the width
+ * @see #width
+ */
+ public double getWidth() {
+ return width;
+ }
+
+ /**
+ * @param width
+ * the width to set
+ * @see #width
+ */
+ public void setWidth(double width) {
+ this.width = width;
+ }
+
+ /**
+ * @return the color
+ * @see #color
+ */
+ public Color getColor() {
+ return color;
+ }
+
+ /**
+ * @param color
+ * the color to set
+ * @see #color
+ */
+ public void setColor(Color color) {
+ this.color = color;
+ }
+
+ /**
+ * @return the type
+ * @see #type
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * @param type
+ * the type to set
+ * @see #type
+ */
+ public void setType(String type) {
+ this.type = type;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/SingleLine.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/SingleLine.java
index 406d3d651c..26dfe344ca 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/SingleLine.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/SingleLine.java
@@ -1,33 +1,33 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
-
-/**
- * Strange CellDEsigner structure to store width of single line...
- *
- * @author Piotr Gawron
- *
- */
-public class SingleLine {
-
- /**
- * Width of the line.
- */
- private Double width;
-
- /**
- * @return the width
- * @see #width
- */
- public Double getWidth() {
- return width;
- }
-
- /**
- * @param width
- * the width to set
- * @see #width
- */
- public void setWidth(Double width) {
- this.width = width;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
+
+/**
+ * Strange CellDEsigner structure to store width of single line...
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class SingleLine {
+
+ /**
+ * Width of the line.
+ */
+ private Double width;
+
+ /**
+ * @return the width
+ * @see #width
+ */
+ public Double getWidth() {
+ return width;
+ }
+
+ /**
+ * @param width
+ * the width to set
+ * @see #width
+ */
+ public void setWidth(Double width) {
+ this.width = width;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/View.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/View.java
index 9960909347..dd0a00f02f 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/View.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/View.java
@@ -1,94 +1,94 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
-
-import java.awt.Color;
-import java.awt.Dimension;
-import java.awt.geom.Point2D;
-
-/**
- * This class represents some layout information in CellDesigner format.
- *
- * @author Piotr Gawron
- *
- */
-public class View {
-
- /**
- * No idea what this parameter describes.
- */
- private Point2D innerPosition;
-
- /**
- * Size of the element.
- */
- private Dimension boxSize;
-
- /**
- * Width of the line.
- */
- private SingleLine singleLine;
-
- /**
- * Color of the element.
- */
- private Color color;
-
- /**
- * @return the innerPosition
- */
- public Point2D getInnerPosition() {
- return innerPosition;
- }
-
- /**
- * @param innerPosition
- * the innerPosition to set
- */
- public void setInnerPosition(Point2D innerPosition) {
- this.innerPosition = innerPosition;
- }
-
- /**
- * @return the boxSize
- */
- public Dimension getBoxSize() {
- return boxSize;
- }
-
- /**
- * @param boxSize
- * the boxSize to set
- */
- public void setBoxSize(Dimension boxSize) {
- this.boxSize = boxSize;
- }
-
- /**
- * @return the singleLine
- */
- public SingleLine getSingleLine() {
- return singleLine;
- }
-
- /**
- * @param singleLine
- * the singleLine to set
- */
- public void setSingleLine(SingleLine singleLine) {
- this.singleLine = singleLine;
- }
-
- /**
- * @return the color
- */
- public Color getColor() {
- return color;
- }
-
- /**
- * @param color
- * the color to set
- */
- public void setColor(Color color) {
- this.color = color;
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.geom.Point2D;
+
+/**
+ * This class represents some layout information in CellDesigner format.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class View {
+
+ /**
+ * No idea what this parameter describes.
+ */
+ private Point2D innerPosition;
+
+ /**
+ * Size of the element.
+ */
+ private Dimension boxSize;
+
+ /**
+ * Width of the line.
+ */
+ private SingleLine singleLine;
+
+ /**
+ * Color of the element.
+ */
+ private Color color;
+
+ /**
+ * @return the innerPosition
+ */
+ public Point2D getInnerPosition() {
+ return innerPosition;
+ }
+
+ /**
+ * @param innerPosition
+ * the innerPosition to set
+ */
+ public void setInnerPosition(Point2D innerPosition) {
+ this.innerPosition = innerPosition;
+ }
+
+ /**
+ * @return the boxSize
+ */
+ public Dimension getBoxSize() {
+ return boxSize;
+ }
+
+ /**
+ * @param boxSize
+ * the boxSize to set
+ */
+ public void setBoxSize(Dimension boxSize) {
+ this.boxSize = boxSize;
+ }
+
+ /**
+ * @return the singleLine
+ */
+ public SingleLine getSingleLine() {
+ return singleLine;
+ }
+
+ /**
+ * @param singleLine
+ * the singleLine to set
+ */
+ public void setSingleLine(SingleLine singleLine) {
+ this.singleLine = singleLine;
+ }
+
+ /**
+ * @return the color
+ */
+ public Color getColor() {
+ return color;
+ }
+
+ /**
+ * @param color
+ * the color to set
+ */
+ public void setColor(Color color) {
+ this.color = color;
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/package-info.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/package-info.java
index aeacb0eda1..67c2f4aafa 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/package-info.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/package-info.java
@@ -1,5 +1,5 @@
-/**
- * This package contains internal CellDesigner structures describing some fields
- * of the Species elements.
- */
-package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
+/**
+ * This package contains internal CellDesigner structures describing some fields
+ * of the Species elements.
+ */
+package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/package-info.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/package-info.java
index 2248a314c6..8c3bb3c4a0 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/package-info.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/package-info.java
@@ -1,6 +1,6 @@
-/**
- * This package contains internal CellDesigner structures used in the xml to
- * store some data. Structures from this package should be used only during
- * convertion from/to CellDEsigner format.
- */
+/**
+ * This package contains internal CellDesigner structures used in the xml to
+ * store some data. Structures from this package should be used only during
+ * convertion from/to CellDEsigner format.
+ */
package lcsb.mapviewer.converter.model.celldesigner.structure;
\ No newline at end of file
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierType.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierType.java
index 69f797da4d..3a907fea11 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierType.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierType.java
@@ -1,202 +1,202 @@
-package lcsb.mapviewer.converter.model.celldesigner.types;
-
-import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesignerConverter;
-import lcsb.mapviewer.model.graphics.ArrowType;
-import lcsb.mapviewer.model.graphics.ArrowTypeData;
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.map.modifier.Catalysis;
-import lcsb.mapviewer.model.map.modifier.Inhibition;
-import lcsb.mapviewer.model.map.modifier.Modulation;
-import lcsb.mapviewer.model.map.modifier.PhysicalStimulation;
-import lcsb.mapviewer.model.map.modifier.Trigger;
-import lcsb.mapviewer.model.map.modifier.UnknownCatalysis;
-import lcsb.mapviewer.model.map.modifier.UnknownInhibition;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-
-/**
- * This enum defines how different types of CellDesigner modifiers should be
- * translated into the reaction {@link Modifier} class.
- *
- * @author Piotr Gawron
- *
- */
-public enum ModifierType {
-
- /**
- * Catalysis.
- */
- CATALYSIS("CATALYSIS", Catalysis.class, ArrowType.CIRCLE, 8.0),
-
- /**
- * Inhibition.
- */
- INHIBITION("INHIBITION", Inhibition.class, ArrowType.CROSSBAR, 8.0, ReactionCellDesignerConverter.RECT_SIZE / 2 - 1),
-
- /**
- * Unknown catalysis.
- */
- UNKNOWN_CATALYSIS("UNKNOWN_CATALYSIS", UnknownCatalysis.class, ArrowType.CIRCLE, 8.0, 0.0, LineType.DASHED),
-
- /**
- * Unknown inhibition.
- */
- UNKNOWN_INHIBITION("UNKNOWN_INHIBITION", UnknownInhibition.class, ArrowType.CROSSBAR, 8.0, ReactionCellDesignerConverter.RECT_SIZE / 2 - 1, LineType.DASHED),
-
- /**
- * Physical stimulation.
- */
- PHYSICAL_STIMULATION("PHYSICAL_STIMULATION", PhysicalStimulation.class, ArrowType.BLANK),
-
- /**
- * Modulation.
- */
- MODULATION_STRING("MODULATION", Modulation.class, ArrowType.DIAMOND),
-
- /**
- * Trigger.
- */
- TRIGGER_STRING("TRIGGER", Trigger.class, ArrowType.BLANK_CROSSBAR);
-
- /**
- * CellDesigner string describing this type.
- */
- private String stringName;
- /**
- * Which class should be used for this type.
- */
- private Class<? extends Modifier> clazz;
- /**
- * How the arrow head of the line should look like.
- */
- private ArrowTypeData atd = new ArrowTypeData();
- /**
- * How much should be the arrow line trimmed.
- */
- private double trimLength = 0;
- /**
- * What line type should be used for this modifier.
- */
- private LineType lineType = LineType.SOLID;
-
- /**
- * Constructor used to create and initialize this enum.
- *
- * @param string
- * {@link #stringName}
- * @param clazz
- * {@link #clazz}
- * @param at
- * type of the arrow
- */
- ModifierType(String string, Class<? extends Modifier> clazz, ArrowType at) {
- this(string, clazz, at, null, null, null);
- }
-
- /**
- * Constructor used to create and initialize this enum.
- *
- * @param string
- * {@link #stringName}
- * @param clazz
- * {@link #clazz}
- * @param at
- * type of the arrow
- * @param arrowLength
- * length of the arrow
- */
- ModifierType(String string, Class<? extends Modifier> clazz, ArrowType at, Double arrowLength) {
- this(string, clazz, at, arrowLength, null, null);
- }
-
- /**
- * Constructor used to create and initialize this enum.
- *
- * @param string
- * {@link #stringName}
- * @param clazz
- * {@link #clazz}
- * @param at
- * type of the arrow
- * @param arrowLength
- * length of the arrow
- * @param trimLength
- * {@link #trimLength}
- */
- ModifierType(String string, Class<? extends Modifier> clazz, ArrowType at, Double arrowLength, Double trimLength) {
- this(string, clazz, at, arrowLength, trimLength, null);
- }
-
- /**
- * Constructor used to create and initialize this enum.
- *
- * @param string
- * {@link #stringName}
- * @param clazz
- * {@link #clazz}
- * @param at
- * type of the arrow
- * @param arrowLength
- * length of the arrow
- * @param trimLength
- * {@link #trimLength}
- * @param lt
- * {@link #lineType}
- */
- ModifierType(String string, Class<? extends Modifier> clazz, ArrowType at, Double arrowLength, Double trimLength, LineType lt) {
- stringName = string;
- this.clazz = clazz;
- if (at != null) {
- atd.setArrowType(at);
- }
- if (arrowLength != null) {
- atd.setLen(arrowLength);
- }
- if (trimLength != null) {
- this.trimLength = trimLength;
- }
- if (lt != null) {
- lineType = lt;
- }
-
- }
-
- /**
- *
- * @return {@link #stringName}
- */
- public String getStringName() {
- return stringName;
- }
-
- /**
- *
- * @return {@link #clazz}
- */
- public Class<? extends Modifier> getClazz() {
- return clazz;
- }
-
- /**
- *
- * @return {@link #atd}
- */
- public ArrowTypeData getAtd() {
- return atd;
- }
-
- /**
- *
- * @return {@link #trimLength}
- */
- public double getTrimLength() {
- return trimLength;
- }
-
- /**
- *
- * @return {@link #lineType}
- */
- public LineType getLineType() {
- return lineType;
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.types;
+
+import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesignerConverter;
+import lcsb.mapviewer.model.graphics.ArrowType;
+import lcsb.mapviewer.model.graphics.ArrowTypeData;
+import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.map.modifier.Catalysis;
+import lcsb.mapviewer.model.map.modifier.Inhibition;
+import lcsb.mapviewer.model.map.modifier.Modulation;
+import lcsb.mapviewer.model.map.modifier.PhysicalStimulation;
+import lcsb.mapviewer.model.map.modifier.Trigger;
+import lcsb.mapviewer.model.map.modifier.UnknownCatalysis;
+import lcsb.mapviewer.model.map.modifier.UnknownInhibition;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+
+/**
+ * This enum defines how different types of CellDesigner modifiers should be
+ * translated into the reaction {@link Modifier} class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum ModifierType {
+
+ /**
+ * Catalysis.
+ */
+ CATALYSIS("CATALYSIS", Catalysis.class, ArrowType.CIRCLE, 8.0),
+
+ /**
+ * Inhibition.
+ */
+ INHIBITION("INHIBITION", Inhibition.class, ArrowType.CROSSBAR, 8.0, ReactionCellDesignerConverter.RECT_SIZE / 2 - 1),
+
+ /**
+ * Unknown catalysis.
+ */
+ UNKNOWN_CATALYSIS("UNKNOWN_CATALYSIS", UnknownCatalysis.class, ArrowType.CIRCLE, 8.0, 0.0, LineType.DASHED),
+
+ /**
+ * Unknown inhibition.
+ */
+ UNKNOWN_INHIBITION("UNKNOWN_INHIBITION", UnknownInhibition.class, ArrowType.CROSSBAR, 8.0, ReactionCellDesignerConverter.RECT_SIZE / 2 - 1, LineType.DASHED),
+
+ /**
+ * Physical stimulation.
+ */
+ PHYSICAL_STIMULATION("PHYSICAL_STIMULATION", PhysicalStimulation.class, ArrowType.BLANK),
+
+ /**
+ * Modulation.
+ */
+ MODULATION_STRING("MODULATION", Modulation.class, ArrowType.DIAMOND),
+
+ /**
+ * Trigger.
+ */
+ TRIGGER_STRING("TRIGGER", Trigger.class, ArrowType.BLANK_CROSSBAR);
+
+ /**
+ * CellDesigner string describing this type.
+ */
+ private String stringName;
+ /**
+ * Which class should be used for this type.
+ */
+ private Class<? extends Modifier> clazz;
+ /**
+ * How the arrow head of the line should look like.
+ */
+ private ArrowTypeData atd = new ArrowTypeData();
+ /**
+ * How much should be the arrow line trimmed.
+ */
+ private double trimLength = 0;
+ /**
+ * What line type should be used for this modifier.
+ */
+ private LineType lineType = LineType.SOLID;
+
+ /**
+ * Constructor used to create and initialize this enum.
+ *
+ * @param string
+ * {@link #stringName}
+ * @param clazz
+ * {@link #clazz}
+ * @param at
+ * type of the arrow
+ */
+ ModifierType(String string, Class<? extends Modifier> clazz, ArrowType at) {
+ this(string, clazz, at, null, null, null);
+ }
+
+ /**
+ * Constructor used to create and initialize this enum.
+ *
+ * @param string
+ * {@link #stringName}
+ * @param clazz
+ * {@link #clazz}
+ * @param at
+ * type of the arrow
+ * @param arrowLength
+ * length of the arrow
+ */
+ ModifierType(String string, Class<? extends Modifier> clazz, ArrowType at, Double arrowLength) {
+ this(string, clazz, at, arrowLength, null, null);
+ }
+
+ /**
+ * Constructor used to create and initialize this enum.
+ *
+ * @param string
+ * {@link #stringName}
+ * @param clazz
+ * {@link #clazz}
+ * @param at
+ * type of the arrow
+ * @param arrowLength
+ * length of the arrow
+ * @param trimLength
+ * {@link #trimLength}
+ */
+ ModifierType(String string, Class<? extends Modifier> clazz, ArrowType at, Double arrowLength, Double trimLength) {
+ this(string, clazz, at, arrowLength, trimLength, null);
+ }
+
+ /**
+ * Constructor used to create and initialize this enum.
+ *
+ * @param string
+ * {@link #stringName}
+ * @param clazz
+ * {@link #clazz}
+ * @param at
+ * type of the arrow
+ * @param arrowLength
+ * length of the arrow
+ * @param trimLength
+ * {@link #trimLength}
+ * @param lt
+ * {@link #lineType}
+ */
+ ModifierType(String string, Class<? extends Modifier> clazz, ArrowType at, Double arrowLength, Double trimLength, LineType lt) {
+ stringName = string;
+ this.clazz = clazz;
+ if (at != null) {
+ atd.setArrowType(at);
+ }
+ if (arrowLength != null) {
+ atd.setLen(arrowLength);
+ }
+ if (trimLength != null) {
+ this.trimLength = trimLength;
+ }
+ if (lt != null) {
+ lineType = lt;
+ }
+
+ }
+
+ /**
+ *
+ * @return {@link #stringName}
+ */
+ public String getStringName() {
+ return stringName;
+ }
+
+ /**
+ *
+ * @return {@link #clazz}
+ */
+ public Class<? extends Modifier> getClazz() {
+ return clazz;
+ }
+
+ /**
+ *
+ * @return {@link #atd}
+ */
+ public ArrowTypeData getAtd() {
+ return atd;
+ }
+
+ /**
+ *
+ * @return {@link #trimLength}
+ */
+ public double getTrimLength() {
+ return trimLength;
+ }
+
+ /**
+ *
+ * @return {@link #lineType}
+ */
+ public LineType getLineType() {
+ return lineType;
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtils.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtils.java
index 5b4f536996..99d3aa1eb1 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtils.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtils.java
@@ -1,305 +1,305 @@
-package lcsb.mapviewer.converter.model.celldesigner.types;
-
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.common.geometry.PointTransformation;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesignerConverter;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.reaction.AbstractNode;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.reaction.NodeOperator;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * Util class that helps in transformation of CellDesigner modifiers into
- * {@link Modifier} object in our model.
- *
- * @author Piotr Gawron
- *
- */
-public class ModifierTypeUtils {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(ModifierTypeUtils.class);
-
- /**
- * Returns {@link ModifierType} that reference to the clazz.
- *
- * @param clazz
- * class type for which result is returned
- * @return {@link ModifierType} that reference to the clazz
- */
- public ModifierType getModifierTypeForClazz(Class<? extends Modifier> clazz) {
- for (ModifierType modType : ModifierType.values()) {
- if (clazz.equals(modType.getClazz())) {
- return modType;
- }
- }
- return null;
- }
-
- /**
- * Returns {@link ModifierType} that reference to the CellDesigner string
- * 'type'.
- *
- * @param type
- * CellDesigner string defining modifier type
- * @return {@link ModifierType} that reference to the CellDesigner 'type'
- */
- public ModifierType getModifierTypeForStringType(String type) {
- for (ModifierType modType : ModifierType.values()) {
- if (type.equalsIgnoreCase(modType.getStringName())) {
- return modType;
- }
- }
- return null;
- }
-
- /**
- * Creates {@link Modifier} for the CellDesigner type.
- *
- * @param type
- * CellDesigner type of the modifier
- * @param alias
- * alias to which modifier point to
- * @return {@link Modifier} for the CellDesigner type
- */
- public Modifier createModifierForStringType(String type, Species alias) {
- ModifierType modType = getModifierTypeForStringType(type);
- if (modType == null) {
- throw new InvalidArgumentException("Unknown modifier type: " + type);
- }
- try {
- Modifier mod = modType.getClazz().getConstructor(Element.class).newInstance(alias);
- return mod;
- } catch (Exception e) {
- throw new InvalidStateException("Problem with instantiation of Modifier class: " + type);
- }
- }
-
- /**
- * Returns CellDesigner string used for modifier creation.
- *
- * @param modifier
- * modifier for which CellDesigner string is looked for
- * @return CellDesigner string used for modifier creation
- */
- public String getStringTypeByModifier(Modifier modifier) {
- ModifierType modifierType = getModifierTypeForClazz(modifier.getClass());
- if (modifierType != null) {
- return modifierType.getStringName();
- }
- return null;
- }
-
- /**
- * Returns string that identfies TargetLine index for the modifier. TargetLine
- * index is a CellDesigner String that identifies to which point on the
- * rectangle in the center line modifier line is connected.
- *
- * @param modifier
- * modifier for target line
- * @return string that identfies TargetLine index for the modifier
- */
- public String getTargetLineIndexByModifier(Modifier modifier) {
- ModifierType modType = getModifierTypeForClazz(modifier.getClass());
- if (modType == null) {
- throw new InvalidArgumentException("Unknown modifier class: " + modifier.getClass());
- }
-
- Reaction reaction = modifier.getReaction();
- PolylineData line = modifier.getLine();
-
- String result = getTragteLineIndex(modType, reaction, line);
- return result;
- }
-
- /**
- * Returns string that identfies TargetLine index for the modifier operator.
- * TargetLine index is a CellDesigner String that identifies to which point on
- * the rectangle in the center line modifier line is connected.
- *
- * @param modifier
- * modifier operator for target line
- * @return string that identfies TargetLine index for the modifier
- */
- public String getTargetLineIndexByModifier(NodeOperator modifier) {
- if (!(modifier.getInputs().get(0) instanceof Modifier)) {
- throw new InvalidArgumentException("Invalid NodeOperator");
- } else {
- ModifierType modType = getModifierTypeForClazz(((Modifier) modifier.getInputs().get(0)).getClass());
-
- if (modType == null) {
- throw new InvalidArgumentException("Unknown modifier class: " + modifier.getClass());
- }
-
- Reaction reaction = modifier.getReaction();
- PolylineData line = modifier.getLine();
-
- String result = getTragteLineIndex(modType, reaction, line);
- return result;
- }
- }
-
- /**
- * Returns string that identfies TargetLine index for the modifier line
- * connected to reaction (target line index is explained here:
- * {@link #getTargetLineIndexByModifier(Modifier)}).
- *
- *
- * @param modType
- * type of modifier for the line
- * @param reaction
- * reaction on which target line index is looked for
- * @param originalLine
- * line that connects modifier to the reaction
- * @return string that identfies TargetLine index for modifier line
- */
- private String getTragteLineIndex(ModifierType modType, Reaction reaction, PolylineData originalLine) {
- PolylineData line = new PolylineData(originalLine);
- line.trimEnd(-modType.getTrimLength());
-
- String[] possibleValues = new String[] { "0,2", "0,3", "0,4", "0,5", "0,6", "0,7" };
- Point2D closestPoint = new Point2D.Double(Double.MAX_VALUE, Double.MAX_VALUE);
- Point2D checkedPoint = line.getEndPoint();
- String result = "0,0";
- for (String string : possibleValues) {
- Point2D point = getAnchorPointOnReactionRect(reaction, string);
- if (point.distance(checkedPoint) < closestPoint.distance(checkedPoint)) {
- closestPoint = point;
- result = string;
- }
- }
- return result;
- }
-
- /**
- * This method get anchor point on the reaction line (the center point of this
- * line is given as a parameter). The anchor point depends on the line and
- * lineConnectionType associated with the modification.
- *
- * @param reaction
- * rection on which we are looking for a point
- * @param lineConnectionType
- * point of connection to the reaction center rectangle
- * @return coordinates of point on the center rectangle
- */
- public Point2D getAnchorPointOnReactionRect(Reaction reaction, String lineConnectionType) {
- Line2D centerLine = reaction.getCenterLine();
- double dx = centerLine.getX2() - centerLine.getX1();
- double dy = centerLine.getY2() - centerLine.getY1();
- double angle = Math.atan2(dy, dx);
- Point2D mid = new Point2D.Double((centerLine.getX1() + centerLine.getX2()) / 2, (centerLine.getY1() + centerLine.getY2()) / 2);
-
- String id = lineConnectionType;
- String[] spr = id.split(",");
- double x = mid.getX();
- double y = mid.getY();
- if (spr.length > 1) {
- id = spr[1];
- if (id.equals("2")) {
- y -= ReactionCellDesignerConverter.RECT_SIZE / 2;
- } else if (id.equals("3")) {
- y += ReactionCellDesignerConverter.RECT_SIZE / 2;
- } else if (id.equals("4")) {
- y -= ReactionCellDesignerConverter.RECT_SIZE / 2;
- x -= ReactionCellDesignerConverter.RECT_SIZE / 2;
- } else if (id.equals("5")) {
- y -= ReactionCellDesignerConverter.RECT_SIZE / 2;
- x += ReactionCellDesignerConverter.RECT_SIZE / 2;
- } else if (id.equals("6")) {
- y += ReactionCellDesignerConverter.RECT_SIZE / 2;
- x -= ReactionCellDesignerConverter.RECT_SIZE / 2;
- } else if (id.equals("7")) {
- y += ReactionCellDesignerConverter.RECT_SIZE / 2;
- x += ReactionCellDesignerConverter.RECT_SIZE / 2;
- } else if (id.equals("0")) {
- // this is only workaround...
- y += ReactionCellDesignerConverter.RECT_SIZE / 2;
- } else {
- throw new InvalidArgumentException("Unknown targetLineIndex: " + id);
- }
-
- } else {
- throw new InvalidArgumentException("Invalid targetLineIndex: " + id);
- }
- Point2D p = new Point2D.Double(x, y);
- PointTransformation pointTransformation = new PointTransformation();
- p = pointTransformation.rotatePoint(p, angle, mid);
- return p;
- }
-
- /**
- * Update line parameters to make it look like a proper modifier.
- *
- * @param modifier
- * modifier for which line will be modified
- */
- public void updateLineEndPoint(Modifier modifier) {
- ModifierType modType = getModifierTypeForClazz(modifier.getClass());
- if (modType == null) {
- throw new InvalidArgumentException("Unknown modifier class: " + modifier.getClass());
- }
- PolylineData line = modifier.getLine();
- updateLineByType(modType, line);
- }
-
- /**
- * Updates line parameters of modifier operator to make it look like a proper
- * modifier.
- *
- * @param operator
- * modifier operator for which line will be modified
- */
- @SuppressWarnings("unchecked")
- public void updateLineEndPoint(NodeOperator operator) {
- Class<? extends AbstractNode> clazz = operator.getInputs().get(1).getClass();
- if (Modifier.class.isAssignableFrom(clazz)) {
- ModifierType modType = getModifierTypeForClazz((Class<? extends Modifier>) clazz);
- if (modType == null) {
- throw new InvalidArgumentException("Unknown modifier class: " + clazz);
- }
- PolylineData line = operator.getLine();
- updateLineByType(modType, line);
- } else {
- throw new InvalidArgumentException("Operator contains invalid input: " + clazz);
- }
- }
-
- /**
- * Updates line parameters to make it look like a proper modifier.
- *
- * @param modType
- * type of modifier
- * @param line
- * line to update
- */
- private void updateLineByType(ModifierType modType, PolylineData line) {
- line.setEndAtd(modType.getAtd().copy());
- line.setType(modType.getLineType());
- line.trimEnd(modType.getTrimLength());
- }
-
- /**
- * Returns type of the modifier in modifier operator.
- *
- * @param modifierOperator
- * opertor for which type will be returned
- * @return type of the modifier in modifier operator
- */
- public ModifierType getModifierTypeForOperator(NodeOperator modifierOperator) {
- Modifier mod = (Modifier) modifierOperator.getInputs().get(0);
- return getModifierTypeForClazz(mod.getClass());
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.types;
+
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.common.geometry.PointTransformation;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesignerConverter;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.reaction.AbstractNode;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.reaction.NodeOperator;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * Util class that helps in transformation of CellDesigner modifiers into
+ * {@link Modifier} object in our model.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ModifierTypeUtils {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(ModifierTypeUtils.class);
+
+ /**
+ * Returns {@link ModifierType} that reference to the clazz.
+ *
+ * @param clazz
+ * class type for which result is returned
+ * @return {@link ModifierType} that reference to the clazz
+ */
+ public ModifierType getModifierTypeForClazz(Class<? extends Modifier> clazz) {
+ for (ModifierType modType : ModifierType.values()) {
+ if (clazz.equals(modType.getClazz())) {
+ return modType;
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Returns {@link ModifierType} that reference to the CellDesigner string
+ * 'type'.
+ *
+ * @param type
+ * CellDesigner string defining modifier type
+ * @return {@link ModifierType} that reference to the CellDesigner 'type'
+ */
+ public ModifierType getModifierTypeForStringType(String type) {
+ for (ModifierType modType : ModifierType.values()) {
+ if (type.equalsIgnoreCase(modType.getStringName())) {
+ return modType;
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Creates {@link Modifier} for the CellDesigner type.
+ *
+ * @param type
+ * CellDesigner type of the modifier
+ * @param alias
+ * alias to which modifier point to
+ * @return {@link Modifier} for the CellDesigner type
+ */
+ public Modifier createModifierForStringType(String type, Species alias) {
+ ModifierType modType = getModifierTypeForStringType(type);
+ if (modType == null) {
+ throw new InvalidArgumentException("Unknown modifier type: " + type);
+ }
+ try {
+ Modifier mod = modType.getClazz().getConstructor(Element.class).newInstance(alias);
+ return mod;
+ } catch (Exception e) {
+ throw new InvalidStateException("Problem with instantiation of Modifier class: " + type);
+ }
+ }
+
+ /**
+ * Returns CellDesigner string used for modifier creation.
+ *
+ * @param modifier
+ * modifier for which CellDesigner string is looked for
+ * @return CellDesigner string used for modifier creation
+ */
+ public String getStringTypeByModifier(Modifier modifier) {
+ ModifierType modifierType = getModifierTypeForClazz(modifier.getClass());
+ if (modifierType != null) {
+ return modifierType.getStringName();
+ }
+ return null;
+ }
+
+ /**
+ * Returns string that identfies TargetLine index for the modifier. TargetLine
+ * index is a CellDesigner String that identifies to which point on the
+ * rectangle in the center line modifier line is connected.
+ *
+ * @param modifier
+ * modifier for target line
+ * @return string that identfies TargetLine index for the modifier
+ */
+ public String getTargetLineIndexByModifier(Modifier modifier) {
+ ModifierType modType = getModifierTypeForClazz(modifier.getClass());
+ if (modType == null) {
+ throw new InvalidArgumentException("Unknown modifier class: " + modifier.getClass());
+ }
+
+ Reaction reaction = modifier.getReaction();
+ PolylineData line = modifier.getLine();
+
+ String result = getTragteLineIndex(modType, reaction, line);
+ return result;
+ }
+
+ /**
+ * Returns string that identfies TargetLine index for the modifier operator.
+ * TargetLine index is a CellDesigner String that identifies to which point on
+ * the rectangle in the center line modifier line is connected.
+ *
+ * @param modifier
+ * modifier operator for target line
+ * @return string that identfies TargetLine index for the modifier
+ */
+ public String getTargetLineIndexByModifier(NodeOperator modifier) {
+ if (!(modifier.getInputs().get(0) instanceof Modifier)) {
+ throw new InvalidArgumentException("Invalid NodeOperator");
+ } else {
+ ModifierType modType = getModifierTypeForClazz(((Modifier) modifier.getInputs().get(0)).getClass());
+
+ if (modType == null) {
+ throw new InvalidArgumentException("Unknown modifier class: " + modifier.getClass());
+ }
+
+ Reaction reaction = modifier.getReaction();
+ PolylineData line = modifier.getLine();
+
+ String result = getTragteLineIndex(modType, reaction, line);
+ return result;
+ }
+ }
+
+ /**
+ * Returns string that identfies TargetLine index for the modifier line
+ * connected to reaction (target line index is explained here:
+ * {@link #getTargetLineIndexByModifier(Modifier)}).
+ *
+ *
+ * @param modType
+ * type of modifier for the line
+ * @param reaction
+ * reaction on which target line index is looked for
+ * @param originalLine
+ * line that connects modifier to the reaction
+ * @return string that identfies TargetLine index for modifier line
+ */
+ private String getTragteLineIndex(ModifierType modType, Reaction reaction, PolylineData originalLine) {
+ PolylineData line = new PolylineData(originalLine);
+ line.trimEnd(-modType.getTrimLength());
+
+ String[] possibleValues = new String[] { "0,2", "0,3", "0,4", "0,5", "0,6", "0,7" };
+ Point2D closestPoint = new Point2D.Double(Double.MAX_VALUE, Double.MAX_VALUE);
+ Point2D checkedPoint = line.getEndPoint();
+ String result = "0,0";
+ for (String string : possibleValues) {
+ Point2D point = getAnchorPointOnReactionRect(reaction, string);
+ if (point.distance(checkedPoint) < closestPoint.distance(checkedPoint)) {
+ closestPoint = point;
+ result = string;
+ }
+ }
+ return result;
+ }
+
+ /**
+ * This method get anchor point on the reaction line (the center point of this
+ * line is given as a parameter). The anchor point depends on the line and
+ * lineConnectionType associated with the modification.
+ *
+ * @param reaction
+ * rection on which we are looking for a point
+ * @param lineConnectionType
+ * point of connection to the reaction center rectangle
+ * @return coordinates of point on the center rectangle
+ */
+ public Point2D getAnchorPointOnReactionRect(Reaction reaction, String lineConnectionType) {
+ Line2D centerLine = reaction.getCenterLine();
+ double dx = centerLine.getX2() - centerLine.getX1();
+ double dy = centerLine.getY2() - centerLine.getY1();
+ double angle = Math.atan2(dy, dx);
+ Point2D mid = new Point2D.Double((centerLine.getX1() + centerLine.getX2()) / 2, (centerLine.getY1() + centerLine.getY2()) / 2);
+
+ String id = lineConnectionType;
+ String[] spr = id.split(",");
+ double x = mid.getX();
+ double y = mid.getY();
+ if (spr.length > 1) {
+ id = spr[1];
+ if (id.equals("2")) {
+ y -= ReactionCellDesignerConverter.RECT_SIZE / 2;
+ } else if (id.equals("3")) {
+ y += ReactionCellDesignerConverter.RECT_SIZE / 2;
+ } else if (id.equals("4")) {
+ y -= ReactionCellDesignerConverter.RECT_SIZE / 2;
+ x -= ReactionCellDesignerConverter.RECT_SIZE / 2;
+ } else if (id.equals("5")) {
+ y -= ReactionCellDesignerConverter.RECT_SIZE / 2;
+ x += ReactionCellDesignerConverter.RECT_SIZE / 2;
+ } else if (id.equals("6")) {
+ y += ReactionCellDesignerConverter.RECT_SIZE / 2;
+ x -= ReactionCellDesignerConverter.RECT_SIZE / 2;
+ } else if (id.equals("7")) {
+ y += ReactionCellDesignerConverter.RECT_SIZE / 2;
+ x += ReactionCellDesignerConverter.RECT_SIZE / 2;
+ } else if (id.equals("0")) {
+ // this is only workaround...
+ y += ReactionCellDesignerConverter.RECT_SIZE / 2;
+ } else {
+ throw new InvalidArgumentException("Unknown targetLineIndex: " + id);
+ }
+
+ } else {
+ throw new InvalidArgumentException("Invalid targetLineIndex: " + id);
+ }
+ Point2D p = new Point2D.Double(x, y);
+ PointTransformation pointTransformation = new PointTransformation();
+ p = pointTransformation.rotatePoint(p, angle, mid);
+ return p;
+ }
+
+ /**
+ * Update line parameters to make it look like a proper modifier.
+ *
+ * @param modifier
+ * modifier for which line will be modified
+ */
+ public void updateLineEndPoint(Modifier modifier) {
+ ModifierType modType = getModifierTypeForClazz(modifier.getClass());
+ if (modType == null) {
+ throw new InvalidArgumentException("Unknown modifier class: " + modifier.getClass());
+ }
+ PolylineData line = modifier.getLine();
+ updateLineByType(modType, line);
+ }
+
+ /**
+ * Updates line parameters of modifier operator to make it look like a proper
+ * modifier.
+ *
+ * @param operator
+ * modifier operator for which line will be modified
+ */
+ @SuppressWarnings("unchecked")
+ public void updateLineEndPoint(NodeOperator operator) {
+ Class<? extends AbstractNode> clazz = operator.getInputs().get(1).getClass();
+ if (Modifier.class.isAssignableFrom(clazz)) {
+ ModifierType modType = getModifierTypeForClazz((Class<? extends Modifier>) clazz);
+ if (modType == null) {
+ throw new InvalidArgumentException("Unknown modifier class: " + clazz);
+ }
+ PolylineData line = operator.getLine();
+ updateLineByType(modType, line);
+ } else {
+ throw new InvalidArgumentException("Operator contains invalid input: " + clazz);
+ }
+ }
+
+ /**
+ * Updates line parameters to make it look like a proper modifier.
+ *
+ * @param modType
+ * type of modifier
+ * @param line
+ * line to update
+ */
+ private void updateLineByType(ModifierType modType, PolylineData line) {
+ line.setEndAtd(modType.getAtd().copy());
+ line.setType(modType.getLineType());
+ line.trimEnd(modType.getTrimLength());
+ }
+
+ /**
+ * Returns type of the modifier in modifier operator.
+ *
+ * @param modifierOperator
+ * opertor for which type will be returned
+ * @return type of the modifier in modifier operator
+ */
+ public ModifierType getModifierTypeForOperator(NodeOperator modifierOperator) {
+ Modifier mod = (Modifier) modifierOperator.getInputs().get(0);
+ return getModifierTypeForClazz(mod.getClass());
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/OperatorType.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/OperatorType.java
index 59f6ff630e..7f6d880876 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/OperatorType.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/OperatorType.java
@@ -1,94 +1,94 @@
-package lcsb.mapviewer.converter.model.celldesigner.types;
-
-import lcsb.mapviewer.model.map.reaction.AndOperator;
-import lcsb.mapviewer.model.map.reaction.NandOperator;
-import lcsb.mapviewer.model.map.reaction.NodeOperator;
-import lcsb.mapviewer.model.map.reaction.OrOperator;
-import lcsb.mapviewer.model.map.reaction.UnknownOperator;
-
-/**
- * This enum defines how different types of CellDesigner operators should be
- * translated into the reaction {@link NodeOperator} class.
- *
- * @author Piotr Gawron
- *
- */
-public enum OperatorType {
-
- /**
- * Boolean and operator.
- */
- AND_OPERATOR_STRING("BOOLEAN_LOGIC_GATE_AND", AndOperator.class),
-
- /**
- * Boolean not and operator.
- */
- NAND_OPERATOR_STRING("BOOLEAN_LOGIC_GATE_NOT", NandOperator.class),
-
- /**
- * Boolean or operator.
- */
- OR_OPERATOR_STRING("BOOLEAN_LOGIC_GATE_OR", OrOperator.class),
-
- /**
- * Boolean unknown operator.
- */
- UNKNOWN_OPERATOR_STRING("BOOLEAN_LOGIC_GATE_UNKNOWN", UnknownOperator.class);
-
- /**
- * CellDEsigner string identifing this operator.
- */
- private String stringName;
- /**
- * Class in our model representing this operator.
- */
- private Class<? extends NodeOperator> clazz;
-
- /**
- * Default constructor. Initialize enum with data.
- *
- * @param string
- * {@link #stringName}
- * @param clazz
- * {@link #clazz}
- */
- OperatorType(String string, Class<? extends NodeOperator> clazz) {
- stringName = string;
- this.clazz = clazz;
- }
-
- /**
- * @return the stringName
- * @see #stringName
- */
- public String getStringName() {
- return stringName;
- }
-
- /**
- * @return the clazz
- * @see #clazz
- */
- public Class<? extends NodeOperator> getClazz() {
- return clazz;
- }
-
- /**
- * Returns {@link OperatorType} that should be applied to a class given in the
- * parameter.
- *
- * @param clazz
- * class for which we are looking for {@link OperatorType}
- * @return {@link OperatorType} that should be applied to a class given in the
- * parameter
- */
- public static OperatorType getTypeByClass(Class<? extends NodeOperator> clazz) {
- for (OperatorType type : OperatorType.values()) {
- if (type.getClazz().equals(clazz)) {
- return type;
- }
- }
- return null;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.types;
+
+import lcsb.mapviewer.model.map.reaction.AndOperator;
+import lcsb.mapviewer.model.map.reaction.NandOperator;
+import lcsb.mapviewer.model.map.reaction.NodeOperator;
+import lcsb.mapviewer.model.map.reaction.OrOperator;
+import lcsb.mapviewer.model.map.reaction.UnknownOperator;
+
+/**
+ * This enum defines how different types of CellDesigner operators should be
+ * translated into the reaction {@link NodeOperator} class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum OperatorType {
+
+ /**
+ * Boolean and operator.
+ */
+ AND_OPERATOR_STRING("BOOLEAN_LOGIC_GATE_AND", AndOperator.class),
+
+ /**
+ * Boolean not and operator.
+ */
+ NAND_OPERATOR_STRING("BOOLEAN_LOGIC_GATE_NOT", NandOperator.class),
+
+ /**
+ * Boolean or operator.
+ */
+ OR_OPERATOR_STRING("BOOLEAN_LOGIC_GATE_OR", OrOperator.class),
+
+ /**
+ * Boolean unknown operator.
+ */
+ UNKNOWN_OPERATOR_STRING("BOOLEAN_LOGIC_GATE_UNKNOWN", UnknownOperator.class);
+
+ /**
+ * CellDEsigner string identifing this operator.
+ */
+ private String stringName;
+ /**
+ * Class in our model representing this operator.
+ */
+ private Class<? extends NodeOperator> clazz;
+
+ /**
+ * Default constructor. Initialize enum with data.
+ *
+ * @param string
+ * {@link #stringName}
+ * @param clazz
+ * {@link #clazz}
+ */
+ OperatorType(String string, Class<? extends NodeOperator> clazz) {
+ stringName = string;
+ this.clazz = clazz;
+ }
+
+ /**
+ * @return the stringName
+ * @see #stringName
+ */
+ public String getStringName() {
+ return stringName;
+ }
+
+ /**
+ * @return the clazz
+ * @see #clazz
+ */
+ public Class<? extends NodeOperator> getClazz() {
+ return clazz;
+ }
+
+ /**
+ * Returns {@link OperatorType} that should be applied to a class given in the
+ * parameter.
+ *
+ * @param clazz
+ * class for which we are looking for {@link OperatorType}
+ * @return {@link OperatorType} that should be applied to a class given in the
+ * parameter
+ */
+ public static OperatorType getTypeByClass(Class<? extends NodeOperator> clazz) {
+ for (OperatorType type : OperatorType.values()) {
+ if (type.getClazz().equals(clazz)) {
+ return type;
+ }
+ }
+ return null;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/OperatorTypeUtils.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/OperatorTypeUtils.java
index 4ba9cfab1f..ccadf86fcc 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/OperatorTypeUtils.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/OperatorTypeUtils.java
@@ -1,92 +1,92 @@
-package lcsb.mapviewer.converter.model.celldesigner.types;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.model.map.reaction.NodeOperator;
-
-/**
- * Util class that helps in transformation of CellDesigner operators into
- * {@link NodeOperator} object in our model.
- *
- * @author Piotr Gawron
- *
- */
-public class OperatorTypeUtils {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(OperatorTypeUtils.class);
-
- /**
- * Return {@link OperatorType} for the operator class.
- *
- * @param clazz
- * clazz for which we are looking for operator type
- * @return {@link OperatorType} corresponding to the given class
- */
- public OperatorType getOperatorTypeForClazz(Class<? extends NodeOperator> clazz) {
- for (OperatorType modType : OperatorType.values()) {
- if (clazz.equals(modType.getClazz())) {
- return modType;
- }
- }
- return null;
- }
-
- /**
- * Return {@link OperatorType} for the CellDesigner string representing
- * operator.
- *
- * @param type
- * CellDesigner string representing operator
- * @return {@link OperatorType} corresponding to the given type
- */
- protected OperatorType getOperatorTypeForStringType(String type) {
- for (OperatorType modType : OperatorType.values()) {
- if (type.equalsIgnoreCase(modType.getStringName())) {
- return modType;
- }
- }
- return null;
- }
-
- /**
- * Creates operator for the type identified by CellDesigner string.
- *
- * @param type
- * CellDesigner string identifing operator type.
- * @return empty {@link NodeOperator} of the type given in parameter
- */
- public NodeOperator createModifierForStringType(String type) {
- NodeOperator operator = null;
- OperatorType opType = getOperatorTypeForStringType(type);
- if (opType == null) {
- throw new InvalidArgumentException("Unknown modifier type: " + type);
- }
- try {
- operator = opType.getClazz().getConstructor().newInstance();
- } catch (Exception e) {
- throw new InvalidStateException("Problem with instantiation of NodeOperator class: " + type, e);
- }
- return operator;
- }
-
- /**
- * Returns CellDesigner string for the operator type.
- *
- * @param modifierOperator
- * operator for which CellDesigner string is looked for
- * @return CellDesigner string for the operator type
- */
- public String getStringTypeByOperator(NodeOperator modifierOperator) {
- OperatorType operatorType = getOperatorTypeForClazz(modifierOperator.getClass());
- if (operatorType != null) {
- return operatorType.getStringName();
- }
- return null;
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.types;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.model.map.reaction.NodeOperator;
+
+/**
+ * Util class that helps in transformation of CellDesigner operators into
+ * {@link NodeOperator} object in our model.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class OperatorTypeUtils {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(OperatorTypeUtils.class);
+
+ /**
+ * Return {@link OperatorType} for the operator class.
+ *
+ * @param clazz
+ * clazz for which we are looking for operator type
+ * @return {@link OperatorType} corresponding to the given class
+ */
+ public OperatorType getOperatorTypeForClazz(Class<? extends NodeOperator> clazz) {
+ for (OperatorType modType : OperatorType.values()) {
+ if (clazz.equals(modType.getClazz())) {
+ return modType;
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Return {@link OperatorType} for the CellDesigner string representing
+ * operator.
+ *
+ * @param type
+ * CellDesigner string representing operator
+ * @return {@link OperatorType} corresponding to the given type
+ */
+ protected OperatorType getOperatorTypeForStringType(String type) {
+ for (OperatorType modType : OperatorType.values()) {
+ if (type.equalsIgnoreCase(modType.getStringName())) {
+ return modType;
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Creates operator for the type identified by CellDesigner string.
+ *
+ * @param type
+ * CellDesigner string identifing operator type.
+ * @return empty {@link NodeOperator} of the type given in parameter
+ */
+ public NodeOperator createModifierForStringType(String type) {
+ NodeOperator operator = null;
+ OperatorType opType = getOperatorTypeForStringType(type);
+ if (opType == null) {
+ throw new InvalidArgumentException("Unknown modifier type: " + type);
+ }
+ try {
+ operator = opType.getClazz().getConstructor().newInstance();
+ } catch (Exception e) {
+ throw new InvalidStateException("Problem with instantiation of NodeOperator class: " + type, e);
+ }
+ return operator;
+ }
+
+ /**
+ * Returns CellDesigner string for the operator type.
+ *
+ * @param modifierOperator
+ * operator for which CellDesigner string is looked for
+ * @return CellDesigner string for the operator type
+ */
+ public String getStringTypeByOperator(NodeOperator modifierOperator) {
+ OperatorType operatorType = getOperatorTypeForClazz(modifierOperator.getClass());
+ if (operatorType != null) {
+ return operatorType.getStringName();
+ }
+ return null;
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/package-info.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/package-info.java
index 783736a997..c61e202f20 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/package-info.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/package-info.java
@@ -1,6 +1,6 @@
-/**
- * Defines enums and utils that helps transforming CellDesigner types into types
- * used in our model.
- */
-package lcsb.mapviewer.converter.model.celldesigner.types;
-
+/**
+ * Defines enums and utils that helps transforming CellDesigner types into types
+ * used in our model.
+ */
+package lcsb.mapviewer.converter.model.celldesigner.types;
+
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/AllCellDesignerTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/AllCellDesignerTests.java
index 16b51dec9d..7f521c9341 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/AllCellDesignerTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/AllCellDesignerTests.java
@@ -1,44 +1,44 @@
-package lcsb.mapviewer.converter.model.celldesigner;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-import lcsb.mapviewer.converter.model.celldesigner.alias.AllAliasTests;
-import lcsb.mapviewer.converter.model.celldesigner.annotation.AllAnnotationTests;
-import lcsb.mapviewer.converter.model.celldesigner.compartment.AllCompartmentTests;
-import lcsb.mapviewer.converter.model.celldesigner.function.AllFunctionTests;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.AllGeometryTests;
-import lcsb.mapviewer.converter.model.celldesigner.parameter.ParameterXmlParserTest;
-import lcsb.mapviewer.converter.model.celldesigner.reaction.AllReactionTests;
-import lcsb.mapviewer.converter.model.celldesigner.species.AllSpeciesTests;
-import lcsb.mapviewer.converter.model.celldesigner.structure.AllStructureTests;
-import lcsb.mapviewer.converter.model.celldesigner.types.AllTypesTests;
-import lcsb.mapviewer.converter.model.celldesigner.unit.UnitXmlParserTest;
-
-@RunWith(Suite.class)
-@SuiteClasses({ //
- AllAnnotationTests.class, //
- AllAliasTests.class, //
- AllCompartmentTests.class, //
- AllFunctionTests.class, //
- AllGeometryTests.class, //
- AllReactionTests.class, //
- AllSpeciesTests.class, //
- AllStructureTests.class, //
- AllTypesTests.class, //
- CellDesignerElementCollectionTest.class, //
- CellDesignerParserExceptionTest.class, //
- CellDesignerXmlParserTest.class, //
- ComplexParserTests.class, //
- InvalidGroupExceptionTest.class, //
- LayerXmlParserTest.class, //
- NestedComplexParsingTests.class, //
- ModificationTest.class, //
- ParameterXmlParserTest.class, //
- ReconDataInCellDesignerXmlParserTest.class, //
- UnitXmlParserTest.class,//
-})
-public class AllCellDesignerTests {
-
-}
+package lcsb.mapviewer.converter.model.celldesigner;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+import lcsb.mapviewer.converter.model.celldesigner.alias.AllAliasTests;
+import lcsb.mapviewer.converter.model.celldesigner.annotation.AllAnnotationTests;
+import lcsb.mapviewer.converter.model.celldesigner.compartment.AllCompartmentTests;
+import lcsb.mapviewer.converter.model.celldesigner.function.AllFunctionTests;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.AllGeometryTests;
+import lcsb.mapviewer.converter.model.celldesigner.parameter.ParameterXmlParserTest;
+import lcsb.mapviewer.converter.model.celldesigner.reaction.AllReactionTests;
+import lcsb.mapviewer.converter.model.celldesigner.species.AllSpeciesTests;
+import lcsb.mapviewer.converter.model.celldesigner.structure.AllStructureTests;
+import lcsb.mapviewer.converter.model.celldesigner.types.AllTypesTests;
+import lcsb.mapviewer.converter.model.celldesigner.unit.UnitXmlParserTest;
+
+@RunWith(Suite.class)
+@SuiteClasses({ //
+ AllAnnotationTests.class, //
+ AllAliasTests.class, //
+ AllCompartmentTests.class, //
+ AllFunctionTests.class, //
+ AllGeometryTests.class, //
+ AllReactionTests.class, //
+ AllSpeciesTests.class, //
+ AllStructureTests.class, //
+ AllTypesTests.class, //
+ CellDesignerElementCollectionTest.class, //
+ CellDesignerParserExceptionTest.class, //
+ CellDesignerXmlParserTest.class, //
+ ComplexParserTests.class, //
+ InvalidGroupExceptionTest.class, //
+ LayerXmlParserTest.class, //
+ NestedComplexParsingTests.class, //
+ ModificationTest.class, //
+ ParameterXmlParserTest.class, //
+ ReconDataInCellDesignerXmlParserTest.class, //
+ UnitXmlParserTest.class,//
+})
+public class AllCellDesignerTests {
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollectionTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollectionTest.java
index 66320431e5..48d06d7037 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollectionTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollectionTest.java
@@ -1,43 +1,43 @@
-package lcsb.mapviewer.converter.model.celldesigner;
-
-import static org.junit.Assert.fail;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
-
-public class CellDesignerElementCollectionTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testAddTheSameElementTwice() {
- try {
- CellDesignerElementCollection collection = new CellDesignerElementCollection();
- CellDesignerComplexSpecies complex = new CellDesignerComplexSpecies();
- complex.setElementId("id");
- collection.addElement(complex);
- collection.addElement(complex);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner;
+
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
+
+public class CellDesignerElementCollectionTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testAddTheSameElementTwice() {
+ try {
+ CellDesignerElementCollection collection = new CellDesignerElementCollection();
+ CellDesignerComplexSpecies complex = new CellDesignerComplexSpecies();
+ complex.setElementId("id");
+ collection.addElement(complex);
+ collection.addElement(complex);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerParserExceptionTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerParserExceptionTest.java
index 648b9bb0be..b586a2cc66 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerParserExceptionTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerParserExceptionTest.java
@@ -1,52 +1,52 @@
-package lcsb.mapviewer.converter.model.celldesigner;
-
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class CellDesignerParserExceptionTest {
-
- private static class Tmp extends CellDesignerParserException {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- public Tmp(String string) {
- super(string);
- }
-
- public Tmp() {
- super();
- }
-
- public Tmp(String string, Exception exception) {
- super(string, exception);
- }
-
- public Tmp(Exception exception) {
- super(exception);
- }
-
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testConstructor() {
- assertNotNull(new Tmp());
- assertNotNull(new Tmp("str"));
- assertNotNull(new Tmp("str2", new Exception()));
- assertNotNull(new Tmp(new Exception()));
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner;
+
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class CellDesignerParserExceptionTest {
+
+ private static class Tmp extends CellDesignerParserException {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ public Tmp(String string) {
+ super(string);
+ }
+
+ public Tmp() {
+ super();
+ }
+
+ public Tmp(String string, Exception exception) {
+ super(string, exception);
+ }
+
+ public Tmp(Exception exception) {
+ super(exception);
+ }
+
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testConstructor() {
+ assertNotNull(new Tmp());
+ assertNotNull(new Tmp("str"));
+ assertNotNull(new Tmp("str2", new Exception()));
+ assertNotNull(new Tmp(new Exception()));
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerTestFunctions.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerTestFunctions.java
index 4710799adc..1b82c92951 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerTestFunctions.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerTestFunctions.java
@@ -1,228 +1,228 @@
-package lcsb.mapviewer.converter.model.celldesigner;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.Reader;
-import java.io.StringReader;
-import java.io.StringWriter;
-import java.io.UnsupportedEncodingException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.util.Arrays;
-import java.util.List;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.transform.OutputKeys;
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerException;
-import javax.xml.transform.TransformerFactory;
-import javax.xml.transform.dom.DOMSource;
-import javax.xml.transform.stream.StreamResult;
-
-import org.apache.log4j.Logger;
-import org.apache.log4j.spi.LoggingEvent;
-import org.junit.After;
-import org.junit.Before;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-import org.xml.sax.InputSource;
-import org.xml.sax.SAXException;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.EventStorageLoggerAppender;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.model.map.model.Model;
-
-public abstract class CellDesignerTestFunctions {
- private Logger logger = Logger.getLogger(CellDesignerTestFunctions.class);
-
- protected static double EPSILON = Configuration.EPSILON;
-
- private EventStorageLoggerAppender appender;
-
- @Before
- public final void _setUp() throws Exception {
- Logger.getRootLogger().removeAppender(appender);
- appender = new EventStorageLoggerAppender();
- Logger.getRootLogger().addAppender(appender);
- }
-
- @After
- public final void _tearDown() throws Exception {
- Logger.getRootLogger().removeAppender(appender);
- }
-
- protected List<LoggingEvent> getWarnings() {
- return appender.getWarnings();
- }
-
- protected String readFile(String file) throws IOException {
- StringBuilder stringBuilder = new StringBuilder();
- BufferedReader reader = new BufferedReader(new FileReader(file));
- try {
- String line = null;
- String ls = System.getProperty("line.separator");
-
- while ((line = reader.readLine()) != null) {
- stringBuilder.append(line);
- stringBuilder.append(ls);
- }
- } finally {
- reader.close();
- }
-
- return stringBuilder.toString();
- }
-
- protected Node getNodeFromXmlString(String text) throws InvalidXmlSchemaException {
- InputSource is = new InputSource();
- is.setCharacterStream(new StringReader(text));
- return getXmlDocumentFromInputSource(is).getChildNodes().item(0);
- }
-
- protected Document getXmlDocumentFromFile(String fileName) throws InvalidXmlSchemaException, IOException {
- File file = new File(fileName);
- InputStream inputStream = new FileInputStream(file);
- Reader reader = null;
- try {
- reader = new InputStreamReader(inputStream, "UTF-8");
- InputSource is = new InputSource(reader);
-
- Document result = getXmlDocumentFromInputSource(is);
- inputStream.close();
- return result;
- } catch (UnsupportedEncodingException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- return null;
- }
-
- protected Document getXmlDocumentFromInputSource(InputSource stream) throws InvalidXmlSchemaException {
- DocumentBuilder db;
- try {
- db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
- } catch (ParserConfigurationException e) {
- throw new InvalidXmlSchemaException("Problem with xml parser");
- }
- Document doc = null;
- try {
- doc = db.parse(stream);
- } catch (SAXException e) {
- logger.error(e);
- } catch (IOException e) {
- logger.error(e);
- }
- return doc;
- }
-
- protected Model getModelForFile(String fileName) throws Exception {
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- return parser.createModel(new ConverterParams().filename(fileName).sizeAutoAdjust(false));
- }
-
- protected String createTmpFileName() {
- try {
- File f = File.createTempFile("prefix", ".txt");
- String filename = f.getName();
- f.delete();
- return filename;
- } catch (IOException e) {
- e.printStackTrace();
- return null;
- }
- }
-
- protected String nodeToString(Node node) {
- return nodeToString(node, false);
- }
-
- protected String nodeToString(Node node, boolean includeHeadNode) {
- if (node == null)
- return null;
- StringWriter sw = new StringWriter();
- try {
- Transformer t = TransformerFactory.newInstance().newTransformer();
- t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
- t.setOutputProperty(OutputKeys.INDENT, "yes");
- t.setOutputProperty(OutputKeys.METHOD, "xml");
-
- NodeList list = node.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node element = list.item(i);
- t.transform(new DOMSource(element), new StreamResult(sw));
- }
- } catch (TransformerException te) {
- logger.debug("nodeToString Transformer Exception");
- }
- if (includeHeadNode) {
- return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
- }
- return sw.toString();
- }
-
- protected boolean equalFiles(String fileA, String fileB) throws IOException {
- int BLOCK_SIZE = 65536;
- FileInputStream inputStreamA = new FileInputStream(fileA);
- FileInputStream inputStreamB = new FileInputStream(fileB);
- // vary BLOCK_SIZE to suit yourself.
- // it should probably a factor or multiple of the size of a disk
- // sector/cluster.
- // Note that your max heap size may need to be adjused
- // if you have a very big block size or lots of these comparators.
-
- // assume inputStreamA and inputStreamB are streams from your two files.
- byte[] streamABlock = new byte[BLOCK_SIZE];
- byte[] streamBBlock = new byte[BLOCK_SIZE];
- boolean match = true;
- int bytesReadA = 0;
- int bytesReadB = 0;
- do {
- bytesReadA = inputStreamA.read(streamABlock);
- bytesReadB = inputStreamB.read(streamBBlock);
- match = ((bytesReadA == bytesReadB) && Arrays.equals(streamABlock, streamBBlock));
- } while (match && (bytesReadA > -1));
- inputStreamA.close();
- inputStreamB.close();
- return match;
- }
-
- public File createTempDirectory() throws IOException {
- final File temp;
-
- temp = File.createTempFile("temp", Long.toString(System.nanoTime()));
-
- if (!(temp.delete())) {
- throw new IOException("Could not delete temp file: " + temp.getAbsolutePath());
- }
-
- if (!(temp.mkdir())) {
- throw new IOException("Could not create temp directory: " + temp.getAbsolutePath());
- }
-
- return (temp);
- }
-
- protected String getWebpage(String accessUrl) throws IOException {
- String inputLine;
- StringBuilder tmp = new StringBuilder();
- URL url = new URL(accessUrl);
- URLConnection urlConn = url.openConnection();
- BufferedReader in = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));
-
- while ((inputLine = in.readLine()) != null) {
- tmp.append(inputLine);
- }
- in.close();
- return tmp.toString();
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.io.StringReader;
+import java.io.StringWriter;
+import java.io.UnsupportedEncodingException;
+import java.net.URL;
+import java.net.URLConnection;
+import java.util.Arrays;
+import java.util.List;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.OutputKeys;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerException;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.dom.DOMSource;
+import javax.xml.transform.stream.StreamResult;
+
+import org.apache.log4j.Logger;
+import org.apache.log4j.spi.LoggingEvent;
+import org.junit.After;
+import org.junit.Before;
+import org.w3c.dom.Document;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.EventStorageLoggerAppender;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.model.map.model.Model;
+
+public abstract class CellDesignerTestFunctions {
+ private Logger logger = Logger.getLogger(CellDesignerTestFunctions.class);
+
+ protected static double EPSILON = Configuration.EPSILON;
+
+ private EventStorageLoggerAppender appender;
+
+ @Before
+ public final void _setUp() throws Exception {
+ Logger.getRootLogger().removeAppender(appender);
+ appender = new EventStorageLoggerAppender();
+ Logger.getRootLogger().addAppender(appender);
+ }
+
+ @After
+ public final void _tearDown() throws Exception {
+ Logger.getRootLogger().removeAppender(appender);
+ }
+
+ protected List<LoggingEvent> getWarnings() {
+ return appender.getWarnings();
+ }
+
+ protected String readFile(String file) throws IOException {
+ StringBuilder stringBuilder = new StringBuilder();
+ BufferedReader reader = new BufferedReader(new FileReader(file));
+ try {
+ String line = null;
+ String ls = System.getProperty("line.separator");
+
+ while ((line = reader.readLine()) != null) {
+ stringBuilder.append(line);
+ stringBuilder.append(ls);
+ }
+ } finally {
+ reader.close();
+ }
+
+ return stringBuilder.toString();
+ }
+
+ protected Node getNodeFromXmlString(String text) throws InvalidXmlSchemaException {
+ InputSource is = new InputSource();
+ is.setCharacterStream(new StringReader(text));
+ return getXmlDocumentFromInputSource(is).getChildNodes().item(0);
+ }
+
+ protected Document getXmlDocumentFromFile(String fileName) throws InvalidXmlSchemaException, IOException {
+ File file = new File(fileName);
+ InputStream inputStream = new FileInputStream(file);
+ Reader reader = null;
+ try {
+ reader = new InputStreamReader(inputStream, "UTF-8");
+ InputSource is = new InputSource(reader);
+
+ Document result = getXmlDocumentFromInputSource(is);
+ inputStream.close();
+ return result;
+ } catch (UnsupportedEncodingException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ return null;
+ }
+
+ protected Document getXmlDocumentFromInputSource(InputSource stream) throws InvalidXmlSchemaException {
+ DocumentBuilder db;
+ try {
+ db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
+ } catch (ParserConfigurationException e) {
+ throw new InvalidXmlSchemaException("Problem with xml parser");
+ }
+ Document doc = null;
+ try {
+ doc = db.parse(stream);
+ } catch (SAXException e) {
+ logger.error(e);
+ } catch (IOException e) {
+ logger.error(e);
+ }
+ return doc;
+ }
+
+ protected Model getModelForFile(String fileName) throws Exception {
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ return parser.createModel(new ConverterParams().filename(fileName).sizeAutoAdjust(false));
+ }
+
+ protected String createTmpFileName() {
+ try {
+ File f = File.createTempFile("prefix", ".txt");
+ String filename = f.getName();
+ f.delete();
+ return filename;
+ } catch (IOException e) {
+ e.printStackTrace();
+ return null;
+ }
+ }
+
+ protected String nodeToString(Node node) {
+ return nodeToString(node, false);
+ }
+
+ protected String nodeToString(Node node, boolean includeHeadNode) {
+ if (node == null)
+ return null;
+ StringWriter sw = new StringWriter();
+ try {
+ Transformer t = TransformerFactory.newInstance().newTransformer();
+ t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
+ t.setOutputProperty(OutputKeys.INDENT, "yes");
+ t.setOutputProperty(OutputKeys.METHOD, "xml");
+
+ NodeList list = node.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node element = list.item(i);
+ t.transform(new DOMSource(element), new StreamResult(sw));
+ }
+ } catch (TransformerException te) {
+ logger.debug("nodeToString Transformer Exception");
+ }
+ if (includeHeadNode) {
+ return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
+ }
+ return sw.toString();
+ }
+
+ protected boolean equalFiles(String fileA, String fileB) throws IOException {
+ int BLOCK_SIZE = 65536;
+ FileInputStream inputStreamA = new FileInputStream(fileA);
+ FileInputStream inputStreamB = new FileInputStream(fileB);
+ // vary BLOCK_SIZE to suit yourself.
+ // it should probably a factor or multiple of the size of a disk
+ // sector/cluster.
+ // Note that your max heap size may need to be adjused
+ // if you have a very big block size or lots of these comparators.
+
+ // assume inputStreamA and inputStreamB are streams from your two files.
+ byte[] streamABlock = new byte[BLOCK_SIZE];
+ byte[] streamBBlock = new byte[BLOCK_SIZE];
+ boolean match = true;
+ int bytesReadA = 0;
+ int bytesReadB = 0;
+ do {
+ bytesReadA = inputStreamA.read(streamABlock);
+ bytesReadB = inputStreamB.read(streamBBlock);
+ match = ((bytesReadA == bytesReadB) && Arrays.equals(streamABlock, streamBBlock));
+ } while (match && (bytesReadA > -1));
+ inputStreamA.close();
+ inputStreamB.close();
+ return match;
+ }
+
+ public File createTempDirectory() throws IOException {
+ final File temp;
+
+ temp = File.createTempFile("temp", Long.toString(System.nanoTime()));
+
+ if (!(temp.delete())) {
+ throw new IOException("Could not delete temp file: " + temp.getAbsolutePath());
+ }
+
+ if (!(temp.mkdir())) {
+ throw new IOException("Could not create temp directory: " + temp.getAbsolutePath());
+ }
+
+ return (temp);
+ }
+
+ protected String getWebpage(String accessUrl) throws IOException {
+ String inputLine;
+ StringBuilder tmp = new StringBuilder();
+ URL url = new URL(accessUrl);
+ URLConnection urlConn = url.openConnection();
+ BufferedReader in = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));
+
+ while ((inputLine = in.readLine()) != null) {
+ tmp.append(inputLine);
+ }
+ in.close();
+ return tmp.toString();
+ }
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java
index 4df1c5bfb3..45723d7b90 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java
@@ -1,425 +1,425 @@
-package lcsb.mapviewer.converter.model.celldesigner;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.field.AbstractSiteModification;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.model.map.species.field.ModificationState;
-import lcsb.mapviewer.model.map.species.field.Residue;
-import lcsb.mapviewer.modelutils.map.ElementUtils;
-
-public class ComplexParserTests extends CellDesignerTestFunctions {
- Logger logger = Logger.getLogger(ComplexParserTests.class);
-
- ElementUtils eu = new ElementUtils();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParseFunctions() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/function.xml");
-
- assertEquals(1, model.getFunctions().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseParameters() throws Exception {
- try {
- Model model = getModelForFile("testFiles/parameter.xml");
-
- assertEquals(1, model.getParameters().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseElementKinetics() throws Exception {
- try {
- Model model = getModelForFile("testFiles/elements_with_kinetic_data.xml");
-
- GenericProtein protein1 = model.getElementByElementId("sa1");
- assertEquals(2.5, protein1.getInitialAmount(), Configuration.EPSILON);
- assertTrue("hasOnlySubstance property is not parsed properly", protein1.hasOnlySubstanceUnits());
- assertTrue("boundaryCondition property is not parsed properly", protein1.isBoundaryCondition());
- assertTrue("constant property is not parsed properly", protein1.isConstant());
- assertEquals(SbmlUnitType.GRAM, protein1.getSubstanceUnits());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseAndSerializeKineticsElements() throws Exception {
- try {
- Model model = getModelForFile("testFiles/elements_with_kinetic_data.xml");
- model.setName(null);
-
- String xml = new CellDesignerXmlParser().toXml(model);
- ByteArrayInputStream bais = new ByteArrayInputStream(xml.getBytes());
- Model model2 = new CellDesignerXmlParser()
- .createModel(new ConverterParams().sizeAutoAdjust(false).inputStream(bais));
-
- ModelComparator modelComparator = new ModelComparator();
- assertEquals(0, modelComparator.compare(model, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseAndSerializeKineticsReaction() throws Exception {
- try {
- Model model = getModelForFile("testFiles/reactions/kinetics.xml");
- model.setName(null);
-
- String xml = new CellDesignerXmlParser().toXml(model);
- ByteArrayInputStream bais = new ByteArrayInputStream(xml.getBytes());
- Model model2 = new CellDesignerXmlParser()
- .createModel(new ConverterParams().sizeAutoAdjust(false).inputStream(bais));
-
- ModelComparator modelComparator = new ModelComparator();
- assertEquals(0, modelComparator.compare(model, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseUnits() throws Exception {
- try {
- Model model = getModelForFile("testFiles/unit.xml");
-
- assertEquals(1, model.getUnits().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseCompartmens() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/centeredAnchorInModifier.xml");
-
- assertEquals(0, model.getCompartments().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseBubbles() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/bubbles.xml");
-
- Element species = model.getElementByElementId("sa6");
- assertNotNull(species);
- Protein protein = (Protein) species;
- assertTrue(protein.getModificationResidues().size() > 0);
- assertNotNull(protein.getStructuralState());
- assertFalse(protein.getStructuralState().equals(""));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseCompartmensRelation() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/problematic/elements_in_compartments.xml");
-
- List<Element> aliases = new ArrayList<>();
- aliases.add(model.getElementByElementId("csa3"));
- aliases.add(model.getElementByElementId("csa4"));
- aliases.add(model.getElementByElementId("csa5"));
- aliases.add(model.getElementByElementId("csa6"));
- aliases.add(model.getElementByElementId("sa3"));
- aliases.add(model.getElementByElementId("sa5"));
- aliases.add(model.getElementByElementId("sa6"));
- aliases.add(model.getElementByElementId("sa7"));
- aliases.add(model.getElementByElementId("sa8"));
- aliases.add(model.getElementByElementId("sa9"));
- aliases.add(model.getElementByElementId("sa10"));
- aliases.add(model.getElementByElementId("sa11"));
- aliases.add(model.getElementByElementId("sa12"));
- aliases.add(model.getElementByElementId("sa13"));
- aliases.add(model.getElementByElementId("sa14"));
- aliases.add(model.getElementByElementId("sa15"));
- aliases.add(model.getElementByElementId("sa16"));
- aliases.add(model.getElementByElementId("sa17"));
- aliases.add(model.getElementByElementId("sa18"));
- aliases.add(model.getElementByElementId("sa19"));
- aliases.add(model.getElementByElementId("sa20"));
- for (Element alias : aliases) {
- assertNotNull(eu.getElementTag(alias) + " does not contain info about compartment", alias.getCompartment());
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseProteins() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/problematic/acetyled_protein.xml");
-
- Set<ModificationState> residues = new HashSet<>();
- for (Element element : model.getElements()) {
- if (element instanceof Species) {
- Protein protein = (Protein) element;
- for (ModificationResidue mr : protein.getModificationResidues()) {
- if (mr instanceof AbstractSiteModification) {
- residues.add(((AbstractSiteModification) mr).getState());
- }
- }
- }
- }
- // we have a protein which is acetylated and not acetylated so two types
- // of residues
- assertEquals(2, residues.size());
-
- AbstractSiteModification modification = (AbstractSiteModification) ((Protein) model.getElementByElementId("sa2"))
- .getModificationResidues().get(0);
- assertEquals(ModificationState.ACETYLATED, modification.getState());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testNotesComplexesInNested() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/includedSpecies.xml");
- Element species = model.getElementByElementId("sa1");
- assertNotNull(species);
- assertNotNull(species.getNotes());
- assertTrue("Wrong notes: " + species.getNotes(), species.getNotes().contains("hello world"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testHypotheticalComplex() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/problematic/hypothetical_complex.xml");
- Complex species = (Complex) model.getElementByElementId("csa1");
- assertTrue(species.isHypothetical());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProblematicAcetylation() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/problematic/problematic_acetylation.xml");
- Protein p1 = (Protein) model.getElementByElementId("sa73");
- Protein p2 = (Protein) model.getElementByElementId("sa27");
- assertEquals(ModificationState.ACETYLATED, ((Residue) p1.getModificationResidues().get(0)).getState());
- assertFalse(ModificationState.ACETYLATED.equals(((Residue) p2.getModificationResidues().get(0)).getState()));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDuplicateMiriam() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/problematic/duplicated_miriam.xml");
- Protein p1 = (Protein) model.getElementByElementId("sa1");
- Set<String> ids = new HashSet<>();
-
- assertTrue(p1.getMiriamData().size() > 0);
- for (MiriamData md : p1.getMiriamData()) {
- if (md.getDataType().equals(MiriamType.PUBMED)) {
- assertFalse("Protein contains double pubmed annotation for pubmed id: " + md.getResource(),
- ids.contains(md.getResource()));
- ids.add(md.getResource());
- }
- }
- assertTrue(ids.size() > 0);
- assertEquals(2, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testKappaInDescription() throws Exception {
- try {
- Model model = getModelForFile("testFiles/problematic/kappa_example.xml");
-
- Element species = model.getElementByElementId("sa1");
-
- assertFalse(species.getName().toLowerCase().contains("kappa"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testMissingXmlNodes() throws Exception {
- try {
- Model model = getModelForFile("testFiles/missing_xml_nodes.xml");
-
- assertTrue(((Species) model.getElementByElementId("sa3")).isHypothetical());
- assertTrue(((Species) model.getElementByElementId("sa4")).isHypothetical());
- assertTrue(((Species) model.getElementByElementId("sa5")).isHypothetical());
-
- assertFalse(((Species) model.getElementByElementId("sa12")).isHypothetical());
- assertFalse(((Species) model.getElementByElementId("sa13")).isHypothetical());
- assertFalse(((Species) model.getElementByElementId("sa14")).isHypothetical());
- assertFalse(((Species) model.getElementByElementId("sa15")).isHypothetical());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParsingSpecialCharactersInName() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
- model.setIdModel("as");
- model.setWidth(100);
- model.setHeight(100);
- GenericProtein alias = new GenericProtein("aid");
- alias.setName("name & no-name");
- model.addElement(alias);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String string = parser.toXml(model);
-
- InputStream stream = new ByteArrayInputStream(string.getBytes(StandardCharsets.UTF_8));
-
- ConverterParams params = new ConverterParams().inputStream(stream).sizeAutoAdjust(false);
-
- Model model2 = parser.createModel(params);
-
- ModelComparator comparator = new ModelComparator();
-
- assertEquals(0, comparator.compare(model, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParsingEndLineInName() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
- model.setIdModel("as");
- model.setWidth(100);
- model.setHeight(100);
- GenericProtein alias = new GenericProtein("aid");
- alias.setName("name\rno-name");
- model.addElement(alias);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String string = parser.toXml(model);
-
- InputStream stream = new ByteArrayInputStream(string.getBytes(StandardCharsets.UTF_8));
-
- ConverterParams params = new ConverterParams().inputStream(stream).sizeAutoAdjust(false);
-
- Model model2 = parser.createModel(params);
-
- ModelComparator comparator = new ModelComparator();
-
- assertEquals(0, comparator.compare(model, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testWarningInParser() throws Exception {
- try {
- getModelForFile("testFiles/problematic/invalid_elements_name.xml");
- assertTrue(getWarnings().size() > 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.AbstractSiteModification;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+import lcsb.mapviewer.model.map.species.field.Residue;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
+
+public class ComplexParserTests extends CellDesignerTestFunctions {
+ Logger logger = Logger.getLogger(ComplexParserTests.class);
+
+ ElementUtils eu = new ElementUtils();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testParseFunctions() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/function.xml");
+
+ assertEquals(1, model.getFunctions().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseParameters() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/parameter.xml");
+
+ assertEquals(1, model.getParameters().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseElementKinetics() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/elements_with_kinetic_data.xml");
+
+ GenericProtein protein1 = model.getElementByElementId("sa1");
+ assertEquals(2.5, protein1.getInitialAmount(), Configuration.EPSILON);
+ assertTrue("hasOnlySubstance property is not parsed properly", protein1.hasOnlySubstanceUnits());
+ assertTrue("boundaryCondition property is not parsed properly", protein1.isBoundaryCondition());
+ assertTrue("constant property is not parsed properly", protein1.isConstant());
+ assertEquals(SbmlUnitType.GRAM, protein1.getSubstanceUnits());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseAndSerializeKineticsElements() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/elements_with_kinetic_data.xml");
+ model.setName(null);
+
+ String xml = new CellDesignerXmlParser().toXml(model);
+ ByteArrayInputStream bais = new ByteArrayInputStream(xml.getBytes());
+ Model model2 = new CellDesignerXmlParser()
+ .createModel(new ConverterParams().sizeAutoAdjust(false).inputStream(bais));
+
+ ModelComparator modelComparator = new ModelComparator();
+ assertEquals(0, modelComparator.compare(model, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseAndSerializeKineticsReaction() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/reactions/kinetics.xml");
+ model.setName(null);
+
+ String xml = new CellDesignerXmlParser().toXml(model);
+ ByteArrayInputStream bais = new ByteArrayInputStream(xml.getBytes());
+ Model model2 = new CellDesignerXmlParser()
+ .createModel(new ConverterParams().sizeAutoAdjust(false).inputStream(bais));
+
+ ModelComparator modelComparator = new ModelComparator();
+ assertEquals(0, modelComparator.compare(model, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseUnits() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/unit.xml");
+
+ assertEquals(1, model.getUnits().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseCompartmens() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/centeredAnchorInModifier.xml");
+
+ assertEquals(0, model.getCompartments().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseBubbles() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/bubbles.xml");
+
+ Element species = model.getElementByElementId("sa6");
+ assertNotNull(species);
+ Protein protein = (Protein) species;
+ assertTrue(protein.getModificationResidues().size() > 0);
+ assertNotNull(protein.getStructuralState());
+ assertFalse(protein.getStructuralState().equals(""));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseCompartmensRelation() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/problematic/elements_in_compartments.xml");
+
+ List<Element> aliases = new ArrayList<>();
+ aliases.add(model.getElementByElementId("csa3"));
+ aliases.add(model.getElementByElementId("csa4"));
+ aliases.add(model.getElementByElementId("csa5"));
+ aliases.add(model.getElementByElementId("csa6"));
+ aliases.add(model.getElementByElementId("sa3"));
+ aliases.add(model.getElementByElementId("sa5"));
+ aliases.add(model.getElementByElementId("sa6"));
+ aliases.add(model.getElementByElementId("sa7"));
+ aliases.add(model.getElementByElementId("sa8"));
+ aliases.add(model.getElementByElementId("sa9"));
+ aliases.add(model.getElementByElementId("sa10"));
+ aliases.add(model.getElementByElementId("sa11"));
+ aliases.add(model.getElementByElementId("sa12"));
+ aliases.add(model.getElementByElementId("sa13"));
+ aliases.add(model.getElementByElementId("sa14"));
+ aliases.add(model.getElementByElementId("sa15"));
+ aliases.add(model.getElementByElementId("sa16"));
+ aliases.add(model.getElementByElementId("sa17"));
+ aliases.add(model.getElementByElementId("sa18"));
+ aliases.add(model.getElementByElementId("sa19"));
+ aliases.add(model.getElementByElementId("sa20"));
+ for (Element alias : aliases) {
+ assertNotNull(eu.getElementTag(alias) + " does not contain info about compartment", alias.getCompartment());
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseProteins() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/problematic/acetyled_protein.xml");
+
+ Set<ModificationState> residues = new HashSet<>();
+ for (Element element : model.getElements()) {
+ if (element instanceof Species) {
+ Protein protein = (Protein) element;
+ for (ModificationResidue mr : protein.getModificationResidues()) {
+ if (mr instanceof AbstractSiteModification) {
+ residues.add(((AbstractSiteModification) mr).getState());
+ }
+ }
+ }
+ }
+ // we have a protein which is acetylated and not acetylated so two types
+ // of residues
+ assertEquals(2, residues.size());
+
+ AbstractSiteModification modification = (AbstractSiteModification) ((Protein) model.getElementByElementId("sa2"))
+ .getModificationResidues().get(0);
+ assertEquals(ModificationState.ACETYLATED, modification.getState());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testNotesComplexesInNested() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/includedSpecies.xml");
+ Element species = model.getElementByElementId("sa1");
+ assertNotNull(species);
+ assertNotNull(species.getNotes());
+ assertTrue("Wrong notes: " + species.getNotes(), species.getNotes().contains("hello world"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testHypotheticalComplex() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/problematic/hypothetical_complex.xml");
+ Complex species = (Complex) model.getElementByElementId("csa1");
+ assertTrue(species.isHypothetical());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProblematicAcetylation() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/problematic/problematic_acetylation.xml");
+ Protein p1 = (Protein) model.getElementByElementId("sa73");
+ Protein p2 = (Protein) model.getElementByElementId("sa27");
+ assertEquals(ModificationState.ACETYLATED, ((Residue) p1.getModificationResidues().get(0)).getState());
+ assertFalse(ModificationState.ACETYLATED.equals(((Residue) p2.getModificationResidues().get(0)).getState()));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDuplicateMiriam() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/problematic/duplicated_miriam.xml");
+ Protein p1 = (Protein) model.getElementByElementId("sa1");
+ Set<String> ids = new HashSet<>();
+
+ assertTrue(p1.getMiriamData().size() > 0);
+ for (MiriamData md : p1.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.PUBMED)) {
+ assertFalse("Protein contains double pubmed annotation for pubmed id: " + md.getResource(),
+ ids.contains(md.getResource()));
+ ids.add(md.getResource());
+ }
+ }
+ assertTrue(ids.size() > 0);
+ assertEquals(2, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testKappaInDescription() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/problematic/kappa_example.xml");
+
+ Element species = model.getElementByElementId("sa1");
+
+ assertFalse(species.getName().toLowerCase().contains("kappa"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testMissingXmlNodes() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/missing_xml_nodes.xml");
+
+ assertTrue(((Species) model.getElementByElementId("sa3")).isHypothetical());
+ assertTrue(((Species) model.getElementByElementId("sa4")).isHypothetical());
+ assertTrue(((Species) model.getElementByElementId("sa5")).isHypothetical());
+
+ assertFalse(((Species) model.getElementByElementId("sa12")).isHypothetical());
+ assertFalse(((Species) model.getElementByElementId("sa13")).isHypothetical());
+ assertFalse(((Species) model.getElementByElementId("sa14")).isHypothetical());
+ assertFalse(((Species) model.getElementByElementId("sa15")).isHypothetical());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParsingSpecialCharactersInName() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+ model.setIdModel("as");
+ model.setWidth(100);
+ model.setHeight(100);
+ GenericProtein alias = new GenericProtein("aid");
+ alias.setName("name & no-name");
+ model.addElement(alias);
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String string = parser.toXml(model);
+
+ InputStream stream = new ByteArrayInputStream(string.getBytes(StandardCharsets.UTF_8));
+
+ ConverterParams params = new ConverterParams().inputStream(stream).sizeAutoAdjust(false);
+
+ Model model2 = parser.createModel(params);
+
+ ModelComparator comparator = new ModelComparator();
+
+ assertEquals(0, comparator.compare(model, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParsingEndLineInName() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+ model.setIdModel("as");
+ model.setWidth(100);
+ model.setHeight(100);
+ GenericProtein alias = new GenericProtein("aid");
+ alias.setName("name\rno-name");
+ model.addElement(alias);
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String string = parser.toXml(model);
+
+ InputStream stream = new ByteArrayInputStream(string.getBytes(StandardCharsets.UTF_8));
+
+ ConverterParams params = new ConverterParams().inputStream(stream).sizeAutoAdjust(false);
+
+ Model model2 = parser.createModel(params);
+
+ ModelComparator comparator = new ModelComparator();
+
+ assertEquals(0, comparator.compare(model, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testWarningInParser() throws Exception {
+ try {
+ getModelForFile("testFiles/problematic/invalid_elements_name.xml");
+ assertTrue(getWarnings().size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/InvalidGroupExceptionTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/InvalidGroupExceptionTest.java
index c04439642a..af15a37f2c 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/InvalidGroupExceptionTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/InvalidGroupExceptionTest.java
@@ -1,27 +1,27 @@
-package lcsb.mapviewer.converter.model.celldesigner;
-
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class InvalidGroupExceptionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testConstructor() {
- assertNotNull(new InvalidGroupException());
- assertNotNull(new InvalidGroupException("str"));
- assertNotNull(new InvalidGroupException("str2", new Exception()));
- assertNotNull(new InvalidGroupException(new Exception()));
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner;
+
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class InvalidGroupExceptionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testConstructor() {
+ assertNotNull(new InvalidGroupException());
+ assertNotNull(new InvalidGroupException("str"));
+ assertNotNull(new InvalidGroupException("str2", new Exception()));
+ assertNotNull(new InvalidGroupException(new Exception()));
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParserTest.java
index 512cb8fe4f..1becaf1367 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParserTest.java
@@ -1,449 +1,449 @@
-package lcsb.mapviewer.converter.model.celldesigner;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.awt.geom.Rectangle2D;
-import java.util.Collection;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.w3c.dom.Node;
-
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.graphics.PolylineDataComparator;
-import lcsb.mapviewer.model.map.layout.ElementGroup;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.layout.graphics.LayerComparator;
-import lcsb.mapviewer.model.map.layout.graphics.LayerOval;
-import lcsb.mapviewer.model.map.layout.graphics.LayerOvalComparator;
-import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
-import lcsb.mapviewer.model.map.layout.graphics.LayerRectComparator;
-import lcsb.mapviewer.model.map.layout.graphics.LayerText;
-import lcsb.mapviewer.model.map.layout.graphics.LayerTextComparator;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class LayerXmlParserTest extends CellDesignerTestFunctions {
- Logger logger = Logger.getLogger(LayerXmlParserTest.class);
-
- LayerXmlParser parser = new LayerXmlParser();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParseLayers() throws Exception {
- LayerComparator comparator = new LayerComparator();
- try {
- String xmlString = readFile("testFiles/xmlNodeTestExamples/layer_collection.xml");
- Node node = getNodeFromXmlString(xmlString);
- Collection<Layer> layers = parser.parseLayers(node);
- assertNotNull(layers);
- assertEquals(1, layers.size());
-
- xmlString = parser.layerCollectionToXml(layers);
- node = getNodeFromXmlString(xmlString);
- Collection<Layer> layers2 = parser.parseLayers(node);
- assertNotNull(layers2);
- assertEquals(1, layers2.size());
- assertEquals(0, comparator.compare(layers.iterator().next(), layers2.iterator().next()));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidLayers() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/layer_collection.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.parseLayers(node);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfLayers"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseBlockDiagrams() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
- String xmlString = readFile("testFiles/xmlNodeTestExamples/block_diagrams.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.parseBlocks(model, node);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidBlockDiagrams() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
- String xmlString = readFile("testFiles/invalid/block_diagrams.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.parseBlocks(model, node);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfBlockDiagrams"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidGroups() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
- String xmlString = readFile("testFiles/invalid/group_collection.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.parseGroups(model, node);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfGroups"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidGroups2() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
- String xmlString = readFile("testFiles/invalid/group_collection2.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.parseGroups(model, node);
- fail("Exception expected");
- } catch (InvalidGroupException e) {
- assertTrue(e.getMessage().contains("such alias doesn't exist in the model"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidGroups3() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
- GenericProtein alias = new GenericProtein("sa1");
- model.addElement(alias);
-
- String xmlString = readFile("testFiles/invalid/group_collection3.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.parseGroups(model, node);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:group"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetLayer() throws Exception {
- LayerComparator comparator = new LayerComparator();
- try {
- String xmlString = readFile("testFiles/xmlNodeTestExamples/layer.xml");
- Node node = getNodeFromXmlString(xmlString);
- Layer layer = parser.getLayer(node);
- assertNotNull(layer);
-
- xmlString = parser.layerToXml(layer);
- node = getNodeFromXmlString(xmlString);
- Layer layers2 = parser.getLayer(node);
- assertNotNull(layers2);
- assertEquals(0, comparator.compare(layer, layers2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidLayer() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/layer.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.getLayer(node);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfTexts"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidLayer2() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/layer2.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.getLayer(node);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown celldesigner:layerCompartmentAlias type"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidLayer3() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/layer3.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.getLayer(node);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfSquares"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidLayer4() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/layer4.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.getLayer(node);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfFreeLines"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidLayer5() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/layer5.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.getLayer(node);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:layer"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetLayerRect() throws Exception {
- try {
- LayerRectComparator comparator = new LayerRectComparator();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/layer_square.xml");
- Node node = getNodeFromXmlString(xmlString);
- LayerRect layer = parser.getLayerRect(node);
- assertNotNull(layer);
-
- xmlString = parser.layerRectToXml(layer);
- node = getNodeFromXmlString(xmlString);
- LayerRect layers2 = parser.getLayerRect(node);
- assertNotNull(layers2);
- assertEquals(0, comparator.compare(layer, layers2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidLayerRect() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/layer_square.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.getLayerRect(node);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:layerCompartmentAlias"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetLayerLine() {
- try {
- PolylineDataComparator comparator = new PolylineDataComparator();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/layer_line.xml");
- Node node = getNodeFromXmlString(xmlString);
- PolylineData layer = parser.getLayerLine(node);
- assertNotNull(layer);
-
- xmlString = parser.layerLineToXml(layer);
- node = getNodeFromXmlString(xmlString);
- PolylineData layers2 = parser.getLayerLine(node);
- assertNotNull(layers2);
- assertEquals(0, comparator.compare(layer, layers2));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
- @Test
- public void testParseInvalidLayerLine() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/layer_line.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.getLayerLine(node);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:layerFreeLine"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetLayerOval() {
- try {
- LayerOvalComparator comparator = new LayerOvalComparator();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/layer_oval.xml");
- Node node = getNodeFromXmlString(xmlString);
- LayerOval layer = parser.getLayerOval(node);
- assertNotNull(layer);
-
- xmlString = parser.layerOvalToXml(layer);
- node = getNodeFromXmlString(xmlString);
- LayerOval layers2 = parser.getLayerOval(node);
- assertNotNull(layers2);
- assertEquals(0, comparator.compare(layer, layers2));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
- @Test
- public void testParseInvalidLayerOval() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/layer_oval.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.getLayerOval(node);
- fail("Exception expected");
-
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:layerCompartmentAlias"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetLayerText() {
- try {
- LayerTextComparator comparator = new LayerTextComparator();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/layer_text.xml");
- Node node = getNodeFromXmlString(xmlString);
- LayerText layer = parser.getLayerText(node);
- assertNotNull(layer);
-
- xmlString = parser.layerTextToXml(layer);
- node = getNodeFromXmlString(xmlString);
- LayerText layers2 = parser.getLayerText(node);
- assertNotNull(layers2);
- assertEquals(0, comparator.compare(layer, layers2));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
- @Test
- public void testParseInvalidLayerText() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/layer_text.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.getLayerText(node);
- fail("Exception expected");
-
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:layerSpeciesAlias"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAliasGroup() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
- Species alias = new GenericProtein("sa1035");
- model.addElement(alias);
-
- alias = new GenericProtein("sa1036");
- model.addElement(alias);
-
- alias = new GenericProtein("sa1037");
- model.addElement(alias);
-
- alias = new GenericProtein("sa1038");
- model.addElement(alias);
-
- String string = "<celldesigner:group id=\"g74\" members=\"sa1035,sa1036,sa1037,sa1038\"/>";
- Node node = getNodeFromXmlString(string);
- ElementGroup group = parser.getAliasGroup(node, model);
- assertNotNull(group);
-
- assertEquals(4, group.getElements().size());
-
- assertEquals("g74", group.getIdGroup());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testLayerTextToXml() throws Exception {
- try {
- LayerText text = new LayerText(new Rectangle2D.Double(1, 2, 3, 4), "DF");
- String xml = parser.layerTextToXml(text);
- assertNotNull(xml);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.awt.geom.Rectangle2D;
+import java.util.Collection;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.w3c.dom.Node;
+
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.graphics.PolylineDataComparator;
+import lcsb.mapviewer.model.map.layout.ElementGroup;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.layout.graphics.LayerComparator;
+import lcsb.mapviewer.model.map.layout.graphics.LayerOval;
+import lcsb.mapviewer.model.map.layout.graphics.LayerOvalComparator;
+import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
+import lcsb.mapviewer.model.map.layout.graphics.LayerRectComparator;
+import lcsb.mapviewer.model.map.layout.graphics.LayerText;
+import lcsb.mapviewer.model.map.layout.graphics.LayerTextComparator;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class LayerXmlParserTest extends CellDesignerTestFunctions {
+ Logger logger = Logger.getLogger(LayerXmlParserTest.class);
+
+ LayerXmlParser parser = new LayerXmlParser();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testParseLayers() throws Exception {
+ LayerComparator comparator = new LayerComparator();
+ try {
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/layer_collection.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Collection<Layer> layers = parser.parseLayers(node);
+ assertNotNull(layers);
+ assertEquals(1, layers.size());
+
+ xmlString = parser.layerCollectionToXml(layers);
+ node = getNodeFromXmlString(xmlString);
+ Collection<Layer> layers2 = parser.parseLayers(node);
+ assertNotNull(layers2);
+ assertEquals(1, layers2.size());
+ assertEquals(0, comparator.compare(layers.iterator().next(), layers2.iterator().next()));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidLayers() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/layer_collection.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.parseLayers(node);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfLayers"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseBlockDiagrams() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/block_diagrams.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.parseBlocks(model, node);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidBlockDiagrams() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+ String xmlString = readFile("testFiles/invalid/block_diagrams.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.parseBlocks(model, node);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfBlockDiagrams"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidGroups() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+ String xmlString = readFile("testFiles/invalid/group_collection.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.parseGroups(model, node);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfGroups"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidGroups2() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+ String xmlString = readFile("testFiles/invalid/group_collection2.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.parseGroups(model, node);
+ fail("Exception expected");
+ } catch (InvalidGroupException e) {
+ assertTrue(e.getMessage().contains("such alias doesn't exist in the model"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidGroups3() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+ GenericProtein alias = new GenericProtein("sa1");
+ model.addElement(alias);
+
+ String xmlString = readFile("testFiles/invalid/group_collection3.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.parseGroups(model, node);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:group"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetLayer() throws Exception {
+ LayerComparator comparator = new LayerComparator();
+ try {
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/layer.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Layer layer = parser.getLayer(node);
+ assertNotNull(layer);
+
+ xmlString = parser.layerToXml(layer);
+ node = getNodeFromXmlString(xmlString);
+ Layer layers2 = parser.getLayer(node);
+ assertNotNull(layers2);
+ assertEquals(0, comparator.compare(layer, layers2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidLayer() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/layer.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.getLayer(node);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfTexts"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidLayer2() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/layer2.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.getLayer(node);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown celldesigner:layerCompartmentAlias type"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidLayer3() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/layer3.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.getLayer(node);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfSquares"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidLayer4() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/layer4.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.getLayer(node);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfFreeLines"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidLayer5() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/layer5.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.getLayer(node);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:layer"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetLayerRect() throws Exception {
+ try {
+ LayerRectComparator comparator = new LayerRectComparator();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/layer_square.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ LayerRect layer = parser.getLayerRect(node);
+ assertNotNull(layer);
+
+ xmlString = parser.layerRectToXml(layer);
+ node = getNodeFromXmlString(xmlString);
+ LayerRect layers2 = parser.getLayerRect(node);
+ assertNotNull(layers2);
+ assertEquals(0, comparator.compare(layer, layers2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidLayerRect() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/layer_square.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.getLayerRect(node);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:layerCompartmentAlias"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetLayerLine() {
+ try {
+ PolylineDataComparator comparator = new PolylineDataComparator();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/layer_line.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ PolylineData layer = parser.getLayerLine(node);
+ assertNotNull(layer);
+
+ xmlString = parser.layerLineToXml(layer);
+ node = getNodeFromXmlString(xmlString);
+ PolylineData layers2 = parser.getLayerLine(node);
+ assertNotNull(layers2);
+ assertEquals(0, comparator.compare(layer, layers2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+ @Test
+ public void testParseInvalidLayerLine() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/layer_line.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.getLayerLine(node);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:layerFreeLine"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetLayerOval() {
+ try {
+ LayerOvalComparator comparator = new LayerOvalComparator();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/layer_oval.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ LayerOval layer = parser.getLayerOval(node);
+ assertNotNull(layer);
+
+ xmlString = parser.layerOvalToXml(layer);
+ node = getNodeFromXmlString(xmlString);
+ LayerOval layers2 = parser.getLayerOval(node);
+ assertNotNull(layers2);
+ assertEquals(0, comparator.compare(layer, layers2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+ @Test
+ public void testParseInvalidLayerOval() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/layer_oval.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.getLayerOval(node);
+ fail("Exception expected");
+
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:layerCompartmentAlias"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetLayerText() {
+ try {
+ LayerTextComparator comparator = new LayerTextComparator();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/layer_text.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ LayerText layer = parser.getLayerText(node);
+ assertNotNull(layer);
+
+ xmlString = parser.layerTextToXml(layer);
+ node = getNodeFromXmlString(xmlString);
+ LayerText layers2 = parser.getLayerText(node);
+ assertNotNull(layers2);
+ assertEquals(0, comparator.compare(layer, layers2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+ @Test
+ public void testParseInvalidLayerText() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/layer_text.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.getLayerText(node);
+ fail("Exception expected");
+
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:layerSpeciesAlias"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAliasGroup() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+ Species alias = new GenericProtein("sa1035");
+ model.addElement(alias);
+
+ alias = new GenericProtein("sa1036");
+ model.addElement(alias);
+
+ alias = new GenericProtein("sa1037");
+ model.addElement(alias);
+
+ alias = new GenericProtein("sa1038");
+ model.addElement(alias);
+
+ String string = "<celldesigner:group id=\"g74\" members=\"sa1035,sa1036,sa1037,sa1038\"/>";
+ Node node = getNodeFromXmlString(string);
+ ElementGroup group = parser.getAliasGroup(node, model);
+ assertNotNull(group);
+
+ assertEquals(4, group.getElements().size());
+
+ assertEquals("g74", group.getIdGroup());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testLayerTextToXml() throws Exception {
+ try {
+ LayerText text = new LayerText(new Rectangle2D.Double(1, 2, 3, 4), "DF");
+ String xml = parser.layerTextToXml(text);
+ assertNotNull(xml);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/NestedComplexParsingTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/NestedComplexParsingTests.java
index f849c74923..e2c9f68fcb 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/NestedComplexParsingTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/NestedComplexParsingTests.java
@@ -1,88 +1,88 @@
-package lcsb.mapviewer.converter.model.celldesigner;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Complex;
-
-public class NestedComplexParsingTests extends CellDesignerTestFunctions {
- Logger logger = Logger.getLogger(NestedComplexParsingTests.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParseCompartmens() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/xmlNodeTestExamples/nested_complex.xml");
-
- Element s1 = model.getElementByElementId("csa1");
- Element s2 = model.getElementByElementId("csa2");
- Element s3 = model.getElementByElementId("csa3");
- Element s4 = model.getElementByElementId("csa4");
- Element s5 = model.getElementByElementId("csa5");
- Element s6 = model.getElementByElementId("csa6");
- Element s7 = model.getElementByElementId("sa1");
- Element s8 = model.getElementByElementId("sa2");
- Element s9 = model.getElementByElementId("sa3");
- Element s10 = model.getElementByElementId("sa4");
- Element s11 = model.getElementByElementId("sa5");
- Element s12 = model.getElementByElementId("sa6");
- assertTrue(s1 instanceof Complex);
- assertTrue(s2 instanceof Complex);
- assertTrue(s3 instanceof Complex);
- assertTrue(s4 instanceof Complex);
- assertTrue(s5 instanceof Complex);
- assertTrue(s6 instanceof Complex);
- Complex cs1 = (Complex) s1;
- Complex cs2 = (Complex) s2;
- Complex cs3 = (Complex) s3;
- Complex cs4 = (Complex) s4;
- Complex cs5 = (Complex) s5;
- Complex cs6 = (Complex) s6;
- assertEquals(2,cs1.getElements().size());
- assertEquals(2,cs2.getElements().size());
- assertEquals(0,cs3.getElements().size());
- assertEquals(0,cs4.getElements().size());
- assertEquals(2,cs5.getElements().size());
- assertEquals(3,cs6.getElements().size());
-
- assertTrue(cs1.getElements().contains(s9));
- assertTrue(cs1.getElements().contains(s3));
-
- assertTrue(cs2.getElements().contains(s7));
- assertTrue(cs2.getElements().contains(s8));
-
- assertTrue(cs5.getElements().contains(s10));
- assertTrue(cs5.getElements().contains(s11));
-
- assertTrue(cs6.getElements().contains(s4));
- assertTrue(cs6.getElements().contains(s5));
- assertTrue(cs6.getElements().contains(s12));
-
- assertEquals(1,cs1.getAllSimpleChildren().size());
- assertEquals(2,cs2.getAllSimpleChildren().size());
- assertEquals(0,cs3.getAllSimpleChildren().size());
- assertEquals(0,cs4.getAllSimpleChildren().size());
- assertEquals(2,cs5.getAllSimpleChildren().size());
- assertEquals(3,cs6.getAllSimpleChildren().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
+
+public class NestedComplexParsingTests extends CellDesignerTestFunctions {
+ Logger logger = Logger.getLogger(NestedComplexParsingTests.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testParseCompartmens() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/xmlNodeTestExamples/nested_complex.xml");
+
+ Element s1 = model.getElementByElementId("csa1");
+ Element s2 = model.getElementByElementId("csa2");
+ Element s3 = model.getElementByElementId("csa3");
+ Element s4 = model.getElementByElementId("csa4");
+ Element s5 = model.getElementByElementId("csa5");
+ Element s6 = model.getElementByElementId("csa6");
+ Element s7 = model.getElementByElementId("sa1");
+ Element s8 = model.getElementByElementId("sa2");
+ Element s9 = model.getElementByElementId("sa3");
+ Element s10 = model.getElementByElementId("sa4");
+ Element s11 = model.getElementByElementId("sa5");
+ Element s12 = model.getElementByElementId("sa6");
+ assertTrue(s1 instanceof Complex);
+ assertTrue(s2 instanceof Complex);
+ assertTrue(s3 instanceof Complex);
+ assertTrue(s4 instanceof Complex);
+ assertTrue(s5 instanceof Complex);
+ assertTrue(s6 instanceof Complex);
+ Complex cs1 = (Complex) s1;
+ Complex cs2 = (Complex) s2;
+ Complex cs3 = (Complex) s3;
+ Complex cs4 = (Complex) s4;
+ Complex cs5 = (Complex) s5;
+ Complex cs6 = (Complex) s6;
+ assertEquals(2,cs1.getElements().size());
+ assertEquals(2,cs2.getElements().size());
+ assertEquals(0,cs3.getElements().size());
+ assertEquals(0,cs4.getElements().size());
+ assertEquals(2,cs5.getElements().size());
+ assertEquals(3,cs6.getElements().size());
+
+ assertTrue(cs1.getElements().contains(s9));
+ assertTrue(cs1.getElements().contains(s3));
+
+ assertTrue(cs2.getElements().contains(s7));
+ assertTrue(cs2.getElements().contains(s8));
+
+ assertTrue(cs5.getElements().contains(s10));
+ assertTrue(cs5.getElements().contains(s11));
+
+ assertTrue(cs6.getElements().contains(s4));
+ assertTrue(cs6.getElements().contains(s5));
+ assertTrue(cs6.getElements().contains(s12));
+
+ assertEquals(1,cs1.getAllSimpleChildren().size());
+ assertEquals(2,cs2.getAllSimpleChildren().size());
+ assertEquals(0,cs3.getAllSimpleChildren().size());
+ assertEquals(0,cs4.getAllSimpleChildren().size());
+ assertEquals(2,cs5.getAllSimpleChildren().size());
+ assertEquals(3,cs6.getAllSimpleChildren().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ReconDataInCellDesignerXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ReconDataInCellDesignerXmlParserTest.java
index 397d38c229..7a182b3e9f 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ReconDataInCellDesignerXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ReconDataInCellDesignerXmlParserTest.java
@@ -1,76 +1,76 @@
-package lcsb.mapviewer.converter.model.celldesigner;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class ReconDataInCellDesignerXmlParserTest extends CellDesignerTestFunctions {
- Logger logger = Logger.getLogger(ReconDataInCellDesignerXmlParserTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParseElement() throws Exception {
- try {
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- Model model = parser.createModel(new ConverterParams().filename("testFiles/annotation/recon_annotation_example.xml"));
- assertNotNull(model);
- Species species = (Species)model.getElementByElementId("sa1");
- assertNotNull(species);
- assertEquals("S1_SYMB",species.getSymbol());
- assertEquals("ABREVIATION",species.getAbbreviation());
- assertEquals("FORMULA",species.getFormula());
- assertEquals((Integer)324,species.getCharge());
- assertEquals(1, species.getSynonyms().size());
- assertTrue(species.getSynonyms().contains("syn44"));
- assertEquals("DESCRIPTION",species.getNotes());
-
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseReaction() throws Exception {
- try {
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- Model model = parser.createModel(new ConverterParams().filename("testFiles/annotation/recon_annotation_example.xml"));
- assertNotNull(model);
- Reaction reaction = model.getReactionByReactionId("re1");
- assertNotNull(reaction);
- assertEquals("SAW",reaction.getSymbol());
- assertEquals("ABREVIATION2",reaction.getAbbreviation());
- assertEquals("FORMULA2",reaction.getFormula());
- assertEquals((Integer)100,reaction.getMechanicalConfidenceScore());
- assertEquals((Double)200.201,reaction.getLowerBound());
- assertEquals((Double)300.301,reaction.getUpperBound());
- assertEquals("SUBSYSTEM2",reaction.getSubsystem());
- assertEquals("(urn:miriam:ccds:CCDS8639.1) or (urn:miriam:ccds:CCDS26.1) or (urn:miriam:ccds:CCDS314.2) or (urn:miriam:ccds:CCDS314.1)",reaction.getGeneProteinReaction());
- assertEquals(1, reaction.getSynonyms().size());
- assertTrue(reaction.getSynonyms().contains("SYN1"));
- assertEquals("DESCRIPTION2",reaction.getNotes());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class ReconDataInCellDesignerXmlParserTest extends CellDesignerTestFunctions {
+ Logger logger = Logger.getLogger(ReconDataInCellDesignerXmlParserTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testParseElement() throws Exception {
+ try {
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ Model model = parser.createModel(new ConverterParams().filename("testFiles/annotation/recon_annotation_example.xml"));
+ assertNotNull(model);
+ Species species = (Species)model.getElementByElementId("sa1");
+ assertNotNull(species);
+ assertEquals("S1_SYMB",species.getSymbol());
+ assertEquals("ABREVIATION",species.getAbbreviation());
+ assertEquals("FORMULA",species.getFormula());
+ assertEquals((Integer)324,species.getCharge());
+ assertEquals(1, species.getSynonyms().size());
+ assertTrue(species.getSynonyms().contains("syn44"));
+ assertEquals("DESCRIPTION",species.getNotes());
+
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseReaction() throws Exception {
+ try {
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ Model model = parser.createModel(new ConverterParams().filename("testFiles/annotation/recon_annotation_example.xml"));
+ assertNotNull(model);
+ Reaction reaction = model.getReactionByReactionId("re1");
+ assertNotNull(reaction);
+ assertEquals("SAW",reaction.getSymbol());
+ assertEquals("ABREVIATION2",reaction.getAbbreviation());
+ assertEquals("FORMULA2",reaction.getFormula());
+ assertEquals((Integer)100,reaction.getMechanicalConfidenceScore());
+ assertEquals((Double)200.201,reaction.getLowerBound());
+ assertEquals((Double)300.301,reaction.getUpperBound());
+ assertEquals("SUBSYSTEM2",reaction.getSubsystem());
+ assertEquals("(urn:miriam:ccds:CCDS8639.1) or (urn:miriam:ccds:CCDS26.1) or (urn:miriam:ccds:CCDS314.2) or (urn:miriam:ccds:CCDS314.1)",reaction.getGeneProteinReaction());
+ assertEquals(1, reaction.getSynonyms().size());
+ assertTrue(reaction.getSynonyms().contains("SYN1"));
+ assertEquals("DESCRIPTION2",reaction.getNotes());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParserTest.java
index e5b4e0509e..f5b99e33d9 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParserTest.java
@@ -1,364 +1,364 @@
-package lcsb.mapviewer.converter.model.celldesigner.alias;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.w3c.dom.Node;
-
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGenericProtein;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.compartment.SquareCompartment;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class AliasCollectionXmlParserTest extends CellDesignerTestFunctions {
-
- AliasCollectionXmlParser parser;
- Model model;
- CellDesignerElementCollection elements;
- Logger logger = Logger.getLogger(AliasCollectionXmlParserTest.class.getName());
-
- @Before
- public void setUp() throws Exception {
- model = new ModelFullIndexed(null);
-
- elements = new CellDesignerElementCollection();
-
- parser = new AliasCollectionXmlParser(elements, model);
-
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParseXmlSpeciesAliasCollection() throws Exception {
- try {
- elements.addElement(new CellDesignerGenericProtein("s2594"));
- elements.addElement(new CellDesignerGenericProtein("s2595"));
- elements.addElement(new CellDesignerGenericProtein("s2596"));
- elements.addElement(new CellDesignerGenericProtein("s2506"));
- String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_species_alias_collection.xml");
- Node node = getNodeFromXmlString(xmlString);
- List<Species> list = parser.parseXmlSpeciesAliasCollection(node);
- assertEquals(0, getWarnings().size());
- assertNotNull(list);
- assertEquals(4, list.size());
- Species aliasSa8 = null;
- Species aliasSa9 = null;
- Species aliasSa10 = null;
- Species aliasSa11 = null;
- for (Species alias : list) {
- if (alias.getElementId().equals("sa8"))
- aliasSa8 = alias;
- if (alias.getElementId().equals("sa9"))
- aliasSa9 = alias;
- if (alias.getElementId().equals("sa10"))
- aliasSa10 = alias;
- if (alias.getElementId().equals("sa11"))
- aliasSa11 = alias;
- }
- assertNotNull(aliasSa8);
- assertNotNull(aliasSa9);
- assertNotNull(aliasSa10);
- assertNotNull(aliasSa11);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlSpeciesAliasCollection() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/species_alias_collection.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.parseXmlSpeciesAliasCollection(node);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfSpeciesAliases"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlComplexAliasCollection() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/complex_alias_collection.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.parseXmlComplexAliasCollection(node);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue("Invalid message: " + e.getMessage(),
- e.getMessage().contains("Unknown element of celldesigner:listOfComplexSpeciesAliases"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlCompartmentAliasCollection() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/compartment_alias_collection.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.parseXmlCompartmentAliasCollection(node);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue("Invalid message: " + e.getMessage(),
- e.getMessage().contains("Unknown element of celldesigner:listOfCompartmentAliases"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSpeciesAliasCollectionToXmlString() throws Exception {
- try {
- List<Species> originalLlist = createSpeciesList();
- String xmlString2 = parser.speciesAliasCollectionToXmlString(originalLlist);
- assertNotNull(xmlString2);
-
- for (Species alias : originalLlist) {
- elements.addElement(new CellDesignerGenericProtein(elements.getElementId(alias)));
- }
-
- Node node = getNodeFromXmlString(xmlString2);
- List<Species> list = parser.parseXmlSpeciesAliasCollection(node);
- assertEquals(0, getWarnings().size());
- assertNotNull(list);
- assertEquals(3, list.size());
- for (Species species : originalLlist) {
- boolean found = false;
- for (Species alias : list) {
- if (alias.getElementId().equals(species.getElementId())) {
- found = true;
- }
- }
- assertTrue(found);
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private List<Species> createSpeciesList() {
- List<Species> result = new ArrayList<>();
- result.add(createProtein("sa1"));
- result.add(createProtein("sa2"));
- result.add(createProtein("sa3"));
- return result;
- }
-
- private Species createProtein(String id) {
- GenericProtein protein = new GenericProtein(id);
- protein.setActivity(true);
- protein.setFontSize(4);
- protein.setHeight(10);
- protein.setWidth(20);
- protein.setX(30);
- protein.setY(40);
- protein.setName(id + "name");
- protein.setStateLabel("xxx");
- protein.setStatePrefix("yyy");
- return protein;
- }
-
- @Test
- public void testParseXmlComplexAliasCollection() throws Exception {
- try {
- elements.addElement(new CellDesignerComplexSpecies("s2597"));
- elements.addElement(new CellDesignerComplexSpecies("s2598"));
- elements.addElement(new CellDesignerComplexSpecies("s2599"));
- String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_complex_alias_collection.xml");
- Node node = getNodeFromXmlString(xmlString);
- List<Complex> list = parser.parseXmlComplexAliasCollection(node);
- assertEquals(0, getWarnings().size());
- assertNotNull(list);
- assertEquals(3, list.size());
- Complex aliasSa1 = null;
- Complex aliasSa2 = null;
- Complex aliasSa3 = null;
- for (Complex alias : list) {
- if (alias.getElementId().equals("csa1"))
- aliasSa1 = alias;
- if (alias.getElementId().equals("csa2"))
- aliasSa2 = alias;
- if (alias.getElementId().equals("csa3"))
- aliasSa3 = alias;
- }
- assertNotNull(aliasSa1);
- assertNotNull(aliasSa2);
- assertNotNull(aliasSa3);
-
- } catch (Exception e) {
- throw e;
- }
- }
-
- @Test
- public void testComplexAliasCollectionToXmlString() throws Exception {
- try {
- List<Complex> list = createComplexAliasList();
- String xmlString2 = parser.complexAliasCollectionToXmlString(list);
- assertNotNull(xmlString2);
-
- for (Complex complexAlias : list) {
- elements.addElement(new CellDesignerComplexSpecies(elements.getElementId(complexAlias)));
- }
-
- Node node = getNodeFromXmlString(xmlString2);
- list = parser.parseXmlComplexAliasCollection(node);
- assertEquals(0, getWarnings().size());
- assertNotNull(list);
- assertEquals(3, list.size());
- Complex aliasSa1 = null;
- Complex aliasSa2 = null;
- Complex aliasSa3 = null;
- for (Complex alias : list) {
- if (alias.getElementId().equals("csa1"))
- aliasSa1 = alias;
- if (alias.getElementId().equals("csa2"))
- aliasSa2 = alias;
- if (alias.getElementId().equals("csa3"))
- aliasSa3 = alias;
- }
- assertNotNull(aliasSa1);
- assertNotNull(aliasSa2);
- assertNotNull(aliasSa3);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private List<Complex> createComplexAliasList() {
- List<Complex> result = new ArrayList<>();
- result.add(createComplex("csa1"));
- result.add(createComplex("csa2"));
- result.add(createComplex("csa3"));
- return result;
- }
-
- private Complex createComplex(String id) {
- Complex complex = new Complex(id);
- complex.setFontSize(13.5);
- complex.setHeight(90);
- complex.setWidth(80);
- complex.setName("name_112_" + id);
- complex.setX(32);
- complex.setY(42);
- return complex;
- }
-
- @Test
- public void testParseXmlCompartmentAliasCollection() throws Exception {
- try {
- elements.addElement(new CellDesignerCompartment("c1"));
- elements.addElement(new CellDesignerCompartment("c2"));
- elements.addElement(new CellDesignerCompartment("c3"));
-
- String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_compartment_alias_collection.xml");
- Node node = getNodeFromXmlString(xmlString);
- List<Compartment> list = parser.parseXmlCompartmentAliasCollection(node);
- assertEquals(0, getWarnings().size());
- assertNotNull(list);
- assertEquals(3, list.size());
- Compartment aliasCa1 = null;
- Compartment aliasCa2 = null;
- Compartment aliasCa3 = null;
- for (Compartment alias : list) {
- if (alias.getElementId().equals("ca1"))
- aliasCa1 = alias;
- if (alias.getElementId().equals("ca2"))
- aliasCa2 = alias;
- if (alias.getElementId().equals("ca3"))
- aliasCa3 = alias;
- }
- assertNotNull(aliasCa1);
- assertNotNull(aliasCa2);
- assertNotNull(aliasCa3);
-
- } catch (Exception e) {
- throw e;
- }
- }
-
- @Test
- public void testCompartmentAliasCollectionToXmlString() throws Exception {
- try {
- List<Compartment> originalLlist = createCompartmentList();
- for (Compartment alias : originalLlist) {
- elements.addElement(new CellDesignerCompartment(elements.getElementId(alias)));
- }
-
- String xmlString2 = parser.compartmentAliasCollectionToXmlString(originalLlist);
-
- Node node = getNodeFromXmlString(xmlString2);
- List<Compartment> list = parser.parseXmlCompartmentAliasCollection(node);
- assertEquals(0, getWarnings().size());
-
- assertNotNull(list);
- assertEquals(originalLlist.size(), list.size());
- for (Compartment species : originalLlist) {
- boolean found = false;
- for (Compartment alias : list) {
- if (alias.getElementId().equals(species.getElementId())) {
- found = true;
- }
- }
- assertTrue(found);
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private List<Compartment> createCompartmentList() {
- List<Compartment> result = new ArrayList<>();
- result.add(createCompartment("ca1"));
- result.add(createCompartment("ca2"));
- result.add(createCompartment("ca3"));
- return result;
- }
-
- private Compartment createCompartment(String id) {
- Compartment compartment = new SquareCompartment(id);
- compartment.setName("name" + id);
- compartment.setX(13);
- compartment.setY(14);
- compartment.setWidth(100);
- compartment.setHeight(120);
- compartment.setNamePoint(new Point2D.Double(0, 1));
-
- return compartment;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.alias;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.w3c.dom.Node;
+
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGenericProtein;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.SquareCompartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class AliasCollectionXmlParserTest extends CellDesignerTestFunctions {
+
+ AliasCollectionXmlParser parser;
+ Model model;
+ CellDesignerElementCollection elements;
+ Logger logger = Logger.getLogger(AliasCollectionXmlParserTest.class.getName());
+
+ @Before
+ public void setUp() throws Exception {
+ model = new ModelFullIndexed(null);
+
+ elements = new CellDesignerElementCollection();
+
+ parser = new AliasCollectionXmlParser(elements, model);
+
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testParseXmlSpeciesAliasCollection() throws Exception {
+ try {
+ elements.addElement(new CellDesignerGenericProtein("s2594"));
+ elements.addElement(new CellDesignerGenericProtein("s2595"));
+ elements.addElement(new CellDesignerGenericProtein("s2596"));
+ elements.addElement(new CellDesignerGenericProtein("s2506"));
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_species_alias_collection.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ List<Species> list = parser.parseXmlSpeciesAliasCollection(node);
+ assertEquals(0, getWarnings().size());
+ assertNotNull(list);
+ assertEquals(4, list.size());
+ Species aliasSa8 = null;
+ Species aliasSa9 = null;
+ Species aliasSa10 = null;
+ Species aliasSa11 = null;
+ for (Species alias : list) {
+ if (alias.getElementId().equals("sa8"))
+ aliasSa8 = alias;
+ if (alias.getElementId().equals("sa9"))
+ aliasSa9 = alias;
+ if (alias.getElementId().equals("sa10"))
+ aliasSa10 = alias;
+ if (alias.getElementId().equals("sa11"))
+ aliasSa11 = alias;
+ }
+ assertNotNull(aliasSa8);
+ assertNotNull(aliasSa9);
+ assertNotNull(aliasSa10);
+ assertNotNull(aliasSa11);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlSpeciesAliasCollection() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/species_alias_collection.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.parseXmlSpeciesAliasCollection(node);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfSpeciesAliases"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlComplexAliasCollection() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/complex_alias_collection.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.parseXmlComplexAliasCollection(node);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue("Invalid message: " + e.getMessage(),
+ e.getMessage().contains("Unknown element of celldesigner:listOfComplexSpeciesAliases"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlCompartmentAliasCollection() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/compartment_alias_collection.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.parseXmlCompartmentAliasCollection(node);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue("Invalid message: " + e.getMessage(),
+ e.getMessage().contains("Unknown element of celldesigner:listOfCompartmentAliases"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSpeciesAliasCollectionToXmlString() throws Exception {
+ try {
+ List<Species> originalLlist = createSpeciesList();
+ String xmlString2 = parser.speciesAliasCollectionToXmlString(originalLlist);
+ assertNotNull(xmlString2);
+
+ for (Species alias : originalLlist) {
+ elements.addElement(new CellDesignerGenericProtein(elements.getElementId(alias)));
+ }
+
+ Node node = getNodeFromXmlString(xmlString2);
+ List<Species> list = parser.parseXmlSpeciesAliasCollection(node);
+ assertEquals(0, getWarnings().size());
+ assertNotNull(list);
+ assertEquals(3, list.size());
+ for (Species species : originalLlist) {
+ boolean found = false;
+ for (Species alias : list) {
+ if (alias.getElementId().equals(species.getElementId())) {
+ found = true;
+ }
+ }
+ assertTrue(found);
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private List<Species> createSpeciesList() {
+ List<Species> result = new ArrayList<>();
+ result.add(createProtein("sa1"));
+ result.add(createProtein("sa2"));
+ result.add(createProtein("sa3"));
+ return result;
+ }
+
+ private Species createProtein(String id) {
+ GenericProtein protein = new GenericProtein(id);
+ protein.setActivity(true);
+ protein.setFontSize(4);
+ protein.setHeight(10);
+ protein.setWidth(20);
+ protein.setX(30);
+ protein.setY(40);
+ protein.setName(id + "name");
+ protein.setStateLabel("xxx");
+ protein.setStatePrefix("yyy");
+ return protein;
+ }
+
+ @Test
+ public void testParseXmlComplexAliasCollection() throws Exception {
+ try {
+ elements.addElement(new CellDesignerComplexSpecies("s2597"));
+ elements.addElement(new CellDesignerComplexSpecies("s2598"));
+ elements.addElement(new CellDesignerComplexSpecies("s2599"));
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_complex_alias_collection.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ List<Complex> list = parser.parseXmlComplexAliasCollection(node);
+ assertEquals(0, getWarnings().size());
+ assertNotNull(list);
+ assertEquals(3, list.size());
+ Complex aliasSa1 = null;
+ Complex aliasSa2 = null;
+ Complex aliasSa3 = null;
+ for (Complex alias : list) {
+ if (alias.getElementId().equals("csa1"))
+ aliasSa1 = alias;
+ if (alias.getElementId().equals("csa2"))
+ aliasSa2 = alias;
+ if (alias.getElementId().equals("csa3"))
+ aliasSa3 = alias;
+ }
+ assertNotNull(aliasSa1);
+ assertNotNull(aliasSa2);
+ assertNotNull(aliasSa3);
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ @Test
+ public void testComplexAliasCollectionToXmlString() throws Exception {
+ try {
+ List<Complex> list = createComplexAliasList();
+ String xmlString2 = parser.complexAliasCollectionToXmlString(list);
+ assertNotNull(xmlString2);
+
+ for (Complex complexAlias : list) {
+ elements.addElement(new CellDesignerComplexSpecies(elements.getElementId(complexAlias)));
+ }
+
+ Node node = getNodeFromXmlString(xmlString2);
+ list = parser.parseXmlComplexAliasCollection(node);
+ assertEquals(0, getWarnings().size());
+ assertNotNull(list);
+ assertEquals(3, list.size());
+ Complex aliasSa1 = null;
+ Complex aliasSa2 = null;
+ Complex aliasSa3 = null;
+ for (Complex alias : list) {
+ if (alias.getElementId().equals("csa1"))
+ aliasSa1 = alias;
+ if (alias.getElementId().equals("csa2"))
+ aliasSa2 = alias;
+ if (alias.getElementId().equals("csa3"))
+ aliasSa3 = alias;
+ }
+ assertNotNull(aliasSa1);
+ assertNotNull(aliasSa2);
+ assertNotNull(aliasSa3);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private List<Complex> createComplexAliasList() {
+ List<Complex> result = new ArrayList<>();
+ result.add(createComplex("csa1"));
+ result.add(createComplex("csa2"));
+ result.add(createComplex("csa3"));
+ return result;
+ }
+
+ private Complex createComplex(String id) {
+ Complex complex = new Complex(id);
+ complex.setFontSize(13.5);
+ complex.setHeight(90);
+ complex.setWidth(80);
+ complex.setName("name_112_" + id);
+ complex.setX(32);
+ complex.setY(42);
+ return complex;
+ }
+
+ @Test
+ public void testParseXmlCompartmentAliasCollection() throws Exception {
+ try {
+ elements.addElement(new CellDesignerCompartment("c1"));
+ elements.addElement(new CellDesignerCompartment("c2"));
+ elements.addElement(new CellDesignerCompartment("c3"));
+
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_compartment_alias_collection.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ List<Compartment> list = parser.parseXmlCompartmentAliasCollection(node);
+ assertEquals(0, getWarnings().size());
+ assertNotNull(list);
+ assertEquals(3, list.size());
+ Compartment aliasCa1 = null;
+ Compartment aliasCa2 = null;
+ Compartment aliasCa3 = null;
+ for (Compartment alias : list) {
+ if (alias.getElementId().equals("ca1"))
+ aliasCa1 = alias;
+ if (alias.getElementId().equals("ca2"))
+ aliasCa2 = alias;
+ if (alias.getElementId().equals("ca3"))
+ aliasCa3 = alias;
+ }
+ assertNotNull(aliasCa1);
+ assertNotNull(aliasCa2);
+ assertNotNull(aliasCa3);
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCompartmentAliasCollectionToXmlString() throws Exception {
+ try {
+ List<Compartment> originalLlist = createCompartmentList();
+ for (Compartment alias : originalLlist) {
+ elements.addElement(new CellDesignerCompartment(elements.getElementId(alias)));
+ }
+
+ String xmlString2 = parser.compartmentAliasCollectionToXmlString(originalLlist);
+
+ Node node = getNodeFromXmlString(xmlString2);
+ List<Compartment> list = parser.parseXmlCompartmentAliasCollection(node);
+ assertEquals(0, getWarnings().size());
+
+ assertNotNull(list);
+ assertEquals(originalLlist.size(), list.size());
+ for (Compartment species : originalLlist) {
+ boolean found = false;
+ for (Compartment alias : list) {
+ if (alias.getElementId().equals(species.getElementId())) {
+ found = true;
+ }
+ }
+ assertTrue(found);
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private List<Compartment> createCompartmentList() {
+ List<Compartment> result = new ArrayList<>();
+ result.add(createCompartment("ca1"));
+ result.add(createCompartment("ca2"));
+ result.add(createCompartment("ca3"));
+ return result;
+ }
+
+ private Compartment createCompartment(String id) {
+ Compartment compartment = new SquareCompartment(id);
+ compartment.setName("name" + id);
+ compartment.setX(13);
+ compartment.setY(14);
+ compartment.setWidth(100);
+ compartment.setHeight(120);
+ compartment.setNamePoint(new Point2D.Double(0, 1));
+
+ return compartment;
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/AllAliasTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/AllAliasTests.java
index 3f405d2a18..82cf2ae958 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/AllAliasTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/AllAliasTests.java
@@ -1,14 +1,14 @@
-package lcsb.mapviewer.converter.model.celldesigner.alias;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-
-@RunWith(Suite.class)
-@Suite.SuiteClasses({ AliasCollectionXmlParserTest.class,//
- ComplexAliasXmlParserTest.class,//
- CompartmentAliasXmlParserTest.class,//
- SpeciesAliasXmlParserTest.class, //
-})
-public class AllAliasTests {
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.alias;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+
+@RunWith(Suite.class)
+@Suite.SuiteClasses({ AliasCollectionXmlParserTest.class,//
+ ComplexAliasXmlParserTest.class,//
+ CompartmentAliasXmlParserTest.class,//
+ SpeciesAliasXmlParserTest.class, //
+})
+public class AllAliasTests {
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParserTest.java
index c0b01bb7d8..766d72f297 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParserTest.java
@@ -1,266 +1,266 @@
-package lcsb.mapviewer.converter.model.celldesigner.alias;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.awt.geom.Point2D;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
-import lcsb.mapviewer.model.map.compartment.BottomSquareCompartment;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.compartment.LeftSquareCompartment;
-import lcsb.mapviewer.model.map.compartment.RightSquareCompartment;
-import lcsb.mapviewer.model.map.compartment.SquareCompartment;
-import lcsb.mapviewer.model.map.compartment.TopSquareCompartment;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-
-public class CompartmentAliasXmlParserTest extends CellDesignerTestFunctions {
- static Logger logger = Logger.getLogger(CompartmentAliasXmlParser.class);
-
- CompartmentAliasXmlParser parser;
- Model model;
- CellDesignerElementCollection elements;
-
- @Before
- public void setUp() throws Exception {
- model = new ModelFullIndexed(null);
- elements = new CellDesignerElementCollection();
- parser = new CompartmentAliasXmlParser(elements, model);
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testToXml() throws Exception {
- try {
- Compartment compartment = createCompartment();
- String xmlString = parser.toXml(compartment);
- assertNotNull(xmlString);
-
- elements.addElement(new CellDesignerCompartment(elements.getElementId(compartment)));
-
- Compartment alias2 = parser.parseXmlAlias(xmlString);
- assertEquals(0, getWarnings().size());
-
- assertEquals(compartment.getElementId(), alias2.getElementId());
- assertNotNull(compartment.getName());
- assertEquals(compartment.getFontSize(), alias2.getFontSize(), 1e-6);
- assertEquals(compartment.getHeight(), alias2.getHeight(), 1e-6);
- assertEquals(compartment.getWidth(), alias2.getWidth(), 1e-6);
- assertEquals(compartment.getX(), alias2.getX(), 1e-6);
- assertEquals(compartment.getY(), alias2.getY(), 1e-6);
- assertEquals(compartment.getNamePoint().getX(), alias2.getNamePoint().getX(), 1e-6);
- assertEquals(compartment.getNamePoint().getY(), alias2.getNamePoint().getY(), 1e-6);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private Compartment createCompartment() {
- Compartment compartment = new SquareCompartment("comp_id");
- compartment.setName("name");
- compartment.setX(13);
- compartment.setY(14);
- compartment.setWidth(100);
- compartment.setHeight(120);
- compartment.setNamePoint(new Point2D.Double(0, 1));
-
- return compartment;
- }
-
- @Test
- public void parseInvalidAlias() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
- parser = new CompartmentAliasXmlParser(elements, model);
- String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_compartment_alias.xml");
- parser.parseXmlAlias(xmlString);
- fail("Exception expceted");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Compartment does not exist in a model"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void parseInvalidAlias2() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
- CellDesignerCompartment comp = new CellDesignerCompartment();
- comp.setElementId("c1");
- elements.addElement(comp);
- parser = new CompartmentAliasXmlParser(elements, model);
- String xmlString = readFile("testFiles/invalid/compartment_alias.xml");
- parser.parseXmlAlias(xmlString);
- fail("Exception expceted");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown compartment type"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void parseInvalidAlias3() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
- CellDesignerCompartment comp = new CellDesignerCompartment();
- comp.setElementId("c1");
- elements.addElement(comp);
- parser = new CompartmentAliasXmlParser(elements, model);
- String xmlString = readFile("testFiles/invalid/compartment_alias2.xml");
- parser.parseXmlAlias(xmlString);
- fail("Exception expceted");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Don't know what to do with celldesigner:point for class"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void parseInvalidAlias4() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
- CellDesignerCompartment comp = new CellDesignerCompartment();
- comp.setElementId("c1");
- elements.addElement(comp);
- parser = new CompartmentAliasXmlParser(elements, model);
- String xmlString = readFile("testFiles/invalid/compartment_alias3.xml");
- parser.parseXmlAlias(xmlString);
- fail("Exception expceted");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:compartmentAlias"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlAliasNode() throws Exception {
- try {
- elements.addElement(new CellDesignerCompartment("c1"));
-
- String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_compartment_alias.xml");
- Compartment alias = (Compartment) parser.parseXmlAlias(xmlString);
- assertEquals(0, getWarnings().size());
- assertNotNull(alias);
- assertEquals("ca1", alias.getElementId());
- assertNotNull(alias.getName());
- assertTrue(alias instanceof SquareCompartment);
- assertEquals(139.0, alias.getX(), 1e-6);
- assertEquals(55.0, alias.getY(), 1e-6);
- assertEquals(522.0, alias.getWidth(), 1e-6);
- assertEquals(392.5, alias.getNamePoint().getX(), 1e-6);
- assertEquals(196.5, alias.getNamePoint().getY(), 1e-6);
- assertEquals(0xffcccc00, alias.getColor().getRGB());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- parser.setCommonParser(null);
-
- assertNull(parser.getCommonParser());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testLeftToXml() throws Exception {
- try {
- Compartment alias = new LeftSquareCompartment("id");
- String xml = parser.toXml(alias);
- assertNotNull(xml);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testRightToXml() throws Exception {
- try {
- Compartment alias = new RightSquareCompartment("id");
- String xml = parser.toXml(alias);
- assertNotNull(xml);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testTopToXml() throws Exception {
- try {
- Compartment alias = new TopSquareCompartment("id");
- String xml = parser.toXml(alias);
- assertNotNull(xml);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testBotttomToXml() throws Exception {
- try {
- Compartment alias = new BottomSquareCompartment("id");
- String xml = parser.toXml(alias);
- assertNotNull(xml);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testUnknownToXml() throws Exception {
- try {
- Compartment alias = Mockito.mock(BottomSquareCompartment.class);
- Mockito.when(alias.getElementId()).thenReturn("some id");
- parser.toXml(alias);
- fail("Exception expected");
- } catch (NotImplementedException e) {
- assertTrue(e.getMessage().contains("Unknown compartment class"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.alias;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.awt.geom.Point2D;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
+import lcsb.mapviewer.model.map.compartment.BottomSquareCompartment;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.LeftSquareCompartment;
+import lcsb.mapviewer.model.map.compartment.RightSquareCompartment;
+import lcsb.mapviewer.model.map.compartment.SquareCompartment;
+import lcsb.mapviewer.model.map.compartment.TopSquareCompartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+
+public class CompartmentAliasXmlParserTest extends CellDesignerTestFunctions {
+ static Logger logger = Logger.getLogger(CompartmentAliasXmlParser.class);
+
+ CompartmentAliasXmlParser parser;
+ Model model;
+ CellDesignerElementCollection elements;
+
+ @Before
+ public void setUp() throws Exception {
+ model = new ModelFullIndexed(null);
+ elements = new CellDesignerElementCollection();
+ parser = new CompartmentAliasXmlParser(elements, model);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testToXml() throws Exception {
+ try {
+ Compartment compartment = createCompartment();
+ String xmlString = parser.toXml(compartment);
+ assertNotNull(xmlString);
+
+ elements.addElement(new CellDesignerCompartment(elements.getElementId(compartment)));
+
+ Compartment alias2 = parser.parseXmlAlias(xmlString);
+ assertEquals(0, getWarnings().size());
+
+ assertEquals(compartment.getElementId(), alias2.getElementId());
+ assertNotNull(compartment.getName());
+ assertEquals(compartment.getFontSize(), alias2.getFontSize(), 1e-6);
+ assertEquals(compartment.getHeight(), alias2.getHeight(), 1e-6);
+ assertEquals(compartment.getWidth(), alias2.getWidth(), 1e-6);
+ assertEquals(compartment.getX(), alias2.getX(), 1e-6);
+ assertEquals(compartment.getY(), alias2.getY(), 1e-6);
+ assertEquals(compartment.getNamePoint().getX(), alias2.getNamePoint().getX(), 1e-6);
+ assertEquals(compartment.getNamePoint().getY(), alias2.getNamePoint().getY(), 1e-6);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Compartment createCompartment() {
+ Compartment compartment = new SquareCompartment("comp_id");
+ compartment.setName("name");
+ compartment.setX(13);
+ compartment.setY(14);
+ compartment.setWidth(100);
+ compartment.setHeight(120);
+ compartment.setNamePoint(new Point2D.Double(0, 1));
+
+ return compartment;
+ }
+
+ @Test
+ public void parseInvalidAlias() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+ parser = new CompartmentAliasXmlParser(elements, model);
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_compartment_alias.xml");
+ parser.parseXmlAlias(xmlString);
+ fail("Exception expceted");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Compartment does not exist in a model"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void parseInvalidAlias2() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+ CellDesignerCompartment comp = new CellDesignerCompartment();
+ comp.setElementId("c1");
+ elements.addElement(comp);
+ parser = new CompartmentAliasXmlParser(elements, model);
+ String xmlString = readFile("testFiles/invalid/compartment_alias.xml");
+ parser.parseXmlAlias(xmlString);
+ fail("Exception expceted");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown compartment type"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void parseInvalidAlias3() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+ CellDesignerCompartment comp = new CellDesignerCompartment();
+ comp.setElementId("c1");
+ elements.addElement(comp);
+ parser = new CompartmentAliasXmlParser(elements, model);
+ String xmlString = readFile("testFiles/invalid/compartment_alias2.xml");
+ parser.parseXmlAlias(xmlString);
+ fail("Exception expceted");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do with celldesigner:point for class"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void parseInvalidAlias4() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+ CellDesignerCompartment comp = new CellDesignerCompartment();
+ comp.setElementId("c1");
+ elements.addElement(comp);
+ parser = new CompartmentAliasXmlParser(elements, model);
+ String xmlString = readFile("testFiles/invalid/compartment_alias3.xml");
+ parser.parseXmlAlias(xmlString);
+ fail("Exception expceted");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:compartmentAlias"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlAliasNode() throws Exception {
+ try {
+ elements.addElement(new CellDesignerCompartment("c1"));
+
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_compartment_alias.xml");
+ Compartment alias = (Compartment) parser.parseXmlAlias(xmlString);
+ assertEquals(0, getWarnings().size());
+ assertNotNull(alias);
+ assertEquals("ca1", alias.getElementId());
+ assertNotNull(alias.getName());
+ assertTrue(alias instanceof SquareCompartment);
+ assertEquals(139.0, alias.getX(), 1e-6);
+ assertEquals(55.0, alias.getY(), 1e-6);
+ assertEquals(522.0, alias.getWidth(), 1e-6);
+ assertEquals(392.5, alias.getNamePoint().getX(), 1e-6);
+ assertEquals(196.5, alias.getNamePoint().getY(), 1e-6);
+ assertEquals(0xffcccc00, alias.getColor().getRGB());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ parser.setCommonParser(null);
+
+ assertNull(parser.getCommonParser());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testLeftToXml() throws Exception {
+ try {
+ Compartment alias = new LeftSquareCompartment("id");
+ String xml = parser.toXml(alias);
+ assertNotNull(xml);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testRightToXml() throws Exception {
+ try {
+ Compartment alias = new RightSquareCompartment("id");
+ String xml = parser.toXml(alias);
+ assertNotNull(xml);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testTopToXml() throws Exception {
+ try {
+ Compartment alias = new TopSquareCompartment("id");
+ String xml = parser.toXml(alias);
+ assertNotNull(xml);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testBotttomToXml() throws Exception {
+ try {
+ Compartment alias = new BottomSquareCompartment("id");
+ String xml = parser.toXml(alias);
+ assertNotNull(xml);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testUnknownToXml() throws Exception {
+ try {
+ Compartment alias = Mockito.mock(BottomSquareCompartment.class);
+ Mockito.when(alias.getElementId()).thenReturn("some id");
+ parser.toXml(alias);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ assertTrue(e.getMessage().contains("Unknown compartment class"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParserTest.java
index 2864a26ee2..9fc8216003 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParserTest.java
@@ -1,89 +1,89 @@
-package lcsb.mapviewer.converter.model.celldesigner.alias;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.Complex;
-
-public class ComplexAliasXmlParserTest extends CellDesignerTestFunctions {
- Model model;
- private ComplexAliasXmlParser parser;
- CellDesignerElementCollection elements;
-
- @Before
- public void setUp() throws Exception {
- model = new ModelFullIndexed(null);
- elements = new CellDesignerElementCollection();
- parser = new ComplexAliasXmlParser(elements, model);
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testToXml() throws Exception {
- try {
- Complex complex = createComplex();
- String xmlString = parser.toXml(complex);
- assertNotNull(xmlString);
-
- elements.addElement(new CellDesignerComplexSpecies(elements.getElementId(complex)));
- Complex complexFromXml = parser.parseXmlAlias(xmlString);
- assertEquals(0, getWarnings().size());
-
- assertEquals(complex.getElementId(), complexFromXml.getElementId());
- assertNotNull(complex.getName());
- assertEquals(complex.getFontSize(), complexFromXml.getFontSize(), Configuration.EPSILON);
- assertEquals(complex.getHeight(), complexFromXml.getHeight(), Configuration.EPSILON);
- assertEquals(complex.getWidth(), complexFromXml.getWidth(), Configuration.EPSILON);
- assertEquals(complex.getX(), complexFromXml.getX(), Configuration.EPSILON);
- assertEquals(complex.getY(), complexFromXml.getY(), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private Complex createComplex() {
- Complex complex = new Complex("id");
- complex.setFontSize(13.5);
- complex.setHeight(90);
- complex.setWidth(80);
- complex.setName("112");
- complex.setX(32);
- complex.setY(42);
- return complex;
- }
-
- @Test
- public void testParseXmlAliasNode() throws Exception {
- try {
- elements.addElement(new CellDesignerComplexSpecies("s2597"));
-
- String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_complex_alias.xml");
- Complex alias = (Complex) parser.parseXmlAlias(xmlString);
- assertEquals(0, getWarnings().size());
- assertEquals(false, alias.getActivity());
- assertEquals("csa1", alias.getElementId());
- assertEquals(12.0, alias.getFontSize(), Configuration.EPSILON);
- assertEquals(120.0, alias.getHeight(), Configuration.EPSILON);
- assertEquals(100.0, alias.getWidth(), Configuration.EPSILON);
- assertEquals(744.0, alias.getX(), Configuration.EPSILON);
- assertEquals(0.0, alias.getY(), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.alias;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Complex;
+
+public class ComplexAliasXmlParserTest extends CellDesignerTestFunctions {
+ Model model;
+ private ComplexAliasXmlParser parser;
+ CellDesignerElementCollection elements;
+
+ @Before
+ public void setUp() throws Exception {
+ model = new ModelFullIndexed(null);
+ elements = new CellDesignerElementCollection();
+ parser = new ComplexAliasXmlParser(elements, model);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testToXml() throws Exception {
+ try {
+ Complex complex = createComplex();
+ String xmlString = parser.toXml(complex);
+ assertNotNull(xmlString);
+
+ elements.addElement(new CellDesignerComplexSpecies(elements.getElementId(complex)));
+ Complex complexFromXml = parser.parseXmlAlias(xmlString);
+ assertEquals(0, getWarnings().size());
+
+ assertEquals(complex.getElementId(), complexFromXml.getElementId());
+ assertNotNull(complex.getName());
+ assertEquals(complex.getFontSize(), complexFromXml.getFontSize(), Configuration.EPSILON);
+ assertEquals(complex.getHeight(), complexFromXml.getHeight(), Configuration.EPSILON);
+ assertEquals(complex.getWidth(), complexFromXml.getWidth(), Configuration.EPSILON);
+ assertEquals(complex.getX(), complexFromXml.getX(), Configuration.EPSILON);
+ assertEquals(complex.getY(), complexFromXml.getY(), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Complex createComplex() {
+ Complex complex = new Complex("id");
+ complex.setFontSize(13.5);
+ complex.setHeight(90);
+ complex.setWidth(80);
+ complex.setName("112");
+ complex.setX(32);
+ complex.setY(42);
+ return complex;
+ }
+
+ @Test
+ public void testParseXmlAliasNode() throws Exception {
+ try {
+ elements.addElement(new CellDesignerComplexSpecies("s2597"));
+
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_complex_alias.xml");
+ Complex alias = (Complex) parser.parseXmlAlias(xmlString);
+ assertEquals(0, getWarnings().size());
+ assertEquals(false, alias.getActivity());
+ assertEquals("csa1", alias.getElementId());
+ assertEquals(12.0, alias.getFontSize(), Configuration.EPSILON);
+ assertEquals(120.0, alias.getHeight(), Configuration.EPSILON);
+ assertEquals(100.0, alias.getWidth(), Configuration.EPSILON);
+ assertEquals(744.0, alias.getX(), Configuration.EPSILON);
+ assertEquals(0.0, alias.getY(), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParserTest.java
index 64bacf8376..392170407b 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParserTest.java
@@ -1,336 +1,336 @@
-package lcsb.mapviewer.converter.model.celldesigner.alias;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-import static org.mockito.Mockito.when;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGenericProtein;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class SpeciesAliasXmlParserTest extends CellDesignerTestFunctions {
- static Logger logger = Logger.getLogger(SpeciesAliasXmlParser.class);
-
- Model model;
- private SpeciesAliasXmlParser parser;
-
- private String testCompartmentAliasId2 = "s3";
- private String testCompartmentAliasId = "s4";
- private String testSpeciesId = "s5";
- private String testAliasId = "s6";
- CellDesignerElementCollection elements;
-
- @Before
- public void setUp() throws Exception {
- elements = new CellDesignerElementCollection();
-
- model = createStubModel();
-
- CellDesignerGenericProtein species = new CellDesignerGenericProtein();
- species.setElementId("s78");
- elements.addElement(species);
-
- parser = new SpeciesAliasXmlParser(elements, model);
- }
-
- private Model createStubModel() {
- Model model = new ModelFullIndexed(null);
- model.addElement(new Compartment("ca1"));
- return model;
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParseXmlAliasNode() throws Exception {
- try {
- String xmlString = readFile("testFiles/xmlNodeTestExamples/species_alias.xml");
- Species alias = parser.parseXmlAlias(xmlString);
- assertEquals(0, getWarnings().size());
- assertEquals(false, alias.getActivity());
- assertEquals("sa36", alias.getElementId());
- assertEquals(16.0, alias.getFontSize(), 1e-6);
- assertEquals(25.0, alias.getHeight(), 1e-6);
- assertEquals(80, alias.getWidth(), 1e-6);
- assertEquals(11813.0, alias.getX(), 1e-6);
- assertEquals(2840.5, alias.getY(), 1e-6);
- assertEquals("ca1", alias.getCompartment().getElementId());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlAliasFont() throws Exception {
- try {
- String xmlString = readFile("testFiles/xmlNodeTestExamples/species_alias_with_font.xml");
- Species alias = parser.parseXmlAlias(xmlString);
- assertEquals(30.0, alias.getFontSize(), 1e-6);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXml() throws Exception {
- try {
- Model model2 = createStubModel();
- Species protein = createProtein();
- protein.setCompartment(model2.getCompartments().iterator().next());
- elements.addElement(new CellDesignerGenericProtein(elements.getElementId(protein)));
- String xmlString = parser.toXml(protein);
-
- parser = new SpeciesAliasXmlParser(elements, model2);
- Species alias2 = parser.parseXmlAlias(xmlString);
- assertEquals(0, getWarnings().size());
-
- assertEquals(protein.getActivity(), alias2.getActivity());
- assertEquals(protein.getElementId(), alias2.getElementId());
- assertEquals(protein.getFontSize(), alias2.getFontSize(), 1e-6);
- assertEquals(protein.getHeight(), alias2.getHeight(), 1e-6);
- assertEquals(protein.getWidth(), alias2.getWidth(), 1e-6);
- assertEquals(protein.getX(), alias2.getX(), 1e-6);
- assertEquals(protein.getY(), alias2.getY(), 1e-6);
- assertEquals(protein.getCompartment().getElementId(), alias2.getCompartment().getElementId());
- assertEquals("Alias state label different", protein.getStateLabel(), alias2.getStateLabel());
- assertEquals("Alias state prefix different", protein.getStatePrefix(), alias2.getStatePrefix());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private Species createProtein() {
- GenericProtein protein = new GenericProtein("id");
- protein.setActivity(true);
- protein.setFontSize(4);
- protein.setHeight(10);
- protein.setWidth(20);
- protein.setX(30);
- protein.setY(40);
- protein.setStateLabel("xxx");
- protein.setStatePrefix("yyy");
- return protein;
- }
-
- @Test
- public void testToXmlAliasWithStateNode() throws Exception {
- try {
- Model model = createStubModel();
- Species protein = createProtein();
- protein.setState("sssstate");
- protein.setCompartment(model.getCompartments().iterator().next());
- elements.addElement(new CellDesignerGenericProtein(elements.getElementId(protein)));
- String xmlString = parser.toXml(protein);
-
- Species alias2 = parser.parseXmlAlias(xmlString);
- assertEquals(0, getWarnings().size());
-
- assertEquals("Alias state label different", protein.getStateLabel(), alias2.getStateLabel());
- assertEquals("Alias state prefix different", protein.getStatePrefix(), alias2.getStatePrefix());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlAliasWithStateNode() throws Exception {
- try {
- String xmlString = readFile("testFiles/xmlNodeTestExamples/species_alias_with_state.xml");
- Species alias = parser.parseXmlAlias(xmlString);
- assertEquals(0, getWarnings().size());
- assertNotNull(alias);
- assertEquals("test", alias.getStateLabel());
- assertEquals("free input", alias.getStatePrefix());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlAliasWithoutStateNode() throws Exception {
- try {
- String xmlString = readFile("testFiles/xmlNodeTestExamples/species_alias_without_state.xml");
- Species alias = parser.parseXmlAlias(xmlString);
- assertEquals(0, getWarnings().size());
- assertNotNull(alias);
- assertNull(alias.getStateLabel());
- assertNull(alias.getStatePrefix());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlAliasNode() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/species_alias.xml");
- parser.parseXmlAlias(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown species for alias"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlAliasNode2() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/species_alias2.xml");
- parser.parseXmlAlias(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:speciesAlias"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlAliasNode3() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/species_alias3.xml");
- parser.parseXmlAlias(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("No view in Alias"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlAliasNode4() throws Exception {
- try {
- parser = new SpeciesAliasXmlParser(elements, model);
-
- String xmlString = readFile("testFiles/invalid/species_alias4.xml");
- parser.parseXmlAlias(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("CompartmentAlias does not exist"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlAliasNode5() throws Exception {
- try {
- parser = new SpeciesAliasXmlParser(elements, model);
-
- String xmlString = readFile("testFiles/invalid/species_alias5.xml");
- parser.parseXmlAlias(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("ComplexAlias does not exist"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlAliasNode6() throws Exception {
- try {
- parser = new SpeciesAliasXmlParser(elements, model);
-
- String xmlString = readFile("testFiles/invalid/species_alias6.xml");
- parser.parseXmlAlias(xmlString);
- fail("Exception expected");
- } catch (NotImplementedException e) {
- assertTrue(e.getMessage().contains("Unkown alias state"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlWithUnknownCompartment() throws Exception {
- try {
- Model model = Mockito.mock(ModelFullIndexed.class);
- ModelData md = new ModelData();
- md.setModel(model);
-
- Compartment ca2 = new Compartment(testCompartmentAliasId2);
- ca2.setElementId(testCompartmentAliasId2);
- ca2.setX(6);
- ca2.setY(6);
- ca2.setWidth(190);
- ca2.setHeight(190);
-
- Compartment ca = new Compartment(testCompartmentAliasId);
- ca.setElementId(testCompartmentAliasId);
- ca.setX(5);
- ca.setY(5);
- ca.setWidth(200);
- ca.setHeight(200);
-
- List<Compartment> list = new ArrayList<>();
- list.add(ca);
- list.add(ca2);
-
- // ensure that we return list (firts bigger compartment, then smaller)
- when(model.getCompartments()).thenReturn(list);
- when(model.getModelData()).thenReturn(md);
-
- Species alias = new Complex(testAliasId);
- alias.setX(10);
- alias.setY(10);
- alias.setWidth(100);
- alias.setHeight(100);
- alias.setModel(model);
- alias.setActivity(true);
-
- elements.addElement(new CellDesignerComplexSpecies(testSpeciesId));
- model.addElement(alias);
- SpeciesAliasXmlParser parser = new SpeciesAliasXmlParser(elements, model);
-
- String xml = parser.toXml(alias);
-
- assertTrue(xml.contains(testAliasId));
- assertTrue(xml.contains(testCompartmentAliasId2));
- assertTrue(xml.contains("<celldesigner:activity>active</celldesigner:activity>"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.alias;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import static org.mockito.Mockito.when;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGenericProtein;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class SpeciesAliasXmlParserTest extends CellDesignerTestFunctions {
+ static Logger logger = Logger.getLogger(SpeciesAliasXmlParser.class);
+
+ Model model;
+ private SpeciesAliasXmlParser parser;
+
+ private String testCompartmentAliasId2 = "s3";
+ private String testCompartmentAliasId = "s4";
+ private String testSpeciesId = "s5";
+ private String testAliasId = "s6";
+ CellDesignerElementCollection elements;
+
+ @Before
+ public void setUp() throws Exception {
+ elements = new CellDesignerElementCollection();
+
+ model = createStubModel();
+
+ CellDesignerGenericProtein species = new CellDesignerGenericProtein();
+ species.setElementId("s78");
+ elements.addElement(species);
+
+ parser = new SpeciesAliasXmlParser(elements, model);
+ }
+
+ private Model createStubModel() {
+ Model model = new ModelFullIndexed(null);
+ model.addElement(new Compartment("ca1"));
+ return model;
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testParseXmlAliasNode() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/species_alias.xml");
+ Species alias = parser.parseXmlAlias(xmlString);
+ assertEquals(0, getWarnings().size());
+ assertEquals(false, alias.getActivity());
+ assertEquals("sa36", alias.getElementId());
+ assertEquals(16.0, alias.getFontSize(), 1e-6);
+ assertEquals(25.0, alias.getHeight(), 1e-6);
+ assertEquals(80, alias.getWidth(), 1e-6);
+ assertEquals(11813.0, alias.getX(), 1e-6);
+ assertEquals(2840.5, alias.getY(), 1e-6);
+ assertEquals("ca1", alias.getCompartment().getElementId());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlAliasFont() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/species_alias_with_font.xml");
+ Species alias = parser.parseXmlAlias(xmlString);
+ assertEquals(30.0, alias.getFontSize(), 1e-6);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXml() throws Exception {
+ try {
+ Model model2 = createStubModel();
+ Species protein = createProtein();
+ protein.setCompartment(model2.getCompartments().iterator().next());
+ elements.addElement(new CellDesignerGenericProtein(elements.getElementId(protein)));
+ String xmlString = parser.toXml(protein);
+
+ parser = new SpeciesAliasXmlParser(elements, model2);
+ Species alias2 = parser.parseXmlAlias(xmlString);
+ assertEquals(0, getWarnings().size());
+
+ assertEquals(protein.getActivity(), alias2.getActivity());
+ assertEquals(protein.getElementId(), alias2.getElementId());
+ assertEquals(protein.getFontSize(), alias2.getFontSize(), 1e-6);
+ assertEquals(protein.getHeight(), alias2.getHeight(), 1e-6);
+ assertEquals(protein.getWidth(), alias2.getWidth(), 1e-6);
+ assertEquals(protein.getX(), alias2.getX(), 1e-6);
+ assertEquals(protein.getY(), alias2.getY(), 1e-6);
+ assertEquals(protein.getCompartment().getElementId(), alias2.getCompartment().getElementId());
+ assertEquals("Alias state label different", protein.getStateLabel(), alias2.getStateLabel());
+ assertEquals("Alias state prefix different", protein.getStatePrefix(), alias2.getStatePrefix());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Species createProtein() {
+ GenericProtein protein = new GenericProtein("id");
+ protein.setActivity(true);
+ protein.setFontSize(4);
+ protein.setHeight(10);
+ protein.setWidth(20);
+ protein.setX(30);
+ protein.setY(40);
+ protein.setStateLabel("xxx");
+ protein.setStatePrefix("yyy");
+ return protein;
+ }
+
+ @Test
+ public void testToXmlAliasWithStateNode() throws Exception {
+ try {
+ Model model = createStubModel();
+ Species protein = createProtein();
+ protein.setState("sssstate");
+ protein.setCompartment(model.getCompartments().iterator().next());
+ elements.addElement(new CellDesignerGenericProtein(elements.getElementId(protein)));
+ String xmlString = parser.toXml(protein);
+
+ Species alias2 = parser.parseXmlAlias(xmlString);
+ assertEquals(0, getWarnings().size());
+
+ assertEquals("Alias state label different", protein.getStateLabel(), alias2.getStateLabel());
+ assertEquals("Alias state prefix different", protein.getStatePrefix(), alias2.getStatePrefix());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlAliasWithStateNode() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/species_alias_with_state.xml");
+ Species alias = parser.parseXmlAlias(xmlString);
+ assertEquals(0, getWarnings().size());
+ assertNotNull(alias);
+ assertEquals("test", alias.getStateLabel());
+ assertEquals("free input", alias.getStatePrefix());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlAliasWithoutStateNode() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/species_alias_without_state.xml");
+ Species alias = parser.parseXmlAlias(xmlString);
+ assertEquals(0, getWarnings().size());
+ assertNotNull(alias);
+ assertNull(alias.getStateLabel());
+ assertNull(alias.getStatePrefix());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlAliasNode() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/species_alias.xml");
+ parser.parseXmlAlias(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown species for alias"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlAliasNode2() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/species_alias2.xml");
+ parser.parseXmlAlias(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:speciesAlias"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlAliasNode3() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/species_alias3.xml");
+ parser.parseXmlAlias(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("No view in Alias"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlAliasNode4() throws Exception {
+ try {
+ parser = new SpeciesAliasXmlParser(elements, model);
+
+ String xmlString = readFile("testFiles/invalid/species_alias4.xml");
+ parser.parseXmlAlias(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("CompartmentAlias does not exist"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlAliasNode5() throws Exception {
+ try {
+ parser = new SpeciesAliasXmlParser(elements, model);
+
+ String xmlString = readFile("testFiles/invalid/species_alias5.xml");
+ parser.parseXmlAlias(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("ComplexAlias does not exist"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlAliasNode6() throws Exception {
+ try {
+ parser = new SpeciesAliasXmlParser(elements, model);
+
+ String xmlString = readFile("testFiles/invalid/species_alias6.xml");
+ parser.parseXmlAlias(xmlString);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ assertTrue(e.getMessage().contains("Unkown alias state"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlWithUnknownCompartment() throws Exception {
+ try {
+ Model model = Mockito.mock(ModelFullIndexed.class);
+ ModelData md = new ModelData();
+ md.setModel(model);
+
+ Compartment ca2 = new Compartment(testCompartmentAliasId2);
+ ca2.setElementId(testCompartmentAliasId2);
+ ca2.setX(6);
+ ca2.setY(6);
+ ca2.setWidth(190);
+ ca2.setHeight(190);
+
+ Compartment ca = new Compartment(testCompartmentAliasId);
+ ca.setElementId(testCompartmentAliasId);
+ ca.setX(5);
+ ca.setY(5);
+ ca.setWidth(200);
+ ca.setHeight(200);
+
+ List<Compartment> list = new ArrayList<>();
+ list.add(ca);
+ list.add(ca2);
+
+ // ensure that we return list (firts bigger compartment, then smaller)
+ when(model.getCompartments()).thenReturn(list);
+ when(model.getModelData()).thenReturn(md);
+
+ Species alias = new Complex(testAliasId);
+ alias.setX(10);
+ alias.setY(10);
+ alias.setWidth(100);
+ alias.setHeight(100);
+ alias.setModel(model);
+ alias.setActivity(true);
+
+ elements.addElement(new CellDesignerComplexSpecies(testSpeciesId));
+ model.addElement(alias);
+ SpeciesAliasXmlParser parser = new SpeciesAliasXmlParser(elements, model);
+
+ String xml = parser.toXml(alias);
+
+ assertTrue(xml.contains(testAliasId));
+ assertTrue(xml.contains(testCompartmentAliasId2));
+ assertTrue(xml.contains("<celldesigner:activity>active</celldesigner:activity>"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/AllAnnotationTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/AllAnnotationTests.java
index 21ab5296be..38b590fa33 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/AllAnnotationTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/AllAnnotationTests.java
@@ -1,13 +1,13 @@
-package lcsb.mapviewer.converter.model.celldesigner.annotation;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ NoteFieldTest.class, //
- RestAnnotationParserTest.class, //
-})
-public class AllAnnotationTests {
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.annotation;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ NoteFieldTest.class, //
+ RestAnnotationParserTest.class, //
+})
+public class AllAnnotationTests {
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteFieldTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteFieldTest.java
index f29d697413..1d4244c0d4 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteFieldTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteFieldTest.java
@@ -1,32 +1,32 @@
-package lcsb.mapviewer.converter.model.celldesigner.annotation;
-
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class NoteFieldTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testVallues() {
- for (NoteField field : NoteField.values()) {
- assertNotNull(NoteField.valueOf(field.toString()));
- assertNotNull(field.getClazz());
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.annotation;
+
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class NoteFieldTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testVallues() {
+ for (NoteField field : NoteField.values()) {
+ assertNotNull(NoteField.valueOf(field.toString()));
+ assertNotNull(field.getClazz());
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/AllCompartmentTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/AllCompartmentTests.java
index 79a9a71bca..800262bfab 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/AllCompartmentTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/AllCompartmentTests.java
@@ -1,14 +1,14 @@
-package lcsb.mapviewer.converter.model.celldesigner.compartment;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ CompartmentCollectionXmlParserTest.class,//
- CompartmentParserTests.class,//
- CompartmentXmlParserTest.class,//
-})
-public class AllCompartmentTests {
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.compartment;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ CompartmentCollectionXmlParserTest.class,//
+ CompartmentParserTests.class,//
+ CompartmentXmlParserTest.class,//
+})
+public class AllCompartmentTests {
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParserTest.java
index 557b7924ea..c8964895b9 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParserTest.java
@@ -1,108 +1,108 @@
-package lcsb.mapviewer.converter.model.celldesigner.compartment;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.w3c.dom.Node;
-
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-
-public class CompartmentCollectionXmlParserTest extends CellDesignerTestFunctions {
- static Logger logger = Logger.getLogger(CompartmentCollectionXmlParserTest.class);
-
- int aliasIdCounter = 0;
-
- CompartmentCollectionXmlParser parser;
- CellDesignerElementCollection elements;
-
- @Before
- public void setUp() throws Exception {
- elements = new CellDesignerElementCollection();
- parser = new CompartmentCollectionXmlParser(elements);
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParseXmlReactionCollection() throws Exception {
- try {
-
- String xmlString = readFile("testFiles/compartment/listOfCompartments.xml");
- Node node = getNodeFromXmlString(xmlString);
- List<CellDesignerCompartment> compartments = parser.parseXmlCompartmentCollection(node);
-
- assertEquals(4, compartments.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlReactionCollection() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/listOfCompartments.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.parseXmlCompartmentCollection(node);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of model/listOfCompartments:"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCompartmentCollectionToXmlString() throws Exception {
- try {
-
- String xmlString = readFile("testFiles/compartment/listOfCompartments.xml");
- Node node = getNodeFromXmlString(xmlString);
- List<CellDesignerCompartment> cellDesignerCompartments = parser.parseXmlCompartmentCollection(node);
-
- List<Compartment> compartments = new ArrayList<>();
- for (CellDesignerCompartment cellDesignerCompartment : cellDesignerCompartments) {
- Compartment comp =cellDesignerCompartment.createModelElement("ca" + aliasIdCounter);
- compartments.add(comp);
- aliasIdCounter++;
- }
-
- String xmlString2 = parser.toXml(compartments);
- assertNotNull(xmlString2);
-
- node = getNodeFromXmlString(xmlString2);
-
- elements = new CellDesignerElementCollection();
- parser = new CompartmentCollectionXmlParser(elements);
-
- List<CellDesignerCompartment> compartments2 = parser.parseXmlCompartmentCollection(node);
- for (int i = 0; i < cellDesignerCompartments.size(); i++) {
- CellDesignerCompartment compartmentA = cellDesignerCompartments.get(i);
- CellDesignerCompartment compartmentB = compartments2.get(i);
- assertEquals(compartmentA.getName(), compartmentB.getName());
- }
-
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.compartment;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.w3c.dom.Node;
+
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+
+public class CompartmentCollectionXmlParserTest extends CellDesignerTestFunctions {
+ static Logger logger = Logger.getLogger(CompartmentCollectionXmlParserTest.class);
+
+ int aliasIdCounter = 0;
+
+ CompartmentCollectionXmlParser parser;
+ CellDesignerElementCollection elements;
+
+ @Before
+ public void setUp() throws Exception {
+ elements = new CellDesignerElementCollection();
+ parser = new CompartmentCollectionXmlParser(elements);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testParseXmlReactionCollection() throws Exception {
+ try {
+
+ String xmlString = readFile("testFiles/compartment/listOfCompartments.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ List<CellDesignerCompartment> compartments = parser.parseXmlCompartmentCollection(node);
+
+ assertEquals(4, compartments.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlReactionCollection() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/listOfCompartments.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.parseXmlCompartmentCollection(node);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of model/listOfCompartments:"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCompartmentCollectionToXmlString() throws Exception {
+ try {
+
+ String xmlString = readFile("testFiles/compartment/listOfCompartments.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ List<CellDesignerCompartment> cellDesignerCompartments = parser.parseXmlCompartmentCollection(node);
+
+ List<Compartment> compartments = new ArrayList<>();
+ for (CellDesignerCompartment cellDesignerCompartment : cellDesignerCompartments) {
+ Compartment comp =cellDesignerCompartment.createModelElement("ca" + aliasIdCounter);
+ compartments.add(comp);
+ aliasIdCounter++;
+ }
+
+ String xmlString2 = parser.toXml(compartments);
+ assertNotNull(xmlString2);
+
+ node = getNodeFromXmlString(xmlString2);
+
+ elements = new CellDesignerElementCollection();
+ parser = new CompartmentCollectionXmlParser(elements);
+
+ List<CellDesignerCompartment> compartments2 = parser.parseXmlCompartmentCollection(node);
+ for (int i = 0; i < cellDesignerCompartments.size(); i++) {
+ CellDesignerCompartment compartmentA = cellDesignerCompartments.get(i);
+ CellDesignerCompartment compartmentB = compartments2.get(i);
+ assertEquals(compartmentA.getName(), compartmentB.getName());
+ }
+
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentParserTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentParserTests.java
index 87cac89e30..8bdf581b7b 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentParserTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentParserTests.java
@@ -1,81 +1,81 @@
-package lcsb.mapviewer.converter.model.celldesigner.compartment;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.fail;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.model.map.model.Model;
-
-public class CompartmentParserTests extends CellDesignerTestFunctions {
- Logger logger = Logger.getLogger(CompartmentParserTests.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParseCompartmensBottom() {
- Model model;
- try {
- model = getModelForFile("testFiles/compartment/bottom_compartment.xml");
-
- assertEquals(1, model.getElements().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unexpected exception");
- }
- }
-
- @Test
- public void testParseCompartmensTop() {
- Model model;
- try {
- model = getModelForFile("testFiles/compartment/top_compartment.xml");
-
- assertEquals(1, model.getElements().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unexpected exception");
- }
- }
-
- @Test
- public void testParseCompartmensRight() {
- Model model;
- try {
- model = getModelForFile("testFiles/compartment/right_compartment.xml");
-
- assertEquals(1, model.getElements().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unexpected exception");
- }
- }
-
- @Test
- public void testParseCompartmensLeft() {
- Model model;
- try {
- model = getModelForFile("testFiles/compartment/left_compartment.xml");
-
- assertEquals(1, model.getElements().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unexpected exception");
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.compartment;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.fail;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.model.map.model.Model;
+
+public class CompartmentParserTests extends CellDesignerTestFunctions {
+ Logger logger = Logger.getLogger(CompartmentParserTests.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testParseCompartmensBottom() {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/compartment/bottom_compartment.xml");
+
+ assertEquals(1, model.getElements().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unexpected exception");
+ }
+ }
+
+ @Test
+ public void testParseCompartmensTop() {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/compartment/top_compartment.xml");
+
+ assertEquals(1, model.getElements().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unexpected exception");
+ }
+ }
+
+ @Test
+ public void testParseCompartmensRight() {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/compartment/right_compartment.xml");
+
+ assertEquals(1, model.getElements().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unexpected exception");
+ }
+ }
+
+ @Test
+ public void testParseCompartmensLeft() {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/compartment/left_compartment.xml");
+
+ assertEquals(1, model.getElements().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unexpected exception");
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParserTest.java
index 1d130d28f0..abda4fa553 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParserTest.java
@@ -1,148 +1,148 @@
-package lcsb.mapviewer.converter.model.celldesigner.compartment;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.io.StringReader;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.w3c.dom.Document;
-import org.w3c.dom.NodeList;
-import org.xml.sax.InputSource;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.converter.model.celldesigner.species.ProteinXmlParserTest;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-
-public class CompartmentXmlParserTest extends CellDesignerTestFunctions {
- protected Logger logger = Logger.getLogger(ProteinXmlParserTest.class.getName());
-
- CompartmentXmlParser compartmentParser;
- CellDesignerElementCollection elements;
- String testProteinFile = "testFiles/xmlNodeTestExamples/compartment.xml";
-
- @Before
- public void setUp() throws Exception {
- elements = new CellDesignerElementCollection();
- compartmentParser = new CompartmentXmlParser(elements);
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParseXmlCompartment() {
- try {
- String xmlString = readFile(testProteinFile);
-
- Pair<String, CellDesignerCompartment> result = compartmentParser.parseXmlElement(xmlString);
- CellDesignerCompartment compartment = result.getRight();
- assertNotNull(compartment);
- assertEquals("c1", compartment.getElementId());
- assertEquals(1, compartment.getMiriamData().size());
- assertEquals("c1", compartment.getName());
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unexpected exception occured");
- }
- }
-
- @Test
- public void testToXml() throws Exception {
- try {
- String xmlString = readFile(testProteinFile);
-
- Pair<String, CellDesignerCompartment> result = compartmentParser.parseXmlElement(xmlString);
- CellDesignerCompartment compartment = result.getRight();
- Compartment alias = compartment.createModelElement("id");
- String transformedXml = compartmentParser.toXml(alias);
- assertNotNull(transformedXml);
- DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
- DocumentBuilder builder = factory.newDocumentBuilder();
- InputSource is = new InputSource(new StringReader(transformedXml));
- Document doc = builder.parse(is);
- NodeList root = doc.getChildNodes();
- assertEquals("compartment", root.item(0).getNodeName());
-
- Pair<String, CellDesignerCompartment> result2 = compartmentParser.parseXmlElement(compartmentParser.toXml(alias));
- CellDesignerCompartment compartment2 = result2.getRight();
- assertEquals(alias.getMiriamData().size(), compartment2.getMiriamData().size());
- assertEquals(alias.getName(), compartment2.getName());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidCompartment() throws Exception {
- try {
- compartmentParser.parseXmlElement(readFile("testFiles/invalid/compartment.xml"));
- fail("Exception expected");
-
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of Compartment"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidCompartment2() throws Exception {
- try {
- compartmentParser.parseXmlElement(readFile("testFiles/invalid/compartment2.xml"));
- fail("Exception expected");
-
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of Compartment/annotation"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidCompartment3() throws Exception {
- try {
- compartmentParser.parseXmlElement(readFile("testFiles/invalid/compartment3.xml"));
- fail("Exception expected");
-
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of Compartment/annotation/extension"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlWithParent() throws Exception {
- try {
- Compartment child = new Compartment("c_1");
- Compartment parent = new Compartment("p_1");
- child.setCompartment(parent);
-
- String xml = compartmentParser.toXml(child);
- assertTrue(xml.contains(parent.getElementId()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.compartment;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.io.StringReader;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.w3c.dom.Document;
+import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.converter.model.celldesigner.species.ProteinXmlParserTest;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+
+public class CompartmentXmlParserTest extends CellDesignerTestFunctions {
+ protected Logger logger = Logger.getLogger(ProteinXmlParserTest.class.getName());
+
+ CompartmentXmlParser compartmentParser;
+ CellDesignerElementCollection elements;
+ String testProteinFile = "testFiles/xmlNodeTestExamples/compartment.xml";
+
+ @Before
+ public void setUp() throws Exception {
+ elements = new CellDesignerElementCollection();
+ compartmentParser = new CompartmentXmlParser(elements);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testParseXmlCompartment() {
+ try {
+ String xmlString = readFile(testProteinFile);
+
+ Pair<String, CellDesignerCompartment> result = compartmentParser.parseXmlElement(xmlString);
+ CellDesignerCompartment compartment = result.getRight();
+ assertNotNull(compartment);
+ assertEquals("c1", compartment.getElementId());
+ assertEquals(1, compartment.getMiriamData().size());
+ assertEquals("c1", compartment.getName());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unexpected exception occured");
+ }
+ }
+
+ @Test
+ public void testToXml() throws Exception {
+ try {
+ String xmlString = readFile(testProteinFile);
+
+ Pair<String, CellDesignerCompartment> result = compartmentParser.parseXmlElement(xmlString);
+ CellDesignerCompartment compartment = result.getRight();
+ Compartment alias = compartment.createModelElement("id");
+ String transformedXml = compartmentParser.toXml(alias);
+ assertNotNull(transformedXml);
+ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ DocumentBuilder builder = factory.newDocumentBuilder();
+ InputSource is = new InputSource(new StringReader(transformedXml));
+ Document doc = builder.parse(is);
+ NodeList root = doc.getChildNodes();
+ assertEquals("compartment", root.item(0).getNodeName());
+
+ Pair<String, CellDesignerCompartment> result2 = compartmentParser.parseXmlElement(compartmentParser.toXml(alias));
+ CellDesignerCompartment compartment2 = result2.getRight();
+ assertEquals(alias.getMiriamData().size(), compartment2.getMiriamData().size());
+ assertEquals(alias.getName(), compartment2.getName());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidCompartment() throws Exception {
+ try {
+ compartmentParser.parseXmlElement(readFile("testFiles/invalid/compartment.xml"));
+ fail("Exception expected");
+
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of Compartment"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidCompartment2() throws Exception {
+ try {
+ compartmentParser.parseXmlElement(readFile("testFiles/invalid/compartment2.xml"));
+ fail("Exception expected");
+
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of Compartment/annotation"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidCompartment3() throws Exception {
+ try {
+ compartmentParser.parseXmlElement(readFile("testFiles/invalid/compartment3.xml"));
+ fail("Exception expected");
+
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of Compartment/annotation/extension"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlWithParent() throws Exception {
+ try {
+ Compartment child = new Compartment("c_1");
+ Compartment parent = new Compartment("p_1");
+ child.setCompartment(parent);
+
+ String xml = compartmentParser.toXml(child);
+ assertTrue(xml.contains(parent.getElementId()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverterTest.java
index a9e13b6344..55b199d6c7 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverterTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverterTest.java
@@ -1,84 +1,84 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import static org.junit.Assert.assertEquals;
-
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.EventStorageLoggerAppender;
-import lcsb.mapviewer.common.geometry.LineTransformation;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerEllipseTransformation;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerPolygonTransformation;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerRectangleTransformation;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class AbstractCellDesignerAliasConverterTest {
- Logger logger = Logger.getLogger(AbstractCellDesignerAliasConverterTest.class);
-
- AbstractCellDesignerAliasConverter<Species> converter = new AbstractCellDesignerAliasConverter<Species>(false) {
- @Override
- public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
- return null;
- }
-
- @Override
- protected PathIterator getBoundPathIterator(Species alias) {
- return null;
- }
- };
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetAnchorPointCoordinatesForInvalidImplementation() {
- EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
- Logger.getRootLogger().addAppender(appender);
- try {
- Protein alias = new GenericProtein("id");
- alias.setWidth(1);
- alias.setHeight(1);
- converter.getAnchorPointCoordinates(alias, 0);
- assertEquals(1, appender.getWarnings().size());
- } finally {
- Logger.getRootLogger().removeAppender(appender);
- }
- }
-
- @Test
- public void testGetters() {
- CellDesignerEllipseTransformation ellipseTransformation = new CellDesignerEllipseTransformation();
- LineTransformation lineTransformation = new LineTransformation();
- CellDesignerPolygonTransformation polygonTransformation = new CellDesignerPolygonTransformation();
- CellDesignerRectangleTransformation rectangleTransformation = new CellDesignerRectangleTransformation();
- converter.setEllipseTransformation(ellipseTransformation);
- converter.setLineTransformation(lineTransformation);
- converter.setPolygonTransformation(polygonTransformation);
- converter.setRectangleTransformation(rectangleTransformation);
-
- assertEquals(ellipseTransformation, converter.getEllipseTransformation());
- assertEquals(lineTransformation, converter.getLineTransformation());
- assertEquals(polygonTransformation, converter.getPolygonTransformation());
- assertEquals(rectangleTransformation, converter.getRectangleTransformation());
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import static org.junit.Assert.assertEquals;
+
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.EventStorageLoggerAppender;
+import lcsb.mapviewer.common.geometry.LineTransformation;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerEllipseTransformation;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerPolygonTransformation;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerRectangleTransformation;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class AbstractCellDesignerAliasConverterTest {
+ Logger logger = Logger.getLogger(AbstractCellDesignerAliasConverterTest.class);
+
+ AbstractCellDesignerAliasConverter<Species> converter = new AbstractCellDesignerAliasConverter<Species>(false) {
+ @Override
+ public Point2D getPointCoordinates(Species alias, CellDesignerAnchor anchor) {
+ return null;
+ }
+
+ @Override
+ protected PathIterator getBoundPathIterator(Species alias) {
+ return null;
+ }
+ };
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetAnchorPointCoordinatesForInvalidImplementation() {
+ EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
+ Logger.getRootLogger().addAppender(appender);
+ try {
+ Protein alias = new GenericProtein("id");
+ alias.setWidth(1);
+ alias.setHeight(1);
+ converter.getAnchorPointCoordinates(alias, 0);
+ assertEquals(1, appender.getWarnings().size());
+ } finally {
+ Logger.getRootLogger().removeAppender(appender);
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ CellDesignerEllipseTransformation ellipseTransformation = new CellDesignerEllipseTransformation();
+ LineTransformation lineTransformation = new LineTransformation();
+ CellDesignerPolygonTransformation polygonTransformation = new CellDesignerPolygonTransformation();
+ CellDesignerRectangleTransformation rectangleTransformation = new CellDesignerRectangleTransformation();
+ converter.setEllipseTransformation(ellipseTransformation);
+ converter.setLineTransformation(lineTransformation);
+ converter.setPolygonTransformation(polygonTransformation);
+ converter.setRectangleTransformation(rectangleTransformation);
+
+ assertEquals(ellipseTransformation, converter.getEllipseTransformation());
+ assertEquals(lineTransformation, converter.getLineTransformation());
+ assertEquals(polygonTransformation, converter.getPolygonTransformation());
+ assertEquals(rectangleTransformation, converter.getRectangleTransformation());
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AllGeometryTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AllGeometryTests.java
index ceea0ca772..514045015c 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AllGeometryTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AllGeometryTests.java
@@ -1,26 +1,26 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.AllHelperTests;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AbstractCellDesignerAliasConverterTest.class, //
- AllHelperTests.class, //
- AntisenseRnaCellDesignerAliasConverterTest.class, //
- CellDesignerAliasConverterTest.class, //
- DegradedCellDesignerAliasConverterTest.class, //
- GeneCellDesignerAliasConverterTest.class, //
- IonCellDesignerAliasConverterTest.class, //
- ProteinConverterTest.class, //
- ProteinCellDesignerAliasConverterTest.class, //
- ReactionCellDesignerConverterTest.class, //
- RnaCellDesignerAliasConverterTest.class, //
- SimpleMoleculeCellDesignerAliasConverterTest.class, //
- UnknownCellDesignerAliasConverterTest.class, //
-})
-public class AllGeometryTests {
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.AllHelperTests;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AbstractCellDesignerAliasConverterTest.class, //
+ AllHelperTests.class, //
+ AntisenseRnaCellDesignerAliasConverterTest.class, //
+ CellDesignerAliasConverterTest.class, //
+ DegradedCellDesignerAliasConverterTest.class, //
+ GeneCellDesignerAliasConverterTest.class, //
+ IonCellDesignerAliasConverterTest.class, //
+ ProteinConverterTest.class, //
+ ProteinCellDesignerAliasConverterTest.class, //
+ ReactionCellDesignerConverterTest.class, //
+ RnaCellDesignerAliasConverterTest.class, //
+ SimpleMoleculeCellDesignerAliasConverterTest.class, //
+ UnknownCellDesignerAliasConverterTest.class, //
+})
+public class AllGeometryTests {
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AntisenseRnaCellDesignerAliasConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AntisenseRnaCellDesignerAliasConverterTest.java
index 9450ab4a24..a12653e3a1 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AntisenseRnaCellDesignerAliasConverterTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AntisenseRnaCellDesignerAliasConverterTest.java
@@ -1,59 +1,59 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import static org.junit.Assert.assertNotNull;
-
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class AntisenseRnaCellDesignerAliasConverterTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetPointCoordinatesForSbgn() {
- AntisenseRnaCellDesignerAliasConverter converter = new AntisenseRnaCellDesignerAliasConverter(true);
-
- Model model = new ModelFullIndexed(null);
- Species alias = new GenericProtein("id");
- alias.setWidth(10);
- alias.setHeight(10);
- alias.setModel(model);
- Point2D point = converter.getPointCoordinates(alias, CellDesignerAnchor.E);
- assertNotNull(point);
- }
-
- @Test
- public void testGetAntisenseRnaPathForSbgn() {
- AntisenseRnaCellDesignerAliasConverter converter = new AntisenseRnaCellDesignerAliasConverter(true);
-
- Model model = new ModelFullIndexed(null);
- Species alias = new GenericProtein("id");
- alias.setWidth(10);
- alias.setHeight(10);
- alias.setModel(model);
- PathIterator path = converter.getBoundPathIterator(alias);
- assertNotNull(path);
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import static org.junit.Assert.assertNotNull;
+
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class AntisenseRnaCellDesignerAliasConverterTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetPointCoordinatesForSbgn() {
+ AntisenseRnaCellDesignerAliasConverter converter = new AntisenseRnaCellDesignerAliasConverter(true);
+
+ Model model = new ModelFullIndexed(null);
+ Species alias = new GenericProtein("id");
+ alias.setWidth(10);
+ alias.setHeight(10);
+ alias.setModel(model);
+ Point2D point = converter.getPointCoordinates(alias, CellDesignerAnchor.E);
+ assertNotNull(point);
+ }
+
+ @Test
+ public void testGetAntisenseRnaPathForSbgn() {
+ AntisenseRnaCellDesignerAliasConverter converter = new AntisenseRnaCellDesignerAliasConverter(true);
+
+ Model model = new ModelFullIndexed(null);
+ Species alias = new GenericProtein("id");
+ alias.setWidth(10);
+ alias.setHeight(10);
+ alias.setModel(model);
+ PathIterator path = converter.getBoundPathIterator(alias);
+ assertNotNull(path);
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/CellDesignerAliasConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/CellDesignerAliasConverterTest.java
index 411e684731..98003ed539 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/CellDesignerAliasConverterTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/CellDesignerAliasConverterTest.java
@@ -1,51 +1,51 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class CellDesignerAliasConverterTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testConstructorWithInvalidArg() {
- try {
- new CellDesignerAliasConverter(null, false);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("element cannot be null"));
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg2() {
- try {
- Species alias = Mockito.mock(Species.class);
- new CellDesignerAliasConverter(alias, false);
- fail("Exception expected");
- } catch (NotImplementedException e) {
- assertTrue(e.getMessage().contains("Unknown converter for class"));
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class CellDesignerAliasConverterTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testConstructorWithInvalidArg() {
+ try {
+ new CellDesignerAliasConverter(null, false);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("element cannot be null"));
+ }
+ }
+
+ @Test
+ public void testConstructorWithInvalidArg2() {
+ try {
+ Species alias = Mockito.mock(Species.class);
+ new CellDesignerAliasConverter(alias, false);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ assertTrue(e.getMessage().contains("Unknown converter for class"));
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/DegradedCellDesignerAliasConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/DegradedCellDesignerAliasConverterTest.java
index e17432ca9a..a91f48f823 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/DegradedCellDesignerAliasConverterTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/DegradedCellDesignerAliasConverterTest.java
@@ -1,57 +1,57 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.geom.Point2D;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Degraded;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class DegradedCellDesignerAliasConverterTest {
-
- DegradedCellDesignerAliasConverter converter = new DegradedCellDesignerAliasConverter(false);
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetAnchorPointCoordinatesForInvalidAlias() {
- Degraded alias = new Degraded("id");
- alias.setWidth(-1);
- Point2D point = converter.getAnchorPointCoordinates(alias, 0);
- assertNotNull(point);
- }
-
- @Test
- public void testGetAnchorPointCoordinatesForInvalidAlias2() {
- Species alias = new Degraded("id");
- Point2D point = converter.getAnchorPointCoordinates(alias, 0);
- assertNotNull(point);
- }
-
- @Test
- public void testNotImplementedMethod() {
- try {
- converter.getBoundPathIterator(null);
- } catch (NotImplementedException e) {
- assertTrue(e.getMessage().contains("This class doesn't have bound"));
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import java.awt.geom.Point2D;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Degraded;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class DegradedCellDesignerAliasConverterTest {
+
+ DegradedCellDesignerAliasConverter converter = new DegradedCellDesignerAliasConverter(false);
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetAnchorPointCoordinatesForInvalidAlias() {
+ Degraded alias = new Degraded("id");
+ alias.setWidth(-1);
+ Point2D point = converter.getAnchorPointCoordinates(alias, 0);
+ assertNotNull(point);
+ }
+
+ @Test
+ public void testGetAnchorPointCoordinatesForInvalidAlias2() {
+ Species alias = new Degraded("id");
+ Point2D point = converter.getAnchorPointCoordinates(alias, 0);
+ assertNotNull(point);
+ }
+
+ @Test
+ public void testNotImplementedMethod() {
+ try {
+ converter.getBoundPathIterator(null);
+ } catch (NotImplementedException e) {
+ assertTrue(e.getMessage().contains("This class doesn't have bound"));
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinCellDesignerAliasConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinCellDesignerAliasConverterTest.java
index 1726362d60..1ef0d295c1 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinCellDesignerAliasConverterTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinCellDesignerAliasConverterTest.java
@@ -1,58 +1,58 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.species.Protein;
-
-public class ProteinCellDesignerAliasConverterTest {
-
- ProteinCellDesignerAliasConverter converter = new ProteinCellDesignerAliasConverter(false);
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testNotImplementedMethod() {
- try {
- Protein alias = Mockito.mock(Protein.class);
- converter.getBoundPathIterator(alias);
- fail("Exception expected");
- } catch (NotImplementedException e) {
- assertTrue(e.getMessage().contains("Not implemented protein converter for type"));
- }
- }
-
- @Test
- public void testGetPointCoordinates() {
- try {
- Protein alias = Mockito.spy(Protein.class);
- alias.setWidth(10);
- alias.setHeight(10);
- converter.getPointCoordinates(alias, CellDesignerAnchor.E);
- fail("Exception expected");
- } catch (NotImplementedException e) {
- assertTrue(e.getMessage().contains("Unknown type"));
- }
- }
-
-
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.model.map.species.Protein;
+
+public class ProteinCellDesignerAliasConverterTest {
+
+ ProteinCellDesignerAliasConverter converter = new ProteinCellDesignerAliasConverter(false);
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testNotImplementedMethod() {
+ try {
+ Protein alias = Mockito.mock(Protein.class);
+ converter.getBoundPathIterator(alias);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ assertTrue(e.getMessage().contains("Not implemented protein converter for type"));
+ }
+ }
+
+ @Test
+ public void testGetPointCoordinates() {
+ try {
+ Protein alias = Mockito.spy(Protein.class);
+ alias.setWidth(10);
+ alias.setHeight(10);
+ converter.getPointCoordinates(alias, CellDesignerAnchor.E);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ assertTrue(e.getMessage().contains("Unknown type"));
+ }
+ }
+
+
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ReactionCellDesignerConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ReactionCellDesignerConverterTest.java
index 3246e8dc02..08dbb62a49 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ReactionCellDesignerConverterTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ReactionCellDesignerConverterTest.java
@@ -1,30 +1,30 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import static org.junit.Assert.*;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ReactionCellDesignerConverterTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testConstructor() {
- ReactionCellDesignerConverter onverter = new ReactionCellDesignerConverter();
- assertNotNull(onverter);
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import static org.junit.Assert.*;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ReactionCellDesignerConverterTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testConstructor() {
+ ReactionCellDesignerConverter onverter = new ReactionCellDesignerConverter();
+ assertNotNull(onverter);
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/RnaCellDesignerAliasConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/RnaCellDesignerAliasConverterTest.java
index fc17ed90ca..e6f8670cc3 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/RnaCellDesignerAliasConverterTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/RnaCellDesignerAliasConverterTest.java
@@ -1,59 +1,59 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import static org.junit.Assert.assertNotNull;
-
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class RnaCellDesignerAliasConverterTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetPointCoordinatesForSbgn() {
- RnaCellDesignerAliasConverter converter = new RnaCellDesignerAliasConverter(true);
-
- Model model = new ModelFullIndexed(null);
- Species alias = new GenericProtein("id");
- alias.setWidth(10);
- alias.setHeight(10);
- alias.setModel(model);
- Point2D point = converter.getPointCoordinates(alias, CellDesignerAnchor.E);
- assertNotNull(point);
- }
-
- @Test
- public void testGetAntisebseRnaPathForSbgn() {
- RnaCellDesignerAliasConverter converter = new RnaCellDesignerAliasConverter(true);
-
- Model model = new ModelFullIndexed(null);
- Species alias = new GenericProtein("id");
- alias.setWidth(10);
- alias.setHeight(10);
- alias.setModel(model);
- PathIterator path = converter.getBoundPathIterator(alias);
- assertNotNull(path);
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry;
+
+import static org.junit.Assert.assertNotNull;
+
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class RnaCellDesignerAliasConverterTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetPointCoordinatesForSbgn() {
+ RnaCellDesignerAliasConverter converter = new RnaCellDesignerAliasConverter(true);
+
+ Model model = new ModelFullIndexed(null);
+ Species alias = new GenericProtein("id");
+ alias.setWidth(10);
+ alias.setHeight(10);
+ alias.setModel(model);
+ Point2D point = converter.getPointCoordinates(alias, CellDesignerAnchor.E);
+ assertNotNull(point);
+ }
+
+ @Test
+ public void testGetAntisebseRnaPathForSbgn() {
+ RnaCellDesignerAliasConverter converter = new RnaCellDesignerAliasConverter(true);
+
+ Model model = new ModelFullIndexed(null);
+ Species alias = new GenericProtein("id");
+ alias.setWidth(10);
+ alias.setHeight(10);
+ alias.setModel(model);
+ PathIterator path = converter.getBoundPathIterator(alias);
+ assertNotNull(path);
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/AllHelperTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/AllHelperTests.java
index 1f2a343843..f4b30b1fa2 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/AllHelperTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/AllHelperTests.java
@@ -1,18 +1,18 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ CellDesignerAnchorTest.class, //
- CellDesignerEllipseTransformationTest.class, //
- CellDesignerLineTransformationTest.class, //
- CellDesignerPointTransformationTest.class, //
- CellDesignerPolygonTransformationTest.class, //
- CellDesignerRectangleTransformationTest.class, //
- PolylineDataFactoryTest.class,//
-})
-public class AllHelperTests {
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ CellDesignerAnchorTest.class, //
+ CellDesignerEllipseTransformationTest.class, //
+ CellDesignerLineTransformationTest.class, //
+ CellDesignerPointTransformationTest.class, //
+ CellDesignerPolygonTransformationTest.class, //
+ CellDesignerRectangleTransformationTest.class, //
+ PolylineDataFactoryTest.class,//
+})
+public class AllHelperTests {
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerAnchorTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerAnchorTest.java
index e58f277fbc..d390e8afd6 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerAnchorTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerAnchorTest.java
@@ -1,31 +1,31 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
-
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class CellDesignerAnchorTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetters() {
- for (CellDesignerAnchor value : CellDesignerAnchor.values()) {
- assertNotNull(value.getName());
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
+
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class CellDesignerAnchorTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetters() {
+ for (CellDesignerAnchor value : CellDesignerAnchor.values()) {
+ assertNotNull(value.getName());
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerEllipseTransformationTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerEllipseTransformationTest.java
index 7d959b6d25..d72af04eab 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerEllipseTransformationTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerEllipseTransformationTest.java
@@ -1,145 +1,145 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
-
-import static org.junit.Assert.assertEquals;
-
-import java.awt.geom.Point2D;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class CellDesignerEllipseTransformationTest {
- CellDesignerEllipseTransformation et = new CellDesignerEllipseTransformation();
- double x = 0;
- double y = 10;
- double width = 20;
- double height = 30;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetPointOnEllipseByAnchorNull() {
- Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, null);
- assertEquals(x + width / 2, p.getX(), 1e-6);
- assertEquals(y + height / 2, p.getY(), 1e-6);
- }
-
- @Test
- public void testGetPointOnEllipseByAnchorE() {
- Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.E);
- assertEquals(x + width, p.getX(), 1e-6);
- assertEquals(y + height / 2, p.getY(), 1e-6);
- }
-
- @Test
- public void testGetPointOnEllipseByAnchorW() {
- Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.W);
- assertEquals(x, p.getX(), 1e-6);
- assertEquals(y + height / 2, p.getY(), 1e-6);
- }
-
- @Test
- public void testGetPointOnEllipseByAnchorN() {
- Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.N);
- assertEquals(x + width / 2, p.getX(), 1e-6);
- assertEquals(y, p.getY(), 1e-6);
- }
-
- @Test
- public void testGetPointOnEllipseByAnchorS() {
- Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.S);
- assertEquals(x + width / 2, p.getX(), 1e-6);
- assertEquals(y + height, p.getY(), 1e-6);
- }
-
- @Test
- public void testGetPointOnEllipseByAnchorESE() {
- Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.ESE);
- assertEquals(x + width / 2 + Math.cos(Math.PI / 8) * width / 2, p.getX(), 1e-6);
- assertEquals(y + height / 2 + Math.sin(Math.PI / 8) * height / 2, p.getY(), 1e-6);
- }
-
- @Test
- public void testGetPointOnEllipseByAnchorSE() {
- Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.SE);
- assertEquals(x + width / 2 + Math.cos(Math.PI / 4) * width / 2, p.getX(), 1e-6);
- assertEquals(y + height / 2 + Math.sin(Math.PI / 4) * height / 2, p.getY(), 1e-6);
- }
-
- @Test
- public void testGetPointOnEllipseByAnchorSSE() {
- Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.SSE);
- assertEquals(x + width / 2 + Math.cos(Math.PI * 3 / 8) * width / 2, p.getX(), 1e-6);
- assertEquals(y + height / 2 + Math.sin(Math.PI * 3 / 8) * height / 2, p.getY(), 1e-6);
-
- }
-
- @Test
- public void testGetPointOnEllipseByAnchorSSW() {
- Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.SSW);
- assertEquals(x + width / 2 - Math.sin(Math.PI / 8) * width / 2, p.getX(), 1e-6);
- assertEquals(y + height / 2 + Math.cos(Math.PI / 8) * height / 2, p.getY(), 1e-6);
- }
-
- @Test
- public void testGetPointOnEllipseByAnchorSW() {
- Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.SW);
- assertEquals(x + width / 2 - Math.sin(Math.PI / 4) * width / 2, p.getX(), 1e-6);
- assertEquals(y + height / 2 + Math.cos(Math.PI / 4) * height / 2, p.getY(), 1e-6);
- }
-
- @Test
- public void testGetPointOnEllipseByAnchorWSW() {
- Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.WSW);
- assertEquals(x + width / 2 - Math.sin(Math.PI * 3 / 8) * width / 2, p.getX(), 1e-6);
- assertEquals(y + height / 2 + Math.cos(Math.PI * 3 / 8) * height / 2, p.getY(), 1e-6);
- }
-
- @Test
- public void testGetPointOnEllipseByAnchorWNW() {
- Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.WNW);
- assertEquals(x + width / 2 - Math.sin(Math.PI * 3 / 8) * width / 2, p.getX(), 1e-6);
- assertEquals(y + height / 2 - Math.cos(Math.PI * 3 / 8) * height / 2, p.getY(), 1e-6);
- }
-
- @Test
- public void testGetPointOnEllipseByAnchorNW() {
- Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.NW);
- assertEquals(x + width / 2 - Math.sin(Math.PI / 4) * width / 2, p.getX(), 1e-6);
- assertEquals(y + height / 2 - Math.cos(Math.PI / 4) * height / 2, p.getY(), 1e-6);
- }
-
- @Test
- public void testGetPointOnEllipseByAnchorNNW() {
- Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.NNW);
- assertEquals(x + width / 2 - Math.sin(Math.PI / 8) * width / 2, p.getX(), 1e-6);
- assertEquals(y + height / 2 - Math.cos(Math.PI / 8) * height / 2, p.getY(), 1e-6);
- }
-
- @Test
- public void testGetPointOnEllipseByAnchorNNE() {
- Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.NNE);
- assertEquals(x + width / 2 + Math.sin(Math.PI / 8) * width / 2, p.getX(), 1e-6);
- assertEquals(y + height / 2 - Math.cos(Math.PI / 8) * height / 2, p.getY(), 1e-6);
- }
-
- @Test
- public void testGetPointOnEllipseByAnchorNE() {
- Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.NE);
- assertEquals(x + width / 2 + Math.sin(Math.PI / 4) * width / 2, p.getX(), 1e-6);
- assertEquals(y + height / 2 - Math.cos(Math.PI / 4) * height / 2, p.getY(), 1e-6);
- }
-
- @Test
- public void testGetPointOnEllipseByAnchorENE() {
- Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.ENE);
- assertEquals(x + width / 2 + Math.sin(Math.PI * 3 / 8) * width / 2, p.getX(), 1e-6);
- assertEquals(y + height / 2 - Math.cos(Math.PI * 3 / 8) * height / 2, p.getY(), 1e-6);
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
+
+import static org.junit.Assert.assertEquals;
+
+import java.awt.geom.Point2D;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class CellDesignerEllipseTransformationTest {
+ CellDesignerEllipseTransformation et = new CellDesignerEllipseTransformation();
+ double x = 0;
+ double y = 10;
+ double width = 20;
+ double height = 30;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetPointOnEllipseByAnchorNull() {
+ Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, null);
+ assertEquals(x + width / 2, p.getX(), 1e-6);
+ assertEquals(y + height / 2, p.getY(), 1e-6);
+ }
+
+ @Test
+ public void testGetPointOnEllipseByAnchorE() {
+ Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.E);
+ assertEquals(x + width, p.getX(), 1e-6);
+ assertEquals(y + height / 2, p.getY(), 1e-6);
+ }
+
+ @Test
+ public void testGetPointOnEllipseByAnchorW() {
+ Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.W);
+ assertEquals(x, p.getX(), 1e-6);
+ assertEquals(y + height / 2, p.getY(), 1e-6);
+ }
+
+ @Test
+ public void testGetPointOnEllipseByAnchorN() {
+ Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.N);
+ assertEquals(x + width / 2, p.getX(), 1e-6);
+ assertEquals(y, p.getY(), 1e-6);
+ }
+
+ @Test
+ public void testGetPointOnEllipseByAnchorS() {
+ Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.S);
+ assertEquals(x + width / 2, p.getX(), 1e-6);
+ assertEquals(y + height, p.getY(), 1e-6);
+ }
+
+ @Test
+ public void testGetPointOnEllipseByAnchorESE() {
+ Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.ESE);
+ assertEquals(x + width / 2 + Math.cos(Math.PI / 8) * width / 2, p.getX(), 1e-6);
+ assertEquals(y + height / 2 + Math.sin(Math.PI / 8) * height / 2, p.getY(), 1e-6);
+ }
+
+ @Test
+ public void testGetPointOnEllipseByAnchorSE() {
+ Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.SE);
+ assertEquals(x + width / 2 + Math.cos(Math.PI / 4) * width / 2, p.getX(), 1e-6);
+ assertEquals(y + height / 2 + Math.sin(Math.PI / 4) * height / 2, p.getY(), 1e-6);
+ }
+
+ @Test
+ public void testGetPointOnEllipseByAnchorSSE() {
+ Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.SSE);
+ assertEquals(x + width / 2 + Math.cos(Math.PI * 3 / 8) * width / 2, p.getX(), 1e-6);
+ assertEquals(y + height / 2 + Math.sin(Math.PI * 3 / 8) * height / 2, p.getY(), 1e-6);
+
+ }
+
+ @Test
+ public void testGetPointOnEllipseByAnchorSSW() {
+ Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.SSW);
+ assertEquals(x + width / 2 - Math.sin(Math.PI / 8) * width / 2, p.getX(), 1e-6);
+ assertEquals(y + height / 2 + Math.cos(Math.PI / 8) * height / 2, p.getY(), 1e-6);
+ }
+
+ @Test
+ public void testGetPointOnEllipseByAnchorSW() {
+ Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.SW);
+ assertEquals(x + width / 2 - Math.sin(Math.PI / 4) * width / 2, p.getX(), 1e-6);
+ assertEquals(y + height / 2 + Math.cos(Math.PI / 4) * height / 2, p.getY(), 1e-6);
+ }
+
+ @Test
+ public void testGetPointOnEllipseByAnchorWSW() {
+ Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.WSW);
+ assertEquals(x + width / 2 - Math.sin(Math.PI * 3 / 8) * width / 2, p.getX(), 1e-6);
+ assertEquals(y + height / 2 + Math.cos(Math.PI * 3 / 8) * height / 2, p.getY(), 1e-6);
+ }
+
+ @Test
+ public void testGetPointOnEllipseByAnchorWNW() {
+ Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.WNW);
+ assertEquals(x + width / 2 - Math.sin(Math.PI * 3 / 8) * width / 2, p.getX(), 1e-6);
+ assertEquals(y + height / 2 - Math.cos(Math.PI * 3 / 8) * height / 2, p.getY(), 1e-6);
+ }
+
+ @Test
+ public void testGetPointOnEllipseByAnchorNW() {
+ Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.NW);
+ assertEquals(x + width / 2 - Math.sin(Math.PI / 4) * width / 2, p.getX(), 1e-6);
+ assertEquals(y + height / 2 - Math.cos(Math.PI / 4) * height / 2, p.getY(), 1e-6);
+ }
+
+ @Test
+ public void testGetPointOnEllipseByAnchorNNW() {
+ Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.NNW);
+ assertEquals(x + width / 2 - Math.sin(Math.PI / 8) * width / 2, p.getX(), 1e-6);
+ assertEquals(y + height / 2 - Math.cos(Math.PI / 8) * height / 2, p.getY(), 1e-6);
+ }
+
+ @Test
+ public void testGetPointOnEllipseByAnchorNNE() {
+ Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.NNE);
+ assertEquals(x + width / 2 + Math.sin(Math.PI / 8) * width / 2, p.getX(), 1e-6);
+ assertEquals(y + height / 2 - Math.cos(Math.PI / 8) * height / 2, p.getY(), 1e-6);
+ }
+
+ @Test
+ public void testGetPointOnEllipseByAnchorNE() {
+ Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.NE);
+ assertEquals(x + width / 2 + Math.sin(Math.PI / 4) * width / 2, p.getX(), 1e-6);
+ assertEquals(y + height / 2 - Math.cos(Math.PI / 4) * height / 2, p.getY(), 1e-6);
+ }
+
+ @Test
+ public void testGetPointOnEllipseByAnchorENE() {
+ Point2D p = et.getPointOnEllipseByAnchor(x, y, width, height, CellDesignerAnchor.ENE);
+ assertEquals(x + width / 2 + Math.sin(Math.PI * 3 / 8) * width / 2, p.getX(), 1e-6);
+ assertEquals(y + height / 2 - Math.cos(Math.PI * 3 / 8) * height / 2, p.getY(), 1e-6);
+ }
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerLineTransformationTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerLineTransformationTest.java
index 903d1c336c..94d9a0f2d3 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerLineTransformationTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerLineTransformationTest.java
@@ -1,218 +1,218 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.geometry.PointTransformation;
-import lcsb.mapviewer.model.graphics.PolylineData;
-
-public class CellDesignerLineTransformationTest {
- Logger logger = Logger.getLogger(CellDesignerLineTransformationTest.class);
-
- CellDesignerLineTransformation lineTransformation = new CellDesignerLineTransformation();
- PointTransformation pointTransformation = new PointTransformation();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetPointsFromLine() {
- try {
- Point2D startPoint = new Point2D.Double(1, 7);
- Point2D endPoint = new Point2D.Double(3, 5);
-
- List<Point2D> points = new ArrayList<Point2D>();
- points.add(new Point2D.Double(1.5, 2.5));
- points.add(new Point2D.Double(12, 13));
- points.add(new Point2D.Double(30, 40));
-
- PolylineData line = new PolylineData(lineTransformation.getLinePointsFromPoints(startPoint, endPoint, points));
-
- List<Point2D> newPoints = lineTransformation.getPointsFromLine(line);
- assertNotNull(newPoints);
-
- assertEquals(points.size(), newPoints.size());
-
- for (int i = 0; i < points.size(); i++) {
- double dist = points.get(i).distance(newPoints.get(i));
- assertTrue("Distance to big: " + dist + " for points " + points.get(i) + " and " + newPoints.get(i), dist < 1e-6);
- assertTrue(pointTransformation.isValidPoint(newPoints.get(i)));
- }
- } catch (Exception e) {
- e.printStackTrace();
- fail("Exception occured: " + e.getMessage());
- }
- }
-
- @Test
- public void testGetProblematicPointsFromLine() {
- try {
- Point2D startPoint = new Point2D.Double(1, 7);
- Point2D endPoint = new Point2D.Double(1, 5);
-
- List<Point2D> points = new ArrayList<Point2D>();
- points.add(new Point2D.Double(1.5, 2.5));
- points.add(new Point2D.Double(12, 13));
- points.add(new Point2D.Double(30, 40));
-
- PolylineData line = new PolylineData(lineTransformation.getLinePointsFromPoints(startPoint, endPoint, points));
-
- List<Point2D> newPoints = lineTransformation.getPointsFromLine(line);
- assertNotNull(newPoints);
-
- assertEquals(points.size(), newPoints.size());
-
- for (int i = 0; i < points.size(); i++) {
- assertTrue("Invalid point after transformation: " + newPoints.get(i), pointTransformation.isValidPoint(newPoints.get(i)));
- double dist = points.get(i).distance(newPoints.get(i));
- assertTrue("Distance to big: " + dist + " for points " + points.get(i) + " and " + newPoints.get(i), dist < 1e-6);
- assertTrue(pointTransformation.isValidPoint(newPoints.get(i)));
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetProblematicPointsFromLine2() {
- try {
- Point2D startPoint = new Point2D.Double(5, 1);
- Point2D endPoint = new Point2D.Double(70, 1);
-
- List<Point2D> points = new ArrayList<Point2D>();
- points.add(new Point2D.Double(1.5, 2.5));
- points.add(new Point2D.Double(12, 13));
- points.add(new Point2D.Double(-12, -13));
- points.add(new Point2D.Double(30, 40));
-
- PolylineData line = new PolylineData(lineTransformation.getLinePointsFromPoints(startPoint, endPoint, points));
-
- List<Point2D> newPoints = lineTransformation.getPointsFromLine(line);
- assertNotNull(newPoints);
-
- assertEquals(points.size(), newPoints.size());
-
- for (int i = 0; i < points.size(); i++) {
- assertTrue("Invalid point after transformation: " + newPoints.get(i), pointTransformation.isValidPoint(newPoints.get(i)));
- double dist = points.get(i).distance(newPoints.get(i));
- assertTrue("Distance to big: " + dist + " for points " + points.get(i) + " and " + newPoints.get(i), dist < 1e-6);
- assertTrue(pointTransformation.isValidPoint(newPoints.get(i)));
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetLinePointsFromInvalidPoints() {
- try {
- Point2D startPoint = new Point2D.Double(Double.POSITIVE_INFINITY, 1);
- Point2D endPoint = new Point2D.Double(70, 1);
-
- lineTransformation.getLinePointsFromPoints(startPoint, endPoint, new ArrayList<>());
- fail("Excepiton expceted");
-
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Invalid start point"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetLinePointsFromInvalidPoints2() {
- try {
- Point2D endPoint = new Point2D.Double(Double.POSITIVE_INFINITY, 1);
- Point2D startPoint = new Point2D.Double(70, 1);
-
- lineTransformation.getLinePointsFromPoints(startPoint, endPoint, new ArrayList<>());
- fail("Excepiton expceted");
-
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Invalid end point"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetLinePointsFromInvalidPoints3() {
- try {
- Point2D endPoint = new Point2D.Double(70, 2);
- Point2D startPoint = new Point2D.Double(70, 1);
- List<Point2D> list = new ArrayList<>();
- list.add(new Point2D.Double(Double.POSITIVE_INFINITY, 1));
-
- lineTransformation.getLinePointsFromPoints(startPoint, endPoint, list);
- fail("Excepiton expceted");
-
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Invalid point"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetPointsFromInvalidLine() {
- try {
-
- lineTransformation.getPointsFromLine(null);
- fail("Excepiton expceted");
-
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Line cannot be null"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetPointsFromInvalidLine2() {
- try {
- lineTransformation.getPointsFromLine(new PolylineData());
- fail("Excepiton expceted");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Invalid line passed as an argument"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetPointsFromInvalidLine3() {
- try {
- lineTransformation.getPointsFromLine(new PolylineData(new Point2D.Double(), new Point2D.Double()));
- fail("Excepiton expceted");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("First and last point in the line must differ but found"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.geometry.PointTransformation;
+import lcsb.mapviewer.model.graphics.PolylineData;
+
+public class CellDesignerLineTransformationTest {
+ Logger logger = Logger.getLogger(CellDesignerLineTransformationTest.class);
+
+ CellDesignerLineTransformation lineTransformation = new CellDesignerLineTransformation();
+ PointTransformation pointTransformation = new PointTransformation();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetPointsFromLine() {
+ try {
+ Point2D startPoint = new Point2D.Double(1, 7);
+ Point2D endPoint = new Point2D.Double(3, 5);
+
+ List<Point2D> points = new ArrayList<Point2D>();
+ points.add(new Point2D.Double(1.5, 2.5));
+ points.add(new Point2D.Double(12, 13));
+ points.add(new Point2D.Double(30, 40));
+
+ PolylineData line = new PolylineData(lineTransformation.getLinePointsFromPoints(startPoint, endPoint, points));
+
+ List<Point2D> newPoints = lineTransformation.getPointsFromLine(line);
+ assertNotNull(newPoints);
+
+ assertEquals(points.size(), newPoints.size());
+
+ for (int i = 0; i < points.size(); i++) {
+ double dist = points.get(i).distance(newPoints.get(i));
+ assertTrue("Distance to big: " + dist + " for points " + points.get(i) + " and " + newPoints.get(i), dist < 1e-6);
+ assertTrue(pointTransformation.isValidPoint(newPoints.get(i)));
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Exception occured: " + e.getMessage());
+ }
+ }
+
+ @Test
+ public void testGetProblematicPointsFromLine() {
+ try {
+ Point2D startPoint = new Point2D.Double(1, 7);
+ Point2D endPoint = new Point2D.Double(1, 5);
+
+ List<Point2D> points = new ArrayList<Point2D>();
+ points.add(new Point2D.Double(1.5, 2.5));
+ points.add(new Point2D.Double(12, 13));
+ points.add(new Point2D.Double(30, 40));
+
+ PolylineData line = new PolylineData(lineTransformation.getLinePointsFromPoints(startPoint, endPoint, points));
+
+ List<Point2D> newPoints = lineTransformation.getPointsFromLine(line);
+ assertNotNull(newPoints);
+
+ assertEquals(points.size(), newPoints.size());
+
+ for (int i = 0; i < points.size(); i++) {
+ assertTrue("Invalid point after transformation: " + newPoints.get(i), pointTransformation.isValidPoint(newPoints.get(i)));
+ double dist = points.get(i).distance(newPoints.get(i));
+ assertTrue("Distance to big: " + dist + " for points " + points.get(i) + " and " + newPoints.get(i), dist < 1e-6);
+ assertTrue(pointTransformation.isValidPoint(newPoints.get(i)));
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetProblematicPointsFromLine2() {
+ try {
+ Point2D startPoint = new Point2D.Double(5, 1);
+ Point2D endPoint = new Point2D.Double(70, 1);
+
+ List<Point2D> points = new ArrayList<Point2D>();
+ points.add(new Point2D.Double(1.5, 2.5));
+ points.add(new Point2D.Double(12, 13));
+ points.add(new Point2D.Double(-12, -13));
+ points.add(new Point2D.Double(30, 40));
+
+ PolylineData line = new PolylineData(lineTransformation.getLinePointsFromPoints(startPoint, endPoint, points));
+
+ List<Point2D> newPoints = lineTransformation.getPointsFromLine(line);
+ assertNotNull(newPoints);
+
+ assertEquals(points.size(), newPoints.size());
+
+ for (int i = 0; i < points.size(); i++) {
+ assertTrue("Invalid point after transformation: " + newPoints.get(i), pointTransformation.isValidPoint(newPoints.get(i)));
+ double dist = points.get(i).distance(newPoints.get(i));
+ assertTrue("Distance to big: " + dist + " for points " + points.get(i) + " and " + newPoints.get(i), dist < 1e-6);
+ assertTrue(pointTransformation.isValidPoint(newPoints.get(i)));
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetLinePointsFromInvalidPoints() {
+ try {
+ Point2D startPoint = new Point2D.Double(Double.POSITIVE_INFINITY, 1);
+ Point2D endPoint = new Point2D.Double(70, 1);
+
+ lineTransformation.getLinePointsFromPoints(startPoint, endPoint, new ArrayList<>());
+ fail("Excepiton expceted");
+
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Invalid start point"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetLinePointsFromInvalidPoints2() {
+ try {
+ Point2D endPoint = new Point2D.Double(Double.POSITIVE_INFINITY, 1);
+ Point2D startPoint = new Point2D.Double(70, 1);
+
+ lineTransformation.getLinePointsFromPoints(startPoint, endPoint, new ArrayList<>());
+ fail("Excepiton expceted");
+
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Invalid end point"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetLinePointsFromInvalidPoints3() {
+ try {
+ Point2D endPoint = new Point2D.Double(70, 2);
+ Point2D startPoint = new Point2D.Double(70, 1);
+ List<Point2D> list = new ArrayList<>();
+ list.add(new Point2D.Double(Double.POSITIVE_INFINITY, 1));
+
+ lineTransformation.getLinePointsFromPoints(startPoint, endPoint, list);
+ fail("Excepiton expceted");
+
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Invalid point"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetPointsFromInvalidLine() {
+ try {
+
+ lineTransformation.getPointsFromLine(null);
+ fail("Excepiton expceted");
+
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Line cannot be null"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetPointsFromInvalidLine2() {
+ try {
+ lineTransformation.getPointsFromLine(new PolylineData());
+ fail("Excepiton expceted");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Invalid line passed as an argument"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetPointsFromInvalidLine3() {
+ try {
+ lineTransformation.getPointsFromLine(new PolylineData(new Point2D.Double(), new Point2D.Double()));
+ fail("Excepiton expceted");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("First and last point in the line must differ but found"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerPointTransformationTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerPointTransformationTest.java
index 8025055a86..f2d00d9edd 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerPointTransformationTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerPointTransformationTest.java
@@ -1,66 +1,66 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.geom.Point2D;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class CellDesignerPointTransformationTest {
- Logger logger = Logger.getLogger(CellDesignerPointTransformationTest .class);
-
- CellDesignerPointTransformation pt = new CellDesignerPointTransformation();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- /**
- * Check if coordinetas are transformed in both ways correctly for this
- * strange transformation with new base constsed of 3 points
- */
- @Test
- public void testConversionOfPointBases() {
- try {
- Point2D pointA = new Point2D.Double(1, 2);
- Point2D pointB = new Point2D.Double(10, 12);
- Point2D pointC = new Point2D.Double(4, 3);
- Point2D pointP = new Point2D.Double(0.1, 2);
-
- Point2D pointO = pt.getCoordinatesInNormalBase(pointA, pointB, pointC, pointP);
- Point2D pointQ = pt.getCoordinatesInCellDesignerBase(pointA, pointB, pointC, pointO);
- assertEquals(0, pointQ.distance(pointP), 1e-6);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testNanTransformation() {
- try {
- Point2D pointA = new Point2D.Double(11429.886363636364, 11966.818181818182);
- Point2D pointB = new Point2D.Double(11300.886363636364, 12056.363636363636);
- Point2D pointC = new Point2D.Double(11429.886363636364, 12170.272727272728);
- Point2D pointP = new Point2D.Double(11430.886363636364, 12052.045875614034);
-
- Point2D pointO = pt.getCoordinatesInNormalBase(pointA, pointB, pointC, pointP);
- Point2D pointQ = pt.getCoordinatesInCellDesignerBase(pointA, pointB, pointC, pointO);
- assertTrue(Double.isFinite(pointQ.getX()));
- assertTrue(Double.isFinite(pointQ.getY()));
- assertEquals(0, pointQ.distance(pointP), 1e-6);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.awt.geom.Point2D;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class CellDesignerPointTransformationTest {
+ Logger logger = Logger.getLogger(CellDesignerPointTransformationTest .class);
+
+ CellDesignerPointTransformation pt = new CellDesignerPointTransformation();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ /**
+ * Check if coordinetas are transformed in both ways correctly for this
+ * strange transformation with new base constsed of 3 points
+ */
+ @Test
+ public void testConversionOfPointBases() {
+ try {
+ Point2D pointA = new Point2D.Double(1, 2);
+ Point2D pointB = new Point2D.Double(10, 12);
+ Point2D pointC = new Point2D.Double(4, 3);
+ Point2D pointP = new Point2D.Double(0.1, 2);
+
+ Point2D pointO = pt.getCoordinatesInNormalBase(pointA, pointB, pointC, pointP);
+ Point2D pointQ = pt.getCoordinatesInCellDesignerBase(pointA, pointB, pointC, pointO);
+ assertEquals(0, pointQ.distance(pointP), 1e-6);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testNanTransformation() {
+ try {
+ Point2D pointA = new Point2D.Double(11429.886363636364, 11966.818181818182);
+ Point2D pointB = new Point2D.Double(11300.886363636364, 12056.363636363636);
+ Point2D pointC = new Point2D.Double(11429.886363636364, 12170.272727272728);
+ Point2D pointP = new Point2D.Double(11430.886363636364, 12052.045875614034);
+
+ Point2D pointO = pt.getCoordinatesInNormalBase(pointA, pointB, pointC, pointP);
+ Point2D pointQ = pt.getCoordinatesInCellDesignerBase(pointA, pointB, pointC, pointO);
+ assertTrue(Double.isFinite(pointQ.getX()));
+ assertTrue(Double.isFinite(pointQ.getY()));
+ assertEquals(0, pointQ.distance(pointP), 1e-6);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerPolygonTransformationTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerPolygonTransformationTest.java
index 342518c0fd..1b1a46ccdb 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerPolygonTransformationTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerPolygonTransformationTest.java
@@ -1,71 +1,71 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
-
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-
-public class CellDesignerPolygonTransformationTest {
- CellDesignerPolygonTransformation tranformation = new CellDesignerPolygonTransformation();
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetPointOnInvalidPolygonByAnchor() {
- try {
- tranformation.getPointOnPolygonByAnchor(new ArrayList<>(), null);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Invalid number of points"));
- }
- }
-
- @Test
- public void testGetPointOnPolygonByInvalidAnchor() {
- try {
- List<Point2D> list = new ArrayList<>();
- for (int i = 0; i < CellDesignerAnchor.DIFFERENT_ANCHORS / 2; i++) {
- list.add(new Point2D.Double());
- }
- tranformation.getPointOnPolygonByAnchor(list, null);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Invalid anchor"));
- }
- }
-
- @Test
- public void testGetPointOnPolygonByInvalidAnchor2() {
- try {
- List<Point2D> list = new ArrayList<>();
- for (int i = 0; i < CellDesignerAnchor.DIFFERENT_ANCHORS; i++) {
- list.add(new Point2D.Double());
- }
- tranformation.getPointOnPolygonByAnchor(list, null);
- tranformation.getPointOnPolygonByAnchor(new ArrayList<>(), null);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Invalid anchor"));
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
+
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+
+public class CellDesignerPolygonTransformationTest {
+ CellDesignerPolygonTransformation tranformation = new CellDesignerPolygonTransformation();
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetPointOnInvalidPolygonByAnchor() {
+ try {
+ tranformation.getPointOnPolygonByAnchor(new ArrayList<>(), null);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Invalid number of points"));
+ }
+ }
+
+ @Test
+ public void testGetPointOnPolygonByInvalidAnchor() {
+ try {
+ List<Point2D> list = new ArrayList<>();
+ for (int i = 0; i < CellDesignerAnchor.DIFFERENT_ANCHORS / 2; i++) {
+ list.add(new Point2D.Double());
+ }
+ tranformation.getPointOnPolygonByAnchor(list, null);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Invalid anchor"));
+ }
+ }
+
+ @Test
+ public void testGetPointOnPolygonByInvalidAnchor2() {
+ try {
+ List<Point2D> list = new ArrayList<>();
+ for (int i = 0; i < CellDesignerAnchor.DIFFERENT_ANCHORS; i++) {
+ list.add(new Point2D.Double());
+ }
+ tranformation.getPointOnPolygonByAnchor(list, null);
+ tranformation.getPointOnPolygonByAnchor(new ArrayList<>(), null);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Invalid anchor"));
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerRectangleTransformationTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerRectangleTransformationTest.java
index 250443ec13..a34cb8711a 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerRectangleTransformationTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerRectangleTransformationTest.java
@@ -1,36 +1,36 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
-
-import static org.junit.Assert.assertEquals;
-
-import java.awt.geom.Point2D;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Configuration;
-
-public class CellDesignerRectangleTransformationTest {
-
- CellDesignerRectangleTransformation transformation = new CellDesignerRectangleTransformation();
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetPointOnRectangleByAnchor() {
- Point2D poitn = transformation.getPointOnRectangleByAnchor(0, 0, 10, 12, null);
- assertEquals(0.0, poitn.distance(new Point2D.Double(5, 6)), Configuration.EPSILON);
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
+
+import static org.junit.Assert.assertEquals;
+
+import java.awt.geom.Point2D;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+
+public class CellDesignerRectangleTransformationTest {
+
+ CellDesignerRectangleTransformation transformation = new CellDesignerRectangleTransformation();
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetPointOnRectangleByAnchor() {
+ Point2D poitn = transformation.getPointOnRectangleByAnchor(0, 0, 10, 12, null);
+ assertEquals(0.0, poitn.distance(new Point2D.Double(5, 6)), Configuration.EPSILON);
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/PolylineDataFactoryTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/PolylineDataFactoryTest.java
index 7ad9b3517b..4661d079e8 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/PolylineDataFactoryTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/PolylineDataFactoryTest.java
@@ -1,37 +1,37 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
-
-import static org.junit.Assert.assertNotNull;
-
-import java.lang.reflect.Constructor;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class PolylineDataFactoryTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testPrivateCotnstructor() throws Exception {
- try {
- Constructor<?> constr = PolylineDataFactory.class.getDeclaredConstructor(new Class<?>[] {});
- constr.setAccessible(true);
- assertNotNull(constr.newInstance(new Object[] {}));
- } catch (Exception e) {
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.geometry.helper;
+
+import static org.junit.Assert.assertNotNull;
+
+import java.lang.reflect.Constructor;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class PolylineDataFactoryTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testPrivateCotnstructor() throws Exception {
+ try {
+ Constructor<?> constr = PolylineDataFactory.class.getDeclaredConstructor(new Class<?>[] {});
+ constr.setAccessible(true);
+ assertNotNull(constr.newInstance(new Object[] {}));
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/AllReactionTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/AllReactionTests.java
index 736069c5d0..3b095692f5 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/AllReactionTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/AllReactionTests.java
@@ -1,20 +1,20 @@
-package lcsb.mapviewer.converter.model.celldesigner.reaction;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ KineticsXmlParserTest.class, //
- ModificationReactionTest.class, //
- ReactionCollectionXmlParserTest.class, //
- ReactionFromXmlTest.class, //
- ReactionLineDataTest.class, //
- ReactionParserExceptionTest.class, //
- ReactionParserTests.class, //
- ReactionToXmlTest.class, //
- UnknownModifierClassExceptionTest.class, //
-})
-public class AllReactionTests {
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.reaction;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ KineticsXmlParserTest.class, //
+ ModificationReactionTest.class, //
+ ReactionCollectionXmlParserTest.class, //
+ ReactionFromXmlTest.class, //
+ ReactionLineDataTest.class, //
+ ReactionParserExceptionTest.class, //
+ ReactionParserTests.class, //
+ ReactionToXmlTest.class, //
+ UnknownModifierClassExceptionTest.class, //
+})
+public class AllReactionTests {
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParserTest.java
index 8abf4a9961..07bf29dd76 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParserTest.java
@@ -1,189 +1,189 @@
-package lcsb.mapviewer.converter.model.celldesigner.reaction;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-
-import java.awt.geom.Line2D;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.w3c.dom.Node;
-
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class ReactionCollectionXmlParserTest extends CellDesignerTestFunctions {
- Logger logger = Logger.getLogger(ReactionCollectionXmlParserTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParseXmlReactionCollection() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
-
- CellDesignerElementCollection elements = new CellDesignerElementCollection();
- ReactionCollectionXmlParser parser = new ReactionCollectionXmlParser(model, elements, false);
-
- String xmlString = readFile("testFiles/reactions/listOfReactions.xml");
- Node node = getNodeFromXmlString(xmlString);
- List<Reaction> reactions = parser.parseXmlReactionCollection(node);
-
- assertEquals(3, reactions.size());
-
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- @Test
- public void testReactionCollectionToXmlString() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
-
- CellDesignerElementCollection elements = new CellDesignerElementCollection();
- ReactionCollectionXmlParser parser = new ReactionCollectionXmlParser(model, elements, false);
-
- String xmlString = readFile("testFiles/reactions/listOfReactions.xml");
- Node node = getNodeFromXmlString(xmlString);
- List<Reaction> reactions = parser.parseXmlReactionCollection(node);
-
- elements = new CellDesignerElementCollection();
- parser = new ReactionCollectionXmlParser(model, elements, false);
- String xmlString2 = parser.reactionCollectionToXmlString(reactions);
- assertNotNull(xmlString2);
-
- elements = new CellDesignerElementCollection();
- parser = new ReactionCollectionXmlParser(model, elements, false);
- node = getNodeFromXmlString(xmlString2);
- List<Reaction> reactions2 = parser.parseXmlReactionCollection(node);
-
- assertEquals(reactions.size(), reactions2.size());
- for (int i = 0; i < reactions.size(); i++) {
- Reaction a = reactions.get(0);
- Reaction b = reactions2.get(0);
-
- List<Line2D> linesA = a.getLines();
- List<Line2D> linesB = b.getLines();
- for (int j = 0; j < linesA.size(); j++) {
- Line2D lineA = linesA.get(j);
- Line2D lineB = linesB.get(j);
- assertEquals(lineA.getX1(), lineB.getX1(), EPSILON);
- assertEquals(lineA.getY1(), lineB.getY1(), EPSILON);
- assertEquals(lineA.getX2(), lineB.getX2(), EPSILON);
- assertEquals(lineA.getY2(), lineB.getY2(), EPSILON);
- }
- }
-
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- private Model getModelFilledWithSpecies() {
- Model model = new ModelFullIndexed(null);
-
- Species sa1 = new GenericProtein("sa1");
- sa1.setX(100.0);
- sa1.setY(200.0);
- sa1.setWidth(300.0);
- sa1.setHeight(400.0);
- model.addElement(sa1);
-
- Species sa2 = new GenericProtein("sa2");
- sa2.setX(1050.0);
- sa2.setY(2050.0);
- sa2.setWidth(300.0);
- sa2.setHeight(450.0);
- model.addElement(sa2);
-
- Species sa3 = new GenericProtein("sa3");
- sa3.setX(600.0);
- sa3.setY(250.0);
- sa3.setWidth(300.0);
- sa3.setHeight(400.0);
- model.addElement(sa3);
-
- Species sa4 = new GenericProtein("sa4");
- sa4.setX(550.0);
- sa4.setY(350.0);
- sa4.setWidth(300.0);
- sa4.setHeight(450.0);
- model.addElement(sa4);
-
- Species sa5 = new GenericProtein("sa5");
- sa5.setX(10.0);
- sa5.setY(250.0);
- sa5.setWidth(300.0);
- sa5.setHeight(450.0);
- model.addElement(sa5);
-
- Species sa6 = new GenericProtein("sa6");
- sa6.setX(10.0);
- sa6.setY(250.0);
- sa6.setWidth(300.0);
- sa6.setHeight(450.0);
- model.addElement(sa6);
-
- Species sa10 = new GenericProtein("sa10");
- sa10.setX(210.0);
- sa10.setY(220.0);
- sa10.setWidth(320.0);
- sa10.setHeight(250.0);
- model.addElement(sa10);
-
- Species sa11 = new GenericProtein("sa11");
- sa11.setX(11.0);
- sa11.setY(320.0);
- sa11.setWidth(321.0);
- sa11.setHeight(150.0);
- model.addElement(sa11);
-
- Species sa12 = new GenericProtein("sa12");
- sa12.setX(12.0);
- sa12.setY(20.0);
- sa12.setWidth(321.0);
- sa12.setHeight(150.0);
- model.addElement(sa12);
-
- Species sa13 = new GenericProtein("sa13");
- sa13.setX(513.0);
- sa13.setY(20.0);
- sa13.setWidth(321.0);
- sa13.setHeight(150.0);
- model.addElement(sa13);
-
- Species sa14 = new GenericProtein("sa14");
- sa14.setX(14.0);
- sa14.setY(820.0);
- sa14.setWidth(321.0);
- sa14.setHeight(150.0);
- model.addElement(sa14);
-
- Species sa15 = new GenericProtein("sa15");
- sa15.setX(815.0);
- sa15.setY(620.0);
- sa15.setWidth(321.0);
- sa15.setHeight(150.0);
- model.addElement(sa15);
-
- return model;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.reaction;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import java.awt.geom.Line2D;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.w3c.dom.Node;
+
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class ReactionCollectionXmlParserTest extends CellDesignerTestFunctions {
+ Logger logger = Logger.getLogger(ReactionCollectionXmlParserTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testParseXmlReactionCollection() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+
+ CellDesignerElementCollection elements = new CellDesignerElementCollection();
+ ReactionCollectionXmlParser parser = new ReactionCollectionXmlParser(model, elements, false);
+
+ String xmlString = readFile("testFiles/reactions/listOfReactions.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ List<Reaction> reactions = parser.parseXmlReactionCollection(node);
+
+ assertEquals(3, reactions.size());
+
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionCollectionToXmlString() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+
+ CellDesignerElementCollection elements = new CellDesignerElementCollection();
+ ReactionCollectionXmlParser parser = new ReactionCollectionXmlParser(model, elements, false);
+
+ String xmlString = readFile("testFiles/reactions/listOfReactions.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ List<Reaction> reactions = parser.parseXmlReactionCollection(node);
+
+ elements = new CellDesignerElementCollection();
+ parser = new ReactionCollectionXmlParser(model, elements, false);
+ String xmlString2 = parser.reactionCollectionToXmlString(reactions);
+ assertNotNull(xmlString2);
+
+ elements = new CellDesignerElementCollection();
+ parser = new ReactionCollectionXmlParser(model, elements, false);
+ node = getNodeFromXmlString(xmlString2);
+ List<Reaction> reactions2 = parser.parseXmlReactionCollection(node);
+
+ assertEquals(reactions.size(), reactions2.size());
+ for (int i = 0; i < reactions.size(); i++) {
+ Reaction a = reactions.get(0);
+ Reaction b = reactions2.get(0);
+
+ List<Line2D> linesA = a.getLines();
+ List<Line2D> linesB = b.getLines();
+ for (int j = 0; j < linesA.size(); j++) {
+ Line2D lineA = linesA.get(j);
+ Line2D lineB = linesB.get(j);
+ assertEquals(lineA.getX1(), lineB.getX1(), EPSILON);
+ assertEquals(lineA.getY1(), lineB.getY1(), EPSILON);
+ assertEquals(lineA.getX2(), lineB.getX2(), EPSILON);
+ assertEquals(lineA.getY2(), lineB.getY2(), EPSILON);
+ }
+ }
+
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ private Model getModelFilledWithSpecies() {
+ Model model = new ModelFullIndexed(null);
+
+ Species sa1 = new GenericProtein("sa1");
+ sa1.setX(100.0);
+ sa1.setY(200.0);
+ sa1.setWidth(300.0);
+ sa1.setHeight(400.0);
+ model.addElement(sa1);
+
+ Species sa2 = new GenericProtein("sa2");
+ sa2.setX(1050.0);
+ sa2.setY(2050.0);
+ sa2.setWidth(300.0);
+ sa2.setHeight(450.0);
+ model.addElement(sa2);
+
+ Species sa3 = new GenericProtein("sa3");
+ sa3.setX(600.0);
+ sa3.setY(250.0);
+ sa3.setWidth(300.0);
+ sa3.setHeight(400.0);
+ model.addElement(sa3);
+
+ Species sa4 = new GenericProtein("sa4");
+ sa4.setX(550.0);
+ sa4.setY(350.0);
+ sa4.setWidth(300.0);
+ sa4.setHeight(450.0);
+ model.addElement(sa4);
+
+ Species sa5 = new GenericProtein("sa5");
+ sa5.setX(10.0);
+ sa5.setY(250.0);
+ sa5.setWidth(300.0);
+ sa5.setHeight(450.0);
+ model.addElement(sa5);
+
+ Species sa6 = new GenericProtein("sa6");
+ sa6.setX(10.0);
+ sa6.setY(250.0);
+ sa6.setWidth(300.0);
+ sa6.setHeight(450.0);
+ model.addElement(sa6);
+
+ Species sa10 = new GenericProtein("sa10");
+ sa10.setX(210.0);
+ sa10.setY(220.0);
+ sa10.setWidth(320.0);
+ sa10.setHeight(250.0);
+ model.addElement(sa10);
+
+ Species sa11 = new GenericProtein("sa11");
+ sa11.setX(11.0);
+ sa11.setY(320.0);
+ sa11.setWidth(321.0);
+ sa11.setHeight(150.0);
+ model.addElement(sa11);
+
+ Species sa12 = new GenericProtein("sa12");
+ sa12.setX(12.0);
+ sa12.setY(20.0);
+ sa12.setWidth(321.0);
+ sa12.setHeight(150.0);
+ model.addElement(sa12);
+
+ Species sa13 = new GenericProtein("sa13");
+ sa13.setX(513.0);
+ sa13.setY(20.0);
+ sa13.setWidth(321.0);
+ sa13.setHeight(150.0);
+ model.addElement(sa13);
+
+ Species sa14 = new GenericProtein("sa14");
+ sa14.setX(14.0);
+ sa14.setY(820.0);
+ sa14.setWidth(321.0);
+ sa14.setHeight(150.0);
+ model.addElement(sa14);
+
+ Species sa15 = new GenericProtein("sa15");
+ sa15.setX(815.0);
+ sa15.setY(620.0);
+ sa15.setWidth(321.0);
+ sa15.setHeight(150.0);
+ model.addElement(sa15);
+
+ return model;
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXmlTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXmlTest.java
index ddcab87314..fca282d661 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXmlTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXmlTest.java
@@ -1,667 +1,667 @@
-package lcsb.mapviewer.converter.model.celldesigner.reaction;
-
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGenericProtein;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.type.TwoProductReactionInterface;
-import lcsb.mapviewer.model.map.reaction.type.TwoReactantReactionInterface;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class ReactionFromXmlTest extends CellDesignerTestFunctions {
- ReactionXmlParser parser;
- Model model = new ModelFullIndexed(null);
-
- CellDesignerElementCollection elements;
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- elements = new CellDesignerElementCollection();
- parser = new ReactionXmlParser(elements, false);
-
- Species alias = new GenericProtein("sa1");
- model.addElement(alias);
-
- alias = new GenericProtein("sa2");
- model.addElement(alias);
-
- alias = new GenericProtein("sa3");
- model.addElement(alias);
-
- alias = new GenericProtein("sa4");
- model.addElement(alias);
-
- elements.addElement(new CellDesignerGenericProtein("s1"));
- elements.addElement(new CellDesignerGenericProtein("s2"));
- elements.addElement(new CellDesignerGenericProtein("s3"));
- elements.addElement(new CellDesignerGenericProtein("s4"));
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testInvalid() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("kineticLaw node doesn't have math subnode"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid3() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction3.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Unknown element of reaction"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid4() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction4.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("No annotation node in reaction"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid5() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction5.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Problem with parsing RDF"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid6() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction6.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Unknown element of reaction/annotation"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid7() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction7.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:baseReactants"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid8() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction8.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:baseProducts"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid9() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction9.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(),
- e.getMessage().contains("Unknown element of celldesigner:connectScheme"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid10() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction10.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Unknown element of reaction/celldesigner:extension"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid11() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction11.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("No connectScheme node"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid12() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction12.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Unknown node type"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid13() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction13.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Too many gate members"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid14() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction14.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Missing gate member connecting members"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid15() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction15.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Couldn't find type of BOOLEAN_LOGIC_GATE"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid16() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction16.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(),
- e.getMessage().contains("Unknown element of celldesigner:listOfReactantLinks"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid17() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction17.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(),
- e.getMessage().contains("Unknown element of celldesigner:reactantLink"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid19() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction19.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Alias doesn't exist"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid20() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction20.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(),
- e.getMessage().contains("Unknown element of celldesigner:listOfProductLinks"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid21() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction21.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(),
- e.getMessage().contains("Unknown element of celldesigner:reactantLink"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid23() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction23.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Alias doesn't exist"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid24() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction24.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(),
- e.getMessage().contains("Unknown element of celldesigner:listOfModification"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid26() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction26.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Unknown alias"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid28() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction28.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(),
- e.getMessage().contains("Unknown element of celldesigner:connectScheme"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid29() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction29.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(),
- e.getMessage().contains("Unknown element of celldesigner:listOfModification"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid30() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction30.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(),
- e.getMessage().contains("Unknown element of reaction/celldesigner:baseReactant"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid31() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction31.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Alias with id"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid33() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction33.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(),
- e.getMessage().contains("Unknown element of reaction/celldesigner:baseReactant"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid34() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction34.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Alias with id"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid36() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction36.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(),
- e.getMessage().contains("Unknown element of reaction/celldesigner:baseProduct"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidReaction() throws Exception {
- try {
- // test situation when createProperTypeReaction returns reaction of
- // unknown type
- ReactionFromXml parser = new ReactionFromXml(null, false) {
- Reaction createProperTypeReaction(String type, Reaction result) {
- return result;
- }
- };
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/xmlNodeTestExamples/reaction_transport.xml")),
- model);
- fail("Exception expected");
-
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Problem with parsing lines. Unknown reaction"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidReaction2() throws Exception {
- try {
- // test situation when createProperTypeReaction returns reaction of
- // unknown type that implements TwoProductReactionInterface
-
- class NewReactionType extends Reaction implements TwoProductReactionInterface {
- private static final long serialVersionUID = 1L;
-
- public NewReactionType(Reaction r) {
- super(r);
- }
- }
-
- ReactionFromXml parser = new ReactionFromXml(null, false) {
- Reaction createProperTypeReaction(String type, Reaction result) {
- return new NewReactionType(result);
- }
- };
- parser.getReaction(
- super.getNodeFromXmlString(readFile("testFiles/xmlNodeTestExamples/reaction_dissociation_with_addition.xml")),
- model);
- fail("Exception expected");
-
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Invalid reaction type"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidReaction3() throws Exception {
- try {
- // test situation when createOperatorsForTwoProductReaction encounter
- // reaction with two many base reactants
-
- ReactionFromXml parser = new ReactionFromXml(null, false) {
- Reaction createProperTypeReaction(String type, Reaction result) throws ReactionParserException {
- Reaction r = super.createProperTypeReaction(type, result);
- r.addReactant(new Reactant());
- return r;
- }
- };
- parser.getReaction(
- super.getNodeFromXmlString(readFile("testFiles/xmlNodeTestExamples/reaction_dissociation_with_addition.xml")),
- model);
- fail("Exception expected");
-
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Reaction has more than one reactant"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidReaction4() throws Exception {
- try {
- // test situation when createOperatorsForTwoProductReaction encounter
- // reaction with two many base products
-
- ReactionFromXml parser = new ReactionFromXml(null, false) {
- Reaction createProperTypeReaction(String type, Reaction result) throws ReactionParserException {
- Reaction r = super.createProperTypeReaction(type, result);
- r.addProduct(new Product());
- return r;
- }
- };
- parser.getReaction(
- super.getNodeFromXmlString(readFile("testFiles/xmlNodeTestExamples/reaction_dissociation_with_addition.xml")),
- model);
- fail("Exception expected");
-
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Too many products"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidReaction5() throws Exception {
- try {
- // test situation when createProperTypeReaction returns reaction of
- // unknown type that implements TwoReactantReactionInterface
-
- class NewReactionType extends Reaction implements TwoReactantReactionInterface {
- private static final long serialVersionUID = 1L;
-
- public NewReactionType(Reaction r) {
- super(r);
- }
- }
-
- ReactionFromXml parser = new ReactionFromXml(null, false) {
- Reaction createProperTypeReaction(String type, Reaction result) {
- return new NewReactionType(result);
- }
- };
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/xmlNodeTestExamples/reaction_heterodimer.xml")),
- model);
- fail("Exception expected");
-
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Unknown class type with two reactants"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidReaction6() throws Exception {
- try {
- // test situation when createOperatorsForTwoReactantReaction encounter
- // reaction with two many base reactants
-
- ReactionFromXml parser = new ReactionFromXml(null, false) {
- Reaction createProperTypeReaction(String type, Reaction result) throws ReactionParserException {
- Reaction r = super.createProperTypeReaction(type, result);
- r.addReactant(new Reactant());
- return r;
- }
- };
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/xmlNodeTestExamples/reaction_heterodimer.xml")),
- model);
- fail("Exception expected");
-
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Too many reactants"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidReaction7() throws Exception {
- try {
- // test situation when createOperatorsForTwoReactantReaction encounter
- // reaction with two many base products
-
- ReactionFromXml parser = new ReactionFromXml(null, false) {
- Reaction createProperTypeReaction(String type, Reaction result) throws ReactionParserException {
- Reaction r = super.createProperTypeReaction(type, result);
- r.addProduct(new Product());
- return r;
- }
- };
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/xmlNodeTestExamples/reaction_heterodimer.xml")),
- model);
- fail("Exception expected");
-
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Reaction has more than one product"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidEditPointsString() throws Exception {
- try {
- ReactionFromXml parser = new ReactionFromXml(null, false);
-
- parser.parseEditPointsString("1");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Invalid editPoint string"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidEditPointsString2() throws Exception {
- try {
- ReactionFromXml parser = new ReactionFromXml(null, false);
-
- parser.parseEditPointsString("1,Infinity");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Invalid point parsed from input string"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.reaction;
+
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGenericProtein;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.type.TwoProductReactionInterface;
+import lcsb.mapviewer.model.map.reaction.type.TwoReactantReactionInterface;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class ReactionFromXmlTest extends CellDesignerTestFunctions {
+ ReactionXmlParser parser;
+ Model model = new ModelFullIndexed(null);
+
+ CellDesignerElementCollection elements;
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ elements = new CellDesignerElementCollection();
+ parser = new ReactionXmlParser(elements, false);
+
+ Species alias = new GenericProtein("sa1");
+ model.addElement(alias);
+
+ alias = new GenericProtein("sa2");
+ model.addElement(alias);
+
+ alias = new GenericProtein("sa3");
+ model.addElement(alias);
+
+ alias = new GenericProtein("sa4");
+ model.addElement(alias);
+
+ elements.addElement(new CellDesignerGenericProtein("s1"));
+ elements.addElement(new CellDesignerGenericProtein("s2"));
+ elements.addElement(new CellDesignerGenericProtein("s3"));
+ elements.addElement(new CellDesignerGenericProtein("s4"));
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testInvalid() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("kineticLaw node doesn't have math subnode"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid3() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction3.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Unknown element of reaction"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid4() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction4.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("No annotation node in reaction"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid5() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction5.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Problem with parsing RDF"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid6() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction6.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Unknown element of reaction/annotation"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid7() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction7.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:baseReactants"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid8() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction8.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:baseProducts"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid9() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction9.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(),
+ e.getMessage().contains("Unknown element of celldesigner:connectScheme"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid10() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction10.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Unknown element of reaction/celldesigner:extension"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid11() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction11.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("No connectScheme node"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid12() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction12.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Unknown node type"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid13() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction13.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Too many gate members"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid14() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction14.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Missing gate member connecting members"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid15() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction15.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Couldn't find type of BOOLEAN_LOGIC_GATE"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid16() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction16.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(),
+ e.getMessage().contains("Unknown element of celldesigner:listOfReactantLinks"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid17() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction17.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(),
+ e.getMessage().contains("Unknown element of celldesigner:reactantLink"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid19() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction19.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Alias doesn't exist"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid20() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction20.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(),
+ e.getMessage().contains("Unknown element of celldesigner:listOfProductLinks"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid21() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction21.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(),
+ e.getMessage().contains("Unknown element of celldesigner:reactantLink"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid23() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction23.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Alias doesn't exist"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid24() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction24.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(),
+ e.getMessage().contains("Unknown element of celldesigner:listOfModification"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid26() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction26.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Unknown alias"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid28() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction28.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(),
+ e.getMessage().contains("Unknown element of celldesigner:connectScheme"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid29() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction29.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(),
+ e.getMessage().contains("Unknown element of celldesigner:listOfModification"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid30() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction30.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(),
+ e.getMessage().contains("Unknown element of reaction/celldesigner:baseReactant"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid31() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction31.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Alias with id"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid33() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction33.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(),
+ e.getMessage().contains("Unknown element of reaction/celldesigner:baseReactant"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid34() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction34.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Alias with id"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid36() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction36.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(),
+ e.getMessage().contains("Unknown element of reaction/celldesigner:baseProduct"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidReaction() throws Exception {
+ try {
+ // test situation when createProperTypeReaction returns reaction of
+ // unknown type
+ ReactionFromXml parser = new ReactionFromXml(null, false) {
+ Reaction createProperTypeReaction(String type, Reaction result) {
+ return result;
+ }
+ };
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/xmlNodeTestExamples/reaction_transport.xml")),
+ model);
+ fail("Exception expected");
+
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Problem with parsing lines. Unknown reaction"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidReaction2() throws Exception {
+ try {
+ // test situation when createProperTypeReaction returns reaction of
+ // unknown type that implements TwoProductReactionInterface
+
+ class NewReactionType extends Reaction implements TwoProductReactionInterface {
+ private static final long serialVersionUID = 1L;
+
+ public NewReactionType(Reaction r) {
+ super(r);
+ }
+ }
+
+ ReactionFromXml parser = new ReactionFromXml(null, false) {
+ Reaction createProperTypeReaction(String type, Reaction result) {
+ return new NewReactionType(result);
+ }
+ };
+ parser.getReaction(
+ super.getNodeFromXmlString(readFile("testFiles/xmlNodeTestExamples/reaction_dissociation_with_addition.xml")),
+ model);
+ fail("Exception expected");
+
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Invalid reaction type"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidReaction3() throws Exception {
+ try {
+ // test situation when createOperatorsForTwoProductReaction encounter
+ // reaction with two many base reactants
+
+ ReactionFromXml parser = new ReactionFromXml(null, false) {
+ Reaction createProperTypeReaction(String type, Reaction result) throws ReactionParserException {
+ Reaction r = super.createProperTypeReaction(type, result);
+ r.addReactant(new Reactant());
+ return r;
+ }
+ };
+ parser.getReaction(
+ super.getNodeFromXmlString(readFile("testFiles/xmlNodeTestExamples/reaction_dissociation_with_addition.xml")),
+ model);
+ fail("Exception expected");
+
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Reaction has more than one reactant"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidReaction4() throws Exception {
+ try {
+ // test situation when createOperatorsForTwoProductReaction encounter
+ // reaction with two many base products
+
+ ReactionFromXml parser = new ReactionFromXml(null, false) {
+ Reaction createProperTypeReaction(String type, Reaction result) throws ReactionParserException {
+ Reaction r = super.createProperTypeReaction(type, result);
+ r.addProduct(new Product());
+ return r;
+ }
+ };
+ parser.getReaction(
+ super.getNodeFromXmlString(readFile("testFiles/xmlNodeTestExamples/reaction_dissociation_with_addition.xml")),
+ model);
+ fail("Exception expected");
+
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Too many products"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidReaction5() throws Exception {
+ try {
+ // test situation when createProperTypeReaction returns reaction of
+ // unknown type that implements TwoReactantReactionInterface
+
+ class NewReactionType extends Reaction implements TwoReactantReactionInterface {
+ private static final long serialVersionUID = 1L;
+
+ public NewReactionType(Reaction r) {
+ super(r);
+ }
+ }
+
+ ReactionFromXml parser = new ReactionFromXml(null, false) {
+ Reaction createProperTypeReaction(String type, Reaction result) {
+ return new NewReactionType(result);
+ }
+ };
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/xmlNodeTestExamples/reaction_heterodimer.xml")),
+ model);
+ fail("Exception expected");
+
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Unknown class type with two reactants"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidReaction6() throws Exception {
+ try {
+ // test situation when createOperatorsForTwoReactantReaction encounter
+ // reaction with two many base reactants
+
+ ReactionFromXml parser = new ReactionFromXml(null, false) {
+ Reaction createProperTypeReaction(String type, Reaction result) throws ReactionParserException {
+ Reaction r = super.createProperTypeReaction(type, result);
+ r.addReactant(new Reactant());
+ return r;
+ }
+ };
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/xmlNodeTestExamples/reaction_heterodimer.xml")),
+ model);
+ fail("Exception expected");
+
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Too many reactants"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidReaction7() throws Exception {
+ try {
+ // test situation when createOperatorsForTwoReactantReaction encounter
+ // reaction with two many base products
+
+ ReactionFromXml parser = new ReactionFromXml(null, false) {
+ Reaction createProperTypeReaction(String type, Reaction result) throws ReactionParserException {
+ Reaction r = super.createProperTypeReaction(type, result);
+ r.addProduct(new Product());
+ return r;
+ }
+ };
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/xmlNodeTestExamples/reaction_heterodimer.xml")),
+ model);
+ fail("Exception expected");
+
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Reaction has more than one product"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidEditPointsString() throws Exception {
+ try {
+ ReactionFromXml parser = new ReactionFromXml(null, false);
+
+ parser.parseEditPointsString("1");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Invalid editPoint string"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidEditPointsString2() throws Exception {
+ try {
+ ReactionFromXml parser = new ReactionFromXml(null, false);
+
+ parser.parseEditPointsString("1,Infinity");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Invalid point parsed from input string"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionLineDataTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionLineDataTest.java
index 76bab8805a..c30d2a3a08 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionLineDataTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionLineDataTest.java
@@ -1,55 +1,55 @@
-package lcsb.mapviewer.converter.model.celldesigner.reaction;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-public class ReactionLineDataTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetByLineType() {
- assertNull(ReactionLineData.getByLineType(null, null));
- }
-
- @Test
- public void test() {
- assertNotNull(ReactionLineData.getByCellDesignerString("UNKNOWN_REDUCED_MODULATION"));
- }
-
- @Test
- public void testAllValues() {
- for (ReactionLineData value : ReactionLineData.values()) {
- assertNotNull(ReactionLineData.valueOf(value.toString()));
- }
- }
-
- @Test
- public void testCreateInvalidReaction() throws Exception {
- try {
- ReactionLineData.TRANSPORT.createReaction(Mockito.mock(Reaction.class));
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Problem with creation the new instance of reaction"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.reaction;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+public class ReactionLineDataTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetByLineType() {
+ assertNull(ReactionLineData.getByLineType(null, null));
+ }
+
+ @Test
+ public void test() {
+ assertNotNull(ReactionLineData.getByCellDesignerString("UNKNOWN_REDUCED_MODULATION"));
+ }
+
+ @Test
+ public void testAllValues() {
+ for (ReactionLineData value : ReactionLineData.values()) {
+ assertNotNull(ReactionLineData.valueOf(value.toString()));
+ }
+ }
+
+ @Test
+ public void testCreateInvalidReaction() throws Exception {
+ try {
+ ReactionLineData.TRANSPORT.createReaction(Mockito.mock(Reaction.class));
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Problem with creation the new instance of reaction"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserExceptionTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserExceptionTest.java
index 25b0bf7c1d..ac6b375532 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserExceptionTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserExceptionTest.java
@@ -1,42 +1,42 @@
-package lcsb.mapviewer.converter.model.celldesigner.reaction;
-
-import static org.junit.Assert.assertEquals;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-public class ReactionParserExceptionTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testConstructor() {
- Reaction reaction = new Reaction();
- reaction.setIdReaction("1");
- ReactionParserException exception = new ReactionParserException("text", reaction);
- assertEquals("1", exception.getReactionId());
- }
-
- @Test
- public void testConstructor2() {
- Reaction reaction = new Reaction();
- reaction.setIdReaction("1");
- ReactionParserException exception = new ReactionParserException("text", reaction, new Exception());
- assertEquals("1", exception.getReactionId());
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.reaction;
+
+import static org.junit.Assert.assertEquals;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+public class ReactionParserExceptionTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testConstructor() {
+ Reaction reaction = new Reaction();
+ reaction.setIdReaction("1");
+ ReactionParserException exception = new ReactionParserException("text", reaction);
+ assertEquals("1", exception.getReactionId());
+ }
+
+ @Test
+ public void testConstructor2() {
+ Reaction reaction = new Reaction();
+ reaction.setIdReaction("1");
+ ReactionParserException exception = new ReactionParserException("text", reaction, new Exception());
+ assertEquals("1", exception.getReactionId());
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserTests.java
index a62c5c340e..9aa869f4e2 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserTests.java
@@ -1,1871 +1,1871 @@
-package lcsb.mapviewer.converter.model.celldesigner.reaction;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
-import java.io.ByteArrayInputStream;
-import java.util.List;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.w3c.dom.Node;
-
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGenericProtein;
-import lcsb.mapviewer.model.graphics.ArrowType;
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.reaction.AndOperator;
-import lcsb.mapviewer.model.map.reaction.AssociationOperator;
-import lcsb.mapviewer.model.map.reaction.DissociationOperator;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.reaction.NandOperator;
-import lcsb.mapviewer.model.map.reaction.NodeOperator;
-import lcsb.mapviewer.model.map.reaction.OrOperator;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.SplitOperator;
-import lcsb.mapviewer.model.map.reaction.TruncationOperator;
-import lcsb.mapviewer.model.map.reaction.UnknownOperator;
-import lcsb.mapviewer.model.map.reaction.type.BooleanLogicGateReaction;
-import lcsb.mapviewer.model.map.reaction.type.DissociationReaction;
-import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
-import lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction;
-import lcsb.mapviewer.model.map.reaction.type.ReactionRect;
-import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
-import lcsb.mapviewer.model.map.reaction.type.TranscriptionReaction;
-import lcsb.mapviewer.model.map.reaction.type.TranslationReaction;
-import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
-import lcsb.mapviewer.model.map.reaction.type.TruncationReaction;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class ReactionParserTests extends CellDesignerTestFunctions {
-
- private Logger logger = Logger.getLogger(ReactionParserTests.class.getName());;
- ReactionXmlParser parser;
- CellDesignerElementCollection elements;
-
- @Before
- public void setUp() throws Exception {
- elements = new CellDesignerElementCollection();
-
- parser = new ReactionXmlParser(elements, false);
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testColorReaction() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/colorfull_reaction.xml");
- Reaction reaction = model.getReactionByReactionId("re1");
- PolylineData line = reaction.getReactants().get(0).getLine();
- assertFalse(
- "000".equals(line.getColor().getRed() + "" + line.getColor().getGreen() + "" + line.getColor().getBlue()));
- line = reaction.getProducts().get(0).getLine();
- assertFalse(
- "000".equals(line.getColor().getRed() + "" + line.getColor().getGreen() + "" + line.getColor().getBlue()));
- line = reaction.getModifiers().get(0).getLine();
- assertFalse(
- "000".equals(line.getColor().getRed() + "" + line.getColor().getGreen() + "" + line.getColor().getBlue()));
- line = reaction.getOperators().get(0).getLine();
- assertFalse(
- "000".equals(line.getColor().getRed() + "" + line.getColor().getGreen() + "" + line.getColor().getBlue()));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testMissingLines() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/problematic/pd_map_with_problematic_reaction_line.xml");
- assertTrue(model.getElementByElementId("sa5003") instanceof GenericProtein);
- Set<Reaction> list = model.getReactions();
- for (Reaction reaction : list) {
- // reaction re1607 in this model was problematic, but in fact the
- // problem
- // can be in any reaction line
- // if (reaction.getId().equals("re1607")) {
- List<Line2D> lines = reaction.getLines();
- for (Line2D line2d : lines) {
- assertFalse(Double.isNaN(line2d.getX1()));
- assertFalse(Double.isNaN(line2d.getX2()));
- assertFalse(Double.isNaN(line2d.getY1()));
- assertFalse(Double.isNaN(line2d.getY2()));
- }
- // }
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testTransitionReaction() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/transition.xml");
- assertEquals(1, model.getReactions().size());
- Reaction reaction = model.getReactions().iterator().next();
- assertTrue(reaction instanceof StateTransitionReaction);
- assertEquals(1, reaction.getReactants().size());
- Reactant reactant = reaction.getReactants().get(0);
-
- assertTrue(reaction.isReversible());
- assertEquals(ArrowType.FULL, reactant.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
- assertEquals(3, reactant.getLine().getLines().size());
-
- Product product = reaction.getProducts().get(0);
- assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
- assertEquals(2, product.getLine().getLines().size());
-
- assertTrue(reactant.getLine().getEndPoint().distance(product.getLine().getPoints().get(0)) < 20);
- assertNotNull(reaction.getReactionRect());
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0,false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCenterLineInSimpleReaction() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/transition.xml");
- assertEquals(1, model.getReactions().size());
- Reaction reaction = model.getReactions().iterator().next();
- Reactant reactant = reaction.getReactants().get(0);
-
- Product product = reaction.getProducts().get(0);
-
- // center of the line should be different than edge points of
- // reactant/product description
- assertFalse(reaction.getCenterLine().getP1().distance(reactant.getLine().getEndPoint()) < 1e-6);
- assertFalse(reaction.getCenterLine().getP2().distance(product.getLine().getBeginPoint()) < 1e-6);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testTransition2() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/transitionWithAdditionalNodes.xml");
- Reaction reaction = model.getReactions().iterator().next();
- assertEquals(2, reaction.getOperators().size());
- for (Reactant reactant : reaction.getReactants()) {
- assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
-
- assertTrue(
- reactant.getLine().getEndPoint().distance(reaction.getReactants().get(0).getLine().getEndPoint()) < 1e-6);
- }
-
- for (Product product : reaction.getProducts()) {
- assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
-
- assertTrue(
- product.getLine().getBeginPoint().distance(reaction.getProducts().get(0).getLine().getBeginPoint()) < 1e-6);
- }
- assertNotNull(reaction.getReactionRect());
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0,false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testTransiotionOmitted() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/transition_omitted.xml");
- Reaction reaction = model.getReactions().iterator().next();
- assertEquals(0, reaction.getOperators().size());
- assertEquals(KnownTransitionOmittedReaction.class, reaction.getClass());
- assertNotNull(reaction.getReactionRect());
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0,false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUnknownTransition() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/unknown_transition.xml");
- Reaction reaction = model.getReactions().iterator().next();
- assertNotNull(reaction.getReactionRect());
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0,false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testTranscription() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/transcription.xml");
- assertEquals(1, model.getReactions().size());
- Reaction reaction = model.getReactions().iterator().next();
- assertTrue(reaction instanceof TranscriptionReaction);
- assertEquals(1, reaction.getReactants().size());
- Reactant reactant = reaction.getReactants().get(0);
- assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
- assertEquals(LineType.DASH_DOT_DOT, reactant.getLine().getType());
- assertEquals(1, reactant.getLine().getLines().size());
-
- Product product = reaction.getProducts().get(0);
- assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
- assertEquals(1, product.getLine().getLines().size());
-
- assertTrue(reactant.getLine().getEndPoint().distance(product.getLine().getPoints().get(0)) < 20);
- assertNotNull(reaction.getReactionRect());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testTranscription2() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/transcription_with_additions.xml");
- assertEquals(1, model.getReactions().size());
- Reaction reaction = model.getReactions().iterator().next();
- assertTrue(reaction instanceof TranscriptionReaction);
- assertEquals(2, reaction.getReactants().size());
- Reactant reactant = reaction.getReactants().get(0);
- assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
- assertEquals(LineType.DASH_DOT_DOT, reactant.getLine().getType());
- assertEquals(1, reactant.getLine().getLines().size());
- NodeOperator operator = null;
- for (NodeOperator operator2 : reaction.getOperators()) {
- if (operator2 instanceof SplitOperator)
- operator = operator2;
- }
- assertEquals(LineType.DASH_DOT_DOT, operator.getLine().getType());
-
- Product product = reaction.getProducts().get(0);
- assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
- assertEquals(1, product.getLine().getLines().size());
-
- assertNotNull(reaction.getReactionRect());
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0,false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testTranslation() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/translation.xml");
- assertEquals(1, model.getReactions().size());
- Reaction reaction = model.getReactions().iterator().next();
- assertTrue(reaction instanceof TranslationReaction);
- assertEquals(2, reaction.getReactants().size());
- Reactant reactant = reaction.getReactants().get(0);
- assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
- assertEquals(LineType.DASH_DOT, reactant.getLine().getType());
- assertEquals(1, reactant.getLine().getLines().size());
- NodeOperator operator = reaction.getOperators().iterator().next();
- assertEquals(LineType.DASH_DOT, operator.getLine().getType());
-
- Product product = reaction.getProducts().get(0);
- assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
- assertEquals(1, product.getLine().getLines().size());
-
- assertNotNull(reaction.getReactionRect());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testTransport() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/transport.xml");
- assertEquals(1, model.getReactions().size());
- Reaction reaction = model.getReactions().iterator().next();
- assertTrue(reaction instanceof TransportReaction);
- assertEquals(1, reaction.getReactants().size());
- Reactant reactant = reaction.getReactants().get(0);
- assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
- assertEquals(1, reactant.getLine().getLines().size());
-
- Product product = reaction.getProducts().get(0);
- assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.FULL_CROSSBAR, product.getLine().getEndAtd().getArrowType());
- assertEquals(1, product.getLine().getLines().size());
-
- assertNotNull(reaction.getReactionRect());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testHeterodimer() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/heterodimer.xml");
- assertEquals(1, model.getReactions().size());
- Reaction reaction = model.getReactions().iterator().next();
- assertTrue(reaction instanceof HeterodimerAssociationReaction);
- assertEquals(2, reaction.getReactants().size());
- Reactant reactant = reaction.getReactants().get(0);
- assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
- assertEquals(2, reactant.getLine().getLines().size());
- reactant = reaction.getReactants().get(1);
- assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
- assertEquals(3, reactant.getLine().getLines().size());
-
- Product product = reaction.getProducts().get(0);
- assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
- assertEquals(3, product.getLine().getLines().size());
-
- NodeOperator operator = reaction.getOperators().iterator().next();
- assertEquals(LineType.SOLID, operator.getLine().getType());
- assertEquals(7, operator.getLine().getLines().size());
-
- assertNotNull(reaction.getReactionRect());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testHeterodimerWithAdditions() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/heterodimerWithAdditions.xml");
-
- assertEquals(1, model.getReactions().size());
- Reaction reaction = model.getReactions().iterator().next();
- assertTrue(reaction instanceof HeterodimerAssociationReaction);
- assertEquals(3, reaction.getReactants().size());
- Reactant reactant = reaction.getReactants().get(0);
- assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
- assertEquals(2, reactant.getLine().getLines().size());
- reactant = reaction.getReactants().get(1);
- assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
- assertEquals(3, reactant.getLine().getLines().size());
-
- for (Product product : reaction.getProducts()) {
- assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
- }
-
- assertEquals(3, reaction.getOperators().size());
- NodeOperator operator = reaction.getOperators().iterator().next();
- assertEquals(LineType.SOLID, operator.getLine().getType());
- assertEquals(7, operator.getLine().getLines().size());
-
- assertNotNull(reaction.getReactionRect());
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0,false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDissociation() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/dissociation.xml");
- assertEquals(2, model.getReactions().size());
- Reaction reaction = null;
- for (Reaction reaction2 : model.getReactions()) {
- if (reaction2.getIdReaction().equals("re1"))
- reaction = reaction2;
- }
- assertTrue(reaction instanceof DissociationReaction);
- assertEquals(1, reaction.getReactants().size());
- Reactant reactant = reaction.getReactants().get(0);
- assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
- assertEquals(2, reactant.getLine().getLines().size());
-
- assertEquals(2, reaction.getProducts().size());
- Product product = reaction.getProducts().get(0);
- assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
- assertEquals(5, product.getLine().getLines().size());
- product = reaction.getProducts().get(1);
- assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
- assertEquals(4, product.getLine().getLines().size());
-
- assertEquals(1, reaction.getOperators().size());
- NodeOperator operator = reaction.getOperators().iterator().next();
- assertEquals(LineType.SOLID, operator.getLine().getType());
- assertEquals(5, operator.getLine().getLines().size());
-
- assertNotNull(reaction.getReactionRect());
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0,false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDissociationWithAddition() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/dissociationWithAddition.xml");
- assertEquals(2, model.getReactions().size());
- Reaction reaction = null;
- for (Reaction reaction2 : model.getReactions()) {
- if (reaction2.getIdReaction().equals("re1"))
- reaction = reaction2;
- }
- assertTrue(reaction instanceof DissociationReaction);
- assertEquals(2, reaction.getReactants().size());
- Reactant reactant = reaction.getReactants().get(0);
- assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
- assertEquals(2, reactant.getLine().getLines().size());
-
- assertEquals(3, reaction.getProducts().size());
- Product product = reaction.getProducts().get(0);
- assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
- assertEquals(5, product.getLine().getLines().size());
- product = reaction.getProducts().get(1);
- assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
- assertEquals(4, product.getLine().getLines().size());
-
- assertEquals(3, reaction.getOperators().size());
- NodeOperator operator = reaction.getOperators().iterator().next();
- assertEquals(LineType.SOLID, operator.getLine().getType());
- assertEquals(5, operator.getLine().getLines().size());
- assertEquals(DissociationOperator.class, operator.getClass());
-
- assertNotNull(reaction.getReactionRect());
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0,false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testTruncation() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/truncation.xml");
- assertEquals(1, model.getReactions().size());
- Reaction reaction = model.getReactions().iterator().next();
- assertTrue(reaction instanceof TruncationReaction);
- assertEquals(1, reaction.getReactants().size());
- Reactant reactant = reaction.getReactants().get(0);
- assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
- assertEquals(2, reactant.getLine().getLines().size());
-
- assertEquals(2, reaction.getProducts().size());
- Product product = reaction.getProducts().get(0);
- assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
- assertEquals(3, product.getLine().getLines().size());
- product = reaction.getProducts().get(1);
- assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
- assertEquals(4, product.getLine().getLines().size());
-
- assertEquals(1, reaction.getOperators().size());
- NodeOperator operator = reaction.getOperators().iterator().next();
- assertEquals(LineType.SOLID, operator.getLine().getType());
- assertEquals(1, operator.getLine().getLines().size());
- assertEquals(TruncationOperator.class, operator.getClass());
- assertEquals(reaction.getReactionRect(), ReactionRect.RECT_BOLT);
-
- assertNotNull(reaction.getReactionRect());
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0,false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testTruncationWithModifier() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/truncationWithModifier.xml");
- Reaction reaction = model.getReactions().iterator().next();
- Modifier m = reaction.getModifiers().get(0);
- assertEquals(ArrowType.CIRCLE, m.getLine().getEndAtd().getArrowType());
-
- m = reaction.getModifiers().get(1);
- assertEquals(ArrowType.CROSSBAR, m.getLine().getEndAtd().getArrowType());
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0,false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testComplexModifier1() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/complexModifier1.xml");
-
- Reaction reaction = model.getReactions().iterator().next();
- assertEquals(1, reaction.getOperators().size());
- assertEquals(2, reaction.getModifiers().size());
-
- NodeOperator operator = reaction.getOperators().iterator().next();
- assertTrue(operator.isModifierOperator());
- assertEquals(AndOperator.class, operator.getClass());
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0,false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testComplexModifier2() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/complexModifier2.xml");
- Reaction reaction = model.getReactions().iterator().next();
- assertEquals(1, reaction.getOperators().size());
- assertEquals(2, reaction.getModifiers().size());
-
- NodeOperator operator = reaction.getOperators().iterator().next();
- assertTrue(operator.isModifierOperator());
- assertEquals(OrOperator.class, operator.getClass());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testComplexModifier3() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/complexModifier3.xml");
- Reaction reaction = model.getReactions().iterator().next();
- assertEquals(1, reaction.getOperators().size());
- assertEquals(2, reaction.getModifiers().size());
-
- NodeOperator operator = reaction.getOperators().iterator().next();
- assertTrue(operator.isModifierOperator());
- assertEquals(NandOperator.class, operator.getClass());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testComplexModifier4() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/complexModifier4.xml");
- Reaction reaction = model.getReactions().iterator().next();
- assertEquals(1, reaction.getOperators().size());
- assertEquals(2, reaction.getModifiers().size());
-
- NodeOperator operator = reaction.getOperators().iterator().next();
- assertTrue(operator.isModifierOperator());
- assertEquals(UnknownOperator.class, operator.getClass());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testComplexReaction() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/complexReaction.xml");
- Reaction reaction = model.getReactions().iterator().next();
- assertEquals(0, reaction.getModifiers().size());
- assertEquals(2, reaction.getOperators().size());
- assertEquals(2, reaction.getProducts().size());
- assertEquals(2, reaction.getReactants().size());
-
- NodeOperator operator = reaction.getOperators().iterator().next();
- assertEquals(AndOperator.class, operator.getClass());
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0,false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testComplexModifiers5() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/complexModifier5.xml");
-
- Reaction reaction = model.getReactions().iterator().next();
- assertEquals(4, reaction.getModifiers().size());
- assertEquals(1, reaction.getOperators().size());
- assertEquals(2, reaction.getOperators().iterator().next().getInputs().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProblematicAnchors() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/problemWithAnchors2.xml");
-
- Reaction reaction1 = null;
- Reaction reaction2 = null;
- for (Reaction reaction : model.getReactions()) {
- if (reaction.getIdReaction().equals("re2"))
- reaction1 = reaction;
- if (reaction.getIdReaction().equals("re3"))
- reaction2 = reaction;
- }
- Reactant reactant = reaction1.getReactants().get(0);
- Element alias1 = reaction1.getReactants().get(0).getElement();
- Element alias2 = reaction1.getProducts().get(0).getElement();
- Product product = reaction1.getProducts().get(0);
- Point2D point = new Point2D.Double(alias1.getX() + alias1.getWidth() / 2, alias1.getY() + alias1.getHeight());
- Point2D point2 = new Point2D.Double(alias2.getX(), alias2.getY() + alias2.getHeight() / 2);
- assertTrue(point.distance(reactant.getLine().getPoints().get(0)) < 1);
- assertTrue(point2.distance(product.getLine().getEndPoint()) < 1);
-
- reactant = reaction2.getReactants().get(0);
- alias1 = reaction2.getReactants().get(0).getElement();
- alias2 = reaction2.getProducts().get(0).getElement();
- product = reaction2.getProducts().get(0);
- point = new Point2D.Double(alias1.getX() + alias1.getWidth(), alias1.getY() + alias1.getHeight() / 2);
- point2 = new Point2D.Double(alias2.getX(), alias2.getY() + alias2.getHeight() / 2);
- assertTrue(point.distance(reactant.getLine().getPoints().get(0)) < 1);
- assertTrue(point2.distance(product.getLine().getEndPoint()) < 1);
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0, false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProblematicAnchors3() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/problemWithAnchors3.xml");
- Reaction reaction = null;
- for (Reaction reaction2 : model.getReactions()) {
- if (reaction2.getIdReaction().equals("re3"))
- reaction = reaction2;
- }
- Point2D point = new Point2D.Double(164.85583789974368, 86.060142902597);
- Point2D point2 = new Point2D.Double(397.06477630152193, 284.99999999999994);
-
- assertTrue(point.distance(reaction.getModifiers().get(0).getLine().getPoints().get(0)) < 1);
- assertTrue(point2.distance(reaction.getModifiers().get(1).getLine().getPoints().get(0)) < 1);
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0, false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testPositiveInfluence() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/positive_influence.xml");
- Reaction reaction = model.getReactions().iterator().next();
- assertNull(reaction.getReactionRect());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProblematicAnchors2() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/complexReactionWithModifier.xml");
- Reaction reaction = model.getReactions().iterator().next();
- assertEquals(reaction.getProducts().get(0).getLine().length(), reaction.getReactants().get(0).getLine().length(),
- 1e-6);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProblematicAnchorsWithTwoReactantReaction() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/centeredAnchorInModifier.xml");
- Reaction reaction = model.getReactions().iterator().next();
- Reactant r = null;
- for (Reactant reactant : reaction.getReactants()) {
- if (reactant.getElement().getName().equals("s3")) {
- r = reactant;
- }
- }
- assertNotNull(r);
- // I think there is still a bug becaue it should work with smaller delta
- // :)
- assertEquals(r.getLine().getPoints().get(1).getX(), r.getLine().getPoints().get(2).getX(), 1);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReactionWithModifiers() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/reactionWithModifiers.xml");
- Reaction reaction = model.getReactions().iterator().next();
- List<Modifier> modifiers = reaction.getModifiers();
- Modifier sa3 = null;
- Modifier sa4 = null;
- for (Modifier modifier : modifiers) {
- if (modifier.getElement().getElementId().equals("sa3")) {
- sa3 = modifier;
- }
- if (modifier.getElement().getElementId().equals("sa4")) {
- sa4 = modifier;
- }
- }
- assertEquals(sa3.getLine().getPoints().get(0).distance(new Point2D.Double(101.9591678008944, 68.0)), 0, EPSILON);
- assertEquals(
- sa3.getLine().getPoints().get(1).distance(new Point2D.Double(101.86750788643532, 112.89589905362774)), 0,
- EPSILON);
- assertEquals(
- sa3.getLine().getPoints().get(2).distance(new Point2D.Double(190.66666666666666, 117.66666666666667)), 0,
- EPSILON);
-
- assertEquals(sa4.getLine().getPoints().get(0).distance(new Point2D.Double(267.7075561388218, 54.00000000000001)),
- 0, EPSILON);
- assertEquals(sa4.getLine().getPoints().get(1).distance(new Point2D.Double(298.3735877669656, 71.67109819284718)),
- 0, EPSILON);
- assertEquals(
- sa4.getLine().getPoints().get(2).distance(new Point2D.Double(190.66666666666666, 117.66666666666667)), 0,
- EPSILON);
-
- // new NormalImageGenerator(1, 0, 0, 1024, 1024, model, true, false, 0,
- // false).saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReactionOperatorsWithOperators() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/reactionWithOperators.xml");
- Reaction reaction = model.getReactions().iterator().next();
- NodeOperator operator1 = reaction.getOperators().get(0);
- NodeOperator operator2 = reaction.getOperators().get(1);
- NodeOperator operator3 = reaction.getOperators().get(2);
-
- // new NormalImageGenerator(1, 0, 0, 1024, 1024, model, true, false, 0,
- // false).saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
-
- assertEquals(operator1.getLine().getPoints().get(0).distance(new Point2D.Double(287.0, 242.00000000000009)), 0,
- EPSILON);
- assertEquals(
- operator1.getLine().getPoints().get(1).distance(new Point2D.Double(287.97349260719136, 204.40292958328325)),
- 0, EPSILON);
- assertEquals(
- operator1.getLine().getPoints().get(2).distance(new Point2D.Double(372.9868291110932, 203.8558964441427)), 0,
- EPSILON);
-
- assertEquals(
- operator2.getLine().getPoints().get(0).distance(new Point2D.Double(359.1840955643148, 203.94471254019686)), 0,
- EPSILON);
- assertEquals(
- operator2.getLine().getPoints().get(1).distance(new Point2D.Double(372.9868291110932, 203.8558964441427)), 0,
- EPSILON);
-
- assertEquals(
- operator3.getLine().getPoints().get(0).distance(new Point2D.Double(394.78939704287654, 203.71560401865366)),
- 0, EPSILON);
- assertEquals(
- operator3.getLine().getPoints().get(1).distance(new Point2D.Double(380.9866634960982, 203.80442011470782)), 0,
- EPSILON);
-
- Product product1 = reaction.getProducts().get(0);
- Product product2 = reaction.getProducts().get(1);
-
- assertEquals(
- product1.getLine().getPoints().get(0).distance(new Point2D.Double(394.78939704287654, 203.71560401865366)), 0,
- EPSILON);
- assertEquals(product1.getLine().getPoints().get(1).distance(new Point2D.Double(466.0, 203.25738697556727)), 0,
- EPSILON);
-
- assertEquals(
- product2.getLine().getPoints().get(0).distance(new Point2D.Double(394.78939704287654, 203.71560401865366)), 0,
- EPSILON);
- assertEquals(
- product2.getLine().getPoints().get(1).distance(new Point2D.Double(452.96894321929705, 107.00000000000001)), 0,
- EPSILON);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReactionProductsWithOperators() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/reactionWithOperators.xml");
- Reaction reaction = model.getReactions().iterator().next();
-
- Product product1 = reaction.getProducts().get(0);
- Product product2 = reaction.getProducts().get(1);
-
- assertEquals(
- product1.getLine().getPoints().get(0).distance(new Point2D.Double(394.78939704287654, 203.71560401865366)), 0,
- EPSILON);
- assertEquals(product1.getLine().getPoints().get(1).distance(new Point2D.Double(466.0, 203.25738697556727)), 0,
- EPSILON);
-
- assertEquals(
- product2.getLine().getPoints().get(0).distance(new Point2D.Double(394.78939704287654, 203.71560401865366)), 0,
- EPSILON);
- assertEquals(
- product2.getLine().getPoints().get(1).distance(new Point2D.Double(452.96894321929705, 107.00000000000001)), 0,
- EPSILON);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReactionReactantsWithOperators() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/reactionWithOperators.xml");
- Reaction reaction = model.getReactions().iterator().next();
-
- Reactant reactant1 = reaction.getReactants().get(0);
- Reactant reactant2 = reaction.getReactants().get(1);
- Reactant reactant3 = reaction.getReactants().get(2);
-
- assertEquals(
- reactant1.getLine().getPoints().get(0).distance(new Point2D.Double(112.53618421052632, 167.46381578947367)),
- 0, EPSILON);
- assertEquals(reactant1.getLine().getPoints().get(1).distance(new Point2D.Double(287.0, 242.00000000000009)), 0,
- EPSILON);
-
- assertEquals(reactant2.getLine().getPoints().get(0).distance(new Point2D.Double(121.0, 242.0)), 0, EPSILON);
- assertEquals(reactant2.getLine().getPoints().get(1).distance(new Point2D.Double(287.0, 242.00000000000009)), 0,
- EPSILON);
-
- assertEquals(
- reactant3.getLine().getPoints().get(0).distance(new Point2D.Double(116.65392247520951, 72.34607752479052)), 0,
- EPSILON);
- assertEquals(
- reactant3.getLine().getPoints().get(1).distance(new Point2D.Double(359.1840955643148, 203.94471254019686)), 0,
- EPSILON);
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0, false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testTransitionReactionToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_transition.xml");
-
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
- Reaction reaction2 = parser.getReaction(node2, model);
-
- assertEquals(reaction1.getClass(), reaction2.getClass());
- assertEquals(reaction1.getReactants().size(), reaction2.getReactants().size());
- Reactant reactant1 = reaction1.getReactants().get(0);
- Reactant reactant2 = reaction2.getReactants().get(0);
- assertEquals(reactant1.getLine().getBeginAtd().getArrowType(), reactant2.getLine().getBeginAtd().getArrowType());
- assertEquals(reactant1.getLine().getEndAtd().getArrowType(), reactant2.getLine().getEndAtd().getArrowType());
- assertEquals(reactant1.getLine().getLines().size(), reactant2.getLine().getLines().size());
-
- Product product1 = reaction1.getProducts().get(0);
- Product product2 = reaction2.getProducts().get(0);
- assertEquals(product1.getLine().getBeginAtd().getArrowType(), product2.getLine().getBeginAtd().getArrowType());
- assertEquals(product1.getLine().getEndAtd().getArrowType(), product2.getLine().getEndAtd().getArrowType());
- assertEquals(product1.getLine().getLines().size(), product2.getLine().getLines().size());
-
- assertEquals(reactant1.getLine().getEndPoint().getX(), reactant2.getLine().getEndPoint().getX(), EPSILON);
- assertEquals(reactant1.getLine().getEndPoint().getY(), reactant2.getLine().getEndPoint().getY(), EPSILON);
-
- assertEquals(reaction1.getReactionRect(), reaction2.getReactionRect());
-
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
-
- assertEquals(product1.getLine().getColor(), product2.getLine().getColor());
- assertEquals(product1.getLine().getWidth(), product2.getLine().getWidth(), 1e-6);
-
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- @Test
- public void testTransitionWidthAdditionalNodelReactionToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_transitionWithAdditionalNodes.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
- Reaction reaction2 = parser.getReaction(node2, model);
-
- assertEquals(reaction1.getClass(), reaction2.getClass());
- assertEquals(reaction1.getReactants().size(), reaction2.getReactants().size());
- Reactant reactant1 = reaction1.getReactants().get(1);
- Reactant reactant2 = reaction2.getReactants().get(1);
- assertEquals(reactant1.getLine().getBeginAtd().getArrowType(), reactant2.getLine().getBeginAtd().getArrowType());
- assertEquals(reactant1.getLine().getEndAtd().getArrowType(), reactant2.getLine().getEndAtd().getArrowType());
- assertEquals(reactant1.getLine().getLines().size(), reactant2.getLine().getLines().size());
-
- Product product1 = reaction1.getProducts().get(1);
- Product product2 = reaction2.getProducts().get(1);
- assertEquals(product1.getLine().getBeginAtd().getArrowType(), product2.getLine().getBeginAtd().getArrowType());
- assertEquals(product1.getLine().getEndAtd().getArrowType(), product2.getLine().getEndAtd().getArrowType());
- assertEquals(product1.getLine().getLines().size(), product2.getLine().getLines().size());
-
- assertTrue(reactant1.getLine().getEndPoint().distance(reactant2.getLine().getEndPoint()) < 1e-6);
- assertEquals(reaction1.getReactionRect(), reaction2.getReactionRect());
-
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
-
- assertEquals(product1.getLine().getColor(), product2.getLine().getColor());
- assertEquals(product1.getLine().getWidth(), product2.getLine().getWidth(), 1e-6);
-
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- @Test
- public void testTranslationToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_translation.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
- Reaction reaction2 = parser.getReaction(node2, model);
-
- assertEquals(reaction1.getClass(), reaction2.getClass());
- assertEquals(reaction1.getReactants().size(), reaction2.getReactants().size());
- Reactant reactant1 = reaction1.getReactants().get(1);
- Reactant reactant2 = reaction2.getReactants().get(1);
- assertEquals(reactant1.getLine().getBeginAtd().getArrowType(), reactant2.getLine().getBeginAtd().getArrowType());
- assertEquals(reactant1.getLine().getEndAtd().getArrowType(), reactant2.getLine().getEndAtd().getArrowType());
- assertEquals(reactant1.getLine().getLines().size(), reactant2.getLine().getLines().size());
-
- Product product1 = reaction1.getProducts().get(1);
- Product product2 = reaction2.getProducts().get(1);
- assertEquals(product1.getLine().getBeginAtd().getArrowType(), product2.getLine().getBeginAtd().getArrowType());
- assertEquals(product1.getLine().getEndAtd().getArrowType(), product2.getLine().getEndAtd().getArrowType());
- assertEquals(product1.getLine().getLines().size(), product2.getLine().getLines().size());
-
- assertTrue(reactant1.getLine().getEndPoint().distance(reactant2.getLine().getEndPoint()) < 1e-6);
- assertEquals(reaction1.getReactionRect(), reaction2.getReactionRect());
-
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
-
- assertEquals(product1.getLine().getColor(), product2.getLine().getColor());
- assertEquals(product1.getLine().getWidth(), product2.getLine().getWidth(), 1e-6);
-
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- @Test
- public void testTransportToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_transport.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
- Reaction reaction2 = parser.getReaction(node2, model);
-
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
- assertEquals(reaction1.getClass(), reaction2.getClass());
- assertEquals(reaction1.getMiriamData().size(), reaction2.getMiriamData().size());
- assertEquals(reaction1.getNotes().trim(), reaction2.getNotes().trim());
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- @Test
- public void testTruncationToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_truncation.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
- Reaction reaction2 = parser.getReaction(node2, model);
-
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
- assertEquals(reaction1.getClass(), reaction2.getClass());
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- @Test
- public void testTruncationWithModifierToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_truncationWithModifier.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
- Reaction reaction2 = parser.getReaction(node2, model);
-
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
-
- assertEquals(reaction1.getClass(), reaction2.getClass());
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- @Test
- public void testUnknownTransitionToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_unknown_transition.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
- Reaction reaction2 = parser.getReaction(node2, model);
-
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
- assertEquals(reaction1.getClass(), reaction2.getClass());
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- @Test
- public void testTransitionOmittedToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_transition_omitted.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
- Reaction reaction2 = parser.getReaction(node2, model);
-
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
- assertEquals(reaction1.getClass(), reaction2.getClass());
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- @Test
- public void testTranscriptionToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_transcription.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
- Reaction reaction2 = parser.getReaction(node2, model);
-
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
- assertEquals(reaction1.getClass(), reaction2.getClass());
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- @Test
- public void testTranscriptionWithAdditionsToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_transcription_with_additions.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
- Reaction reaction2 = parser.getReaction(node2, model);
-
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
- assertEquals(reaction1.getClass(), reaction2.getClass());
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- @Test
- public void testReactionWithOperatorsToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_with_operators.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
- Reaction reaction2 = parser.getReaction(node2, model);
-
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
- assertEquals(reaction1.getClass(), reaction2.getClass());
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- @Test
- public void testReactionWithModifiersToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_with_modifiers.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
-
- Reaction reaction2 = parser.getReaction(node2, model);
-
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
- assertEquals(reaction1.getClass(), reaction2.getClass());
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- @Test
- public void testReactionPositiveInfluenceToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_positive_influence.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
- Reaction reaction2 = parser.getReaction(node2, model);
-
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
- assertEquals(reaction1.getClass(), reaction2.getClass());
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- @Test
- public void testReactionHeterodimerWithAdditionsToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_heterodimer_with_additions.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
- Reaction reaction2 = parser.getReaction(node2, model);
-
- assertEquals(reaction1.getNodes().size(), reaction2.getNodes().size());
-
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
- assertEquals(reaction1.getClass(), reaction2.getClass());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReactionHeterodimerToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_heterodimer.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
- Reaction reaction2 = parser.getReaction(node2, model);
-
- assertEquals(reaction1.getNodes().size(), reaction2.getNodes().size());
-
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
- assertEquals(reaction1.getClass(), reaction2.getClass());
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- @Test
- public void testOperatorInReactionHeterodimer() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_heterodimer.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
- for (NodeOperator operator : reaction1.getOperators()) {
- assertTrue(operator instanceof AssociationOperator);
- }
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- @Test
- public void testReactionDissociationWithAdditionToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_dissociation_with_addition.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
- Reaction reaction2 = parser.getReaction(node2, model);
-
- assertEquals(reaction1.getName(), reaction2.getName());
- assertNotNull(reaction1.getName());
- assertFalse(reaction1.getName().trim().equals(""));
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
- assertEquals(reaction1.getClass(), reaction2.getClass());
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- private Model getModelFilledWithSpecies() {
- Model model = new ModelFullIndexed(null);
-
- Species sa1 = new GenericProtein("sa1");
- sa1.setX(100.0);
- sa1.setY(200.0);
- sa1.setWidth(300.0);
- sa1.setHeight(400.0);
- model.addElement(sa1);
- elements.addModelElement(sa1, new CellDesignerGenericProtein("s1"));
-
- Species sa2 = new GenericProtein("sa2");
- sa2.setX(1050.0);
- sa2.setY(2050.0);
- sa2.setWidth(300.0);
- sa2.setHeight(450.0);
- model.addElement(sa2);
- elements.addModelElement(sa2, new CellDesignerGenericProtein("s2"));
-
- Species sa3 = new GenericProtein("sa3");
- sa3.setX(600.0);
- sa3.setY(250.0);
- sa3.setWidth(300.0);
- sa3.setHeight(400.0);
- model.addElement(sa3);
- elements.addModelElement(sa3, new CellDesignerGenericProtein("s3"));
-
- Species sa4 = new GenericProtein("sa4");
- sa4.setX(550.0);
- sa4.setY(350.0);
- sa4.setWidth(300.0);
- sa4.setHeight(450.0);
- model.addElement(sa4);
- elements.addElement(new CellDesignerGenericProtein("s4"));
-
- Species sa5 = new GenericProtein("sa5");
- sa5.setX(10.0);
- sa5.setY(250.0);
- sa5.setWidth(300.0);
- sa5.setHeight(450.0);
- model.addElement(sa5);
- elements.addElement(new CellDesignerGenericProtein("s5"));
-
- Species sa6 = new GenericProtein("sa6");
- sa6.setX(10.0);
- sa6.setY(250.0);
- sa6.setWidth(300.0);
- sa6.setHeight(450.0);
- model.addElement(sa6);
-
- elements.addElement(new CellDesignerGenericProtein("s6"));
-
- Species sa10 = new GenericProtein("sa10");
- sa10.setX(210.0);
- sa10.setY(220.0);
- sa10.setWidth(320.0);
- sa10.setHeight(250.0);
- model.addElement(sa10);
- elements.addElement(new CellDesignerGenericProtein("s10"));
-
- Species sa11 = new GenericProtein("sa11");
- sa11.setX(11.0);
- sa11.setY(320.0);
- sa11.setWidth(321.0);
- sa11.setHeight(150.0);
- model.addElement(sa11);
- elements.addElement(new CellDesignerGenericProtein("s11"));
-
- Species sa12 = new GenericProtein("sa12");
- sa12.setX(12.0);
- sa12.setY(20.0);
- sa12.setWidth(321.0);
- sa12.setHeight(150.0);
- model.addElement(sa12);
- elements.addElement(new CellDesignerGenericProtein("s12"));
-
- Species sa13 = new GenericProtein("sa13");
- sa13.setX(513.0);
- sa13.setY(20.0);
- sa13.setWidth(321.0);
- sa13.setHeight(150.0);
- model.addElement(sa13);
- elements.addElement(new CellDesignerGenericProtein("s13"));
-
- Species sa14 = new GenericProtein("sa14");
- sa14.setX(14.0);
- sa14.setY(820.0);
- sa14.setWidth(321.0);
- sa14.setHeight(150.0);
- model.addElement(sa14);
- elements.addElement(new CellDesignerGenericProtein("s14"));
-
- Species sa15 = new GenericProtein("sa15");
- sa15.setX(815.0);
- sa15.setY(620.0);
- sa15.setWidth(321.0);
- sa15.setHeight(150.0);
- model.addElement(sa15);
- elements.addElement(new CellDesignerGenericProtein("s15"));
-
- return model;
- }
-
- @Test
- public void testLogiGateAndReaction() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/logicGateAnd.xml");
- assertEquals(1, model.getReactions().size());
- Reaction reaction = model.getReactions().iterator().next();
- assertTrue(reaction instanceof BooleanLogicGateReaction);
- assertEquals(1, reaction.getOperators().size());
- assertTrue(reaction.getOperators().get(0) instanceof AndOperator);
- assertEquals(2, reaction.getReactants().size());
- assertEquals(1, reaction.getProducts().size());
-
- assertEquals(0.0, reaction.getReactants().get(0).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
- assertEquals(0.0, reaction.getReactants().get(1).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
- assertEquals(0.0, reaction.getProducts().get(0).getLine().getBeginPoint().distance(200.0, 127.0), EPSILON);
-
- CellDesignerXmlParser cellDesignerXmlParser = new CellDesignerXmlParser();
-
- model.setName(null);
- String xmlString = cellDesignerXmlParser.toXml(model);
-
- ByteArrayInputStream bais = new ByteArrayInputStream(xmlString.getBytes("UTF-8"));
- Model model2 = cellDesignerXmlParser.createModel(new ConverterParams().inputStream(bais).sizeAutoAdjust(false));
-
- ModelComparator mc = new ModelComparator();
- assertEquals("After CellDesigner xml serialization models are different", 0, mc.compare(model, model2));
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0, false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testLogiGateOrReaction() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/logicGateOr.xml");
- assertEquals(1, model.getReactions().size());
- Reaction reaction = model.getReactions().iterator().next();
- assertTrue(reaction instanceof BooleanLogicGateReaction);
- assertEquals(1, reaction.getOperators().size());
- assertTrue(reaction.getOperators().get(0) instanceof OrOperator);
- assertEquals(2, reaction.getReactants().size());
- assertEquals(1, reaction.getProducts().size());
-
- assertEquals(0.0, reaction.getReactants().get(0).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
- assertEquals(0.0, reaction.getReactants().get(1).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
- assertEquals(0.0, reaction.getProducts().get(0).getLine().getBeginPoint().distance(200.0, 127.0), EPSILON);
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0, false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testLogiGateNotReaction() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/logicGateNot.xml");
- assertEquals(1, model.getReactions().size());
- Reaction reaction = model.getReactions().iterator().next();
- assertTrue(reaction instanceof BooleanLogicGateReaction);
- assertEquals(1, reaction.getOperators().size());
- assertTrue(reaction.getOperators().get(0) instanceof NandOperator);
- assertEquals(2, reaction.getReactants().size());
- assertEquals(1, reaction.getProducts().size());
-
- assertEquals(0.0, reaction.getReactants().get(0).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
- assertEquals(0.0, reaction.getReactants().get(1).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
- assertEquals(0.0, reaction.getProducts().get(0).getLine().getBeginPoint().distance(200.0, 127.0), EPSILON);
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0, false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testLogiGateUnknownReaction() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/logicGateUnknown.xml");
- assertEquals(1, model.getReactions().size());
- Reaction reaction = model.getReactions().iterator().next();
- assertTrue(reaction instanceof BooleanLogicGateReaction);
- assertEquals(1, reaction.getOperators().size());
- assertTrue(reaction.getOperators().get(0) instanceof UnknownOperator);
- assertEquals(2, reaction.getReactants().size());
- assertEquals(1, reaction.getProducts().size());
-
- assertEquals(0.0, reaction.getReactants().get(0).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
- assertEquals(0.0, reaction.getReactants().get(1).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
- assertEquals(0.0, reaction.getProducts().get(0).getLine().getBeginPoint().distance(200.0, 127.0), EPSILON);
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0, false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProblematicDrawing() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/problematic/reaction_drawing_problem.xml");
- Reaction reaction = model.getReactionByReactionId("re1");
- assertEquals(0, reaction.getCenterPoint().distance(new Point2D.Double(258.5, 145.0)), EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProteinsInsideComplex() throws Exception {
- try {
- Model model = getModelForFile("testFiles/problematic/proteins_inside_complex.xml");
- for (Element el : model.getElements()) {
- assertFalse(el.getClass().equals(Protein.class));
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testKinetcs() throws Exception {
- try {
- Model model = getModelForFile("testFiles/reactions/kinetics.xml");
- Reaction reaction = model.getReactionByReactionId("re1");
- assertNotNull(reaction.getKinetics());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testKinetcsWithCompartment() throws Exception {
- try {
- Model model = getModelForFile("testFiles/reactions/kinetics_with_compartment.xml");
- Reaction reaction = model.getReactionByReactionId("re1");
- assertNotNull(reaction.getKinetics());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.reaction;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+import java.io.ByteArrayInputStream;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.w3c.dom.Node;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGenericProtein;
+import lcsb.mapviewer.model.graphics.ArrowType;
+import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.reaction.AndOperator;
+import lcsb.mapviewer.model.map.reaction.AssociationOperator;
+import lcsb.mapviewer.model.map.reaction.DissociationOperator;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.reaction.NandOperator;
+import lcsb.mapviewer.model.map.reaction.NodeOperator;
+import lcsb.mapviewer.model.map.reaction.OrOperator;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.SplitOperator;
+import lcsb.mapviewer.model.map.reaction.TruncationOperator;
+import lcsb.mapviewer.model.map.reaction.UnknownOperator;
+import lcsb.mapviewer.model.map.reaction.type.BooleanLogicGateReaction;
+import lcsb.mapviewer.model.map.reaction.type.DissociationReaction;
+import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
+import lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction;
+import lcsb.mapviewer.model.map.reaction.type.ReactionRect;
+import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
+import lcsb.mapviewer.model.map.reaction.type.TranscriptionReaction;
+import lcsb.mapviewer.model.map.reaction.type.TranslationReaction;
+import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
+import lcsb.mapviewer.model.map.reaction.type.TruncationReaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class ReactionParserTests extends CellDesignerTestFunctions {
+
+ private Logger logger = Logger.getLogger(ReactionParserTests.class.getName());;
+ ReactionXmlParser parser;
+ CellDesignerElementCollection elements;
+
+ @Before
+ public void setUp() throws Exception {
+ elements = new CellDesignerElementCollection();
+
+ parser = new ReactionXmlParser(elements, false);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testColorReaction() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/colorfull_reaction.xml");
+ Reaction reaction = model.getReactionByReactionId("re1");
+ PolylineData line = reaction.getReactants().get(0).getLine();
+ assertFalse(
+ "000".equals(line.getColor().getRed() + "" + line.getColor().getGreen() + "" + line.getColor().getBlue()));
+ line = reaction.getProducts().get(0).getLine();
+ assertFalse(
+ "000".equals(line.getColor().getRed() + "" + line.getColor().getGreen() + "" + line.getColor().getBlue()));
+ line = reaction.getModifiers().get(0).getLine();
+ assertFalse(
+ "000".equals(line.getColor().getRed() + "" + line.getColor().getGreen() + "" + line.getColor().getBlue()));
+ line = reaction.getOperators().get(0).getLine();
+ assertFalse(
+ "000".equals(line.getColor().getRed() + "" + line.getColor().getGreen() + "" + line.getColor().getBlue()));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testMissingLines() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/problematic/pd_map_with_problematic_reaction_line.xml");
+ assertTrue(model.getElementByElementId("sa5003") instanceof GenericProtein);
+ Set<Reaction> list = model.getReactions();
+ for (Reaction reaction : list) {
+ // reaction re1607 in this model was problematic, but in fact the
+ // problem
+ // can be in any reaction line
+ // if (reaction.getId().equals("re1607")) {
+ List<Line2D> lines = reaction.getLines();
+ for (Line2D line2d : lines) {
+ assertFalse(Double.isNaN(line2d.getX1()));
+ assertFalse(Double.isNaN(line2d.getX2()));
+ assertFalse(Double.isNaN(line2d.getY1()));
+ assertFalse(Double.isNaN(line2d.getY2()));
+ }
+ // }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTransitionReaction() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/transition.xml");
+ assertEquals(1, model.getReactions().size());
+ Reaction reaction = model.getReactions().iterator().next();
+ assertTrue(reaction instanceof StateTransitionReaction);
+ assertEquals(1, reaction.getReactants().size());
+ Reactant reactant = reaction.getReactants().get(0);
+
+ assertTrue(reaction.isReversible());
+ assertEquals(ArrowType.FULL, reactant.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
+ assertEquals(3, reactant.getLine().getLines().size());
+
+ Product product = reaction.getProducts().get(0);
+ assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
+ assertEquals(2, product.getLine().getLines().size());
+
+ assertTrue(reactant.getLine().getEndPoint().distance(product.getLine().getPoints().get(0)) < 20);
+ assertNotNull(reaction.getReactionRect());
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0,false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCenterLineInSimpleReaction() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/transition.xml");
+ assertEquals(1, model.getReactions().size());
+ Reaction reaction = model.getReactions().iterator().next();
+ Reactant reactant = reaction.getReactants().get(0);
+
+ Product product = reaction.getProducts().get(0);
+
+ // center of the line should be different than edge points of
+ // reactant/product description
+ assertFalse(reaction.getCenterLine().getP1().distance(reactant.getLine().getEndPoint()) < 1e-6);
+ assertFalse(reaction.getCenterLine().getP2().distance(product.getLine().getBeginPoint()) < 1e-6);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTransition2() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/transitionWithAdditionalNodes.xml");
+ Reaction reaction = model.getReactions().iterator().next();
+ assertEquals(2, reaction.getOperators().size());
+ for (Reactant reactant : reaction.getReactants()) {
+ assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
+
+ assertTrue(
+ reactant.getLine().getEndPoint().distance(reaction.getReactants().get(0).getLine().getEndPoint()) < 1e-6);
+ }
+
+ for (Product product : reaction.getProducts()) {
+ assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
+
+ assertTrue(
+ product.getLine().getBeginPoint().distance(reaction.getProducts().get(0).getLine().getBeginPoint()) < 1e-6);
+ }
+ assertNotNull(reaction.getReactionRect());
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0,false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTransiotionOmitted() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/transition_omitted.xml");
+ Reaction reaction = model.getReactions().iterator().next();
+ assertEquals(0, reaction.getOperators().size());
+ assertEquals(KnownTransitionOmittedReaction.class, reaction.getClass());
+ assertNotNull(reaction.getReactionRect());
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0,false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUnknownTransition() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/unknown_transition.xml");
+ Reaction reaction = model.getReactions().iterator().next();
+ assertNotNull(reaction.getReactionRect());
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0,false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTranscription() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/transcription.xml");
+ assertEquals(1, model.getReactions().size());
+ Reaction reaction = model.getReactions().iterator().next();
+ assertTrue(reaction instanceof TranscriptionReaction);
+ assertEquals(1, reaction.getReactants().size());
+ Reactant reactant = reaction.getReactants().get(0);
+ assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
+ assertEquals(LineType.DASH_DOT_DOT, reactant.getLine().getType());
+ assertEquals(1, reactant.getLine().getLines().size());
+
+ Product product = reaction.getProducts().get(0);
+ assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
+ assertEquals(1, product.getLine().getLines().size());
+
+ assertTrue(reactant.getLine().getEndPoint().distance(product.getLine().getPoints().get(0)) < 20);
+ assertNotNull(reaction.getReactionRect());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTranscription2() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/transcription_with_additions.xml");
+ assertEquals(1, model.getReactions().size());
+ Reaction reaction = model.getReactions().iterator().next();
+ assertTrue(reaction instanceof TranscriptionReaction);
+ assertEquals(2, reaction.getReactants().size());
+ Reactant reactant = reaction.getReactants().get(0);
+ assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
+ assertEquals(LineType.DASH_DOT_DOT, reactant.getLine().getType());
+ assertEquals(1, reactant.getLine().getLines().size());
+ NodeOperator operator = null;
+ for (NodeOperator operator2 : reaction.getOperators()) {
+ if (operator2 instanceof SplitOperator)
+ operator = operator2;
+ }
+ assertEquals(LineType.DASH_DOT_DOT, operator.getLine().getType());
+
+ Product product = reaction.getProducts().get(0);
+ assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
+ assertEquals(1, product.getLine().getLines().size());
+
+ assertNotNull(reaction.getReactionRect());
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0,false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTranslation() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/translation.xml");
+ assertEquals(1, model.getReactions().size());
+ Reaction reaction = model.getReactions().iterator().next();
+ assertTrue(reaction instanceof TranslationReaction);
+ assertEquals(2, reaction.getReactants().size());
+ Reactant reactant = reaction.getReactants().get(0);
+ assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
+ assertEquals(LineType.DASH_DOT, reactant.getLine().getType());
+ assertEquals(1, reactant.getLine().getLines().size());
+ NodeOperator operator = reaction.getOperators().iterator().next();
+ assertEquals(LineType.DASH_DOT, operator.getLine().getType());
+
+ Product product = reaction.getProducts().get(0);
+ assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
+ assertEquals(1, product.getLine().getLines().size());
+
+ assertNotNull(reaction.getReactionRect());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTransport() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/transport.xml");
+ assertEquals(1, model.getReactions().size());
+ Reaction reaction = model.getReactions().iterator().next();
+ assertTrue(reaction instanceof TransportReaction);
+ assertEquals(1, reaction.getReactants().size());
+ Reactant reactant = reaction.getReactants().get(0);
+ assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
+ assertEquals(1, reactant.getLine().getLines().size());
+
+ Product product = reaction.getProducts().get(0);
+ assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.FULL_CROSSBAR, product.getLine().getEndAtd().getArrowType());
+ assertEquals(1, product.getLine().getLines().size());
+
+ assertNotNull(reaction.getReactionRect());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testHeterodimer() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/heterodimer.xml");
+ assertEquals(1, model.getReactions().size());
+ Reaction reaction = model.getReactions().iterator().next();
+ assertTrue(reaction instanceof HeterodimerAssociationReaction);
+ assertEquals(2, reaction.getReactants().size());
+ Reactant reactant = reaction.getReactants().get(0);
+ assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
+ assertEquals(2, reactant.getLine().getLines().size());
+ reactant = reaction.getReactants().get(1);
+ assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
+ assertEquals(3, reactant.getLine().getLines().size());
+
+ Product product = reaction.getProducts().get(0);
+ assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
+ assertEquals(3, product.getLine().getLines().size());
+
+ NodeOperator operator = reaction.getOperators().iterator().next();
+ assertEquals(LineType.SOLID, operator.getLine().getType());
+ assertEquals(7, operator.getLine().getLines().size());
+
+ assertNotNull(reaction.getReactionRect());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testHeterodimerWithAdditions() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/heterodimerWithAdditions.xml");
+
+ assertEquals(1, model.getReactions().size());
+ Reaction reaction = model.getReactions().iterator().next();
+ assertTrue(reaction instanceof HeterodimerAssociationReaction);
+ assertEquals(3, reaction.getReactants().size());
+ Reactant reactant = reaction.getReactants().get(0);
+ assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
+ assertEquals(2, reactant.getLine().getLines().size());
+ reactant = reaction.getReactants().get(1);
+ assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
+ assertEquals(3, reactant.getLine().getLines().size());
+
+ for (Product product : reaction.getProducts()) {
+ assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
+ }
+
+ assertEquals(3, reaction.getOperators().size());
+ NodeOperator operator = reaction.getOperators().iterator().next();
+ assertEquals(LineType.SOLID, operator.getLine().getType());
+ assertEquals(7, operator.getLine().getLines().size());
+
+ assertNotNull(reaction.getReactionRect());
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0,false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDissociation() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/dissociation.xml");
+ assertEquals(2, model.getReactions().size());
+ Reaction reaction = null;
+ for (Reaction reaction2 : model.getReactions()) {
+ if (reaction2.getIdReaction().equals("re1"))
+ reaction = reaction2;
+ }
+ assertTrue(reaction instanceof DissociationReaction);
+ assertEquals(1, reaction.getReactants().size());
+ Reactant reactant = reaction.getReactants().get(0);
+ assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
+ assertEquals(2, reactant.getLine().getLines().size());
+
+ assertEquals(2, reaction.getProducts().size());
+ Product product = reaction.getProducts().get(0);
+ assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
+ assertEquals(5, product.getLine().getLines().size());
+ product = reaction.getProducts().get(1);
+ assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
+ assertEquals(4, product.getLine().getLines().size());
+
+ assertEquals(1, reaction.getOperators().size());
+ NodeOperator operator = reaction.getOperators().iterator().next();
+ assertEquals(LineType.SOLID, operator.getLine().getType());
+ assertEquals(5, operator.getLine().getLines().size());
+
+ assertNotNull(reaction.getReactionRect());
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0,false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDissociationWithAddition() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/dissociationWithAddition.xml");
+ assertEquals(2, model.getReactions().size());
+ Reaction reaction = null;
+ for (Reaction reaction2 : model.getReactions()) {
+ if (reaction2.getIdReaction().equals("re1"))
+ reaction = reaction2;
+ }
+ assertTrue(reaction instanceof DissociationReaction);
+ assertEquals(2, reaction.getReactants().size());
+ Reactant reactant = reaction.getReactants().get(0);
+ assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
+ assertEquals(2, reactant.getLine().getLines().size());
+
+ assertEquals(3, reaction.getProducts().size());
+ Product product = reaction.getProducts().get(0);
+ assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
+ assertEquals(5, product.getLine().getLines().size());
+ product = reaction.getProducts().get(1);
+ assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
+ assertEquals(4, product.getLine().getLines().size());
+
+ assertEquals(3, reaction.getOperators().size());
+ NodeOperator operator = reaction.getOperators().iterator().next();
+ assertEquals(LineType.SOLID, operator.getLine().getType());
+ assertEquals(5, operator.getLine().getLines().size());
+ assertEquals(DissociationOperator.class, operator.getClass());
+
+ assertNotNull(reaction.getReactionRect());
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0,false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTruncation() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/truncation.xml");
+ assertEquals(1, model.getReactions().size());
+ Reaction reaction = model.getReactions().iterator().next();
+ assertTrue(reaction instanceof TruncationReaction);
+ assertEquals(1, reaction.getReactants().size());
+ Reactant reactant = reaction.getReactants().get(0);
+ assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
+ assertEquals(2, reactant.getLine().getLines().size());
+
+ assertEquals(2, reaction.getProducts().size());
+ Product product = reaction.getProducts().get(0);
+ assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
+ assertEquals(3, product.getLine().getLines().size());
+ product = reaction.getProducts().get(1);
+ assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
+ assertEquals(4, product.getLine().getLines().size());
+
+ assertEquals(1, reaction.getOperators().size());
+ NodeOperator operator = reaction.getOperators().iterator().next();
+ assertEquals(LineType.SOLID, operator.getLine().getType());
+ assertEquals(1, operator.getLine().getLines().size());
+ assertEquals(TruncationOperator.class, operator.getClass());
+ assertEquals(reaction.getReactionRect(), ReactionRect.RECT_BOLT);
+
+ assertNotNull(reaction.getReactionRect());
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0,false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTruncationWithModifier() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/truncationWithModifier.xml");
+ Reaction reaction = model.getReactions().iterator().next();
+ Modifier m = reaction.getModifiers().get(0);
+ assertEquals(ArrowType.CIRCLE, m.getLine().getEndAtd().getArrowType());
+
+ m = reaction.getModifiers().get(1);
+ assertEquals(ArrowType.CROSSBAR, m.getLine().getEndAtd().getArrowType());
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0,false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testComplexModifier1() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/complexModifier1.xml");
+
+ Reaction reaction = model.getReactions().iterator().next();
+ assertEquals(1, reaction.getOperators().size());
+ assertEquals(2, reaction.getModifiers().size());
+
+ NodeOperator operator = reaction.getOperators().iterator().next();
+ assertTrue(operator.isModifierOperator());
+ assertEquals(AndOperator.class, operator.getClass());
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0,false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testComplexModifier2() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/complexModifier2.xml");
+ Reaction reaction = model.getReactions().iterator().next();
+ assertEquals(1, reaction.getOperators().size());
+ assertEquals(2, reaction.getModifiers().size());
+
+ NodeOperator operator = reaction.getOperators().iterator().next();
+ assertTrue(operator.isModifierOperator());
+ assertEquals(OrOperator.class, operator.getClass());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testComplexModifier3() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/complexModifier3.xml");
+ Reaction reaction = model.getReactions().iterator().next();
+ assertEquals(1, reaction.getOperators().size());
+ assertEquals(2, reaction.getModifiers().size());
+
+ NodeOperator operator = reaction.getOperators().iterator().next();
+ assertTrue(operator.isModifierOperator());
+ assertEquals(NandOperator.class, operator.getClass());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testComplexModifier4() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/complexModifier4.xml");
+ Reaction reaction = model.getReactions().iterator().next();
+ assertEquals(1, reaction.getOperators().size());
+ assertEquals(2, reaction.getModifiers().size());
+
+ NodeOperator operator = reaction.getOperators().iterator().next();
+ assertTrue(operator.isModifierOperator());
+ assertEquals(UnknownOperator.class, operator.getClass());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testComplexReaction() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/complexReaction.xml");
+ Reaction reaction = model.getReactions().iterator().next();
+ assertEquals(0, reaction.getModifiers().size());
+ assertEquals(2, reaction.getOperators().size());
+ assertEquals(2, reaction.getProducts().size());
+ assertEquals(2, reaction.getReactants().size());
+
+ NodeOperator operator = reaction.getOperators().iterator().next();
+ assertEquals(AndOperator.class, operator.getClass());
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0,false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testComplexModifiers5() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/complexModifier5.xml");
+
+ Reaction reaction = model.getReactions().iterator().next();
+ assertEquals(4, reaction.getModifiers().size());
+ assertEquals(1, reaction.getOperators().size());
+ assertEquals(2, reaction.getOperators().iterator().next().getInputs().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProblematicAnchors() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/problemWithAnchors2.xml");
+
+ Reaction reaction1 = null;
+ Reaction reaction2 = null;
+ for (Reaction reaction : model.getReactions()) {
+ if (reaction.getIdReaction().equals("re2"))
+ reaction1 = reaction;
+ if (reaction.getIdReaction().equals("re3"))
+ reaction2 = reaction;
+ }
+ Reactant reactant = reaction1.getReactants().get(0);
+ Element alias1 = reaction1.getReactants().get(0).getElement();
+ Element alias2 = reaction1.getProducts().get(0).getElement();
+ Product product = reaction1.getProducts().get(0);
+ Point2D point = new Point2D.Double(alias1.getX() + alias1.getWidth() / 2, alias1.getY() + alias1.getHeight());
+ Point2D point2 = new Point2D.Double(alias2.getX(), alias2.getY() + alias2.getHeight() / 2);
+ assertTrue(point.distance(reactant.getLine().getPoints().get(0)) < 1);
+ assertTrue(point2.distance(product.getLine().getEndPoint()) < 1);
+
+ reactant = reaction2.getReactants().get(0);
+ alias1 = reaction2.getReactants().get(0).getElement();
+ alias2 = reaction2.getProducts().get(0).getElement();
+ product = reaction2.getProducts().get(0);
+ point = new Point2D.Double(alias1.getX() + alias1.getWidth(), alias1.getY() + alias1.getHeight() / 2);
+ point2 = new Point2D.Double(alias2.getX(), alias2.getY() + alias2.getHeight() / 2);
+ assertTrue(point.distance(reactant.getLine().getPoints().get(0)) < 1);
+ assertTrue(point2.distance(product.getLine().getEndPoint()) < 1);
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0, false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProblematicAnchors3() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/problemWithAnchors3.xml");
+ Reaction reaction = null;
+ for (Reaction reaction2 : model.getReactions()) {
+ if (reaction2.getIdReaction().equals("re3"))
+ reaction = reaction2;
+ }
+ Point2D point = new Point2D.Double(164.85583789974368, 86.060142902597);
+ Point2D point2 = new Point2D.Double(397.06477630152193, 284.99999999999994);
+
+ assertTrue(point.distance(reaction.getModifiers().get(0).getLine().getPoints().get(0)) < 1);
+ assertTrue(point2.distance(reaction.getModifiers().get(1).getLine().getPoints().get(0)) < 1);
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0, false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testPositiveInfluence() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/positive_influence.xml");
+ Reaction reaction = model.getReactions().iterator().next();
+ assertNull(reaction.getReactionRect());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProblematicAnchors2() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/complexReactionWithModifier.xml");
+ Reaction reaction = model.getReactions().iterator().next();
+ assertEquals(reaction.getProducts().get(0).getLine().length(), reaction.getReactants().get(0).getLine().length(),
+ 1e-6);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProblematicAnchorsWithTwoReactantReaction() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/centeredAnchorInModifier.xml");
+ Reaction reaction = model.getReactions().iterator().next();
+ Reactant r = null;
+ for (Reactant reactant : reaction.getReactants()) {
+ if (reactant.getElement().getName().equals("s3")) {
+ r = reactant;
+ }
+ }
+ assertNotNull(r);
+ // I think there is still a bug becaue it should work with smaller delta
+ // :)
+ assertEquals(r.getLine().getPoints().get(1).getX(), r.getLine().getPoints().get(2).getX(), 1);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionWithModifiers() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/reactionWithModifiers.xml");
+ Reaction reaction = model.getReactions().iterator().next();
+ List<Modifier> modifiers = reaction.getModifiers();
+ Modifier sa3 = null;
+ Modifier sa4 = null;
+ for (Modifier modifier : modifiers) {
+ if (modifier.getElement().getElementId().equals("sa3")) {
+ sa3 = modifier;
+ }
+ if (modifier.getElement().getElementId().equals("sa4")) {
+ sa4 = modifier;
+ }
+ }
+ assertEquals(sa3.getLine().getPoints().get(0).distance(new Point2D.Double(101.9591678008944, 68.0)), 0, EPSILON);
+ assertEquals(
+ sa3.getLine().getPoints().get(1).distance(new Point2D.Double(101.86750788643532, 112.89589905362774)), 0,
+ EPSILON);
+ assertEquals(
+ sa3.getLine().getPoints().get(2).distance(new Point2D.Double(190.66666666666666, 117.66666666666667)), 0,
+ EPSILON);
+
+ assertEquals(sa4.getLine().getPoints().get(0).distance(new Point2D.Double(267.7075561388218, 54.00000000000001)),
+ 0, EPSILON);
+ assertEquals(sa4.getLine().getPoints().get(1).distance(new Point2D.Double(298.3735877669656, 71.67109819284718)),
+ 0, EPSILON);
+ assertEquals(
+ sa4.getLine().getPoints().get(2).distance(new Point2D.Double(190.66666666666666, 117.66666666666667)), 0,
+ EPSILON);
+
+ // new NormalImageGenerator(1, 0, 0, 1024, 1024, model, true, false, 0,
+ // false).saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionOperatorsWithOperators() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/reactionWithOperators.xml");
+ Reaction reaction = model.getReactions().iterator().next();
+ NodeOperator operator1 = reaction.getOperators().get(0);
+ NodeOperator operator2 = reaction.getOperators().get(1);
+ NodeOperator operator3 = reaction.getOperators().get(2);
+
+ // new NormalImageGenerator(1, 0, 0, 1024, 1024, model, true, false, 0,
+ // false).saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+
+ assertEquals(operator1.getLine().getPoints().get(0).distance(new Point2D.Double(287.0, 242.00000000000009)), 0,
+ EPSILON);
+ assertEquals(
+ operator1.getLine().getPoints().get(1).distance(new Point2D.Double(287.97349260719136, 204.40292958328325)),
+ 0, EPSILON);
+ assertEquals(
+ operator1.getLine().getPoints().get(2).distance(new Point2D.Double(372.9868291110932, 203.8558964441427)), 0,
+ EPSILON);
+
+ assertEquals(
+ operator2.getLine().getPoints().get(0).distance(new Point2D.Double(359.1840955643148, 203.94471254019686)), 0,
+ EPSILON);
+ assertEquals(
+ operator2.getLine().getPoints().get(1).distance(new Point2D.Double(372.9868291110932, 203.8558964441427)), 0,
+ EPSILON);
+
+ assertEquals(
+ operator3.getLine().getPoints().get(0).distance(new Point2D.Double(394.78939704287654, 203.71560401865366)),
+ 0, EPSILON);
+ assertEquals(
+ operator3.getLine().getPoints().get(1).distance(new Point2D.Double(380.9866634960982, 203.80442011470782)), 0,
+ EPSILON);
+
+ Product product1 = reaction.getProducts().get(0);
+ Product product2 = reaction.getProducts().get(1);
+
+ assertEquals(
+ product1.getLine().getPoints().get(0).distance(new Point2D.Double(394.78939704287654, 203.71560401865366)), 0,
+ EPSILON);
+ assertEquals(product1.getLine().getPoints().get(1).distance(new Point2D.Double(466.0, 203.25738697556727)), 0,
+ EPSILON);
+
+ assertEquals(
+ product2.getLine().getPoints().get(0).distance(new Point2D.Double(394.78939704287654, 203.71560401865366)), 0,
+ EPSILON);
+ assertEquals(
+ product2.getLine().getPoints().get(1).distance(new Point2D.Double(452.96894321929705, 107.00000000000001)), 0,
+ EPSILON);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionProductsWithOperators() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/reactionWithOperators.xml");
+ Reaction reaction = model.getReactions().iterator().next();
+
+ Product product1 = reaction.getProducts().get(0);
+ Product product2 = reaction.getProducts().get(1);
+
+ assertEquals(
+ product1.getLine().getPoints().get(0).distance(new Point2D.Double(394.78939704287654, 203.71560401865366)), 0,
+ EPSILON);
+ assertEquals(product1.getLine().getPoints().get(1).distance(new Point2D.Double(466.0, 203.25738697556727)), 0,
+ EPSILON);
+
+ assertEquals(
+ product2.getLine().getPoints().get(0).distance(new Point2D.Double(394.78939704287654, 203.71560401865366)), 0,
+ EPSILON);
+ assertEquals(
+ product2.getLine().getPoints().get(1).distance(new Point2D.Double(452.96894321929705, 107.00000000000001)), 0,
+ EPSILON);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionReactantsWithOperators() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/reactionWithOperators.xml");
+ Reaction reaction = model.getReactions().iterator().next();
+
+ Reactant reactant1 = reaction.getReactants().get(0);
+ Reactant reactant2 = reaction.getReactants().get(1);
+ Reactant reactant3 = reaction.getReactants().get(2);
+
+ assertEquals(
+ reactant1.getLine().getPoints().get(0).distance(new Point2D.Double(112.53618421052632, 167.46381578947367)),
+ 0, EPSILON);
+ assertEquals(reactant1.getLine().getPoints().get(1).distance(new Point2D.Double(287.0, 242.00000000000009)), 0,
+ EPSILON);
+
+ assertEquals(reactant2.getLine().getPoints().get(0).distance(new Point2D.Double(121.0, 242.0)), 0, EPSILON);
+ assertEquals(reactant2.getLine().getPoints().get(1).distance(new Point2D.Double(287.0, 242.00000000000009)), 0,
+ EPSILON);
+
+ assertEquals(
+ reactant3.getLine().getPoints().get(0).distance(new Point2D.Double(116.65392247520951, 72.34607752479052)), 0,
+ EPSILON);
+ assertEquals(
+ reactant3.getLine().getPoints().get(1).distance(new Point2D.Double(359.1840955643148, 203.94471254019686)), 0,
+ EPSILON);
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0, false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTransitionReactionToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_transition.xml");
+
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ assertEquals(reaction1.getReactants().size(), reaction2.getReactants().size());
+ Reactant reactant1 = reaction1.getReactants().get(0);
+ Reactant reactant2 = reaction2.getReactants().get(0);
+ assertEquals(reactant1.getLine().getBeginAtd().getArrowType(), reactant2.getLine().getBeginAtd().getArrowType());
+ assertEquals(reactant1.getLine().getEndAtd().getArrowType(), reactant2.getLine().getEndAtd().getArrowType());
+ assertEquals(reactant1.getLine().getLines().size(), reactant2.getLine().getLines().size());
+
+ Product product1 = reaction1.getProducts().get(0);
+ Product product2 = reaction2.getProducts().get(0);
+ assertEquals(product1.getLine().getBeginAtd().getArrowType(), product2.getLine().getBeginAtd().getArrowType());
+ assertEquals(product1.getLine().getEndAtd().getArrowType(), product2.getLine().getEndAtd().getArrowType());
+ assertEquals(product1.getLine().getLines().size(), product2.getLine().getLines().size());
+
+ assertEquals(reactant1.getLine().getEndPoint().getX(), reactant2.getLine().getEndPoint().getX(), EPSILON);
+ assertEquals(reactant1.getLine().getEndPoint().getY(), reactant2.getLine().getEndPoint().getY(), EPSILON);
+
+ assertEquals(reaction1.getReactionRect(), reaction2.getReactionRect());
+
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+
+ assertEquals(product1.getLine().getColor(), product2.getLine().getColor());
+ assertEquals(product1.getLine().getWidth(), product2.getLine().getWidth(), 1e-6);
+
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTransitionWidthAdditionalNodelReactionToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_transitionWithAdditionalNodes.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ assertEquals(reaction1.getReactants().size(), reaction2.getReactants().size());
+ Reactant reactant1 = reaction1.getReactants().get(1);
+ Reactant reactant2 = reaction2.getReactants().get(1);
+ assertEquals(reactant1.getLine().getBeginAtd().getArrowType(), reactant2.getLine().getBeginAtd().getArrowType());
+ assertEquals(reactant1.getLine().getEndAtd().getArrowType(), reactant2.getLine().getEndAtd().getArrowType());
+ assertEquals(reactant1.getLine().getLines().size(), reactant2.getLine().getLines().size());
+
+ Product product1 = reaction1.getProducts().get(1);
+ Product product2 = reaction2.getProducts().get(1);
+ assertEquals(product1.getLine().getBeginAtd().getArrowType(), product2.getLine().getBeginAtd().getArrowType());
+ assertEquals(product1.getLine().getEndAtd().getArrowType(), product2.getLine().getEndAtd().getArrowType());
+ assertEquals(product1.getLine().getLines().size(), product2.getLine().getLines().size());
+
+ assertTrue(reactant1.getLine().getEndPoint().distance(reactant2.getLine().getEndPoint()) < 1e-6);
+ assertEquals(reaction1.getReactionRect(), reaction2.getReactionRect());
+
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+
+ assertEquals(product1.getLine().getColor(), product2.getLine().getColor());
+ assertEquals(product1.getLine().getWidth(), product2.getLine().getWidth(), 1e-6);
+
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTranslationToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_translation.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ assertEquals(reaction1.getReactants().size(), reaction2.getReactants().size());
+ Reactant reactant1 = reaction1.getReactants().get(1);
+ Reactant reactant2 = reaction2.getReactants().get(1);
+ assertEquals(reactant1.getLine().getBeginAtd().getArrowType(), reactant2.getLine().getBeginAtd().getArrowType());
+ assertEquals(reactant1.getLine().getEndAtd().getArrowType(), reactant2.getLine().getEndAtd().getArrowType());
+ assertEquals(reactant1.getLine().getLines().size(), reactant2.getLine().getLines().size());
+
+ Product product1 = reaction1.getProducts().get(1);
+ Product product2 = reaction2.getProducts().get(1);
+ assertEquals(product1.getLine().getBeginAtd().getArrowType(), product2.getLine().getBeginAtd().getArrowType());
+ assertEquals(product1.getLine().getEndAtd().getArrowType(), product2.getLine().getEndAtd().getArrowType());
+ assertEquals(product1.getLine().getLines().size(), product2.getLine().getLines().size());
+
+ assertTrue(reactant1.getLine().getEndPoint().distance(reactant2.getLine().getEndPoint()) < 1e-6);
+ assertEquals(reaction1.getReactionRect(), reaction2.getReactionRect());
+
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+
+ assertEquals(product1.getLine().getColor(), product2.getLine().getColor());
+ assertEquals(product1.getLine().getWidth(), product2.getLine().getWidth(), 1e-6);
+
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTransportToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_transport.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ assertEquals(reaction1.getMiriamData().size(), reaction2.getMiriamData().size());
+ assertEquals(reaction1.getNotes().trim(), reaction2.getNotes().trim());
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTruncationToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_truncation.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTruncationWithModifierToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_truncationWithModifier.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUnknownTransitionToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_unknown_transition.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTransitionOmittedToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_transition_omitted.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTranscriptionToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_transcription.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTranscriptionWithAdditionsToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_transcription_with_additions.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionWithOperatorsToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_with_operators.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionWithModifiersToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_with_modifiers.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionPositiveInfluenceToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_positive_influence.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionHeterodimerWithAdditionsToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_heterodimer_with_additions.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ assertEquals(reaction1.getNodes().size(), reaction2.getNodes().size());
+
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionHeterodimerToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_heterodimer.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ assertEquals(reaction1.getNodes().size(), reaction2.getNodes().size());
+
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ @Test
+ public void testOperatorInReactionHeterodimer() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_heterodimer.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+ for (NodeOperator operator : reaction1.getOperators()) {
+ assertTrue(operator instanceof AssociationOperator);
+ }
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionDissociationWithAdditionToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_dissociation_with_addition.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ assertEquals(reaction1.getName(), reaction2.getName());
+ assertNotNull(reaction1.getName());
+ assertFalse(reaction1.getName().trim().equals(""));
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ private Model getModelFilledWithSpecies() {
+ Model model = new ModelFullIndexed(null);
+
+ Species sa1 = new GenericProtein("sa1");
+ sa1.setX(100.0);
+ sa1.setY(200.0);
+ sa1.setWidth(300.0);
+ sa1.setHeight(400.0);
+ model.addElement(sa1);
+ elements.addModelElement(sa1, new CellDesignerGenericProtein("s1"));
+
+ Species sa2 = new GenericProtein("sa2");
+ sa2.setX(1050.0);
+ sa2.setY(2050.0);
+ sa2.setWidth(300.0);
+ sa2.setHeight(450.0);
+ model.addElement(sa2);
+ elements.addModelElement(sa2, new CellDesignerGenericProtein("s2"));
+
+ Species sa3 = new GenericProtein("sa3");
+ sa3.setX(600.0);
+ sa3.setY(250.0);
+ sa3.setWidth(300.0);
+ sa3.setHeight(400.0);
+ model.addElement(sa3);
+ elements.addModelElement(sa3, new CellDesignerGenericProtein("s3"));
+
+ Species sa4 = new GenericProtein("sa4");
+ sa4.setX(550.0);
+ sa4.setY(350.0);
+ sa4.setWidth(300.0);
+ sa4.setHeight(450.0);
+ model.addElement(sa4);
+ elements.addElement(new CellDesignerGenericProtein("s4"));
+
+ Species sa5 = new GenericProtein("sa5");
+ sa5.setX(10.0);
+ sa5.setY(250.0);
+ sa5.setWidth(300.0);
+ sa5.setHeight(450.0);
+ model.addElement(sa5);
+ elements.addElement(new CellDesignerGenericProtein("s5"));
+
+ Species sa6 = new GenericProtein("sa6");
+ sa6.setX(10.0);
+ sa6.setY(250.0);
+ sa6.setWidth(300.0);
+ sa6.setHeight(450.0);
+ model.addElement(sa6);
+
+ elements.addElement(new CellDesignerGenericProtein("s6"));
+
+ Species sa10 = new GenericProtein("sa10");
+ sa10.setX(210.0);
+ sa10.setY(220.0);
+ sa10.setWidth(320.0);
+ sa10.setHeight(250.0);
+ model.addElement(sa10);
+ elements.addElement(new CellDesignerGenericProtein("s10"));
+
+ Species sa11 = new GenericProtein("sa11");
+ sa11.setX(11.0);
+ sa11.setY(320.0);
+ sa11.setWidth(321.0);
+ sa11.setHeight(150.0);
+ model.addElement(sa11);
+ elements.addElement(new CellDesignerGenericProtein("s11"));
+
+ Species sa12 = new GenericProtein("sa12");
+ sa12.setX(12.0);
+ sa12.setY(20.0);
+ sa12.setWidth(321.0);
+ sa12.setHeight(150.0);
+ model.addElement(sa12);
+ elements.addElement(new CellDesignerGenericProtein("s12"));
+
+ Species sa13 = new GenericProtein("sa13");
+ sa13.setX(513.0);
+ sa13.setY(20.0);
+ sa13.setWidth(321.0);
+ sa13.setHeight(150.0);
+ model.addElement(sa13);
+ elements.addElement(new CellDesignerGenericProtein("s13"));
+
+ Species sa14 = new GenericProtein("sa14");
+ sa14.setX(14.0);
+ sa14.setY(820.0);
+ sa14.setWidth(321.0);
+ sa14.setHeight(150.0);
+ model.addElement(sa14);
+ elements.addElement(new CellDesignerGenericProtein("s14"));
+
+ Species sa15 = new GenericProtein("sa15");
+ sa15.setX(815.0);
+ sa15.setY(620.0);
+ sa15.setWidth(321.0);
+ sa15.setHeight(150.0);
+ model.addElement(sa15);
+ elements.addElement(new CellDesignerGenericProtein("s15"));
+
+ return model;
+ }
+
+ @Test
+ public void testLogiGateAndReaction() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/logicGateAnd.xml");
+ assertEquals(1, model.getReactions().size());
+ Reaction reaction = model.getReactions().iterator().next();
+ assertTrue(reaction instanceof BooleanLogicGateReaction);
+ assertEquals(1, reaction.getOperators().size());
+ assertTrue(reaction.getOperators().get(0) instanceof AndOperator);
+ assertEquals(2, reaction.getReactants().size());
+ assertEquals(1, reaction.getProducts().size());
+
+ assertEquals(0.0, reaction.getReactants().get(0).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
+ assertEquals(0.0, reaction.getReactants().get(1).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
+ assertEquals(0.0, reaction.getProducts().get(0).getLine().getBeginPoint().distance(200.0, 127.0), EPSILON);
+
+ CellDesignerXmlParser cellDesignerXmlParser = new CellDesignerXmlParser();
+
+ model.setName(null);
+ String xmlString = cellDesignerXmlParser.toXml(model);
+
+ ByteArrayInputStream bais = new ByteArrayInputStream(xmlString.getBytes("UTF-8"));
+ Model model2 = cellDesignerXmlParser.createModel(new ConverterParams().inputStream(bais).sizeAutoAdjust(false));
+
+ ModelComparator mc = new ModelComparator();
+ assertEquals("After CellDesigner xml serialization models are different", 0, mc.compare(model, model2));
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0, false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testLogiGateOrReaction() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/logicGateOr.xml");
+ assertEquals(1, model.getReactions().size());
+ Reaction reaction = model.getReactions().iterator().next();
+ assertTrue(reaction instanceof BooleanLogicGateReaction);
+ assertEquals(1, reaction.getOperators().size());
+ assertTrue(reaction.getOperators().get(0) instanceof OrOperator);
+ assertEquals(2, reaction.getReactants().size());
+ assertEquals(1, reaction.getProducts().size());
+
+ assertEquals(0.0, reaction.getReactants().get(0).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
+ assertEquals(0.0, reaction.getReactants().get(1).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
+ assertEquals(0.0, reaction.getProducts().get(0).getLine().getBeginPoint().distance(200.0, 127.0), EPSILON);
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0, false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testLogiGateNotReaction() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/logicGateNot.xml");
+ assertEquals(1, model.getReactions().size());
+ Reaction reaction = model.getReactions().iterator().next();
+ assertTrue(reaction instanceof BooleanLogicGateReaction);
+ assertEquals(1, reaction.getOperators().size());
+ assertTrue(reaction.getOperators().get(0) instanceof NandOperator);
+ assertEquals(2, reaction.getReactants().size());
+ assertEquals(1, reaction.getProducts().size());
+
+ assertEquals(0.0, reaction.getReactants().get(0).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
+ assertEquals(0.0, reaction.getReactants().get(1).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
+ assertEquals(0.0, reaction.getProducts().get(0).getLine().getBeginPoint().distance(200.0, 127.0), EPSILON);
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0, false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testLogiGateUnknownReaction() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/logicGateUnknown.xml");
+ assertEquals(1, model.getReactions().size());
+ Reaction reaction = model.getReactions().iterator().next();
+ assertTrue(reaction instanceof BooleanLogicGateReaction);
+ assertEquals(1, reaction.getOperators().size());
+ assertTrue(reaction.getOperators().get(0) instanceof UnknownOperator);
+ assertEquals(2, reaction.getReactants().size());
+ assertEquals(1, reaction.getProducts().size());
+
+ assertEquals(0.0, reaction.getReactants().get(0).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
+ assertEquals(0.0, reaction.getReactants().get(1).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
+ assertEquals(0.0, reaction.getProducts().get(0).getLine().getBeginPoint().distance(200.0, 127.0), EPSILON);
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0, false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProblematicDrawing() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/problematic/reaction_drawing_problem.xml");
+ Reaction reaction = model.getReactionByReactionId("re1");
+ assertEquals(0, reaction.getCenterPoint().distance(new Point2D.Double(258.5, 145.0)), EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProteinsInsideComplex() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/problematic/proteins_inside_complex.xml");
+ for (Element el : model.getElements()) {
+ assertFalse(el.getClass().equals(Protein.class));
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testKinetcs() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/reactions/kinetics.xml");
+ Reaction reaction = model.getReactionByReactionId("re1");
+ assertNotNull(reaction.getKinetics());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testKinetcsWithCompartment() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/reactions/kinetics_with_compartment.xml");
+ Reaction reaction = model.getReactionByReactionId("re1");
+ assertNotNull(reaction.getKinetics());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXmlTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXmlTest.java
index 892243e5b3..3e6ca41a0a 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXmlTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXmlTest.java
@@ -1,265 +1,265 @@
-package lcsb.mapviewer.converter.model.celldesigner.reaction;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.EventStorageLoggerAppender;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.InconsistentModelException;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.modifier.Catalysis;
-import lcsb.mapviewer.model.map.reaction.AndOperator;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.reaction.NodeOperator;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.type.DissociationReaction;
-import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class ReactionToXmlTest {
- Logger logger = Logger.getLogger(ReactionToXmlTest.class);
-
- CellDesignerElementCollection elements;
- ReactionToXml toXmlParser;
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- elements = new CellDesignerElementCollection();
- toXmlParser = new ReactionToXml(elements, false);
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testInvalidModification() throws InconsistentModelException {
- Model model = new ModelFullIndexed(null);
- Species protein1 = new GenericProtein("2");
- Species protein2 = new GenericProtein("3");
-
- model.addElement(protein1);
- model.addElement(protein2);
-
- Reaction reaction = new TransportReaction();
-
- Reactant reactant = new Reactant(protein1);
- reactant.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double(10, 0)));
- Product product = new Product(protein2);
- product.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double(20, 0)));
-
- reaction.addReactant(reactant);
- reaction.addProduct(product);
-
- Modifier modifier = new Catalysis(protein1);
- modifier.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double(30, 0)));
-
- Modifier modifier2 = new Catalysis(protein1);
- List<Point2D> points = new ArrayList<>();
- points.add(new Point2D.Double(0, 0));
- points.add(new Point2D.Double(30, 30));
- points.add(new Point2D.Double(20, 20));
- points.add(new Point2D.Double(20, 10));
- points.add(new Point2D.Double(40, 0));
- modifier2.setLine(new PolylineData(points));
-
- NodeOperator andOperator = new AndOperator();
- andOperator.addInput(modifier);
- andOperator.addInput(modifier2);
- points = new ArrayList<>();
- points.add(new Point2D.Double(1, 0));
- points.add(new Point2D.Double(30, 30));
- points.add(new Point2D.Double(20, 20));
- points.add(new Point2D.Double(20, 10));
- points.add(new Point2D.Double(30, 0));
- andOperator.setLine(new PolylineData(points));
-
- reaction.addModifier(modifier);
- reaction.addModifier(modifier2);
- reaction.addNode(andOperator);
-
- EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
- Logger.getRootLogger().addAppender(appender);
-
- try {
- toXmlParser.toXml(reaction);
- assertEquals(2, appender.getWarnings().size());
- } finally {
- Logger.getRootLogger().removeAppender(appender);
- }
-
- }
-
- @Test
- public void testModificationFromInsideComplex() throws InconsistentModelException {
-
- Model model = new ModelFullIndexed(null);
- Species protein1 = new GenericProtein("2");
- Species protein2 = new GenericProtein("3");
-
- model.addElement(protein1);
- model.addElement(protein2);
-
- Complex complex = new Complex("4");
- complex.addSpecies(protein1);
-
- protein1.setComplex(complex);
-
- model.addElement(complex);
-
- Reaction reaction = new TransportReaction();
-
- Reactant reactant = new Reactant(protein1);
- reactant.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double(10, 0)));
- Product product = new Product(protein2);
- product.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double(20, 0)));
-
- reaction.addReactant(reactant);
- reaction.addProduct(product);
-
- Modifier modifier = new Catalysis(protein1);
- modifier.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double(30, 0)));
-
- reaction.addModifier(modifier);
-
- String xml = toXmlParser.toXml(reaction);
-
- assertTrue(xml.contains("species=\"" + elements.getElementId(complex) + "\""));
-
- }
-
- @Test
- public void testInvalidToXml() throws InconsistentModelException {
-
- Model model = new ModelFullIndexed(null);
-
- Complex complex = new Complex("4");
- complex.setComplex(complex);
- model.addElement(complex);
-
- Species protein1 = new GenericProtein("2");
-
- model.addElement(protein1);
-
-
- Reaction reaction = new TransportReaction();
-
- Reactant reactant = new Reactant(complex);
- reactant.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double(10, 0)));
- Product product = new Product(protein1);
- product.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double(20, 0)));
-
- reaction.addReactant(reactant);
- reaction.addProduct(product);
-
- try {
- toXmlParser.toXml(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- }
-
- }
-
- @Test
- public void testInvalidReaction() throws InconsistentModelException {
-
- Model model = new ModelFullIndexed(null);
- Species protein1 = new GenericProtein("2");
- Species protein2 = new GenericProtein("3");
-
- model.addElement(protein1);
- model.addElement(protein2);
-
- Reaction reaction = new Reaction();
-
- Reactant reactant = new Reactant(protein1);
- reactant.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double(10, 0)));
- Product product = new Product(protein2);
- product.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double(20, 0)));
-
- reaction.addReactant(reactant);
- reaction.addProduct(product);
-
- try {
- toXmlParser.toXml(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Unknown reaction type"));
- }
-
- }
-
- @Test
- public void testGetEditPointsXmlStringForInvalidReaction() {
- try {
- toXmlParser.getEditPointsXmlStringForReaction(new Reaction());
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Unhandled reaction type"));
- }
-
- }
-
- @Test
- public void testGetConnectSchemeXmlStringForReaction() {
- try {
- toXmlParser.getConnectSchemeXmlStringForReaction(new Reaction());
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Unknown reaction type"));
- }
-
- }
-
- @Test
- public void testGetConnectSchemeXmlStringForReaction2() {
- try {
- // test internal implementation
- toXmlParser = new ReactionToXml(elements, false) {
- @Override
- String getEditPointsXmlStringForReaction(Reaction reaction) {
- return "";
- }
- };
- toXmlParser.getConnectSchemeXmlStringForReaction(new DissociationReaction());
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Invalid editPoints string"));
- }
-
- }
-
- @Test
- public void testGetConnectSchemeXmlStringForLines() {
- // this test checks currently not used part of the code (for test coverage
- // purpose)
- String xml = toXmlParser.getConnectSchemeXmlStringForLines(
- new PolylineData[] { new PolylineData(new Point2D.Double(), new Point2D.Double()), new PolylineData() });
- assertTrue(xml.contains("arm"));
-
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.reaction;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.EventStorageLoggerAppender;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.modifier.Catalysis;
+import lcsb.mapviewer.model.map.reaction.AndOperator;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.reaction.NodeOperator;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.type.DissociationReaction;
+import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class ReactionToXmlTest {
+ Logger logger = Logger.getLogger(ReactionToXmlTest.class);
+
+ CellDesignerElementCollection elements;
+ ReactionToXml toXmlParser;
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ elements = new CellDesignerElementCollection();
+ toXmlParser = new ReactionToXml(elements, false);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testInvalidModification() throws InconsistentModelException {
+ Model model = new ModelFullIndexed(null);
+ Species protein1 = new GenericProtein("2");
+ Species protein2 = new GenericProtein("3");
+
+ model.addElement(protein1);
+ model.addElement(protein2);
+
+ Reaction reaction = new TransportReaction();
+
+ Reactant reactant = new Reactant(protein1);
+ reactant.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double(10, 0)));
+ Product product = new Product(protein2);
+ product.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double(20, 0)));
+
+ reaction.addReactant(reactant);
+ reaction.addProduct(product);
+
+ Modifier modifier = new Catalysis(protein1);
+ modifier.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double(30, 0)));
+
+ Modifier modifier2 = new Catalysis(protein1);
+ List<Point2D> points = new ArrayList<>();
+ points.add(new Point2D.Double(0, 0));
+ points.add(new Point2D.Double(30, 30));
+ points.add(new Point2D.Double(20, 20));
+ points.add(new Point2D.Double(20, 10));
+ points.add(new Point2D.Double(40, 0));
+ modifier2.setLine(new PolylineData(points));
+
+ NodeOperator andOperator = new AndOperator();
+ andOperator.addInput(modifier);
+ andOperator.addInput(modifier2);
+ points = new ArrayList<>();
+ points.add(new Point2D.Double(1, 0));
+ points.add(new Point2D.Double(30, 30));
+ points.add(new Point2D.Double(20, 20));
+ points.add(new Point2D.Double(20, 10));
+ points.add(new Point2D.Double(30, 0));
+ andOperator.setLine(new PolylineData(points));
+
+ reaction.addModifier(modifier);
+ reaction.addModifier(modifier2);
+ reaction.addNode(andOperator);
+
+ EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
+ Logger.getRootLogger().addAppender(appender);
+
+ try {
+ toXmlParser.toXml(reaction);
+ assertEquals(2, appender.getWarnings().size());
+ } finally {
+ Logger.getRootLogger().removeAppender(appender);
+ }
+
+ }
+
+ @Test
+ public void testModificationFromInsideComplex() throws InconsistentModelException {
+
+ Model model = new ModelFullIndexed(null);
+ Species protein1 = new GenericProtein("2");
+ Species protein2 = new GenericProtein("3");
+
+ model.addElement(protein1);
+ model.addElement(protein2);
+
+ Complex complex = new Complex("4");
+ complex.addSpecies(protein1);
+
+ protein1.setComplex(complex);
+
+ model.addElement(complex);
+
+ Reaction reaction = new TransportReaction();
+
+ Reactant reactant = new Reactant(protein1);
+ reactant.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double(10, 0)));
+ Product product = new Product(protein2);
+ product.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double(20, 0)));
+
+ reaction.addReactant(reactant);
+ reaction.addProduct(product);
+
+ Modifier modifier = new Catalysis(protein1);
+ modifier.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double(30, 0)));
+
+ reaction.addModifier(modifier);
+
+ String xml = toXmlParser.toXml(reaction);
+
+ assertTrue(xml.contains("species=\"" + elements.getElementId(complex) + "\""));
+
+ }
+
+ @Test
+ public void testInvalidToXml() throws InconsistentModelException {
+
+ Model model = new ModelFullIndexed(null);
+
+ Complex complex = new Complex("4");
+ complex.setComplex(complex);
+ model.addElement(complex);
+
+ Species protein1 = new GenericProtein("2");
+
+ model.addElement(protein1);
+
+
+ Reaction reaction = new TransportReaction();
+
+ Reactant reactant = new Reactant(complex);
+ reactant.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double(10, 0)));
+ Product product = new Product(protein1);
+ product.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double(20, 0)));
+
+ reaction.addReactant(reactant);
+ reaction.addProduct(product);
+
+ try {
+ toXmlParser.toXml(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ }
+
+ }
+
+ @Test
+ public void testInvalidReaction() throws InconsistentModelException {
+
+ Model model = new ModelFullIndexed(null);
+ Species protein1 = new GenericProtein("2");
+ Species protein2 = new GenericProtein("3");
+
+ model.addElement(protein1);
+ model.addElement(protein2);
+
+ Reaction reaction = new Reaction();
+
+ Reactant reactant = new Reactant(protein1);
+ reactant.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double(10, 0)));
+ Product product = new Product(protein2);
+ product.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double(20, 0)));
+
+ reaction.addReactant(reactant);
+ reaction.addProduct(product);
+
+ try {
+ toXmlParser.toXml(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Unknown reaction type"));
+ }
+
+ }
+
+ @Test
+ public void testGetEditPointsXmlStringForInvalidReaction() {
+ try {
+ toXmlParser.getEditPointsXmlStringForReaction(new Reaction());
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Unhandled reaction type"));
+ }
+
+ }
+
+ @Test
+ public void testGetConnectSchemeXmlStringForReaction() {
+ try {
+ toXmlParser.getConnectSchemeXmlStringForReaction(new Reaction());
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Unknown reaction type"));
+ }
+
+ }
+
+ @Test
+ public void testGetConnectSchemeXmlStringForReaction2() {
+ try {
+ // test internal implementation
+ toXmlParser = new ReactionToXml(elements, false) {
+ @Override
+ String getEditPointsXmlStringForReaction(Reaction reaction) {
+ return "";
+ }
+ };
+ toXmlParser.getConnectSchemeXmlStringForReaction(new DissociationReaction());
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Invalid editPoints string"));
+ }
+
+ }
+
+ @Test
+ public void testGetConnectSchemeXmlStringForLines() {
+ // this test checks currently not used part of the code (for test coverage
+ // purpose)
+ String xml = toXmlParser.getConnectSchemeXmlStringForLines(
+ new PolylineData[] { new PolylineData(new Point2D.Double(), new Point2D.Double()), new PolylineData() });
+ assertTrue(xml.contains("arm"));
+
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/UnknownModifierClassExceptionTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/UnknownModifierClassExceptionTest.java
index 9707a0ded8..88d28638b1 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/UnknownModifierClassExceptionTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/UnknownModifierClassExceptionTest.java
@@ -1,32 +1,32 @@
-package lcsb.mapviewer.converter.model.celldesigner.reaction;
-
-import static org.junit.Assert.*;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class UnknownModifierClassExceptionTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetters() {
- String modificationType = "str";
- UnknownModifierClassException exception = new UnknownModifierClassException(null, null, null);
- exception.setModificationType(modificationType);
- assertEquals(modificationType, exception.getModificationType());
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.reaction;
+
+import static org.junit.Assert.*;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class UnknownModifierClassExceptionTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetters() {
+ String modificationType = "str";
+ UnknownModifierClassException exception = new UnknownModifierClassException(null, null, null);
+ exception.setModificationType(modificationType);
+ assertEquals(modificationType, exception.getModificationType());
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/AllSpeciesTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/AllSpeciesTests.java
index cffa09dcd8..f6b46cd415 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/AllSpeciesTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/AllSpeciesTests.java
@@ -1,21 +1,21 @@
-package lcsb.mapviewer.converter.model.celldesigner.species;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-
-@RunWith(Suite.class)
-@Suite.SuiteClasses({ AntisenseRnaXmlParserTest.class, //
- ComplexParserTest.class, //
- GeneXmlParserTest.class, //
- InternalModelSpeciesDataTest.class, //
- ProteinMappingTest.class, //
- ProteinXmlParserTest.class, //
- RnaXmlParserTest.class, //
- SpeciesCollectionTest.class, //
- SpeciesCollectionXmlParserTest.class, //
- SpeciesMappingTest.class, //
- SpeciesSbmlParserTest.class,//
-})
-public class AllSpeciesTests {
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.species;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+
+@RunWith(Suite.class)
+@Suite.SuiteClasses({ AntisenseRnaXmlParserTest.class, //
+ ComplexParserTest.class, //
+ GeneXmlParserTest.class, //
+ InternalModelSpeciesDataTest.class, //
+ ProteinMappingTest.class, //
+ ProteinXmlParserTest.class, //
+ RnaXmlParserTest.class, //
+ SpeciesCollectionTest.class, //
+ SpeciesCollectionXmlParserTest.class, //
+ SpeciesMappingTest.class, //
+ SpeciesSbmlParserTest.class,//
+})
+public class AllSpeciesTests {
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParserTest.java
index 0bad270ff1..32345985cb 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParserTest.java
@@ -1,158 +1,158 @@
-package lcsb.mapviewer.converter.model.celldesigner.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.io.StringReader;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.w3c.dom.Document;
-import org.w3c.dom.NodeList;
-import org.xml.sax.InputSource;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRna;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.ModificationType;
-
-public class AntisenseRnaXmlParserTest extends CellDesignerTestFunctions {
- protected Logger logger = Logger.getLogger(AntisenseRnaXmlParserTest.class.getName());
-
- AntisenseRnaXmlParser antisenseRnaParser;
- String testAntisenseRnaFile = "testFiles" + System.getProperty("file.separator") + "xmlNodeTestExamples"
- + System.getProperty("file.separator") + "antisense_rna.xml";
- CellDesignerElementCollection elements;
-
- @Before
- public void setUp() throws Exception {
- elements = new CellDesignerElementCollection();
- antisenseRnaParser = new AntisenseRnaXmlParser(elements);
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParseXmlSpecies() throws Exception {
- try {
- String xmlString = readFile(testAntisenseRnaFile);
- Pair<String, CellDesignerAntisenseRna> result = antisenseRnaParser.parseXmlElement(xmlString);
- CellDesignerAntisenseRna antisenseRna = result.getRight();
- assertEquals("arn1", result.getLeft());
- assertEquals("s1", antisenseRna.getName());
- assertTrue(antisenseRna.getNotes().contains("some notes"));
- assertEquals(1, antisenseRna.getRegions().size());
- CellDesignerModificationResidue region = antisenseRna.getRegions().get(0);
- assertEquals("tr1", region.getIdModificationResidue());
- assertEquals("zzz", region.getName());
- assertEquals(0.3, region.getSize(), 1e-6);
- assertEquals(0.29999999999999993, region.getPos(), 1e-6);
- assertEquals(ModificationType.CODING_REGION, region.getModificationType());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlSpecies() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/antisense_rna.xml");
- antisenseRnaParser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfRegions"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlSpecies2() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/antisense_rna2.xml");
- antisenseRnaParser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:antisenseRna"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlSpecies3() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/antisense_rna3.xml");
- antisenseRnaParser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlSpecies4() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/antisense_rna4.xml");
- antisenseRnaParser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:region"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXml() throws Exception {
- try {
- String xmlString = readFile(testAntisenseRnaFile);
- Pair<String, CellDesignerAntisenseRna> result = antisenseRnaParser.parseXmlElement(xmlString);
- CellDesignerAntisenseRna antisenseRna = result.getRight();
-
- String transformedXml = antisenseRnaParser.toXml(antisenseRna.createModelElement());
- DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
- DocumentBuilder builder = factory.newDocumentBuilder();
- InputSource is = new InputSource(new StringReader(transformedXml));
- Document doc = builder.parse(is);
- NodeList root = doc.getChildNodes();
- assertEquals("celldesigner:AntisenseRNA", root.item(0).getNodeName());
-
- Pair<String, CellDesignerAntisenseRna> result2 = antisenseRnaParser.parseXmlElement(xmlString);
- CellDesignerAntisenseRna antisenseRna2 = result2.getRight();
- assertEquals(result.getLeft(), result2.getLeft());
- assertEquals(antisenseRna.getName(), antisenseRna2.getName());
- assertEquals(antisenseRna.getNotes().trim(), antisenseRna2.getNotes().trim());
-
- assertEquals(1, antisenseRna2.getRegions().size());
- CellDesignerModificationResidue region = antisenseRna.getRegions().get(0);
- CellDesignerModificationResidue region2 = antisenseRna2.getRegions().get(0);
- assertEquals(region.getIdModificationResidue(), region2.getIdModificationResidue());
- assertEquals(region.getName(), region2.getName());
- assertEquals(region.getSize(), region2.getSize(), 1e-6);
- assertEquals(region.getPos(), region2.getPos(), 1e-6);
- assertEquals(region.getModificationType(), region2.getModificationType());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.io.StringReader;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.w3c.dom.Document;
+import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.ModificationType;
+
+public class AntisenseRnaXmlParserTest extends CellDesignerTestFunctions {
+ protected Logger logger = Logger.getLogger(AntisenseRnaXmlParserTest.class.getName());
+
+ AntisenseRnaXmlParser antisenseRnaParser;
+ String testAntisenseRnaFile = "testFiles" + System.getProperty("file.separator") + "xmlNodeTestExamples"
+ + System.getProperty("file.separator") + "antisense_rna.xml";
+ CellDesignerElementCollection elements;
+
+ @Before
+ public void setUp() throws Exception {
+ elements = new CellDesignerElementCollection();
+ antisenseRnaParser = new AntisenseRnaXmlParser(elements);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testParseXmlSpecies() throws Exception {
+ try {
+ String xmlString = readFile(testAntisenseRnaFile);
+ Pair<String, CellDesignerAntisenseRna> result = antisenseRnaParser.parseXmlElement(xmlString);
+ CellDesignerAntisenseRna antisenseRna = result.getRight();
+ assertEquals("arn1", result.getLeft());
+ assertEquals("s1", antisenseRna.getName());
+ assertTrue(antisenseRna.getNotes().contains("some notes"));
+ assertEquals(1, antisenseRna.getRegions().size());
+ CellDesignerModificationResidue region = antisenseRna.getRegions().get(0);
+ assertEquals("tr1", region.getIdModificationResidue());
+ assertEquals("zzz", region.getName());
+ assertEquals(0.3, region.getSize(), 1e-6);
+ assertEquals(0.29999999999999993, region.getPos(), 1e-6);
+ assertEquals(ModificationType.CODING_REGION, region.getModificationType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlSpecies() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/antisense_rna.xml");
+ antisenseRnaParser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfRegions"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlSpecies2() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/antisense_rna2.xml");
+ antisenseRnaParser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:antisenseRna"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlSpecies3() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/antisense_rna3.xml");
+ antisenseRnaParser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlSpecies4() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/antisense_rna4.xml");
+ antisenseRnaParser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:region"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXml() throws Exception {
+ try {
+ String xmlString = readFile(testAntisenseRnaFile);
+ Pair<String, CellDesignerAntisenseRna> result = antisenseRnaParser.parseXmlElement(xmlString);
+ CellDesignerAntisenseRna antisenseRna = result.getRight();
+
+ String transformedXml = antisenseRnaParser.toXml(antisenseRna.createModelElement());
+ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ DocumentBuilder builder = factory.newDocumentBuilder();
+ InputSource is = new InputSource(new StringReader(transformedXml));
+ Document doc = builder.parse(is);
+ NodeList root = doc.getChildNodes();
+ assertEquals("celldesigner:AntisenseRNA", root.item(0).getNodeName());
+
+ Pair<String, CellDesignerAntisenseRna> result2 = antisenseRnaParser.parseXmlElement(xmlString);
+ CellDesignerAntisenseRna antisenseRna2 = result2.getRight();
+ assertEquals(result.getLeft(), result2.getLeft());
+ assertEquals(antisenseRna.getName(), antisenseRna2.getName());
+ assertEquals(antisenseRna.getNotes().trim(), antisenseRna2.getNotes().trim());
+
+ assertEquals(1, antisenseRna2.getRegions().size());
+ CellDesignerModificationResidue region = antisenseRna.getRegions().get(0);
+ CellDesignerModificationResidue region2 = antisenseRna2.getRegions().get(0);
+ assertEquals(region.getIdModificationResidue(), region2.getIdModificationResidue());
+ assertEquals(region.getName(), region2.getName());
+ assertEquals(region.getSize(), region2.getSize(), 1e-6);
+ assertEquals(region.getPos(), region2.getPos(), 1e-6);
+ assertEquals(region.getModificationType(), region2.getModificationType());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ComplexParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ComplexParserTest.java
index 943e53b846..10d6269550 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ComplexParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ComplexParserTest.java
@@ -1,352 +1,352 @@
-package lcsb.mapviewer.converter.model.celldesigner.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-import static org.mockito.Mockito.when;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.converter.model.celldesigner.alias.ComplexAliasXmlParser;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.Complex;
-
-public class ComplexParserTest extends CellDesignerTestFunctions {
- Logger logger = Logger.getLogger(ComplexParserTest.class);
-
- String testSpeciesId = "s3";
- String testAliasId = "sa3";
- String testCompartmentAliasId = "ca3";
- String testCompartmentId = "c3";
- String testCompartmentAliasId2 = "ca4";
- String testCompartmentId2 = "c4";
-
- CellDesignerElementCollection elements;
-
- @Before
- public void setUp() throws Exception {
- elements = new CellDesignerElementCollection();
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testComplexState() throws Exception {
- try {
- Model model = getModelForFile("testFiles/problematic/complex_with_state.xml");
- Complex complex = (Complex) model.getElementByElementId("csa1");
- assertEquals("test state", complex.getStructuralState());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidInputNode() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
- ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
-
- parser.parseXmlAlias(readFile("testFiles/invalid/invalid_complex_alias.xml"));
- fail("Exceptione expected");
-
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("No species"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidInputNode2() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
- CellDesignerComplexSpecies element = new CellDesignerComplexSpecies();
- element.setElementId("s3");
- elements.addElement(element);
- ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
-
- parser.parseXmlAlias(readFile("testFiles/invalid/invalid_complex_alias2.xml"));
- fail("Exceptione expected");
-
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("celldesigner:bla"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidInputNode3() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
- CellDesignerComplexSpecies element = new CellDesignerComplexSpecies();
- element.setElementId("s3");
- elements.addElement(element);
- ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
-
- parser.parseXmlAlias(readFile("testFiles/invalid/invalid_complex_alias3.xml"));
- fail("Exceptione expected");
-
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("unusual"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidInputNode4() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
- CellDesignerComplexSpecies element = new CellDesignerComplexSpecies();
- element.setElementId("s3");
- elements.addElement(element);
- ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
-
- parser.parseXmlAlias(readFile("testFiles/invalid/invalid_complex_alias4.xml"));
- fail("Exceptione expected");
-
- } catch (NotImplementedException e) {
- assertTrue(e.getMessage().contains("unkown state"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidInputNode5() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
- CellDesignerComplexSpecies element = new CellDesignerComplexSpecies();
- element.setElementId("s3");
- elements.addElement(element);
- ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
-
- parser.parseXmlAlias(readFile("testFiles/invalid/invalid_complex_alias5.xml"));
- fail("Exceptione expected");
-
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("CompartmentAlias does not exist"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlWithParent() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
-
- Compartment compartment = new Compartment(testCompartmentAliasId);
-
- Complex alias = new Complex(testAliasId);
-
- alias.setCompartment(compartment);
-
- model.addElement(alias);
- ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
-
- String xml = parser.toXml(alias);
-
- assertTrue(xml.contains(testAliasId));
- assertTrue(xml.contains(testCompartmentAliasId));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlWithCompartment() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
-
- Compartment ca = new Compartment(testCompartmentAliasId);
-
- Complex alias = new Complex(testAliasId);
-
- alias.setCompartment(ca);
-
- model.addElement(alias);
- ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
-
- String xml = parser.toXml(alias);
-
- assertTrue(xml.contains(testAliasId));
- assertTrue(xml.contains(testCompartmentAliasId));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlWithUnknownCompartment() throws Exception {
- try {
- Model model = Mockito.mock(ModelFullIndexed.class);
- ModelData md = new ModelData();
- md.setModel(model);
-
- Compartment ca2 = new Compartment(testCompartmentAliasId2);
- ca2.setX(6);
- ca2.setY(6);
- ca2.setWidth(190);
- ca2.setHeight(190);
-
- Compartment ca = new Compartment(testCompartmentAliasId);
- ca.setX(5);
- ca.setY(5);
- ca.setWidth(200);
- ca.setHeight(200);
-
- List<Compartment> list = new ArrayList<>();
- list.add(ca);
- list.add(ca2);
-
- // ensure that we return list (firts bigger compartment, then smaller)
- when(model.getCompartments()).thenReturn(list);
- when(model.getModelData()).thenReturn(md);
-
- Complex alias = new Complex(testAliasId);
- alias.setX(10);
- alias.setY(10);
- alias.setWidth(100);
- alias.setHeight(100);
- alias.setModel(model);
-
- model.addElement(alias);
- ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
-
- String xml = parser.toXml(alias);
-
- assertTrue(xml.contains(testAliasId));
- assertTrue(xml.contains(testCompartmentAliasId2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlWithComplexParent() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
-
- Complex complex = new Complex(testCompartmentAliasId);
-
- Complex alias = new Complex(testAliasId);
-
- alias.setComplex(complex);
-
- model.addElement(alias);
- ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
-
- String xml = parser.toXml(alias);
-
- assertTrue(xml.contains(testAliasId));
- assertTrue(xml.contains(testCompartmentAliasId));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlWithActiveComplex() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
-
- Complex alias = new Complex(testAliasId);
-
- alias.setActivity(true);
-
- model.addElement(alias);
- ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
-
- String xml = parser.toXml(alias);
-
- assertTrue(xml.contains(testAliasId));
- assertTrue(xml.contains("<celldesigner:activity>active</celldesigner:activity>"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddInvalidReference() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
- CellDesignerComplexSpecies element = new CellDesignerComplexSpecies();
- element.setElementId("s2");
- elements.addElement(element);
-
- ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
-
- Complex child = parser.parseXmlAlias(readFile("testFiles/xmlNodeTestExamples/cd_complex_alias_with_parent.xml"));
-
- parser.addReference(child);
- fail("Exception expected");
-
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Parent complex alias does not exist"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseWithEmptyState() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
- CellDesignerComplexSpecies element = new CellDesignerComplexSpecies("s2597");
- elements.addElement(element);
-
- ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
-
- Complex child = parser.parseXmlAlias(readFile("testFiles/xmlNodeTestExamples/cd_complex_alias_with_empty_state.xml"));
-
- assertNotNull(child);
- assertNull(child.getStateLabel());
- assertNull(child.getStatePrefix());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import static org.mockito.Mockito.when;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.converter.model.celldesigner.alias.ComplexAliasXmlParser;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Complex;
+
+public class ComplexParserTest extends CellDesignerTestFunctions {
+ Logger logger = Logger.getLogger(ComplexParserTest.class);
+
+ String testSpeciesId = "s3";
+ String testAliasId = "sa3";
+ String testCompartmentAliasId = "ca3";
+ String testCompartmentId = "c3";
+ String testCompartmentAliasId2 = "ca4";
+ String testCompartmentId2 = "c4";
+
+ CellDesignerElementCollection elements;
+
+ @Before
+ public void setUp() throws Exception {
+ elements = new CellDesignerElementCollection();
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testComplexState() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/problematic/complex_with_state.xml");
+ Complex complex = (Complex) model.getElementByElementId("csa1");
+ assertEquals("test state", complex.getStructuralState());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidInputNode() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+ ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
+
+ parser.parseXmlAlias(readFile("testFiles/invalid/invalid_complex_alias.xml"));
+ fail("Exceptione expected");
+
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("No species"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidInputNode2() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+ CellDesignerComplexSpecies element = new CellDesignerComplexSpecies();
+ element.setElementId("s3");
+ elements.addElement(element);
+ ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
+
+ parser.parseXmlAlias(readFile("testFiles/invalid/invalid_complex_alias2.xml"));
+ fail("Exceptione expected");
+
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("celldesigner:bla"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidInputNode3() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+ CellDesignerComplexSpecies element = new CellDesignerComplexSpecies();
+ element.setElementId("s3");
+ elements.addElement(element);
+ ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
+
+ parser.parseXmlAlias(readFile("testFiles/invalid/invalid_complex_alias3.xml"));
+ fail("Exceptione expected");
+
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("unusual"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidInputNode4() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+ CellDesignerComplexSpecies element = new CellDesignerComplexSpecies();
+ element.setElementId("s3");
+ elements.addElement(element);
+ ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
+
+ parser.parseXmlAlias(readFile("testFiles/invalid/invalid_complex_alias4.xml"));
+ fail("Exceptione expected");
+
+ } catch (NotImplementedException e) {
+ assertTrue(e.getMessage().contains("unkown state"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidInputNode5() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+ CellDesignerComplexSpecies element = new CellDesignerComplexSpecies();
+ element.setElementId("s3");
+ elements.addElement(element);
+ ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
+
+ parser.parseXmlAlias(readFile("testFiles/invalid/invalid_complex_alias5.xml"));
+ fail("Exceptione expected");
+
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("CompartmentAlias does not exist"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlWithParent() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+
+ Compartment compartment = new Compartment(testCompartmentAliasId);
+
+ Complex alias = new Complex(testAliasId);
+
+ alias.setCompartment(compartment);
+
+ model.addElement(alias);
+ ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
+
+ String xml = parser.toXml(alias);
+
+ assertTrue(xml.contains(testAliasId));
+ assertTrue(xml.contains(testCompartmentAliasId));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlWithCompartment() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+
+ Compartment ca = new Compartment(testCompartmentAliasId);
+
+ Complex alias = new Complex(testAliasId);
+
+ alias.setCompartment(ca);
+
+ model.addElement(alias);
+ ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
+
+ String xml = parser.toXml(alias);
+
+ assertTrue(xml.contains(testAliasId));
+ assertTrue(xml.contains(testCompartmentAliasId));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlWithUnknownCompartment() throws Exception {
+ try {
+ Model model = Mockito.mock(ModelFullIndexed.class);
+ ModelData md = new ModelData();
+ md.setModel(model);
+
+ Compartment ca2 = new Compartment(testCompartmentAliasId2);
+ ca2.setX(6);
+ ca2.setY(6);
+ ca2.setWidth(190);
+ ca2.setHeight(190);
+
+ Compartment ca = new Compartment(testCompartmentAliasId);
+ ca.setX(5);
+ ca.setY(5);
+ ca.setWidth(200);
+ ca.setHeight(200);
+
+ List<Compartment> list = new ArrayList<>();
+ list.add(ca);
+ list.add(ca2);
+
+ // ensure that we return list (firts bigger compartment, then smaller)
+ when(model.getCompartments()).thenReturn(list);
+ when(model.getModelData()).thenReturn(md);
+
+ Complex alias = new Complex(testAliasId);
+ alias.setX(10);
+ alias.setY(10);
+ alias.setWidth(100);
+ alias.setHeight(100);
+ alias.setModel(model);
+
+ model.addElement(alias);
+ ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
+
+ String xml = parser.toXml(alias);
+
+ assertTrue(xml.contains(testAliasId));
+ assertTrue(xml.contains(testCompartmentAliasId2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlWithComplexParent() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+
+ Complex complex = new Complex(testCompartmentAliasId);
+
+ Complex alias = new Complex(testAliasId);
+
+ alias.setComplex(complex);
+
+ model.addElement(alias);
+ ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
+
+ String xml = parser.toXml(alias);
+
+ assertTrue(xml.contains(testAliasId));
+ assertTrue(xml.contains(testCompartmentAliasId));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlWithActiveComplex() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+
+ Complex alias = new Complex(testAliasId);
+
+ alias.setActivity(true);
+
+ model.addElement(alias);
+ ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
+
+ String xml = parser.toXml(alias);
+
+ assertTrue(xml.contains(testAliasId));
+ assertTrue(xml.contains("<celldesigner:activity>active</celldesigner:activity>"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddInvalidReference() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+ CellDesignerComplexSpecies element = new CellDesignerComplexSpecies();
+ element.setElementId("s2");
+ elements.addElement(element);
+
+ ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
+
+ Complex child = parser.parseXmlAlias(readFile("testFiles/xmlNodeTestExamples/cd_complex_alias_with_parent.xml"));
+
+ parser.addReference(child);
+ fail("Exception expected");
+
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Parent complex alias does not exist"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseWithEmptyState() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+ CellDesignerComplexSpecies element = new CellDesignerComplexSpecies("s2597");
+ elements.addElement(element);
+
+ ComplexAliasXmlParser parser = new ComplexAliasXmlParser(elements, model);
+
+ Complex child = parser.parseXmlAlias(readFile("testFiles/xmlNodeTestExamples/cd_complex_alias_with_empty_state.xml"));
+
+ assertNotNull(child);
+ assertNull(child.getStateLabel());
+ assertNull(child.getStatePrefix());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/InternalModelSpeciesDataTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/InternalModelSpeciesDataTest.java
index 314077d9dc..495605edbc 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/InternalModelSpeciesDataTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/InternalModelSpeciesDataTest.java
@@ -1,51 +1,51 @@
-package lcsb.mapviewer.converter.model.celldesigner.species;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-
-public class InternalModelSpeciesDataTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetters() {
- InternalModelSpeciesData data = new InternalModelSpeciesData();
- assertNotNull(data.getAll());
- assertNotNull(data.getAntisenseRnas());
- assertNotNull(data.getGenes());
- assertNotNull(data.getProteins());
- assertNotNull(data.getRnas());
- }
-
- @Test
- public void testUpdateUnknownSpecies() {
- InternalModelSpeciesData data = new InternalModelSpeciesData();
- try {
- data.updateSpecies(new CellDesignerSpecies<GenericProtein>(), null);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Unknown species type"));
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.species;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+
+public class InternalModelSpeciesDataTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetters() {
+ InternalModelSpeciesData data = new InternalModelSpeciesData();
+ assertNotNull(data.getAll());
+ assertNotNull(data.getAntisenseRnas());
+ assertNotNull(data.getGenes());
+ assertNotNull(data.getProteins());
+ assertNotNull(data.getRnas());
+ }
+
+ @Test
+ public void testUpdateUnknownSpecies() {
+ InternalModelSpeciesData data = new InternalModelSpeciesData();
+ try {
+ data.updateSpecies(new CellDesignerSpecies<GenericProtein>(), null);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Unknown species type"));
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinMappingTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinMappingTest.java
index 4404192113..76fff7ecd1 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinMappingTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinMappingTest.java
@@ -1,81 +1,81 @@
-package lcsb.mapviewer.converter.model.celldesigner.species;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import java.lang.reflect.Field;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
-import lcsb.mapviewer.model.map.species.TruncatedProtein;
-
-public class ProteinMappingTest {
- Logger logger = Logger.getLogger(ProteinMappingTest.class);
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testAllValues() {
- for (ProteinMapping value : ProteinMapping.values()) {
- assertNotNull(ProteinMapping.valueOf(value.toString()));
- }
- }
-
- @Test
- public void testCreateInvalidProteinImpl() throws Exception {
- // artificial implementation of Protein that is invalid
- class InvalidProtein extends CellDesignerProtein<TruncatedProtein> {
- private static final long serialVersionUID = 1L;
-
- @SuppressWarnings("unused")
- public InvalidProtein() {
- throw new NotImplementedException();
- }
- }
-
- // mopdify one of the elements of ProteinMapping so it will have invalid
- // implementation
- ProteinMapping typeToModify = ProteinMapping.GENERIC_PROTEIN;
- Class<? extends CellDesignerProtein<?>> clazz = typeToModify.getCellDesignerClazz();
-
- try {
- Field field = typeToModify.getClass().getDeclaredField("cellDesignerClazz");
- field.setAccessible(true);
- field.set(typeToModify, InvalidProtein.class);
-
- // and check if we catch properly information about problematic
- // implementation
- typeToModify.createProtein();
- fail("Exception expected");
- } catch (InvalidStateException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- // restore correct values for the modified type (if not then other test
- // might fail...)
- Field field = typeToModify.getClass().getDeclaredField("cellDesignerClazz");
- field.setAccessible(true);
- field.set(typeToModify, clazz);
- }
-
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.species;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import java.lang.reflect.Field;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
+import lcsb.mapviewer.model.map.species.TruncatedProtein;
+
+public class ProteinMappingTest {
+ Logger logger = Logger.getLogger(ProteinMappingTest.class);
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testAllValues() {
+ for (ProteinMapping value : ProteinMapping.values()) {
+ assertNotNull(ProteinMapping.valueOf(value.toString()));
+ }
+ }
+
+ @Test
+ public void testCreateInvalidProteinImpl() throws Exception {
+ // artificial implementation of Protein that is invalid
+ class InvalidProtein extends CellDesignerProtein<TruncatedProtein> {
+ private static final long serialVersionUID = 1L;
+
+ @SuppressWarnings("unused")
+ public InvalidProtein() {
+ throw new NotImplementedException();
+ }
+ }
+
+ // mopdify one of the elements of ProteinMapping so it will have invalid
+ // implementation
+ ProteinMapping typeToModify = ProteinMapping.GENERIC_PROTEIN;
+ Class<? extends CellDesignerProtein<?>> clazz = typeToModify.getCellDesignerClazz();
+
+ try {
+ Field field = typeToModify.getClass().getDeclaredField("cellDesignerClazz");
+ field.setAccessible(true);
+ field.set(typeToModify, InvalidProtein.class);
+
+ // and check if we catch properly information about problematic
+ // implementation
+ typeToModify.createProtein();
+ fail("Exception expected");
+ } catch (InvalidStateException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ // restore correct values for the modified type (if not then other test
+ // might fail...)
+ Field field = typeToModify.getClass().getDeclaredField("cellDesignerClazz");
+ field.setAccessible(true);
+ field.set(typeToModify, clazz);
+ }
+
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionTest.java
index c44b0e7632..a1d9e75448 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionTest.java
@@ -1,121 +1,121 @@
-package lcsb.mapviewer.converter.model.celldesigner.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGene;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGenericProtein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class SpeciesCollectionTest {
- Logger logger = Logger.getLogger(SpeciesCollectionTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testAdd() {
- try {
- SpeciesCollection<CellDesignerGene> coll = new SpeciesCollection<CellDesignerGene>();
- CellDesignerGene g = new CellDesignerGene();
- g.setElementId("general Id");
- coll.add(g, "geneId");
- assertNotNull(coll.getSpeciesListByLocalId("geneId"));
- assertEquals(1, coll.getSpeciesListByLocalId("geneId").size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate() {
- try {
- SpeciesCollection<CellDesignerProtein<?>> coll = new SpeciesCollection<>();
- CellDesignerProtein<?> protein = new CellDesignerGenericProtein();
- protein.setElementId("");
- coll.add(protein, "prot id");
-
- CellDesignerProtein<?> p2 = new CellDesignerGenericProtein();
- p2.setElementId("id2");
- coll.updateSpeciesByLocalId(p2, "prot id");
- assertEquals(1, coll.getSpeciesListByLocalId("prot id").size());
- CellDesignerProtein<?> p3 = coll.getSpeciesListByLocalId("prot id").get(0);
-
- assertEquals(protein, p3);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdateWithTypeChange() {
- try {
- SpeciesCollection<CellDesignerProtein<?>> coll = new SpeciesCollection<>();
- CellDesignerProtein<?> p = new CellDesignerProtein<>();
- p.setElementId("");
- coll.add(p, "prot id");
-
- CellDesignerGenericProtein p2 = new CellDesignerGenericProtein();
- p2.setElementId("id2");
- coll.updateSpeciesByLocalId(p2, "prot id");
- assertEquals(1, coll.getSpeciesListByLocalId("prot id").size());
- CellDesignerProtein<?> p3 = coll.getSpeciesListByLocalId("prot id").get(0);
-
- // we don't have generic data anymore but new instance
- assertFalse(p3.equals(p));
- assertFalse(p3.equals(p2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateNewInstance() {
- try {
- SpeciesCollection<CellDesignerSpecies<?>> coll = new SpeciesCollection<>();
- class InvalidSpecies extends CellDesignerSpecies<Species> {
- private static final long serialVersionUID = 1L;
-
- public InvalidSpecies() {
- }
-
- @SuppressWarnings("unused")
- public InvalidSpecies(final CellDesignerSpecies<?> sp) {
- throw new NotImplementedException();
- }
- }
-
- InvalidSpecies p = new InvalidSpecies();
- p.setElementId("");
-
- coll.createNewInstance(p.getClass(), p);
-
- } catch (InvalidStateException e) {
- assertTrue(e.getMessage().contains("Problem with creating object"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGene;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGenericProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class SpeciesCollectionTest {
+ Logger logger = Logger.getLogger(SpeciesCollectionTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testAdd() {
+ try {
+ SpeciesCollection<CellDesignerGene> coll = new SpeciesCollection<CellDesignerGene>();
+ CellDesignerGene g = new CellDesignerGene();
+ g.setElementId("general Id");
+ coll.add(g, "geneId");
+ assertNotNull(coll.getSpeciesListByLocalId("geneId"));
+ assertEquals(1, coll.getSpeciesListByLocalId("geneId").size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdate() {
+ try {
+ SpeciesCollection<CellDesignerProtein<?>> coll = new SpeciesCollection<>();
+ CellDesignerProtein<?> protein = new CellDesignerGenericProtein();
+ protein.setElementId("");
+ coll.add(protein, "prot id");
+
+ CellDesignerProtein<?> p2 = new CellDesignerGenericProtein();
+ p2.setElementId("id2");
+ coll.updateSpeciesByLocalId(p2, "prot id");
+ assertEquals(1, coll.getSpeciesListByLocalId("prot id").size());
+ CellDesignerProtein<?> p3 = coll.getSpeciesListByLocalId("prot id").get(0);
+
+ assertEquals(protein, p3);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdateWithTypeChange() {
+ try {
+ SpeciesCollection<CellDesignerProtein<?>> coll = new SpeciesCollection<>();
+ CellDesignerProtein<?> p = new CellDesignerProtein<>();
+ p.setElementId("");
+ coll.add(p, "prot id");
+
+ CellDesignerGenericProtein p2 = new CellDesignerGenericProtein();
+ p2.setElementId("id2");
+ coll.updateSpeciesByLocalId(p2, "prot id");
+ assertEquals(1, coll.getSpeciesListByLocalId("prot id").size());
+ CellDesignerProtein<?> p3 = coll.getSpeciesListByLocalId("prot id").get(0);
+
+ // we don't have generic data anymore but new instance
+ assertFalse(p3.equals(p));
+ assertFalse(p3.equals(p2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCreateNewInstance() {
+ try {
+ SpeciesCollection<CellDesignerSpecies<?>> coll = new SpeciesCollection<>();
+ class InvalidSpecies extends CellDesignerSpecies<Species> {
+ private static final long serialVersionUID = 1L;
+
+ public InvalidSpecies() {
+ }
+
+ @SuppressWarnings("unused")
+ public InvalidSpecies(final CellDesignerSpecies<?> sp) {
+ throw new NotImplementedException();
+ }
+ }
+
+ InvalidSpecies p = new InvalidSpecies();
+ p.setElementId("");
+
+ coll.createNewInstance(p.getClass(), p);
+
+ } catch (InvalidStateException e) {
+ assertTrue(e.getMessage().contains("Problem with creating object"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionXmlParserTest.java
index f442ea96fd..3d781303f9 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionXmlParserTest.java
@@ -1,458 +1,458 @@
-package lcsb.mapviewer.converter.model.celldesigner.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.lang.reflect.Field;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.w3c.dom.Node;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRna;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGene;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGenericProtein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class SpeciesCollectionXmlParserTest extends CellDesignerTestFunctions {
- static Logger logger = Logger.getLogger(SpeciesCollectionXmlParserTest.class);
- Model model = new ModelFullIndexed(null);
- SpeciesCollectionXmlParser parser = null;
-
- String testDirectory = "testFiles" + System.getProperty("file.separator") + "xmlNodeTestExamples"
- + System.getProperty("file.separator");
-
- String testRnaListXmlFile = "cd_rna_collection.xml";
- String testGeneListXmlFile = "cd_gene_collection.xml";
- String testAntisenseRnaListXmlFile = "cd_antisense_rna_collection.xml";
- String testIncludedListXmlFile = "cd_included_species_collection.xml";
- String testProteinListXmlFile = "cd_protein_collection.xml";
- String testSbmlListXmlFile = "cd_sbml_collection.xml";
-
- CellDesignerElementCollection elements;
-
- int idCounter = 0;
-
- @Before
- public void setUp() throws Exception {
- elements = new CellDesignerElementCollection();
- parser = new SpeciesCollectionXmlParser(elements);
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParseXmlRnaCollection() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testRnaListXmlFile);
- Node node = getNodeFromXmlString(xmlString);
- List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseXmlRnaCollection(node);
- assertEquals(2, list.size());
- assertTrue(list.get(0).getRight() instanceof CellDesignerRna);
- } catch (Exception e) {
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlRnaCollection() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/rna_collection.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.parseXmlRnaCollection(node);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfRNAs"));
- } catch (Exception e) {
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlGeneCollection() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/gene_collection.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.parseXmlGeneCollection(node);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfGenes"));
- } catch (Exception e) {
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlAntisenseRnaCollection() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/antisense_rna_collection.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.parseXmlAntisenseRnaCollection(node);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfAntisenseRNAs"));
- } catch (Exception e) {
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlPRoteinCollection() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/protein_collection.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.parseXmlProteinCollection(node);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfProteins"));
- } catch (Exception e) {
- throw e;
- }
- }
-
- @Test
- public void testToXmlStringRnaCollection() {
- try {
- String xmlString = readFile(testDirectory + testRnaListXmlFile);
- Node node = getNodeFromXmlString(xmlString);
- List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseXmlRnaCollection(node);
- List<Rna> arList = new ArrayList<>();
- for (Pair<String, ? extends CellDesignerSpecies<?>> pair : list) {
- arList.add((Rna) pair.getRight().createModelElement(""+(idCounter++)));
- }
- String convertedString = parser.rnaCollectionToXmlString(arList);
- assertNotNull(convertedString);
- node = getNodeFromXmlString(convertedString);
- assertEquals("celldesigner:listOfRNAs", node.getNodeName());
- List<Pair<String, ? extends CellDesignerSpecies<?>>> list2 = parser.parseXmlRnaCollection(node);
- assertNotNull(list2);
- assertEquals(list.size(), list2.size());
- assertEquals(list.get(0).getClass().getName(), list2.get(0).getClass().getName());
- } catch (Exception exception) {
- fail("Unexpected exception occurred");
- }
- }
-
- @Test
- public void testParseXmlGeneCollection() {
- try {
- String xmlString = readFile(testDirectory + testGeneListXmlFile);
- Node node = getNodeFromXmlString(xmlString);
- List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseXmlGeneCollection(node);
- assertEquals(2, list.size());
- assertTrue(list.get(0).getRight() instanceof CellDesignerGene);
- } catch (Exception exception) {
- fail("Unexpected exception occurred");
- }
- }
-
- @Test
- public void testToXmlStringGeneCollection() {
- try {
- String xmlString = readFile(testDirectory + testGeneListXmlFile);
- Node node = getNodeFromXmlString(xmlString);
- List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseXmlGeneCollection(node);
- List<Gene> arList = new ArrayList<>();
- for (Pair<String, ? extends CellDesignerSpecies<?>> pair : list) {
- arList.add((Gene) pair.getRight().createModelElement(""+(idCounter++)));
- }
- String convertedString = parser.geneCollectionToXmlString(arList);
- assertNotNull(convertedString);
- node = getNodeFromXmlString(convertedString);
- assertEquals("celldesigner:listOfGenes", node.getNodeName());
- List<Pair<String, ? extends CellDesignerSpecies<?>>> list2 = parser.parseXmlGeneCollection(node);
- assertNotNull(list2);
- assertEquals(list.size(), list2.size());
- assertEquals(list.get(0).getClass().getName(), list2.get(0).getClass().getName());
- } catch (Exception exception) {
- fail("Unexpected exception occurred");
- }
- }
-
- @Test
- public void testParseXmlProteinCollection() {
- try {
- String xmlString = readFile(testDirectory + testProteinListXmlFile);
- Node node = getNodeFromXmlString(xmlString);
- List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseXmlProteinCollection(node);
- assertEquals(4, list.size());
- assertTrue(list.get(0).getRight() instanceof CellDesignerProtein);
- } catch (Exception exception) {
- fail("Unexpected exception occurred");
- }
- }
-
- @Test
- public void testToXmlStringProteinCollection() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testProteinListXmlFile);
- Node node = getNodeFromXmlString(xmlString);
- List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseXmlProteinCollection(node);
- List<Protein> arList = new ArrayList<>();
- for (Pair<String, ? extends CellDesignerSpecies<?>> pair : list) {
- arList.add((Protein) pair.getRight().createModelElement("" + idCounter++));
- }
- String convertedString = parser.proteinCollectionToXmlString(arList);
- assertNotNull(convertedString);
- node = getNodeFromXmlString(convertedString);
- assertEquals("celldesigner:listOfProteins", node.getNodeName());
- List<Pair<String, ? extends CellDesignerSpecies<?>>> list2 = parser.parseXmlProteinCollection(node);
- assertNotNull(list2);
- assertEquals(list.size(), list2.size());
- assertEquals(list.get(0).getClass().getName(), list2.get(0).getClass().getName());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlAntisenseRnaCollection() {
- try {
- String xmlString = readFile(testDirectory + testAntisenseRnaListXmlFile);
- Node node = getNodeFromXmlString(xmlString);
- List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseXmlAntisenseRnaCollection(node);
- assertEquals(2, list.size());
- assertTrue(list.get(0).getRight() instanceof CellDesignerAntisenseRna);
- } catch (Exception exception) {
- fail("Unexpected exception occurred");
- }
- }
-
- @Test
- public void testToXmlStringAntisenseRnaCollection() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testAntisenseRnaListXmlFile);
- Node node = getNodeFromXmlString(xmlString);
- List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseXmlAntisenseRnaCollection(node);
- List<AntisenseRna> arList = new ArrayList<>();
- for (Pair<String, ? extends CellDesignerSpecies<?>> pair : list) {
- arList.add((AntisenseRna) pair.getRight().createModelElement(""+(idCounter++)));
- }
- String convertedString = parser.antisenseRnaCollectionToXmlString(arList);
- assertNotNull(convertedString);
- node = getNodeFromXmlString(convertedString);
- assertEquals("celldesigner:listOfAntisenseRNAs", node.getNodeName());
- List<Pair<String, ? extends CellDesignerSpecies<?>>> list2 = parser.parseXmlAntisenseRnaCollection(node);
- assertNotNull(list2);
- assertEquals(list.size(), list2.size());
- assertEquals(list.get(0).getClass().getName(), list2.get(0).getClass().getName());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseSbmlSpeciesCollection() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testSbmlListXmlFile);
- Node node = getNodeFromXmlString(xmlString);
- List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseSbmlSpeciesCollection(node);
- assertEquals(9, list.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidSbmlSpeciesCollection() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/sbml_collection.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.parseSbmlSpeciesCollection(node);
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of listOfSpecies"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToSbmlStringSpeciesCollection() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testSbmlListXmlFile);
- Node node = getNodeFromXmlString(xmlString);
- List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseSbmlSpeciesCollection(node);
- Model model = new ModelFullIndexed(null);
- int x = 0;
- List<Species> speciesList = new ArrayList<>();
- for (Pair<String, ? extends CellDesignerSpecies<?>> el : list) {
- CellDesignerSpecies<?> species = el.getRight();
- if (species.getClass() == CellDesignerProtein.class) {
- species = new CellDesignerGenericProtein(species);
- }
-
- Species alias = species.createModelElement("alias" + (x++));
- model.addElement(alias);
- speciesList.add(alias);
- }
- model.addElement(new Compartment("default"));
- String convertedString = parser.speciesCollectionToSbmlString(speciesList);
- assertNotNull(convertedString);
- node = getNodeFromXmlString(convertedString);
- assertEquals("listOfSpecies", node.getNodeName());
- List<Pair<String, ? extends CellDesignerSpecies<?>>> list2 = parser.parseSbmlSpeciesCollection(node);
- assertNotNull(list2);
- assertEquals(list.size(), list2.size());
- assertEquals(list.get(0).getClass().getName(), list2.get(0).getClass().getName());
- } catch (Exception exception) {
- exception.printStackTrace();
- throw exception;
- }
- }
-
- @Test
- public void testParseIncludedSpeciesCollection() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testIncludedListXmlFile);
- Node node = getNodeFromXmlString(xmlString);
- List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseIncludedSpeciesCollection(node);
- assertEquals(3, list.size());
- int complexes = 0;
- int proteins = 0;
- for (Pair<String, ? extends CellDesignerSpecies<?>> species : list) {
- if (species.getRight() instanceof CellDesignerComplexSpecies)
- complexes++;
- if (species.getRight() instanceof CellDesignerProtein)
- proteins++;
- }
- assertEquals(1, complexes);
- assertEquals(2, proteins);
- } catch (Exception exception) {
- exception.printStackTrace();
- throw exception;
- }
- }
-
- @Test
- public void testParseInvalidIncludedSpeciesCollection() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/included_species_collection.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.parseIncludedSpeciesCollection(node);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException exception) {
- assertTrue(exception.getMessage().contains("Included species does not contain id"));
- } catch (Exception exception) {
- exception.printStackTrace();
- throw exception;
- }
- }
-
- @Test
- public void testParseInvalidIncludedSpeciesCollection2() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/included_species_collection2.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.parseIncludedSpeciesCollection(node);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException exception) {
- assertTrue(exception.getMessage().contains("Unknown element of celldesigner:species"));
- } catch (Exception exception) {
- exception.printStackTrace();
- throw exception;
- }
- }
-
- @Test
- public void testParseInvalidIncludedSpeciesCollection3() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/included_species_collection3.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.parseIncludedSpeciesCollection(node);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException exception) {
- assertTrue(exception.getMessage().contains("Included species does not contain annotation node"));
- } catch (Exception exception) {
- exception.printStackTrace();
- throw exception;
- }
- }
-
- @Test
- public void testParseInvalidIncludedSpeciesCollection4() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/included_species_collection4.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.parseIncludedSpeciesCollection(node);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException exception) {
- assertTrue(exception.getMessage().contains("No celldesigner:speciesIdentity node in included tag"));
- } catch (Exception exception) {
- exception.printStackTrace();
- throw exception;
- }
- }
-
- @Test
- public void testParseInvalidIncludedSpeciesCollection5() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/included_species_collection5.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.parseIncludedSpeciesCollection(node);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException exception) {
- assertTrue(exception.getMessage().contains("Unknown element of celldesigner:listOfIncludedSpecies"));
- } catch (Exception exception) {
- exception.printStackTrace();
- throw exception;
- }
- }
-
- @Test
- public void artifitialTest() throws Exception {
- try {
- // tests some parts of the code that should never be called and therefore
- // throw exceptions
-
- // this is only for test coverage puropse
-
- SpeciesCollectionXmlParser parser = new SpeciesCollectionXmlParser(elements);
- Field field = SpeciesCollectionXmlParser.class.getDeclaredField("helpParser");
- field.setAccessible(true);
- try {
- ((AbstractElementXmlParser<?, ?>) field.get(parser)).toXml(null);
- fail("Exception expected");
- } catch (NotImplementedException e) {
-
- }
- try {
- ((AbstractElementXmlParser<?, ?>) field.get(parser)).parseXmlElement((Node) null);
- fail("Exception expected");
- } catch (NotImplementedException e) {
-
- }
- } catch (Exception exception) {
- exception.printStackTrace();
- throw exception;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.lang.reflect.Field;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.w3c.dom.Node;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGene;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGenericProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class SpeciesCollectionXmlParserTest extends CellDesignerTestFunctions {
+ static Logger logger = Logger.getLogger(SpeciesCollectionXmlParserTest.class);
+ Model model = new ModelFullIndexed(null);
+ SpeciesCollectionXmlParser parser = null;
+
+ String testDirectory = "testFiles" + System.getProperty("file.separator") + "xmlNodeTestExamples"
+ + System.getProperty("file.separator");
+
+ String testRnaListXmlFile = "cd_rna_collection.xml";
+ String testGeneListXmlFile = "cd_gene_collection.xml";
+ String testAntisenseRnaListXmlFile = "cd_antisense_rna_collection.xml";
+ String testIncludedListXmlFile = "cd_included_species_collection.xml";
+ String testProteinListXmlFile = "cd_protein_collection.xml";
+ String testSbmlListXmlFile = "cd_sbml_collection.xml";
+
+ CellDesignerElementCollection elements;
+
+ int idCounter = 0;
+
+ @Before
+ public void setUp() throws Exception {
+ elements = new CellDesignerElementCollection();
+ parser = new SpeciesCollectionXmlParser(elements);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testParseXmlRnaCollection() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testRnaListXmlFile);
+ Node node = getNodeFromXmlString(xmlString);
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseXmlRnaCollection(node);
+ assertEquals(2, list.size());
+ assertTrue(list.get(0).getRight() instanceof CellDesignerRna);
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlRnaCollection() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/rna_collection.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.parseXmlRnaCollection(node);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfRNAs"));
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlGeneCollection() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/gene_collection.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.parseXmlGeneCollection(node);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfGenes"));
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlAntisenseRnaCollection() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/antisense_rna_collection.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.parseXmlAntisenseRnaCollection(node);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfAntisenseRNAs"));
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlPRoteinCollection() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/protein_collection.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.parseXmlProteinCollection(node);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfProteins"));
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlStringRnaCollection() {
+ try {
+ String xmlString = readFile(testDirectory + testRnaListXmlFile);
+ Node node = getNodeFromXmlString(xmlString);
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseXmlRnaCollection(node);
+ List<Rna> arList = new ArrayList<>();
+ for (Pair<String, ? extends CellDesignerSpecies<?>> pair : list) {
+ arList.add((Rna) pair.getRight().createModelElement(""+(idCounter++)));
+ }
+ String convertedString = parser.rnaCollectionToXmlString(arList);
+ assertNotNull(convertedString);
+ node = getNodeFromXmlString(convertedString);
+ assertEquals("celldesigner:listOfRNAs", node.getNodeName());
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list2 = parser.parseXmlRnaCollection(node);
+ assertNotNull(list2);
+ assertEquals(list.size(), list2.size());
+ assertEquals(list.get(0).getClass().getName(), list2.get(0).getClass().getName());
+ } catch (Exception exception) {
+ fail("Unexpected exception occurred");
+ }
+ }
+
+ @Test
+ public void testParseXmlGeneCollection() {
+ try {
+ String xmlString = readFile(testDirectory + testGeneListXmlFile);
+ Node node = getNodeFromXmlString(xmlString);
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseXmlGeneCollection(node);
+ assertEquals(2, list.size());
+ assertTrue(list.get(0).getRight() instanceof CellDesignerGene);
+ } catch (Exception exception) {
+ fail("Unexpected exception occurred");
+ }
+ }
+
+ @Test
+ public void testToXmlStringGeneCollection() {
+ try {
+ String xmlString = readFile(testDirectory + testGeneListXmlFile);
+ Node node = getNodeFromXmlString(xmlString);
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseXmlGeneCollection(node);
+ List<Gene> arList = new ArrayList<>();
+ for (Pair<String, ? extends CellDesignerSpecies<?>> pair : list) {
+ arList.add((Gene) pair.getRight().createModelElement(""+(idCounter++)));
+ }
+ String convertedString = parser.geneCollectionToXmlString(arList);
+ assertNotNull(convertedString);
+ node = getNodeFromXmlString(convertedString);
+ assertEquals("celldesigner:listOfGenes", node.getNodeName());
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list2 = parser.parseXmlGeneCollection(node);
+ assertNotNull(list2);
+ assertEquals(list.size(), list2.size());
+ assertEquals(list.get(0).getClass().getName(), list2.get(0).getClass().getName());
+ } catch (Exception exception) {
+ fail("Unexpected exception occurred");
+ }
+ }
+
+ @Test
+ public void testParseXmlProteinCollection() {
+ try {
+ String xmlString = readFile(testDirectory + testProteinListXmlFile);
+ Node node = getNodeFromXmlString(xmlString);
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseXmlProteinCollection(node);
+ assertEquals(4, list.size());
+ assertTrue(list.get(0).getRight() instanceof CellDesignerProtein);
+ } catch (Exception exception) {
+ fail("Unexpected exception occurred");
+ }
+ }
+
+ @Test
+ public void testToXmlStringProteinCollection() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testProteinListXmlFile);
+ Node node = getNodeFromXmlString(xmlString);
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseXmlProteinCollection(node);
+ List<Protein> arList = new ArrayList<>();
+ for (Pair<String, ? extends CellDesignerSpecies<?>> pair : list) {
+ arList.add((Protein) pair.getRight().createModelElement("" + idCounter++));
+ }
+ String convertedString = parser.proteinCollectionToXmlString(arList);
+ assertNotNull(convertedString);
+ node = getNodeFromXmlString(convertedString);
+ assertEquals("celldesigner:listOfProteins", node.getNodeName());
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list2 = parser.parseXmlProteinCollection(node);
+ assertNotNull(list2);
+ assertEquals(list.size(), list2.size());
+ assertEquals(list.get(0).getClass().getName(), list2.get(0).getClass().getName());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlAntisenseRnaCollection() {
+ try {
+ String xmlString = readFile(testDirectory + testAntisenseRnaListXmlFile);
+ Node node = getNodeFromXmlString(xmlString);
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseXmlAntisenseRnaCollection(node);
+ assertEquals(2, list.size());
+ assertTrue(list.get(0).getRight() instanceof CellDesignerAntisenseRna);
+ } catch (Exception exception) {
+ fail("Unexpected exception occurred");
+ }
+ }
+
+ @Test
+ public void testToXmlStringAntisenseRnaCollection() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testAntisenseRnaListXmlFile);
+ Node node = getNodeFromXmlString(xmlString);
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseXmlAntisenseRnaCollection(node);
+ List<AntisenseRna> arList = new ArrayList<>();
+ for (Pair<String, ? extends CellDesignerSpecies<?>> pair : list) {
+ arList.add((AntisenseRna) pair.getRight().createModelElement(""+(idCounter++)));
+ }
+ String convertedString = parser.antisenseRnaCollectionToXmlString(arList);
+ assertNotNull(convertedString);
+ node = getNodeFromXmlString(convertedString);
+ assertEquals("celldesigner:listOfAntisenseRNAs", node.getNodeName());
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list2 = parser.parseXmlAntisenseRnaCollection(node);
+ assertNotNull(list2);
+ assertEquals(list.size(), list2.size());
+ assertEquals(list.get(0).getClass().getName(), list2.get(0).getClass().getName());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseSbmlSpeciesCollection() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testSbmlListXmlFile);
+ Node node = getNodeFromXmlString(xmlString);
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseSbmlSpeciesCollection(node);
+ assertEquals(9, list.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidSbmlSpeciesCollection() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/sbml_collection.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.parseSbmlSpeciesCollection(node);
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of listOfSpecies"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToSbmlStringSpeciesCollection() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testSbmlListXmlFile);
+ Node node = getNodeFromXmlString(xmlString);
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseSbmlSpeciesCollection(node);
+ Model model = new ModelFullIndexed(null);
+ int x = 0;
+ List<Species> speciesList = new ArrayList<>();
+ for (Pair<String, ? extends CellDesignerSpecies<?>> el : list) {
+ CellDesignerSpecies<?> species = el.getRight();
+ if (species.getClass() == CellDesignerProtein.class) {
+ species = new CellDesignerGenericProtein(species);
+ }
+
+ Species alias = species.createModelElement("alias" + (x++));
+ model.addElement(alias);
+ speciesList.add(alias);
+ }
+ model.addElement(new Compartment("default"));
+ String convertedString = parser.speciesCollectionToSbmlString(speciesList);
+ assertNotNull(convertedString);
+ node = getNodeFromXmlString(convertedString);
+ assertEquals("listOfSpecies", node.getNodeName());
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list2 = parser.parseSbmlSpeciesCollection(node);
+ assertNotNull(list2);
+ assertEquals(list.size(), list2.size());
+ assertEquals(list.get(0).getClass().getName(), list2.get(0).getClass().getName());
+ } catch (Exception exception) {
+ exception.printStackTrace();
+ throw exception;
+ }
+ }
+
+ @Test
+ public void testParseIncludedSpeciesCollection() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testIncludedListXmlFile);
+ Node node = getNodeFromXmlString(xmlString);
+ List<Pair<String, ? extends CellDesignerSpecies<?>>> list = parser.parseIncludedSpeciesCollection(node);
+ assertEquals(3, list.size());
+ int complexes = 0;
+ int proteins = 0;
+ for (Pair<String, ? extends CellDesignerSpecies<?>> species : list) {
+ if (species.getRight() instanceof CellDesignerComplexSpecies)
+ complexes++;
+ if (species.getRight() instanceof CellDesignerProtein)
+ proteins++;
+ }
+ assertEquals(1, complexes);
+ assertEquals(2, proteins);
+ } catch (Exception exception) {
+ exception.printStackTrace();
+ throw exception;
+ }
+ }
+
+ @Test
+ public void testParseInvalidIncludedSpeciesCollection() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/included_species_collection.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.parseIncludedSpeciesCollection(node);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException exception) {
+ assertTrue(exception.getMessage().contains("Included species does not contain id"));
+ } catch (Exception exception) {
+ exception.printStackTrace();
+ throw exception;
+ }
+ }
+
+ @Test
+ public void testParseInvalidIncludedSpeciesCollection2() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/included_species_collection2.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.parseIncludedSpeciesCollection(node);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException exception) {
+ assertTrue(exception.getMessage().contains("Unknown element of celldesigner:species"));
+ } catch (Exception exception) {
+ exception.printStackTrace();
+ throw exception;
+ }
+ }
+
+ @Test
+ public void testParseInvalidIncludedSpeciesCollection3() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/included_species_collection3.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.parseIncludedSpeciesCollection(node);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException exception) {
+ assertTrue(exception.getMessage().contains("Included species does not contain annotation node"));
+ } catch (Exception exception) {
+ exception.printStackTrace();
+ throw exception;
+ }
+ }
+
+ @Test
+ public void testParseInvalidIncludedSpeciesCollection4() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/included_species_collection4.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.parseIncludedSpeciesCollection(node);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException exception) {
+ assertTrue(exception.getMessage().contains("No celldesigner:speciesIdentity node in included tag"));
+ } catch (Exception exception) {
+ exception.printStackTrace();
+ throw exception;
+ }
+ }
+
+ @Test
+ public void testParseInvalidIncludedSpeciesCollection5() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/included_species_collection5.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.parseIncludedSpeciesCollection(node);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException exception) {
+ assertTrue(exception.getMessage().contains("Unknown element of celldesigner:listOfIncludedSpecies"));
+ } catch (Exception exception) {
+ exception.printStackTrace();
+ throw exception;
+ }
+ }
+
+ @Test
+ public void artifitialTest() throws Exception {
+ try {
+ // tests some parts of the code that should never be called and therefore
+ // throw exceptions
+
+ // this is only for test coverage puropse
+
+ SpeciesCollectionXmlParser parser = new SpeciesCollectionXmlParser(elements);
+ Field field = SpeciesCollectionXmlParser.class.getDeclaredField("helpParser");
+ field.setAccessible(true);
+ try {
+ ((AbstractElementXmlParser<?, ?>) field.get(parser)).toXml(null);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+
+ }
+ try {
+ ((AbstractElementXmlParser<?, ?>) field.get(parser)).parseXmlElement((Node) null);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+
+ }
+ } catch (Exception exception) {
+ exception.printStackTrace();
+ throw exception;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParserTest.java
index 786cd6cd40..6e90f40f00 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParserTest.java
@@ -1,1143 +1,1143 @@
-package lcsb.mapviewer.converter.model.celldesigner.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.io.StringReader;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-import org.w3c.dom.Document;
-import org.w3c.dom.NodeList;
-import org.xml.sax.InputSource;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRna;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerDegraded;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerDrug;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGene;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGenericProtein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerIon;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerPhenotype;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSimpleMolecule;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerUnknown;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.SpeciesState;
-import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(SpeciesSbmlParserTest.class.getName());
-
- SpeciesSbmlParser parser;
-
- String testDirectory = "testFiles" + System.getProperty("file.separator") + "xmlNodeTestExamples"
- + System.getProperty("file.separator");
- String testGeneFile = "sbml_gene.xml";
- String testDegradedFile = "sbml_degraded.xml";
- String testDrugFile = "sbml_drug.xml";
- String testIonFile = "sbml_ion.xml";
- String testPhenotypeFile = "sbml_phenotype.xml";
- String testProteinFile = "sbml_protein.xml";
- String testRnaFile = "sbml_rna.xml";
- String testSimpleMoleculeFile = "sbml_simple_molecule.xml";
- String testUnknownFile = "sbml_unknown.xml";
-
- CellDesignerElementCollection elements;
-
- int idCounter = 0;
-
- @Before
- public void setUp() throws Exception {
- elements = new CellDesignerElementCollection();
- parser = new SpeciesSbmlParser(elements);
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParseXmlSpeciesAntisenseRna() throws Exception {
- try {
- String xmlString = readFile(testDirectory + "sbml_antisense_rna.xml");
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerAntisenseRna species = (CellDesignerAntisenseRna) result.getRight();
- assertEquals("s2", species.getElementId());
- assertEquals("s3", species.getName());
- assertEquals(2, species.getInitialAmount(), Configuration.EPSILON);
- assertEquals(Boolean.TRUE, species.hasOnlySubstanceUnits());
- assertEquals(new Integer(0), species.getCharge());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlSpeciesWithKineticsData() throws Exception {
- try {
- String xmlString = readFile("testFiles/kinetics/species_with_kinetics_param.xml");
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerProtein<?> species = (CellDesignerProtein<?>) result.getRight();
- assertEquals(3.7, species.getInitialConcentration(), Configuration.EPSILON);
- assertEquals(SbmlUnitType.MOLE, species.getSubstanceUnit());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSpeciesUnitsToXml() throws Exception {
- try {
- GenericProtein protein = new GenericProtein("s1");
- protein.setSubstanceUnits(SbmlUnitType.MOLE);
- String xml = parser.toXml(protein);
- assertTrue("Cannot find substance unit in xml", xml.indexOf("mole") >= 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSpeciesConstantToXml() throws Exception {
- try {
- GenericProtein protein = new GenericProtein("s1");
- protein.setConstant(true);
- String xml = parser.toXml(protein);
- assertTrue("Cannot find constant in xml", xml.indexOf("constant") >= 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSpeciesBoundaryConditionToXml() throws Exception {
- try {
- GenericProtein protein = new GenericProtein("s1");
- protein.setBoundaryCondition(true);
- String xml = parser.toXml(protein);
- assertTrue("Cannot find boundary condition in xml", xml.indexOf("boundaryCondition") >= 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlSpeciesWithKineticsData2() throws Exception {
- try {
- String xmlString = readFile("testFiles/kinetics/species_with_kinetics_param2.xml");
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerProtein<?> species = (CellDesignerProtein<?>) result.getRight();
- assertEquals(2.5, species.getInitialAmount(), Configuration.EPSILON);
- assertEquals(SbmlUnitType.GRAM, species.getSubstanceUnit());
- assertEquals(Boolean.TRUE, species.hasOnlySubstanceUnits());
- assertEquals("Boundary condition wasn't parsed", Boolean.TRUE, species.isBoundaryCondition());
- assertEquals("Constant property wasn't parsed", Boolean.TRUE, species.isConstant());
- assertEquals(new Integer(0), species.getCharge());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlAntisenseRna() throws Exception {
- try {
- String xmlString = readFile(testDirectory + "sbml_antisense_rna.xml");
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerAntisenseRna species = (CellDesignerAntisenseRna) result.getRight();
-
- String transformedXml = parser.toXml(species.createModelElement());
- assertNotNull(transformedXml);
- DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
- DocumentBuilder builder = factory.newDocumentBuilder();
- InputSource is = new InputSource(new StringReader(transformedXml));
- Document doc = builder.parse(is);
- NodeList root = doc.getChildNodes();
- assertEquals("species", root.item(0).getNodeName());
-
- Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser
- .parseXmlElement(parser.toXml(species.createModelElement()));
- CellDesignerAntisenseRna species2 = (CellDesignerAntisenseRna) result2.getRight();
-
- assertEquals(species.getName(), species2.getName());
- assertEquals(species.getParent(), species2.getParent());
- assertEquals(species.getInitialAmount(), species2.getInitialAmount());
- assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
- assertEquals(species.getCharge(), species2.getCharge());
- assertEquals(species.getPositionToCompartment(), species2.getPositionToCompartment());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlSpeciesComplex() throws Exception {
- try {
- String xmlString = readFile(testDirectory + "sbml_complex.xml");
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerComplexSpecies species = (CellDesignerComplexSpecies) result.getRight();
- assertNotNull(species);
- assertEquals("s6549", species.getElementId());
- assertEquals("LC3-II", species.getName());
- assertEquals(0.0, species.getInitialAmount(), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlComplex() throws Exception {
- try {
- String xmlString = readFile(testDirectory + "sbml_complex.xml");
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerComplexSpecies species = (CellDesignerComplexSpecies) result.getRight();
-
- String transformedXml = parser.toXml(species.createModelElement());
- assertNotNull(transformedXml);
- DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
- DocumentBuilder builder = factory.newDocumentBuilder();
- InputSource is = new InputSource(new StringReader(transformedXml));
- Document doc = builder.parse(is);
- NodeList root = doc.getChildNodes();
- assertEquals("species", root.item(0).getNodeName());
-
- Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser
- .parseXmlElement(parser.toXml(species.createModelElement()));
- CellDesignerComplexSpecies species2 = (CellDesignerComplexSpecies) result2.getRight();
-
- assertNotNull(species2);
- assertEquals(species.getName(), species2.getName());
- assertEquals(species.getParent(), species2.getParent());
- assertEquals(species.getInitialAmount(), species2.getInitialAmount());
- assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
- assertEquals(species.getCharge(), species2.getCharge());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlSpeciesDegraded() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testDegradedFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerDegraded species = (CellDesignerDegraded) result.getRight();
- assertNotNull(species);
- assertEquals("s1275", species.getElementId());
- assertEquals("s1275", species.getName());
- assertEquals(0, species.getInitialAmount(), Configuration.EPSILON);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlDegraded() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testDegradedFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerDegraded species = (CellDesignerDegraded) result.getRight();
-
- String transformedXml = parser.toXml(species.createModelElement());
- assertNotNull(transformedXml);
- DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
- DocumentBuilder builder = factory.newDocumentBuilder();
- InputSource is = new InputSource(new StringReader(transformedXml));
- Document doc = builder.parse(is);
- NodeList root = doc.getChildNodes();
- assertEquals("species", root.item(0).getNodeName());
-
- Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser
- .parseXmlElement(parser.toXml(species.createModelElement()));
- CellDesignerDegraded species2 = (CellDesignerDegraded) result2.getRight();
-
- assertNotNull(species2);
- assertEquals(species.getName(), species2.getName());
- assertEquals(species.getParent(), species2.getParent());
- assertEquals(species.getInitialAmount(), species2.getInitialAmount());
- assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
- assertEquals(species.getCharge(), species2.getCharge());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlSpeciesDrug() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testDrugFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerDrug species = (CellDesignerDrug) result.getRight();
- assertEquals("s6104", species.getElementId());
- assertEquals("geldanamycin", species.getName());
- assertEquals(new Integer(0), species.getCharge());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlDrug() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testDrugFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerDrug species = (CellDesignerDrug) result.getRight();
-
- String transformedXml = parser.toXml(species.createModelElement());
- assertNotNull(transformedXml);
- DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
- DocumentBuilder builder = factory.newDocumentBuilder();
- InputSource is = new InputSource(new StringReader(transformedXml));
- Document doc = builder.parse(is);
- NodeList root = doc.getChildNodes();
- assertEquals("species", root.item(0).getNodeName());
-
- Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser
- .parseXmlElement(parser.toXml(species.createModelElement()));
- CellDesignerDrug species2 = (CellDesignerDrug) result2.getRight();
-
- assertNotNull(species2);
- assertEquals(species.getName(), species2.getName());
- assertEquals(species.getParent(), species2.getParent());
- assertEquals(species.getInitialAmount(), species2.getInitialAmount());
- assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
- assertEquals(species.getCharge(), species2.getCharge());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlSpeciesGene() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testGeneFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerGene species = (CellDesignerGene) result.getRight();
-
- assertEquals("s5916", species.getElementId());
- assertEquals("Ptgr1", species.getName());
- assertEquals(new Integer(0), species.getCharge());
- assertEquals(0, species.getInitialAmount(), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlSpeciesGeneWithModelUpdate() throws Exception {
- try {
- CellDesignerSpecies<?> gene = new CellDesignerGene();
- gene.setElementId("s5916");
- InternalModelSpeciesData modelData = new InternalModelSpeciesData();
- modelData.updateSpecies(gene, "");
-
- SpeciesSbmlParser complexParser = new SpeciesSbmlParser(elements);
- CellDesignerGene oldGene = new CellDesignerGene();
- oldGene.setElementId("s5916");
- oldGene.setName("Ptgr1");
- modelData.updateSpecies(oldGene, "gn95");
-
- String xmlString = readFile(testDirectory + testGeneFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = complexParser.parseXmlElement(xmlString);
- CellDesignerGene species = (CellDesignerGene) result.getRight();
- modelData.updateSpecies(species, result.getLeft());
-
- assertEquals("s5916", species.getElementId());
- assertEquals("Ptgr1", species.getName());
- assertTrue(species.getNotes().contains("prostaglandin reductase 1"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlGene() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testGeneFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerGene species = (CellDesignerGene) result.getRight();
-
- String transformedXml = parser.toXml(species.createModelElement());
- assertNotNull(transformedXml);
- DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
- DocumentBuilder builder = factory.newDocumentBuilder();
- InputSource is = new InputSource(new StringReader(transformedXml));
- Document doc = builder.parse(is);
- NodeList root = doc.getChildNodes();
- assertEquals("species", root.item(0).getNodeName());
-
- Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser
- .parseXmlElement(parser.toXml(species.createModelElement()));
- CellDesignerGene species2 = (CellDesignerGene) result2.getRight();
-
- assertNotNull(species2);
- assertEquals(species.getName(), species2.getName());
- assertEquals(species.getParent(), species2.getParent());
- assertEquals(species.getInitialAmount(), species2.getInitialAmount());
- assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
- assertEquals(species.getCharge(), species2.getCharge());
- assertTrue(species2.getNotes().trim().contains(species.getNotes().trim()));
- assertEquals(species.getMiriamData().size(), species2.getMiriamData().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlSpeciesIon() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testIonFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerIon species = (CellDesignerIon) result.getRight();
-
- assertEquals("s6029", species.getElementId());
- assertEquals("Pi", species.getName());
- assertEquals(new Integer(0), species.getCharge());
- assertEquals(0, species.getInitialConcentration(), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlIon() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testIonFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerIon species = (CellDesignerIon) result.getRight();
-
- String transformedXml = parser.toXml(species.createModelElement());
- assertNotNull(transformedXml);
- DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
- DocumentBuilder builder = factory.newDocumentBuilder();
- InputSource is = new InputSource(new StringReader(transformedXml));
- Document doc = builder.parse(is);
- NodeList root = doc.getChildNodes();
- assertEquals("species", root.item(0).getNodeName());
-
- Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser.parseXmlElement(xmlString);
- CellDesignerIon species2 = (CellDesignerIon) result2.getRight();
-
- assertNotNull(species2);
- assertEquals(species.getElementId(), species2.getElementId());
- assertEquals(species.getName(), species2.getName());
- assertEquals(species.getParent(), species2.getParent());
- assertEquals(species.getInitialAmount(), species2.getInitialAmount());
- assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
- assertEquals(species.getCharge(), species2.getCharge());
- assertEquals(species.getInitialConcentration(), species2.getInitialConcentration());
- assertEquals(species.getNotes().trim(), species2.getNotes().trim());
- assertEquals(species.getMiriamData().size(), species2.getMiriamData().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlSpeciesPhenotype() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testPhenotypeFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerPhenotype species = (CellDesignerPhenotype) result.getRight();
-
- assertEquals("s5462", species.getElementId());
- assertEquals("Neuronal damage and death", species.getName());
- assertEquals(0, species.getInitialAmount(), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlPhenotype() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testPhenotypeFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerPhenotype species = (CellDesignerPhenotype) result.getRight();
-
- String transformedXml = parser.toXml(species.createModelElement());
- assertNotNull(transformedXml);
- DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
- DocumentBuilder builder = factory.newDocumentBuilder();
- InputSource is = new InputSource(new StringReader(transformedXml));
- Document doc = builder.parse(is);
- NodeList root = doc.getChildNodes();
- assertEquals("species", root.item(0).getNodeName());
-
- Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser
- .parseXmlElement(parser.toXml(species.createModelElement()));
- CellDesignerPhenotype species2 = (CellDesignerPhenotype) result2.getRight();
-
- assertNotNull(species2);
- assertEquals(species.getName(), species2.getName());
- assertEquals(species.getParent(), species2.getParent());
- assertEquals(species.getInitialAmount(), species2.getInitialAmount());
- assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
- assertEquals(species.getCharge(), species2.getCharge());
- assertEquals(species.getInitialConcentration(), species2.getInitialConcentration());
- assertEquals(species.getNotes(), species2.getNotes());
- assertEquals(species.getMiriamData().size(), species2.getMiriamData().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlSpeciesProtein() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testProteinFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerProtein<?> species = (CellDesignerProtein<?>) result.getRight();
-
- assertEquals("s5456", species.getElementId());
- assertEquals("PTPRC", species.getName());
- assertEquals(0, species.getInitialAmount(), Configuration.EPSILON);
- assertEquals(new Integer(0), species.getCharge());
- assertTrue(species.getNotes().contains("protein tyrosine phosphatase, receptor type, C"));
- assertNull(species.getStructuralState());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlProtein() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testProteinFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerGenericProtein species = new CellDesignerGenericProtein(result.getRight());
-
- String transformedXml = parser.toXml(species.createModelElement("" + idCounter++));
- assertNotNull(transformedXml);
- DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
- DocumentBuilder builder = factory.newDocumentBuilder();
- InputSource is = new InputSource(new StringReader(transformedXml));
- Document doc = builder.parse(is);
- NodeList root = doc.getChildNodes();
- assertEquals("species", root.item(0).getNodeName());
-
- Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser
- .parseXmlElement(parser.toXml(species.createModelElement("" + idCounter++)));
- CellDesignerProtein<?> species2 = (CellDesignerProtein<?>) result2.getRight();
-
- assertNotNull(species2);
- assertEquals(species.getName(), species2.getName());
- assertEquals(species.getParent(), species2.getParent());
- assertEquals(species.getInitialAmount(), species2.getInitialAmount());
- assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
- assertEquals(species.getCharge(), species2.getCharge());
- assertEquals(species.getInitialConcentration(), species2.getInitialConcentration());
- assertTrue(species2.getNotes().contains(species.getNotes()));
- assertEquals(species.getMiriamData().size(), species2.getMiriamData().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlSpeciesRna() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testRnaFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerRna species = (CellDesignerRna) result.getRight();
-
- assertEquals("s5914", species.getElementId());
- assertEquals("Fmo3", species.getName());
- assertEquals(0, species.getInitialAmount(), Configuration.EPSILON);
- assertEquals(new Integer(0), species.getCharge());
- assertTrue(species.getNotes().contains("Dimethylaniline monooxygenase [N-oxide-forming] 3"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlRna() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testRnaFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerRna species = (CellDesignerRna) result.getRight();
-
- String transformedXml = parser.toXml(species.createModelElement());
- assertNotNull(transformedXml);
- DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
- DocumentBuilder builder = factory.newDocumentBuilder();
- InputSource is = new InputSource(new StringReader(transformedXml));
- Document doc = builder.parse(is);
- NodeList root = doc.getChildNodes();
- assertEquals("species", root.item(0).getNodeName());
-
- Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser
- .parseXmlElement(parser.toXml(species.createModelElement()));
- CellDesignerRna species2 = (CellDesignerRna) result2.getRight();
-
- assertNotNull(species2);
- assertEquals(species.getName(), species2.getName());
- assertEquals(species.getParent(), species2.getParent());
- assertEquals(species.getInitialAmount(), species2.getInitialAmount());
- assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
- assertEquals(species.getCharge(), species2.getCharge());
- assertEquals(species.getInitialConcentration(), species2.getInitialConcentration());
- assertTrue(species2.getNotes().trim().contains(species.getNotes().trim()));
- assertEquals(species.getMiriamData().size(), species2.getMiriamData().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlSpeciesSimpleMolecule() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testSimpleMoleculeFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerSimpleMolecule species = (CellDesignerSimpleMolecule) result.getRight();
- assertEquals("s5463", species.getElementId());
- assertEquals("Peroxides", species.getName());
- assertEquals(0, species.getInitialAmount(), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlSimpleMolecule() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testSimpleMoleculeFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerSimpleMolecule species = (CellDesignerSimpleMolecule) result.getRight();
-
- String transformedXml = parser.toXml(species.createModelElement("" + idCounter++));
- assertNotNull(transformedXml);
- DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
- DocumentBuilder builder = factory.newDocumentBuilder();
- InputSource is = new InputSource(new StringReader(transformedXml));
- Document doc = builder.parse(is);
- NodeList root = doc.getChildNodes();
- assertEquals("species", root.item(0).getNodeName());
-
- Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser
- .parseXmlElement(parser.toXml(species.createModelElement("" + idCounter++)));
- CellDesignerSimpleMolecule species2 = (CellDesignerSimpleMolecule) result2.getRight();
-
- assertNotNull(species2);
- assertEquals(species.getName(), species2.getName());
- assertEquals(species.getParent(), species2.getParent());
- assertEquals(species.getInitialAmount(), species2.getInitialAmount());
- assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
- assertEquals(species.getCharge(), species2.getCharge());
- assertEquals(species.getInitialConcentration(), species2.getInitialConcentration());
- assertEquals(species.getNotes(), species2.getNotes());
- assertEquals(species.getMiriamData().size(), species2.getMiriamData().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlSpeciesUnknown() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testUnknownFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerUnknown species = (CellDesignerUnknown) result.getRight();
- assertEquals("s1356", species.getElementId());
- assertEquals("unidentified caspase acting on Occludin", species.getName());
- assertEquals(0, species.getInitialAmount(), Configuration.EPSILON);
- assertEquals(new Integer(0), species.getCharge());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlUnknown() throws Exception {
- try {
- String xmlString = readFile(testDirectory + testUnknownFile);
- Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
- CellDesignerUnknown species = (CellDesignerUnknown) result.getRight();
-
- String transformedXml = parser.toXml(species.createModelElement());
- assertNotNull(transformedXml);
- DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
- DocumentBuilder builder = factory.newDocumentBuilder();
- InputSource is = new InputSource(new StringReader(transformedXml));
- Document doc = builder.parse(is);
- NodeList root = doc.getChildNodes();
- assertEquals("species", root.item(0).getNodeName());
-
- Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser
- .parseXmlElement(parser.toXml(species.createModelElement()));
- CellDesignerUnknown species2 = (CellDesignerUnknown) result2.getRight();
-
- assertNotNull(species2);
- assertEquals(species.getName(), species2.getName());
- assertEquals(species.getParent(), species2.getParent());
- assertEquals(species.getInitialAmount(), species2.getInitialAmount());
- assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
- assertEquals(species.getCharge(), species2.getCharge());
- assertEquals(species.getInitialConcentration(), species2.getInitialConcentration());
- assertEquals(species.getNotes(), species2.getNotes());
- assertEquals(species.getMiriamData().size(), species2.getMiriamData().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalid() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/invalid_sbml_protein.xml");
- parser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("No annotation node"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalid2() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/invalid_sbml_protein2.xml");
- parser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("bla"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalid3() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/invalid_sbml_protein3.xml");
- parser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("unk_bla"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalid4() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/invalid_sbml_protein4.xml");
- parser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("No celldesigner:extension"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalid5() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/invalid_sbml_protein5.xml");
- parser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("ann_unk"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalid6() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/invalid_sbml_protein6.xml");
- parser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("No celldesigner:speciesIdentity"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalid7() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/invalid_sbml_protein7.xml");
- parser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("unkPos"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalid8() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/invalid_sbml_protein8.xml");
- parser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Species node in Sbml model doesn't contain"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalid9() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/invalid_sbml_protein9.xml");
- parser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("unknown_protein_class"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalid10() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/invalid_sbml_protein10.xml");
- parser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Wrong class type for protein reference"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalid11() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/invalid_sbml_protein11.xml");
- parser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Wrong class type for gene reference"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalid12() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/invalid_sbml_protein12.xml");
- parser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Wrong class type for rna reference"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalid13() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/invalid_sbml_protein13.xml");
- parser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Wrong class type for antisense rna reference"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalid14() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/invalid_sbml_protein14.xml");
- parser.parseXmlElement(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("uknNode"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlWithDefaultCompartment() throws Exception {
- try {
- CellDesignerGenericProtein species = new CellDesignerGenericProtein();
- String xml = parser.toXml(species.createModelElement("EL_ID"));
- assertTrue(xml.contains("EL_ID"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidSpeciesIdentityToXml() throws Exception {
- try {
- Species species = Mockito.mock(Species.class);
- parser.speciesIdentityToXml(species);
- fail("Excepiton expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Invalid species class"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSpeciesIdentityToXml() throws Exception {
- try {
- GenericProtein species = new GenericProtein("xx");
- species.setHypothetical(true);
- String xml = parser.speciesIdentityToXml(species);
- assertTrue(xml.contains("<celldesigner:hypothetical>true</celldesigner:hypothetical>"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSpeciesStateToXml() throws Exception {
- try {
- SpeciesState state = new SpeciesState();
- state.setHomodimer(2);
- state.setStructuralState("xxxState");
- String xml = parser.speciesStateToXml(state);
- assertTrue(xml.contains("xxxState"));
- assertTrue(xml.contains("celldesigner:homodimer"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProcessInvalidStateDataInSpecies() throws Exception {
- try {
- SpeciesState state = new SpeciesState();
- state.addModificationResidue(new CellDesignerModificationResidue());
- CellDesignerComplexSpecies species = new CellDesignerComplexSpecies();
-
- parser.processStateDataInSpecies(species, state);
- fail("Exception expected");
- } catch (NotImplementedException e) {
- assertTrue(e.getMessage().contains("Modification not supported in Complex"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProcessInvalidStateDataInSpecies2() throws Exception {
- try {
- SpeciesState state = new SpeciesState();
- state.setStructuralState("state");
- CellDesignerGene species = new CellDesignerGene();
-
- parser.processStateDataInSpecies(species, state);
- fail("Exception expected");
- } catch (NotImplementedException e) {
- assertTrue(e.getMessage().contains("StructuralState not supported in Gene"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProcessInvalidStateDataInSpecies3() throws Exception {
- try {
- SpeciesState state = new SpeciesState();
- state.setStructuralState("state");
- CellDesignerRna species = new CellDesignerRna();
-
- parser.processStateDataInSpecies(species, state);
- fail("Exception expected");
- } catch (NotImplementedException e) {
- assertTrue(e.getMessage().contains("Structural state not supported in RNA"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProcessInvalidStateDataInSpecies4() throws Exception {
- try {
- SpeciesState state = new SpeciesState();
- state.addModificationResidue(new CellDesignerModificationResidue());
- CellDesignerSimpleMolecule species = new CellDesignerSimpleMolecule();
-
- parser.processStateDataInSpecies(species, state);
- fail("Exception expected");
- } catch (NotImplementedException e) {
- assertTrue(e.getMessage().contains("Modification not supported in SimpleMolecule"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProcessInvalidStateDataInSpecies5() throws Exception {
- try {
- SpeciesState state = new SpeciesState();
- state.setStructuralState("state");
- CellDesignerSimpleMolecule species = new CellDesignerSimpleMolecule();
-
- parser.processStateDataInSpecies(species, state);
- fail("Exception expected");
- } catch (NotImplementedException e) {
- assertTrue(e.getMessage().contains("Structural state not supported in SimpleMolecule"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProcessInvalidStateDataInSpecies6() throws Exception {
- try {
- SpeciesState state = new SpeciesState();
- state.setStructuralState("state");
- CellDesignerAntisenseRna species = new CellDesignerAntisenseRna();
-
- parser.processStateDataInSpecies(species, state);
- fail("Exception expected");
- } catch (NotImplementedException e) {
- assertTrue(e.getMessage().contains("Structural state not supported in AntisenseRna"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProcessInvalidStateDataInSpecies7() throws Exception {
- try {
- SpeciesState state = new SpeciesState();
- state.setStructuralState("state");
- CellDesignerSpecies<?> species = new CellDesignerSpecies<Gene>();
-
- parser.processStateDataInSpecies(species, state);
- fail("Exception expected");
- } catch (NotImplementedException e) {
- assertTrue(e.getMessage().contains("Structural state not supported"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProcessInvalidStateDataInSpecies8() throws Exception {
- try {
- SpeciesState state = new SpeciesState();
- state.addModificationResidue(new CellDesignerModificationResidue());
- CellDesignerSpecies<?> species = new CellDesignerSpecies<Gene>();
-
- parser.processStateDataInSpecies(species, state);
- fail("Exception expected");
- } catch (NotImplementedException e) {
- assertTrue(e.getMessage().contains("Modification not supported in"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProcessAntisenseRnaStateDataInSpecies() throws Exception {
- try {
- SpeciesState state = new SpeciesState();
- state.addModificationResidue(new CellDesignerModificationResidue());
- CellDesignerAntisenseRna species = new CellDesignerAntisenseRna();
-
- parser.processStateDataInSpecies(species, state);
-
- assertEquals(1, species.getRegions().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.io.StringReader;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+import org.w3c.dom.Document;
+import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerDegraded;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerDrug;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGene;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGenericProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerIon;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerPhenotype;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSimpleMolecule;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerUnknown;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.SpeciesState;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class SpeciesSbmlParserTest extends CellDesignerTestFunctions {
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(SpeciesSbmlParserTest.class.getName());
+
+ SpeciesSbmlParser parser;
+
+ String testDirectory = "testFiles" + System.getProperty("file.separator") + "xmlNodeTestExamples"
+ + System.getProperty("file.separator");
+ String testGeneFile = "sbml_gene.xml";
+ String testDegradedFile = "sbml_degraded.xml";
+ String testDrugFile = "sbml_drug.xml";
+ String testIonFile = "sbml_ion.xml";
+ String testPhenotypeFile = "sbml_phenotype.xml";
+ String testProteinFile = "sbml_protein.xml";
+ String testRnaFile = "sbml_rna.xml";
+ String testSimpleMoleculeFile = "sbml_simple_molecule.xml";
+ String testUnknownFile = "sbml_unknown.xml";
+
+ CellDesignerElementCollection elements;
+
+ int idCounter = 0;
+
+ @Before
+ public void setUp() throws Exception {
+ elements = new CellDesignerElementCollection();
+ parser = new SpeciesSbmlParser(elements);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testParseXmlSpeciesAntisenseRna() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + "sbml_antisense_rna.xml");
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerAntisenseRna species = (CellDesignerAntisenseRna) result.getRight();
+ assertEquals("s2", species.getElementId());
+ assertEquals("s3", species.getName());
+ assertEquals(2, species.getInitialAmount(), Configuration.EPSILON);
+ assertEquals(Boolean.TRUE, species.hasOnlySubstanceUnits());
+ assertEquals(new Integer(0), species.getCharge());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlSpeciesWithKineticsData() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/kinetics/species_with_kinetics_param.xml");
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerProtein<?> species = (CellDesignerProtein<?>) result.getRight();
+ assertEquals(3.7, species.getInitialConcentration(), Configuration.EPSILON);
+ assertEquals(SbmlUnitType.MOLE, species.getSubstanceUnit());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSpeciesUnitsToXml() throws Exception {
+ try {
+ GenericProtein protein = new GenericProtein("s1");
+ protein.setSubstanceUnits(SbmlUnitType.MOLE);
+ String xml = parser.toXml(protein);
+ assertTrue("Cannot find substance unit in xml", xml.indexOf("mole") >= 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSpeciesConstantToXml() throws Exception {
+ try {
+ GenericProtein protein = new GenericProtein("s1");
+ protein.setConstant(true);
+ String xml = parser.toXml(protein);
+ assertTrue("Cannot find constant in xml", xml.indexOf("constant") >= 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSpeciesBoundaryConditionToXml() throws Exception {
+ try {
+ GenericProtein protein = new GenericProtein("s1");
+ protein.setBoundaryCondition(true);
+ String xml = parser.toXml(protein);
+ assertTrue("Cannot find boundary condition in xml", xml.indexOf("boundaryCondition") >= 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlSpeciesWithKineticsData2() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/kinetics/species_with_kinetics_param2.xml");
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerProtein<?> species = (CellDesignerProtein<?>) result.getRight();
+ assertEquals(2.5, species.getInitialAmount(), Configuration.EPSILON);
+ assertEquals(SbmlUnitType.GRAM, species.getSubstanceUnit());
+ assertEquals(Boolean.TRUE, species.hasOnlySubstanceUnits());
+ assertEquals("Boundary condition wasn't parsed", Boolean.TRUE, species.isBoundaryCondition());
+ assertEquals("Constant property wasn't parsed", Boolean.TRUE, species.isConstant());
+ assertEquals(new Integer(0), species.getCharge());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlAntisenseRna() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + "sbml_antisense_rna.xml");
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerAntisenseRna species = (CellDesignerAntisenseRna) result.getRight();
+
+ String transformedXml = parser.toXml(species.createModelElement());
+ assertNotNull(transformedXml);
+ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ DocumentBuilder builder = factory.newDocumentBuilder();
+ InputSource is = new InputSource(new StringReader(transformedXml));
+ Document doc = builder.parse(is);
+ NodeList root = doc.getChildNodes();
+ assertEquals("species", root.item(0).getNodeName());
+
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser
+ .parseXmlElement(parser.toXml(species.createModelElement()));
+ CellDesignerAntisenseRna species2 = (CellDesignerAntisenseRna) result2.getRight();
+
+ assertEquals(species.getName(), species2.getName());
+ assertEquals(species.getParent(), species2.getParent());
+ assertEquals(species.getInitialAmount(), species2.getInitialAmount());
+ assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
+ assertEquals(species.getCharge(), species2.getCharge());
+ assertEquals(species.getPositionToCompartment(), species2.getPositionToCompartment());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlSpeciesComplex() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + "sbml_complex.xml");
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerComplexSpecies species = (CellDesignerComplexSpecies) result.getRight();
+ assertNotNull(species);
+ assertEquals("s6549", species.getElementId());
+ assertEquals("LC3-II", species.getName());
+ assertEquals(0.0, species.getInitialAmount(), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlComplex() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + "sbml_complex.xml");
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerComplexSpecies species = (CellDesignerComplexSpecies) result.getRight();
+
+ String transformedXml = parser.toXml(species.createModelElement());
+ assertNotNull(transformedXml);
+ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ DocumentBuilder builder = factory.newDocumentBuilder();
+ InputSource is = new InputSource(new StringReader(transformedXml));
+ Document doc = builder.parse(is);
+ NodeList root = doc.getChildNodes();
+ assertEquals("species", root.item(0).getNodeName());
+
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser
+ .parseXmlElement(parser.toXml(species.createModelElement()));
+ CellDesignerComplexSpecies species2 = (CellDesignerComplexSpecies) result2.getRight();
+
+ assertNotNull(species2);
+ assertEquals(species.getName(), species2.getName());
+ assertEquals(species.getParent(), species2.getParent());
+ assertEquals(species.getInitialAmount(), species2.getInitialAmount());
+ assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
+ assertEquals(species.getCharge(), species2.getCharge());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlSpeciesDegraded() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testDegradedFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerDegraded species = (CellDesignerDegraded) result.getRight();
+ assertNotNull(species);
+ assertEquals("s1275", species.getElementId());
+ assertEquals("s1275", species.getName());
+ assertEquals(0, species.getInitialAmount(), Configuration.EPSILON);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlDegraded() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testDegradedFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerDegraded species = (CellDesignerDegraded) result.getRight();
+
+ String transformedXml = parser.toXml(species.createModelElement());
+ assertNotNull(transformedXml);
+ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ DocumentBuilder builder = factory.newDocumentBuilder();
+ InputSource is = new InputSource(new StringReader(transformedXml));
+ Document doc = builder.parse(is);
+ NodeList root = doc.getChildNodes();
+ assertEquals("species", root.item(0).getNodeName());
+
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser
+ .parseXmlElement(parser.toXml(species.createModelElement()));
+ CellDesignerDegraded species2 = (CellDesignerDegraded) result2.getRight();
+
+ assertNotNull(species2);
+ assertEquals(species.getName(), species2.getName());
+ assertEquals(species.getParent(), species2.getParent());
+ assertEquals(species.getInitialAmount(), species2.getInitialAmount());
+ assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
+ assertEquals(species.getCharge(), species2.getCharge());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlSpeciesDrug() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testDrugFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerDrug species = (CellDesignerDrug) result.getRight();
+ assertEquals("s6104", species.getElementId());
+ assertEquals("geldanamycin", species.getName());
+ assertEquals(new Integer(0), species.getCharge());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlDrug() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testDrugFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerDrug species = (CellDesignerDrug) result.getRight();
+
+ String transformedXml = parser.toXml(species.createModelElement());
+ assertNotNull(transformedXml);
+ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ DocumentBuilder builder = factory.newDocumentBuilder();
+ InputSource is = new InputSource(new StringReader(transformedXml));
+ Document doc = builder.parse(is);
+ NodeList root = doc.getChildNodes();
+ assertEquals("species", root.item(0).getNodeName());
+
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser
+ .parseXmlElement(parser.toXml(species.createModelElement()));
+ CellDesignerDrug species2 = (CellDesignerDrug) result2.getRight();
+
+ assertNotNull(species2);
+ assertEquals(species.getName(), species2.getName());
+ assertEquals(species.getParent(), species2.getParent());
+ assertEquals(species.getInitialAmount(), species2.getInitialAmount());
+ assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
+ assertEquals(species.getCharge(), species2.getCharge());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlSpeciesGene() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testGeneFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerGene species = (CellDesignerGene) result.getRight();
+
+ assertEquals("s5916", species.getElementId());
+ assertEquals("Ptgr1", species.getName());
+ assertEquals(new Integer(0), species.getCharge());
+ assertEquals(0, species.getInitialAmount(), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlSpeciesGeneWithModelUpdate() throws Exception {
+ try {
+ CellDesignerSpecies<?> gene = new CellDesignerGene();
+ gene.setElementId("s5916");
+ InternalModelSpeciesData modelData = new InternalModelSpeciesData();
+ modelData.updateSpecies(gene, "");
+
+ SpeciesSbmlParser complexParser = new SpeciesSbmlParser(elements);
+ CellDesignerGene oldGene = new CellDesignerGene();
+ oldGene.setElementId("s5916");
+ oldGene.setName("Ptgr1");
+ modelData.updateSpecies(oldGene, "gn95");
+
+ String xmlString = readFile(testDirectory + testGeneFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = complexParser.parseXmlElement(xmlString);
+ CellDesignerGene species = (CellDesignerGene) result.getRight();
+ modelData.updateSpecies(species, result.getLeft());
+
+ assertEquals("s5916", species.getElementId());
+ assertEquals("Ptgr1", species.getName());
+ assertTrue(species.getNotes().contains("prostaglandin reductase 1"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlGene() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testGeneFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerGene species = (CellDesignerGene) result.getRight();
+
+ String transformedXml = parser.toXml(species.createModelElement());
+ assertNotNull(transformedXml);
+ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ DocumentBuilder builder = factory.newDocumentBuilder();
+ InputSource is = new InputSource(new StringReader(transformedXml));
+ Document doc = builder.parse(is);
+ NodeList root = doc.getChildNodes();
+ assertEquals("species", root.item(0).getNodeName());
+
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser
+ .parseXmlElement(parser.toXml(species.createModelElement()));
+ CellDesignerGene species2 = (CellDesignerGene) result2.getRight();
+
+ assertNotNull(species2);
+ assertEquals(species.getName(), species2.getName());
+ assertEquals(species.getParent(), species2.getParent());
+ assertEquals(species.getInitialAmount(), species2.getInitialAmount());
+ assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
+ assertEquals(species.getCharge(), species2.getCharge());
+ assertTrue(species2.getNotes().trim().contains(species.getNotes().trim()));
+ assertEquals(species.getMiriamData().size(), species2.getMiriamData().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlSpeciesIon() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testIonFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerIon species = (CellDesignerIon) result.getRight();
+
+ assertEquals("s6029", species.getElementId());
+ assertEquals("Pi", species.getName());
+ assertEquals(new Integer(0), species.getCharge());
+ assertEquals(0, species.getInitialConcentration(), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlIon() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testIonFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerIon species = (CellDesignerIon) result.getRight();
+
+ String transformedXml = parser.toXml(species.createModelElement());
+ assertNotNull(transformedXml);
+ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ DocumentBuilder builder = factory.newDocumentBuilder();
+ InputSource is = new InputSource(new StringReader(transformedXml));
+ Document doc = builder.parse(is);
+ NodeList root = doc.getChildNodes();
+ assertEquals("species", root.item(0).getNodeName());
+
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser.parseXmlElement(xmlString);
+ CellDesignerIon species2 = (CellDesignerIon) result2.getRight();
+
+ assertNotNull(species2);
+ assertEquals(species.getElementId(), species2.getElementId());
+ assertEquals(species.getName(), species2.getName());
+ assertEquals(species.getParent(), species2.getParent());
+ assertEquals(species.getInitialAmount(), species2.getInitialAmount());
+ assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
+ assertEquals(species.getCharge(), species2.getCharge());
+ assertEquals(species.getInitialConcentration(), species2.getInitialConcentration());
+ assertEquals(species.getNotes().trim(), species2.getNotes().trim());
+ assertEquals(species.getMiriamData().size(), species2.getMiriamData().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlSpeciesPhenotype() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testPhenotypeFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerPhenotype species = (CellDesignerPhenotype) result.getRight();
+
+ assertEquals("s5462", species.getElementId());
+ assertEquals("Neuronal damage and death", species.getName());
+ assertEquals(0, species.getInitialAmount(), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlPhenotype() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testPhenotypeFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerPhenotype species = (CellDesignerPhenotype) result.getRight();
+
+ String transformedXml = parser.toXml(species.createModelElement());
+ assertNotNull(transformedXml);
+ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ DocumentBuilder builder = factory.newDocumentBuilder();
+ InputSource is = new InputSource(new StringReader(transformedXml));
+ Document doc = builder.parse(is);
+ NodeList root = doc.getChildNodes();
+ assertEquals("species", root.item(0).getNodeName());
+
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser
+ .parseXmlElement(parser.toXml(species.createModelElement()));
+ CellDesignerPhenotype species2 = (CellDesignerPhenotype) result2.getRight();
+
+ assertNotNull(species2);
+ assertEquals(species.getName(), species2.getName());
+ assertEquals(species.getParent(), species2.getParent());
+ assertEquals(species.getInitialAmount(), species2.getInitialAmount());
+ assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
+ assertEquals(species.getCharge(), species2.getCharge());
+ assertEquals(species.getInitialConcentration(), species2.getInitialConcentration());
+ assertEquals(species.getNotes(), species2.getNotes());
+ assertEquals(species.getMiriamData().size(), species2.getMiriamData().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlSpeciesProtein() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testProteinFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerProtein<?> species = (CellDesignerProtein<?>) result.getRight();
+
+ assertEquals("s5456", species.getElementId());
+ assertEquals("PTPRC", species.getName());
+ assertEquals(0, species.getInitialAmount(), Configuration.EPSILON);
+ assertEquals(new Integer(0), species.getCharge());
+ assertTrue(species.getNotes().contains("protein tyrosine phosphatase, receptor type, C"));
+ assertNull(species.getStructuralState());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlProtein() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testProteinFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerGenericProtein species = new CellDesignerGenericProtein(result.getRight());
+
+ String transformedXml = parser.toXml(species.createModelElement("" + idCounter++));
+ assertNotNull(transformedXml);
+ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ DocumentBuilder builder = factory.newDocumentBuilder();
+ InputSource is = new InputSource(new StringReader(transformedXml));
+ Document doc = builder.parse(is);
+ NodeList root = doc.getChildNodes();
+ assertEquals("species", root.item(0).getNodeName());
+
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser
+ .parseXmlElement(parser.toXml(species.createModelElement("" + idCounter++)));
+ CellDesignerProtein<?> species2 = (CellDesignerProtein<?>) result2.getRight();
+
+ assertNotNull(species2);
+ assertEquals(species.getName(), species2.getName());
+ assertEquals(species.getParent(), species2.getParent());
+ assertEquals(species.getInitialAmount(), species2.getInitialAmount());
+ assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
+ assertEquals(species.getCharge(), species2.getCharge());
+ assertEquals(species.getInitialConcentration(), species2.getInitialConcentration());
+ assertTrue(species2.getNotes().contains(species.getNotes()));
+ assertEquals(species.getMiriamData().size(), species2.getMiriamData().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlSpeciesRna() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testRnaFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerRna species = (CellDesignerRna) result.getRight();
+
+ assertEquals("s5914", species.getElementId());
+ assertEquals("Fmo3", species.getName());
+ assertEquals(0, species.getInitialAmount(), Configuration.EPSILON);
+ assertEquals(new Integer(0), species.getCharge());
+ assertTrue(species.getNotes().contains("Dimethylaniline monooxygenase [N-oxide-forming] 3"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlRna() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testRnaFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerRna species = (CellDesignerRna) result.getRight();
+
+ String transformedXml = parser.toXml(species.createModelElement());
+ assertNotNull(transformedXml);
+ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ DocumentBuilder builder = factory.newDocumentBuilder();
+ InputSource is = new InputSource(new StringReader(transformedXml));
+ Document doc = builder.parse(is);
+ NodeList root = doc.getChildNodes();
+ assertEquals("species", root.item(0).getNodeName());
+
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser
+ .parseXmlElement(parser.toXml(species.createModelElement()));
+ CellDesignerRna species2 = (CellDesignerRna) result2.getRight();
+
+ assertNotNull(species2);
+ assertEquals(species.getName(), species2.getName());
+ assertEquals(species.getParent(), species2.getParent());
+ assertEquals(species.getInitialAmount(), species2.getInitialAmount());
+ assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
+ assertEquals(species.getCharge(), species2.getCharge());
+ assertEquals(species.getInitialConcentration(), species2.getInitialConcentration());
+ assertTrue(species2.getNotes().trim().contains(species.getNotes().trim()));
+ assertEquals(species.getMiriamData().size(), species2.getMiriamData().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlSpeciesSimpleMolecule() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testSimpleMoleculeFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerSimpleMolecule species = (CellDesignerSimpleMolecule) result.getRight();
+ assertEquals("s5463", species.getElementId());
+ assertEquals("Peroxides", species.getName());
+ assertEquals(0, species.getInitialAmount(), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlSimpleMolecule() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testSimpleMoleculeFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerSimpleMolecule species = (CellDesignerSimpleMolecule) result.getRight();
+
+ String transformedXml = parser.toXml(species.createModelElement("" + idCounter++));
+ assertNotNull(transformedXml);
+ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ DocumentBuilder builder = factory.newDocumentBuilder();
+ InputSource is = new InputSource(new StringReader(transformedXml));
+ Document doc = builder.parse(is);
+ NodeList root = doc.getChildNodes();
+ assertEquals("species", root.item(0).getNodeName());
+
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser
+ .parseXmlElement(parser.toXml(species.createModelElement("" + idCounter++)));
+ CellDesignerSimpleMolecule species2 = (CellDesignerSimpleMolecule) result2.getRight();
+
+ assertNotNull(species2);
+ assertEquals(species.getName(), species2.getName());
+ assertEquals(species.getParent(), species2.getParent());
+ assertEquals(species.getInitialAmount(), species2.getInitialAmount());
+ assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
+ assertEquals(species.getCharge(), species2.getCharge());
+ assertEquals(species.getInitialConcentration(), species2.getInitialConcentration());
+ assertEquals(species.getNotes(), species2.getNotes());
+ assertEquals(species.getMiriamData().size(), species2.getMiriamData().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlSpeciesUnknown() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testUnknownFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerUnknown species = (CellDesignerUnknown) result.getRight();
+ assertEquals("s1356", species.getElementId());
+ assertEquals("unidentified caspase acting on Occludin", species.getName());
+ assertEquals(0, species.getInitialAmount(), Configuration.EPSILON);
+ assertEquals(new Integer(0), species.getCharge());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlUnknown() throws Exception {
+ try {
+ String xmlString = readFile(testDirectory + testUnknownFile);
+ Pair<String, ? extends CellDesignerSpecies<?>> result = parser.parseXmlElement(xmlString);
+ CellDesignerUnknown species = (CellDesignerUnknown) result.getRight();
+
+ String transformedXml = parser.toXml(species.createModelElement());
+ assertNotNull(transformedXml);
+ DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+ DocumentBuilder builder = factory.newDocumentBuilder();
+ InputSource is = new InputSource(new StringReader(transformedXml));
+ Document doc = builder.parse(is);
+ NodeList root = doc.getChildNodes();
+ assertEquals("species", root.item(0).getNodeName());
+
+ Pair<String, ? extends CellDesignerSpecies<?>> result2 = parser
+ .parseXmlElement(parser.toXml(species.createModelElement()));
+ CellDesignerUnknown species2 = (CellDesignerUnknown) result2.getRight();
+
+ assertNotNull(species2);
+ assertEquals(species.getName(), species2.getName());
+ assertEquals(species.getParent(), species2.getParent());
+ assertEquals(species.getInitialAmount(), species2.getInitialAmount());
+ assertEquals(species.hasOnlySubstanceUnits(), species2.hasOnlySubstanceUnits());
+ assertEquals(species.getCharge(), species2.getCharge());
+ assertEquals(species.getInitialConcentration(), species2.getInitialConcentration());
+ assertEquals(species.getNotes(), species2.getNotes());
+ assertEquals(species.getMiriamData().size(), species2.getMiriamData().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalid() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/invalid_sbml_protein.xml");
+ parser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("No annotation node"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalid2() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/invalid_sbml_protein2.xml");
+ parser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("bla"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalid3() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/invalid_sbml_protein3.xml");
+ parser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("unk_bla"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalid4() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/invalid_sbml_protein4.xml");
+ parser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("No celldesigner:extension"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalid5() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/invalid_sbml_protein5.xml");
+ parser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("ann_unk"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalid6() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/invalid_sbml_protein6.xml");
+ parser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("No celldesigner:speciesIdentity"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalid7() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/invalid_sbml_protein7.xml");
+ parser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("unkPos"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalid8() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/invalid_sbml_protein8.xml");
+ parser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Species node in Sbml model doesn't contain"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalid9() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/invalid_sbml_protein9.xml");
+ parser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("unknown_protein_class"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalid10() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/invalid_sbml_protein10.xml");
+ parser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Wrong class type for protein reference"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalid11() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/invalid_sbml_protein11.xml");
+ parser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Wrong class type for gene reference"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalid12() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/invalid_sbml_protein12.xml");
+ parser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Wrong class type for rna reference"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalid13() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/invalid_sbml_protein13.xml");
+ parser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Wrong class type for antisense rna reference"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalid14() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/invalid_sbml_protein14.xml");
+ parser.parseXmlElement(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("uknNode"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlWithDefaultCompartment() throws Exception {
+ try {
+ CellDesignerGenericProtein species = new CellDesignerGenericProtein();
+ String xml = parser.toXml(species.createModelElement("EL_ID"));
+ assertTrue(xml.contains("EL_ID"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidSpeciesIdentityToXml() throws Exception {
+ try {
+ Species species = Mockito.mock(Species.class);
+ parser.speciesIdentityToXml(species);
+ fail("Excepiton expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Invalid species class"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSpeciesIdentityToXml() throws Exception {
+ try {
+ GenericProtein species = new GenericProtein("xx");
+ species.setHypothetical(true);
+ String xml = parser.speciesIdentityToXml(species);
+ assertTrue(xml.contains("<celldesigner:hypothetical>true</celldesigner:hypothetical>"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSpeciesStateToXml() throws Exception {
+ try {
+ SpeciesState state = new SpeciesState();
+ state.setHomodimer(2);
+ state.setStructuralState("xxxState");
+ String xml = parser.speciesStateToXml(state);
+ assertTrue(xml.contains("xxxState"));
+ assertTrue(xml.contains("celldesigner:homodimer"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProcessInvalidStateDataInSpecies() throws Exception {
+ try {
+ SpeciesState state = new SpeciesState();
+ state.addModificationResidue(new CellDesignerModificationResidue());
+ CellDesignerComplexSpecies species = new CellDesignerComplexSpecies();
+
+ parser.processStateDataInSpecies(species, state);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ assertTrue(e.getMessage().contains("Modification not supported in Complex"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProcessInvalidStateDataInSpecies2() throws Exception {
+ try {
+ SpeciesState state = new SpeciesState();
+ state.setStructuralState("state");
+ CellDesignerGene species = new CellDesignerGene();
+
+ parser.processStateDataInSpecies(species, state);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ assertTrue(e.getMessage().contains("StructuralState not supported in Gene"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProcessInvalidStateDataInSpecies3() throws Exception {
+ try {
+ SpeciesState state = new SpeciesState();
+ state.setStructuralState("state");
+ CellDesignerRna species = new CellDesignerRna();
+
+ parser.processStateDataInSpecies(species, state);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ assertTrue(e.getMessage().contains("Structural state not supported in RNA"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProcessInvalidStateDataInSpecies4() throws Exception {
+ try {
+ SpeciesState state = new SpeciesState();
+ state.addModificationResidue(new CellDesignerModificationResidue());
+ CellDesignerSimpleMolecule species = new CellDesignerSimpleMolecule();
+
+ parser.processStateDataInSpecies(species, state);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ assertTrue(e.getMessage().contains("Modification not supported in SimpleMolecule"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProcessInvalidStateDataInSpecies5() throws Exception {
+ try {
+ SpeciesState state = new SpeciesState();
+ state.setStructuralState("state");
+ CellDesignerSimpleMolecule species = new CellDesignerSimpleMolecule();
+
+ parser.processStateDataInSpecies(species, state);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ assertTrue(e.getMessage().contains("Structural state not supported in SimpleMolecule"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProcessInvalidStateDataInSpecies6() throws Exception {
+ try {
+ SpeciesState state = new SpeciesState();
+ state.setStructuralState("state");
+ CellDesignerAntisenseRna species = new CellDesignerAntisenseRna();
+
+ parser.processStateDataInSpecies(species, state);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ assertTrue(e.getMessage().contains("Structural state not supported in AntisenseRna"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProcessInvalidStateDataInSpecies7() throws Exception {
+ try {
+ SpeciesState state = new SpeciesState();
+ state.setStructuralState("state");
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<Gene>();
+
+ parser.processStateDataInSpecies(species, state);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ assertTrue(e.getMessage().contains("Structural state not supported"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProcessInvalidStateDataInSpecies8() throws Exception {
+ try {
+ SpeciesState state = new SpeciesState();
+ state.addModificationResidue(new CellDesignerModificationResidue());
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<Gene>();
+
+ parser.processStateDataInSpecies(species, state);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ assertTrue(e.getMessage().contains("Modification not supported in"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProcessAntisenseRnaStateDataInSpecies() throws Exception {
+ try {
+ SpeciesState state = new SpeciesState();
+ state.addModificationResidue(new CellDesignerModificationResidue());
+ CellDesignerAntisenseRna species = new CellDesignerAntisenseRna();
+
+ parser.processStateDataInSpecies(species, state);
+
+ assertEquals(1, species.getRegions().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AllStructureTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AllStructureTests.java
index 6afe5cf8ea..2cf4d96ad2 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AllStructureTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/AllStructureTests.java
@@ -1,38 +1,38 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.AllFieldsTests;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AllFieldsTests.class, //
- AntisenseRnaTest.class, //
- CellDesignerChemicalTest.class, //
- CompartmentTest.class, //
- ComplexSpeciesTest.class, //
- ConnectSchemeTest.class, //
- DegradedTest.class, //
- DrugTest.class, //
- ElementTest.class, //
- GenericProteinTest.class, //
- GeneTest.class, //
- IonChannelProteinTest.class, //
- IonTest.class, //
- LinePropertiesTest.class, //
- ModificationResidueTest.class, //
- PhenotypeTest.class, //
- ProteinTest.class, //
- ReceptorProteinTest.class, //
- RnaTest.class, //
- SimpleMoleculeTest.class, //
- SpeciesStateTest.class, //
- SpeciesTest.class, //
- TruncatedProteinTest.class, //
- UnknownTest.class, //
- ViewTest.class, //
-})
-public class AllStructureTests {
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.AllFieldsTests;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AllFieldsTests.class, //
+ AntisenseRnaTest.class, //
+ CellDesignerChemicalTest.class, //
+ CompartmentTest.class, //
+ ComplexSpeciesTest.class, //
+ ConnectSchemeTest.class, //
+ DegradedTest.class, //
+ DrugTest.class, //
+ ElementTest.class, //
+ GenericProteinTest.class, //
+ GeneTest.class, //
+ IonChannelProteinTest.class, //
+ IonTest.class, //
+ LinePropertiesTest.class, //
+ ModificationResidueTest.class, //
+ PhenotypeTest.class, //
+ ProteinTest.class, //
+ ReceptorProteinTest.class, //
+ RnaTest.class, //
+ SimpleMoleculeTest.class, //
+ SpeciesStateTest.class, //
+ SpeciesTest.class, //
+ TruncatedProteinTest.class, //
+ UnknownTest.class, //
+ ViewTest.class, //
+})
+public class AllStructureTests {
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerChemicalTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerChemicalTest.java
index da6753e8ae..aef53547d4 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerChemicalTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerChemicalTest.java
@@ -1,40 +1,40 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import static org.junit.Assert.assertEquals;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class CellDesignerChemicalTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetters() {
- String smiles = "smiles";
- String inChI = "inchi";
- String inChIKey = "key";
-
- CellDesignerChemical<?> chemical = new CellDesignerIon();
- chemical.setSmiles(smiles);
- chemical.setInChI(inChI);
- chemical.setInChIKey(inChIKey);
-
- assertEquals(smiles, chemical.getSmiles());
- assertEquals(inChI, chemical.getInChI());
- assertEquals(inChIKey, chemical.getInChIKey());
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import static org.junit.Assert.assertEquals;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class CellDesignerChemicalTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetters() {
+ String smiles = "smiles";
+ String inChI = "inchi";
+ String inChIKey = "key";
+
+ CellDesignerChemical<?> chemical = new CellDesignerIon();
+ chemical.setSmiles(smiles);
+ chemical.setInChI(inChI);
+ chemical.setInChIKey(inChIKey);
+
+ assertEquals(smiles, chemical.getSmiles());
+ assertEquals(inChI, chemical.getInChI());
+ assertEquals(inChIKey, chemical.getInChIKey());
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentTest.java
index e0316dca58..7393585314 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/CompartmentTest.java
@@ -1,172 +1,172 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class CompartmentTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new CellDesignerCompartment());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- CellDesignerCompartment original = new CellDesignerCompartment();
- original.addElement(new CellDesignerGenericProtein());
- CellDesignerCompartment compartment = new CellDesignerCompartment(original);
- assertNotNull(compartment);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testEquals() {
- try {
- CellDesignerCompartment original = new CellDesignerCompartment();
- original.setName("anme");
- CellDesignerCompartment compartment = new CellDesignerCompartment(original);
- CellDesignerCompartment compartment2 = new CellDesignerCompartment();
-
- CellDesignerCompartment compartment3 = new CellDesignerCompartment();
- compartment3.setElementId("q");
-
- assertEquals(0, compartment.compareTo(original));
- assertTrue(compartment.equals(original));
-
- assertEquals(0, compartment.compareTo(compartment));
- assertTrue(compartment.equals(compartment));
- assertTrue(compartment.compareTo(compartment2) != 0);
- assertFalse(compartment.equals(compartment2));
-
- assertTrue(compartment.compareTo(compartment3) != 0);
-
- assertFalse(compartment.equals(new Object()));
-
- assertTrue(compartment.compareTo(null) != 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- CellDesignerCompartment compartment = new CellDesignerCompartment().copy();
- assertNotNull(compartment);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- String elementId = "id";
-
- CellDesignerCompartment compartment = new CellDesignerCompartment();
-
- compartment.setElementId(elementId);
- assertEquals(elementId, compartment.getElementId());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddElements() {
- try {
- CellDesignerGenericProtein protein = new CellDesignerGenericProtein();
-
- CellDesignerCompartment compartment = new CellDesignerCompartment();
-
- assertEquals(0, compartment.getElements().size());
- compartment.addElement(protein);
- assertEquals(1, compartment.getElements().size());
- compartment.addElement(protein);
- assertEquals(1, compartment.getElements().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testHashCode() {
- try {
- CellDesignerCompartment compartment = new CellDesignerCompartment();
- compartment.setName("name");
-
- int code = compartment.hashCode();
- compartment.setName("name2");
- int code2 = compartment.hashCode();
-
- assertTrue(code != code2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- CellDesignerCompartment compartment = Mockito.spy(CellDesignerCompartment.class);
- compartment.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateModelElementWithProblems() {
- try {
- CellDesignerCompartment compartment = new CellDesignerCompartment();
- compartment.addElement(new CellDesignerAntisenseRna());
- compartment.createModelElement();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class CompartmentTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new CellDesignerCompartment());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ CellDesignerCompartment original = new CellDesignerCompartment();
+ original.addElement(new CellDesignerGenericProtein());
+ CellDesignerCompartment compartment = new CellDesignerCompartment(original);
+ assertNotNull(compartment);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ CellDesignerCompartment original = new CellDesignerCompartment();
+ original.setName("anme");
+ CellDesignerCompartment compartment = new CellDesignerCompartment(original);
+ CellDesignerCompartment compartment2 = new CellDesignerCompartment();
+
+ CellDesignerCompartment compartment3 = new CellDesignerCompartment();
+ compartment3.setElementId("q");
+
+ assertEquals(0, compartment.compareTo(original));
+ assertTrue(compartment.equals(original));
+
+ assertEquals(0, compartment.compareTo(compartment));
+ assertTrue(compartment.equals(compartment));
+ assertTrue(compartment.compareTo(compartment2) != 0);
+ assertFalse(compartment.equals(compartment2));
+
+ assertTrue(compartment.compareTo(compartment3) != 0);
+
+ assertFalse(compartment.equals(new Object()));
+
+ assertTrue(compartment.compareTo(null) != 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ CellDesignerCompartment compartment = new CellDesignerCompartment().copy();
+ assertNotNull(compartment);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ String elementId = "id";
+
+ CellDesignerCompartment compartment = new CellDesignerCompartment();
+
+ compartment.setElementId(elementId);
+ assertEquals(elementId, compartment.getElementId());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddElements() {
+ try {
+ CellDesignerGenericProtein protein = new CellDesignerGenericProtein();
+
+ CellDesignerCompartment compartment = new CellDesignerCompartment();
+
+ assertEquals(0, compartment.getElements().size());
+ compartment.addElement(protein);
+ assertEquals(1, compartment.getElements().size());
+ compartment.addElement(protein);
+ assertEquals(1, compartment.getElements().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testHashCode() {
+ try {
+ CellDesignerCompartment compartment = new CellDesignerCompartment();
+ compartment.setName("name");
+
+ int code = compartment.hashCode();
+ compartment.setName("name2");
+ int code2 = compartment.hashCode();
+
+ assertTrue(code != code2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ CellDesignerCompartment compartment = Mockito.spy(CellDesignerCompartment.class);
+ compartment.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCreateModelElementWithProblems() {
+ try {
+ CellDesignerCompartment compartment = new CellDesignerCompartment();
+ compartment.addElement(new CellDesignerAntisenseRna());
+ compartment.createModelElement();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesTest.java
index 674e14a750..43b18cfa93 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ComplexSpeciesTest.java
@@ -1,148 +1,148 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import java.util.HashSet;
-import java.util.Set;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-
-public class ComplexSpeciesTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new CellDesignerComplexSpecies());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- CellDesignerComplexSpecies degraded = new CellDesignerComplexSpecies(new CellDesignerSpecies<AntisenseRna>());
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- CellDesignerComplexSpecies species = new CellDesignerComplexSpecies();
- species.addElement(new CellDesignerSpecies<AntisenseRna>());
- CellDesignerComplexSpecies complex = new CellDesignerComplexSpecies(species);
-
- Set<CellDesignerElement<?>> elements = new HashSet<>();
- complex.setElements(elements);
- assertEquals(elements, complex.getElements());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddElement() {
- try {
- CellDesignerComplexSpecies species = new CellDesignerComplexSpecies();
- species.addElement(new CellDesignerSpecies<AntisenseRna>());
- species.addElement(new CellDesignerSpecies<AntisenseRna>());
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetStructuralState() {
- try {
- CellDesignerComplexSpecies species = new CellDesignerComplexSpecies();
- species.setStructuralState("a");
- species.setStructuralState("b");
- assertEquals("b", species.getStructuralState());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAllSimpleChildren() {
- try {
- CellDesignerComplexSpecies species = new CellDesignerComplexSpecies();
- species.addElement(new CellDesignerSpecies<AntisenseRna>());
- CellDesignerComplexSpecies complex = new CellDesignerComplexSpecies("a");
- complex.addElement(new CellDesignerSpecies<AntisenseRna>("s"));
- complex.addElement(new CellDesignerSpecies<AntisenseRna>("d"));
- species.addElement(complex);
- assertEquals(3, species.getAllSimpleChildren().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- CellDesignerComplexSpecies degraded = new CellDesignerComplexSpecies().copy();
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- CellDesignerComplexSpecies complex = Mockito.spy(CellDesignerComplexSpecies.class);
- complex.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateInvalidElement() {
- try {
- CellDesignerComplexSpecies complex = new CellDesignerComplexSpecies();
- complex.addElement(new CellDesignerGene());
- complex.createModelElement();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+
+public class ComplexSpeciesTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new CellDesignerComplexSpecies());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ CellDesignerComplexSpecies degraded = new CellDesignerComplexSpecies(new CellDesignerSpecies<AntisenseRna>());
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ CellDesignerComplexSpecies species = new CellDesignerComplexSpecies();
+ species.addElement(new CellDesignerSpecies<AntisenseRna>());
+ CellDesignerComplexSpecies complex = new CellDesignerComplexSpecies(species);
+
+ Set<CellDesignerElement<?>> elements = new HashSet<>();
+ complex.setElements(elements);
+ assertEquals(elements, complex.getElements());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddElement() {
+ try {
+ CellDesignerComplexSpecies species = new CellDesignerComplexSpecies();
+ species.addElement(new CellDesignerSpecies<AntisenseRna>());
+ species.addElement(new CellDesignerSpecies<AntisenseRna>());
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetStructuralState() {
+ try {
+ CellDesignerComplexSpecies species = new CellDesignerComplexSpecies();
+ species.setStructuralState("a");
+ species.setStructuralState("b");
+ assertEquals("b", species.getStructuralState());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAllSimpleChildren() {
+ try {
+ CellDesignerComplexSpecies species = new CellDesignerComplexSpecies();
+ species.addElement(new CellDesignerSpecies<AntisenseRna>());
+ CellDesignerComplexSpecies complex = new CellDesignerComplexSpecies("a");
+ complex.addElement(new CellDesignerSpecies<AntisenseRna>("s"));
+ complex.addElement(new CellDesignerSpecies<AntisenseRna>("d"));
+ species.addElement(complex);
+ assertEquals(3, species.getAllSimpleChildren().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ CellDesignerComplexSpecies degraded = new CellDesignerComplexSpecies().copy();
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ CellDesignerComplexSpecies complex = Mockito.spy(CellDesignerComplexSpecies.class);
+ complex.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCreateInvalidElement() {
+ try {
+ CellDesignerComplexSpecies complex = new CellDesignerComplexSpecies();
+ complex.addElement(new CellDesignerGene());
+ complex.createModelElement();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ConnectSchemeTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ConnectSchemeTest.java
index e427ca6477..5b5ba309a6 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ConnectSchemeTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ConnectSchemeTest.java
@@ -1,45 +1,45 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import static org.junit.Assert.assertEquals;
-
-import java.util.HashMap;
-import java.util.Map;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.ConnectScheme;
-
-public class ConnectSchemeTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetters() {
- String connectIndex = "1";
- Integer integerConnectIndex = 1;
- String connectPolicy = "2";
- Map<String, String> directions = new HashMap<>();
- ConnectScheme cs = new ConnectScheme();
- cs.setConnectPolicy(connectPolicy);
- cs.setConnectIndex(connectIndex);
- cs.setLineDirections(directions);
-
- assertEquals(integerConnectIndex, cs.getConnectIndex());
- assertEquals(connectPolicy, cs.getConnectPolicy());
- assertEquals(directions, cs.getLineDirections());
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import static org.junit.Assert.assertEquals;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.ConnectScheme;
+
+public class ConnectSchemeTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetters() {
+ String connectIndex = "1";
+ Integer integerConnectIndex = 1;
+ String connectPolicy = "2";
+ Map<String, String> directions = new HashMap<>();
+ ConnectScheme cs = new ConnectScheme();
+ cs.setConnectPolicy(connectPolicy);
+ cs.setConnectIndex(connectIndex);
+ cs.setLineDirections(directions);
+
+ assertEquals(integerConnectIndex, cs.getConnectIndex());
+ assertEquals(connectPolicy, cs.getConnectPolicy());
+ assertEquals(directions, cs.getLineDirections());
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedTest.java
index 636f4bb559..c9575803d2 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DegradedTest.java
@@ -1,70 +1,70 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Degraded;
-
-public class DegradedTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new CellDesignerDegraded());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- CellDesignerDegraded degraded = new CellDesignerDegraded(new CellDesignerSpecies<Degraded>());
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- CellDesignerDegraded degraded = new CellDesignerDegraded().copy();
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- CellDesignerDegraded degraded = Mockito.spy(CellDesignerDegraded.class);
- degraded.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Degraded;
+
+public class DegradedTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new CellDesignerDegraded());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ CellDesignerDegraded degraded = new CellDesignerDegraded(new CellDesignerSpecies<Degraded>());
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ CellDesignerDegraded degraded = new CellDesignerDegraded().copy();
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ CellDesignerDegraded degraded = Mockito.spy(CellDesignerDegraded.class);
+ degraded.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugTest.java
index b0354518a9..322c4ab051 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/DrugTest.java
@@ -1,70 +1,70 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Drug;
-
-public class DrugTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new CellDesignerDrug());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- CellDesignerDrug degraded = new CellDesignerDrug(new CellDesignerSpecies<Drug>());
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- CellDesignerDrug degraded = new CellDesignerDrug().copy();
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- CellDesignerDrug drug = Mockito.spy(CellDesignerDrug.class);
- drug.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Drug;
+
+public class DrugTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new CellDesignerDrug());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ CellDesignerDrug degraded = new CellDesignerDrug(new CellDesignerSpecies<Drug>());
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ CellDesignerDrug degraded = new CellDesignerDrug().copy();
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ CellDesignerDrug drug = Mockito.spy(CellDesignerDrug.class);
+ drug.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementTest.java
index 214e436b0a..015b044475 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ElementTest.java
@@ -1,129 +1,129 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-
-public class ElementTest extends CellDesignerTestFunctions {
- Logger logger = Logger.getLogger(ElementTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testConstructor() {
- try {
- CellDesignerSpecies<?> element = Mockito.spy(CellDesignerSpecies.class);
- element.addMiriamData(new MiriamData());
- CellDesignerElement<?> copy = new CellDesignerGenericProtein(element);
- assertNotNull(copy);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddMiriamCollection() {
- try {
- List<MiriamData> list = new ArrayList<>();
- list.add(new MiriamData(MiriamType.CAS, "1"));
- list.add(new MiriamData(MiriamType.CAS, "1"));
- CellDesignerElement<?> element = Mockito.spy(CellDesignerElement.class);
- element.addMiriamData(list);
- assertEquals(1, element.getMiriamData().size());
- assertEquals(1, getWarnings().size());
-
- element.addMiriamData(list);
- assertEquals(3, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetNotes() {
- try {
- CellDesignerElement<?> element = Mockito.spy(CellDesignerElement.class);
- element.setNotes("</html>");
- fail("Exception epxected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddSynonym() {
- try {
- CellDesignerElement<?> element = Mockito.spy(CellDesignerElement.class);
- List<String> synonyms = new ArrayList<>();
- synonyms.add("syn");
- element.addSynonyms(synonyms);
- assertEquals("syn", element.getSynonyms().get(0));
- StringBuilder sb = new StringBuilder();
- for (int i = 0; i < 300; i++) {
- sb.append("a");
- }
- String syn = sb.toString();
- synonyms = new ArrayList<>();
- synonyms.add(syn);
- element.addSynonyms(synonyms);
- assertFalse(syn.equals(element.getSynonyms().get(1)));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- CellDesignerElement<?> element = Mockito.spy(CellDesignerElement.class);
- List<String> synonyms = new ArrayList<>();
- List<String> formerSymbols = new ArrayList<>();
- CellDesignerComplexSpecies complex = new CellDesignerComplexSpecies();
- String formula = "str";
- String abbreviation = "abr";
-
- element.setSynonyms(synonyms);
- element.setFormerSymbols(formerSymbols);
- element.setComplex(complex);
- element.setFormula(formula);
- element.setAbbreviation(abbreviation);
-
- assertEquals(synonyms, element.getSynonyms());
- assertEquals(formerSymbols, element.getFormerSymbols());
- assertEquals(complex, element.getComplex());
- assertEquals(formula, element.getFormula());
- assertEquals(abbreviation, element.getAbbreviation());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+
+public class ElementTest extends CellDesignerTestFunctions {
+ Logger logger = Logger.getLogger(ElementTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ CellDesignerSpecies<?> element = Mockito.spy(CellDesignerSpecies.class);
+ element.addMiriamData(new MiriamData());
+ CellDesignerElement<?> copy = new CellDesignerGenericProtein(element);
+ assertNotNull(copy);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddMiriamCollection() {
+ try {
+ List<MiriamData> list = new ArrayList<>();
+ list.add(new MiriamData(MiriamType.CAS, "1"));
+ list.add(new MiriamData(MiriamType.CAS, "1"));
+ CellDesignerElement<?> element = Mockito.spy(CellDesignerElement.class);
+ element.addMiriamData(list);
+ assertEquals(1, element.getMiriamData().size());
+ assertEquals(1, getWarnings().size());
+
+ element.addMiriamData(list);
+ assertEquals(3, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetNotes() {
+ try {
+ CellDesignerElement<?> element = Mockito.spy(CellDesignerElement.class);
+ element.setNotes("</html>");
+ fail("Exception epxected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddSynonym() {
+ try {
+ CellDesignerElement<?> element = Mockito.spy(CellDesignerElement.class);
+ List<String> synonyms = new ArrayList<>();
+ synonyms.add("syn");
+ element.addSynonyms(synonyms);
+ assertEquals("syn", element.getSynonyms().get(0));
+ StringBuilder sb = new StringBuilder();
+ for (int i = 0; i < 300; i++) {
+ sb.append("a");
+ }
+ String syn = sb.toString();
+ synonyms = new ArrayList<>();
+ synonyms.add(syn);
+ element.addSynonyms(synonyms);
+ assertFalse(syn.equals(element.getSynonyms().get(1)));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ CellDesignerElement<?> element = Mockito.spy(CellDesignerElement.class);
+ List<String> synonyms = new ArrayList<>();
+ List<String> formerSymbols = new ArrayList<>();
+ CellDesignerComplexSpecies complex = new CellDesignerComplexSpecies();
+ String formula = "str";
+ String abbreviation = "abr";
+
+ element.setSynonyms(synonyms);
+ element.setFormerSymbols(formerSymbols);
+ element.setComplex(complex);
+ element.setFormula(formula);
+ element.setAbbreviation(abbreviation);
+
+ assertEquals(synonyms, element.getSynonyms());
+ assertEquals(formerSymbols, element.getFormerSymbols());
+ assertEquals(complex, element.getComplex());
+ assertEquals(formula, element.getFormula());
+ assertEquals(abbreviation, element.getAbbreviation());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GenericProteinTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GenericProteinTest.java
index 866399a63a..1fdf0313a1 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GenericProteinTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GenericProteinTest.java
@@ -1,69 +1,69 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-
-public class GenericProteinTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new CellDesignerGenericProtein());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- CellDesignerGenericProtein species = new CellDesignerGenericProtein(new CellDesignerSpecies<GenericProtein>());
- assertNotNull(species);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy1() {
- try {
- CellDesignerGenericProtein species = new CellDesignerGenericProtein(new CellDesignerSpecies<GenericProtein>()).copy();
- assertNotNull(species);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy2() {
- try {
- CellDesignerGenericProtein protein = Mockito.spy(CellDesignerGenericProtein.class);
- protein.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+
+public class GenericProteinTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new CellDesignerGenericProtein());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ CellDesignerGenericProtein species = new CellDesignerGenericProtein(new CellDesignerSpecies<GenericProtein>());
+ assertNotNull(species);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy1() {
+ try {
+ CellDesignerGenericProtein species = new CellDesignerGenericProtein(new CellDesignerSpecies<GenericProtein>()).copy();
+ assertNotNull(species);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy2() {
+ try {
+ CellDesignerGenericProtein protein = Mockito.spy(CellDesignerGenericProtein.class);
+ protein.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonChannelProteinTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonChannelProteinTest.java
index e4c9423343..3751fa3540 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonChannelProteinTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/IonChannelProteinTest.java
@@ -1,70 +1,70 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.IonChannelProtein;
-
-public class IonChannelProteinTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new CellDesignerIonChannelProtein());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- CellDesignerIonChannelProtein species = new CellDesignerIonChannelProtein(new CellDesignerSpecies<IonChannelProtein>());
- assertNotNull(species);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy1() {
- try {
- CellDesignerIonChannelProtein species = new CellDesignerIonChannelProtein(new CellDesignerSpecies<IonChannelProtein>()).copy();
- assertNotNull(species);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy2() {
- try {
- CellDesignerIonChannelProtein protein = Mockito.spy(CellDesignerIonChannelProtein.class);
- protein.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.IonChannelProtein;
+
+public class IonChannelProteinTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new CellDesignerIonChannelProtein());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ CellDesignerIonChannelProtein species = new CellDesignerIonChannelProtein(new CellDesignerSpecies<IonChannelProtein>());
+ assertNotNull(species);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy1() {
+ try {
+ CellDesignerIonChannelProtein species = new CellDesignerIonChannelProtein(new CellDesignerSpecies<IonChannelProtein>()).copy();
+ assertNotNull(species);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy2() {
+ try {
+ CellDesignerIonChannelProtein protein = Mockito.spy(CellDesignerIonChannelProtein.class);
+ protein.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/LinePropertiesTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/LinePropertiesTest.java
index 501161070d..ad1c9dcc49 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/LinePropertiesTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/LinePropertiesTest.java
@@ -1,34 +1,34 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import static org.junit.Assert.*;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.LineProperties;
-
-public class LinePropertiesTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetters() {
- String type = "str_t";
- LineProperties lp = new LineProperties();
- lp.setType(type);
- assertEquals(type,lp.getType());
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import static org.junit.Assert.*;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.LineProperties;
+
+public class LinePropertiesTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetters() {
+ String type = "str_t";
+ LineProperties lp = new LineProperties();
+ lp.setType(type);
+ assertEquals(type,lp.getType());
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidueTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidueTest.java
index 992af01828..4bddfd2566 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidueTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ModificationResidueTest.java
@@ -1,153 +1,153 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
-import lcsb.mapviewer.model.map.species.IonChannelProtein;
-import lcsb.mapviewer.model.map.species.field.ModificationState;
-
-public class ModificationResidueTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new CellDesignerModificationResidue());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- CellDesignerModificationResidue original = new CellDesignerModificationResidue();
- CellDesignerModificationResidue copy = new CellDesignerModificationResidue(original);
- assertNotNull(copy);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate() {
- try {
- CellDesignerModificationResidue original = new CellDesignerModificationResidue();
- CellDesignerModificationResidue update = new CellDesignerModificationResidue();
-
- String name = "n";
- String side = "s";
- ModificationState state = ModificationState.ACETYLATED;
- Double angle = 3.9;
- Double size = 5.0;
-
- update.setName(name);
- update.setSide(side);
- update.setAngle(angle);
- update.setSize(size);
- update.setState(state);
-
- original.update(update);
-
- assertEquals(name, original.getName());
- assertEquals(side, original.getSide());
- assertEquals(angle, original.getAngle());
- assertEquals(size, original.getSize());
- assertEquals(state, original.getState());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- CellDesignerModificationResidue original = new CellDesignerModificationResidue();
-
- String doubleStr = "2.0";
- String invalidDoubleStr = "a2.0";
- String nullStr = null;
- Double angle = 2.0;
- CellDesignerSpecies<?> species = new CellDesignerSpecies<IonChannelProtein>();
-
- original.setAngle(doubleStr);
- assertEquals(angle, original.getAngle(), Configuration.EPSILON);
- try {
- original.setAngle(invalidDoubleStr);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- original.setAngle(nullStr);
- assertNull(original.getAngle());
-
- original.setSize(doubleStr);
- assertEquals(angle, original.getSize(), Configuration.EPSILON);
- try {
- original.setSize(invalidDoubleStr);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- original.setSize(doubleStr);
- original.setSize(nullStr);
- assertNull(original.getSize());
-
- original.setSpecies(species);
- assertEquals(species, original.getSpecies());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- CellDesignerModificationResidue degraded = new CellDesignerModificationResidue().copy();
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new CellDesignerModificationResidue() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.model.map.species.IonChannelProtein;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+
+public class ModificationResidueTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new CellDesignerModificationResidue());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ CellDesignerModificationResidue original = new CellDesignerModificationResidue();
+ CellDesignerModificationResidue copy = new CellDesignerModificationResidue(original);
+ assertNotNull(copy);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdate() {
+ try {
+ CellDesignerModificationResidue original = new CellDesignerModificationResidue();
+ CellDesignerModificationResidue update = new CellDesignerModificationResidue();
+
+ String name = "n";
+ String side = "s";
+ ModificationState state = ModificationState.ACETYLATED;
+ Double angle = 3.9;
+ Double size = 5.0;
+
+ update.setName(name);
+ update.setSide(side);
+ update.setAngle(angle);
+ update.setSize(size);
+ update.setState(state);
+
+ original.update(update);
+
+ assertEquals(name, original.getName());
+ assertEquals(side, original.getSide());
+ assertEquals(angle, original.getAngle());
+ assertEquals(size, original.getSize());
+ assertEquals(state, original.getState());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ CellDesignerModificationResidue original = new CellDesignerModificationResidue();
+
+ String doubleStr = "2.0";
+ String invalidDoubleStr = "a2.0";
+ String nullStr = null;
+ Double angle = 2.0;
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<IonChannelProtein>();
+
+ original.setAngle(doubleStr);
+ assertEquals(angle, original.getAngle(), Configuration.EPSILON);
+ try {
+ original.setAngle(invalidDoubleStr);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ original.setAngle(nullStr);
+ assertNull(original.getAngle());
+
+ original.setSize(doubleStr);
+ assertEquals(angle, original.getSize(), Configuration.EPSILON);
+ try {
+ original.setSize(invalidDoubleStr);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ original.setSize(doubleStr);
+ original.setSize(nullStr);
+ assertNull(original.getSize());
+
+ original.setSpecies(species);
+ assertEquals(species, original.getSpecies());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ CellDesignerModificationResidue degraded = new CellDesignerModificationResidue().copy();
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new CellDesignerModificationResidue() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeTest.java
index 2e0508828c..dc63317e6a 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/PhenotypeTest.java
@@ -1,70 +1,70 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class PhenotypeTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new CellDesignerPhenotype());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- CellDesignerPhenotype original = new CellDesignerPhenotype();
- CellDesignerPhenotype copy = new CellDesignerPhenotype(original);
- assertNotNull(copy);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- CellDesignerPhenotype degraded = new CellDesignerPhenotype().copy();
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- CellDesignerPhenotype phenotype = Mockito.spy(CellDesignerPhenotype.class);
- phenotype.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class PhenotypeTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new CellDesignerPhenotype());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ CellDesignerPhenotype original = new CellDesignerPhenotype();
+ CellDesignerPhenotype copy = new CellDesignerPhenotype(original);
+ assertNotNull(copy);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ CellDesignerPhenotype degraded = new CellDesignerPhenotype().copy();
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ CellDesignerPhenotype phenotype = Mockito.spy(CellDesignerPhenotype.class);
+ phenotype.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinTest.java
index 8894d14ba9..be726bf744 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ProteinTest.java
@@ -1,135 +1,135 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-
-public class ProteinTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new CellDesignerGenericProtein());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- CellDesignerProtein<?> protein = new CellDesignerGenericProtein();
- protein.setStructuralState("srt");
- List<CellDesignerModificationResidue> residues = new ArrayList<>();
- residues.add(new CellDesignerModificationResidue());
-
- protein.setModificationResidues(residues);
- CellDesignerProtein<?> protein2 = new CellDesignerGenericProtein(protein);
- assertNotNull(protein2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate() {
- try {
- CellDesignerProtein<?> protein = new CellDesignerGenericProtein();
- protein.setStructuralState("");
- CellDesignerProtein<?> protein2 = new CellDesignerGenericProtein();
- protein2.setStructuralState("srt");
- List<CellDesignerModificationResidue> residues = new ArrayList<>();
- residues.add(new CellDesignerModificationResidue());
-
- protein2.setModificationResidues(residues);
-
- protein.update(protein2);
- assertEquals(protein2.getStructuralState(), protein.getStructuralState());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddModificationResidue() {
- try {
- CellDesignerProtein<?> protein = new CellDesignerGenericProtein();
- CellDesignerModificationResidue mr = new CellDesignerModificationResidue();
- mr.setIdModificationResidue("id1");
-
- CellDesignerModificationResidue mr2 = new CellDesignerModificationResidue();
- mr2.setIdModificationResidue("id1");
-
- protein.addModificationResidue(mr);
- assertEquals(1, protein.getModificationResidues().size());
- protein.addModificationResidue(mr2);
- assertEquals(1, protein.getModificationResidues().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetStructuralState() {
- try {
- CellDesignerProtein<?> protein = new CellDesignerGenericProtein();
- protein.setStructuralState("str");
- protein.setStructuralState("str1");
-
- assertEquals("str1", protein.getStructuralState());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- CellDesignerProtein<?> protein = new CellDesignerProtein<GenericProtein>().copy();
- assertNotNull(protein);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- CellDesignerProtein<?> mock = Mockito.spy(CellDesignerProtein.class);
- mock.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+
+public class ProteinTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new CellDesignerGenericProtein());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ CellDesignerProtein<?> protein = new CellDesignerGenericProtein();
+ protein.setStructuralState("srt");
+ List<CellDesignerModificationResidue> residues = new ArrayList<>();
+ residues.add(new CellDesignerModificationResidue());
+
+ protein.setModificationResidues(residues);
+ CellDesignerProtein<?> protein2 = new CellDesignerGenericProtein(protein);
+ assertNotNull(protein2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdate() {
+ try {
+ CellDesignerProtein<?> protein = new CellDesignerGenericProtein();
+ protein.setStructuralState("");
+ CellDesignerProtein<?> protein2 = new CellDesignerGenericProtein();
+ protein2.setStructuralState("srt");
+ List<CellDesignerModificationResidue> residues = new ArrayList<>();
+ residues.add(new CellDesignerModificationResidue());
+
+ protein2.setModificationResidues(residues);
+
+ protein.update(protein2);
+ assertEquals(protein2.getStructuralState(), protein.getStructuralState());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddModificationResidue() {
+ try {
+ CellDesignerProtein<?> protein = new CellDesignerGenericProtein();
+ CellDesignerModificationResidue mr = new CellDesignerModificationResidue();
+ mr.setIdModificationResidue("id1");
+
+ CellDesignerModificationResidue mr2 = new CellDesignerModificationResidue();
+ mr2.setIdModificationResidue("id1");
+
+ protein.addModificationResidue(mr);
+ assertEquals(1, protein.getModificationResidues().size());
+ protein.addModificationResidue(mr2);
+ assertEquals(1, protein.getModificationResidues().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetStructuralState() {
+ try {
+ CellDesignerProtein<?> protein = new CellDesignerGenericProtein();
+ protein.setStructuralState("str");
+ protein.setStructuralState("str1");
+
+ assertEquals("str1", protein.getStructuralState());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ CellDesignerProtein<?> protein = new CellDesignerProtein<GenericProtein>().copy();
+ assertNotNull(protein);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ CellDesignerProtein<?> mock = Mockito.spy(CellDesignerProtein.class);
+ mock.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ReceptorProteinTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ReceptorProteinTest.java
index f9b3b8a7a7..0ce73dfe6a 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ReceptorProteinTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ReceptorProteinTest.java
@@ -1,70 +1,70 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.ReceptorProtein;
-
-public class ReceptorProteinTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new CellDesignerReceptorProtein());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- CellDesignerReceptorProtein species = new CellDesignerReceptorProtein(new CellDesignerSpecies<ReceptorProtein>());
- assertNotNull(species);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy1() {
- try {
- CellDesignerReceptorProtein species = new CellDesignerReceptorProtein(new CellDesignerSpecies<ReceptorProtein>()).copy();
- assertNotNull(species);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy2() {
- try {
- CellDesignerReceptorProtein protein = Mockito.spy(CellDesignerReceptorProtein.class);
- protein.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.ReceptorProtein;
+
+public class ReceptorProteinTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new CellDesignerReceptorProtein());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ CellDesignerReceptorProtein species = new CellDesignerReceptorProtein(new CellDesignerSpecies<ReceptorProtein>());
+ assertNotNull(species);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy1() {
+ try {
+ CellDesignerReceptorProtein species = new CellDesignerReceptorProtein(new CellDesignerSpecies<ReceptorProtein>()).copy();
+ assertNotNull(species);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy2() {
+ try {
+ CellDesignerReceptorProtein protein = Mockito.spy(CellDesignerReceptorProtein.class);
+ protein.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeTest.java
index 12ba41b5c9..39c8e9c01a 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SimpleMoleculeTest.java
@@ -1,70 +1,70 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
-
-public class SimpleMoleculeTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new CellDesignerSimpleMolecule());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- CellDesignerSimpleMolecule degraded = new CellDesignerSimpleMolecule(new CellDesignerSpecies<SimpleMolecule>());
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- CellDesignerSimpleMolecule degraded = new CellDesignerSimpleMolecule().copy();
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- CellDesignerSimpleMolecule simpleMolecule = Mockito.spy(CellDesignerSimpleMolecule.class);
- simpleMolecule.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+
+public class SimpleMoleculeTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new CellDesignerSimpleMolecule());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ CellDesignerSimpleMolecule degraded = new CellDesignerSimpleMolecule(new CellDesignerSpecies<SimpleMolecule>());
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ CellDesignerSimpleMolecule degraded = new CellDesignerSimpleMolecule().copy();
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ CellDesignerSimpleMolecule simpleMolecule = Mockito.spy(CellDesignerSimpleMolecule.class);
+ simpleMolecule.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesTest.java
index 6bf57cf435..733e2a7dbd 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesTest.java
@@ -1,358 +1,358 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Rna;
-
-public class SpeciesTest extends CellDesignerTestFunctions {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new CellDesignerSpecies<GenericProtein>());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
- String elementId = "51";
- Double initialAmount = 54.0;
- Double initialConcentration = 58.0;
- Integer charge = 59;
- Boolean onlySubstanceUnits = true;
-
- String trueStr = "true";
- assertFalse(species.isHypothetical());
- species.setHypothetical(trueStr);
- assertTrue(species.isHypothetical());
-
- species.setElementId(elementId);
- assertEquals(elementId, species.getElementId());
-
- species.setInitialAmount(initialAmount);
- assertEquals(initialAmount, species.getInitialAmount());
-
- species.setOnlySubstanceUnits(onlySubstanceUnits);
- assertEquals(onlySubstanceUnits, species.getOnlySubstanceUnits());
-
- species.setInitialConcentration(initialConcentration);
- assertEquals(initialConcentration, species.getInitialConcentration());
-
- species.setCharge(charge);
-
- assertEquals(charge, species.getCharge());
-
- species.setElementId("");
- assertEquals("", species.getElementId());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- String id = "as_id";
- CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>(id);
- assertEquals(id, species.getElementId());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- String id = "as_id";
- CellDesignerSpecies<GenericProtein> species = new CellDesignerSpecies<>(id);
- species.setBoundaryCondition(true);
- species.setConstant(true);
- species.setSubstanceUnits(SbmlUnitType.COULUMB);
- CellDesignerSpecies<?> copy = species.copy();
- assertEquals(id, species.getElementId());
- assertEquals(Boolean.TRUE, copy.isBoundaryCondition());
- assertEquals(Boolean.TRUE, copy.isConstant());
- assertEquals(SbmlUnitType.COULUMB, copy.getSubstanceUnit());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetId() {
- try {
- CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
- species.setElementId("");
- species.setElementId("xx");
- try {
- species.setElementId("yy");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate1() {
- try {
- int warningsCount = getWarnings().size();
- CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
- species.setName("A");
- species.setNotes("XXX");
- CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
- species2.setName("B");
- species.update(species2);
- int warningsCount2 = getWarnings().size();
- assertEquals(1, warningsCount2 - warningsCount);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate2() {
- try {
- CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
- species.setNotes("XXX");
- CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
- species2.addMiriamData(new MiriamData());
- species.update(species2);
- int warningsCount = getWarnings().size();
- assertEquals(0, warningsCount);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate3() {
- try {
- CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
- species.setNotes("XXX");
- CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
- species2.setNotes("xx");
- species.update(species2);
- int warningsCount = getWarnings().size();
- assertEquals(0, warningsCount);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate4() {
- try {
- CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
- species.setNotes("XX");
- CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
- species2.setNotes("xxX");
- species.update(species2);
- int warningsCount = getWarnings().size();
- assertEquals(0, warningsCount);
- assertEquals(3, species.getNotes().length());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate5() {
- try {
- CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
- species.setNotes("XX");
- CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
- species2.setNotes("a as x");
- species2.setHypothetical(true);
- species2.setSymbol("sym");
- species2.setHomodimer(2);
- species.update(species2);
- int warningsCount = getWarnings().size();
- assertEquals(0, warningsCount);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate6() {
- try {
- CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
- species.setSymbol("sym1");
- species.setFullName("a_sym1");
- CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
- species2.setSymbol("sym2");
- species2.setFullName("b_sym1");
- species.update(species2);
- int warningsCount = getWarnings().size();
- assertEquals(2, warningsCount);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate7() {
- try {
- CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
- CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
- species2.addSynonym("syn");
- species2.addFormerSymbol("sym");
- species.update(species2);
- int warningsCount = getWarnings().size();
- assertEquals(0, warningsCount);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetInitialAmount() {
- try {
- CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
- species.setInitialAmount("1");
- assertEquals(1, species.getInitialAmount(), Configuration.EPSILON);
- try {
- species.setInitialAmount("a1");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- species.setInitialAmount("1");
- species.setInitialAmount((String) null);
- assertNull(species.getInitialAmount());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetCharge() {
- try {
- CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
- species.setCharge("1");
- assertEquals((Integer) 1, species.getCharge());
- try {
- species.setCharge("a1");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- species.setCharge("1");
- species.setCharge((String) null);
- assertNull(species.getCharge());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetOnlySubstanceUnits() {
- try {
- CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
- species.setOnlySubstanceUnits("true");
- assertTrue(species.getOnlySubstanceUnits());
- try {
- species.setOnlySubstanceUnits("a1");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- species.setOnlySubstanceUnits("false");
- assertFalse(species.getOnlySubstanceUnits());
- species.setOnlySubstanceUnits((String) null);
- assertNull(species.getOnlySubstanceUnits());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetInitialConcentration() {
- try {
- CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
- species.setInitialConcentration("1");
- assertEquals(1, species.getInitialConcentration(), Configuration.EPSILON);
- try {
- species.setInitialConcentration("a1");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- species.setInitialConcentration("1");
- species.setInitialConcentration((String) null);
- assertNull(species.getInitialConcentration());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateInvalidElement() {
- try {
- CellDesignerSpecies<?> complex = new CellDesignerSpecies<Rna>();
- complex.createModelElement("id");
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Rna;
+
+public class SpeciesTest extends CellDesignerTestFunctions {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new CellDesignerSpecies<GenericProtein>());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
+ String elementId = "51";
+ Double initialAmount = 54.0;
+ Double initialConcentration = 58.0;
+ Integer charge = 59;
+ Boolean onlySubstanceUnits = true;
+
+ String trueStr = "true";
+ assertFalse(species.isHypothetical());
+ species.setHypothetical(trueStr);
+ assertTrue(species.isHypothetical());
+
+ species.setElementId(elementId);
+ assertEquals(elementId, species.getElementId());
+
+ species.setInitialAmount(initialAmount);
+ assertEquals(initialAmount, species.getInitialAmount());
+
+ species.setOnlySubstanceUnits(onlySubstanceUnits);
+ assertEquals(onlySubstanceUnits, species.getOnlySubstanceUnits());
+
+ species.setInitialConcentration(initialConcentration);
+ assertEquals(initialConcentration, species.getInitialConcentration());
+
+ species.setCharge(charge);
+
+ assertEquals(charge, species.getCharge());
+
+ species.setElementId("");
+ assertEquals("", species.getElementId());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ String id = "as_id";
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>(id);
+ assertEquals(id, species.getElementId());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ String id = "as_id";
+ CellDesignerSpecies<GenericProtein> species = new CellDesignerSpecies<>(id);
+ species.setBoundaryCondition(true);
+ species.setConstant(true);
+ species.setSubstanceUnits(SbmlUnitType.COULUMB);
+ CellDesignerSpecies<?> copy = species.copy();
+ assertEquals(id, species.getElementId());
+ assertEquals(Boolean.TRUE, copy.isBoundaryCondition());
+ assertEquals(Boolean.TRUE, copy.isConstant());
+ assertEquals(SbmlUnitType.COULUMB, copy.getSubstanceUnit());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetId() {
+ try {
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
+ species.setElementId("");
+ species.setElementId("xx");
+ try {
+ species.setElementId("yy");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdate1() {
+ try {
+ int warningsCount = getWarnings().size();
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
+ species.setName("A");
+ species.setNotes("XXX");
+ CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
+ species2.setName("B");
+ species.update(species2);
+ int warningsCount2 = getWarnings().size();
+ assertEquals(1, warningsCount2 - warningsCount);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdate2() {
+ try {
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
+ species.setNotes("XXX");
+ CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
+ species2.addMiriamData(new MiriamData());
+ species.update(species2);
+ int warningsCount = getWarnings().size();
+ assertEquals(0, warningsCount);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdate3() {
+ try {
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
+ species.setNotes("XXX");
+ CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
+ species2.setNotes("xx");
+ species.update(species2);
+ int warningsCount = getWarnings().size();
+ assertEquals(0, warningsCount);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdate4() {
+ try {
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
+ species.setNotes("XX");
+ CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
+ species2.setNotes("xxX");
+ species.update(species2);
+ int warningsCount = getWarnings().size();
+ assertEquals(0, warningsCount);
+ assertEquals(3, species.getNotes().length());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdate5() {
+ try {
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
+ species.setNotes("XX");
+ CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
+ species2.setNotes("a as x");
+ species2.setHypothetical(true);
+ species2.setSymbol("sym");
+ species2.setHomodimer(2);
+ species.update(species2);
+ int warningsCount = getWarnings().size();
+ assertEquals(0, warningsCount);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdate6() {
+ try {
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
+ species.setSymbol("sym1");
+ species.setFullName("a_sym1");
+ CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
+ species2.setSymbol("sym2");
+ species2.setFullName("b_sym1");
+ species.update(species2);
+ int warningsCount = getWarnings().size();
+ assertEquals(2, warningsCount);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdate7() {
+ try {
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
+ CellDesignerSpecies<?> species2 = new CellDesignerSpecies<GenericProtein>();
+ species2.addSynonym("syn");
+ species2.addFormerSymbol("sym");
+ species.update(species2);
+ int warningsCount = getWarnings().size();
+ assertEquals(0, warningsCount);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetInitialAmount() {
+ try {
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
+ species.setInitialAmount("1");
+ assertEquals(1, species.getInitialAmount(), Configuration.EPSILON);
+ try {
+ species.setInitialAmount("a1");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ species.setInitialAmount("1");
+ species.setInitialAmount((String) null);
+ assertNull(species.getInitialAmount());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetCharge() {
+ try {
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
+ species.setCharge("1");
+ assertEquals((Integer) 1, species.getCharge());
+ try {
+ species.setCharge("a1");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ species.setCharge("1");
+ species.setCharge((String) null);
+ assertNull(species.getCharge());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetOnlySubstanceUnits() {
+ try {
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
+ species.setOnlySubstanceUnits("true");
+ assertTrue(species.getOnlySubstanceUnits());
+ try {
+ species.setOnlySubstanceUnits("a1");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ species.setOnlySubstanceUnits("false");
+ assertFalse(species.getOnlySubstanceUnits());
+ species.setOnlySubstanceUnits((String) null);
+ assertNull(species.getOnlySubstanceUnits());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetInitialConcentration() {
+ try {
+ CellDesignerSpecies<?> species = new CellDesignerSpecies<GenericProtein>();
+ species.setInitialConcentration("1");
+ assertEquals(1, species.getInitialConcentration(), Configuration.EPSILON);
+ try {
+ species.setInitialConcentration("a1");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ species.setInitialConcentration("1");
+ species.setInitialConcentration((String) null);
+ assertNull(species.getInitialConcentration());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCreateInvalidElement() {
+ try {
+ CellDesignerSpecies<?> complex = new CellDesignerSpecies<Rna>();
+ complex.createModelElement("id");
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/TruncatedProteinTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/TruncatedProteinTest.java
index 9171a2ff8c..d7a38ce9f3 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/TruncatedProteinTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/TruncatedProteinTest.java
@@ -1,70 +1,70 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.TruncatedProtein;
-
-public class TruncatedProteinTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new CellDesignerTruncatedProtein());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- CellDesignerTruncatedProtein species = new CellDesignerTruncatedProtein(new CellDesignerSpecies<TruncatedProtein>());
- assertNotNull(species);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy1() {
- try {
- CellDesignerTruncatedProtein species = new CellDesignerTruncatedProtein(new CellDesignerSpecies<TruncatedProtein>()).copy();
- assertNotNull(species);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy2() {
- try {
- CellDesignerTruncatedProtein protein = Mockito.spy(CellDesignerTruncatedProtein.class);
- protein.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.TruncatedProtein;
+
+public class TruncatedProteinTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new CellDesignerTruncatedProtein());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ CellDesignerTruncatedProtein species = new CellDesignerTruncatedProtein(new CellDesignerSpecies<TruncatedProtein>());
+ assertNotNull(species);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy1() {
+ try {
+ CellDesignerTruncatedProtein species = new CellDesignerTruncatedProtein(new CellDesignerSpecies<TruncatedProtein>()).copy();
+ assertNotNull(species);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy2() {
+ try {
+ CellDesignerTruncatedProtein protein = Mockito.spy(CellDesignerTruncatedProtein.class);
+ protein.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownTest.java
index 1c5b80fe1f..bdf5cd4c26 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/UnknownTest.java
@@ -1,70 +1,70 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Unknown;
-
-public class UnknownTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new CellDesignerUnknown());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- CellDesignerUnknown degraded = new CellDesignerUnknown(new CellDesignerSpecies<Unknown>());
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- CellDesignerUnknown degraded = new CellDesignerUnknown().copy();
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- CellDesignerUnknown unknown = Mockito.spy(CellDesignerUnknown.class);
- unknown.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Unknown;
+
+public class UnknownTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new CellDesignerUnknown());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ CellDesignerUnknown degraded = new CellDesignerUnknown(new CellDesignerSpecies<Unknown>());
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ CellDesignerUnknown degraded = new CellDesignerUnknown().copy();
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ CellDesignerUnknown unknown = Mockito.spy(CellDesignerUnknown.class);
+ unknown.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ViewTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ViewTest.java
index 818365ca41..ae6f2152a3 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ViewTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/ViewTest.java
@@ -1,36 +1,36 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import static org.junit.Assert.*;
-
-import java.awt.geom.Point2D;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.View;
-
-public class ViewTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetters() {
- Point2D innerPosition = new Point2D.Double();
- View view = new View();
- view.setInnerPosition(innerPosition);
- assertEquals(innerPosition, view.getInnerPosition());
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import static org.junit.Assert.*;
+
+import java.awt.geom.Point2D;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.View;
+
+public class ViewTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetters() {
+ Point2D innerPosition = new Point2D.Double();
+ View view = new View();
+ view.setInnerPosition(innerPosition);
+ assertEquals(innerPosition, view.getInnerPosition());
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/AllFieldsTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/AllFieldsTests.java
index 54887f8d0d..bc93824a6c 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/AllFieldsTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/AllFieldsTests.java
@@ -1,12 +1,12 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ CellDesignerModificationResidueTest.class, //
-})
-public class AllFieldsTests {
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ CellDesignerModificationResidueTest.class, //
+})
+public class AllFieldsTests {
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidueTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidueTest.java
index 96aa3aa79b..41d152d0db 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidueTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidueTest.java
@@ -1,30 +1,30 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
-
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class CellDesignerModificationResidueTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void test() {
- CellDesignerModificationResidue region = new CellDesignerModificationResidue();
- assertNotNull(region.toString());
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
+
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class CellDesignerModificationResidueTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void test() {
+ CellDesignerModificationResidue region = new CellDesignerModificationResidue();
+ assertNotNull(region.toString());
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/AllTypesTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/AllTypesTests.java
index 5a6c7a9b9d..dd93d8d0e7 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/AllTypesTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/AllTypesTests.java
@@ -1,15 +1,15 @@
-package lcsb.mapviewer.converter.model.celldesigner.types;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ ModifierTypeTest.class, //
- ModifierTypeUtilsTest.class, //
- OperatorTypeTest.class, //
- OperatorTypeUtilsTest.class, //
-})
-public class AllTypesTests {
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.types;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ ModifierTypeTest.class, //
+ ModifierTypeUtilsTest.class, //
+ OperatorTypeTest.class, //
+ OperatorTypeUtilsTest.class, //
+})
+public class AllTypesTests {
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeTest.java
index 29008c9c5c..b10acf49c6 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeTest.java
@@ -1,31 +1,31 @@
-package lcsb.mapviewer.converter.model.celldesigner.types;
-
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ModifierTypeTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void test() {
- for (ModifierType type : ModifierType.values()) {
- assertNotNull(ModifierType.valueOf(type.toString()));
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.types;
+
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ModifierTypeTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void test() {
+ for (ModifierType type : ModifierType.values()) {
+ assertNotNull(ModifierType.valueOf(type.toString()));
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtilsTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtilsTest.java
index 8d1cc6df9c..96ab7dcfe8 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtilsTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtilsTest.java
@@ -1,263 +1,263 @@
-package lcsb.mapviewer.converter.model.celldesigner.types;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.awt.geom.Point2D;
-import java.lang.reflect.Field;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.reaction.AndOperator;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.reaction.NodeOperator;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class ModifierTypeUtilsTest {
-
- ModifierTypeUtils utils = new ModifierTypeUtils();
-
- Modifier invalidModifier = Mockito.mock(Modifier.class, Mockito.CALLS_REAL_METHODS);
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetInvalidModifierTypeForClazz() {
- ModifierType type = utils.getModifierTypeForClazz(invalidModifier.getClass());
- assertNull(type);
- }
-
- @Test
- public void testGetInvalidStringTypeByModifier() {
- String type = utils.getStringTypeByModifier(invalidModifier);
- assertNull(type);
- }
-
- @Test
- public void testGetTargetLineIndexByInvalidModifier() {
- try {
- utils.getTargetLineIndexByModifier(invalidModifier);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Unknown modifier class"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetTargetLineIndexByInvalidModifier2() {
- try {
- NodeOperator operator = new AndOperator();
- operator.addInput(new Reactant());
- utils.getTargetLineIndexByModifier(operator);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Invalid NodeOperator"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetTargetLineIndexByInvalidModifier3() {
- try {
- NodeOperator operator = new AndOperator();
- operator.addInput(invalidModifier);
- utils.getTargetLineIndexByModifier(operator);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Unknown modifier class"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAnchorPointOnReactionRectByInvalidType() {
- try {
- Reaction reaction = new Reaction();
- Reactant reactant = new Reactant();
- Product product = new Product();
- reactant.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double()));
- product.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double()));
- reaction.addReactant(reactant);
- reaction.addProduct(product);
- Point2D point = utils.getAnchorPointOnReactionRect(reaction, "0,0");
- assertNotNull(point);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAnchorPointOnReactionRectByInvalidType2() {
- try {
- Reaction reaction = new Reaction();
- Reactant reactant = new Reactant();
- Product product = new Product();
- reactant.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double()));
- product.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double()));
- reaction.addReactant(reactant);
- reaction.addProduct(product);
- utils.getAnchorPointOnReactionRect(reaction, "0");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Invalid targetLineIndex"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAnchorPointOnReactionRectByInvalidType3() {
- try {
- Reaction reaction = new Reaction();
- Reactant reactant = new Reactant();
- Product product = new Product();
- reactant.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double()));
- product.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double()));
- reaction.addReactant(reactant);
- reaction.addProduct(product);
- utils.getAnchorPointOnReactionRect(reaction, "10,10");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Unknown targetLineIndex"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdateLineEndPointForInvalidModifier() {
- try {
- utils.updateLineEndPoint(invalidModifier);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Unknown modifier class"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdateLineEndPointForInvalidModifier2() {
- try {
- NodeOperator operator = new AndOperator();
- operator.addInput(new Product());
- operator.addInput(invalidModifier);
- utils.updateLineEndPoint(operator);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Unknown modifier class"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdateLineEndPointForInvalidModifier3() {
- try {
- NodeOperator operator = new AndOperator();
- operator.addInput(new Product());
- operator.addInput(new Product());
- utils.updateLineEndPoint(operator);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Operator contains invalid input"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateInvalidModifierForStringType2() throws Exception {
- // artificial implementation of Modifier that is invalid
- class InvalidModifier extends Modifier {
- private static final long serialVersionUID = 1L;
-
- @SuppressWarnings("unused")
- public InvalidModifier() {
- throw new NotImplementedException();
- }
-
- @SuppressWarnings("unused")
- public InvalidModifier(Species alias, CellDesignerElement<?> element) {
- throw new NotImplementedException();
- }
- }
-
- // mopdify one of the elements of OperatorType so it will have invalid
- // implementation
- ModifierType typeToModify = ModifierType.CATALYSIS;
- Class<? extends Modifier> clazz = typeToModify.getClazz();
-
- try {
- Field field = typeToModify.getClass().getDeclaredField("clazz");
- field.setAccessible(true);
- field.set(typeToModify, InvalidModifier.class);
-
- // and check if we catch properly information about problematic
- // implementation
- utils.createModifierForStringType(typeToModify.getStringName(), new GenericProtein("id"));
- fail("Exceptione expected");
- } catch (InvalidStateException e) {
- assertTrue(e.getMessage().contains("Problem with instantiation of Modifier class"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- // restore correct values for the modified type (if not then other test
- // might fail...)
- Field field = typeToModify.getClass().getDeclaredField("clazz");
- field.setAccessible(true);
- field.set(typeToModify, clazz);
- }
- }
-
- @Test
- public void testCreateModifierForStringType2() throws Exception {
- try {
- utils.createModifierForStringType("unjkType", null);
- fail("Exceptione expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Unknown modifier type"));
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.types;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.awt.geom.Point2D;
+import java.lang.reflect.Field;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.reaction.AndOperator;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.reaction.NodeOperator;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class ModifierTypeUtilsTest {
+
+ ModifierTypeUtils utils = new ModifierTypeUtils();
+
+ Modifier invalidModifier = Mockito.mock(Modifier.class, Mockito.CALLS_REAL_METHODS);
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetInvalidModifierTypeForClazz() {
+ ModifierType type = utils.getModifierTypeForClazz(invalidModifier.getClass());
+ assertNull(type);
+ }
+
+ @Test
+ public void testGetInvalidStringTypeByModifier() {
+ String type = utils.getStringTypeByModifier(invalidModifier);
+ assertNull(type);
+ }
+
+ @Test
+ public void testGetTargetLineIndexByInvalidModifier() {
+ try {
+ utils.getTargetLineIndexByModifier(invalidModifier);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Unknown modifier class"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetTargetLineIndexByInvalidModifier2() {
+ try {
+ NodeOperator operator = new AndOperator();
+ operator.addInput(new Reactant());
+ utils.getTargetLineIndexByModifier(operator);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Invalid NodeOperator"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetTargetLineIndexByInvalidModifier3() {
+ try {
+ NodeOperator operator = new AndOperator();
+ operator.addInput(invalidModifier);
+ utils.getTargetLineIndexByModifier(operator);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Unknown modifier class"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAnchorPointOnReactionRectByInvalidType() {
+ try {
+ Reaction reaction = new Reaction();
+ Reactant reactant = new Reactant();
+ Product product = new Product();
+ reactant.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double()));
+ product.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double()));
+ reaction.addReactant(reactant);
+ reaction.addProduct(product);
+ Point2D point = utils.getAnchorPointOnReactionRect(reaction, "0,0");
+ assertNotNull(point);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAnchorPointOnReactionRectByInvalidType2() {
+ try {
+ Reaction reaction = new Reaction();
+ Reactant reactant = new Reactant();
+ Product product = new Product();
+ reactant.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double()));
+ product.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double()));
+ reaction.addReactant(reactant);
+ reaction.addProduct(product);
+ utils.getAnchorPointOnReactionRect(reaction, "0");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Invalid targetLineIndex"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAnchorPointOnReactionRectByInvalidType3() {
+ try {
+ Reaction reaction = new Reaction();
+ Reactant reactant = new Reactant();
+ Product product = new Product();
+ reactant.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double()));
+ product.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double()));
+ reaction.addReactant(reactant);
+ reaction.addProduct(product);
+ utils.getAnchorPointOnReactionRect(reaction, "10,10");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Unknown targetLineIndex"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdateLineEndPointForInvalidModifier() {
+ try {
+ utils.updateLineEndPoint(invalidModifier);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Unknown modifier class"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdateLineEndPointForInvalidModifier2() {
+ try {
+ NodeOperator operator = new AndOperator();
+ operator.addInput(new Product());
+ operator.addInput(invalidModifier);
+ utils.updateLineEndPoint(operator);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Unknown modifier class"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdateLineEndPointForInvalidModifier3() {
+ try {
+ NodeOperator operator = new AndOperator();
+ operator.addInput(new Product());
+ operator.addInput(new Product());
+ utils.updateLineEndPoint(operator);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Operator contains invalid input"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCreateInvalidModifierForStringType2() throws Exception {
+ // artificial implementation of Modifier that is invalid
+ class InvalidModifier extends Modifier {
+ private static final long serialVersionUID = 1L;
+
+ @SuppressWarnings("unused")
+ public InvalidModifier() {
+ throw new NotImplementedException();
+ }
+
+ @SuppressWarnings("unused")
+ public InvalidModifier(Species alias, CellDesignerElement<?> element) {
+ throw new NotImplementedException();
+ }
+ }
+
+ // mopdify one of the elements of OperatorType so it will have invalid
+ // implementation
+ ModifierType typeToModify = ModifierType.CATALYSIS;
+ Class<? extends Modifier> clazz = typeToModify.getClazz();
+
+ try {
+ Field field = typeToModify.getClass().getDeclaredField("clazz");
+ field.setAccessible(true);
+ field.set(typeToModify, InvalidModifier.class);
+
+ // and check if we catch properly information about problematic
+ // implementation
+ utils.createModifierForStringType(typeToModify.getStringName(), new GenericProtein("id"));
+ fail("Exceptione expected");
+ } catch (InvalidStateException e) {
+ assertTrue(e.getMessage().contains("Problem with instantiation of Modifier class"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ // restore correct values for the modified type (if not then other test
+ // might fail...)
+ Field field = typeToModify.getClass().getDeclaredField("clazz");
+ field.setAccessible(true);
+ field.set(typeToModify, clazz);
+ }
+ }
+
+ @Test
+ public void testCreateModifierForStringType2() throws Exception {
+ try {
+ utils.createModifierForStringType("unjkType", null);
+ fail("Exceptione expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Unknown modifier type"));
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/OperatorTypeTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/OperatorTypeTest.java
index b8f6865acf..51c5880ba5 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/OperatorTypeTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/OperatorTypeTest.java
@@ -1,31 +1,31 @@
-package lcsb.mapviewer.converter.model.celldesigner.types;
-
-import static org.junit.Assert.*;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class OperatorTypeTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void test() {
- for (OperatorType type : OperatorType.values()) {
- assertNotNull(OperatorType.valueOf(type.toString()));
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.types;
+
+import static org.junit.Assert.*;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class OperatorTypeTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void test() {
+ for (OperatorType type : OperatorType.values()) {
+ assertNotNull(OperatorType.valueOf(type.toString()));
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/OperatorTypeUtilsTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/OperatorTypeUtilsTest.java
index a0cfa67eb8..0da1a339e7 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/OperatorTypeUtilsTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/OperatorTypeUtilsTest.java
@@ -1,111 +1,111 @@
-package lcsb.mapviewer.converter.model.celldesigner.types;
-
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.lang.reflect.Field;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.reaction.NodeOperator;
-
-public class OperatorTypeUtilsTest {
-
- OperatorTypeUtils utils = new OperatorTypeUtils();
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetUnknownOperatorTypeForClazz() {
-
- OperatorType result = utils
- .getOperatorTypeForClazz(Mockito.mock(NodeOperator.class, Mockito.CALLS_REAL_METHODS).getClass());
-
- assertNull(result);
- }
-
- @Test
- public void testGetUnkownOperatorTypeForStringType() {
- OperatorType result = utils.getOperatorTypeForStringType("unknown");
-
- assertNull(result);
- }
-
- @Test
- public void testGetUnknownStringTypeByOperator() {
-
- String result = utils.getStringTypeByOperator(Mockito.mock(NodeOperator.class, Mockito.CALLS_REAL_METHODS));
-
- assertNull(result);
- }
-
- @Test
- public void testCreateUnknownModifierForStringType() {
- try {
- utils.createModifierForStringType("blabla");
- fail("Exceptione expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Unknown modifier type"));
- }
- }
-
- @Test
- public void testCreateInvalidModifierForStringType() throws Exception {
- // artificial implementation of Modifier that is invalid
- class InvalidModifier extends Modifier {
- private static final long serialVersionUID = 1L;
-
- @SuppressWarnings("unused")
- public InvalidModifier() {
- throw new NotImplementedException();
- }
- }
-
- // mopdify one of the elements of OperatorType so it will have invalid
- // implementation
- OperatorType typeToModify = OperatorType.AND_OPERATOR_STRING;
- Class<? extends NodeOperator> clazz = typeToModify.getClazz();
-
- try {
- Field field = typeToModify.getClass().getDeclaredField("clazz");
- field.setAccessible(true);
- field.set(typeToModify, InvalidModifier.class);
-
- // and check if we catch properly information about problematic
- // implementation
- utils.createModifierForStringType(typeToModify.getStringName());
- fail("Exceptione expected");
- } catch (InvalidStateException e) {
- assertTrue(e.getMessage().contains("Problem with instantiation of NodeOperator class"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- // restore correct values for the modified type (if not then other test
- // might fail...)
- Field field = typeToModify.getClass().getDeclaredField("clazz");
- field.setAccessible(true);
- field.set(typeToModify, clazz);
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.types;
+
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.lang.reflect.Field;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.reaction.NodeOperator;
+
+public class OperatorTypeUtilsTest {
+
+ OperatorTypeUtils utils = new OperatorTypeUtils();
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetUnknownOperatorTypeForClazz() {
+
+ OperatorType result = utils
+ .getOperatorTypeForClazz(Mockito.mock(NodeOperator.class, Mockito.CALLS_REAL_METHODS).getClass());
+
+ assertNull(result);
+ }
+
+ @Test
+ public void testGetUnkownOperatorTypeForStringType() {
+ OperatorType result = utils.getOperatorTypeForStringType("unknown");
+
+ assertNull(result);
+ }
+
+ @Test
+ public void testGetUnknownStringTypeByOperator() {
+
+ String result = utils.getStringTypeByOperator(Mockito.mock(NodeOperator.class, Mockito.CALLS_REAL_METHODS));
+
+ assertNull(result);
+ }
+
+ @Test
+ public void testCreateUnknownModifierForStringType() {
+ try {
+ utils.createModifierForStringType("blabla");
+ fail("Exceptione expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Unknown modifier type"));
+ }
+ }
+
+ @Test
+ public void testCreateInvalidModifierForStringType() throws Exception {
+ // artificial implementation of Modifier that is invalid
+ class InvalidModifier extends Modifier {
+ private static final long serialVersionUID = 1L;
+
+ @SuppressWarnings("unused")
+ public InvalidModifier() {
+ throw new NotImplementedException();
+ }
+ }
+
+ // mopdify one of the elements of OperatorType so it will have invalid
+ // implementation
+ OperatorType typeToModify = OperatorType.AND_OPERATOR_STRING;
+ Class<? extends NodeOperator> clazz = typeToModify.getClazz();
+
+ try {
+ Field field = typeToModify.getClass().getDeclaredField("clazz");
+ field.setAccessible(true);
+ field.set(typeToModify, InvalidModifier.class);
+
+ // and check if we catch properly information about problematic
+ // implementation
+ utils.createModifierForStringType(typeToModify.getStringName());
+ fail("Exceptione expected");
+ } catch (InvalidStateException e) {
+ assertTrue(e.getMessage().contains("Problem with instantiation of NodeOperator class"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ // restore correct values for the modified type (if not then other test
+ // might fail...)
+ Field field = typeToModify.getClass().getDeclaredField("clazz");
+ field.setAccessible(true);
+ field.set(typeToModify, clazz);
+ }
+ }
+
+}
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlConverter.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlConverter.java
index 344454f9cf..3618c14e95 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlConverter.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlConverter.java
@@ -1,84 +1,84 @@
-/**
- *
- */
-package lcsb.mapviewer.converter.model.sbgnml;
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-
-import javax.xml.bind.JAXBException;
-
-import lcsb.mapviewer.common.MimeType;
-import lcsb.mapviewer.converter.ConverterException;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.IConverter;
-import lcsb.mapviewer.converter.InvalidInputDataExecption;
-import lcsb.mapviewer.model.map.InconsistentModelException;
-import lcsb.mapviewer.model.map.model.Model;
-
-import org.sbgn.SbgnUtil;
-import org.sbgn.bindings.Sbgn;
-
-/**
- * @author Michał Kuźma
- *
- */
-public class SbgnmlXmlConverter implements IConverter {
-
- @Override
- public Model createModel(ConverterParams params) throws InvalidInputDataExecption {
- SbgnmlXmlParser parser = new SbgnmlXmlParser();
- return parser.createModel(params);
- }
-
- @Override
- public InputStream exportModelToInputStream(Model model) throws InconsistentModelException, ConverterException {
- SbgnmlXmlExporter exporter = new SbgnmlXmlExporter();
- Sbgn exportedData = exporter.toSbgnml(model);
- File tempFile;
- try {
- tempFile = File.createTempFile("sbgnmlExportTempFile", ".tmp");
- SbgnUtil.writeToFile(exportedData, tempFile);
- InputStream result = new FileInputStream(tempFile);
- return result;
- } catch (IOException e) {
- throw new ConverterException(e);
- } catch (JAXBException e) {
- throw new ConverterException(e);
- }
- }
-
- @Override
- public File exportModelToFile(Model model, String filePath) throws InconsistentModelException, ConverterException {
- SbgnmlXmlExporter exporter = new SbgnmlXmlExporter();
- Sbgn exportedData = exporter.toSbgnml(model);
- File exportedFile = new File(filePath);
- if (exportedFile.getParentFile() != null) {
- exportedFile.getParentFile().mkdirs();
- }
- try {
- SbgnUtil.writeToFile(exportedData, exportedFile);
- } catch (JAXBException e) {
- throw new ConverterException(e);
- }
- return exportedFile;
- }
-
- @Override
- public String getCommonName() {
- return "SBGN-ML";
- }
-
- @Override
- public MimeType getMimeType() {
- return MimeType.TEXT;
- }
-
- @Override
- public String getFileExtension() {
- return "sbgn";
- }
-
-}
+/**
+ *
+ */
+package lcsb.mapviewer.converter.model.sbgnml;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+
+import javax.xml.bind.JAXBException;
+
+import lcsb.mapviewer.common.MimeType;
+import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.model.Model;
+
+import org.sbgn.SbgnUtil;
+import org.sbgn.bindings.Sbgn;
+
+/**
+ * @author Michał Kuźma
+ *
+ */
+public class SbgnmlXmlConverter implements IConverter {
+
+ @Override
+ public Model createModel(ConverterParams params) throws InvalidInputDataExecption {
+ SbgnmlXmlParser parser = new SbgnmlXmlParser();
+ return parser.createModel(params);
+ }
+
+ @Override
+ public InputStream exportModelToInputStream(Model model) throws InconsistentModelException, ConverterException {
+ SbgnmlXmlExporter exporter = new SbgnmlXmlExporter();
+ Sbgn exportedData = exporter.toSbgnml(model);
+ File tempFile;
+ try {
+ tempFile = File.createTempFile("sbgnmlExportTempFile", ".tmp");
+ SbgnUtil.writeToFile(exportedData, tempFile);
+ InputStream result = new FileInputStream(tempFile);
+ return result;
+ } catch (IOException e) {
+ throw new ConverterException(e);
+ } catch (JAXBException e) {
+ throw new ConverterException(e);
+ }
+ }
+
+ @Override
+ public File exportModelToFile(Model model, String filePath) throws InconsistentModelException, ConverterException {
+ SbgnmlXmlExporter exporter = new SbgnmlXmlExporter();
+ Sbgn exportedData = exporter.toSbgnml(model);
+ File exportedFile = new File(filePath);
+ if (exportedFile.getParentFile() != null) {
+ exportedFile.getParentFile().mkdirs();
+ }
+ try {
+ SbgnUtil.writeToFile(exportedData, exportedFile);
+ } catch (JAXBException e) {
+ throw new ConverterException(e);
+ }
+ return exportedFile;
+ }
+
+ @Override
+ public String getCommonName() {
+ return "SBGN-ML";
+ }
+
+ @Override
+ public MimeType getMimeType() {
+ return MimeType.TEXT;
+ }
+
+ @Override
+ public String getFileExtension() {
+ return "sbgn";
+ }
+
+}
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/console/SbgnmlConsoleConverter.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/console/SbgnmlConsoleConverter.java
index dd0b751b04..18466ee85c 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/console/SbgnmlConsoleConverter.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/console/SbgnmlConsoleConverter.java
@@ -1,120 +1,120 @@
-package lcsb.mapviewer.converter.model.sbgnml.console;
-
-import java.io.FileNotFoundException;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.IConverter;
-import lcsb.mapviewer.converter.InvalidInputDataExecption;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter;
-import lcsb.mapviewer.converter.model.sbgnml.console.gui.GraphicalInterface;
-import lcsb.mapviewer.model.map.model.Model;
-
-/**
- * This class is entry point for console tool to convert data from CellDesigner
- * file to SBGN-ML format and back.
- *
- * @author Michał Kuźma
- *
- */
-public class SbgnmlConsoleConverter {
-
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(SbgnmlConsoleConverter.class.getName());
-
- /**
- * Options from the input.
- */
- private SbgnmlRunOptions inputOptions;
-
- /**
- * Default constructor.
- *
- * @param args
- * parameters with which the program was run
- */
- public SbgnmlConsoleConverter(String[] args) {
- inputOptions = new SbgnmlRunOptions(args);
- }
-
- /**
- * Main entry point to the program.
- *
- * @param args
- * parameters with which the program was run
- */
- public static void main(String[] args) {
- SbgnmlConsoleConverter main = new SbgnmlConsoleConverter(args);
- try {
- main.run();
- } catch (Exception e) {
- main.logger.error(e, e);
- }
- }
-
- /**
- * Method used to convert data from one file format to another.
- *
- * @param inputFilename
- * path to the input file
- * @param outputFilename
- * path to the output file
- * @param reversed
- * true if conversion should be done from CellDesigner to SBGN-ML
- * file
- * @throws InvalidInputDataExecption
- * thrown when there is a problem with conversion
- */
- public static void convert(String inputFilename, String outputFilename, boolean reversed) throws InvalidInputDataExecption {
- IConverter parser;
- IConverter exporter;
- if (reversed) {
- parser = new CellDesignerXmlParser();
- exporter = new SbgnmlXmlConverter();
- } else {
- parser = new SbgnmlXmlConverter();
- exporter = new CellDesignerXmlParser();
- }
-
- Model model;
- try {
- model = parser.createModel(new ConverterParams().filename(inputFilename));
- } catch (FileNotFoundException e) {
- throw new InvalidInputDataExecption("Problem with input file: " + inputFilename, e);
- }
-
- try {
- exporter.exportModelToFile(model, outputFilename);
- } catch (Exception e) {
- throw new InvalidInputDataExecption("Problem with output file: " + outputFilename, e);
- }
- }
-
- /**
- * This method transform {@link #inputOptions input data}.
- *
- * @throws InvalidInputDataExecption
- * thrown when the input data are invalid
- */
- private void run() throws InvalidInputDataExecption {
- if (inputOptions.noOptionsGiven()) {
- GraphicalInterface gui = new GraphicalInterface();
- gui.execute();
- } else {
- if (!inputOptions.isValidInput() || inputOptions.isHelpOption()) {
- if (!inputOptions.isValidInput()) {
- logger.warn("Invalid input data");
- }
- inputOptions.printHelp();
- } else {
- logger.debug("Running...");
-
- convert(inputOptions.getInputFilename(), inputOptions.getOutputFilename(), inputOptions.isReversedOption());
- }
- }
- }
-}
+package lcsb.mapviewer.converter.model.sbgnml.console;
+
+import java.io.FileNotFoundException;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter;
+import lcsb.mapviewer.converter.model.sbgnml.console.gui.GraphicalInterface;
+import lcsb.mapviewer.model.map.model.Model;
+
+/**
+ * This class is entry point for console tool to convert data from CellDesigner
+ * file to SBGN-ML format and back.
+ *
+ * @author Michał Kuźma
+ *
+ */
+public class SbgnmlConsoleConverter {
+
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(SbgnmlConsoleConverter.class.getName());
+
+ /**
+ * Options from the input.
+ */
+ private SbgnmlRunOptions inputOptions;
+
+ /**
+ * Default constructor.
+ *
+ * @param args
+ * parameters with which the program was run
+ */
+ public SbgnmlConsoleConverter(String[] args) {
+ inputOptions = new SbgnmlRunOptions(args);
+ }
+
+ /**
+ * Main entry point to the program.
+ *
+ * @param args
+ * parameters with which the program was run
+ */
+ public static void main(String[] args) {
+ SbgnmlConsoleConverter main = new SbgnmlConsoleConverter(args);
+ try {
+ main.run();
+ } catch (Exception e) {
+ main.logger.error(e, e);
+ }
+ }
+
+ /**
+ * Method used to convert data from one file format to another.
+ *
+ * @param inputFilename
+ * path to the input file
+ * @param outputFilename
+ * path to the output file
+ * @param reversed
+ * true if conversion should be done from CellDesigner to SBGN-ML
+ * file
+ * @throws InvalidInputDataExecption
+ * thrown when there is a problem with conversion
+ */
+ public static void convert(String inputFilename, String outputFilename, boolean reversed) throws InvalidInputDataExecption {
+ IConverter parser;
+ IConverter exporter;
+ if (reversed) {
+ parser = new CellDesignerXmlParser();
+ exporter = new SbgnmlXmlConverter();
+ } else {
+ parser = new SbgnmlXmlConverter();
+ exporter = new CellDesignerXmlParser();
+ }
+
+ Model model;
+ try {
+ model = parser.createModel(new ConverterParams().filename(inputFilename));
+ } catch (FileNotFoundException e) {
+ throw new InvalidInputDataExecption("Problem with input file: " + inputFilename, e);
+ }
+
+ try {
+ exporter.exportModelToFile(model, outputFilename);
+ } catch (Exception e) {
+ throw new InvalidInputDataExecption("Problem with output file: " + outputFilename, e);
+ }
+ }
+
+ /**
+ * This method transform {@link #inputOptions input data}.
+ *
+ * @throws InvalidInputDataExecption
+ * thrown when the input data are invalid
+ */
+ private void run() throws InvalidInputDataExecption {
+ if (inputOptions.noOptionsGiven()) {
+ GraphicalInterface gui = new GraphicalInterface();
+ gui.execute();
+ } else {
+ if (!inputOptions.isValidInput() || inputOptions.isHelpOption()) {
+ if (!inputOptions.isValidInput()) {
+ logger.warn("Invalid input data");
+ }
+ inputOptions.printHelp();
+ } else {
+ logger.debug("Running...");
+
+ convert(inputOptions.getInputFilename(), inputOptions.getOutputFilename(), inputOptions.isReversedOption());
+ }
+ }
+ }
+}
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/console/SbgnmlRunOptions.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/console/SbgnmlRunOptions.java
index 33822ca578..3889115cfe 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/console/SbgnmlRunOptions.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/console/SbgnmlRunOptions.java
@@ -1,250 +1,250 @@
-package lcsb.mapviewer.converter.model.sbgnml.console;
-
-import org.apache.commons.cli.BasicParser;
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.HelpFormatter;
-import org.apache.commons.cli.Option;
-import org.apache.commons.cli.OptionBuilder;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.ParseException;
-import org.apache.log4j.Logger;
-
-/**
- * This class is used to parse and store input data for {@link SbgnmlConsoleConverter}
- * .
- *
- * @author Michał Kuźma
- *
- */
-public class SbgnmlRunOptions {
-
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(SbgnmlRunOptions.class.getName());
-
- /**
- * What is the abbreviation of help option.
- */
- private static final String HELP_OPTION = "h";
-
-
- /**
- * What is the abbreviation of output file option.
- */
- private static final String OUTPUT_OPTION = "o";
-
-
- /**
- * What is the abbreviation of input file option.
- */
- private static final String INPUT_OPTION = "i";
-
- /**
- * What is the abbreviation of reversed converter mode option (CellDesigner to SBGN-ML).
- */
- private static final String REVERSED_OPTION = "r";
-
- /**
- * Object with available input options.
- */
- private Options options;
-
- /**
- * What should be the command line to run the program.
- */
- private String commandLineRun = null;
-
- /**
- * Was the input valid?
- */
- private boolean validInput = false;
-
- /**
- * Data parsed from input.
- */
- private CommandLine commandLine;
-
- /**
- * Default constructor that parses data.
- *
- * @param args
- * parameters used to run the program
- */
- public SbgnmlRunOptions(String[] args) {
- options = new Options();
- options.addOption(createOption("input", INPUT_OPTION, true, "input-file", "input file"));
- options.addOption(createOption("output", OUTPUT_OPTION, true, "output-file", "converted output file"));
- OptionBuilder.isRequired(false);
- options.addOption(REVERSED_OPTION, false, "convert from CellDesigner to SBGN-ML");
- options.addOption(HELP_OPTION, false, "print this help menu");
-
- commandLineRun = "java -jar " + new java.io.File(SbgnmlConsoleConverter.class.getProtectionDomain().getCodeSource().getLocation().getPath()).getName()
- + " [options]";
-
- CommandLineParser parser = new BasicParser();
-
- try {
- validInput = true;
- commandLine = parser.parse(options, args);
- if (getInputFilename() == null || getOutputFilename() == null
- || (isReversedOption() && (!getInputFilename().endsWith(".xml") || !getOutputFilename().endsWith(".sbgn")))
- || (!isReversedOption() && (!getInputFilename().endsWith(".sbgn") || !getOutputFilename().endsWith(".xml")))) {
- validInput = false;
- }
- } catch (ParseException e) {
- validInput = false;
- logger.info(e.getMessage());
- }
-
- }
-
- /**
- * Creates new {@link Option} object.
- *
- * @param optionName
- * full name of the option
- * @param optionAbbreviation
- * abbreviation of the option
- * @param hasArgument
- * has the option argument
- * @param argumentName
- * name of the argument
- * @param description
- * description of the option
- * @return {@link Option} created from input values
- */
- private Option createOption(String optionName, String optionAbbreviation, boolean hasArgument, String argumentName, String description) {
- OptionBuilder.hasArg(hasArgument);
- if (hasArgument) {
- OptionBuilder.withArgName(argumentName);
- }
- OptionBuilder.withDescription(description);
- OptionBuilder.withLongOpt(optionName);
- return OptionBuilder.create(optionAbbreviation);
- }
-
- /**
- * @return the options
- * @see #options
- */
- public Options getOptions() {
- return options;
- }
-
- /**
- * @param options
- * the options to set
- * @see #options
- */
- public void setOptions(Options options) {
- this.options = options;
- }
-
- /**
- * @return the commandLineRun
- * @see #commandLineRun
- */
- public String getCommandLineRun() {
- return commandLineRun;
- }
-
- /**
- * @param commandLineRun
- * the commandLineRun to set
- * @see #commandLineRun
- */
- public void setCommandLineRun(String commandLineRun) {
- this.commandLineRun = commandLineRun;
- }
-
- /**
- * @return the validInput
- * @see #validInput
- */
- public boolean isValidInput() {
- return validInput;
- }
-
- /**
- * @param validInput
- * the validInput to set
- * @see #validInput
- */
- public void setValidInput(boolean validInput) {
- this.validInput = validInput;
- }
-
- /**
- * @return the commandLine
- * @see #commandLine
- */
- public CommandLine getCommandLine() {
- return commandLine;
- }
-
- /**
- * @param commandLine
- * the commandLine to set
- * @see #commandLine
- */
- public void setCommandLine(CommandLine commandLine) {
- this.commandLine = commandLine;
- }
-
- /**
- * Prints help to the console how to used the program (what parameters to put
- * and what are they used for).
- */
- public void printHelp() {
- HelpFormatter formatter = new HelpFormatter();
- formatter.printHelp(commandLineRun, options);
- }
-
- /**
- * Checks if {@link #HELP_OPTION} was selected in the input.
- *
- * @return <code>true</code> if {@link #HELP_OPTION} was selected,
- * <code>false</code> otherwise
- */
- public boolean isHelpOption() {
- return commandLine.hasOption(HELP_OPTION);
- }
-
- /**
- * Checks if {@link #REVERSED} was selected in the input.
- *
- * @return <code>true</code> if {@link #REVERSED_OPTION} was selected,
- * <code>false</code> otherwise
- */
- public boolean isReversedOption() {
- return commandLine.hasOption(REVERSED_OPTION);
- }
-
- /**
- * Returns name of the input file.
- *
- * @return name of the input file
- */
- public String getInputFilename() {
- return commandLine.getOptionValue(INPUT_OPTION);
- }
-
- /**
- * Returns name of the output file.
- *
- * @return name of the output file
- */
- public String getOutputFilename() {
- return commandLine.getOptionValue(OUTPUT_OPTION);
- }
-
- /**
- * Returns true if no options were given when executing application.
- * @return true if no options were given when executing application
- */
- public boolean noOptionsGiven() {
- return commandLine.getOptions().length == 0;
- }
-}
+package lcsb.mapviewer.converter.model.sbgnml.console;
+
+import org.apache.commons.cli.BasicParser;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.HelpFormatter;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.OptionBuilder;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
+import org.apache.log4j.Logger;
+
+/**
+ * This class is used to parse and store input data for {@link SbgnmlConsoleConverter}
+ * .
+ *
+ * @author Michał Kuźma
+ *
+ */
+public class SbgnmlRunOptions {
+
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(SbgnmlRunOptions.class.getName());
+
+ /**
+ * What is the abbreviation of help option.
+ */
+ private static final String HELP_OPTION = "h";
+
+
+ /**
+ * What is the abbreviation of output file option.
+ */
+ private static final String OUTPUT_OPTION = "o";
+
+
+ /**
+ * What is the abbreviation of input file option.
+ */
+ private static final String INPUT_OPTION = "i";
+
+ /**
+ * What is the abbreviation of reversed converter mode option (CellDesigner to SBGN-ML).
+ */
+ private static final String REVERSED_OPTION = "r";
+
+ /**
+ * Object with available input options.
+ */
+ private Options options;
+
+ /**
+ * What should be the command line to run the program.
+ */
+ private String commandLineRun = null;
+
+ /**
+ * Was the input valid?
+ */
+ private boolean validInput = false;
+
+ /**
+ * Data parsed from input.
+ */
+ private CommandLine commandLine;
+
+ /**
+ * Default constructor that parses data.
+ *
+ * @param args
+ * parameters used to run the program
+ */
+ public SbgnmlRunOptions(String[] args) {
+ options = new Options();
+ options.addOption(createOption("input", INPUT_OPTION, true, "input-file", "input file"));
+ options.addOption(createOption("output", OUTPUT_OPTION, true, "output-file", "converted output file"));
+ OptionBuilder.isRequired(false);
+ options.addOption(REVERSED_OPTION, false, "convert from CellDesigner to SBGN-ML");
+ options.addOption(HELP_OPTION, false, "print this help menu");
+
+ commandLineRun = "java -jar " + new java.io.File(SbgnmlConsoleConverter.class.getProtectionDomain().getCodeSource().getLocation().getPath()).getName()
+ + " [options]";
+
+ CommandLineParser parser = new BasicParser();
+
+ try {
+ validInput = true;
+ commandLine = parser.parse(options, args);
+ if (getInputFilename() == null || getOutputFilename() == null
+ || (isReversedOption() && (!getInputFilename().endsWith(".xml") || !getOutputFilename().endsWith(".sbgn")))
+ || (!isReversedOption() && (!getInputFilename().endsWith(".sbgn") || !getOutputFilename().endsWith(".xml")))) {
+ validInput = false;
+ }
+ } catch (ParseException e) {
+ validInput = false;
+ logger.info(e.getMessage());
+ }
+
+ }
+
+ /**
+ * Creates new {@link Option} object.
+ *
+ * @param optionName
+ * full name of the option
+ * @param optionAbbreviation
+ * abbreviation of the option
+ * @param hasArgument
+ * has the option argument
+ * @param argumentName
+ * name of the argument
+ * @param description
+ * description of the option
+ * @return {@link Option} created from input values
+ */
+ private Option createOption(String optionName, String optionAbbreviation, boolean hasArgument, String argumentName, String description) {
+ OptionBuilder.hasArg(hasArgument);
+ if (hasArgument) {
+ OptionBuilder.withArgName(argumentName);
+ }
+ OptionBuilder.withDescription(description);
+ OptionBuilder.withLongOpt(optionName);
+ return OptionBuilder.create(optionAbbreviation);
+ }
+
+ /**
+ * @return the options
+ * @see #options
+ */
+ public Options getOptions() {
+ return options;
+ }
+
+ /**
+ * @param options
+ * the options to set
+ * @see #options
+ */
+ public void setOptions(Options options) {
+ this.options = options;
+ }
+
+ /**
+ * @return the commandLineRun
+ * @see #commandLineRun
+ */
+ public String getCommandLineRun() {
+ return commandLineRun;
+ }
+
+ /**
+ * @param commandLineRun
+ * the commandLineRun to set
+ * @see #commandLineRun
+ */
+ public void setCommandLineRun(String commandLineRun) {
+ this.commandLineRun = commandLineRun;
+ }
+
+ /**
+ * @return the validInput
+ * @see #validInput
+ */
+ public boolean isValidInput() {
+ return validInput;
+ }
+
+ /**
+ * @param validInput
+ * the validInput to set
+ * @see #validInput
+ */
+ public void setValidInput(boolean validInput) {
+ this.validInput = validInput;
+ }
+
+ /**
+ * @return the commandLine
+ * @see #commandLine
+ */
+ public CommandLine getCommandLine() {
+ return commandLine;
+ }
+
+ /**
+ * @param commandLine
+ * the commandLine to set
+ * @see #commandLine
+ */
+ public void setCommandLine(CommandLine commandLine) {
+ this.commandLine = commandLine;
+ }
+
+ /**
+ * Prints help to the console how to used the program (what parameters to put
+ * and what are they used for).
+ */
+ public void printHelp() {
+ HelpFormatter formatter = new HelpFormatter();
+ formatter.printHelp(commandLineRun, options);
+ }
+
+ /**
+ * Checks if {@link #HELP_OPTION} was selected in the input.
+ *
+ * @return <code>true</code> if {@link #HELP_OPTION} was selected,
+ * <code>false</code> otherwise
+ */
+ public boolean isHelpOption() {
+ return commandLine.hasOption(HELP_OPTION);
+ }
+
+ /**
+ * Checks if {@link #REVERSED} was selected in the input.
+ *
+ * @return <code>true</code> if {@link #REVERSED_OPTION} was selected,
+ * <code>false</code> otherwise
+ */
+ public boolean isReversedOption() {
+ return commandLine.hasOption(REVERSED_OPTION);
+ }
+
+ /**
+ * Returns name of the input file.
+ *
+ * @return name of the input file
+ */
+ public String getInputFilename() {
+ return commandLine.getOptionValue(INPUT_OPTION);
+ }
+
+ /**
+ * Returns name of the output file.
+ *
+ * @return name of the output file
+ */
+ public String getOutputFilename() {
+ return commandLine.getOptionValue(OUTPUT_OPTION);
+ }
+
+ /**
+ * Returns true if no options were given when executing application.
+ * @return true if no options were given when executing application
+ */
+ public boolean noOptionsGiven() {
+ return commandLine.getOptions().length == 0;
+ }
+}
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/console/gui/GraphicalInterface.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/console/gui/GraphicalInterface.java
index fe0414321e..7fbddc4658 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/console/gui/GraphicalInterface.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/console/gui/GraphicalInterface.java
@@ -1,320 +1,320 @@
-package lcsb.mapviewer.converter.model.sbgnml.console.gui;
-
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.io.ByteArrayOutputStream;
-import java.io.FileDescriptor;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.PrintStream;
-import java.io.PrintWriter;
-
-import javax.swing.JButton;
-import javax.swing.JFileChooser;
-import javax.swing.JFrame;
-import javax.swing.JLabel;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JTextField;
-import javax.swing.filechooser.FileNameExtensionFilter;
-
-import lcsb.mapviewer.converter.InvalidInputDataExecption;
-import lcsb.mapviewer.converter.model.sbgnml.console.SbgnmlConsoleConverter;
-
-/**
- * Graphical User Interface for SBGN-ML, CellDesigner converter.
- **/
-public class GraphicalInterface {
-
- /**
- * Path of the input file.
- */
- private String szInputFilePath = null;
-
- /**
- * Path of the output file.
- */
- private String szOutputFilePath = null;
-
- /**
- * Path of the log file.
- */
- private String szLogsFilePath = null;
-
- /**
- * Should the conversion go from CellDesigner to SBGN-ML file.
- */
- private boolean cellDesigner2Sbgnml = false;
-
- /**
- * Input text with path to input file.
- */
- private JTextField jtfOpenFilePath;
-
- /**
- * Input text with path to output file.
- */
- private JTextField jtfSaveFilePath;
-
- /**
- * Input text with path to log file.
- */
- private JTextField jtfLogFilePath;
-
- /**
- * Button used for opening files.
- */
- private JButton btnOpenInput;
-
- /**
- * Button used for saving converted files.
- */
- private JButton btnSaveOutput;
-
- /**
- * Button used for saving log file.
- */
- private JButton btnLogsFile;
-
- /**
- * Button for staring conversion.
- */
- private JButton btnParse;
-
- /**
- * Button for closing application.
- */
- private JButton btnClose;
-
- /**
- * Label with copyrights.
- */
- private JLabel fundingLabel;
-
- /**
- * Launch the application.
- *
- * @param args
- */
- public void execute() {
- try {
- final JFrame frame = new JFrame("SBGN-ML to SBML Converter");
-
- JPanel panel = new JPanel();
-
- panel.setLayout(null);
-
- // CHECKSTYLE:OFF
- jtfOpenFilePath = new JTextField(70);
- jtfSaveFilePath = new JTextField(70);
- jtfLogFilePath = new JTextField(70);
-
- jtfOpenFilePath.setBounds(265, 5, 600, 28);
- jtfSaveFilePath.setBounds(265, 55, 600, 28);
- jtfLogFilePath.setBounds(265, 105, 600, 28);
-
- jtfLogFilePath.setEditable(false);
- jtfOpenFilePath.setEditable(false);
- jtfSaveFilePath.setEditable(false);
-
- btnOpenInput = new JButton();
- btnOpenInput.setBounds(10, 5, 218, 28);
- btnOpenInput.setText("Open Input File");
- btnOpenInput.addActionListener(createOpenButtonListener());
-
- btnSaveOutput = new JButton();
- btnSaveOutput.setBounds(10, 55, 218, 28);
- btnSaveOutput.setText("Save output file");
- btnSaveOutput.addActionListener(createSaveButtonListener());
-
- btnLogsFile = new JButton();
- btnLogsFile.setBounds(10, 105, 218, 28);
- btnLogsFile.setText("Save Model consistency logs");
- btnLogsFile.addActionListener(createSaveLogsListener());
-
- btnParse = new JButton();
- btnParse.setBounds(10, 205, 218, 28);
- btnParse.setText("Convert");
- btnParse.addActionListener(new ActionListener() {
- public void actionPerformed(ActionEvent e) {
- if (null == szInputFilePath) {
- JOptionPane.showMessageDialog(
- frame, "Error: No path for the input file! Press " + btnOpenInput.getText() + " button to load input file!", "No input file!",
- JOptionPane.ERROR_MESSAGE);
- }
-
- else if (null == szOutputFilePath) {
- JOptionPane.showMessageDialog(
- frame, "Error: No path for the output file! Press " + btnSaveOutput.getText() + " button to save output file!", "No output file path!",
- JOptionPane.ERROR_MESSAGE);
- }
-
- else {
- if (null == szLogsFilePath) {
- int reply = JOptionPane.showConfirmDialog(
- frame, "Warning: No path for the model consistency check logs file! Do you want to add it now?", "No model consistency check file path!",
- JOptionPane.YES_NO_OPTION);
-
- if (reply == JOptionPane.YES_OPTION) {
- JFileChooser fileChooser = new JFileChooser();
- fileChooser.setDialogTitle("Specify a file to save Logs");
-
- int userSelection = fileChooser.showSaveDialog(null);
-
- if (userSelection == JFileChooser.APPROVE_OPTION) {
- szLogsFilePath = fileChooser.getSelectedFile().getAbsolutePath();
- int iPathSize = szLogsFilePath.length();
- String strExtension = szLogsFilePath.substring(iPathSize - 4, iPathSize);
- if (!strExtension.toLowerCase().equals(".txt")) {
- szLogsFilePath = szLogsFilePath.concat(".txt");
- }
-
- jtfLogFilePath.setText(szLogsFilePath);
- }
- }
- }
-
- ByteArrayOutputStream baos = new ByteArrayOutputStream();
- System.setOut(new PrintStream(baos));
-
- try {
- SbgnmlConsoleConverter.convert(szInputFilePath, szOutputFilePath, cellDesigner2Sbgnml);
- } catch (InvalidInputDataExecption e1) {
- JOptionPane.showMessageDialog(frame, "Problems, when converting the file:\n" + e1.getMessage(), "Converter problem!", JOptionPane.ERROR_MESSAGE);
- return;
- }
-
- System.setOut(new PrintStream(new FileOutputStream(FileDescriptor.out)));
- if (null != szLogsFilePath) {
- PrintWriter logsFile = null;
- try {
- logsFile = new PrintWriter(szLogsFilePath);
- } catch (FileNotFoundException ex) {
- JOptionPane.showMessageDialog(frame, "Error: Couldn't open the logs file ", "Problems with opening logs file!", JOptionPane.ERROR_MESSAGE);
- }
- logsFile.println(baos.toString());
- logsFile.close();
-
- JOptionPane.showMessageDialog(
- frame, "Parsing finished: output file available at: " + szOutputFilePath
- + "\nIf anything went wrong, logs with all warnings can be found at: " + szLogsFilePath);
- } else {
- JOptionPane.showMessageDialog(frame, "Parsing finished: output file available at: " + szOutputFilePath);
- }
- }
- }
- });
-
- btnClose = new JButton();
- btnClose.setBounds(520, 205, 147, 28);
- btnClose.setText("Close");
- btnClose.addActionListener(new ActionListener() {
- public void actionPerformed(ActionEvent e) {
- frame.dispose();
- }
- });
-
- fundingLabel = new JLabel("@Copyright: EISBM - eTRIKS");
- fundingLabel.setBounds(700, 205, 300, 28);
-
- panel.add(btnOpenInput);
- panel.add(btnSaveOutput);
- panel.add(btnLogsFile);
- panel.add(btnParse);
- panel.add(btnClose);
-
- panel.add(jtfOpenFilePath);
- panel.add(jtfSaveFilePath);
- panel.add(jtfLogFilePath);
-
- frame.add(panel);
- frame.setSize(900, 280);
- frame.setLocationRelativeTo(null);
- frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
- frame.setVisible(true);
-
- // CHECKSTYLE:ON
- } catch (Exception e) {
- e.printStackTrace();
- }
- }
-
- /**
- * Creates listener to open dialog for saving logs.
- *
- * @return listener resposinble to open dialog for saving log file
- */
- public ActionListener createSaveLogsListener() {
- return new ActionListener() {
- public void actionPerformed(ActionEvent e) {
- JFileChooser fileChooser = new JFileChooser();
- fileChooser.setDialogTitle("Specify a file to save Logs");
-
- int userSelection = fileChooser.showSaveDialog(null);
-
- if (userSelection == JFileChooser.APPROVE_OPTION) {
- szLogsFilePath = fileChooser.getSelectedFile().getAbsolutePath();
- if (!szLogsFilePath.toLowerCase().endsWith(".txt")) {
- szLogsFilePath = szLogsFilePath.concat(".txt");
- }
-
- jtfLogFilePath.setText(szLogsFilePath);
- }
- }
- };
- }
-
- /**
- * Creates listener to open dialog for saving output.
- *
- * @return listener resposinble to open dialog for saving output
- */
- public ActionListener createSaveButtonListener() {
- return new ActionListener() {
- public void actionPerformed(ActionEvent e) {
- JFileChooser fileChooser = new JFileChooser();
- fileChooser.setDialogTitle("Specify a file to save");
- fileChooser.addChoosableFileFilter(new FileNameExtensionFilter("JSON Files", "json"));
- fileChooser.addChoosableFileFilter(new FileNameExtensionFilter("SBML Files", "xml"));
-
- int userSelection = fileChooser.showSaveDialog(null);
-
- if (userSelection == JFileChooser.APPROVE_OPTION) {
- szOutputFilePath = fileChooser.getSelectedFile().getAbsolutePath();
- jtfSaveFilePath.setText(szOutputFilePath);
- }
- }
- };
- }
-
- /**
- * Creates listener to open dialog for opening input file.
- *
- * @return listener resposinble to open dialog for input file
- */
- public ActionListener createOpenButtonListener() {
- return new ActionListener() {
- public void actionPerformed(ActionEvent e) {
- JFileChooser fileChooser = new JFileChooser();
- fileChooser.setDialogTitle("Open a file to parse");
- fileChooser.addChoosableFileFilter(new FileNameExtensionFilter("JSON Files", "json"));
- fileChooser.addChoosableFileFilter(new FileNameExtensionFilter("SBML Files", "xml"));
- int userSelection = fileChooser.showOpenDialog(null);
- if (userSelection == JFileChooser.APPROVE_OPTION) {
- szInputFilePath = fileChooser.getSelectedFile().getAbsolutePath();
- cellDesigner2Sbgnml = szInputFilePath.endsWith(".xml");
- jtfOpenFilePath.setText(szInputFilePath);
- szOutputFilePath = szInputFilePath.substring(0, szInputFilePath.lastIndexOf('.'));
- if (cellDesigner2Sbgnml) {
- szOutputFilePath = szOutputFilePath.concat("_converted.sbgn");
- } else {
- szOutputFilePath = szOutputFilePath.concat("_converted.xml");
- }
- jtfSaveFilePath.setText(szOutputFilePath);
- szLogsFilePath = szInputFilePath.substring(0, szInputFilePath.lastIndexOf('.')).concat("_logs.txt");
- jtfLogFilePath.setText(szLogsFilePath);
- }
- }
- };
- }
-}
+package lcsb.mapviewer.converter.model.sbgnml.console.gui;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.ByteArrayOutputStream;
+import java.io.FileDescriptor;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.PrintStream;
+import java.io.PrintWriter;
+
+import javax.swing.JButton;
+import javax.swing.JFileChooser;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+import javax.swing.filechooser.FileNameExtensionFilter;
+
+import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.model.sbgnml.console.SbgnmlConsoleConverter;
+
+/**
+ * Graphical User Interface for SBGN-ML, CellDesigner converter.
+ **/
+public class GraphicalInterface {
+
+ /**
+ * Path of the input file.
+ */
+ private String szInputFilePath = null;
+
+ /**
+ * Path of the output file.
+ */
+ private String szOutputFilePath = null;
+
+ /**
+ * Path of the log file.
+ */
+ private String szLogsFilePath = null;
+
+ /**
+ * Should the conversion go from CellDesigner to SBGN-ML file.
+ */
+ private boolean cellDesigner2Sbgnml = false;
+
+ /**
+ * Input text with path to input file.
+ */
+ private JTextField jtfOpenFilePath;
+
+ /**
+ * Input text with path to output file.
+ */
+ private JTextField jtfSaveFilePath;
+
+ /**
+ * Input text with path to log file.
+ */
+ private JTextField jtfLogFilePath;
+
+ /**
+ * Button used for opening files.
+ */
+ private JButton btnOpenInput;
+
+ /**
+ * Button used for saving converted files.
+ */
+ private JButton btnSaveOutput;
+
+ /**
+ * Button used for saving log file.
+ */
+ private JButton btnLogsFile;
+
+ /**
+ * Button for staring conversion.
+ */
+ private JButton btnParse;
+
+ /**
+ * Button for closing application.
+ */
+ private JButton btnClose;
+
+ /**
+ * Label with copyrights.
+ */
+ private JLabel fundingLabel;
+
+ /**
+ * Launch the application.
+ *
+ * @param args
+ */
+ public void execute() {
+ try {
+ final JFrame frame = new JFrame("SBGN-ML to SBML Converter");
+
+ JPanel panel = new JPanel();
+
+ panel.setLayout(null);
+
+ // CHECKSTYLE:OFF
+ jtfOpenFilePath = new JTextField(70);
+ jtfSaveFilePath = new JTextField(70);
+ jtfLogFilePath = new JTextField(70);
+
+ jtfOpenFilePath.setBounds(265, 5, 600, 28);
+ jtfSaveFilePath.setBounds(265, 55, 600, 28);
+ jtfLogFilePath.setBounds(265, 105, 600, 28);
+
+ jtfLogFilePath.setEditable(false);
+ jtfOpenFilePath.setEditable(false);
+ jtfSaveFilePath.setEditable(false);
+
+ btnOpenInput = new JButton();
+ btnOpenInput.setBounds(10, 5, 218, 28);
+ btnOpenInput.setText("Open Input File");
+ btnOpenInput.addActionListener(createOpenButtonListener());
+
+ btnSaveOutput = new JButton();
+ btnSaveOutput.setBounds(10, 55, 218, 28);
+ btnSaveOutput.setText("Save output file");
+ btnSaveOutput.addActionListener(createSaveButtonListener());
+
+ btnLogsFile = new JButton();
+ btnLogsFile.setBounds(10, 105, 218, 28);
+ btnLogsFile.setText("Save Model consistency logs");
+ btnLogsFile.addActionListener(createSaveLogsListener());
+
+ btnParse = new JButton();
+ btnParse.setBounds(10, 205, 218, 28);
+ btnParse.setText("Convert");
+ btnParse.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ if (null == szInputFilePath) {
+ JOptionPane.showMessageDialog(
+ frame, "Error: No path for the input file! Press " + btnOpenInput.getText() + " button to load input file!", "No input file!",
+ JOptionPane.ERROR_MESSAGE);
+ }
+
+ else if (null == szOutputFilePath) {
+ JOptionPane.showMessageDialog(
+ frame, "Error: No path for the output file! Press " + btnSaveOutput.getText() + " button to save output file!", "No output file path!",
+ JOptionPane.ERROR_MESSAGE);
+ }
+
+ else {
+ if (null == szLogsFilePath) {
+ int reply = JOptionPane.showConfirmDialog(
+ frame, "Warning: No path for the model consistency check logs file! Do you want to add it now?", "No model consistency check file path!",
+ JOptionPane.YES_NO_OPTION);
+
+ if (reply == JOptionPane.YES_OPTION) {
+ JFileChooser fileChooser = new JFileChooser();
+ fileChooser.setDialogTitle("Specify a file to save Logs");
+
+ int userSelection = fileChooser.showSaveDialog(null);
+
+ if (userSelection == JFileChooser.APPROVE_OPTION) {
+ szLogsFilePath = fileChooser.getSelectedFile().getAbsolutePath();
+ int iPathSize = szLogsFilePath.length();
+ String strExtension = szLogsFilePath.substring(iPathSize - 4, iPathSize);
+ if (!strExtension.toLowerCase().equals(".txt")) {
+ szLogsFilePath = szLogsFilePath.concat(".txt");
+ }
+
+ jtfLogFilePath.setText(szLogsFilePath);
+ }
+ }
+ }
+
+ ByteArrayOutputStream baos = new ByteArrayOutputStream();
+ System.setOut(new PrintStream(baos));
+
+ try {
+ SbgnmlConsoleConverter.convert(szInputFilePath, szOutputFilePath, cellDesigner2Sbgnml);
+ } catch (InvalidInputDataExecption e1) {
+ JOptionPane.showMessageDialog(frame, "Problems, when converting the file:\n" + e1.getMessage(), "Converter problem!", JOptionPane.ERROR_MESSAGE);
+ return;
+ }
+
+ System.setOut(new PrintStream(new FileOutputStream(FileDescriptor.out)));
+ if (null != szLogsFilePath) {
+ PrintWriter logsFile = null;
+ try {
+ logsFile = new PrintWriter(szLogsFilePath);
+ } catch (FileNotFoundException ex) {
+ JOptionPane.showMessageDialog(frame, "Error: Couldn't open the logs file ", "Problems with opening logs file!", JOptionPane.ERROR_MESSAGE);
+ }
+ logsFile.println(baos.toString());
+ logsFile.close();
+
+ JOptionPane.showMessageDialog(
+ frame, "Parsing finished: output file available at: " + szOutputFilePath
+ + "\nIf anything went wrong, logs with all warnings can be found at: " + szLogsFilePath);
+ } else {
+ JOptionPane.showMessageDialog(frame, "Parsing finished: output file available at: " + szOutputFilePath);
+ }
+ }
+ }
+ });
+
+ btnClose = new JButton();
+ btnClose.setBounds(520, 205, 147, 28);
+ btnClose.setText("Close");
+ btnClose.addActionListener(new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ frame.dispose();
+ }
+ });
+
+ fundingLabel = new JLabel("@Copyright: EISBM - eTRIKS");
+ fundingLabel.setBounds(700, 205, 300, 28);
+
+ panel.add(btnOpenInput);
+ panel.add(btnSaveOutput);
+ panel.add(btnLogsFile);
+ panel.add(btnParse);
+ panel.add(btnClose);
+
+ panel.add(jtfOpenFilePath);
+ panel.add(jtfSaveFilePath);
+ panel.add(jtfLogFilePath);
+
+ frame.add(panel);
+ frame.setSize(900, 280);
+ frame.setLocationRelativeTo(null);
+ frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+ frame.setVisible(true);
+
+ // CHECKSTYLE:ON
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+
+ /**
+ * Creates listener to open dialog for saving logs.
+ *
+ * @return listener resposinble to open dialog for saving log file
+ */
+ public ActionListener createSaveLogsListener() {
+ return new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ JFileChooser fileChooser = new JFileChooser();
+ fileChooser.setDialogTitle("Specify a file to save Logs");
+
+ int userSelection = fileChooser.showSaveDialog(null);
+
+ if (userSelection == JFileChooser.APPROVE_OPTION) {
+ szLogsFilePath = fileChooser.getSelectedFile().getAbsolutePath();
+ if (!szLogsFilePath.toLowerCase().endsWith(".txt")) {
+ szLogsFilePath = szLogsFilePath.concat(".txt");
+ }
+
+ jtfLogFilePath.setText(szLogsFilePath);
+ }
+ }
+ };
+ }
+
+ /**
+ * Creates listener to open dialog for saving output.
+ *
+ * @return listener resposinble to open dialog for saving output
+ */
+ public ActionListener createSaveButtonListener() {
+ return new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ JFileChooser fileChooser = new JFileChooser();
+ fileChooser.setDialogTitle("Specify a file to save");
+ fileChooser.addChoosableFileFilter(new FileNameExtensionFilter("JSON Files", "json"));
+ fileChooser.addChoosableFileFilter(new FileNameExtensionFilter("SBML Files", "xml"));
+
+ int userSelection = fileChooser.showSaveDialog(null);
+
+ if (userSelection == JFileChooser.APPROVE_OPTION) {
+ szOutputFilePath = fileChooser.getSelectedFile().getAbsolutePath();
+ jtfSaveFilePath.setText(szOutputFilePath);
+ }
+ }
+ };
+ }
+
+ /**
+ * Creates listener to open dialog for opening input file.
+ *
+ * @return listener resposinble to open dialog for input file
+ */
+ public ActionListener createOpenButtonListener() {
+ return new ActionListener() {
+ public void actionPerformed(ActionEvent e) {
+ JFileChooser fileChooser = new JFileChooser();
+ fileChooser.setDialogTitle("Open a file to parse");
+ fileChooser.addChoosableFileFilter(new FileNameExtensionFilter("JSON Files", "json"));
+ fileChooser.addChoosableFileFilter(new FileNameExtensionFilter("SBML Files", "xml"));
+ int userSelection = fileChooser.showOpenDialog(null);
+ if (userSelection == JFileChooser.APPROVE_OPTION) {
+ szInputFilePath = fileChooser.getSelectedFile().getAbsolutePath();
+ cellDesigner2Sbgnml = szInputFilePath.endsWith(".xml");
+ jtfOpenFilePath.setText(szInputFilePath);
+ szOutputFilePath = szInputFilePath.substring(0, szInputFilePath.lastIndexOf('.'));
+ if (cellDesigner2Sbgnml) {
+ szOutputFilePath = szOutputFilePath.concat("_converted.sbgn");
+ } else {
+ szOutputFilePath = szOutputFilePath.concat("_converted.xml");
+ }
+ jtfSaveFilePath.setText(szOutputFilePath);
+ szLogsFilePath = szInputFilePath.substring(0, szInputFilePath.lastIndexOf('.')).concat("_logs.txt");
+ jtfLogFilePath.setText(szLogsFilePath);
+ }
+ }
+ };
+ }
+}
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/console/gui/package-info.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/console/gui/package-info.java
index f8bc6639ee..008594e788 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/console/gui/package-info.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/console/gui/package-info.java
@@ -1,8 +1,8 @@
-/**
- *
- */
-/**
- * @author Michał Kuźma
- *
- */
+/**
+ *
+ */
+/**
+ * @author Michał Kuźma
+ *
+ */
package lcsb.mapviewer.converter.model.sbgnml.console.gui;
\ No newline at end of file
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/console/package-info.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/console/package-info.java
index a9546d7b6d..5e70c83f6b 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/console/package-info.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/console/package-info.java
@@ -1,5 +1,5 @@
-/**
- * Package where console application interface for CellDesigner-SBGNML
- * transformation is implemented.
- */
+/**
+ * Package where console application interface for CellDesigner-SBGNML
+ * transformation is implemented.
+ */
package lcsb.mapviewer.converter.model.sbgnml.console;
\ No newline at end of file
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/package-info.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/package-info.java
index 4f4bf039cf..a2833a7d9d 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/package-info.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/package-info.java
@@ -1,4 +1,4 @@
-/**
- * lcsb.mapviewer.converter.model.sbgnml is the main package of SBGN-ML converter.
- */
+/**
+ * lcsb.mapviewer.converter.model.sbgnml is the main package of SBGN-ML converter.
+ */
package lcsb.mapviewer.converter.model.sbgnml;
\ No newline at end of file
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/structures/Process.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/structures/Process.java
index 2ac0bfca5a..1a12c70805 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/structures/Process.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/structures/Process.java
@@ -1,237 +1,237 @@
-package lcsb.mapviewer.converter.model.sbgnml.structures;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.stream.Collectors;
-
-import org.sbgn.bindings.Arc;
-import org.sbgn.bindings.Glyph;
-import org.sbgn.bindings.Port;
-
-import lcsb.mapviewer.common.comparator.DoubleComparator;
-
-/**
- * This class represents a reaction in the map.
- *
- * @author Michał Kuźma
- *
- */
-public class Process {
-
- /**
- * Central point of a reaction represented by a glyph.
- */
- private Glyph centralPoint;
-
- /**
- * Product arcs.
- */
- private List<Arc> productArcs = new ArrayList<Arc>();
-
- /**
- * Reagent arcs.
- */
- private List<Arc> reagentArcs = new ArrayList<Arc>();
-
- /**
- * Modifier arcs.
- */
- private List<Arc> modifierArcs = new ArrayList<Arc>();
-
- /**
- * Port for all reagents.
- */
- private Port reagentsPort;
-
- /**
- * Port for all products.
- */
- private Port productsPort;
-
- /**
- * Is the process reversible.
- */
- private boolean reversible;
-
- /**
- * Default constructor.
- *
- * @param centralPoint
- * central point of the process
- */
- public Process(Glyph centralPoint) {
- this.reversible = false;
- this.productsPort = null;
- this.reagentsPort = null;
- this.centralPoint = centralPoint;
- }
-
- /**
- * Adds a product arc to the process.
- *
- * @param a
- * the arc to be added
- */
- public void addProductArc(Arc a) {
- if (this.getCentralPoint().getPort().size() == 2) {
- double dx = a.getEnd().getX() - a.getStart().getX();
- double dy = a.getEnd().getY() - a.getStart().getY();
- double centralDx = this.getCentralPoint().getPort().get(0).getX() - this.getCentralPoint().getPort().get(1).getX();
- double centralDy = this.getCentralPoint().getPort().get(0).getY() - this.getCentralPoint().getPort().get(1).getY();
- DoubleComparator comparator = new DoubleComparator();
- if (comparator.compare(dy / dx, centralDy / centralDx) == 0) {
- productArcs.add(0, a);
- } else {
- productArcs.add(a);
- }
- } else {
- productArcs.add(a);
- }
- }
-
- /**
- * Adds a reagent arc to the process.
- *
- * @param a
- * the arc to be added
- */
- public void addReagentArc(Arc a) {
- if (this.getCentralPoint().getPort().size() == 2) {
- double dx = a.getEnd().getX() - a.getStart().getX();
- double dy = a.getEnd().getY() - a.getStart().getY();
- double centralDx = this.getCentralPoint().getPort().get(0).getX() - this.getCentralPoint().getPort().get(1).getX();
- double centralDy = this.getCentralPoint().getPort().get(0).getY() - this.getCentralPoint().getPort().get(1).getY();
- DoubleComparator comparator = new DoubleComparator();
- if (comparator.compare(dy / dx, centralDy / centralDx) == 0) {
- reagentArcs.add(0, a);
- } else {
- reagentArcs.add(a);
- }
- } else {
- reagentArcs.add(a);
- }
- }
-
- /**
- * Adds a influence arc to the process.
- *
- * @param a
- * the arc to be added
- */
- public void addInfluenceArc(Arc a) {
- modifierArcs.add(a);
- }
-
- /**
- * @return the reagentArcs
- * @see #reagentArcs
- */
- public List<Arc> getReagentArcs() {
- return reagentArcs;
- }
-
- /**
- * @return the productArcs
- * @see #productArcs
- */
- public List<Arc> getProductArcs() {
- return productArcs;
- }
-
- /**
- * @return the centralPoint
- * @see #centralPoint
- */
- public Glyph getCentralPoint() {
- return centralPoint;
- }
-
- /**
- * @param centralPoint
- * the centralPoint to set
- * @see #centralPoint
- */
- public void setCentralPoint(Glyph centralPoint) {
- this.centralPoint = centralPoint;
- }
-
- /**
- * @return the modifierArcs
- * @see #modifierArcs
- */
- public List<Arc> getModifierArcs() {
- return modifierArcs;
- }
-
- /**
- * @return the reagentsPort
- * @see #reagentsPort
- */
- public Port getReagentsPort() {
- return reagentsPort;
- }
-
- /**
- * @param reagentsPort
- * the reagentsPort to set
- * @see #reagentsPort
- */
- public void setReagentsPort(Port reagentsPort) {
- this.reagentsPort = reagentsPort;
- }
-
- /**
- * @return the productsPort
- * @see #productsPort
- */
- public Port getProductsPort() {
- return productsPort;
- }
-
- /**
- * @param productsPort
- * the productsPort to set
- * @see #productsPort
- */
- public void setProductsPort(Port productsPort) {
- this.productsPort = productsPort;
- }
-
- /**
- * @return the reversible
- * @see #reversible
- */
- public boolean isReversible() {
- return reversible;
- }
-
- /**
- * @param reversible
- * the reversible to set
- * @see #reversible
- */
- public void setReversible(boolean reversible) {
- this.reversible = reversible;
- }
-
- /**
- * Method used to retrieve product arcs in reversible process.
- *
- * @return list of product arcs
- */
- public List<Arc> getRevProductArcs() {
- List<Arc> result = productArcs.stream().filter(a -> a.getSource().equals(productsPort)).collect(Collectors.toList());
- return result;
- }
-
- /**
- * Method used to retrieve reagent arcs in reversible process.
- *
- * @return list of reagent arcs
- */
- public List<Arc> getRevReagentArcs() {
- List<Arc> result = productArcs.stream().filter(a -> a.getSource().equals(reagentsPort)).collect(Collectors.toList());
- return result;
- }
-
-}
+package lcsb.mapviewer.converter.model.sbgnml.structures;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import org.sbgn.bindings.Arc;
+import org.sbgn.bindings.Glyph;
+import org.sbgn.bindings.Port;
+
+import lcsb.mapviewer.common.comparator.DoubleComparator;
+
+/**
+ * This class represents a reaction in the map.
+ *
+ * @author Michał Kuźma
+ *
+ */
+public class Process {
+
+ /**
+ * Central point of a reaction represented by a glyph.
+ */
+ private Glyph centralPoint;
+
+ /**
+ * Product arcs.
+ */
+ private List<Arc> productArcs = new ArrayList<Arc>();
+
+ /**
+ * Reagent arcs.
+ */
+ private List<Arc> reagentArcs = new ArrayList<Arc>();
+
+ /**
+ * Modifier arcs.
+ */
+ private List<Arc> modifierArcs = new ArrayList<Arc>();
+
+ /**
+ * Port for all reagents.
+ */
+ private Port reagentsPort;
+
+ /**
+ * Port for all products.
+ */
+ private Port productsPort;
+
+ /**
+ * Is the process reversible.
+ */
+ private boolean reversible;
+
+ /**
+ * Default constructor.
+ *
+ * @param centralPoint
+ * central point of the process
+ */
+ public Process(Glyph centralPoint) {
+ this.reversible = false;
+ this.productsPort = null;
+ this.reagentsPort = null;
+ this.centralPoint = centralPoint;
+ }
+
+ /**
+ * Adds a product arc to the process.
+ *
+ * @param a
+ * the arc to be added
+ */
+ public void addProductArc(Arc a) {
+ if (this.getCentralPoint().getPort().size() == 2) {
+ double dx = a.getEnd().getX() - a.getStart().getX();
+ double dy = a.getEnd().getY() - a.getStart().getY();
+ double centralDx = this.getCentralPoint().getPort().get(0).getX() - this.getCentralPoint().getPort().get(1).getX();
+ double centralDy = this.getCentralPoint().getPort().get(0).getY() - this.getCentralPoint().getPort().get(1).getY();
+ DoubleComparator comparator = new DoubleComparator();
+ if (comparator.compare(dy / dx, centralDy / centralDx) == 0) {
+ productArcs.add(0, a);
+ } else {
+ productArcs.add(a);
+ }
+ } else {
+ productArcs.add(a);
+ }
+ }
+
+ /**
+ * Adds a reagent arc to the process.
+ *
+ * @param a
+ * the arc to be added
+ */
+ public void addReagentArc(Arc a) {
+ if (this.getCentralPoint().getPort().size() == 2) {
+ double dx = a.getEnd().getX() - a.getStart().getX();
+ double dy = a.getEnd().getY() - a.getStart().getY();
+ double centralDx = this.getCentralPoint().getPort().get(0).getX() - this.getCentralPoint().getPort().get(1).getX();
+ double centralDy = this.getCentralPoint().getPort().get(0).getY() - this.getCentralPoint().getPort().get(1).getY();
+ DoubleComparator comparator = new DoubleComparator();
+ if (comparator.compare(dy / dx, centralDy / centralDx) == 0) {
+ reagentArcs.add(0, a);
+ } else {
+ reagentArcs.add(a);
+ }
+ } else {
+ reagentArcs.add(a);
+ }
+ }
+
+ /**
+ * Adds a influence arc to the process.
+ *
+ * @param a
+ * the arc to be added
+ */
+ public void addInfluenceArc(Arc a) {
+ modifierArcs.add(a);
+ }
+
+ /**
+ * @return the reagentArcs
+ * @see #reagentArcs
+ */
+ public List<Arc> getReagentArcs() {
+ return reagentArcs;
+ }
+
+ /**
+ * @return the productArcs
+ * @see #productArcs
+ */
+ public List<Arc> getProductArcs() {
+ return productArcs;
+ }
+
+ /**
+ * @return the centralPoint
+ * @see #centralPoint
+ */
+ public Glyph getCentralPoint() {
+ return centralPoint;
+ }
+
+ /**
+ * @param centralPoint
+ * the centralPoint to set
+ * @see #centralPoint
+ */
+ public void setCentralPoint(Glyph centralPoint) {
+ this.centralPoint = centralPoint;
+ }
+
+ /**
+ * @return the modifierArcs
+ * @see #modifierArcs
+ */
+ public List<Arc> getModifierArcs() {
+ return modifierArcs;
+ }
+
+ /**
+ * @return the reagentsPort
+ * @see #reagentsPort
+ */
+ public Port getReagentsPort() {
+ return reagentsPort;
+ }
+
+ /**
+ * @param reagentsPort
+ * the reagentsPort to set
+ * @see #reagentsPort
+ */
+ public void setReagentsPort(Port reagentsPort) {
+ this.reagentsPort = reagentsPort;
+ }
+
+ /**
+ * @return the productsPort
+ * @see #productsPort
+ */
+ public Port getProductsPort() {
+ return productsPort;
+ }
+
+ /**
+ * @param productsPort
+ * the productsPort to set
+ * @see #productsPort
+ */
+ public void setProductsPort(Port productsPort) {
+ this.productsPort = productsPort;
+ }
+
+ /**
+ * @return the reversible
+ * @see #reversible
+ */
+ public boolean isReversible() {
+ return reversible;
+ }
+
+ /**
+ * @param reversible
+ * the reversible to set
+ * @see #reversible
+ */
+ public void setReversible(boolean reversible) {
+ this.reversible = reversible;
+ }
+
+ /**
+ * Method used to retrieve product arcs in reversible process.
+ *
+ * @return list of product arcs
+ */
+ public List<Arc> getRevProductArcs() {
+ List<Arc> result = productArcs.stream().filter(a -> a.getSource().equals(productsPort)).collect(Collectors.toList());
+ return result;
+ }
+
+ /**
+ * Method used to retrieve reagent arcs in reversible process.
+ *
+ * @return list of reagent arcs
+ */
+ public List<Arc> getRevReagentArcs() {
+ List<Arc> result = productArcs.stream().filter(a -> a.getSource().equals(reagentsPort)).collect(Collectors.toList());
+ return result;
+ }
+
+}
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/structures/package-info.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/structures/package-info.java
index 19b2356a37..b463f7a41a 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/structures/package-info.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/structures/package-info.java
@@ -1,4 +1,4 @@
-/**
- * lcsb.mapviewer.converter.model.sbgnml.structures is a group of additional structures used in the process of parsing SBGN-ML file.
- */
+/**
+ * lcsb.mapviewer.converter.model.sbgnml.structures is a group of additional structures used in the process of parsing SBGN-ML file.
+ */
package lcsb.mapviewer.converter.model.sbgnml.structures;
\ No newline at end of file
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/AllSbgnmlTests.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/AllSbgnmlTests.java
index 255c144623..dd9c78c762 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/AllSbgnmlTests.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/AllSbgnmlTests.java
@@ -1,17 +1,17 @@
-package lcsb.mapviewer.converter.model.sbgnml;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ CellDesigner2SbgnmlConversionTest.class, //
- CellDesignerToSbgnTest.class, //
- DbSerializationTest.class, //
- SbgnmlXmlExporterTest.class, //
- SbgnmlXmlParserTest.class, //
- SbgnmlXmlParserTest2.class, //
-})
-public class AllSbgnmlTests {
-
-}
+package lcsb.mapviewer.converter.model.sbgnml;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ CellDesigner2SbgnmlConversionTest.class, //
+ CellDesignerToSbgnTest.class, //
+ DbSerializationTest.class, //
+ SbgnmlXmlExporterTest.class, //
+ SbgnmlXmlParserTest.class, //
+ SbgnmlXmlParserTest2.class, //
+})
+public class AllSbgnmlTests {
+
+}
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesigner2SbgnmlConversionTest.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesigner2SbgnmlConversionTest.java
index e2a8401386..0dcf4d8818 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesigner2SbgnmlConversionTest.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesigner2SbgnmlConversionTest.java
@@ -1,90 +1,90 @@
-package lcsb.mapviewer.converter.model.sbgnml;
-
-import java.io.File;
-import java.io.IOException;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.util.ArrayList;
-import java.util.Collection;
-
-import org.apache.commons.io.FileUtils;
-import org.apache.log4j.Logger;
-import org.junit.Test;
-import org.junit.runner.RunWith;
-import org.junit.runners.Parameterized;
-import org.junit.runners.Parameterized.Parameters;
-
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.IConverter;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.model.Model;
-
-@RunWith(Parameterized.class)
-public class CellDesigner2SbgnmlConversionTest {
-
- private static Logger logger = Logger.getLogger(CellDesigner2SbgnmlConversionTest.class.getName());
-
- private Path testPath;
-
- public CellDesigner2SbgnmlConversionTest(Path testPath) {
- this.testPath = testPath;
- }
-
- @Parameters(name = "{index} : {0}")
- public static Collection<Object[]> data() throws IOException {
- Collection<Object[]> data = new ArrayList<>();
- Files.walk(Paths.get("../converter-CellDesigner/testFiles")).forEach(fPath -> {
- if (Files.isRegularFile(fPath) && fPath.toString().endsWith(".xml")&& fPath.toString().indexOf("invalid")==-1) {
- try {
- String tempPath = fPath.toString().substring(fPath.toString().indexOf("testFiles") + "testFiles".length() + 1);
- if (!tempPath.contains("_full")) {
- String content = FileUtils.readFileToString(fPath.toFile());
- if (content.indexOf("xmlns:celldesigner") >= 0) {
- data.add(new Object[] { fPath });
- }
- }
- } catch (Exception e) {
- throw new RuntimeException();
- }
- }
- });
- return data;
- }
-
- private void parseAndExport(Path testPath) throws Exception {
- IConverter cellDesignerConverter = new CellDesignerXmlParser();
- IConverter sbgnmlConverter = new SbgnmlXmlConverter();
-
- String testName = "";
- Path tempPath = testPath;
- while (!tempPath.getParent().toString().endsWith("testFiles")) {
- // Add parent folder to path
- tempPath = tempPath.getParent();
- testName = tempPath.getFileName().toString().concat("/").concat(testName);
- }
- testName = testName.concat(testPath.getFileName().toString().substring(0, testPath.getFileName().toString().indexOf(".xml")));
- Model model;
- try {
- model = cellDesignerConverter.createModel(new ConverterParams().filename("../converter-CellDesigner/testFiles/".concat(testName).concat(".xml")));
- } catch (Exception ex) {
- logger.warn("Problem encountered when parsing CellDesigner file: " + testName);
- return;
- }
-
- String outputFile = "testFiles/sbgnmlExporterTestFiles/fromCellDesigner/".concat(testName).concat(".sbgn");
- sbgnmlConverter.exportModelToFile(model, outputFile);
- new File(outputFile).delete();
- }
-
- @Test
- public void test() throws Exception {
- try {
- parseAndExport(testPath);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.sbgnml;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.Collection;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.log4j.Logger;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameters;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+
+@RunWith(Parameterized.class)
+public class CellDesigner2SbgnmlConversionTest {
+
+ private static Logger logger = Logger.getLogger(CellDesigner2SbgnmlConversionTest.class.getName());
+
+ private Path testPath;
+
+ public CellDesigner2SbgnmlConversionTest(Path testPath) {
+ this.testPath = testPath;
+ }
+
+ @Parameters(name = "{index} : {0}")
+ public static Collection<Object[]> data() throws IOException {
+ Collection<Object[]> data = new ArrayList<>();
+ Files.walk(Paths.get("../converter-CellDesigner/testFiles")).forEach(fPath -> {
+ if (Files.isRegularFile(fPath) && fPath.toString().endsWith(".xml")&& fPath.toString().indexOf("invalid")==-1) {
+ try {
+ String tempPath = fPath.toString().substring(fPath.toString().indexOf("testFiles") + "testFiles".length() + 1);
+ if (!tempPath.contains("_full")) {
+ String content = FileUtils.readFileToString(fPath.toFile());
+ if (content.indexOf("xmlns:celldesigner") >= 0) {
+ data.add(new Object[] { fPath });
+ }
+ }
+ } catch (Exception e) {
+ throw new RuntimeException();
+ }
+ }
+ });
+ return data;
+ }
+
+ private void parseAndExport(Path testPath) throws Exception {
+ IConverter cellDesignerConverter = new CellDesignerXmlParser();
+ IConverter sbgnmlConverter = new SbgnmlXmlConverter();
+
+ String testName = "";
+ Path tempPath = testPath;
+ while (!tempPath.getParent().toString().endsWith("testFiles")) {
+ // Add parent folder to path
+ tempPath = tempPath.getParent();
+ testName = tempPath.getFileName().toString().concat("/").concat(testName);
+ }
+ testName = testName.concat(testPath.getFileName().toString().substring(0, testPath.getFileName().toString().indexOf(".xml")));
+ Model model;
+ try {
+ model = cellDesignerConverter.createModel(new ConverterParams().filename("../converter-CellDesigner/testFiles/".concat(testName).concat(".xml")));
+ } catch (Exception ex) {
+ logger.warn("Problem encountered when parsing CellDesigner file: " + testName);
+ return;
+ }
+
+ String outputFile = "testFiles/sbgnmlExporterTestFiles/fromCellDesigner/".concat(testName).concat(".sbgn");
+ sbgnmlConverter.exportModelToFile(model, outputFile);
+ new File(outputFile).delete();
+ }
+
+ @Test
+ public void test() throws Exception {
+ try {
+ parseAndExport(testPath);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesignerToSbgnTest.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesignerToSbgnTest.java
index a711f585ac..bc4b09114b 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesignerToSbgnTest.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesignerToSbgnTest.java
@@ -1,62 +1,62 @@
-package lcsb.mapviewer.converter.model.sbgnml;
-
-import java.io.File;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.IConverter;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.model.Model;
-
-public class CellDesignerToSbgnTest {
- Logger logger = Logger.getLogger(CellDesignerToSbgnTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSample() throws Exception {
- try {
- IConverter converter = new CellDesignerXmlParser();
- IConverter converter2 = new SbgnmlXmlConverter();
-
- Model model;
- model = converter.createModel(new ConverterParams().filename("testFiles/cellDesigner/sample.xml"));
-
- String output = File.createTempFile("temp-sbgn-output", ".sbgn").getAbsolutePath();
- converter2.exportModelToFile(model, output);
- new File(output).delete();
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSample2() throws Exception {
- try {
- IConverter converter = new CellDesignerXmlParser();
- IConverter converter2 = new SbgnmlXmlConverter();
-
- Model model;
- model = converter.createModel(new ConverterParams().filename("testFiles/cellDesigner/bubbles.xml"));
-
- String output = File.createTempFile("temp-sbgn-output", ".sbgn").getAbsolutePath();
- converter2.exportModelToFile(model, output);
- new File(output).delete();
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.sbgnml;
+
+import java.io.File;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+
+public class CellDesignerToSbgnTest {
+ Logger logger = Logger.getLogger(CellDesignerToSbgnTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSample() throws Exception {
+ try {
+ IConverter converter = new CellDesignerXmlParser();
+ IConverter converter2 = new SbgnmlXmlConverter();
+
+ Model model;
+ model = converter.createModel(new ConverterParams().filename("testFiles/cellDesigner/sample.xml"));
+
+ String output = File.createTempFile("temp-sbgn-output", ".sbgn").getAbsolutePath();
+ converter2.exportModelToFile(model, output);
+ new File(output).delete();
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSample2() throws Exception {
+ try {
+ IConverter converter = new CellDesignerXmlParser();
+ IConverter converter2 = new SbgnmlXmlConverter();
+
+ Model model;
+ model = converter.createModel(new ConverterParams().filename("testFiles/cellDesigner/bubbles.xml"));
+
+ String output = File.createTempFile("temp-sbgn-output", ".sbgn").getAbsolutePath();
+ converter2.exportModelToFile(model, output);
+ new File(output).delete();
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java
index 450cf7a2aa..f11a593cbb 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java
@@ -1,69 +1,69 @@
-package lcsb.mapviewer.converter.model.sbgnml;
-
-import java.io.File;
-import java.io.IOException;
-import java.nio.file.Files;
-import java.nio.file.Paths;
-import java.util.ArrayList;
-import java.util.Collection;
-
-import org.apache.log4j.Logger;
-import org.junit.Test;
-import org.junit.runner.RunWith;
-import org.junit.runners.Parameterized;
-import org.junit.runners.Parameterized.Parameters;
-
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.IConverter;
-import lcsb.mapviewer.model.map.model.Model;
-
-@RunWith(Parameterized.class)
-public class SbgnmlXmlExporterTest {
-
- Logger logger = Logger.getLogger(SbgnmlXmlExporterTest.class.getName());
-
- private String testName;
-
- public SbgnmlXmlExporterTest(String testName) {
- this.testName = testName;
- }
-
- @Parameters(name = "{index} : {0}")
- public static Collection<Object[]> data() throws IOException {
- Collection<Object[]> data = new ArrayList<Object[]>();
- Files.walk(Paths.get("testFiles/sbgnmlParserTestFiles/sbgnmlFiles")).forEach(fPath -> {
- if (Files.isRegularFile(fPath) && fPath.toString().endsWith(".sbgn")) {
- String tName = fPath.getFileName().toString().substring(0, fPath.getFileName().toString().indexOf(".sbgn"));
- data.add(new Object[] { tName });
- }
- });
- return data;
- }
-
- private void parseAndExport(String testName) throws Exception {
- IConverter converter = new SbgnmlXmlConverter();
-
- Model model = converter.createModel(new ConverterParams().filename("testFiles/sbgnmlParserTestFiles/sbgnmlFiles/".concat(testName).concat(".sbgn")));
-
- converter.exportModelToFile(model, File.createTempFile("temp-sbgn-output", ".sbgn").getAbsolutePath());
- }
-
- /*
- * @Test public void simpleTest() throws JAXBException {
- * parseAndExport("simpleTest"); }
- *
- * @Test public void VANTEDdiagram() throws JAXBException {
- * parseAndExport("VANTEDdiagram"); }
- */
-
- @Test
- public void test() throws Exception {
- try {
- parseAndExport(testName);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.sbgnml;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.Collection;
+
+import org.apache.log4j.Logger;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameters;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.model.map.model.Model;
+
+@RunWith(Parameterized.class)
+public class SbgnmlXmlExporterTest {
+
+ Logger logger = Logger.getLogger(SbgnmlXmlExporterTest.class.getName());
+
+ private String testName;
+
+ public SbgnmlXmlExporterTest(String testName) {
+ this.testName = testName;
+ }
+
+ @Parameters(name = "{index} : {0}")
+ public static Collection<Object[]> data() throws IOException {
+ Collection<Object[]> data = new ArrayList<Object[]>();
+ Files.walk(Paths.get("testFiles/sbgnmlParserTestFiles/sbgnmlFiles")).forEach(fPath -> {
+ if (Files.isRegularFile(fPath) && fPath.toString().endsWith(".sbgn")) {
+ String tName = fPath.getFileName().toString().substring(0, fPath.getFileName().toString().indexOf(".sbgn"));
+ data.add(new Object[] { tName });
+ }
+ });
+ return data;
+ }
+
+ private void parseAndExport(String testName) throws Exception {
+ IConverter converter = new SbgnmlXmlConverter();
+
+ Model model = converter.createModel(new ConverterParams().filename("testFiles/sbgnmlParserTestFiles/sbgnmlFiles/".concat(testName).concat(".sbgn")));
+
+ converter.exportModelToFile(model, File.createTempFile("temp-sbgn-output", ".sbgn").getAbsolutePath());
+ }
+
+ /*
+ * @Test public void simpleTest() throws JAXBException {
+ * parseAndExport("simpleTest"); }
+ *
+ * @Test public void VANTEDdiagram() throws JAXBException {
+ * parseAndExport("VANTEDdiagram"); }
+ */
+
+ @Test
+ public void test() throws Exception {
+ try {
+ parseAndExport(testName);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
index fcf4410236..50350a9247 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
@@ -1,1162 +1,1162 @@
-package lcsb.mapviewer.converter.graphics;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.RenderingHints;
-import java.awt.geom.Line2D;
-import java.awt.geom.Rectangle2D;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.commands.SemanticZoomLevelMatcher;
-import lcsb.mapviewer.common.MimeType;
-import lcsb.mapviewer.converter.graphics.bioEntity.BioEntityConverterImpl;
-import lcsb.mapviewer.converter.graphics.layer.LayerConverter;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.modelutils.map.ElementUtils;
-
-/**
- * This class is responsible for creation of the image from the model. It's an
- * abstract class that implements the conversion of a model into drawing on
- * Graphics2D object with specified zoom level. However, it does't implement
- * transformation of a graphics2D to an output file. Among many parameters there
- * are two main modes:
- * <ul>
- * <li><i>classical</i> - in this mode everything is drawn as it's visible</li>
- * <li><i>nested</i> - in this mode, on some levels, compartments, complexes and
- * pathways cover big part of the map hiding underlying complexity. In this mode
- * very important thing is to understand difference between
- * {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator.level level}
- * and {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator.scale
- * scale} parameters. Scale defines magnification of the image (it's a double
- * value), whereas level defines how far from the top we are in hierarchical
- * view (it's an integer usually in the range <0..7>. Usually there is
- * corellation between scale and level, but it's not obligatory. Level=0 means
- * that we want to see as little elements as possible, whereas level=infinity
- * means that we want to see everything</li>
- * </ul>
- *
- * <p>
- * All draw operations are performed in default constractor. Therefore if we
- * want to create image of a different part of the map we have to create new
- * object. There are few reasons of that:
- * <ul>
- * <li>drawing is quite expensive, so lets do it once</li>
- * <li>we can draw only with the defined zoom level</li>
- * <li>when we have everything drawn we can extract different parts of the image
- * from graphics2D and save it into separate files</li>
- * </ul>
- *
- *
- *
- * @author Piotr Gawron
- *
- */
-public abstract class AbstractImageGenerator {
-
- /**
- * Class that allows to check if element is visible (or transparent) when
- * drawing. It's used to filter out invisible elements when drawing
- * semantic/hierarchy view.
- */
- private SemanticZoomLevelMatcher zoomLevelMatcher = new SemanticZoomLevelMatcher();
-
- /**
- * Model is drawn as a partial image (x,y,width,height parameters of
- * {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params
- * Params} class. This partial image sometimes contains some object that
- * doesn't intersect with this border (usually text descriptions). This margin
- * defines how far extend drawing.
- *
- * TODO maybe more effecient (and safe) solution would be to include text
- * desciption as parts of the object border
- */
- private static final int SINGLE_FRAME_MARGIN = 100;
-
- /**
- * On which level in hierarchical view we should visualize map.
- */
- private int level = Integer.MAX_VALUE;
-
- /**
- * Zoom factor of the drawing.
- */
- private double scale = 1;
-
- /**
- * This is a frame border from which we take all elements to draw.
- */
- private Rectangle2D.Double border = null;
-
- /**
- * Object that helps to convert {@link ColorSchema} values into colors.
- */
- private ColorExtractor colorExtractor = null;
-
- /**
- * Util class for simple operations on {@link Element elements}.
- */
- private ElementUtils eu = new ElementUtils();
-
- /**
- * This class contains a list of params that are used for drawing.
- *
- * @author Piotr Gawron
- *
- */
- public static class Params {
-
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(Params.class);
-
- /**
- * Scale at which we want to visualize the map. The default value is 1.0 (no
- * magnification).
- */
- private double scale = 1;
-
- /**
- * x coordinate from which we start to draw a map. This is absolute value on
- * the map (scale doesn't influence it).
- */
-
- private double x = 0;
-
- /**
- * y coordinate from which we start to draw a map. This is absolute value on
- * the map (scale doesn't influence it).
- */
- private double y = 0;
-
- /**
- * width of the generated image. It's an absolute value in pixels, therefore
- * when scale is set to value different than 1.0 the width on the map will
- * also be modified to fit into width pixels.
- */
- private Double width = null;
-
- /**
- * height of the generated image. It's an absolute value in pixels,
- * therefore when scale is set to value different than 1.0 the height on the
- * map will also be modified to fit into height pixels.
- */
- private Double height = null;
-
- /**
- * Model to be visualized.
- */
- private Model model = null;
-
- /**
- * Should we draw white background.
- */
- private boolean background = true;
-
- /**
- * At which hierarchy level we visualize map. Level=0 means that we want to
- * see as little elements as possible, whereas level=infinity means that we
- * want to see everything.
- */
- private int level = Integer.MAX_VALUE;
-
- /**
- * Should the visualization include hierarchical view or not.
- */
- private boolean nested = false;
-
- /**
- * Should sbgn standard be used.
- */
- private boolean sbgn = false;
-
- /**
- * List of objects containging information about layouts visualized in the
- * javascript (on client side). Every object (map) represents data for
- * single layout. In this map we have pairs between {@link Element}/
- * {@link Reaction} and {@link ColorSchema} used to visualize the element.
- *
- */
- private List<Map<Object, ColorSchema>> visibleLayouts = new ArrayList<>();
-
- /**
- * Color that should be used for drawing overlays with minimum value.
- */
- private Color minColor = Color.BLACK;
-
- /**
- * Color that should be used for drawing overlays with maximum value.
- */
- private Color maxColor = Color.BLACK;
-
- private Color simpleColor = Color.BLACK;
-
- /**
- * @param scale
- * scale to set
- * @return object with all parameters
- * @see #scale
- */
- public Params scale(final double scale) {
- this.scale = scale;
- return this;
- }
-
- /**
- * @param scale
- * scale to set
- * @return object with all parameters
- * @see #scale
- */
- public Params scale(final int scale) {
- this.scale = scale;
- return this;
- }
-
- /**
- *
- * @param x
- * x coordinate to be set
- * @return object with all parameters
- * @see #x
- */
- public Params x(final double x) {
- this.x = x;
- return this;
- }
-
- /**
- * @param x
- * x coordinate to be set
- * @return object with all parameters
- * @see #x
- */
- public Params x(final int x) {
- this.x = x;
- return this;
- }
-
- /**
- * @param y
- * y coordinate to be set
- * @return object with all parameters
- * @see #y
- */
- public Params y(final double y) {
- this.y = y;
- return this;
- }
-
- /**
- * @param y
- * y coordinate to be set
- * @return object with all parameters
- * @see #y
- */
- public Params y(final int y) {
- this.y = y;
- return this;
- }
-
- /**
- * @param width
- * width to set
- * @return object with all parameters
- * @see #width
- */
- public Params width(final double width) {
- this.width = width;
- return this;
- }
-
- /**
- * @param width
- * width to set
- * @return object with all parameters
- * @see #width
- */
- public Params width(final int width) {
- this.width = (double) width;
- return this;
- }
-
- /**
- *
- * @param height
- * height to set
- * @return object with all parameters
- * @see #height
- */
- public Params height(final double height) {
- this.height = height;
- return this;
- }
-
- /**
- * @param height
- * height to set
- * @return object with all parameters
- * @see #height
- */
- public Params height(final int height) {
- this.height = (double) height;
- return this;
- }
-
- /**
- *
- * @param background
- * background flag to set
- * @return object with all parameters
- * @see #background
- */
- public Params background(final boolean background) {
- this.background = background;
- return this;
- }
-
- /**
- *
- * @param nested
- * nested flag to set
- * @return object with all parameters
- * @see #nested
- */
- public Params nested(final boolean nested) {
- this.nested = nested;
- return this;
- }
-
- /**
- *
- * @param model
- * model to set
- * @return object with all parameters
- * @see #model
- */
- public Params model(final Model model) {
- this.model = model;
- if (this.width == null) {
- this.width = model.getWidth();
- }
- if (this.height == null) {
- this.height = model.getHeight();
- }
- return this;
- }
-
- /**
- *
- * @param level
- * level to set
- * @return object with all parameters
- * @see #level
- */
- public Params level(final int level) {
- this.level = level;
- return this;
- }
-
- /**
- *
- * @return scale value
- * @see #scale
- */
- public double getScale() {
- return scale;
- }
-
- /**
- *
- * @return x coordinate value
- * @see #x
- */
- public double getX() {
- return x;
- }
-
- /**
- *
- * @return y coordinate value
- * @see #y
- */
- public double getY() {
- return y;
- }
-
- /**
- *
- * @return width value
- * @see #width
- */
- public double getWidth() {
- return width;
- }
-
- /**
- *
- * @return height value
- * @see #height
- */
- public double getHeight() {
- return height;
- }
-
- /**
- *
- * @return model object
- * @see #model
- */
- public Model getModel() {
- return model;
- }
-
- /**
- *
- * @return background value
- * @see #background
- */
- public boolean isBackground() {
- return background;
- }
-
- /**
- *
- * @return nested value
- * @see #nested
- */
- public boolean isNested() {
- return nested;
- }
-
- /**
- * @return the level
- * @see #level
- */
- public int getLevel() {
- return level;
- }
-
- /**
- * Sets {@link #level} parameter from {@link String}.
- *
- * @param zoomLevel
- * new {@link #level} value
- * @return object with all parameters
- */
- public Params level(String zoomLevel) {
- if (zoomLevel == null) {
- logger.warn("Parameter equals to null...");
- } else {
- this.level = Integer.valueOf(zoomLevel);
- }
- return this;
- }
-
- @Override
- public String toString() {
- String result = "[" + this.getClass().getSimpleName() + "] " + "Model:" + model + "," + //
- "scale:" + scale + "," + //
- "x:" + x + "," + //
- "y:" + y + "," + //
- "width:" + width + "," + //
- "height:" + height + "," + //
- "background:" + background + "," + //
- "level:" + level + "," + //
- "nested:" + nested + ",";
- return result;
- }
-
- /**
- * Adds layout data that is visualized on the client side. Layout data
- * contains mapping between {@link Element}/{@link Reaction} and
- * {@link ColorSchema} used for coloring specific element.
- *
- * @param map
- * layout data containing mapping between {@link Element}/
- * {@link Reaction} and {@link ColorSchema} used for coloring
- * specific element
- */
- public void addVisibleLayout(Map<Object, ColorSchema> map) {
- visibleLayouts.add(map);
- }
-
- /**
- * @return the visibleLayouts
- * @see #visibleLayouts
- */
- public List<Map<Object, ColorSchema>> getVisibleLayouts() {
- return visibleLayouts;
- }
-
- /**
- * Returns list with {@link ColorSchema} used to visualize the specific
- * object in layouts visualized in the javascript.
- *
- * @param object
- * object ({@link Element} or {@link Reaction}) for which we return
- * list of {@link ColorSchema} in different layouts
- * @return list with {@link ColorSchema} used to visualize the specific
- * object in layouts visualized in the javascript
- * @see #visibleLayouts
- */
- public List<ColorSchema> getVisibleLayoutsForElement(Object object) {
- List<ColorSchema> result = new ArrayList<>();
- for (Map<Object, ColorSchema> map : visibleLayouts) {
- result.add(map.get(object));
- }
- return result;
- }
-
- /**
- * Returns {@link Color} that should be used for drawing overlays with
- * maximum value.
- *
- * @return {@link Color} that should be used for drawing overlays with
- * maximum value
- */
- public Color getMaxColor() {
- return maxColor;
- }
-
- public Color getSimpleColor() {
- return simpleColor;
- }
-
- /**
- * Returns {@link Color} that should be used for drawing overlays with
- * minimum value.
- *
- * @return {@link Color} that should be used for drawing overlays with
- * minimum value
- */
- public Color getMinColor() {
- return minColor;
- }
-
- /**
- * @param minColor
- * minColor to set
- * @return object with all parameters
- * @see #minColor
- */
- public Params minColor(Color minColor) {
- this.minColor = minColor;
- return this;
- }
-
- /**
- * @param maxColor
- * maxColor to set
- * @return object with all parameters
- * @see #maxColor
- */
- public Params maxColor(Color maxColor) {
- this.maxColor = maxColor;
- return this;
- }
-
- /**
- * @param simpleColor
- * simpleColor to set
- * @return object with all parameters
- * @see #simpleColor
- */
- public Params simpleColor(Color simpleColor) {
- this.simpleColor = simpleColor;
- return this;
- }
-
- /**
- * @return the sbgn
- * @see #sbgn
- */
- public boolean isSbgn() {
- return sbgn;
- }
-
- /**
- * @param sbgn
- * the sbgn to set
- * @see #sbgn
- * @return object with all parameters
- */
- public Params sbgn(boolean sbgn) {
- this.sbgn = sbgn;
- return this;
- }
-
- public Params colorExtractor(ColorExtractor colorExtractor) {
- return minColor(colorExtractor.getMinColor()).//
- maxColor(colorExtractor.getMaxColor()).//
- simpleColor(colorExtractor.getSimpleColor());
- }
-
- }
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(AbstractImageGenerator.class);
-
- /**
- * Graphics object which allows to draw objects.
- */
- private Graphics2D graphics;
-
- /**
- * SBGN display format.
- */
- private boolean sbgnFormat = false;
-
- /**
- * List of params used for drawing.
- */
- private Params params;
-
- /**
- * This method creates a graphics object for different implementations of
- * canvas with fixed width and height.
- *
- * @param width
- * width of the canvas (graphics2d) to be created
- * @param height
- * height of the canvas (graphics2d) to be created
- */
- protected abstract void createImageObject(double width, double height);
-
- /**
- * Default constructor. Create an image that is described by params. For more
- * information see
- * {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params
- * params}.
- *
- * @param params
- * list of all params to create apropriate image
- * @throws DrawingException
- * thrown when there was a problem with drawing a map
- *
- */
- protected AbstractImageGenerator(final Params params) {
- this.params = params;
- }
-
- /**
- * Flag indicating {@link #draw()} method was executed.
- */
- private boolean drawn = false;
-
- /**
- * Draw a model into {@link #getGraphics()} object.
- *
- * @throws DrawingException
- * thrown when there is a problem with drawing
- */
- protected void draw() throws DrawingException {
- if (isDrawn()) {
- logger.warn("Model was already drawn. Skipping");
- return;
- }
- this.level = params.getLevel();
- this.scale = params.getScale();
-
- colorExtractor = new ColorExtractor(params.getMinColor(), params.getMaxColor(), params.getSimpleColor());
-
- // set border frame extended by a margin
- border = new Rectangle2D.Double(
- params.getX() - SINGLE_FRAME_MARGIN, params.getY() - SINGLE_FRAME_MARGIN, params.getWidth() * scale + 2 * SINGLE_FRAME_MARGIN,
- params.getHeight() * scale + 2 * SINGLE_FRAME_MARGIN);
- createImageObject(params.getWidth(), params.getHeight());
-
- // turn on anti-aliasing
- graphics.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
-
- graphics.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
-
- graphics.setRenderingHint(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY);
-
- // set scale
- graphics.scale(1 / scale, 1 / scale);
-
- // move the upper left corner to coordinates
- graphics.translate(-params.getX(), -params.getY());
-
- if (params.isBackground()) {
- // create a background
- graphics.setColor(Color.WHITE);
- graphics.fillRect(
- (int) params.getX() - 1, (int) params.getY() - 1, ((int) Math.ceil(params.getWidth() * scale)) + 2,
- ((int) Math.ceil(params.getHeight() * scale)) + 2);
- graphics.setColor(Color.BLACK);
- }
-
- // Get the SBGN display format option from the model
- this.sbgnFormat = params.isSbgn();
-
- // Correct order of displaying is: elements, reactions, compartments,
- // layers.
- // In this way we can display all reactions and overlay them by compartments
- // or layers if they should be solid and hide complexity behind it
-
- // draw all elements
- for (Element element : params.getModel().getSortedSpeciesList()) {
- // draw only elements that don't have parents (aren't included in any
- // compartment/complexes)
- if (element instanceof Species) {
- if (((Species) element).getComplex() == null && element.getCompartment() == null) {
- drawSpecies((Species) element);
- }
- }
- }
- // draw all reactions
- for (Reaction reaction : params.getModel().getSortedReactions()) {
- drawReaction(reaction);
- }
- // draw all compartments
- for (Compartment compartment : params.getModel().getSortedCompartments()) {
- // draw only compartment that don't have parents (aren't included in any
- // compartment/complexes)
- if (compartment.getCompartment() == null) {
- drawCompartment(compartment);
- }
- }
-
- // draw all layers
- for (Layer layer : params.getModel().getLayers()) {
- drawLayer(layer);
- }
- closeImageObject();
- setDrawn(true);
- }
-
- /**
- * Method called after drawing. It should close drawing canvas properly.
- */
- protected abstract void closeImageObject();
-
- /**
- * This method draw layer on the graphics.
- *
- * @param layer
- * layer to be drawn
- */
- private void drawLayer(final Layer layer) {
- // get a converter nad set text borders to no
- LayerConverter converter = new LayerConverter(false);
- converter.drawLayer(layer, graphics);
- }
-
- /**
- * Don't allow to create default public constructors with empty list of
- * parameters.
- */
- protected AbstractImageGenerator() {
- super();
- }
-
- /**
- * This method draw a {@link Compartment} on a graphics.
- *
- * @param compartment
- * object that we want to draw
- * @throws DrawingException
- * thrown when there was a problem with drawing {@link Compartment}
- */
- protected void drawCompartment(final Compartment compartment) throws DrawingException {
- // get a converter for this compartment
- BioEntityConverterImpl converter = new BioEntityConverterImpl(compartment, colorExtractor);
- ConverterParams compartmentParams = new ConverterParams().level(level).nested(params.nested);
-
- if (params.nested) {
- compartmentParams.scale(Math.max(scale, 1));
- }
-
- // we draw compartment only when we have hierarchical view or it's
- // standard compartment (not the pathway)
- if (params.nested || !(compartment instanceof PathwayCompartment)) {
- converter.draw(compartment, graphics, compartmentParams, params.getVisibleLayoutsForElement(compartment));
- }
-
- // If compartment should be filled, then we could skip drawing the inside
- // compartments.
-
- if (zoomLevelMatcher.isTransparent(level, compartment.getTransparencyLevel()) || !params.nested) {
- List<Element> result = new ArrayList<>();
- result.addAll(compartment.getElements());
- Collections.sort(result, Element.SIZE_COMPARATOR);
-
- // draw all children of this compartment
- for (Element child : result) {
- // if a child is a standard species
- if (child instanceof Species) {
- drawSpecies((Species) child);
- } else if (child instanceof Compartment) {
- drawCompartment((Compartment) child);
- } else {
- // if a child is not a compartment or a species then we have a
- // problem
- throw new DrawingException(eu.getElementTag(child) + "Unknown Element type");
- }
-
- }
- if (!compartment.containsIdenticalSpecies()) {
- if (!(compartment instanceof PathwayCompartment)) {
- converter.drawText(compartment, graphics, compartmentParams);
- }
- }
- }
- }
-
- /**
- * This method draw a {@link Species} on a graphics.
- *
- * @param species
- * object to be drawn
- * @throws DrawingException
- * thrown when there was a problem with drawing a {@link Species}
- */
- protected void drawSpecies(final Species species) throws DrawingException {
- if (!cross(species.getBorder())) {
- return;
- }
-
- boolean rescale = false;
- if (species instanceof Complex) {
- Complex complex = (Complex) species;
- if (complex.getElements().size() == 0) {
- rescale = true;
- } else {
- rescale = true;
- for (Element child : complex.getElements()) {
- if ((zoomLevelMatcher.isVisible(level, child.getVisibilityLevel())) || !params.nested) {
- rescale = false;
- }
- }
- }
- }
-
- // at the beginning try to find an appropriate converter
- BioEntityConverterImpl converter = new BioEntityConverterImpl(species, sbgnFormat, colorExtractor);
- double customScale = 1;
- if (rescale) {
- customScale = scale;
- }
- converter.draw(
- species, graphics, new ConverterParams().scale(customScale).level(level).sbgnFormat(sbgnFormat).nested(params.nested),
- params.getVisibleLayoutsForElement(species));
-
- // if the species is a complex then we may want to draw children
- // objects
- if (species instanceof Complex) {
- Complex complex = (Complex) species;
- // before drawing children check if the view is not set to brief
- // mode
- if (!complex.getState().equalsIgnoreCase("brief")) {
- // depending on current zoom level, children are drawn or not
- if (zoomLevelMatcher.isTransparent(level, complex.getTransparencyLevel()) || !params.nested) {
- for (Species child : complex.getElements()) {
- drawSpecies(child);
- }
- }
- }
- }
- }
-
- /**
- * This method draw a reaction on a graphics.
- *
- * @param reaction
- * object to be drawn
- * @throws DrawingException
- * thrown when there was a problem with drawing a {@link Reaction}
- */
- protected void drawReaction(final Reaction reaction) throws DrawingException {
- if (!cross(reaction.getLines())) {
- return;
- }
- BioEntityConverterImpl converter = new BioEntityConverterImpl(reaction, sbgnFormat, colorExtractor);
- converter.draw(
- reaction, graphics, new ConverterParams().sbgnFormat(sbgnFormat).nested(params.nested).level(level), params.getVisibleLayoutsForElement(reaction));
- }
-
- /**
- * Checks if one of the lines in parameter cross the frame.
- *
- * @param lines
- * list of lines to check
- * @return true if the cross point exist, false otherwise
- */
- private boolean cross(final List<Line2D> lines) {
- for (Line2D line2d : lines) {
- if (border.intersectsLine(line2d)) {
- return true;
- }
- }
- return false;
- }
-
- /**
- * Checks if the rectangle in the parameters cross the fram in which we are
- * currently draw image.
- *
- * @param rect
- * rectangle to check
- * @return true if rectangle check the frame, false otherwise
- */
- protected boolean cross(final Rectangle2D rect) {
- return border.intersects(rect);
- }
-
- /**
- * @return the graphics
- */
- protected Graphics2D getGraphics() {
- return graphics;
- }
-
- /**
- * @param graphics
- * the graphics to set
- */
- protected void setGraphics(Graphics2D graphics) {
- this.graphics = graphics;
- }
-
- /**
- * Saves generated image into file.
- *
- * @param fileName
- * file where the images should be saved
- * @throws IOException
- * thrown when there is problem with output file
- * @throws DrawingException
- * thrown when there was a problem with drawing map
- */
- public final void saveToFile(String fileName) throws IOException, DrawingException {
- if (!isDrawn()) {
- draw();
- }
- saveToFileImplementation(fileName);
- };
-
- /**
- * Saves generated image from {@link #getGraphics()} into file.
- *
- * @param fileName
- * file where the images should be saved
- * @throws IOException
- * thrown when there is problem with output file
- * @throws DrawingException
- * thrown when there was a problem with drawing map
- */
- protected abstract void saveToFileImplementation(String fileName) throws IOException;
-
- /**
- * Saves generated image into {@link OutputStream}.
- *
- * @param os
- * stream where the images should be saved
- * @throws IOException
- * thrown when there is problem with output stream
- * @throws DrawingException
- * thrown when there was a problem with drawing map
- */
- public final void saveToOutputStream(OutputStream os) throws IOException, DrawingException {
- if (!isDrawn()) {
- draw();
- }
- saveToOutputStream(os);
- }
-
- /**
- * Saves generated image from {@link #getGraphics()} into {@link OutputStream}
- * .
- *
- * @param os
- * stream where the images should be saved
- * @throws IOException
- * thrown when there is problem with output stream
- * @throws DrawingException
- * thrown when there was a problem with drawing map
- */
- protected abstract void saveToOutputStreamImplementation(OutputStream os) throws IOException;
-
- /**
- * Saves part of the generated image file.
- *
- * @param fileName
- * file where the images should be saved
- * @param x
- * x left margin of the image part
- * @param y
- * y top margin of the image part
- * @param width
- * width of the image part
- * @param height
- * hieght of the image part
- * @throws IOException
- * thrown when there is problem with output file
- * @throws DrawingException
- * thrown when there was a problem with drawing map
- */
- public final void savePartToFile(final int x, final int y, final int width, final int height, final String fileName) throws IOException, DrawingException {
- if (!isDrawn()) {
- draw();
- }
- savePartToFileImplementation(x, y, width, height, fileName);
- }
-
- /**
- * Saves part of the generated image from {@link #getGraphics()} into file.
- *
- * @param fileName
- * file where the images should be saved
- * @param x
- * x left margin of the image part
- * @param y
- * y top margin of the image part
- * @param width
- * width of the image part
- * @param height
- * hieght of the image part
- * @throws IOException
- * thrown when there is problem with output file
- */
- protected abstract void savePartToFileImplementation(final int x, final int y, final int width, final int height, final String fileName) throws IOException;
-
- /**
- * Saves part of the generated image into {@link OutputStream}.
- *
- * @param os
- * stream where the images should be saved
- * @param x
- * x left margin of the image part
- * @param y
- * y top margin of the image part
- * @param width
- * width of the image part
- * @param height
- * hieght of the image part
- * @throws IOException
- * thrown when there is problem with output file
- * @throws DrawingException
- * thrown when there was a problem with drawing map
- */
- public final void savePartToOutputStream(final int x, final int y, final int width, final int height, final OutputStream os)
- throws IOException, DrawingException {
- if (!isDrawn()) {
- draw();
- }
- savePartToOutputStreamImplementation(x, y, width, height, os);
- }
-
- /**
- * Saves part of the generated image from {@link #getGraphics()} into
- * {@link OutputStream}.
- *
- * @param os
- * stream where the images should be saved
- * @param x
- * x left margin of the image part
- * @param y
- * y top margin of the image part
- * @param width
- * width of the image part
- * @param height
- * hieght of the image part
- * @throws IOException
- * thrown when there is problem with output file
- * @throws DrawingException
- * thrown when there was a problem with drawing map
- */
- protected abstract void savePartToOutputStreamImplementation(final int x, final int y, final int width, final int height, final OutputStream os)
- throws IOException;
-
- /**
- * Returns name of the format to which this graphic converter will transform.
- *
- * @return name of the format to which this graphic converter will transform
- */
- public abstract String getFormatName();
-
- /**
- * Returns {@link MimeType} that should be used for files generated by this
- * image generator.
- *
- * @return {@link MimeType} that should be used for files generated by this
- * image generator
- */
- public abstract MimeType getMimeType();
-
- /**
- * Returns default file extension used by this image generator.
- *
- * @return default file extension used by this image generator
- */
- public abstract String getFileExtension();
-
- /**
- * @return the sbgnFormat
- */
- protected boolean isSbgnFormat() {
- return sbgnFormat;
- }
-
- /**
- * @param sbgnFormat
- * the sbgnFormat to set
- */
- protected void sbgnFormat(boolean sbgnFormat) {
- this.sbgnFormat = sbgnFormat;
- }
-
- /**
- * @return the drawn
- * @see #drawn
- */
- private boolean isDrawn() {
- return drawn;
- }
-
- /**
- * @param drawn
- * the drawn to set
- * @see #drawn
- */
- private void setDrawn(boolean drawn) {
- this.drawn = drawn;
- }
-
- /**
- * @return the params
- * @see #params
- */
- protected Params getParams() {
- return params;
- }
-
- /**
- * @param params
- * the params to set
- * @see #params
- */
- protected void setParams(Params params) {
- this.params = params;
- }
+package lcsb.mapviewer.converter.graphics;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.RenderingHints;
+import java.awt.geom.Line2D;
+import java.awt.geom.Rectangle2D;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.commands.SemanticZoomLevelMatcher;
+import lcsb.mapviewer.common.MimeType;
+import lcsb.mapviewer.converter.graphics.bioEntity.BioEntityConverterImpl;
+import lcsb.mapviewer.converter.graphics.layer.LayerConverter;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
+
+/**
+ * This class is responsible for creation of the image from the model. It's an
+ * abstract class that implements the conversion of a model into drawing on
+ * Graphics2D object with specified zoom level. However, it does't implement
+ * transformation of a graphics2D to an output file. Among many parameters there
+ * are two main modes:
+ * <ul>
+ * <li><i>classical</i> - in this mode everything is drawn as it's visible</li>
+ * <li><i>nested</i> - in this mode, on some levels, compartments, complexes and
+ * pathways cover big part of the map hiding underlying complexity. In this mode
+ * very important thing is to understand difference between
+ * {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator.level level}
+ * and {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator.scale
+ * scale} parameters. Scale defines magnification of the image (it's a double
+ * value), whereas level defines how far from the top we are in hierarchical
+ * view (it's an integer usually in the range <0..7>. Usually there is
+ * corellation between scale and level, but it's not obligatory. Level=0 means
+ * that we want to see as little elements as possible, whereas level=infinity
+ * means that we want to see everything</li>
+ * </ul>
+ *
+ * <p>
+ * All draw operations are performed in default constractor. Therefore if we
+ * want to create image of a different part of the map we have to create new
+ * object. There are few reasons of that:
+ * <ul>
+ * <li>drawing is quite expensive, so lets do it once</li>
+ * <li>we can draw only with the defined zoom level</li>
+ * <li>when we have everything drawn we can extract different parts of the image
+ * from graphics2D and save it into separate files</li>
+ * </ul>
+ *
+ *
+ *
+ * @author Piotr Gawron
+ *
+ */
+public abstract class AbstractImageGenerator {
+
+ /**
+ * Class that allows to check if element is visible (or transparent) when
+ * drawing. It's used to filter out invisible elements when drawing
+ * semantic/hierarchy view.
+ */
+ private SemanticZoomLevelMatcher zoomLevelMatcher = new SemanticZoomLevelMatcher();
+
+ /**
+ * Model is drawn as a partial image (x,y,width,height parameters of
+ * {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params
+ * Params} class. This partial image sometimes contains some object that
+ * doesn't intersect with this border (usually text descriptions). This margin
+ * defines how far extend drawing.
+ *
+ * TODO maybe more effecient (and safe) solution would be to include text
+ * desciption as parts of the object border
+ */
+ private static final int SINGLE_FRAME_MARGIN = 100;
+
+ /**
+ * On which level in hierarchical view we should visualize map.
+ */
+ private int level = Integer.MAX_VALUE;
+
+ /**
+ * Zoom factor of the drawing.
+ */
+ private double scale = 1;
+
+ /**
+ * This is a frame border from which we take all elements to draw.
+ */
+ private Rectangle2D.Double border = null;
+
+ /**
+ * Object that helps to convert {@link ColorSchema} values into colors.
+ */
+ private ColorExtractor colorExtractor = null;
+
+ /**
+ * Util class for simple operations on {@link Element elements}.
+ */
+ private ElementUtils eu = new ElementUtils();
+
+ /**
+ * This class contains a list of params that are used for drawing.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ public static class Params {
+
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(Params.class);
+
+ /**
+ * Scale at which we want to visualize the map. The default value is 1.0 (no
+ * magnification).
+ */
+ private double scale = 1;
+
+ /**
+ * x coordinate from which we start to draw a map. This is absolute value on
+ * the map (scale doesn't influence it).
+ */
+
+ private double x = 0;
+
+ /**
+ * y coordinate from which we start to draw a map. This is absolute value on
+ * the map (scale doesn't influence it).
+ */
+ private double y = 0;
+
+ /**
+ * width of the generated image. It's an absolute value in pixels, therefore
+ * when scale is set to value different than 1.0 the width on the map will
+ * also be modified to fit into width pixels.
+ */
+ private Double width = null;
+
+ /**
+ * height of the generated image. It's an absolute value in pixels,
+ * therefore when scale is set to value different than 1.0 the height on the
+ * map will also be modified to fit into height pixels.
+ */
+ private Double height = null;
+
+ /**
+ * Model to be visualized.
+ */
+ private Model model = null;
+
+ /**
+ * Should we draw white background.
+ */
+ private boolean background = true;
+
+ /**
+ * At which hierarchy level we visualize map. Level=0 means that we want to
+ * see as little elements as possible, whereas level=infinity means that we
+ * want to see everything.
+ */
+ private int level = Integer.MAX_VALUE;
+
+ /**
+ * Should the visualization include hierarchical view or not.
+ */
+ private boolean nested = false;
+
+ /**
+ * Should sbgn standard be used.
+ */
+ private boolean sbgn = false;
+
+ /**
+ * List of objects containging information about layouts visualized in the
+ * javascript (on client side). Every object (map) represents data for
+ * single layout. In this map we have pairs between {@link Element}/
+ * {@link Reaction} and {@link ColorSchema} used to visualize the element.
+ *
+ */
+ private List<Map<Object, ColorSchema>> visibleLayouts = new ArrayList<>();
+
+ /**
+ * Color that should be used for drawing overlays with minimum value.
+ */
+ private Color minColor = Color.BLACK;
+
+ /**
+ * Color that should be used for drawing overlays with maximum value.
+ */
+ private Color maxColor = Color.BLACK;
+
+ private Color simpleColor = Color.BLACK;
+
+ /**
+ * @param scale
+ * scale to set
+ * @return object with all parameters
+ * @see #scale
+ */
+ public Params scale(final double scale) {
+ this.scale = scale;
+ return this;
+ }
+
+ /**
+ * @param scale
+ * scale to set
+ * @return object with all parameters
+ * @see #scale
+ */
+ public Params scale(final int scale) {
+ this.scale = scale;
+ return this;
+ }
+
+ /**
+ *
+ * @param x
+ * x coordinate to be set
+ * @return object with all parameters
+ * @see #x
+ */
+ public Params x(final double x) {
+ this.x = x;
+ return this;
+ }
+
+ /**
+ * @param x
+ * x coordinate to be set
+ * @return object with all parameters
+ * @see #x
+ */
+ public Params x(final int x) {
+ this.x = x;
+ return this;
+ }
+
+ /**
+ * @param y
+ * y coordinate to be set
+ * @return object with all parameters
+ * @see #y
+ */
+ public Params y(final double y) {
+ this.y = y;
+ return this;
+ }
+
+ /**
+ * @param y
+ * y coordinate to be set
+ * @return object with all parameters
+ * @see #y
+ */
+ public Params y(final int y) {
+ this.y = y;
+ return this;
+ }
+
+ /**
+ * @param width
+ * width to set
+ * @return object with all parameters
+ * @see #width
+ */
+ public Params width(final double width) {
+ this.width = width;
+ return this;
+ }
+
+ /**
+ * @param width
+ * width to set
+ * @return object with all parameters
+ * @see #width
+ */
+ public Params width(final int width) {
+ this.width = (double) width;
+ return this;
+ }
+
+ /**
+ *
+ * @param height
+ * height to set
+ * @return object with all parameters
+ * @see #height
+ */
+ public Params height(final double height) {
+ this.height = height;
+ return this;
+ }
+
+ /**
+ * @param height
+ * height to set
+ * @return object with all parameters
+ * @see #height
+ */
+ public Params height(final int height) {
+ this.height = (double) height;
+ return this;
+ }
+
+ /**
+ *
+ * @param background
+ * background flag to set
+ * @return object with all parameters
+ * @see #background
+ */
+ public Params background(final boolean background) {
+ this.background = background;
+ return this;
+ }
+
+ /**
+ *
+ * @param nested
+ * nested flag to set
+ * @return object with all parameters
+ * @see #nested
+ */
+ public Params nested(final boolean nested) {
+ this.nested = nested;
+ return this;
+ }
+
+ /**
+ *
+ * @param model
+ * model to set
+ * @return object with all parameters
+ * @see #model
+ */
+ public Params model(final Model model) {
+ this.model = model;
+ if (this.width == null) {
+ this.width = model.getWidth();
+ }
+ if (this.height == null) {
+ this.height = model.getHeight();
+ }
+ return this;
+ }
+
+ /**
+ *
+ * @param level
+ * level to set
+ * @return object with all parameters
+ * @see #level
+ */
+ public Params level(final int level) {
+ this.level = level;
+ return this;
+ }
+
+ /**
+ *
+ * @return scale value
+ * @see #scale
+ */
+ public double getScale() {
+ return scale;
+ }
+
+ /**
+ *
+ * @return x coordinate value
+ * @see #x
+ */
+ public double getX() {
+ return x;
+ }
+
+ /**
+ *
+ * @return y coordinate value
+ * @see #y
+ */
+ public double getY() {
+ return y;
+ }
+
+ /**
+ *
+ * @return width value
+ * @see #width
+ */
+ public double getWidth() {
+ return width;
+ }
+
+ /**
+ *
+ * @return height value
+ * @see #height
+ */
+ public double getHeight() {
+ return height;
+ }
+
+ /**
+ *
+ * @return model object
+ * @see #model
+ */
+ public Model getModel() {
+ return model;
+ }
+
+ /**
+ *
+ * @return background value
+ * @see #background
+ */
+ public boolean isBackground() {
+ return background;
+ }
+
+ /**
+ *
+ * @return nested value
+ * @see #nested
+ */
+ public boolean isNested() {
+ return nested;
+ }
+
+ /**
+ * @return the level
+ * @see #level
+ */
+ public int getLevel() {
+ return level;
+ }
+
+ /**
+ * Sets {@link #level} parameter from {@link String}.
+ *
+ * @param zoomLevel
+ * new {@link #level} value
+ * @return object with all parameters
+ */
+ public Params level(String zoomLevel) {
+ if (zoomLevel == null) {
+ logger.warn("Parameter equals to null...");
+ } else {
+ this.level = Integer.valueOf(zoomLevel);
+ }
+ return this;
+ }
+
+ @Override
+ public String toString() {
+ String result = "[" + this.getClass().getSimpleName() + "] " + "Model:" + model + "," + //
+ "scale:" + scale + "," + //
+ "x:" + x + "," + //
+ "y:" + y + "," + //
+ "width:" + width + "," + //
+ "height:" + height + "," + //
+ "background:" + background + "," + //
+ "level:" + level + "," + //
+ "nested:" + nested + ",";
+ return result;
+ }
+
+ /**
+ * Adds layout data that is visualized on the client side. Layout data
+ * contains mapping between {@link Element}/{@link Reaction} and
+ * {@link ColorSchema} used for coloring specific element.
+ *
+ * @param map
+ * layout data containing mapping between {@link Element}/
+ * {@link Reaction} and {@link ColorSchema} used for coloring
+ * specific element
+ */
+ public void addVisibleLayout(Map<Object, ColorSchema> map) {
+ visibleLayouts.add(map);
+ }
+
+ /**
+ * @return the visibleLayouts
+ * @see #visibleLayouts
+ */
+ public List<Map<Object, ColorSchema>> getVisibleLayouts() {
+ return visibleLayouts;
+ }
+
+ /**
+ * Returns list with {@link ColorSchema} used to visualize the specific
+ * object in layouts visualized in the javascript.
+ *
+ * @param object
+ * object ({@link Element} or {@link Reaction}) for which we return
+ * list of {@link ColorSchema} in different layouts
+ * @return list with {@link ColorSchema} used to visualize the specific
+ * object in layouts visualized in the javascript
+ * @see #visibleLayouts
+ */
+ public List<ColorSchema> getVisibleLayoutsForElement(Object object) {
+ List<ColorSchema> result = new ArrayList<>();
+ for (Map<Object, ColorSchema> map : visibleLayouts) {
+ result.add(map.get(object));
+ }
+ return result;
+ }
+
+ /**
+ * Returns {@link Color} that should be used for drawing overlays with
+ * maximum value.
+ *
+ * @return {@link Color} that should be used for drawing overlays with
+ * maximum value
+ */
+ public Color getMaxColor() {
+ return maxColor;
+ }
+
+ public Color getSimpleColor() {
+ return simpleColor;
+ }
+
+ /**
+ * Returns {@link Color} that should be used for drawing overlays with
+ * minimum value.
+ *
+ * @return {@link Color} that should be used for drawing overlays with
+ * minimum value
+ */
+ public Color getMinColor() {
+ return minColor;
+ }
+
+ /**
+ * @param minColor
+ * minColor to set
+ * @return object with all parameters
+ * @see #minColor
+ */
+ public Params minColor(Color minColor) {
+ this.minColor = minColor;
+ return this;
+ }
+
+ /**
+ * @param maxColor
+ * maxColor to set
+ * @return object with all parameters
+ * @see #maxColor
+ */
+ public Params maxColor(Color maxColor) {
+ this.maxColor = maxColor;
+ return this;
+ }
+
+ /**
+ * @param simpleColor
+ * simpleColor to set
+ * @return object with all parameters
+ * @see #simpleColor
+ */
+ public Params simpleColor(Color simpleColor) {
+ this.simpleColor = simpleColor;
+ return this;
+ }
+
+ /**
+ * @return the sbgn
+ * @see #sbgn
+ */
+ public boolean isSbgn() {
+ return sbgn;
+ }
+
+ /**
+ * @param sbgn
+ * the sbgn to set
+ * @see #sbgn
+ * @return object with all parameters
+ */
+ public Params sbgn(boolean sbgn) {
+ this.sbgn = sbgn;
+ return this;
+ }
+
+ public Params colorExtractor(ColorExtractor colorExtractor) {
+ return minColor(colorExtractor.getMinColor()).//
+ maxColor(colorExtractor.getMaxColor()).//
+ simpleColor(colorExtractor.getSimpleColor());
+ }
+
+ }
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(AbstractImageGenerator.class);
+
+ /**
+ * Graphics object which allows to draw objects.
+ */
+ private Graphics2D graphics;
+
+ /**
+ * SBGN display format.
+ */
+ private boolean sbgnFormat = false;
+
+ /**
+ * List of params used for drawing.
+ */
+ private Params params;
+
+ /**
+ * This method creates a graphics object for different implementations of
+ * canvas with fixed width and height.
+ *
+ * @param width
+ * width of the canvas (graphics2d) to be created
+ * @param height
+ * height of the canvas (graphics2d) to be created
+ */
+ protected abstract void createImageObject(double width, double height);
+
+ /**
+ * Default constructor. Create an image that is described by params. For more
+ * information see
+ * {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params
+ * params}.
+ *
+ * @param params
+ * list of all params to create apropriate image
+ * @throws DrawingException
+ * thrown when there was a problem with drawing a map
+ *
+ */
+ protected AbstractImageGenerator(final Params params) {
+ this.params = params;
+ }
+
+ /**
+ * Flag indicating {@link #draw()} method was executed.
+ */
+ private boolean drawn = false;
+
+ /**
+ * Draw a model into {@link #getGraphics()} object.
+ *
+ * @throws DrawingException
+ * thrown when there is a problem with drawing
+ */
+ protected void draw() throws DrawingException {
+ if (isDrawn()) {
+ logger.warn("Model was already drawn. Skipping");
+ return;
+ }
+ this.level = params.getLevel();
+ this.scale = params.getScale();
+
+ colorExtractor = new ColorExtractor(params.getMinColor(), params.getMaxColor(), params.getSimpleColor());
+
+ // set border frame extended by a margin
+ border = new Rectangle2D.Double(
+ params.getX() - SINGLE_FRAME_MARGIN, params.getY() - SINGLE_FRAME_MARGIN, params.getWidth() * scale + 2 * SINGLE_FRAME_MARGIN,
+ params.getHeight() * scale + 2 * SINGLE_FRAME_MARGIN);
+ createImageObject(params.getWidth(), params.getHeight());
+
+ // turn on anti-aliasing
+ graphics.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
+
+ graphics.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
+
+ graphics.setRenderingHint(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY);
+
+ // set scale
+ graphics.scale(1 / scale, 1 / scale);
+
+ // move the upper left corner to coordinates
+ graphics.translate(-params.getX(), -params.getY());
+
+ if (params.isBackground()) {
+ // create a background
+ graphics.setColor(Color.WHITE);
+ graphics.fillRect(
+ (int) params.getX() - 1, (int) params.getY() - 1, ((int) Math.ceil(params.getWidth() * scale)) + 2,
+ ((int) Math.ceil(params.getHeight() * scale)) + 2);
+ graphics.setColor(Color.BLACK);
+ }
+
+ // Get the SBGN display format option from the model
+ this.sbgnFormat = params.isSbgn();
+
+ // Correct order of displaying is: elements, reactions, compartments,
+ // layers.
+ // In this way we can display all reactions and overlay them by compartments
+ // or layers if they should be solid and hide complexity behind it
+
+ // draw all elements
+ for (Element element : params.getModel().getSortedSpeciesList()) {
+ // draw only elements that don't have parents (aren't included in any
+ // compartment/complexes)
+ if (element instanceof Species) {
+ if (((Species) element).getComplex() == null && element.getCompartment() == null) {
+ drawSpecies((Species) element);
+ }
+ }
+ }
+ // draw all reactions
+ for (Reaction reaction : params.getModel().getSortedReactions()) {
+ drawReaction(reaction);
+ }
+ // draw all compartments
+ for (Compartment compartment : params.getModel().getSortedCompartments()) {
+ // draw only compartment that don't have parents (aren't included in any
+ // compartment/complexes)
+ if (compartment.getCompartment() == null) {
+ drawCompartment(compartment);
+ }
+ }
+
+ // draw all layers
+ for (Layer layer : params.getModel().getLayers()) {
+ drawLayer(layer);
+ }
+ closeImageObject();
+ setDrawn(true);
+ }
+
+ /**
+ * Method called after drawing. It should close drawing canvas properly.
+ */
+ protected abstract void closeImageObject();
+
+ /**
+ * This method draw layer on the graphics.
+ *
+ * @param layer
+ * layer to be drawn
+ */
+ private void drawLayer(final Layer layer) {
+ // get a converter nad set text borders to no
+ LayerConverter converter = new LayerConverter(false);
+ converter.drawLayer(layer, graphics);
+ }
+
+ /**
+ * Don't allow to create default public constructors with empty list of
+ * parameters.
+ */
+ protected AbstractImageGenerator() {
+ super();
+ }
+
+ /**
+ * This method draw a {@link Compartment} on a graphics.
+ *
+ * @param compartment
+ * object that we want to draw
+ * @throws DrawingException
+ * thrown when there was a problem with drawing {@link Compartment}
+ */
+ protected void drawCompartment(final Compartment compartment) throws DrawingException {
+ // get a converter for this compartment
+ BioEntityConverterImpl converter = new BioEntityConverterImpl(compartment, colorExtractor);
+ ConverterParams compartmentParams = new ConverterParams().level(level).nested(params.nested);
+
+ if (params.nested) {
+ compartmentParams.scale(Math.max(scale, 1));
+ }
+
+ // we draw compartment only when we have hierarchical view or it's
+ // standard compartment (not the pathway)
+ if (params.nested || !(compartment instanceof PathwayCompartment)) {
+ converter.draw(compartment, graphics, compartmentParams, params.getVisibleLayoutsForElement(compartment));
+ }
+
+ // If compartment should be filled, then we could skip drawing the inside
+ // compartments.
+
+ if (zoomLevelMatcher.isTransparent(level, compartment.getTransparencyLevel()) || !params.nested) {
+ List<Element> result = new ArrayList<>();
+ result.addAll(compartment.getElements());
+ Collections.sort(result, Element.SIZE_COMPARATOR);
+
+ // draw all children of this compartment
+ for (Element child : result) {
+ // if a child is a standard species
+ if (child instanceof Species) {
+ drawSpecies((Species) child);
+ } else if (child instanceof Compartment) {
+ drawCompartment((Compartment) child);
+ } else {
+ // if a child is not a compartment or a species then we have a
+ // problem
+ throw new DrawingException(eu.getElementTag(child) + "Unknown Element type");
+ }
+
+ }
+ if (!compartment.containsIdenticalSpecies()) {
+ if (!(compartment instanceof PathwayCompartment)) {
+ converter.drawText(compartment, graphics, compartmentParams);
+ }
+ }
+ }
+ }
+
+ /**
+ * This method draw a {@link Species} on a graphics.
+ *
+ * @param species
+ * object to be drawn
+ * @throws DrawingException
+ * thrown when there was a problem with drawing a {@link Species}
+ */
+ protected void drawSpecies(final Species species) throws DrawingException {
+ if (!cross(species.getBorder())) {
+ return;
+ }
+
+ boolean rescale = false;
+ if (species instanceof Complex) {
+ Complex complex = (Complex) species;
+ if (complex.getElements().size() == 0) {
+ rescale = true;
+ } else {
+ rescale = true;
+ for (Element child : complex.getElements()) {
+ if ((zoomLevelMatcher.isVisible(level, child.getVisibilityLevel())) || !params.nested) {
+ rescale = false;
+ }
+ }
+ }
+ }
+
+ // at the beginning try to find an appropriate converter
+ BioEntityConverterImpl converter = new BioEntityConverterImpl(species, sbgnFormat, colorExtractor);
+ double customScale = 1;
+ if (rescale) {
+ customScale = scale;
+ }
+ converter.draw(
+ species, graphics, new ConverterParams().scale(customScale).level(level).sbgnFormat(sbgnFormat).nested(params.nested),
+ params.getVisibleLayoutsForElement(species));
+
+ // if the species is a complex then we may want to draw children
+ // objects
+ if (species instanceof Complex) {
+ Complex complex = (Complex) species;
+ // before drawing children check if the view is not set to brief
+ // mode
+ if (!complex.getState().equalsIgnoreCase("brief")) {
+ // depending on current zoom level, children are drawn or not
+ if (zoomLevelMatcher.isTransparent(level, complex.getTransparencyLevel()) || !params.nested) {
+ for (Species child : complex.getElements()) {
+ drawSpecies(child);
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * This method draw a reaction on a graphics.
+ *
+ * @param reaction
+ * object to be drawn
+ * @throws DrawingException
+ * thrown when there was a problem with drawing a {@link Reaction}
+ */
+ protected void drawReaction(final Reaction reaction) throws DrawingException {
+ if (!cross(reaction.getLines())) {
+ return;
+ }
+ BioEntityConverterImpl converter = new BioEntityConverterImpl(reaction, sbgnFormat, colorExtractor);
+ converter.draw(
+ reaction, graphics, new ConverterParams().sbgnFormat(sbgnFormat).nested(params.nested).level(level), params.getVisibleLayoutsForElement(reaction));
+ }
+
+ /**
+ * Checks if one of the lines in parameter cross the frame.
+ *
+ * @param lines
+ * list of lines to check
+ * @return true if the cross point exist, false otherwise
+ */
+ private boolean cross(final List<Line2D> lines) {
+ for (Line2D line2d : lines) {
+ if (border.intersectsLine(line2d)) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Checks if the rectangle in the parameters cross the fram in which we are
+ * currently draw image.
+ *
+ * @param rect
+ * rectangle to check
+ * @return true if rectangle check the frame, false otherwise
+ */
+ protected boolean cross(final Rectangle2D rect) {
+ return border.intersects(rect);
+ }
+
+ /**
+ * @return the graphics
+ */
+ protected Graphics2D getGraphics() {
+ return graphics;
+ }
+
+ /**
+ * @param graphics
+ * the graphics to set
+ */
+ protected void setGraphics(Graphics2D graphics) {
+ this.graphics = graphics;
+ }
+
+ /**
+ * Saves generated image into file.
+ *
+ * @param fileName
+ * file where the images should be saved
+ * @throws IOException
+ * thrown when there is problem with output file
+ * @throws DrawingException
+ * thrown when there was a problem with drawing map
+ */
+ public final void saveToFile(String fileName) throws IOException, DrawingException {
+ if (!isDrawn()) {
+ draw();
+ }
+ saveToFileImplementation(fileName);
+ };
+
+ /**
+ * Saves generated image from {@link #getGraphics()} into file.
+ *
+ * @param fileName
+ * file where the images should be saved
+ * @throws IOException
+ * thrown when there is problem with output file
+ * @throws DrawingException
+ * thrown when there was a problem with drawing map
+ */
+ protected abstract void saveToFileImplementation(String fileName) throws IOException;
+
+ /**
+ * Saves generated image into {@link OutputStream}.
+ *
+ * @param os
+ * stream where the images should be saved
+ * @throws IOException
+ * thrown when there is problem with output stream
+ * @throws DrawingException
+ * thrown when there was a problem with drawing map
+ */
+ public final void saveToOutputStream(OutputStream os) throws IOException, DrawingException {
+ if (!isDrawn()) {
+ draw();
+ }
+ saveToOutputStream(os);
+ }
+
+ /**
+ * Saves generated image from {@link #getGraphics()} into {@link OutputStream}
+ * .
+ *
+ * @param os
+ * stream where the images should be saved
+ * @throws IOException
+ * thrown when there is problem with output stream
+ * @throws DrawingException
+ * thrown when there was a problem with drawing map
+ */
+ protected abstract void saveToOutputStreamImplementation(OutputStream os) throws IOException;
+
+ /**
+ * Saves part of the generated image file.
+ *
+ * @param fileName
+ * file where the images should be saved
+ * @param x
+ * x left margin of the image part
+ * @param y
+ * y top margin of the image part
+ * @param width
+ * width of the image part
+ * @param height
+ * hieght of the image part
+ * @throws IOException
+ * thrown when there is problem with output file
+ * @throws DrawingException
+ * thrown when there was a problem with drawing map
+ */
+ public final void savePartToFile(final int x, final int y, final int width, final int height, final String fileName) throws IOException, DrawingException {
+ if (!isDrawn()) {
+ draw();
+ }
+ savePartToFileImplementation(x, y, width, height, fileName);
+ }
+
+ /**
+ * Saves part of the generated image from {@link #getGraphics()} into file.
+ *
+ * @param fileName
+ * file where the images should be saved
+ * @param x
+ * x left margin of the image part
+ * @param y
+ * y top margin of the image part
+ * @param width
+ * width of the image part
+ * @param height
+ * hieght of the image part
+ * @throws IOException
+ * thrown when there is problem with output file
+ */
+ protected abstract void savePartToFileImplementation(final int x, final int y, final int width, final int height, final String fileName) throws IOException;
+
+ /**
+ * Saves part of the generated image into {@link OutputStream}.
+ *
+ * @param os
+ * stream where the images should be saved
+ * @param x
+ * x left margin of the image part
+ * @param y
+ * y top margin of the image part
+ * @param width
+ * width of the image part
+ * @param height
+ * hieght of the image part
+ * @throws IOException
+ * thrown when there is problem with output file
+ * @throws DrawingException
+ * thrown when there was a problem with drawing map
+ */
+ public final void savePartToOutputStream(final int x, final int y, final int width, final int height, final OutputStream os)
+ throws IOException, DrawingException {
+ if (!isDrawn()) {
+ draw();
+ }
+ savePartToOutputStreamImplementation(x, y, width, height, os);
+ }
+
+ /**
+ * Saves part of the generated image from {@link #getGraphics()} into
+ * {@link OutputStream}.
+ *
+ * @param os
+ * stream where the images should be saved
+ * @param x
+ * x left margin of the image part
+ * @param y
+ * y top margin of the image part
+ * @param width
+ * width of the image part
+ * @param height
+ * hieght of the image part
+ * @throws IOException
+ * thrown when there is problem with output file
+ * @throws DrawingException
+ * thrown when there was a problem with drawing map
+ */
+ protected abstract void savePartToOutputStreamImplementation(final int x, final int y, final int width, final int height, final OutputStream os)
+ throws IOException;
+
+ /**
+ * Returns name of the format to which this graphic converter will transform.
+ *
+ * @return name of the format to which this graphic converter will transform
+ */
+ public abstract String getFormatName();
+
+ /**
+ * Returns {@link MimeType} that should be used for files generated by this
+ * image generator.
+ *
+ * @return {@link MimeType} that should be used for files generated by this
+ * image generator
+ */
+ public abstract MimeType getMimeType();
+
+ /**
+ * Returns default file extension used by this image generator.
+ *
+ * @return default file extension used by this image generator
+ */
+ public abstract String getFileExtension();
+
+ /**
+ * @return the sbgnFormat
+ */
+ protected boolean isSbgnFormat() {
+ return sbgnFormat;
+ }
+
+ /**
+ * @param sbgnFormat
+ * the sbgnFormat to set
+ */
+ protected void sbgnFormat(boolean sbgnFormat) {
+ this.sbgnFormat = sbgnFormat;
+ }
+
+ /**
+ * @return the drawn
+ * @see #drawn
+ */
+ private boolean isDrawn() {
+ return drawn;
+ }
+
+ /**
+ * @param drawn
+ * the drawn to set
+ * @see #drawn
+ */
+ private void setDrawn(boolean drawn) {
+ this.drawn = drawn;
+ }
+
+ /**
+ * @return the params
+ * @see #params
+ */
+ protected Params getParams() {
+ return params;
+ }
+
+ /**
+ * @param params
+ * the params to set
+ * @see #params
+ */
+ protected void setParams(Params params) {
+ this.params = params;
+ }
}
\ No newline at end of file
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ConverterParams.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ConverterParams.java
index d46ccdf508..9e07193401 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ConverterParams.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ConverterParams.java
@@ -1,118 +1,118 @@
-package lcsb.mapviewer.converter.graphics;
-
-/**
- * Set of parameters used for drawing elements (Aliases) on the Graphics2D.
- *
- * @author Piotr Gawron
- *
- */
-public class ConverterParams {
-
- /**
- * At which level the object is visualized. It helps to deterimine font size.
- * However it's possible that this value is not required.
- */
- private int level = 0;
-
- /**
- * What is the scale. It allows to adjust font size to be readable.
- */
- private double scale = 1;
-
- /**
- * Should the map be displayed in SBGN format.
- */
- private boolean sbgnFormat = false;
-
- /**
- * Does the visualization include nesting/hierarchy.
- */
- private boolean nested = false;
-
- /**
- * @param scale
- * the scale to set
- * @return object with all parameters
- * @see #scale
- */
- public ConverterParams scale(final double scale) {
- this.scale = scale;
- return this;
- }
-
- /**
- * @param nested
- * the nested to set
- * @return object with all parameters
- * @see #nested
- */
- public ConverterParams nested(final boolean nested) {
- this.nested = nested;
- return this;
- }
-
- /**
- * @return the level
- * @see #level
- */
- public int getLevel() {
- return level;
- }
-
- /**
- * @param level
- * the level to set
- * @return ConverterParams object with all parameters
- * @see #level
- */
- public ConverterParams level(int level) {
- this.level = level;
- return this;
- }
-
- /**
- * @param sbgnFormat
- * the sbgnFormat to set
- * @return ConverterParams object with all parameters
- * @see #sbgnFormat
- */
- public ConverterParams sbgnFormat(boolean sbgnFormat) {
- this.sbgnFormat = sbgnFormat;
- return this;
- }
-
- /**
- * @return the scale
- * @see #scale
- */
- public double getScale() {
- return scale;
- }
-
- /**
- * @return the sbgnFormat
- * @see #sbgnFormat
- */
- public boolean isSbgnFormat() {
- return sbgnFormat;
- }
-
- /**
- * @return the nested
- * @see #nested
- */
- public boolean isNested() {
- return nested;
- }
-
- @Override
- public String toString() {
- String result = "[" + this.getClass().getSimpleName() + "] " + //
- "level:" + level + "," + //
- "scale:" + scale + "," + //
- "nested:" + nested + "," + //
- "sbgnFormat:" + sbgnFormat;
- return result;
- }
-
-}
+package lcsb.mapviewer.converter.graphics;
+
+/**
+ * Set of parameters used for drawing elements (Aliases) on the Graphics2D.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ConverterParams {
+
+ /**
+ * At which level the object is visualized. It helps to deterimine font size.
+ * However it's possible that this value is not required.
+ */
+ private int level = 0;
+
+ /**
+ * What is the scale. It allows to adjust font size to be readable.
+ */
+ private double scale = 1;
+
+ /**
+ * Should the map be displayed in SBGN format.
+ */
+ private boolean sbgnFormat = false;
+
+ /**
+ * Does the visualization include nesting/hierarchy.
+ */
+ private boolean nested = false;
+
+ /**
+ * @param scale
+ * the scale to set
+ * @return object with all parameters
+ * @see #scale
+ */
+ public ConverterParams scale(final double scale) {
+ this.scale = scale;
+ return this;
+ }
+
+ /**
+ * @param nested
+ * the nested to set
+ * @return object with all parameters
+ * @see #nested
+ */
+ public ConverterParams nested(final boolean nested) {
+ this.nested = nested;
+ return this;
+ }
+
+ /**
+ * @return the level
+ * @see #level
+ */
+ public int getLevel() {
+ return level;
+ }
+
+ /**
+ * @param level
+ * the level to set
+ * @return ConverterParams object with all parameters
+ * @see #level
+ */
+ public ConverterParams level(int level) {
+ this.level = level;
+ return this;
+ }
+
+ /**
+ * @param sbgnFormat
+ * the sbgnFormat to set
+ * @return ConverterParams object with all parameters
+ * @see #sbgnFormat
+ */
+ public ConverterParams sbgnFormat(boolean sbgnFormat) {
+ this.sbgnFormat = sbgnFormat;
+ return this;
+ }
+
+ /**
+ * @return the scale
+ * @see #scale
+ */
+ public double getScale() {
+ return scale;
+ }
+
+ /**
+ * @return the sbgnFormat
+ * @see #sbgnFormat
+ */
+ public boolean isSbgnFormat() {
+ return sbgnFormat;
+ }
+
+ /**
+ * @return the nested
+ * @see #nested
+ */
+ public boolean isNested() {
+ return nested;
+ }
+
+ @Override
+ public String toString() {
+ String result = "[" + this.getClass().getSimpleName() + "] " + //
+ "level:" + level + "," + //
+ "scale:" + scale + "," + //
+ "nested:" + nested + "," + //
+ "sbgnFormat:" + sbgnFormat;
+ return result;
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/DrawingException.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/DrawingException.java
index fd059380f6..bf1d439e69 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/DrawingException.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/DrawingException.java
@@ -1,38 +1,38 @@
-package lcsb.mapviewer.converter.graphics;
-
-/**
- * Exception thrown when there are some problems with drawing.
- *
- * @author Piotr Gawron
- *
- */
-public class DrawingException extends Exception {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- *
- * @param string
- * exception message
- * @param e
- * super exception
- */
- public DrawingException(String string, Exception e) {
- super(string, e);
- }
-
- /**
- * Default constructor.
- *
- * @param string
- * exception message
- */
- public DrawingException(String string) {
- super(string);
- }
-
-}
+package lcsb.mapviewer.converter.graphics;
+
+/**
+ * Exception thrown when there are some problems with drawing.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class DrawingException extends Exception {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ *
+ * @param string
+ * exception message
+ * @param e
+ * super exception
+ */
+ public DrawingException(String string, Exception e) {
+ super(string, e);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param string
+ * exception message
+ */
+ public DrawingException(String string) {
+ super(string);
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ImageGenerators.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ImageGenerators.java
index 96bc681dfb..7436591a33 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ImageGenerators.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ImageGenerators.java
@@ -1,178 +1,178 @@
-package lcsb.mapviewer.converter.graphics;
-
-import java.awt.Color;
-import java.io.IOException;
-import java.lang.reflect.InvocationTargetException;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.MimeType;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-
-/**
- * This class is a util class containing information about all currently
- * available implementations of {@link AbstractImageGenerator} class.
- *
- * @author Piotr Gawron
- *
- */
-public class ImageGenerators {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(ImageGenerators.class);
- /**
- * List of {@link AbstractImageGenerator} classes available in the system.
- */
- private List<Pair<String, Class<? extends AbstractImageGenerator>>> availableGenerators;
-
- /**
- * List of all possible objects extending {@link AbstractImageGenerator}
- * interface that are available in the system.
- */
- private List<AbstractImageGenerator> generatorInstances = null;
-
- /**
- * Default constructor.
- */
- public ImageGenerators() {
- try {
- availableGenerators = new ArrayList<Pair<String, Class<? extends AbstractImageGenerator>>>();
- Model model = new ModelFullIndexed(null);
- AbstractImageGenerator.Params params = new AbstractImageGenerator.Params().//
- model(model).//
- width(1).//
- minColor(Color.WHITE).maxColor(Color.WHITE).height(1);
- generatorInstances = new ArrayList<>();
- generatorInstances.add(new PngImageGenerator(params));
- generatorInstances.add(new PdfImageGenerator(params));
- generatorInstances.add(new SvgImageGenerator(params));
- // generatorInstances.add(new JpgImageGenerator(params));
- for (AbstractImageGenerator abstractImageGenerator : generatorInstances) {
- availableGenerators
- .add(new Pair<String, Class<? extends AbstractImageGenerator>>(abstractImageGenerator.getFormatName(), abstractImageGenerator.getClass()));
- }
-
- } catch (DrawingException e) {
- throw new InvalidStateException("Problem with ImageGenarater instance creation...", e);
- }
- }
-
- /**
- * Returns {@link #availableGenerators}.
- *
- * @return {@link #availableGenerators}
- */
- public List<Pair<String, Class<? extends AbstractImageGenerator>>> getAvailableImageGenerators() {
- return availableGenerators;
- }
-
- /**
- * Generates image and saves it to a file.
- *
- * @param generatorClass
- * which {@link AbstractImageGenerator} should be used to generate an
- * image
- * @param params
- * parameters of the image generation process (scaling, size,
- * nesting, etc)
- * @param filename
- * name of the file where result should be saved
- * @return {@link MimeType} of the generated object
- * @throws IOException
- * thrown when there is a problem with output file
- * @throws DrawingException
- * thrown when there is a problem drawing map
- */
- public MimeType generate(Class<? extends AbstractImageGenerator> generatorClass, AbstractImageGenerator.Params params, String filename)
- throws IOException, DrawingException {
- try {
- AbstractImageGenerator generator = generatorClass.getConstructor(AbstractImageGenerator.Params.class).newInstance(params);
- generator.saveToFile(filename);
- return generator.getMimeType();
- } catch (InstantiationException e) {
- throw new InvalidStateException("Problem with ImageGenarater instance creation...", e);
- } catch (IllegalAccessException e) {
- throw new InvalidStateException("Problem with ImageGenarater instance creation...", e);
- } catch (IllegalArgumentException e) {
- throw new InvalidStateException("Problem with ImageGenarater instance creation...", e);
- } catch (InvocationTargetException e) {
- throw new InvalidStateException("Problem with ImageGenarater instance creation...", e);
- } catch (NoSuchMethodException e) {
- throw new InvalidStateException("Problem with ImageGenarater instance creation...", e);
- } catch (SecurityException e) {
- throw new InvalidStateException("Problem with ImageGenarater instance creation...", e);
- }
- }
-
- /**
- * Generates image and saves it to a file.
- *
- * @param generatorClass
- * name of the {@link AbstractImageGenerator} implementation that
- * should be used to generate an image
- * @param params
- * parameters of the image generation process (scaling, size,
- * nesting, etc)
- * @param filename
- * name of the file where result should be saved
- * @return {@link MimeType} of the generated object
- * @throws IOException
- * thrown when there is a problem with output file
- * @throws DrawingException
- * thrown when there is a problem drawing map
- */
- public MimeType generate(String generatorClass, Params params, String filename) throws IOException, DrawingException {
- for (Pair<String, Class<? extends AbstractImageGenerator>> element : availableGenerators) {
- if (element.getRight().getCanonicalName().equals(generatorClass)) {
- return generate(element.getRight(), params, filename);
- }
- }
- throw new InvalidArgumentException("Unknown class type: " + generatorClass);
-
- }
-
- /**
- * Returns file extension that should be used for files generated by
- * implementation of {@link AbstractImageGenerator} class.
- *
- * @param generatorClass
- * name of the class that extends {@link AbstractImageGenerator}
- * @return file extension that should be used for files generated by
- * implementation of {@link AbstractImageGenerator} class
- */
- public String getExtension(String generatorClass) {
- for (Pair<String, Class<? extends AbstractImageGenerator>> element : availableGenerators) {
- if (element.getRight().getCanonicalName().equals(generatorClass)) {
- return getExtension(element.getRight());
- }
- }
- throw new InvalidArgumentException("Unknown class type: " + generatorClass);
- }
-
- /**
- * Returns file extension that should be used for files generated by
- * implementation of {@link AbstractImageGenerator} class.
- *
- * @param generatorClass
- * class that extends {@link AbstractImageGenerator}
- * @return file extension that should be used for files generated by
- * implementation of {@link AbstractImageGenerator} class
- */
- public String getExtension(Class<? extends AbstractImageGenerator> generatorClass) {
- for (AbstractImageGenerator imageGenerator : generatorInstances) {
- if (generatorClass.isAssignableFrom(imageGenerator.getClass())) {
- return imageGenerator.getFileExtension();
- }
- }
- throw new InvalidArgumentException("Unknown class type: " + generatorClass);
- }
-}
+package lcsb.mapviewer.converter.graphics;
+
+import java.awt.Color;
+import java.io.IOException;
+import java.lang.reflect.InvocationTargetException;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.MimeType;
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+
+/**
+ * This class is a util class containing information about all currently
+ * available implementations of {@link AbstractImageGenerator} class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ImageGenerators {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(ImageGenerators.class);
+ /**
+ * List of {@link AbstractImageGenerator} classes available in the system.
+ */
+ private List<Pair<String, Class<? extends AbstractImageGenerator>>> availableGenerators;
+
+ /**
+ * List of all possible objects extending {@link AbstractImageGenerator}
+ * interface that are available in the system.
+ */
+ private List<AbstractImageGenerator> generatorInstances = null;
+
+ /**
+ * Default constructor.
+ */
+ public ImageGenerators() {
+ try {
+ availableGenerators = new ArrayList<Pair<String, Class<? extends AbstractImageGenerator>>>();
+ Model model = new ModelFullIndexed(null);
+ AbstractImageGenerator.Params params = new AbstractImageGenerator.Params().//
+ model(model).//
+ width(1).//
+ minColor(Color.WHITE).maxColor(Color.WHITE).height(1);
+ generatorInstances = new ArrayList<>();
+ generatorInstances.add(new PngImageGenerator(params));
+ generatorInstances.add(new PdfImageGenerator(params));
+ generatorInstances.add(new SvgImageGenerator(params));
+ // generatorInstances.add(new JpgImageGenerator(params));
+ for (AbstractImageGenerator abstractImageGenerator : generatorInstances) {
+ availableGenerators
+ .add(new Pair<String, Class<? extends AbstractImageGenerator>>(abstractImageGenerator.getFormatName(), abstractImageGenerator.getClass()));
+ }
+
+ } catch (DrawingException e) {
+ throw new InvalidStateException("Problem with ImageGenarater instance creation...", e);
+ }
+ }
+
+ /**
+ * Returns {@link #availableGenerators}.
+ *
+ * @return {@link #availableGenerators}
+ */
+ public List<Pair<String, Class<? extends AbstractImageGenerator>>> getAvailableImageGenerators() {
+ return availableGenerators;
+ }
+
+ /**
+ * Generates image and saves it to a file.
+ *
+ * @param generatorClass
+ * which {@link AbstractImageGenerator} should be used to generate an
+ * image
+ * @param params
+ * parameters of the image generation process (scaling, size,
+ * nesting, etc)
+ * @param filename
+ * name of the file where result should be saved
+ * @return {@link MimeType} of the generated object
+ * @throws IOException
+ * thrown when there is a problem with output file
+ * @throws DrawingException
+ * thrown when there is a problem drawing map
+ */
+ public MimeType generate(Class<? extends AbstractImageGenerator> generatorClass, AbstractImageGenerator.Params params, String filename)
+ throws IOException, DrawingException {
+ try {
+ AbstractImageGenerator generator = generatorClass.getConstructor(AbstractImageGenerator.Params.class).newInstance(params);
+ generator.saveToFile(filename);
+ return generator.getMimeType();
+ } catch (InstantiationException e) {
+ throw new InvalidStateException("Problem with ImageGenarater instance creation...", e);
+ } catch (IllegalAccessException e) {
+ throw new InvalidStateException("Problem with ImageGenarater instance creation...", e);
+ } catch (IllegalArgumentException e) {
+ throw new InvalidStateException("Problem with ImageGenarater instance creation...", e);
+ } catch (InvocationTargetException e) {
+ throw new InvalidStateException("Problem with ImageGenarater instance creation...", e);
+ } catch (NoSuchMethodException e) {
+ throw new InvalidStateException("Problem with ImageGenarater instance creation...", e);
+ } catch (SecurityException e) {
+ throw new InvalidStateException("Problem with ImageGenarater instance creation...", e);
+ }
+ }
+
+ /**
+ * Generates image and saves it to a file.
+ *
+ * @param generatorClass
+ * name of the {@link AbstractImageGenerator} implementation that
+ * should be used to generate an image
+ * @param params
+ * parameters of the image generation process (scaling, size,
+ * nesting, etc)
+ * @param filename
+ * name of the file where result should be saved
+ * @return {@link MimeType} of the generated object
+ * @throws IOException
+ * thrown when there is a problem with output file
+ * @throws DrawingException
+ * thrown when there is a problem drawing map
+ */
+ public MimeType generate(String generatorClass, Params params, String filename) throws IOException, DrawingException {
+ for (Pair<String, Class<? extends AbstractImageGenerator>> element : availableGenerators) {
+ if (element.getRight().getCanonicalName().equals(generatorClass)) {
+ return generate(element.getRight(), params, filename);
+ }
+ }
+ throw new InvalidArgumentException("Unknown class type: " + generatorClass);
+
+ }
+
+ /**
+ * Returns file extension that should be used for files generated by
+ * implementation of {@link AbstractImageGenerator} class.
+ *
+ * @param generatorClass
+ * name of the class that extends {@link AbstractImageGenerator}
+ * @return file extension that should be used for files generated by
+ * implementation of {@link AbstractImageGenerator} class
+ */
+ public String getExtension(String generatorClass) {
+ for (Pair<String, Class<? extends AbstractImageGenerator>> element : availableGenerators) {
+ if (element.getRight().getCanonicalName().equals(generatorClass)) {
+ return getExtension(element.getRight());
+ }
+ }
+ throw new InvalidArgumentException("Unknown class type: " + generatorClass);
+ }
+
+ /**
+ * Returns file extension that should be used for files generated by
+ * implementation of {@link AbstractImageGenerator} class.
+ *
+ * @param generatorClass
+ * class that extends {@link AbstractImageGenerator}
+ * @return file extension that should be used for files generated by
+ * implementation of {@link AbstractImageGenerator} class
+ */
+ public String getExtension(Class<? extends AbstractImageGenerator> generatorClass) {
+ for (AbstractImageGenerator imageGenerator : generatorInstances) {
+ if (generatorClass.isAssignableFrom(imageGenerator.getClass())) {
+ return imageGenerator.getFileExtension();
+ }
+ }
+ throw new InvalidArgumentException("Unknown class type: " + generatorClass);
+ }
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/JpgImageGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/JpgImageGenerator.java
index c903920061..e5c57e4b79 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/JpgImageGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/JpgImageGenerator.java
@@ -1,84 +1,84 @@
-package lcsb.mapviewer.converter.graphics;
-
-import java.awt.Graphics2D;
-import java.awt.image.BufferedImage;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.OutputStream;
-
-import javax.imageio.ImageIO;
-
-import lcsb.mapviewer.common.MimeType;
-
-/**
- * This implementation of {@link AbstractImageGenerator} allows to generate JPG
- * images.
- *
- * @author Piotr Gawron
- *
- */
-public class JpgImageGenerator extends NormalImageGenerator {
-
- /**
- * Default constructor. Create an image that is described by params. For more
- * information see
- * {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params
- * params}.
- *
- * @param params
- * parameters used for the image creation.
- * @throws DrawingException
- * thrown when there was a problem with drawing a map
- */
- public JpgImageGenerator(Params params) throws DrawingException {
- super(params);
- }
-
- @Override
- public void saveToFileImplementation(String fileName) throws IOException {
- FileOutputStream fos = new FileOutputStream(new File(fileName));
- saveToOutputStreamImplementation(fos);
- fos.close();
- }
-
- @Override
- public void saveToOutputStreamImplementation(OutputStream os) throws IOException {
- ImageIO.write(getBi(), "JPG", os);
- }
-
- @Override
- public void savePartToFileImplementation(int x, int y, int width, int height, String fileName) throws IOException {
- FileOutputStream fos = new FileOutputStream(new File(fileName));
- savePartToOutputStreamImplementation(x, y, width, height, fos);
- fos.close();
- }
-
- @Override
- public void savePartToOutputStreamImplementation(int x, int y, int width, int height, OutputStream os) throws IOException {
- BufferedImage tmpBI = new BufferedImage(width, height, BufferedImage.TYPE_INT_ARGB);
- Graphics2D tmpGraphics = tmpBI.createGraphics();
- tmpGraphics.drawImage(getBi(), 0, 0, width, height, x, y, x + width, y + width, null);
- ImageIO.write(tmpBI, "JPG", os);
- }
-
- @Override
- public String getFormatName() {
- return "JPG image";
- }
-
- @Override
- public MimeType getMimeType() {
- return MimeType.JPG;
- }
-
- @Override
- public String getFileExtension() {
- return "jpg";
- }
-
- @Override
- protected void closeImageObject() {
- }
-
-}
+package lcsb.mapviewer.converter.graphics;
+
+import java.awt.Graphics2D;
+import java.awt.image.BufferedImage;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStream;
+
+import javax.imageio.ImageIO;
+
+import lcsb.mapviewer.common.MimeType;
+
+/**
+ * This implementation of {@link AbstractImageGenerator} allows to generate JPG
+ * images.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class JpgImageGenerator extends NormalImageGenerator {
+
+ /**
+ * Default constructor. Create an image that is described by params. For more
+ * information see
+ * {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params
+ * params}.
+ *
+ * @param params
+ * parameters used for the image creation.
+ * @throws DrawingException
+ * thrown when there was a problem with drawing a map
+ */
+ public JpgImageGenerator(Params params) throws DrawingException {
+ super(params);
+ }
+
+ @Override
+ public void saveToFileImplementation(String fileName) throws IOException {
+ FileOutputStream fos = new FileOutputStream(new File(fileName));
+ saveToOutputStreamImplementation(fos);
+ fos.close();
+ }
+
+ @Override
+ public void saveToOutputStreamImplementation(OutputStream os) throws IOException {
+ ImageIO.write(getBi(), "JPG", os);
+ }
+
+ @Override
+ public void savePartToFileImplementation(int x, int y, int width, int height, String fileName) throws IOException {
+ FileOutputStream fos = new FileOutputStream(new File(fileName));
+ savePartToOutputStreamImplementation(x, y, width, height, fos);
+ fos.close();
+ }
+
+ @Override
+ public void savePartToOutputStreamImplementation(int x, int y, int width, int height, OutputStream os) throws IOException {
+ BufferedImage tmpBI = new BufferedImage(width, height, BufferedImage.TYPE_INT_ARGB);
+ Graphics2D tmpGraphics = tmpBI.createGraphics();
+ tmpGraphics.drawImage(getBi(), 0, 0, width, height, x, y, x + width, y + width, null);
+ ImageIO.write(tmpBI, "JPG", os);
+ }
+
+ @Override
+ public String getFormatName() {
+ return "JPG image";
+ }
+
+ @Override
+ public MimeType getMimeType() {
+ return MimeType.JPG;
+ }
+
+ @Override
+ public String getFileExtension() {
+ return "jpg";
+ }
+
+ @Override
+ protected void closeImageObject() {
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/MapGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/MapGenerator.java
index 4500e81c15..499b408609 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/MapGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/MapGenerator.java
@@ -1,405 +1,405 @@
-package lcsb.mapviewer.converter.graphics;
-
-import java.io.File;
-import java.io.IOException;
-
-import org.apache.commons.io.FileUtils;
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.model.Model;
-
-/**
- * This class allows to generate set of images that could be later on used by
- * Google Maps API.
- *
- * @author Piotr Gawron
- *
- */
-public class MapGenerator {
-
- /**
- * Parameter class with information for generating set of images:
- * <ul>
- * <li>{@link #model}</li>
- * <li>{@link #directory}</li>
- * <li>{@link #nested}</li>
- * <li>{@link #removeEmpty}</li>
- * <li>{@link #updater}</li>
- * <li>{@link #zoomFactor}</li>
- * <li>{@link #levels}</li>.
- * </ul>
- *
- *
- * @author Piotr Gawron
- *
- */
- public class MapGeneratorParams {
- /**
- * Information about map to be generated.
- *
- */
- private Model model;
- /**
- * Where we want to put the files. The structure of the directory will be as
- * follows: directory/subDirA/subDirB/file.PNG. subDirA is a level of
- * zooming. subDirB is x coordinate of the image. file is y coordinate of
- * the image.
- *
- */
- private String directory;
- /**
- * Do we want to generate images in hierarchical view or normal.
- *
- */
- private boolean nested = false;
- /**
- * Should we remove empty elements in nested view.
- *
- */
- private boolean removeEmpty = false;
- /**
- * Callback function that update progress information.
- *
- */
- private IProgressUpdater updater = new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- };
-
- /**
- * Zoom factor on the lowest level.
- */
- private Double zoomFactor;
-
- /**
- * How many levels.
- */
- private Integer levels;
-
- /**
- * Should sbgn standard be used.
- */
- private boolean sbgn;
-
- /**
- * @param model
- * the model to set
- * @see #model
- * @return full {@link MapGeneratorParams} object
- */
- public MapGeneratorParams model(Model model) {
- this.model = model;
- if (zoomFactor == null) {
- zoomFactor = computeZoomFactor(model);
- }
- if (levels == null) {
- levels = computeZoomLevels(model);
- }
- return this;
- }
-
- /**
- * @param directory
- * the directory to set
- * @see #directory
- * @return full {@link MapGeneratorParams} object
- */
- public MapGeneratorParams directory(String directory) {
- this.directory = directory;
- return this;
- }
-
- /**
- * @return the nested
- * @see #nested
- */
- public boolean isNested() {
- return nested;
- }
-
- /**
- * @param nested
- * the nested to set
- * @see #nested
- * @return full {@link MapGeneratorParams} object
- */
- public MapGeneratorParams nested(boolean nested) {
- this.nested = nested;
- return this;
- }
-
- /**
- * @return the removeEmpty
- * @see #removeEmpty
- */
- public boolean isRemoveEmpty() {
- return removeEmpty;
- }
-
- /**
- * @param removeEmpty
- * the removeEmpty to set
- * @see #removeEmpty
- * @return full {@link MapGeneratorParams} object
- */
- public MapGeneratorParams removeEmpty(boolean removeEmpty) {
- this.removeEmpty = removeEmpty;
- return this;
- }
-
- /**
- * @return the updater
- * @see #updater
- */
- public IProgressUpdater getUpdater() {
- return updater;
- }
-
- /**
- * @param updater
- * the updater to set
- * @see #updater
- * @return full {@link MapGeneratorParams} object
- */
- public MapGeneratorParams updater(IProgressUpdater updater) {
- this.updater = updater;
- return this;
- }
-
- /**
- * @return the zoomFactor
- * @see #zoomFactor
- */
- public Double getZoomFactor() {
- return zoomFactor;
- }
-
- /**
- * @param zoomFactor
- * the zoomFactor to set
- * @see #zoomFactor
- * @return full {@link MapGeneratorParams} object
- */
- public MapGeneratorParams zoomFactor(Double zoomFactor) {
- this.zoomFactor = zoomFactor;
- return this;
- }
-
- /**
- * @return the levels
- * @see #levels
- */
- public Integer getLevels() {
- return levels;
- }
-
- /**
- * @param levels
- * the levels to set
- * @see #levels
- * @return full {@link MapGeneratorParams} object
- */
- public MapGeneratorParams levels(Integer levels) {
- this.levels = levels;
- return this;
- }
-
- /**
- * @return the sbgn
- * @see #sbgn
- */
- public boolean isSbgn() {
- return sbgn;
- }
-
- /**
- * @param sbgn
- * the sbgn to set
- * @see #sbgn
- * @return object with all parameters
- */
- public MapGeneratorParams sbgn(boolean sbgn) {
- this.sbgn = sbgn;
- return this;
- }
-
- }
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(MapGenerator.class.getName());
-
- /**
- * Default tile size. It must be 256px*256px, if different value is chosen
- * then there are problems with positioning all elements by GoogleMaps API
- * (like putting markers, line, getting position etc).
- */
- public static final int TILE_SIZE = 256;
-
- /**
- * Because generating of PNG file require to transform the whole Model class
- * into canvas, the bigger image is created and after the image is created
- * small chunks are sliced and saved to files. For instance if
- * TILES_CACHE_NUM=4 and TILE_SIZE=256, then ImageGenerator will create PNG
- * images 1024px*1024px and this images are sliced into 256px*256px images. Of
- * course TILES_CACHE_NUM cannot be too big due to Out of Memory problem.
- */
-
- static final int TILES_CACHE_NUM = 4;
-
- /**
- * This method generates PNG images used by GoogleMaps API.
- *
- * @param params
- * {@link MapGeneratorParams params} used for generating images
- * @throws IOException
- * exception thrown when there are some problems with creating
- * images
- * @throws DrawingException
- * thrown when there was a problem with drawing a map
- */
- public void generateMapImages(MapGeneratorParams params) throws IOException, DrawingException {
-
- if (params.nested) {
- logger.debug("Creating nested model with " + params.levels + " levels and maximum zoom rate: " + params.zoomFactor);
- } else {
- logger.debug("Creating not nested model with " + params.levels + " levels and maximum zoom rate: " + params.zoomFactor);
- }
-
- // compute number of tiles (for progress bar)
- double num = 0;
- for (int i = 0; i <= params.levels; i++) {
- double m = Math.ceil((int) Math.pow(2, i)) / TILES_CACHE_NUM;
- m = Math.ceil(m);
- m *= TILES_CACHE_NUM;
- num += m * m;
- }
-
- String zoomDirStr = params.directory;
- File zoomDir = new File(zoomDirStr);
- if (zoomDir.isDirectory()) {
- logger.warn("Removing directory: " + zoomDir.getAbsolutePath());
- FileUtils.deleteDirectory(zoomDir);
- } else if (zoomDir.isFile()) {
- logger.warn("Removing file: " + zoomDir.getAbsolutePath());
- zoomDir.delete();
- }
-
- int progress = 0;
- for (int i = 0; i <= params.levels; i++) {
- zoomDirStr = params.directory + System.getProperty("file.separator") + (i + Configuration.MIN_ZOOM_LEVEL) + System.getProperty("file.separator");
- int tiles = (int) (Math.pow(2, i));
- for (int j = 0; j < tiles + TILES_CACHE_NUM; j++) {
- zoomDir = new File(zoomDirStr + System.getProperty("file.separator") + j);
- if (!zoomDir.exists()) {
-
- if (!zoomDir.mkdirs()) {
- logger.warn("Problem with creating dir: " + zoomDir.getAbsolutePath());
- }
- }
- }
- for (int j = 0; j < tiles; j += TILES_CACHE_NUM) {
- for (int k = 0; k < tiles; k += TILES_CACHE_NUM) {
- params.updater.setProgress((IProgressUpdater.MAX_PROGRESS * progress / num));
- progress += TILES_CACHE_NUM * TILES_CACHE_NUM;
- if (j * TILE_SIZE * params.zoomFactor > params.model.getWidth() || k * TILE_SIZE * params.zoomFactor > params.model.getHeight()) {
- continue;
- } else {
- Params imgParams = new Params();
- imgParams.scale(params.zoomFactor);
- imgParams.x(j * TILE_SIZE * params.zoomFactor);
- imgParams.y(k * TILE_SIZE * params.zoomFactor);
- imgParams.width(TILE_SIZE * TILES_CACHE_NUM);
- imgParams.height(TILE_SIZE * TILES_CACHE_NUM);
- imgParams.model(params.model);
- imgParams.sbgn(params.sbgn);
- imgParams.level(i);
- imgParams.nested(params.nested);
- PngImageGenerator generator = new PngImageGenerator(imgParams);
- for (int cx = 0; cx < TILES_CACHE_NUM; cx++) {
- for (int cy = 0; cy < TILES_CACHE_NUM; cy++) {
- if ((j + cx) * TILE_SIZE * params.zoomFactor >= params.model.getWidth()
- || (k + cy) * TILE_SIZE * params.zoomFactor >= params.model.getHeight()) {
- continue;
- } else {
- String fileName = zoomDirStr + (j + cx) + System.getProperty("file.separator") + (k + cy) + ".PNG";
- generator.savePartToFile(cx * TILE_SIZE, cy * TILE_SIZE, TILE_SIZE, TILE_SIZE, fileName);
- }
- }
- }
- }
- }
- }
- params.zoomFactor /= 2;
- }
- }
-
- /**
- * Computes how many zoom levels should exists for the map model.
- *
- * @param model
- * map model
- * @return zoom levels for the model
- */
- public int computeZoomLevels(final Model model) {
- return (int) Math.ceil(Math.log(computeZoomFactor(model)) / Math.log(2));
- }
-
- /**
- * Computes the scale that should be used on the top zoom level.
- *
- * @param model
- * model for which computation is done
- * @return scale on the top zoom level
- */
- public double computeZoomFactor(final Model model) {
- return Math.max(model.getHeight(), model.getWidth()) / (TILE_SIZE);
- }
-
- /**
- * Removes files that were generated for the layout.
- *
- * @param dbLayout
- * layout object for which images will be removed
- * @throws IOException
- * thrown whene there are some problems with removing files
- */
- public void removeLayout(final Layout dbLayout) throws IOException {
- removeLayout(dbLayout, null);
- }
-
- /**
- * Removes files that were generated for the layout.
- *
- * @param dbLayout
- * layout object for which images will be removed
- * @param homeDir
- * determines the directory where images are stored (it's optional)
- * @throws IOException
- * thrown whene there are some problems with removing files
- */
- public void removeLayout(final Layout dbLayout, String homeDir) throws IOException {
- String directory = dbLayout.getDirectory();
- File dir = new File(directory);
- if (!dir.isAbsolute() && homeDir != null) {
- dir = new File(homeDir + "/" + directory);
- }
- if (dir.exists()) {
- FileUtils.deleteDirectory(dir);
- } else {
- logger.warn("Trying to remove dir that doesn't exist: " + dir.getAbsolutePath() + " (" + directory + ")");
- }
- if (dbLayout.getParentLayout() == null) {
- for (Layout child : dbLayout.getLayouts()) {
- removeLayout(child, homeDir);
- }
- }
- }
-
-}
+package lcsb.mapviewer.converter.graphics;
+
+import java.io.File;
+import java.io.IOException;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
+import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.model.Model;
+
+/**
+ * This class allows to generate set of images that could be later on used by
+ * Google Maps API.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class MapGenerator {
+
+ /**
+ * Parameter class with information for generating set of images:
+ * <ul>
+ * <li>{@link #model}</li>
+ * <li>{@link #directory}</li>
+ * <li>{@link #nested}</li>
+ * <li>{@link #removeEmpty}</li>
+ * <li>{@link #updater}</li>
+ * <li>{@link #zoomFactor}</li>
+ * <li>{@link #levels}</li>.
+ * </ul>
+ *
+ *
+ * @author Piotr Gawron
+ *
+ */
+ public class MapGeneratorParams {
+ /**
+ * Information about map to be generated.
+ *
+ */
+ private Model model;
+ /**
+ * Where we want to put the files. The structure of the directory will be as
+ * follows: directory/subDirA/subDirB/file.PNG. subDirA is a level of
+ * zooming. subDirB is x coordinate of the image. file is y coordinate of
+ * the image.
+ *
+ */
+ private String directory;
+ /**
+ * Do we want to generate images in hierarchical view or normal.
+ *
+ */
+ private boolean nested = false;
+ /**
+ * Should we remove empty elements in nested view.
+ *
+ */
+ private boolean removeEmpty = false;
+ /**
+ * Callback function that update progress information.
+ *
+ */
+ private IProgressUpdater updater = new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ };
+
+ /**
+ * Zoom factor on the lowest level.
+ */
+ private Double zoomFactor;
+
+ /**
+ * How many levels.
+ */
+ private Integer levels;
+
+ /**
+ * Should sbgn standard be used.
+ */
+ private boolean sbgn;
+
+ /**
+ * @param model
+ * the model to set
+ * @see #model
+ * @return full {@link MapGeneratorParams} object
+ */
+ public MapGeneratorParams model(Model model) {
+ this.model = model;
+ if (zoomFactor == null) {
+ zoomFactor = computeZoomFactor(model);
+ }
+ if (levels == null) {
+ levels = computeZoomLevels(model);
+ }
+ return this;
+ }
+
+ /**
+ * @param directory
+ * the directory to set
+ * @see #directory
+ * @return full {@link MapGeneratorParams} object
+ */
+ public MapGeneratorParams directory(String directory) {
+ this.directory = directory;
+ return this;
+ }
+
+ /**
+ * @return the nested
+ * @see #nested
+ */
+ public boolean isNested() {
+ return nested;
+ }
+
+ /**
+ * @param nested
+ * the nested to set
+ * @see #nested
+ * @return full {@link MapGeneratorParams} object
+ */
+ public MapGeneratorParams nested(boolean nested) {
+ this.nested = nested;
+ return this;
+ }
+
+ /**
+ * @return the removeEmpty
+ * @see #removeEmpty
+ */
+ public boolean isRemoveEmpty() {
+ return removeEmpty;
+ }
+
+ /**
+ * @param removeEmpty
+ * the removeEmpty to set
+ * @see #removeEmpty
+ * @return full {@link MapGeneratorParams} object
+ */
+ public MapGeneratorParams removeEmpty(boolean removeEmpty) {
+ this.removeEmpty = removeEmpty;
+ return this;
+ }
+
+ /**
+ * @return the updater
+ * @see #updater
+ */
+ public IProgressUpdater getUpdater() {
+ return updater;
+ }
+
+ /**
+ * @param updater
+ * the updater to set
+ * @see #updater
+ * @return full {@link MapGeneratorParams} object
+ */
+ public MapGeneratorParams updater(IProgressUpdater updater) {
+ this.updater = updater;
+ return this;
+ }
+
+ /**
+ * @return the zoomFactor
+ * @see #zoomFactor
+ */
+ public Double getZoomFactor() {
+ return zoomFactor;
+ }
+
+ /**
+ * @param zoomFactor
+ * the zoomFactor to set
+ * @see #zoomFactor
+ * @return full {@link MapGeneratorParams} object
+ */
+ public MapGeneratorParams zoomFactor(Double zoomFactor) {
+ this.zoomFactor = zoomFactor;
+ return this;
+ }
+
+ /**
+ * @return the levels
+ * @see #levels
+ */
+ public Integer getLevels() {
+ return levels;
+ }
+
+ /**
+ * @param levels
+ * the levels to set
+ * @see #levels
+ * @return full {@link MapGeneratorParams} object
+ */
+ public MapGeneratorParams levels(Integer levels) {
+ this.levels = levels;
+ return this;
+ }
+
+ /**
+ * @return the sbgn
+ * @see #sbgn
+ */
+ public boolean isSbgn() {
+ return sbgn;
+ }
+
+ /**
+ * @param sbgn
+ * the sbgn to set
+ * @see #sbgn
+ * @return object with all parameters
+ */
+ public MapGeneratorParams sbgn(boolean sbgn) {
+ this.sbgn = sbgn;
+ return this;
+ }
+
+ }
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(MapGenerator.class.getName());
+
+ /**
+ * Default tile size. It must be 256px*256px, if different value is chosen
+ * then there are problems with positioning all elements by GoogleMaps API
+ * (like putting markers, line, getting position etc).
+ */
+ public static final int TILE_SIZE = 256;
+
+ /**
+ * Because generating of PNG file require to transform the whole Model class
+ * into canvas, the bigger image is created and after the image is created
+ * small chunks are sliced and saved to files. For instance if
+ * TILES_CACHE_NUM=4 and TILE_SIZE=256, then ImageGenerator will create PNG
+ * images 1024px*1024px and this images are sliced into 256px*256px images. Of
+ * course TILES_CACHE_NUM cannot be too big due to Out of Memory problem.
+ */
+
+ static final int TILES_CACHE_NUM = 4;
+
+ /**
+ * This method generates PNG images used by GoogleMaps API.
+ *
+ * @param params
+ * {@link MapGeneratorParams params} used for generating images
+ * @throws IOException
+ * exception thrown when there are some problems with creating
+ * images
+ * @throws DrawingException
+ * thrown when there was a problem with drawing a map
+ */
+ public void generateMapImages(MapGeneratorParams params) throws IOException, DrawingException {
+
+ if (params.nested) {
+ logger.debug("Creating nested model with " + params.levels + " levels and maximum zoom rate: " + params.zoomFactor);
+ } else {
+ logger.debug("Creating not nested model with " + params.levels + " levels and maximum zoom rate: " + params.zoomFactor);
+ }
+
+ // compute number of tiles (for progress bar)
+ double num = 0;
+ for (int i = 0; i <= params.levels; i++) {
+ double m = Math.ceil((int) Math.pow(2, i)) / TILES_CACHE_NUM;
+ m = Math.ceil(m);
+ m *= TILES_CACHE_NUM;
+ num += m * m;
+ }
+
+ String zoomDirStr = params.directory;
+ File zoomDir = new File(zoomDirStr);
+ if (zoomDir.isDirectory()) {
+ logger.warn("Removing directory: " + zoomDir.getAbsolutePath());
+ FileUtils.deleteDirectory(zoomDir);
+ } else if (zoomDir.isFile()) {
+ logger.warn("Removing file: " + zoomDir.getAbsolutePath());
+ zoomDir.delete();
+ }
+
+ int progress = 0;
+ for (int i = 0; i <= params.levels; i++) {
+ zoomDirStr = params.directory + System.getProperty("file.separator") + (i + Configuration.MIN_ZOOM_LEVEL) + System.getProperty("file.separator");
+ int tiles = (int) (Math.pow(2, i));
+ for (int j = 0; j < tiles + TILES_CACHE_NUM; j++) {
+ zoomDir = new File(zoomDirStr + System.getProperty("file.separator") + j);
+ if (!zoomDir.exists()) {
+
+ if (!zoomDir.mkdirs()) {
+ logger.warn("Problem with creating dir: " + zoomDir.getAbsolutePath());
+ }
+ }
+ }
+ for (int j = 0; j < tiles; j += TILES_CACHE_NUM) {
+ for (int k = 0; k < tiles; k += TILES_CACHE_NUM) {
+ params.updater.setProgress((IProgressUpdater.MAX_PROGRESS * progress / num));
+ progress += TILES_CACHE_NUM * TILES_CACHE_NUM;
+ if (j * TILE_SIZE * params.zoomFactor > params.model.getWidth() || k * TILE_SIZE * params.zoomFactor > params.model.getHeight()) {
+ continue;
+ } else {
+ Params imgParams = new Params();
+ imgParams.scale(params.zoomFactor);
+ imgParams.x(j * TILE_SIZE * params.zoomFactor);
+ imgParams.y(k * TILE_SIZE * params.zoomFactor);
+ imgParams.width(TILE_SIZE * TILES_CACHE_NUM);
+ imgParams.height(TILE_SIZE * TILES_CACHE_NUM);
+ imgParams.model(params.model);
+ imgParams.sbgn(params.sbgn);
+ imgParams.level(i);
+ imgParams.nested(params.nested);
+ PngImageGenerator generator = new PngImageGenerator(imgParams);
+ for (int cx = 0; cx < TILES_CACHE_NUM; cx++) {
+ for (int cy = 0; cy < TILES_CACHE_NUM; cy++) {
+ if ((j + cx) * TILE_SIZE * params.zoomFactor >= params.model.getWidth()
+ || (k + cy) * TILE_SIZE * params.zoomFactor >= params.model.getHeight()) {
+ continue;
+ } else {
+ String fileName = zoomDirStr + (j + cx) + System.getProperty("file.separator") + (k + cy) + ".PNG";
+ generator.savePartToFile(cx * TILE_SIZE, cy * TILE_SIZE, TILE_SIZE, TILE_SIZE, fileName);
+ }
+ }
+ }
+ }
+ }
+ }
+ params.zoomFactor /= 2;
+ }
+ }
+
+ /**
+ * Computes how many zoom levels should exists for the map model.
+ *
+ * @param model
+ * map model
+ * @return zoom levels for the model
+ */
+ public int computeZoomLevels(final Model model) {
+ return (int) Math.ceil(Math.log(computeZoomFactor(model)) / Math.log(2));
+ }
+
+ /**
+ * Computes the scale that should be used on the top zoom level.
+ *
+ * @param model
+ * model for which computation is done
+ * @return scale on the top zoom level
+ */
+ public double computeZoomFactor(final Model model) {
+ return Math.max(model.getHeight(), model.getWidth()) / (TILE_SIZE);
+ }
+
+ /**
+ * Removes files that were generated for the layout.
+ *
+ * @param dbLayout
+ * layout object for which images will be removed
+ * @throws IOException
+ * thrown whene there are some problems with removing files
+ */
+ public void removeLayout(final Layout dbLayout) throws IOException {
+ removeLayout(dbLayout, null);
+ }
+
+ /**
+ * Removes files that were generated for the layout.
+ *
+ * @param dbLayout
+ * layout object for which images will be removed
+ * @param homeDir
+ * determines the directory where images are stored (it's optional)
+ * @throws IOException
+ * thrown whene there are some problems with removing files
+ */
+ public void removeLayout(final Layout dbLayout, String homeDir) throws IOException {
+ String directory = dbLayout.getDirectory();
+ File dir = new File(directory);
+ if (!dir.isAbsolute() && homeDir != null) {
+ dir = new File(homeDir + "/" + directory);
+ }
+ if (dir.exists()) {
+ FileUtils.deleteDirectory(dir);
+ } else {
+ logger.warn("Trying to remove dir that doesn't exist: " + dir.getAbsolutePath() + " (" + directory + ")");
+ }
+ if (dbLayout.getParentLayout() == null) {
+ for (Layout child : dbLayout.getLayouts()) {
+ removeLayout(child, homeDir);
+ }
+ }
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/NormalImageGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/NormalImageGenerator.java
index 5c6e6fa3d3..aa325fef7d 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/NormalImageGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/NormalImageGenerator.java
@@ -1,65 +1,65 @@
-package lcsb.mapviewer.converter.graphics;
-
-import java.awt.image.BufferedImage;
-
-import org.apache.log4j.Logger;
-
-/**
- * Extension of the image generator class that use standard awt implementation
- * taht allows basic export.
- *
- * @author Piotr Gawron
- *
- */
-public abstract class NormalImageGenerator extends AbstractImageGenerator {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(NormalImageGenerator.class);
-
- /**
- * Buffered image structure used for image generating.
- */
- private BufferedImage bi;
-
- /**
- * Default constructor. Create an image that is described by params. For more
- * information see
- * {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params
- * params}.
- *
- * @param params
- * parameters used for the image creation.
- * @throws DrawingException
- * thrown when there was a problem with drawing a map
- */
- protected NormalImageGenerator(final Params params) throws DrawingException {
- super(params);
- }
-
- @Override
- protected void createImageObject(final double width, final double height) {
- bi = new BufferedImage((int) width, (int) height, BufferedImage.TYPE_INT_ARGB);
- setGraphics(bi.createGraphics());
- }
-
- /**
- * @return the bi
- * @throws DrawingException
- * @see #bi
- */
- protected BufferedImage getBi() {
- return bi;
- }
-
- /**
- * @param bi
- * the bi to set
- * @see #bi
- */
- protected void setBi(BufferedImage bi) {
- this.bi = bi;
- }
-
-}
+package lcsb.mapviewer.converter.graphics;
+
+import java.awt.image.BufferedImage;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Extension of the image generator class that use standard awt implementation
+ * taht allows basic export.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public abstract class NormalImageGenerator extends AbstractImageGenerator {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(NormalImageGenerator.class);
+
+ /**
+ * Buffered image structure used for image generating.
+ */
+ private BufferedImage bi;
+
+ /**
+ * Default constructor. Create an image that is described by params. For more
+ * information see
+ * {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params
+ * params}.
+ *
+ * @param params
+ * parameters used for the image creation.
+ * @throws DrawingException
+ * thrown when there was a problem with drawing a map
+ */
+ protected NormalImageGenerator(final Params params) throws DrawingException {
+ super(params);
+ }
+
+ @Override
+ protected void createImageObject(final double width, final double height) {
+ bi = new BufferedImage((int) width, (int) height, BufferedImage.TYPE_INT_ARGB);
+ setGraphics(bi.createGraphics());
+ }
+
+ /**
+ * @return the bi
+ * @throws DrawingException
+ * @see #bi
+ */
+ protected BufferedImage getBi() {
+ return bi;
+ }
+
+ /**
+ * @param bi
+ * the bi to set
+ * @see #bi
+ */
+ protected void setBi(BufferedImage bi) {
+ this.bi = bi;
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/PdfImageGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/PdfImageGenerator.java
index 504b4e2d1c..3fd3fab697 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/PdfImageGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/PdfImageGenerator.java
@@ -1,115 +1,115 @@
-package lcsb.mapviewer.converter.graphics;
-
-import java.awt.Graphics2D;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.OutputStream;
-
-import org.apache.commons.io.output.ByteArrayOutputStream;
-
-import com.itextpdf.awt.PdfGraphics2D;
-import com.itextpdf.text.Document;
-import com.itextpdf.text.DocumentException;
-import com.itextpdf.text.Rectangle;
-import com.itextpdf.text.pdf.PdfContentByte;
-import com.itextpdf.text.pdf.PdfWriter;
-
-import lcsb.mapviewer.common.MimeType;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-/**
- * This class implements PDF generator for the image object. This class uses
- * itext library to create all converters.
- *
- * @author Piotr Gawron
- *
- */
-public class PdfImageGenerator extends AbstractImageGenerator {
- /**
- * Stream where pdf data will be generated. When request to save pdf appears
- * this stream is used to generate file.
- */
- private ByteArrayOutputStream inMemoryOutputStream;
-
- /**
- * Object representing pdf document.
- */
- private Document pdfDocument;
-
- @Override
- protected void createImageObject(final double width, final double height) {
- try {
- inMemoryOutputStream = new ByteArrayOutputStream();
- pdfDocument = new Document(new Rectangle((int) width, (int) height));
- PdfWriter writer = PdfWriter.getInstance(pdfDocument, inMemoryOutputStream);
- pdfDocument.open();
- PdfContentByte cb = writer.getDirectContent();
- Graphics2D g2d = new PdfGraphics2D(cb, (float) width, (float) height);
-
- setGraphics(g2d);
- } catch (DocumentException e) {
- throw new InvalidStateException("Problem with initializing pdf generator", e);
- }
-
- }
-
- @Override
- public void saveToFileImplementation(final String fileName) throws IOException {
- FileOutputStream fos = new FileOutputStream(fileName);
- saveToOutputStreamImplementation(fos);
- fos.close();
- }
-
- /**
- * Default constructor. Create an image that is described by params. For more
- * information see
- * {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params
- * params}.
- *
- * @param params
- * parameters used for the image creation.
- * @throws DrawingException
- * thrown when there was a problem with drawing a map
- */
- public PdfImageGenerator(final Params params) throws DrawingException {
- super(params);
- }
-
- @Override
- protected void closeImageObject() {
- getGraphics().dispose();
- pdfDocument.close();
- }
-
- @Override
- public void saveToOutputStreamImplementation(OutputStream os) throws IOException {
- inMemoryOutputStream.writeTo(os);
- }
-
- @Override
- public void savePartToFileImplementation(int x, int y, int width, int height, String fileName) throws IOException {
- throw new NotImplementedException("Partial save is not implemented in PNG image generator");
- }
-
- @Override
- public void savePartToOutputStreamImplementation(int x, int y, int width, int height, OutputStream os) throws IOException {
- throw new NotImplementedException("Partial save is not implemented in PNG image generator");
- }
-
- @Override
- public String getFormatName() {
- return "PDF";
- }
-
- @Override
- public MimeType getMimeType() {
- return MimeType.PDF;
- }
-
- @Override
- public String getFileExtension() {
- return "pdf";
- }
-
-}
+package lcsb.mapviewer.converter.graphics;
+
+import java.awt.Graphics2D;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStream;
+
+import org.apache.commons.io.output.ByteArrayOutputStream;
+
+import com.itextpdf.awt.PdfGraphics2D;
+import com.itextpdf.text.Document;
+import com.itextpdf.text.DocumentException;
+import com.itextpdf.text.Rectangle;
+import com.itextpdf.text.pdf.PdfContentByte;
+import com.itextpdf.text.pdf.PdfWriter;
+
+import lcsb.mapviewer.common.MimeType;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * This class implements PDF generator for the image object. This class uses
+ * itext library to create all converters.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class PdfImageGenerator extends AbstractImageGenerator {
+ /**
+ * Stream where pdf data will be generated. When request to save pdf appears
+ * this stream is used to generate file.
+ */
+ private ByteArrayOutputStream inMemoryOutputStream;
+
+ /**
+ * Object representing pdf document.
+ */
+ private Document pdfDocument;
+
+ @Override
+ protected void createImageObject(final double width, final double height) {
+ try {
+ inMemoryOutputStream = new ByteArrayOutputStream();
+ pdfDocument = new Document(new Rectangle((int) width, (int) height));
+ PdfWriter writer = PdfWriter.getInstance(pdfDocument, inMemoryOutputStream);
+ pdfDocument.open();
+ PdfContentByte cb = writer.getDirectContent();
+ Graphics2D g2d = new PdfGraphics2D(cb, (float) width, (float) height);
+
+ setGraphics(g2d);
+ } catch (DocumentException e) {
+ throw new InvalidStateException("Problem with initializing pdf generator", e);
+ }
+
+ }
+
+ @Override
+ public void saveToFileImplementation(final String fileName) throws IOException {
+ FileOutputStream fos = new FileOutputStream(fileName);
+ saveToOutputStreamImplementation(fos);
+ fos.close();
+ }
+
+ /**
+ * Default constructor. Create an image that is described by params. For more
+ * information see
+ * {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params
+ * params}.
+ *
+ * @param params
+ * parameters used for the image creation.
+ * @throws DrawingException
+ * thrown when there was a problem with drawing a map
+ */
+ public PdfImageGenerator(final Params params) throws DrawingException {
+ super(params);
+ }
+
+ @Override
+ protected void closeImageObject() {
+ getGraphics().dispose();
+ pdfDocument.close();
+ }
+
+ @Override
+ public void saveToOutputStreamImplementation(OutputStream os) throws IOException {
+ inMemoryOutputStream.writeTo(os);
+ }
+
+ @Override
+ public void savePartToFileImplementation(int x, int y, int width, int height, String fileName) throws IOException {
+ throw new NotImplementedException("Partial save is not implemented in PNG image generator");
+ }
+
+ @Override
+ public void savePartToOutputStreamImplementation(int x, int y, int width, int height, OutputStream os) throws IOException {
+ throw new NotImplementedException("Partial save is not implemented in PNG image generator");
+ }
+
+ @Override
+ public String getFormatName() {
+ return "PDF";
+ }
+
+ @Override
+ public MimeType getMimeType() {
+ return MimeType.PDF;
+ }
+
+ @Override
+ public String getFileExtension() {
+ return "pdf";
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/PngImageGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/PngImageGenerator.java
index 77f65da695..59a2601c5a 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/PngImageGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/PngImageGenerator.java
@@ -1,92 +1,92 @@
-package lcsb.mapviewer.converter.graphics;
-
-import java.awt.Graphics2D;
-import java.awt.image.BufferedImage;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.OutputStream;
-
-import javax.imageio.ImageIO;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.MimeType;
-
-/**
- * This implementation of {@link AbstractImageGenerator} allows to generate PNG
- * images.
- *
- * @author Piotr Gawron
- *
- */
-public class PngImageGenerator extends NormalImageGenerator {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(PngImageGenerator.class);
-
- /**
- * Default constructor. Create an image that is described by params. For more
- * information see
- * {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params
- * params}.
- *
- * @param params
- * parameters used for the image creation.
- * @throws DrawingException
- * thrown when there was a problem with drawing a map
- */
- public PngImageGenerator(Params params) throws DrawingException {
- super(params);
- }
-
- @Override
- protected void closeImageObject() {
- }
-
- @Override
- public void saveToFileImplementation(String fileName) throws IOException {
- FileOutputStream fos = new FileOutputStream(new File(fileName));
- saveToOutputStreamImplementation(fos);
- fos.close();
- }
-
- @Override
- public void saveToOutputStreamImplementation(OutputStream os) throws IOException {
- ImageIO.write(getBi(), "PNG", os);
- }
-
- @Override
- public void savePartToFileImplementation(int x, int y, int width, int height, String fileName) throws IOException {
- FileOutputStream fos = new FileOutputStream(new File(fileName));
- savePartToOutputStreamImplementation(x, y, width, height, fos);
- fos.close();
- }
-
- @Override
- public void savePartToOutputStreamImplementation(int x, int y, int width, int height, OutputStream os) throws IOException {
- BufferedImage tmpBI = new BufferedImage(width, height, BufferedImage.TYPE_INT_ARGB);
- Graphics2D tmpGraphics = tmpBI.createGraphics();
- tmpGraphics.drawImage(getBi(), 0, 0, width, height, x, y, x + width, y + width, null);
- ImageIO.write(tmpBI, "PNG", os);
- }
-
- @Override
- public String getFormatName() {
- return "PNG image";
- }
-
- @Override
- public MimeType getMimeType() {
- return MimeType.PNG;
- }
-
- @Override
- public String getFileExtension() {
- return "png";
- }
-
-}
+package lcsb.mapviewer.converter.graphics;
+
+import java.awt.Graphics2D;
+import java.awt.image.BufferedImage;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStream;
+
+import javax.imageio.ImageIO;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.MimeType;
+
+/**
+ * This implementation of {@link AbstractImageGenerator} allows to generate PNG
+ * images.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class PngImageGenerator extends NormalImageGenerator {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(PngImageGenerator.class);
+
+ /**
+ * Default constructor. Create an image that is described by params. For more
+ * information see
+ * {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params
+ * params}.
+ *
+ * @param params
+ * parameters used for the image creation.
+ * @throws DrawingException
+ * thrown when there was a problem with drawing a map
+ */
+ public PngImageGenerator(Params params) throws DrawingException {
+ super(params);
+ }
+
+ @Override
+ protected void closeImageObject() {
+ }
+
+ @Override
+ public void saveToFileImplementation(String fileName) throws IOException {
+ FileOutputStream fos = new FileOutputStream(new File(fileName));
+ saveToOutputStreamImplementation(fos);
+ fos.close();
+ }
+
+ @Override
+ public void saveToOutputStreamImplementation(OutputStream os) throws IOException {
+ ImageIO.write(getBi(), "PNG", os);
+ }
+
+ @Override
+ public void savePartToFileImplementation(int x, int y, int width, int height, String fileName) throws IOException {
+ FileOutputStream fos = new FileOutputStream(new File(fileName));
+ savePartToOutputStreamImplementation(x, y, width, height, fos);
+ fos.close();
+ }
+
+ @Override
+ public void savePartToOutputStreamImplementation(int x, int y, int width, int height, OutputStream os) throws IOException {
+ BufferedImage tmpBI = new BufferedImage(width, height, BufferedImage.TYPE_INT_ARGB);
+ Graphics2D tmpGraphics = tmpBI.createGraphics();
+ tmpGraphics.drawImage(getBi(), 0, 0, width, height, x, y, x + width, y + width, null);
+ ImageIO.write(tmpBI, "PNG", os);
+ }
+
+ @Override
+ public String getFormatName() {
+ return "PNG image";
+ }
+
+ @Override
+ public MimeType getMimeType() {
+ return MimeType.PNG;
+ }
+
+ @Override
+ public String getFileExtension() {
+ return "png";
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/SvgImageGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/SvgImageGenerator.java
index bf97fec4fd..6a1aa4f203 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/SvgImageGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/SvgImageGenerator.java
@@ -1,95 +1,95 @@
-package lcsb.mapviewer.converter.graphics;
-
-import java.io.IOException;
-import java.io.OutputStream;
-import java.io.OutputStreamWriter;
-
-import lcsb.mapviewer.common.MimeType;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-import org.apache.batik.dom.GenericDOMImplementation;
-import org.apache.batik.svggen.SVGGraphics2D;
-import org.apache.batik.svggen.SVGGraphics2DIOException;
-import org.w3c.dom.DOMImplementation;
-import org.w3c.dom.Document;
-
-/**
- * This class implements SVG generator for the image object.This class uses
- * batik library to create all converters.
- *
- * @author Piotr Gawron
- *
- */
-public class SvgImageGenerator extends AbstractImageGenerator {
-
- @Override
- protected void createImageObject(final double width, final double height) {
-
- // Get a DOMImplementation.
- DOMImplementation domImpl = GenericDOMImplementation.getDOMImplementation();
-
- // Create an instance of org.w3c.dom.Document.
- String svgNS = "http://www.w3.org/2000/svg";
- Document document = domImpl.createDocument(svgNS, "svg", null);
-
- // Create an instance of the SVG Generator.
- setGraphics(new SVGGraphics2D(document));
-
- }
-
- @Override
- public void saveToFileImplementation(final String fileName) throws SVGGraphics2DIOException {
- ((SVGGraphics2D) getGraphics()).stream(fileName);
- }
-
- /**
- * Default constructor. Create an image that is described by params. For more
- * information see
- * {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params
- * params}.
- *
- * @param params
- * parameters used for the image creation.
- * @throws DrawingException
- * thrown when there was a problem with drawing a map
- */
- public SvgImageGenerator(final Params params) throws DrawingException {
- super(params);
- }
-
- @Override
- protected void closeImageObject() {
- }
-
- @Override
- public void saveToOutputStreamImplementation(OutputStream os) throws IOException {
- ((SVGGraphics2D) getGraphics()).stream(new OutputStreamWriter(os));
-
- }
-
- @Override
- public void savePartToFileImplementation(int x, int y, int width, int height, String fileName) throws IOException {
- throw new NotImplementedException("Partial save is not implemented in SVG image generator");
- }
-
- @Override
- public void savePartToOutputStreamImplementation(int x, int y, int width, int height, OutputStream os) throws IOException {
- throw new NotImplementedException("Partial save is not implemented in SVG image generator");
- }
-
- @Override
- public String getFormatName() {
- return "SVG image";
- }
-
- @Override
- public MimeType getMimeType() {
- return MimeType.SVG;
- }
-
- @Override
- public String getFileExtension() {
- return "svg";
- }
-
-}
+package lcsb.mapviewer.converter.graphics;
+
+import java.io.IOException;
+import java.io.OutputStream;
+import java.io.OutputStreamWriter;
+
+import lcsb.mapviewer.common.MimeType;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+import org.apache.batik.dom.GenericDOMImplementation;
+import org.apache.batik.svggen.SVGGraphics2D;
+import org.apache.batik.svggen.SVGGraphics2DIOException;
+import org.w3c.dom.DOMImplementation;
+import org.w3c.dom.Document;
+
+/**
+ * This class implements SVG generator for the image object.This class uses
+ * batik library to create all converters.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class SvgImageGenerator extends AbstractImageGenerator {
+
+ @Override
+ protected void createImageObject(final double width, final double height) {
+
+ // Get a DOMImplementation.
+ DOMImplementation domImpl = GenericDOMImplementation.getDOMImplementation();
+
+ // Create an instance of org.w3c.dom.Document.
+ String svgNS = "http://www.w3.org/2000/svg";
+ Document document = domImpl.createDocument(svgNS, "svg", null);
+
+ // Create an instance of the SVG Generator.
+ setGraphics(new SVGGraphics2D(document));
+
+ }
+
+ @Override
+ public void saveToFileImplementation(final String fileName) throws SVGGraphics2DIOException {
+ ((SVGGraphics2D) getGraphics()).stream(fileName);
+ }
+
+ /**
+ * Default constructor. Create an image that is described by params. For more
+ * information see
+ * {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params
+ * params}.
+ *
+ * @param params
+ * parameters used for the image creation.
+ * @throws DrawingException
+ * thrown when there was a problem with drawing a map
+ */
+ public SvgImageGenerator(final Params params) throws DrawingException {
+ super(params);
+ }
+
+ @Override
+ protected void closeImageObject() {
+ }
+
+ @Override
+ public void saveToOutputStreamImplementation(OutputStream os) throws IOException {
+ ((SVGGraphics2D) getGraphics()).stream(new OutputStreamWriter(os));
+
+ }
+
+ @Override
+ public void savePartToFileImplementation(int x, int y, int width, int height, String fileName) throws IOException {
+ throw new NotImplementedException("Partial save is not implemented in SVG image generator");
+ }
+
+ @Override
+ public void savePartToOutputStreamImplementation(int x, int y, int width, int height, OutputStream os) throws IOException {
+ throw new NotImplementedException("Partial save is not implemented in SVG image generator");
+ }
+
+ @Override
+ public String getFormatName() {
+ return "SVG image";
+ }
+
+ @Override
+ public MimeType getMimeType() {
+ return MimeType.SVG;
+ }
+
+ @Override
+ public String getFileExtension() {
+ return "svg";
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java
index 373ee420b1..ed93a346a0 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java
@@ -1,250 +1,250 @@
-package lcsb.mapviewer.converter.graphics.bioEntity;
-
-import java.awt.Graphics2D;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.commands.SemanticZoomLevelMatcher;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.converter.graphics.DrawingException;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.reaction.AbstractNode;
-import lcsb.mapviewer.model.map.reaction.NodeOperator;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.ReactionNode;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * This interface defines what operations should be possible to convert
- * {@link BioEntity} into a graphics on Graphics2D object.
- *
- * @author Piotr Gawron
- *
- * @param <T>
- * class of alias to convert
- */
-public abstract class BioEntityConverter<T extends BioEntity> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(BioEntityConverter.class);
-
- /**
- * Class that allows to check if element is visible (or transparent) when
- * drawing. It's used to filter out invisible elements when drawing
- * semantic/hierarchy view.
- */
- private SemanticZoomLevelMatcher zoomLevelMatcher = new SemanticZoomLevelMatcher();
-
- /**
- * Alpha value (0..255) used for visualizing overlay data that are normally
- * visualized in javascript.
- */
- public static final int LAYOUT_ALPHA = 200;
-
- /**
- * This function draw {@link BioEntity} on the {@link Graphics2D} object.
- *
- * @param bioEntity
- * {@link BioEntity} that should be drawn
- * @param graphics
- * where we want to draw bioEntity
- * @param params
- * visuzalization params (like, should the object be filled with
- * solid color, etc.), for more information see
- * {@link ConverterParams}
- * @throws DrawingException
- * thrown when there is a problem with drawing {@link BioEntity}
- *
- */
- public void draw(T bioEntity, Graphics2D graphics, ConverterParams params) throws DrawingException {
- draw(bioEntity, graphics, params, new ArrayList<>());
- }
-
- /**
- * This function draw representation of the alias on the graphics object.
- *
- * @param bioEntity
- * {@link BioEntity} that should be drawn
- * @param graphics
- * where we want to draw bioEntity
- * @param params
- * visuzalization params (like, should the object be filled with
- * solid color, etc.), for more information see
- * {@link ConverterParams}
- * @param visualizedOverlaysColorSchemas
- * list of {@link ColorSchema} that were used for visualizing this
- * bioentity in different data overlays that should be overlayed on
- * the alias
- * @throws DrawingException
- * thrown when there is a problem with drawing {@link BioEntity}
- *
- */
- public abstract void draw(T bioEntity, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedOverlaysColorSchemas)
- throws DrawingException;
-
- /**
- * This function will find proper font size to display text within it. Then it
- * will print this text.
- *
- * @param bioEntity
- * {@link BioEntity} with description to be drawn
- * @param graphics
- * where the description should be drawn
- * @param params
- * parameters of visualization (centering, scale)
- * @throws DrawingException
- * thrown when there is a problem with drawing {@link BioEntity}
- */
- public abstract void drawText(T bioEntity, Graphics2D graphics, ConverterParams params) throws DrawingException;
-
- /**
- * Checks if {@link AbstractNode} is visible according to visualization given
- * in params.
- *
- * @param node
- * visibility of this object will be checked
- * @param params
- * visualization params
- * @return true if object is visible
- */
- protected boolean isVisible(AbstractNode node, ConverterParams params) {
- if (node instanceof NodeOperator) {
- return isVisible((NodeOperator) node, params);
- } else if (node instanceof ReactionNode) {
- return isVisible(((ReactionNode) node).getElement(), params);
- } else {
- throw new InvalidArgumentException("Unknown class type: " + node.getClass());
- }
- }
-
- /**
- * Checks if {@link NodeOperator} is visible according to visualization given
- * in params.
- *
- * @param operator
- * visibility of this object will be checked
- * @param params
- * visualization params
- * @return true if object is visible
- */
- protected boolean isVisible(NodeOperator operator, ConverterParams params) {
- boolean result = false;
- if (operator.isModifierOperator() || operator.isReactantOperator()) {
- for (AbstractNode input : operator.getInputs()) {
- result |= isVisible(input, params);
- }
- } else if (operator.isProductOperator()) {
- for (AbstractNode output : operator.getOutputs()) {
- result |= isVisible(output, params);
- }
- } else {
- throw new InvalidStateException("Unknown class state: " + operator);
- }
- return result;
- }
-
- /**
- * Checks if {@link BioEntity} is visible according to visualization given in
- * params.
- *
- * @param bioEntity
- * visibility of this object will be checked
- * @param params
- * visualization params
- * @return true if object is visible
- */
- protected boolean isVisible(BioEntity bioEntity, ConverterParams params) {
- if (params.isNested()) {
- boolean result = zoomLevelMatcher.isVisible(params.getLevel(), bioEntity.getVisibilityLevel());
- if (bioEntity instanceof Element) {
- Compartment compartment = ((Element) bioEntity).getCompartment();
- if (compartment != null) {
- result &= isVisible(compartment, params);
- }
- if (bioEntity instanceof Species) {
- Complex complex = ((Species) bioEntity).getComplex();
- if (complex != null) {
- result &= isVisible(complex, params);
- }
- }
- } else if (bioEntity instanceof Reaction) {
- if (!isAnyProductVisible(((Reaction) bioEntity).getProducts(), params)) {
- result = false;
- } else if (!isAnyReactantVisible(((Reaction) bioEntity).getReactants(), params)) {
- result = false;
- }
- } else {
- throw new InvalidArgumentException("Unknown class type: " + bioEntity.getClass());
- }
- return result;
- }
- return true;
- }
-
- /**
- * Checks if {@link Element} given in the argument is transparent accordind to
- * the level given in the {@link ConverterParams}.
- *
- * @param bioEntity
- * {@link BioEntity} to be checked
- * @param params
- * params against which check is run
- * @return <code>true</code> if object is transparent, <code>false</code>
- * otherwise
- */
- protected boolean isTransparent(Element bioEntity, ConverterParams params) {
- return zoomLevelMatcher.isTransparent(params.getLevel(), bioEntity.getTransparencyLevel()) || !params.isNested();
- }
-
- /**
- * Checks if at least one reactant is visible.
- *
- * @param reactants
- * list of reactants
- * @param params
- * params against which check is run
- * @return true if at least one reactant is visible
- */
- private boolean isAnyReactantVisible(List<Reactant> reactants, ConverterParams params) {
- boolean result = false;
- for (Reactant reactant : reactants) {
- if (isVisible(reactant, params)) {
- result = true;
- }
- }
- return result;
- }
-
- /**
- * Checks if at least one product is visible.
- *
- * @param products
- * list of products
- * @param params
- * params against which check is run
- * @return true if at least one product is visible
- */
- private boolean isAnyProductVisible(List<Product> products, ConverterParams params) {
- boolean result = false;
- for (Product product : products) {
- if (isVisible(product, params)) {
- result = true;
- }
- }
- return result;
- }
-
-}
+package lcsb.mapviewer.converter.graphics.bioEntity;
+
+import java.awt.Graphics2D;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.SemanticZoomLevelMatcher;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.DrawingException;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.reaction.AbstractNode;
+import lcsb.mapviewer.model.map.reaction.NodeOperator;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This interface defines what operations should be possible to convert
+ * {@link BioEntity} into a graphics on Graphics2D object.
+ *
+ * @author Piotr Gawron
+ *
+ * @param <T>
+ * class of alias to convert
+ */
+public abstract class BioEntityConverter<T extends BioEntity> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(BioEntityConverter.class);
+
+ /**
+ * Class that allows to check if element is visible (or transparent) when
+ * drawing. It's used to filter out invisible elements when drawing
+ * semantic/hierarchy view.
+ */
+ private SemanticZoomLevelMatcher zoomLevelMatcher = new SemanticZoomLevelMatcher();
+
+ /**
+ * Alpha value (0..255) used for visualizing overlay data that are normally
+ * visualized in javascript.
+ */
+ public static final int LAYOUT_ALPHA = 200;
+
+ /**
+ * This function draw {@link BioEntity} on the {@link Graphics2D} object.
+ *
+ * @param bioEntity
+ * {@link BioEntity} that should be drawn
+ * @param graphics
+ * where we want to draw bioEntity
+ * @param params
+ * visuzalization params (like, should the object be filled with
+ * solid color, etc.), for more information see
+ * {@link ConverterParams}
+ * @throws DrawingException
+ * thrown when there is a problem with drawing {@link BioEntity}
+ *
+ */
+ public void draw(T bioEntity, Graphics2D graphics, ConverterParams params) throws DrawingException {
+ draw(bioEntity, graphics, params, new ArrayList<>());
+ }
+
+ /**
+ * This function draw representation of the alias on the graphics object.
+ *
+ * @param bioEntity
+ * {@link BioEntity} that should be drawn
+ * @param graphics
+ * where we want to draw bioEntity
+ * @param params
+ * visuzalization params (like, should the object be filled with
+ * solid color, etc.), for more information see
+ * {@link ConverterParams}
+ * @param visualizedOverlaysColorSchemas
+ * list of {@link ColorSchema} that were used for visualizing this
+ * bioentity in different data overlays that should be overlayed on
+ * the alias
+ * @throws DrawingException
+ * thrown when there is a problem with drawing {@link BioEntity}
+ *
+ */
+ public abstract void draw(T bioEntity, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedOverlaysColorSchemas)
+ throws DrawingException;
+
+ /**
+ * This function will find proper font size to display text within it. Then it
+ * will print this text.
+ *
+ * @param bioEntity
+ * {@link BioEntity} with description to be drawn
+ * @param graphics
+ * where the description should be drawn
+ * @param params
+ * parameters of visualization (centering, scale)
+ * @throws DrawingException
+ * thrown when there is a problem with drawing {@link BioEntity}
+ */
+ public abstract void drawText(T bioEntity, Graphics2D graphics, ConverterParams params) throws DrawingException;
+
+ /**
+ * Checks if {@link AbstractNode} is visible according to visualization given
+ * in params.
+ *
+ * @param node
+ * visibility of this object will be checked
+ * @param params
+ * visualization params
+ * @return true if object is visible
+ */
+ protected boolean isVisible(AbstractNode node, ConverterParams params) {
+ if (node instanceof NodeOperator) {
+ return isVisible((NodeOperator) node, params);
+ } else if (node instanceof ReactionNode) {
+ return isVisible(((ReactionNode) node).getElement(), params);
+ } else {
+ throw new InvalidArgumentException("Unknown class type: " + node.getClass());
+ }
+ }
+
+ /**
+ * Checks if {@link NodeOperator} is visible according to visualization given
+ * in params.
+ *
+ * @param operator
+ * visibility of this object will be checked
+ * @param params
+ * visualization params
+ * @return true if object is visible
+ */
+ protected boolean isVisible(NodeOperator operator, ConverterParams params) {
+ boolean result = false;
+ if (operator.isModifierOperator() || operator.isReactantOperator()) {
+ for (AbstractNode input : operator.getInputs()) {
+ result |= isVisible(input, params);
+ }
+ } else if (operator.isProductOperator()) {
+ for (AbstractNode output : operator.getOutputs()) {
+ result |= isVisible(output, params);
+ }
+ } else {
+ throw new InvalidStateException("Unknown class state: " + operator);
+ }
+ return result;
+ }
+
+ /**
+ * Checks if {@link BioEntity} is visible according to visualization given in
+ * params.
+ *
+ * @param bioEntity
+ * visibility of this object will be checked
+ * @param params
+ * visualization params
+ * @return true if object is visible
+ */
+ protected boolean isVisible(BioEntity bioEntity, ConverterParams params) {
+ if (params.isNested()) {
+ boolean result = zoomLevelMatcher.isVisible(params.getLevel(), bioEntity.getVisibilityLevel());
+ if (bioEntity instanceof Element) {
+ Compartment compartment = ((Element) bioEntity).getCompartment();
+ if (compartment != null) {
+ result &= isVisible(compartment, params);
+ }
+ if (bioEntity instanceof Species) {
+ Complex complex = ((Species) bioEntity).getComplex();
+ if (complex != null) {
+ result &= isVisible(complex, params);
+ }
+ }
+ } else if (bioEntity instanceof Reaction) {
+ if (!isAnyProductVisible(((Reaction) bioEntity).getProducts(), params)) {
+ result = false;
+ } else if (!isAnyReactantVisible(((Reaction) bioEntity).getReactants(), params)) {
+ result = false;
+ }
+ } else {
+ throw new InvalidArgumentException("Unknown class type: " + bioEntity.getClass());
+ }
+ return result;
+ }
+ return true;
+ }
+
+ /**
+ * Checks if {@link Element} given in the argument is transparent accordind to
+ * the level given in the {@link ConverterParams}.
+ *
+ * @param bioEntity
+ * {@link BioEntity} to be checked
+ * @param params
+ * params against which check is run
+ * @return <code>true</code> if object is transparent, <code>false</code>
+ * otherwise
+ */
+ protected boolean isTransparent(Element bioEntity, ConverterParams params) {
+ return zoomLevelMatcher.isTransparent(params.getLevel(), bioEntity.getTransparencyLevel()) || !params.isNested();
+ }
+
+ /**
+ * Checks if at least one reactant is visible.
+ *
+ * @param reactants
+ * list of reactants
+ * @param params
+ * params against which check is run
+ * @return true if at least one reactant is visible
+ */
+ private boolean isAnyReactantVisible(List<Reactant> reactants, ConverterParams params) {
+ boolean result = false;
+ for (Reactant reactant : reactants) {
+ if (isVisible(reactant, params)) {
+ result = true;
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Checks if at least one product is visible.
+ *
+ * @param products
+ * list of products
+ * @param params
+ * params against which check is run
+ * @return true if at least one product is visible
+ */
+ private boolean isAnyProductVisible(List<Product> products, ConverterParams params) {
+ boolean result = false;
+ for (Product product : products) {
+ if (isVisible(product, params)) {
+ result = true;
+ }
+ }
+ return result;
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImpl.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImpl.java
index 48c0d1f37e..f4e895661f 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImpl.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImpl.java
@@ -1,202 +1,202 @@
-package lcsb.mapviewer.converter.graphics.bioEntity;
-
-import java.awt.Graphics2D;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.converter.graphics.DrawingException;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.BottomSquareCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.LeftSquareCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.OvalCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.PathwayCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.RightSquareCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.SquareCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.TopSquareCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.AntisenseRnaConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.ComplexConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.DegradedConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.DrugConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.GeneConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.IonConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.PhenotypeConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.ProteinConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.RnaConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.SBGNNucleicAcidFeatureConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.SimpleMoleculeConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.UnknownConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.reaction.ReactionConverter;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.compartment.BottomSquareCompartment;
-import lcsb.mapviewer.model.map.compartment.LeftSquareCompartment;
-import lcsb.mapviewer.model.map.compartment.OvalCompartment;
-import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
-import lcsb.mapviewer.model.map.compartment.RightSquareCompartment;
-import lcsb.mapviewer.model.map.compartment.SquareCompartment;
-import lcsb.mapviewer.model.map.compartment.TopSquareCompartment;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Degraded;
-import lcsb.mapviewer.model.map.species.Drug;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Ion;
-import lcsb.mapviewer.model.map.species.IonChannelProtein;
-import lcsb.mapviewer.model.map.species.Phenotype;
-import lcsb.mapviewer.model.map.species.ReceptorProtein;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
-import lcsb.mapviewer.model.map.species.TruncatedProtein;
-import lcsb.mapviewer.model.map.species.Unknown;
-import lcsb.mapviewer.modelutils.map.ElementUtils;
-
-/**
- * This class is designed to convert any type of {@link Element} into a graphic
- * glyph that will be visualized on the {@link Graphics2D} object.
- *
- * @author Piotr Gawron
- *
- */
-public class BioEntityConverterImpl extends BioEntityConverter<BioEntity> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(BioEntityConverterImpl.class.getName());
-
- /**
- * Returns a converter for given element. If converter doesn't exist then
- * exception is thrown.
- *
- * @param element
- * {@link Element} for which we are looking for a converter
- * @param colorExtractor
- * object that helps to convert overlay values into colors
- * @return converter that can be applied for the given element
- */
- private BioEntityConverter<? extends BioEntity> getConverterForElement(BioEntity element, ColorExtractor colorExtractor) {
- if (element == null) {
- throw new InvalidArgumentException("element cannot be null");
- }
- if (element instanceof GenericProtein) {
- return new ProteinConverter(colorExtractor);
- } else if (element instanceof IonChannelProtein) {
- return new ProteinConverter(colorExtractor);
- } else if (element instanceof ReceptorProtein) {
- return new ProteinConverter(colorExtractor);
- } else if (element instanceof TruncatedProtein) {
- return new ProteinConverter(colorExtractor);
- } else if (element instanceof Degraded) {
- return new DegradedConverter(colorExtractor);
- } else if (element instanceof Complex) {
- return new ComplexConverter(colorExtractor);
- } else if (element instanceof SimpleMolecule) {
- return new SimpleMoleculeConverter(colorExtractor);
- } else if (element instanceof Drug) {
- return new DrugConverter(colorExtractor);
- } else if (element instanceof Ion) {
- return new IonConverter(colorExtractor);
- } else if (element instanceof Phenotype) {
- return new PhenotypeConverter(colorExtractor);
- } else if (element instanceof Rna) {
- return new RnaConverter(colorExtractor);
- } else if (element instanceof AntisenseRna) {
- return new AntisenseRnaConverter(colorExtractor);
- } else if (element instanceof Gene) {
- return new GeneConverter(colorExtractor);
- } else if (element instanceof Unknown) {
- return new UnknownConverter(colorExtractor);
- } else if (element instanceof SquareCompartment) {
- return new SquareCompartmentConverter(colorExtractor);
- } else if (element instanceof OvalCompartment) {
- return new OvalCompartmentConverter(colorExtractor);
- } else if (element instanceof PathwayCompartment) {
- return new PathwayCompartmentConverter(colorExtractor);
- } else if (element instanceof BottomSquareCompartment) {
- return new BottomSquareCompartmentConverter(colorExtractor);
- } else if (element instanceof TopSquareCompartment) {
- return new TopSquareCompartmentConverter(colorExtractor);
- } else if (element instanceof LeftSquareCompartment) {
- return new LeftSquareCompartmentConverter(colorExtractor);
- } else if (element instanceof RightSquareCompartment) {
- return new RightSquareCompartmentConverter(colorExtractor);
- } else if (element instanceof Reaction) {
- return new ReactionConverter(colorExtractor);
- } else {
- throw new NotImplementedException(new ElementUtils().getElementTag(element) + "Unknown element class");
- }
- }
-
- /**
- * Converter used for conversion of the {@link Element} given in constructor.
- */
- @SuppressWarnings("rawtypes")
- private BioEntityConverter elementConverter = null;
-
- /**
- * Support constructor. Used in case of SBGN format display
- *
- * @param element
- * {@link Element} for which this converter will be used
- * @param colorExtractor
- * object that helps to convert overlay values into colors
- * @param sbgnFormat
- * boolean value indicating if SBGN display format should be used
- */
- public BioEntityConverterImpl(final BioEntity element, final boolean sbgnFormat, ColorExtractor colorExtractor) {
-
- // If element is a nucleic acid feature to be displayed in SBGN
- if (sbgnFormat && (element instanceof AntisenseRna || element instanceof Rna || element instanceof Gene)) {
- elementConverter = new SBGNNucleicAcidFeatureConverter(colorExtractor);
- } else {
- // If not, at the beginning try to find an appropriate converter
- elementConverter = getConverterForElement(element, colorExtractor);
- }
-
- // if we don't know which converter to use then throw an exception
- if (elementConverter == null) {
- throw new InvalidArgumentException(new ElementUtils().getElementTag(element) + "Unknown converter for class: " + element.getClass());
- }
- }
-
- /**
- * Default constructor.
- *
- * @param colorExtractor
- * object that helps to convert overlay values into colors
- * @param element
- * {@link Element} for which this converter will be used
- */
- public BioEntityConverterImpl(final Element element, ColorExtractor colorExtractor) {
- this(element, false, colorExtractor);
- }
-
- @SuppressWarnings("unchecked")
- @Override
- public void drawText(final BioEntity element, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
- if (isVisible(element, params)) {
- elementConverter.drawText(element, graphics, params);
- }
- }
-
- @SuppressWarnings("unchecked")
- @Override
- public void draw(BioEntity element, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) throws DrawingException {
- try {
- if (isVisible(element, params)) {
- elementConverter.draw(element, graphics, params, visualizedLayoutsColorSchemas);
- }
- } catch (Exception e) {
- throw new DrawingException(new ElementUtils().getElementTag(element) + "Problem with drawing element.", e);
- }
- }
-
-}
+package lcsb.mapviewer.converter.graphics.bioEntity;
+
+import java.awt.Graphics2D;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.DrawingException;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.BottomSquareCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.LeftSquareCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.OvalCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.PathwayCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.RightSquareCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.SquareCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.TopSquareCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.AntisenseRnaConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.ComplexConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.DegradedConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.DrugConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.GeneConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.IonConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.PhenotypeConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.ProteinConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.RnaConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.SBGNNucleicAcidFeatureConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.SimpleMoleculeConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.UnknownConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.reaction.ReactionConverter;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.compartment.BottomSquareCompartment;
+import lcsb.mapviewer.model.map.compartment.LeftSquareCompartment;
+import lcsb.mapviewer.model.map.compartment.OvalCompartment;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
+import lcsb.mapviewer.model.map.compartment.RightSquareCompartment;
+import lcsb.mapviewer.model.map.compartment.SquareCompartment;
+import lcsb.mapviewer.model.map.compartment.TopSquareCompartment;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Degraded;
+import lcsb.mapviewer.model.map.species.Drug;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.model.map.species.IonChannelProtein;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.ReceptorProtein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.TruncatedProtein;
+import lcsb.mapviewer.model.map.species.Unknown;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
+
+/**
+ * This class is designed to convert any type of {@link Element} into a graphic
+ * glyph that will be visualized on the {@link Graphics2D} object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class BioEntityConverterImpl extends BioEntityConverter<BioEntity> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(BioEntityConverterImpl.class.getName());
+
+ /**
+ * Returns a converter for given element. If converter doesn't exist then
+ * exception is thrown.
+ *
+ * @param element
+ * {@link Element} for which we are looking for a converter
+ * @param colorExtractor
+ * object that helps to convert overlay values into colors
+ * @return converter that can be applied for the given element
+ */
+ private BioEntityConverter<? extends BioEntity> getConverterForElement(BioEntity element, ColorExtractor colorExtractor) {
+ if (element == null) {
+ throw new InvalidArgumentException("element cannot be null");
+ }
+ if (element instanceof GenericProtein) {
+ return new ProteinConverter(colorExtractor);
+ } else if (element instanceof IonChannelProtein) {
+ return new ProteinConverter(colorExtractor);
+ } else if (element instanceof ReceptorProtein) {
+ return new ProteinConverter(colorExtractor);
+ } else if (element instanceof TruncatedProtein) {
+ return new ProteinConverter(colorExtractor);
+ } else if (element instanceof Degraded) {
+ return new DegradedConverter(colorExtractor);
+ } else if (element instanceof Complex) {
+ return new ComplexConverter(colorExtractor);
+ } else if (element instanceof SimpleMolecule) {
+ return new SimpleMoleculeConverter(colorExtractor);
+ } else if (element instanceof Drug) {
+ return new DrugConverter(colorExtractor);
+ } else if (element instanceof Ion) {
+ return new IonConverter(colorExtractor);
+ } else if (element instanceof Phenotype) {
+ return new PhenotypeConverter(colorExtractor);
+ } else if (element instanceof Rna) {
+ return new RnaConverter(colorExtractor);
+ } else if (element instanceof AntisenseRna) {
+ return new AntisenseRnaConverter(colorExtractor);
+ } else if (element instanceof Gene) {
+ return new GeneConverter(colorExtractor);
+ } else if (element instanceof Unknown) {
+ return new UnknownConverter(colorExtractor);
+ } else if (element instanceof SquareCompartment) {
+ return new SquareCompartmentConverter(colorExtractor);
+ } else if (element instanceof OvalCompartment) {
+ return new OvalCompartmentConverter(colorExtractor);
+ } else if (element instanceof PathwayCompartment) {
+ return new PathwayCompartmentConverter(colorExtractor);
+ } else if (element instanceof BottomSquareCompartment) {
+ return new BottomSquareCompartmentConverter(colorExtractor);
+ } else if (element instanceof TopSquareCompartment) {
+ return new TopSquareCompartmentConverter(colorExtractor);
+ } else if (element instanceof LeftSquareCompartment) {
+ return new LeftSquareCompartmentConverter(colorExtractor);
+ } else if (element instanceof RightSquareCompartment) {
+ return new RightSquareCompartmentConverter(colorExtractor);
+ } else if (element instanceof Reaction) {
+ return new ReactionConverter(colorExtractor);
+ } else {
+ throw new NotImplementedException(new ElementUtils().getElementTag(element) + "Unknown element class");
+ }
+ }
+
+ /**
+ * Converter used for conversion of the {@link Element} given in constructor.
+ */
+ @SuppressWarnings("rawtypes")
+ private BioEntityConverter elementConverter = null;
+
+ /**
+ * Support constructor. Used in case of SBGN format display
+ *
+ * @param element
+ * {@link Element} for which this converter will be used
+ * @param colorExtractor
+ * object that helps to convert overlay values into colors
+ * @param sbgnFormat
+ * boolean value indicating if SBGN display format should be used
+ */
+ public BioEntityConverterImpl(final BioEntity element, final boolean sbgnFormat, ColorExtractor colorExtractor) {
+
+ // If element is a nucleic acid feature to be displayed in SBGN
+ if (sbgnFormat && (element instanceof AntisenseRna || element instanceof Rna || element instanceof Gene)) {
+ elementConverter = new SBGNNucleicAcidFeatureConverter(colorExtractor);
+ } else {
+ // If not, at the beginning try to find an appropriate converter
+ elementConverter = getConverterForElement(element, colorExtractor);
+ }
+
+ // if we don't know which converter to use then throw an exception
+ if (elementConverter == null) {
+ throw new InvalidArgumentException(new ElementUtils().getElementTag(element) + "Unknown converter for class: " + element.getClass());
+ }
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * object that helps to convert overlay values into colors
+ * @param element
+ * {@link Element} for which this converter will be used
+ */
+ public BioEntityConverterImpl(final Element element, ColorExtractor colorExtractor) {
+ this(element, false, colorExtractor);
+ }
+
+ @SuppressWarnings("unchecked")
+ @Override
+ public void drawText(final BioEntity element, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
+ if (isVisible(element, params)) {
+ elementConverter.drawText(element, graphics, params);
+ }
+ }
+
+ @SuppressWarnings("unchecked")
+ @Override
+ public void draw(BioEntity element, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) throws DrawingException {
+ try {
+ if (isVisible(element, params)) {
+ elementConverter.draw(element, graphics, params, visualizedLayoutsColorSchemas);
+ }
+ } catch (Exception e) {
+ throw new DrawingException(new ElementUtils().getElementTag(element) + "Problem with drawing element.", e);
+ }
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/ElementConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/ElementConverter.java
index 1bec6b8f64..3f108b2a44 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/ElementConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/ElementConverter.java
@@ -1,17 +1,17 @@
-package lcsb.mapviewer.converter.graphics.bioEntity.element;
-
-import lcsb.mapviewer.converter.graphics.bioEntity.BioEntityConverter;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * This interface defines what operations should be possible to convert
- * {@link Element} into a graphics on Graphics2D object.
- *
- * @author Piotr Gawron
- *
- * @param <T>
- * class of alias to convert
- */
-public abstract class ElementConverter<T extends Element> extends BioEntityConverter<T> {
-
-}
+package lcsb.mapviewer.converter.graphics.bioEntity.element;
+
+import lcsb.mapviewer.converter.graphics.bioEntity.BioEntityConverter;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * This interface defines what operations should be possible to convert
+ * {@link Element} into a graphics on Graphics2D object.
+ *
+ * @author Piotr Gawron
+ *
+ * @param <T>
+ * class of alias to convert
+ */
+public abstract class ElementConverter<T extends Element> extends BioEntityConverter<T> {
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/BottomSquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/BottomSquareCompartmentConverter.java
index de023622f3..06b04ff84b 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/BottomSquareCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/BottomSquareCompartmentConverter.java
@@ -1,96 +1,96 @@
-package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.Shape;
-import java.awt.Stroke;
-import java.awt.geom.Area;
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.converter.graphics.DrawingException;
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.map.compartment.BottomSquareCompartment;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * Class responsible for drawing BottomSquareCompartment on the Graphics2D.
- *
- * @author Piotr Gawron
- *
- */
-public class BottomSquareCompartmentConverter extends CompartmentConverter<BottomSquareCompartment> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(BottomSquareCompartmentConverter.class.getName());
-
- /**
- * Default constructor.
- *
- * @param colorExtractor
- * Object that helps to convert {@link ColorSchema} values into
- * colors when drawing {@link Species}
- */
- public BottomSquareCompartmentConverter(ColorExtractor colorExtractor) {
- super(colorExtractor);
- }
-
- @Override
- public void draw(final BottomSquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
- // keep the old values of colors and line
- Color oldColor = graphics.getColor();
- Stroke oldStroke = graphics.getStroke();
-
- // create shape of the compartment
- Shape s1 = new Line2D.Double(0, compartment.getY(), compartment.getWidth(), compartment.getY());
- Shape s3 = new Line2D.Double(0, compartment.getY() + compartment.getThickness(), compartment.getWidth(), compartment.getY() + compartment.getThickness());
- Area a1 = new Area(new Rectangle2D.Double(0.0, compartment.getY(), compartment.getWidth(), compartment.getHeight()));
-
- Color c1 = compartment.getColor();
- Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
- if (c1.equals(Color.WHITE)) {
- c1 = Color.BLACK;
- }
-
- // fill the background
- boolean fill = !isTransparent(compartment, params);
- if (fill) {
- graphics.setColor(c1);
- } else {
- Color bgAlphaColor = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), getAlphaLevel());
- graphics.setColor(bgAlphaColor);
- }
- graphics.fill(s1);
-
- // create borders
- graphics.setColor(c1);
- graphics.setStroke(LineType.SOLID_BOLD.getStroke());
- graphics.draw(s1);
- graphics.setStroke(LineType.SOLID.getStroke());
- graphics.draw(s3);
- graphics.setColor(c2);
- if (fill) {
- graphics.fill(a1);
- }
- // restore color and line type
- graphics.setColor(oldColor);
- graphics.setStroke(oldStroke);
-
- // draw description
- if (fill) {
- Point2D tmpPoint = compartment.getNamePoint();
- compartment.setNamePoint(compartment.getCenter());
- drawText(compartment, graphics, params);
- compartment.setNamePoint(tmpPoint);
- }
- }
-}
+package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.Shape;
+import java.awt.Stroke;
+import java.awt.geom.Area;
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.DrawingException;
+import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.map.compartment.BottomSquareCompartment;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * Class responsible for drawing BottomSquareCompartment on the Graphics2D.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class BottomSquareCompartmentConverter extends CompartmentConverter<BottomSquareCompartment> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(BottomSquareCompartmentConverter.class.getName());
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing {@link Species}
+ */
+ public BottomSquareCompartmentConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
+ @Override
+ public void draw(final BottomSquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
+ // keep the old values of colors and line
+ Color oldColor = graphics.getColor();
+ Stroke oldStroke = graphics.getStroke();
+
+ // create shape of the compartment
+ Shape s1 = new Line2D.Double(0, compartment.getY(), compartment.getWidth(), compartment.getY());
+ Shape s3 = new Line2D.Double(0, compartment.getY() + compartment.getThickness(), compartment.getWidth(), compartment.getY() + compartment.getThickness());
+ Area a1 = new Area(new Rectangle2D.Double(0.0, compartment.getY(), compartment.getWidth(), compartment.getHeight()));
+
+ Color c1 = compartment.getColor();
+ Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
+ if (c1.equals(Color.WHITE)) {
+ c1 = Color.BLACK;
+ }
+
+ // fill the background
+ boolean fill = !isTransparent(compartment, params);
+ if (fill) {
+ graphics.setColor(c1);
+ } else {
+ Color bgAlphaColor = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), getAlphaLevel());
+ graphics.setColor(bgAlphaColor);
+ }
+ graphics.fill(s1);
+
+ // create borders
+ graphics.setColor(c1);
+ graphics.setStroke(LineType.SOLID_BOLD.getStroke());
+ graphics.draw(s1);
+ graphics.setStroke(LineType.SOLID.getStroke());
+ graphics.draw(s3);
+ graphics.setColor(c2);
+ if (fill) {
+ graphics.fill(a1);
+ }
+ // restore color and line type
+ graphics.setColor(oldColor);
+ graphics.setStroke(oldStroke);
+
+ // draw description
+ if (fill) {
+ Point2D tmpPoint = compartment.getNamePoint();
+ compartment.setNamePoint(compartment.getCenter());
+ drawText(compartment, graphics, params);
+ compartment.setNamePoint(tmpPoint);
+ }
+ }
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/CompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/CompartmentConverter.java
index 0846c804c8..9c6769776f 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/CompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/CompartmentConverter.java
@@ -1,205 +1,205 @@
-package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
-
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.Graphics2D;
-import java.awt.geom.Rectangle2D;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.geometry.EllipseTransformation;
-import lcsb.mapviewer.common.geometry.LineTransformation;
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.converter.graphics.DrawingException;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.ElementConverter;
-import lcsb.mapviewer.converter.graphics.geometry.FontFinder;
-import lcsb.mapviewer.converter.graphics.geometry.RectangleTooSmallException;
-import lcsb.mapviewer.converter.graphics.placefinder.PlaceFinder;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.modelutils.map.ElementUtils;
-
-/**
- * Abstract class responsible for common methods to draw compartmentAliases on
- * Graphics2D.
- *
- * @author Piotr Gawron
- *
- * @param <T>
- * class for which the comparator is created
- *
- */
-public abstract class CompartmentConverter<T extends Compartment> extends ElementConverter<T> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(CompartmentConverter.class.getName());
-
- /**
- * Default font size.
- */
- private static final int DEFAULT_FONT_SIZE = 10;
-
- /**
- * Alpha level for inside of the transparent compartments.
- */
- public static final int DEFAULT_ALPHA_LEVEL = 8;
-
- /**
- * Class used for transformation of lines.
- */
- private LineTransformation lineTransformation = new LineTransformation();
-
- /**
- * Class used for transformation of ellipses.
- */
- private EllipseTransformation ellipseTransformation = new EllipseTransformation();
-
- /**
- * Default alpha level for transparent compartments.
- */
- private static int alphaLevel = DEFAULT_ALPHA_LEVEL;
-
- /**
- * Default alpha level for semi-transparent borders.
- */
- protected static final int HIGH_ALPHA_LEVEL = 127;
-
- /**
- * Class used for finding place to draw desciption of the compartment.
- */
- private PlaceFinder placeFinder;
-
- /**
- * Object used for synchronization when accessing {@link #placeFinder}.
- */
- private String placeFinderSynchronization = "";
-
- /**
- * Object that helps to convert {@link ColorSchema} values into colors.
- */
- private ColorExtractor colorExtractor;
-
- /**
- * Default constructor.
- *
- * @param colorExtractor
- * Object that helps to convert {@link ColorSchema} values into
- * colors when drawing elements
- *
- */
- protected CompartmentConverter(ColorExtractor colorExtractor) {
- this.colorExtractor = colorExtractor;
- };
-
- @Override
- public void drawText(final T compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
- if (compartment.getWidth() < Configuration.EPSILON || compartment.getHeight() < Configuration.EPSILON) {
- throw new DrawingException(new ElementUtils().getElementTag(compartment) + "Dimension of the alias must be bigger than 0.");
- }
- boolean textCentered = !isTransparent(compartment, params);
- Rectangle2D border;
- if (textCentered) {
- synchronized (placeFinderSynchronization) {
- if (placeFinder == null || placeFinder.getModel() != compartment.getModelData()) {
- placeFinder = new PlaceFinder(compartment.getModelData().getModel());
- }
- border = placeFinder.getRetangle(compartment, params.getLevel());
- }
- } else {
- border = new Rectangle2D.Double(
- compartment.getNamePoint().getX(), compartment.getNamePoint().getY(),
- compartment.getWidth() - (compartment.getNamePoint().getX() - compartment.getX()),
- compartment.getHeight() - (compartment.getNamePoint().getY() - compartment.getY()));
-
- }
- double fontSize = DEFAULT_FONT_SIZE * params.getScale();
- if (compartment.getFontSize() != null) {
- fontSize = compartment.getFontSize() * params.getScale();
- }
- String fontName = Font.SANS_SERIF;
- try {
- fontSize = FontFinder.findMaxFontSize((int) Math.round(fontSize), fontName, graphics, border, compartment.getName());
- FontFinder.drawText((int) fontSize, fontName, graphics, border, compartment.getName(), textCentered);
- } catch (RectangleTooSmallException e) {
- // if it's too small then don't draw
- return;
- }
- }
-
- /**
- * @return the lineTransformation
- */
- protected LineTransformation getLineTransformation() {
- return lineTransformation;
- }
-
- /**
- * @param lineTransformation
- * the lineTransformation to set
- */
- protected void setLineTransformation(LineTransformation lineTransformation) {
- this.lineTransformation = lineTransformation;
- }
-
- /**
- * @return the ellipseTransformation
- */
- protected EllipseTransformation getEllipseTransformation() {
- return ellipseTransformation;
- }
-
- /**
- * @param ellipseTransformation
- * the ellipseTransformation to set
- */
- protected void setEllipseTransformation(EllipseTransformation ellipseTransformation) {
- this.ellipseTransformation = ellipseTransformation;
- }
-
- /**
- * @return the alphaLevel
- */
- public static int getAlphaLevel() {
- return alphaLevel;
- }
-
- /**
- * @param alphaLevel
- * the alphaLevel to set
- */
- public static void setAlphaLevel(int alphaLevel) {
- CompartmentConverter.alphaLevel = alphaLevel;
- }
-
- @Override
- public void draw(T alias, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) throws DrawingException {
- draw(alias, graphics, params);
-
- Color oldColor = graphics.getColor();
- int count = 0;
- double width = alias.getWidth() / visualizedLayoutsColorSchemas.size();
- for (ColorSchema schema : visualizedLayoutsColorSchemas) {
- if (schema != null) {
- double startX = (double) count / (double) visualizedLayoutsColorSchemas.size();
- graphics.setColor(Color.BLACK);
-
- int x = (int) (startX * alias.getWidth() + alias.getX());
- graphics.drawRect(x, alias.getY().intValue(), (int) width, alias.getHeight().intValue());
-
- Color color = colorExtractor.getNormalizedColor(schema);
- Color bgAlphaColor = new Color(color.getRed(), color.getGreen(), color.getBlue(), LAYOUT_ALPHA);
- graphics.setColor(bgAlphaColor);
- graphics.fillRect(x, alias.getY().intValue(), (int) width, alias.getHeight().intValue());
- }
- count++;
- }
- graphics.setColor(oldColor);
- }
-
-}
+package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Graphics2D;
+import java.awt.geom.Rectangle2D;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.geometry.EllipseTransformation;
+import lcsb.mapviewer.common.geometry.LineTransformation;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.DrawingException;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.ElementConverter;
+import lcsb.mapviewer.converter.graphics.geometry.FontFinder;
+import lcsb.mapviewer.converter.graphics.geometry.RectangleTooSmallException;
+import lcsb.mapviewer.converter.graphics.placefinder.PlaceFinder;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
+
+/**
+ * Abstract class responsible for common methods to draw compartmentAliases on
+ * Graphics2D.
+ *
+ * @author Piotr Gawron
+ *
+ * @param <T>
+ * class for which the comparator is created
+ *
+ */
+public abstract class CompartmentConverter<T extends Compartment> extends ElementConverter<T> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(CompartmentConverter.class.getName());
+
+ /**
+ * Default font size.
+ */
+ private static final int DEFAULT_FONT_SIZE = 10;
+
+ /**
+ * Alpha level for inside of the transparent compartments.
+ */
+ public static final int DEFAULT_ALPHA_LEVEL = 8;
+
+ /**
+ * Class used for transformation of lines.
+ */
+ private LineTransformation lineTransformation = new LineTransformation();
+
+ /**
+ * Class used for transformation of ellipses.
+ */
+ private EllipseTransformation ellipseTransformation = new EllipseTransformation();
+
+ /**
+ * Default alpha level for transparent compartments.
+ */
+ private static int alphaLevel = DEFAULT_ALPHA_LEVEL;
+
+ /**
+ * Default alpha level for semi-transparent borders.
+ */
+ protected static final int HIGH_ALPHA_LEVEL = 127;
+
+ /**
+ * Class used for finding place to draw desciption of the compartment.
+ */
+ private PlaceFinder placeFinder;
+
+ /**
+ * Object used for synchronization when accessing {@link #placeFinder}.
+ */
+ private String placeFinderSynchronization = "";
+
+ /**
+ * Object that helps to convert {@link ColorSchema} values into colors.
+ */
+ private ColorExtractor colorExtractor;
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing elements
+ *
+ */
+ protected CompartmentConverter(ColorExtractor colorExtractor) {
+ this.colorExtractor = colorExtractor;
+ };
+
+ @Override
+ public void drawText(final T compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
+ if (compartment.getWidth() < Configuration.EPSILON || compartment.getHeight() < Configuration.EPSILON) {
+ throw new DrawingException(new ElementUtils().getElementTag(compartment) + "Dimension of the alias must be bigger than 0.");
+ }
+ boolean textCentered = !isTransparent(compartment, params);
+ Rectangle2D border;
+ if (textCentered) {
+ synchronized (placeFinderSynchronization) {
+ if (placeFinder == null || placeFinder.getModel() != compartment.getModelData()) {
+ placeFinder = new PlaceFinder(compartment.getModelData().getModel());
+ }
+ border = placeFinder.getRetangle(compartment, params.getLevel());
+ }
+ } else {
+ border = new Rectangle2D.Double(
+ compartment.getNamePoint().getX(), compartment.getNamePoint().getY(),
+ compartment.getWidth() - (compartment.getNamePoint().getX() - compartment.getX()),
+ compartment.getHeight() - (compartment.getNamePoint().getY() - compartment.getY()));
+
+ }
+ double fontSize = DEFAULT_FONT_SIZE * params.getScale();
+ if (compartment.getFontSize() != null) {
+ fontSize = compartment.getFontSize() * params.getScale();
+ }
+ String fontName = Font.SANS_SERIF;
+ try {
+ fontSize = FontFinder.findMaxFontSize((int) Math.round(fontSize), fontName, graphics, border, compartment.getName());
+ FontFinder.drawText((int) fontSize, fontName, graphics, border, compartment.getName(), textCentered);
+ } catch (RectangleTooSmallException e) {
+ // if it's too small then don't draw
+ return;
+ }
+ }
+
+ /**
+ * @return the lineTransformation
+ */
+ protected LineTransformation getLineTransformation() {
+ return lineTransformation;
+ }
+
+ /**
+ * @param lineTransformation
+ * the lineTransformation to set
+ */
+ protected void setLineTransformation(LineTransformation lineTransformation) {
+ this.lineTransformation = lineTransformation;
+ }
+
+ /**
+ * @return the ellipseTransformation
+ */
+ protected EllipseTransformation getEllipseTransformation() {
+ return ellipseTransformation;
+ }
+
+ /**
+ * @param ellipseTransformation
+ * the ellipseTransformation to set
+ */
+ protected void setEllipseTransformation(EllipseTransformation ellipseTransformation) {
+ this.ellipseTransformation = ellipseTransformation;
+ }
+
+ /**
+ * @return the alphaLevel
+ */
+ public static int getAlphaLevel() {
+ return alphaLevel;
+ }
+
+ /**
+ * @param alphaLevel
+ * the alphaLevel to set
+ */
+ public static void setAlphaLevel(int alphaLevel) {
+ CompartmentConverter.alphaLevel = alphaLevel;
+ }
+
+ @Override
+ public void draw(T alias, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) throws DrawingException {
+ draw(alias, graphics, params);
+
+ Color oldColor = graphics.getColor();
+ int count = 0;
+ double width = alias.getWidth() / visualizedLayoutsColorSchemas.size();
+ for (ColorSchema schema : visualizedLayoutsColorSchemas) {
+ if (schema != null) {
+ double startX = (double) count / (double) visualizedLayoutsColorSchemas.size();
+ graphics.setColor(Color.BLACK);
+
+ int x = (int) (startX * alias.getWidth() + alias.getX());
+ graphics.drawRect(x, alias.getY().intValue(), (int) width, alias.getHeight().intValue());
+
+ Color color = colorExtractor.getNormalizedColor(schema);
+ Color bgAlphaColor = new Color(color.getRed(), color.getGreen(), color.getBlue(), LAYOUT_ALPHA);
+ graphics.setColor(bgAlphaColor);
+ graphics.fillRect(x, alias.getY().intValue(), (int) width, alias.getHeight().intValue());
+ }
+ count++;
+ }
+ graphics.setColor(oldColor);
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/LeftSquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/LeftSquareCompartmentConverter.java
index 5b8b989f13..fa24065489 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/LeftSquareCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/LeftSquareCompartmentConverter.java
@@ -1,98 +1,98 @@
-package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.Shape;
-import java.awt.Stroke;
-import java.awt.geom.Area;
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.converter.graphics.DrawingException;
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.map.compartment.LeftSquareCompartment;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-
-import org.apache.log4j.Logger;
-
-/**
- * Class responsible for drawing LeftSquareCompartment on the Graphics2D.
- *
- * @author Piotr Gawron
- *
- */
-public class LeftSquareCompartmentConverter extends CompartmentConverter<LeftSquareCompartment> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(LeftSquareCompartmentConverter.class.getName());
-
- /**
- * Default constructor.
- *
- * @param colorExtractor
- * Object that helps to convert {@link ColorSchema} values into
- * colors when drawing elements
- *
- */
- public LeftSquareCompartmentConverter(ColorExtractor colorExtractor) {
- super(colorExtractor);
- }
-
- @Override
- public void draw(final LeftSquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
- // keep the old values of color and line type
- Color oldColor = graphics.getColor();
- Stroke oldStroke = graphics.getStroke();
-
- // create shape of the compartment
- Shape s1 = new Line2D.Double(compartment.getWidth(), compartment.getHeight(), compartment.getWidth(), 0);
- Shape s3 = new Line2D.Double(
- compartment.getWidth() - compartment.getThickness(), 0, compartment.getWidth() - compartment.getThickness(), compartment.getHeight());
- Area a1 = new Area(new Rectangle2D.Double(0.0, 0.0, compartment.getWidth(), compartment.getHeight()));
-
- Color c1 = compartment.getColor();
- Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
- if (c1.equals(Color.WHITE)) {
- c1 = Color.BLACK;
- }
-
- // fill the background
- boolean fill = !isTransparent(compartment, params);
- if (fill) {
- graphics.setColor(c1);
- } else {
- Color bgAlphaColor = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), getAlphaLevel());
- graphics.setColor(bgAlphaColor);
- }
- graphics.fill(s1);
-
- // create borders
- graphics.setColor(c1);
- graphics.setStroke(LineType.SOLID_BOLD.getStroke());
- graphics.draw(s1);
- graphics.setStroke(LineType.SOLID.getStroke());
- graphics.draw(s3);
- graphics.setColor(c2);
- if (fill) {
- graphics.fill(a1);
- }
-
- // restore color and line type
- graphics.setColor(oldColor);
- graphics.setStroke(oldStroke);
-
- // draw description
- if (fill) {
- Point2D tmpPoint = compartment.getNamePoint();
- compartment.setNamePoint(compartment.getCenter());
- drawText(compartment, graphics, params);
- compartment.setNamePoint(tmpPoint);
- }
- }
-}
+package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.Shape;
+import java.awt.Stroke;
+import java.awt.geom.Area;
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.DrawingException;
+import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.map.compartment.LeftSquareCompartment;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Class responsible for drawing LeftSquareCompartment on the Graphics2D.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class LeftSquareCompartmentConverter extends CompartmentConverter<LeftSquareCompartment> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(LeftSquareCompartmentConverter.class.getName());
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing elements
+ *
+ */
+ public LeftSquareCompartmentConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
+ @Override
+ public void draw(final LeftSquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
+ // keep the old values of color and line type
+ Color oldColor = graphics.getColor();
+ Stroke oldStroke = graphics.getStroke();
+
+ // create shape of the compartment
+ Shape s1 = new Line2D.Double(compartment.getWidth(), compartment.getHeight(), compartment.getWidth(), 0);
+ Shape s3 = new Line2D.Double(
+ compartment.getWidth() - compartment.getThickness(), 0, compartment.getWidth() - compartment.getThickness(), compartment.getHeight());
+ Area a1 = new Area(new Rectangle2D.Double(0.0, 0.0, compartment.getWidth(), compartment.getHeight()));
+
+ Color c1 = compartment.getColor();
+ Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
+ if (c1.equals(Color.WHITE)) {
+ c1 = Color.BLACK;
+ }
+
+ // fill the background
+ boolean fill = !isTransparent(compartment, params);
+ if (fill) {
+ graphics.setColor(c1);
+ } else {
+ Color bgAlphaColor = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), getAlphaLevel());
+ graphics.setColor(bgAlphaColor);
+ }
+ graphics.fill(s1);
+
+ // create borders
+ graphics.setColor(c1);
+ graphics.setStroke(LineType.SOLID_BOLD.getStroke());
+ graphics.draw(s1);
+ graphics.setStroke(LineType.SOLID.getStroke());
+ graphics.draw(s3);
+ graphics.setColor(c2);
+ if (fill) {
+ graphics.fill(a1);
+ }
+
+ // restore color and line type
+ graphics.setColor(oldColor);
+ graphics.setStroke(oldStroke);
+
+ // draw description
+ if (fill) {
+ Point2D tmpPoint = compartment.getNamePoint();
+ compartment.setNamePoint(compartment.getCenter());
+ drawText(compartment, graphics, params);
+ compartment.setNamePoint(tmpPoint);
+ }
+ }
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/OvalCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/OvalCompartmentConverter.java
index f570a7937d..07addb7e2a 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/OvalCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/OvalCompartmentConverter.java
@@ -1,107 +1,107 @@
-package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.Shape;
-import java.awt.Stroke;
-import java.awt.geom.Area;
-import java.awt.geom.Ellipse2D;
-import java.awt.geom.Point2D;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.converter.graphics.DrawingException;
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.compartment.OvalCompartment;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * Class responsible for drawing OvalCompartment on the Graphics2D.
- *
- * @author Piotr Gawron
- *
- */
-public class OvalCompartmentConverter extends CompartmentConverter<OvalCompartment> {
-
- /**
- * Default constructor.
- *
- * @param colorExtractor
- * Object that helps to convert {@link ColorSchema} values into
- * colors when drawing {@link Species}
- */
- public OvalCompartmentConverter(ColorExtractor colorExtractor) {
- super(colorExtractor);
- }
-
- /**
- * Returns shape representing alias.
- *
- * @param compartment
- * alias for which we are looking for a Shape
- * @return Shape object that represents alias
- */
- private Shape getShape(final Compartment compartment) {
- return new Ellipse2D.Double(compartment.getX(), compartment.getY(), compartment.getWidth(), compartment.getHeight());
- }
-
- @Override
- public void draw(final OvalCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
- // keep the old values of color and line type
- Color oldColor = graphics.getColor();
- Stroke oldStroke = graphics.getStroke();
-
- // create shape of the compartment
- Shape s1 = getShape(compartment);
- compartment.increaseBorder(-compartment.getThickness());
- Shape s3 = getShape(compartment);
- compartment.increaseBorder(compartment.getThickness());
-
- Color c1 = compartment.getColor();
- Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
- if (c1.equals(Color.WHITE)) {
- c1 = Color.BLACK;
- }
-
- Area a1 = new Area(s1);
- a1.subtract(new Area(s3));
-
- // fill the background
- boolean fill = !isTransparent(compartment, params);
- if (fill) {
- graphics.setColor(c1);
- } else {
- Color bgAlphaColor = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), getAlphaLevel());
- graphics.setColor(bgAlphaColor);
- }
- graphics.fill(s1);
-
- // create borders
- graphics.setColor(c1);
- graphics.setStroke(LineType.SOLID_BOLD.getStroke());
- graphics.draw(s1);
- graphics.setStroke(LineType.SOLID.getStroke());
- graphics.draw(s3);
- graphics.setColor(c2);
- graphics.fill(a1);
-
- // restore color and line type
- graphics.setColor(oldColor);
- graphics.setStroke(oldStroke);
-
- // draw description
- if (fill) {
- Point2D tmpPoint = compartment.getNamePoint();
- compartment.setNamePoint(compartment.getCenter());
- drawText(compartment, graphics, params);
- compartment.setNamePoint(tmpPoint);
- } else {
- if (!compartment.containsIdenticalSpecies()) {
- drawText(compartment, graphics, params);
- }
- }
- }
-
-}
+package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.Shape;
+import java.awt.Stroke;
+import java.awt.geom.Area;
+import java.awt.geom.Ellipse2D;
+import java.awt.geom.Point2D;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.DrawingException;
+import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.OvalCompartment;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * Class responsible for drawing OvalCompartment on the Graphics2D.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class OvalCompartmentConverter extends CompartmentConverter<OvalCompartment> {
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing {@link Species}
+ */
+ public OvalCompartmentConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
+ /**
+ * Returns shape representing alias.
+ *
+ * @param compartment
+ * alias for which we are looking for a Shape
+ * @return Shape object that represents alias
+ */
+ private Shape getShape(final Compartment compartment) {
+ return new Ellipse2D.Double(compartment.getX(), compartment.getY(), compartment.getWidth(), compartment.getHeight());
+ }
+
+ @Override
+ public void draw(final OvalCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
+ // keep the old values of color and line type
+ Color oldColor = graphics.getColor();
+ Stroke oldStroke = graphics.getStroke();
+
+ // create shape of the compartment
+ Shape s1 = getShape(compartment);
+ compartment.increaseBorder(-compartment.getThickness());
+ Shape s3 = getShape(compartment);
+ compartment.increaseBorder(compartment.getThickness());
+
+ Color c1 = compartment.getColor();
+ Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
+ if (c1.equals(Color.WHITE)) {
+ c1 = Color.BLACK;
+ }
+
+ Area a1 = new Area(s1);
+ a1.subtract(new Area(s3));
+
+ // fill the background
+ boolean fill = !isTransparent(compartment, params);
+ if (fill) {
+ graphics.setColor(c1);
+ } else {
+ Color bgAlphaColor = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), getAlphaLevel());
+ graphics.setColor(bgAlphaColor);
+ }
+ graphics.fill(s1);
+
+ // create borders
+ graphics.setColor(c1);
+ graphics.setStroke(LineType.SOLID_BOLD.getStroke());
+ graphics.draw(s1);
+ graphics.setStroke(LineType.SOLID.getStroke());
+ graphics.draw(s3);
+ graphics.setColor(c2);
+ graphics.fill(a1);
+
+ // restore color and line type
+ graphics.setColor(oldColor);
+ graphics.setStroke(oldStroke);
+
+ // draw description
+ if (fill) {
+ Point2D tmpPoint = compartment.getNamePoint();
+ compartment.setNamePoint(compartment.getCenter());
+ drawText(compartment, graphics, params);
+ compartment.setNamePoint(tmpPoint);
+ } else {
+ if (!compartment.containsIdenticalSpecies()) {
+ drawText(compartment, graphics, params);
+ }
+ }
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/PathwayCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/PathwayCompartmentConverter.java
index 9440065afb..60d3d808c0 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/PathwayCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/PathwayCompartmentConverter.java
@@ -1,85 +1,85 @@
-package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.Shape;
-import java.awt.Stroke;
-import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.converter.graphics.DrawingException;
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * This class allows to draw {@link PathwayCompartment} on the
- * {@link Graphics2D} class.
- *
- * @author Piotr Gawron
- *
- */
-public class PathwayCompartmentConverter extends CompartmentConverter<PathwayCompartment> {
-
- /**
- * Default constructor.
- *
- * @param colorExtractor
- * Object that helps to convert {@link ColorSchema} values into
- * colors when drawing {@link Species}
- */
- public PathwayCompartmentConverter(ColorExtractor colorExtractor) {
- super(colorExtractor);
- }
-
- /**
- * Background color of drawn compartments.
- */
- private Color backgroundColor = Color.LIGHT_GRAY;
-
- @Override
- public void draw(final PathwayCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
- // keep the old values of colors and line
- Color oldColor = graphics.getColor();
- Stroke oldStroke = graphics.getStroke();
-
- Shape shape = new Rectangle2D.Double(compartment.getX(), compartment.getY(), compartment.getWidth(), compartment.getHeight());
-
- Color color = compartment.getColor();
-
- // fill the background
- boolean fill = !isTransparent(compartment, params);
- if (fill) {
- graphics.setColor(backgroundColor);
- } else {
- Color bgAlphaColor = new Color(0, 0, 0, getAlphaLevel());
- graphics.setColor(bgAlphaColor);
- }
- graphics.fill(shape);
-
- // draw the border
- graphics.setColor(color);
- graphics.setStroke(LineType.SOLID_BOLD.getStroke());
- graphics.draw(shape);
-
- // restore old color and line type
- graphics.setColor(oldColor);
- graphics.setStroke(oldStroke);
-
- // draw description of the compartment
- if (fill) {
- Point2D tmpPoint = compartment.getNamePoint();
- compartment.setNamePoint(compartment.getCenter());
- drawText(compartment, graphics, params);
- compartment.setNamePoint(tmpPoint);
- } else {
- if (!compartment.containsIdenticalSpecies()) {
- drawText(compartment, graphics, params);
- }
- }
- }
-
-}
+package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.Shape;
+import java.awt.Stroke;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.DrawingException;
+import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This class allows to draw {@link PathwayCompartment} on the
+ * {@link Graphics2D} class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class PathwayCompartmentConverter extends CompartmentConverter<PathwayCompartment> {
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing {@link Species}
+ */
+ public PathwayCompartmentConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
+ /**
+ * Background color of drawn compartments.
+ */
+ private Color backgroundColor = Color.LIGHT_GRAY;
+
+ @Override
+ public void draw(final PathwayCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
+ // keep the old values of colors and line
+ Color oldColor = graphics.getColor();
+ Stroke oldStroke = graphics.getStroke();
+
+ Shape shape = new Rectangle2D.Double(compartment.getX(), compartment.getY(), compartment.getWidth(), compartment.getHeight());
+
+ Color color = compartment.getColor();
+
+ // fill the background
+ boolean fill = !isTransparent(compartment, params);
+ if (fill) {
+ graphics.setColor(backgroundColor);
+ } else {
+ Color bgAlphaColor = new Color(0, 0, 0, getAlphaLevel());
+ graphics.setColor(bgAlphaColor);
+ }
+ graphics.fill(shape);
+
+ // draw the border
+ graphics.setColor(color);
+ graphics.setStroke(LineType.SOLID_BOLD.getStroke());
+ graphics.draw(shape);
+
+ // restore old color and line type
+ graphics.setColor(oldColor);
+ graphics.setStroke(oldStroke);
+
+ // draw description of the compartment
+ if (fill) {
+ Point2D tmpPoint = compartment.getNamePoint();
+ compartment.setNamePoint(compartment.getCenter());
+ drawText(compartment, graphics, params);
+ compartment.setNamePoint(tmpPoint);
+ } else {
+ if (!compartment.containsIdenticalSpecies()) {
+ drawText(compartment, graphics, params);
+ }
+ }
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/RightSquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/RightSquareCompartmentConverter.java
index 0dde9a347e..4431113ae6 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/RightSquareCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/RightSquareCompartmentConverter.java
@@ -1,103 +1,103 @@
-package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.Shape;
-import java.awt.Stroke;
-import java.awt.geom.Area;
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.converter.graphics.DrawingException;
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.map.compartment.RightSquareCompartment;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.species.Species;
-
-import org.apache.log4j.Logger;
-
-/**
- * Class responsible for drawing RightSquareCompartment on the Graphics2D.
- *
- * @author Piotr Gawron
- *
- */
-public class RightSquareCompartmentConverter extends CompartmentConverter<RightSquareCompartment> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(RightSquareCompartmentConverter.class.getName());
-
- /**
- * Default constructor.
- *
- * @param colorExtractor
- * Object that helps to convert {@link ColorSchema} values into
- * colors when drawing {@link Species}
- */
- public RightSquareCompartmentConverter(ColorExtractor colorExtractor) {
- super(colorExtractor);
- }
-
- @Override
- public void draw(final RightSquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
- // keep the old values of color and line type
- Color oldColor = graphics.getColor();
- Stroke oldStroke = graphics.getStroke();
-
- // create shape of the compartment
- Shape s1 = new Line2D.Double(compartment.getX(), compartment.getHeight(), compartment.getX(), 0);
- Shape s3 = new Line2D.Double(compartment.getX() + compartment.getThickness(), compartment.getHeight(), compartment.getX(), 0);
- Area a1 = new Area(new Rectangle2D.Double(compartment.getX(), 0.0, compartment.getWidth(), compartment.getHeight()));
-
- Color c1 = compartment.getColor();
- Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
- if (c1.equals(Color.WHITE)) {
- c1 = Color.BLACK;
- }
-
- // fill the background
- boolean fill = !isTransparent(compartment, params);
- if (fill) {
- graphics.setColor(c1);
- } else {
- Color bgAlphaColor = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), getAlphaLevel());
- graphics.setColor(bgAlphaColor);
- }
- graphics.fill(s1);
-
- // create borders
- graphics.setColor(c1);
- graphics.setStroke(LineType.SOLID_BOLD.getStroke());
- graphics.draw(s1);
- graphics.setStroke(LineType.SOLID.getStroke());
- graphics.draw(s3);
- graphics.setColor(c2);
- if (fill) {
- graphics.fill(a1);
- }
- // restore color and line type
- graphics.setColor(oldColor);
- graphics.setStroke(oldStroke);
-
- // three lines below are only temporary fix...
- double x = compartment.getNamePoint().getX() - compartment.getX();
- double y = compartment.getNamePoint().getY();
- compartment.getNamePoint().setLocation(x, y);
-
- // draw description
- if (fill) {
- Point2D tmpPoint = compartment.getNamePoint();
- compartment.setNamePoint(compartment.getCenter());
- drawText(compartment, graphics, params);
- compartment.setNamePoint(tmpPoint);
- }
- x += compartment.getX();
- compartment.getNamePoint().setLocation(x, y);
- }
-}
+package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.Shape;
+import java.awt.Stroke;
+import java.awt.geom.Area;
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.DrawingException;
+import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.map.compartment.RightSquareCompartment;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.species.Species;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Class responsible for drawing RightSquareCompartment on the Graphics2D.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class RightSquareCompartmentConverter extends CompartmentConverter<RightSquareCompartment> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(RightSquareCompartmentConverter.class.getName());
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing {@link Species}
+ */
+ public RightSquareCompartmentConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
+ @Override
+ public void draw(final RightSquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
+ // keep the old values of color and line type
+ Color oldColor = graphics.getColor();
+ Stroke oldStroke = graphics.getStroke();
+
+ // create shape of the compartment
+ Shape s1 = new Line2D.Double(compartment.getX(), compartment.getHeight(), compartment.getX(), 0);
+ Shape s3 = new Line2D.Double(compartment.getX() + compartment.getThickness(), compartment.getHeight(), compartment.getX(), 0);
+ Area a1 = new Area(new Rectangle2D.Double(compartment.getX(), 0.0, compartment.getWidth(), compartment.getHeight()));
+
+ Color c1 = compartment.getColor();
+ Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
+ if (c1.equals(Color.WHITE)) {
+ c1 = Color.BLACK;
+ }
+
+ // fill the background
+ boolean fill = !isTransparent(compartment, params);
+ if (fill) {
+ graphics.setColor(c1);
+ } else {
+ Color bgAlphaColor = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), getAlphaLevel());
+ graphics.setColor(bgAlphaColor);
+ }
+ graphics.fill(s1);
+
+ // create borders
+ graphics.setColor(c1);
+ graphics.setStroke(LineType.SOLID_BOLD.getStroke());
+ graphics.draw(s1);
+ graphics.setStroke(LineType.SOLID.getStroke());
+ graphics.draw(s3);
+ graphics.setColor(c2);
+ if (fill) {
+ graphics.fill(a1);
+ }
+ // restore color and line type
+ graphics.setColor(oldColor);
+ graphics.setStroke(oldStroke);
+
+ // three lines below are only temporary fix...
+ double x = compartment.getNamePoint().getX() - compartment.getX();
+ double y = compartment.getNamePoint().getY();
+ compartment.getNamePoint().setLocation(x, y);
+
+ // draw description
+ if (fill) {
+ Point2D tmpPoint = compartment.getNamePoint();
+ compartment.setNamePoint(compartment.getCenter());
+ drawText(compartment, graphics, params);
+ compartment.setNamePoint(tmpPoint);
+ }
+ x += compartment.getX();
+ compartment.getNamePoint().setLocation(x, y);
+ }
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/SquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/SquareCompartmentConverter.java
index 8f320bf9a3..a524860740 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/SquareCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/SquareCompartmentConverter.java
@@ -1,115 +1,115 @@
-package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.Shape;
-import java.awt.Stroke;
-import java.awt.geom.Area;
-import java.awt.geom.Point2D;
-import java.awt.geom.RoundRectangle2D;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.converter.graphics.DrawingException;
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.compartment.SquareCompartment;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * Class responsible for drawing SquareCompartment on the {@link Graphics2D}.
- *
- * @author Piotr Gawron
- *
- */
-public class SquareCompartmentConverter extends CompartmentConverter<SquareCompartment> {
- /**
- * How big is the arc in the corner of rectangle that represents square
- * compartment.
- */
- private static final int RECTANGLE_CORNER_ARC_SIZE = 20;
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(SquareCompartmentConverter.class.getName());
-
- /**
- * Default constructor.
- *
- * @param colorExtractor
- * Object that helps to convert {@link ColorSchema} values into
- * colors when drawing {@link Species}
- */
- public SquareCompartmentConverter(ColorExtractor colorExtractor) {
- super(colorExtractor);
- }
-
- /**
- * Returns shape representing compartment.
- *
- * @param compartment
- * compartment for which we are looking for a {@link Shape}
- * @return {@link Shape} object that represents compartment
- */
- private Shape getShape(final Compartment compartment) {
- return new RoundRectangle2D.Double(
- compartment.getX(), compartment.getY(), compartment.getWidth(), compartment.getHeight(), RECTANGLE_CORNER_ARC_SIZE, RECTANGLE_CORNER_ARC_SIZE);
- }
-
- @Override
- public void draw(final SquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
- // keep the old values of color and line type
- Color oldColor = graphics.getColor();
- Stroke oldStroke = graphics.getStroke();
-
- // create shape of the compartment
- Shape s1 = getShape(compartment);
- compartment.increaseBorder(-compartment.getThickness());
- Shape s3 = getShape(compartment);
- compartment.increaseBorder(compartment.getThickness());
-
- Color c1 = compartment.getColor();
- Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
- if (c1.equals(Color.WHITE)) {
- c1 = Color.BLACK;
- }
-
- Area a1 = new Area(s1);
- a1.subtract(new Area(s3));
-
- // fill the background
- boolean fill = !isTransparent(compartment, params);
- if (fill) {
- graphics.setColor(c1);
- } else {
- Color bgAlphaColor = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), getAlphaLevel());
- graphics.setColor(bgAlphaColor);
- }
- graphics.fill(s1);
-
- // create borders
- graphics.setColor(c1);
- graphics.setStroke(LineType.SOLID_BOLD.getStroke());
- graphics.draw(s1);
- graphics.setStroke(LineType.SOLID.getStroke());
- graphics.draw(s3);
- graphics.setColor(c2);
- graphics.fill(a1);
-
- // restore color and line type
- graphics.setColor(oldColor);
- graphics.setStroke(oldStroke);
-
- // draw description
- if (fill) {
- Point2D tmpPoint = compartment.getNamePoint();
- compartment.setNamePoint(compartment.getCenter());
- drawText(compartment, graphics, params);
- compartment.setNamePoint(tmpPoint);
- }
- }
-}
+package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.Shape;
+import java.awt.Stroke;
+import java.awt.geom.Area;
+import java.awt.geom.Point2D;
+import java.awt.geom.RoundRectangle2D;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.DrawingException;
+import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.SquareCompartment;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * Class responsible for drawing SquareCompartment on the {@link Graphics2D}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class SquareCompartmentConverter extends CompartmentConverter<SquareCompartment> {
+ /**
+ * How big is the arc in the corner of rectangle that represents square
+ * compartment.
+ */
+ private static final int RECTANGLE_CORNER_ARC_SIZE = 20;
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(SquareCompartmentConverter.class.getName());
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing {@link Species}
+ */
+ public SquareCompartmentConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
+ /**
+ * Returns shape representing compartment.
+ *
+ * @param compartment
+ * compartment for which we are looking for a {@link Shape}
+ * @return {@link Shape} object that represents compartment
+ */
+ private Shape getShape(final Compartment compartment) {
+ return new RoundRectangle2D.Double(
+ compartment.getX(), compartment.getY(), compartment.getWidth(), compartment.getHeight(), RECTANGLE_CORNER_ARC_SIZE, RECTANGLE_CORNER_ARC_SIZE);
+ }
+
+ @Override
+ public void draw(final SquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
+ // keep the old values of color and line type
+ Color oldColor = graphics.getColor();
+ Stroke oldStroke = graphics.getStroke();
+
+ // create shape of the compartment
+ Shape s1 = getShape(compartment);
+ compartment.increaseBorder(-compartment.getThickness());
+ Shape s3 = getShape(compartment);
+ compartment.increaseBorder(compartment.getThickness());
+
+ Color c1 = compartment.getColor();
+ Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
+ if (c1.equals(Color.WHITE)) {
+ c1 = Color.BLACK;
+ }
+
+ Area a1 = new Area(s1);
+ a1.subtract(new Area(s3));
+
+ // fill the background
+ boolean fill = !isTransparent(compartment, params);
+ if (fill) {
+ graphics.setColor(c1);
+ } else {
+ Color bgAlphaColor = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), getAlphaLevel());
+ graphics.setColor(bgAlphaColor);
+ }
+ graphics.fill(s1);
+
+ // create borders
+ graphics.setColor(c1);
+ graphics.setStroke(LineType.SOLID_BOLD.getStroke());
+ graphics.draw(s1);
+ graphics.setStroke(LineType.SOLID.getStroke());
+ graphics.draw(s3);
+ graphics.setColor(c2);
+ graphics.fill(a1);
+
+ // restore color and line type
+ graphics.setColor(oldColor);
+ graphics.setStroke(oldStroke);
+
+ // draw description
+ if (fill) {
+ Point2D tmpPoint = compartment.getNamePoint();
+ compartment.setNamePoint(compartment.getCenter());
+ drawText(compartment, graphics, params);
+ compartment.setNamePoint(tmpPoint);
+ }
+ }
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/TopSquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/TopSquareCompartmentConverter.java
index 2e1ef6dfcd..c30a6ae45e 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/TopSquareCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/TopSquareCompartmentConverter.java
@@ -1,94 +1,94 @@
-package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.Shape;
-import java.awt.Stroke;
-import java.awt.geom.Area;
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.converter.graphics.DrawingException;
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.map.compartment.TopSquareCompartment;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.species.Species;
-
-import org.apache.log4j.Logger;
-
-/**
- * Class responsible for drawing TopSquareCompartment on the {@link Graphics2D}.
- *
- * @author Piotr Gawron
- *
- */
-public class TopSquareCompartmentConverter extends CompartmentConverter<TopSquareCompartment> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(TopSquareCompartmentConverter.class.getName());
-
- /**
- * Default constructor.
- *
- * @param colorExtractor
- * Object that helps to convert {@link ColorSchema} values into
- * colors when drawing {@link Species}
- */
- public TopSquareCompartmentConverter(ColorExtractor colorExtractor) {
- super(colorExtractor);
- }
-
- @Override
- public void draw(final TopSquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
- Color oldColor = graphics.getColor();
- Stroke oldStroke = graphics.getStroke();
-
- Shape s1 = new Line2D.Double(0, compartment.getHeight(), compartment.getWidth(), compartment.getHeight());
- Shape s3 = new Line2D.Double(
- 0, compartment.getHeight() - compartment.getThickness(), compartment.getWidth(), compartment.getHeight() - compartment.getThickness());
- Area a1 = new Area(new Rectangle2D.Double(0.0, 0.0, compartment.getWidth(), compartment.getHeight()));
-
- Color c1 = compartment.getColor();
- Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
- if (c1.equals(Color.WHITE)) {
- c1 = Color.BLACK;
- }
-
- // fill the background
- boolean fill = !isTransparent(compartment, params);
- if (fill) {
- graphics.setColor(c1);
- } else {
- Color bgAlphaColor = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), getAlphaLevel());
- graphics.setColor(bgAlphaColor);
- }
- graphics.fill(s1);
-
- graphics.setColor(c1);
- graphics.setStroke(LineType.SOLID_BOLD.getStroke());
- graphics.draw(s1);
- graphics.setStroke(LineType.SOLID.getStroke());
- graphics.draw(s3);
- graphics.setColor(c2);
- if (fill) {
- graphics.fill(a1);
- }
-
- // restore color and line type
- graphics.setColor(oldColor);
- graphics.setStroke(oldStroke);
- // draw description
- if (fill) {
- Point2D tmpPoint = compartment.getNamePoint();
- compartment.setNamePoint(compartment.getCenter());
- drawText(compartment, graphics, params);
- compartment.setNamePoint(tmpPoint);
- }
- }
-}
+package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.Shape;
+import java.awt.Stroke;
+import java.awt.geom.Area;
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.DrawingException;
+import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.map.compartment.TopSquareCompartment;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.species.Species;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Class responsible for drawing TopSquareCompartment on the {@link Graphics2D}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class TopSquareCompartmentConverter extends CompartmentConverter<TopSquareCompartment> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(TopSquareCompartmentConverter.class.getName());
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing {@link Species}
+ */
+ public TopSquareCompartmentConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
+ @Override
+ public void draw(final TopSquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
+ Color oldColor = graphics.getColor();
+ Stroke oldStroke = graphics.getStroke();
+
+ Shape s1 = new Line2D.Double(0, compartment.getHeight(), compartment.getWidth(), compartment.getHeight());
+ Shape s3 = new Line2D.Double(
+ 0, compartment.getHeight() - compartment.getThickness(), compartment.getWidth(), compartment.getHeight() - compartment.getThickness());
+ Area a1 = new Area(new Rectangle2D.Double(0.0, 0.0, compartment.getWidth(), compartment.getHeight()));
+
+ Color c1 = compartment.getColor();
+ Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
+ if (c1.equals(Color.WHITE)) {
+ c1 = Color.BLACK;
+ }
+
+ // fill the background
+ boolean fill = !isTransparent(compartment, params);
+ if (fill) {
+ graphics.setColor(c1);
+ } else {
+ Color bgAlphaColor = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), getAlphaLevel());
+ graphics.setColor(bgAlphaColor);
+ }
+ graphics.fill(s1);
+
+ graphics.setColor(c1);
+ graphics.setStroke(LineType.SOLID_BOLD.getStroke());
+ graphics.draw(s1);
+ graphics.setStroke(LineType.SOLID.getStroke());
+ graphics.draw(s3);
+ graphics.setColor(c2);
+ if (fill) {
+ graphics.fill(a1);
+ }
+
+ // restore color and line type
+ graphics.setColor(oldColor);
+ graphics.setStroke(oldStroke);
+ // draw description
+ if (fill) {
+ Point2D tmpPoint = compartment.getNamePoint();
+ compartment.setNamePoint(compartment.getCenter());
+ drawText(compartment, graphics, params);
+ compartment.setNamePoint(tmpPoint);
+ }
+ }
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/package-info.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/package-info.java
index 992fd5cbdd..cda3756654 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/package-info.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/package-info.java
@@ -1,5 +1,5 @@
-/**
- * Provides classes that draws different implemention of
- * {@link Compartment} on the {@link Graphics2D}.
- */
-package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
+/**
+ * Provides classes that draws different implemention of
+ * {@link Compartment} on the {@link Graphics2D}.
+ */
+package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/package-info.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/package-info.java
index 2a4ce8bf83..e7a0b3d9dc 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/package-info.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/package-info.java
@@ -1,5 +1,5 @@
-/**
- * Provides classes that draws {@link lcsb.mapviewer.model.map.species.Element
- * Elements} on the Graphics2D object.
- */
-package lcsb.mapviewer.converter.graphics.bioEntity.element;
+/**
+ * Provides classes that draws {@link lcsb.mapviewer.model.map.species.Element
+ * Elements} on the Graphics2D object.
+ */
+package lcsb.mapviewer.converter.graphics.bioEntity.element;
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexConverter.java
index 2fa74bcc72..cb11dd86e9 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexConverter.java
@@ -1,190 +1,190 @@
-package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
-
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.Graphics2D;
-import java.awt.Stroke;
-import java.awt.geom.AffineTransform;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.Path2D;
-import java.awt.geom.PathIterator;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.converter.graphics.geometry.FontFinder;
-import lcsb.mapviewer.converter.graphics.geometry.RectangleTooSmallException;
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * This class defines methods used for drawing ComplexAlias on the graphics2d
- * object.
- *
- * @author Piotr Gawron
- *
- */
-public class ComplexConverter extends SpeciesConverter<Complex> {
-
- /**
- * How big is the triangle trimmed part of the complex.
- */
- private static final int TRIMMED_CORNER_SIZE = 5;
-
- /**
- * Describes the distance between border of complex and internal border in
- * brief view (without children).
- */
- private static final double INTERNAL_BORDER_DIST = 5.0;
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ComplexConverter.class.getName());
-
- /**
- * Default constructor.
- *
- * @param colorExtractor
- * Object that helps to convert {@link ColorSchema} values into
- * colors when drawing {@link Species}
- */
- public ComplexConverter(ColorExtractor colorExtractor) {
- super(colorExtractor);
- }
-
- @Override
- public void draw(final Complex alias, final Graphics2D graphics, final ConverterParams params) {
- if (alias.getState().equalsIgnoreCase("complexnoborder")) {
- return;
- }
-
- int homodir;
- if (params.isSbgnFormat()) {
- // If the SBGN display mode is set, multimer is shown as two stacked
- // glyphs
- if (alias.getHomodimer() > 1) {
- homodir = 2;
- } else {
- homodir = 1;
- }
- } else {
- homodir = alias.getHomodimer();
- }
-
- alias.setWidth(alias.getWidth() - SpeciesConverter.HOMODIMER_OFFSET * (alias.getHomodimer() - 1));
- alias.setHeight(alias.getHeight() - SpeciesConverter.HOMODIMER_OFFSET * (alias.getHomodimer() - 1));
-
- alias.setX(alias.getX() + SpeciesConverter.HOMODIMER_OFFSET * (homodir));
- alias.setY(alias.getY() + SpeciesConverter.HOMODIMER_OFFSET * (homodir));
-
- for (int i = 0; i < homodir; i++) {
- alias.setX(alias.getX() - SpeciesConverter.HOMODIMER_OFFSET);
- alias.setY(alias.getY() - SpeciesConverter.HOMODIMER_OFFSET);
-
- GeneralPath path = getAliasPath(alias);
-
- Color c = graphics.getColor();
- Stroke stroke = graphics.getStroke();
- graphics.setColor(alias.getColor());
- graphics.fill(path);
- graphics.setColor(c);
- graphics.setStroke(getBorderLine(alias));
- graphics.draw(path);
-
- if (alias.getState().equals("brief")) {
- alias.increaseBorder(-INTERNAL_BORDER_DIST);
- path = getAliasPath(alias);
- alias.increaseBorder(INTERNAL_BORDER_DIST);
- graphics.setStroke(LineType.DOTTED.getStroke());
- graphics.draw(path);
- }
- if (alias.getActivity() && !params.isSbgnFormat()) {
- alias.increaseBorder(INTERNAL_BORDER_DIST);
- path = getAliasPath(alias);
- alias.increaseBorder(-INTERNAL_BORDER_DIST);
- graphics.setStroke(LineType.DOTTED.getStroke());
- graphics.draw(path);
- }
- graphics.setStroke(stroke);
- }
-
- alias.setWidth(alias.getWidth() + SpeciesConverter.HOMODIMER_OFFSET * (alias.getHomodimer() - 1));
- alias.setHeight(alias.getHeight() + SpeciesConverter.HOMODIMER_OFFSET * (alias.getHomodimer() - 1));
-
- // SBGN view - multimers are displayed with a unit of information containing
- // cardinality
- if (params.isSbgnFormat()) {
- String unitOfInformationText = null;
- if (alias.getStatePrefix() != null && alias.getStateLabel() != null) {
- unitOfInformationText = alias.getStatePrefix() + ":" + alias.getStateLabel();
- }
- if (homodir == 2 && (unitOfInformationText == null || !unitOfInformationText.contains("N:"))) {
- if (unitOfInformationText != null) {
- unitOfInformationText += "; ";
- } else {
- unitOfInformationText = "";
- }
- unitOfInformationText += "N:" + alias.getHomodimer();
- }
-
- drawUnitOfInformation(unitOfInformationText, alias, graphics);
- }
-
- String text = alias.getStructuralState();
-
- drawStructuralState(text, alias, graphics);
-
- drawText(alias, graphics, params);
- }
-
- @Override
- public void drawText(final Complex complex, final Graphics2D graphics, final ConverterParams params) {
- if (complex.getElements().size() > 0) {
- if (isTransparent(complex, params)) {
- super.drawText(complex, graphics, params);
- return;
- }
- }
- String text = getText(complex);
- try {
- double fontSize = DEFAULT_SPECIES_FONT_SIZE;
- if (complex.getFontSize() != null) {
- fontSize = complex.getFontSize();
- }
- int size = (int) FontFinder.findMaxFontSize(params.getScale() * fontSize, Font.SANS_SERIF, graphics, complex.getBorder(), text);
- FontFinder.drawText(size, Font.SANS_SERIF, graphics, complex.getBorder(), text);
- } catch (RectangleTooSmallException e) {
- logger.warn("Problem with finding font size", e);
- super.drawText(complex, graphics, params);
- }
- }
-
- /**
- * Returns the border of {@link Complex}.
- *
- * @param complex
- * exact object for which we want to get a border
- * @return border of the {@link Complex}
- */
- private GeneralPath getAliasPath(final Complex complex) {
- GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD);
- path.moveTo(complex.getX() + TRIMMED_CORNER_SIZE, complex.getY());
- path.lineTo(complex.getX() + complex.getWidth() - TRIMMED_CORNER_SIZE, complex.getY());
- path.lineTo(complex.getX() + complex.getWidth(), complex.getY() + TRIMMED_CORNER_SIZE);
- path.lineTo(complex.getX() + complex.getWidth(), complex.getY() + complex.getHeight() - TRIMMED_CORNER_SIZE);
- path.lineTo(complex.getX() + complex.getWidth() - TRIMMED_CORNER_SIZE, complex.getY() + complex.getHeight());
- path.lineTo(complex.getX() + TRIMMED_CORNER_SIZE, complex.getY() + complex.getHeight());
- path.lineTo(complex.getX(), complex.getY() + complex.getHeight() - TRIMMED_CORNER_SIZE);
- path.lineTo(complex.getX(), complex.getY() + TRIMMED_CORNER_SIZE);
- path.closePath();
- return path;
- }
-
- @Override
- public PathIterator getBoundPathIterator(final Complex complex) {
- return getAliasPath(complex).getPathIterator(new AffineTransform());
- }
-}
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Graphics2D;
+import java.awt.Stroke;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.Path2D;
+import java.awt.geom.PathIterator;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.geometry.FontFinder;
+import lcsb.mapviewer.converter.graphics.geometry.RectangleTooSmallException;
+import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This class defines methods used for drawing ComplexAlias on the graphics2d
+ * object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ComplexConverter extends SpeciesConverter<Complex> {
+
+ /**
+ * How big is the triangle trimmed part of the complex.
+ */
+ private static final int TRIMMED_CORNER_SIZE = 5;
+
+ /**
+ * Describes the distance between border of complex and internal border in
+ * brief view (without children).
+ */
+ private static final double INTERNAL_BORDER_DIST = 5.0;
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ComplexConverter.class.getName());
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing {@link Species}
+ */
+ public ComplexConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
+ @Override
+ public void draw(final Complex alias, final Graphics2D graphics, final ConverterParams params) {
+ if (alias.getState().equalsIgnoreCase("complexnoborder")) {
+ return;
+ }
+
+ int homodir;
+ if (params.isSbgnFormat()) {
+ // If the SBGN display mode is set, multimer is shown as two stacked
+ // glyphs
+ if (alias.getHomodimer() > 1) {
+ homodir = 2;
+ } else {
+ homodir = 1;
+ }
+ } else {
+ homodir = alias.getHomodimer();
+ }
+
+ alias.setWidth(alias.getWidth() - SpeciesConverter.HOMODIMER_OFFSET * (alias.getHomodimer() - 1));
+ alias.setHeight(alias.getHeight() - SpeciesConverter.HOMODIMER_OFFSET * (alias.getHomodimer() - 1));
+
+ alias.setX(alias.getX() + SpeciesConverter.HOMODIMER_OFFSET * (homodir));
+ alias.setY(alias.getY() + SpeciesConverter.HOMODIMER_OFFSET * (homodir));
+
+ for (int i = 0; i < homodir; i++) {
+ alias.setX(alias.getX() - SpeciesConverter.HOMODIMER_OFFSET);
+ alias.setY(alias.getY() - SpeciesConverter.HOMODIMER_OFFSET);
+
+ GeneralPath path = getAliasPath(alias);
+
+ Color c = graphics.getColor();
+ Stroke stroke = graphics.getStroke();
+ graphics.setColor(alias.getColor());
+ graphics.fill(path);
+ graphics.setColor(c);
+ graphics.setStroke(getBorderLine(alias));
+ graphics.draw(path);
+
+ if (alias.getState().equals("brief")) {
+ alias.increaseBorder(-INTERNAL_BORDER_DIST);
+ path = getAliasPath(alias);
+ alias.increaseBorder(INTERNAL_BORDER_DIST);
+ graphics.setStroke(LineType.DOTTED.getStroke());
+ graphics.draw(path);
+ }
+ if (alias.getActivity() && !params.isSbgnFormat()) {
+ alias.increaseBorder(INTERNAL_BORDER_DIST);
+ path = getAliasPath(alias);
+ alias.increaseBorder(-INTERNAL_BORDER_DIST);
+ graphics.setStroke(LineType.DOTTED.getStroke());
+ graphics.draw(path);
+ }
+ graphics.setStroke(stroke);
+ }
+
+ alias.setWidth(alias.getWidth() + SpeciesConverter.HOMODIMER_OFFSET * (alias.getHomodimer() - 1));
+ alias.setHeight(alias.getHeight() + SpeciesConverter.HOMODIMER_OFFSET * (alias.getHomodimer() - 1));
+
+ // SBGN view - multimers are displayed with a unit of information containing
+ // cardinality
+ if (params.isSbgnFormat()) {
+ String unitOfInformationText = null;
+ if (alias.getStatePrefix() != null && alias.getStateLabel() != null) {
+ unitOfInformationText = alias.getStatePrefix() + ":" + alias.getStateLabel();
+ }
+ if (homodir == 2 && (unitOfInformationText == null || !unitOfInformationText.contains("N:"))) {
+ if (unitOfInformationText != null) {
+ unitOfInformationText += "; ";
+ } else {
+ unitOfInformationText = "";
+ }
+ unitOfInformationText += "N:" + alias.getHomodimer();
+ }
+
+ drawUnitOfInformation(unitOfInformationText, alias, graphics);
+ }
+
+ String text = alias.getStructuralState();
+
+ drawStructuralState(text, alias, graphics);
+
+ drawText(alias, graphics, params);
+ }
+
+ @Override
+ public void drawText(final Complex complex, final Graphics2D graphics, final ConverterParams params) {
+ if (complex.getElements().size() > 0) {
+ if (isTransparent(complex, params)) {
+ super.drawText(complex, graphics, params);
+ return;
+ }
+ }
+ String text = getText(complex);
+ try {
+ double fontSize = DEFAULT_SPECIES_FONT_SIZE;
+ if (complex.getFontSize() != null) {
+ fontSize = complex.getFontSize();
+ }
+ int size = (int) FontFinder.findMaxFontSize(params.getScale() * fontSize, Font.SANS_SERIF, graphics, complex.getBorder(), text);
+ FontFinder.drawText(size, Font.SANS_SERIF, graphics, complex.getBorder(), text);
+ } catch (RectangleTooSmallException e) {
+ logger.warn("Problem with finding font size", e);
+ super.drawText(complex, graphics, params);
+ }
+ }
+
+ /**
+ * Returns the border of {@link Complex}.
+ *
+ * @param complex
+ * exact object for which we want to get a border
+ * @return border of the {@link Complex}
+ */
+ private GeneralPath getAliasPath(final Complex complex) {
+ GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD);
+ path.moveTo(complex.getX() + TRIMMED_CORNER_SIZE, complex.getY());
+ path.lineTo(complex.getX() + complex.getWidth() - TRIMMED_CORNER_SIZE, complex.getY());
+ path.lineTo(complex.getX() + complex.getWidth(), complex.getY() + TRIMMED_CORNER_SIZE);
+ path.lineTo(complex.getX() + complex.getWidth(), complex.getY() + complex.getHeight() - TRIMMED_CORNER_SIZE);
+ path.lineTo(complex.getX() + complex.getWidth() - TRIMMED_CORNER_SIZE, complex.getY() + complex.getHeight());
+ path.lineTo(complex.getX() + TRIMMED_CORNER_SIZE, complex.getY() + complex.getHeight());
+ path.lineTo(complex.getX(), complex.getY() + complex.getHeight() - TRIMMED_CORNER_SIZE);
+ path.lineTo(complex.getX(), complex.getY() + TRIMMED_CORNER_SIZE);
+ path.closePath();
+ return path;
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(final Complex complex) {
+ return getAliasPath(complex).getPathIterator(new AffineTransform());
+ }
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DegradedConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DegradedConverter.java
index 2b8c6d163a..e51b68f673 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DegradedConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DegradedConverter.java
@@ -1,135 +1,135 @@
-package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.Stroke;
-import java.awt.geom.Area;
-import java.awt.geom.Ellipse2D;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.Path2D;
-import java.awt.geom.PathIterator;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.species.Degraded;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * This class defines methods used for drawing {@link Degraded} on the
- * {@link Graphics2D} object.
- *
- * @author Piotr Gawron
- *
- */
-public class DegradedConverter extends SpeciesConverter<Degraded> {
- /**
- * Part of height of the line used to cross degraded circle that goes behind
- * this circle.
- */
- private static final int CROSS_LINE_EXTENDED_LENGTH = 7;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(DegradedConverter.class.getName());
-
- /**
- * Default constructor.
- *
- * @param colorExtractor
- * Object that helps to convert {@link ColorSchema} values into
- * colors when drawing {@link Species}
- */
- public DegradedConverter(ColorExtractor colorExtractor) {
- super(colorExtractor);
- }
-
- @Override
- public void draw(final Degraded degraded, final Graphics2D graphics, final ConverterParams params) {
- double diameter = getDiameter(degraded);
- double x = getXCoord(degraded, diameter);
- double y = getYCoord(degraded);
- Area a1 = new Area(new Ellipse2D.Double(x, y, diameter, diameter));
-
- double lineX1 = degraded.getX() + degraded.getWidth() / 2 + CROSS_LINE_EXTENDED_LENGTH;
- double lineY1 = degraded.getY();
-
- double lineX2 = degraded.getX() + degraded.getWidth() / 2 - CROSS_LINE_EXTENDED_LENGTH;
- double lineY2 = degraded.getY() + diameter + 2 * CROSS_LINE_EXTENDED_LENGTH;
-
- GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD, 2);
- path.moveTo(lineX1, lineY1);
- path.lineTo(lineX1 + 1, lineY1);
- path.lineTo(lineX2 + 1, lineY2);
- path.lineTo(lineX2, lineY2);
- path.closePath();
-
- a1.exclusiveOr(new Area(path));
- Color c = graphics.getColor();
- graphics.setColor(degraded.getColor());
- graphics.fill(a1);
- graphics.setColor(c);
- Stroke stroke = graphics.getStroke();
- graphics.setStroke(getBorderLine(degraded));
- graphics.draw(a1);
- graphics.setStroke(stroke);
- drawText(degraded, graphics, params);
- }
-
- /**
- * Returns transformed y coordinate for the {@link Degraded} bioentity.
- *
- * @param degraded
- * {@link Degraded} to to which we are looking for y coordinate
- * @return y coordinate of the alias
- */
- private double getYCoord(final Degraded degraded) {
- double y = degraded.getY() + CROSS_LINE_EXTENDED_LENGTH;
- return y;
- }
-
- /**
- * Returns transformed x coordinate for the degraded alias.
- *
- * @param degraded
- * object alias to to which we are looking for x coordinate
- * @param diameter
- * diameter of cross line used in this alias
- * @return x coordinate of the {@link Degraded} bioentity.
- */
- private double getXCoord(final Degraded degraded, final double diameter) {
- double x = degraded.getX() + (degraded.getWidth() - diameter) / 2;
- return x;
- }
-
- /**
- * Computes diameter of cross line for the degraded alias.
- *
- * @param degraded
- * object alias to to which we are looking for diameter.
- * @return diameter of the cross line
- */
- private double getDiameter(final Degraded degraded) {
- double diameter = Math.min(degraded.getWidth(), degraded.getHeight()) - 2 * CROSS_LINE_EXTENDED_LENGTH;
- if (diameter < 0) {
- logger.warn("Diameter cannot be negative...");
- diameter = 0;
- }
- return diameter;
- }
-
- @Override
- public String getText(Degraded degraded) {
- return "";
- }
-
- @Override
- public PathIterator getBoundPathIterator(Degraded degraded) {
- throw new InvalidStateException("This class doesn't have bound");
- }
-
-}
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.Stroke;
+import java.awt.geom.Area;
+import java.awt.geom.Ellipse2D;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.Path2D;
+import java.awt.geom.PathIterator;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.species.Degraded;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This class defines methods used for drawing {@link Degraded} on the
+ * {@link Graphics2D} object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class DegradedConverter extends SpeciesConverter<Degraded> {
+ /**
+ * Part of height of the line used to cross degraded circle that goes behind
+ * this circle.
+ */
+ private static final int CROSS_LINE_EXTENDED_LENGTH = 7;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(DegradedConverter.class.getName());
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing {@link Species}
+ */
+ public DegradedConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
+ @Override
+ public void draw(final Degraded degraded, final Graphics2D graphics, final ConverterParams params) {
+ double diameter = getDiameter(degraded);
+ double x = getXCoord(degraded, diameter);
+ double y = getYCoord(degraded);
+ Area a1 = new Area(new Ellipse2D.Double(x, y, diameter, diameter));
+
+ double lineX1 = degraded.getX() + degraded.getWidth() / 2 + CROSS_LINE_EXTENDED_LENGTH;
+ double lineY1 = degraded.getY();
+
+ double lineX2 = degraded.getX() + degraded.getWidth() / 2 - CROSS_LINE_EXTENDED_LENGTH;
+ double lineY2 = degraded.getY() + diameter + 2 * CROSS_LINE_EXTENDED_LENGTH;
+
+ GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD, 2);
+ path.moveTo(lineX1, lineY1);
+ path.lineTo(lineX1 + 1, lineY1);
+ path.lineTo(lineX2 + 1, lineY2);
+ path.lineTo(lineX2, lineY2);
+ path.closePath();
+
+ a1.exclusiveOr(new Area(path));
+ Color c = graphics.getColor();
+ graphics.setColor(degraded.getColor());
+ graphics.fill(a1);
+ graphics.setColor(c);
+ Stroke stroke = graphics.getStroke();
+ graphics.setStroke(getBorderLine(degraded));
+ graphics.draw(a1);
+ graphics.setStroke(stroke);
+ drawText(degraded, graphics, params);
+ }
+
+ /**
+ * Returns transformed y coordinate for the {@link Degraded} bioentity.
+ *
+ * @param degraded
+ * {@link Degraded} to to which we are looking for y coordinate
+ * @return y coordinate of the alias
+ */
+ private double getYCoord(final Degraded degraded) {
+ double y = degraded.getY() + CROSS_LINE_EXTENDED_LENGTH;
+ return y;
+ }
+
+ /**
+ * Returns transformed x coordinate for the degraded alias.
+ *
+ * @param degraded
+ * object alias to to which we are looking for x coordinate
+ * @param diameter
+ * diameter of cross line used in this alias
+ * @return x coordinate of the {@link Degraded} bioentity.
+ */
+ private double getXCoord(final Degraded degraded, final double diameter) {
+ double x = degraded.getX() + (degraded.getWidth() - diameter) / 2;
+ return x;
+ }
+
+ /**
+ * Computes diameter of cross line for the degraded alias.
+ *
+ * @param degraded
+ * object alias to to which we are looking for diameter.
+ * @return diameter of the cross line
+ */
+ private double getDiameter(final Degraded degraded) {
+ double diameter = Math.min(degraded.getWidth(), degraded.getHeight()) - 2 * CROSS_LINE_EXTENDED_LENGTH;
+ if (diameter < 0) {
+ logger.warn("Diameter cannot be negative...");
+ diameter = 0;
+ }
+ return diameter;
+ }
+
+ @Override
+ public String getText(Degraded degraded) {
+ return "";
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(Degraded degraded) {
+ throw new InvalidStateException("This class doesn't have bound");
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DrugConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DrugConverter.java
index 8765dd6e30..e21d696918 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DrugConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DrugConverter.java
@@ -1,122 +1,122 @@
-package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.Shape;
-import java.awt.Stroke;
-import java.awt.geom.AffineTransform;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-import java.awt.geom.RoundRectangle2D;
-import java.util.ArrayList;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.species.Drug;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * This class defines methods used for drawing Drug SpeciesAlias on the
- * graphics2d object.
- *
- * @author Piotr Gawron
- *
- */
-public class DrugConverter extends SpeciesConverter<Drug> {
-
- /**
- * Distance between internal and external border of drug graphical
- * representation.
- */
- private static final int OFFSET_BETWEEN_BORDERS = 4;
-
- /**
- * How big should be the arc in rectangle for drug representation.
- */
- private static final int RECTANGLE_CORNER_ARC_SIZE = 40;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(DrugConverter.class.getName());
-
- /**
- * Default constructor.
- *
- * @param colorExtractor
- * Object that helps to convert {@link ColorSchema} values into
- * colors when drawing {@link Species}
- */
- public DrugConverter(ColorExtractor colorExtractor) {
- super(colorExtractor);
- }
-
- /**
- * Returns shape of the Drug .
- *
- * @param drug
- * {@link Drug} for which we are looking for a border
- * @return Shape object defining given alias
- */
- private Shape getDrugShape(final Drug drug) {
- return new RoundRectangle2D.Double(drug.getX(), drug.getY(), drug.getWidth(), drug.getHeight(), RECTANGLE_CORNER_ARC_SIZE, RECTANGLE_CORNER_ARC_SIZE);
- }
-
- @Override
- public void draw(Drug drug, final Graphics2D graphics, final ConverterParams params) {
- Shape a1 = getDrugShape(drug);
- double offset = OFFSET_BETWEEN_BORDERS;
- Shape a2 = new RoundRectangle2D.Double(
- drug.getX() + offset, drug.getY() + offset, drug.getWidth() - 2 * offset, drug.getHeight() - 2 * offset, RECTANGLE_CORNER_ARC_SIZE,
- RECTANGLE_CORNER_ARC_SIZE);
- Color c = graphics.getColor();
- graphics.setColor(drug.getColor());
- graphics.fill(a1);
- graphics.setColor(c);
- Stroke stroke = graphics.getStroke();
- graphics.setStroke(getBorderLine(drug));
- graphics.draw(a1);
- graphics.draw(a2);
- graphics.setStroke(stroke);
- drawText(drug, graphics, params);
- }
-
- /**
- * Returns shape of the {@link Drug} as a list of points.
- *
- * @param drug
- * {@link Drug} for which we are looking for a border
- * @return list of points defining border of the given {@link Drug}
- */
- protected ArrayList<Point2D> getDrugPoints(final Drug drug) {
- ArrayList<Point2D> list = new ArrayList<Point2D>();
-
- double x = drug.getX();
- double y = drug.getY();
- double width = drug.getWidth();
- double height = drug.getHeight();
-
- // CHECKSTYLE:OFF
- list.add(new Point2D.Double(x, y + height / 2));
- list.add(new Point2D.Double(x + width / 12, y));
- list.add(new Point2D.Double(x + width / 2, y));
- list.add(new Point2D.Double(x + width * 11 / 12, y));
- list.add(new Point2D.Double(x + width, y + height / 2));
- list.add(new Point2D.Double(x + width * 11 / 12, y + height));
- list.add(new Point2D.Double(x + width / 2, y + height));
- list.add(new Point2D.Double(x + width / 12, y + height));
- // CHECKSTYLE:ON
-
- return list;
- }
-
- @Override
- public PathIterator getBoundPathIterator(Drug drug) {
- return getDrugShape(drug).getPathIterator(new AffineTransform());
- }
-
-}
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.Shape;
+import java.awt.Stroke;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+import java.awt.geom.RoundRectangle2D;
+import java.util.ArrayList;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.species.Drug;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This class defines methods used for drawing Drug SpeciesAlias on the
+ * graphics2d object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class DrugConverter extends SpeciesConverter<Drug> {
+
+ /**
+ * Distance between internal and external border of drug graphical
+ * representation.
+ */
+ private static final int OFFSET_BETWEEN_BORDERS = 4;
+
+ /**
+ * How big should be the arc in rectangle for drug representation.
+ */
+ private static final int RECTANGLE_CORNER_ARC_SIZE = 40;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(DrugConverter.class.getName());
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing {@link Species}
+ */
+ public DrugConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
+ /**
+ * Returns shape of the Drug .
+ *
+ * @param drug
+ * {@link Drug} for which we are looking for a border
+ * @return Shape object defining given alias
+ */
+ private Shape getDrugShape(final Drug drug) {
+ return new RoundRectangle2D.Double(drug.getX(), drug.getY(), drug.getWidth(), drug.getHeight(), RECTANGLE_CORNER_ARC_SIZE, RECTANGLE_CORNER_ARC_SIZE);
+ }
+
+ @Override
+ public void draw(Drug drug, final Graphics2D graphics, final ConverterParams params) {
+ Shape a1 = getDrugShape(drug);
+ double offset = OFFSET_BETWEEN_BORDERS;
+ Shape a2 = new RoundRectangle2D.Double(
+ drug.getX() + offset, drug.getY() + offset, drug.getWidth() - 2 * offset, drug.getHeight() - 2 * offset, RECTANGLE_CORNER_ARC_SIZE,
+ RECTANGLE_CORNER_ARC_SIZE);
+ Color c = graphics.getColor();
+ graphics.setColor(drug.getColor());
+ graphics.fill(a1);
+ graphics.setColor(c);
+ Stroke stroke = graphics.getStroke();
+ graphics.setStroke(getBorderLine(drug));
+ graphics.draw(a1);
+ graphics.draw(a2);
+ graphics.setStroke(stroke);
+ drawText(drug, graphics, params);
+ }
+
+ /**
+ * Returns shape of the {@link Drug} as a list of points.
+ *
+ * @param drug
+ * {@link Drug} for which we are looking for a border
+ * @return list of points defining border of the given {@link Drug}
+ */
+ protected ArrayList<Point2D> getDrugPoints(final Drug drug) {
+ ArrayList<Point2D> list = new ArrayList<Point2D>();
+
+ double x = drug.getX();
+ double y = drug.getY();
+ double width = drug.getWidth();
+ double height = drug.getHeight();
+
+ // CHECKSTYLE:OFF
+ list.add(new Point2D.Double(x, y + height / 2));
+ list.add(new Point2D.Double(x + width / 12, y));
+ list.add(new Point2D.Double(x + width / 2, y));
+ list.add(new Point2D.Double(x + width * 11 / 12, y));
+ list.add(new Point2D.Double(x + width, y + height / 2));
+ list.add(new Point2D.Double(x + width * 11 / 12, y + height));
+ list.add(new Point2D.Double(x + width / 2, y + height));
+ list.add(new Point2D.Double(x + width / 12, y + height));
+ // CHECKSTYLE:ON
+
+ return list;
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(Drug drug) {
+ return getDrugShape(drug).getPathIterator(new AffineTransform());
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/IonConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/IonConverter.java
index b8d1220e40..5f261cb19b 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/IonConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/IonConverter.java
@@ -1,110 +1,110 @@
-package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.Shape;
-import java.awt.Stroke;
-import java.awt.geom.Ellipse2D;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.species.Ion;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * This class defines methods used for drawing SpeciesAlias of {@link Ion} on
- * the {@link Graphics2D} object.
- *
- * @author Piotr Gawron
- *
- */
-public class IonConverter extends SpeciesConverter<Ion> {
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(IonConverter.class.getName());
-
- /**
- * Default constructor.
- *
- * @param colorExtractor
- * Object that helps to convert {@link ColorSchema} values into colors
- * when drawing {@link Species}
- */
- public IonConverter(ColorExtractor colorExtractor) {
- super(colorExtractor);
- }
-
- @Override
- public void draw(Ion ion, final Graphics2D graphics, final ConverterParams params) {
- double diameter = getDiameter(ion);
- double x = getXCoord(ion, diameter);
- double y = getYCoord(ion);
- Shape shape = new Ellipse2D.Double(x, y, diameter, diameter);
- Color c = graphics.getColor();
- graphics.setColor(ion.getColor());
- graphics.fill(shape);
- graphics.setColor(c);
- Stroke stroke = graphics.getStroke();
- graphics.setStroke(getBorderLine(ion));
- graphics.draw(shape);
- graphics.setStroke(stroke);
- drawText(ion, graphics, params);
- }
-
- /**
- * Returns transformed y coordinate for the {@link Ion}.
- *
- * @param ion
- * {@link Ion} to to which we are looking for y coordinate
- * @return y coordinate of the {@link Ion}
- */
- private double getYCoord(final Ion ion) {
- double y = ion.getY();
- return y;
- }
-
- /**
- * Returns transformed x coordinate for the {@link Ion}.
- *
- * @param ion
- * {@link Ion} to which we are looking for x coordinate
- * @param diameter
- * diameter of circle representation of ion
- * @return x coordinate of the {@link Ion}
- */
- private double getXCoord(final Ion ion, final double diameter) {
- double x = ion.getX() + (ion.getWidth() - diameter) / 2;
- return x;
- }
-
- /**
- * Returns diameter of circle representation of an {@link Ion}.
- *
- * @param ion
- * {@link Ion} to to which we are looking for diameter.
- * @return diameter of {@link Ion} circle representation
- */
- private double getDiameter(final Ion ion) {
- double diameter = Math.min(ion.getWidth(), ion.getHeight());
- if (diameter < 0) {
- logger.warn("Something is wrong. Size cannot be negative");
- diameter = 0;
- }
-
- return diameter;
- }
-
- @Override
- public PathIterator getBoundPathIterator(Ion ion) {
- throw new InvalidStateException("This class doesn't have bound");
- }
-
-}
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.Shape;
+import java.awt.Stroke;
+import java.awt.geom.Ellipse2D;
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This class defines methods used for drawing SpeciesAlias of {@link Ion} on
+ * the {@link Graphics2D} object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class IonConverter extends SpeciesConverter<Ion> {
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(IonConverter.class.getName());
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into colors
+ * when drawing {@link Species}
+ */
+ public IonConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
+ @Override
+ public void draw(Ion ion, final Graphics2D graphics, final ConverterParams params) {
+ double diameter = getDiameter(ion);
+ double x = getXCoord(ion, diameter);
+ double y = getYCoord(ion);
+ Shape shape = new Ellipse2D.Double(x, y, diameter, diameter);
+ Color c = graphics.getColor();
+ graphics.setColor(ion.getColor());
+ graphics.fill(shape);
+ graphics.setColor(c);
+ Stroke stroke = graphics.getStroke();
+ graphics.setStroke(getBorderLine(ion));
+ graphics.draw(shape);
+ graphics.setStroke(stroke);
+ drawText(ion, graphics, params);
+ }
+
+ /**
+ * Returns transformed y coordinate for the {@link Ion}.
+ *
+ * @param ion
+ * {@link Ion} to to which we are looking for y coordinate
+ * @return y coordinate of the {@link Ion}
+ */
+ private double getYCoord(final Ion ion) {
+ double y = ion.getY();
+ return y;
+ }
+
+ /**
+ * Returns transformed x coordinate for the {@link Ion}.
+ *
+ * @param ion
+ * {@link Ion} to which we are looking for x coordinate
+ * @param diameter
+ * diameter of circle representation of ion
+ * @return x coordinate of the {@link Ion}
+ */
+ private double getXCoord(final Ion ion, final double diameter) {
+ double x = ion.getX() + (ion.getWidth() - diameter) / 2;
+ return x;
+ }
+
+ /**
+ * Returns diameter of circle representation of an {@link Ion}.
+ *
+ * @param ion
+ * {@link Ion} to to which we are looking for diameter.
+ * @return diameter of {@link Ion} circle representation
+ */
+ private double getDiameter(final Ion ion) {
+ double diameter = Math.min(ion.getWidth(), ion.getHeight());
+ if (diameter < 0) {
+ logger.warn("Something is wrong. Size cannot be negative");
+ diameter = 0;
+ }
+
+ return diameter;
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(Ion ion) {
+ throw new InvalidStateException("This class doesn't have bound");
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/PhenotypeConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/PhenotypeConverter.java
index b9674dc864..5d73019e9a 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/PhenotypeConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/PhenotypeConverter.java
@@ -1,86 +1,86 @@
-package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.Stroke;
-import java.awt.geom.AffineTransform;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.Path2D;
-import java.awt.geom.PathIterator;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.species.Phenotype;
-
-/**
- * This class defines methods used for drawing SpeciesAlias of {@link Phenotype}
- * on the {@link Graphics2D} object.
- *
- * @author Piotr Gawron
- *
- */
-public class PhenotypeConverter extends SpeciesConverter<Phenotype> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(PhenotypeConverter.class.getName());
-
- /**
- * Default constructor.
- *
- * @param colorExtractor
- * Object that helps to convert {@link ColorSchema} values into
- * colors when drawing elements
- *
- */
- public PhenotypeConverter(ColorExtractor colorExtractor) {
- super(colorExtractor);
- }
-
- @Override
- public void draw(Phenotype phenotype, final Graphics2D graphics, final ConverterParams params) {
- GeneralPath path = getPhenotypePath(phenotype);
-
- Color c = graphics.getColor();
- graphics.setColor(phenotype.getColor());
- graphics.fill(path);
- graphics.setColor(c);
- Stroke stroke = graphics.getStroke();
- graphics.setStroke(getBorderLine(phenotype));
- graphics.draw(path);
- graphics.setStroke(stroke);
- drawText(phenotype, graphics, params);
- }
-
- /**
- * Returns shape of the {@link Phenotype} as a {@link GeneralPath} object.
- *
- * @param phenotype
- * {@link Phenotype} for which we are looking for a border
- * @return {@link GeneralPath} object defining border of the given
- * {@link Phenotype}
- */
- private GeneralPath getPhenotypePath(final Phenotype phenotype) {
- // CHECKSTYLE:OFF
- GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD, 6);
- path.moveTo(phenotype.getX() + phenotype.getWidth() / 6, phenotype.getY());
- path.lineTo(phenotype.getX() + phenotype.getWidth() * 5 / 6, phenotype.getY());
- path.lineTo(phenotype.getX() + phenotype.getWidth(), phenotype.getY() + phenotype.getHeight() / 2);
- path.lineTo(phenotype.getX() + phenotype.getWidth() * 5 / 6, phenotype.getY() + phenotype.getHeight());
- path.lineTo(phenotype.getX() + phenotype.getWidth() / 6, phenotype.getY() + phenotype.getHeight());
- path.lineTo(phenotype.getX(), phenotype.getY() + phenotype.getHeight() / 2);
- // CHECKSTYLE:ON
- path.closePath();
- return path;
- }
-
- @Override
- public PathIterator getBoundPathIterator(Phenotype phenotype) {
- return getPhenotypePath(phenotype).getPathIterator(new AffineTransform());
- }
-
-}
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.Stroke;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.Path2D;
+import java.awt.geom.PathIterator;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.species.Phenotype;
+
+/**
+ * This class defines methods used for drawing SpeciesAlias of {@link Phenotype}
+ * on the {@link Graphics2D} object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class PhenotypeConverter extends SpeciesConverter<Phenotype> {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(PhenotypeConverter.class.getName());
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing elements
+ *
+ */
+ public PhenotypeConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
+ @Override
+ public void draw(Phenotype phenotype, final Graphics2D graphics, final ConverterParams params) {
+ GeneralPath path = getPhenotypePath(phenotype);
+
+ Color c = graphics.getColor();
+ graphics.setColor(phenotype.getColor());
+ graphics.fill(path);
+ graphics.setColor(c);
+ Stroke stroke = graphics.getStroke();
+ graphics.setStroke(getBorderLine(phenotype));
+ graphics.draw(path);
+ graphics.setStroke(stroke);
+ drawText(phenotype, graphics, params);
+ }
+
+ /**
+ * Returns shape of the {@link Phenotype} as a {@link GeneralPath} object.
+ *
+ * @param phenotype
+ * {@link Phenotype} for which we are looking for a border
+ * @return {@link GeneralPath} object defining border of the given
+ * {@link Phenotype}
+ */
+ private GeneralPath getPhenotypePath(final Phenotype phenotype) {
+ // CHECKSTYLE:OFF
+ GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD, 6);
+ path.moveTo(phenotype.getX() + phenotype.getWidth() / 6, phenotype.getY());
+ path.lineTo(phenotype.getX() + phenotype.getWidth() * 5 / 6, phenotype.getY());
+ path.lineTo(phenotype.getX() + phenotype.getWidth(), phenotype.getY() + phenotype.getHeight() / 2);
+ path.lineTo(phenotype.getX() + phenotype.getWidth() * 5 / 6, phenotype.getY() + phenotype.getHeight());
+ path.lineTo(phenotype.getX() + phenotype.getWidth() / 6, phenotype.getY() + phenotype.getHeight());
+ path.lineTo(phenotype.getX(), phenotype.getY() + phenotype.getHeight() / 2);
+ // CHECKSTYLE:ON
+ path.closePath();
+ return path;
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(Phenotype phenotype) {
+ return getPhenotypePath(phenotype).getPathIterator(new AffineTransform());
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SBGNNucleicAcidFeatureConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SBGNNucleicAcidFeatureConverter.java
index cd82b37bc9..4c7ead26d0 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SBGNNucleicAcidFeatureConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SBGNNucleicAcidFeatureConverter.java
@@ -1,132 +1,132 @@
-package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.Shape;
-import java.awt.Stroke;
-import java.awt.geom.AffineTransform;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.PathIterator;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * This class defines methods used for drawing {@link Species} of nucleic acid
- * feature in the SBGN way on the {@link Graphics2D} object.
- *
- * @author Michał Kuźma
- *
- */
-
-public class SBGNNucleicAcidFeatureConverter extends SpeciesConverter<Species> {
-
- /**
- * How big should be the arc in rectangle for nucleic acid feature
- * representation.
- */
- private static final int RECTANGLE_CORNER_ARC_SIZE = 5;
-
- /**
- * Default constructor.
- *
- * @param colorExtractor
- * Object that helps to convert {@link ColorSchema} values into
- * colors when drawing {@link Species}
- */
- public SBGNNucleicAcidFeatureConverter(ColorExtractor colorExtractor) {
- super(colorExtractor);
- }
-
- /**
- * Returns shape of SBGN Nucleic acid feature.
- *
- * @param species
- * {@link Species} for which the shape should be returned
- * @return shape of the SBGN Nucleic acid feature for given alias
- */
- private Shape getShape(final Species species) {
- GeneralPath bottomRoundedRectangle = new GeneralPath(GeneralPath.WIND_EVEN_ODD);
- double x = species.getX(), y = species.getY(), width = species.getWidth(), height = species.getHeight();
-
- bottomRoundedRectangle.moveTo(x, y);
- bottomRoundedRectangle.lineTo(x, y + height - RECTANGLE_CORNER_ARC_SIZE);
- bottomRoundedRectangle.curveTo(x, y + height, x + RECTANGLE_CORNER_ARC_SIZE, y + height, x + RECTANGLE_CORNER_ARC_SIZE, y + height);
- bottomRoundedRectangle.lineTo(x + width - RECTANGLE_CORNER_ARC_SIZE, y + height);
- bottomRoundedRectangle
- .curveTo(x + width, y + height, x + width, y + height - RECTANGLE_CORNER_ARC_SIZE, x + width, y + height - RECTANGLE_CORNER_ARC_SIZE);
- bottomRoundedRectangle.lineTo(x + width, y);
- bottomRoundedRectangle.closePath();
- return bottomRoundedRectangle;
- }
-
- @Override
- public void draw(Species species, Graphics2D graphics, ConverterParams params) {
- // Unit of information text - multimer cardinality
- String unitOfInformationText = null;
- if (species.getStatePrefix() != null && species.getStateLabel() != null) {
- if (species.getStatePrefix().equals("free input")) {
- unitOfInformationText = species.getStateLabel();
- } else {
- unitOfInformationText = species.getStatePrefix() + ":" + species.getStateLabel();
- }
- }
-
- int homodir = species.getHomodimer();
-
- species.setWidth(species.getWidth() - SpeciesConverter.HOMODIMER_OFFSET * (species.getHomodimer() - 1));
- species.setHeight(species.getHeight() - SpeciesConverter.HOMODIMER_OFFSET * (species.getHomodimer() - 1));
-
- species.setX(species.getX() + SpeciesConverter.HOMODIMER_OFFSET * homodir);
- species.setY(species.getY() + SpeciesConverter.HOMODIMER_OFFSET * homodir);
-
- int glyphCount;
- if (homodir > 1) {
- glyphCount = 2;
- } else {
- glyphCount = 1;
- }
- for (int i = 0; i < glyphCount; i++) {
- species.setX(species.getX() - SpeciesConverter.HOMODIMER_OFFSET);
- species.setY(species.getY() - SpeciesConverter.HOMODIMER_OFFSET);
-
- Shape shape = getShape(species);
-
- Color c = graphics.getColor();
- graphics.setColor(species.getColor());
- graphics.fill(shape);
- graphics.setColor(c);
-
- Stroke stroke = graphics.getStroke();
- graphics.setStroke(getBorderLine(species));
- graphics.draw(shape);
- graphics.setStroke(stroke);
-
- if (i == 1) {
- if (homodir > 1 && (unitOfInformationText == null || !unitOfInformationText.contains("N:"))) {
- if (unitOfInformationText == null) {
- unitOfInformationText = "";
- } else {
- unitOfInformationText = unitOfInformationText.concat("; ");
- }
- unitOfInformationText = unitOfInformationText.concat("N:").concat(Integer.toString(homodir));
- }
- }
-
- }
-
- drawUnitOfInformation(unitOfInformationText, species, graphics);
- drawText(species, graphics, params);
-
- species.setWidth(species.getWidth() + SpeciesConverter.HOMODIMER_OFFSET * (homodir - 1));
- species.setHeight(species.getHeight() + SpeciesConverter.HOMODIMER_OFFSET * (homodir - 1));
- }
-
- @Override
- protected PathIterator getBoundPathIterator(Species species) {
- return getShape(species).getPathIterator(new AffineTransform());
- }
-
-}
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.Shape;
+import java.awt.Stroke;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.PathIterator;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This class defines methods used for drawing {@link Species} of nucleic acid
+ * feature in the SBGN way on the {@link Graphics2D} object.
+ *
+ * @author Michał Kuźma
+ *
+ */
+
+public class SBGNNucleicAcidFeatureConverter extends SpeciesConverter<Species> {
+
+ /**
+ * How big should be the arc in rectangle for nucleic acid feature
+ * representation.
+ */
+ private static final int RECTANGLE_CORNER_ARC_SIZE = 5;
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing {@link Species}
+ */
+ public SBGNNucleicAcidFeatureConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
+ /**
+ * Returns shape of SBGN Nucleic acid feature.
+ *
+ * @param species
+ * {@link Species} for which the shape should be returned
+ * @return shape of the SBGN Nucleic acid feature for given alias
+ */
+ private Shape getShape(final Species species) {
+ GeneralPath bottomRoundedRectangle = new GeneralPath(GeneralPath.WIND_EVEN_ODD);
+ double x = species.getX(), y = species.getY(), width = species.getWidth(), height = species.getHeight();
+
+ bottomRoundedRectangle.moveTo(x, y);
+ bottomRoundedRectangle.lineTo(x, y + height - RECTANGLE_CORNER_ARC_SIZE);
+ bottomRoundedRectangle.curveTo(x, y + height, x + RECTANGLE_CORNER_ARC_SIZE, y + height, x + RECTANGLE_CORNER_ARC_SIZE, y + height);
+ bottomRoundedRectangle.lineTo(x + width - RECTANGLE_CORNER_ARC_SIZE, y + height);
+ bottomRoundedRectangle
+ .curveTo(x + width, y + height, x + width, y + height - RECTANGLE_CORNER_ARC_SIZE, x + width, y + height - RECTANGLE_CORNER_ARC_SIZE);
+ bottomRoundedRectangle.lineTo(x + width, y);
+ bottomRoundedRectangle.closePath();
+ return bottomRoundedRectangle;
+ }
+
+ @Override
+ public void draw(Species species, Graphics2D graphics, ConverterParams params) {
+ // Unit of information text - multimer cardinality
+ String unitOfInformationText = null;
+ if (species.getStatePrefix() != null && species.getStateLabel() != null) {
+ if (species.getStatePrefix().equals("free input")) {
+ unitOfInformationText = species.getStateLabel();
+ } else {
+ unitOfInformationText = species.getStatePrefix() + ":" + species.getStateLabel();
+ }
+ }
+
+ int homodir = species.getHomodimer();
+
+ species.setWidth(species.getWidth() - SpeciesConverter.HOMODIMER_OFFSET * (species.getHomodimer() - 1));
+ species.setHeight(species.getHeight() - SpeciesConverter.HOMODIMER_OFFSET * (species.getHomodimer() - 1));
+
+ species.setX(species.getX() + SpeciesConverter.HOMODIMER_OFFSET * homodir);
+ species.setY(species.getY() + SpeciesConverter.HOMODIMER_OFFSET * homodir);
+
+ int glyphCount;
+ if (homodir > 1) {
+ glyphCount = 2;
+ } else {
+ glyphCount = 1;
+ }
+ for (int i = 0; i < glyphCount; i++) {
+ species.setX(species.getX() - SpeciesConverter.HOMODIMER_OFFSET);
+ species.setY(species.getY() - SpeciesConverter.HOMODIMER_OFFSET);
+
+ Shape shape = getShape(species);
+
+ Color c = graphics.getColor();
+ graphics.setColor(species.getColor());
+ graphics.fill(shape);
+ graphics.setColor(c);
+
+ Stroke stroke = graphics.getStroke();
+ graphics.setStroke(getBorderLine(species));
+ graphics.draw(shape);
+ graphics.setStroke(stroke);
+
+ if (i == 1) {
+ if (homodir > 1 && (unitOfInformationText == null || !unitOfInformationText.contains("N:"))) {
+ if (unitOfInformationText == null) {
+ unitOfInformationText = "";
+ } else {
+ unitOfInformationText = unitOfInformationText.concat("; ");
+ }
+ unitOfInformationText = unitOfInformationText.concat("N:").concat(Integer.toString(homodir));
+ }
+ }
+
+ }
+
+ drawUnitOfInformation(unitOfInformationText, species, graphics);
+ drawText(species, graphics, params);
+
+ species.setWidth(species.getWidth() + SpeciesConverter.HOMODIMER_OFFSET * (homodir - 1));
+ species.setHeight(species.getHeight() + SpeciesConverter.HOMODIMER_OFFSET * (homodir - 1));
+ }
+
+ @Override
+ protected PathIterator getBoundPathIterator(Species species) {
+ return getShape(species).getPathIterator(new AffineTransform());
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/package-info.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/package-info.java
index bb5eba0424..eae247edf8 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/package-info.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/package-info.java
@@ -1,6 +1,6 @@
-/**
- * Provides classes that draws
- * {@link lcsb.mapviewer.db.model.map.species.Species Species} on the Graphics2D
- * object.
- */
-package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
+/**
+ * Provides classes that draws
+ * {@link lcsb.mapviewer.db.model.map.species.Species Species} on the Graphics2D
+ * object.
+ */
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/package-info.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/package-info.java
index 1c4360d074..57afe77f28 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/package-info.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/package-info.java
@@ -1,5 +1,5 @@
-/**
- * Provides classes that draws {@link lcsb.mapviewer.model.map.BioEntity
- * BioEntites} on the Graphics2D object.
- */
-package lcsb.mapviewer.converter.graphics.bioEntity;
+/**
+ * Provides classes that draws {@link lcsb.mapviewer.model.map.BioEntity
+ * BioEntites} on the Graphics2D object.
+ */
+package lcsb.mapviewer.converter.graphics.bioEntity;
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverter.java
index 1881210ae7..284ff3493d 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverter.java
@@ -1,445 +1,445 @@
-package lcsb.mapviewer.converter.graphics.bioEntity.reaction;
-
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.Graphics2D;
-import java.awt.geom.Ellipse2D;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.geometry.LineTransformation;
-import lcsb.mapviewer.common.geometry.PointTransformation;
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.converter.graphics.DrawingException;
-import lcsb.mapviewer.converter.graphics.bioEntity.BioEntityConverter;
-import lcsb.mapviewer.converter.graphics.geometry.ArrowTransformation;
-import lcsb.mapviewer.model.graphics.ArrowType;
-import lcsb.mapviewer.model.graphics.ArrowTypeData;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.layout.GenericColorSchema;
-import lcsb.mapviewer.model.map.reaction.AbstractNode;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.reaction.NodeOperator;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.type.ReactionRect;
-
-/**
- * Thics class allows to draw reaction on the graphics2D.
- *
- * @author Piotr Gawron
- *
- */
-public class ReactionConverter extends BioEntityConverter<Reaction> {
-
- /**
- * When drawing operator this value defines radius of the joining operator
- * circle.
- */
- private static final int DEFAULT_OPERATOR_RADIUS = 6;
-
- /**
- * Size of the rectangle drawn on the central line of the reaction.
- */
- public static final double RECT_SIZE = 10;
-
- /**
- * Default font size of reaction description.
- */
- public static final int DESCRIPTION_FONT_SIZE = 10;
-
- /**
- * Radius multiplier for bigger logic operators circles in SBGN view.
- */
- public static final double SBGN_RADIUS_MULTIPLIER = 2.5;
-
- /**
- * {@link ColorSchema} used for coloring reactions where we have more than one
- * layout.
- */
- public static final ColorSchema DEFAULT_COLOR_SCHEMA = new GenericColorSchema();
-
- /**
- * Line width of #DEFAULT_COLOR_SCHEMA used for coloring reactions where we
- * have more than one layout.
- */
- private static final double DEFAULT_COLOR_SCHEMA_LINE_WIDTH = 3.0;
-
- static {
- DEFAULT_COLOR_SCHEMA.setColor(Color.BLACK);
- DEFAULT_COLOR_SCHEMA.setLineWidth(DEFAULT_COLOR_SCHEMA_LINE_WIDTH);
- }
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(ReactionConverter.class.getName());
-
- /**
- * Font used for drawing reaction description on the map.
- */
- private Font descFont = null;
-
- /**
- * Graphical helper object with line transformation functions.
- */
- private LineTransformation lineTransformation = new LineTransformation();
-
- /**
- * This objects helps drawing arrows.
- */
- private ArrowTransformation arrowTransformation = new ArrowTransformation();
-
- /**
- * Object used to perform transformations on point objects.
- */
- private PointTransformation pointTransformation = new PointTransformation();
-
- /**
- * Object that helps to convert {@link ColorSchema} values into colors.
- */
- private ColorExtractor colorExtractor;
-
- /**
- * Default constructor.
- *
- * @param colorExtractor
- * Object that helps to convert {@link ColorSchema} values into
- * colors when drawing {@link Reaction}
- */
- public ReactionConverter(ColorExtractor colorExtractor) {
- super();
- descFont = new Font(Font.SANS_SERIF, Font.BOLD, DESCRIPTION_FONT_SIZE);
- this.colorExtractor = colorExtractor;
- }
-
- /**
- * This method draws a rectangle in the center of reaction (defined by line).
- *
- * @param line
- * line on which the rectangle is drawn
- * @param insideType
- * type of the rectangle to be drawn
- * @param graphics
- * where the rectangle should be drawn
- */
- protected void drawRectangleData(final Line2D line, final ReactionRect insideType, final Graphics2D graphics) {
- if (insideType == null) {
- graphics.draw(line);
- } else {
- Point2D startPoint = line.getP1();
- Point2D endPoint = line.getP2();
- double dx = endPoint.getX() - startPoint.getX();
- double dy = endPoint.getY() - startPoint.getY();
- double angle = Math.atan2(dy, dx);
-
- // find rectangle
- Rectangle2D rect = new Rectangle2D.Double();
- double pointX = (startPoint.getX() + endPoint.getX()) / 2;
- double pointY = (startPoint.getY() + endPoint.getY()) / 2;
- rect.setRect(pointX - RECT_SIZE / 2, pointY - RECT_SIZE / 2, RECT_SIZE, RECT_SIZE);
-
- // rotate graphics by the angle defined by line (instead of rotating
- // rectangle)
- graphics.rotate(angle, pointX, pointY);
- // fill rect
- Color color = graphics.getColor();
- graphics.setColor(Color.white);
- graphics.fill(rect);
- graphics.setColor(color);
- // draw rect border
- graphics.draw(rect);
-
- // draw text inside rect
- Font tmpFont = graphics.getFont();
- graphics.setFont(descFont);
- String insideDesc = insideType.getText();
- double textWidth = graphics.getFontMetrics().stringWidth(insideDesc);
- double textHeight = graphics.getFontMetrics().getAscent() - 2;
- graphics.drawString(insideDesc, (int) (pointX - textWidth / 2), (int) (pointY + textHeight / 2));
- graphics.setFont(tmpFont);
-
- // if we should put bolt character inside then do it
- if (insideType == ReactionRect.RECT_BOLT) {
- GeneralPath path = new GeneralPath();
- // CHECKSTYLE:OFF
- path.moveTo(pointX + 2, pointY - RECT_SIZE / 2 + 1);
- path.lineTo(pointX + 2, pointY + RECT_SIZE / 2 - 3);
- path.lineTo(pointX - 2, pointY - RECT_SIZE / 2 + 3);
- path.lineTo(pointX - 2, pointY + RECT_SIZE / 2 - 1);
- // CHECKSTYLE:ON
- graphics.draw(path);
- }
-
- // unrotate the graphics
- graphics.rotate(-angle, pointX, pointY);
- }
- }
-
- @Override
- public void draw(final Reaction reaction, final Graphics2D graphics, final ConverterParams params) {
- Color color = graphics.getColor();
- graphics.setColor(reaction.getReactants().get(0).getLine().getColor());
- // first reactants
- for (Reactant reactant : reaction.getReactants()) {
- if (isVisible(reactant, params)) {
- drawReactant(graphics, reactant);
- }
- }
- // now products
- for (Product product : reaction.getProducts()) {
- if (isVisible(product, params)) {
- drawProduct(graphics, product);
- }
- }
- // draw modifiers
- for (Modifier modifier : reaction.getModifiers()) {
- if (isVisible(modifier, params)) {
- drawModifier(graphics, modifier);
- }
- }
-
- // and operators
- for (NodeOperator operator : reaction.getOperators()) {
- if (isVisible(operator, params)) {
- drawOperator(graphics, operator, params.isSbgnFormat());
- }
- }
-
- // in the end we draw rectangle in the middle
- drawRectangleData(reaction.getCenterLine(), reaction.getReactionRect(), graphics);
- graphics.setColor(color);
- }
-
- @Override
- public void draw(final Reaction reaction, final Graphics2D graphics, final ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) {
- if (visualizedLayoutsColorSchemas.size() == 0) {
- draw(reaction, graphics, params);
- } else if (visualizedLayoutsColorSchemas.size() == 1) {
- if (visualizedLayoutsColorSchemas.get(0) == null) {
- draw(reaction, graphics, params);
- } else {
- List<Pair<AbstractNode, PolylineData>> oldData = new ArrayList<>();
- for (AbstractNode node : reaction.getNodes()) {
- oldData.add(new Pair<AbstractNode, PolylineData>(node, node.getLine()));
- }
- applyColorSchema(reaction, visualizedLayoutsColorSchemas.get(0));
- draw(reaction, graphics, params);
- for (Pair<AbstractNode, PolylineData> pair : oldData) {
- pair.getLeft().setLine(pair.getRight());
- }
- }
- } else {
- int count = 0;
- for (ColorSchema schema : visualizedLayoutsColorSchemas) {
- if (schema != null) {
- count++;
- }
- }
- if (count == 0) {
- draw(reaction, graphics, params);
- } else {
- List<Pair<AbstractNode, PolylineData>> oldData = new ArrayList<>();
- for (AbstractNode node : reaction.getNodes()) {
- oldData.add(new Pair<AbstractNode, PolylineData>(node, node.getLine()));
- }
- applyColorSchema(reaction, DEFAULT_COLOR_SCHEMA);
- draw(reaction, graphics, params);
- for (Pair<AbstractNode, PolylineData> pair : oldData) {
- pair.getLeft().setLine(pair.getRight());
- }
- }
- }
- }
-
- /**
- * Modify reaction with data from {@link ColorSchema}.
- *
- * @param reaction
- * reaction to modify
- * @param colorSchema
- * {@link ColorSchema} to modify reaction
- */
- private void applyColorSchema(Reaction reaction, ColorSchema colorSchema) {
- for (AbstractNode node : reaction.getNodes()) {
- PolylineData pd = new PolylineData(node.getLine());
- pd.setColor(colorExtractor.getNormalizedColor(colorSchema));
- if (colorSchema.getLineWidth() != null) {
- pd.setWidth(colorSchema.getLineWidth());
- }
- if (colorSchema.getReverseReaction() != null && colorSchema.getReverseReaction()) {
- ArrowTypeData atd = pd.getBeginAtd();
- pd.setBeginAtd(pd.getEndAtd());
- pd.setEndAtd(atd);
- }
- node.setLine(pd);
- }
-
- }
-
- /**
- * Draw modifier on the graphics2d.
- *
- * @param graphics
- * where we want to draw the object
- * @param modifier
- * object to be drawn
- */
- private void drawModifier(final Graphics2D graphics, final Modifier modifier) {
- // modifier consists only from the arrow
- arrowTransformation.drawLine(modifier.getLine(), graphics);
- }
-
- /**
- * Draw operator on the graphics2d.
- *
- * @param graphics
- * where we want to draw the object
- * @param operator
- * object to be drawn
- * @param sbgnFormat
- * true if operator is to be drawn in SBGN format
- */
- private void drawOperator(final Graphics2D graphics, final NodeOperator operator, boolean sbgnFormat) {
- // draw line
- arrowTransformation.drawLine(operator.getLine(), graphics);
-
- // in SBGN view - draw connecting point only if it's not connected to
- // reactants or products
- if (!sbgnFormat || operator.getLine().getEndAtd().getArrowType() != ArrowType.NONE
- || (!operator.getOutputs().isEmpty() && operator.getOutputs().get(0) instanceof NodeOperator)) {
- // and now connecting point
- Point2D centerPoint = operator.getLine().getPoints().get(0);
- int radius = DEFAULT_OPERATOR_RADIUS;
- // bigger connecting point circles in SBGN view
- if (sbgnFormat) {
- radius *= SBGN_RADIUS_MULTIPLIER;
- }
- // it's a circle
- Ellipse2D cir = new Ellipse2D.Double(centerPoint.getX() - radius, centerPoint.getY() - radius, 2 * radius, 2 * radius);
- Color color = graphics.getColor();
- graphics.setColor(Color.white);
- graphics.fill(cir);
- graphics.setColor(operator.getLine().getColor());
- graphics.draw(cir);
- // and text defined by operator
- String text;
- if (!sbgnFormat) {
- text = operator.getOperatorText();
- } else {
- text = operator.getSBGNOperatorText();
- }
- Rectangle2D rect = graphics.getFontMetrics().getStringBounds(text, graphics);
- graphics.drawString(text, (int) (centerPoint.getX() - rect.getWidth() / 2 + 1), (int) (centerPoint.getY() + rect.getHeight() / 2) - 2);
- graphics.setColor(color);
- }
- }
-
- /**
- * Draw product on the graphics2D.
- *
- * @param graphics
- * where we want to draw the object
- * @param product
- * object to be drawn
- */
- private void drawProduct(final Graphics2D graphics, final Product product) {
- arrowTransformation.drawLine(product.getLine(), graphics);
- }
-
- /**
- * Draw reactant on the graphics2D.
- *
- * @param graphics
- * where the reactant should be drawn
- * @param reactant
- * object to be drawn on the graphics
- */
- private void drawReactant(final Graphics2D graphics, final Reactant reactant) {
- arrowTransformation.drawLine(reactant.getLine(), graphics);
- }
-
- /**
- *
- * @return {@link #descFont}
- */
- protected Font getDescFont() {
- return descFont;
- }
-
- /**
- *
- * @param descFont
- * new {@link #descFont} value
- */
- protected void setDescFont(final Font descFont) {
- this.descFont = descFont;
- }
-
- /**
- *
- * @return {@link #lineTransformation}
- */
- protected LineTransformation getLineTransformation() {
- return lineTransformation;
- }
-
- /**
- *
- * @param lineTransformation
- * new {@link #lineTransformation}
- */
- protected void setLineTransformation(final LineTransformation lineTransformation) {
- this.lineTransformation = lineTransformation;
- }
-
- /**
- *
- * @return {@link #arrowTransformation}
- */
- protected ArrowTransformation getArrowTransformation() {
- return arrowTransformation;
- }
-
- /**
- *
- * @param arrowTransformation
- * new {@link #arrowTransformation}
- */
- protected void setArrowTransformation(final ArrowTransformation arrowTransformation) {
- this.arrowTransformation = arrowTransformation;
- }
-
- /**
- *
- * @return {@link #pointTransformation}
- */
- protected PointTransformation getPointTransformation() {
- return pointTransformation;
- }
-
- /**
- *
- * @param pointTransformation
- * new {@link #pointTransformation}
- */
- protected void setPointTransformation(final PointTransformation pointTransformation) {
- this.pointTransformation = pointTransformation;
- }
-
- @Override
- public void drawText(Reaction bioEntity, Graphics2D graphics, ConverterParams params) throws DrawingException {
- }
-
+package lcsb.mapviewer.converter.graphics.bioEntity.reaction;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Graphics2D;
+import java.awt.geom.Ellipse2D;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.geometry.LineTransformation;
+import lcsb.mapviewer.common.geometry.PointTransformation;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.DrawingException;
+import lcsb.mapviewer.converter.graphics.bioEntity.BioEntityConverter;
+import lcsb.mapviewer.converter.graphics.geometry.ArrowTransformation;
+import lcsb.mapviewer.model.graphics.ArrowType;
+import lcsb.mapviewer.model.graphics.ArrowTypeData;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.layout.GenericColorSchema;
+import lcsb.mapviewer.model.map.reaction.AbstractNode;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.reaction.NodeOperator;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.type.ReactionRect;
+
+/**
+ * Thics class allows to draw reaction on the graphics2D.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ReactionConverter extends BioEntityConverter<Reaction> {
+
+ /**
+ * When drawing operator this value defines radius of the joining operator
+ * circle.
+ */
+ private static final int DEFAULT_OPERATOR_RADIUS = 6;
+
+ /**
+ * Size of the rectangle drawn on the central line of the reaction.
+ */
+ public static final double RECT_SIZE = 10;
+
+ /**
+ * Default font size of reaction description.
+ */
+ public static final int DESCRIPTION_FONT_SIZE = 10;
+
+ /**
+ * Radius multiplier for bigger logic operators circles in SBGN view.
+ */
+ public static final double SBGN_RADIUS_MULTIPLIER = 2.5;
+
+ /**
+ * {@link ColorSchema} used for coloring reactions where we have more than one
+ * layout.
+ */
+ public static final ColorSchema DEFAULT_COLOR_SCHEMA = new GenericColorSchema();
+
+ /**
+ * Line width of #DEFAULT_COLOR_SCHEMA used for coloring reactions where we
+ * have more than one layout.
+ */
+ private static final double DEFAULT_COLOR_SCHEMA_LINE_WIDTH = 3.0;
+
+ static {
+ DEFAULT_COLOR_SCHEMA.setColor(Color.BLACK);
+ DEFAULT_COLOR_SCHEMA.setLineWidth(DEFAULT_COLOR_SCHEMA_LINE_WIDTH);
+ }
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(ReactionConverter.class.getName());
+
+ /**
+ * Font used for drawing reaction description on the map.
+ */
+ private Font descFont = null;
+
+ /**
+ * Graphical helper object with line transformation functions.
+ */
+ private LineTransformation lineTransformation = new LineTransformation();
+
+ /**
+ * This objects helps drawing arrows.
+ */
+ private ArrowTransformation arrowTransformation = new ArrowTransformation();
+
+ /**
+ * Object used to perform transformations on point objects.
+ */
+ private PointTransformation pointTransformation = new PointTransformation();
+
+ /**
+ * Object that helps to convert {@link ColorSchema} values into colors.
+ */
+ private ColorExtractor colorExtractor;
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into
+ * colors when drawing {@link Reaction}
+ */
+ public ReactionConverter(ColorExtractor colorExtractor) {
+ super();
+ descFont = new Font(Font.SANS_SERIF, Font.BOLD, DESCRIPTION_FONT_SIZE);
+ this.colorExtractor = colorExtractor;
+ }
+
+ /**
+ * This method draws a rectangle in the center of reaction (defined by line).
+ *
+ * @param line
+ * line on which the rectangle is drawn
+ * @param insideType
+ * type of the rectangle to be drawn
+ * @param graphics
+ * where the rectangle should be drawn
+ */
+ protected void drawRectangleData(final Line2D line, final ReactionRect insideType, final Graphics2D graphics) {
+ if (insideType == null) {
+ graphics.draw(line);
+ } else {
+ Point2D startPoint = line.getP1();
+ Point2D endPoint = line.getP2();
+ double dx = endPoint.getX() - startPoint.getX();
+ double dy = endPoint.getY() - startPoint.getY();
+ double angle = Math.atan2(dy, dx);
+
+ // find rectangle
+ Rectangle2D rect = new Rectangle2D.Double();
+ double pointX = (startPoint.getX() + endPoint.getX()) / 2;
+ double pointY = (startPoint.getY() + endPoint.getY()) / 2;
+ rect.setRect(pointX - RECT_SIZE / 2, pointY - RECT_SIZE / 2, RECT_SIZE, RECT_SIZE);
+
+ // rotate graphics by the angle defined by line (instead of rotating
+ // rectangle)
+ graphics.rotate(angle, pointX, pointY);
+ // fill rect
+ Color color = graphics.getColor();
+ graphics.setColor(Color.white);
+ graphics.fill(rect);
+ graphics.setColor(color);
+ // draw rect border
+ graphics.draw(rect);
+
+ // draw text inside rect
+ Font tmpFont = graphics.getFont();
+ graphics.setFont(descFont);
+ String insideDesc = insideType.getText();
+ double textWidth = graphics.getFontMetrics().stringWidth(insideDesc);
+ double textHeight = graphics.getFontMetrics().getAscent() - 2;
+ graphics.drawString(insideDesc, (int) (pointX - textWidth / 2), (int) (pointY + textHeight / 2));
+ graphics.setFont(tmpFont);
+
+ // if we should put bolt character inside then do it
+ if (insideType == ReactionRect.RECT_BOLT) {
+ GeneralPath path = new GeneralPath();
+ // CHECKSTYLE:OFF
+ path.moveTo(pointX + 2, pointY - RECT_SIZE / 2 + 1);
+ path.lineTo(pointX + 2, pointY + RECT_SIZE / 2 - 3);
+ path.lineTo(pointX - 2, pointY - RECT_SIZE / 2 + 3);
+ path.lineTo(pointX - 2, pointY + RECT_SIZE / 2 - 1);
+ // CHECKSTYLE:ON
+ graphics.draw(path);
+ }
+
+ // unrotate the graphics
+ graphics.rotate(-angle, pointX, pointY);
+ }
+ }
+
+ @Override
+ public void draw(final Reaction reaction, final Graphics2D graphics, final ConverterParams params) {
+ Color color = graphics.getColor();
+ graphics.setColor(reaction.getReactants().get(0).getLine().getColor());
+ // first reactants
+ for (Reactant reactant : reaction.getReactants()) {
+ if (isVisible(reactant, params)) {
+ drawReactant(graphics, reactant);
+ }
+ }
+ // now products
+ for (Product product : reaction.getProducts()) {
+ if (isVisible(product, params)) {
+ drawProduct(graphics, product);
+ }
+ }
+ // draw modifiers
+ for (Modifier modifier : reaction.getModifiers()) {
+ if (isVisible(modifier, params)) {
+ drawModifier(graphics, modifier);
+ }
+ }
+
+ // and operators
+ for (NodeOperator operator : reaction.getOperators()) {
+ if (isVisible(operator, params)) {
+ drawOperator(graphics, operator, params.isSbgnFormat());
+ }
+ }
+
+ // in the end we draw rectangle in the middle
+ drawRectangleData(reaction.getCenterLine(), reaction.getReactionRect(), graphics);
+ graphics.setColor(color);
+ }
+
+ @Override
+ public void draw(final Reaction reaction, final Graphics2D graphics, final ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) {
+ if (visualizedLayoutsColorSchemas.size() == 0) {
+ draw(reaction, graphics, params);
+ } else if (visualizedLayoutsColorSchemas.size() == 1) {
+ if (visualizedLayoutsColorSchemas.get(0) == null) {
+ draw(reaction, graphics, params);
+ } else {
+ List<Pair<AbstractNode, PolylineData>> oldData = new ArrayList<>();
+ for (AbstractNode node : reaction.getNodes()) {
+ oldData.add(new Pair<AbstractNode, PolylineData>(node, node.getLine()));
+ }
+ applyColorSchema(reaction, visualizedLayoutsColorSchemas.get(0));
+ draw(reaction, graphics, params);
+ for (Pair<AbstractNode, PolylineData> pair : oldData) {
+ pair.getLeft().setLine(pair.getRight());
+ }
+ }
+ } else {
+ int count = 0;
+ for (ColorSchema schema : visualizedLayoutsColorSchemas) {
+ if (schema != null) {
+ count++;
+ }
+ }
+ if (count == 0) {
+ draw(reaction, graphics, params);
+ } else {
+ List<Pair<AbstractNode, PolylineData>> oldData = new ArrayList<>();
+ for (AbstractNode node : reaction.getNodes()) {
+ oldData.add(new Pair<AbstractNode, PolylineData>(node, node.getLine()));
+ }
+ applyColorSchema(reaction, DEFAULT_COLOR_SCHEMA);
+ draw(reaction, graphics, params);
+ for (Pair<AbstractNode, PolylineData> pair : oldData) {
+ pair.getLeft().setLine(pair.getRight());
+ }
+ }
+ }
+ }
+
+ /**
+ * Modify reaction with data from {@link ColorSchema}.
+ *
+ * @param reaction
+ * reaction to modify
+ * @param colorSchema
+ * {@link ColorSchema} to modify reaction
+ */
+ private void applyColorSchema(Reaction reaction, ColorSchema colorSchema) {
+ for (AbstractNode node : reaction.getNodes()) {
+ PolylineData pd = new PolylineData(node.getLine());
+ pd.setColor(colorExtractor.getNormalizedColor(colorSchema));
+ if (colorSchema.getLineWidth() != null) {
+ pd.setWidth(colorSchema.getLineWidth());
+ }
+ if (colorSchema.getReverseReaction() != null && colorSchema.getReverseReaction()) {
+ ArrowTypeData atd = pd.getBeginAtd();
+ pd.setBeginAtd(pd.getEndAtd());
+ pd.setEndAtd(atd);
+ }
+ node.setLine(pd);
+ }
+
+ }
+
+ /**
+ * Draw modifier on the graphics2d.
+ *
+ * @param graphics
+ * where we want to draw the object
+ * @param modifier
+ * object to be drawn
+ */
+ private void drawModifier(final Graphics2D graphics, final Modifier modifier) {
+ // modifier consists only from the arrow
+ arrowTransformation.drawLine(modifier.getLine(), graphics);
+ }
+
+ /**
+ * Draw operator on the graphics2d.
+ *
+ * @param graphics
+ * where we want to draw the object
+ * @param operator
+ * object to be drawn
+ * @param sbgnFormat
+ * true if operator is to be drawn in SBGN format
+ */
+ private void drawOperator(final Graphics2D graphics, final NodeOperator operator, boolean sbgnFormat) {
+ // draw line
+ arrowTransformation.drawLine(operator.getLine(), graphics);
+
+ // in SBGN view - draw connecting point only if it's not connected to
+ // reactants or products
+ if (!sbgnFormat || operator.getLine().getEndAtd().getArrowType() != ArrowType.NONE
+ || (!operator.getOutputs().isEmpty() && operator.getOutputs().get(0) instanceof NodeOperator)) {
+ // and now connecting point
+ Point2D centerPoint = operator.getLine().getPoints().get(0);
+ int radius = DEFAULT_OPERATOR_RADIUS;
+ // bigger connecting point circles in SBGN view
+ if (sbgnFormat) {
+ radius *= SBGN_RADIUS_MULTIPLIER;
+ }
+ // it's a circle
+ Ellipse2D cir = new Ellipse2D.Double(centerPoint.getX() - radius, centerPoint.getY() - radius, 2 * radius, 2 * radius);
+ Color color = graphics.getColor();
+ graphics.setColor(Color.white);
+ graphics.fill(cir);
+ graphics.setColor(operator.getLine().getColor());
+ graphics.draw(cir);
+ // and text defined by operator
+ String text;
+ if (!sbgnFormat) {
+ text = operator.getOperatorText();
+ } else {
+ text = operator.getSBGNOperatorText();
+ }
+ Rectangle2D rect = graphics.getFontMetrics().getStringBounds(text, graphics);
+ graphics.drawString(text, (int) (centerPoint.getX() - rect.getWidth() / 2 + 1), (int) (centerPoint.getY() + rect.getHeight() / 2) - 2);
+ graphics.setColor(color);
+ }
+ }
+
+ /**
+ * Draw product on the graphics2D.
+ *
+ * @param graphics
+ * where we want to draw the object
+ * @param product
+ * object to be drawn
+ */
+ private void drawProduct(final Graphics2D graphics, final Product product) {
+ arrowTransformation.drawLine(product.getLine(), graphics);
+ }
+
+ /**
+ * Draw reactant on the graphics2D.
+ *
+ * @param graphics
+ * where the reactant should be drawn
+ * @param reactant
+ * object to be drawn on the graphics
+ */
+ private void drawReactant(final Graphics2D graphics, final Reactant reactant) {
+ arrowTransformation.drawLine(reactant.getLine(), graphics);
+ }
+
+ /**
+ *
+ * @return {@link #descFont}
+ */
+ protected Font getDescFont() {
+ return descFont;
+ }
+
+ /**
+ *
+ * @param descFont
+ * new {@link #descFont} value
+ */
+ protected void setDescFont(final Font descFont) {
+ this.descFont = descFont;
+ }
+
+ /**
+ *
+ * @return {@link #lineTransformation}
+ */
+ protected LineTransformation getLineTransformation() {
+ return lineTransformation;
+ }
+
+ /**
+ *
+ * @param lineTransformation
+ * new {@link #lineTransformation}
+ */
+ protected void setLineTransformation(final LineTransformation lineTransformation) {
+ this.lineTransformation = lineTransformation;
+ }
+
+ /**
+ *
+ * @return {@link #arrowTransformation}
+ */
+ protected ArrowTransformation getArrowTransformation() {
+ return arrowTransformation;
+ }
+
+ /**
+ *
+ * @param arrowTransformation
+ * new {@link #arrowTransformation}
+ */
+ protected void setArrowTransformation(final ArrowTransformation arrowTransformation) {
+ this.arrowTransformation = arrowTransformation;
+ }
+
+ /**
+ *
+ * @return {@link #pointTransformation}
+ */
+ protected PointTransformation getPointTransformation() {
+ return pointTransformation;
+ }
+
+ /**
+ *
+ * @param pointTransformation
+ * new {@link #pointTransformation}
+ */
+ protected void setPointTransformation(final PointTransformation pointTransformation) {
+ this.pointTransformation = pointTransformation;
+ }
+
+ @Override
+ public void drawText(Reaction bioEntity, Graphics2D graphics, ConverterParams params) throws DrawingException {
+ }
+
}
\ No newline at end of file
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/package-info.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/package-info.java
index d3b737737c..679fb7d63c 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/package-info.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/package-info.java
@@ -1,7 +1,7 @@
-/**
- * Provides classes that draws
- * {@link lcsb.mapviewer.db.model.map.reaction.Reaction reactions} on the
- * {@link java.awt.Graphics2D Graphics2D} object.
- */
-package lcsb.mapviewer.converter.graphics.bioEntity.reaction;
-
+/**
+ * Provides classes that draws
+ * {@link lcsb.mapviewer.db.model.map.reaction.Reaction reactions} on the
+ * {@link java.awt.Graphics2D Graphics2D} object.
+ */
+package lcsb.mapviewer.converter.graphics.bioEntity.reaction;
+
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/geometry/ArrowTransformation.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/geometry/ArrowTransformation.java
index 8a24e0e356..0b1744f6c5 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/geometry/ArrowTransformation.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/geometry/ArrowTransformation.java
@@ -1,467 +1,467 @@
-package lcsb.mapviewer.converter.graphics.geometry;
-
-import java.awt.BasicStroke;
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.Stroke;
-import java.awt.geom.Ellipse2D;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.List;
-
-import lcsb.mapviewer.common.geometry.PointTransformation;
-import lcsb.mapviewer.model.graphics.ArrowType;
-import lcsb.mapviewer.model.graphics.ArrowTypeData;
-import lcsb.mapviewer.model.graphics.PolylineData;
-
-import org.apache.log4j.Logger;
-
-/**
- * Class containing basic function for drawing arrows.
- *
- * @author Piotr Gawron
- *
- */
-public class ArrowTransformation {
- /**
- * Distance of the crossbar from main arrow in the crossbar arrow end.
- */
- private static final int CROSSBAR_ARROW_END = 5;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ArrowTransformation.class.getName());
-
- /**
- * Object used to perform transformations on point objects.
- */
- private PointTransformation pointTransformation = new PointTransformation();
-
- /**
- * Draw normal arrow head (with white filling).
- *
- * @param line
- * line on which we draw arrow end
- * @param graphics
- * graphics object on which we draw
- * @param len
- * length of the arrow part
- * @param angle
- * angle of the arrow head
- */
- private void drawBlankEnd(final Line2D line, final Graphics2D graphics, final double len, final double angle) {
-
- Point2D startPoint = line.getP1();
- Point2D endPoint = line.getP2();
-
- double dx = startPoint.getX() - endPoint.getX();
- double dy = startPoint.getY() - endPoint.getY();
- double dist = Math.sqrt(dx * dx + dy * dy);
- double coef = len / dist;
- double arrowX = endPoint.getX() - coef * dx;
- double arrowY = endPoint.getY() - coef * dy;
- Point2D p1 = new Point2D.Double(arrowX, arrowY);
- p1 = pointTransformation.rotatePoint(p1, angle, endPoint);
- Point2D p2 = new Point2D.Double(arrowX, arrowY);
- p2 = pointTransformation.rotatePoint(p2, -angle, endPoint);
-
- GeneralPath triangle = new GeneralPath();
- triangle.moveTo(endPoint.getX(), endPoint.getY());
- triangle.lineTo(p1.getX(), p1.getY());
- triangle.lineTo(p2.getX(), p2.getY());
- triangle.closePath();
-
- Color color = graphics.getColor();
- graphics.setColor(Color.WHITE);
- graphics.fill(triangle);
- graphics.setColor(color);
- graphics.draw(triangle);
-
- }
-
- /**
- * Draw normal arrow head (with white filling) with a crossbar (short
- * perpendicular line to the one given as input) behind it.
- *
- * @param line
- * line on which we draw arrow end
- * @param graphics
- * graphics object on which we draw
- * @param len
- * length of the arrow part
- * @param angle
- * angle of the arrow head
- */
- private void drawBlankCrossbarEnd(final Line2D line, final Graphics2D graphics, final double len, final double angle) {
-
- double len1 = len;
- double len2 = len + CROSSBAR_ARROW_END;
-
- Point2D startPoint = line.getP1();
- Point2D endPoint = line.getP2();
-
- double dx = startPoint.getX() - endPoint.getX();
- double dy = startPoint.getY() - endPoint.getY();
- double dist = Math.sqrt(dx * dx + dy * dy);
-
- GeneralPath triangle = getArrowTriangle(line, len1, angle, false);
- Color color = graphics.getColor();
- graphics.setColor(Color.WHITE);
- graphics.fill(triangle);
- graphics.setColor(color);
- graphics.draw(triangle);
-
- double coef = (len2 - len1) / dist;
- ArrayList<Point2D> points = getArrowTrianglePoints(line, len1, angle);
- Point2D p1 = points.get(0);
- Point2D p2 = points.get(1);
-
- p1.setLocation(p1.getX() + coef * dx, p1.getY() + coef * dy);
- p2.setLocation(p2.getX() + coef * dx, p2.getY() + coef * dy);
- Line2D l = new Line2D.Double(p1, p2);
- graphics.draw(l);
-
- }
-
- /**
- * Draw arrow head (without filling and perpedicular closing) as an arrow end.
- *
- * @param line
- * line on which we draw arrow end
- * @param graphics
- * graphics object on which we draw
- * @param len
- * length of the arrow part
- * @param angle
- * angle of the arrow head
- */
- private void drawOpenEnd(final Line2D line, final Graphics2D graphics, final double len, final double angle) {
- GeneralPath triangle = getArrowTriangle(line, len, angle, true);
- graphics.draw(triangle);
- }
-
- /**
- * Draw normal arrow head with a crossbar (short perpendicular line to the one
- * given as input) behind it .
- *
- * @param line
- * line on which we draw arrow end
- * @param graphics
- * graphics object on which we draw
- * @param len
- * length of the arrow part
- * @param angle
- * angle of the arrow head
- */
- private void drawFullCrossbarEnd(final Line2D line, final Graphics2D graphics, final double len, final double angle) {
- double len1 = len;
- double len2 = len1 + CROSSBAR_ARROW_END;
-
- Point2D startPoint = line.getP1();
- Point2D endPoint = line.getP2();
-
- double dx = startPoint.getX() - endPoint.getX();
- double dy = startPoint.getY() - endPoint.getY();
- double dist = Math.sqrt(dx * dx + dy * dy);
-
- GeneralPath triangle = getArrowTriangle(line, len1, angle, false);
- graphics.fill(triangle);
-
- double coef = (len2 - len1) / dist;
- ArrayList<Point2D> points = getArrowTrianglePoints(line, len1, angle);
- Point2D p1 = points.get(0);
- Point2D p2 = points.get(1);
-
- p1.setLocation(p1.getX() + coef * dx, p1.getY() + coef * dy);
- p2.setLocation(p2.getX() + coef * dx, p2.getY() + coef * dy);
- Line2D l = new Line2D.Double(p1, p2);
- graphics.draw(l);
- }
-
- /**
- * Draw crossbar as arrow head (short perpendicular line to the one given as
- * input).
- *
- * @param line
- * line on which we draw arrow end
- * @param graphics
- * graphics object on which we draw
- */
- private void drawCrossbarEnd(final Line2D line, final Graphics2D graphics) {
- double len = CROSSBAR_ARROW_END;
- double angle = Math.PI / 2;
-
- ArrayList<Point2D> points = getArrowTrianglePoints(line, len, angle);
-
- Line2D l = new Line2D.Double(points.get(0), points.get(1));
- graphics.draw(l);
-
- }
-
- /**
- * Draw diamond as an arrow head.
- *
- * @param line
- * line on which we draw arrow end
- * @param graphics
- * graphics object on which we draw
- * @param length
- * length of the diamond part
- * @param angle
- * angle of the diamond head
- */
- private void drawDiamondEnd(final Line2D line, final Graphics2D graphics, final double length, final double angle) {
- double len = length / 2;
-
- Point2D startPoint = line.getP1();
- Point2D endPoint = line.getP2();
-
- double dx = startPoint.getX() - endPoint.getX();
- double dy = startPoint.getY() - endPoint.getY();
- double dist = Math.sqrt(dx * dx + dy * dy);
- double coef = len / dist;
- double arrowX = endPoint.getX() - coef * dx;
- double arrowY = endPoint.getY() - coef * dy;
- Point2D p1 = new Point2D.Double(arrowX, arrowY);
- p1 = pointTransformation.rotatePoint(p1, angle, endPoint);
- Point2D p2 = new Point2D.Double(arrowX, arrowY);
- p2 = pointTransformation.rotatePoint(p2, -angle, endPoint);
- arrowX = endPoint.getX() + 2 * coef * dx;
- arrowY = endPoint.getY() + 2 * coef * dy;
- Point2D p3 = new Point2D.Double(arrowX, arrowY);
-
- GeneralPath diamond = new GeneralPath();
- diamond.moveTo(endPoint.getX(), endPoint.getY());
- diamond.lineTo(p1.getX(), p1.getY());
- diamond.lineTo(p3.getX(), p3.getY());
- diamond.lineTo(p2.getX(), p2.getY());
- diamond.closePath();
-
- Color color = graphics.getColor();
- graphics.setColor(Color.WHITE);
- graphics.fill(diamond);
- graphics.setColor(color);
- graphics.draw(diamond);
-
- }
-
- /**
- * Draw standard filled arrow as an arrow head.
- *
- * @param line
- * line on which we draw arrow end
- * @param graphics
- * graphics object on which we draw
- * @param len
- * length of the arrow part
- * @param angle
- * angle of the arrow head
- */
- private void drawFullArrowEnd(final Line2D line, final Graphics2D graphics, final double len, final double angle) {
- GeneralPath triangle = getArrowTriangle(line, len, angle, false);
- graphics.fill(triangle);
- }
-
- /**
- * Draw circle as an arrow head.
- *
- * @param line
- * line on which we draw circle end
- * @param graphics
- * graphics object on which we draw
- * @param len
- * size (diamater) of the circle
- */
- private void drawCircleEnd(final Line2D line, final Graphics2D graphics, final double len) {
- double diameter = len;
-
- Point2D startPoint = line.getP1();
- Point2D endPoint = line.getP2();
-
- double dx = startPoint.getX() - endPoint.getX();
- double dy = startPoint.getY() - endPoint.getY();
- double dist = Math.sqrt(dx * dx + dy * dy);
- double coef = diameter / dist / 2;
- double x = endPoint.getX() + coef * dx;
- double y = endPoint.getY() + coef * dy;
-
- Ellipse2D circle = new Ellipse2D.Double(x - diameter / 2, y - diameter / 2, diameter, diameter);
-
- Color color = graphics.getColor();
- graphics.setColor(Color.WHITE);
- graphics.fill(circle);
- graphics.setColor(color);
- graphics.draw(circle);
- }
-
- /**
- * This method creates a General Path that describes triangle end of an arrow.
- * The parameters determine position of segement line (line), the length of
- * arrow end (len) and angle of an arrow. The open field determines if
- * triangle should be closed or not.
- *
- * @param line
- * line to which we want to add arrow end
- * @param len
- * length of the arrow end
- * @param angle
- * angle of the arrow head
- * @param open
- * should the returned triangle be closed or not
- * @return GeneralPath object that describes arrow head of the arrow
- */
- private GeneralPath getArrowTriangle(final Line2D line, final double len, final double angle, final boolean open) {
- GeneralPath result = new GeneralPath();
- ArrayList<Point2D> points = getArrowTrianglePoints(line, len, angle);
- result.moveTo(points.get(0).getX(), points.get(0).getY());
- result.lineTo(line.getX2(), line.getY2());
- result.lineTo(points.get(1).getX(), points.get(1).getY());
- if (!open) {
- result.closePath();
- }
- return result;
- }
-
- /**
- * This method computes two points to be used as the end of an arrow. The
- * parameters determine position of segement line (line), the length of arrow
- * end (len) and angle of an arrow.
- *
- * @param line
- * line to which we want to find arrow head points
- * @param len
- * length of the arrow end
- * @param angle
- * angle of the arrow head
- * @return list of two points that determines the points of an arrow
- */
- private ArrayList<Point2D> getArrowTrianglePoints(final Line2D line, final double len, final double angle) {
- Point2D startPoint = line.getP1();
- Point2D endPoint = line.getP2();
-
- double dx = startPoint.getX() - endPoint.getX();
- double dy = startPoint.getY() - endPoint.getY();
- // compute the length of line segment
- double dist = Math.sqrt(dx * dx + dy * dy);
- if (dist == 0) {
- logger.error("Cannot draw arrow segment with length equal to 0.0");
- }
- double coef = len / dist;
- // compute the coordinates of a point on the line that will have to be
- // rotated
- double arrowX = endPoint.getX() - coef * dx;
- double arrowY = endPoint.getY() - coef * dy;
- // rotate first point
- Point2D p1 = new Point2D.Double(arrowX, arrowY);
- p1 = pointTransformation.rotatePoint(p1, angle, endPoint);
- // rotate and the second one
- Point2D p2 = new Point2D.Double(arrowX, arrowY);
- p2 = pointTransformation.rotatePoint(p2, -angle, endPoint);
- ArrayList<Point2D> result = new ArrayList<Point2D>();
- result.add(p1);
- result.add(p2);
- return result;
-
- }
-
- /**
- * This method draws a line ld on the graphics.
- *
- * @param ld
- * line to be drawn (containing information about arrow ends)
- * @param graphics
- * where we want to draw the object
- * @param arrowType
- */
- public void drawLine(final PolylineData ld, final Graphics2D graphics) {
- // get current color
- Color color = graphics.getColor();
- graphics.setColor(ld.getColor());
-
- // transform ld to a line
- GeneralPath path = ld.toGeneralPath();
- // get current stroke
- Stroke stroke = graphics.getStroke();
- // set stroke and draw line
-
- Stroke newStroke = ld.getType().getStroke();
- if (ld.getWidth() != 1.0 && newStroke instanceof BasicStroke) {
- BasicStroke basicStroke = (BasicStroke) newStroke;
- newStroke = new BasicStroke(
- (float) ld.getWidth(), basicStroke.getEndCap(), basicStroke.getLineJoin(), basicStroke.getMiterLimit(), basicStroke.getDashArray(),
- basicStroke.getDashPhase());
- }
-
- graphics.setStroke(newStroke);
- graphics.draw(path);
-
- // and now try to draw an arrow end
-
- List<Point2D> points = ld.getPoints();
-
- ArrowTypeData arrowType = ld.getEndAtd();
- Point2D p1 = points.get(points.size() - 2);
- Point2D p2 = points.get(points.size() - 1);
- drawArrowEnd(graphics, arrowType, p1, p2);
-
- arrowType = ld.getBeginAtd();
- p1 = points.get(1);
- p2 = points.get(0);
- drawArrowEnd(graphics, arrowType, p1, p2);
-
- // restore default stroke type
- graphics.setStroke(stroke);
- graphics.setColor(color);
-
- }
-
- /**
- * Draws head of the arrow on the graphics2d element. The line is defined by
- * two points: startPoint, endPoint. Where endPoint defines the end with the
- * arrow.
- *
- * @param graphics
- * where we ant to draw an arrow head
- * @param arrowType
- * what kind of arrow head we want to draw
- * @param startPoint
- * first point of the line
- * @param endPoint
- * second point of the line (with the arrow head)
- */
- protected void drawArrowEnd(final Graphics2D graphics, final ArrowTypeData arrowType, final Point2D startPoint, final Point2D endPoint) {
- graphics.setStroke(arrowType.getArrowLineType().getStroke());
-
- // get the last segment of polyline - this segment will determine the
- // position of arrow end
- Line2D line = new Line2D.Double(startPoint, endPoint);
-
- // basing on a type call different drawing method
- if (arrowType.getArrowType() == ArrowType.FULL) {
- drawFullArrowEnd(line, graphics, arrowType.getLen(), arrowType.getAngle());
- } else if (arrowType.getArrowType() == ArrowType.CIRCLE) {
- drawCircleEnd(line, graphics, arrowType.getLen());
- } else if (arrowType.getArrowType() == ArrowType.NONE) {
- //
- return;
- } else if (arrowType.getArrowType() == ArrowType.BLANK) {
- drawBlankEnd(line, graphics, arrowType.getLen(), arrowType.getAngle());
- } else if (arrowType.getArrowType() == ArrowType.CROSSBAR) {
- drawCrossbarEnd(line, graphics);
- } else if (arrowType.getArrowType() == ArrowType.DIAMOND) {
- drawDiamondEnd(line, graphics, arrowType.getLen(), arrowType.getAngle());
- } else if (arrowType.getArrowType() == ArrowType.FULL_CROSSBAR) {
- drawFullCrossbarEnd(line, graphics, arrowType.getLen(), arrowType.getAngle());
- } else if (arrowType.getArrowType() == ArrowType.BLANK_CROSSBAR) {
- drawBlankCrossbarEnd(line, graphics, arrowType.getLen(), arrowType.getAngle());
- } else if (arrowType.getArrowType() == ArrowType.OPEN) {
- drawOpenEnd(line, graphics, arrowType.getLen(), arrowType.getAngle());
- } else {
- logger.debug("Unknown arrow type: " + arrowType.getArrowType());
- }
- }
-
-}
+package lcsb.mapviewer.converter.graphics.geometry;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.Stroke;
+import java.awt.geom.Ellipse2D;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.List;
+
+import lcsb.mapviewer.common.geometry.PointTransformation;
+import lcsb.mapviewer.model.graphics.ArrowType;
+import lcsb.mapviewer.model.graphics.ArrowTypeData;
+import lcsb.mapviewer.model.graphics.PolylineData;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Class containing basic function for drawing arrows.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ArrowTransformation {
+ /**
+ * Distance of the crossbar from main arrow in the crossbar arrow end.
+ */
+ private static final int CROSSBAR_ARROW_END = 5;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ArrowTransformation.class.getName());
+
+ /**
+ * Object used to perform transformations on point objects.
+ */
+ private PointTransformation pointTransformation = new PointTransformation();
+
+ /**
+ * Draw normal arrow head (with white filling).
+ *
+ * @param line
+ * line on which we draw arrow end
+ * @param graphics
+ * graphics object on which we draw
+ * @param len
+ * length of the arrow part
+ * @param angle
+ * angle of the arrow head
+ */
+ private void drawBlankEnd(final Line2D line, final Graphics2D graphics, final double len, final double angle) {
+
+ Point2D startPoint = line.getP1();
+ Point2D endPoint = line.getP2();
+
+ double dx = startPoint.getX() - endPoint.getX();
+ double dy = startPoint.getY() - endPoint.getY();
+ double dist = Math.sqrt(dx * dx + dy * dy);
+ double coef = len / dist;
+ double arrowX = endPoint.getX() - coef * dx;
+ double arrowY = endPoint.getY() - coef * dy;
+ Point2D p1 = new Point2D.Double(arrowX, arrowY);
+ p1 = pointTransformation.rotatePoint(p1, angle, endPoint);
+ Point2D p2 = new Point2D.Double(arrowX, arrowY);
+ p2 = pointTransformation.rotatePoint(p2, -angle, endPoint);
+
+ GeneralPath triangle = new GeneralPath();
+ triangle.moveTo(endPoint.getX(), endPoint.getY());
+ triangle.lineTo(p1.getX(), p1.getY());
+ triangle.lineTo(p2.getX(), p2.getY());
+ triangle.closePath();
+
+ Color color = graphics.getColor();
+ graphics.setColor(Color.WHITE);
+ graphics.fill(triangle);
+ graphics.setColor(color);
+ graphics.draw(triangle);
+
+ }
+
+ /**
+ * Draw normal arrow head (with white filling) with a crossbar (short
+ * perpendicular line to the one given as input) behind it.
+ *
+ * @param line
+ * line on which we draw arrow end
+ * @param graphics
+ * graphics object on which we draw
+ * @param len
+ * length of the arrow part
+ * @param angle
+ * angle of the arrow head
+ */
+ private void drawBlankCrossbarEnd(final Line2D line, final Graphics2D graphics, final double len, final double angle) {
+
+ double len1 = len;
+ double len2 = len + CROSSBAR_ARROW_END;
+
+ Point2D startPoint = line.getP1();
+ Point2D endPoint = line.getP2();
+
+ double dx = startPoint.getX() - endPoint.getX();
+ double dy = startPoint.getY() - endPoint.getY();
+ double dist = Math.sqrt(dx * dx + dy * dy);
+
+ GeneralPath triangle = getArrowTriangle(line, len1, angle, false);
+ Color color = graphics.getColor();
+ graphics.setColor(Color.WHITE);
+ graphics.fill(triangle);
+ graphics.setColor(color);
+ graphics.draw(triangle);
+
+ double coef = (len2 - len1) / dist;
+ ArrayList<Point2D> points = getArrowTrianglePoints(line, len1, angle);
+ Point2D p1 = points.get(0);
+ Point2D p2 = points.get(1);
+
+ p1.setLocation(p1.getX() + coef * dx, p1.getY() + coef * dy);
+ p2.setLocation(p2.getX() + coef * dx, p2.getY() + coef * dy);
+ Line2D l = new Line2D.Double(p1, p2);
+ graphics.draw(l);
+
+ }
+
+ /**
+ * Draw arrow head (without filling and perpedicular closing) as an arrow end.
+ *
+ * @param line
+ * line on which we draw arrow end
+ * @param graphics
+ * graphics object on which we draw
+ * @param len
+ * length of the arrow part
+ * @param angle
+ * angle of the arrow head
+ */
+ private void drawOpenEnd(final Line2D line, final Graphics2D graphics, final double len, final double angle) {
+ GeneralPath triangle = getArrowTriangle(line, len, angle, true);
+ graphics.draw(triangle);
+ }
+
+ /**
+ * Draw normal arrow head with a crossbar (short perpendicular line to the one
+ * given as input) behind it .
+ *
+ * @param line
+ * line on which we draw arrow end
+ * @param graphics
+ * graphics object on which we draw
+ * @param len
+ * length of the arrow part
+ * @param angle
+ * angle of the arrow head
+ */
+ private void drawFullCrossbarEnd(final Line2D line, final Graphics2D graphics, final double len, final double angle) {
+ double len1 = len;
+ double len2 = len1 + CROSSBAR_ARROW_END;
+
+ Point2D startPoint = line.getP1();
+ Point2D endPoint = line.getP2();
+
+ double dx = startPoint.getX() - endPoint.getX();
+ double dy = startPoint.getY() - endPoint.getY();
+ double dist = Math.sqrt(dx * dx + dy * dy);
+
+ GeneralPath triangle = getArrowTriangle(line, len1, angle, false);
+ graphics.fill(triangle);
+
+ double coef = (len2 - len1) / dist;
+ ArrayList<Point2D> points = getArrowTrianglePoints(line, len1, angle);
+ Point2D p1 = points.get(0);
+ Point2D p2 = points.get(1);
+
+ p1.setLocation(p1.getX() + coef * dx, p1.getY() + coef * dy);
+ p2.setLocation(p2.getX() + coef * dx, p2.getY() + coef * dy);
+ Line2D l = new Line2D.Double(p1, p2);
+ graphics.draw(l);
+ }
+
+ /**
+ * Draw crossbar as arrow head (short perpendicular line to the one given as
+ * input).
+ *
+ * @param line
+ * line on which we draw arrow end
+ * @param graphics
+ * graphics object on which we draw
+ */
+ private void drawCrossbarEnd(final Line2D line, final Graphics2D graphics) {
+ double len = CROSSBAR_ARROW_END;
+ double angle = Math.PI / 2;
+
+ ArrayList<Point2D> points = getArrowTrianglePoints(line, len, angle);
+
+ Line2D l = new Line2D.Double(points.get(0), points.get(1));
+ graphics.draw(l);
+
+ }
+
+ /**
+ * Draw diamond as an arrow head.
+ *
+ * @param line
+ * line on which we draw arrow end
+ * @param graphics
+ * graphics object on which we draw
+ * @param length
+ * length of the diamond part
+ * @param angle
+ * angle of the diamond head
+ */
+ private void drawDiamondEnd(final Line2D line, final Graphics2D graphics, final double length, final double angle) {
+ double len = length / 2;
+
+ Point2D startPoint = line.getP1();
+ Point2D endPoint = line.getP2();
+
+ double dx = startPoint.getX() - endPoint.getX();
+ double dy = startPoint.getY() - endPoint.getY();
+ double dist = Math.sqrt(dx * dx + dy * dy);
+ double coef = len / dist;
+ double arrowX = endPoint.getX() - coef * dx;
+ double arrowY = endPoint.getY() - coef * dy;
+ Point2D p1 = new Point2D.Double(arrowX, arrowY);
+ p1 = pointTransformation.rotatePoint(p1, angle, endPoint);
+ Point2D p2 = new Point2D.Double(arrowX, arrowY);
+ p2 = pointTransformation.rotatePoint(p2, -angle, endPoint);
+ arrowX = endPoint.getX() + 2 * coef * dx;
+ arrowY = endPoint.getY() + 2 * coef * dy;
+ Point2D p3 = new Point2D.Double(arrowX, arrowY);
+
+ GeneralPath diamond = new GeneralPath();
+ diamond.moveTo(endPoint.getX(), endPoint.getY());
+ diamond.lineTo(p1.getX(), p1.getY());
+ diamond.lineTo(p3.getX(), p3.getY());
+ diamond.lineTo(p2.getX(), p2.getY());
+ diamond.closePath();
+
+ Color color = graphics.getColor();
+ graphics.setColor(Color.WHITE);
+ graphics.fill(diamond);
+ graphics.setColor(color);
+ graphics.draw(diamond);
+
+ }
+
+ /**
+ * Draw standard filled arrow as an arrow head.
+ *
+ * @param line
+ * line on which we draw arrow end
+ * @param graphics
+ * graphics object on which we draw
+ * @param len
+ * length of the arrow part
+ * @param angle
+ * angle of the arrow head
+ */
+ private void drawFullArrowEnd(final Line2D line, final Graphics2D graphics, final double len, final double angle) {
+ GeneralPath triangle = getArrowTriangle(line, len, angle, false);
+ graphics.fill(triangle);
+ }
+
+ /**
+ * Draw circle as an arrow head.
+ *
+ * @param line
+ * line on which we draw circle end
+ * @param graphics
+ * graphics object on which we draw
+ * @param len
+ * size (diamater) of the circle
+ */
+ private void drawCircleEnd(final Line2D line, final Graphics2D graphics, final double len) {
+ double diameter = len;
+
+ Point2D startPoint = line.getP1();
+ Point2D endPoint = line.getP2();
+
+ double dx = startPoint.getX() - endPoint.getX();
+ double dy = startPoint.getY() - endPoint.getY();
+ double dist = Math.sqrt(dx * dx + dy * dy);
+ double coef = diameter / dist / 2;
+ double x = endPoint.getX() + coef * dx;
+ double y = endPoint.getY() + coef * dy;
+
+ Ellipse2D circle = new Ellipse2D.Double(x - diameter / 2, y - diameter / 2, diameter, diameter);
+
+ Color color = graphics.getColor();
+ graphics.setColor(Color.WHITE);
+ graphics.fill(circle);
+ graphics.setColor(color);
+ graphics.draw(circle);
+ }
+
+ /**
+ * This method creates a General Path that describes triangle end of an arrow.
+ * The parameters determine position of segement line (line), the length of
+ * arrow end (len) and angle of an arrow. The open field determines if
+ * triangle should be closed or not.
+ *
+ * @param line
+ * line to which we want to add arrow end
+ * @param len
+ * length of the arrow end
+ * @param angle
+ * angle of the arrow head
+ * @param open
+ * should the returned triangle be closed or not
+ * @return GeneralPath object that describes arrow head of the arrow
+ */
+ private GeneralPath getArrowTriangle(final Line2D line, final double len, final double angle, final boolean open) {
+ GeneralPath result = new GeneralPath();
+ ArrayList<Point2D> points = getArrowTrianglePoints(line, len, angle);
+ result.moveTo(points.get(0).getX(), points.get(0).getY());
+ result.lineTo(line.getX2(), line.getY2());
+ result.lineTo(points.get(1).getX(), points.get(1).getY());
+ if (!open) {
+ result.closePath();
+ }
+ return result;
+ }
+
+ /**
+ * This method computes two points to be used as the end of an arrow. The
+ * parameters determine position of segement line (line), the length of arrow
+ * end (len) and angle of an arrow.
+ *
+ * @param line
+ * line to which we want to find arrow head points
+ * @param len
+ * length of the arrow end
+ * @param angle
+ * angle of the arrow head
+ * @return list of two points that determines the points of an arrow
+ */
+ private ArrayList<Point2D> getArrowTrianglePoints(final Line2D line, final double len, final double angle) {
+ Point2D startPoint = line.getP1();
+ Point2D endPoint = line.getP2();
+
+ double dx = startPoint.getX() - endPoint.getX();
+ double dy = startPoint.getY() - endPoint.getY();
+ // compute the length of line segment
+ double dist = Math.sqrt(dx * dx + dy * dy);
+ if (dist == 0) {
+ logger.error("Cannot draw arrow segment with length equal to 0.0");
+ }
+ double coef = len / dist;
+ // compute the coordinates of a point on the line that will have to be
+ // rotated
+ double arrowX = endPoint.getX() - coef * dx;
+ double arrowY = endPoint.getY() - coef * dy;
+ // rotate first point
+ Point2D p1 = new Point2D.Double(arrowX, arrowY);
+ p1 = pointTransformation.rotatePoint(p1, angle, endPoint);
+ // rotate and the second one
+ Point2D p2 = new Point2D.Double(arrowX, arrowY);
+ p2 = pointTransformation.rotatePoint(p2, -angle, endPoint);
+ ArrayList<Point2D> result = new ArrayList<Point2D>();
+ result.add(p1);
+ result.add(p2);
+ return result;
+
+ }
+
+ /**
+ * This method draws a line ld on the graphics.
+ *
+ * @param ld
+ * line to be drawn (containing information about arrow ends)
+ * @param graphics
+ * where we want to draw the object
+ * @param arrowType
+ */
+ public void drawLine(final PolylineData ld, final Graphics2D graphics) {
+ // get current color
+ Color color = graphics.getColor();
+ graphics.setColor(ld.getColor());
+
+ // transform ld to a line
+ GeneralPath path = ld.toGeneralPath();
+ // get current stroke
+ Stroke stroke = graphics.getStroke();
+ // set stroke and draw line
+
+ Stroke newStroke = ld.getType().getStroke();
+ if (ld.getWidth() != 1.0 && newStroke instanceof BasicStroke) {
+ BasicStroke basicStroke = (BasicStroke) newStroke;
+ newStroke = new BasicStroke(
+ (float) ld.getWidth(), basicStroke.getEndCap(), basicStroke.getLineJoin(), basicStroke.getMiterLimit(), basicStroke.getDashArray(),
+ basicStroke.getDashPhase());
+ }
+
+ graphics.setStroke(newStroke);
+ graphics.draw(path);
+
+ // and now try to draw an arrow end
+
+ List<Point2D> points = ld.getPoints();
+
+ ArrowTypeData arrowType = ld.getEndAtd();
+ Point2D p1 = points.get(points.size() - 2);
+ Point2D p2 = points.get(points.size() - 1);
+ drawArrowEnd(graphics, arrowType, p1, p2);
+
+ arrowType = ld.getBeginAtd();
+ p1 = points.get(1);
+ p2 = points.get(0);
+ drawArrowEnd(graphics, arrowType, p1, p2);
+
+ // restore default stroke type
+ graphics.setStroke(stroke);
+ graphics.setColor(color);
+
+ }
+
+ /**
+ * Draws head of the arrow on the graphics2d element. The line is defined by
+ * two points: startPoint, endPoint. Where endPoint defines the end with the
+ * arrow.
+ *
+ * @param graphics
+ * where we ant to draw an arrow head
+ * @param arrowType
+ * what kind of arrow head we want to draw
+ * @param startPoint
+ * first point of the line
+ * @param endPoint
+ * second point of the line (with the arrow head)
+ */
+ protected void drawArrowEnd(final Graphics2D graphics, final ArrowTypeData arrowType, final Point2D startPoint, final Point2D endPoint) {
+ graphics.setStroke(arrowType.getArrowLineType().getStroke());
+
+ // get the last segment of polyline - this segment will determine the
+ // position of arrow end
+ Line2D line = new Line2D.Double(startPoint, endPoint);
+
+ // basing on a type call different drawing method
+ if (arrowType.getArrowType() == ArrowType.FULL) {
+ drawFullArrowEnd(line, graphics, arrowType.getLen(), arrowType.getAngle());
+ } else if (arrowType.getArrowType() == ArrowType.CIRCLE) {
+ drawCircleEnd(line, graphics, arrowType.getLen());
+ } else if (arrowType.getArrowType() == ArrowType.NONE) {
+ //
+ return;
+ } else if (arrowType.getArrowType() == ArrowType.BLANK) {
+ drawBlankEnd(line, graphics, arrowType.getLen(), arrowType.getAngle());
+ } else if (arrowType.getArrowType() == ArrowType.CROSSBAR) {
+ drawCrossbarEnd(line, graphics);
+ } else if (arrowType.getArrowType() == ArrowType.DIAMOND) {
+ drawDiamondEnd(line, graphics, arrowType.getLen(), arrowType.getAngle());
+ } else if (arrowType.getArrowType() == ArrowType.FULL_CROSSBAR) {
+ drawFullCrossbarEnd(line, graphics, arrowType.getLen(), arrowType.getAngle());
+ } else if (arrowType.getArrowType() == ArrowType.BLANK_CROSSBAR) {
+ drawBlankCrossbarEnd(line, graphics, arrowType.getLen(), arrowType.getAngle());
+ } else if (arrowType.getArrowType() == ArrowType.OPEN) {
+ drawOpenEnd(line, graphics, arrowType.getLen(), arrowType.getAngle());
+ } else {
+ logger.debug("Unknown arrow type: " + arrowType.getArrowType());
+ }
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/geometry/FontFinder.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/geometry/FontFinder.java
index 766c6fb240..7a70eeee40 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/geometry/FontFinder.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/geometry/FontFinder.java
@@ -1,247 +1,247 @@
-package lcsb.mapviewer.converter.graphics.geometry;
-
-import java.awt.Font;
-import java.awt.Graphics2D;
-import java.awt.geom.Rectangle2D;
-import java.util.ArrayList;
-import java.util.List;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-
-import org.apache.log4j.Logger;
-
-/**
- * This is utility class that helps to find optimal font to fit text into
- * rectangle.
- *
- * @author Piotr Gawron
- *
- */
-public final class FontFinder {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(FontFinder.class);
-
- /**
- * Constructor that prevents class from instantiate.
- */
- protected FontFinder() {
-
- }
-
- /**
- * Methods looks for the biggest font size that allows to fit text into
- * rectangle, but is not bigger then initialFontSze. IMPORTANT: it's not
- * optimal, so don't set initialFontSize into infinity :).
- *
- * @param initialFontSize
- * maximum font size that we consider
- * @param fontName
- * name of the font that we use
- * @param graphics
- * what is the graphics implementation that we use
- * @param border
- * border of the rectangle where we want to place our text
- * @param text
- * text to draw
- * @return max font size that allows to draw the text into borders (but not
- * bigger then initialFontSize)
- * @throws RectangleTooSmallException
- * if the border is too small to draw text
- */
- public static double findMaxFontSize(double initialFontSize, String fontName, Graphics2D graphics, Rectangle2D border, String text)
- throws RectangleTooSmallException {
- if (border.getWidth() <= 0 || border.getHeight() <= 0) {
- throw new RectangleTooSmallException("Size of the rectangle must be grater then 0.0");
- }
- int result = (int) initialFontSize;
- if (result <= 0) {
- throw new InvalidArgumentException("initialFontSize must be at least 1.0");
- }
- Font oldFont = graphics.getFont();
- graphics.setFont(new Font(fontName, 0, result));
- while (!textFits(graphics, border, text)) {
- result--;
- if (result <= 0) {
- throw new RectangleTooSmallException("Cannot fit text into the border.");
- }
- graphics.setFont(new Font(fontName, 0, result));
- }
-
- graphics.setFont(oldFont);
- return result;
- }
-
- /**
- * Check if the font in graphics allows to draw text in the rectangle.
- *
- * @param graphics
- * implementation of the graphics (with font property)
- * @param border
- * border of the text in which we want put text
- * @param text
- * text that we want to draw
- * @return true if the text can be drawn in the border, false othrerwise
- */
- private static boolean textFits(Graphics2D graphics, Rectangle2D border, String text) {
- double width = border.getWidth();
- double height = border.getHeight();
-
- int lines = 1;
- int index = 0;
- StringBuilder line = new StringBuilder();
- while (index < text.length()) {
- StringBuilder word = new StringBuilder();
- while (index < text.length()) {
- if (text.charAt(index) == ' ' || text.charAt(index) == '\t' || text.charAt(index) == '\n') {
- break;
- } else {
- word.append(text.charAt(index));
- index++;
- }
- }
- if (!lineFits(graphics, width, line.toString() + word.toString())) {
- if (line.length() == 0) {
- return false;
- }
- lines++;
- if (index == text.length() || text.charAt(index) == '\n') {
- line = new StringBuilder();
- lines++;
- } else {
- line = word;
- line.append(text.charAt(index));
- }
- } else if (index < text.length()) {
- line.append(word.toString());
- if (text.charAt(index) == '\n') {
- line = new StringBuilder();
- lines++;
- } else {
- line.append(text.charAt(index));
- }
- }
- index++;
- }
-
- return lines * (graphics.getFontMetrics().getHeight()) <= height;
- }
-
- /**
- * Check if width of the text line is not bigger then required.
- *
- * @param graphics
- * font property
- * @param width
- * max width of the text
- * @param text
- * text that we want to check
- * @return true if width of the text line is not bigger then required, false
- * otherwise
- */
- private static boolean lineFits(Graphics2D graphics, double width, String text) {
- return width >= graphics.getFontMetrics().stringWidth(text);
- }
-
- /**
- * Writes centered text in rectangle using fontSize given as a parameter.
- *
- * @param fontSize
- * font size
- * @param fontName
- * font name
- * @param graphics
- * where we want to write a text
- * @param border
- * what are the borders
- * @param text
- * what text we want to write
- * @param center
- * should the text be centered
- */
- public static void drawText(int fontSize, String fontName, Graphics2D graphics, Rectangle2D border, String text, boolean center) {
- Font oldFont = graphics.getFont();
- graphics.setFont(new Font(fontName, 0, fontSize));
-
- double width = border.getWidth();
-
- List<String> lines = new ArrayList<String>();
- int index = 0;
- StringBuilder line = new StringBuilder();
- while (index < text.length()) {
- StringBuilder word = new StringBuilder();
- while (index < text.length()) {
- if (text.charAt(index) == ' ' || text.charAt(index) == '\t' || text.charAt(index) == '\n') {
- break;
- } else {
- word.append(text.charAt(index));
- index++;
- }
- }
- if (!lineFits(graphics, width, line.toString() + word.toString())) {
- if (line.length() == 0) {
- throw new InvalidArgumentException("Font too big.");
- }
- lines.add(line.toString());
- if (index == text.length() || text.charAt(index) == '\n') {
- line = new StringBuilder();
- lines.add(word.toString());
- } else {
- line = word;
- line.append(text.charAt(index));
- }
- } else {
- line.append(word.toString());
- if (index < text.length()) {
- if (text.charAt(index) == '\n') {
- lines.add(line.toString());
- line = new StringBuilder();
- } else {
- line.append(text.charAt(index));
- }
- }
- }
- index++;
- }
- lines.add(line.toString());
-
- double lineHeight = graphics.getFontMetrics().getHeight();
- double y = (int) (border.getCenterY() - lineHeight * lines.size() / 2.0 + graphics.getFontMetrics().getAscent());
- // if text is not centerd then lets start from left top corner
- if (!center) {
- y = border.getY() + lineHeight / 2;
- }
-
- for (String string : lines) {
- double textWidth = graphics.getFontMetrics().stringWidth(string);
- if (center) {
- graphics.drawString(string, (int) (border.getCenterX() - textWidth / 2), (int) y);
- } else {
- graphics.drawString(string, (int) border.getX(), (int) y);
- }
- y += lineHeight;
- }
-
- graphics.setFont(oldFont);
- }
-
- /**
- * Writes centered text in rectangle using fontSize given as a parameter.
- *
- * @param fontSize
- * font size
- * @param fontName
- * font name
- * @param graphics
- * where we want to write a text
- * @param border
- * what are the borders
- * @param text
- * what text we want to write
- */
- public static void drawText(int fontSize, String fontName, Graphics2D graphics, Rectangle2D border, String text) {
- drawText(fontSize, fontName, graphics, border, text, true);
- }
-}
+package lcsb.mapviewer.converter.graphics.geometry;
+
+import java.awt.Font;
+import java.awt.Graphics2D;
+import java.awt.geom.Rectangle2D;
+import java.util.ArrayList;
+import java.util.List;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+
+import org.apache.log4j.Logger;
+
+/**
+ * This is utility class that helps to find optimal font to fit text into
+ * rectangle.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public final class FontFinder {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(FontFinder.class);
+
+ /**
+ * Constructor that prevents class from instantiate.
+ */
+ protected FontFinder() {
+
+ }
+
+ /**
+ * Methods looks for the biggest font size that allows to fit text into
+ * rectangle, but is not bigger then initialFontSze. IMPORTANT: it's not
+ * optimal, so don't set initialFontSize into infinity :).
+ *
+ * @param initialFontSize
+ * maximum font size that we consider
+ * @param fontName
+ * name of the font that we use
+ * @param graphics
+ * what is the graphics implementation that we use
+ * @param border
+ * border of the rectangle where we want to place our text
+ * @param text
+ * text to draw
+ * @return max font size that allows to draw the text into borders (but not
+ * bigger then initialFontSize)
+ * @throws RectangleTooSmallException
+ * if the border is too small to draw text
+ */
+ public static double findMaxFontSize(double initialFontSize, String fontName, Graphics2D graphics, Rectangle2D border, String text)
+ throws RectangleTooSmallException {
+ if (border.getWidth() <= 0 || border.getHeight() <= 0) {
+ throw new RectangleTooSmallException("Size of the rectangle must be grater then 0.0");
+ }
+ int result = (int) initialFontSize;
+ if (result <= 0) {
+ throw new InvalidArgumentException("initialFontSize must be at least 1.0");
+ }
+ Font oldFont = graphics.getFont();
+ graphics.setFont(new Font(fontName, 0, result));
+ while (!textFits(graphics, border, text)) {
+ result--;
+ if (result <= 0) {
+ throw new RectangleTooSmallException("Cannot fit text into the border.");
+ }
+ graphics.setFont(new Font(fontName, 0, result));
+ }
+
+ graphics.setFont(oldFont);
+ return result;
+ }
+
+ /**
+ * Check if the font in graphics allows to draw text in the rectangle.
+ *
+ * @param graphics
+ * implementation of the graphics (with font property)
+ * @param border
+ * border of the text in which we want put text
+ * @param text
+ * text that we want to draw
+ * @return true if the text can be drawn in the border, false othrerwise
+ */
+ private static boolean textFits(Graphics2D graphics, Rectangle2D border, String text) {
+ double width = border.getWidth();
+ double height = border.getHeight();
+
+ int lines = 1;
+ int index = 0;
+ StringBuilder line = new StringBuilder();
+ while (index < text.length()) {
+ StringBuilder word = new StringBuilder();
+ while (index < text.length()) {
+ if (text.charAt(index) == ' ' || text.charAt(index) == '\t' || text.charAt(index) == '\n') {
+ break;
+ } else {
+ word.append(text.charAt(index));
+ index++;
+ }
+ }
+ if (!lineFits(graphics, width, line.toString() + word.toString())) {
+ if (line.length() == 0) {
+ return false;
+ }
+ lines++;
+ if (index == text.length() || text.charAt(index) == '\n') {
+ line = new StringBuilder();
+ lines++;
+ } else {
+ line = word;
+ line.append(text.charAt(index));
+ }
+ } else if (index < text.length()) {
+ line.append(word.toString());
+ if (text.charAt(index) == '\n') {
+ line = new StringBuilder();
+ lines++;
+ } else {
+ line.append(text.charAt(index));
+ }
+ }
+ index++;
+ }
+
+ return lines * (graphics.getFontMetrics().getHeight()) <= height;
+ }
+
+ /**
+ * Check if width of the text line is not bigger then required.
+ *
+ * @param graphics
+ * font property
+ * @param width
+ * max width of the text
+ * @param text
+ * text that we want to check
+ * @return true if width of the text line is not bigger then required, false
+ * otherwise
+ */
+ private static boolean lineFits(Graphics2D graphics, double width, String text) {
+ return width >= graphics.getFontMetrics().stringWidth(text);
+ }
+
+ /**
+ * Writes centered text in rectangle using fontSize given as a parameter.
+ *
+ * @param fontSize
+ * font size
+ * @param fontName
+ * font name
+ * @param graphics
+ * where we want to write a text
+ * @param border
+ * what are the borders
+ * @param text
+ * what text we want to write
+ * @param center
+ * should the text be centered
+ */
+ public static void drawText(int fontSize, String fontName, Graphics2D graphics, Rectangle2D border, String text, boolean center) {
+ Font oldFont = graphics.getFont();
+ graphics.setFont(new Font(fontName, 0, fontSize));
+
+ double width = border.getWidth();
+
+ List<String> lines = new ArrayList<String>();
+ int index = 0;
+ StringBuilder line = new StringBuilder();
+ while (index < text.length()) {
+ StringBuilder word = new StringBuilder();
+ while (index < text.length()) {
+ if (text.charAt(index) == ' ' || text.charAt(index) == '\t' || text.charAt(index) == '\n') {
+ break;
+ } else {
+ word.append(text.charAt(index));
+ index++;
+ }
+ }
+ if (!lineFits(graphics, width, line.toString() + word.toString())) {
+ if (line.length() == 0) {
+ throw new InvalidArgumentException("Font too big.");
+ }
+ lines.add(line.toString());
+ if (index == text.length() || text.charAt(index) == '\n') {
+ line = new StringBuilder();
+ lines.add(word.toString());
+ } else {
+ line = word;
+ line.append(text.charAt(index));
+ }
+ } else {
+ line.append(word.toString());
+ if (index < text.length()) {
+ if (text.charAt(index) == '\n') {
+ lines.add(line.toString());
+ line = new StringBuilder();
+ } else {
+ line.append(text.charAt(index));
+ }
+ }
+ }
+ index++;
+ }
+ lines.add(line.toString());
+
+ double lineHeight = graphics.getFontMetrics().getHeight();
+ double y = (int) (border.getCenterY() - lineHeight * lines.size() / 2.0 + graphics.getFontMetrics().getAscent());
+ // if text is not centerd then lets start from left top corner
+ if (!center) {
+ y = border.getY() + lineHeight / 2;
+ }
+
+ for (String string : lines) {
+ double textWidth = graphics.getFontMetrics().stringWidth(string);
+ if (center) {
+ graphics.drawString(string, (int) (border.getCenterX() - textWidth / 2), (int) y);
+ } else {
+ graphics.drawString(string, (int) border.getX(), (int) y);
+ }
+ y += lineHeight;
+ }
+
+ graphics.setFont(oldFont);
+ }
+
+ /**
+ * Writes centered text in rectangle using fontSize given as a parameter.
+ *
+ * @param fontSize
+ * font size
+ * @param fontName
+ * font name
+ * @param graphics
+ * where we want to write a text
+ * @param border
+ * what are the borders
+ * @param text
+ * what text we want to write
+ */
+ public static void drawText(int fontSize, String fontName, Graphics2D graphics, Rectangle2D border, String text) {
+ drawText(fontSize, fontName, graphics, border, text, true);
+ }
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/geometry/RectangleTooSmallException.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/geometry/RectangleTooSmallException.java
index 1c904da435..e9618b89bb 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/geometry/RectangleTooSmallException.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/geometry/RectangleTooSmallException.java
@@ -1,26 +1,26 @@
-package lcsb.mapviewer.converter.graphics.geometry;
-
-/**
- * Exception thrown when the rectangle in which we want to draw description is
- * too small.
- *
- * @author Piotr Gawron
- *
- */
-public class RectangleTooSmallException extends Exception {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor with text message.
- *
- * @param message
- * string message for this exception
- */
- public RectangleTooSmallException(String message) {
- super(message);
- }
-}
+package lcsb.mapviewer.converter.graphics.geometry;
+
+/**
+ * Exception thrown when the rectangle in which we want to draw description is
+ * too small.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class RectangleTooSmallException extends Exception {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor with text message.
+ *
+ * @param message
+ * string message for this exception
+ */
+ public RectangleTooSmallException(String message) {
+ super(message);
+ }
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/geometry/package-info.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/geometry/package-info.java
index 5b09be4667..4ca2ad7a80 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/geometry/package-info.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/geometry/package-info.java
@@ -1,6 +1,6 @@
-/**
- * This package contains some graphical util classes.
- *
- */
-package lcsb.mapviewer.converter.graphics.geometry;
-
+/**
+ * This package contains some graphical util classes.
+ *
+ */
+package lcsb.mapviewer.converter.graphics.geometry;
+
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/layer/LayerConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/layer/LayerConverter.java
index 261eba7a0b..02b225525a 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/layer/LayerConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/layer/LayerConverter.java
@@ -1,155 +1,155 @@
-package lcsb.mapviewer.converter.graphics.layer;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.geom.Ellipse2D;
-import java.awt.geom.Rectangle2D;
-
-import lcsb.mapviewer.converter.graphics.geometry.ArrowTransformation;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.layout.graphics.LayerOval;
-import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
-import lcsb.mapviewer.model.map.layout.graphics.LayerText;
-
-import org.apache.log4j.Logger;
-
-/**
- * This class allows to draw layer on Graphics2D.
- *
- * @author Piotr Gawron
- *
- */
-public class LayerConverter {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(LayerConverter.class.getName());
-
- /**
- * Color used for text frames.
- */
- private static final Color FRAME_COLOR = Color.LIGHT_GRAY;
-
- /**
- * Should the border around text be visible.
- */
- private boolean visibleTextBorder = true;
-
- /**
- * This objects helps drawing arrows.
- */
- private ArrowTransformation arrowTransformation = new ArrowTransformation();
-
- /**
- * Default constructor.
- *
- * @param visibleTextBorder
- * should the text hav border
- */
- public LayerConverter(final boolean visibleTextBorder) {
- this.visibleTextBorder = visibleTextBorder;
- }
-
- /**
- * Draw the whole layer on the Graphics2D.
- *
- * @param layer
- * object to be drawn
- * @param graphics
- * where we want to draw the object
- */
- public void drawLayer(final Layer layer, final Graphics2D graphics) {
- if (layer.isVisible()) {
- for (LayerText text : layer.getTexts()) {
- drawLayerText(text, graphics);
- }
- for (LayerRect rect : layer.getRectangles()) {
- drawLayerRect(rect, graphics);
- }
- for (LayerOval oval : layer.getOvals()) {
- drawLayerOval(oval, graphics);
- }
- for (PolylineData line : layer.getLines()) {
- drawLayerLine(line, graphics);
- }
- }
-
- }
-
- /**
- * Draw text on the Graphics2D.
- *
- * @param text
- * object to be drawn
- * @param graphics
- * where we want to draw the object
- */
- private void drawLayerText(final LayerText text, final Graphics2D graphics) {
- if (visibleTextBorder) {
- Color tmpColor = graphics.getColor();
- graphics.setColor(FRAME_COLOR);
- Rectangle2D rect = new Rectangle2D.Double(text.getX(), text.getY(), text.getWidth(), text.getHeight());
- graphics.draw(rect);
- graphics.setColor(tmpColor);
- }
- int x = text.getX().intValue() + 2;
- int y = text.getY().intValue();
- y += graphics.getFontMetrics().getHeight();
- graphics.drawString(text.getNotes(), x, y);
-
- }
-
- /**
- * Draws rectangle on the Graphics2D.
- *
- * @param rect
- * object to be drawn
- * @param graphics
- * where we want to draw the object
- */
- private void drawLayerRect(final LayerRect rect, final Graphics2D graphics) {
- Color tmpColor = graphics.getColor();
- graphics.setColor(rect.getColor());
- Rectangle2D rectangle = new Rectangle2D.Double(rect.getX(), rect.getY(), rect.getWidth(), rect.getHeight());
- graphics.draw(rectangle);
- graphics.setColor(tmpColor);
-
- }
-
- /**
- * Draws line on the Graphics2D.
- *
- * @param line
- * object to be drawn
- * @param graphics
- * where we want to draw the object
- */
- private void drawLayerLine(final PolylineData line, final Graphics2D graphics) {
- Color tmpColor = graphics.getColor();
- graphics.setColor(line.getColor());
- arrowTransformation.drawLine(line, graphics);
-
- graphics.setColor(tmpColor);
-
- }
-
- /**
- * Draws oval on the Graphics2D.
- *
- * @param oval
- * object to be drawn
- * @param graphics
- * where we want to draw the object
- */
- private void drawLayerOval(final LayerOval oval, final Graphics2D graphics) {
- Color tmpColor = graphics.getColor();
- graphics.setColor(oval.getColor());
- Ellipse2D o = new Ellipse2D.Double(oval.getX(), oval.getY(), oval.getWidth(), oval.getHeight());
- graphics.draw(o);
- graphics.setColor(tmpColor);
-
- }
+package lcsb.mapviewer.converter.graphics.layer;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.geom.Ellipse2D;
+import java.awt.geom.Rectangle2D;
+
+import lcsb.mapviewer.converter.graphics.geometry.ArrowTransformation;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.layout.graphics.LayerOval;
+import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
+import lcsb.mapviewer.model.map.layout.graphics.LayerText;
+
+import org.apache.log4j.Logger;
+
+/**
+ * This class allows to draw layer on Graphics2D.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class LayerConverter {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(LayerConverter.class.getName());
+
+ /**
+ * Color used for text frames.
+ */
+ private static final Color FRAME_COLOR = Color.LIGHT_GRAY;
+
+ /**
+ * Should the border around text be visible.
+ */
+ private boolean visibleTextBorder = true;
+
+ /**
+ * This objects helps drawing arrows.
+ */
+ private ArrowTransformation arrowTransformation = new ArrowTransformation();
+
+ /**
+ * Default constructor.
+ *
+ * @param visibleTextBorder
+ * should the text hav border
+ */
+ public LayerConverter(final boolean visibleTextBorder) {
+ this.visibleTextBorder = visibleTextBorder;
+ }
+
+ /**
+ * Draw the whole layer on the Graphics2D.
+ *
+ * @param layer
+ * object to be drawn
+ * @param graphics
+ * where we want to draw the object
+ */
+ public void drawLayer(final Layer layer, final Graphics2D graphics) {
+ if (layer.isVisible()) {
+ for (LayerText text : layer.getTexts()) {
+ drawLayerText(text, graphics);
+ }
+ for (LayerRect rect : layer.getRectangles()) {
+ drawLayerRect(rect, graphics);
+ }
+ for (LayerOval oval : layer.getOvals()) {
+ drawLayerOval(oval, graphics);
+ }
+ for (PolylineData line : layer.getLines()) {
+ drawLayerLine(line, graphics);
+ }
+ }
+
+ }
+
+ /**
+ * Draw text on the Graphics2D.
+ *
+ * @param text
+ * object to be drawn
+ * @param graphics
+ * where we want to draw the object
+ */
+ private void drawLayerText(final LayerText text, final Graphics2D graphics) {
+ if (visibleTextBorder) {
+ Color tmpColor = graphics.getColor();
+ graphics.setColor(FRAME_COLOR);
+ Rectangle2D rect = new Rectangle2D.Double(text.getX(), text.getY(), text.getWidth(), text.getHeight());
+ graphics.draw(rect);
+ graphics.setColor(tmpColor);
+ }
+ int x = text.getX().intValue() + 2;
+ int y = text.getY().intValue();
+ y += graphics.getFontMetrics().getHeight();
+ graphics.drawString(text.getNotes(), x, y);
+
+ }
+
+ /**
+ * Draws rectangle on the Graphics2D.
+ *
+ * @param rect
+ * object to be drawn
+ * @param graphics
+ * where we want to draw the object
+ */
+ private void drawLayerRect(final LayerRect rect, final Graphics2D graphics) {
+ Color tmpColor = graphics.getColor();
+ graphics.setColor(rect.getColor());
+ Rectangle2D rectangle = new Rectangle2D.Double(rect.getX(), rect.getY(), rect.getWidth(), rect.getHeight());
+ graphics.draw(rectangle);
+ graphics.setColor(tmpColor);
+
+ }
+
+ /**
+ * Draws line on the Graphics2D.
+ *
+ * @param line
+ * object to be drawn
+ * @param graphics
+ * where we want to draw the object
+ */
+ private void drawLayerLine(final PolylineData line, final Graphics2D graphics) {
+ Color tmpColor = graphics.getColor();
+ graphics.setColor(line.getColor());
+ arrowTransformation.drawLine(line, graphics);
+
+ graphics.setColor(tmpColor);
+
+ }
+
+ /**
+ * Draws oval on the Graphics2D.
+ *
+ * @param oval
+ * object to be drawn
+ * @param graphics
+ * where we want to draw the object
+ */
+ private void drawLayerOval(final LayerOval oval, final Graphics2D graphics) {
+ Color tmpColor = graphics.getColor();
+ graphics.setColor(oval.getColor());
+ Ellipse2D o = new Ellipse2D.Double(oval.getX(), oval.getY(), oval.getWidth(), oval.getHeight());
+ graphics.draw(o);
+ graphics.setColor(tmpColor);
+
+ }
}
\ No newline at end of file
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/layer/package-info.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/layer/package-info.java
index ac74dcb94a..62859860b8 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/layer/package-info.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/layer/package-info.java
@@ -1,6 +1,6 @@
-/**
- * Provides classes that draws layouts with additional graphics elements on the
- * Graphics2D.
- */
-package lcsb.mapviewer.converter.graphics.layer;
-
+/**
+ * Provides classes that draws layouts with additional graphics elements on the
+ * Graphics2D.
+ */
+package lcsb.mapviewer.converter.graphics.layer;
+
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/package-info.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/package-info.java
index 93304e1639..405d155a7b 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/package-info.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/package-info.java
@@ -1,27 +1,27 @@
-/**
- * This package contains converter from our model into a graphic representation
- * that can be saved in the graphic file. There are two main application:
- * <ul>
- * <li>generation of the single graphic file that represents the map - in this
- * case direct usage of implementation of
- * {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator
- * AbstractImageGenerator} is recommended. There are two implementation of this
- * class:
- * <ul>
- * <li> {@link lcsb.mapviewer.converter.graphics.NormalImageGenerator
- * NormalImageGenerator} - allows to generate images in PNG and JPG format.</li>
- * <li> {@link lcsb.mapviewer.converter.graphics.SvgImageGenerator
- * SvgImageGenerator} - allows to generate images in SVG format.</li>
- * </ul>
- * It is crucial to remember that too big maps will create very big files which
- * might cause Out of Memory exception</li>
- * <li>generation of the set of files that represent whole image as set of small
- * non-overlapping parts - in this case
- * {@link lcsb.mapviewer.converter.graphics.MapGenerator MapGenerator} class
- * provides interface that generates these images. The images can be used later
- * on by <a href="https://developers.google.com/maps/">Google Maps API</a>.</li>
- * </ul>
- *
- */
-package lcsb.mapviewer.converter.graphics;
-
+/**
+ * This package contains converter from our model into a graphic representation
+ * that can be saved in the graphic file. There are two main application:
+ * <ul>
+ * <li>generation of the single graphic file that represents the map - in this
+ * case direct usage of implementation of
+ * {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator
+ * AbstractImageGenerator} is recommended. There are two implementation of this
+ * class:
+ * <ul>
+ * <li> {@link lcsb.mapviewer.converter.graphics.NormalImageGenerator
+ * NormalImageGenerator} - allows to generate images in PNG and JPG format.</li>
+ * <li> {@link lcsb.mapviewer.converter.graphics.SvgImageGenerator
+ * SvgImageGenerator} - allows to generate images in SVG format.</li>
+ * </ul>
+ * It is crucial to remember that too big maps will create very big files which
+ * might cause Out of Memory exception</li>
+ * <li>generation of the set of files that represent whole image as set of small
+ * non-overlapping parts - in this case
+ * {@link lcsb.mapviewer.converter.graphics.MapGenerator MapGenerator} class
+ * provides interface that generates these images. The images can be used later
+ * on by <a href="https://developers.google.com/maps/">Google Maps API</a>.</li>
+ * </ul>
+ *
+ */
+package lcsb.mapviewer.converter.graphics;
+
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/placefinder/PlaceFinder.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/placefinder/PlaceFinder.java
index 48de38bd01..9e12099a0d 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/placefinder/PlaceFinder.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/placefinder/PlaceFinder.java
@@ -1,482 +1,482 @@
-package lcsb.mapviewer.converter.graphics.placefinder;
-
-import java.awt.geom.Rectangle2D;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeSet;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.commands.SemanticZoomLevelMatcher;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * This class allows to find free space where description should appear for the
- * alias in hierarchical view.
- *
- * @author Piotr Gawron
- *
- */
-public class PlaceFinder {
-
- /**
- * Class that allows to check if element is visible (or transparent) when
- * drawing. It's used to filter out invisible elements when drawing
- * semantic/hierarchy view.
- */
- private SemanticZoomLevelMatcher zoomLevelMatcher = new SemanticZoomLevelMatcher();
-
- /**
- * Represents small part of the map (enclosed by cuting lines) where something
- * can be put. Contains borders (height, weight, location etc). Informatin if
- * it can be used or no and range (magic field that describes how much to the
- * bottom rectangle can be extended).
- *
- * @author Piotr Gawron
- *
- */
- private class Field {
- /**
- * Border of the field.
- */
- private Rectangle2D border;
- /**
- * Can the field be used for something or is occupied?
- */
- private boolean available = true;
- /**
- * How many fields to the bottom are free (how much could we extend empty
- * rectangle.
- */
- private int range = -1;
-
- /**
- * @return the border
- * @see #border
- */
- Rectangle2D getBorder() {
- return border;
- }
-
- /**
- * @param border
- * the border to set
- * @see #border
- */
- void setBorder(Rectangle2D border) {
- this.border = border;
- }
-
- /**
- * @return the available
- * @see #available
- */
- public boolean isAvailable() {
- return available;
- }
-
- /**
- * @param available
- * the available to set
- * @see #available
- */
- public void setAvailable(boolean available) {
- this.available = available;
- }
-
- /**
- * @return the range
- * @see #range
- */
- public int getRange() {
- return range;
- }
-
- /**
- * @param range
- * the range to set
- * @see #range
- */
- public void setRange(int range) {
- this.range = range;
- }
- }
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(PlaceFinder.class.getName());
- /**
- * Whole surface is split into rectangular regions. The lines that cut the
- * surface correspond to borders of aliases that overlap current alias. This
- * matrix defines which of these regions can be used for description.
- */
- private Field[][] matrix;
-
- /**
- * List of {@link Compartment compartment aliases} that split surface into
- * regions.
- */
- private List<Compartment> aliases;
-
- /**
- * Alias for which computation is done.
- */
- private Element mainAlias;
-
- /**
- * Left boundary of the rectangle in which we want to fit our description.
- */
- private double leftBound;
- /**
- * Right boundary of the rectangle in which we want to fit our description.
- */
- private double rightBound;
- /**
- * Top boundary of the rectangle in which we want to fit our description.
- */
- private double upBound;
- /**
- * Bottom boundary of the rectangle in which we want to fit our description.
- */
- private double bottomBound;
-
- /**
- * Model for which this {@link PlaceFinder} was created.
- */
- private Model model;
-
- /**
- * Map with aliases that should be considered when looking for a place to put
- * text.
- */
- private Map<Element, Map<Integer, List<Compartment>>> otherAliases = new HashMap<>();
-
- /**
- * Default constructor for place finder in a model.
- *
- * @param model
- * model
- *
- */
- public PlaceFinder(Model model) {
- this.model = model;
- }
-
- /**
- * Finds the biggest rectangle.
- *
- * @return the biggest rectangle
- */
- private Rectangle2D findRectangle() {
- Rectangle2D biggestRectangle = new Rectangle2D.Double();
- Rectangle2D temporaryRectangle = null;
- for (int y = 0; y < getSizeY(); y++) {
- for (int x = 0; x < getSizeX(); x++) {
- temporaryRectangle = computeRectangleMaxArea(x, y);
- double newArea = temporaryRectangle.getWidth() * temporaryRectangle.getHeight();
- double oldArea = biggestRectangle.getWidth() * biggestRectangle.getHeight();
- if (newArea > oldArea) {
- biggestRectangle = temporaryRectangle;
- }
- }
- }
-
- return biggestRectangle;
- }
-
- /**
- * Computes the biggest rectangle that starts in the region on the position
- * [x,y].
- *
- * @param x
- * x index of the region
- * @param y
- * y index of the region
- * @return the biggest rectangle that starts in the region on the given
- * position
- */
- private Rectangle2D computeRectangleMaxArea(int x, int y) {
- Rectangle2D result = new Rectangle2D.Double();
- int possibleMaximumOfHeight = matrix[x][y].getRange();
- for (int k = x; k >= 0 && matrix[k][y].isAvailable(); k--) {
- if (matrix[k][y].getRange() < possibleMaximumOfHeight) {
- possibleMaximumOfHeight = matrix[k][y].getRange();
- }
- Rectangle2D temporary = computeRectangle(x, y, k, possibleMaximumOfHeight);
- double newArea = temporary.getWidth() * temporary.getHeight();
- double oldArea = result.getWidth() * result.getHeight();
- if (newArea > oldArea) {
- result = temporary;
- }
- }
- return result;
- }
-
- /**
- * Computes rectangle in region range [k..x][y..y+height].
- *
- * @param x
- * end x coordinate
- * @param y
- * start y coordinate
- * @param k
- * start x coordinate
- * @param height
- * height in y coordinate
- * @return rectangle in region range
- */
- private Rectangle2D computeRectangle(int x, int y, int k, int height) {
- double resX = matrix[k][y].getBorder().getX();
- double resY = matrix[k][y].getBorder().getY();
- double resWidth = matrix[x][y + height - 1].getBorder().getX() - resX + matrix[x][y + height - 1].getBorder().getWidth();
- double resHeight = matrix[x][y + height - 1].getBorder().getY() - resY + matrix[x][y + height - 1].getBorder().getHeight();
-
- return new Rectangle2D.Double(resX, resY, resWidth, resHeight);
- }
-
- /**
- * Computes how deep in y axis can regions be extended from starting x,y
- * region.
- */
- private void findRanges() {
- for (int i = 0; i < getSizeX(); i++) {
- for (int j = 0; j < getSizeY(); j++) {
- if (!matrix[i][j].isAvailable()) {
- int k = j;
- int temporaryRange = 0;
- while (k >= 0 && matrix[i][k].getRange() == -1) {
- matrix[i][k--].setRange(temporaryRange++);
- }
- }
- }
- if (matrix[i][getSizeY() - 1].isAvailable()) {
- int k = getSizeY() - 1;
- int temporaryRange = 1;
- while (k >= 0 && matrix[i][k].getRange() == -1) {
- matrix[i][k--].setRange(temporaryRange++);
- }
- }
-
- }
- }
-
- /**
- * Disables regions for all aliases.
- */
- private void fillMatrixWithAliases() {
- for (Element alias : aliases) {
- if (alias != mainAlias) {
- fillMatrixWithAlias(alias);
- }
- }
- }
-
- /**
- * Disable regions for given alias.
- *
- * @param alias
- * alias that should disable regions
- */
- private void fillMatrixWithAlias(Element alias) {
- Double a, b, c, d;
-
- a = alias.getX();
- b = alias.getX() + alias.getWidth();
- c = alias.getY() + alias.getHeight();
- d = alias.getY();
-
- fillWithPoints(a, b, c, d);
- }
-
- /**
- * Disable regions between given coordinates.
- *
- * @param x
- * starting x coordinate
- * @param xw
- * ending x coordinate
- * @param yh
- * ending y coordinate
- * @param y
- * starting y coordinate
- */
- private void fillWithPoints(Double x, Double xw, Double yh, Double y) {
- Integer widthStart = 0;
- Integer widthEnd = matrix.length;
- Integer heightStart = 0;
- Integer heightEnd = matrix[0].length;
-
- for (int i = 0; i < matrix.length; i++) {
- if (matrix[i][0].getBorder().getX() <= x) {
- widthStart = i;
- }
- if (matrix[i][0].getBorder().getX() <= xw) {
- widthEnd = i;
- }
- }
- if (matrix[matrix.length - 1][0].getBorder().getX() + matrix[matrix.length - 1][0].getBorder().getWidth() <= xw) {
- widthEnd = matrix.length;
- }
- for (int i = 0; i < matrix[0].length; i++) {
- if (matrix[0][i].getBorder().getY() <= y) {
- heightStart = i;
- }
- if (matrix[0][i].getBorder().getY() <= yh) {
- heightEnd = i;
- }
- }
- if (matrix[0][matrix[0].length - 1].getBorder().getY() + matrix[0][matrix[0].length - 1].getBorder().getHeight() <= yh) {
- heightEnd = matrix[0].length;
- }
-
- for (int i = widthStart; i < widthEnd; i++) {
- for (int j = heightStart; j < heightEnd; j++) {
- matrix[i][j].setAvailable(false);
- }
- }
- }
-
- /**
- * This method looks for a place to put description of the {@link Compartment}
- * on the map.
- *
- * @param compartment
- * {@link Compartment} for which we try to determine text position
- * @param level
- * level at which we will visualize element
- * @return bounds where text could be put
- */
- public Rectangle2D getRetangle(Compartment compartment, int level) {
- Map<Integer, List<Compartment>> lists = otherAliases.get(compartment);
- if (lists == null) {
- lists = new HashMap<>();
- otherAliases.put(compartment, lists);
- }
- List<Compartment> list = lists.get(level);
- if (list == null) {
- list = new ArrayList<Compartment>();
- for (Compartment compAlias : model.getCompartments()) {
- if (zoomLevelMatcher.isVisible(level, compAlias.getVisibilityLevel()) && !zoomLevelMatcher.isTransparent(level, compAlias.getTransparencyLevel())) {
- if (compAlias.cross(compartment) && compAlias.getSize() <= compartment.getSize()) {
- list.add(compAlias);
- }
- }
- }
- lists.put(level, list);
- }
-
- this.mainAlias = compartment;
- this.aliases = list;
-
- leftBound = compartment.getX();
- rightBound = (compartment.getX() + compartment.getWidth());
- upBound = compartment.getY();
- bottomBound = (compartment.getY() + compartment.getHeight());
-
- createMatrix();
-
- fillMatrixWithAliases();
-
- findRanges(); // 2*O(n^2)
-
- return findRectangle();
- }
-
- /**
- * Create empty matrix with fields.
- *
- * @see #matrix
- */
- protected void createMatrix() {
- Set<Double> xs = new TreeSet<Double>();
- Set<Double> ys = new TreeSet<Double>();
- List<Double> widths = new ArrayList<Double>();
- List<Double> xCoordsOfBegginingOfRectangle = new ArrayList<Double>();
- List<Double> heights = new ArrayList<Double>();
- List<Double> yCoordsOfBegginingOfRectangle = new ArrayList<Double>();
-
- for (Element alias : aliases) {
- double x1 = alias.getX();
- double x2 = alias.getX() + alias.getWidth();
- double y1 = alias.getY();
- double y2 = alias.getY() + alias.getHeight();
- if (x1 >= leftBound && x1 <= rightBound) {
- xs.add(x1);
- }
- if (x2 >= leftBound && x2 <= rightBound) {
- xs.add(x2);
- }
-
- if (y1 >= upBound && y1 <= bottomBound) {
- ys.add(y1);
- }
- if (y2 >= upBound && y2 <= bottomBound) {
- ys.add(y2);
- }
- }
- Double previous = null;
- for (Double width : xs) {
- if (previous != null) {
- widths.add(width - previous);
- }
- xCoordsOfBegginingOfRectangle.add(width);
- previous = width;
- }
- previous = null;
- for (Double height : ys) {
- if (previous != null) {
- heights.add(height - previous);
- }
- yCoordsOfBegginingOfRectangle.add(height);
- previous = height;
- }
-
- matrix = new Field[xs.size() - 1][ys.size() - 1];
-
- for (int i = 0; i < getSizeX(); i++) {
- for (int j = 0; j < getSizeY(); j++) {
- Field field = new Field();
- xCoordsOfBegginingOfRectangle.get(i);
- yCoordsOfBegginingOfRectangle.get(j);
- widths.get(i);
- heights.get(j);
- field.setBorder(new Rectangle2D.Double(xCoordsOfBegginingOfRectangle.get(i), yCoordsOfBegginingOfRectangle.get(j), widths.get(i), heights.get(j)));
- matrix[i][j] = field;
- }
- }
- }
-
- /**
- *
- * @return {@link #model}
- */
- public Model getModel() {
- return model;
- }
-
- /**
- * Returns width of the {@link #matrix}.
- *
- * @return width of the {@link #matrix}
- */
- private int getSizeX() {
- return matrix.length;
- }
-
- /**
- * Returns height of the {@link #matrix}.
- *
- * @return height of the {@link #matrix}
- */
- private int getSizeY() {
- return matrix[0].length;
- }
-
-}
+package lcsb.mapviewer.converter.graphics.placefinder;
+
+import java.awt.geom.Rectangle2D;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeSet;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.SemanticZoomLevelMatcher;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * This class allows to find free space where description should appear for the
+ * alias in hierarchical view.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class PlaceFinder {
+
+ /**
+ * Class that allows to check if element is visible (or transparent) when
+ * drawing. It's used to filter out invisible elements when drawing
+ * semantic/hierarchy view.
+ */
+ private SemanticZoomLevelMatcher zoomLevelMatcher = new SemanticZoomLevelMatcher();
+
+ /**
+ * Represents small part of the map (enclosed by cuting lines) where something
+ * can be put. Contains borders (height, weight, location etc). Informatin if
+ * it can be used or no and range (magic field that describes how much to the
+ * bottom rectangle can be extended).
+ *
+ * @author Piotr Gawron
+ *
+ */
+ private class Field {
+ /**
+ * Border of the field.
+ */
+ private Rectangle2D border;
+ /**
+ * Can the field be used for something or is occupied?
+ */
+ private boolean available = true;
+ /**
+ * How many fields to the bottom are free (how much could we extend empty
+ * rectangle.
+ */
+ private int range = -1;
+
+ /**
+ * @return the border
+ * @see #border
+ */
+ Rectangle2D getBorder() {
+ return border;
+ }
+
+ /**
+ * @param border
+ * the border to set
+ * @see #border
+ */
+ void setBorder(Rectangle2D border) {
+ this.border = border;
+ }
+
+ /**
+ * @return the available
+ * @see #available
+ */
+ public boolean isAvailable() {
+ return available;
+ }
+
+ /**
+ * @param available
+ * the available to set
+ * @see #available
+ */
+ public void setAvailable(boolean available) {
+ this.available = available;
+ }
+
+ /**
+ * @return the range
+ * @see #range
+ */
+ public int getRange() {
+ return range;
+ }
+
+ /**
+ * @param range
+ * the range to set
+ * @see #range
+ */
+ public void setRange(int range) {
+ this.range = range;
+ }
+ }
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(PlaceFinder.class.getName());
+ /**
+ * Whole surface is split into rectangular regions. The lines that cut the
+ * surface correspond to borders of aliases that overlap current alias. This
+ * matrix defines which of these regions can be used for description.
+ */
+ private Field[][] matrix;
+
+ /**
+ * List of {@link Compartment compartment aliases} that split surface into
+ * regions.
+ */
+ private List<Compartment> aliases;
+
+ /**
+ * Alias for which computation is done.
+ */
+ private Element mainAlias;
+
+ /**
+ * Left boundary of the rectangle in which we want to fit our description.
+ */
+ private double leftBound;
+ /**
+ * Right boundary of the rectangle in which we want to fit our description.
+ */
+ private double rightBound;
+ /**
+ * Top boundary of the rectangle in which we want to fit our description.
+ */
+ private double upBound;
+ /**
+ * Bottom boundary of the rectangle in which we want to fit our description.
+ */
+ private double bottomBound;
+
+ /**
+ * Model for which this {@link PlaceFinder} was created.
+ */
+ private Model model;
+
+ /**
+ * Map with aliases that should be considered when looking for a place to put
+ * text.
+ */
+ private Map<Element, Map<Integer, List<Compartment>>> otherAliases = new HashMap<>();
+
+ /**
+ * Default constructor for place finder in a model.
+ *
+ * @param model
+ * model
+ *
+ */
+ public PlaceFinder(Model model) {
+ this.model = model;
+ }
+
+ /**
+ * Finds the biggest rectangle.
+ *
+ * @return the biggest rectangle
+ */
+ private Rectangle2D findRectangle() {
+ Rectangle2D biggestRectangle = new Rectangle2D.Double();
+ Rectangle2D temporaryRectangle = null;
+ for (int y = 0; y < getSizeY(); y++) {
+ for (int x = 0; x < getSizeX(); x++) {
+ temporaryRectangle = computeRectangleMaxArea(x, y);
+ double newArea = temporaryRectangle.getWidth() * temporaryRectangle.getHeight();
+ double oldArea = biggestRectangle.getWidth() * biggestRectangle.getHeight();
+ if (newArea > oldArea) {
+ biggestRectangle = temporaryRectangle;
+ }
+ }
+ }
+
+ return biggestRectangle;
+ }
+
+ /**
+ * Computes the biggest rectangle that starts in the region on the position
+ * [x,y].
+ *
+ * @param x
+ * x index of the region
+ * @param y
+ * y index of the region
+ * @return the biggest rectangle that starts in the region on the given
+ * position
+ */
+ private Rectangle2D computeRectangleMaxArea(int x, int y) {
+ Rectangle2D result = new Rectangle2D.Double();
+ int possibleMaximumOfHeight = matrix[x][y].getRange();
+ for (int k = x; k >= 0 && matrix[k][y].isAvailable(); k--) {
+ if (matrix[k][y].getRange() < possibleMaximumOfHeight) {
+ possibleMaximumOfHeight = matrix[k][y].getRange();
+ }
+ Rectangle2D temporary = computeRectangle(x, y, k, possibleMaximumOfHeight);
+ double newArea = temporary.getWidth() * temporary.getHeight();
+ double oldArea = result.getWidth() * result.getHeight();
+ if (newArea > oldArea) {
+ result = temporary;
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Computes rectangle in region range [k..x][y..y+height].
+ *
+ * @param x
+ * end x coordinate
+ * @param y
+ * start y coordinate
+ * @param k
+ * start x coordinate
+ * @param height
+ * height in y coordinate
+ * @return rectangle in region range
+ */
+ private Rectangle2D computeRectangle(int x, int y, int k, int height) {
+ double resX = matrix[k][y].getBorder().getX();
+ double resY = matrix[k][y].getBorder().getY();
+ double resWidth = matrix[x][y + height - 1].getBorder().getX() - resX + matrix[x][y + height - 1].getBorder().getWidth();
+ double resHeight = matrix[x][y + height - 1].getBorder().getY() - resY + matrix[x][y + height - 1].getBorder().getHeight();
+
+ return new Rectangle2D.Double(resX, resY, resWidth, resHeight);
+ }
+
+ /**
+ * Computes how deep in y axis can regions be extended from starting x,y
+ * region.
+ */
+ private void findRanges() {
+ for (int i = 0; i < getSizeX(); i++) {
+ for (int j = 0; j < getSizeY(); j++) {
+ if (!matrix[i][j].isAvailable()) {
+ int k = j;
+ int temporaryRange = 0;
+ while (k >= 0 && matrix[i][k].getRange() == -1) {
+ matrix[i][k--].setRange(temporaryRange++);
+ }
+ }
+ }
+ if (matrix[i][getSizeY() - 1].isAvailable()) {
+ int k = getSizeY() - 1;
+ int temporaryRange = 1;
+ while (k >= 0 && matrix[i][k].getRange() == -1) {
+ matrix[i][k--].setRange(temporaryRange++);
+ }
+ }
+
+ }
+ }
+
+ /**
+ * Disables regions for all aliases.
+ */
+ private void fillMatrixWithAliases() {
+ for (Element alias : aliases) {
+ if (alias != mainAlias) {
+ fillMatrixWithAlias(alias);
+ }
+ }
+ }
+
+ /**
+ * Disable regions for given alias.
+ *
+ * @param alias
+ * alias that should disable regions
+ */
+ private void fillMatrixWithAlias(Element alias) {
+ Double a, b, c, d;
+
+ a = alias.getX();
+ b = alias.getX() + alias.getWidth();
+ c = alias.getY() + alias.getHeight();
+ d = alias.getY();
+
+ fillWithPoints(a, b, c, d);
+ }
+
+ /**
+ * Disable regions between given coordinates.
+ *
+ * @param x
+ * starting x coordinate
+ * @param xw
+ * ending x coordinate
+ * @param yh
+ * ending y coordinate
+ * @param y
+ * starting y coordinate
+ */
+ private void fillWithPoints(Double x, Double xw, Double yh, Double y) {
+ Integer widthStart = 0;
+ Integer widthEnd = matrix.length;
+ Integer heightStart = 0;
+ Integer heightEnd = matrix[0].length;
+
+ for (int i = 0; i < matrix.length; i++) {
+ if (matrix[i][0].getBorder().getX() <= x) {
+ widthStart = i;
+ }
+ if (matrix[i][0].getBorder().getX() <= xw) {
+ widthEnd = i;
+ }
+ }
+ if (matrix[matrix.length - 1][0].getBorder().getX() + matrix[matrix.length - 1][0].getBorder().getWidth() <= xw) {
+ widthEnd = matrix.length;
+ }
+ for (int i = 0; i < matrix[0].length; i++) {
+ if (matrix[0][i].getBorder().getY() <= y) {
+ heightStart = i;
+ }
+ if (matrix[0][i].getBorder().getY() <= yh) {
+ heightEnd = i;
+ }
+ }
+ if (matrix[0][matrix[0].length - 1].getBorder().getY() + matrix[0][matrix[0].length - 1].getBorder().getHeight() <= yh) {
+ heightEnd = matrix[0].length;
+ }
+
+ for (int i = widthStart; i < widthEnd; i++) {
+ for (int j = heightStart; j < heightEnd; j++) {
+ matrix[i][j].setAvailable(false);
+ }
+ }
+ }
+
+ /**
+ * This method looks for a place to put description of the {@link Compartment}
+ * on the map.
+ *
+ * @param compartment
+ * {@link Compartment} for which we try to determine text position
+ * @param level
+ * level at which we will visualize element
+ * @return bounds where text could be put
+ */
+ public Rectangle2D getRetangle(Compartment compartment, int level) {
+ Map<Integer, List<Compartment>> lists = otherAliases.get(compartment);
+ if (lists == null) {
+ lists = new HashMap<>();
+ otherAliases.put(compartment, lists);
+ }
+ List<Compartment> list = lists.get(level);
+ if (list == null) {
+ list = new ArrayList<Compartment>();
+ for (Compartment compAlias : model.getCompartments()) {
+ if (zoomLevelMatcher.isVisible(level, compAlias.getVisibilityLevel()) && !zoomLevelMatcher.isTransparent(level, compAlias.getTransparencyLevel())) {
+ if (compAlias.cross(compartment) && compAlias.getSize() <= compartment.getSize()) {
+ list.add(compAlias);
+ }
+ }
+ }
+ lists.put(level, list);
+ }
+
+ this.mainAlias = compartment;
+ this.aliases = list;
+
+ leftBound = compartment.getX();
+ rightBound = (compartment.getX() + compartment.getWidth());
+ upBound = compartment.getY();
+ bottomBound = (compartment.getY() + compartment.getHeight());
+
+ createMatrix();
+
+ fillMatrixWithAliases();
+
+ findRanges(); // 2*O(n^2)
+
+ return findRectangle();
+ }
+
+ /**
+ * Create empty matrix with fields.
+ *
+ * @see #matrix
+ */
+ protected void createMatrix() {
+ Set<Double> xs = new TreeSet<Double>();
+ Set<Double> ys = new TreeSet<Double>();
+ List<Double> widths = new ArrayList<Double>();
+ List<Double> xCoordsOfBegginingOfRectangle = new ArrayList<Double>();
+ List<Double> heights = new ArrayList<Double>();
+ List<Double> yCoordsOfBegginingOfRectangle = new ArrayList<Double>();
+
+ for (Element alias : aliases) {
+ double x1 = alias.getX();
+ double x2 = alias.getX() + alias.getWidth();
+ double y1 = alias.getY();
+ double y2 = alias.getY() + alias.getHeight();
+ if (x1 >= leftBound && x1 <= rightBound) {
+ xs.add(x1);
+ }
+ if (x2 >= leftBound && x2 <= rightBound) {
+ xs.add(x2);
+ }
+
+ if (y1 >= upBound && y1 <= bottomBound) {
+ ys.add(y1);
+ }
+ if (y2 >= upBound && y2 <= bottomBound) {
+ ys.add(y2);
+ }
+ }
+ Double previous = null;
+ for (Double width : xs) {
+ if (previous != null) {
+ widths.add(width - previous);
+ }
+ xCoordsOfBegginingOfRectangle.add(width);
+ previous = width;
+ }
+ previous = null;
+ for (Double height : ys) {
+ if (previous != null) {
+ heights.add(height - previous);
+ }
+ yCoordsOfBegginingOfRectangle.add(height);
+ previous = height;
+ }
+
+ matrix = new Field[xs.size() - 1][ys.size() - 1];
+
+ for (int i = 0; i < getSizeX(); i++) {
+ for (int j = 0; j < getSizeY(); j++) {
+ Field field = new Field();
+ xCoordsOfBegginingOfRectangle.get(i);
+ yCoordsOfBegginingOfRectangle.get(j);
+ widths.get(i);
+ heights.get(j);
+ field.setBorder(new Rectangle2D.Double(xCoordsOfBegginingOfRectangle.get(i), yCoordsOfBegginingOfRectangle.get(j), widths.get(i), heights.get(j)));
+ matrix[i][j] = field;
+ }
+ }
+ }
+
+ /**
+ *
+ * @return {@link #model}
+ */
+ public Model getModel() {
+ return model;
+ }
+
+ /**
+ * Returns width of the {@link #matrix}.
+ *
+ * @return width of the {@link #matrix}
+ */
+ private int getSizeX() {
+ return matrix.length;
+ }
+
+ /**
+ * Returns height of the {@link #matrix}.
+ *
+ * @return height of the {@link #matrix}
+ */
+ private int getSizeY() {
+ return matrix[0].length;
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/placefinder/package-info.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/placefinder/package-info.java
index 415632a6c2..8968ad062e 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/placefinder/package-info.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/placefinder/package-info.java
@@ -1,6 +1,6 @@
-/**
- * This package contains utility to find place where description can be put
- * among many overlapping rectangles.
- */
-package lcsb.mapviewer.converter.graphics.placefinder;
-
+/**
+ * This package contains utility to find place where description can be put
+ * among many overlapping rectangles.
+ */
+package lcsb.mapviewer.converter.graphics.placefinder;
+
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/AllGraphicsTests.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/AllGraphicsTests.java
index 582a1ddc39..b6eeeff919 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/AllGraphicsTests.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/AllGraphicsTests.java
@@ -1,26 +1,26 @@
-package lcsb.mapviewer.converter.graphics;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-import lcsb.mapviewer.converter.graphics.bioEntity.AllBioEntityTests;
-import lcsb.mapviewer.converter.graphics.geometry.AllGeometryTests;
-import lcsb.mapviewer.converter.graphics.placefinder.AllPlaceFinderTest;
-
-@RunWith(Suite.class)
-@SuiteClasses({ //
- AbstractImageGeneratorTest.class, //
- AllBioEntityTests.class, //
- AllGeometryTests.class, //
- AllPlaceFinderTest.class, //
- ConverterTest.class, //
- ImageGeneratorsTest.class, //
- MapGeneratorTest.class, //
- NormalImageGeneratorTest.class, //
- PdfImageGeneratorTest.class,//
-
-})
-public class AllGraphicsTests {
-
-}
+package lcsb.mapviewer.converter.graphics;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+import lcsb.mapviewer.converter.graphics.bioEntity.AllBioEntityTests;
+import lcsb.mapviewer.converter.graphics.geometry.AllGeometryTests;
+import lcsb.mapviewer.converter.graphics.placefinder.AllPlaceFinderTest;
+
+@RunWith(Suite.class)
+@SuiteClasses({ //
+ AbstractImageGeneratorTest.class, //
+ AllBioEntityTests.class, //
+ AllGeometryTests.class, //
+ AllPlaceFinderTest.class, //
+ ConverterTest.class, //
+ ImageGeneratorsTest.class, //
+ MapGeneratorTest.class, //
+ NormalImageGeneratorTest.class, //
+ PdfImageGeneratorTest.class,//
+
+})
+public class AllGraphicsTests {
+
+}
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java
index af923b647b..c4f3038875 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java
@@ -1,86 +1,86 @@
-package lcsb.mapviewer.converter.graphics;
-
-import java.awt.Color;
-import java.awt.Desktop;
-import java.awt.Graphics2D;
-import java.awt.image.BufferedImage;
-import java.io.File;
-import java.io.IOException;
-
-import javax.imageio.ImageIO;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Ignore;
-import org.junit.Test;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.converter.graphics.bioEntity.BioEntityConverterImpl;
-import lcsb.mapviewer.model.map.compartment.BottomSquareCompartment;
-import lcsb.mapviewer.model.map.compartment.LeftSquareCompartment;
-import lcsb.mapviewer.model.map.compartment.RightSquareCompartment;
-import lcsb.mapviewer.model.map.compartment.TopSquareCompartment;
-
-public class ConverterTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void test() {
- try {
- ColorExtractor colorExtractor = new ColorExtractor(Color.BLUE, Color.RED, Color.BLUE);
- new BioEntityConverterImpl(new BottomSquareCompartment("id1"), colorExtractor);
- new BioEntityConverterImpl(new TopSquareCompartment("id2"), colorExtractor);
- new BioEntityConverterImpl(new LeftSquareCompartment("id3"), colorExtractor);
- new BioEntityConverterImpl(new RightSquareCompartment("id4"), colorExtractor);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- @Ignore("it's just code for generating scale")
- public void testX() throws IOException {
- BufferedImage tmpBI = new BufferedImage(900, 100, BufferedImage.TYPE_INT_ARGB);
- Graphics2D tmpGraphics = tmpBI.createGraphics();
- int startX = 10;
- int startY = 15;
- int stepSize = 40;
- int height = 25;
- tmpGraphics.setColor(Color.BLACK);
- for (int i = 0; i < 21; i++) {
- tmpGraphics.drawLine(startX + i * stepSize, height+startY, startX + i * stepSize, height*2);
- String str = ""+((double)(i-10))/((double)(10));
- tmpGraphics.drawString(str, startX + i * stepSize, height*2+startY);
- }
- for (int i = 0; i < 10 * stepSize; i++) {
- double ratio = ((double) i) / ((double) (10 * stepSize));
- tmpGraphics.setBackground(getColor(ratio, Color.BLUE, Color.WHITE));
- tmpGraphics.setColor(getColor(ratio, Color.BLUE, Color.WHITE));
- tmpGraphics.drawRect(startX + i, startY , 1, height);
- }
- for (int i = 0; i < 10 * stepSize; i++) {
- double ratio = ((double) i) / ((double) (10 * stepSize));
- tmpGraphics.setBackground(getColor(ratio, Color.WHITE, Color.RED));
- tmpGraphics.setColor(getColor(ratio, Color.WHITE, Color.RED));
- tmpGraphics.drawRect(10 * stepSize + startX + i, startY , 1, height);
- }
- ImageIO.write(tmpBI, "PNG", new File("tmp.png"));
- Desktop.getDesktop().open(new File("tmp.png"));
- }
-
- private Color getColor(double d, Color startColor, Color endColor) {
-
- return new Color((int) (startColor.getRed() + d * (endColor.getRed() - startColor.getRed())), //
- (int) (startColor.getGreen() + d * (endColor.getGreen() - startColor.getGreen())), //
- (int) (startColor.getBlue() + d * (endColor.getBlue() - startColor.getBlue())));
- }
-
-}
+package lcsb.mapviewer.converter.graphics;
+
+import java.awt.Color;
+import java.awt.Desktop;
+import java.awt.Graphics2D;
+import java.awt.image.BufferedImage;
+import java.io.File;
+import java.io.IOException;
+
+import javax.imageio.ImageIO;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Ignore;
+import org.junit.Test;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.converter.graphics.bioEntity.BioEntityConverterImpl;
+import lcsb.mapviewer.model.map.compartment.BottomSquareCompartment;
+import lcsb.mapviewer.model.map.compartment.LeftSquareCompartment;
+import lcsb.mapviewer.model.map.compartment.RightSquareCompartment;
+import lcsb.mapviewer.model.map.compartment.TopSquareCompartment;
+
+public class ConverterTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void test() {
+ try {
+ ColorExtractor colorExtractor = new ColorExtractor(Color.BLUE, Color.RED, Color.BLUE);
+ new BioEntityConverterImpl(new BottomSquareCompartment("id1"), colorExtractor);
+ new BioEntityConverterImpl(new TopSquareCompartment("id2"), colorExtractor);
+ new BioEntityConverterImpl(new LeftSquareCompartment("id3"), colorExtractor);
+ new BioEntityConverterImpl(new RightSquareCompartment("id4"), colorExtractor);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ @Ignore("it's just code for generating scale")
+ public void testX() throws IOException {
+ BufferedImage tmpBI = new BufferedImage(900, 100, BufferedImage.TYPE_INT_ARGB);
+ Graphics2D tmpGraphics = tmpBI.createGraphics();
+ int startX = 10;
+ int startY = 15;
+ int stepSize = 40;
+ int height = 25;
+ tmpGraphics.setColor(Color.BLACK);
+ for (int i = 0; i < 21; i++) {
+ tmpGraphics.drawLine(startX + i * stepSize, height+startY, startX + i * stepSize, height*2);
+ String str = ""+((double)(i-10))/((double)(10));
+ tmpGraphics.drawString(str, startX + i * stepSize, height*2+startY);
+ }
+ for (int i = 0; i < 10 * stepSize; i++) {
+ double ratio = ((double) i) / ((double) (10 * stepSize));
+ tmpGraphics.setBackground(getColor(ratio, Color.BLUE, Color.WHITE));
+ tmpGraphics.setColor(getColor(ratio, Color.BLUE, Color.WHITE));
+ tmpGraphics.drawRect(startX + i, startY , 1, height);
+ }
+ for (int i = 0; i < 10 * stepSize; i++) {
+ double ratio = ((double) i) / ((double) (10 * stepSize));
+ tmpGraphics.setBackground(getColor(ratio, Color.WHITE, Color.RED));
+ tmpGraphics.setColor(getColor(ratio, Color.WHITE, Color.RED));
+ tmpGraphics.drawRect(10 * stepSize + startX + i, startY , 1, height);
+ }
+ ImageIO.write(tmpBI, "PNG", new File("tmp.png"));
+ Desktop.getDesktop().open(new File("tmp.png"));
+ }
+
+ private Color getColor(double d, Color startColor, Color endColor) {
+
+ return new Color((int) (startColor.getRed() + d * (endColor.getRed() - startColor.getRed())), //
+ (int) (startColor.getGreen() + d * (endColor.getGreen() - startColor.getGreen())), //
+ (int) (startColor.getBlue() + d * (endColor.getBlue() - startColor.getBlue())));
+ }
+
+}
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ImageGeneratorsTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ImageGeneratorsTest.java
index adb7f266c3..acfa32d3db 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ImageGeneratorsTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ImageGeneratorsTest.java
@@ -1,45 +1,45 @@
-package lcsb.mapviewer.converter.graphics;
-
-import static org.junit.Assert.*;
-import lcsb.mapviewer.common.Pair;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ImageGeneratorsTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testAvailableGenerators() {
- try {
- ImageGenerators imageGenerators = new ImageGenerators();
-
- boolean pngGenFound = false;
- boolean pdfGenFound = false;
- for (Pair<String, Class<? extends AbstractImageGenerator>> element : imageGenerators.getAvailableImageGenerators()) {
- if (element.getRight().equals(PngImageGenerator.class)) {
- pngGenFound = true;
- }
- if (element.getRight().equals(PdfImageGenerator.class)) {
- pdfGenFound = true;
- }
- }
- assertTrue(pngGenFound);
- assertTrue(pdfGenFound);
-// assertTrue(jpgGenFound);
-// assertTrue(svgGenFound);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.graphics;
+
+import static org.junit.Assert.*;
+import lcsb.mapviewer.common.Pair;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ImageGeneratorsTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testAvailableGenerators() {
+ try {
+ ImageGenerators imageGenerators = new ImageGenerators();
+
+ boolean pngGenFound = false;
+ boolean pdfGenFound = false;
+ for (Pair<String, Class<? extends AbstractImageGenerator>> element : imageGenerators.getAvailableImageGenerators()) {
+ if (element.getRight().equals(PngImageGenerator.class)) {
+ pngGenFound = true;
+ }
+ if (element.getRight().equals(PdfImageGenerator.class)) {
+ pdfGenFound = true;
+ }
+ }
+ assertTrue(pngGenFound);
+ assertTrue(pdfGenFound);
+// assertTrue(jpgGenFound);
+// assertTrue(svgGenFound);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/MapGeneratorTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/MapGeneratorTest.java
index 2138d0f0dd..8b58c565a1 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/MapGeneratorTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/MapGeneratorTest.java
@@ -1,85 +1,85 @@
-package lcsb.mapviewer.converter.graphics;
-
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.io.File;
-
-import lcsb.mapviewer.converter.graphics.MapGenerator.MapGeneratorParams;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-
-import org.apache.commons.io.FileUtils;
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class MapGeneratorTest {
- Logger logger = Logger.getLogger(MapGeneratorTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGenerateMapImagesModelStringBoolean() {
- try {
- String dir = "test_images";
- File f = new File(dir);
- if (f.exists()) {
- FileUtils.deleteDirectory(f);
- }
-
- Model model = createModel();
- MapGenerator generator = new MapGenerator();
- MapGeneratorParams params = generator.new MapGeneratorParams().model(model).directory(dir);
- generator.generateMapImages(params);
-
- File f1 = new File(dir + "/2/0/0.PNG");
- assertTrue(f1.exists());
- File f2 = new File(dir + "/4/1/1.PNG");
- assertTrue(f2.exists());
-
- f = new File(dir);
- FileUtils.deleteDirectory(f);
- } catch (Exception e) {
- e.printStackTrace();
- fail("Exception occurred");
- }
- }
-
- private Model createModel() {
- Model model = new ModelFullIndexed(null);
- model.setWidth(1305.7682370820667);
- model.setHeight(473.0);
- return model;
- }
-
- @Test
- public void testRemoveLayout() throws Exception {
- try {
- String dir = "test_images";
- File f = new File(dir);
-
- Model model = createModel();
- model.addLayout(new Layout("a", dir, true));
- MapGenerator generator = new MapGenerator();
- MapGeneratorParams params = generator.new MapGeneratorParams().model(model).directory(dir);
- generator.generateMapImages(params);
- assertTrue(f.exists());
- generator.removeLayout(model.getLayouts().get(0));
-
- assertFalse(f.exists());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.converter.graphics;
+
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.io.File;
+
+import lcsb.mapviewer.converter.graphics.MapGenerator.MapGeneratorParams;
+import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class MapGeneratorTest {
+ Logger logger = Logger.getLogger(MapGeneratorTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGenerateMapImagesModelStringBoolean() {
+ try {
+ String dir = "test_images";
+ File f = new File(dir);
+ if (f.exists()) {
+ FileUtils.deleteDirectory(f);
+ }
+
+ Model model = createModel();
+ MapGenerator generator = new MapGenerator();
+ MapGeneratorParams params = generator.new MapGeneratorParams().model(model).directory(dir);
+ generator.generateMapImages(params);
+
+ File f1 = new File(dir + "/2/0/0.PNG");
+ assertTrue(f1.exists());
+ File f2 = new File(dir + "/4/1/1.PNG");
+ assertTrue(f2.exists());
+
+ f = new File(dir);
+ FileUtils.deleteDirectory(f);
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Exception occurred");
+ }
+ }
+
+ private Model createModel() {
+ Model model = new ModelFullIndexed(null);
+ model.setWidth(1305.7682370820667);
+ model.setHeight(473.0);
+ return model;
+ }
+
+ @Test
+ public void testRemoveLayout() throws Exception {
+ try {
+ String dir = "test_images";
+ File f = new File(dir);
+
+ Model model = createModel();
+ model.addLayout(new Layout("a", dir, true));
+ MapGenerator generator = new MapGenerator();
+ MapGeneratorParams params = generator.new MapGeneratorParams().model(model).directory(dir);
+ generator.generateMapImages(params);
+ assertTrue(f.exists());
+ generator.removeLayout(model.getLayouts().get(0));
+
+ assertFalse(f.exists());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java
index fbb7a6f4c7..347ca0dbaa 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java
@@ -1,147 +1,147 @@
-package lcsb.mapviewer.converter.graphics;
-
-import static org.junit.Assert.assertFalse;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.commands.CreateHierarchyCommand;
-import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.ComplexConverter;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.layout.graphics.LayerText;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.Complex;
-
-public class NormalImageGeneratorTest {
- static Logger logger = Logger.getLogger(NormalImageGenerator.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- Double scale;
- private Boolean artifitialCalled;
-
- public void setScale(Double sc) {
- scale = sc;
- }
-
- class TmpComplexConverter extends ComplexConverter {
- public TmpComplexConverter(ColorExtractor colorExtractor) {
- super(colorExtractor);
- }
-
- @Override
- public void drawText(Complex compAlias, Graphics2D graphics, ConverterParams params) {
- setScale(params.getScale());
- super.drawText(compAlias, graphics, params);
- }
-
- }
-
- private Model createCompartmentModel() {
- Model model = new ModelFullIndexed(null);
- model.setWidth(526);
- model.setHeight(346);
-
- LayerText compAlias = new LayerText();
- compAlias.setX(256.0);
- compAlias.setY(79.0);
- compAlias.setWidth(233.0);
- compAlias.setHeight(188.0);
- compAlias.setNotes("asd as");
- compAlias.setColor(Color.BLACK);
- Layer layer = new Layer();
- layer.addLayerText(compAlias);
- layer.setVisible(true);
- model.addLayer(layer);
-
- layer.addLayerLine(new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(100, 100)));
-
- Complex alias = new Complex("1");
- alias.setName("a");
- alias.setX(300);
- alias.setY(90);
- alias.setWidth(100);
- alias.setHeight(50);
- model.addElement(alias);
-
- return model;
- }
-
- @Test
- public void testArtifitialInNonHierarchicalView() throws Exception {
- scale = null;
- try {
- // TODO fix it
- // AliasConverter.addAliasConverter(PathwayCompartment.class, new
- // TmpArtifitialConverter());
-
- setArtifitialCalled(false);
- Model model = createCompartmentModel();
- new CreateHierarchyCommand(model, 2, 2).execute();
- new PngImageGenerator(new Params().scale(2).width(600).height(600).model(model));
-
- assertFalse(getArtifitialCalled());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- /**
- * @return the artifitialCalled
- * @see #artifitialCalled
- */
- public Boolean getArtifitialCalled() {
- return artifitialCalled;
- }
-
- /**
- * @param artifitialCalled
- * the artifitialCalled to set
- * @see #artifitialCalled
- */
- public void setArtifitialCalled(Boolean artifitialCalled) {
- this.artifitialCalled = artifitialCalled;
- }
-
- @Test
- public void testArtifitialInHierarchicalView() throws Exception {
- try {
- Model model = createCompartmentModel();
- Layer layer = model.getLayers().iterator().next();
-
- layer.addLayerText(new LayerText(new Rectangle2D.Double(10, 10, 500, 500), "X asd"));
- layer.addLayerText(new LayerText(new Rectangle2D.Double(20, 20, 200, 200), "Y qwe ret"));
- layer.addLayerText(new LayerText(new Rectangle2D.Double(100, 100, 199, 220), "Z dgf fsd aaewq ret"));
-
- new CreateHierarchyCommand(model, 1, 8).execute();
- model.getCompartments().get(1).setTransparencyLevel("2");
- model.getCompartments().get(0).setTransparencyLevel("2");
- model.getCompartments().get(3).setTransparencyLevel("2");
- new PngImageGenerator(new Params().level(2).scale(4).width(600).height(600).model(model).nested(true));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.graphics;
+
+import static org.junit.Assert.assertFalse;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.commands.CreateHierarchyCommand;
+import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.ComplexConverter;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.layout.graphics.LayerText;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Complex;
+
+public class NormalImageGeneratorTest {
+ static Logger logger = Logger.getLogger(NormalImageGenerator.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ Double scale;
+ private Boolean artifitialCalled;
+
+ public void setScale(Double sc) {
+ scale = sc;
+ }
+
+ class TmpComplexConverter extends ComplexConverter {
+ public TmpComplexConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
+ @Override
+ public void drawText(Complex compAlias, Graphics2D graphics, ConverterParams params) {
+ setScale(params.getScale());
+ super.drawText(compAlias, graphics, params);
+ }
+
+ }
+
+ private Model createCompartmentModel() {
+ Model model = new ModelFullIndexed(null);
+ model.setWidth(526);
+ model.setHeight(346);
+
+ LayerText compAlias = new LayerText();
+ compAlias.setX(256.0);
+ compAlias.setY(79.0);
+ compAlias.setWidth(233.0);
+ compAlias.setHeight(188.0);
+ compAlias.setNotes("asd as");
+ compAlias.setColor(Color.BLACK);
+ Layer layer = new Layer();
+ layer.addLayerText(compAlias);
+ layer.setVisible(true);
+ model.addLayer(layer);
+
+ layer.addLayerLine(new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(100, 100)));
+
+ Complex alias = new Complex("1");
+ alias.setName("a");
+ alias.setX(300);
+ alias.setY(90);
+ alias.setWidth(100);
+ alias.setHeight(50);
+ model.addElement(alias);
+
+ return model;
+ }
+
+ @Test
+ public void testArtifitialInNonHierarchicalView() throws Exception {
+ scale = null;
+ try {
+ // TODO fix it
+ // AliasConverter.addAliasConverter(PathwayCompartment.class, new
+ // TmpArtifitialConverter());
+
+ setArtifitialCalled(false);
+ Model model = createCompartmentModel();
+ new CreateHierarchyCommand(model, 2, 2).execute();
+ new PngImageGenerator(new Params().scale(2).width(600).height(600).model(model));
+
+ assertFalse(getArtifitialCalled());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ /**
+ * @return the artifitialCalled
+ * @see #artifitialCalled
+ */
+ public Boolean getArtifitialCalled() {
+ return artifitialCalled;
+ }
+
+ /**
+ * @param artifitialCalled
+ * the artifitialCalled to set
+ * @see #artifitialCalled
+ */
+ public void setArtifitialCalled(Boolean artifitialCalled) {
+ this.artifitialCalled = artifitialCalled;
+ }
+
+ @Test
+ public void testArtifitialInHierarchicalView() throws Exception {
+ try {
+ Model model = createCompartmentModel();
+ Layer layer = model.getLayers().iterator().next();
+
+ layer.addLayerText(new LayerText(new Rectangle2D.Double(10, 10, 500, 500), "X asd"));
+ layer.addLayerText(new LayerText(new Rectangle2D.Double(20, 20, 200, 200), "Y qwe ret"));
+ layer.addLayerText(new LayerText(new Rectangle2D.Double(100, 100, 199, 220), "Z dgf fsd aaewq ret"));
+
+ new CreateHierarchyCommand(model, 1, 8).execute();
+ model.getCompartments().get(1).setTransparencyLevel("2");
+ model.getCompartments().get(0).setTransparencyLevel("2");
+ model.getCompartments().get(3).setTransparencyLevel("2");
+ new PngImageGenerator(new Params().level(2).scale(4).width(600).height(600).model(model).nested(true));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/PdfImageGeneratorTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/PdfImageGeneratorTest.java
index 6109ab544d..b8785d7c89 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/PdfImageGeneratorTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/PdfImageGeneratorTest.java
@@ -1,102 +1,102 @@
-package lcsb.mapviewer.converter.graphics;
-
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.Color;
-import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
-import java.io.File;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.commands.CreateHierarchyCommand;
-import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.layout.graphics.LayerText;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.Complex;
-
-public class PdfImageGeneratorTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSaveToFile() throws Exception {
- try {
- String filename = "tmp.pdf";
-
- File f = new File(filename);
- if (f.exists()) {
- f.delete();
- }
-
- assertFalse(f.exists());
-
- Model model = createCompartmentModel();
- Layer layer = model.getLayers().iterator().next();
-
- layer.addLayerText(new LayerText(new Rectangle2D.Double(10, 10, 500, 500), "X asd"));
- layer.addLayerText(new LayerText(new Rectangle2D.Double(20, 20, 200, 200), "Y qwe ret"));
- layer.addLayerText(new LayerText(new Rectangle2D.Double(100, 100, 199, 220), "Z dgf fsd aaewq ret"));
-
- new CreateHierarchyCommand(model, 1, 8).execute();
- model.getCompartments().get(1).setTransparencyLevel("2");
- model.getCompartments().get(0).setTransparencyLevel("2");
- model.getCompartments().get(3).setTransparencyLevel("2");
-
- PdfImageGenerator pig = new PdfImageGenerator(new Params().level(2).scale(4).width(600).height(600).model(model).nested(true));
-
- pig.saveToFile("tmp.pdf");
-
- assertTrue(f.exists());
- f.delete();
- assertFalse(f.exists());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private Model createCompartmentModel() {
- Model model = new ModelFullIndexed(null);
- model.setWidth(526);
- model.setHeight(346);
-
- LayerText compAlias = new LayerText();
- compAlias.setX(256.0);
- compAlias.setY(79.0);
- compAlias.setWidth(233.0);
- compAlias.setHeight(188.0);
- compAlias.setNotes("asd as");
- compAlias.setColor(Color.BLACK);
- Layer layer = new Layer();
- layer.addLayerText(compAlias);
- layer.setVisible(true);
- model.addLayer(layer);
-
- layer.addLayerLine(new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(100, 100)));
-
- Complex alias = new Complex("1");
- alias.setName("a");
- alias.setX(300);
- alias.setY(90);
- alias.setWidth(100);
- alias.setHeight(50);
- model.addElement(alias);
-
- return model;
- }
-
-}
+package lcsb.mapviewer.converter.graphics;
+
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import java.awt.Color;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+import java.io.File;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.commands.CreateHierarchyCommand;
+import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.layout.graphics.LayerText;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Complex;
+
+public class PdfImageGeneratorTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSaveToFile() throws Exception {
+ try {
+ String filename = "tmp.pdf";
+
+ File f = new File(filename);
+ if (f.exists()) {
+ f.delete();
+ }
+
+ assertFalse(f.exists());
+
+ Model model = createCompartmentModel();
+ Layer layer = model.getLayers().iterator().next();
+
+ layer.addLayerText(new LayerText(new Rectangle2D.Double(10, 10, 500, 500), "X asd"));
+ layer.addLayerText(new LayerText(new Rectangle2D.Double(20, 20, 200, 200), "Y qwe ret"));
+ layer.addLayerText(new LayerText(new Rectangle2D.Double(100, 100, 199, 220), "Z dgf fsd aaewq ret"));
+
+ new CreateHierarchyCommand(model, 1, 8).execute();
+ model.getCompartments().get(1).setTransparencyLevel("2");
+ model.getCompartments().get(0).setTransparencyLevel("2");
+ model.getCompartments().get(3).setTransparencyLevel("2");
+
+ PdfImageGenerator pig = new PdfImageGenerator(new Params().level(2).scale(4).width(600).height(600).model(model).nested(true));
+
+ pig.saveToFile("tmp.pdf");
+
+ assertTrue(f.exists());
+ f.delete();
+ assertFalse(f.exists());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Model createCompartmentModel() {
+ Model model = new ModelFullIndexed(null);
+ model.setWidth(526);
+ model.setHeight(346);
+
+ LayerText compAlias = new LayerText();
+ compAlias.setX(256.0);
+ compAlias.setY(79.0);
+ compAlias.setWidth(233.0);
+ compAlias.setHeight(188.0);
+ compAlias.setNotes("asd as");
+ compAlias.setColor(Color.BLACK);
+ Layer layer = new Layer();
+ layer.addLayerText(compAlias);
+ layer.setVisible(true);
+ model.addLayer(layer);
+
+ layer.addLayerLine(new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(100, 100)));
+
+ Complex alias = new Complex("1");
+ alias.setName("a");
+ alias.setX(300);
+ alias.setY(90);
+ alias.setWidth(100);
+ alias.setHeight(50);
+ model.addElement(alias);
+
+ return model;
+ }
+
+}
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AllSpeciesConverterTests.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AllSpeciesConverterTests.java
index 69e9b97b05..12de6ac30b 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AllSpeciesConverterTests.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AllSpeciesConverterTests.java
@@ -1,11 +1,11 @@
-package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ SpeciesConverterTest.class })
-public class AllSpeciesConverterTests {
-
-}
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ SpeciesConverterTest.class })
+public class AllSpeciesConverterTests {
+
+}
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/AllReactionTests.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/AllReactionTests.java
index eb1ffeb4e9..57d3835f9a 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/AllReactionTests.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/AllReactionTests.java
@@ -1,11 +1,11 @@
-package lcsb.mapviewer.converter.graphics.bioEntity.reaction;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ ReactionConverterTest.class })
-public class AllReactionTests {
-
-}
+package lcsb.mapviewer.converter.graphics.bioEntity.reaction;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ ReactionConverterTest.class })
+public class AllReactionTests {
+
+}
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java
index 6c54f92d23..05b4508daa 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java
@@ -1,394 +1,394 @@
-package lcsb.mapviewer.converter.graphics.bioEntity.reaction;
-
-import static org.junit.Assert.assertTrue;
-import static org.mockito.Matchers.any;
-import static org.mockito.Mockito.times;
-import static org.mockito.Mockito.verify;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.Point2D;
-import java.awt.image.BufferedImage;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-import javax.imageio.ImageIO;
-
-import org.apache.commons.io.output.ByteArrayOutputStream;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.converter.graphics.GraphicsTestFunctions;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.layout.GenericColorSchema;
-import lcsb.mapviewer.model.map.modifier.Catalysis;
-import lcsb.mapviewer.model.map.reaction.AndOperator;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.reaction.OrOperator;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.SplitOperator;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-
-public class ReactionConverterTest extends GraphicsTestFunctions {
-
- ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testDrawReactionWithLayouts() throws Exception {
- try {
- BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
- Graphics2D graphics = bi.createGraphics();
- ReactionConverter rc = new ReactionConverter(colorExtractor);
-
- Reaction reaction = createReaction(5.0);
- rc.draw(reaction, graphics, new ConverterParams().sbgnFormat(false));
-
- ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
- ImageIO.write(bi, "PNG", outputStream);
- byte[] output1 = outputStream.toByteArray();
-
- Reaction reaction2 = createReaction(1.0);
-
- bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
- graphics = bi.createGraphics();
-
- ColorSchema schema = new GenericColorSchema();
- schema.setColor(Color.BLACK);
- schema.setLineWidth(5.0);
- List<ColorSchema> schemas = new ArrayList<>();
- schemas.add(schema);
-
- rc.draw(reaction2, graphics, new ConverterParams().sbgnFormat(false), schemas);
-
- outputStream = new ByteArrayOutputStream();
- ImageIO.write(bi, "PNG", outputStream);
- byte[] output2 = outputStream.toByteArray();
-
- // FileUtils.writeByteArrayToFile(new File("tmp.png"), output1);
- // FileUtils.writeByteArrayToFile(new File("tmp2.png"), output2);
- //
- // Desktop.getDesktop().open(new File("tmp.png"));
- // Desktop.getDesktop().open(new File("tmp2.png"));
-
- assertTrue(Arrays.equals(output1, output2));
-
- } catch (Exception e) {
- throw e;
- }
- }
-
- @Test
- public void testDrawAfterDrawingReactionWithLayouts() throws Exception {
- try {
- BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
- Graphics2D graphics = bi.createGraphics();
- ReactionConverter rc = new ReactionConverter(colorExtractor);
-
- Reaction reaction = createReaction(1.0);
- rc.draw(reaction, graphics, new ConverterParams().sbgnFormat(false));
-
- ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
- ImageIO.write(bi, "PNG", outputStream);
- byte[] output1 = outputStream.toByteArray();
-
- Reaction reaction2 = createReaction(1.0);
-
- bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
- graphics = bi.createGraphics();
-
- ColorSchema schema = new GenericColorSchema();
- schema.setColor(Color.BLACK);
- schema.setLineWidth(5.0);
- List<ColorSchema> schemas = new ArrayList<>();
- schemas.add(schema);
-
- rc.draw(reaction2, graphics, new ConverterParams().sbgnFormat(false), schemas);
- bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
- graphics = bi.createGraphics();
- rc.draw(reaction2, graphics, new ConverterParams().sbgnFormat(false), new ArrayList<>());
-
- outputStream = new ByteArrayOutputStream();
- ImageIO.write(bi, "PNG", outputStream);
- byte[] output2 = outputStream.toByteArray();
-
- // FileUtils.writeByteArrayToFile(new File("tmp.png"), output1);
- // FileUtils.writeByteArrayToFile(new File("tmp2.png"), output2);
- //
- // Desktop.getDesktop().open(new File("tmp.png"));
- // Desktop.getDesktop().open(new File("tmp2.png"));
-
- assertTrue(Arrays.equals(output1, output2));
-
- } catch (Exception e) {
- throw e;
- }
- }
-
- @Test
- public void testDrawReactionWithFewLayouts() throws Exception {
- try {
- BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
- Graphics2D graphics = bi.createGraphics();
- ReactionConverter rc = new ReactionConverter(colorExtractor);
-
- Reaction reaction = createReaction(3.0);
- rc.draw(reaction, graphics, new ConverterParams().sbgnFormat(false));
-
- ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
- ImageIO.write(bi, "PNG", outputStream);
- byte[] output1 = outputStream.toByteArray();
-
- Reaction reaction2 = createReaction(1.0);
-
- bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
- graphics = bi.createGraphics();
-
- ColorSchema schema = new GenericColorSchema();
- schema.setColor(Color.BLACK);
- schema.setLineWidth(5.0);
- List<ColorSchema> schemas = new ArrayList<>();
- schemas.add(schema);
- schemas.add(schema);
-
- rc.draw(reaction2, graphics, new ConverterParams().sbgnFormat(false), schemas);
-
- outputStream = new ByteArrayOutputStream();
- ImageIO.write(bi, "PNG", outputStream);
- byte[] output2 = outputStream.toByteArray();
-
- // FileUtils.writeByteArrayToFile(new File("tmp.png"), output1);
- // FileUtils.writeByteArrayToFile(new File("tmp2.png"), output2);
- //
- // Desktop.getDesktop().open(new File("tmp.png"));
- // Desktop.getDesktop().open(new File("tmp2.png"));
-
- assertTrue(Arrays.equals(output1, output2));
-
- } catch (Exception e) {
- throw e;
- }
- }
-
- private Reaction createReaction(double lineWidth) {
- Reaction result = new Reaction();
-
- Modifier modifier = new Catalysis(new GenericProtein("s1"));
- modifier.setLine(new PolylineData(new Point2D.Double(100, 20), new Point2D.Double(100, 80)));
- modifier.getLine().setWidth(lineWidth);
-
- Reactant reactant = new Reactant(new GenericProtein("s2"));
- reactant.setLine(new PolylineData(new Point2D.Double(90, 90), new Point2D.Double(10, 90)));
- reactant.getLine().setWidth(lineWidth);
- Product product = new Product(new GenericProtein("s3"));
- product.setLine(new PolylineData(new Point2D.Double(200, 90), new Point2D.Double(110, 90)));
- product.getLine().setWidth(lineWidth);
- result.addModifier(modifier);
- result.addProduct(product);
- result.addReactant(reactant);
- return result;
- }
-
- private Reaction createComplexReaction(double lineWidth) {
- Reaction result = new Reaction();
-
- Modifier modifier1 = new Catalysis(new GenericProtein("s1-1"));
- modifier1.setLine(new PolylineData(new Point2D.Double(80, 20), new Point2D.Double(100, 40)));
- modifier1.getLine().setWidth(lineWidth);
-
- Modifier modifier2 = new Catalysis(new GenericProtein("s1-2"));
- modifier2.setLine(new PolylineData(new Point2D.Double(120, 20), new Point2D.Double(100, 40)));
- modifier2.getLine().setWidth(lineWidth);
-
- AndOperator modifierOperator = new AndOperator();
- modifierOperator.addInput(modifier1);
- modifierOperator.addInput(modifier2);
- modifierOperator.setLine(new PolylineData(new Point2D.Double(100, 40), new Point2D.Double(100, 80)));
-
- Reactant reactant1 = new Reactant(new GenericProtein("s2-1"));
- reactant1.setLine(new PolylineData(new Point2D.Double(60, 90), new Point2D.Double(10, 70)));
- reactant1.getLine().setWidth(lineWidth);
- Reactant reactant2 = new Reactant(new GenericProtein("s2-1"));
- reactant2.setLine(new PolylineData(new Point2D.Double(60, 90), new Point2D.Double(10, 110)));
- reactant2.getLine().setWidth(lineWidth);
- OrOperator reactantOperator = new OrOperator();
- reactantOperator.addInput(reactant1);
- reactantOperator.addInput(reactant2);
- reactantOperator.setLine(new PolylineData(new Point2D.Double(60, 90), new Point2D.Double(90, 90)));
-
- Product product1 = new Product(new GenericProtein("s3-1"));
- product1.setLine(new PolylineData(new Point2D.Double(200, 70), new Point2D.Double(130, 90)));
- product1.getLine().setWidth(lineWidth);
- Product product2 = new Product(new GenericProtein("s3-2"));
- product2.setLine(new PolylineData(new Point2D.Double(200, 110), new Point2D.Double(130, 90)));
- product2.getLine().setWidth(lineWidth);
- SplitOperator productOperator = new SplitOperator();
- productOperator.addOutput(product1);
- productOperator.addOutput(product2);
- productOperator.setLine(new PolylineData(new Point2D.Double(130, 90), new Point2D.Double(110, 90)));
-
- result.addModifier(modifier1);
- result.addModifier(modifier2);
- result.addNode(modifierOperator);
- result.addProduct(product1);
- result.addProduct(product2);
- result.addNode(productOperator);
- result.addReactant(reactant1);
- result.addReactant(reactant2);
- result.addNode(reactantOperator);
- return result;
- }
-
- @Test
- public void testDrawReactionWithSemanticZooming() throws Exception {
- try {
- Graphics2D graphics = Mockito.mock(Graphics2D.class);
- ReactionConverter rc = new ReactionConverter(colorExtractor);
-
- Reaction reaction = createReaction(1.0);
- rc.draw(reaction, graphics, new ConverterParams().nested(true).level(10));
-
- verify(graphics, times(4)).draw(any(GeneralPath.class));
-
- } catch (Exception e) {
- throw e;
- }
- }
-
- @Test
- public void testDrawReactionWithSemanticZoomingAndModifierOff() throws Exception {
- try {
- Graphics2D graphics = Mockito.mock(Graphics2D.class);
- ReactionConverter rc = new ReactionConverter(colorExtractor);
-
- Reaction reaction = createReaction(1.0);
- reaction.getModifiers().get(0).getElement().setVisibilityLevel("11");
- rc.draw(reaction, graphics, new ConverterParams().nested(true).level(10));
-
- verify(graphics, times(3)).draw(any(GeneralPath.class));
-
- } catch (Exception e) {
- throw e;
- }
- }
-
- @Test
- public void testDrawReactionWithSemanticZoomingAndReactantOff() throws Exception {
- try {
- Graphics2D graphics = Mockito.mock(Graphics2D.class);
- ReactionConverter rc = new ReactionConverter(colorExtractor);
-
- Reaction reaction = createReaction(1.0);
- reaction.getReactants().get(0).getElement().setVisibilityLevel("11");
- rc.draw(reaction, graphics, new ConverterParams().nested(true).level(10));
-
- verify(graphics, times(3)).draw(any(GeneralPath.class));
-
- } catch (Exception e) {
- throw e;
- }
- }
-
- @Test
- public void testDrawReactionWithSemanticZoomingAndProductOff() throws Exception {
- try {
- Graphics2D graphics = Mockito.mock(Graphics2D.class);
- ReactionConverter rc = new ReactionConverter(colorExtractor);
-
- Reaction reaction = createReaction(1.0);
- reaction.getProducts().get(0).getElement().setVisibilityLevel("11");
- rc.draw(reaction, graphics, new ConverterParams().nested(true).level(10));
-
- verify(graphics, times(3)).draw(any(GeneralPath.class));
-
- } catch (Exception e) {
- throw e;
- }
- }
-
- @Test
- public void testDrawComplexReactionWithSemanticZoomingAndModiferOff() throws Exception {
- try {
- Graphics2D graphics = createGraphicsMock();
- ReactionConverter rc = new ReactionConverter(colorExtractor);
-
- Reaction reaction = createComplexReaction(1.0);
- reaction.getModifiers().get(0).getElement().setVisibilityLevel("11");
- rc.draw(reaction, graphics, new ConverterParams().nested(true).level(10));
-
- verify(graphics, times(12)).draw(any(GeneralPath.class));
-
- } catch (Exception e) {
- throw e;
- }
- }
-
- @Test
- public void testDrawComplexReactionWithSemanticZoomingAndAllModifersOff() throws Exception {
- try {
- Graphics2D graphics = createGraphicsMock();
- ReactionConverter rc = new ReactionConverter(colorExtractor);
-
- Reaction reaction = createComplexReaction(1.0);
- reaction.getModifiers().get(0).getElement().setVisibilityLevel("11");
- reaction.getModifiers().get(1).getElement().setVisibilityLevel("11");
- rc.draw(reaction, graphics, new ConverterParams().nested(true).level(10));
-
- verify(graphics, times(9)).draw(any(GeneralPath.class));
-
- } catch (Exception e) {
- throw e;
- }
- }
-
- @Test
- public void testDrawComplexReactionWithSemanticZoomingAndReactantOff() throws Exception {
- try {
- Graphics2D graphics = createGraphicsMock();
- ReactionConverter rc = new ReactionConverter(colorExtractor);
-
- Reaction reaction = createComplexReaction(1.0);
- reaction.getReactants().get(0).getElement().setVisibilityLevel("11");
- rc.draw(reaction, graphics, new ConverterParams().nested(true).level(10));
-
- verify(graphics, times(12)).draw(any(GeneralPath.class));
-
- } catch (Exception e) {
- throw e;
- }
- }
-
- @Test
- public void testDrawComplexReactionWithSemanticZoomingAndProductOff() throws Exception {
- try {
- Graphics2D graphics = createGraphicsMock();
- ReactionConverter rc = new ReactionConverter(colorExtractor);
-
- Reaction reaction = createComplexReaction(1.0);
- reaction.getProducts().get(0).getElement().setVisibilityLevel("11");
- rc.draw(reaction, graphics, new ConverterParams().nested(true).level(10));
-
- verify(graphics, times(12)).draw(any(GeneralPath.class));
-
- } catch (Exception e) {
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.graphics.bioEntity.reaction;
+
+import static org.junit.Assert.assertTrue;
+import static org.mockito.Matchers.any;
+import static org.mockito.Mockito.times;
+import static org.mockito.Mockito.verify;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.Point2D;
+import java.awt.image.BufferedImage;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import javax.imageio.ImageIO;
+
+import org.apache.commons.io.output.ByteArrayOutputStream;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.GraphicsTestFunctions;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.layout.GenericColorSchema;
+import lcsb.mapviewer.model.map.modifier.Catalysis;
+import lcsb.mapviewer.model.map.reaction.AndOperator;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.reaction.OrOperator;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.SplitOperator;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+
+public class ReactionConverterTest extends GraphicsTestFunctions {
+
+ ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testDrawReactionWithLayouts() throws Exception {
+ try {
+ BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
+ Graphics2D graphics = bi.createGraphics();
+ ReactionConverter rc = new ReactionConverter(colorExtractor);
+
+ Reaction reaction = createReaction(5.0);
+ rc.draw(reaction, graphics, new ConverterParams().sbgnFormat(false));
+
+ ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
+ ImageIO.write(bi, "PNG", outputStream);
+ byte[] output1 = outputStream.toByteArray();
+
+ Reaction reaction2 = createReaction(1.0);
+
+ bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
+ graphics = bi.createGraphics();
+
+ ColorSchema schema = new GenericColorSchema();
+ schema.setColor(Color.BLACK);
+ schema.setLineWidth(5.0);
+ List<ColorSchema> schemas = new ArrayList<>();
+ schemas.add(schema);
+
+ rc.draw(reaction2, graphics, new ConverterParams().sbgnFormat(false), schemas);
+
+ outputStream = new ByteArrayOutputStream();
+ ImageIO.write(bi, "PNG", outputStream);
+ byte[] output2 = outputStream.toByteArray();
+
+ // FileUtils.writeByteArrayToFile(new File("tmp.png"), output1);
+ // FileUtils.writeByteArrayToFile(new File("tmp2.png"), output2);
+ //
+ // Desktop.getDesktop().open(new File("tmp.png"));
+ // Desktop.getDesktop().open(new File("tmp2.png"));
+
+ assertTrue(Arrays.equals(output1, output2));
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDrawAfterDrawingReactionWithLayouts() throws Exception {
+ try {
+ BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
+ Graphics2D graphics = bi.createGraphics();
+ ReactionConverter rc = new ReactionConverter(colorExtractor);
+
+ Reaction reaction = createReaction(1.0);
+ rc.draw(reaction, graphics, new ConverterParams().sbgnFormat(false));
+
+ ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
+ ImageIO.write(bi, "PNG", outputStream);
+ byte[] output1 = outputStream.toByteArray();
+
+ Reaction reaction2 = createReaction(1.0);
+
+ bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
+ graphics = bi.createGraphics();
+
+ ColorSchema schema = new GenericColorSchema();
+ schema.setColor(Color.BLACK);
+ schema.setLineWidth(5.0);
+ List<ColorSchema> schemas = new ArrayList<>();
+ schemas.add(schema);
+
+ rc.draw(reaction2, graphics, new ConverterParams().sbgnFormat(false), schemas);
+ bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
+ graphics = bi.createGraphics();
+ rc.draw(reaction2, graphics, new ConverterParams().sbgnFormat(false), new ArrayList<>());
+
+ outputStream = new ByteArrayOutputStream();
+ ImageIO.write(bi, "PNG", outputStream);
+ byte[] output2 = outputStream.toByteArray();
+
+ // FileUtils.writeByteArrayToFile(new File("tmp.png"), output1);
+ // FileUtils.writeByteArrayToFile(new File("tmp2.png"), output2);
+ //
+ // Desktop.getDesktop().open(new File("tmp.png"));
+ // Desktop.getDesktop().open(new File("tmp2.png"));
+
+ assertTrue(Arrays.equals(output1, output2));
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDrawReactionWithFewLayouts() throws Exception {
+ try {
+ BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
+ Graphics2D graphics = bi.createGraphics();
+ ReactionConverter rc = new ReactionConverter(colorExtractor);
+
+ Reaction reaction = createReaction(3.0);
+ rc.draw(reaction, graphics, new ConverterParams().sbgnFormat(false));
+
+ ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
+ ImageIO.write(bi, "PNG", outputStream);
+ byte[] output1 = outputStream.toByteArray();
+
+ Reaction reaction2 = createReaction(1.0);
+
+ bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
+ graphics = bi.createGraphics();
+
+ ColorSchema schema = new GenericColorSchema();
+ schema.setColor(Color.BLACK);
+ schema.setLineWidth(5.0);
+ List<ColorSchema> schemas = new ArrayList<>();
+ schemas.add(schema);
+ schemas.add(schema);
+
+ rc.draw(reaction2, graphics, new ConverterParams().sbgnFormat(false), schemas);
+
+ outputStream = new ByteArrayOutputStream();
+ ImageIO.write(bi, "PNG", outputStream);
+ byte[] output2 = outputStream.toByteArray();
+
+ // FileUtils.writeByteArrayToFile(new File("tmp.png"), output1);
+ // FileUtils.writeByteArrayToFile(new File("tmp2.png"), output2);
+ //
+ // Desktop.getDesktop().open(new File("tmp.png"));
+ // Desktop.getDesktop().open(new File("tmp2.png"));
+
+ assertTrue(Arrays.equals(output1, output2));
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ private Reaction createReaction(double lineWidth) {
+ Reaction result = new Reaction();
+
+ Modifier modifier = new Catalysis(new GenericProtein("s1"));
+ modifier.setLine(new PolylineData(new Point2D.Double(100, 20), new Point2D.Double(100, 80)));
+ modifier.getLine().setWidth(lineWidth);
+
+ Reactant reactant = new Reactant(new GenericProtein("s2"));
+ reactant.setLine(new PolylineData(new Point2D.Double(90, 90), new Point2D.Double(10, 90)));
+ reactant.getLine().setWidth(lineWidth);
+ Product product = new Product(new GenericProtein("s3"));
+ product.setLine(new PolylineData(new Point2D.Double(200, 90), new Point2D.Double(110, 90)));
+ product.getLine().setWidth(lineWidth);
+ result.addModifier(modifier);
+ result.addProduct(product);
+ result.addReactant(reactant);
+ return result;
+ }
+
+ private Reaction createComplexReaction(double lineWidth) {
+ Reaction result = new Reaction();
+
+ Modifier modifier1 = new Catalysis(new GenericProtein("s1-1"));
+ modifier1.setLine(new PolylineData(new Point2D.Double(80, 20), new Point2D.Double(100, 40)));
+ modifier1.getLine().setWidth(lineWidth);
+
+ Modifier modifier2 = new Catalysis(new GenericProtein("s1-2"));
+ modifier2.setLine(new PolylineData(new Point2D.Double(120, 20), new Point2D.Double(100, 40)));
+ modifier2.getLine().setWidth(lineWidth);
+
+ AndOperator modifierOperator = new AndOperator();
+ modifierOperator.addInput(modifier1);
+ modifierOperator.addInput(modifier2);
+ modifierOperator.setLine(new PolylineData(new Point2D.Double(100, 40), new Point2D.Double(100, 80)));
+
+ Reactant reactant1 = new Reactant(new GenericProtein("s2-1"));
+ reactant1.setLine(new PolylineData(new Point2D.Double(60, 90), new Point2D.Double(10, 70)));
+ reactant1.getLine().setWidth(lineWidth);
+ Reactant reactant2 = new Reactant(new GenericProtein("s2-1"));
+ reactant2.setLine(new PolylineData(new Point2D.Double(60, 90), new Point2D.Double(10, 110)));
+ reactant2.getLine().setWidth(lineWidth);
+ OrOperator reactantOperator = new OrOperator();
+ reactantOperator.addInput(reactant1);
+ reactantOperator.addInput(reactant2);
+ reactantOperator.setLine(new PolylineData(new Point2D.Double(60, 90), new Point2D.Double(90, 90)));
+
+ Product product1 = new Product(new GenericProtein("s3-1"));
+ product1.setLine(new PolylineData(new Point2D.Double(200, 70), new Point2D.Double(130, 90)));
+ product1.getLine().setWidth(lineWidth);
+ Product product2 = new Product(new GenericProtein("s3-2"));
+ product2.setLine(new PolylineData(new Point2D.Double(200, 110), new Point2D.Double(130, 90)));
+ product2.getLine().setWidth(lineWidth);
+ SplitOperator productOperator = new SplitOperator();
+ productOperator.addOutput(product1);
+ productOperator.addOutput(product2);
+ productOperator.setLine(new PolylineData(new Point2D.Double(130, 90), new Point2D.Double(110, 90)));
+
+ result.addModifier(modifier1);
+ result.addModifier(modifier2);
+ result.addNode(modifierOperator);
+ result.addProduct(product1);
+ result.addProduct(product2);
+ result.addNode(productOperator);
+ result.addReactant(reactant1);
+ result.addReactant(reactant2);
+ result.addNode(reactantOperator);
+ return result;
+ }
+
+ @Test
+ public void testDrawReactionWithSemanticZooming() throws Exception {
+ try {
+ Graphics2D graphics = Mockito.mock(Graphics2D.class);
+ ReactionConverter rc = new ReactionConverter(colorExtractor);
+
+ Reaction reaction = createReaction(1.0);
+ rc.draw(reaction, graphics, new ConverterParams().nested(true).level(10));
+
+ verify(graphics, times(4)).draw(any(GeneralPath.class));
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDrawReactionWithSemanticZoomingAndModifierOff() throws Exception {
+ try {
+ Graphics2D graphics = Mockito.mock(Graphics2D.class);
+ ReactionConverter rc = new ReactionConverter(colorExtractor);
+
+ Reaction reaction = createReaction(1.0);
+ reaction.getModifiers().get(0).getElement().setVisibilityLevel("11");
+ rc.draw(reaction, graphics, new ConverterParams().nested(true).level(10));
+
+ verify(graphics, times(3)).draw(any(GeneralPath.class));
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDrawReactionWithSemanticZoomingAndReactantOff() throws Exception {
+ try {
+ Graphics2D graphics = Mockito.mock(Graphics2D.class);
+ ReactionConverter rc = new ReactionConverter(colorExtractor);
+
+ Reaction reaction = createReaction(1.0);
+ reaction.getReactants().get(0).getElement().setVisibilityLevel("11");
+ rc.draw(reaction, graphics, new ConverterParams().nested(true).level(10));
+
+ verify(graphics, times(3)).draw(any(GeneralPath.class));
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDrawReactionWithSemanticZoomingAndProductOff() throws Exception {
+ try {
+ Graphics2D graphics = Mockito.mock(Graphics2D.class);
+ ReactionConverter rc = new ReactionConverter(colorExtractor);
+
+ Reaction reaction = createReaction(1.0);
+ reaction.getProducts().get(0).getElement().setVisibilityLevel("11");
+ rc.draw(reaction, graphics, new ConverterParams().nested(true).level(10));
+
+ verify(graphics, times(3)).draw(any(GeneralPath.class));
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDrawComplexReactionWithSemanticZoomingAndModiferOff() throws Exception {
+ try {
+ Graphics2D graphics = createGraphicsMock();
+ ReactionConverter rc = new ReactionConverter(colorExtractor);
+
+ Reaction reaction = createComplexReaction(1.0);
+ reaction.getModifiers().get(0).getElement().setVisibilityLevel("11");
+ rc.draw(reaction, graphics, new ConverterParams().nested(true).level(10));
+
+ verify(graphics, times(12)).draw(any(GeneralPath.class));
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDrawComplexReactionWithSemanticZoomingAndAllModifersOff() throws Exception {
+ try {
+ Graphics2D graphics = createGraphicsMock();
+ ReactionConverter rc = new ReactionConverter(colorExtractor);
+
+ Reaction reaction = createComplexReaction(1.0);
+ reaction.getModifiers().get(0).getElement().setVisibilityLevel("11");
+ reaction.getModifiers().get(1).getElement().setVisibilityLevel("11");
+ rc.draw(reaction, graphics, new ConverterParams().nested(true).level(10));
+
+ verify(graphics, times(9)).draw(any(GeneralPath.class));
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDrawComplexReactionWithSemanticZoomingAndReactantOff() throws Exception {
+ try {
+ Graphics2D graphics = createGraphicsMock();
+ ReactionConverter rc = new ReactionConverter(colorExtractor);
+
+ Reaction reaction = createComplexReaction(1.0);
+ reaction.getReactants().get(0).getElement().setVisibilityLevel("11");
+ rc.draw(reaction, graphics, new ConverterParams().nested(true).level(10));
+
+ verify(graphics, times(12)).draw(any(GeneralPath.class));
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDrawComplexReactionWithSemanticZoomingAndProductOff() throws Exception {
+ try {
+ Graphics2D graphics = createGraphicsMock();
+ ReactionConverter rc = new ReactionConverter(colorExtractor);
+
+ Reaction reaction = createComplexReaction(1.0);
+ reaction.getProducts().get(0).getElement().setVisibilityLevel("11");
+ rc.draw(reaction, graphics, new ConverterParams().nested(true).level(10));
+
+ verify(graphics, times(12)).draw(any(GeneralPath.class));
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/geometry/AllGeometryTests.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/geometry/AllGeometryTests.java
index 35098e610f..f7310c88fe 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/geometry/AllGeometryTests.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/geometry/AllGeometryTests.java
@@ -1,11 +1,11 @@
-package lcsb.mapviewer.converter.graphics.geometry;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ FontFinderTest.class, ArrowTransformationTest.class })
-public class AllGeometryTests {
-
-}
+package lcsb.mapviewer.converter.graphics.geometry;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ FontFinderTest.class, ArrowTransformationTest.class })
+public class AllGeometryTests {
+
+}
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/geometry/ArrowTransformationTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/geometry/ArrowTransformationTest.java
index e83a261227..32e10229a8 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/geometry/ArrowTransformationTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/geometry/ArrowTransformationTest.java
@@ -1,59 +1,59 @@
-package lcsb.mapviewer.converter.graphics.geometry;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.geom.Point2D;
-import java.awt.image.BufferedImage;
-
-import lcsb.mapviewer.model.graphics.ArrowType;
-import lcsb.mapviewer.model.graphics.PolylineData;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ArrowTransformationTest {
-
- ArrowTransformation at = new ArrowTransformation();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testDrawingArrows() throws Exception {
- try {
- int coordX = 0;
- int coordY = 10;
- int height = 60;
-
- for (ArrowType type : ArrowType.values()) {
- BufferedImage bi = new BufferedImage((int) 65, (int) 20, BufferedImage.TYPE_INT_ARGB);
- Graphics2D graphics = bi.createGraphics();
-
-// graphics.fill(new Rectangle2D.Double(0, 0, 100, 40));
- graphics.setColor(Color.BLACK);
-
- PolylineData pd = new PolylineData(new Point2D.Double(coordX, coordY), new Point2D.Double(coordX + height, coordY));
- pd.getEndAtd().setArrowType(type);
- at.drawLine(pd, graphics);
-
-// FileOutputStream fos = new FileOutputStream(new File(type.name() + ".png"));
-// ImageIO.write(bi, "PNG", fos);
-// fos.close();
-//
-// Desktop.getDesktop().open(new File(type.name() + ".png"));
-
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.graphics.geometry;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.geom.Point2D;
+import java.awt.image.BufferedImage;
+
+import lcsb.mapviewer.model.graphics.ArrowType;
+import lcsb.mapviewer.model.graphics.PolylineData;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ArrowTransformationTest {
+
+ ArrowTransformation at = new ArrowTransformation();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testDrawingArrows() throws Exception {
+ try {
+ int coordX = 0;
+ int coordY = 10;
+ int height = 60;
+
+ for (ArrowType type : ArrowType.values()) {
+ BufferedImage bi = new BufferedImage((int) 65, (int) 20, BufferedImage.TYPE_INT_ARGB);
+ Graphics2D graphics = bi.createGraphics();
+
+// graphics.fill(new Rectangle2D.Double(0, 0, 100, 40));
+ graphics.setColor(Color.BLACK);
+
+ PolylineData pd = new PolylineData(new Point2D.Double(coordX, coordY), new Point2D.Double(coordX + height, coordY));
+ pd.getEndAtd().setArrowType(type);
+ at.drawLine(pd, graphics);
+
+// FileOutputStream fos = new FileOutputStream(new File(type.name() + ".png"));
+// ImageIO.write(bi, "PNG", fos);
+// fos.close();
+//
+// Desktop.getDesktop().open(new File(type.name() + ".png"));
+
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/geometry/FontFinderTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/geometry/FontFinderTest.java
index 1acd2cf74b..9d77bdff06 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/geometry/FontFinderTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/geometry/FontFinderTest.java
@@ -1,145 +1,145 @@
-package lcsb.mapviewer.converter.graphics.geometry;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.Graphics2D;
-import java.awt.geom.Rectangle2D;
-import java.awt.image.BufferedImage;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class FontFinderTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testFindFontSize1() throws Exception {
- try {
- String text = "Some text to write";
- int coordX = 20;
- int coordY = 40;
- int height = 20;
-
- BufferedImage bi = new BufferedImage((int) 400, (int) 400, BufferedImage.TYPE_INT_ARGB);
- Graphics2D graphics = bi.createGraphics();
- graphics.fill(new Rectangle2D.Double(0, 0, 400, 400));
-
- Rectangle2D border = new Rectangle2D.Double(coordX, coordY, 100, height);
-
- double size = FontFinder.findMaxFontSize(13, Font.SANS_SERIF, graphics, border, text);
-
- assertTrue(size < 13);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testFindFontSize2() throws Exception {
- try {
- String text = "Some text to write";
- int coordX = 20;
- int coordY = 40;
- int height = 60;
-
- BufferedImage bi = new BufferedImage((int) 400, (int) 400, BufferedImage.TYPE_INT_ARGB);
- Graphics2D graphics = bi.createGraphics();
- graphics.fill(new Rectangle2D.Double(0, 0, 400, 400));
-
- Rectangle2D border = new Rectangle2D.Double(coordX, coordY, 100, height);
-
- double size = FontFinder.findMaxFontSize(20, Font.SANS_SERIF, graphics, border, text);
-
- graphics.setColor(Color.BLACK);
- graphics.draw(border);
- // graphics.setFont(new Font(Font.SANS_SERIF, 0, (int) size));
- FontFinder.drawText((int) size, Font.SANS_SERIF, graphics, border, text);
-
- // graphics.drawString(text, coordX, coordY + height);
- //
- // FileOutputStream fos = new FileOutputStream(new File("tmp.png"));
- // ImageIO.write(bi, "PNG", fos);
- // fos.close();
- //
- // Desktop.getDesktop().open(new File("tmp.png"));
-
- //different os compute it differnetly ...
- assertTrue(size>18);
- assertTrue(size<=20);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testFindFontSize3() throws Exception {
- try {
- String text = "Some\ntext\n to write";
- int coordX = 20;
- int coordY = 40;
- int height = 60;
-
- BufferedImage bi = new BufferedImage((int) 400, (int) 400, BufferedImage.TYPE_INT_ARGB);
- Graphics2D graphics = bi.createGraphics();
- graphics.fill(new Rectangle2D.Double(0, 0, 400, 400));
-
- Rectangle2D border = new Rectangle2D.Double(coordX, coordY, 100, height);
-
- double size = FontFinder.findMaxFontSize(20, Font.SANS_SERIF, graphics, border, text);
-
- graphics.setColor(Color.BLACK);
- graphics.draw(border);
- // graphics.setFont(new Font(Font.SANS_SERIF, 0, (int) size));
- FontFinder.drawText((int) size, Font.SANS_SERIF, graphics, border, text);
-
- assertTrue(size < 20);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testFindFontSize4() throws Exception {
- try {
- String text = "";
- int coordX = 20;
- int coordY = 40;
- int height = 60;
-
- BufferedImage bi = new BufferedImage((int) 400, (int) 400, BufferedImage.TYPE_INT_ARGB);
- Graphics2D graphics = bi.createGraphics();
- graphics.fill(new Rectangle2D.Double(0, 0, 400, 400));
-
- Rectangle2D border = new Rectangle2D.Double(coordX, coordY, 100, height);
-
- double size = FontFinder.findMaxFontSize(20, Font.SANS_SERIF, graphics, border, text);
-
- assertEquals(20, (int) size);
- size = FontFinder.findMaxFontSize(20, Font.SANS_SERIF, graphics, border, " ");
-
- assertEquals(20, (int) size);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
-}
+package lcsb.mapviewer.converter.graphics.geometry;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Graphics2D;
+import java.awt.geom.Rectangle2D;
+import java.awt.image.BufferedImage;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class FontFinderTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testFindFontSize1() throws Exception {
+ try {
+ String text = "Some text to write";
+ int coordX = 20;
+ int coordY = 40;
+ int height = 20;
+
+ BufferedImage bi = new BufferedImage((int) 400, (int) 400, BufferedImage.TYPE_INT_ARGB);
+ Graphics2D graphics = bi.createGraphics();
+ graphics.fill(new Rectangle2D.Double(0, 0, 400, 400));
+
+ Rectangle2D border = new Rectangle2D.Double(coordX, coordY, 100, height);
+
+ double size = FontFinder.findMaxFontSize(13, Font.SANS_SERIF, graphics, border, text);
+
+ assertTrue(size < 13);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testFindFontSize2() throws Exception {
+ try {
+ String text = "Some text to write";
+ int coordX = 20;
+ int coordY = 40;
+ int height = 60;
+
+ BufferedImage bi = new BufferedImage((int) 400, (int) 400, BufferedImage.TYPE_INT_ARGB);
+ Graphics2D graphics = bi.createGraphics();
+ graphics.fill(new Rectangle2D.Double(0, 0, 400, 400));
+
+ Rectangle2D border = new Rectangle2D.Double(coordX, coordY, 100, height);
+
+ double size = FontFinder.findMaxFontSize(20, Font.SANS_SERIF, graphics, border, text);
+
+ graphics.setColor(Color.BLACK);
+ graphics.draw(border);
+ // graphics.setFont(new Font(Font.SANS_SERIF, 0, (int) size));
+ FontFinder.drawText((int) size, Font.SANS_SERIF, graphics, border, text);
+
+ // graphics.drawString(text, coordX, coordY + height);
+ //
+ // FileOutputStream fos = new FileOutputStream(new File("tmp.png"));
+ // ImageIO.write(bi, "PNG", fos);
+ // fos.close();
+ //
+ // Desktop.getDesktop().open(new File("tmp.png"));
+
+ //different os compute it differnetly ...
+ assertTrue(size>18);
+ assertTrue(size<=20);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testFindFontSize3() throws Exception {
+ try {
+ String text = "Some\ntext\n to write";
+ int coordX = 20;
+ int coordY = 40;
+ int height = 60;
+
+ BufferedImage bi = new BufferedImage((int) 400, (int) 400, BufferedImage.TYPE_INT_ARGB);
+ Graphics2D graphics = bi.createGraphics();
+ graphics.fill(new Rectangle2D.Double(0, 0, 400, 400));
+
+ Rectangle2D border = new Rectangle2D.Double(coordX, coordY, 100, height);
+
+ double size = FontFinder.findMaxFontSize(20, Font.SANS_SERIF, graphics, border, text);
+
+ graphics.setColor(Color.BLACK);
+ graphics.draw(border);
+ // graphics.setFont(new Font(Font.SANS_SERIF, 0, (int) size));
+ FontFinder.drawText((int) size, Font.SANS_SERIF, graphics, border, text);
+
+ assertTrue(size < 20);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testFindFontSize4() throws Exception {
+ try {
+ String text = "";
+ int coordX = 20;
+ int coordY = 40;
+ int height = 60;
+
+ BufferedImage bi = new BufferedImage((int) 400, (int) 400, BufferedImage.TYPE_INT_ARGB);
+ Graphics2D graphics = bi.createGraphics();
+ graphics.fill(new Rectangle2D.Double(0, 0, 400, 400));
+
+ Rectangle2D border = new Rectangle2D.Double(coordX, coordY, 100, height);
+
+ double size = FontFinder.findMaxFontSize(20, Font.SANS_SERIF, graphics, border, text);
+
+ assertEquals(20, (int) size);
+ size = FontFinder.findMaxFontSize(20, Font.SANS_SERIF, graphics, border, " ");
+
+ assertEquals(20, (int) size);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+}
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/placefinder/AllPlaceFinderTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/placefinder/AllPlaceFinderTest.java
index de5f85db23..3ab34b1d27 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/placefinder/AllPlaceFinderTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/placefinder/AllPlaceFinderTest.java
@@ -1,147 +1,147 @@
-package lcsb.mapviewer.converter.graphics.placefinder;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.geom.Rectangle2D;
-import java.io.IOException;
-import java.util.Arrays;
-
-import org.apache.log4j.Logger;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.compartment.SquareCompartment;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-
-public class AllPlaceFinderTest {
- Logger logger = Logger.getLogger(AllPlaceFinderTest.class);
- final String out = "map_images/testOutput";
- final String folder = "testFiles/placeFinderFiles/";
-
- int id = 10;
-
- @Test
- public void oneEmptyCompartments() throws InvalidXmlSchemaException, IOException {
- String actual = null;
- Model model = new ModelFullIndexed(null);
- model.addElement(createCompartmentAlias(94.0, 70.0, 355.0, 173.0));
-
- for (Compartment alias : model.getCompartments()) {
- PlaceFinder pf = new PlaceFinder(model);
- actual = pf.getRetangle(alias, Integer.valueOf(alias.getVisibilityLevel())).toString();
- }
- String expected = "";
- Rectangle2D result = model.getCompartments().get(0).getBorder();
- expected = result.toString();
- assertEquals(expected, actual);
- }
-
- @Test
- public void twoSeparatedCompartments() throws InvalidXmlSchemaException, IOException {
- String actual = null;
- Model model = new ModelFullIndexed(null);
- model.addElement(createCompartmentAlias(70.0, 81.0, 229.0, 213.0));
- model.addElement(createCompartmentAlias(332.0, 66.0, 188.0, 255.0));
-
- String expected = "";
- for (Compartment alias : model.getCompartments()) {
- PlaceFinder pf = new PlaceFinder(model);
- actual = pf.getRetangle(alias, Integer.valueOf(alias.getVisibilityLevel())).toString();
- Rectangle2D result = alias.getBorder();
- expected = result.toString();
- assertEquals(expected, actual);
- }
- }
-
- @Test
- public void twoIntersectingCompartments() throws InvalidXmlSchemaException, IOException {
- Model model = new ModelFullIndexed(null);
- Compartment alias = createCompartmentAlias(87.0, 56.0, 235.0, 219.0);
- model.addElement(alias);
- Compartment alias2 = createCompartmentAlias(227.0, 17.0, 290.0, 317.0);
- model.addElement(alias2);
-
- PlaceFinder pf = new PlaceFinder(model);
- Rectangle2D rect = pf.getRetangle(alias2, Integer.valueOf(alias.getVisibilityLevel()));
- double actual = rect.getWidth() * rect.getHeight();
- double expected = alias2.getWidth() * alias2.getHeight();
- assertTrue(actual < expected);
- }
-
- @Test
- public void oneCompartmentCompletlyOverlapSecondOne() throws InvalidXmlSchemaException, IOException {
- Model model = new ModelFullIndexed(null);
- model.addElement(createCompartmentAlias(45.0, 38.0, 174.0, 169.0));
- model.addElement(createCompartmentAlias(118.0, 85.0, 60.0, 68.0));
- double actual = 0.0;
- for (Compartment alias : model.getCompartments()) {
- PlaceFinder pf = new PlaceFinder(model);
- Rectangle2D rect = pf.getRetangle(alias, Integer.valueOf(alias.getVisibilityLevel()));
- actual = rect.getWidth() * rect.getHeight();
- assertTrue(actual > 0);
- }
- }
-
- @Test
- public void perfectOverlapingOfThreeCompartments() throws InvalidXmlSchemaException, IOException {
- Model model = new ModelFullIndexed(null);
- model.addElement(createCompartmentAlias(226.0, 70.0, 138.0, 112.0));
- model.addElement(createCompartmentAlias(163.0, 70.0, 138.0, 112.0));
- model.addElement(createCompartmentAlias(88.0, 70.0, 138.0, 112.0));
- double actual = 0.0;
- Rectangle2D result = null;
- for (Compartment alias : model.getCompartments()) {
- PlaceFinder pf = new PlaceFinder(model);
- Rectangle2D rect = pf.getRetangle(alias, Integer.valueOf(alias.getVisibilityLevel()));
- actual += rect.getWidth() * rect.getHeight();
- }
- result = model.getCompartments().get(0).getBorder();
- assertEquals(result.getWidth() * result.getHeight(), actual, 0.01);
- }
-
- boolean equals(boolean[][] a, boolean[][] b) {
- int ax = a.length;
- int bx = b.length;
- // logger.debug("Length of second table is " + bx);
- boolean tru = false;
- if (ax == bx) {
- tru = true;
- for (int i = 0; i < ax; i++) {
- if (!Arrays.equals(a[i], b[i])) {
- tru = false;
- }
- }
- }
- return tru;
- }
-
- private Compartment createCompartmentAlias(double x, double y, double width, double height) {
- Compartment result = new SquareCompartment("" + id++);
- result.setX(x);
- result.setY(y);
- result.setWidth(width);
- result.setHeight(height);
- result.setTransparencyLevel("10");
- result.setVisibilityLevel("9");
-
- return result;
- }
-
- @Test
- public void problematic() throws InvalidXmlSchemaException, IOException {
- Model model = new ModelFullIndexed(null);
- model.addElement(createCompartmentAlias(4521.0, 0.0, 10000.0, 6000.0));
- model.addElement(createCompartmentAlias(4828.0, 0.0, 5172.0, 6000.0));
- double actual = 0.0;
- for (Compartment alias : model.getCompartments()) {
- PlaceFinder pf = new PlaceFinder(model);
- Rectangle2D rect = pf.getRetangle(alias, Integer.valueOf(alias.getVisibilityLevel()));
- actual = rect.getWidth() * rect.getHeight();
- assertTrue(actual > 0);
- }
- }
-
-}
+package lcsb.mapviewer.converter.graphics.placefinder;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.awt.geom.Rectangle2D;
+import java.io.IOException;
+import java.util.Arrays;
+
+import org.apache.log4j.Logger;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.SquareCompartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+
+public class AllPlaceFinderTest {
+ Logger logger = Logger.getLogger(AllPlaceFinderTest.class);
+ final String out = "map_images/testOutput";
+ final String folder = "testFiles/placeFinderFiles/";
+
+ int id = 10;
+
+ @Test
+ public void oneEmptyCompartments() throws InvalidXmlSchemaException, IOException {
+ String actual = null;
+ Model model = new ModelFullIndexed(null);
+ model.addElement(createCompartmentAlias(94.0, 70.0, 355.0, 173.0));
+
+ for (Compartment alias : model.getCompartments()) {
+ PlaceFinder pf = new PlaceFinder(model);
+ actual = pf.getRetangle(alias, Integer.valueOf(alias.getVisibilityLevel())).toString();
+ }
+ String expected = "";
+ Rectangle2D result = model.getCompartments().get(0).getBorder();
+ expected = result.toString();
+ assertEquals(expected, actual);
+ }
+
+ @Test
+ public void twoSeparatedCompartments() throws InvalidXmlSchemaException, IOException {
+ String actual = null;
+ Model model = new ModelFullIndexed(null);
+ model.addElement(createCompartmentAlias(70.0, 81.0, 229.0, 213.0));
+ model.addElement(createCompartmentAlias(332.0, 66.0, 188.0, 255.0));
+
+ String expected = "";
+ for (Compartment alias : model.getCompartments()) {
+ PlaceFinder pf = new PlaceFinder(model);
+ actual = pf.getRetangle(alias, Integer.valueOf(alias.getVisibilityLevel())).toString();
+ Rectangle2D result = alias.getBorder();
+ expected = result.toString();
+ assertEquals(expected, actual);
+ }
+ }
+
+ @Test
+ public void twoIntersectingCompartments() throws InvalidXmlSchemaException, IOException {
+ Model model = new ModelFullIndexed(null);
+ Compartment alias = createCompartmentAlias(87.0, 56.0, 235.0, 219.0);
+ model.addElement(alias);
+ Compartment alias2 = createCompartmentAlias(227.0, 17.0, 290.0, 317.0);
+ model.addElement(alias2);
+
+ PlaceFinder pf = new PlaceFinder(model);
+ Rectangle2D rect = pf.getRetangle(alias2, Integer.valueOf(alias.getVisibilityLevel()));
+ double actual = rect.getWidth() * rect.getHeight();
+ double expected = alias2.getWidth() * alias2.getHeight();
+ assertTrue(actual < expected);
+ }
+
+ @Test
+ public void oneCompartmentCompletlyOverlapSecondOne() throws InvalidXmlSchemaException, IOException {
+ Model model = new ModelFullIndexed(null);
+ model.addElement(createCompartmentAlias(45.0, 38.0, 174.0, 169.0));
+ model.addElement(createCompartmentAlias(118.0, 85.0, 60.0, 68.0));
+ double actual = 0.0;
+ for (Compartment alias : model.getCompartments()) {
+ PlaceFinder pf = new PlaceFinder(model);
+ Rectangle2D rect = pf.getRetangle(alias, Integer.valueOf(alias.getVisibilityLevel()));
+ actual = rect.getWidth() * rect.getHeight();
+ assertTrue(actual > 0);
+ }
+ }
+
+ @Test
+ public void perfectOverlapingOfThreeCompartments() throws InvalidXmlSchemaException, IOException {
+ Model model = new ModelFullIndexed(null);
+ model.addElement(createCompartmentAlias(226.0, 70.0, 138.0, 112.0));
+ model.addElement(createCompartmentAlias(163.0, 70.0, 138.0, 112.0));
+ model.addElement(createCompartmentAlias(88.0, 70.0, 138.0, 112.0));
+ double actual = 0.0;
+ Rectangle2D result = null;
+ for (Compartment alias : model.getCompartments()) {
+ PlaceFinder pf = new PlaceFinder(model);
+ Rectangle2D rect = pf.getRetangle(alias, Integer.valueOf(alias.getVisibilityLevel()));
+ actual += rect.getWidth() * rect.getHeight();
+ }
+ result = model.getCompartments().get(0).getBorder();
+ assertEquals(result.getWidth() * result.getHeight(), actual, 0.01);
+ }
+
+ boolean equals(boolean[][] a, boolean[][] b) {
+ int ax = a.length;
+ int bx = b.length;
+ // logger.debug("Length of second table is " + bx);
+ boolean tru = false;
+ if (ax == bx) {
+ tru = true;
+ for (int i = 0; i < ax; i++) {
+ if (!Arrays.equals(a[i], b[i])) {
+ tru = false;
+ }
+ }
+ }
+ return tru;
+ }
+
+ private Compartment createCompartmentAlias(double x, double y, double width, double height) {
+ Compartment result = new SquareCompartment("" + id++);
+ result.setX(x);
+ result.setY(y);
+ result.setWidth(width);
+ result.setHeight(height);
+ result.setTransparencyLevel("10");
+ result.setVisibilityLevel("9");
+
+ return result;
+ }
+
+ @Test
+ public void problematic() throws InvalidXmlSchemaException, IOException {
+ Model model = new ModelFullIndexed(null);
+ model.addElement(createCompartmentAlias(4521.0, 0.0, 10000.0, 6000.0));
+ model.addElement(createCompartmentAlias(4828.0, 0.0, 5172.0, 6000.0));
+ double actual = 0.0;
+ for (Compartment alias : model.getCompartments()) {
+ PlaceFinder pf = new PlaceFinder(model);
+ Rectangle2D rect = pf.getRetangle(alias, Integer.valueOf(alias.getVisibilityLevel()));
+ actual = rect.getWidth() * rect.getHeight();
+ assertTrue(actual > 0);
+ }
+ }
+
+}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlParserTest.java
index 026f607a24..409a17a491 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlParserTest.java
@@ -1,104 +1,104 @@
-package lcsb.mapviewer.converter.model.sbml;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-
-import java.io.ByteArrayInputStream;
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.util.ArrayList;
-import java.util.Collection;
-
-import org.apache.commons.io.FileUtils;
-import org.apache.log4j.Logger;
-import org.junit.Test;
-import org.junit.runner.RunWith;
-import org.junit.runners.Parameterized;
-import org.junit.runners.Parameterized.Parameters;
-
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.IConverter;
-import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
-import lcsb.mapviewer.converter.graphics.NormalImageGenerator;
-import lcsb.mapviewer.converter.graphics.PngImageGenerator;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-
-@RunWith(Parameterized.class)
-public class GenericSbmlParserTest {
-
- static Logger logger = Logger.getLogger(GenericSbmlParserTest.class.getName());
-
- private Path filePath;
-
- public GenericSbmlParserTest(Path filePath) {
- this.filePath = filePath;
- }
-
- @Parameters(name = "{index} : {0}")
- public static Collection<Object[]> data() throws IOException {
- Collection<Object[]> data = new ArrayList<Object[]>();
- Files.walk(Paths.get("testFiles/layoutExample")).forEach(fPath -> {
- if (Files.isRegularFile(fPath) && fPath.toString().endsWith(".xml")) {
- data.add(new Object[] { fPath });
- }
- });
- Files.walk(Paths.get("testFiles/invalidButParseable")).forEach(fPath -> {
- if (Files.isRegularFile(fPath) && fPath.toString().endsWith(".xml")) {
- data.add(new Object[] { fPath });
- }
- });
- return data;
- }
-
- @Test
- public void createModelTest() throws Exception {
- try {
- String dir = Files.createTempDirectory("sbml-temp-images-dir").toFile().getAbsolutePath();
-
- IConverter converter = new SbmlParser();
-
- Model model = converter.createModel(new ConverterParams().filename(filePath.toString()));
- model.setName(null);
-
- // Create and display image of parsed map
- AbstractImageGenerator.Params params = new AbstractImageGenerator.Params().height(model.getHeight())
- .width(model.getWidth()).nested(true).scale(1).level(20).x(0).y(0).model(model);
- NormalImageGenerator nig = new PngImageGenerator(params);
- String pathWithouExtension = dir + "/"
- + filePath.getFileName().toString().substring(0, filePath.getFileName().toString().indexOf(".xml"));
- String pngFilePath = pathWithouExtension.concat(".png");
- nig.saveToFile(pngFilePath);
- // Desktop.getDesktop().open(new File(pngFilePath));
-
- CellDesignerXmlParser cellDesignerXmlParser = new CellDesignerXmlParser();
- String xmlString = cellDesignerXmlParser.toXml(model);
-
- InputStream is = new ByteArrayInputStream(xmlString.getBytes("UTF-8"));
-
- Model model2 = cellDesignerXmlParser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- AbstractImageGenerator.Params params2 = new AbstractImageGenerator.Params().height(model2.getHeight())
- .width(model2.getWidth()).nested(true).scale(1).level(20).x(0).y(0).model(model2);
- NormalImageGenerator nig2 = new PngImageGenerator(params2);
- String pngFilePath2 = pathWithouExtension.concat("_2.png");
- nig2.saveToFile(pngFilePath2);
-
- assertNotNull(model2);
- ModelComparator comparator = new ModelComparator(1.0);
- assertEquals(0, comparator.compare(model, model2));
- FileUtils.deleteDirectory(new File(dir));
-
- } catch (Exception e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.sbml;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.Collection;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.log4j.Logger;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameters;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
+import lcsb.mapviewer.converter.graphics.NormalImageGenerator;
+import lcsb.mapviewer.converter.graphics.PngImageGenerator;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+
+@RunWith(Parameterized.class)
+public class GenericSbmlParserTest {
+
+ static Logger logger = Logger.getLogger(GenericSbmlParserTest.class.getName());
+
+ private Path filePath;
+
+ public GenericSbmlParserTest(Path filePath) {
+ this.filePath = filePath;
+ }
+
+ @Parameters(name = "{index} : {0}")
+ public static Collection<Object[]> data() throws IOException {
+ Collection<Object[]> data = new ArrayList<Object[]>();
+ Files.walk(Paths.get("testFiles/layoutExample")).forEach(fPath -> {
+ if (Files.isRegularFile(fPath) && fPath.toString().endsWith(".xml")) {
+ data.add(new Object[] { fPath });
+ }
+ });
+ Files.walk(Paths.get("testFiles/invalidButParseable")).forEach(fPath -> {
+ if (Files.isRegularFile(fPath) && fPath.toString().endsWith(".xml")) {
+ data.add(new Object[] { fPath });
+ }
+ });
+ return data;
+ }
+
+ @Test
+ public void createModelTest() throws Exception {
+ try {
+ String dir = Files.createTempDirectory("sbml-temp-images-dir").toFile().getAbsolutePath();
+
+ IConverter converter = new SbmlParser();
+
+ Model model = converter.createModel(new ConverterParams().filename(filePath.toString()));
+ model.setName(null);
+
+ // Create and display image of parsed map
+ AbstractImageGenerator.Params params = new AbstractImageGenerator.Params().height(model.getHeight())
+ .width(model.getWidth()).nested(true).scale(1).level(20).x(0).y(0).model(model);
+ NormalImageGenerator nig = new PngImageGenerator(params);
+ String pathWithouExtension = dir + "/"
+ + filePath.getFileName().toString().substring(0, filePath.getFileName().toString().indexOf(".xml"));
+ String pngFilePath = pathWithouExtension.concat(".png");
+ nig.saveToFile(pngFilePath);
+ // Desktop.getDesktop().open(new File(pngFilePath));
+
+ CellDesignerXmlParser cellDesignerXmlParser = new CellDesignerXmlParser();
+ String xmlString = cellDesignerXmlParser.toXml(model);
+
+ InputStream is = new ByteArrayInputStream(xmlString.getBytes("UTF-8"));
+
+ Model model2 = cellDesignerXmlParser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ AbstractImageGenerator.Params params2 = new AbstractImageGenerator.Params().height(model2.getHeight())
+ .width(model2.getWidth()).nested(true).scale(1).level(20).x(0).y(0).model(model2);
+ NormalImageGenerator nig2 = new PngImageGenerator(params2);
+ String pngFilePath2 = pathWithouExtension.concat("_2.png");
+ nig2.saveToFile(pngFilePath2);
+
+ assertNotNull(model2);
+ ModelComparator comparator = new ModelComparator(1.0);
+ assertEquals(0, comparator.compare(model, model2));
+ FileUtils.deleteDirectory(new File(dir));
+
+ } catch (Exception e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
index 7f589568fd..10843990e9 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
@@ -1,84 +1,84 @@
-package lcsb.mapviewer.converter.model.sbml;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-
-import java.io.File;
-import java.io.IOException;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.util.ArrayList;
-import java.util.Collection;
-
-import org.apache.commons.io.FileUtils;
-import org.apache.log4j.Logger;
-import org.junit.Test;
-import org.junit.runner.RunWith;
-import org.junit.runners.Parameterized;
-import org.junit.runners.Parameterized.Parameters;
-
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.IConverter;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-
-@RunWith(Parameterized.class)
-public class GenericSbmlToXmlParserTest {
-
- static Logger logger = Logger.getLogger(GenericSbmlToXmlParserTest.class.getName());
-
- private Path filePath;
-
- public GenericSbmlToXmlParserTest(Path filePath) {
- this.filePath = filePath;
- }
-
- @Parameters(name = "{index} : {0}")
- public static Collection<Object[]> data() throws IOException {
- Collection<Object[]> data = new ArrayList<Object[]>();
- Files.walk(Paths.get("testFiles/layoutExample")).forEach(fPath -> {
- if (Files.isRegularFile(fPath) && fPath.toString().endsWith(".xml")) {
- data.add(new Object[] { fPath });
- }
- });
- Files.walk(Paths.get("testFiles/small")).forEach(fPath -> {
- if (Files.isRegularFile(fPath) && fPath.toString().endsWith(".xml")) {
- data.add(new Object[] { fPath });
- }
- });
- return data;
- }
-
- @Test
- public void toXmlModelTest() throws Exception {
- try {
-
- String dir = Files.createTempDirectory("sbgn-temp-images-dir").toFile().getAbsolutePath();
-
- IConverter converter = new SbmlParser();
-
- Model model = converter.createModel(new ConverterParams().filename(filePath.toString()));
- model.setName(null);
-
- String pathWithouExtension = dir + "/"
- + filePath.getFileName().toString().substring(0, filePath.getFileName().toString().indexOf(".xml"));
- String xmlFilePath = pathWithouExtension.concat(".xml");
- converter.exportModelToFile(model, xmlFilePath);
-
- Model model2 = converter.createModel(new ConverterParams().filename(xmlFilePath).sizeAutoAdjust(false));
- model2.setName(null);
-
- assertNotNull(model2);
- ModelComparator comparator = new ModelComparator(1.0);
- assertEquals(0, comparator.compare(model, model2));
- FileUtils.deleteDirectory(new File(dir));
-
- } catch (Exception e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.sbml;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.Collection;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.log4j.Logger;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameters;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+
+@RunWith(Parameterized.class)
+public class GenericSbmlToXmlParserTest {
+
+ static Logger logger = Logger.getLogger(GenericSbmlToXmlParserTest.class.getName());
+
+ private Path filePath;
+
+ public GenericSbmlToXmlParserTest(Path filePath) {
+ this.filePath = filePath;
+ }
+
+ @Parameters(name = "{index} : {0}")
+ public static Collection<Object[]> data() throws IOException {
+ Collection<Object[]> data = new ArrayList<Object[]>();
+ Files.walk(Paths.get("testFiles/layoutExample")).forEach(fPath -> {
+ if (Files.isRegularFile(fPath) && fPath.toString().endsWith(".xml")) {
+ data.add(new Object[] { fPath });
+ }
+ });
+ Files.walk(Paths.get("testFiles/small")).forEach(fPath -> {
+ if (Files.isRegularFile(fPath) && fPath.toString().endsWith(".xml")) {
+ data.add(new Object[] { fPath });
+ }
+ });
+ return data;
+ }
+
+ @Test
+ public void toXmlModelTest() throws Exception {
+ try {
+
+ String dir = Files.createTempDirectory("sbgn-temp-images-dir").toFile().getAbsolutePath();
+
+ IConverter converter = new SbmlParser();
+
+ Model model = converter.createModel(new ConverterParams().filename(filePath.toString()));
+ model.setName(null);
+
+ String pathWithouExtension = dir + "/"
+ + filePath.getFileName().toString().substring(0, filePath.getFileName().toString().indexOf(".xml"));
+ String xmlFilePath = pathWithouExtension.concat(".xml");
+ converter.exportModelToFile(model, xmlFilePath);
+
+ Model model2 = converter.createModel(new ConverterParams().filename(xmlFilePath).sizeAutoAdjust(false));
+ model2.setName(null);
+
+ assertNotNull(model2);
+ ModelComparator comparator = new ModelComparator(1.0);
+ assertEquals(0, comparator.compare(model, model2));
+ FileUtils.deleteDirectory(new File(dir));
+
+ } catch (Exception e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlPareserForInvalidReactionTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlPareserForInvalidReactionTest.java
index 09c74b274e..d1dd68b432 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlPareserForInvalidReactionTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlPareserForInvalidReactionTest.java
@@ -1,58 +1,58 @@
-package lcsb.mapviewer.converter.model.sbml;
-
-import static org.junit.Assert.fail;
-
-import java.io.IOException;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.util.ArrayList;
-import java.util.Collection;
-
-import org.apache.log4j.Logger;
-import org.junit.Test;
-import org.junit.runner.RunWith;
-import org.junit.runners.Parameterized;
-import org.junit.runners.Parameterized.Parameters;
-
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.IConverter;
-import lcsb.mapviewer.converter.InvalidInputDataExecption;
-
-@RunWith(Parameterized.class)
-public class SbmlPareserForInvalidReactionTest {
-
- static Logger logger = Logger.getLogger(SbmlPareserForInvalidReactionTest.class.getName());
-
- private Path filePath;
-
- public SbmlPareserForInvalidReactionTest(Path filePath) {
- this.filePath = filePath;
- }
-
- @Parameters(name = "{index} : {0}")
- public static Collection<Object[]> data() throws IOException {
- Collection<Object[]> data = new ArrayList<Object[]>();
- Files.walk(Paths.get("testFiles/invalidReaction")).forEach(fPath -> {
- if (Files.isRegularFile(fPath) && fPath.toString().endsWith(".xml")) {
- data.add(new Object[] { fPath });
- }
- });
- return data;
- }
-
- @Test
- public void createModelTest() throws Exception {
- try {
- IConverter converter = new SbmlParser();
-
- converter.createModel(new ConverterParams().filename(filePath.toString()));
- fail("Exception expected when parsing file: " + filePath.toString());
- } catch (InvalidInputDataExecption e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.sbml;
+
+import static org.junit.Assert.fail;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.Collection;
+
+import org.apache.log4j.Logger;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameters;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.InvalidInputDataExecption;
+
+@RunWith(Parameterized.class)
+public class SbmlPareserForInvalidReactionTest {
+
+ static Logger logger = Logger.getLogger(SbmlPareserForInvalidReactionTest.class.getName());
+
+ private Path filePath;
+
+ public SbmlPareserForInvalidReactionTest(Path filePath) {
+ this.filePath = filePath;
+ }
+
+ @Parameters(name = "{index} : {0}")
+ public static Collection<Object[]> data() throws IOException {
+ Collection<Object[]> data = new ArrayList<Object[]>();
+ Files.walk(Paths.get("testFiles/invalidReaction")).forEach(fPath -> {
+ if (Files.isRegularFile(fPath) && fPath.toString().endsWith(".xml")) {
+ data.add(new Object[] { fPath });
+ }
+ });
+ return data;
+ }
+
+ @Test
+ public void createModelTest() throws Exception {
+ try {
+ IConverter converter = new SbmlParser();
+
+ converter.createModel(new ConverterParams().filename(filePath.toString()));
+ fail("Exception expected when parsing file: " + filePath.toString());
+ } catch (InvalidInputDataExecption e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
index 93b03b62af..43df7989f4 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
@@ -1,399 +1,399 @@
-package lcsb.mapviewer.converter;
-
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.lang.reflect.Modifier;
-import java.util.ArrayList;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipFile;
-
-import org.apache.commons.io.FilenameUtils;
-import org.apache.commons.io.IOUtils;
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidClassException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
-import lcsb.mapviewer.converter.zip.LayoutZipEntryFile;
-import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
-import lcsb.mapviewer.converter.zip.ZipEntryFile;
-import lcsb.mapviewer.model.cache.UploadedFileEntry;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
-import lcsb.mapviewer.model.map.model.SubmodelType;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Phenotype;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * This class allows to create complex {@link Model} that contains submaps. It's
- * written in generic way and use {@link IConverter} as a class to parse single
- * submap.
- *
- * @author Piotr Gawron
- *
- */
-public class ComplexZipConverter {
-
- /**
- * Size of the buffer used for accessing single chunk of data from input stream.
- */
- private static final int BUFFER_SIZE = 1024;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ComplexZipConverter.class);
-
- /**
- * Class used to create single submap from a file.
- */
- private Class<? extends IConverter> converterClazz;
-
- /**
- * Default constructor. Checks if the class given in the parameter is proper
- * {@link IConverter} implementation.
- *
- * @param clazz
- * {@link IConverter} class used for creation of the single submap
- */
- public ComplexZipConverter(Class<? extends IConverter> clazz) {
- if (Modifier.isAbstract(clazz.getModifiers())) {
- throw new InvalidClassException("Param class cannot be abstract");
- }
-
- if (Modifier.isInterface(clazz.getModifiers())) {
- throw new InvalidClassException("Param class cannot be an interface");
- }
-
- converterClazz = clazz;
- }
-
- /**
- * Creates complex {@link Model} that contains submaps.
- *
- * @param params
- * {@link ComplexZipConverterParams object} with information about data
- * from which result is going to be created
- * @return complex {@link Model} created from input data
- * @throws InvalidInputDataExecption
- * thrown when there is a problem with accessing input data
- */
- public Model createModel(ComplexZipConverterParams params) throws InvalidInputDataExecption {
- try {
- ZipFile zipFile = params.getZipFile();
- Enumeration<? extends ZipEntry> entries;
- String mapping = validateSubmodelInformation(params, zipFile);
-
- IConverter converter = createConverterInstance();
- Map<String, Model> filenameModelMap = new HashMap<>();
- Map<String, Model> nameModelMap = new HashMap<>();
-
- entries = zipFile.entries();
- Model result = null;
- int overlayOrder = 1;
- List<Layout> layouts = new ArrayList<>();
- while (entries.hasMoreElements()) {
- ZipEntry entry = entries.nextElement();
- if (!entry.isDirectory()) {
- ZipEntryFile zef = params.getEntry(entry.getName());
- if (zef instanceof ModelZipEntryFile) {
- ModelZipEntryFile modelEntryFile = (ModelZipEntryFile) zef;
- InputStream is = zipFile.getInputStream(entry);
- ConverterParams cParams = new ConverterParams();
- cParams.inputStream(is);
- Model model = converter.createModel(cParams);
- model.setName(modelEntryFile.getName());
- filenameModelMap.put(entry.getName(), model);
- nameModelMap.put(FilenameUtils.getBaseName(modelEntryFile.getFilename()).toLowerCase(), model);
- if (modelEntryFile.isRoot()) {
- result = model;
- }
- } else if (zef instanceof LayoutZipEntryFile) {
- layouts.add(layoutZipEntryFileToLayout(params, zipFile, entry, (LayoutZipEntryFile) zef, overlayOrder++));
- } else if (zef instanceof ImageZipEntryFile) {
- continue;
- // imageEntries.add((ImageZipEntryFile) zef);
- } else if (!isIgnoredFile(entry.getName())) {
- throw new NotImplementedException("Unknwon entry type: " + zef.getClass());
- }
- }
- }
-
- for (Entry<String, Model> entry : filenameModelMap.entrySet()) {
- String filename = entry.getKey();
- Model model = entry.getValue();
- ZipEntryFile zef = params.getEntry(filename);
- if (zef instanceof ModelZipEntryFile) {
- ModelZipEntryFile modelEntryFile = (ModelZipEntryFile) zef;
- if (!modelEntryFile.isRoot() && !modelEntryFile.isMappingFile()) {
- ModelSubmodelConnection submodel = new ModelSubmodelConnection(model, modelEntryFile.getType());
- submodel.setName(modelEntryFile.getName());
- result.addSubmodelConnection(submodel);
- }
- }
- }
- for (Layout layout : layouts) {
- Layout topLayout = new Layout(layout);
- result.addLayout(topLayout);
- int modelId = 0;
- topLayout.setDirectory(topLayout.getDirectory() + modelId);
- modelId++;
- for (ModelSubmodelConnection connection : result.getSubmodelConnections()) {
- Layout childLayout = new Layout(layout);
- // we need to set separate directory names for different submodels
- childLayout.setDirectory(childLayout.getDirectory() + modelId);
- modelId++;
- childLayout.setParentLayout(topLayout);
- connection.getSubmodel().addLayout(childLayout);
- }
- }
- Model mappingModel = filenameModelMap.get(mapping);
- if (mappingModel != null) {
- for (Reaction reaction : mappingModel.getReactions()) {
- processReaction(mapping, nameModelMap, result, reaction);
- }
- }
- return result;
- } catch (IOException e) {
- throw new InvalidArgumentException(e);
- }
- }
-
- protected boolean isIgnoredFile(String name) {
- if (name == null) {
- return true;
- } else if (name.isEmpty()) {
- return true;
- } else if (name.startsWith(".DS_Store")) {
- return true;
- } else if (name.startsWith("__MACOSX")) {
- return true;
- }
- return false;
- }
-
- /**
- * Process a single reaction in mapping file (transfomring reaction into
- * connection between submodels).
- *
- * @param mapping
- * name of the mapping file
- * @param nameModelMap
- * mapping between file names and models
- * @param topModel
- * top model
- * @param reaction
- * reaction to transform into connection
- */
- public void processReaction(String mapping, Map<String, Model> nameModelMap, Model topModel, Reaction reaction) {
- if (reaction.getReactants().size() > 1) {
- logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping
- + ") contains too many reactants. Skipped");
- } else if (reaction.getProducts().size() > 1) {
- logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping
- + ") contains too many products. Skipped");
- } else if (reaction.getModifiers().size() > 0) {
- logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping
- + ") contains modifiers. Skipped");
- } else {
- Element fromAlias = reaction.getReactants().get(0).getElement();
- Element toAlias = reaction.getProducts().get(0).getElement();
- if (!(fromAlias instanceof Species)) {
- logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping
- + ") contains doesn't start in species. Skipped");
- } else if (!(toAlias instanceof Species)) {
- logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping
- + ") contains doesn't end in species. Skipped");
- } else {
- Complex complexFrom = ((Species) fromAlias).getComplex();
- Complex complexTo = ((Species) toAlias).getComplex();
- if (complexFrom == null) {
- logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping
- + ") contains doesn't start inside complex. Skipped");
- } else if (complexTo == null && (!(toAlias instanceof Complex))) {
- logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping
- + ") contains doesn't end inside complex. Skipped");
- } else {
- if (complexTo == null) {
- complexTo = (Complex) toAlias;
- }
- String fromName = complexFrom.getName().toLowerCase();
- String toName = complexTo.getName().toLowerCase();
- Model fromModel = nameModelMap.get(fromName);
- Model toModel = nameModelMap.get(toName);
- if (fromModel == null) {
- throw new InvalidArgumentException(
- "Mapping file references to " + fromName + " submodel. But such model doesn't exist");
- } else if (toModel == null) {
- throw new InvalidArgumentException(
- "Mapping file references to " + toName + " submodel. But such model doesn't exist");
- }
- Element source = fromModel.getElementByElementId(fromAlias.getName());
- if (source == null) {
- throw new InvalidArgumentException("Mapping file references to element with alias: " + fromAlias.getName()
- + ". But such element doesn't exist");
- }
- Element dest = null;
- if (!(toAlias instanceof Complex)) {
- dest = fromModel.getElementByElementId(toAlias.getName());
- }
- SubmodelType type = SubmodelType.UNKNOWN;
- if (fromAlias instanceof Protein) {
- type = SubmodelType.DOWNSTREAM_TARGETS;
- } else if (fromAlias instanceof Phenotype) {
- type = SubmodelType.PATHWAY;
- }
- ElementSubmodelConnection connection = new ElementSubmodelConnection(toModel, type);
- connection.setFromElement(source);
- connection.setToElement(dest);
- connection.setName(toModel.getName());
- source.setSubmodel(connection);
- }
- }
- }
- }
-
- /**
- * This method validates if information about model and submodels in the params
- * are sufficient. If not then appropriate exception will be thrown.
- *
- * @param params
- * parameters to validate
- * @param zipFile
- * original {@link ZipFile}
- * @return name of the file containing mapping between submodels
- */
- protected String validateSubmodelInformation(ComplexZipConverterParams params, ZipFile zipFile) {
- Enumeration<? extends ZipEntry> entries = zipFile.entries();
- Set<String> processed = new HashSet<>();
-
- String root = null;
- String mapping = null;
- while (entries.hasMoreElements()) {
- ZipEntry entry = entries.nextElement();
- if (!entry.isDirectory()) {
- String name = entry.getName();
- ZipEntryFile zef = params.getEntry(name);
- if (zef == null && !isIgnoredFile(name)) {
- throw new InvalidArgumentException("No information found in params about file: " + name);
- }
- if (zef instanceof ModelZipEntryFile) {
- ModelZipEntryFile modelEntryFile = (ModelZipEntryFile) zef;
- if (modelEntryFile.isRoot()) {
- if (root != null) {
- throw new InvalidArgumentException("Two roots found: " + name + ", " + root + ". There can be only one.");
- }
- root = name;
- }
- if (modelEntryFile.isMappingFile()) {
- if (mapping != null) {
- throw new InvalidArgumentException(
- "Two mapping files found: " + name + ", " + mapping + ". There can be only one.");
- }
- mapping = name;
- }
- }
- processed.add(name.toLowerCase());
- }
- }
- if (root == null) {
- throw new InvalidArgumentException("No root map found.");
- }
- for (String entryName : params.getFilenames()) {
- if (!processed.contains(entryName)) {
- throw new InvalidArgumentException("Entry " + entryName + " doesn't exists in the zip file.");
- }
- }
- return mapping;
- }
-
- /**
- * Transforms {@link LayoutZipEntryFile} into {@link Layout}.
- *
- * @param zipFile
- * original {@link ZipFile}
- * @param entry
- * entry in a zip file
- * @param params
- * parameters used to make general conversion (we use directory where
- * layout should be stored)
- * @param layoutEntry
- * {@link LayoutZipEntryFile} to transform
- * @return {@link LAyout} for a given {@link LayoutZipEntryFile}
- * @throws IOException
- * thrown when there is a problem with accessing {@link ZipFile}
- */
- protected Layout layoutZipEntryFileToLayout(ComplexZipConverterParams params, ZipFile zipFile, ZipEntry entry,
- LayoutZipEntryFile layoutEntry, int order) throws IOException {
- Layout layout = new Layout();
- layout.setDescription(layoutEntry.getDescription());
- layout.setDirectory(params.getVisualizationDir() + "/" + layoutEntry.getName().replaceAll(" ", "_"));
- UploadedFileEntry fileEntry = new UploadedFileEntry();
- fileEntry.setFileContent(IOUtils.toByteArray(zipFile.getInputStream(entry)));
- fileEntry.setOriginalFileName(entry.getName());
- fileEntry.setLength(fileEntry.getFileContent().length);
- layout.setInputData(fileEntry);
- layout.setPublicLayout(true);
- layout.setTitle(layoutEntry.getName());
- layout.setOrderIndex(order);
- return layout;
- }
-
- /**
- * Copy file from zip entry into temporary file.
- *
- * @param zipFile
- * input zip file
- * @param entry
- * entry in the zip file
- * @return {@link File} with a copy of data from zip entry
- * @throws IOException
- * thrown when there is a problem with input or output file
- */
- protected File saveFileFromZipFile(ZipFile zipFile, ZipEntry entry) throws IOException {
- InputStream is = zipFile.getInputStream(entry);
- File result = File.createTempFile("temp-file-name", ".png");
- FileOutputStream fos = new FileOutputStream(result);
- byte[] bytes = new byte[BUFFER_SIZE];
- int length;
- while ((length = is.read(bytes)) >= 0) {
- fos.write(bytes, 0, length);
- }
- fos.close();
- return result;
- }
-
- /**
- * Creates inctance of {@link IConverter} used as a template parameter for this
- * class instatiation.
- *
- * @return inctance of {@link IConverter}
- */
- protected IConverter createConverterInstance() {
- IConverter converter;
- try {
- converter = converterClazz.newInstance();
- } catch (InstantiationException e) {
- throw new InvalidClassException("Problem with instantation of the class: " + converterClazz, e);
- } catch (IllegalAccessException e) {
- throw new InvalidClassException("Problem with instantation of the class: " + converterClazz, e);
- }
- return converter;
- }
-}
+package lcsb.mapviewer.converter;
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.lang.reflect.Modifier;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipFile;
+
+import org.apache.commons.io.FilenameUtils;
+import org.apache.commons.io.IOUtils;
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidClassException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
+import lcsb.mapviewer.converter.zip.LayoutZipEntryFile;
+import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
+import lcsb.mapviewer.converter.zip.ZipEntryFile;
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
+import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
+import lcsb.mapviewer.model.map.model.SubmodelType;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This class allows to create complex {@link Model} that contains submaps. It's
+ * written in generic way and use {@link IConverter} as a class to parse single
+ * submap.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ComplexZipConverter {
+
+ /**
+ * Size of the buffer used for accessing single chunk of data from input stream.
+ */
+ private static final int BUFFER_SIZE = 1024;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ComplexZipConverter.class);
+
+ /**
+ * Class used to create single submap from a file.
+ */
+ private Class<? extends IConverter> converterClazz;
+
+ /**
+ * Default constructor. Checks if the class given in the parameter is proper
+ * {@link IConverter} implementation.
+ *
+ * @param clazz
+ * {@link IConverter} class used for creation of the single submap
+ */
+ public ComplexZipConverter(Class<? extends IConverter> clazz) {
+ if (Modifier.isAbstract(clazz.getModifiers())) {
+ throw new InvalidClassException("Param class cannot be abstract");
+ }
+
+ if (Modifier.isInterface(clazz.getModifiers())) {
+ throw new InvalidClassException("Param class cannot be an interface");
+ }
+
+ converterClazz = clazz;
+ }
+
+ /**
+ * Creates complex {@link Model} that contains submaps.
+ *
+ * @param params
+ * {@link ComplexZipConverterParams object} with information about data
+ * from which result is going to be created
+ * @return complex {@link Model} created from input data
+ * @throws InvalidInputDataExecption
+ * thrown when there is a problem with accessing input data
+ */
+ public Model createModel(ComplexZipConverterParams params) throws InvalidInputDataExecption {
+ try {
+ ZipFile zipFile = params.getZipFile();
+ Enumeration<? extends ZipEntry> entries;
+ String mapping = validateSubmodelInformation(params, zipFile);
+
+ IConverter converter = createConverterInstance();
+ Map<String, Model> filenameModelMap = new HashMap<>();
+ Map<String, Model> nameModelMap = new HashMap<>();
+
+ entries = zipFile.entries();
+ Model result = null;
+ int overlayOrder = 1;
+ List<Layout> layouts = new ArrayList<>();
+ while (entries.hasMoreElements()) {
+ ZipEntry entry = entries.nextElement();
+ if (!entry.isDirectory()) {
+ ZipEntryFile zef = params.getEntry(entry.getName());
+ if (zef instanceof ModelZipEntryFile) {
+ ModelZipEntryFile modelEntryFile = (ModelZipEntryFile) zef;
+ InputStream is = zipFile.getInputStream(entry);
+ ConverterParams cParams = new ConverterParams();
+ cParams.inputStream(is);
+ Model model = converter.createModel(cParams);
+ model.setName(modelEntryFile.getName());
+ filenameModelMap.put(entry.getName(), model);
+ nameModelMap.put(FilenameUtils.getBaseName(modelEntryFile.getFilename()).toLowerCase(), model);
+ if (modelEntryFile.isRoot()) {
+ result = model;
+ }
+ } else if (zef instanceof LayoutZipEntryFile) {
+ layouts.add(layoutZipEntryFileToLayout(params, zipFile, entry, (LayoutZipEntryFile) zef, overlayOrder++));
+ } else if (zef instanceof ImageZipEntryFile) {
+ continue;
+ // imageEntries.add((ImageZipEntryFile) zef);
+ } else if (!isIgnoredFile(entry.getName())) {
+ throw new NotImplementedException("Unknwon entry type: " + zef.getClass());
+ }
+ }
+ }
+
+ for (Entry<String, Model> entry : filenameModelMap.entrySet()) {
+ String filename = entry.getKey();
+ Model model = entry.getValue();
+ ZipEntryFile zef = params.getEntry(filename);
+ if (zef instanceof ModelZipEntryFile) {
+ ModelZipEntryFile modelEntryFile = (ModelZipEntryFile) zef;
+ if (!modelEntryFile.isRoot() && !modelEntryFile.isMappingFile()) {
+ ModelSubmodelConnection submodel = new ModelSubmodelConnection(model, modelEntryFile.getType());
+ submodel.setName(modelEntryFile.getName());
+ result.addSubmodelConnection(submodel);
+ }
+ }
+ }
+ for (Layout layout : layouts) {
+ Layout topLayout = new Layout(layout);
+ result.addLayout(topLayout);
+ int modelId = 0;
+ topLayout.setDirectory(topLayout.getDirectory() + modelId);
+ modelId++;
+ for (ModelSubmodelConnection connection : result.getSubmodelConnections()) {
+ Layout childLayout = new Layout(layout);
+ // we need to set separate directory names for different submodels
+ childLayout.setDirectory(childLayout.getDirectory() + modelId);
+ modelId++;
+ childLayout.setParentLayout(topLayout);
+ connection.getSubmodel().addLayout(childLayout);
+ }
+ }
+ Model mappingModel = filenameModelMap.get(mapping);
+ if (mappingModel != null) {
+ for (Reaction reaction : mappingModel.getReactions()) {
+ processReaction(mapping, nameModelMap, result, reaction);
+ }
+ }
+ return result;
+ } catch (IOException e) {
+ throw new InvalidArgumentException(e);
+ }
+ }
+
+ protected boolean isIgnoredFile(String name) {
+ if (name == null) {
+ return true;
+ } else if (name.isEmpty()) {
+ return true;
+ } else if (name.startsWith(".DS_Store")) {
+ return true;
+ } else if (name.startsWith("__MACOSX")) {
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Process a single reaction in mapping file (transfomring reaction into
+ * connection between submodels).
+ *
+ * @param mapping
+ * name of the mapping file
+ * @param nameModelMap
+ * mapping between file names and models
+ * @param topModel
+ * top model
+ * @param reaction
+ * reaction to transform into connection
+ */
+ public void processReaction(String mapping, Map<String, Model> nameModelMap, Model topModel, Reaction reaction) {
+ if (reaction.getReactants().size() > 1) {
+ logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping
+ + ") contains too many reactants. Skipped");
+ } else if (reaction.getProducts().size() > 1) {
+ logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping
+ + ") contains too many products. Skipped");
+ } else if (reaction.getModifiers().size() > 0) {
+ logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping
+ + ") contains modifiers. Skipped");
+ } else {
+ Element fromAlias = reaction.getReactants().get(0).getElement();
+ Element toAlias = reaction.getProducts().get(0).getElement();
+ if (!(fromAlias instanceof Species)) {
+ logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping
+ + ") contains doesn't start in species. Skipped");
+ } else if (!(toAlias instanceof Species)) {
+ logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping
+ + ") contains doesn't end in species. Skipped");
+ } else {
+ Complex complexFrom = ((Species) fromAlias).getComplex();
+ Complex complexTo = ((Species) toAlias).getComplex();
+ if (complexFrom == null) {
+ logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping
+ + ") contains doesn't start inside complex. Skipped");
+ } else if (complexTo == null && (!(toAlias instanceof Complex))) {
+ logger.warn("[SUBMODEL MAPPING] Reaction " + reaction.getIdReaction() + " in mapping file (" + mapping
+ + ") contains doesn't end inside complex. Skipped");
+ } else {
+ if (complexTo == null) {
+ complexTo = (Complex) toAlias;
+ }
+ String fromName = complexFrom.getName().toLowerCase();
+ String toName = complexTo.getName().toLowerCase();
+ Model fromModel = nameModelMap.get(fromName);
+ Model toModel = nameModelMap.get(toName);
+ if (fromModel == null) {
+ throw new InvalidArgumentException(
+ "Mapping file references to " + fromName + " submodel. But such model doesn't exist");
+ } else if (toModel == null) {
+ throw new InvalidArgumentException(
+ "Mapping file references to " + toName + " submodel. But such model doesn't exist");
+ }
+ Element source = fromModel.getElementByElementId(fromAlias.getName());
+ if (source == null) {
+ throw new InvalidArgumentException("Mapping file references to element with alias: " + fromAlias.getName()
+ + ". But such element doesn't exist");
+ }
+ Element dest = null;
+ if (!(toAlias instanceof Complex)) {
+ dest = fromModel.getElementByElementId(toAlias.getName());
+ }
+ SubmodelType type = SubmodelType.UNKNOWN;
+ if (fromAlias instanceof Protein) {
+ type = SubmodelType.DOWNSTREAM_TARGETS;
+ } else if (fromAlias instanceof Phenotype) {
+ type = SubmodelType.PATHWAY;
+ }
+ ElementSubmodelConnection connection = new ElementSubmodelConnection(toModel, type);
+ connection.setFromElement(source);
+ connection.setToElement(dest);
+ connection.setName(toModel.getName());
+ source.setSubmodel(connection);
+ }
+ }
+ }
+ }
+
+ /**
+ * This method validates if information about model and submodels in the params
+ * are sufficient. If not then appropriate exception will be thrown.
+ *
+ * @param params
+ * parameters to validate
+ * @param zipFile
+ * original {@link ZipFile}
+ * @return name of the file containing mapping between submodels
+ */
+ protected String validateSubmodelInformation(ComplexZipConverterParams params, ZipFile zipFile) {
+ Enumeration<? extends ZipEntry> entries = zipFile.entries();
+ Set<String> processed = new HashSet<>();
+
+ String root = null;
+ String mapping = null;
+ while (entries.hasMoreElements()) {
+ ZipEntry entry = entries.nextElement();
+ if (!entry.isDirectory()) {
+ String name = entry.getName();
+ ZipEntryFile zef = params.getEntry(name);
+ if (zef == null && !isIgnoredFile(name)) {
+ throw new InvalidArgumentException("No information found in params about file: " + name);
+ }
+ if (zef instanceof ModelZipEntryFile) {
+ ModelZipEntryFile modelEntryFile = (ModelZipEntryFile) zef;
+ if (modelEntryFile.isRoot()) {
+ if (root != null) {
+ throw new InvalidArgumentException("Two roots found: " + name + ", " + root + ". There can be only one.");
+ }
+ root = name;
+ }
+ if (modelEntryFile.isMappingFile()) {
+ if (mapping != null) {
+ throw new InvalidArgumentException(
+ "Two mapping files found: " + name + ", " + mapping + ". There can be only one.");
+ }
+ mapping = name;
+ }
+ }
+ processed.add(name.toLowerCase());
+ }
+ }
+ if (root == null) {
+ throw new InvalidArgumentException("No root map found.");
+ }
+ for (String entryName : params.getFilenames()) {
+ if (!processed.contains(entryName)) {
+ throw new InvalidArgumentException("Entry " + entryName + " doesn't exists in the zip file.");
+ }
+ }
+ return mapping;
+ }
+
+ /**
+ * Transforms {@link LayoutZipEntryFile} into {@link Layout}.
+ *
+ * @param zipFile
+ * original {@link ZipFile}
+ * @param entry
+ * entry in a zip file
+ * @param params
+ * parameters used to make general conversion (we use directory where
+ * layout should be stored)
+ * @param layoutEntry
+ * {@link LayoutZipEntryFile} to transform
+ * @return {@link LAyout} for a given {@link LayoutZipEntryFile}
+ * @throws IOException
+ * thrown when there is a problem with accessing {@link ZipFile}
+ */
+ protected Layout layoutZipEntryFileToLayout(ComplexZipConverterParams params, ZipFile zipFile, ZipEntry entry,
+ LayoutZipEntryFile layoutEntry, int order) throws IOException {
+ Layout layout = new Layout();
+ layout.setDescription(layoutEntry.getDescription());
+ layout.setDirectory(params.getVisualizationDir() + "/" + layoutEntry.getName().replaceAll(" ", "_"));
+ UploadedFileEntry fileEntry = new UploadedFileEntry();
+ fileEntry.setFileContent(IOUtils.toByteArray(zipFile.getInputStream(entry)));
+ fileEntry.setOriginalFileName(entry.getName());
+ fileEntry.setLength(fileEntry.getFileContent().length);
+ layout.setInputData(fileEntry);
+ layout.setPublicLayout(true);
+ layout.setTitle(layoutEntry.getName());
+ layout.setOrderIndex(order);
+ return layout;
+ }
+
+ /**
+ * Copy file from zip entry into temporary file.
+ *
+ * @param zipFile
+ * input zip file
+ * @param entry
+ * entry in the zip file
+ * @return {@link File} with a copy of data from zip entry
+ * @throws IOException
+ * thrown when there is a problem with input or output file
+ */
+ protected File saveFileFromZipFile(ZipFile zipFile, ZipEntry entry) throws IOException {
+ InputStream is = zipFile.getInputStream(entry);
+ File result = File.createTempFile("temp-file-name", ".png");
+ FileOutputStream fos = new FileOutputStream(result);
+ byte[] bytes = new byte[BUFFER_SIZE];
+ int length;
+ while ((length = is.read(bytes)) >= 0) {
+ fos.write(bytes, 0, length);
+ }
+ fos.close();
+ return result;
+ }
+
+ /**
+ * Creates inctance of {@link IConverter} used as a template parameter for this
+ * class instatiation.
+ *
+ * @return inctance of {@link IConverter}
+ */
+ protected IConverter createConverterInstance() {
+ IConverter converter;
+ try {
+ converter = converterClazz.newInstance();
+ } catch (InstantiationException e) {
+ throw new InvalidClassException("Problem with instantation of the class: " + converterClazz, e);
+ } catch (IllegalAccessException e) {
+ throw new InvalidClassException("Problem with instantation of the class: " + converterClazz, e);
+ }
+ return converter;
+ }
+}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverterParams.java b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverterParams.java
index 8d8daf907d..78946c93d3 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverterParams.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverterParams.java
@@ -1,130 +1,130 @@
-package lcsb.mapviewer.converter;
-
-import java.io.IOException;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Set;
-import java.util.zip.ZipFile;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.converter.zip.ZipEntryFile;
-
-/**
- * Class that contains information about input data used for creation of the
- * complex {@link lcsb.mapviewer.model.map.model.Model Model} with submaps.
- *
- * @author Piotr Gawron
- *
- */
-public class ComplexZipConverterParams {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(ComplexZipConverterParams.class);
-
- /**
- * Zip file where all maps are stored.
- */
- private ZipFile zipFile;
-
- /**
- * Mapping between filename and information provided by the user about the file.
- */
- private Map<String, ZipEntryFile> entries = new HashMap<>();
-
- /**
- * Directory where additional visualization files should be stored.
- */
- private String visualizationDir = null;
-
- /**
- * Sets {@link #zipFile}.
- *
- * @param zipFile
- * {@link #zipFile}
- * @return object with all parameters
- */
- public ComplexZipConverterParams zipFile(ZipFile zipFile) {
- this.zipFile = zipFile;
- return this;
- }
-
- /**
- * Sets {@link #zipFile}.
- *
- * @param filename
- * name of the {@link #zipFile}
- * @return object with all parameters
- * @throws IOException
- * throw when there is a problem with a file
- */
- public ComplexZipConverterParams zipFile(String filename) throws IOException {
- this.zipFile = new ZipFile(filename);
- return this;
- }
-
- /**
- * Sets information about single entry in the zip file.
- *
- * @param entry
- * set of information about single zip entry
- * @return object with all parameters
- */
- public ComplexZipConverterParams entry(ZipEntryFile entry) {
- this.entries.put(entry.getFilename().toLowerCase(), entry);
- return this;
- }
-
- /**
- * @return the zipFile
- * @see #zipFile
- */
- public ZipFile getZipFile() {
- return zipFile;
- }
-
- /**
- * Returns set of filenames put in this param object.
- *
- * @return set of filenames put in this param object
- */
- public Set<String> getFilenames() {
- return entries.keySet();
- }
-
- /**
- * Sets {@link #visualizationDir} value.
- *
- * @param string
- * new value
- * @return instance of this class
- */
- public ComplexZipConverterParams visualizationDir(String string) {
- this.visualizationDir = string;
- return this;
- }
-
- /**
- * Returns {@link #visualizationDir}.
- *
- * @return {@link #visualizationDir}
- */
- public String getVisualizationDir() {
- return visualizationDir;
- }
-
- /**
- * Return {@link ZipEntryFile entry} with information about single file in the
- * zip archive identified by file name (file name is case insensitive).
- *
- * @param name
- * name of the file in zip archive
- * @return {@link ZipEntryFile entry} with information about file
- */
- public ZipEntryFile getEntry(String name) {
- return entries.get(name.toLowerCase());
- }
-}
+package lcsb.mapviewer.converter;
+
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Set;
+import java.util.zip.ZipFile;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.converter.zip.ZipEntryFile;
+
+/**
+ * Class that contains information about input data used for creation of the
+ * complex {@link lcsb.mapviewer.model.map.model.Model Model} with submaps.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ComplexZipConverterParams {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(ComplexZipConverterParams.class);
+
+ /**
+ * Zip file where all maps are stored.
+ */
+ private ZipFile zipFile;
+
+ /**
+ * Mapping between filename and information provided by the user about the file.
+ */
+ private Map<String, ZipEntryFile> entries = new HashMap<>();
+
+ /**
+ * Directory where additional visualization files should be stored.
+ */
+ private String visualizationDir = null;
+
+ /**
+ * Sets {@link #zipFile}.
+ *
+ * @param zipFile
+ * {@link #zipFile}
+ * @return object with all parameters
+ */
+ public ComplexZipConverterParams zipFile(ZipFile zipFile) {
+ this.zipFile = zipFile;
+ return this;
+ }
+
+ /**
+ * Sets {@link #zipFile}.
+ *
+ * @param filename
+ * name of the {@link #zipFile}
+ * @return object with all parameters
+ * @throws IOException
+ * throw when there is a problem with a file
+ */
+ public ComplexZipConverterParams zipFile(String filename) throws IOException {
+ this.zipFile = new ZipFile(filename);
+ return this;
+ }
+
+ /**
+ * Sets information about single entry in the zip file.
+ *
+ * @param entry
+ * set of information about single zip entry
+ * @return object with all parameters
+ */
+ public ComplexZipConverterParams entry(ZipEntryFile entry) {
+ this.entries.put(entry.getFilename().toLowerCase(), entry);
+ return this;
+ }
+
+ /**
+ * @return the zipFile
+ * @see #zipFile
+ */
+ public ZipFile getZipFile() {
+ return zipFile;
+ }
+
+ /**
+ * Returns set of filenames put in this param object.
+ *
+ * @return set of filenames put in this param object
+ */
+ public Set<String> getFilenames() {
+ return entries.keySet();
+ }
+
+ /**
+ * Sets {@link #visualizationDir} value.
+ *
+ * @param string
+ * new value
+ * @return instance of this class
+ */
+ public ComplexZipConverterParams visualizationDir(String string) {
+ this.visualizationDir = string;
+ return this;
+ }
+
+ /**
+ * Returns {@link #visualizationDir}.
+ *
+ * @return {@link #visualizationDir}
+ */
+ public String getVisualizationDir() {
+ return visualizationDir;
+ }
+
+ /**
+ * Return {@link ZipEntryFile entry} with information about single file in the
+ * zip archive identified by file name (file name is case insensitive).
+ *
+ * @param name
+ * name of the file in zip archive
+ * @return {@link ZipEntryFile entry} with information about file
+ */
+ public ZipEntryFile getEntry(String name) {
+ return entries.get(name.toLowerCase());
+ }
+}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ConverterException.java b/converter/src/main/java/lcsb/mapviewer/converter/ConverterException.java
index c0d120bae1..ffc14cefd6 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ConverterException.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ConverterException.java
@@ -1,56 +1,56 @@
-package lcsb.mapviewer.converter;
-
-/**
- * Generic exception thrown when implementation of {@link IConverter} encounter
- * a problem.
- *
- * @author Piotr Gawron
- *
- */
-public class ConverterException extends Exception {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor with exception message.
- *
- * @param message
- * error message
- */
- public ConverterException(String message) {
- super(message);
- }
-
- /**
- * Default constructor with super exception as a source.
- *
- * @param e
- * super exception
- */
- public ConverterException(Exception e) {
- super(e);
- }
-
- /**
- * Default constructor - initializes instance variable to unknown.
- */
-
- public ConverterException() {
- super(); // call superclass constructor
- }
-
- /**
- * Default constructor.
- *
- * @param message
- * exception message
- * @param e
- * super exception
- */
- public ConverterException(String message, Exception e) {
- super(message, e);
- }
+package lcsb.mapviewer.converter;
+
+/**
+ * Generic exception thrown when implementation of {@link IConverter} encounter
+ * a problem.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ConverterException extends Exception {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor with exception message.
+ *
+ * @param message
+ * error message
+ */
+ public ConverterException(String message) {
+ super(message);
+ }
+
+ /**
+ * Default constructor with super exception as a source.
+ *
+ * @param e
+ * super exception
+ */
+ public ConverterException(Exception e) {
+ super(e);
+ }
+
+ /**
+ * Default constructor - initializes instance variable to unknown.
+ */
+
+ public ConverterException() {
+ super(); // call superclass constructor
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * exception message
+ * @param e
+ * super exception
+ */
+ public ConverterException(String message, Exception e) {
+ super(message, e);
+ }
}
\ No newline at end of file
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ConverterParams.java b/converter/src/main/java/lcsb/mapviewer/converter/ConverterParams.java
index f1db067a8b..20400e0c80 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ConverterParams.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ConverterParams.java
@@ -1,124 +1,124 @@
-package lcsb.mapviewer.converter;
-
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.InputStream;
-
-import org.apache.xerces.xni.parser.XMLInputSource;
-
-/**
- * Class with params for {@link IConverter} interface.
- *
- * @author Piotr Gawron
- */
-public class ConverterParams {
- /**
- * Input stream for the parser.
- */
- private InputStream inputStream;
-
- /**
- * Name of the file used as a data input. (not obligatory)
- */
- private String filename;
- /**
- * Should the map be autoresized after parsing or not. Autoresizing will equal
- * right with left margin and top with bottom margin.
- */
- private boolean sizeAutoAdjust = true;
-
- /**
- * Should the map be formated as SBGN.
- */
- private boolean sbgnFormat = false;
-
- /**
- * Set file as input source.
- *
- * @param fileName
- * path to a file that should be parsed.
- * @return object with all set parameters
- * @throws FileNotFoundException
- */
- public ConverterParams filename(String fileName) throws FileNotFoundException {
- inputStream = new FileInputStream(fileName);
- this.filename = fileName;
- return this;
- }
-
- /**
- *
- * Set input stream as input source.
- *
- * @param is
- * input stream that should be parsed
- * @return object with all set parameters
- */
- public ConverterParams inputStream(InputStream is) {
- this.inputStream = is;
- return this;
- }
-
- /**
- * @return the source
- * @see #source
- */
- public XMLInputSource getSource() {
- return new XMLInputSource(null, null, null, this.inputStream, null);
- }
-
- /**
- *
- * @param value
- * the sizeAutoAdjust to set
- * @see #sizeAutoAdjust
- * @return object with all parameters
- */
- public ConverterParams sizeAutoAdjust(boolean value) {
- sizeAutoAdjust = value;
- return this;
- }
-
- /**
- * @return the inputStream
- * @see #inputStream
- */
- public InputStream getInputStream() {
- return this.inputStream;
- }
-
- /**
- * @return the sizeAutoAdjust
- * @see #sizeAutoAdjust
- */
- public boolean isSizeAutoAdjust() {
- return sizeAutoAdjust;
- }
-
- /**
- * @return the filename
- * @see #filename
- */
- public String getFilename() {
- return filename;
- }
-
- /**
- * @return the sbgnFormat
- * @see #sbgnFormat
- */
- public boolean isSbgnFormat() {
- return sbgnFormat;
- }
-
- /**
- * @param sbgnFormat the sbgnFormat to set
- * @return ConverterParams object with all parameters
- * @see #sbgnFormat
- */
- public ConverterParams sbgnFormat(boolean sbgnFormat) {
- this.sbgnFormat = sbgnFormat;
- return this;
- }
-
-}
+package lcsb.mapviewer.converter;
+
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.InputStream;
+
+import org.apache.xerces.xni.parser.XMLInputSource;
+
+/**
+ * Class with params for {@link IConverter} interface.
+ *
+ * @author Piotr Gawron
+ */
+public class ConverterParams {
+ /**
+ * Input stream for the parser.
+ */
+ private InputStream inputStream;
+
+ /**
+ * Name of the file used as a data input. (not obligatory)
+ */
+ private String filename;
+ /**
+ * Should the map be autoresized after parsing or not. Autoresizing will equal
+ * right with left margin and top with bottom margin.
+ */
+ private boolean sizeAutoAdjust = true;
+
+ /**
+ * Should the map be formated as SBGN.
+ */
+ private boolean sbgnFormat = false;
+
+ /**
+ * Set file as input source.
+ *
+ * @param fileName
+ * path to a file that should be parsed.
+ * @return object with all set parameters
+ * @throws FileNotFoundException
+ */
+ public ConverterParams filename(String fileName) throws FileNotFoundException {
+ inputStream = new FileInputStream(fileName);
+ this.filename = fileName;
+ return this;
+ }
+
+ /**
+ *
+ * Set input stream as input source.
+ *
+ * @param is
+ * input stream that should be parsed
+ * @return object with all set parameters
+ */
+ public ConverterParams inputStream(InputStream is) {
+ this.inputStream = is;
+ return this;
+ }
+
+ /**
+ * @return the source
+ * @see #source
+ */
+ public XMLInputSource getSource() {
+ return new XMLInputSource(null, null, null, this.inputStream, null);
+ }
+
+ /**
+ *
+ * @param value
+ * the sizeAutoAdjust to set
+ * @see #sizeAutoAdjust
+ * @return object with all parameters
+ */
+ public ConverterParams sizeAutoAdjust(boolean value) {
+ sizeAutoAdjust = value;
+ return this;
+ }
+
+ /**
+ * @return the inputStream
+ * @see #inputStream
+ */
+ public InputStream getInputStream() {
+ return this.inputStream;
+ }
+
+ /**
+ * @return the sizeAutoAdjust
+ * @see #sizeAutoAdjust
+ */
+ public boolean isSizeAutoAdjust() {
+ return sizeAutoAdjust;
+ }
+
+ /**
+ * @return the filename
+ * @see #filename
+ */
+ public String getFilename() {
+ return filename;
+ }
+
+ /**
+ * @return the sbgnFormat
+ * @see #sbgnFormat
+ */
+ public boolean isSbgnFormat() {
+ return sbgnFormat;
+ }
+
+ /**
+ * @param sbgnFormat the sbgnFormat to set
+ * @return ConverterParams object with all parameters
+ * @see #sbgnFormat
+ */
+ public ConverterParams sbgnFormat(boolean sbgnFormat) {
+ this.sbgnFormat = sbgnFormat;
+ return this;
+ }
+
+}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/IConverter.java b/converter/src/main/java/lcsb/mapviewer/converter/IConverter.java
index bcc0546a33..f1e0095ad6 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/IConverter.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/IConverter.java
@@ -1,82 +1,82 @@
-package lcsb.mapviewer.converter;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-
-import lcsb.mapviewer.common.MimeType;
-import lcsb.mapviewer.model.map.InconsistentModelException;
-import lcsb.mapviewer.model.map.model.Model;
-
-/**
- * Interface used for reading data from file and putting it into {@link Model}
- * object.
- *
- * @author Piotr Gawron
- *
- */
-public interface IConverter {
-
- /**
- * Parse input source and transformes it into a model object.
- *
- * @param params
- * input params used for reading data
- * @return model obtained from inut source
- * @throws InvalidInputDataExecption
- * thrown when input parameters are invalid
- */
-
- Model createModel(ConverterParams params) throws InvalidInputDataExecption;
-
- /**
- * Export model to {@link InputStream}.
- *
- * @param model
- * model to be exported
- * @return {@link InputStream} with exported data
- * @throws InconsistentModelException
- * thrown when given model is inconsistent and unable to be exported
- * @throws ConverterException
- * thrown when there is unknown problem in a converter
- */
- InputStream exportModelToInputStream(Model model) throws ConverterException, InconsistentModelException;
-
- /**
- * Export model to {@link File}.
- *
- * @param model
- * model to be exported
- * @param filePath
- * exported file path
- * @return {@link File} with exported data
- * @throws InconsistentModelException
- * thrown when given model is inconsistent and unable to be exported
- * @throws ConverterException
- * thrown when there is unknown problem in a converter
- * @throws IOException thrown when there is a problem with writing to file
- */
- File exportModelToFile(Model model, String filePath) throws ConverterException, InconsistentModelException, IOException;
-
- /**
- * Returns a common name of data format used in the converter.
- *
- * @return common name of data format used in the converter
- */
- String getCommonName();
-
- /**
- * Returns {@link MimeType} of the exported data.
- *
- * @return {@link MimeType} of the exported data
- */
- MimeType getMimeType();
-
- /**
- * Returns extension of the exported file.
- *
- * @return extension of the exported file
- */
- String getFileExtension();
-
-}
+package lcsb.mapviewer.converter;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+
+import lcsb.mapviewer.common.MimeType;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.model.Model;
+
+/**
+ * Interface used for reading data from file and putting it into {@link Model}
+ * object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface IConverter {
+
+ /**
+ * Parse input source and transformes it into a model object.
+ *
+ * @param params
+ * input params used for reading data
+ * @return model obtained from inut source
+ * @throws InvalidInputDataExecption
+ * thrown when input parameters are invalid
+ */
+
+ Model createModel(ConverterParams params) throws InvalidInputDataExecption;
+
+ /**
+ * Export model to {@link InputStream}.
+ *
+ * @param model
+ * model to be exported
+ * @return {@link InputStream} with exported data
+ * @throws InconsistentModelException
+ * thrown when given model is inconsistent and unable to be exported
+ * @throws ConverterException
+ * thrown when there is unknown problem in a converter
+ */
+ InputStream exportModelToInputStream(Model model) throws ConverterException, InconsistentModelException;
+
+ /**
+ * Export model to {@link File}.
+ *
+ * @param model
+ * model to be exported
+ * @param filePath
+ * exported file path
+ * @return {@link File} with exported data
+ * @throws InconsistentModelException
+ * thrown when given model is inconsistent and unable to be exported
+ * @throws ConverterException
+ * thrown when there is unknown problem in a converter
+ * @throws IOException thrown when there is a problem with writing to file
+ */
+ File exportModelToFile(Model model, String filePath) throws ConverterException, InconsistentModelException, IOException;
+
+ /**
+ * Returns a common name of data format used in the converter.
+ *
+ * @return common name of data format used in the converter
+ */
+ String getCommonName();
+
+ /**
+ * Returns {@link MimeType} of the exported data.
+ *
+ * @return {@link MimeType} of the exported data
+ */
+ MimeType getMimeType();
+
+ /**
+ * Returns extension of the exported file.
+ *
+ * @return extension of the exported file
+ */
+ String getFileExtension();
+
+}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/InvalidCoordinatesFile.java b/converter/src/main/java/lcsb/mapviewer/converter/InvalidCoordinatesFile.java
index 5f3a86226f..cf6037be29 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/InvalidCoordinatesFile.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/InvalidCoordinatesFile.java
@@ -1,51 +1,51 @@
-package lcsb.mapviewer.converter;
-
-
-/**
- * Exception thrown when the {@link OverviewParser#COORDINATES_FILENAME image
- * link coordinates file} in {@link lcsb.mapviewer.converter.zip.InputFileType#OVERLAY_IMAGE_DATA input file}
- * is invalid.
- *
- * @author Piotr Gawron
- *
- */
-public class InvalidCoordinatesFile extends InvalidOverviewFile {
-
- /**
- * Default constructor.
- *
- * @param e
- * parent exception (reason)
- */
- public InvalidCoordinatesFile(Exception e) {
- super(e);
- }
-
- /**
- * Default constructor.
- *
- * @param message
- * exception message
- * @param e
- * parent exception (reason)
- */
- public InvalidCoordinatesFile(String message, Exception e) {
- super(message, e);
- }
-
- /**
- * Default constructor.
- *
- * @param message
- * exception message
- */
- public InvalidCoordinatesFile(String message) {
- super(message);
- }
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
-}
+package lcsb.mapviewer.converter;
+
+
+/**
+ * Exception thrown when the {@link OverviewParser#COORDINATES_FILENAME image
+ * link coordinates file} in {@link lcsb.mapviewer.converter.zip.InputFileType#OVERLAY_IMAGE_DATA input file}
+ * is invalid.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class InvalidCoordinatesFile extends InvalidOverviewFile {
+
+ /**
+ * Default constructor.
+ *
+ * @param e
+ * parent exception (reason)
+ */
+ public InvalidCoordinatesFile(Exception e) {
+ super(e);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * exception message
+ * @param e
+ * parent exception (reason)
+ */
+ public InvalidCoordinatesFile(String message, Exception e) {
+ super(message, e);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * exception message
+ */
+ public InvalidCoordinatesFile(String message) {
+ super(message);
+ }
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/InvalidInputDataExecption.java b/converter/src/main/java/lcsb/mapviewer/converter/InvalidInputDataExecption.java
index 8f0e98c9ac..ebc92805a1 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/InvalidInputDataExecption.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/InvalidInputDataExecption.java
@@ -1,68 +1,68 @@
-package lcsb.mapviewer.converter;
-
-/**
- * Exception that should be thrown when there is a problem with input data.
- *
- * @author Piotr Gawron
- *
- */
-public class InvalidInputDataExecption extends Exception {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor with exception message.
- *
- * @param message
- * error message
- */
- public InvalidInputDataExecption(String message) {
- super(message);
- }
-
- /**
- * Default constructor with super exception as a source.
- *
- * @param e
- * super exception
- */
- public InvalidInputDataExecption(Exception e) {
- super(e);
- }
-
- /**
- * Default constructor - initializes instance variable to unknown.
- */
-
- public InvalidInputDataExecption() {
- super(); // call superclass constructor
- }
-
- /**
- * Default constructor.
- *
- * @param message
- * exception message
- * @param e
- * super exception
- */
- public InvalidInputDataExecption(String message, Exception e) {
- super(message, e);
- }
-
- /**
- * Default constructor with exception message.
- *
- * @param message
- * error message
- * @param filename
- * name of the file where data is invalid
- */
- public InvalidInputDataExecption(String message, String filename) {
- super("[File \"" + filename + "\"]: " + message.trim());
- }
-
-}
+package lcsb.mapviewer.converter;
+
+/**
+ * Exception that should be thrown when there is a problem with input data.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class InvalidInputDataExecption extends Exception {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor with exception message.
+ *
+ * @param message
+ * error message
+ */
+ public InvalidInputDataExecption(String message) {
+ super(message);
+ }
+
+ /**
+ * Default constructor with super exception as a source.
+ *
+ * @param e
+ * super exception
+ */
+ public InvalidInputDataExecption(Exception e) {
+ super(e);
+ }
+
+ /**
+ * Default constructor - initializes instance variable to unknown.
+ */
+
+ public InvalidInputDataExecption() {
+ super(); // call superclass constructor
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * exception message
+ * @param e
+ * super exception
+ */
+ public InvalidInputDataExecption(String message, Exception e) {
+ super(message, e);
+ }
+
+ /**
+ * Default constructor with exception message.
+ *
+ * @param message
+ * error message
+ * @param filename
+ * name of the file where data is invalid
+ */
+ public InvalidInputDataExecption(String message, String filename) {
+ super("[File \"" + filename + "\"]: " + message.trim());
+ }
+
+}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/InvalidOverviewFile.java b/converter/src/main/java/lcsb/mapviewer/converter/InvalidOverviewFile.java
index f326b97be1..45c1a26809 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/InvalidOverviewFile.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/InvalidOverviewFile.java
@@ -1,51 +1,51 @@
-package lcsb.mapviewer.converter;
-
-
-/**
- * Exception thrown when the {@link lcsb.mapviewer.converter.zip.InputFileType#OVERLAY_IMAGE_DATA input file
- * * } containing data about {@link lcsb.mapviewer.model.map.OverviewImage
- * overview images} is invalid.
- *
- * @author Piotr Gawron
- *
- */
-public class InvalidOverviewFile extends InvalidInputDataExecption {
-
- /**
- * Default constructor.
- *
- * @param e
- * parent exception (reason)
- */
- public InvalidOverviewFile(Exception e) {
- super(e);
- }
-
- /**
- * Default constructor.
- *
- * @param message
- * exception message
- * @param e
- * parent exception (reason)
- */
- public InvalidOverviewFile(String message, Exception e) {
- super(message, e);
- }
-
- /**
- * Default constructor.
- *
- * @param message
- * exception message
- */
- public InvalidOverviewFile(String message) {
- super(message);
- }
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
-}
+package lcsb.mapviewer.converter;
+
+
+/**
+ * Exception thrown when the {@link lcsb.mapviewer.converter.zip.InputFileType#OVERLAY_IMAGE_DATA input file
+ * * } containing data about {@link lcsb.mapviewer.model.map.OverviewImage
+ * overview images} is invalid.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class InvalidOverviewFile extends InvalidInputDataExecption {
+
+ /**
+ * Default constructor.
+ *
+ * @param e
+ * parent exception (reason)
+ */
+ public InvalidOverviewFile(Exception e) {
+ super(e);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * exception message
+ * @param e
+ * parent exception (reason)
+ */
+ public InvalidOverviewFile(String message, Exception e) {
+ super(message, e);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * exception message
+ */
+ public InvalidOverviewFile(String message) {
+ super(message);
+ }
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/OverviewParser.java b/converter/src/main/java/lcsb/mapviewer/converter/OverviewParser.java
index 0e2473ec1b..adcf556305 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/OverviewParser.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/OverviewParser.java
@@ -1,459 +1,459 @@
-package lcsb.mapviewer.converter;
-
-import java.awt.Polygon;
-import java.awt.geom.Area;
-import java.awt.geom.Point2D;
-import java.awt.image.BufferedImage;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.ArrayList;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipFile;
-
-import javax.imageio.ImageIO;
-
-import org.apache.commons.io.FilenameUtils;
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
-import lcsb.mapviewer.model.map.OverviewImage;
-import lcsb.mapviewer.model.map.OverviewImageLink;
-import lcsb.mapviewer.model.map.OverviewLink;
-import lcsb.mapviewer.model.map.OverviewModelLink;
-import lcsb.mapviewer.model.map.OverviewSearchLink;
-import lcsb.mapviewer.model.map.model.Model;
-
-/**
- * Parser used to extract data about {@link OverviewImage overview images} from
- * zip file.
- *
- * @author Piotr Gawron
- *
- */
-public class OverviewParser {
- /**
- * Name of the file in zip archive where information about connections between
- * {@link OverviewImage images} and models are stored. This file is tab
- * separated file where every row contains information about single connection.
- */
- private static final String COORDINATES_FILENAME = "coords.txt";
-
- /**
- * Name of the column in {@link #COORDINATES_FILENAME} where information about
- * {@link OverviewModelLink#zoomLevel} is stored.
- */
- private static final String ZOOM_LEVEL_COORDINATES_COLUMN = "MODEL_ZOOM_LEVEL";
- /**
- * Name of the column in {@link #COORDINATES_FILENAME} where information about
- * {@link OverviewModelLink#xCoord},{@link OverviewModelLink#yCoord} is stored.
- */
- private static final String REDIRECTION_COORDINATES_COORDINATE_COLUMN = "MODEL_COORDINATES";
- /**
- * Name of the column in {@link #COORDINATES_FILENAME} where information about
- * {@link OverviewModelLink#linkedModel} or
- * {@link OverviewImageLink#linkedOverviewImage} is stored.
- */
- private static final String TARGET_FILENAME_COORDINATE_COLUMN = "LINK_TARGET";
- /**
- * Name of the column in {@link #COORDINATES_FILENAME} where information about
- * {@link OverviewLink#polygon} is stored.
- */
- private static final String POLYGON_COORDINATE_COLUMN = "POLYGON";
- /**
- * Name of the column in {@link #COORDINATES_FILENAME} where information about
- * {@link OverviewLink#overviewImage source of the image} is stored.
- */
- private static final String FILENAME_COORDINATE_COLUMN = "FILE";
-
- /**
- * Name of the column in {@link #COORDINATES_FILENAME} where information about
- * type of the link (implementation of {@link OverviewLink} class) is stored.
- */
- private static final String TARGET_TYPE_COORDINATE_COLUMN = "LINK_TYPE";
-
- /**
- * Name of the column in {@link #COORDINATES_FILENAME} where comment about link
- * is stored.
- */
- private static final String COMMENT_COORDINATE_COLUMN = "COMMENT";
-
- /**
- * Size of the buffer used to access data from input stream.
- */
- private static final Integer BUFFER_SIZE = 1024;
-
- /**
- * String identifying {@link OverviewModelLink} connections.
- */
- private static final String MODEL_LINK_TYPE = "MODEL";
-
- /**
- * String identifying {@link OverviewImageLink} connections between images.
- */
- private static final String IMAGE_LINK_TYPE = "IMAGE";
-
- /**
- * String identifying {@link OverviewSearchLink} connections.
- */
- private static final String SEARCH_LINK_TYPE = "SEARCH";
-
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(OverviewParser.class);
-
- /**
- * Method that parse zip file and creates list of {@link OverviewImage images}
- * from it.
- *
- * @param models
- * map with models where the key is name of the file and value is model
- * that was parsed from the file
- * @param files
- * list with files to parse
- * @param outputDirectory
- * directory where images should be stored, directory path should be
- * absolute
- * @return list of {@link OverviewImage images}
- * @throws InvalidOverviewFile
- * thrown when the zip file contains invalid data
- */
- public List<OverviewImage> parseOverviewLinks(Set<Model> models, List<ImageZipEntryFile> files,
- String outputDirectory, ZipFile zipFile) throws InvalidOverviewFile {
- if (outputDirectory != null) {
- File f = new File(outputDirectory);
- if (!f.exists()) {
- logger.info("Directory \"" + outputDirectory + "\" doesn't exist. Creating...");
- if (!f.mkdirs()) {
- throw new InvalidArgumentException("Problem with crating directory: " + outputDirectory);
- }
- }
- }
- List<OverviewImage> result = new ArrayList<>();
-
- Map<String, ZipEntry> zipEntriesByLowerCaseName = new HashMap<>();
-
- Enumeration<? extends ZipEntry> entries = zipFile.entries();
- while (entries.hasMoreElements()) {
- ZipEntry entry = entries.nextElement();
- if (!entry.isDirectory()) {
- zipEntriesByLowerCaseName.put(entry.getName().toLowerCase(), entry);
- }
- }
-
- String coordinates = null;
-
- try {
- for (ImageZipEntryFile entry : files) {
- String filename = FilenameUtils.getName(entry.getFilename());
- // process image
- if (filename.toLowerCase().endsWith("png")) {
- OverviewImage oi = new OverviewImage();
- oi.setFilename(filename);
-
- File imageFile = null;
- // copy file to file system
- if (outputDirectory != null) {
- imageFile = new File(outputDirectory + "/" + filename);
- } else { // or temporary file
- imageFile = File.createTempFile("temp-file-name", ".png");
- imageFile.deleteOnExit();
- }
- FileOutputStream fos = new FileOutputStream(imageFile);
- byte[] bytes = new byte[BUFFER_SIZE];
- int length;
- InputStream is = zipFile.getInputStream(zipEntriesByLowerCaseName.get(entry.getFilename().toLowerCase()));
- while ((length = is.read(bytes)) >= 0) {
- fos.write(bytes, 0, length);
- }
- fos.close();
-
- // read info about image
- BufferedImage bimg = ImageIO.read(imageFile);
- oi.setWidth(bimg.getWidth());
- oi.setHeight(bimg.getHeight());
- result.add(oi);
-
- // store coordinates file
- } else if (filename.equalsIgnoreCase(COORDINATES_FILENAME)) {
- StringBuilder sb = new StringBuilder("");
- byte[] buffer = new byte[BUFFER_SIZE];
- int read = 0;
- InputStream is = zipFile.getInputStream(zipEntriesByLowerCaseName.get(entry.getFilename().toLowerCase()));
- while ((read = is.read(buffer)) >= 0) {
- sb.append(new String(buffer, 0, read));
- }
- coordinates = sb.toString();
- } else {
- throw new InvalidOverviewFile("Unknown file in overview images zip archive: " + filename);
- }
- }
- } catch (IOException e) {
- throw new InvalidOverviewFile("Problem with overview images file", e);
- }
- if (coordinates == null) {
- throw new InvalidOverviewFile(
- "File with coordinates (\"" + COORDINATES_FILENAME + "\") doesn't exist in overview images zip archive.");
- }
-
- processCoordinates(models, result, coordinates);
- return result;
- }
-
- private Map<String, Model> createMapping(Set<Model> models) {
- Map<String, Model> result = new HashMap<>();
- for (Model model : models) {
- result.put(model.getName().toLowerCase(), model);
- }
- return result;
- }
-
- /**
- * This method process data from {@link #COORDINATES_FILENAME} in zip archive.
- * This method adds connections between images and between images and models.
- *
- * @param models
- * map with models where the key is name of the file and value is model
- * that was parsed from the file
- * @param images
- * list of {@link OverviewImage images} that should be connected
- * @param coordinatesData
- * {@link String} with the data taken from
- * {@link #COORDINATES_FILENAME} file
- * @throws InvalidOverviewFile
- * thrown when the data are invalid
- */
- protected void processCoordinates(Set<Model> models, List<OverviewImage> images, String coordinatesData)
- throws InvalidOverviewFile {
- Map<String, Model> modelMapping = createMapping(models);
- String[] rows = coordinatesData.replaceAll("\r", "\n").split("\n");
- Integer filenameColumn = null;
- Integer polygonColumn = null;
- Integer targetFilenameColumn = null;
- Integer targetTypeColumn = null;
- Integer redirectionCoordinatesColumn = null;
- Integer zoomLevelColumn = null;
- Integer commentColumn = null;
- String[] columns = {};
- int headerLine = -1;
- for (int i = 0; i < rows.length; i++) {
- if (!rows[i].startsWith("#") && (!rows[i].isEmpty())) {
- columns = rows[i].split("\t", -1);
- headerLine = i;
- break;
- }
- }
- int headerColumns = columns.length;
- for (int i = 0; i < columns.length; i++) {
- String string = columns[i].trim();
- if (string.equals(ZOOM_LEVEL_COORDINATES_COLUMN)) {
- if (zoomLevelColumn != null) {
- throw new InvalidCoordinatesFile("Column \"" + string + "\" is redefined.");
- }
- zoomLevelColumn = i;
- } else if (string.equals(REDIRECTION_COORDINATES_COORDINATE_COLUMN)) {
- if (redirectionCoordinatesColumn != null) {
- throw new InvalidCoordinatesFile("Column \"" + string + "\" is redefined.");
- }
- redirectionCoordinatesColumn = i;
- } else if (string.equals(TARGET_FILENAME_COORDINATE_COLUMN)) {
- if (targetFilenameColumn != null) {
- throw new InvalidCoordinatesFile("Column \"" + string + "\" is redefined.");
- }
- targetFilenameColumn = i;
- } else if (string.equals(POLYGON_COORDINATE_COLUMN)) {
- if (polygonColumn != null) {
- throw new InvalidCoordinatesFile("Column \"" + string + "\" is redefined.");
- }
- polygonColumn = i;
- } else if (string.equals(FILENAME_COORDINATE_COLUMN)) {
- if (filenameColumn != null) {
- throw new InvalidCoordinatesFile("Column \"" + string + "\" is redefined.");
- }
- filenameColumn = i;
- } else if (string.equals(TARGET_TYPE_COORDINATE_COLUMN)) {
- if (targetTypeColumn != null) {
- throw new InvalidCoordinatesFile("Column \"" + string + "\" is redefined.");
- }
- targetTypeColumn = i;
- } else if (string.equals(COMMENT_COORDINATE_COLUMN)) {
- if (commentColumn != null) {
- throw new InvalidCoordinatesFile("Column \"" + string + "\" is redefined.");
- }
- commentColumn = i;
- } else {
- throw new InvalidCoordinatesFile("Unknown column name: \"" + string + "\".");
- }
- }
-
- if (filenameColumn == null) {
- throw new InvalidCoordinatesFile(
- "Column \"" + FILENAME_COORDINATE_COLUMN + "\" is not defined, but is required.");
- }
- if (polygonColumn == null) {
- throw new InvalidCoordinatesFile("Column \"" + POLYGON_COORDINATE_COLUMN + "\" is not defined, but is required.");
- }
- if (targetFilenameColumn == null) {
- throw new InvalidCoordinatesFile(
- "Column \"" + TARGET_FILENAME_COORDINATE_COLUMN + "\" is not defined, but is required.");
- }
- if (targetTypeColumn == null) {
- throw new InvalidCoordinatesFile(
- "Column \"" + TARGET_TYPE_COORDINATE_COLUMN + "\" is not defined, but is required.");
- }
- if (redirectionCoordinatesColumn == null) {
- throw new InvalidCoordinatesFile(
- "Column \"" + REDIRECTION_COORDINATES_COORDINATE_COLUMN + "\" is not defined, but is required.");
- }
- if (zoomLevelColumn == null) {
- throw new InvalidCoordinatesFile(
- "Column \"" + ZOOM_LEVEL_COORDINATES_COLUMN + "\" is not defined, but is required.");
- }
-
- for (int i = headerLine + 1; i < rows.length; i++) {
- String row = rows[i];
- if (!row.isEmpty() && !row.startsWith("#")) {
- columns = row.split("\t", -1);
- if (columns.length != headerColumns) {
- throw new InvalidCoordinatesFile("Invalid number of columns (" + columns.length + " found, but "
- + headerColumns + " expected). Row: \"" + row + "\"");
- }
- String filename = columns[filenameColumn];
- String polygon = columns[polygonColumn];
- String modelName = FilenameUtils.getBaseName(columns[targetFilenameColumn]);
- String coord = columns[redirectionCoordinatesColumn];
- String zoomLevel = columns[zoomLevelColumn];
- String linkType = columns[targetTypeColumn];
- createOverviewLink(filename, polygon, modelName, coord, zoomLevel, linkType, images, modelMapping);
- }
- }
- for (OverviewImage image : images) {
- for (int i = 0; i < image.getLinks().size(); i++) {
- for (int j = i + 1; j < image.getLinks().size(); j++) {
- OverviewLink ol = image.getLinks().get(i);
- OverviewLink ol2 = image.getLinks().get(j);
-
- Polygon polygon = new Polygon();
- for (Point2D point : ol.getPolygonCoordinates()) {
- polygon.addPoint((int) point.getX(), (int) point.getY());
- }
- Polygon polygon2 = new Polygon();
- for (Point2D point : ol2.getPolygonCoordinates()) {
- polygon2.addPoint((int) point.getX(), (int) point.getY());
- }
- Area area = new Area(polygon);
- Area area2 = new Area(polygon2);
- area.intersect(area2);
- if (!area.isEmpty()) {
- throw new InvalidOverviewFile("Polygon coordinates in " + COORDINATES_FILENAME + " file overlap. Image: "
- + image.getFilename() + "; polgyon1 = " + ol.getPolygon() + "; polygon2 = " + ol2.getPolygon());
- }
- }
- }
- }
-
- }
-
- /**
- * Creates a link from parameters and place it in appropriate
- * {@link OverviewImage}.
- *
- * @param filename
- * {@link OverviewImage#filename name of the image}
- * @param polygon
- * {@link OverviewImage#polygon polygon} describing link
- * @param linkTarget
- * defines target that should be invoked when the link is activated.
- * This target is either a file name (in case of
- * {@link #MODEL_LINK_TYPE} or {@link #IMAGE_LINK_TYPE}) or a search
- * string (in case of {@link #SEARCH_LINK_TYPE}).
- * @param coord
- * coordinates on the model where redirection should be placed in case
- * of {@link #MODEL_LINK_TYPE} connection
- * @param zoomLevel
- * zoom level on the model where redirection should be placed in case
- * of {@link #MODEL_LINK_TYPE} connection
- * @param linkType
- * type of the connection. This will define implementation of
- * {@link OverviewImage} that will be used. For now three values are
- * acceptable: {@link #MODEL_LINK_TYPE}, {@link #IMAGE_LINK_TYPE},
- * {@link #SEARCH_LINK_TYPE}.
- * @param images
- * list of images that are available
- * @param models
- * list of models that are available
- * @throws InvalidCoordinatesFile
- * thrown when one of the input parameters is invalid
- */
- private void createOverviewLink(String filename, String polygon, String linkTarget, String coord, String zoomLevel,
- String linkType, List<OverviewImage> images, Map<String, Model> models) throws InvalidCoordinatesFile {
- OverviewImage image = null;
- for (OverviewImage oi : images) {
- if (oi.getFilename().equalsIgnoreCase(filename)) {
- image = oi;
- }
- }
- if (image == null) {
- throw new InvalidCoordinatesFile("Unknown image filename in \"" + COORDINATES_FILENAME + "\": " + filename);
- }
- OverviewLink ol = null;
- if (linkType.equals(MODEL_LINK_TYPE)) {
- Model model = models.get(linkTarget.toLowerCase());
- if (model == null) {
- throw new InvalidCoordinatesFile("Unknown model in \"" + COORDINATES_FILENAME + "\" file: " + linkTarget);
- }
- OverviewModelLink oml = new OverviewModelLink();
- oml.setLinkedModel(model);
- try {
- oml.setxCoord(Double.valueOf(coord.split(",")[0]));
- oml.setyCoord(Double.valueOf(coord.split(",")[1]));
- } catch (NumberFormatException | ArrayIndexOutOfBoundsException e) {
- throw new InvalidCoordinatesFile("Problem with parsing coordinates in file \"" + COORDINATES_FILENAME
- + "\". Problematic text: \"" + coord + "\"", e);
- }
- try {
- oml.setZoomLevel(Integer.valueOf(zoomLevel.trim()));
- } catch (NumberFormatException e) {
- throw new InvalidCoordinatesFile("Problem with parsing zoom level in file \"" + COORDINATES_FILENAME
- + "\". Problematic text: \"" + zoomLevel + "\"", e);
- }
- ol = oml;
- } else if (linkType.equals(IMAGE_LINK_TYPE)) {
- OverviewImage targetImage = null;
- for (OverviewImage oi : images) {
- if (FilenameUtils.removeExtension(oi.getFilename()).equalsIgnoreCase(linkTarget)) {
- targetImage = oi;
- }
- }
- if (targetImage == null) {
- throw new InvalidCoordinatesFile("Unknown image filename in \"" + COORDINATES_FILENAME + "\": " + linkTarget);
- }
- OverviewImageLink oml = new OverviewImageLink();
- oml.setLinkedOverviewImage(targetImage);
- ol = oml;
- } else if (linkType.equals(SEARCH_LINK_TYPE)) {
- OverviewSearchLink osl = new OverviewSearchLink();
- osl.setQuery(linkTarget);
- ol = osl;
- } else {
- throw new InvalidCoordinatesFile("Unknown link in \"" + COORDINATES_FILENAME + "\" file: " + linkTarget);
- }
- ol.setPolygon(polygon);
- for (Point2D point : ol.getPolygonCoordinates()) {
- if (point.getX() > image.getWidth() || point.getY() > image.getHeight() || point.getX() < 0 || point.getY() < 0) {
- throw new InvalidCoordinatesFile("Problem with parsing numbers in file \"" + COORDINATES_FILENAME
- + "\". Polygon coordinates outside image: " + point);
- }
- }
- image.addLink(ol);
-
- }
-}
+package lcsb.mapviewer.converter;
+
+import java.awt.Polygon;
+import java.awt.geom.Area;
+import java.awt.geom.Point2D;
+import java.awt.image.BufferedImage;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipFile;
+
+import javax.imageio.ImageIO;
+
+import org.apache.commons.io.FilenameUtils;
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
+import lcsb.mapviewer.model.map.OverviewImage;
+import lcsb.mapviewer.model.map.OverviewImageLink;
+import lcsb.mapviewer.model.map.OverviewLink;
+import lcsb.mapviewer.model.map.OverviewModelLink;
+import lcsb.mapviewer.model.map.OverviewSearchLink;
+import lcsb.mapviewer.model.map.model.Model;
+
+/**
+ * Parser used to extract data about {@link OverviewImage overview images} from
+ * zip file.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class OverviewParser {
+ /**
+ * Name of the file in zip archive where information about connections between
+ * {@link OverviewImage images} and models are stored. This file is tab
+ * separated file where every row contains information about single connection.
+ */
+ private static final String COORDINATES_FILENAME = "coords.txt";
+
+ /**
+ * Name of the column in {@link #COORDINATES_FILENAME} where information about
+ * {@link OverviewModelLink#zoomLevel} is stored.
+ */
+ private static final String ZOOM_LEVEL_COORDINATES_COLUMN = "MODEL_ZOOM_LEVEL";
+ /**
+ * Name of the column in {@link #COORDINATES_FILENAME} where information about
+ * {@link OverviewModelLink#xCoord},{@link OverviewModelLink#yCoord} is stored.
+ */
+ private static final String REDIRECTION_COORDINATES_COORDINATE_COLUMN = "MODEL_COORDINATES";
+ /**
+ * Name of the column in {@link #COORDINATES_FILENAME} where information about
+ * {@link OverviewModelLink#linkedModel} or
+ * {@link OverviewImageLink#linkedOverviewImage} is stored.
+ */
+ private static final String TARGET_FILENAME_COORDINATE_COLUMN = "LINK_TARGET";
+ /**
+ * Name of the column in {@link #COORDINATES_FILENAME} where information about
+ * {@link OverviewLink#polygon} is stored.
+ */
+ private static final String POLYGON_COORDINATE_COLUMN = "POLYGON";
+ /**
+ * Name of the column in {@link #COORDINATES_FILENAME} where information about
+ * {@link OverviewLink#overviewImage source of the image} is stored.
+ */
+ private static final String FILENAME_COORDINATE_COLUMN = "FILE";
+
+ /**
+ * Name of the column in {@link #COORDINATES_FILENAME} where information about
+ * type of the link (implementation of {@link OverviewLink} class) is stored.
+ */
+ private static final String TARGET_TYPE_COORDINATE_COLUMN = "LINK_TYPE";
+
+ /**
+ * Name of the column in {@link #COORDINATES_FILENAME} where comment about link
+ * is stored.
+ */
+ private static final String COMMENT_COORDINATE_COLUMN = "COMMENT";
+
+ /**
+ * Size of the buffer used to access data from input stream.
+ */
+ private static final Integer BUFFER_SIZE = 1024;
+
+ /**
+ * String identifying {@link OverviewModelLink} connections.
+ */
+ private static final String MODEL_LINK_TYPE = "MODEL";
+
+ /**
+ * String identifying {@link OverviewImageLink} connections between images.
+ */
+ private static final String IMAGE_LINK_TYPE = "IMAGE";
+
+ /**
+ * String identifying {@link OverviewSearchLink} connections.
+ */
+ private static final String SEARCH_LINK_TYPE = "SEARCH";
+
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(OverviewParser.class);
+
+ /**
+ * Method that parse zip file and creates list of {@link OverviewImage images}
+ * from it.
+ *
+ * @param models
+ * map with models where the key is name of the file and value is model
+ * that was parsed from the file
+ * @param files
+ * list with files to parse
+ * @param outputDirectory
+ * directory where images should be stored, directory path should be
+ * absolute
+ * @return list of {@link OverviewImage images}
+ * @throws InvalidOverviewFile
+ * thrown when the zip file contains invalid data
+ */
+ public List<OverviewImage> parseOverviewLinks(Set<Model> models, List<ImageZipEntryFile> files,
+ String outputDirectory, ZipFile zipFile) throws InvalidOverviewFile {
+ if (outputDirectory != null) {
+ File f = new File(outputDirectory);
+ if (!f.exists()) {
+ logger.info("Directory \"" + outputDirectory + "\" doesn't exist. Creating...");
+ if (!f.mkdirs()) {
+ throw new InvalidArgumentException("Problem with crating directory: " + outputDirectory);
+ }
+ }
+ }
+ List<OverviewImage> result = new ArrayList<>();
+
+ Map<String, ZipEntry> zipEntriesByLowerCaseName = new HashMap<>();
+
+ Enumeration<? extends ZipEntry> entries = zipFile.entries();
+ while (entries.hasMoreElements()) {
+ ZipEntry entry = entries.nextElement();
+ if (!entry.isDirectory()) {
+ zipEntriesByLowerCaseName.put(entry.getName().toLowerCase(), entry);
+ }
+ }
+
+ String coordinates = null;
+
+ try {
+ for (ImageZipEntryFile entry : files) {
+ String filename = FilenameUtils.getName(entry.getFilename());
+ // process image
+ if (filename.toLowerCase().endsWith("png")) {
+ OverviewImage oi = new OverviewImage();
+ oi.setFilename(filename);
+
+ File imageFile = null;
+ // copy file to file system
+ if (outputDirectory != null) {
+ imageFile = new File(outputDirectory + "/" + filename);
+ } else { // or temporary file
+ imageFile = File.createTempFile("temp-file-name", ".png");
+ imageFile.deleteOnExit();
+ }
+ FileOutputStream fos = new FileOutputStream(imageFile);
+ byte[] bytes = new byte[BUFFER_SIZE];
+ int length;
+ InputStream is = zipFile.getInputStream(zipEntriesByLowerCaseName.get(entry.getFilename().toLowerCase()));
+ while ((length = is.read(bytes)) >= 0) {
+ fos.write(bytes, 0, length);
+ }
+ fos.close();
+
+ // read info about image
+ BufferedImage bimg = ImageIO.read(imageFile);
+ oi.setWidth(bimg.getWidth());
+ oi.setHeight(bimg.getHeight());
+ result.add(oi);
+
+ // store coordinates file
+ } else if (filename.equalsIgnoreCase(COORDINATES_FILENAME)) {
+ StringBuilder sb = new StringBuilder("");
+ byte[] buffer = new byte[BUFFER_SIZE];
+ int read = 0;
+ InputStream is = zipFile.getInputStream(zipEntriesByLowerCaseName.get(entry.getFilename().toLowerCase()));
+ while ((read = is.read(buffer)) >= 0) {
+ sb.append(new String(buffer, 0, read));
+ }
+ coordinates = sb.toString();
+ } else {
+ throw new InvalidOverviewFile("Unknown file in overview images zip archive: " + filename);
+ }
+ }
+ } catch (IOException e) {
+ throw new InvalidOverviewFile("Problem with overview images file", e);
+ }
+ if (coordinates == null) {
+ throw new InvalidOverviewFile(
+ "File with coordinates (\"" + COORDINATES_FILENAME + "\") doesn't exist in overview images zip archive.");
+ }
+
+ processCoordinates(models, result, coordinates);
+ return result;
+ }
+
+ private Map<String, Model> createMapping(Set<Model> models) {
+ Map<String, Model> result = new HashMap<>();
+ for (Model model : models) {
+ result.put(model.getName().toLowerCase(), model);
+ }
+ return result;
+ }
+
+ /**
+ * This method process data from {@link #COORDINATES_FILENAME} in zip archive.
+ * This method adds connections between images and between images and models.
+ *
+ * @param models
+ * map with models where the key is name of the file and value is model
+ * that was parsed from the file
+ * @param images
+ * list of {@link OverviewImage images} that should be connected
+ * @param coordinatesData
+ * {@link String} with the data taken from
+ * {@link #COORDINATES_FILENAME} file
+ * @throws InvalidOverviewFile
+ * thrown when the data are invalid
+ */
+ protected void processCoordinates(Set<Model> models, List<OverviewImage> images, String coordinatesData)
+ throws InvalidOverviewFile {
+ Map<String, Model> modelMapping = createMapping(models);
+ String[] rows = coordinatesData.replaceAll("\r", "\n").split("\n");
+ Integer filenameColumn = null;
+ Integer polygonColumn = null;
+ Integer targetFilenameColumn = null;
+ Integer targetTypeColumn = null;
+ Integer redirectionCoordinatesColumn = null;
+ Integer zoomLevelColumn = null;
+ Integer commentColumn = null;
+ String[] columns = {};
+ int headerLine = -1;
+ for (int i = 0; i < rows.length; i++) {
+ if (!rows[i].startsWith("#") && (!rows[i].isEmpty())) {
+ columns = rows[i].split("\t", -1);
+ headerLine = i;
+ break;
+ }
+ }
+ int headerColumns = columns.length;
+ for (int i = 0; i < columns.length; i++) {
+ String string = columns[i].trim();
+ if (string.equals(ZOOM_LEVEL_COORDINATES_COLUMN)) {
+ if (zoomLevelColumn != null) {
+ throw new InvalidCoordinatesFile("Column \"" + string + "\" is redefined.");
+ }
+ zoomLevelColumn = i;
+ } else if (string.equals(REDIRECTION_COORDINATES_COORDINATE_COLUMN)) {
+ if (redirectionCoordinatesColumn != null) {
+ throw new InvalidCoordinatesFile("Column \"" + string + "\" is redefined.");
+ }
+ redirectionCoordinatesColumn = i;
+ } else if (string.equals(TARGET_FILENAME_COORDINATE_COLUMN)) {
+ if (targetFilenameColumn != null) {
+ throw new InvalidCoordinatesFile("Column \"" + string + "\" is redefined.");
+ }
+ targetFilenameColumn = i;
+ } else if (string.equals(POLYGON_COORDINATE_COLUMN)) {
+ if (polygonColumn != null) {
+ throw new InvalidCoordinatesFile("Column \"" + string + "\" is redefined.");
+ }
+ polygonColumn = i;
+ } else if (string.equals(FILENAME_COORDINATE_COLUMN)) {
+ if (filenameColumn != null) {
+ throw new InvalidCoordinatesFile("Column \"" + string + "\" is redefined.");
+ }
+ filenameColumn = i;
+ } else if (string.equals(TARGET_TYPE_COORDINATE_COLUMN)) {
+ if (targetTypeColumn != null) {
+ throw new InvalidCoordinatesFile("Column \"" + string + "\" is redefined.");
+ }
+ targetTypeColumn = i;
+ } else if (string.equals(COMMENT_COORDINATE_COLUMN)) {
+ if (commentColumn != null) {
+ throw new InvalidCoordinatesFile("Column \"" + string + "\" is redefined.");
+ }
+ commentColumn = i;
+ } else {
+ throw new InvalidCoordinatesFile("Unknown column name: \"" + string + "\".");
+ }
+ }
+
+ if (filenameColumn == null) {
+ throw new InvalidCoordinatesFile(
+ "Column \"" + FILENAME_COORDINATE_COLUMN + "\" is not defined, but is required.");
+ }
+ if (polygonColumn == null) {
+ throw new InvalidCoordinatesFile("Column \"" + POLYGON_COORDINATE_COLUMN + "\" is not defined, but is required.");
+ }
+ if (targetFilenameColumn == null) {
+ throw new InvalidCoordinatesFile(
+ "Column \"" + TARGET_FILENAME_COORDINATE_COLUMN + "\" is not defined, but is required.");
+ }
+ if (targetTypeColumn == null) {
+ throw new InvalidCoordinatesFile(
+ "Column \"" + TARGET_TYPE_COORDINATE_COLUMN + "\" is not defined, but is required.");
+ }
+ if (redirectionCoordinatesColumn == null) {
+ throw new InvalidCoordinatesFile(
+ "Column \"" + REDIRECTION_COORDINATES_COORDINATE_COLUMN + "\" is not defined, but is required.");
+ }
+ if (zoomLevelColumn == null) {
+ throw new InvalidCoordinatesFile(
+ "Column \"" + ZOOM_LEVEL_COORDINATES_COLUMN + "\" is not defined, but is required.");
+ }
+
+ for (int i = headerLine + 1; i < rows.length; i++) {
+ String row = rows[i];
+ if (!row.isEmpty() && !row.startsWith("#")) {
+ columns = row.split("\t", -1);
+ if (columns.length != headerColumns) {
+ throw new InvalidCoordinatesFile("Invalid number of columns (" + columns.length + " found, but "
+ + headerColumns + " expected). Row: \"" + row + "\"");
+ }
+ String filename = columns[filenameColumn];
+ String polygon = columns[polygonColumn];
+ String modelName = FilenameUtils.getBaseName(columns[targetFilenameColumn]);
+ String coord = columns[redirectionCoordinatesColumn];
+ String zoomLevel = columns[zoomLevelColumn];
+ String linkType = columns[targetTypeColumn];
+ createOverviewLink(filename, polygon, modelName, coord, zoomLevel, linkType, images, modelMapping);
+ }
+ }
+ for (OverviewImage image : images) {
+ for (int i = 0; i < image.getLinks().size(); i++) {
+ for (int j = i + 1; j < image.getLinks().size(); j++) {
+ OverviewLink ol = image.getLinks().get(i);
+ OverviewLink ol2 = image.getLinks().get(j);
+
+ Polygon polygon = new Polygon();
+ for (Point2D point : ol.getPolygonCoordinates()) {
+ polygon.addPoint((int) point.getX(), (int) point.getY());
+ }
+ Polygon polygon2 = new Polygon();
+ for (Point2D point : ol2.getPolygonCoordinates()) {
+ polygon2.addPoint((int) point.getX(), (int) point.getY());
+ }
+ Area area = new Area(polygon);
+ Area area2 = new Area(polygon2);
+ area.intersect(area2);
+ if (!area.isEmpty()) {
+ throw new InvalidOverviewFile("Polygon coordinates in " + COORDINATES_FILENAME + " file overlap. Image: "
+ + image.getFilename() + "; polgyon1 = " + ol.getPolygon() + "; polygon2 = " + ol2.getPolygon());
+ }
+ }
+ }
+ }
+
+ }
+
+ /**
+ * Creates a link from parameters and place it in appropriate
+ * {@link OverviewImage}.
+ *
+ * @param filename
+ * {@link OverviewImage#filename name of the image}
+ * @param polygon
+ * {@link OverviewImage#polygon polygon} describing link
+ * @param linkTarget
+ * defines target that should be invoked when the link is activated.
+ * This target is either a file name (in case of
+ * {@link #MODEL_LINK_TYPE} or {@link #IMAGE_LINK_TYPE}) or a search
+ * string (in case of {@link #SEARCH_LINK_TYPE}).
+ * @param coord
+ * coordinates on the model where redirection should be placed in case
+ * of {@link #MODEL_LINK_TYPE} connection
+ * @param zoomLevel
+ * zoom level on the model where redirection should be placed in case
+ * of {@link #MODEL_LINK_TYPE} connection
+ * @param linkType
+ * type of the connection. This will define implementation of
+ * {@link OverviewImage} that will be used. For now three values are
+ * acceptable: {@link #MODEL_LINK_TYPE}, {@link #IMAGE_LINK_TYPE},
+ * {@link #SEARCH_LINK_TYPE}.
+ * @param images
+ * list of images that are available
+ * @param models
+ * list of models that are available
+ * @throws InvalidCoordinatesFile
+ * thrown when one of the input parameters is invalid
+ */
+ private void createOverviewLink(String filename, String polygon, String linkTarget, String coord, String zoomLevel,
+ String linkType, List<OverviewImage> images, Map<String, Model> models) throws InvalidCoordinatesFile {
+ OverviewImage image = null;
+ for (OverviewImage oi : images) {
+ if (oi.getFilename().equalsIgnoreCase(filename)) {
+ image = oi;
+ }
+ }
+ if (image == null) {
+ throw new InvalidCoordinatesFile("Unknown image filename in \"" + COORDINATES_FILENAME + "\": " + filename);
+ }
+ OverviewLink ol = null;
+ if (linkType.equals(MODEL_LINK_TYPE)) {
+ Model model = models.get(linkTarget.toLowerCase());
+ if (model == null) {
+ throw new InvalidCoordinatesFile("Unknown model in \"" + COORDINATES_FILENAME + "\" file: " + linkTarget);
+ }
+ OverviewModelLink oml = new OverviewModelLink();
+ oml.setLinkedModel(model);
+ try {
+ oml.setxCoord(Double.valueOf(coord.split(",")[0]));
+ oml.setyCoord(Double.valueOf(coord.split(",")[1]));
+ } catch (NumberFormatException | ArrayIndexOutOfBoundsException e) {
+ throw new InvalidCoordinatesFile("Problem with parsing coordinates in file \"" + COORDINATES_FILENAME
+ + "\". Problematic text: \"" + coord + "\"", e);
+ }
+ try {
+ oml.setZoomLevel(Integer.valueOf(zoomLevel.trim()));
+ } catch (NumberFormatException e) {
+ throw new InvalidCoordinatesFile("Problem with parsing zoom level in file \"" + COORDINATES_FILENAME
+ + "\". Problematic text: \"" + zoomLevel + "\"", e);
+ }
+ ol = oml;
+ } else if (linkType.equals(IMAGE_LINK_TYPE)) {
+ OverviewImage targetImage = null;
+ for (OverviewImage oi : images) {
+ if (FilenameUtils.removeExtension(oi.getFilename()).equalsIgnoreCase(linkTarget)) {
+ targetImage = oi;
+ }
+ }
+ if (targetImage == null) {
+ throw new InvalidCoordinatesFile("Unknown image filename in \"" + COORDINATES_FILENAME + "\": " + linkTarget);
+ }
+ OverviewImageLink oml = new OverviewImageLink();
+ oml.setLinkedOverviewImage(targetImage);
+ ol = oml;
+ } else if (linkType.equals(SEARCH_LINK_TYPE)) {
+ OverviewSearchLink osl = new OverviewSearchLink();
+ osl.setQuery(linkTarget);
+ ol = osl;
+ } else {
+ throw new InvalidCoordinatesFile("Unknown link in \"" + COORDINATES_FILENAME + "\" file: " + linkTarget);
+ }
+ ol.setPolygon(polygon);
+ for (Point2D point : ol.getPolygonCoordinates()) {
+ if (point.getX() > image.getWidth() || point.getY() > image.getHeight() || point.getX() < 0 || point.getY() < 0) {
+ throw new InvalidCoordinatesFile("Problem with parsing numbers in file \"" + COORDINATES_FILENAME
+ + "\". Polygon coordinates outside image: " + point);
+ }
+ }
+ image.addLink(ol);
+
+ }
+}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParser.java b/converter/src/main/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParser.java
index c6ebc15d1c..c5562b249b 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParser.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParser.java
@@ -1,193 +1,193 @@
-package lcsb.mapviewer.converter.annotation;
-
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import lcsb.mapviewer.common.XmlParser;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
-
-/**
- * This class allow to parse xml nodes responsible for species annotations in
- * CellDesigner.
- *
- * @author Piotr Gawron
- *
- */
-public class XmlAnnotationParser extends XmlParser {
-
- /**
- * Deafult logger.
- */
- private static Logger logger = Logger.getLogger(XmlAnnotationParser.class.getName());
-
- /**
- * Default constructor.
- */
- public XmlAnnotationParser() {
- }
-
- /**
- * This method parse the xml string passed as an argument. All information
- * obtained by the method are stored in local variables: miriamDataSet,
- * speciesId and can be accessed later on.
- *
- * @param data
- * - xml string to be parsed
- *
- * @return collection of miriam objects that were obtained from the xml node
- * @throws InvalidXmlSchemaException
- * thrown when there is a problem with xml
- */
- public Set<MiriamData> parse(String data) throws InvalidXmlSchemaException {
- // start from creating a DOM parser and parse the whole document
- Document doc = getXmlDocumentFromString(data);
-
- NodeList root = doc.getChildNodes();
-
- // process the whole schema
- return parseRdfNode(root);
- }
-
- /**
- * Retrieves set of Miriam annotation from xml rdf node.
- *
- * @param root
- * xml node list
- * @return set of miriam annotations.
- * @throws InvalidXmlSchemaException
- * thrown when there is a problem with xml
- */
- public Set<MiriamData> parseRdfNode(NodeList root) throws InvalidXmlSchemaException {
- Node rdf = getNode("rdf:RDF", root);
- return parseRdfNode(rdf);
- }
-
- /**
- * Retrieves set of Miriam annotation from xml rdf node.
- *
- * @param rdf
- * xml node
- * @return set of miriam annotations.
- * @throws InvalidXmlSchemaException
- * thrown when there is a problem with xml
- */
- public Set<MiriamData> parseRdfNode(Node rdf) throws InvalidXmlSchemaException {
- Set<MiriamData> miriamDataSet = new HashSet<MiriamData>();
- if (rdf != null) {
- Node description = getNode("rdf:Description", rdf.getChildNodes());
- if (description != null) {
- NodeList list = description.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- miriamDataSet.addAll(parseMiriamNode(node));
- }
- }
- } else {
- throw new InvalidXmlSchemaException("rdf:Description node not found");
- }
- } else {
- throw new InvalidXmlSchemaException("rdf:Rdf node not found");
- }
- return miriamDataSet;
- }
-
- /**
- * This method converts a xml node into MiriamData object (annotation of a
- * species).
- *
- * @param node
- * - xml node that contains representation of a single annotation of
- * a species
- * @return MiriamData object that represents annotation of a species
- * @throws InvalidXmlSchemaException
- * thrown when there is a problem with xml
- */
- public Set<MiriamData> parseMiriamNode(Node node) throws InvalidXmlSchemaException {
- Set<MiriamData> result = new HashSet<MiriamData>();
- NodeList list = node.getChildNodes();
- String relationTypeString = node.getNodeName();
- MiriamRelationType relationType = MiriamRelationType.getTypeByStringRepresentation(relationTypeString);
- Node bag = getNode("rdf:Bag", list);
- if (bag == null) {
- throw new InvalidXmlSchemaException("No rdf:Bag node found");
- }
- list = bag.getChildNodes();
- List<Node> nodes = getNodes("rdf:li", list);
- for (Node li : nodes) {
- String dataTypeUri = getNodeAttr("rdf:resource", li);
- if (dataTypeUri == null || dataTypeUri.isEmpty()) {
- throw new InvalidXmlSchemaException("rdf:li does not have a rdf:resource attribute");
- }
-
- try {
- MiriamData md = MiriamType.getMiriamByUri(dataTypeUri);
- if (relationType == null) {
- logger.warn("Unknown relation type: " + relationTypeString + ". For miriam uri: " + dataTypeUri + ".");
- } else {
- if (!MiriamType.PUBMED.equals(md.getDataType())) {
- md.setRelationType(relationType);
- }
- result.add(md);
- }
- } catch (InvalidArgumentException e) {
- logger.warn(e.getMessage());
- }
- }
- return result;
- }
-
- /**
- * This method converts a set of MiriamData into xml string that can be put to
- * CellDesigner schema.
- *
- * @param data
- * - a set of MiriamData to be converted.
- * @return xml string representation of the input data
- */
- public String dataSetToXmlString(Collection<MiriamData> data) {
- StringBuilder result = new StringBuilder("");
- result.append(
- "<rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" " + "xmlns:dc=\"http://purl.org/dc/elements/1.1/\" "
- + "xmlns:dcterms=\"http://purl.org/dc/terms/\" " + "xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" "
- + "xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" " + "xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n");
- result.append("<rdf:Description rdf:about=\"#\">\n");
- for (MiriamData miriamData : data) {
- result.append(miriamDataToXmlString(miriamData));
- }
- result.append("</rdf:Description>\n");
- result.append("</rdf:RDF>\n");
- return result.toString();
- }
-
- /**
- * This method converts a single MiriamData into xml string that can be put to
- * CellDesigner schema.
- *
- * @param data
- * - a MiriamData to be converted.
- * @return xml string representation of the input data
- */
- public String miriamDataToXmlString(MiriamData data) {
- StringBuilder result = new StringBuilder("");
- result.append("<" + data.getRelationType().getStringRepresentation() + ">\n");
- result.append("<rdf:Bag>\n");
- result.append("<rdf:li rdf:resource=\"" + data.getDataType().getUris().get(0) + ":" + data.getResource().replaceAll(":", "%3A") + "\"/>\n");
- result.append("</rdf:Bag>\n");
- result.append("</" + data.getRelationType().getStringRepresentation() + ">\n");
-
- return result.toString();
- }
-
-}
+package lcsb.mapviewer.converter.annotation;
+
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.w3c.dom.Document;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
+
+/**
+ * This class allow to parse xml nodes responsible for species annotations in
+ * CellDesigner.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class XmlAnnotationParser extends XmlParser {
+
+ /**
+ * Deafult logger.
+ */
+ private static Logger logger = Logger.getLogger(XmlAnnotationParser.class.getName());
+
+ /**
+ * Default constructor.
+ */
+ public XmlAnnotationParser() {
+ }
+
+ /**
+ * This method parse the xml string passed as an argument. All information
+ * obtained by the method are stored in local variables: miriamDataSet,
+ * speciesId and can be accessed later on.
+ *
+ * @param data
+ * - xml string to be parsed
+ *
+ * @return collection of miriam objects that were obtained from the xml node
+ * @throws InvalidXmlSchemaException
+ * thrown when there is a problem with xml
+ */
+ public Set<MiriamData> parse(String data) throws InvalidXmlSchemaException {
+ // start from creating a DOM parser and parse the whole document
+ Document doc = getXmlDocumentFromString(data);
+
+ NodeList root = doc.getChildNodes();
+
+ // process the whole schema
+ return parseRdfNode(root);
+ }
+
+ /**
+ * Retrieves set of Miriam annotation from xml rdf node.
+ *
+ * @param root
+ * xml node list
+ * @return set of miriam annotations.
+ * @throws InvalidXmlSchemaException
+ * thrown when there is a problem with xml
+ */
+ public Set<MiriamData> parseRdfNode(NodeList root) throws InvalidXmlSchemaException {
+ Node rdf = getNode("rdf:RDF", root);
+ return parseRdfNode(rdf);
+ }
+
+ /**
+ * Retrieves set of Miriam annotation from xml rdf node.
+ *
+ * @param rdf
+ * xml node
+ * @return set of miriam annotations.
+ * @throws InvalidXmlSchemaException
+ * thrown when there is a problem with xml
+ */
+ public Set<MiriamData> parseRdfNode(Node rdf) throws InvalidXmlSchemaException {
+ Set<MiriamData> miriamDataSet = new HashSet<MiriamData>();
+ if (rdf != null) {
+ Node description = getNode("rdf:Description", rdf.getChildNodes());
+ if (description != null) {
+ NodeList list = description.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ miriamDataSet.addAll(parseMiriamNode(node));
+ }
+ }
+ } else {
+ throw new InvalidXmlSchemaException("rdf:Description node not found");
+ }
+ } else {
+ throw new InvalidXmlSchemaException("rdf:Rdf node not found");
+ }
+ return miriamDataSet;
+ }
+
+ /**
+ * This method converts a xml node into MiriamData object (annotation of a
+ * species).
+ *
+ * @param node
+ * - xml node that contains representation of a single annotation of
+ * a species
+ * @return MiriamData object that represents annotation of a species
+ * @throws InvalidXmlSchemaException
+ * thrown when there is a problem with xml
+ */
+ public Set<MiriamData> parseMiriamNode(Node node) throws InvalidXmlSchemaException {
+ Set<MiriamData> result = new HashSet<MiriamData>();
+ NodeList list = node.getChildNodes();
+ String relationTypeString = node.getNodeName();
+ MiriamRelationType relationType = MiriamRelationType.getTypeByStringRepresentation(relationTypeString);
+ Node bag = getNode("rdf:Bag", list);
+ if (bag == null) {
+ throw new InvalidXmlSchemaException("No rdf:Bag node found");
+ }
+ list = bag.getChildNodes();
+ List<Node> nodes = getNodes("rdf:li", list);
+ for (Node li : nodes) {
+ String dataTypeUri = getNodeAttr("rdf:resource", li);
+ if (dataTypeUri == null || dataTypeUri.isEmpty()) {
+ throw new InvalidXmlSchemaException("rdf:li does not have a rdf:resource attribute");
+ }
+
+ try {
+ MiriamData md = MiriamType.getMiriamByUri(dataTypeUri);
+ if (relationType == null) {
+ logger.warn("Unknown relation type: " + relationTypeString + ". For miriam uri: " + dataTypeUri + ".");
+ } else {
+ if (!MiriamType.PUBMED.equals(md.getDataType())) {
+ md.setRelationType(relationType);
+ }
+ result.add(md);
+ }
+ } catch (InvalidArgumentException e) {
+ logger.warn(e.getMessage());
+ }
+ }
+ return result;
+ }
+
+ /**
+ * This method converts a set of MiriamData into xml string that can be put to
+ * CellDesigner schema.
+ *
+ * @param data
+ * - a set of MiriamData to be converted.
+ * @return xml string representation of the input data
+ */
+ public String dataSetToXmlString(Collection<MiriamData> data) {
+ StringBuilder result = new StringBuilder("");
+ result.append(
+ "<rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" " + "xmlns:dc=\"http://purl.org/dc/elements/1.1/\" "
+ + "xmlns:dcterms=\"http://purl.org/dc/terms/\" " + "xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" "
+ + "xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" " + "xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n");
+ result.append("<rdf:Description rdf:about=\"#\">\n");
+ for (MiriamData miriamData : data) {
+ result.append(miriamDataToXmlString(miriamData));
+ }
+ result.append("</rdf:Description>\n");
+ result.append("</rdf:RDF>\n");
+ return result.toString();
+ }
+
+ /**
+ * This method converts a single MiriamData into xml string that can be put to
+ * CellDesigner schema.
+ *
+ * @param data
+ * - a MiriamData to be converted.
+ * @return xml string representation of the input data
+ */
+ public String miriamDataToXmlString(MiriamData data) {
+ StringBuilder result = new StringBuilder("");
+ result.append("<" + data.getRelationType().getStringRepresentation() + ">\n");
+ result.append("<rdf:Bag>\n");
+ result.append("<rdf:li rdf:resource=\"" + data.getDataType().getUris().get(0) + ":" + data.getResource().replaceAll(":", "%3A") + "\"/>\n");
+ result.append("</rdf:Bag>\n");
+ result.append("</" + data.getRelationType().getStringRepresentation() + ">\n");
+
+ return result.toString();
+ }
+
+}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/package-info.java b/converter/src/main/java/lcsb/mapviewer/converter/package-info.java
index fb1838ce22..4ebbd0ce6b 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/package-info.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/package-info.java
@@ -1,7 +1,7 @@
-/**
- * Provides generic interface used for reading data and transforming it into
- * {@link lcsb.mapviewer.model.map.model.Model Model} structure.
- *
- */
-package lcsb.mapviewer.converter;
-
+/**
+ * Provides generic interface used for reading data and transforming it into
+ * {@link lcsb.mapviewer.model.map.model.Model Model} structure.
+ *
+ */
+package lcsb.mapviewer.converter;
+
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/zip/ImageZipEntryFile.java b/converter/src/main/java/lcsb/mapviewer/converter/zip/ImageZipEntryFile.java
index cef2d1956b..a7bf34b2c7 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/zip/ImageZipEntryFile.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/zip/ImageZipEntryFile.java
@@ -1,42 +1,42 @@
-package lcsb.mapviewer.converter.zip;
-
-import java.io.IOException;
-import java.io.Serializable;
-
-/**
- * Structure used to describe a file in a zip archive with single entry about
- * {@link lcsb.mapviewer.model.map.OverviewImage}.
- *
- * @author Piotr Gawron
- *
- */
-public class ImageZipEntryFile extends ZipEntryFile implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public ImageZipEntryFile() {
-
- }
-
- /**
- * Default constructor.
- *
- * @param filename
- * {@link ZipEntryFile#filename}
- * @param inputStream
- * input stream with the data for this entry.
- * @see #baos
- * @throws IOException
- * thrown when there is a problem with accessing input stream
- */
- public ImageZipEntryFile(String filename) {
- super(filename);
- }
-
-}
+package lcsb.mapviewer.converter.zip;
+
+import java.io.IOException;
+import java.io.Serializable;
+
+/**
+ * Structure used to describe a file in a zip archive with single entry about
+ * {@link lcsb.mapviewer.model.map.OverviewImage}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ImageZipEntryFile extends ZipEntryFile implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public ImageZipEntryFile() {
+
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param filename
+ * {@link ZipEntryFile#filename}
+ * @param inputStream
+ * input stream with the data for this entry.
+ * @see #baos
+ * @throws IOException
+ * thrown when there is a problem with accessing input stream
+ */
+ public ImageZipEntryFile(String filename) {
+ super(filename);
+ }
+
+}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/zip/InputFileType.java b/converter/src/main/java/lcsb/mapviewer/converter/zip/InputFileType.java
index bb89fecbdb..5c933d2fca 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/zip/InputFileType.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/zip/InputFileType.java
@@ -1,43 +1,43 @@
-package lcsb.mapviewer.converter.zip;
-
-/**
- * This enum identifies type of input file inside zip archive given as the input
- * to MINERVa framework.
- *
- * @author Piotr Gawron
- *
- */
-public enum InputFileType {
- /**
- * Identifies file which is CellDesigner file.
- */
- CELLDESIGNER("CellDesigner (*.xml)"),
-
- /**
- * Unknown file type.
- */
- UNKNOWN("Unknown (*.*)");
-
- /**
- * Common name used for the type.
- */
- private String commonName;
-
- /**
- * Default constructor.
- *
- * @param commonName
- * {@link #commonName}
- */
- InputFileType(String commonName) {
- this.commonName = commonName;
- }
-
- /**
- * @return the commonName
- * @see #commonName
- */
- public String getCommonName() {
- return commonName;
- }
-}
+package lcsb.mapviewer.converter.zip;
+
+/**
+ * This enum identifies type of input file inside zip archive given as the input
+ * to MINERVa framework.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum InputFileType {
+ /**
+ * Identifies file which is CellDesigner file.
+ */
+ CELLDESIGNER("CellDesigner (*.xml)"),
+
+ /**
+ * Unknown file type.
+ */
+ UNKNOWN("Unknown (*.*)");
+
+ /**
+ * Common name used for the type.
+ */
+ private String commonName;
+
+ /**
+ * Default constructor.
+ *
+ * @param commonName
+ * {@link #commonName}
+ */
+ InputFileType(String commonName) {
+ this.commonName = commonName;
+ }
+
+ /**
+ * @return the commonName
+ * @see #commonName
+ */
+ public String getCommonName() {
+ return commonName;
+ }
+}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/zip/LayoutZipEntryFile.java b/converter/src/main/java/lcsb/mapviewer/converter/zip/LayoutZipEntryFile.java
index 99b30c9a5e..3b0c877195 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/zip/LayoutZipEntryFile.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/zip/LayoutZipEntryFile.java
@@ -1,82 +1,82 @@
-package lcsb.mapviewer.converter.zip;
-
-import java.io.Serializable;
-
-/**
- * Structure used to describe a file in a zip archive with single entry about
- * {@link lcsb.mapviewer.model.map.layout.Layout Layout}.
- *
- * @author Piotr Gawron
- *
- */
-public class LayoutZipEntryFile extends ZipEntryFile implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Name of the layout.
- */
- private String name = "";
-
- /**
- * Description of the layout.
- */
- private String description = "";
-
- /**
- * Default constructor.
- */
- public LayoutZipEntryFile() {
-
- }
-
- /**
- * Default constructor.
- *
- * @param filename
- * {@link ZipEntryFile#filename}
- */
- public LayoutZipEntryFile(String filename, String name, String description) {
- super(filename);
- this.name = name;
- this.description = description;
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return the description
- * @see #description
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * @param description
- * the description to set
- * @see #description
- */
- public void setDescription(String description) {
- this.description = description;
- }
-
-}
+package lcsb.mapviewer.converter.zip;
+
+import java.io.Serializable;
+
+/**
+ * Structure used to describe a file in a zip archive with single entry about
+ * {@link lcsb.mapviewer.model.map.layout.Layout Layout}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class LayoutZipEntryFile extends ZipEntryFile implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Name of the layout.
+ */
+ private String name = "";
+
+ /**
+ * Description of the layout.
+ */
+ private String description = "";
+
+ /**
+ * Default constructor.
+ */
+ public LayoutZipEntryFile() {
+
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param filename
+ * {@link ZipEntryFile#filename}
+ */
+ public LayoutZipEntryFile(String filename, String name, String description) {
+ super(filename);
+ this.name = name;
+ this.description = description;
+ }
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * @return the description
+ * @see #description
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * @param description
+ * the description to set
+ * @see #description
+ */
+ public void setDescription(String description) {
+ this.description = description;
+ }
+
+}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/zip/ModelZipEntryFile.java b/converter/src/main/java/lcsb/mapviewer/converter/zip/ModelZipEntryFile.java
index 44db1861ac..b2569f492f 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/zip/ModelZipEntryFile.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/zip/ModelZipEntryFile.java
@@ -1,200 +1,200 @@
-package lcsb.mapviewer.converter.zip;
-
-import java.io.Serializable;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.model.SubmodelType;
-
-/**
- * Structure used to describe a file in a zip archive with single entry about
- * {@link lcsb.mapviewer.model.map.model.Model model} or submodel.
- *
- * @author Piotr Gawron
- *
- */
-public class ModelZipEntryFile extends ZipEntryFile implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Name that should be used for the file.
- */
- private String name;
-
- /**
- * Is the file root (top) model in the project.
- */
- private String root = "false";
-
- /**
- * Is the file a mapping file.
- */
- private String mapping = "false";
-
- /**
- * What kind of submodel it is.
- */
- private SubmodelType type = SubmodelType.UNKNOWN;
-
- /**
- * Type of the input file. For now we accept only CellDesigner files, but in
- * future it will change.
- */
- private InputFileType fileType = InputFileType.UNKNOWN;
-
- /**
- * Default constructor.
- */
- public ModelZipEntryFile() {
-
- }
-
- /**
- * Constructor that initializes all params.
- *
- * @param filename
- * {@link #filename}
- * @param name
- * {@link #name}
- * @param root
- * {@link #root}
- * @param mapping
- * {@link #mapping}
- * @param type
- * {@link #type}
- */
- public ModelZipEntryFile(String filename, String name, boolean root, boolean mapping, SubmodelType type) {
- setFilename(filename);
- if (name == null && !mapping) {
- throw new InvalidArgumentException("Name cannot be null for submap");
- }
- this.name = name;
- this.root = root + "";
- this.mapping = mapping + "";
- this.type = type;
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return the type
- * @see #type
- */
- public SubmodelType getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(SubmodelType type) {
- this.type = type;
- }
-
- /**
- * @return the root
- * @see #root
- */
- public String getRoot() {
- return root;
- }
-
- /**
- * @param root
- * the root to set
- * @see #root
- */
- public void setRoot(String root) {
- this.root = root;
- }
-
- /**
- * @return the mapping
- * @see #mapping
- */
- public String getMapping() {
- return mapping;
- }
-
- /**
- * @param mapping
- * the mapping to set
- * @see #mapping
- */
- public void setMapping(String mapping) {
- this.mapping = mapping;
- }
-
- /**
- * @return the fileType
- * @see #fileType
- */
- public InputFileType getFileType() {
- return fileType;
- }
-
- /**
- * @param fileType
- * the fileType to set
- * @see #fileType
- */
- public void setFileType(InputFileType fileType) {
- this.fileType = fileType;
- }
-
- /**
- * Sets {@link #root} vale.
- *
- * @param root
- * new {@link #root} value
- */
- public void setRoot(boolean root) {
- if (root) {
- setRoot("true");
- } else {
- setRoot("false");
- }
- }
-
- /**
- * Returns <code>true</code> if {@link #root} is positive, <code>false</code>
- * otherwise.
- *
- * @return <code>true</code> if {@link #root} is positive, <code>false</code>
- * otherwise
- */
- public boolean isRoot() {
- return "true".equalsIgnoreCase(root);
- }
-
- /**
- * Returns <code>true</code> if {@link #mapping} is positive,
- * <code>false</code> otherwise.
- *
- * @return <code>true</code> if {@link #mapping} is positive,
- * <code>false</code> otherwise
- */
- public boolean isMappingFile() {
- return "true".equalsIgnoreCase(mapping);
- }
-
-}
+package lcsb.mapviewer.converter.zip;
+
+import java.io.Serializable;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.model.SubmodelType;
+
+/**
+ * Structure used to describe a file in a zip archive with single entry about
+ * {@link lcsb.mapviewer.model.map.model.Model model} or submodel.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ModelZipEntryFile extends ZipEntryFile implements Serializable {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Name that should be used for the file.
+ */
+ private String name;
+
+ /**
+ * Is the file root (top) model in the project.
+ */
+ private String root = "false";
+
+ /**
+ * Is the file a mapping file.
+ */
+ private String mapping = "false";
+
+ /**
+ * What kind of submodel it is.
+ */
+ private SubmodelType type = SubmodelType.UNKNOWN;
+
+ /**
+ * Type of the input file. For now we accept only CellDesigner files, but in
+ * future it will change.
+ */
+ private InputFileType fileType = InputFileType.UNKNOWN;
+
+ /**
+ * Default constructor.
+ */
+ public ModelZipEntryFile() {
+
+ }
+
+ /**
+ * Constructor that initializes all params.
+ *
+ * @param filename
+ * {@link #filename}
+ * @param name
+ * {@link #name}
+ * @param root
+ * {@link #root}
+ * @param mapping
+ * {@link #mapping}
+ * @param type
+ * {@link #type}
+ */
+ public ModelZipEntryFile(String filename, String name, boolean root, boolean mapping, SubmodelType type) {
+ setFilename(filename);
+ if (name == null && !mapping) {
+ throw new InvalidArgumentException("Name cannot be null for submap");
+ }
+ this.name = name;
+ this.root = root + "";
+ this.mapping = mapping + "";
+ this.type = type;
+ }
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * @return the type
+ * @see #type
+ */
+ public SubmodelType getType() {
+ return type;
+ }
+
+ /**
+ * @param type
+ * the type to set
+ * @see #type
+ */
+ public void setType(SubmodelType type) {
+ this.type = type;
+ }
+
+ /**
+ * @return the root
+ * @see #root
+ */
+ public String getRoot() {
+ return root;
+ }
+
+ /**
+ * @param root
+ * the root to set
+ * @see #root
+ */
+ public void setRoot(String root) {
+ this.root = root;
+ }
+
+ /**
+ * @return the mapping
+ * @see #mapping
+ */
+ public String getMapping() {
+ return mapping;
+ }
+
+ /**
+ * @param mapping
+ * the mapping to set
+ * @see #mapping
+ */
+ public void setMapping(String mapping) {
+ this.mapping = mapping;
+ }
+
+ /**
+ * @return the fileType
+ * @see #fileType
+ */
+ public InputFileType getFileType() {
+ return fileType;
+ }
+
+ /**
+ * @param fileType
+ * the fileType to set
+ * @see #fileType
+ */
+ public void setFileType(InputFileType fileType) {
+ this.fileType = fileType;
+ }
+
+ /**
+ * Sets {@link #root} vale.
+ *
+ * @param root
+ * new {@link #root} value
+ */
+ public void setRoot(boolean root) {
+ if (root) {
+ setRoot("true");
+ } else {
+ setRoot("false");
+ }
+ }
+
+ /**
+ * Returns <code>true</code> if {@link #root} is positive, <code>false</code>
+ * otherwise.
+ *
+ * @return <code>true</code> if {@link #root} is positive, <code>false</code>
+ * otherwise
+ */
+ public boolean isRoot() {
+ return "true".equalsIgnoreCase(root);
+ }
+
+ /**
+ * Returns <code>true</code> if {@link #mapping} is positive,
+ * <code>false</code> otherwise.
+ *
+ * @return <code>true</code> if {@link #mapping} is positive,
+ * <code>false</code> otherwise
+ */
+ public boolean isMappingFile() {
+ return "true".equalsIgnoreCase(mapping);
+ }
+
+}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/zip/ZipEntryFile.java b/converter/src/main/java/lcsb/mapviewer/converter/zip/ZipEntryFile.java
index 30ac1c8ea5..5eb83c136b 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/zip/ZipEntryFile.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/zip/ZipEntryFile.java
@@ -1,85 +1,85 @@
-package lcsb.mapviewer.converter.zip;
-
-import java.util.HashMap;
-import java.util.Map;
-
-/**
- * Class defining entry file for zip containing complex model (consisting of
- * many submodels and other files).
- *
- * @author Piotr Gawron
- *
- */
-public abstract class ZipEntryFile {
- /**
- * Name of the file in zip archive.
- */
- private String filename;
-
- /**
- * This map contains information that are stored in the header (first few
- * lines) in a text file. This information is stored as a pair:
- *
- * <pre>
- * # key=value
- * </pre>
- */
- private Map<String, String> headerParameters = new HashMap<String, String>();
-
- /**
- * Default constructor.
- */
- public ZipEntryFile() {
- }
-
- /**
- * Default constructor.
- *
- * @param filename
- * {@link #filename}
- */
- public ZipEntryFile(String filename) {
- this.filename = filename;
- }
-
- /**
- * @return the filename
- * @see #filename
- */
- public String getFilename() {
- return filename;
- }
-
- /**
- * @param filename
- * the filename to set
- * @see #filename
- */
- public void setFilename(String filename) {
- this.filename = filename;
- }
-
- /**
- * Adds new param (or replace old one) to {@link #headerParameters}.
- *
- * @param key
- * key identifing param
- * @param value
- * value of the param
- */
- public void setHeaderParameter(String key, String value) {
- headerParameters.put(key, value);
- }
-
- /**
- * Returns value of the param identified by string key.
- *
- * @param key
- * key used to identify param
- * @return value of the param identified by string key
- */
- public String getHeaderParameter(String key) {
- return headerParameters.get(key);
- }
-
-}
+package lcsb.mapviewer.converter.zip;
+
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * Class defining entry file for zip containing complex model (consisting of
+ * many submodels and other files).
+ *
+ * @author Piotr Gawron
+ *
+ */
+public abstract class ZipEntryFile {
+ /**
+ * Name of the file in zip archive.
+ */
+ private String filename;
+
+ /**
+ * This map contains information that are stored in the header (first few
+ * lines) in a text file. This information is stored as a pair:
+ *
+ * <pre>
+ * # key=value
+ * </pre>
+ */
+ private Map<String, String> headerParameters = new HashMap<String, String>();
+
+ /**
+ * Default constructor.
+ */
+ public ZipEntryFile() {
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param filename
+ * {@link #filename}
+ */
+ public ZipEntryFile(String filename) {
+ this.filename = filename;
+ }
+
+ /**
+ * @return the filename
+ * @see #filename
+ */
+ public String getFilename() {
+ return filename;
+ }
+
+ /**
+ * @param filename
+ * the filename to set
+ * @see #filename
+ */
+ public void setFilename(String filename) {
+ this.filename = filename;
+ }
+
+ /**
+ * Adds new param (or replace old one) to {@link #headerParameters}.
+ *
+ * @param key
+ * key identifing param
+ * @param value
+ * value of the param
+ */
+ public void setHeaderParameter(String key, String value) {
+ headerParameters.put(key, value);
+ }
+
+ /**
+ * Returns value of the param identified by string key.
+ *
+ * @param key
+ * key used to identify param
+ * @return value of the param identified by string key
+ */
+ public String getHeaderParameter(String key) {
+ return headerParameters.get(key);
+ }
+
+}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/zip/ZipEntryFileFactory.java b/converter/src/main/java/lcsb/mapviewer/converter/zip/ZipEntryFileFactory.java
index 977b64c498..1dc84388e4 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/zip/ZipEntryFileFactory.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/zip/ZipEntryFileFactory.java
@@ -1,168 +1,168 @@
-package lcsb.mapviewer.converter.zip;
-
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.Map;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipFile;
-
-import org.apache.commons.io.FilenameUtils;
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.TextFileUtils;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-
-/**
- * Factory class used to create {@link ZipEntryFile} objects.
- *
- * @author Piotr Gawron
- *
- */
-public class ZipEntryFileFactory {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(ZipEntryFileFactory.class);
-
- /**
- * Directory in a zip file where information about submodels is stored. These
- * entries should be by default transformed into {@link ModelZipEntryFile}.
- */
- private static final String SUBMODEL_DIRECTORY = "submaps/";
-
- /**
- * Directory in a zip file where information about
- * {@link lcsb.mapviewer.model.map.OverviewImage OverviewImage} is stored. These
- * entries should be by default transformed into {@link ImageZipEntryFile}.
- */
- private static final String IMAGES_DIRECTORY = "images/";
-
- /**
- * Directory in a zip file where information about
- * {@link lcsb.mapviewer.model.map.layout.Layout Layout} is stored. These
- * entries should be by default transformed into {@link LayoutZipEntryFile}.
- */
- private static final String LAYOUT_DIRECTORY = "layouts/";
-
- /**
- * Name of the parameter in {@link LayoutZipEntryFile file describing layout}
- * corresponding to the {@link LayoutZipEntryFile#name layout name}.
- */
- private static final String LAYOUT_HEADER_PARAM_NAME = "NAME";
-
- /**
- * Name of the parameter in {@link LayoutZipEntryFile file describing layout}
- * corresponding to the {@link LayoutZipEntryFile#description layout
- * description}.
- */
- private static final String LAYOUT_HEADER_PARAM_DESCRIPTION = "DESCRIPTION";
-
- /**
- * Name of the parameter in {@link LayoutZipEntryFile file describing layout}
- * corresponding to the {@link LayoutZipEntryFile#type type}.
- */
- public static final String LAYOUT_HEADER_PARAM_TYPE = "TYPE";
-
- /**
- * Name of the parameter in {@link LayoutZipEntryFile file describing layout}
- * corresponding to the {@link LayoutZipEntryFile#genomeType genome type}.
- */
- public static final String LAYOUT_HEADER_PARAM_GENOME_TYPE = "GENOME_TYPE";
-
- /**
- * Name of the parameter in {@link LayoutZipEntryFile file describing layout}
- * corresponding to the {@link LayoutZipEntryFile#genomeVersion genome version}.
- */
- public static final String LAYOUT_HEADER_PARAM_GENOME_VERSION = "GENOME_VERSION";
-
- /**
- * Generates instance of {@link ZipEntryFile} representing entry in the zip file
- * with pre-parsed structural data (like: type, name, description, etc).
- *
- * @param entry
- * {@link ZipEntry entry} in the {@link ZipFile}
- * @param zipFile
- * original {@link ZipFile}
- * @return {@link ZipEntryFile} for the given {@link ZipEntry}
- * @throws IOException
- * thrown when there is a problem with accessing zip file
- */
- public ZipEntryFile createZipEntryFile(ZipEntry entry, ZipFile zipFile) throws IOException {
- if (entry.isDirectory()) {
- return null;
- } else {
- String directory = null;
- String[] tmp = entry.getName().split("/");
- String name = tmp[tmp.length - 1];
- if (tmp.length > 1) {
- directory = entry.getName().replace(name, "");
- }
-
- if (directory == null) {
- ModelZipEntryFile zesf = new ModelZipEntryFile();
- zesf.setFilename(entry.getName());
- zesf.setName(FilenameUtils.getBaseName(entry.getName()));
- zesf.setRoot(true);
- if ("xml".equalsIgnoreCase(FilenameUtils.getExtension(entry.getName()))) {
- zesf.setFileType(InputFileType.CELLDESIGNER);
- } else {
- throw new InvalidArgumentException("Don't know what to do with entry: " + entry.getName());
- }
- return zesf;
- } else if (directory.equals(SUBMODEL_DIRECTORY)) {
- ModelZipEntryFile zesf = new ModelZipEntryFile();
- zesf.setFilename(entry.getName());
- zesf.setName(FilenameUtils.getBaseName(entry.getName()));
- if ("mapping".equalsIgnoreCase(zesf.getName())) {
- zesf.setMapping("true");
- } else {
- zesf.setMapping("false");
- }
- if ("xml".equalsIgnoreCase(FilenameUtils.getExtension(entry.getName()))) {
- zesf.setFileType(InputFileType.CELLDESIGNER);
- } else {
- throw new InvalidArgumentException("Don't know what to do with entry: " + entry.getName());
- }
- return zesf;
- } else if (directory.equals(IMAGES_DIRECTORY)) {
- ImageZipEntryFile result = new ImageZipEntryFile(entry.getName());
- return result;
- } else if (directory.equals(LAYOUT_DIRECTORY)) {
- LayoutZipEntryFile result = createLayoutZipEntryFile(entry.getName(), zipFile.getInputStream(entry));
- return result;
- } else {
- throw new InvalidArgumentException("Don't know what to do with entry: " + entry.getName());
- }
- }
- }
-
- /**
- * Creates {@link LayoutZipEntryFile layout entry} from input stream and given
- * name of the layout.
- *
- * @param name
- * name of the layout
- * @param inputStream
- * stream where data is stored
- * @return {@link LayoutZipEntryFile} processed from input data
- * @throws IOException
- * thrown when there is problem with accessing input data
- */
- public LayoutZipEntryFile createLayoutZipEntryFile(String name, InputStream inputStream) throws IOException {
- LayoutZipEntryFile result = new LayoutZipEntryFile();
- result.setFilename(name);
- result.setName(FilenameUtils.getBaseName(name));
- for (Map.Entry<String, String> mapEntry : TextFileUtils.getHeaderParametersFromFile(inputStream).entrySet()) {
- result.setHeaderParameter(mapEntry.getKey(), mapEntry.getValue());
- }
- if (result.getHeaderParameter(LAYOUT_HEADER_PARAM_NAME) != null) {
- result.setName(result.getHeaderParameter(LAYOUT_HEADER_PARAM_NAME));
- }
- if (result.getHeaderParameter(LAYOUT_HEADER_PARAM_DESCRIPTION) != null) {
- result.setDescription(result.getHeaderParameter(LAYOUT_HEADER_PARAM_DESCRIPTION));
- }
- return result;
- }
-
-}
+package lcsb.mapviewer.converter.zip;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.Map;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipFile;
+
+import org.apache.commons.io.FilenameUtils;
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.TextFileUtils;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+
+/**
+ * Factory class used to create {@link ZipEntryFile} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ZipEntryFileFactory {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(ZipEntryFileFactory.class);
+
+ /**
+ * Directory in a zip file where information about submodels is stored. These
+ * entries should be by default transformed into {@link ModelZipEntryFile}.
+ */
+ private static final String SUBMODEL_DIRECTORY = "submaps/";
+
+ /**
+ * Directory in a zip file where information about
+ * {@link lcsb.mapviewer.model.map.OverviewImage OverviewImage} is stored. These
+ * entries should be by default transformed into {@link ImageZipEntryFile}.
+ */
+ private static final String IMAGES_DIRECTORY = "images/";
+
+ /**
+ * Directory in a zip file where information about
+ * {@link lcsb.mapviewer.model.map.layout.Layout Layout} is stored. These
+ * entries should be by default transformed into {@link LayoutZipEntryFile}.
+ */
+ private static final String LAYOUT_DIRECTORY = "layouts/";
+
+ /**
+ * Name of the parameter in {@link LayoutZipEntryFile file describing layout}
+ * corresponding to the {@link LayoutZipEntryFile#name layout name}.
+ */
+ private static final String LAYOUT_HEADER_PARAM_NAME = "NAME";
+
+ /**
+ * Name of the parameter in {@link LayoutZipEntryFile file describing layout}
+ * corresponding to the {@link LayoutZipEntryFile#description layout
+ * description}.
+ */
+ private static final String LAYOUT_HEADER_PARAM_DESCRIPTION = "DESCRIPTION";
+
+ /**
+ * Name of the parameter in {@link LayoutZipEntryFile file describing layout}
+ * corresponding to the {@link LayoutZipEntryFile#type type}.
+ */
+ public static final String LAYOUT_HEADER_PARAM_TYPE = "TYPE";
+
+ /**
+ * Name of the parameter in {@link LayoutZipEntryFile file describing layout}
+ * corresponding to the {@link LayoutZipEntryFile#genomeType genome type}.
+ */
+ public static final String LAYOUT_HEADER_PARAM_GENOME_TYPE = "GENOME_TYPE";
+
+ /**
+ * Name of the parameter in {@link LayoutZipEntryFile file describing layout}
+ * corresponding to the {@link LayoutZipEntryFile#genomeVersion genome version}.
+ */
+ public static final String LAYOUT_HEADER_PARAM_GENOME_VERSION = "GENOME_VERSION";
+
+ /**
+ * Generates instance of {@link ZipEntryFile} representing entry in the zip file
+ * with pre-parsed structural data (like: type, name, description, etc).
+ *
+ * @param entry
+ * {@link ZipEntry entry} in the {@link ZipFile}
+ * @param zipFile
+ * original {@link ZipFile}
+ * @return {@link ZipEntryFile} for the given {@link ZipEntry}
+ * @throws IOException
+ * thrown when there is a problem with accessing zip file
+ */
+ public ZipEntryFile createZipEntryFile(ZipEntry entry, ZipFile zipFile) throws IOException {
+ if (entry.isDirectory()) {
+ return null;
+ } else {
+ String directory = null;
+ String[] tmp = entry.getName().split("/");
+ String name = tmp[tmp.length - 1];
+ if (tmp.length > 1) {
+ directory = entry.getName().replace(name, "");
+ }
+
+ if (directory == null) {
+ ModelZipEntryFile zesf = new ModelZipEntryFile();
+ zesf.setFilename(entry.getName());
+ zesf.setName(FilenameUtils.getBaseName(entry.getName()));
+ zesf.setRoot(true);
+ if ("xml".equalsIgnoreCase(FilenameUtils.getExtension(entry.getName()))) {
+ zesf.setFileType(InputFileType.CELLDESIGNER);
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with entry: " + entry.getName());
+ }
+ return zesf;
+ } else if (directory.equals(SUBMODEL_DIRECTORY)) {
+ ModelZipEntryFile zesf = new ModelZipEntryFile();
+ zesf.setFilename(entry.getName());
+ zesf.setName(FilenameUtils.getBaseName(entry.getName()));
+ if ("mapping".equalsIgnoreCase(zesf.getName())) {
+ zesf.setMapping("true");
+ } else {
+ zesf.setMapping("false");
+ }
+ if ("xml".equalsIgnoreCase(FilenameUtils.getExtension(entry.getName()))) {
+ zesf.setFileType(InputFileType.CELLDESIGNER);
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with entry: " + entry.getName());
+ }
+ return zesf;
+ } else if (directory.equals(IMAGES_DIRECTORY)) {
+ ImageZipEntryFile result = new ImageZipEntryFile(entry.getName());
+ return result;
+ } else if (directory.equals(LAYOUT_DIRECTORY)) {
+ LayoutZipEntryFile result = createLayoutZipEntryFile(entry.getName(), zipFile.getInputStream(entry));
+ return result;
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with entry: " + entry.getName());
+ }
+ }
+ }
+
+ /**
+ * Creates {@link LayoutZipEntryFile layout entry} from input stream and given
+ * name of the layout.
+ *
+ * @param name
+ * name of the layout
+ * @param inputStream
+ * stream where data is stored
+ * @return {@link LayoutZipEntryFile} processed from input data
+ * @throws IOException
+ * thrown when there is problem with accessing input data
+ */
+ public LayoutZipEntryFile createLayoutZipEntryFile(String name, InputStream inputStream) throws IOException {
+ LayoutZipEntryFile result = new LayoutZipEntryFile();
+ result.setFilename(name);
+ result.setName(FilenameUtils.getBaseName(name));
+ for (Map.Entry<String, String> mapEntry : TextFileUtils.getHeaderParametersFromFile(inputStream).entrySet()) {
+ result.setHeaderParameter(mapEntry.getKey(), mapEntry.getValue());
+ }
+ if (result.getHeaderParameter(LAYOUT_HEADER_PARAM_NAME) != null) {
+ result.setName(result.getHeaderParameter(LAYOUT_HEADER_PARAM_NAME));
+ }
+ if (result.getHeaderParameter(LAYOUT_HEADER_PARAM_DESCRIPTION) != null) {
+ result.setDescription(result.getHeaderParameter(LAYOUT_HEADER_PARAM_DESCRIPTION));
+ }
+ return result;
+ }
+
+}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/zip/package-info.java b/converter/src/main/java/lcsb/mapviewer/converter/zip/package-info.java
index 713063013d..fdbf9c0a4c 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/zip/package-info.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/zip/package-info.java
@@ -1,5 +1,5 @@
-/**
- * Package with structures describing zip file entries.
- */
-package lcsb.mapviewer.converter.zip;
-
+/**
+ * Package with structures describing zip file entries.
+ */
+package lcsb.mapviewer.converter.zip;
+
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/ClearColorModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/ClearColorModelCommand.java
index 64a211a664..541db6b893 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/ClearColorModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/ClearColorModelCommand.java
@@ -1,46 +1,46 @@
-package lcsb.mapviewer.commands;
-
-import java.awt.Color;
-import java.util.ArrayList;
-
-import lcsb.mapviewer.model.map.model.Model;
-
-/**
- * This {@link ModelCommand} clear info about colors in a model.
- *
- * @author Piotr Gawron
- *
- */
-public class ClearColorModelCommand extends ModelCommand {
-
- /**
- * Coloring command that will clear colors.
- */
- private ColorModelCommand colorModelCommand;
-
- /**
- * Default constructor.
- *
- * @param model
- * original model
- */
- public ClearColorModelCommand(Model model) {
- super(model);
- colorModelCommand = new ColorModelCommand(model, new ArrayList<>(), new ColorExtractor(Color.WHITE, Color.WHITE, Color.WHITE));
- }
-
- @Override
- protected void undoImplementation() throws CommandExecutionException {
- colorModelCommand.undo();
- }
-
- @Override
- protected void redoImplementation() throws CommandExecutionException {
- colorModelCommand.redo();
- }
-
- @Override
- protected void executeImplementation() throws CommandExecutionException {
- colorModelCommand.execute();
- }
-}
+package lcsb.mapviewer.commands;
+
+import java.awt.Color;
+import java.util.ArrayList;
+
+import lcsb.mapviewer.model.map.model.Model;
+
+/**
+ * This {@link ModelCommand} clear info about colors in a model.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ClearColorModelCommand extends ModelCommand {
+
+ /**
+ * Coloring command that will clear colors.
+ */
+ private ColorModelCommand colorModelCommand;
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * original model
+ */
+ public ClearColorModelCommand(Model model) {
+ super(model);
+ colorModelCommand = new ColorModelCommand(model, new ArrayList<>(), new ColorExtractor(Color.WHITE, Color.WHITE, Color.WHITE));
+ }
+
+ @Override
+ protected void undoImplementation() throws CommandExecutionException {
+ colorModelCommand.undo();
+ }
+
+ @Override
+ protected void redoImplementation() throws CommandExecutionException {
+ colorModelCommand.redo();
+ }
+
+ @Override
+ protected void executeImplementation() throws CommandExecutionException {
+ colorModelCommand.execute();
+ }
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/ColorExtractor.java b/model-command/src/main/java/lcsb/mapviewer/commands/ColorExtractor.java
index 0638978854..e08bdca655 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/ColorExtractor.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/ColorExtractor.java
@@ -1,105 +1,105 @@
-package lcsb.mapviewer.commands;
-
-import java.awt.Color;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-
-/**
- * Class that extracts color that should be used for drawing from
- * {@link ColorSchema}.
- *
- * @author Piotr Gawron
- *
- */
-public class ColorExtractor {
-
- /**
- * Color that should be used for min values of {@link ColorSchema#value}.
- */
- private Color minColor;
-
- /**
- * Color that should be used for maxvalues of {@link ColorSchema#value}.
- */
- private Color maxColor;
-
- private Color simpleColor;
-
- /**
- * Default constructor.
- *
- * @param minColor
- * Color that should be used for min values of
- * {@link ColorSchema#value}
- * @param maxColor
- * Color that should be used for max values of
- * {@link ColorSchema#value}
- */
- public ColorExtractor(Color minColor, Color maxColor, Color simpleColor) {
- if (minColor == null || maxColor == null || simpleColor == null) {
- throw new InvalidArgumentException("Parameters cannot be null");
- }
- this.minColor = minColor;
- this.maxColor = maxColor;
- this.simpleColor = simpleColor;
- }
-
- /**
- * Extracts color from {@link ColorSchema} object.
- *
- * @param colorSchema
- * {@link ColorSchema} from which {@link Color} should be extracted
- *
- * @return color from {@link ColorSchema} object
- */
- public Color getNormalizedColor(ColorSchema colorSchema) {
- if (colorSchema.getColor() != null) {
- return colorSchema.getColor();
- } else if (colorSchema.getValue() == null) {
- return simpleColor;
- } else {
- return getColorForValue(colorSchema.getValue());
- }
- }
-
- /**
- * Returns color from red - green scale for the given normalized double value
- * (from range -1,1).
- *
- * @param value
- * double value that should be converted into color
- * @return color for the double value
- */
- protected Color getColorForValue(Double value) {
- if (value > 0) {
- double ratio = value;
- return new Color((int) (maxColor.getRed() * ratio), (int) (maxColor.getGreen() * ratio), (int) (maxColor.getBlue() * ratio));
- }
- if (value < 0) {
- double ratio = -value;
- return new Color((int) (minColor.getRed() * ratio), (int) (minColor.getGreen() * ratio), (int) (minColor.getBlue() * ratio));
- }
- return Color.WHITE;
- }
-
- /**
- * @return the minColor
- * @see #minColor
- */
- public Color getMinColor() {
- return minColor;
- }
-
- /**
- * @return the maxColor
- * @see #maxColor
- */
- public Color getMaxColor() {
- return maxColor;
- }
-
- public Color getSimpleColor() {
- return simpleColor;
- }
-}
+package lcsb.mapviewer.commands;
+
+import java.awt.Color;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+
+/**
+ * Class that extracts color that should be used for drawing from
+ * {@link ColorSchema}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ColorExtractor {
+
+ /**
+ * Color that should be used for min values of {@link ColorSchema#value}.
+ */
+ private Color minColor;
+
+ /**
+ * Color that should be used for maxvalues of {@link ColorSchema#value}.
+ */
+ private Color maxColor;
+
+ private Color simpleColor;
+
+ /**
+ * Default constructor.
+ *
+ * @param minColor
+ * Color that should be used for min values of
+ * {@link ColorSchema#value}
+ * @param maxColor
+ * Color that should be used for max values of
+ * {@link ColorSchema#value}
+ */
+ public ColorExtractor(Color minColor, Color maxColor, Color simpleColor) {
+ if (minColor == null || maxColor == null || simpleColor == null) {
+ throw new InvalidArgumentException("Parameters cannot be null");
+ }
+ this.minColor = minColor;
+ this.maxColor = maxColor;
+ this.simpleColor = simpleColor;
+ }
+
+ /**
+ * Extracts color from {@link ColorSchema} object.
+ *
+ * @param colorSchema
+ * {@link ColorSchema} from which {@link Color} should be extracted
+ *
+ * @return color from {@link ColorSchema} object
+ */
+ public Color getNormalizedColor(ColorSchema colorSchema) {
+ if (colorSchema.getColor() != null) {
+ return colorSchema.getColor();
+ } else if (colorSchema.getValue() == null) {
+ return simpleColor;
+ } else {
+ return getColorForValue(colorSchema.getValue());
+ }
+ }
+
+ /**
+ * Returns color from red - green scale for the given normalized double value
+ * (from range -1,1).
+ *
+ * @param value
+ * double value that should be converted into color
+ * @return color for the double value
+ */
+ protected Color getColorForValue(Double value) {
+ if (value > 0) {
+ double ratio = value;
+ return new Color((int) (maxColor.getRed() * ratio), (int) (maxColor.getGreen() * ratio), (int) (maxColor.getBlue() * ratio));
+ }
+ if (value < 0) {
+ double ratio = -value;
+ return new Color((int) (minColor.getRed() * ratio), (int) (minColor.getGreen() * ratio), (int) (minColor.getBlue() * ratio));
+ }
+ return Color.WHITE;
+ }
+
+ /**
+ * @return the minColor
+ * @see #minColor
+ */
+ public Color getMinColor() {
+ return minColor;
+ }
+
+ /**
+ * @return the maxColor
+ * @see #maxColor
+ */
+ public Color getMaxColor() {
+ return maxColor;
+ }
+
+ public Color getSimpleColor() {
+ return simpleColor;
+ }
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/CommandExecutionException.java b/model-command/src/main/java/lcsb/mapviewer/commands/CommandExecutionException.java
index ac6585bebd..ae9195d4b2 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CommandExecutionException.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CommandExecutionException.java
@@ -1,55 +1,55 @@
-package lcsb.mapviewer.commands;
-
-/**
- * Exception that is thrown when the data for {@link ModelCommand} is invalid.
- *
- * @author Piotr Gawron
- *
- */
-public class CommandExecutionException extends Exception {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public CommandExecutionException() {
- super();
- }
-
- /**
- * Default constructor with message passed in the argument.
- *
- * @param string
- * message of this exception
- */
- public CommandExecutionException(String string) {
- super(string);
- }
-
- /**
- * Public constructor with parent exception that was catched.
- *
- * @param e
- * parent exception
- */
- public CommandExecutionException(Exception e) {
- super(e.getMessage(), e);
- }
-
- /**
- * Public constructor with parent exception that was catched.
- *
- * @param string
- * message of this exception
- * @param e
- * parent exception
- */
- public CommandExecutionException(String string, Exception e) {
- super(string, e);
- }
-
-}
+package lcsb.mapviewer.commands;
+
+/**
+ * Exception that is thrown when the data for {@link ModelCommand} is invalid.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CommandExecutionException extends Exception {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public CommandExecutionException() {
+ super();
+ }
+
+ /**
+ * Default constructor with message passed in the argument.
+ *
+ * @param string
+ * message of this exception
+ */
+ public CommandExecutionException(String string) {
+ super(string);
+ }
+
+ /**
+ * Public constructor with parent exception that was catched.
+ *
+ * @param e
+ * parent exception
+ */
+ public CommandExecutionException(Exception e) {
+ super(e.getMessage(), e);
+ }
+
+ /**
+ * Public constructor with parent exception that was catched.
+ *
+ * @param string
+ * message of this exception
+ * @param e
+ * parent exception
+ */
+ public CommandExecutionException(String string, Exception e) {
+ super(string, e);
+ }
+
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
index 535b0f3fad..40a14f584c 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
@@ -1,424 +1,424 @@
-package lcsb.mapviewer.commands;
-
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidClassException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.kinetics.SbmlArgument;
-import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
-import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
-import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
-import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
-import lcsb.mapviewer.model.map.model.SubmodelConnection;
-import lcsb.mapviewer.model.map.reaction.AbstractNode;
-import lcsb.mapviewer.model.map.reaction.NodeOperator;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.ReactionNode;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * Command that creates a new instance of the model with the same data.
- *
- */
-
-public class CopyCommand extends NewModelCommand {
- /**
- * Defaul class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(CopyCommand.class);
-
- /**
- * Default constructor.
- *
- * @param model
- * {@link #model}
- */
- public CopyCommand(Model model) {
- super(model);
- }
-
- /**
- * Executed the operation.
- *
- * @return copy of the model
- */
- public Model execute() {
- Map<Model, Model> copies = new HashMap<>();
-
- Model model = getModel();
-
- if (model.getModelData().getParentModels().size() > 0) {
- ModelSubmodelConnection parent = null;
- for (SubmodelConnection connection : model.getModelData().getParentModels()) {
- if (connection instanceof ModelSubmodelConnection) {
- if (parent != null) {
- throw new InvalidArgumentException(
- "It looks like the model is a submodel, but has more than one parent...");
- } else {
- parent = (ModelSubmodelConnection) connection;
- }
- }
- }
- if (parent != null) {
- CopyCommand copyParentCommand = new CopyCommand(parent.getParentModel().getModel());
- Model copy = copyParentCommand.execute();
- for (ModelSubmodelConnection submodel : copy.getSubmodelConnections()) {
- if (submodel.getName().equals(parent.getName())) {
- return submodel.getSubmodel().getModel();
- }
- }
- throw new InvalidStateException("Problem with copying submodel of a model");
- }
- }
-
- Model result = createNotNestedCopy(model);
-
- copies.put(model, result);
-
- for (ModelSubmodelConnection submodelConnection : model.getSubmodelConnections()) {
- Model submodel = submodelConnection.getSubmodel().getModel();
- Model submodelCopy = createNotNestedCopy(submodel);
- copies.put(submodel, submodelCopy);
- }
- for (Model modelCopy : copies.values()) {
- try {
- assignModelCopies(modelCopy, copies);
- } catch (InvalidModelException e) {
- throw new InvalidArgumentException(e);
- }
- }
- return result;
-
- }
-
- /**
- * Assign information about submodel to the copied links.
- *
- * @param modelCopy
- * copy of a model where substitution should be made
- * @param copies
- * map with map copies
- * @throws InvalidModelException
- * when there is inconsistency in data
- */
- private void assignModelCopies(Model modelCopy, Map<Model, Model> copies) throws InvalidModelException {
- for (ModelSubmodelConnection connection : modelCopy.getSubmodelConnections()) {
- // copy connection reference
- Model original = connection.getSubmodel().getModel();
- Model copy = copies.get(original);
- if (copy == null) {
- throw new InvalidModelException("Original model contain reference to model that wasn't copied");
- }
- connection.setSubmodel(copy);
-
- // copy connection parent reference
- if (connection.getParentModel() != null) {
- original = connection.getParentModel().getModel();
- if (original != null) {
- copy = copies.get(original);
- if (copy == null) {
- if (!copies.values().contains(original)) {
- throw new InvalidModelException("Original model contain reference to model that wasn't copied");
- }
- } else {
- connection.setParentModel(copy);
- }
- }
- }
- }
- for (Element alias : modelCopy.getElements()) {
- // if alias has connection to submodel
- if (alias.getSubmodel() != null) {
- ElementSubmodelConnection connection = alias.getSubmodel();
- // copy information about submodel
- Model original = connection.getSubmodel().getModel();
- Model copy = copies.get(original);
- if (copy == null) {
- throw new InvalidModelException("Original model contain reference to model that wasn't copied");
- }
- connection.setSubmodel(copy);
-
- // copy information about original alias
- if (connection.getFromElement() != null) {
- connection.setFromElement(modelCopy.getElementByElementId(connection.getFromElement().getElementId()));
- }
- // copy information about reference alias
- if (connection.getToElement() != null) {
- connection.setToElement(modelCopy.getElementByElementId(connection.getToElement().getElementId()));
- }
- }
- }
- }
-
- /**
- * Creates copy of the model without modifying information about submodels
- * (information about original submodels will be left in the copy).
- *
- * @param model
- * original model to copy
- * @return copy of the model
- */
- protected Model createNotNestedCopy(Model model) {
- Model result = new ModelFullIndexed(null);
-
- for (SbmlUnit unit : model.getUnits()) {
- result.addUnit(unit.copy());
- }
-
- for (SbmlFunction function : model.getFunctions()) {
- result.addFunction(function.copy());
- }
-
- for (SbmlParameter parameter : model.getParameters()) {
- result.addParameter(parameter.copy());
- }
-
- for (Element alias : model.getElements()) {
- if (alias instanceof Compartment) {
- Compartment copy = ((Compartment) alias).copy();
- copy.getElements().clear();
- copy.setCompartment(null);
- result.addElement(copy);
- }
-
- }
-
- for (Element alias : model.getElements()) {
- if (alias instanceof Species) {
- Species copy = ((Species) alias).copy();
- copy.setCompartment(null);
- result.addElement(copy);
-
- Compartment parentCompartment = alias.getCompartment();
-
- if (parentCompartment != null) {
- parentCompartment = result.getElementByElementId(parentCompartment.getElementId());
- copy.setCompartment(parentCompartment);
- }
-
- } else if (alias instanceof Compartment) {
-
- Compartment parentCompartment = alias.getCompartment();
-
- if (parentCompartment != null) {
- Compartment copy = result.getElementByElementId(alias.getElementId());
- parentCompartment = result.getElementByElementId(parentCompartment.getElementId());
- copy.setCompartment(parentCompartment);
- }
- } else {
- throw new InvalidClassException("Don't know what to do with: " + alias.getClass());
- }
- }
-
- for (Layer layer : model.getLayers()) {
- result.addLayer(layer.copy());
- }
-
- for (Reaction reaction : model.getReactions()) {
- result.addReaction(createCopy(reaction));
- }
-
- assignSimpleDataToCopy(result, model);
- for (Layout layout : model.getLayouts()) {
- result.addLayout(layout.copy());
- }
- result.setProject(model.getProject());
-
- for (Element element : result.getElements()) {
- updateElementReferences(element, result, model);
- }
- for (Reaction reaction : result.getReactions()) {
- updateReactionReferences(reaction, result);
- }
- for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
- result.addSubmodelConnection(connection.copy());
- }
- return result;
- }
-
- /**
- * Copies simple information about model to the copy.
- *
- * @param copy
- * to this model data will be copied
- * @param original
- * original model
- */
- private void assignSimpleDataToCopy(Model copy, Model original) {
- copy.setName(original.getName());
-
- copy.setCreationDate(original.getCreationDate());
-
- copy.setWidth(original.getWidth());
- copy.setHeight(original.getHeight());
- copy.setNotes(original.getNotes());
- copy.setIdModel(original.getIdModel());
- copy.setZoomLevels(original.getZoomLevels());
- copy.setTileSize(original.getTileSize());
- }
-
- /**
- * Creates copy of the reaction that doesn't contain any references to the
- * original (so we have to substitute all references with the new ones...).
- *
- * @param reaction
- * original reaction
- * @return copy of the reaction
- */
- private Reaction createCopy(Reaction reaction) {
- Reaction copy = reaction.copy();
- reaction.getNodes().clear();
- for (AbstractNode node : copy.getNodes()) {
- reaction.addNode(node);
- }
- copy.getNodes().clear();
-
- for (AbstractNode node : reaction.getNodes()) {
- AbstractNode nodeCopy = node.copy();
- nodeCopy.setLine(new PolylineData(nodeCopy.getLine()));
- copy.addNode(nodeCopy);
- }
-
- for (int i = 0; i < copy.getOperators().size(); i++) {
- NodeOperator nodeCopy = copy.getOperators().get(i);
- NodeOperator nodeOriginal = reaction.getOperators().get(i);
- for (int j = 0; j < nodeCopy.getInputs().size(); j++) {
- AbstractNode input = nodeCopy.getInputs().get(j);
- int index1 = reaction.getOperators().indexOf(input);
- int index2 = reaction.getNodes().indexOf(input);
- if (index1 >= 0) {
- nodeCopy.getInputs().set(j, copy.getOperators().get(index1));
- copy.getOperators().get(index1).setNodeOperatorForInput(nodeCopy);
-
- reaction.getOperators().get(index1).setNodeOperatorForInput(nodeOriginal);
- } else if (index2 >= 0) {
- nodeCopy.getInputs().set(j, copy.getNodes().get(index2));
- copy.getNodes().get(index2).setNodeOperatorForInput(nodeCopy);
-
- reaction.getNodes().get(index2).setNodeOperatorForInput(nodeOriginal);
- } else {
- throw new InvalidStateException("WTF");
- }
- }
-
- for (int j = 0; j < nodeCopy.getOutputs().size(); j++) {
- AbstractNode output = nodeCopy.getOutputs().get(j);
- int index1 = reaction.getOperators().indexOf(output);
- int index2 = reaction.getNodes().indexOf(output);
- if (index1 >= 0) {
- nodeCopy.getOutputs().set(j, copy.getOperators().get(index1));
- copy.getOperators().get(index1).setNodeOperatorForOutput(nodeCopy);
-
- reaction.getOperators().get(index1).setNodeOperatorForOutput(nodeOriginal);
- } else if (index2 >= 0) {
- nodeCopy.getOutputs().set(j, copy.getNodes().get(index2));
- copy.getNodes().get(index2).setNodeOperatorForOutput(nodeCopy);
-
- reaction.getNodes().get(index2).setNodeOperatorForOutput(nodeOriginal);
- } else {
- throw new InvalidStateException("WTF");
- }
- }
- }
-
- return copy;
- }
-
- /**
- * Updates references to elements and aliases in reaction to the objects taken
- * from model.
- *
- * @param reaction
- * references in this reaction will be updated
- * @param model
- * references from this model will be taken
- */
- private void updateReactionReferences(Reaction reaction, Model model) {
- reaction.setModel(model);
- for (ReactionNode rNode : reaction.getReactionNodes()) {
- rNode.setElement(model.getElementByElementId(rNode.getElement().getElementId()));
- }
- SbmlKinetics kinetics = reaction.getKinetics();
- if (kinetics != null) {
- Collection<SbmlArgument> arguments = new HashSet<>();
- for (SbmlArgument argument : kinetics.getArguments()) {
- if (argument instanceof Element) {
- arguments.add(model.getElementByElementId(argument.getElementId()));
- } else if (argument instanceof SbmlParameter) {
- if (model.getParameterById(argument.getElementId()) != null) {
- arguments.add(model.getParameterById(argument.getElementId()));
- } else {
- arguments.add(argument);
- }
- } else if (argument instanceof SbmlFunction) {
- arguments.add(model.getFunctionById(argument.getElementId()));
- } else {
- throw new InvalidStateException("Don't know what to do with class: " + argument.getClass());
- }
- }
- kinetics.removeArguments(kinetics.getArguments());
- kinetics.addArguments(arguments);
- }
-
- }
-
- /**
- * Updates information (like elements, parent aliases) in the alias with the
- * data from new model.
- *
- * @param element
- * object to be updated
- * @param model
- * data from this model will be used for update
- * @param originalModel
- * original model from which alias copy was created
- */
- private void updateElementReferences(Element element, Model model, Model originalModel) {
- if (element instanceof Compartment) {
- Compartment compartment = (Compartment) element;
- Compartment original = originalModel.getElementByElementId(element.getElementId());
- for (Element child : original.getElements()) {
- compartment.addElement(model.getElementByElementId(child.getElementId()));
- }
- }
-
- if (element instanceof Complex) {
- Complex complex = (Complex) element;
- for (int i = 0; i < complex.getElements().size(); i++) {
- Species newElement = model.getElementByElementId(complex.getElements().get(i).getElementId());
- complex.getElements().set(i, newElement);
- }
- }
- if (element instanceof Species) {
- Species species = (Species) element;
-
- if (species.getComplex() != null) {
- species.setComplex((Complex) model.getElementByElementId(species.getComplex().getElementId()));
- }
-
- }
-
- element.setModel(model);
-
- if (element.getCompartment() != null) {
- element.setCompartment(model.getElementByElementId(element.getCompartment().getElementId()));
- }
- }
-}
+package lcsb.mapviewer.commands;
+
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidClassException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.kinetics.SbmlArgument;
+import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
+import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
+import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
+import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
+import lcsb.mapviewer.model.map.model.SubmodelConnection;
+import lcsb.mapviewer.model.map.reaction.AbstractNode;
+import lcsb.mapviewer.model.map.reaction.NodeOperator;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * Command that creates a new instance of the model with the same data.
+ *
+ */
+
+public class CopyCommand extends NewModelCommand {
+ /**
+ * Defaul class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(CopyCommand.class);
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * {@link #model}
+ */
+ public CopyCommand(Model model) {
+ super(model);
+ }
+
+ /**
+ * Executed the operation.
+ *
+ * @return copy of the model
+ */
+ public Model execute() {
+ Map<Model, Model> copies = new HashMap<>();
+
+ Model model = getModel();
+
+ if (model.getModelData().getParentModels().size() > 0) {
+ ModelSubmodelConnection parent = null;
+ for (SubmodelConnection connection : model.getModelData().getParentModels()) {
+ if (connection instanceof ModelSubmodelConnection) {
+ if (parent != null) {
+ throw new InvalidArgumentException(
+ "It looks like the model is a submodel, but has more than one parent...");
+ } else {
+ parent = (ModelSubmodelConnection) connection;
+ }
+ }
+ }
+ if (parent != null) {
+ CopyCommand copyParentCommand = new CopyCommand(parent.getParentModel().getModel());
+ Model copy = copyParentCommand.execute();
+ for (ModelSubmodelConnection submodel : copy.getSubmodelConnections()) {
+ if (submodel.getName().equals(parent.getName())) {
+ return submodel.getSubmodel().getModel();
+ }
+ }
+ throw new InvalidStateException("Problem with copying submodel of a model");
+ }
+ }
+
+ Model result = createNotNestedCopy(model);
+
+ copies.put(model, result);
+
+ for (ModelSubmodelConnection submodelConnection : model.getSubmodelConnections()) {
+ Model submodel = submodelConnection.getSubmodel().getModel();
+ Model submodelCopy = createNotNestedCopy(submodel);
+ copies.put(submodel, submodelCopy);
+ }
+ for (Model modelCopy : copies.values()) {
+ try {
+ assignModelCopies(modelCopy, copies);
+ } catch (InvalidModelException e) {
+ throw new InvalidArgumentException(e);
+ }
+ }
+ return result;
+
+ }
+
+ /**
+ * Assign information about submodel to the copied links.
+ *
+ * @param modelCopy
+ * copy of a model where substitution should be made
+ * @param copies
+ * map with map copies
+ * @throws InvalidModelException
+ * when there is inconsistency in data
+ */
+ private void assignModelCopies(Model modelCopy, Map<Model, Model> copies) throws InvalidModelException {
+ for (ModelSubmodelConnection connection : modelCopy.getSubmodelConnections()) {
+ // copy connection reference
+ Model original = connection.getSubmodel().getModel();
+ Model copy = copies.get(original);
+ if (copy == null) {
+ throw new InvalidModelException("Original model contain reference to model that wasn't copied");
+ }
+ connection.setSubmodel(copy);
+
+ // copy connection parent reference
+ if (connection.getParentModel() != null) {
+ original = connection.getParentModel().getModel();
+ if (original != null) {
+ copy = copies.get(original);
+ if (copy == null) {
+ if (!copies.values().contains(original)) {
+ throw new InvalidModelException("Original model contain reference to model that wasn't copied");
+ }
+ } else {
+ connection.setParentModel(copy);
+ }
+ }
+ }
+ }
+ for (Element alias : modelCopy.getElements()) {
+ // if alias has connection to submodel
+ if (alias.getSubmodel() != null) {
+ ElementSubmodelConnection connection = alias.getSubmodel();
+ // copy information about submodel
+ Model original = connection.getSubmodel().getModel();
+ Model copy = copies.get(original);
+ if (copy == null) {
+ throw new InvalidModelException("Original model contain reference to model that wasn't copied");
+ }
+ connection.setSubmodel(copy);
+
+ // copy information about original alias
+ if (connection.getFromElement() != null) {
+ connection.setFromElement(modelCopy.getElementByElementId(connection.getFromElement().getElementId()));
+ }
+ // copy information about reference alias
+ if (connection.getToElement() != null) {
+ connection.setToElement(modelCopy.getElementByElementId(connection.getToElement().getElementId()));
+ }
+ }
+ }
+ }
+
+ /**
+ * Creates copy of the model without modifying information about submodels
+ * (information about original submodels will be left in the copy).
+ *
+ * @param model
+ * original model to copy
+ * @return copy of the model
+ */
+ protected Model createNotNestedCopy(Model model) {
+ Model result = new ModelFullIndexed(null);
+
+ for (SbmlUnit unit : model.getUnits()) {
+ result.addUnit(unit.copy());
+ }
+
+ for (SbmlFunction function : model.getFunctions()) {
+ result.addFunction(function.copy());
+ }
+
+ for (SbmlParameter parameter : model.getParameters()) {
+ result.addParameter(parameter.copy());
+ }
+
+ for (Element alias : model.getElements()) {
+ if (alias instanceof Compartment) {
+ Compartment copy = ((Compartment) alias).copy();
+ copy.getElements().clear();
+ copy.setCompartment(null);
+ result.addElement(copy);
+ }
+
+ }
+
+ for (Element alias : model.getElements()) {
+ if (alias instanceof Species) {
+ Species copy = ((Species) alias).copy();
+ copy.setCompartment(null);
+ result.addElement(copy);
+
+ Compartment parentCompartment = alias.getCompartment();
+
+ if (parentCompartment != null) {
+ parentCompartment = result.getElementByElementId(parentCompartment.getElementId());
+ copy.setCompartment(parentCompartment);
+ }
+
+ } else if (alias instanceof Compartment) {
+
+ Compartment parentCompartment = alias.getCompartment();
+
+ if (parentCompartment != null) {
+ Compartment copy = result.getElementByElementId(alias.getElementId());
+ parentCompartment = result.getElementByElementId(parentCompartment.getElementId());
+ copy.setCompartment(parentCompartment);
+ }
+ } else {
+ throw new InvalidClassException("Don't know what to do with: " + alias.getClass());
+ }
+ }
+
+ for (Layer layer : model.getLayers()) {
+ result.addLayer(layer.copy());
+ }
+
+ for (Reaction reaction : model.getReactions()) {
+ result.addReaction(createCopy(reaction));
+ }
+
+ assignSimpleDataToCopy(result, model);
+ for (Layout layout : model.getLayouts()) {
+ result.addLayout(layout.copy());
+ }
+ result.setProject(model.getProject());
+
+ for (Element element : result.getElements()) {
+ updateElementReferences(element, result, model);
+ }
+ for (Reaction reaction : result.getReactions()) {
+ updateReactionReferences(reaction, result);
+ }
+ for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
+ result.addSubmodelConnection(connection.copy());
+ }
+ return result;
+ }
+
+ /**
+ * Copies simple information about model to the copy.
+ *
+ * @param copy
+ * to this model data will be copied
+ * @param original
+ * original model
+ */
+ private void assignSimpleDataToCopy(Model copy, Model original) {
+ copy.setName(original.getName());
+
+ copy.setCreationDate(original.getCreationDate());
+
+ copy.setWidth(original.getWidth());
+ copy.setHeight(original.getHeight());
+ copy.setNotes(original.getNotes());
+ copy.setIdModel(original.getIdModel());
+ copy.setZoomLevels(original.getZoomLevels());
+ copy.setTileSize(original.getTileSize());
+ }
+
+ /**
+ * Creates copy of the reaction that doesn't contain any references to the
+ * original (so we have to substitute all references with the new ones...).
+ *
+ * @param reaction
+ * original reaction
+ * @return copy of the reaction
+ */
+ private Reaction createCopy(Reaction reaction) {
+ Reaction copy = reaction.copy();
+ reaction.getNodes().clear();
+ for (AbstractNode node : copy.getNodes()) {
+ reaction.addNode(node);
+ }
+ copy.getNodes().clear();
+
+ for (AbstractNode node : reaction.getNodes()) {
+ AbstractNode nodeCopy = node.copy();
+ nodeCopy.setLine(new PolylineData(nodeCopy.getLine()));
+ copy.addNode(nodeCopy);
+ }
+
+ for (int i = 0; i < copy.getOperators().size(); i++) {
+ NodeOperator nodeCopy = copy.getOperators().get(i);
+ NodeOperator nodeOriginal = reaction.getOperators().get(i);
+ for (int j = 0; j < nodeCopy.getInputs().size(); j++) {
+ AbstractNode input = nodeCopy.getInputs().get(j);
+ int index1 = reaction.getOperators().indexOf(input);
+ int index2 = reaction.getNodes().indexOf(input);
+ if (index1 >= 0) {
+ nodeCopy.getInputs().set(j, copy.getOperators().get(index1));
+ copy.getOperators().get(index1).setNodeOperatorForInput(nodeCopy);
+
+ reaction.getOperators().get(index1).setNodeOperatorForInput(nodeOriginal);
+ } else if (index2 >= 0) {
+ nodeCopy.getInputs().set(j, copy.getNodes().get(index2));
+ copy.getNodes().get(index2).setNodeOperatorForInput(nodeCopy);
+
+ reaction.getNodes().get(index2).setNodeOperatorForInput(nodeOriginal);
+ } else {
+ throw new InvalidStateException("WTF");
+ }
+ }
+
+ for (int j = 0; j < nodeCopy.getOutputs().size(); j++) {
+ AbstractNode output = nodeCopy.getOutputs().get(j);
+ int index1 = reaction.getOperators().indexOf(output);
+ int index2 = reaction.getNodes().indexOf(output);
+ if (index1 >= 0) {
+ nodeCopy.getOutputs().set(j, copy.getOperators().get(index1));
+ copy.getOperators().get(index1).setNodeOperatorForOutput(nodeCopy);
+
+ reaction.getOperators().get(index1).setNodeOperatorForOutput(nodeOriginal);
+ } else if (index2 >= 0) {
+ nodeCopy.getOutputs().set(j, copy.getNodes().get(index2));
+ copy.getNodes().get(index2).setNodeOperatorForOutput(nodeCopy);
+
+ reaction.getNodes().get(index2).setNodeOperatorForOutput(nodeOriginal);
+ } else {
+ throw new InvalidStateException("WTF");
+ }
+ }
+ }
+
+ return copy;
+ }
+
+ /**
+ * Updates references to elements and aliases in reaction to the objects taken
+ * from model.
+ *
+ * @param reaction
+ * references in this reaction will be updated
+ * @param model
+ * references from this model will be taken
+ */
+ private void updateReactionReferences(Reaction reaction, Model model) {
+ reaction.setModel(model);
+ for (ReactionNode rNode : reaction.getReactionNodes()) {
+ rNode.setElement(model.getElementByElementId(rNode.getElement().getElementId()));
+ }
+ SbmlKinetics kinetics = reaction.getKinetics();
+ if (kinetics != null) {
+ Collection<SbmlArgument> arguments = new HashSet<>();
+ for (SbmlArgument argument : kinetics.getArguments()) {
+ if (argument instanceof Element) {
+ arguments.add(model.getElementByElementId(argument.getElementId()));
+ } else if (argument instanceof SbmlParameter) {
+ if (model.getParameterById(argument.getElementId()) != null) {
+ arguments.add(model.getParameterById(argument.getElementId()));
+ } else {
+ arguments.add(argument);
+ }
+ } else if (argument instanceof SbmlFunction) {
+ arguments.add(model.getFunctionById(argument.getElementId()));
+ } else {
+ throw new InvalidStateException("Don't know what to do with class: " + argument.getClass());
+ }
+ }
+ kinetics.removeArguments(kinetics.getArguments());
+ kinetics.addArguments(arguments);
+ }
+
+ }
+
+ /**
+ * Updates information (like elements, parent aliases) in the alias with the
+ * data from new model.
+ *
+ * @param element
+ * object to be updated
+ * @param model
+ * data from this model will be used for update
+ * @param originalModel
+ * original model from which alias copy was created
+ */
+ private void updateElementReferences(Element element, Model model, Model originalModel) {
+ if (element instanceof Compartment) {
+ Compartment compartment = (Compartment) element;
+ Compartment original = originalModel.getElementByElementId(element.getElementId());
+ for (Element child : original.getElements()) {
+ compartment.addElement(model.getElementByElementId(child.getElementId()));
+ }
+ }
+
+ if (element instanceof Complex) {
+ Complex complex = (Complex) element;
+ for (int i = 0; i < complex.getElements().size(); i++) {
+ Species newElement = model.getElementByElementId(complex.getElements().get(i).getElementId());
+ complex.getElements().set(i, newElement);
+ }
+ }
+ if (element instanceof Species) {
+ Species species = (Species) element;
+
+ if (species.getComplex() != null) {
+ species.setComplex((Complex) model.getElementByElementId(species.getComplex().getElementId()));
+ }
+
+ }
+
+ element.setModel(model);
+
+ if (element.getCompartment() != null) {
+ element.setCompartment(model.getElementByElementId(element.getCompartment().getElementId()));
+ }
+ }
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
index e89bcdf5a4..57800a7e4f 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
@@ -1,385 +1,385 @@
-package lcsb.mapviewer.commands;
-
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
-import lcsb.mapviewer.model.map.layout.graphics.LayerText;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * This {@link ModelCommand command} class allows to transform model into
- * multilevel (nested) component structure. Some artificial compartments will
- * appear. All compartments have information about children compartments. All
- * objects have information about parents.
- *
- *
- */
-public class CreateHierarchyCommand extends ModelCommand {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(CreateHierarchyCommand.class);
- /**
- * Natural logarithm of four.
- */
- private static final double LOG_4 = Math.log(4);
-
- /**
- * Top left corner x coordinate of the text associated with compratment.
- */
- private static final double DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT = 10;
- /**
- * Top left corner y coordinate of the text associated with compratment.
- */
- private static final double DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT = 10;
-
- /**
- * How many levels are possible.
- */
- private int zoomLevels;
- /**
- * What is the maximum zoom factor in the view.
- */
- private double maxZoomFactor;
-
- /**
- * Default constructor that intializes data.
- *
- * @param model
- * model on which command will be executed
- * @param maxZoomFactor
- * what is the maximum zoom out factor
- * @param zoomLevels
- * how many levels are possible
- */
- public CreateHierarchyCommand(Model model, int zoomLevels, double maxZoomFactor) {
- super(model);
- this.zoomLevels = zoomLevels;
- this.maxZoomFactor = maxZoomFactor;
- }
-
- @Override
- protected void undoImplementation() {
- throw new NotImplementedException();
- }
-
- @Override
- protected void executeImplementation() {
- if (!ModelCommandStatus.CREATED.equals(getStatus()) && !ModelCommandStatus.UNDONE.equals(getStatus())) {
- throw new InvalidStateException("To execute command, the command must be in CREATED or UNDONE state. " + getStatus() + " found.");
- }
- Model model = getModel();
- List<Species> compacts = new ArrayList<>();
- for (Element alias : model.getElements()) {
- if (alias instanceof Complex) {
- if (((Complex) alias).getState().contains("brief")) {
- compacts.add((Species) alias);
- compacts.addAll(((Complex) alias).getElements());
- }
- }
- }
- model.getElements().removeAll(compacts);
- clean();
- createArtificials();
- assignAliases();
-
- List<Element> sortedAliases = model.getElementsSortedBySize();
- setParentingAndChildreningOfNonComplexChildrens(sortedAliases);
- model.getElements().addAll(compacts);
- sortedAliases = model.getElementsSortedBySize();
- preSettingOfVisibilityLevel(sortedAliases, maxZoomFactor);
- settingOfTransparencyLevel(sortedAliases);
-
- setStatus(ModelCommandStatus.EXECUTED);
- }
-
- @Override
- protected void redoImplementation() {
- throw new NotImplementedException();
- }
-
- /**
- * Cleans hierarchical information from the model.
- */
- protected void clean() {
- for (Element alias : getModel().getElements()) {
- alias.setCompartment(null);
- alias.setTransparencyLevel("");
- }
- for (BioEntity bioEntity : getModel().getBioEntities()) {
- bioEntity.setVisibilityLevel("0");
- }
- Set<Compartment> toRemove = new HashSet<>();
- for (Compartment alias : getModel().getCompartments()) {
- if (alias instanceof PathwayCompartment) {
- toRemove.add(alias);
- }
- }
- for (Compartment alias : toRemove) {
- getModel().removeElement(alias);
- }
- }
-
- /**
- * Creates artifitial compartment alias for rectangles and texts object on
- * additional graphic layers.
- */
- private void createArtificials() {
- Model model = getModel();
- int id = 0;
- for (Layer layer : model.getLayers()) {
- for (LayerRect rect : layer.getRectangles()) {
- PathwayCompartment alias = new PathwayCompartment("art" + (id++));
- alias.setX(rect.getX());
- alias.setY(rect.getY());
- alias.setWidth(rect.getWidth());
- alias.setHeight(rect.getHeight());
- alias.setColor(rect.getColor());
- alias.setNamePoint(
- new Point2D.Double(rect.getX() + DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT, rect.getY() + DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT));
-
- model.addElement(alias);
- }
- for (LayerText text : layer.getTexts()) {
- PathwayCompartment alias = new PathwayCompartment("art" + (id++));
- alias.setX(text.getX());
- alias.setY(text.getY());
- alias.setWidth(text.getWidth());
- alias.setHeight(text.getHeight());
- alias.setColor(text.getColor());
- alias.setName(text.getNotes().trim());
- alias.setNamePoint(
- new Point2D.Double(text.getX() + DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT, text.getY() + DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT));
-
- model.addElement(alias);
-
- }
- }
- }
-
- /**
- * Assign aliases in hierarchical structure.
- */
- private void assignAliases() {
- assignToCompartments();
- }
-
- /**
- * Computes visibility levels for aliases based on the size.
- *
- * @param sortedAliases
- * list of aliases
- * @param maxZoomFactor
- * max scale used on the map
- */
- private void preSettingOfVisibilityLevel(List<Element> sortedAliases, double maxZoomFactor) {
- for (Element alias : sortedAliases) {
- double rate = computeRate(alias, Configuration.MIN_VISIBLE_OBJECT_SIZE);
- int logValue = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
- boolean hasCompartment = alias.getCompartment() != null;
- boolean hasComplex = false;
- if (alias instanceof Species) {
- hasComplex = ((Species) alias).getComplex() != null;
- }
- if (!hasCompartment && !hasComplex) {
- logValue = 0;
- }
- if (logValue >= zoomLevels) {
- if (hasComplex) {
- logValue = zoomLevels - 1;
- } else {
- logValue = zoomLevels;
- }
- }
- alias.setVisibilityLevel(logValue + "");
- }
- }
-
- /**
- * Sets transparency level in hierarchical view for compartment alias.
- *
- * @param compartment
- * comaprtment alias
- */
- private void settingTransparencyLevelForCompartment(Compartment compartment) {
- int maxVisibilityLevel = Integer.MAX_VALUE;
- double rate = computeRate(compartment, Configuration.MAX_VISIBLE_OBJECT_SIZE);
- maxVisibilityLevel = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
- for (Element child : compartment.getElements()) {
- maxVisibilityLevel = Math.min(maxVisibilityLevel, Integer.valueOf(child.getVisibilityLevel()));
- }
- if (maxVisibilityLevel >= zoomLevels) {
- maxVisibilityLevel = zoomLevels;
- }
- if (maxVisibilityLevel <= 0) {
- maxVisibilityLevel = 1;
- }
- compartment.setTransparencyLevel(maxVisibilityLevel + "");
- for (Element child : compartment.getElements()) {
- child.setVisibilityLevel(compartment.getTransparencyLevel());
- }
- }
-
- /**
- * Sets transparency level in hierarchical view for complex alias.
- *
- * @param complex
- * complex alias
- */
- private void settingTransparencyLevelForComplex(Complex complex) {
- int maxVisibilityLevel = Integer.MAX_VALUE;
- double rate = computeRate(complex, Configuration.MAX_VISIBLE_OBJECT_SIZE);
- maxVisibilityLevel = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
- for (Element child : complex.getElements()) {
- maxVisibilityLevel = Math.min(maxVisibilityLevel, Integer.valueOf(child.getVisibilityLevel()));
- }
- if (maxVisibilityLevel >= zoomLevels) {
- maxVisibilityLevel = zoomLevels;
- }
- if (maxVisibilityLevel <= 0) {
- maxVisibilityLevel = 1;
- }
- complex.setTransparencyLevel(maxVisibilityLevel + "");
- for (Element child : complex.getElements()) {
- child.setVisibilityLevel(complex.getTransparencyLevel());
- }
- }
-
- /**
- * Sets transparency level in hierarchical view for all elements.
- *
- * @param sortedAliases
- * list of aliases
- */
- private void settingOfTransparencyLevel(List<Element> sortedAliases) {
- for (Element alias : sortedAliases) {
- if (alias instanceof Compartment) {
- settingTransparencyLevelForCompartment((Compartment) alias);
- } else if (alias instanceof Complex) {
- settingTransparencyLevelForComplex((Complex) alias);
- } else {
- alias.setTransparencyLevel("0");
- }
- }
- }
-
- /**
- * Removes invalid compartment children.
- *
- * @param sortedAliases
- * list of aliases
- */
- private void setChildrening(List<Element> sortedAliases) {
- for (Element compartment : sortedAliases) {
- if (compartment instanceof Compartment) {
- Set<Element> removable = new HashSet<>();
- for (Element alias : ((Compartment) compartment).getElements()) {
- if (alias.getCompartment() != compartment) {
- removable.add(alias);
- }
- }
- ((Compartment) compartment).getElements().removeAll(removable);
- }
- }
- }
-
- /**
- * Sets parent for elements.
- *
- * @param sortedAliases
- * list of aliases
- */
- private void setParentingOfNonComplexChildrens(List<Element> sortedAliases) {
- for (Element element : getModel().getElements()) {
- if (element.getCompartment() == null) {
- for (Element compartment : sortedAliases) {
- if (compartment instanceof Compartment) {
- if (((Compartment) compartment).getElements().contains(element)) {
- element.setCompartment((Compartment) compartment);
- }
- }
- }
-
- }
- if (element instanceof Species) {
- Species species = (Species) element;
- if (species.getComplex() == null) {
- for (Element complex : sortedAliases) {
- if (complex instanceof Complex) {
- if (((Complex) complex).getElements().contains(element)) {
- species.setComplex((Complex) complex);
- }
- }
- }
- }
- }
- }
- }
-
- /**
- * Set parents for the elements in hierarchical view.
- *
- * @param sortedAliases
- * list of aliases
- */
- private void setParentingAndChildreningOfNonComplexChildrens(List<Element> sortedAliases) {
- setParentingOfNonComplexChildrens(sortedAliases);
- setChildrening(sortedAliases);
- }
-
- /**
- * Assign aliases to compartments.
- */
- private void assignToCompartments() {
- Compartment nullCompartment = new Compartment("null");
- nullCompartment.setWidth(Double.MAX_VALUE);
- nullCompartment.setHeight(Double.MAX_VALUE);
- for (Element element : getModel().getElements()) {
- Compartment supposedParent = nullCompartment;
- for (Compartment alias : getModel().getCompartments()) {
- if (alias.contains(element) && alias.getSize() < supposedParent.getSize()) {
- supposedParent = alias;
- }
- }
- if (supposedParent != nullCompartment) {
- supposedParent.addElement(element);
- }
- }
- }
-
- /**
- * Computes the ratio between the minimal object that should be visible, and
- * alias visible on the top level.
- *
- * @param alias
- * alias for which computation is done
- * @param limit
- * size of the minimal visibe object
- * @return ratio between the minimal object that should be visible, and alias
- * visible on the top level
- */
- private double computeRate(Element alias, double limit) {
- double length = alias.getWidth() / maxZoomFactor;
- double height = alias.getHeight() / maxZoomFactor;
- double size = length * height;
- return (double) Math.ceil(limit / size);
- }
-
-}
+package lcsb.mapviewer.commands;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
+import lcsb.mapviewer.model.map.layout.graphics.LayerText;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This {@link ModelCommand command} class allows to transform model into
+ * multilevel (nested) component structure. Some artificial compartments will
+ * appear. All compartments have information about children compartments. All
+ * objects have information about parents.
+ *
+ *
+ */
+public class CreateHierarchyCommand extends ModelCommand {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(CreateHierarchyCommand.class);
+ /**
+ * Natural logarithm of four.
+ */
+ private static final double LOG_4 = Math.log(4);
+
+ /**
+ * Top left corner x coordinate of the text associated with compratment.
+ */
+ private static final double DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT = 10;
+ /**
+ * Top left corner y coordinate of the text associated with compratment.
+ */
+ private static final double DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT = 10;
+
+ /**
+ * How many levels are possible.
+ */
+ private int zoomLevels;
+ /**
+ * What is the maximum zoom factor in the view.
+ */
+ private double maxZoomFactor;
+
+ /**
+ * Default constructor that intializes data.
+ *
+ * @param model
+ * model on which command will be executed
+ * @param maxZoomFactor
+ * what is the maximum zoom out factor
+ * @param zoomLevels
+ * how many levels are possible
+ */
+ public CreateHierarchyCommand(Model model, int zoomLevels, double maxZoomFactor) {
+ super(model);
+ this.zoomLevels = zoomLevels;
+ this.maxZoomFactor = maxZoomFactor;
+ }
+
+ @Override
+ protected void undoImplementation() {
+ throw new NotImplementedException();
+ }
+
+ @Override
+ protected void executeImplementation() {
+ if (!ModelCommandStatus.CREATED.equals(getStatus()) && !ModelCommandStatus.UNDONE.equals(getStatus())) {
+ throw new InvalidStateException("To execute command, the command must be in CREATED or UNDONE state. " + getStatus() + " found.");
+ }
+ Model model = getModel();
+ List<Species> compacts = new ArrayList<>();
+ for (Element alias : model.getElements()) {
+ if (alias instanceof Complex) {
+ if (((Complex) alias).getState().contains("brief")) {
+ compacts.add((Species) alias);
+ compacts.addAll(((Complex) alias).getElements());
+ }
+ }
+ }
+ model.getElements().removeAll(compacts);
+ clean();
+ createArtificials();
+ assignAliases();
+
+ List<Element> sortedAliases = model.getElementsSortedBySize();
+ setParentingAndChildreningOfNonComplexChildrens(sortedAliases);
+ model.getElements().addAll(compacts);
+ sortedAliases = model.getElementsSortedBySize();
+ preSettingOfVisibilityLevel(sortedAliases, maxZoomFactor);
+ settingOfTransparencyLevel(sortedAliases);
+
+ setStatus(ModelCommandStatus.EXECUTED);
+ }
+
+ @Override
+ protected void redoImplementation() {
+ throw new NotImplementedException();
+ }
+
+ /**
+ * Cleans hierarchical information from the model.
+ */
+ protected void clean() {
+ for (Element alias : getModel().getElements()) {
+ alias.setCompartment(null);
+ alias.setTransparencyLevel("");
+ }
+ for (BioEntity bioEntity : getModel().getBioEntities()) {
+ bioEntity.setVisibilityLevel("0");
+ }
+ Set<Compartment> toRemove = new HashSet<>();
+ for (Compartment alias : getModel().getCompartments()) {
+ if (alias instanceof PathwayCompartment) {
+ toRemove.add(alias);
+ }
+ }
+ for (Compartment alias : toRemove) {
+ getModel().removeElement(alias);
+ }
+ }
+
+ /**
+ * Creates artifitial compartment alias for rectangles and texts object on
+ * additional graphic layers.
+ */
+ private void createArtificials() {
+ Model model = getModel();
+ int id = 0;
+ for (Layer layer : model.getLayers()) {
+ for (LayerRect rect : layer.getRectangles()) {
+ PathwayCompartment alias = new PathwayCompartment("art" + (id++));
+ alias.setX(rect.getX());
+ alias.setY(rect.getY());
+ alias.setWidth(rect.getWidth());
+ alias.setHeight(rect.getHeight());
+ alias.setColor(rect.getColor());
+ alias.setNamePoint(
+ new Point2D.Double(rect.getX() + DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT, rect.getY() + DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT));
+
+ model.addElement(alias);
+ }
+ for (LayerText text : layer.getTexts()) {
+ PathwayCompartment alias = new PathwayCompartment("art" + (id++));
+ alias.setX(text.getX());
+ alias.setY(text.getY());
+ alias.setWidth(text.getWidth());
+ alias.setHeight(text.getHeight());
+ alias.setColor(text.getColor());
+ alias.setName(text.getNotes().trim());
+ alias.setNamePoint(
+ new Point2D.Double(text.getX() + DEFAULT_TITLE_X_COORD_IN_ARTIFITIAL_COMPARTMENT, text.getY() + DEFAULT_TITLE_Y_COORD_IN_ARTIFITIAL_COMPARTMENT));
+
+ model.addElement(alias);
+
+ }
+ }
+ }
+
+ /**
+ * Assign aliases in hierarchical structure.
+ */
+ private void assignAliases() {
+ assignToCompartments();
+ }
+
+ /**
+ * Computes visibility levels for aliases based on the size.
+ *
+ * @param sortedAliases
+ * list of aliases
+ * @param maxZoomFactor
+ * max scale used on the map
+ */
+ private void preSettingOfVisibilityLevel(List<Element> sortedAliases, double maxZoomFactor) {
+ for (Element alias : sortedAliases) {
+ double rate = computeRate(alias, Configuration.MIN_VISIBLE_OBJECT_SIZE);
+ int logValue = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
+ boolean hasCompartment = alias.getCompartment() != null;
+ boolean hasComplex = false;
+ if (alias instanceof Species) {
+ hasComplex = ((Species) alias).getComplex() != null;
+ }
+ if (!hasCompartment && !hasComplex) {
+ logValue = 0;
+ }
+ if (logValue >= zoomLevels) {
+ if (hasComplex) {
+ logValue = zoomLevels - 1;
+ } else {
+ logValue = zoomLevels;
+ }
+ }
+ alias.setVisibilityLevel(logValue + "");
+ }
+ }
+
+ /**
+ * Sets transparency level in hierarchical view for compartment alias.
+ *
+ * @param compartment
+ * comaprtment alias
+ */
+ private void settingTransparencyLevelForCompartment(Compartment compartment) {
+ int maxVisibilityLevel = Integer.MAX_VALUE;
+ double rate = computeRate(compartment, Configuration.MAX_VISIBLE_OBJECT_SIZE);
+ maxVisibilityLevel = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
+ for (Element child : compartment.getElements()) {
+ maxVisibilityLevel = Math.min(maxVisibilityLevel, Integer.valueOf(child.getVisibilityLevel()));
+ }
+ if (maxVisibilityLevel >= zoomLevels) {
+ maxVisibilityLevel = zoomLevels;
+ }
+ if (maxVisibilityLevel <= 0) {
+ maxVisibilityLevel = 1;
+ }
+ compartment.setTransparencyLevel(maxVisibilityLevel + "");
+ for (Element child : compartment.getElements()) {
+ child.setVisibilityLevel(compartment.getTransparencyLevel());
+ }
+ }
+
+ /**
+ * Sets transparency level in hierarchical view for complex alias.
+ *
+ * @param complex
+ * complex alias
+ */
+ private void settingTransparencyLevelForComplex(Complex complex) {
+ int maxVisibilityLevel = Integer.MAX_VALUE;
+ double rate = computeRate(complex, Configuration.MAX_VISIBLE_OBJECT_SIZE);
+ maxVisibilityLevel = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
+ for (Element child : complex.getElements()) {
+ maxVisibilityLevel = Math.min(maxVisibilityLevel, Integer.valueOf(child.getVisibilityLevel()));
+ }
+ if (maxVisibilityLevel >= zoomLevels) {
+ maxVisibilityLevel = zoomLevels;
+ }
+ if (maxVisibilityLevel <= 0) {
+ maxVisibilityLevel = 1;
+ }
+ complex.setTransparencyLevel(maxVisibilityLevel + "");
+ for (Element child : complex.getElements()) {
+ child.setVisibilityLevel(complex.getTransparencyLevel());
+ }
+ }
+
+ /**
+ * Sets transparency level in hierarchical view for all elements.
+ *
+ * @param sortedAliases
+ * list of aliases
+ */
+ private void settingOfTransparencyLevel(List<Element> sortedAliases) {
+ for (Element alias : sortedAliases) {
+ if (alias instanceof Compartment) {
+ settingTransparencyLevelForCompartment((Compartment) alias);
+ } else if (alias instanceof Complex) {
+ settingTransparencyLevelForComplex((Complex) alias);
+ } else {
+ alias.setTransparencyLevel("0");
+ }
+ }
+ }
+
+ /**
+ * Removes invalid compartment children.
+ *
+ * @param sortedAliases
+ * list of aliases
+ */
+ private void setChildrening(List<Element> sortedAliases) {
+ for (Element compartment : sortedAliases) {
+ if (compartment instanceof Compartment) {
+ Set<Element> removable = new HashSet<>();
+ for (Element alias : ((Compartment) compartment).getElements()) {
+ if (alias.getCompartment() != compartment) {
+ removable.add(alias);
+ }
+ }
+ ((Compartment) compartment).getElements().removeAll(removable);
+ }
+ }
+ }
+
+ /**
+ * Sets parent for elements.
+ *
+ * @param sortedAliases
+ * list of aliases
+ */
+ private void setParentingOfNonComplexChildrens(List<Element> sortedAliases) {
+ for (Element element : getModel().getElements()) {
+ if (element.getCompartment() == null) {
+ for (Element compartment : sortedAliases) {
+ if (compartment instanceof Compartment) {
+ if (((Compartment) compartment).getElements().contains(element)) {
+ element.setCompartment((Compartment) compartment);
+ }
+ }
+ }
+
+ }
+ if (element instanceof Species) {
+ Species species = (Species) element;
+ if (species.getComplex() == null) {
+ for (Element complex : sortedAliases) {
+ if (complex instanceof Complex) {
+ if (((Complex) complex).getElements().contains(element)) {
+ species.setComplex((Complex) complex);
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Set parents for the elements in hierarchical view.
+ *
+ * @param sortedAliases
+ * list of aliases
+ */
+ private void setParentingAndChildreningOfNonComplexChildrens(List<Element> sortedAliases) {
+ setParentingOfNonComplexChildrens(sortedAliases);
+ setChildrening(sortedAliases);
+ }
+
+ /**
+ * Assign aliases to compartments.
+ */
+ private void assignToCompartments() {
+ Compartment nullCompartment = new Compartment("null");
+ nullCompartment.setWidth(Double.MAX_VALUE);
+ nullCompartment.setHeight(Double.MAX_VALUE);
+ for (Element element : getModel().getElements()) {
+ Compartment supposedParent = nullCompartment;
+ for (Compartment alias : getModel().getCompartments()) {
+ if (alias.contains(element) && alias.getSize() < supposedParent.getSize()) {
+ supposedParent = alias;
+ }
+ }
+ if (supposedParent != nullCompartment) {
+ supposedParent.addElement(element);
+ }
+ }
+ }
+
+ /**
+ * Computes the ratio between the minimal object that should be visible, and
+ * alias visible on the top level.
+ *
+ * @param alias
+ * alias for which computation is done
+ * @param limit
+ * size of the minimal visibe object
+ * @return ratio between the minimal object that should be visible, and alias
+ * visible on the top level
+ */
+ private double computeRate(Element alias, double limit) {
+ double length = alias.getWidth() / maxZoomFactor;
+ double height = alias.getHeight() / maxZoomFactor;
+ double size = length * height;
+ return (double) Math.ceil(limit / size);
+ }
+
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/InvalidModelException.java b/model-command/src/main/java/lcsb/mapviewer/commands/InvalidModelException.java
index c2368577ac..b0d70db8e0 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/InvalidModelException.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/InvalidModelException.java
@@ -1,26 +1,26 @@
-package lcsb.mapviewer.commands;
-
-/**
- * Exception thrown when the {@link lcsb.mapviewer.model.map.model.Model Model}
- * is inconsitent.
- *
- * @author Piotr Gawron
- *
- */
-public class InvalidModelException extends Exception {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor with message passed in the argument.
- *
- * @param string
- * message of this exception
- */
- public InvalidModelException(String string) {
- super(string);
- }
-
-}
+package lcsb.mapviewer.commands;
+
+/**
+ * Exception thrown when the {@link lcsb.mapviewer.model.map.model.Model Model}
+ * is inconsitent.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class InvalidModelException extends Exception {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor with message passed in the argument.
+ *
+ * @param string
+ * message of this exception
+ */
+ public InvalidModelException(String string) {
+ super(string);
+ }
+
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/ModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/ModelCommand.java
index aefcf90fff..56394014f0 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/ModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/ModelCommand.java
@@ -1,230 +1,230 @@
-package lcsb.mapviewer.commands;
-
-import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
-
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.AbstractNode;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * Abstract class representing operation on the model. There are following steps
- * during processing command:
- * <ul>
- * <li>initialization with some data (constructor)</li>
- * <li>execution - command is performed</li>
- * <li>undo - if command was performed then this method will undo the operation
- * </li>
- * <li>redo - if command was undone then operation is redone</li>
- * </ul>
- *
- * @author Piotr Gawron
- *
- */
-public abstract class ModelCommand {
-
- /**
- * Status of the command.
- */
- private ModelCommandStatus status = ModelCommandStatus.CREATED;
-
- /**
- * Model on which command is performed.
- */
- private Model model;
-
- /**
- * Region that is affected by this command. If null then command didn't
- * affected layout.
- */
- private Rectangle2D affectedRegion;
-
- /**
- * Undo the operation.
- *
- * @throws CommandExecutionException
- * thrown when undo cannot be performed due to invalid input data
- */
- public void undo() throws CommandExecutionException {
- if (!ModelCommandStatus.EXECUTED.equals(getStatus())) {
- throw new InvalidStateException("To undo command, the command must be executed first. " + getStatus() + " found.");
- } else {
- affectedRegion = null;
- undoImplementation();
- }
- }
-
- /**
- * Redo the operation if the command was undone.
- *
- * @throws CommandExecutionException
- * thrown when undo cannot be executed due to problemtaic input data
- */
- public void redo() throws CommandExecutionException {
- if (!ModelCommandStatus.UNDONE.equals(getStatus())) {
- throw new InvalidStateException("To redo command, the command must be undone first. " + getStatus() + " found.");
- } else {
- affectedRegion = null;
- redoImplementation();
- }
- }
-
- /**
- * Executed the operation.
- *
- * @throws CommandExecutionException
- * thrown when execution cannot be performed due to invalid input
- * data
- */
- public void execute() throws CommandExecutionException {
- if (!ModelCommandStatus.CREATED.equals(getStatus()) && !ModelCommandStatus.UNDONE.equals(getStatus())) {
- throw new InvalidStateException("To execute command, the command must be in CREATED or UNDONE state. " + getStatus() + " found.");
- } else {
- affectedRegion = null;
- executeImplementation();
- setStatus(ModelCommandStatus.EXECUTED);
- }
- }
-
- /**
- * Command specific implementation of {@link #undo()} operation.
- *
- * @throws CommandExecutionException
- * thrown when undo cannot be executed due to problematic input data
- */
- protected abstract void undoImplementation() throws CommandExecutionException;
-
- /**
- * Command specific implementation of {@link #redo()} operation.
- *
- * @throws CommandExecutionException
- * thrown when redo cannot be executed due to problematic input data
- */
- protected abstract void redoImplementation() throws CommandExecutionException;
-
- /**
- * Command specific implementation how to execute this command.
- *
- * @throws CommandExecutionException
- * thrown when command cannot be executed due to problematic input
- * data
- */
- protected abstract void executeImplementation() throws CommandExecutionException;
-
- /**
- * Default constructor.
- *
- * @param model
- * {@link #model}
- */
- public ModelCommand(Model model) {
- this.model = model;
- }
-
- /**
- * @return the status
- * @see #status
- */
- public ModelCommandStatus getStatus() {
- return status;
- }
-
- /**
- * @return the model
- * @see #model
- */
- protected Model getModel() {
- return model;
- }
-
- /**
- * @param model
- * the model to set
- * @see #model
- */
- protected void setModel(Model model) {
- this.model = model;
- }
-
- /**
- * @param status
- * the status to set
- * @see #status
- */
- protected void setStatus(ModelCommandStatus status) {
- this.status = status;
- }
-
- /**
- * @return the affectedRegion
- * @see #affectedRegion
- */
- public Rectangle2D getAffectedRegion() {
- return affectedRegion;
- }
-
- /**
- * Adds point to {@link #affectedRegion}.
- *
- * @param point
- * point to be included in affected region
- */
- protected void includeInAffectedRegion(Point2D point) {
- if (affectedRegion == null) {
- affectedRegion = new Rectangle2D.Double(point.getY(), point.getY(), 0, 0);
- } else {
- affectedRegion.add(point);
- }
- }
-
- /**
- * Adds line to {@link #affectedRegion}.
- *
- * @param pd
- * line to be included in affected region
- */
- protected void includeInAffectedRegion(PolylineData pd) {
- if (affectedRegion == null) {
- affectedRegion = new Rectangle2D.Double(pd.getBeginPoint().getX(), pd.getBeginPoint().getY(), 0, 0);
- }
- for (Point2D point : pd.getPoints()) {
- affectedRegion.add(point);
- }
- }
-
- /**
- * Adds alias to {@link #affectedRegion}.
- *
- * @param alias
- * alias to be included in affected region
- */
- protected void includeInAffectedRegion(Element alias) {
- if (affectedRegion == null) {
- affectedRegion = new Rectangle2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight());
- } else {
- affectedRegion.add(alias.getX(), alias.getY());
- affectedRegion.add(alias.getX() + alias.getWidth(), alias.getY() + alias.getHeight());
- }
- }
-
- /**
- * Adds reaction to {@link #affectedRegion}.
- *
- * @param reaction
- * reaction to be included in affected region
- */
- protected void includeInAffectedRegion(Reaction reaction) {
- if (affectedRegion == null) {
- Point2D point = reaction.getNodes().iterator().next().getLine().getBeginPoint();
- affectedRegion = new Rectangle2D.Double(point.getX(), point.getY(), 0, 0);
- }
- for (AbstractNode node : reaction.getNodes()) {
- includeInAffectedRegion(node.getLine());
- }
-
- }
-
-}
+package lcsb.mapviewer.commands;
+
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.AbstractNode;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * Abstract class representing operation on the model. There are following steps
+ * during processing command:
+ * <ul>
+ * <li>initialization with some data (constructor)</li>
+ * <li>execution - command is performed</li>
+ * <li>undo - if command was performed then this method will undo the operation
+ * </li>
+ * <li>redo - if command was undone then operation is redone</li>
+ * </ul>
+ *
+ * @author Piotr Gawron
+ *
+ */
+public abstract class ModelCommand {
+
+ /**
+ * Status of the command.
+ */
+ private ModelCommandStatus status = ModelCommandStatus.CREATED;
+
+ /**
+ * Model on which command is performed.
+ */
+ private Model model;
+
+ /**
+ * Region that is affected by this command. If null then command didn't
+ * affected layout.
+ */
+ private Rectangle2D affectedRegion;
+
+ /**
+ * Undo the operation.
+ *
+ * @throws CommandExecutionException
+ * thrown when undo cannot be performed due to invalid input data
+ */
+ public void undo() throws CommandExecutionException {
+ if (!ModelCommandStatus.EXECUTED.equals(getStatus())) {
+ throw new InvalidStateException("To undo command, the command must be executed first. " + getStatus() + " found.");
+ } else {
+ affectedRegion = null;
+ undoImplementation();
+ }
+ }
+
+ /**
+ * Redo the operation if the command was undone.
+ *
+ * @throws CommandExecutionException
+ * thrown when undo cannot be executed due to problemtaic input data
+ */
+ public void redo() throws CommandExecutionException {
+ if (!ModelCommandStatus.UNDONE.equals(getStatus())) {
+ throw new InvalidStateException("To redo command, the command must be undone first. " + getStatus() + " found.");
+ } else {
+ affectedRegion = null;
+ redoImplementation();
+ }
+ }
+
+ /**
+ * Executed the operation.
+ *
+ * @throws CommandExecutionException
+ * thrown when execution cannot be performed due to invalid input
+ * data
+ */
+ public void execute() throws CommandExecutionException {
+ if (!ModelCommandStatus.CREATED.equals(getStatus()) && !ModelCommandStatus.UNDONE.equals(getStatus())) {
+ throw new InvalidStateException("To execute command, the command must be in CREATED or UNDONE state. " + getStatus() + " found.");
+ } else {
+ affectedRegion = null;
+ executeImplementation();
+ setStatus(ModelCommandStatus.EXECUTED);
+ }
+ }
+
+ /**
+ * Command specific implementation of {@link #undo()} operation.
+ *
+ * @throws CommandExecutionException
+ * thrown when undo cannot be executed due to problematic input data
+ */
+ protected abstract void undoImplementation() throws CommandExecutionException;
+
+ /**
+ * Command specific implementation of {@link #redo()} operation.
+ *
+ * @throws CommandExecutionException
+ * thrown when redo cannot be executed due to problematic input data
+ */
+ protected abstract void redoImplementation() throws CommandExecutionException;
+
+ /**
+ * Command specific implementation how to execute this command.
+ *
+ * @throws CommandExecutionException
+ * thrown when command cannot be executed due to problematic input
+ * data
+ */
+ protected abstract void executeImplementation() throws CommandExecutionException;
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * {@link #model}
+ */
+ public ModelCommand(Model model) {
+ this.model = model;
+ }
+
+ /**
+ * @return the status
+ * @see #status
+ */
+ public ModelCommandStatus getStatus() {
+ return status;
+ }
+
+ /**
+ * @return the model
+ * @see #model
+ */
+ protected Model getModel() {
+ return model;
+ }
+
+ /**
+ * @param model
+ * the model to set
+ * @see #model
+ */
+ protected void setModel(Model model) {
+ this.model = model;
+ }
+
+ /**
+ * @param status
+ * the status to set
+ * @see #status
+ */
+ protected void setStatus(ModelCommandStatus status) {
+ this.status = status;
+ }
+
+ /**
+ * @return the affectedRegion
+ * @see #affectedRegion
+ */
+ public Rectangle2D getAffectedRegion() {
+ return affectedRegion;
+ }
+
+ /**
+ * Adds point to {@link #affectedRegion}.
+ *
+ * @param point
+ * point to be included in affected region
+ */
+ protected void includeInAffectedRegion(Point2D point) {
+ if (affectedRegion == null) {
+ affectedRegion = new Rectangle2D.Double(point.getY(), point.getY(), 0, 0);
+ } else {
+ affectedRegion.add(point);
+ }
+ }
+
+ /**
+ * Adds line to {@link #affectedRegion}.
+ *
+ * @param pd
+ * line to be included in affected region
+ */
+ protected void includeInAffectedRegion(PolylineData pd) {
+ if (affectedRegion == null) {
+ affectedRegion = new Rectangle2D.Double(pd.getBeginPoint().getX(), pd.getBeginPoint().getY(), 0, 0);
+ }
+ for (Point2D point : pd.getPoints()) {
+ affectedRegion.add(point);
+ }
+ }
+
+ /**
+ * Adds alias to {@link #affectedRegion}.
+ *
+ * @param alias
+ * alias to be included in affected region
+ */
+ protected void includeInAffectedRegion(Element alias) {
+ if (affectedRegion == null) {
+ affectedRegion = new Rectangle2D.Double(alias.getX(), alias.getY(), alias.getWidth(), alias.getHeight());
+ } else {
+ affectedRegion.add(alias.getX(), alias.getY());
+ affectedRegion.add(alias.getX() + alias.getWidth(), alias.getY() + alias.getHeight());
+ }
+ }
+
+ /**
+ * Adds reaction to {@link #affectedRegion}.
+ *
+ * @param reaction
+ * reaction to be included in affected region
+ */
+ protected void includeInAffectedRegion(Reaction reaction) {
+ if (affectedRegion == null) {
+ Point2D point = reaction.getNodes().iterator().next().getLine().getBeginPoint();
+ affectedRegion = new Rectangle2D.Double(point.getX(), point.getY(), 0, 0);
+ }
+ for (AbstractNode node : reaction.getNodes()) {
+ includeInAffectedRegion(node.getLine());
+ }
+
+ }
+
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/ModelCommandStatus.java b/model-command/src/main/java/lcsb/mapviewer/commands/ModelCommandStatus.java
index 4fb30a4951..5bcf5084fe 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/ModelCommandStatus.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/ModelCommandStatus.java
@@ -1,22 +1,22 @@
-package lcsb.mapviewer.commands;
-
-/**
- * Describes status of the {@link ModelCommand}.
- *
- * @author Piotr Gawron
- *
- */
-public enum ModelCommandStatus {
- /**
- * {@link ModelCommand} was created.
- */
- CREATED,
- /**
- * {@link ModelCommand} was executed.
- */
- EXECUTED,
- /**
- * {@link ModelCommand} was undone.
- */
- UNDONE;
-}
+package lcsb.mapviewer.commands;
+
+/**
+ * Describes status of the {@link ModelCommand}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum ModelCommandStatus {
+ /**
+ * {@link ModelCommand} was created.
+ */
+ CREATED,
+ /**
+ * {@link ModelCommand} was executed.
+ */
+ EXECUTED,
+ /**
+ * {@link ModelCommand} was undone.
+ */
+ UNDONE;
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/MoveCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/MoveCommand.java
index 9451c64f4e..42aa36319f 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/MoveCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/MoveCommand.java
@@ -1,76 +1,76 @@
-package lcsb.mapviewer.commands;
-
-import java.awt.geom.Point2D;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.AbstractNode;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * Command which moves model by dx, dy coordinates.
- *
- * @author Piotr Gawron
- *
- */
-public class MoveCommand extends ModelCommand {
-
- /**
- * Delta x.
- */
- private double dx;
- /**
- * Delta y.
- */
- private double dy;
-
- /**
- * Default constructor.
- *
- * @param model
- * model to move
- * @param dx
- * delta x
- * @param dy
- * delat y
- */
- public MoveCommand(Model model, double dx, double dy) {
- super(model);
- this.dx = dx;
- this.dy = dy;
- }
-
- @Override
- protected void undoImplementation() {
- throw new NotImplementedException();
- }
-
- @Override
- protected void redoImplementation() {
- throw new NotImplementedException();
- }
-
- @Override
- protected void executeImplementation() {
-
- Model model = getModel();
-
- for (Element alias : model.getElements()) {
- alias.setX(alias.getX() + dx);
- alias.setY(alias.getY() + dy);
- if (alias instanceof Compartment) {
- ((Compartment) alias).setNamePoint(((Compartment) alias).getNamePoint().getX() + dx, ((Compartment) alias).getNamePoint().getY() + dy);
- }
- }
- for (Reaction reaction : model.getReactions()) {
- for (AbstractNode node : reaction.getNodes()) {
- for (Point2D point : node.getLine().getPoints()) {
- point.setLocation(point.getX() + dx, point.getY() + dy);
- }
- }
- }
- }
-
-}
+package lcsb.mapviewer.commands;
+
+import java.awt.geom.Point2D;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.AbstractNode;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * Command which moves model by dx, dy coordinates.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class MoveCommand extends ModelCommand {
+
+ /**
+ * Delta x.
+ */
+ private double dx;
+ /**
+ * Delta y.
+ */
+ private double dy;
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * model to move
+ * @param dx
+ * delta x
+ * @param dy
+ * delat y
+ */
+ public MoveCommand(Model model, double dx, double dy) {
+ super(model);
+ this.dx = dx;
+ this.dy = dy;
+ }
+
+ @Override
+ protected void undoImplementation() {
+ throw new NotImplementedException();
+ }
+
+ @Override
+ protected void redoImplementation() {
+ throw new NotImplementedException();
+ }
+
+ @Override
+ protected void executeImplementation() {
+
+ Model model = getModel();
+
+ for (Element alias : model.getElements()) {
+ alias.setX(alias.getX() + dx);
+ alias.setY(alias.getY() + dy);
+ if (alias instanceof Compartment) {
+ ((Compartment) alias).setNamePoint(((Compartment) alias).getNamePoint().getX() + dx, ((Compartment) alias).getNamePoint().getY() + dy);
+ }
+ }
+ for (Reaction reaction : model.getReactions()) {
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Point2D point : node.getLine().getPoints()) {
+ point.setLocation(point.getX() + dx, point.getY() + dy);
+ }
+ }
+ }
+ }
+
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/MoveElementsCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/MoveElementsCommand.java
index 9910d2e812..ab6002da40 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/MoveElementsCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/MoveElementsCommand.java
@@ -1,181 +1,181 @@
-package lcsb.mapviewer.commands;
-
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.reaction.NodeOperator;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.ReactionNode;
-import lcsb.mapviewer.model.map.species.Element;
-
-import org.apache.log4j.Logger;
-
-/**
- * Command which moves elements in model by dx, dy coordinates.
- *
- * @author Piotr Gawron
- *
- */
-public class MoveElementsCommand extends ModelCommand {
-
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(MoveElementsCommand.class);
-
- /**
- * Delta x.
- */
- private double dx;
-
- /**
- * Delta y.
- */
- private double dy;
-
- /**
- * List of objects to move.
- */
- private List<Object> objectsToMove = new ArrayList<>();
-
- /**
- * Default constructor.
- *
- * @param model
- * model to move
- * @param elements
- * elements that should be moved
- * @param dx
- * delta x
- * @param dy
- * delat y
- */
- public MoveElementsCommand(Model model, List<Object> elements, double dx, double dy) {
- super(model);
- this.dx = dx;
- this.dy = dy;
- for (Object object : elements) {
- if (object instanceof Element) {
- if (((Element) object).getModel() != model) {
- throw new InvalidArgumentException("Object doesnt belong to specified model: " + object);
- }
- } else if (object instanceof Reaction) {
- if (((Reaction) object).getModel() != model) {
- throw new InvalidArgumentException("Object doesnt belong to specified model: " + object);
- }
- } else {
- throw new InvalidArgumentException("Cannot move element: " + object);
- }
- }
- objectsToMove = elements;
- }
-
- @Override
- protected void undoImplementation() {
- dx = -dx;
- dy = -dy;
- executeImplementation();
- dx = -dx;
- dy = -dy;
- setStatus(ModelCommandStatus.UNDONE);
- }
-
- @Override
- protected void redoImplementation() {
- executeImplementation();
- setStatus(ModelCommandStatus.EXECUTED);
- }
-
- @Override
- protected void executeImplementation() {
- Set<Element> aliases = new HashSet<>();
-
- for (Object object : objectsToMove) {
- if (object instanceof Element) {
- Element alias = (Element) object;
-
- includeInAffectedRegion(alias);
-
- alias.setX(alias.getX() + dx);
- alias.setY(alias.getY() + dy);
- if (alias instanceof Compartment) {
- ((Compartment) alias)
- .setNamePoint(((Compartment) alias).getNamePoint().getX() + dx, ((Compartment) alias).getNamePoint().getY() + dy);
- }
-
- includeInAffectedRegion(alias);
-
- aliases.add(alias);
- } else if (object instanceof Reaction) {
- Reaction reaction = (Reaction) object;
- for (Reactant node : reaction.getReactants()) {
- for (int i = 1; i < node.getLine().getPoints().size(); i++) {
- Point2D point = node.getLine().getPoints().get(i);
- logger.debug("Moving point: " + point);
- point.setLocation(point.getX() + dx, point.getY() + dy);
- }
- }
- for (Product node : reaction.getProducts()) {
- for (int i = 0; i < node.getLine().getPoints().size() - 1; i++) {
- Point2D point = node.getLine().getPoints().get(i);
- point.setLocation(point.getX() + dx, point.getY() + dy);
- }
- }
- for (Modifier node : reaction.getModifiers()) {
- for (int i = 1; i < node.getLine().getPoints().size(); i++) {
- Point2D point = node.getLine().getPoints().get(i);
- point.setLocation(point.getX() + dx, point.getY() + dy);
- }
- }
- for (NodeOperator node : reaction.getOperators()) {
- for (int i = 0; i < node.getLine().getPoints().size(); i++) {
- Point2D point = node.getLine().getPoints().get(i);
- point.setLocation(point.getX() + dx, point.getY() + dy);
- }
- }
- includeInAffectedRegion(reaction);
- } else {
- throw new InvalidStateException("Unknown class type: " + object);
- }
- }
- if (aliases.size() > 0) {
- // TODO this must be improved, we cannot do full search on every move
- for (Reaction reaction : getModel().getReactions()) {
- for (ReactionNode node : reaction.getReactionNodes()) {
- if (aliases.contains(node.getElement())) {
- if (node instanceof Reactant) {
- Point2D point = node.getLine().getBeginPoint();
- point.setLocation(point.getX() + dx, point.getY() + dy);
-
- // we don't have to include point that we change as it's already
- // on the border of the element
- includeInAffectedRegion(node.getLine().getPoints().get(1));
- } else if (node instanceof Modifier) {
- Point2D point = node.getLine().getBeginPoint();
- point.setLocation(point.getX() + dx, point.getY() + dy);
- // we don't have to include point that we change as it's already
- // on the border of the element
- includeInAffectedRegion(node.getLine().getPoints().get(1));
- } else if (node instanceof Product) {
- Point2D point = node.getLine().getEndPoint();
- point.setLocation(point.getX() + dx, point.getY() + dy);
- // we don't have to include point that we change as it's already
- // on the border of the element
- includeInAffectedRegion(node.getLine().getPoints().get(node.getLine().getPoints().size() - 1));
- }
- }
- }
- }
- }
- }
-}
+package lcsb.mapviewer.commands;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.reaction.NodeOperator;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.Element;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Command which moves elements in model by dx, dy coordinates.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class MoveElementsCommand extends ModelCommand {
+
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(MoveElementsCommand.class);
+
+ /**
+ * Delta x.
+ */
+ private double dx;
+
+ /**
+ * Delta y.
+ */
+ private double dy;
+
+ /**
+ * List of objects to move.
+ */
+ private List<Object> objectsToMove = new ArrayList<>();
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * model to move
+ * @param elements
+ * elements that should be moved
+ * @param dx
+ * delta x
+ * @param dy
+ * delat y
+ */
+ public MoveElementsCommand(Model model, List<Object> elements, double dx, double dy) {
+ super(model);
+ this.dx = dx;
+ this.dy = dy;
+ for (Object object : elements) {
+ if (object instanceof Element) {
+ if (((Element) object).getModel() != model) {
+ throw new InvalidArgumentException("Object doesnt belong to specified model: " + object);
+ }
+ } else if (object instanceof Reaction) {
+ if (((Reaction) object).getModel() != model) {
+ throw new InvalidArgumentException("Object doesnt belong to specified model: " + object);
+ }
+ } else {
+ throw new InvalidArgumentException("Cannot move element: " + object);
+ }
+ }
+ objectsToMove = elements;
+ }
+
+ @Override
+ protected void undoImplementation() {
+ dx = -dx;
+ dy = -dy;
+ executeImplementation();
+ dx = -dx;
+ dy = -dy;
+ setStatus(ModelCommandStatus.UNDONE);
+ }
+
+ @Override
+ protected void redoImplementation() {
+ executeImplementation();
+ setStatus(ModelCommandStatus.EXECUTED);
+ }
+
+ @Override
+ protected void executeImplementation() {
+ Set<Element> aliases = new HashSet<>();
+
+ for (Object object : objectsToMove) {
+ if (object instanceof Element) {
+ Element alias = (Element) object;
+
+ includeInAffectedRegion(alias);
+
+ alias.setX(alias.getX() + dx);
+ alias.setY(alias.getY() + dy);
+ if (alias instanceof Compartment) {
+ ((Compartment) alias)
+ .setNamePoint(((Compartment) alias).getNamePoint().getX() + dx, ((Compartment) alias).getNamePoint().getY() + dy);
+ }
+
+ includeInAffectedRegion(alias);
+
+ aliases.add(alias);
+ } else if (object instanceof Reaction) {
+ Reaction reaction = (Reaction) object;
+ for (Reactant node : reaction.getReactants()) {
+ for (int i = 1; i < node.getLine().getPoints().size(); i++) {
+ Point2D point = node.getLine().getPoints().get(i);
+ logger.debug("Moving point: " + point);
+ point.setLocation(point.getX() + dx, point.getY() + dy);
+ }
+ }
+ for (Product node : reaction.getProducts()) {
+ for (int i = 0; i < node.getLine().getPoints().size() - 1; i++) {
+ Point2D point = node.getLine().getPoints().get(i);
+ point.setLocation(point.getX() + dx, point.getY() + dy);
+ }
+ }
+ for (Modifier node : reaction.getModifiers()) {
+ for (int i = 1; i < node.getLine().getPoints().size(); i++) {
+ Point2D point = node.getLine().getPoints().get(i);
+ point.setLocation(point.getX() + dx, point.getY() + dy);
+ }
+ }
+ for (NodeOperator node : reaction.getOperators()) {
+ for (int i = 0; i < node.getLine().getPoints().size(); i++) {
+ Point2D point = node.getLine().getPoints().get(i);
+ point.setLocation(point.getX() + dx, point.getY() + dy);
+ }
+ }
+ includeInAffectedRegion(reaction);
+ } else {
+ throw new InvalidStateException("Unknown class type: " + object);
+ }
+ }
+ if (aliases.size() > 0) {
+ // TODO this must be improved, we cannot do full search on every move
+ for (Reaction reaction : getModel().getReactions()) {
+ for (ReactionNode node : reaction.getReactionNodes()) {
+ if (aliases.contains(node.getElement())) {
+ if (node instanceof Reactant) {
+ Point2D point = node.getLine().getBeginPoint();
+ point.setLocation(point.getX() + dx, point.getY() + dy);
+
+ // we don't have to include point that we change as it's already
+ // on the border of the element
+ includeInAffectedRegion(node.getLine().getPoints().get(1));
+ } else if (node instanceof Modifier) {
+ Point2D point = node.getLine().getBeginPoint();
+ point.setLocation(point.getX() + dx, point.getY() + dy);
+ // we don't have to include point that we change as it's already
+ // on the border of the element
+ includeInAffectedRegion(node.getLine().getPoints().get(1));
+ } else if (node instanceof Product) {
+ Point2D point = node.getLine().getEndPoint();
+ point.setLocation(point.getX() + dx, point.getY() + dy);
+ // we don't have to include point that we change as it's already
+ // on the border of the element
+ includeInAffectedRegion(node.getLine().getPoints().get(node.getLine().getPoints().size() - 1));
+ }
+ }
+ }
+ }
+ }
+ }
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/NewModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/NewModelCommand.java
index a753344c35..0c89b1852c 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/NewModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/NewModelCommand.java
@@ -1,52 +1,52 @@
-package lcsb.mapviewer.commands;
-
-import lcsb.mapviewer.model.map.model.Model;
-
-/**
- * Abstract class representing operation on the model that creates a new model
- * without changing the old one (kind of creational pattern).
- *
- * @author Piotr Gawron
- *
- */
-public abstract class NewModelCommand {
-
- /**
- * Model on which command is performed.
- */
- private Model model;
-
- /**
- * Executed the operation.
- *
- * @return new {@link Model} object accoriding to initialization params
- */
- public abstract Model execute();
-
- /**
- * Default constructor.
- *
- * @param model
- * {@link #model}
- */
- public NewModelCommand(Model model) {
- this.model = model;
- }
-
- /**
- * @return the model
- * @see #model
- */
- protected Model getModel() {
- return model;
- }
-
- /**
- * @param model
- * the model to set
- * @see #model
- */
- protected void setModel(Model model) {
- this.model = model;
- }
-}
+package lcsb.mapviewer.commands;
+
+import lcsb.mapviewer.model.map.model.Model;
+
+/**
+ * Abstract class representing operation on the model that creates a new model
+ * without changing the old one (kind of creational pattern).
+ *
+ * @author Piotr Gawron
+ *
+ */
+public abstract class NewModelCommand {
+
+ /**
+ * Model on which command is performed.
+ */
+ private Model model;
+
+ /**
+ * Executed the operation.
+ *
+ * @return new {@link Model} object accoriding to initialization params
+ */
+ public abstract Model execute();
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * {@link #model}
+ */
+ public NewModelCommand(Model model) {
+ this.model = model;
+ }
+
+ /**
+ * @return the model
+ * @see #model
+ */
+ protected Model getModel() {
+ return model;
+ }
+
+ /**
+ * @param model
+ * the model to set
+ * @see #model
+ */
+ protected void setModel(Model model) {
+ this.model = model;
+ }
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/SetFixedHierarchyLevelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/SetFixedHierarchyLevelCommand.java
index b6c341cbaf..27d69c1334 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/SetFixedHierarchyLevelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/SetFixedHierarchyLevelCommand.java
@@ -1,61 +1,61 @@
-package lcsb.mapviewer.commands;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.model.Model;
-
-/**
- * This {@link ModelCommand command} class allows to transform model into
- * multilevel (nested) component structure. Some artificial compartments will
- * appear. All compartments have information about children compartments. All
- * objects have information about parents.
- *
- *
- */
-public class SetFixedHierarchyLevelCommand extends ModelCommand {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(SetFixedHierarchyLevelCommand.class);
- private Integer level;
-
- public SetFixedHierarchyLevelCommand(Model model, Integer level) {
- super(model);
- this.level = level;
- }
-
- @Override
- protected void undoImplementation() {
- throw new NotImplementedException();
- }
-
- @Override
- protected void executeImplementation() {
- if (!ModelCommandStatus.CREATED.equals(getStatus()) && !ModelCommandStatus.UNDONE.equals(getStatus())) {
- throw new InvalidStateException("To execute command, the command must be in CREATED or UNDONE state. " + getStatus() + " found.");
- }
- if (level != null) {
- SemanticZoomLevelMatcher matcher = new SemanticZoomLevelMatcher();
- Model output = getModel();
- for (BioEntity bioEntity : output.getBioEntities()) {
- if (matcher.isVisible(level, bioEntity.getVisibilityLevel())) {
- bioEntity.setVisibilityLevel("0");
- } else {
- bioEntity.setVisibilityLevel(Integer.MAX_VALUE + "");
- }
- }
- }
-
- setStatus(ModelCommandStatus.EXECUTED);
- }
-
- @Override
- protected void redoImplementation() {
- throw new NotImplementedException();
- }
-
-}
+package lcsb.mapviewer.commands;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.model.Model;
+
+/**
+ * This {@link ModelCommand command} class allows to transform model into
+ * multilevel (nested) component structure. Some artificial compartments will
+ * appear. All compartments have information about children compartments. All
+ * objects have information about parents.
+ *
+ *
+ */
+public class SetFixedHierarchyLevelCommand extends ModelCommand {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(SetFixedHierarchyLevelCommand.class);
+ private Integer level;
+
+ public SetFixedHierarchyLevelCommand(Model model, Integer level) {
+ super(model);
+ this.level = level;
+ }
+
+ @Override
+ protected void undoImplementation() {
+ throw new NotImplementedException();
+ }
+
+ @Override
+ protected void executeImplementation() {
+ if (!ModelCommandStatus.CREATED.equals(getStatus()) && !ModelCommandStatus.UNDONE.equals(getStatus())) {
+ throw new InvalidStateException("To execute command, the command must be in CREATED or UNDONE state. " + getStatus() + " found.");
+ }
+ if (level != null) {
+ SemanticZoomLevelMatcher matcher = new SemanticZoomLevelMatcher();
+ Model output = getModel();
+ for (BioEntity bioEntity : output.getBioEntities()) {
+ if (matcher.isVisible(level, bioEntity.getVisibilityLevel())) {
+ bioEntity.setVisibilityLevel("0");
+ } else {
+ bioEntity.setVisibilityLevel(Integer.MAX_VALUE + "");
+ }
+ }
+ }
+
+ setStatus(ModelCommandStatus.EXECUTED);
+ }
+
+ @Override
+ protected void redoImplementation() {
+ throw new NotImplementedException();
+ }
+
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/SubModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/SubModelCommand.java
index f01a762985..0ab7ea8d34 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/SubModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/SubModelCommand.java
@@ -1,141 +1,141 @@
-package lcsb.mapviewer.commands;
-
-import java.awt.geom.Path2D;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.layout.graphics.LayerText;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.AbstractNode;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.ReactionNode;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * Creates a new instance of the model with data limited to region described by
- * polygon.
- *
- * @author Piotr Gawron
- *
- */
-public class SubModelCommand extends NewModelCommand {
-
- /**
- * Polygon that limits the area for the new model.
- *
- */
- private Path2D polygon;
-
- /**
- * Default constructor.
- *
- * @param model
- * original {@link NewModelCommand#model}
- * @param polygon
- * #polygon that limits the area for the new model
- */
- public SubModelCommand(Model model, Path2D polygon) {
- super(model);
- this.polygon = polygon;
- }
-
- @Override
- public Model execute() {
- CopyCommand copy = new CopyCommand(getModel());
- Model result = copy.execute();
-
- Set<Element> aliasNotToRemove = new HashSet<Element>();
-
- for (Element alias : result.getElements()) {
- if (polygon.intersects(alias.getBorder())) {
- aliasNotToRemove.add(alias);
- }
- }
- boolean added = false;
- do {
- Set<Element> iterativeAliasNotToRemove = new HashSet<>();
- for (Element alias : aliasNotToRemove) {
- Element parent = alias.getCompartment();
- if (parent != null) {
- if (!aliasNotToRemove.contains(parent)) {
- iterativeAliasNotToRemove.add(parent);
- }
- }
- if (alias instanceof Species) {
- parent = ((Species) alias).getComplex();
- if (parent != null) {
- if (!aliasNotToRemove.contains(parent)) {
- iterativeAliasNotToRemove.add(parent);
- }
- }
- }
- }
-
- added = iterativeAliasNotToRemove.size() != 0;
- aliasNotToRemove.addAll(iterativeAliasNotToRemove);
- } while (added);
-
- List<Element> aliasToRemove = new ArrayList<Element>();
- for (Element alias : result.getElements()) {
- if (!(polygon.intersects(alias.getBorder()))) {
- boolean remove = true;
- if (alias instanceof Species) {
- remove = ((Species) alias).getComplex() == null;
- }
- if (aliasNotToRemove.contains(alias)) {
- remove = false;
- }
- if (remove) {
- aliasToRemove.add(alias);
- if (alias instanceof Complex) {
- List<Species> aliases = ((Complex) alias).getAllChildren();
- aliasToRemove.addAll(aliases);
- }
- }
- }
-
- }
- for (Element alias : aliasToRemove) {
- result.removeElement(alias);
- }
-
- List<Reaction> reactionsToRemove = new ArrayList<Reaction>();
- for (Reaction reaction : result.getReactions()) {
- boolean remove = false;
- for (AbstractNode node : reaction.getNodes()) {
- if (node instanceof ReactionNode) {
- if (!result.getElements().contains(((ReactionNode) node).getElement())) {
- remove = true;
- break;
- }
- }
- }
- if (remove) {
- reactionsToRemove.add(reaction);
- }
- }
- for (Reaction reaction : reactionsToRemove) {
- result.removeReaction(reaction);
- }
-
- for (Layer layer : result.getLayers()) {
- List<LayerText> textToRemove = new ArrayList<LayerText>();
- for (LayerText text : layer.getTexts()) {
- if (!(polygon.intersects(text.getBorder()))) {
- textToRemove.add(text);
- }
- }
- for (LayerText text : textToRemove) {
- layer.removeLayerText(text);
- }
- }
-
- return result;
- }
-
-}
+package lcsb.mapviewer.commands;
+
+import java.awt.geom.Path2D;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.layout.graphics.LayerText;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.AbstractNode;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * Creates a new instance of the model with data limited to region described by
+ * polygon.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class SubModelCommand extends NewModelCommand {
+
+ /**
+ * Polygon that limits the area for the new model.
+ *
+ */
+ private Path2D polygon;
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * original {@link NewModelCommand#model}
+ * @param polygon
+ * #polygon that limits the area for the new model
+ */
+ public SubModelCommand(Model model, Path2D polygon) {
+ super(model);
+ this.polygon = polygon;
+ }
+
+ @Override
+ public Model execute() {
+ CopyCommand copy = new CopyCommand(getModel());
+ Model result = copy.execute();
+
+ Set<Element> aliasNotToRemove = new HashSet<Element>();
+
+ for (Element alias : result.getElements()) {
+ if (polygon.intersects(alias.getBorder())) {
+ aliasNotToRemove.add(alias);
+ }
+ }
+ boolean added = false;
+ do {
+ Set<Element> iterativeAliasNotToRemove = new HashSet<>();
+ for (Element alias : aliasNotToRemove) {
+ Element parent = alias.getCompartment();
+ if (parent != null) {
+ if (!aliasNotToRemove.contains(parent)) {
+ iterativeAliasNotToRemove.add(parent);
+ }
+ }
+ if (alias instanceof Species) {
+ parent = ((Species) alias).getComplex();
+ if (parent != null) {
+ if (!aliasNotToRemove.contains(parent)) {
+ iterativeAliasNotToRemove.add(parent);
+ }
+ }
+ }
+ }
+
+ added = iterativeAliasNotToRemove.size() != 0;
+ aliasNotToRemove.addAll(iterativeAliasNotToRemove);
+ } while (added);
+
+ List<Element> aliasToRemove = new ArrayList<Element>();
+ for (Element alias : result.getElements()) {
+ if (!(polygon.intersects(alias.getBorder()))) {
+ boolean remove = true;
+ if (alias instanceof Species) {
+ remove = ((Species) alias).getComplex() == null;
+ }
+ if (aliasNotToRemove.contains(alias)) {
+ remove = false;
+ }
+ if (remove) {
+ aliasToRemove.add(alias);
+ if (alias instanceof Complex) {
+ List<Species> aliases = ((Complex) alias).getAllChildren();
+ aliasToRemove.addAll(aliases);
+ }
+ }
+ }
+
+ }
+ for (Element alias : aliasToRemove) {
+ result.removeElement(alias);
+ }
+
+ List<Reaction> reactionsToRemove = new ArrayList<Reaction>();
+ for (Reaction reaction : result.getReactions()) {
+ boolean remove = false;
+ for (AbstractNode node : reaction.getNodes()) {
+ if (node instanceof ReactionNode) {
+ if (!result.getElements().contains(((ReactionNode) node).getElement())) {
+ remove = true;
+ break;
+ }
+ }
+ }
+ if (remove) {
+ reactionsToRemove.add(reaction);
+ }
+ }
+ for (Reaction reaction : reactionsToRemove) {
+ result.removeReaction(reaction);
+ }
+
+ for (Layer layer : result.getLayers()) {
+ List<LayerText> textToRemove = new ArrayList<LayerText>();
+ for (LayerText text : layer.getTexts()) {
+ if (!(polygon.intersects(text.getBorder()))) {
+ textToRemove.add(text);
+ }
+ }
+ for (LayerText text : textToRemove) {
+ layer.removeLayerText(text);
+ }
+ }
+
+ return result;
+ }
+
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/package-info.java b/model-command/src/main/java/lcsb/mapviewer/commands/package-info.java
index 11522cc6b1..912c51cf99 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/package-info.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/package-info.java
@@ -1,7 +1,7 @@
-/**
- * This package contains commands (some standalone operations) that can be
- * performed on {@link lcsb.mapviewer.model.map.model.Model}.
- *
- */
-package lcsb.mapviewer.commands;
-
+/**
+ * This package contains commands (some standalone operations) that can be
+ * performed on {@link lcsb.mapviewer.model.map.model.Model}.
+ *
+ */
+package lcsb.mapviewer.commands;
+
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementFormerSymbolsCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementFormerSymbolsCommand.java
index f4bb75b0a1..27c1f94649 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementFormerSymbolsCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementFormerSymbolsCommand.java
@@ -1,74 +1,74 @@
-package lcsb.mapviewer.commands.properties;
-
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes former
- * sybmols of the {@link Element element}.
- *
- * @author Piotr Gawron
- *
- */
-public class AddElementFormerSymbolsCommand extends AddElementPropertyListEntryCommand<String> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(AddElementFormerSymbolsCommand.class);
-
- /**
- * Default constructor.
- *
- * @param model
- * {@link lcsb.mapviewer.commands.ModelCommand#model}
- * @param alias
- * {@link ChangeElementPropertyCommand#alias}
- * @param values
- * new {@link Element#synonym} values to be added
- */
- public AddElementFormerSymbolsCommand(Model model, Element alias, List<String> values) {
- super(model, alias, values);
- }
-
- @Override
- protected void executeImplementation() throws CommandExecutionException {
-
- // former symbols are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
-
- for (String string : getNewValues()) {
- if (getAlias().getFormerSymbols().contains(string)) {
- throw new CommandExecutionException("Cannot add former synonym \"" + string + "\"to the list. Element already exists.");
- }
- }
-
- getAlias().getFormerSymbols().addAll(getNewValues());
-
- // former symbols are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
- }
-
- @Override
- protected void undoImplementation() {
- // former symbols are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
-
- getAlias().getFormerSymbols().removeAll(getNewValues());
-
- // former symbols are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
-
- }
-
-}
+package lcsb.mapviewer.commands.properties;
+
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.CommandExecutionException;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes former
+ * sybmols of the {@link Element element}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class AddElementFormerSymbolsCommand extends AddElementPropertyListEntryCommand<String> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(AddElementFormerSymbolsCommand.class);
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * {@link lcsb.mapviewer.commands.ModelCommand#model}
+ * @param alias
+ * {@link ChangeElementPropertyCommand#alias}
+ * @param values
+ * new {@link Element#synonym} values to be added
+ */
+ public AddElementFormerSymbolsCommand(Model model, Element alias, List<String> values) {
+ super(model, alias, values);
+ }
+
+ @Override
+ protected void executeImplementation() throws CommandExecutionException {
+
+ // former symbols are not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+
+ for (String string : getNewValues()) {
+ if (getAlias().getFormerSymbols().contains(string)) {
+ throw new CommandExecutionException("Cannot add former synonym \"" + string + "\"to the list. Element already exists.");
+ }
+ }
+
+ getAlias().getFormerSymbols().addAll(getNewValues());
+
+ // former symbols are not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+ }
+
+ @Override
+ protected void undoImplementation() {
+ // former symbols are not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+
+ getAlias().getFormerSymbols().removeAll(getNewValues());
+
+ // former symbols are not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+
+ }
+
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementMiriamDataCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementMiriamDataCommand.java
index d2ab757f64..d39ea3a322 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementMiriamDataCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementMiriamDataCommand.java
@@ -1,74 +1,74 @@
-package lcsb.mapviewer.commands.properties;
-
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes
- * {@link MiriamData annotations} of the {@link Element Element} .
- *
- * @author Piotr Gawron
- *
- */
-public class AddElementMiriamDataCommand extends AddElementPropertyListEntryCommand<MiriamData> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(AddElementMiriamDataCommand.class);
-
- /**
- * Default constructor.
- *
- * @param model
- * {@link lcsb.mapviewer.commands.ModelCommand#model}
- * @param alias
- * {@link ChangeElementPropertyCommand#alias}
- * @param values
- * new annotation values to be added
- */
- public AddElementMiriamDataCommand(Model model, Element alias, List<MiriamData> values) {
- super(model, alias, values);
- }
-
- @Override
- protected void executeImplementation() throws CommandExecutionException {
-
- // miriam data is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
-
- for (MiriamData md : getNewValues()) {
- if (getAlias().getMiriamData().contains(md)) {
- throw new CommandExecutionException("Cannot add miriam \"" + md + "\" to the list. Element already exists.");
- }
- }
-
- getAlias().getMiriamData().addAll(getNewValues());
-
- // miriam data is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
- }
-
- @Override
- protected void undoImplementation() {
- // miriam data is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
-
- getAlias().getMiriamData().removeAll(getNewValues());
-
- // miriam data is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
-
- }
-}
+package lcsb.mapviewer.commands.properties;
+
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.CommandExecutionException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes
+ * {@link MiriamData annotations} of the {@link Element Element} .
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class AddElementMiriamDataCommand extends AddElementPropertyListEntryCommand<MiriamData> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(AddElementMiriamDataCommand.class);
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * {@link lcsb.mapviewer.commands.ModelCommand#model}
+ * @param alias
+ * {@link ChangeElementPropertyCommand#alias}
+ * @param values
+ * new annotation values to be added
+ */
+ public AddElementMiriamDataCommand(Model model, Element alias, List<MiriamData> values) {
+ super(model, alias, values);
+ }
+
+ @Override
+ protected void executeImplementation() throws CommandExecutionException {
+
+ // miriam data is not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+
+ for (MiriamData md : getNewValues()) {
+ if (getAlias().getMiriamData().contains(md)) {
+ throw new CommandExecutionException("Cannot add miriam \"" + md + "\" to the list. Element already exists.");
+ }
+ }
+
+ getAlias().getMiriamData().addAll(getNewValues());
+
+ // miriam data is not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+ }
+
+ @Override
+ protected void undoImplementation() {
+ // miriam data is not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+
+ getAlias().getMiriamData().removeAll(getNewValues());
+
+ // miriam data is not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+
+ }
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementPropertyListEntryCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementPropertyListEntryCommand.java
index 2a390f6e6b..921b7c72af 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementPropertyListEntryCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementPropertyListEntryCommand.java
@@ -1,91 +1,91 @@
-package lcsb.mapviewer.commands.properties;
-
-import java.util.List;
-
-import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.commands.ModelCommand;
-import lcsb.mapviewer.commands.ModelCommandStatus;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that add entries
- * into a property of the {@link Element Element} that is list.
- *
- * @param <T>
- * class of property to edit
- *
- * @author Piotr Gawron
- *
- */
-public abstract class AddElementPropertyListEntryCommand<T> extends ModelCommand {
-
- /**
- * List of new values that should be added to property.
- */
- private List<T> newValues;
-
- /**
- * {@link Element} for which we will change the property.
- */
- private Element alias;
-
- /**
- * Default constructor.
- *
- * @param model
- * model to move
- *
- * @param alias
- * alias to be changed
- *
- * @param newValues
- * new values of the element property that will be added
- *
- */
- public AddElementPropertyListEntryCommand(Model model, Element alias, List<T> newValues) {
- super(model);
- this.alias = alias;
- this.newValues = newValues;
- }
-
- @Override
- protected void redoImplementation() throws CommandExecutionException {
- executeImplementation();
- setStatus(ModelCommandStatus.EXECUTED);
- }
-
- /**
- * @return the alias
- * @see #alias
- */
- protected Element getAlias() {
- return alias;
- }
-
- /**
- * @param alias
- * the alias to set
- * @see #alias
- */
- protected void setAlias(Element alias) {
- this.alias = alias;
- }
-
- /**
- * @return the newValue
- * @see #newValue
- */
- protected List<T> getNewValues() {
- return newValues;
- }
-
- /**
- * @param newValue
- * the newValue to set
- * @see #newValue
- */
- protected void setNewValues(List<T> newValue) {
- this.newValues = newValue;
- }
-}
+package lcsb.mapviewer.commands.properties;
+
+import java.util.List;
+
+import lcsb.mapviewer.commands.CommandExecutionException;
+import lcsb.mapviewer.commands.ModelCommand;
+import lcsb.mapviewer.commands.ModelCommandStatus;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that add entries
+ * into a property of the {@link Element Element} that is list.
+ *
+ * @param <T>
+ * class of property to edit
+ *
+ * @author Piotr Gawron
+ *
+ */
+public abstract class AddElementPropertyListEntryCommand<T> extends ModelCommand {
+
+ /**
+ * List of new values that should be added to property.
+ */
+ private List<T> newValues;
+
+ /**
+ * {@link Element} for which we will change the property.
+ */
+ private Element alias;
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * model to move
+ *
+ * @param alias
+ * alias to be changed
+ *
+ * @param newValues
+ * new values of the element property that will be added
+ *
+ */
+ public AddElementPropertyListEntryCommand(Model model, Element alias, List<T> newValues) {
+ super(model);
+ this.alias = alias;
+ this.newValues = newValues;
+ }
+
+ @Override
+ protected void redoImplementation() throws CommandExecutionException {
+ executeImplementation();
+ setStatus(ModelCommandStatus.EXECUTED);
+ }
+
+ /**
+ * @return the alias
+ * @see #alias
+ */
+ protected Element getAlias() {
+ return alias;
+ }
+
+ /**
+ * @param alias
+ * the alias to set
+ * @see #alias
+ */
+ protected void setAlias(Element alias) {
+ this.alias = alias;
+ }
+
+ /**
+ * @return the newValue
+ * @see #newValue
+ */
+ protected List<T> getNewValues() {
+ return newValues;
+ }
+
+ /**
+ * @param newValue
+ * the newValue to set
+ * @see #newValue
+ */
+ protected void setNewValues(List<T> newValue) {
+ this.newValues = newValue;
+ }
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementSynonymsCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementSynonymsCommand.java
index 6c4587b949..8b9d921335 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementSynonymsCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/AddElementSynonymsCommand.java
@@ -1,73 +1,73 @@
-package lcsb.mapviewer.commands.properties;
-
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes
- * synonyms of the {@link Element Element}.
- *
- * @author Piotr Gawron
- *
- */
-public class AddElementSynonymsCommand extends AddElementPropertyListEntryCommand<String> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(AddElementSynonymsCommand.class);
-
- /**
- * Default constructor.
- *
- * @param model
- * {@link lcsb.mapviewer.commands.ModelCommand#model}
- * @param alias
- * {@link ChangeElementPropertyCommand#alias}
- * @param values
- * new {@link Element#synonym} values to be added
- */
- public AddElementSynonymsCommand(Model model, Element alias, List<String> values) {
- super(model, alias, values);
- }
-
- @Override
- protected void executeImplementation() throws CommandExecutionException {
-
- // synonyms are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
-
- for (String string : getNewValues()) {
- if (getAlias().getSynonyms().contains(string)) {
- throw new CommandExecutionException("Cannot add synonym to the list: " + string + ". Element already exists.");
- }
- }
-
- getAlias().getSynonyms().addAll(getNewValues());
-
- // synonyms are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
- }
-
- @Override
- protected void undoImplementation() {
- // synonyms are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
-
- getAlias().getSynonyms().removeAll(getNewValues());
-
- // synonyms are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
-
- }
-}
+package lcsb.mapviewer.commands.properties;
+
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.CommandExecutionException;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes
+ * synonyms of the {@link Element Element}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class AddElementSynonymsCommand extends AddElementPropertyListEntryCommand<String> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(AddElementSynonymsCommand.class);
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * {@link lcsb.mapviewer.commands.ModelCommand#model}
+ * @param alias
+ * {@link ChangeElementPropertyCommand#alias}
+ * @param values
+ * new {@link Element#synonym} values to be added
+ */
+ public AddElementSynonymsCommand(Model model, Element alias, List<String> values) {
+ super(model, alias, values);
+ }
+
+ @Override
+ protected void executeImplementation() throws CommandExecutionException {
+
+ // synonyms are not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+
+ for (String string : getNewValues()) {
+ if (getAlias().getSynonyms().contains(string)) {
+ throw new CommandExecutionException("Cannot add synonym to the list: " + string + ". Element already exists.");
+ }
+ }
+
+ getAlias().getSynonyms().addAll(getNewValues());
+
+ // synonyms are not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+ }
+
+ @Override
+ protected void undoImplementation() {
+ // synonyms are not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+
+ getAlias().getSynonyms().removeAll(getNewValues());
+
+ // synonyms are not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+
+ }
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementAbbreviationCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementAbbreviationCommand.java
index f0db3c5b9d..61854ce6f8 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementAbbreviationCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementAbbreviationCommand.java
@@ -1,50 +1,50 @@
-package lcsb.mapviewer.commands.properties;
-
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-
-import org.apache.log4j.Logger;
-
-/**
- * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes name
- * of the element connected to {@link Element}.
- *
- * @author Piotr Gawron
- *
- */
-public class ChangeElementAbbreviationCommand extends ChangeElementPropertyCommand<String> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(ChangeElementAbbreviationCommand.class);
-
- /**
- * Default constructor.
- *
- * @param model
- * {@link lcsb.mapviewer.commands.ModelCommand#model}
- * @param alias
- * {@link ChangeElementPropertyCommand#alias}
- * @param newName
- * new name of the elemnt
- */
- public ChangeElementAbbreviationCommand(Model model, Element alias, String newName) {
- super(model, alias, newName);
- }
-
- @Override
- protected void executeImplementation() {
- // abbreviation is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
-
- setOldValue(getAlias().getAbbreviation());
- getAlias().setAbbreviation((String) getNewValue());
-
- // abbreviation is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
- }
-}
+package lcsb.mapviewer.commands.properties;
+
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+import org.apache.log4j.Logger;
+
+/**
+ * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes name
+ * of the element connected to {@link Element}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ChangeElementAbbreviationCommand extends ChangeElementPropertyCommand<String> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(ChangeElementAbbreviationCommand.class);
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * {@link lcsb.mapviewer.commands.ModelCommand#model}
+ * @param alias
+ * {@link ChangeElementPropertyCommand#alias}
+ * @param newName
+ * new name of the elemnt
+ */
+ public ChangeElementAbbreviationCommand(Model model, Element alias, String newName) {
+ super(model, alias, newName);
+ }
+
+ @Override
+ protected void executeImplementation() {
+ // abbreviation is not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+
+ setOldValue(getAlias().getAbbreviation());
+ getAlias().setAbbreviation((String) getNewValue());
+
+ // abbreviation is not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+ }
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementColorCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementColorCommand.java
index 334ddb8961..c6a4694441 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementColorCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementColorCommand.java
@@ -1,49 +1,49 @@
-package lcsb.mapviewer.commands.properties;
-
-import java.awt.Color;
-
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-
-import org.apache.log4j.Logger;
-
-/**
- * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that
- * {@link Element#color}.
- *
- * @author Piotr Gawron
- *
- */
-public class ChangeElementColorCommand extends ChangeElementPropertyCommand<Color> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(ChangeElementColorCommand.class);
-
- /**
- * Default constructor.
- *
- * @param model
- * {@link lcsb.mapviewer.commands.ModelCommand#model}
- * @param alias
- * {@link ChangeElementPropertyCommand#alias}
- * @param newName
- * new {@link Element#color} value
- */
- public ChangeElementColorCommand(Model model, Element alias, Color newName) {
- super(model, alias, newName);
- }
-
- @Override
- protected void executeImplementation() {
-
- includeInAffectedRegion(getAlias());
-
- setOldValue(getAlias().getColor());
- getAlias().setColor((Color) getNewValue());
-
- includeInAffectedRegion(getAlias());
- }
-}
+package lcsb.mapviewer.commands.properties;
+
+import java.awt.Color;
+
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+import org.apache.log4j.Logger;
+
+/**
+ * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that
+ * {@link Element#color}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ChangeElementColorCommand extends ChangeElementPropertyCommand<Color> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(ChangeElementColorCommand.class);
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * {@link lcsb.mapviewer.commands.ModelCommand#model}
+ * @param alias
+ * {@link ChangeElementPropertyCommand#alias}
+ * @param newName
+ * new {@link Element#color} value
+ */
+ public ChangeElementColorCommand(Model model, Element alias, Color newName) {
+ super(model, alias, newName);
+ }
+
+ @Override
+ protected void executeImplementation() {
+
+ includeInAffectedRegion(getAlias());
+
+ setOldValue(getAlias().getColor());
+ getAlias().setColor((Color) getNewValue());
+
+ includeInAffectedRegion(getAlias());
+ }
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFontSizeCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFontSizeCommand.java
index bd8a4fbcc7..a00d9de774 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFontSizeCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFontSizeCommand.java
@@ -1,51 +1,51 @@
-package lcsb.mapviewer.commands.properties;
-
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-
-import org.apache.log4j.Logger;
-
-/**
- * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes
- * {@link Element#fontSize}.
- *
- * @author Piotr Gawron
- *
- */
-public class ChangeElementFontSizeCommand extends ChangeElementPropertyCommand<Double> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(ChangeElementFontSizeCommand.class);
-
- /**
- * Default constructor.
- *
- * @param model
- * {@link lcsb.mapviewer.commands.ModelCommand#model}
- * @param alias
- * {@link ChangeElementPropertyCommand#alias}
- * @param newName
- * new {@link Element#fontSize} value
- */
- public ChangeElementFontSizeCommand(Model model, Element alias, Double newName) {
- super(model, alias, newName);
- }
-
- @Override
- protected void executeImplementation() {
-
- // abbreviation is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
-
- setOldValue(getAlias().getFontSize());
- getAlias().setFontSize((Double) getNewValue());
-
- // abbreviation is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
- }
-}
+package lcsb.mapviewer.commands.properties;
+
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+import org.apache.log4j.Logger;
+
+/**
+ * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes
+ * {@link Element#fontSize}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ChangeElementFontSizeCommand extends ChangeElementPropertyCommand<Double> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(ChangeElementFontSizeCommand.class);
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * {@link lcsb.mapviewer.commands.ModelCommand#model}
+ * @param alias
+ * {@link ChangeElementPropertyCommand#alias}
+ * @param newName
+ * new {@link Element#fontSize} value
+ */
+ public ChangeElementFontSizeCommand(Model model, Element alias, Double newName) {
+ super(model, alias, newName);
+ }
+
+ @Override
+ protected void executeImplementation() {
+
+ // abbreviation is not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+
+ setOldValue(getAlias().getFontSize());
+ getAlias().setFontSize((Double) getNewValue());
+
+ // abbreviation is not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+ }
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFormerSymbolCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFormerSymbolCommand.java
index fc5adb281f..01fc85e437 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFormerSymbolCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFormerSymbolCommand.java
@@ -1,64 +1,64 @@
-package lcsb.mapviewer.commands.properties;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes former
- * symbol of the {@link Element Element}.
- *
- * @author Piotr Gawron
- *
- */
-public class ChangeElementFormerSymbolCommand extends ChangeElementPropertyListEntryCommand<String> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(ChangeElementFormerSymbolCommand.class);
-
- /**
- * Default constructor.
- *
- * @param model
- * {@link lcsb.mapviewer.commands.ModelCommand#model}
- * @param alias
- * {@link ChangeElementPropertyCommand#alias}
- * @param newValue
- * new {@link Element#synonym} value
- * @param oldValue
- * old {@link Element#synonym} value
- */
- public ChangeElementFormerSymbolCommand(Model model, Element alias, String newValue, String oldValue) {
- super(model, alias, newValue, oldValue);
- }
-
- @Override
- protected void executeImplementation() throws CommandExecutionException {
- if (getOldValue().equals(getNewValue())) {
- return;
- }
-
- // former symbols are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
-
- int index = getAlias().getFormerSymbols().indexOf(getOldValue());
- if (index < 0) {
- throw new CommandExecutionException("Former symbol " + getOldValue() + " doesn't exist.");
- }
- int index2 = getAlias().getFormerSymbols().indexOf(getNewValue());
- if (index2 >= 0) {
- throw new CommandExecutionException("Former symbol " + getNewValue() + " already exist.");
- }
- getAlias().getFormerSymbols().set(index, (String) getNewValue());
-
- // former symbols are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
- }
-}
+package lcsb.mapviewer.commands.properties;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.CommandExecutionException;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes former
+ * symbol of the {@link Element Element}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ChangeElementFormerSymbolCommand extends ChangeElementPropertyListEntryCommand<String> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(ChangeElementFormerSymbolCommand.class);
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * {@link lcsb.mapviewer.commands.ModelCommand#model}
+ * @param alias
+ * {@link ChangeElementPropertyCommand#alias}
+ * @param newValue
+ * new {@link Element#synonym} value
+ * @param oldValue
+ * old {@link Element#synonym} value
+ */
+ public ChangeElementFormerSymbolCommand(Model model, Element alias, String newValue, String oldValue) {
+ super(model, alias, newValue, oldValue);
+ }
+
+ @Override
+ protected void executeImplementation() throws CommandExecutionException {
+ if (getOldValue().equals(getNewValue())) {
+ return;
+ }
+
+ // former symbols are not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+
+ int index = getAlias().getFormerSymbols().indexOf(getOldValue());
+ if (index < 0) {
+ throw new CommandExecutionException("Former symbol " + getOldValue() + " doesn't exist.");
+ }
+ int index2 = getAlias().getFormerSymbols().indexOf(getNewValue());
+ if (index2 >= 0) {
+ throw new CommandExecutionException("Former symbol " + getNewValue() + " already exist.");
+ }
+ getAlias().getFormerSymbols().set(index, (String) getNewValue());
+
+ // former symbols are not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+ }
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFormulaCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFormulaCommand.java
index 5f3dc88d6f..e0c3f23b81 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFormulaCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFormulaCommand.java
@@ -1,51 +1,51 @@
-package lcsb.mapviewer.commands.properties;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes
- * formula of the element connected to {@link Element}.
- *
- * @author Piotr Gawron
- *
- */
-public class ChangeElementFormulaCommand extends ChangeElementPropertyCommand<String> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(ChangeElementFormulaCommand.class);
-
- /**
- * Default constructor.
- *
- * @param model
- * {@link lcsb.mapviewer.commands.ModelCommand#model}
- * @param alias
- * {@link ChangeElementPropertyCommand#alias}
- * @param newName
- * new {@link Element#formula} value
- */
- public ChangeElementFormulaCommand(Model model, Element alias, String newName) {
- super(model, alias, newName);
- }
-
- @Override
- protected void executeImplementation() {
-
- // formula is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
-
- setOldValue(getAlias().getFormula());
- getAlias().setFormula((String) getNewValue());
-
- // formula is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
- }
-}
+package lcsb.mapviewer.commands.properties;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes
+ * formula of the element connected to {@link Element}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ChangeElementFormulaCommand extends ChangeElementPropertyCommand<String> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(ChangeElementFormulaCommand.class);
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * {@link lcsb.mapviewer.commands.ModelCommand#model}
+ * @param alias
+ * {@link ChangeElementPropertyCommand#alias}
+ * @param newName
+ * new {@link Element#formula} value
+ */
+ public ChangeElementFormulaCommand(Model model, Element alias, String newName) {
+ super(model, alias, newName);
+ }
+
+ @Override
+ protected void executeImplementation() {
+
+ // formula is not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+
+ setOldValue(getAlias().getFormula());
+ getAlias().setFormula((String) getNewValue());
+
+ // formula is not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+ }
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFullNameCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFullNameCommand.java
index db9f6841c0..63d4e41550 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFullNameCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementFullNameCommand.java
@@ -1,51 +1,51 @@
-package lcsb.mapviewer.commands.properties;
-
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-
-import org.apache.log4j.Logger;
-
-/**
- * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes full
- * name of the element connected to {@link Element}.
- *
- * @author Piotr Gawron
- *
- */
-public class ChangeElementFullNameCommand extends ChangeElementPropertyCommand<String> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(ChangeElementFullNameCommand.class);
-
- /**
- * Default constructor.
- *
- * @param model
- * {@link lcsb.mapviewer.commands.ModelCommand#model}
- * @param alias
- * {@link ChangeElementPropertyCommand#alias}
- * @param newName
- * new {@link Element#fullName} value
- */
- public ChangeElementFullNameCommand(Model model, Element alias, String newName) {
- super(model, alias, newName);
- }
-
- @Override
- protected void executeImplementation() {
-
- // fullname is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
-
- setOldValue(getAlias().getFullName());
- getAlias().setFullName((String) getNewValue());
-
- // fullname is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
- }
-}
+package lcsb.mapviewer.commands.properties;
+
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+import org.apache.log4j.Logger;
+
+/**
+ * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes full
+ * name of the element connected to {@link Element}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ChangeElementFullNameCommand extends ChangeElementPropertyCommand<String> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(ChangeElementFullNameCommand.class);
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * {@link lcsb.mapviewer.commands.ModelCommand#model}
+ * @param alias
+ * {@link ChangeElementPropertyCommand#alias}
+ * @param newName
+ * new {@link Element#fullName} value
+ */
+ public ChangeElementFullNameCommand(Model model, Element alias, String newName) {
+ super(model, alias, newName);
+ }
+
+ @Override
+ protected void executeImplementation() {
+
+ // fullname is not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+
+ setOldValue(getAlias().getFullName());
+ getAlias().setFullName((String) getNewValue());
+
+ // fullname is not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+ }
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementMiriamDataCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementMiriamDataCommand.java
index 34db575c45..fc97cf1e54 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementMiriamDataCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementMiriamDataCommand.java
@@ -1,68 +1,68 @@
-package lcsb.mapviewer.commands.properties;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes
- * annotations of the {@link Element Element}.
- *
- * @author Piotr Gawron
- *
- */
-public class ChangeElementMiriamDataCommand extends ChangeElementPropertyListEntryCommand<MiriamData> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(ChangeElementMiriamDataCommand.class);
-
- /**
- * Default constructor.
- *
- * @param model
- * {@link lcsb.mapviewer.commands.ModelCommand#model}
- * @param alias
- * {@link ChangeElementPropertyCommand#alias}
- * @param newValue
- * new annotation value
- * @param oldValue
- * old annotation value
- */
- public ChangeElementMiriamDataCommand(Model model, Element alias, MiriamData newValue, MiriamData oldValue) {
- super(model, alias, newValue, oldValue);
- }
-
- @Override
- protected void executeImplementation() throws CommandExecutionException {
- // if there is no change then return
- if (getOldValue().equals(getNewValue())) {
- return;
- }
-
- // miriam data is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
-
- if (!getAlias().getMiriamData().contains(getOldValue())) {
- throw new CommandExecutionException("Miriam " + getOldValue() + " doesn't exist.");
- }
- if (getAlias().getMiriamData().contains(getNewValue())) {
- throw new CommandExecutionException("Miriam " + getNewValue() + " already exist.");
- }
- getAlias().getMiriamData().remove(getOldValue());
- getOldValue().setDataType(getNewValue().getDataType());
- getOldValue().setRelationType(getNewValue().getRelationType());
- getOldValue().setResource(getNewValue().getResource());
- getAlias().getMiriamData().add(getOldValue());
-
- // miriam data is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
- }
-}
+package lcsb.mapviewer.commands.properties;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.CommandExecutionException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes
+ * annotations of the {@link Element Element}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ChangeElementMiriamDataCommand extends ChangeElementPropertyListEntryCommand<MiriamData> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(ChangeElementMiriamDataCommand.class);
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * {@link lcsb.mapviewer.commands.ModelCommand#model}
+ * @param alias
+ * {@link ChangeElementPropertyCommand#alias}
+ * @param newValue
+ * new annotation value
+ * @param oldValue
+ * old annotation value
+ */
+ public ChangeElementMiriamDataCommand(Model model, Element alias, MiriamData newValue, MiriamData oldValue) {
+ super(model, alias, newValue, oldValue);
+ }
+
+ @Override
+ protected void executeImplementation() throws CommandExecutionException {
+ // if there is no change then return
+ if (getOldValue().equals(getNewValue())) {
+ return;
+ }
+
+ // miriam data is not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+
+ if (!getAlias().getMiriamData().contains(getOldValue())) {
+ throw new CommandExecutionException("Miriam " + getOldValue() + " doesn't exist.");
+ }
+ if (getAlias().getMiriamData().contains(getNewValue())) {
+ throw new CommandExecutionException("Miriam " + getNewValue() + " already exist.");
+ }
+ getAlias().getMiriamData().remove(getOldValue());
+ getOldValue().setDataType(getNewValue().getDataType());
+ getOldValue().setRelationType(getNewValue().getRelationType());
+ getOldValue().setResource(getNewValue().getResource());
+ getAlias().getMiriamData().add(getOldValue());
+
+ // miriam data is not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+ }
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementNameCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementNameCommand.java
index 82bfff0c28..584a8a7317 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementNameCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementNameCommand.java
@@ -1,47 +1,47 @@
-package lcsb.mapviewer.commands.properties;
-
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-
-import org.apache.log4j.Logger;
-
-/**
- * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes name
- * of the element connected to {@link Element}.
- *
- * @author Piotr Gawron
- *
- */
-public class ChangeElementNameCommand extends ChangeElementPropertyCommand<String> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(ChangeElementNameCommand.class);
-
- /**
- * Default constructor.
- *
- * @param model
- * {@link lcsb.mapviewer.commands.ModelCommand#model}
- * @param alias
- * {@link ChangeElementPropertyCommand#alias}
- * @param newName
- * new name of the elemnt
- */
- public ChangeElementNameCommand(Model model, Element alias, String newName) {
- super(model, alias, newName);
- }
-
- @Override
- protected void executeImplementation() {
-
- includeInAffectedRegion(getAlias());
-
- setOldValue(getAlias().getName());
- getAlias().setName((String) getNewValue());
-
- includeInAffectedRegion(getAlias());
- }
-}
+package lcsb.mapviewer.commands.properties;
+
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+import org.apache.log4j.Logger;
+
+/**
+ * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes name
+ * of the element connected to {@link Element}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ChangeElementNameCommand extends ChangeElementPropertyCommand<String> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(ChangeElementNameCommand.class);
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * {@link lcsb.mapviewer.commands.ModelCommand#model}
+ * @param alias
+ * {@link ChangeElementPropertyCommand#alias}
+ * @param newName
+ * new name of the elemnt
+ */
+ public ChangeElementNameCommand(Model model, Element alias, String newName) {
+ super(model, alias, newName);
+ }
+
+ @Override
+ protected void executeImplementation() {
+
+ includeInAffectedRegion(getAlias());
+
+ setOldValue(getAlias().getName());
+ getAlias().setName((String) getNewValue());
+
+ includeInAffectedRegion(getAlias());
+ }
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementNotesCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementNotesCommand.java
index 8e4be7669b..4a9cfb50c1 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementNotesCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementNotesCommand.java
@@ -1,51 +1,51 @@
-package lcsb.mapviewer.commands.properties;
-
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-
-import org.apache.log4j.Logger;
-
-/**
- * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes notes
- * of the element connected to {@link Element}.
- *
- * @author Piotr Gawron
- *
- */
-public class ChangeElementNotesCommand extends ChangeElementPropertyCommand<String> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(ChangeElementNotesCommand.class);
-
- /**
- * Default constructor.
- *
- * @param model
- * {@link lcsb.mapviewer.commands.ModelCommand#model}
- * @param alias
- * {@link ChangeElementPropertyCommand#alias}
- * @param newName
- * new {@link Element#notes} value
- */
- public ChangeElementNotesCommand(Model model, Element alias, String newName) {
- super(model, alias, newName);
- }
-
- @Override
- protected void executeImplementation() {
-
- // notes is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
-
- setOldValue(getAlias().getNotes());
- getAlias().setNotes((String) getNewValue());
-
- // notes is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
- }
-}
+package lcsb.mapviewer.commands.properties;
+
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+import org.apache.log4j.Logger;
+
+/**
+ * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes notes
+ * of the element connected to {@link Element}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ChangeElementNotesCommand extends ChangeElementPropertyCommand<String> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(ChangeElementNotesCommand.class);
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * {@link lcsb.mapviewer.commands.ModelCommand#model}
+ * @param alias
+ * {@link ChangeElementPropertyCommand#alias}
+ * @param newName
+ * new {@link Element#notes} value
+ */
+ public ChangeElementNotesCommand(Model model, Element alias, String newName) {
+ super(model, alias, newName);
+ }
+
+ @Override
+ protected void executeImplementation() {
+
+ // notes is not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+
+ setOldValue(getAlias().getNotes());
+ getAlias().setNotes((String) getNewValue());
+
+ // notes is not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+ }
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementPropertyCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementPropertyCommand.java
index fa157fb75e..6613c69e48 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementPropertyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementPropertyCommand.java
@@ -1,120 +1,120 @@
-package lcsb.mapviewer.commands.properties;
-
-import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.commands.ModelCommand;
-import lcsb.mapviewer.commands.ModelCommandStatus;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes single
- * property of the element connected to {@link Element}.
- *
- * @param <T>
- * class of property to edit
- *
- * @author Piotr Gawron
- *
- */
-public abstract class ChangeElementPropertyCommand<T> extends ModelCommand {
-
- /**
- * New element property value.
- */
- private T newValue;
-
- /**
- * Old element property value.
- */
- private T oldValue;
-
- /**
- * {@link Element} for which we will change the property.
- */
- private Element alias;
-
- /**
- * Default constructor.
- *
- * @param model
- * model to move
- *
- * @param alias
- * alias to be changed
- *
- * @param newValue
- * new value of the element property
- */
- public ChangeElementPropertyCommand(Model model, Element alias, T newValue) {
- super(model);
- this.alias = alias;
- this.newValue = newValue;
- }
-
- @Override
- protected void undoImplementation() throws CommandExecutionException {
- T tmp = newValue;
- newValue = oldValue;
- executeImplementation();
- newValue = tmp;
- oldValue = null;
- setStatus(ModelCommandStatus.UNDONE);
- }
-
- @Override
- protected void redoImplementation() throws CommandExecutionException {
- executeImplementation();
- setStatus(ModelCommandStatus.EXECUTED);
- }
-
- /**
- * @return the alias
- * @see #alias
- */
- protected Element getAlias() {
- return alias;
- }
-
- /**
- * @param alias
- * the alias to set
- * @see #alias
- */
- protected void setAlias(Element alias) {
- this.alias = alias;
- }
-
- /**
- * @return the oldValue
- * @see #oldValue
- */
- protected Object getOldValue() {
- return oldValue;
- }
-
- /**
- * @param oldValue
- * the oldValue to set
- * @see #oldValue
- */
- protected void setOldValue(T oldValue) {
- this.oldValue = oldValue;
- }
-
- /**
- * @return the newValue
- * @see #newValue
- */
- protected Object getNewValue() {
- return newValue;
- }
-
- /**
- * @param newValue
- * the newValue to set
- * @see #newValue
- */
- protected void setNewValue(T newValue) {
- this.newValue = newValue;
- }
-}
+package lcsb.mapviewer.commands.properties;
+
+import lcsb.mapviewer.commands.CommandExecutionException;
+import lcsb.mapviewer.commands.ModelCommand;
+import lcsb.mapviewer.commands.ModelCommandStatus;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes single
+ * property of the element connected to {@link Element}.
+ *
+ * @param <T>
+ * class of property to edit
+ *
+ * @author Piotr Gawron
+ *
+ */
+public abstract class ChangeElementPropertyCommand<T> extends ModelCommand {
+
+ /**
+ * New element property value.
+ */
+ private T newValue;
+
+ /**
+ * Old element property value.
+ */
+ private T oldValue;
+
+ /**
+ * {@link Element} for which we will change the property.
+ */
+ private Element alias;
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * model to move
+ *
+ * @param alias
+ * alias to be changed
+ *
+ * @param newValue
+ * new value of the element property
+ */
+ public ChangeElementPropertyCommand(Model model, Element alias, T newValue) {
+ super(model);
+ this.alias = alias;
+ this.newValue = newValue;
+ }
+
+ @Override
+ protected void undoImplementation() throws CommandExecutionException {
+ T tmp = newValue;
+ newValue = oldValue;
+ executeImplementation();
+ newValue = tmp;
+ oldValue = null;
+ setStatus(ModelCommandStatus.UNDONE);
+ }
+
+ @Override
+ protected void redoImplementation() throws CommandExecutionException {
+ executeImplementation();
+ setStatus(ModelCommandStatus.EXECUTED);
+ }
+
+ /**
+ * @return the alias
+ * @see #alias
+ */
+ protected Element getAlias() {
+ return alias;
+ }
+
+ /**
+ * @param alias
+ * the alias to set
+ * @see #alias
+ */
+ protected void setAlias(Element alias) {
+ this.alias = alias;
+ }
+
+ /**
+ * @return the oldValue
+ * @see #oldValue
+ */
+ protected Object getOldValue() {
+ return oldValue;
+ }
+
+ /**
+ * @param oldValue
+ * the oldValue to set
+ * @see #oldValue
+ */
+ protected void setOldValue(T oldValue) {
+ this.oldValue = oldValue;
+ }
+
+ /**
+ * @return the newValue
+ * @see #newValue
+ */
+ protected Object getNewValue() {
+ return newValue;
+ }
+
+ /**
+ * @param newValue
+ * the newValue to set
+ * @see #newValue
+ */
+ protected void setNewValue(T newValue) {
+ this.newValue = newValue;
+ }
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementPropertyListEntryCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementPropertyListEntryCommand.java
index 00218400a4..b842c08eca 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementPropertyListEntryCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementPropertyListEntryCommand.java
@@ -1,127 +1,127 @@
-package lcsb.mapviewer.commands.properties;
-
-import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.commands.ModelCommand;
-import lcsb.mapviewer.commands.ModelCommandStatus;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes single
- * entry in a property of the {@link Element Element}
- * that is list.
- *
- * @param <T>
- * class of property to edit
- *
- * @author Piotr Gawron
- *
- */
-public abstract class ChangeElementPropertyListEntryCommand<T> extends ModelCommand {
-
- /**
- * New element property value.
- */
- private T newValue;
-
- /**
- * Old element property value.
- */
- private T oldValue;
-
- /**
- * {@link Element} for which we will change the property.
- */
- private Element alias;
-
- /**
- * Default constructor.
- *
- * @param model
- * model to move
- *
- * @param alias
- * alias to be changed
- *
- * @param newValue
- * new value of the element property
- *
- * @param oldValue
- * old value of the element property
- */
- public ChangeElementPropertyListEntryCommand(Model model, Element alias, T newValue, T oldValue) {
- super(model);
- this.alias = alias;
- this.oldValue = oldValue;
- this.newValue = newValue;
- }
-
- @Override
- protected void undoImplementation() throws CommandExecutionException {
- T tmpNewValue = newValue;
- T tmpOldValue = oldValue;
- newValue = tmpOldValue;
- oldValue = tmpNewValue;
- executeImplementation();
- newValue = tmpNewValue;
- oldValue = tmpOldValue;
- setStatus(ModelCommandStatus.UNDONE);
- }
-
- @Override
- protected void redoImplementation() throws CommandExecutionException {
- executeImplementation();
- setStatus(ModelCommandStatus.EXECUTED);
- }
-
- /**
- * @return the alias
- * @see #alias
- */
- protected Element getAlias() {
- return alias;
- }
-
- /**
- * @param alias
- * the alias to set
- * @see #alias
- */
- protected void setAlias(Element alias) {
- this.alias = alias;
- }
-
- /**
- * @return the oldValue
- * @see #oldValue
- */
- protected T getOldValue() {
- return oldValue;
- }
-
- /**
- * @param oldValue
- * the oldValue to set
- * @see #oldValue
- */
- protected void setOldValue(T oldValue) {
- this.oldValue = oldValue;
- }
-
- /**
- * @return the newValue
- * @see #newValue
- */
- protected T getNewValue() {
- return newValue;
- }
-
- /**
- * @param newValue
- * the newValue to set
- * @see #newValue
- */
- protected void setNewValue(T newValue) {
- this.newValue = newValue;
- }
-}
+package lcsb.mapviewer.commands.properties;
+
+import lcsb.mapviewer.commands.CommandExecutionException;
+import lcsb.mapviewer.commands.ModelCommand;
+import lcsb.mapviewer.commands.ModelCommandStatus;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes single
+ * entry in a property of the {@link Element Element}
+ * that is list.
+ *
+ * @param <T>
+ * class of property to edit
+ *
+ * @author Piotr Gawron
+ *
+ */
+public abstract class ChangeElementPropertyListEntryCommand<T> extends ModelCommand {
+
+ /**
+ * New element property value.
+ */
+ private T newValue;
+
+ /**
+ * Old element property value.
+ */
+ private T oldValue;
+
+ /**
+ * {@link Element} for which we will change the property.
+ */
+ private Element alias;
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * model to move
+ *
+ * @param alias
+ * alias to be changed
+ *
+ * @param newValue
+ * new value of the element property
+ *
+ * @param oldValue
+ * old value of the element property
+ */
+ public ChangeElementPropertyListEntryCommand(Model model, Element alias, T newValue, T oldValue) {
+ super(model);
+ this.alias = alias;
+ this.oldValue = oldValue;
+ this.newValue = newValue;
+ }
+
+ @Override
+ protected void undoImplementation() throws CommandExecutionException {
+ T tmpNewValue = newValue;
+ T tmpOldValue = oldValue;
+ newValue = tmpOldValue;
+ oldValue = tmpNewValue;
+ executeImplementation();
+ newValue = tmpNewValue;
+ oldValue = tmpOldValue;
+ setStatus(ModelCommandStatus.UNDONE);
+ }
+
+ @Override
+ protected void redoImplementation() throws CommandExecutionException {
+ executeImplementation();
+ setStatus(ModelCommandStatus.EXECUTED);
+ }
+
+ /**
+ * @return the alias
+ * @see #alias
+ */
+ protected Element getAlias() {
+ return alias;
+ }
+
+ /**
+ * @param alias
+ * the alias to set
+ * @see #alias
+ */
+ protected void setAlias(Element alias) {
+ this.alias = alias;
+ }
+
+ /**
+ * @return the oldValue
+ * @see #oldValue
+ */
+ protected T getOldValue() {
+ return oldValue;
+ }
+
+ /**
+ * @param oldValue
+ * the oldValue to set
+ * @see #oldValue
+ */
+ protected void setOldValue(T oldValue) {
+ this.oldValue = oldValue;
+ }
+
+ /**
+ * @return the newValue
+ * @see #newValue
+ */
+ protected T getNewValue() {
+ return newValue;
+ }
+
+ /**
+ * @param newValue
+ * the newValue to set
+ * @see #newValue
+ */
+ protected void setNewValue(T newValue) {
+ this.newValue = newValue;
+ }
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementSymbolCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementSymbolCommand.java
index 20fb9cc8df..8d0ccf5680 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementSymbolCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementSymbolCommand.java
@@ -1,51 +1,51 @@
-package lcsb.mapviewer.commands.properties;
-
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-
-import org.apache.log4j.Logger;
-
-/**
- * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes symbol
- * of the element connected to {@link Element}.
- *
- * @author Piotr Gawron
- *
- */
-public class ChangeElementSymbolCommand extends ChangeElementPropertyCommand<String> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(ChangeElementSymbolCommand.class);
-
- /**
- * Default constructor.
- *
- * @param model
- * {@link lcsb.mapviewer.commands.ModelCommand#model}
- * @param alias
- * {@link ChangeElementPropertyCommand#alias}
- * @param newName
- * new {@link Element#symbol} value
- */
- public ChangeElementSymbolCommand(Model model, Element alias, String newName) {
- super(model, alias, newName);
- }
-
- @Override
- protected void executeImplementation() {
-
- // symbol is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
-
- setOldValue(getAlias().getSymbol());
- getAlias().setSymbol((String) getNewValue());
-
- // symbol is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
- }
-}
+package lcsb.mapviewer.commands.properties;
+
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+import org.apache.log4j.Logger;
+
+/**
+ * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes symbol
+ * of the element connected to {@link Element}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ChangeElementSymbolCommand extends ChangeElementPropertyCommand<String> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(ChangeElementSymbolCommand.class);
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * {@link lcsb.mapviewer.commands.ModelCommand#model}
+ * @param alias
+ * {@link ChangeElementPropertyCommand#alias}
+ * @param newName
+ * new {@link Element#symbol} value
+ */
+ public ChangeElementSymbolCommand(Model model, Element alias, String newName) {
+ super(model, alias, newName);
+ }
+
+ @Override
+ protected void executeImplementation() {
+
+ // symbol is not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+
+ setOldValue(getAlias().getSymbol());
+ getAlias().setSymbol((String) getNewValue());
+
+ // symbol is not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+ }
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementSynonymCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementSynonymCommand.java
index 9f669ca8c4..48de685439 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementSynonymCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementSynonymCommand.java
@@ -1,64 +1,64 @@
-package lcsb.mapviewer.commands.properties;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes
- * synonym of the {@link Element Element}.
- *
- * @author Piotr Gawron
- *
- */
-public class ChangeElementSynonymCommand extends ChangeElementPropertyListEntryCommand<String> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(ChangeElementSynonymCommand.class);
-
- /**
- * Default constructor.
- *
- * @param model
- * {@link lcsb.mapviewer.commands.ModelCommand#model}
- * @param alias
- * {@link ChangeElementPropertyCommand#alias}
- * @param newValue
- * new {@link Element#synonym} value
- * @param oldValue
- * old {@link Element#synonym} value
- */
- public ChangeElementSynonymCommand(Model model, Element alias, String newValue, String oldValue) {
- super(model, alias, newValue, oldValue);
- }
-
- @Override
- protected void executeImplementation() throws CommandExecutionException {
- if (getOldValue().equals(getNewValue())) {
- return;
- }
-
- // synonyms are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
-
- int index = getAlias().getSynonyms().indexOf(getOldValue());
- if (index < 0) {
- throw new CommandExecutionException("Synonym " + getOldValue() + " doesn't exist.");
- }
- int index2 = getAlias().getSynonyms().indexOf(getNewValue());
- if (index2 >= 0) {
- throw new CommandExecutionException("Synonym " + getNewValue() + " already exist.");
- }
- getAlias().getSynonyms().set(index, getNewValue());
-
- // synonyms are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
- }
-}
+package lcsb.mapviewer.commands.properties;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.CommandExecutionException;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that changes
+ * synonym of the {@link Element Element}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ChangeElementSynonymCommand extends ChangeElementPropertyListEntryCommand<String> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(ChangeElementSynonymCommand.class);
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * {@link lcsb.mapviewer.commands.ModelCommand#model}
+ * @param alias
+ * {@link ChangeElementPropertyCommand#alias}
+ * @param newValue
+ * new {@link Element#synonym} value
+ * @param oldValue
+ * old {@link Element#synonym} value
+ */
+ public ChangeElementSynonymCommand(Model model, Element alias, String newValue, String oldValue) {
+ super(model, alias, newValue, oldValue);
+ }
+
+ @Override
+ protected void executeImplementation() throws CommandExecutionException {
+ if (getOldValue().equals(getNewValue())) {
+ return;
+ }
+
+ // synonyms are not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+
+ int index = getAlias().getSynonyms().indexOf(getOldValue());
+ if (index < 0) {
+ throw new CommandExecutionException("Synonym " + getOldValue() + " doesn't exist.");
+ }
+ int index2 = getAlias().getSynonyms().indexOf(getNewValue());
+ if (index2 >= 0) {
+ throw new CommandExecutionException("Synonym " + getNewValue() + " already exist.");
+ }
+ getAlias().getSynonyms().set(index, getNewValue());
+
+ // synonyms are not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+ }
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementFormerSymbolsCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementFormerSymbolsCommand.java
index 9f21a2c821..e4d2d18926 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementFormerSymbolsCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementFormerSymbolsCommand.java
@@ -1,73 +1,73 @@
-package lcsb.mapviewer.commands.properties;
-
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that removes former
- * symbols from {@link Element Element}.
- *
- * @author Piotr Gawron
- *
- */
-public class RemoveElementFormerSymbolsCommand extends RemoveElementPropertyListEntryCommand<String> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(RemoveElementFormerSymbolsCommand.class);
-
- /**
- * Default constructor.
- *
- * @param model
- * {@link lcsb.mapviewer.commands.ModelCommand#model}
- * @param alias
- * {@link ChangeElementPropertyCommand#alias}
- * @param values
- * {@link Element#synonym} values to be removed
- */
- public RemoveElementFormerSymbolsCommand(Model model, Element alias, List<String> values) {
- super(model, alias, values);
- }
-
- @Override
- protected void executeImplementation() throws CommandExecutionException {
-
- // former symbols are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
-
- for (String string : getValues()) {
- if (!getAlias().getFormerSymbols().contains(string)) {
- throw new CommandExecutionException("Cannot remove former symbol \"" + string + "\" from the list. Element doesn't exist.");
- }
- }
-
- getAlias().getFormerSymbols().removeAll(getValues());
-
- // former symbols are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
- }
-
- @Override
- protected void undoImplementation() {
- // former symbols are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
-
- getAlias().getFormerSymbols().addAll(getValues());
-
- // former symbols are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
-
- }
-}
+package lcsb.mapviewer.commands.properties;
+
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.CommandExecutionException;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that removes former
+ * symbols from {@link Element Element}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class RemoveElementFormerSymbolsCommand extends RemoveElementPropertyListEntryCommand<String> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(RemoveElementFormerSymbolsCommand.class);
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * {@link lcsb.mapviewer.commands.ModelCommand#model}
+ * @param alias
+ * {@link ChangeElementPropertyCommand#alias}
+ * @param values
+ * {@link Element#synonym} values to be removed
+ */
+ public RemoveElementFormerSymbolsCommand(Model model, Element alias, List<String> values) {
+ super(model, alias, values);
+ }
+
+ @Override
+ protected void executeImplementation() throws CommandExecutionException {
+
+ // former symbols are not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+
+ for (String string : getValues()) {
+ if (!getAlias().getFormerSymbols().contains(string)) {
+ throw new CommandExecutionException("Cannot remove former symbol \"" + string + "\" from the list. Element doesn't exist.");
+ }
+ }
+
+ getAlias().getFormerSymbols().removeAll(getValues());
+
+ // former symbols are not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+ }
+
+ @Override
+ protected void undoImplementation() {
+ // former symbols are not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+
+ getAlias().getFormerSymbols().addAll(getValues());
+
+ // former symbols are not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+
+ }
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementMiriamDataCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementMiriamDataCommand.java
index d7d6f7f9e7..f8d9dec4d6 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementMiriamDataCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementMiriamDataCommand.java
@@ -1,74 +1,74 @@
-package lcsb.mapviewer.commands.properties;
-
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that removes
- * annotations from {@link Element Element}.
- *
- * @author Piotr Gawron
- *
- */
-public class RemoveElementMiriamDataCommand extends RemoveElementPropertyListEntryCommand<MiriamData> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(RemoveElementMiriamDataCommand.class);
-
- /**
- * Default constructor.
- *
- * @param model
- * {@link lcsb.mapviewer.commands.ModelCommand#model}
- * @param alias
- * {@link ChangeElementPropertyCommand#alias}
- * @param values
- * {@link Element#synonym} values to be removed
- */
- public RemoveElementMiriamDataCommand(Model model, Element alias, List<MiriamData> values) {
- super(model, alias, values);
- }
-
- @Override
- protected void executeImplementation() throws CommandExecutionException {
-
- // miriam data is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
-
- for (MiriamData string : getValues()) {
- if (!getAlias().getMiriamData().contains(string)) {
- throw new CommandExecutionException("Cannot remove miriam \"" + string + "\" from the list. Element doesn't exist.");
- }
- }
-
- getAlias().getMiriamData().removeAll(getValues());
-
- // miriam data is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
- }
-
- @Override
- protected void undoImplementation() {
- // miriam data is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
-
- getAlias().getMiriamData().addAll(getValues());
-
- // miriam data is not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
-
- }
-}
+package lcsb.mapviewer.commands.properties;
+
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.CommandExecutionException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that removes
+ * annotations from {@link Element Element}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class RemoveElementMiriamDataCommand extends RemoveElementPropertyListEntryCommand<MiriamData> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(RemoveElementMiriamDataCommand.class);
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * {@link lcsb.mapviewer.commands.ModelCommand#model}
+ * @param alias
+ * {@link ChangeElementPropertyCommand#alias}
+ * @param values
+ * {@link Element#synonym} values to be removed
+ */
+ public RemoveElementMiriamDataCommand(Model model, Element alias, List<MiriamData> values) {
+ super(model, alias, values);
+ }
+
+ @Override
+ protected void executeImplementation() throws CommandExecutionException {
+
+ // miriam data is not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+
+ for (MiriamData string : getValues()) {
+ if (!getAlias().getMiriamData().contains(string)) {
+ throw new CommandExecutionException("Cannot remove miriam \"" + string + "\" from the list. Element doesn't exist.");
+ }
+ }
+
+ getAlias().getMiriamData().removeAll(getValues());
+
+ // miriam data is not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+ }
+
+ @Override
+ protected void undoImplementation() {
+ // miriam data is not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+
+ getAlias().getMiriamData().addAll(getValues());
+
+ // miriam data is not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+
+ }
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementPropertyListEntryCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementPropertyListEntryCommand.java
index 9e883c7777..b61167bc40 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementPropertyListEntryCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementPropertyListEntryCommand.java
@@ -1,92 +1,92 @@
-package lcsb.mapviewer.commands.properties;
-
-import java.util.List;
-
-import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.commands.ModelCommand;
-import lcsb.mapviewer.commands.ModelCommandStatus;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that removes
- * entries from a property of the {@link Element
- * Element} that is list.
- *
- * @param <T>
- * class of property to edit
- *
- * @author Piotr Gawron
- *
- */
-public abstract class RemoveElementPropertyListEntryCommand<T> extends ModelCommand {
-
- /**
- * Rlement property values to be removed.
- */
- private List<T> values;
-
- /**
- * {@link Element} for which we will change the property.
- */
- private Element alias;
-
- /**
- * Default constructor.
- *
- * @param model
- * model to move
- *
- * @param alias
- * alias to be changed
- *
- * @param values
- * values of the element property to remove
- */
- public RemoveElementPropertyListEntryCommand(Model model, Element alias, List<T> values) {
- super(model);
- this.alias = alias;
- this.values = values;
- }
-
- @Override
- protected void redoImplementation() throws CommandExecutionException {
- executeImplementation();
- setStatus(ModelCommandStatus.EXECUTED);
- }
-
- /**
- * @return the alias
- * @see #alias
- */
- protected Element getAlias() {
- return alias;
- }
-
- /**
- * @param alias
- * the alias to set
- * @see #alias
- */
- protected void setAlias(Element alias) {
- this.alias = alias;
- }
-
- /**
- * @return the values
- * @see #values
- */
- public List<T> getValues() {
- return values;
- }
-
- /**
- * @param values
- * the values to set
- * @see #values
- */
- public void setValues(List<T> values) {
- this.values = values;
- }
-
-}
+package lcsb.mapviewer.commands.properties;
+
+import java.util.List;
+
+import lcsb.mapviewer.commands.CommandExecutionException;
+import lcsb.mapviewer.commands.ModelCommand;
+import lcsb.mapviewer.commands.ModelCommandStatus;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that removes
+ * entries from a property of the {@link Element
+ * Element} that is list.
+ *
+ * @param <T>
+ * class of property to edit
+ *
+ * @author Piotr Gawron
+ *
+ */
+public abstract class RemoveElementPropertyListEntryCommand<T> extends ModelCommand {
+
+ /**
+ * Rlement property values to be removed.
+ */
+ private List<T> values;
+
+ /**
+ * {@link Element} for which we will change the property.
+ */
+ private Element alias;
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * model to move
+ *
+ * @param alias
+ * alias to be changed
+ *
+ * @param values
+ * values of the element property to remove
+ */
+ public RemoveElementPropertyListEntryCommand(Model model, Element alias, List<T> values) {
+ super(model);
+ this.alias = alias;
+ this.values = values;
+ }
+
+ @Override
+ protected void redoImplementation() throws CommandExecutionException {
+ executeImplementation();
+ setStatus(ModelCommandStatus.EXECUTED);
+ }
+
+ /**
+ * @return the alias
+ * @see #alias
+ */
+ protected Element getAlias() {
+ return alias;
+ }
+
+ /**
+ * @param alias
+ * the alias to set
+ * @see #alias
+ */
+ protected void setAlias(Element alias) {
+ this.alias = alias;
+ }
+
+ /**
+ * @return the values
+ * @see #values
+ */
+ public List<T> getValues() {
+ return values;
+ }
+
+ /**
+ * @param values
+ * the values to set
+ * @see #values
+ */
+ public void setValues(List<T> values) {
+ this.values = values;
+ }
+
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementSynonymsCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementSynonymsCommand.java
index fe8a7bbe3d..2c39a42095 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementSynonymsCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/RemoveElementSynonymsCommand.java
@@ -1,73 +1,73 @@
-package lcsb.mapviewer.commands.properties;
-
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that removes
- * synonym from {@link Element Element}.
- *
- * @author Piotr Gawron
- *
- */
-public class RemoveElementSynonymsCommand extends RemoveElementPropertyListEntryCommand<String> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(RemoveElementSynonymsCommand.class);
-
- /**
- * Default constructor.
- *
- * @param model
- * {@link lcsb.mapviewer.commands.ModelCommand#model}
- * @param alias
- * {@link ChangeElementPropertyCommand#alias}
- * @param values
- * {@link Element#synonym} values to be removed
- */
- public RemoveElementSynonymsCommand(Model model, Element alias, List<String> values) {
- super(model, alias, values);
- }
-
- @Override
- protected void executeImplementation() throws CommandExecutionException {
-
- // synonyms are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
-
- for (String string : getValues()) {
- if (!getAlias().getSynonyms().contains(string)) {
- throw new CommandExecutionException("Cannot remove synonym from the list: " + string + ". Element doesn't exist.");
- }
- }
-
- getAlias().getSynonyms().removeAll(getValues());
-
- // synonyms are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
- }
-
- @Override
- protected void undoImplementation() {
- // synonyms are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
-
- getAlias().getSynonyms().addAll(getValues());
-
- // synonyms are not visualized, so we don't need to report any
- // visualization changes
- // includeInAffectedRegion(getAlias());
-
- }
-}
+package lcsb.mapviewer.commands.properties;
+
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.CommandExecutionException;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * {@link lcsb.mapviewer.commands.ModelCommand ModelCommand} that removes
+ * synonym from {@link Element Element}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class RemoveElementSynonymsCommand extends RemoveElementPropertyListEntryCommand<String> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(RemoveElementSynonymsCommand.class);
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * {@link lcsb.mapviewer.commands.ModelCommand#model}
+ * @param alias
+ * {@link ChangeElementPropertyCommand#alias}
+ * @param values
+ * {@link Element#synonym} values to be removed
+ */
+ public RemoveElementSynonymsCommand(Model model, Element alias, List<String> values) {
+ super(model, alias, values);
+ }
+
+ @Override
+ protected void executeImplementation() throws CommandExecutionException {
+
+ // synonyms are not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+
+ for (String string : getValues()) {
+ if (!getAlias().getSynonyms().contains(string)) {
+ throw new CommandExecutionException("Cannot remove synonym from the list: " + string + ". Element doesn't exist.");
+ }
+ }
+
+ getAlias().getSynonyms().removeAll(getValues());
+
+ // synonyms are not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+ }
+
+ @Override
+ protected void undoImplementation() {
+ // synonyms are not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+
+ getAlias().getSynonyms().addAll(getValues());
+
+ // synonyms are not visualized, so we don't need to report any
+ // visualization changes
+ // includeInAffectedRegion(getAlias());
+
+ }
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/package-info.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/package-info.java
index 4d500fc4a0..900c3f4675 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/package-info.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/package-info.java
@@ -1,8 +1,8 @@
-/**
- * This package contains {@link lcsb.mapviewer.commands.ModelCommand commands}
- * that change properies of {@link java.lang.reflect.AnnotatedElement elements }
- * or {@link lcsb.mapviewer.model.map.species.Element aliases}.
- *
- */
-package lcsb.mapviewer.commands.properties;
-
+/**
+ * This package contains {@link lcsb.mapviewer.commands.ModelCommand commands}
+ * that change properies of {@link java.lang.reflect.AnnotatedElement elements }
+ * or {@link lcsb.mapviewer.model.map.species.Element aliases}.
+ *
+ */
+package lcsb.mapviewer.commands.properties;
+
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/AllCommandsTests.java b/model-command/src/test/java/lcsb/mapviewer/commands/AllCommandsTests.java
index 71fece55e5..d391ec54da 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/AllCommandsTests.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/AllCommandsTests.java
@@ -1,21 +1,21 @@
-package lcsb.mapviewer.commands;
-
-import lcsb.mapviewer.commands.layout.AllLayoutTests;
-import lcsb.mapviewer.commands.properties.AllPropertyCommandTests;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AllLayoutTests.class, //
- AllPropertyCommandTests.class, //
- ColorModelCommandTest.class, //
- CopyCommandTest.class, //
- CreateHierarchyCommandTest.class, //
- MoveElementsCommandTest.class, //
- SubModelCommandTest.class,//
-})
-public class AllCommandsTests {
-
-}
+package lcsb.mapviewer.commands;
+
+import lcsb.mapviewer.commands.layout.AllLayoutTests;
+import lcsb.mapviewer.commands.properties.AllPropertyCommandTests;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AllLayoutTests.class, //
+ AllPropertyCommandTests.class, //
+ ColorModelCommandTest.class, //
+ CopyCommandTest.class, //
+ CreateHierarchyCommandTest.class, //
+ MoveElementsCommandTest.class, //
+ SubModelCommandTest.class,//
+})
+public class AllCommandsTests {
+
+}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java b/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java
index 145d6e000e..f975548de2 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java
@@ -1,65 +1,65 @@
-package lcsb.mapviewer.commands;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-
-public abstract class CommandTestFunctions {
- public double EPSILON = 1e-6;
-
- Logger logger = Logger.getLogger(CommandTestFunctions.class);
-
- private static Map<String, Model> models = new HashMap<String, Model>();
-
- protected Model getModelForFile(String fileName, boolean fromCache) throws Exception {
- if (!fromCache) {
- logger.debug("File without cache: " + fileName);
- Model result = new CellDesignerXmlParser().createModel(new ConverterParams().filename(fileName));
- result.setName(null);
- return result;
- }
- Model result = models.get(fileName);
- if (result == null) {
- logger.debug("File to cache: " + fileName);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- result = parser.createModel(new ConverterParams().filename(fileName).sizeAutoAdjust(false));
- result.setName(null);
- models.put(fileName, result);
- }
- return result;
- }
-
- protected Model createSimpleModel() {
- Model model = new ModelFullIndexed(null);
-
- GenericProtein alias = new GenericProtein("alias_id");
- alias.setNotes(null);
- List<String> list = new ArrayList<>();
- list.add("synonym");
- alias.addSynonyms(list);
- List<String> list2 = new ArrayList<>();
- list2.add("f_symbol");
- alias.setFormerSymbols(list2);
-
- Complex complexAlias = new Complex("complex_alias_id");
- model.addElement(complexAlias);
-
- complexAlias.addSpecies(alias);
-
- model.addElement(alias);
-
- return model;
- }
-
-}
+package lcsb.mapviewer.commands;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+
+public abstract class CommandTestFunctions {
+ public double EPSILON = 1e-6;
+
+ Logger logger = Logger.getLogger(CommandTestFunctions.class);
+
+ private static Map<String, Model> models = new HashMap<String, Model>();
+
+ protected Model getModelForFile(String fileName, boolean fromCache) throws Exception {
+ if (!fromCache) {
+ logger.debug("File without cache: " + fileName);
+ Model result = new CellDesignerXmlParser().createModel(new ConverterParams().filename(fileName));
+ result.setName(null);
+ return result;
+ }
+ Model result = models.get(fileName);
+ if (result == null) {
+ logger.debug("File to cache: " + fileName);
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ result = parser.createModel(new ConverterParams().filename(fileName).sizeAutoAdjust(false));
+ result.setName(null);
+ models.put(fileName, result);
+ }
+ return result;
+ }
+
+ protected Model createSimpleModel() {
+ Model model = new ModelFullIndexed(null);
+
+ GenericProtein alias = new GenericProtein("alias_id");
+ alias.setNotes(null);
+ List<String> list = new ArrayList<>();
+ list.add("synonym");
+ alias.addSynonyms(list);
+ List<String> list2 = new ArrayList<>();
+ list2.add("f_symbol");
+ alias.setFormerSymbols(list2);
+
+ Complex complexAlias = new Complex("complex_alias_id");
+ model.addElement(complexAlias);
+
+ complexAlias.addSpecies(alias);
+
+ model.addElement(alias);
+
+ return model;
+ }
+
+}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
index d942482d7b..c7ddbc5442 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
@@ -1,389 +1,389 @@
-package lcsb.mapviewer.commands;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.awt.geom.Point2D;
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.compartment.SquareCompartment;
-import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
-import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
-import lcsb.mapviewer.model.map.model.SubmodelType;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-
-public class CopyCommandTest extends CommandTestFunctions {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testCopyModel() {
- try {
- Model model = getModelForFile("testFiles/sample.xml", false);
- Model copy = new CopyCommand(model).execute();
-
- ModelComparator comparator = new ModelComparator();
-
- assertEquals(0, comparator.compare(model, copy));
- } catch (Exception e) {
- e.printStackTrace();
- fail("exception occurred");
- }
- }
-
- @Test
- public void testCopyModelWithKinetics() throws Exception {
- try {
- Model model = getModelForFile("testFiles/kinetics_with_compartment.xml", false);
- Model copy = new CopyCommand(model).execute();
-
- ModelComparator comparator = new ModelComparator();
-
- assertEquals(0, comparator.compare(model, copy));
- for (Reaction reaction : copy.getReactions()) {
- if (reaction.getKinetics() != null) {
- for (Element element : reaction.getKinetics().getElements()) {
- assertTrue("Element in the copy doesn't belong to copy", copy.getElements().contains(element));
- }
- for (SbmlFunction function : reaction.getKinetics().getFunctions()) {
- assertTrue("Function in the copy doesn't belong to copy", copy.getFunctions().contains(function));
- }
- for (SbmlParameter parameter : reaction.getKinetics().getParameters()) {
- if (parameter.getParameterId().equals("k2")) {
- assertTrue("Global parameter in the function copy doesn't belong to copy",
- copy.getParameters().contains(parameter));
- }
- }
- }
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopyCustomModel() {
- try {
- Model model = new ModelFullIndexed(null);
-
- GenericProtein protein = new GenericProtein("A");
- protein.setNotes(null);
-
- model.addElement(protein);
-
- Model copy = new CopyCommand(model).execute();
-
- ModelComparator comparator = new ModelComparator();
-
- assertEquals(0, comparator.compare(model, copy));
- } catch (Exception e) {
- e.printStackTrace();
- fail("exception occurred");
- }
- }
-
- @Test
- public void testCopyCustomModel2() {
- try {
- Model model = new ModelFullIndexed(null);
-
- Complex complexAlias = new Complex("id2");
- GenericProtein protein = new GenericProtein("A");
- protein.setNotes(null);
- complexAlias.addSpecies(protein);
- model.addElement(protein);
- model.addElement(complexAlias);
-
- GenericProtein alias = new GenericProtein("B");
- alias.setNotes(null);
-
- complexAlias.addSpecies(alias);
- model.addElement(alias);
-
- Model copy = new CopyCommand(model).execute();
-
- ModelComparator comparator = new ModelComparator();
-
- assertEquals(0, comparator.compare(model, copy));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopyModel3() throws Exception {
- try {
- Model model = getModelForFile("testFiles/complex_with_state.xml", true);
-
- Model copy = new CopyCommand(model).execute();
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(copy);
-
- InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
- ModelComparator comparator = new ModelComparator();
-
- // check if after conversion to xml everything works
- assertEquals(0, comparator.compare(copy, copy2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopyModel4() throws Exception {
- try {
- Model model = getModelForFile("testFiles/problematic_description.xml", true);
-
- Model copy = new CopyCommand(model).execute();
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(copy);
-
- InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
- ModelComparator comparator = new ModelComparator();
-
- // check if after conversion to xml everything works
- assertEquals(0, comparator.compare(copy, copy2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopyModelWithArtifitialAliases() throws Exception {
- try {
- Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
- new CreateHierarchyCommand(model, 2, 2).execute();
-
- Model copy = new CopyCommand(model).execute();
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(copy);
-
- InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
- ModelComparator comparator = new ModelComparator();
-
- new CreateHierarchyCommand(copy2, 2, 2).execute();
-
- // check if after conversion to xml everything works
- assertEquals(0, comparator.compare(copy, copy2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopyModelWithSubmodels() throws Exception {
- try {
- Model model = getModel();
- Model model2 = getModel();
- model2.setNotes("ASDSA");
- model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
- Model copy = new CopyCommand(model).execute();
-
- ModelComparator comparator = new ModelComparator();
-
- assertEquals(0, comparator.compare(model, copy));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopySubmodel() throws Exception {
- try {
- Model model = getModel();
- Model model2 = getModel();
- model2.setNotes("ASDSA");
- model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS, "name a"));
-
- Model model3 = getModel();
- model3.setNotes("ASDSA");
- model.addSubmodelConnection(new ModelSubmodelConnection(model3, SubmodelType.DOWNSTREAM_TARGETS, "name b"));
- Element alias = model2.getElementByElementId("a_id");
- alias.setSubmodel(new ElementSubmodelConnection(model3, SubmodelType.DOWNSTREAM_TARGETS, "name c"));
- Model copy = new CopyCommand(model2).execute();
-
- ModelComparator comparator = new ModelComparator();
-
- assertEquals(0, comparator.compare(model2, copy));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopyModelWithSubmodels2() throws Exception {
- try {
- Model model = getModel();
- Model model2 = getModel();
- model2.setNotes("ASDSA2");
-
- model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
- model.getElementByElementId("a_id")
- .setSubmodel(new ElementSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
- Model copy = new CopyCommand(model).execute();
-
- ModelComparator comparator = new ModelComparator();
-
- assertEquals(0, comparator.compare(model, copy));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopyModelWithName() throws Exception {
- try {
- Model model = getModel();
- model.setName("ASDSA2");
-
- Model copy = new CopyCommand(model).execute();
-
- ModelComparator comparator = new ModelComparator();
-
- assertEquals(0, comparator.compare(model, copy));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopyModelWithSubmodelsThrowException() throws Exception {
- try {
- Model model = getModel();
- Model model2 = getModel();
- model2.setNotes("ASDSA2");
-
- model.getElementByElementId("a_id")
- .setSubmodel(new ElementSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
- try {
- new CopyCommand(model).execute();
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private Model getModel() {
- Model model = new ModelFullIndexed(null);
- model.setNotes("Some description");
-
- GenericProtein alias = new GenericProtein("a_id");
- alias.setName("ad");
- model.addElement(alias);
-
- Layer layer = new Layer();
- layer.setName("layer name");
- model.addLayer(layer);
-
- model.addReaction(new Reaction());
- return model;
- }
-
- @Test
- public void testCopyModelReaction() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
-
- Compartment c1 = new SquareCompartment("c1");
- Compartment c2 = new SquareCompartment("c2");
- c1.setVisibilityLevel("2");
- c2.setVisibilityLevel("3");
-
- model.addElement(c1);
- model.addElement(c2);
-
- GenericProtein s1 = new GenericProtein("s1");
- s1.setCompartment(c1);
- model.addElement(s1);
-
- GenericProtein s2 = new GenericProtein("s2");
- s2.setCompartment(c2);
- model.addElement(s2);
-
- StateTransitionReaction reaction = new StateTransitionReaction();
- Reactant reactant = new Reactant(s1);
- reactant.setLine(new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10)));
- reaction.addReactant(reactant);
- Product product = new Product(s2);
- product.setLine(new PolylineData(new Point2D.Double(10, 0), new Point2D.Double(120, 10)));
- reaction.addProduct(product);
- reaction.setVisibilityLevel("4");
-
- model.addReaction(reaction);
-
- assertTrue(s1.equals(reaction.getReactants().get(0).getElement()));
- assertTrue(s2.equals(reaction.getProducts().get(0).getElement()));
-
- Model model2 = new CopyCommand(model).execute();
- Reaction reaction2 = model2.getReactions().iterator().next();
-
- assertTrue(s1.equals(reaction.getReactants().get(0).getElement()));
- assertTrue(s2.equals(reaction.getProducts().get(0).getElement()));
-
- assertFalse(s1.equals(reaction2.getReactants().get(0).getElement()));
- assertFalse(s2.equals(reaction2.getProducts().get(0).getElement()));
-
- assertNotNull(reaction2.getReactants().get(0).getElement().getCompartment());
- assertNotNull(reaction2.getProducts().get(0).getElement().getCompartment());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.commands;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.awt.geom.Point2D;
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.SquareCompartment;
+import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
+import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
+import lcsb.mapviewer.model.map.model.SubmodelType;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+
+public class CopyCommandTest extends CommandTestFunctions {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testCopyModel() {
+ try {
+ Model model = getModelForFile("testFiles/sample.xml", false);
+ Model copy = new CopyCommand(model).execute();
+
+ ModelComparator comparator = new ModelComparator();
+
+ assertEquals(0, comparator.compare(model, copy));
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("exception occurred");
+ }
+ }
+
+ @Test
+ public void testCopyModelWithKinetics() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/kinetics_with_compartment.xml", false);
+ Model copy = new CopyCommand(model).execute();
+
+ ModelComparator comparator = new ModelComparator();
+
+ assertEquals(0, comparator.compare(model, copy));
+ for (Reaction reaction : copy.getReactions()) {
+ if (reaction.getKinetics() != null) {
+ for (Element element : reaction.getKinetics().getElements()) {
+ assertTrue("Element in the copy doesn't belong to copy", copy.getElements().contains(element));
+ }
+ for (SbmlFunction function : reaction.getKinetics().getFunctions()) {
+ assertTrue("Function in the copy doesn't belong to copy", copy.getFunctions().contains(function));
+ }
+ for (SbmlParameter parameter : reaction.getKinetics().getParameters()) {
+ if (parameter.getParameterId().equals("k2")) {
+ assertTrue("Global parameter in the function copy doesn't belong to copy",
+ copy.getParameters().contains(parameter));
+ }
+ }
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyCustomModel() {
+ try {
+ Model model = new ModelFullIndexed(null);
+
+ GenericProtein protein = new GenericProtein("A");
+ protein.setNotes(null);
+
+ model.addElement(protein);
+
+ Model copy = new CopyCommand(model).execute();
+
+ ModelComparator comparator = new ModelComparator();
+
+ assertEquals(0, comparator.compare(model, copy));
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("exception occurred");
+ }
+ }
+
+ @Test
+ public void testCopyCustomModel2() {
+ try {
+ Model model = new ModelFullIndexed(null);
+
+ Complex complexAlias = new Complex("id2");
+ GenericProtein protein = new GenericProtein("A");
+ protein.setNotes(null);
+ complexAlias.addSpecies(protein);
+ model.addElement(protein);
+ model.addElement(complexAlias);
+
+ GenericProtein alias = new GenericProtein("B");
+ alias.setNotes(null);
+
+ complexAlias.addSpecies(alias);
+ model.addElement(alias);
+
+ Model copy = new CopyCommand(model).execute();
+
+ ModelComparator comparator = new ModelComparator();
+
+ assertEquals(0, comparator.compare(model, copy));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyModel3() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/complex_with_state.xml", true);
+
+ Model copy = new CopyCommand(model).execute();
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(copy);
+
+ InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
+ ModelComparator comparator = new ModelComparator();
+
+ // check if after conversion to xml everything works
+ assertEquals(0, comparator.compare(copy, copy2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyModel4() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/problematic_description.xml", true);
+
+ Model copy = new CopyCommand(model).execute();
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(copy);
+
+ InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
+ ModelComparator comparator = new ModelComparator();
+
+ // check if after conversion to xml everything works
+ assertEquals(0, comparator.compare(copy, copy2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyModelWithArtifitialAliases() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
+ new CreateHierarchyCommand(model, 2, 2).execute();
+
+ Model copy = new CopyCommand(model).execute();
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(copy);
+
+ InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
+ ModelComparator comparator = new ModelComparator();
+
+ new CreateHierarchyCommand(copy2, 2, 2).execute();
+
+ // check if after conversion to xml everything works
+ assertEquals(0, comparator.compare(copy, copy2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyModelWithSubmodels() throws Exception {
+ try {
+ Model model = getModel();
+ Model model2 = getModel();
+ model2.setNotes("ASDSA");
+ model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
+ Model copy = new CopyCommand(model).execute();
+
+ ModelComparator comparator = new ModelComparator();
+
+ assertEquals(0, comparator.compare(model, copy));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopySubmodel() throws Exception {
+ try {
+ Model model = getModel();
+ Model model2 = getModel();
+ model2.setNotes("ASDSA");
+ model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS, "name a"));
+
+ Model model3 = getModel();
+ model3.setNotes("ASDSA");
+ model.addSubmodelConnection(new ModelSubmodelConnection(model3, SubmodelType.DOWNSTREAM_TARGETS, "name b"));
+ Element alias = model2.getElementByElementId("a_id");
+ alias.setSubmodel(new ElementSubmodelConnection(model3, SubmodelType.DOWNSTREAM_TARGETS, "name c"));
+ Model copy = new CopyCommand(model2).execute();
+
+ ModelComparator comparator = new ModelComparator();
+
+ assertEquals(0, comparator.compare(model2, copy));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyModelWithSubmodels2() throws Exception {
+ try {
+ Model model = getModel();
+ Model model2 = getModel();
+ model2.setNotes("ASDSA2");
+
+ model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
+ model.getElementByElementId("a_id")
+ .setSubmodel(new ElementSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
+ Model copy = new CopyCommand(model).execute();
+
+ ModelComparator comparator = new ModelComparator();
+
+ assertEquals(0, comparator.compare(model, copy));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyModelWithName() throws Exception {
+ try {
+ Model model = getModel();
+ model.setName("ASDSA2");
+
+ Model copy = new CopyCommand(model).execute();
+
+ ModelComparator comparator = new ModelComparator();
+
+ assertEquals(0, comparator.compare(model, copy));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyModelWithSubmodelsThrowException() throws Exception {
+ try {
+ Model model = getModel();
+ Model model2 = getModel();
+ model2.setNotes("ASDSA2");
+
+ model.getElementByElementId("a_id")
+ .setSubmodel(new ElementSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
+ try {
+ new CopyCommand(model).execute();
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Model getModel() {
+ Model model = new ModelFullIndexed(null);
+ model.setNotes("Some description");
+
+ GenericProtein alias = new GenericProtein("a_id");
+ alias.setName("ad");
+ model.addElement(alias);
+
+ Layer layer = new Layer();
+ layer.setName("layer name");
+ model.addLayer(layer);
+
+ model.addReaction(new Reaction());
+ return model;
+ }
+
+ @Test
+ public void testCopyModelReaction() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+
+ Compartment c1 = new SquareCompartment("c1");
+ Compartment c2 = new SquareCompartment("c2");
+ c1.setVisibilityLevel("2");
+ c2.setVisibilityLevel("3");
+
+ model.addElement(c1);
+ model.addElement(c2);
+
+ GenericProtein s1 = new GenericProtein("s1");
+ s1.setCompartment(c1);
+ model.addElement(s1);
+
+ GenericProtein s2 = new GenericProtein("s2");
+ s2.setCompartment(c2);
+ model.addElement(s2);
+
+ StateTransitionReaction reaction = new StateTransitionReaction();
+ Reactant reactant = new Reactant(s1);
+ reactant.setLine(new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10)));
+ reaction.addReactant(reactant);
+ Product product = new Product(s2);
+ product.setLine(new PolylineData(new Point2D.Double(10, 0), new Point2D.Double(120, 10)));
+ reaction.addProduct(product);
+ reaction.setVisibilityLevel("4");
+
+ model.addReaction(reaction);
+
+ assertTrue(s1.equals(reaction.getReactants().get(0).getElement()));
+ assertTrue(s2.equals(reaction.getProducts().get(0).getElement()));
+
+ Model model2 = new CopyCommand(model).execute();
+ Reaction reaction2 = model2.getReactions().iterator().next();
+
+ assertTrue(s1.equals(reaction.getReactants().get(0).getElement()));
+ assertTrue(s2.equals(reaction.getProducts().get(0).getElement()));
+
+ assertFalse(s1.equals(reaction2.getReactants().get(0).getElement()));
+ assertFalse(s2.equals(reaction2.getProducts().get(0).getElement()));
+
+ assertNotNull(reaction2.getReactants().get(0).getElement().getCompartment());
+ assertNotNull(reaction2.getProducts().get(0).getElement().getCompartment());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/MoveElementsCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/MoveElementsCommandTest.java
index 8b7637362c..17bb618520 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/MoveElementsCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/MoveElementsCommandTest.java
@@ -1,277 +1,277 @@
-package lcsb.mapviewer.commands;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.awt.geom.Rectangle2D;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
-
-public class MoveElementsCommandTest extends CommandTestFunctions {
-
- ModelComparator modelComparator = new ModelComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testMoveAlias() throws Exception {
- try {
- Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
- Model model2 = getModelForFile("testFiles/spliting_test_Case.xml", false);
- Element alias = model.getElementByElementId("sa2");
- Element alias2 = model.getElementByElementId("sa1");
- double anotherAliasX = alias2.getX();
- double anotherAliasY = alias2.getY();
-
- List<Object> list = new ArrayList<>();
- list.add(alias);
- double x = alias.getX();
- double y = alias.getY();
-
- double dx = 10;
- double dy = 2;
-
- // models should be equal before move
- assertEquals(0, modelComparator.compare(model, model2));
-
- MoveElementsCommand moveCommand = new MoveElementsCommand(model, list, dx, dy);
- moveCommand.execute();
-
- // after move models should be different
- assertTrue(0 != modelComparator.compare(model, model2));
-
- // check new coordinates
- assertEquals(x + dx, alias.getX(), Configuration.EPSILON);
- assertEquals(y + dy, alias.getY(), Configuration.EPSILON);
-
- // and check if another alias didn't change coordinates
- assertEquals(anotherAliasX, alias2.getX(), Configuration.EPSILON);
- assertEquals(anotherAliasY, alias2.getY(), Configuration.EPSILON);
-
- list = new ArrayList<>();
- list.add(model2.getElementByElementId("sa2"));
- MoveElementsCommand moveCommand2 = new MoveElementsCommand(model2, list, dx, dy);
- moveCommand2.execute();
-
- // if we perfomr the same operator on the second model then they should be
- // equal
- assertEquals(0, modelComparator.compare(model, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testMoveSpecies() throws Exception {
- try {
- Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
- List<Object> list = new ArrayList<>();
- list.add(new Object());
-
- MoveElementsCommand moveCommand = new MoveElementsCommand(model, list, 10, 10);
- moveCommand.execute();
- fail("Exception expected");
-
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAliasWithReaction() throws Exception {
- try {
- Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
- Model model2 = getModelForFile("testFiles/spliting_test_Case.xml", false);
- Element alias = model.getElementByElementId("sa1");
- Element alias2 = model.getElementByElementId("sa2");
- double anotherAliasX = alias2.getX();
- double anotherAliasY = alias2.getY();
- Reaction reaction = model.getReactionByReactionId("re1");
-
- List<Object> list = new ArrayList<>();
- list.add(alias);
- double x = reaction.getReactants().get(0).getLine().getBeginPoint().getX();
- double y = reaction.getReactants().get(0).getLine().getBeginPoint().getY();
-
- double dx = 10;
- double dy = 2;
-
- // models should be equal before move
- assertEquals(0, modelComparator.compare(model, model2));
-
- MoveElementsCommand moveCommand = new MoveElementsCommand(model, list, dx, dy);
- moveCommand.execute();
-
- // after move models should be different
- assertTrue(0 != modelComparator.compare(model, model2));
-
- // check new coordinates of reaction
- assertEquals(x + dx, reaction.getReactants().get(0).getLine().getBeginPoint().getX(), Configuration.EPSILON);
- assertEquals(y + dy, reaction.getReactants().get(0).getLine().getBeginPoint().getY(), Configuration.EPSILON);
-
- // and check if another alias didn't change coordinates
- assertEquals(anotherAliasX, alias2.getX(), Configuration.EPSILON);
- assertEquals(anotherAliasY, alias2.getY(), Configuration.EPSILON);
-
- list = new ArrayList<>();
- list.add(model2.getElementByElementId("sa1"));
- MoveElementsCommand moveCommand2 = new MoveElementsCommand(model2, list, dx, dy);
- moveCommand2.execute();
-
- // if we perfomr the same operator on the second model then they should be
- // equal
- assertEquals(0, modelComparator.compare(model, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testMoveReaction() throws Exception {
- try {
- Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
- Element alias2 = model.getElementByElementId("sa1");
- double anotherAliasX = alias2.getX();
- double anotherAliasY = alias2.getY();
- Reaction reaction = model.getReactionByReactionId("re1");
-
- List<Object> list = new ArrayList<>();
- list.add(reaction);
- double x = reaction.getReactants().get(0).getLine().getBeginPoint().getX();
- double y = reaction.getReactants().get(0).getLine().getBeginPoint().getY();
-
- double x2 = reaction.getReactants().get(0).getLine().getEndPoint().getX();
- double y2 = reaction.getReactants().get(0).getLine().getEndPoint().getY();
-
- double dx = 10;
- double dy = 2;
-
- MoveElementsCommand moveCommand = new MoveElementsCommand(model, list, dx, dy);
- moveCommand.execute();
-
- // check new coordinates of reaction (point attached to alias shouldn't
- // move, the one not attached should move)
- assertEquals(x, reaction.getReactants().get(0).getLine().getBeginPoint().getX(), Configuration.EPSILON);
- assertEquals(y, reaction.getReactants().get(0).getLine().getBeginPoint().getY(), Configuration.EPSILON);
- assertEquals(x2 + dx, reaction.getReactants().get(0).getLine().getEndPoint().getX(), Configuration.EPSILON);
- assertEquals(y2 + dy, reaction.getReactants().get(0).getLine().getEndPoint().getY(), Configuration.EPSILON);
-
- // and check if another alias didn't change coordinates
- assertEquals(anotherAliasX, alias2.getX(), Configuration.EPSILON);
- assertEquals(anotherAliasY, alias2.getY(), Configuration.EPSILON);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUndo() throws Exception {
- try {
- Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
- Model model2 = getModelForFile("testFiles/spliting_test_Case.xml", false);
- Element alias = model.getElementByElementId("sa2");
-
- List<Object> list = new ArrayList<>();
- list.add(alias);
-
- double dx = 10;
- double dy = 2;
-
- // models should be equal before move
- assertEquals(0, modelComparator.compare(model, model2));
-
- MoveElementsCommand moveCommand = new MoveElementsCommand(model, list, dx, dy);
- moveCommand.execute();
-
- // after move models should be different
- assertTrue(0 != modelComparator.compare(model, model2));
-
- // undo command
- moveCommand.undo();
-
- // after undo they should be the same again
- assertEquals(0, modelComparator.compare(model, model2));
-
- moveCommand.redo();
-
- // after redo they should be different again
- assertTrue(0 != modelComparator.compare(model, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAffectedRegion() throws Exception {
- try {
- Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
- Element alias = model.getElementByElementId("sa2");
-
- List<Object> list = new ArrayList<>();
- list.add(alias);
- double x = alias.getX();
- double y = alias.getY();
-
- double dx = 10;
- double dy = 2;
-
- double minx = x;
- double maxx = alias.getWidth() + x + dx;
-
- double miny = y;
- double maxy = alias.getHeight() + y + dy;
-
- MoveElementsCommand moveCommand = new MoveElementsCommand(model, list, dx, dy);
- assertNull(moveCommand.getAffectedRegion());
- moveCommand.execute();
- assertNotNull(moveCommand.getAffectedRegion());
- Rectangle2D affectedRegion = moveCommand.getAffectedRegion();
- assertEquals(minx, affectedRegion.getX(), Configuration.EPSILON);
- assertEquals(miny, affectedRegion.getY(), Configuration.EPSILON);
- assertEquals(maxx, affectedRegion.getX() + affectedRegion.getWidth(), Configuration.EPSILON);
- assertEquals(maxy, affectedRegion.getY() + affectedRegion.getHeight(), Configuration.EPSILON);
-
- moveCommand.undo();
-
- affectedRegion = moveCommand.getAffectedRegion();
- assertEquals(minx, affectedRegion.getX(), Configuration.EPSILON);
- assertEquals(miny, affectedRegion.getY(), Configuration.EPSILON);
- assertEquals(maxx, affectedRegion.getX() + affectedRegion.getWidth(), Configuration.EPSILON);
- assertEquals(maxy, affectedRegion.getY() + affectedRegion.getHeight(), Configuration.EPSILON);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.commands;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.awt.geom.Rectangle2D;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+
+public class MoveElementsCommandTest extends CommandTestFunctions {
+
+ ModelComparator modelComparator = new ModelComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testMoveAlias() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
+ Model model2 = getModelForFile("testFiles/spliting_test_Case.xml", false);
+ Element alias = model.getElementByElementId("sa2");
+ Element alias2 = model.getElementByElementId("sa1");
+ double anotherAliasX = alias2.getX();
+ double anotherAliasY = alias2.getY();
+
+ List<Object> list = new ArrayList<>();
+ list.add(alias);
+ double x = alias.getX();
+ double y = alias.getY();
+
+ double dx = 10;
+ double dy = 2;
+
+ // models should be equal before move
+ assertEquals(0, modelComparator.compare(model, model2));
+
+ MoveElementsCommand moveCommand = new MoveElementsCommand(model, list, dx, dy);
+ moveCommand.execute();
+
+ // after move models should be different
+ assertTrue(0 != modelComparator.compare(model, model2));
+
+ // check new coordinates
+ assertEquals(x + dx, alias.getX(), Configuration.EPSILON);
+ assertEquals(y + dy, alias.getY(), Configuration.EPSILON);
+
+ // and check if another alias didn't change coordinates
+ assertEquals(anotherAliasX, alias2.getX(), Configuration.EPSILON);
+ assertEquals(anotherAliasY, alias2.getY(), Configuration.EPSILON);
+
+ list = new ArrayList<>();
+ list.add(model2.getElementByElementId("sa2"));
+ MoveElementsCommand moveCommand2 = new MoveElementsCommand(model2, list, dx, dy);
+ moveCommand2.execute();
+
+ // if we perfomr the same operator on the second model then they should be
+ // equal
+ assertEquals(0, modelComparator.compare(model, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testMoveSpecies() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
+ List<Object> list = new ArrayList<>();
+ list.add(new Object());
+
+ MoveElementsCommand moveCommand = new MoveElementsCommand(model, list, 10, 10);
+ moveCommand.execute();
+ fail("Exception expected");
+
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAliasWithReaction() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
+ Model model2 = getModelForFile("testFiles/spliting_test_Case.xml", false);
+ Element alias = model.getElementByElementId("sa1");
+ Element alias2 = model.getElementByElementId("sa2");
+ double anotherAliasX = alias2.getX();
+ double anotherAliasY = alias2.getY();
+ Reaction reaction = model.getReactionByReactionId("re1");
+
+ List<Object> list = new ArrayList<>();
+ list.add(alias);
+ double x = reaction.getReactants().get(0).getLine().getBeginPoint().getX();
+ double y = reaction.getReactants().get(0).getLine().getBeginPoint().getY();
+
+ double dx = 10;
+ double dy = 2;
+
+ // models should be equal before move
+ assertEquals(0, modelComparator.compare(model, model2));
+
+ MoveElementsCommand moveCommand = new MoveElementsCommand(model, list, dx, dy);
+ moveCommand.execute();
+
+ // after move models should be different
+ assertTrue(0 != modelComparator.compare(model, model2));
+
+ // check new coordinates of reaction
+ assertEquals(x + dx, reaction.getReactants().get(0).getLine().getBeginPoint().getX(), Configuration.EPSILON);
+ assertEquals(y + dy, reaction.getReactants().get(0).getLine().getBeginPoint().getY(), Configuration.EPSILON);
+
+ // and check if another alias didn't change coordinates
+ assertEquals(anotherAliasX, alias2.getX(), Configuration.EPSILON);
+ assertEquals(anotherAliasY, alias2.getY(), Configuration.EPSILON);
+
+ list = new ArrayList<>();
+ list.add(model2.getElementByElementId("sa1"));
+ MoveElementsCommand moveCommand2 = new MoveElementsCommand(model2, list, dx, dy);
+ moveCommand2.execute();
+
+ // if we perfomr the same operator on the second model then they should be
+ // equal
+ assertEquals(0, modelComparator.compare(model, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testMoveReaction() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
+ Element alias2 = model.getElementByElementId("sa1");
+ double anotherAliasX = alias2.getX();
+ double anotherAliasY = alias2.getY();
+ Reaction reaction = model.getReactionByReactionId("re1");
+
+ List<Object> list = new ArrayList<>();
+ list.add(reaction);
+ double x = reaction.getReactants().get(0).getLine().getBeginPoint().getX();
+ double y = reaction.getReactants().get(0).getLine().getBeginPoint().getY();
+
+ double x2 = reaction.getReactants().get(0).getLine().getEndPoint().getX();
+ double y2 = reaction.getReactants().get(0).getLine().getEndPoint().getY();
+
+ double dx = 10;
+ double dy = 2;
+
+ MoveElementsCommand moveCommand = new MoveElementsCommand(model, list, dx, dy);
+ moveCommand.execute();
+
+ // check new coordinates of reaction (point attached to alias shouldn't
+ // move, the one not attached should move)
+ assertEquals(x, reaction.getReactants().get(0).getLine().getBeginPoint().getX(), Configuration.EPSILON);
+ assertEquals(y, reaction.getReactants().get(0).getLine().getBeginPoint().getY(), Configuration.EPSILON);
+ assertEquals(x2 + dx, reaction.getReactants().get(0).getLine().getEndPoint().getX(), Configuration.EPSILON);
+ assertEquals(y2 + dy, reaction.getReactants().get(0).getLine().getEndPoint().getY(), Configuration.EPSILON);
+
+ // and check if another alias didn't change coordinates
+ assertEquals(anotherAliasX, alias2.getX(), Configuration.EPSILON);
+ assertEquals(anotherAliasY, alias2.getY(), Configuration.EPSILON);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUndo() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
+ Model model2 = getModelForFile("testFiles/spliting_test_Case.xml", false);
+ Element alias = model.getElementByElementId("sa2");
+
+ List<Object> list = new ArrayList<>();
+ list.add(alias);
+
+ double dx = 10;
+ double dy = 2;
+
+ // models should be equal before move
+ assertEquals(0, modelComparator.compare(model, model2));
+
+ MoveElementsCommand moveCommand = new MoveElementsCommand(model, list, dx, dy);
+ moveCommand.execute();
+
+ // after move models should be different
+ assertTrue(0 != modelComparator.compare(model, model2));
+
+ // undo command
+ moveCommand.undo();
+
+ // after undo they should be the same again
+ assertEquals(0, modelComparator.compare(model, model2));
+
+ moveCommand.redo();
+
+ // after redo they should be different again
+ assertTrue(0 != modelComparator.compare(model, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAffectedRegion() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
+ Element alias = model.getElementByElementId("sa2");
+
+ List<Object> list = new ArrayList<>();
+ list.add(alias);
+ double x = alias.getX();
+ double y = alias.getY();
+
+ double dx = 10;
+ double dy = 2;
+
+ double minx = x;
+ double maxx = alias.getWidth() + x + dx;
+
+ double miny = y;
+ double maxy = alias.getHeight() + y + dy;
+
+ MoveElementsCommand moveCommand = new MoveElementsCommand(model, list, dx, dy);
+ assertNull(moveCommand.getAffectedRegion());
+ moveCommand.execute();
+ assertNotNull(moveCommand.getAffectedRegion());
+ Rectangle2D affectedRegion = moveCommand.getAffectedRegion();
+ assertEquals(minx, affectedRegion.getX(), Configuration.EPSILON);
+ assertEquals(miny, affectedRegion.getY(), Configuration.EPSILON);
+ assertEquals(maxx, affectedRegion.getX() + affectedRegion.getWidth(), Configuration.EPSILON);
+ assertEquals(maxy, affectedRegion.getY() + affectedRegion.getHeight(), Configuration.EPSILON);
+
+ moveCommand.undo();
+
+ affectedRegion = moveCommand.getAffectedRegion();
+ assertEquals(minx, affectedRegion.getX(), Configuration.EPSILON);
+ assertEquals(miny, affectedRegion.getY(), Configuration.EPSILON);
+ assertEquals(maxx, affectedRegion.getX() + affectedRegion.getWidth(), Configuration.EPSILON);
+ assertEquals(maxy, affectedRegion.getY() + affectedRegion.getHeight(), Configuration.EPSILON);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/SubModelCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/SubModelCommandTest.java
index 9521e94745..ccfb0bb1ad 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/SubModelCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/SubModelCommandTest.java
@@ -1,168 +1,168 @@
-package lcsb.mapviewer.commands;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-
-import java.awt.geom.Path2D;
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
-
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class SubModelCommandTest extends CommandTestFunctions {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetSubmodel1() throws Exception {
- try {
- Model model = getModelForFile("testFiles/spliting_test_Case.xml", true);
-
- Path2D polygon = new Path2D.Double();
- polygon.moveTo(0, 0);
- polygon.lineTo(0, 100);
- polygon.lineTo(100, 100);
- polygon.lineTo(100, 0);
- polygon.closePath();
-
- Model copy = new SubModelCommand(model, polygon).execute();
-
- assertEquals(2, copy.getElements().size());
- assertEquals(0, copy.getReactions().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetSubmodel2() throws Exception {
- try {
- Model model = getModelForFile("testFiles/spliting_test_Case.xml", true);
-
- Path2D polygon = new Path2D.Double();
- polygon.moveTo(50, 50);
- polygon.lineTo(350, 50);
- polygon.lineTo(350, 200);
- polygon.lineTo(50, 200);
- polygon.closePath();
-
- Model copy = new SubModelCommand(model, polygon).execute();
-
- assertEquals(9, copy.getElements().size());
- assertEquals(1, copy.getReactions().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetSubmodel3() throws Exception {
- try {
- Model model = getModelForFile("testFiles/spliting_test_Case.xml", true);
-
- Path2D polygon = new Path2D.Double();
- polygon.moveTo(0, 200);
- polygon.lineTo(350, 200);
- polygon.lineTo(350, 400);
- polygon.lineTo(0, 400);
- polygon.closePath();
-
- Model copy = new SubModelCommand(model, polygon).execute();
-
- double dx = 10;
- double dy = -10;
-
- new MoveCommand(copy, dx, dy).execute();
-
- assertEquals(model.getElementByElementId("sa3").getCenterX(), copy.getElementByElementId("sa3").getCenterX() - dx, EPSILON);
- assertEquals(model.getElementByElementId("sa3").getCenterY(), copy.getElementByElementId("sa3").getCenterY() - dy, EPSILON);
-
- assertEquals(model.getReactionByReactionId("re3").getLines().get(0).getX2(), copy.getReactionByReactionId("re3").getLines().get(0).getX2() - dx, EPSILON);
- assertEquals(model.getReactionByReactionId("re3").getLines().get(0).getY2(), copy.getReactionByReactionId("re3").getLines().get(0).getY2() - dy, EPSILON);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(copy);
-
- InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
- ModelComparator comparator = new ModelComparator();
-
- // check if after conversion to xml everything works
- assertEquals(0, comparator.compare(copy, copy2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetSubmodelWithoutCompartments() throws Exception {
- try {
- Model model = getModelForFile("testFiles/compartments.xml", true);
-
- Path2D polygon = new Path2D.Double();
- polygon.moveTo(0, 10);
- polygon.lineTo(10, 10);
- polygon.lineTo(10, 0);
- polygon.lineTo(0, 0);
- polygon.closePath();
-
- Model copy = new SubModelCommand(model, polygon).execute();
-
- // we should cut off some of compartmets
- assertFalse(model.getLayers().iterator().next().getTexts().size() == copy.getLayers().iterator().next().getTexts().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetSubmodelWithoutCompartments2() throws Exception {
- try {
- Model model = getModelForFile("testFiles/problematic/cutting_without_compartment.xml", true);
-
- Path2D polygon = new Path2D.Double();
- polygon.moveTo(0, 0);
- polygon.lineTo(0, 500);
- polygon.lineTo(300, 500);
- polygon.lineTo(300, 0);
- polygon.closePath();
-
- Model copy = new SubModelCommand(model, polygon).execute();
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xmlString = parser.toXml(copy);
-
- InputStream stream = new ByteArrayInputStream(xmlString.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
-
- ModelComparator mc = new ModelComparator();
- assertEquals(0, mc.compare(copy, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.commands;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+
+import java.awt.geom.Path2D;
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class SubModelCommandTest extends CommandTestFunctions {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetSubmodel1() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/spliting_test_Case.xml", true);
+
+ Path2D polygon = new Path2D.Double();
+ polygon.moveTo(0, 0);
+ polygon.lineTo(0, 100);
+ polygon.lineTo(100, 100);
+ polygon.lineTo(100, 0);
+ polygon.closePath();
+
+ Model copy = new SubModelCommand(model, polygon).execute();
+
+ assertEquals(2, copy.getElements().size());
+ assertEquals(0, copy.getReactions().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetSubmodel2() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/spliting_test_Case.xml", true);
+
+ Path2D polygon = new Path2D.Double();
+ polygon.moveTo(50, 50);
+ polygon.lineTo(350, 50);
+ polygon.lineTo(350, 200);
+ polygon.lineTo(50, 200);
+ polygon.closePath();
+
+ Model copy = new SubModelCommand(model, polygon).execute();
+
+ assertEquals(9, copy.getElements().size());
+ assertEquals(1, copy.getReactions().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetSubmodel3() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/spliting_test_Case.xml", true);
+
+ Path2D polygon = new Path2D.Double();
+ polygon.moveTo(0, 200);
+ polygon.lineTo(350, 200);
+ polygon.lineTo(350, 400);
+ polygon.lineTo(0, 400);
+ polygon.closePath();
+
+ Model copy = new SubModelCommand(model, polygon).execute();
+
+ double dx = 10;
+ double dy = -10;
+
+ new MoveCommand(copy, dx, dy).execute();
+
+ assertEquals(model.getElementByElementId("sa3").getCenterX(), copy.getElementByElementId("sa3").getCenterX() - dx, EPSILON);
+ assertEquals(model.getElementByElementId("sa3").getCenterY(), copy.getElementByElementId("sa3").getCenterY() - dy, EPSILON);
+
+ assertEquals(model.getReactionByReactionId("re3").getLines().get(0).getX2(), copy.getReactionByReactionId("re3").getLines().get(0).getX2() - dx, EPSILON);
+ assertEquals(model.getReactionByReactionId("re3").getLines().get(0).getY2(), copy.getReactionByReactionId("re3").getLines().get(0).getY2() - dy, EPSILON);
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(copy);
+
+ InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
+ ModelComparator comparator = new ModelComparator();
+
+ // check if after conversion to xml everything works
+ assertEquals(0, comparator.compare(copy, copy2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetSubmodelWithoutCompartments() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/compartments.xml", true);
+
+ Path2D polygon = new Path2D.Double();
+ polygon.moveTo(0, 10);
+ polygon.lineTo(10, 10);
+ polygon.lineTo(10, 0);
+ polygon.lineTo(0, 0);
+ polygon.closePath();
+
+ Model copy = new SubModelCommand(model, polygon).execute();
+
+ // we should cut off some of compartmets
+ assertFalse(model.getLayers().iterator().next().getTexts().size() == copy.getLayers().iterator().next().getTexts().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetSubmodelWithoutCompartments2() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/problematic/cutting_without_compartment.xml", true);
+
+ Path2D polygon = new Path2D.Double();
+ polygon.moveTo(0, 0);
+ polygon.lineTo(0, 500);
+ polygon.lineTo(300, 500);
+ polygon.lineTo(300, 0);
+ polygon.closePath();
+
+ Model copy = new SubModelCommand(model, polygon).execute();
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xmlString = parser.toXml(copy);
+
+ InputStream stream = new ByteArrayInputStream(xmlString.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
+
+ ModelComparator mc = new ModelComparator();
+ assertEquals(0, mc.compare(copy, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/properties/AllPropertyCommandTests.java b/model-command/src/test/java/lcsb/mapviewer/commands/properties/AllPropertyCommandTests.java
index 53f1636b82..3253f2fbbd 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/properties/AllPropertyCommandTests.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/properties/AllPropertyCommandTests.java
@@ -1,23 +1,23 @@
-package lcsb.mapviewer.commands.properties;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ ChangeElementAbbreviationCommandTest.class,//
- ChangeElementColorCommandTest.class,//
- ChangeElementFontSizeCommandTest.class,//
- ChangeElementFormerSymbolCommandTest.class,//
- ChangeElementFormulaCommandTest.class,//
- ChangeElementFullNameCommandTest.class,//
- ChangeElementMiriamDataCommandTest.class,//
- ChangeElementNameCommandTest.class,//
- ChangeElementNotesCommandTest.class,//
- ChangeElementSymbolCommandTest.class,//
- ChangeElementSynonymCommandTest.class,//
-
-})
-public class AllPropertyCommandTests {
-
-}
+package lcsb.mapviewer.commands.properties;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ ChangeElementAbbreviationCommandTest.class,//
+ ChangeElementColorCommandTest.class,//
+ ChangeElementFontSizeCommandTest.class,//
+ ChangeElementFormerSymbolCommandTest.class,//
+ ChangeElementFormulaCommandTest.class,//
+ ChangeElementFullNameCommandTest.class,//
+ ChangeElementMiriamDataCommandTest.class,//
+ ChangeElementNameCommandTest.class,//
+ ChangeElementNotesCommandTest.class,//
+ ChangeElementSymbolCommandTest.class,//
+ ChangeElementSynonymCommandTest.class,//
+
+})
+public class AllPropertyCommandTests {
+
+}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementAbbreviationCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementAbbreviationCommandTest.java
index 3d571c0d55..9ae8adbad7 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementAbbreviationCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementAbbreviationCommandTest.java
@@ -1,75 +1,75 @@
-package lcsb.mapviewer.commands.properties;
-
-import static org.junit.Assert.*;
-import lcsb.mapviewer.commands.CommandTestFunctions;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.species.Element;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ChangeElementAbbreviationCommandTest extends CommandTestFunctions{
-
- Model model;
-
- ModelComparator modelComparator= new ModelComparator();
-
- @Before
- public void setUp() throws Exception {
- model = createSimpleModel();
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testChangeAliasAbbreviation() throws Exception {
- try {
- Element alias = model.getElementByElementId("alias_id");
- ChangeElementAbbreviationCommand command = new ChangeElementAbbreviationCommand(model, alias, "test");
- assertFalse("test".equalsIgnoreCase(alias.getAbbreviation()));
- command.execute();
- assertTrue(alias.getAbbreviation().equalsIgnoreCase("test"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUndo() throws Exception {
- try {
- Model model2 = createSimpleModel();
- Element alias = model.getElementByElementId("alias_id");
-
- // models should be equal before move
- assertEquals(0, modelComparator.compare(model, model2));
-
- ChangeElementAbbreviationCommand command = new ChangeElementAbbreviationCommand(model, alias, "test");
- command.execute();
-
- // after move models should be different
- assertTrue(0 != modelComparator.compare(model, model2));
-
- // undo command
- command.undo();
-
- // after undo they should be the same again
- assertEquals(0, modelComparator.compare(model, model2));
-
- command.redo();
-
- // after redo they should be different again
- assertTrue(0 != modelComparator.compare(model, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.commands.properties;
+
+import static org.junit.Assert.*;
+import lcsb.mapviewer.commands.CommandTestFunctions;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.species.Element;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ChangeElementAbbreviationCommandTest extends CommandTestFunctions{
+
+ Model model;
+
+ ModelComparator modelComparator= new ModelComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ model = createSimpleModel();
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testChangeAliasAbbreviation() throws Exception {
+ try {
+ Element alias = model.getElementByElementId("alias_id");
+ ChangeElementAbbreviationCommand command = new ChangeElementAbbreviationCommand(model, alias, "test");
+ assertFalse("test".equalsIgnoreCase(alias.getAbbreviation()));
+ command.execute();
+ assertTrue(alias.getAbbreviation().equalsIgnoreCase("test"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUndo() throws Exception {
+ try {
+ Model model2 = createSimpleModel();
+ Element alias = model.getElementByElementId("alias_id");
+
+ // models should be equal before move
+ assertEquals(0, modelComparator.compare(model, model2));
+
+ ChangeElementAbbreviationCommand command = new ChangeElementAbbreviationCommand(model, alias, "test");
+ command.execute();
+
+ // after move models should be different
+ assertTrue(0 != modelComparator.compare(model, model2));
+
+ // undo command
+ command.undo();
+
+ // after undo they should be the same again
+ assertEquals(0, modelComparator.compare(model, model2));
+
+ command.redo();
+
+ // after redo they should be different again
+ assertTrue(0 != modelComparator.compare(model, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementColorCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementColorCommandTest.java
index f42942a0dc..f8e0b3c319 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementColorCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementColorCommandTest.java
@@ -1,78 +1,78 @@
-package lcsb.mapviewer.commands.properties;
-
-import static org.junit.Assert.*;
-
-import java.awt.Color;
-
-import lcsb.mapviewer.commands.CommandTestFunctions;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.species.Element;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ChangeElementColorCommandTest extends CommandTestFunctions {
-
- Model model;
-
- ModelComparator modelComparator = new ModelComparator();
-
- @Before
- public void setUp() throws Exception {
- model = createSimpleModel();
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testChangeAliasColor() throws Exception {
- try {
- Element alias = model.getElementByElementId("alias_id");
- ChangeElementColorCommand command = new ChangeElementColorCommand(model, alias, Color.PINK);
- assertFalse(alias.getColor().equals(Color.PINK));
- command.execute();
- assertTrue(alias.getColor().equals(Color.PINK));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUndo() throws Exception {
- try {
- Model model2 = createSimpleModel();
- Element alias = model.getElementByElementId("alias_id");
-
- // models should be equal before move
- assertEquals(0, modelComparator.compare(model, model2));
-
- ChangeElementColorCommand command = new ChangeElementColorCommand(model, alias, Color.PINK);
- command.execute();
-
- // after move models should be different
- assertTrue(0 != modelComparator.compare(model, model2));
-
- // undo command
- command.undo();
-
- // after undo they should be the same again
- assertEquals(0, modelComparator.compare(model, model2));
-
- command.redo();
-
- // after redo they should be different again
- assertTrue(0 != modelComparator.compare(model, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.commands.properties;
+
+import static org.junit.Assert.*;
+
+import java.awt.Color;
+
+import lcsb.mapviewer.commands.CommandTestFunctions;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.species.Element;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ChangeElementColorCommandTest extends CommandTestFunctions {
+
+ Model model;
+
+ ModelComparator modelComparator = new ModelComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ model = createSimpleModel();
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testChangeAliasColor() throws Exception {
+ try {
+ Element alias = model.getElementByElementId("alias_id");
+ ChangeElementColorCommand command = new ChangeElementColorCommand(model, alias, Color.PINK);
+ assertFalse(alias.getColor().equals(Color.PINK));
+ command.execute();
+ assertTrue(alias.getColor().equals(Color.PINK));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUndo() throws Exception {
+ try {
+ Model model2 = createSimpleModel();
+ Element alias = model.getElementByElementId("alias_id");
+
+ // models should be equal before move
+ assertEquals(0, modelComparator.compare(model, model2));
+
+ ChangeElementColorCommand command = new ChangeElementColorCommand(model, alias, Color.PINK);
+ command.execute();
+
+ // after move models should be different
+ assertTrue(0 != modelComparator.compare(model, model2));
+
+ // undo command
+ command.undo();
+
+ // after undo they should be the same again
+ assertEquals(0, modelComparator.compare(model, model2));
+
+ command.redo();
+
+ // after redo they should be different again
+ assertTrue(0 != modelComparator.compare(model, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFontSizeCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFontSizeCommandTest.java
index 99570345e3..29a6e22e21 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFontSizeCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFontSizeCommandTest.java
@@ -1,75 +1,75 @@
-package lcsb.mapviewer.commands.properties;
-
-import static org.junit.Assert.*;
-import lcsb.mapviewer.commands.CommandTestFunctions;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.species.Element;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ChangeElementFontSizeCommandTest extends CommandTestFunctions{
-
- Model model;
-
- ModelComparator modelComparator= new ModelComparator();
-
- @Before
- public void setUp() throws Exception {
- model = createSimpleModel();
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testChangeAliasFontSize() throws Exception {
- try {
- Element alias = model.getElementByElementId("alias_id");
- ChangeElementFontSizeCommand command = new ChangeElementFontSizeCommand(model, alias, 15.0);
- assertFalse(alias.getFontSize().equals(15.0));
- command.execute();
- assertTrue(alias.getFontSize().equals(15.0));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUndo() throws Exception {
- try {
- Model model2 = createSimpleModel();
- Element alias = model.getElementByElementId("alias_id");
-
- // models should be equal before move
- assertEquals(0, modelComparator.compare(model, model2));
-
- ChangeElementFontSizeCommand command = new ChangeElementFontSizeCommand(model, alias, 15.0);
- command.execute();
-
- // after move models should be different
- assertTrue(0 != modelComparator.compare(model, model2));
-
- // undo command
- command.undo();
-
- // after undo they should be the same again
- assertEquals(0, modelComparator.compare(model, model2));
-
- command.redo();
-
- // after redo they should be different again
- assertTrue(0 != modelComparator.compare(model, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.commands.properties;
+
+import static org.junit.Assert.*;
+import lcsb.mapviewer.commands.CommandTestFunctions;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.species.Element;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ChangeElementFontSizeCommandTest extends CommandTestFunctions{
+
+ Model model;
+
+ ModelComparator modelComparator= new ModelComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ model = createSimpleModel();
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testChangeAliasFontSize() throws Exception {
+ try {
+ Element alias = model.getElementByElementId("alias_id");
+ ChangeElementFontSizeCommand command = new ChangeElementFontSizeCommand(model, alias, 15.0);
+ assertFalse(alias.getFontSize().equals(15.0));
+ command.execute();
+ assertTrue(alias.getFontSize().equals(15.0));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUndo() throws Exception {
+ try {
+ Model model2 = createSimpleModel();
+ Element alias = model.getElementByElementId("alias_id");
+
+ // models should be equal before move
+ assertEquals(0, modelComparator.compare(model, model2));
+
+ ChangeElementFontSizeCommand command = new ChangeElementFontSizeCommand(model, alias, 15.0);
+ command.execute();
+
+ // after move models should be different
+ assertTrue(0 != modelComparator.compare(model, model2));
+
+ // undo command
+ command.undo();
+
+ // after undo they should be the same again
+ assertEquals(0, modelComparator.compare(model, model2));
+
+ command.redo();
+
+ // after redo they should be different again
+ assertTrue(0 != modelComparator.compare(model, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFormerSymbolCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFormerSymbolCommandTest.java
index acebff81a6..3d96d5e87d 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFormerSymbolCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFormerSymbolCommandTest.java
@@ -1,44 +1,44 @@
-package lcsb.mapviewer.commands.properties;
-
-import static org.junit.Assert.*;
-import lcsb.mapviewer.commands.CommandTestFunctions;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.species.Element;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ChangeElementFormerSymbolCommandTest extends CommandTestFunctions {
-
- Model model;
-
- ModelComparator modelComparator = new ModelComparator();
-
- @Before
- public void setUp() throws Exception {
- model = createSimpleModel();
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
-
- @Test
- public void testChangeToTheSame() throws Exception {
- try {
- Element alias = model.getElementByElementId("alias_id");
- ChangeElementFormerSymbolCommand command = new ChangeElementFormerSymbolCommand(model, alias, "f_symbol","f_symbol");
- assertTrue(alias.getFormerSymbols().contains("f_symbol"));
- command.execute();
- assertTrue(alias.getFormerSymbols().contains("f_symbol"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.commands.properties;
+
+import static org.junit.Assert.*;
+import lcsb.mapviewer.commands.CommandTestFunctions;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.species.Element;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ChangeElementFormerSymbolCommandTest extends CommandTestFunctions {
+
+ Model model;
+
+ ModelComparator modelComparator = new ModelComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ model = createSimpleModel();
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+
+ @Test
+ public void testChangeToTheSame() throws Exception {
+ try {
+ Element alias = model.getElementByElementId("alias_id");
+ ChangeElementFormerSymbolCommand command = new ChangeElementFormerSymbolCommand(model, alias, "f_symbol","f_symbol");
+ assertTrue(alias.getFormerSymbols().contains("f_symbol"));
+ command.execute();
+ assertTrue(alias.getFormerSymbols().contains("f_symbol"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFormulaCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFormulaCommandTest.java
index 3417b371cc..d4a9b62beb 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFormulaCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFormulaCommandTest.java
@@ -1,75 +1,75 @@
-package lcsb.mapviewer.commands.properties;
-
-import static org.junit.Assert.*;
-import lcsb.mapviewer.commands.CommandTestFunctions;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.species.Element;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ChangeElementFormulaCommandTest extends CommandTestFunctions{
-
- Model model;
-
- ModelComparator modelComparator= new ModelComparator();
-
- @Before
- public void setUp() throws Exception {
- model = createSimpleModel();
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testChangeAliasFormula() throws Exception {
- try {
- Element alias = model.getElementByElementId("alias_id");
- ChangeElementFormulaCommand command = new ChangeElementFormulaCommand(model, alias, "test");
- assertFalse("test".equals(alias.getFormula()));
- command.execute();
- assertTrue(alias.getFormula().equalsIgnoreCase("test"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUndo() throws Exception {
- try {
- Model model2 = createSimpleModel();
- Element alias = model.getElementByElementId("alias_id");
-
- // models should be equal before move
- assertEquals(0, modelComparator.compare(model, model2));
-
- ChangeElementFormulaCommand command = new ChangeElementFormulaCommand(model, alias, "test");
- command.execute();
-
- // after move models should be different
- assertTrue(0 != modelComparator.compare(model, model2));
-
- // undo command
- command.undo();
-
- // after undo they should be the same again
- assertEquals(0, modelComparator.compare(model, model2));
-
- command.redo();
-
- // after redo they should be different again
- assertTrue(0 != modelComparator.compare(model, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.commands.properties;
+
+import static org.junit.Assert.*;
+import lcsb.mapviewer.commands.CommandTestFunctions;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.species.Element;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ChangeElementFormulaCommandTest extends CommandTestFunctions{
+
+ Model model;
+
+ ModelComparator modelComparator= new ModelComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ model = createSimpleModel();
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testChangeAliasFormula() throws Exception {
+ try {
+ Element alias = model.getElementByElementId("alias_id");
+ ChangeElementFormulaCommand command = new ChangeElementFormulaCommand(model, alias, "test");
+ assertFalse("test".equals(alias.getFormula()));
+ command.execute();
+ assertTrue(alias.getFormula().equalsIgnoreCase("test"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUndo() throws Exception {
+ try {
+ Model model2 = createSimpleModel();
+ Element alias = model.getElementByElementId("alias_id");
+
+ // models should be equal before move
+ assertEquals(0, modelComparator.compare(model, model2));
+
+ ChangeElementFormulaCommand command = new ChangeElementFormulaCommand(model, alias, "test");
+ command.execute();
+
+ // after move models should be different
+ assertTrue(0 != modelComparator.compare(model, model2));
+
+ // undo command
+ command.undo();
+
+ // after undo they should be the same again
+ assertEquals(0, modelComparator.compare(model, model2));
+
+ command.redo();
+
+ // after redo they should be different again
+ assertTrue(0 != modelComparator.compare(model, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFullNameCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFullNameCommandTest.java
index 2be5eb71b5..48647ec2c7 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFullNameCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementFullNameCommandTest.java
@@ -1,75 +1,75 @@
-package lcsb.mapviewer.commands.properties;
-
-import static org.junit.Assert.*;
-import lcsb.mapviewer.commands.CommandTestFunctions;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.species.Element;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ChangeElementFullNameCommandTest extends CommandTestFunctions{
-
- Model model;
-
- ModelComparator modelComparator= new ModelComparator();
-
- @Before
- public void setUp() throws Exception {
- model = createSimpleModel();
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testChangeAliasFullName() throws Exception {
- try {
- Element alias = model.getElementByElementId("alias_id");
- ChangeElementFullNameCommand command = new ChangeElementFullNameCommand(model, alias, "test");
- assertFalse("test".equals(alias.getFullName()));
- command.execute();
- assertTrue(alias.getFullName().equalsIgnoreCase("test"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUndo() throws Exception {
- try {
- Model model2 = createSimpleModel();
- Element alias = model.getElementByElementId("alias_id");
-
- // models should be equal before move
- assertEquals(0, modelComparator.compare(model, model2));
-
- ChangeElementFullNameCommand command = new ChangeElementFullNameCommand(model, alias, "test");
- command.execute();
-
- // after move models should be different
- assertTrue(0 != modelComparator.compare(model, model2));
-
- // undo command
- command.undo();
-
- // after undo they should be the same again
- assertEquals(0, modelComparator.compare(model, model2));
-
- command.redo();
-
- // after redo they should be different again
- assertTrue(0 != modelComparator.compare(model, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.commands.properties;
+
+import static org.junit.Assert.*;
+import lcsb.mapviewer.commands.CommandTestFunctions;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.species.Element;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ChangeElementFullNameCommandTest extends CommandTestFunctions{
+
+ Model model;
+
+ ModelComparator modelComparator= new ModelComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ model = createSimpleModel();
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testChangeAliasFullName() throws Exception {
+ try {
+ Element alias = model.getElementByElementId("alias_id");
+ ChangeElementFullNameCommand command = new ChangeElementFullNameCommand(model, alias, "test");
+ assertFalse("test".equals(alias.getFullName()));
+ command.execute();
+ assertTrue(alias.getFullName().equalsIgnoreCase("test"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUndo() throws Exception {
+ try {
+ Model model2 = createSimpleModel();
+ Element alias = model.getElementByElementId("alias_id");
+
+ // models should be equal before move
+ assertEquals(0, modelComparator.compare(model, model2));
+
+ ChangeElementFullNameCommand command = new ChangeElementFullNameCommand(model, alias, "test");
+ command.execute();
+
+ // after move models should be different
+ assertTrue(0 != modelComparator.compare(model, model2));
+
+ // undo command
+ command.undo();
+
+ // after undo they should be the same again
+ assertEquals(0, modelComparator.compare(model, model2));
+
+ command.redo();
+
+ // after redo they should be different again
+ assertTrue(0 != modelComparator.compare(model, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementMiriamDataCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementMiriamDataCommandTest.java
index 423ae61121..b00c1a0919 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementMiriamDataCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementMiriamDataCommandTest.java
@@ -1,88 +1,88 @@
-package lcsb.mapviewer.commands.properties;
-
-import static org.junit.Assert.*;
-import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.commands.CommandTestFunctions;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ChangeElementMiriamDataCommandTest extends CommandTestFunctions {
-
- Model model;
-
- @Before
- public void setUp() throws Exception {
- model = createSimpleModel();
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testWithoutChange() throws Exception {
- try {
- Element alias = model.getElementByElementId("alias_id");
- MiriamData md = new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA");
- MiriamData md2 = new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA");
- alias.addMiriamData(md);
- ChangeElementMiriamDataCommand command = new ChangeElementMiriamDataCommand(model, alias, md2, md);
- command.execute();
- assertTrue(alias.getMiriamData().contains(md2));
- assertEquals(1, alias.getMiriamData().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidChange() throws Exception {
- try {
- Element alias = model.getElementByElementId("alias_id");
- MiriamData md = new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA");
- MiriamData md2 = new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA2");
- alias.addMiriamData(md);
- alias.addMiriamData(md2);
- ChangeElementMiriamDataCommand command = new ChangeElementMiriamDataCommand(model, alias, md2, md);
- try {
- command.execute();
- fail("Exception expected");
- } catch (CommandExecutionException e) {
- assertTrue(alias.getMiriamData().contains(md));
- assertTrue(alias.getMiriamData().contains(md2));
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
- @Test
- public void testChange() throws Exception {
- try {
- Element alias = model.getElementByElementId("alias_id");
- MiriamData md = new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA");
- MiriamData md2 = new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA2");
- MiriamData md3 = new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA");
- alias.addMiriamData(md);
- ChangeElementMiriamDataCommand command = new ChangeElementMiriamDataCommand(model, alias, md2, md);
- command.execute();
- assertTrue(alias.getMiriamData().contains(md2));
- assertFalse(alias.getMiriamData().contains(md3));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.commands.properties;
+
+import static org.junit.Assert.*;
+import lcsb.mapviewer.commands.CommandExecutionException;
+import lcsb.mapviewer.commands.CommandTestFunctions;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ChangeElementMiriamDataCommandTest extends CommandTestFunctions {
+
+ Model model;
+
+ @Before
+ public void setUp() throws Exception {
+ model = createSimpleModel();
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testWithoutChange() throws Exception {
+ try {
+ Element alias = model.getElementByElementId("alias_id");
+ MiriamData md = new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA");
+ MiriamData md2 = new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA");
+ alias.addMiriamData(md);
+ ChangeElementMiriamDataCommand command = new ChangeElementMiriamDataCommand(model, alias, md2, md);
+ command.execute();
+ assertTrue(alias.getMiriamData().contains(md2));
+ assertEquals(1, alias.getMiriamData().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidChange() throws Exception {
+ try {
+ Element alias = model.getElementByElementId("alias_id");
+ MiriamData md = new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA");
+ MiriamData md2 = new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA2");
+ alias.addMiriamData(md);
+ alias.addMiriamData(md2);
+ ChangeElementMiriamDataCommand command = new ChangeElementMiriamDataCommand(model, alias, md2, md);
+ try {
+ command.execute();
+ fail("Exception expected");
+ } catch (CommandExecutionException e) {
+ assertTrue(alias.getMiriamData().contains(md));
+ assertTrue(alias.getMiriamData().contains(md2));
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
+ @Test
+ public void testChange() throws Exception {
+ try {
+ Element alias = model.getElementByElementId("alias_id");
+ MiriamData md = new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA");
+ MiriamData md2 = new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA2");
+ MiriamData md3 = new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA");
+ alias.addMiriamData(md);
+ ChangeElementMiriamDataCommand command = new ChangeElementMiriamDataCommand(model, alias, md2, md);
+ command.execute();
+ assertTrue(alias.getMiriamData().contains(md2));
+ assertFalse(alias.getMiriamData().contains(md3));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementNameCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementNameCommandTest.java
index c4a801bdd4..a8d6643ba8 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementNameCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementNameCommandTest.java
@@ -1,77 +1,77 @@
-package lcsb.mapviewer.commands.properties;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-import lcsb.mapviewer.commands.CommandTestFunctions;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.species.Element;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ChangeElementNameCommandTest extends CommandTestFunctions {
-
- Model model;
-
- ModelComparator modelComparator= new ModelComparator();
-
- @Before
- public void setUp() throws Exception {
- model = createSimpleModel();
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testChangeAliasName() throws Exception {
- try {
- Element alias = model.getElementByElementId("alias_id");
- ChangeElementNameCommand command = new ChangeElementNameCommand(model, alias, "test");
- assertFalse(alias.getName().equalsIgnoreCase("test"));
- command.execute();
- assertTrue(alias.getName().equalsIgnoreCase("test"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUndo() throws Exception {
- try {
- Model model2 = createSimpleModel();
- Element alias = model.getElementByElementId("alias_id");
-
- // models should be equal before move
- assertEquals(0, modelComparator.compare(model, model2));
-
- ChangeElementNameCommand command = new ChangeElementNameCommand(model, alias, "test");
- command.execute();
-
- // after move models should be different
- assertTrue(0 != modelComparator.compare(model, model2));
-
- // undo command
- command.undo();
-
- // after undo they should be the same again
- assertEquals(0, modelComparator.compare(model, model2));
-
- command.redo();
-
- // after redo they should be different again
- assertTrue(0 != modelComparator.compare(model, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.commands.properties;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+import lcsb.mapviewer.commands.CommandTestFunctions;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.species.Element;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ChangeElementNameCommandTest extends CommandTestFunctions {
+
+ Model model;
+
+ ModelComparator modelComparator= new ModelComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ model = createSimpleModel();
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testChangeAliasName() throws Exception {
+ try {
+ Element alias = model.getElementByElementId("alias_id");
+ ChangeElementNameCommand command = new ChangeElementNameCommand(model, alias, "test");
+ assertFalse(alias.getName().equalsIgnoreCase("test"));
+ command.execute();
+ assertTrue(alias.getName().equalsIgnoreCase("test"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUndo() throws Exception {
+ try {
+ Model model2 = createSimpleModel();
+ Element alias = model.getElementByElementId("alias_id");
+
+ // models should be equal before move
+ assertEquals(0, modelComparator.compare(model, model2));
+
+ ChangeElementNameCommand command = new ChangeElementNameCommand(model, alias, "test");
+ command.execute();
+
+ // after move models should be different
+ assertTrue(0 != modelComparator.compare(model, model2));
+
+ // undo command
+ command.undo();
+
+ // after undo they should be the same again
+ assertEquals(0, modelComparator.compare(model, model2));
+
+ command.redo();
+
+ // after redo they should be different again
+ assertTrue(0 != modelComparator.compare(model, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementNotesCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementNotesCommandTest.java
index e14108358e..a2189d27ae 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementNotesCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementNotesCommandTest.java
@@ -1,75 +1,75 @@
-package lcsb.mapviewer.commands.properties;
-
-import static org.junit.Assert.*;
-import lcsb.mapviewer.commands.CommandTestFunctions;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.species.Element;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ChangeElementNotesCommandTest extends CommandTestFunctions{
-
- Model model;
-
- ModelComparator modelComparator= new ModelComparator();
-
- @Before
- public void setUp() throws Exception {
- model = createSimpleModel();
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testChangeAliasNotes() throws Exception {
- try {
- Element alias = model.getElementByElementId("alias_id");
- ChangeElementNotesCommand command = new ChangeElementNotesCommand(model, alias, "test");
- assertFalse("test".equals(alias.getNotes()));
- command.execute();
- assertTrue(alias.getNotes().equalsIgnoreCase("test"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUndo() throws Exception {
- try {
- Model model2 = createSimpleModel();
- Element alias = model.getElementByElementId("alias_id");
-
- // models should be equal before move
- assertEquals(0, modelComparator.compare(model, model2));
-
- ChangeElementNotesCommand command = new ChangeElementNotesCommand(model, alias, "test");
- command.execute();
-
- // after move models should be different
- assertTrue(0 != modelComparator.compare(model, model2));
-
- // undo command
- command.undo();
-
- // after undo they should be the same again
- assertEquals(0, modelComparator.compare(model, model2));
-
- command.redo();
-
- // after redo they should be different again
- assertTrue(0 != modelComparator.compare(model, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.commands.properties;
+
+import static org.junit.Assert.*;
+import lcsb.mapviewer.commands.CommandTestFunctions;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.species.Element;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ChangeElementNotesCommandTest extends CommandTestFunctions{
+
+ Model model;
+
+ ModelComparator modelComparator= new ModelComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ model = createSimpleModel();
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testChangeAliasNotes() throws Exception {
+ try {
+ Element alias = model.getElementByElementId("alias_id");
+ ChangeElementNotesCommand command = new ChangeElementNotesCommand(model, alias, "test");
+ assertFalse("test".equals(alias.getNotes()));
+ command.execute();
+ assertTrue(alias.getNotes().equalsIgnoreCase("test"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUndo() throws Exception {
+ try {
+ Model model2 = createSimpleModel();
+ Element alias = model.getElementByElementId("alias_id");
+
+ // models should be equal before move
+ assertEquals(0, modelComparator.compare(model, model2));
+
+ ChangeElementNotesCommand command = new ChangeElementNotesCommand(model, alias, "test");
+ command.execute();
+
+ // after move models should be different
+ assertTrue(0 != modelComparator.compare(model, model2));
+
+ // undo command
+ command.undo();
+
+ // after undo they should be the same again
+ assertEquals(0, modelComparator.compare(model, model2));
+
+ command.redo();
+
+ // after redo they should be different again
+ assertTrue(0 != modelComparator.compare(model, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementSymbolCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementSymbolCommandTest.java
index 091ca65d9b..721358b838 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementSymbolCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementSymbolCommandTest.java
@@ -1,75 +1,75 @@
-package lcsb.mapviewer.commands.properties;
-
-import static org.junit.Assert.*;
-import lcsb.mapviewer.commands.CommandTestFunctions;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.species.Element;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ChangeElementSymbolCommandTest extends CommandTestFunctions{
-
- Model model;
-
- ModelComparator modelComparator= new ModelComparator();
-
- @Before
- public void setUp() throws Exception {
- model = createSimpleModel();
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testChangeAliasSymbol() throws Exception {
- try {
- Element alias = model.getElementByElementId("alias_id");
- ChangeElementSymbolCommand command = new ChangeElementSymbolCommand(model, alias, "test");
- assertFalse("test".equals(alias.getSymbol()));
- command.execute();
- assertTrue(alias.getSymbol().equalsIgnoreCase("test"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUndo() throws Exception {
- try {
- Model model2 = createSimpleModel();
- Element alias = model.getElementByElementId("alias_id");
-
- // models should be equal before move
- assertEquals(0, modelComparator.compare(model, model2));
-
- ChangeElementSymbolCommand command = new ChangeElementSymbolCommand(model, alias, "test");
- command.execute();
-
- // after move models should be different
- assertTrue(0 != modelComparator.compare(model, model2));
-
- // undo command
- command.undo();
-
- // after undo they should be the same again
- assertEquals(0, modelComparator.compare(model, model2));
-
- command.redo();
-
- // after redo they should be different again
- assertTrue(0 != modelComparator.compare(model, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.commands.properties;
+
+import static org.junit.Assert.*;
+import lcsb.mapviewer.commands.CommandTestFunctions;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.species.Element;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ChangeElementSymbolCommandTest extends CommandTestFunctions{
+
+ Model model;
+
+ ModelComparator modelComparator= new ModelComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ model = createSimpleModel();
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testChangeAliasSymbol() throws Exception {
+ try {
+ Element alias = model.getElementByElementId("alias_id");
+ ChangeElementSymbolCommand command = new ChangeElementSymbolCommand(model, alias, "test");
+ assertFalse("test".equals(alias.getSymbol()));
+ command.execute();
+ assertTrue(alias.getSymbol().equalsIgnoreCase("test"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUndo() throws Exception {
+ try {
+ Model model2 = createSimpleModel();
+ Element alias = model.getElementByElementId("alias_id");
+
+ // models should be equal before move
+ assertEquals(0, modelComparator.compare(model, model2));
+
+ ChangeElementSymbolCommand command = new ChangeElementSymbolCommand(model, alias, "test");
+ command.execute();
+
+ // after move models should be different
+ assertTrue(0 != modelComparator.compare(model, model2));
+
+ // undo command
+ command.undo();
+
+ // after undo they should be the same again
+ assertEquals(0, modelComparator.compare(model, model2));
+
+ command.redo();
+
+ // after redo they should be different again
+ assertTrue(0 != modelComparator.compare(model, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementSynonymCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementSynonymCommandTest.java
index 5ff47be58e..6cad5a9b42 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementSynonymCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementSynonymCommandTest.java
@@ -1,90 +1,90 @@
-package lcsb.mapviewer.commands.properties;
-
-import static org.junit.Assert.*;
-import lcsb.mapviewer.commands.CommandTestFunctions;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.species.Element;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ChangeElementSynonymCommandTest extends CommandTestFunctions {
-
- Model model;
-
- ModelComparator modelComparator = new ModelComparator();
-
- @Before
- public void setUp() throws Exception {
- model = createSimpleModel();
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testChangeAliasSynonym() throws Exception {
- try {
- Element alias = model.getElementByElementId("alias_id");
- ChangeElementSynonymCommand command = new ChangeElementSynonymCommand(model, alias, "test","synonym");
- assertFalse(alias.getSynonyms().contains("test"));
- command.execute();
- assertTrue(alias.getSynonyms().contains("test"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testChangeToTheSame() throws Exception {
- try {
- Element alias = model.getElementByElementId("alias_id");
- ChangeElementSynonymCommand command = new ChangeElementSynonymCommand(model, alias, "synonym","synonym");
- assertTrue(alias.getSynonyms().contains("synonym"));
- command.execute();
- assertTrue(alias.getSynonyms().contains("synonym"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUndo() throws Exception {
- try {
- Model model2 = createSimpleModel();
- Element alias = model.getElementByElementId("alias_id");
-
- // models should be equal before move
- assertEquals(0, modelComparator.compare(model, model2));
-
- ChangeElementSynonymCommand command = new ChangeElementSynonymCommand(model, alias, "test", "synonym");
- command.execute();
-
- // after move models should be different
- assertTrue(0 != modelComparator.compare(model, model2));
-
- // undo command
- command.undo();
-
- // after undo they should be the same again
- assertEquals(0, modelComparator.compare(model, model2));
-
- command.redo();
-
- // after redo they should be different again
- assertTrue(0 != modelComparator.compare(model, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.commands.properties;
+
+import static org.junit.Assert.*;
+import lcsb.mapviewer.commands.CommandTestFunctions;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.species.Element;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ChangeElementSynonymCommandTest extends CommandTestFunctions {
+
+ Model model;
+
+ ModelComparator modelComparator = new ModelComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ model = createSimpleModel();
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testChangeAliasSynonym() throws Exception {
+ try {
+ Element alias = model.getElementByElementId("alias_id");
+ ChangeElementSynonymCommand command = new ChangeElementSynonymCommand(model, alias, "test","synonym");
+ assertFalse(alias.getSynonyms().contains("test"));
+ command.execute();
+ assertTrue(alias.getSynonyms().contains("test"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testChangeToTheSame() throws Exception {
+ try {
+ Element alias = model.getElementByElementId("alias_id");
+ ChangeElementSynonymCommand command = new ChangeElementSynonymCommand(model, alias, "synonym","synonym");
+ assertTrue(alias.getSynonyms().contains("synonym"));
+ command.execute();
+ assertTrue(alias.getSynonyms().contains("synonym"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUndo() throws Exception {
+ try {
+ Model model2 = createSimpleModel();
+ Element alias = model.getElementByElementId("alias_id");
+
+ // models should be equal before move
+ assertEquals(0, modelComparator.compare(model, model2));
+
+ ChangeElementSynonymCommand command = new ChangeElementSynonymCommand(model, alias, "test", "synonym");
+ command.execute();
+
+ // after move models should be different
+ assertTrue(0 != modelComparator.compare(model, model2));
+
+ // undo command
+ command.undo();
+
+ // after undo they should be the same again
+ assertEquals(0, modelComparator.compare(model, model2));
+
+ command.redo();
+
+ // after redo they should be different again
+ assertTrue(0 != modelComparator.compare(model, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/Project.java b/model/src/main/java/lcsb/mapviewer/model/Project.java
index 1d829734bb..52ce21efdb 100644
--- a/model/src/main/java/lcsb/mapviewer/model/Project.java
+++ b/model/src/main/java/lcsb/mapviewer/model/Project.java
@@ -1,625 +1,625 @@
-package lcsb.mapviewer.model;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.EnumType;
-import javax.persistence.Enumerated;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.OneToMany;
-import javax.persistence.OneToOne;
-import javax.persistence.OrderBy;
-import javax.persistence.Table;
-
-import org.apache.log4j.Appender;
-import org.apache.log4j.Logger;
-import org.apache.log4j.spi.LoggingEvent;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-import org.hibernate.annotations.LazyCollection;
-import org.hibernate.annotations.LazyCollectionOption;
-
-import lcsb.mapviewer.common.EventStorageLoggerAppender;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.cache.UploadedFileEntry;
-import lcsb.mapviewer.model.graphics.MapCanvasType;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.OverviewImage;
-import lcsb.mapviewer.model.map.OverviewImageLink;
-import lcsb.mapviewer.model.map.OverviewLink;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
-
-/**
- * Top level structure in the system. It describes single project and contains
- * all data in it.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "project_table")
-public class Project implements Serializable {
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(Project.class);
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Unique database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- /**
- * Project identifier defined by the user (some meaningful string).
- */
- @Column(name = "project_id", unique = true, nullable = false)
- private String projectId;
-
- /**
- * Project disease.
- */
- @Cascade({ CascadeType.ALL })
- @OneToOne
- private MiriamData disease;
-
- /**
- * Name of the project.
- */
- private String name;
-
- /**
- * Version of the project.
- */
- private String version;
-
- /**
- * Email of the user who should be notified when some serious modification to
- * the map were performed.
- */
- private String notifyEmail;
-
- /**
- * Directory where the images on the server will be stored for this project.
- */
- private String directory;
-
- /**
- * Status of the project used during uploading the project to the system.
- */
- @Enumerated(EnumType.STRING)
- private ProjectStatus status = ProjectStatus.UNKNOWN;
-
- /**
- * Progress of single step of project uploading.
- */
- private double progress = 0;
-
- /**
- * Errors connected with the project.
- */
- private String errors = null;
-
- /**
- * Short description of the map.
- */
- @Column(columnDefinition = "TEXT")
- private String warnings;
-
- /**
- * Which "maps" implementation should be used for frontend visualization.
- */
- @Enumerated(EnumType.STRING)
- @Column(name = "map_canvas_type")
- private MapCanvasType mapCanvasType = MapCanvasType.OPEN_LAYERS;
-
- @Column(name = "google_map_license_accept_date")
- private Calendar googleMapLicenseAcceptDate;
-
- /**
- * Map models in the project.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(mappedBy = "project", orphanRemoval = true)
- private Set<ModelData> models = new HashSet<>();
-
- /**
- * Here we store input file.
- */
- @Cascade({ CascadeType.SAVE_UPDATE })
- @OneToOne(fetch = FetchType.LAZY)
- @JoinColumn(name = "file_entry_iddb")
- private UploadedFileEntry inputData;
-
- /**
- * Organism associated with the project.
- */
- @Cascade({ CascadeType.ALL })
- @OneToOne
- private MiriamData organism;
-
- /**
- * SBGN format selection. Set, if map is to be displayed in SBGN format
- */
- private boolean sbgnFormat = false;
-
- /**
- * List of overview images describing this {@link Project}. The elements on the
- * list can create a hierarchy that describe dependencies, however now matter if
- * the image is a top-level object or a leaf it should be placed on this list.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(mappedBy = "project", orphanRemoval = true)
- @OrderBy("id")
- @LazyCollection(LazyCollectionOption.FALSE)
- private List<OverviewImage> overviewImages = new ArrayList<>();
-
- /**
- * Default constructor.
- */
- public Project() {
- }
-
- /**
- * Constructor with the project name in the parameter.
- *
- * @param projectName
- * name of the project
- */
- public Project(String projectName) {
- this.projectId = projectName;
- }
-
- /**
- * Adds map model to the project.
- *
- * @param model
- * map to be added
- */
- public void addModel(ModelData model) {
- models.add(model);
- model.setProject(this);
- }
-
- /**
- * Adds map model to the project.
- *
- * @param model
- * map to be added
- */
- public void addModel(Model model) {
- models.add(model.getModelData());
- model.setProject(this);
- }
-
- /**
- * Removes map model from the project.
- *
- * @param model
- * map model to remove
- */
- public void removeModel(ModelData model) {
- models.remove(model);
- }
-
- /**
- * @return the id
- * @see #id
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
- /**
- * @return user defined project identifier
- * @see #projectId
- */
- public String getProjectId() {
- return projectId;
- }
-
- /**
- * @param projectId
- * user defined project identifier
- * @see #projectId
- */
- public void setProjectId(String projectId) {
- this.projectId = projectId;
- }
-
- /**
- * @return the status
- * @see #status
- */
- public ProjectStatus getStatus() {
- return status;
- }
-
- /**
- * @param status
- * the status to set
- * @see #status
- */
- public void setStatus(ProjectStatus status) {
- this.status = status;
- }
-
- /**
- * @return the progress
- * @see #progress
- */
- public double getProgress() {
- return progress;
- }
-
- /**
- * @param progress
- * the progress to set
- * @see #progress
- */
- public void setProgress(double progress) {
- this.progress = progress;
- }
-
- /**
- * @return the models
- * @see #models
- */
- public Set<ModelData> getModels() {
- return models;
- }
-
- /**
- * @param models
- * the models to set
- * @see #models
- */
- public void setModels(Set<ModelData> models) {
- this.models = models;
- }
-
- /**
- * @return the errors
- * @see #errors
- */
- public String getErrors() {
- return errors;
- }
-
- /**
- * @param errors
- * the errors to set
- * @see #errors
- */
- public void setErrors(String errors) {
- this.errors = errors;
- }
-
- /**
- * @return the directory
- * @see #directory
- */
- public String getDirectory() {
- return directory;
- }
-
- /**
- * @param directory
- * the directory to set
- * @see #directory
- */
- public void setDirectory(String directory) {
- this.directory = directory;
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return disease
- */
- public MiriamData getDisease() {
- return disease;
- }
-
- /**
- * @param disease
- * the disease
- */
- public void setDisease(MiriamData disease) {
- this.disease = disease;
- }
-
- /**
- * @param organism
- * the organism to set
- * @see #organism
- */
- public void setOrganism(MiriamData organism) {
- this.organism = organism;
- }
-
- /**
- * @return the organism
- * @see #organism
- */
- public MiriamData getOrganism() {
- return organism;
- }
-
- /**
- * Adds a warning to a list of warnings generated during model creation.
- *
- * @param warning
- * warning to add
- */
- public void addWarning(String warning) {
- if (warning.trim().contains("\n")) {
- throw new InvalidArgumentException("Warning must be one line of text");
- }
- if (warning.trim().equals("")) {
- return;
- }
- if (warnings == null) {
- warnings = warning.trim();
- } else {
- warnings = warnings + "\n" + warning.trim();
- }
- }
-
- /**
- * Returns list of warnings set during creation of mode.
- *
- * @return list of warnings set during creation of mode
- */
- public List<String> getWarnings() {
- List<String> result = new ArrayList<>();
- if (warnings == null) {
- return result;
- }
- String[] warningsArray = warnings.split("\n");
- for (String string : warningsArray) {
- result.add(string);
- }
- return result;
- }
-
- /**
- * Adds warnings to a list of warnings generated during model creation.
- *
- * @param warnings
- * list of warnings to add
- */
- public void addWarnings(List<String> warnings) {
- StringBuilder sb = new StringBuilder("");
- if (this.warnings != null) {
- sb.append(this.warnings);
- }
- for (String string : warnings) {
- if (string.trim().equals("")) {
- continue;
- }
- if (string.contains("\n")) {
- throw new InvalidArgumentException("Warning must be one line of text, but found:\n" + string);
- }
- if (sb.length() > 0) {
- sb.append("\n");
- }
- sb.append(string.trim());
- }
- if (sb.length() != 0) {
- this.warnings = sb.toString();
- }
- }
-
- /**
- * Adds warning log information to a project.
- *
- * @param appender
- * {@link Appender log4j appender} that gathered logs
- */
- public void addLoggingInfo(EventStorageLoggerAppender appender) {
- List<String> warnings = new ArrayList<>();
- for (LoggingEvent event : appender.getWarnings()) {
- if (event.getMessage() instanceof String) {
- warnings.add(((String) event.getMessage()).replaceAll("\n", "_NEW_LINE_"));
- } else {
- logger.warn("Unknown message class: " + event.getClass());
- }
- }
- addWarnings(warnings);
- }
-
- /**
- * @return the sbgnFormat
- * @see #sbgnFormat
- */
- public boolean isSbgnFormat() {
- return sbgnFormat;
- }
-
- /**
- * @param sbgnFormat
- * the sbgnFormat to set
- * @see #sbgnFormat
- */
- public void setSbgnFormat(boolean sbgnFormat) {
- this.sbgnFormat = sbgnFormat;
- }
-
- /**
- * @return the version
- * @see #version
- */
- public String getVersion() {
- return version;
- }
-
- /**
- * @param version
- * the version to set
- * @see #version
- */
- public void setVersion(String version) {
- this.version = version;
- }
-
- /**
- * @return the overviewImages
- * @see #overviewImages
- */
- public List<OverviewImage> getOverviewImages() {
- return overviewImages;
- }
-
- /**
- * @param overviewImages
- * the overviewImages to set
- * @see #overviewImages
- */
- public void setOverviewImages(List<OverviewImage> overviewImages) {
- this.overviewImages = overviewImages;
- for (OverviewImage overviewImage : overviewImages) {
- overviewImage.setProject(this);
- }
- }
-
- /**
- * Returns top level {@link OverviewImage} that should be present as a first one
- * when switching to view data by the overview images.
- *
- * @return top level {@link OverviewImage}
- */
- public OverviewImage getTopOverviewImage() {
- Set<OverviewImage> set = new HashSet<OverviewImage>();
- set.addAll(getOverviewImages());
- for (OverviewImage image : getOverviewImages()) {
- for (OverviewLink ol : image.getLinks()) {
- if (ol instanceof OverviewImageLink) {
- set.remove(((OverviewImageLink) ol).getLinkedOverviewImage());
- }
- }
- }
- if (set.size() > 0) {
- return set.iterator().next();
- } else if (getOverviewImages().size() > 0) {
- logger.warn("Cannot determine top level image. Taking first one: " + getOverviewImages().get(0).getFilename());
- return getOverviewImages().get(0);
- } else {
- return null;
- }
- }
-
- public void addOverviewImage(OverviewImage oi) {
- this.overviewImages.add(oi);
- oi.setProject(this);
- }
-
- public void addOverviewImages(List<OverviewImage> parseOverviewLinks) {
- for (OverviewImage overviewImage : parseOverviewLinks) {
- this.addOverviewImage(overviewImage);
- }
-
- }
-
- /**
- * @return the inputData
- * @see #inputData
- */
- public UploadedFileEntry getInputData() {
- return inputData;
- }
-
- /**
- * @param inputData
- * the inputData to set
- * @see #inputData
- */
- public void setInputData(UploadedFileEntry inputData) {
- this.inputData = inputData;
- }
-
- /**
- * @return the notifyEmail
- * @see #notifyEmail
- */
- public String getNotifyEmail() {
- return notifyEmail;
- }
-
- /**
- * @param notifyEmail
- * the notifyEmail to set
- * @see #notifyEmail
- */
- public void setNotifyEmail(String notifyEmail) {
- this.notifyEmail = notifyEmail;
- }
-
- public MapCanvasType getMapCanvasType() {
- return mapCanvasType;
- }
-
- public void setMapCanvasType(MapCanvasType mapCanvasType) {
- MapCanvasType oldMapCanvasType = this.mapCanvasType;
- this.mapCanvasType = mapCanvasType;
- if (!mapCanvasType.equals(oldMapCanvasType)) {
- if (mapCanvasType.equals(MapCanvasType.GOOGLE_MAPS_API)) {
- this.setGoogleMapLicenseAcceptDate(Calendar.getInstance());
- } else {
- this.setGoogleMapLicenseAcceptDate(null);
- }
- }
- }
-
- public Calendar getGoogleMapLicenseAcceptDate() {
- return googleMapLicenseAcceptDate;
- }
-
- public void setGoogleMapLicenseAcceptDate(Calendar googleMapLicenseAcceptDate) {
- this.googleMapLicenseAcceptDate = googleMapLicenseAcceptDate;
- }
-
-}
+package lcsb.mapviewer.model;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Calendar;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.EnumType;
+import javax.persistence.Enumerated;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.OneToMany;
+import javax.persistence.OneToOne;
+import javax.persistence.OrderBy;
+import javax.persistence.Table;
+
+import org.apache.log4j.Appender;
+import org.apache.log4j.Logger;
+import org.apache.log4j.spi.LoggingEvent;
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+import org.hibernate.annotations.LazyCollection;
+import org.hibernate.annotations.LazyCollectionOption;
+
+import lcsb.mapviewer.common.EventStorageLoggerAppender;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
+import lcsb.mapviewer.model.graphics.MapCanvasType;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.OverviewImage;
+import lcsb.mapviewer.model.map.OverviewImageLink;
+import lcsb.mapviewer.model.map.OverviewLink;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+
+/**
+ * Top level structure in the system. It describes single project and contains
+ * all data in it.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "project_table")
+public class Project implements Serializable {
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(Project.class);
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Unique database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * Project identifier defined by the user (some meaningful string).
+ */
+ @Column(name = "project_id", unique = true, nullable = false)
+ private String projectId;
+
+ /**
+ * Project disease.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToOne
+ private MiriamData disease;
+
+ /**
+ * Name of the project.
+ */
+ private String name;
+
+ /**
+ * Version of the project.
+ */
+ private String version;
+
+ /**
+ * Email of the user who should be notified when some serious modification to
+ * the map were performed.
+ */
+ private String notifyEmail;
+
+ /**
+ * Directory where the images on the server will be stored for this project.
+ */
+ private String directory;
+
+ /**
+ * Status of the project used during uploading the project to the system.
+ */
+ @Enumerated(EnumType.STRING)
+ private ProjectStatus status = ProjectStatus.UNKNOWN;
+
+ /**
+ * Progress of single step of project uploading.
+ */
+ private double progress = 0;
+
+ /**
+ * Errors connected with the project.
+ */
+ private String errors = null;
+
+ /**
+ * Short description of the map.
+ */
+ @Column(columnDefinition = "TEXT")
+ private String warnings;
+
+ /**
+ * Which "maps" implementation should be used for frontend visualization.
+ */
+ @Enumerated(EnumType.STRING)
+ @Column(name = "map_canvas_type")
+ private MapCanvasType mapCanvasType = MapCanvasType.OPEN_LAYERS;
+
+ @Column(name = "google_map_license_accept_date")
+ private Calendar googleMapLicenseAcceptDate;
+
+ /**
+ * Map models in the project.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(mappedBy = "project", orphanRemoval = true)
+ private Set<ModelData> models = new HashSet<>();
+
+ /**
+ * Here we store input file.
+ */
+ @Cascade({ CascadeType.SAVE_UPDATE })
+ @OneToOne(fetch = FetchType.LAZY)
+ @JoinColumn(name = "file_entry_iddb")
+ private UploadedFileEntry inputData;
+
+ /**
+ * Organism associated with the project.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToOne
+ private MiriamData organism;
+
+ /**
+ * SBGN format selection. Set, if map is to be displayed in SBGN format
+ */
+ private boolean sbgnFormat = false;
+
+ /**
+ * List of overview images describing this {@link Project}. The elements on the
+ * list can create a hierarchy that describe dependencies, however now matter if
+ * the image is a top-level object or a leaf it should be placed on this list.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(mappedBy = "project", orphanRemoval = true)
+ @OrderBy("id")
+ @LazyCollection(LazyCollectionOption.FALSE)
+ private List<OverviewImage> overviewImages = new ArrayList<>();
+
+ /**
+ * Default constructor.
+ */
+ public Project() {
+ }
+
+ /**
+ * Constructor with the project name in the parameter.
+ *
+ * @param projectName
+ * name of the project
+ */
+ public Project(String projectName) {
+ this.projectId = projectName;
+ }
+
+ /**
+ * Adds map model to the project.
+ *
+ * @param model
+ * map to be added
+ */
+ public void addModel(ModelData model) {
+ models.add(model);
+ model.setProject(this);
+ }
+
+ /**
+ * Adds map model to the project.
+ *
+ * @param model
+ * map to be added
+ */
+ public void addModel(Model model) {
+ models.add(model.getModelData());
+ model.setProject(this);
+ }
+
+ /**
+ * Removes map model from the project.
+ *
+ * @param model
+ * map model to remove
+ */
+ public void removeModel(ModelData model) {
+ models.remove(model);
+ }
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ /**
+ * @return user defined project identifier
+ * @see #projectId
+ */
+ public String getProjectId() {
+ return projectId;
+ }
+
+ /**
+ * @param projectId
+ * user defined project identifier
+ * @see #projectId
+ */
+ public void setProjectId(String projectId) {
+ this.projectId = projectId;
+ }
+
+ /**
+ * @return the status
+ * @see #status
+ */
+ public ProjectStatus getStatus() {
+ return status;
+ }
+
+ /**
+ * @param status
+ * the status to set
+ * @see #status
+ */
+ public void setStatus(ProjectStatus status) {
+ this.status = status;
+ }
+
+ /**
+ * @return the progress
+ * @see #progress
+ */
+ public double getProgress() {
+ return progress;
+ }
+
+ /**
+ * @param progress
+ * the progress to set
+ * @see #progress
+ */
+ public void setProgress(double progress) {
+ this.progress = progress;
+ }
+
+ /**
+ * @return the models
+ * @see #models
+ */
+ public Set<ModelData> getModels() {
+ return models;
+ }
+
+ /**
+ * @param models
+ * the models to set
+ * @see #models
+ */
+ public void setModels(Set<ModelData> models) {
+ this.models = models;
+ }
+
+ /**
+ * @return the errors
+ * @see #errors
+ */
+ public String getErrors() {
+ return errors;
+ }
+
+ /**
+ * @param errors
+ * the errors to set
+ * @see #errors
+ */
+ public void setErrors(String errors) {
+ this.errors = errors;
+ }
+
+ /**
+ * @return the directory
+ * @see #directory
+ */
+ public String getDirectory() {
+ return directory;
+ }
+
+ /**
+ * @param directory
+ * the directory to set
+ * @see #directory
+ */
+ public void setDirectory(String directory) {
+ this.directory = directory;
+ }
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * @return disease
+ */
+ public MiriamData getDisease() {
+ return disease;
+ }
+
+ /**
+ * @param disease
+ * the disease
+ */
+ public void setDisease(MiriamData disease) {
+ this.disease = disease;
+ }
+
+ /**
+ * @param organism
+ * the organism to set
+ * @see #organism
+ */
+ public void setOrganism(MiriamData organism) {
+ this.organism = organism;
+ }
+
+ /**
+ * @return the organism
+ * @see #organism
+ */
+ public MiriamData getOrganism() {
+ return organism;
+ }
+
+ /**
+ * Adds a warning to a list of warnings generated during model creation.
+ *
+ * @param warning
+ * warning to add
+ */
+ public void addWarning(String warning) {
+ if (warning.trim().contains("\n")) {
+ throw new InvalidArgumentException("Warning must be one line of text");
+ }
+ if (warning.trim().equals("")) {
+ return;
+ }
+ if (warnings == null) {
+ warnings = warning.trim();
+ } else {
+ warnings = warnings + "\n" + warning.trim();
+ }
+ }
+
+ /**
+ * Returns list of warnings set during creation of mode.
+ *
+ * @return list of warnings set during creation of mode
+ */
+ public List<String> getWarnings() {
+ List<String> result = new ArrayList<>();
+ if (warnings == null) {
+ return result;
+ }
+ String[] warningsArray = warnings.split("\n");
+ for (String string : warningsArray) {
+ result.add(string);
+ }
+ return result;
+ }
+
+ /**
+ * Adds warnings to a list of warnings generated during model creation.
+ *
+ * @param warnings
+ * list of warnings to add
+ */
+ public void addWarnings(List<String> warnings) {
+ StringBuilder sb = new StringBuilder("");
+ if (this.warnings != null) {
+ sb.append(this.warnings);
+ }
+ for (String string : warnings) {
+ if (string.trim().equals("")) {
+ continue;
+ }
+ if (string.contains("\n")) {
+ throw new InvalidArgumentException("Warning must be one line of text, but found:\n" + string);
+ }
+ if (sb.length() > 0) {
+ sb.append("\n");
+ }
+ sb.append(string.trim());
+ }
+ if (sb.length() != 0) {
+ this.warnings = sb.toString();
+ }
+ }
+
+ /**
+ * Adds warning log information to a project.
+ *
+ * @param appender
+ * {@link Appender log4j appender} that gathered logs
+ */
+ public void addLoggingInfo(EventStorageLoggerAppender appender) {
+ List<String> warnings = new ArrayList<>();
+ for (LoggingEvent event : appender.getWarnings()) {
+ if (event.getMessage() instanceof String) {
+ warnings.add(((String) event.getMessage()).replaceAll("\n", "_NEW_LINE_"));
+ } else {
+ logger.warn("Unknown message class: " + event.getClass());
+ }
+ }
+ addWarnings(warnings);
+ }
+
+ /**
+ * @return the sbgnFormat
+ * @see #sbgnFormat
+ */
+ public boolean isSbgnFormat() {
+ return sbgnFormat;
+ }
+
+ /**
+ * @param sbgnFormat
+ * the sbgnFormat to set
+ * @see #sbgnFormat
+ */
+ public void setSbgnFormat(boolean sbgnFormat) {
+ this.sbgnFormat = sbgnFormat;
+ }
+
+ /**
+ * @return the version
+ * @see #version
+ */
+ public String getVersion() {
+ return version;
+ }
+
+ /**
+ * @param version
+ * the version to set
+ * @see #version
+ */
+ public void setVersion(String version) {
+ this.version = version;
+ }
+
+ /**
+ * @return the overviewImages
+ * @see #overviewImages
+ */
+ public List<OverviewImage> getOverviewImages() {
+ return overviewImages;
+ }
+
+ /**
+ * @param overviewImages
+ * the overviewImages to set
+ * @see #overviewImages
+ */
+ public void setOverviewImages(List<OverviewImage> overviewImages) {
+ this.overviewImages = overviewImages;
+ for (OverviewImage overviewImage : overviewImages) {
+ overviewImage.setProject(this);
+ }
+ }
+
+ /**
+ * Returns top level {@link OverviewImage} that should be present as a first one
+ * when switching to view data by the overview images.
+ *
+ * @return top level {@link OverviewImage}
+ */
+ public OverviewImage getTopOverviewImage() {
+ Set<OverviewImage> set = new HashSet<OverviewImage>();
+ set.addAll(getOverviewImages());
+ for (OverviewImage image : getOverviewImages()) {
+ for (OverviewLink ol : image.getLinks()) {
+ if (ol instanceof OverviewImageLink) {
+ set.remove(((OverviewImageLink) ol).getLinkedOverviewImage());
+ }
+ }
+ }
+ if (set.size() > 0) {
+ return set.iterator().next();
+ } else if (getOverviewImages().size() > 0) {
+ logger.warn("Cannot determine top level image. Taking first one: " + getOverviewImages().get(0).getFilename());
+ return getOverviewImages().get(0);
+ } else {
+ return null;
+ }
+ }
+
+ public void addOverviewImage(OverviewImage oi) {
+ this.overviewImages.add(oi);
+ oi.setProject(this);
+ }
+
+ public void addOverviewImages(List<OverviewImage> parseOverviewLinks) {
+ for (OverviewImage overviewImage : parseOverviewLinks) {
+ this.addOverviewImage(overviewImage);
+ }
+
+ }
+
+ /**
+ * @return the inputData
+ * @see #inputData
+ */
+ public UploadedFileEntry getInputData() {
+ return inputData;
+ }
+
+ /**
+ * @param inputData
+ * the inputData to set
+ * @see #inputData
+ */
+ public void setInputData(UploadedFileEntry inputData) {
+ this.inputData = inputData;
+ }
+
+ /**
+ * @return the notifyEmail
+ * @see #notifyEmail
+ */
+ public String getNotifyEmail() {
+ return notifyEmail;
+ }
+
+ /**
+ * @param notifyEmail
+ * the notifyEmail to set
+ * @see #notifyEmail
+ */
+ public void setNotifyEmail(String notifyEmail) {
+ this.notifyEmail = notifyEmail;
+ }
+
+ public MapCanvasType getMapCanvasType() {
+ return mapCanvasType;
+ }
+
+ public void setMapCanvasType(MapCanvasType mapCanvasType) {
+ MapCanvasType oldMapCanvasType = this.mapCanvasType;
+ this.mapCanvasType = mapCanvasType;
+ if (!mapCanvasType.equals(oldMapCanvasType)) {
+ if (mapCanvasType.equals(MapCanvasType.GOOGLE_MAPS_API)) {
+ this.setGoogleMapLicenseAcceptDate(Calendar.getInstance());
+ } else {
+ this.setGoogleMapLicenseAcceptDate(null);
+ }
+ }
+ }
+
+ public Calendar getGoogleMapLicenseAcceptDate() {
+ return googleMapLicenseAcceptDate;
+ }
+
+ public void setGoogleMapLicenseAcceptDate(Calendar googleMapLicenseAcceptDate) {
+ this.googleMapLicenseAcceptDate = googleMapLicenseAcceptDate;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/ProjectStatus.java b/model/src/main/java/lcsb/mapviewer/model/ProjectStatus.java
index f3b2d02eee..a59e22ca3f 100644
--- a/model/src/main/java/lcsb/mapviewer/model/ProjectStatus.java
+++ b/model/src/main/java/lcsb/mapviewer/model/ProjectStatus.java
@@ -1,103 +1,103 @@
-package lcsb.mapviewer.model;
-
-/**
- * Defines possible statuses when uploading project into system.
- *
- * @author Piotr Gawron
- *
- */
-public enum ProjectStatus {
-
- /**
- * Unknown status.
- */
- UNKNOWN("uninitialized"),
-
- /**
- * Data are parsed by the CellDesigner parser.
- */
- PARSING_DATA("Parsing data"),
-
- /**
- * Model is annotated by the annotation tool.
- */
- ANNOTATING("Annotating"),
-
- /**
- * Model is being uploaded to the database.
- */
- UPLOADING_TO_DB("Uploading to db"),
-
- /**
- * Images for the projects are being generated.
- */
- GENERATING_IMAGES("Generating images"),
-
- /**
- * Data that are linked to pubmed articles are being cached.
- */
- CACHING("Caching pubmed data"),
-
- /**
- * Project is ready to use.
- */
- DONE("Ok"),
-
- /**
- * There was problem during project creation.
- */
- FAIL("Failure"),
-
- /**
- * Data that are linked to miriam are being cached.
- */
- CACHING_MIRIAM("Caching miriam data"),
-
- /**
- * Miriam data validation.
- */
- VALIDATING_MIRIAM("Validating miriam data"),
-
- /**
- * Removing of the project.
- */
- REMOVING("Project removing"),
-
- /**
- * All chemicals that can be found by map elements are cached.
- */
- CACHING_CHEMICAL("Caching chemical data"),
-
- /**
- * All drugs that can be found by map elements are cached.
- */
- CACHING_DRUG("Caching drug data"),
-
- /**
- * All mirna that can be found by map elements are cached.
- */
- CACHING_MI_RNA("Caching miRNA data");
-
- /**
- * Message used to present the status on the client side.
- */
- private String readableString;
-
- /**
- * Default constructor of the enum with {@link #readableString} parameter.
- *
- * @param readableForm
- * {@link #readableString}
- */
- ProjectStatus(String readableForm) {
- this.readableString = readableForm;
- }
-
- /**
- * @return {@link #readableString}
- */
- public String toString() {
- return readableString;
- }
-
-}
+package lcsb.mapviewer.model;
+
+/**
+ * Defines possible statuses when uploading project into system.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum ProjectStatus {
+
+ /**
+ * Unknown status.
+ */
+ UNKNOWN("uninitialized"),
+
+ /**
+ * Data are parsed by the CellDesigner parser.
+ */
+ PARSING_DATA("Parsing data"),
+
+ /**
+ * Model is annotated by the annotation tool.
+ */
+ ANNOTATING("Annotating"),
+
+ /**
+ * Model is being uploaded to the database.
+ */
+ UPLOADING_TO_DB("Uploading to db"),
+
+ /**
+ * Images for the projects are being generated.
+ */
+ GENERATING_IMAGES("Generating images"),
+
+ /**
+ * Data that are linked to pubmed articles are being cached.
+ */
+ CACHING("Caching pubmed data"),
+
+ /**
+ * Project is ready to use.
+ */
+ DONE("Ok"),
+
+ /**
+ * There was problem during project creation.
+ */
+ FAIL("Failure"),
+
+ /**
+ * Data that are linked to miriam are being cached.
+ */
+ CACHING_MIRIAM("Caching miriam data"),
+
+ /**
+ * Miriam data validation.
+ */
+ VALIDATING_MIRIAM("Validating miriam data"),
+
+ /**
+ * Removing of the project.
+ */
+ REMOVING("Project removing"),
+
+ /**
+ * All chemicals that can be found by map elements are cached.
+ */
+ CACHING_CHEMICAL("Caching chemical data"),
+
+ /**
+ * All drugs that can be found by map elements are cached.
+ */
+ CACHING_DRUG("Caching drug data"),
+
+ /**
+ * All mirna that can be found by map elements are cached.
+ */
+ CACHING_MI_RNA("Caching miRNA data");
+
+ /**
+ * Message used to present the status on the client side.
+ */
+ private String readableString;
+
+ /**
+ * Default constructor of the enum with {@link #readableString} parameter.
+ *
+ * @param readableForm
+ * {@link #readableString}
+ */
+ ProjectStatus(String readableForm) {
+ this.readableString = readableForm;
+ }
+
+ /**
+ * @return {@link #readableString}
+ */
+ public String toString() {
+ return readableString;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/cache/BigFileEntry.java b/model/src/main/java/lcsb/mapviewer/model/cache/BigFileEntry.java
index a56b7c135b..460b07ec14 100644
--- a/model/src/main/java/lcsb/mapviewer/model/cache/BigFileEntry.java
+++ b/model/src/main/java/lcsb/mapviewer/model/cache/BigFileEntry.java
@@ -1,116 +1,116 @@
-package lcsb.mapviewer.model.cache;
-
-import java.io.Serializable;
-import java.util.Calendar;
-
-import javax.persistence.Column;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.IProgressUpdater;
-
-/**
- * Database object representing big file cached in filesystem.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("BIG_FILE_ENTRY")
-public class BigFileEntry extends FileEntry implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Url from which file was obtained.
- */
- @Column(columnDefinition = "TEXT")
- private String url;
-
- /**
- * When file was downloaded.
- */
- private Calendar downloadDate;
-
- /**
- * What is the download progress (value between 0 and
- * {@link IProgressUpdater#MAX_PROGRESS 100}).
- */
- private Double downloadProgress;
-
- /**
- * {@link Thread} identifier that is downloading the file.
- */
- private Long downloadThreadId;
-
- /**
- * @return the url
- * @see #url
- */
- public String getUrl() {
- return url;
- }
-
- /**
- * @param url
- * the url to set
- * @see #url
- */
- public void setUrl(String url) {
- this.url = url;
- }
-
- /**
- * @return the downloadDate
- * @see #downloadDate
- */
- public Calendar getDownloadDate() {
- return downloadDate;
- }
-
- /**
- * @param downloadDate
- * the downloadDate to set
- * @see #downloadDate
- */
- public void setDownloadDate(Calendar downloadDate) {
- this.downloadDate = downloadDate;
- }
-
- /**
- * @return the downloadProgress
- * @see #downloadProgress
- */
- public Double getDownloadProgress() {
- return downloadProgress;
- }
-
- /**
- * @param downloadProgress
- * the downloadProgress to set
- * @see #downloadProgress
- */
- public void setDownloadProgress(Double downloadProgress) {
- this.downloadProgress = downloadProgress;
- }
-
- /**
- * @return the downloadThreadId
- * @see #downloadThreadId
- */
- public Long getDownloadThreadId() {
- return downloadThreadId;
- }
-
- /**
- * @param downloadThreadId
- * the downloadThreadId to set
- * @see #downloadThreadId
- */
- public void setDownloadThreadId(Long downloadThreadId) {
- this.downloadThreadId = downloadThreadId;
- }
-
-}
+package lcsb.mapviewer.model.cache;
+
+import java.io.Serializable;
+import java.util.Calendar;
+
+import javax.persistence.Column;
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.IProgressUpdater;
+
+/**
+ * Database object representing big file cached in filesystem.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("BIG_FILE_ENTRY")
+public class BigFileEntry extends FileEntry implements Serializable {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Url from which file was obtained.
+ */
+ @Column(columnDefinition = "TEXT")
+ private String url;
+
+ /**
+ * When file was downloaded.
+ */
+ private Calendar downloadDate;
+
+ /**
+ * What is the download progress (value between 0 and
+ * {@link IProgressUpdater#MAX_PROGRESS 100}).
+ */
+ private Double downloadProgress;
+
+ /**
+ * {@link Thread} identifier that is downloading the file.
+ */
+ private Long downloadThreadId;
+
+ /**
+ * @return the url
+ * @see #url
+ */
+ public String getUrl() {
+ return url;
+ }
+
+ /**
+ * @param url
+ * the url to set
+ * @see #url
+ */
+ public void setUrl(String url) {
+ this.url = url;
+ }
+
+ /**
+ * @return the downloadDate
+ * @see #downloadDate
+ */
+ public Calendar getDownloadDate() {
+ return downloadDate;
+ }
+
+ /**
+ * @param downloadDate
+ * the downloadDate to set
+ * @see #downloadDate
+ */
+ public void setDownloadDate(Calendar downloadDate) {
+ this.downloadDate = downloadDate;
+ }
+
+ /**
+ * @return the downloadProgress
+ * @see #downloadProgress
+ */
+ public Double getDownloadProgress() {
+ return downloadProgress;
+ }
+
+ /**
+ * @param downloadProgress
+ * the downloadProgress to set
+ * @see #downloadProgress
+ */
+ public void setDownloadProgress(Double downloadProgress) {
+ this.downloadProgress = downloadProgress;
+ }
+
+ /**
+ * @return the downloadThreadId
+ * @see #downloadThreadId
+ */
+ public Long getDownloadThreadId() {
+ return downloadThreadId;
+ }
+
+ /**
+ * @param downloadThreadId
+ * the downloadThreadId to set
+ * @see #downloadThreadId
+ */
+ public void setDownloadThreadId(Long downloadThreadId) {
+ this.downloadThreadId = downloadThreadId;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/cache/CacheQuery.java b/model/src/main/java/lcsb/mapviewer/model/cache/CacheQuery.java
index ec3c7826f3..3e8a2d997e 100644
--- a/model/src/main/java/lcsb/mapviewer/model/cache/CacheQuery.java
+++ b/model/src/main/java/lcsb/mapviewer/model/cache/CacheQuery.java
@@ -1,184 +1,184 @@
-package lcsb.mapviewer.model.cache;
-
-import java.io.Serializable;
-import java.util.Calendar;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Temporal;
-import javax.persistence.TemporalType;
-
-/**
- * Object that defines cached value retrieved from external resource. The key in
- * external resource can be any String.
- *
- * @author Piotr Gawron
- *
- * @see CacheEntry
- *
- */
-@Entity
-public class CacheQuery implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Unique local database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- /**
- * Unique external identifier. It can contain any String (for instance url to
- * a webpage), however shorter strings are prefered due to performance
- * reasons.
- */
- @Column(name = "query", columnDefinition = "TEXT")
- private String query;
-
- /**
- * Value in the external resource.
- */
- @Column(name = "value", columnDefinition = "TEXT")
- private String value;
-
- /**
- * What kind of resource. Type allows to refresh value from original resource
- * if needed
- */
- @Column(nullable = false)
- private Integer type;
-
- /**
- * When the value expires.
- */
- @Column
- @Temporal(TemporalType.TIMESTAMP)
- private Calendar expires = Calendar.getInstance();
-
- /**
- * When this value was accessed.
- */
- @Column
- @Temporal(TemporalType.TIMESTAMP)
- private Calendar accessed = Calendar.getInstance();
-
- /**
- * @return the id
- * @see #id
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
- /**
- * @return the query
- * @see #query
- */
- public String getQuery() {
- return query;
- }
-
- /**
- * @param query
- * the query to set
- * @see #query
- */
- public void setQuery(String query) {
- this.query = query;
- }
-
- /**
- * @return the value
- * @see #value
- */
- public String getValue() {
- return value;
- }
-
- /**
- * @param value
- * the value to set
- * @see #value
- */
- public void setValue(String value) {
- this.value = value;
- }
-
- /**
- * @return the type
- * @see #type
- */
- public Integer getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(Integer type) {
- this.type = type;
- }
-
- /**
- * @return the expires
- * @see #expires
- */
- public Calendar getExpires() {
- return expires;
- }
-
- /**
- * @param expires
- * the expires to set
- * @see #expires
- */
- public void setExpires(Calendar expires) {
- this.expires = expires;
- }
-
- /**
- * @return the accessed
- * @see #accessed
- */
- public Calendar getAccessed() {
- return accessed;
- }
-
- /**
- * @param accessed
- * the accessed to set
- * @see #accessed
- */
- public void setAccessed(Calendar accessed) {
- this.accessed = accessed;
- }
-
- /**
- *
- * @param type2
- * new {@link #type} value
- */
- public void setType(CacheType type2) {
- this.type = type2.getId();
- }
-
-}
+package lcsb.mapviewer.model.cache;
+
+import java.io.Serializable;
+import java.util.Calendar;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.Temporal;
+import javax.persistence.TemporalType;
+
+/**
+ * Object that defines cached value retrieved from external resource. The key in
+ * external resource can be any String.
+ *
+ * @author Piotr Gawron
+ *
+ * @see CacheEntry
+ *
+ */
+@Entity
+public class CacheQuery implements Serializable {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Unique local database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * Unique external identifier. It can contain any String (for instance url to
+ * a webpage), however shorter strings are prefered due to performance
+ * reasons.
+ */
+ @Column(name = "query", columnDefinition = "TEXT")
+ private String query;
+
+ /**
+ * Value in the external resource.
+ */
+ @Column(name = "value", columnDefinition = "TEXT")
+ private String value;
+
+ /**
+ * What kind of resource. Type allows to refresh value from original resource
+ * if needed
+ */
+ @Column(nullable = false)
+ private Integer type;
+
+ /**
+ * When the value expires.
+ */
+ @Column
+ @Temporal(TemporalType.TIMESTAMP)
+ private Calendar expires = Calendar.getInstance();
+
+ /**
+ * When this value was accessed.
+ */
+ @Column
+ @Temporal(TemporalType.TIMESTAMP)
+ private Calendar accessed = Calendar.getInstance();
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ /**
+ * @return the query
+ * @see #query
+ */
+ public String getQuery() {
+ return query;
+ }
+
+ /**
+ * @param query
+ * the query to set
+ * @see #query
+ */
+ public void setQuery(String query) {
+ this.query = query;
+ }
+
+ /**
+ * @return the value
+ * @see #value
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * @param value
+ * the value to set
+ * @see #value
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ /**
+ * @return the type
+ * @see #type
+ */
+ public Integer getType() {
+ return type;
+ }
+
+ /**
+ * @param type
+ * the type to set
+ * @see #type
+ */
+ public void setType(Integer type) {
+ this.type = type;
+ }
+
+ /**
+ * @return the expires
+ * @see #expires
+ */
+ public Calendar getExpires() {
+ return expires;
+ }
+
+ /**
+ * @param expires
+ * the expires to set
+ * @see #expires
+ */
+ public void setExpires(Calendar expires) {
+ this.expires = expires;
+ }
+
+ /**
+ * @return the accessed
+ * @see #accessed
+ */
+ public Calendar getAccessed() {
+ return accessed;
+ }
+
+ /**
+ * @param accessed
+ * the accessed to set
+ * @see #accessed
+ */
+ public void setAccessed(Calendar accessed) {
+ this.accessed = accessed;
+ }
+
+ /**
+ *
+ * @param type2
+ * new {@link #type} value
+ */
+ public void setType(CacheType type2) {
+ this.type = type2.getId();
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/cache/CacheType.java b/model/src/main/java/lcsb/mapviewer/model/cache/CacheType.java
index 0807d3e244..c2adbeface 100644
--- a/model/src/main/java/lcsb/mapviewer/model/cache/CacheType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/cache/CacheType.java
@@ -1,102 +1,102 @@
-package lcsb.mapviewer.model.cache;
-
-import java.io.Serializable;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Table;
-
-/**
- * Defines types of objects stored in the cache and interfaces used for
- * refreshing them.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "cache_type")
-public class CacheType implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Class of object that will refresh the data of given type.
- */
- private String className;
-
- /**
- * Unique local database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- /**
- * How many days cached value is valid.
- */
- private int validity;
-
- /**
- * @return the validity
- * @see #validity
- */
- public int getValidity() {
- return validity;
- }
-
- /**
- * @param validity
- * the validity to set
- * @see #validity
- */
- public void setValidity(int validity) {
- this.validity = validity;
- }
-
- /**
- * @return the className
- * @see #className
- */
- public String getClassName() {
- return className;
- }
-
- /**
- * @param className
- * the className to set
- * @see #className
- */
- public void setClassName(String className) {
- this.className = className;
- }
-
- /**
- * @return the id
- * @see #id
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
- @Override
- public String toString() {
- return className + " [id: " + id + "]";
- }
-
-}
+package lcsb.mapviewer.model.cache;
+
+import java.io.Serializable;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.Table;
+
+/**
+ * Defines types of objects stored in the cache and interfaces used for
+ * refreshing them.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "cache_type")
+public class CacheType implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Class of object that will refresh the data of given type.
+ */
+ private String className;
+
+ /**
+ * Unique local database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * How many days cached value is valid.
+ */
+ private int validity;
+
+ /**
+ * @return the validity
+ * @see #validity
+ */
+ public int getValidity() {
+ return validity;
+ }
+
+ /**
+ * @param validity
+ * the validity to set
+ * @see #validity
+ */
+ public void setValidity(int validity) {
+ this.validity = validity;
+ }
+
+ /**
+ * @return the className
+ * @see #className
+ */
+ public String getClassName() {
+ return className;
+ }
+
+ /**
+ * @param className
+ * the className to set
+ * @see #className
+ */
+ public void setClassName(String className) {
+ this.className = className;
+ }
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ @Override
+ public String toString() {
+ return className + " [id: " + id + "]";
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/cache/FileEntry.java b/model/src/main/java/lcsb/mapviewer/model/cache/FileEntry.java
index 2f7cfb037a..7d3ceb0d41 100644
--- a/model/src/main/java/lcsb/mapviewer/model/cache/FileEntry.java
+++ b/model/src/main/java/lcsb/mapviewer/model/cache/FileEntry.java
@@ -1,172 +1,172 @@
-package lcsb.mapviewer.model.cache;
-
-import java.io.Serializable;
-
-import javax.persistence.Column;
-import javax.persistence.DiscriminatorColumn;
-import javax.persistence.DiscriminatorType;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Inheritance;
-import javax.persistence.InheritanceType;
-import javax.persistence.Table;
-
-/**
- * Database object representing file put in the system (it can be some cached
- * file, or uploaded file). There are two ways of storing file. First is by
- * storing the content in database directly (in the {@link #fileContent}
- * field). Second way should be used for all big files - it stores content in
- * the local file system (relative path is stored in {@link #localPath} field).
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "file_entry")
-@Inheritance(strategy = InheritanceType.SINGLE_TABLE)
-@DiscriminatorColumn(name = "file_type_db", discriminatorType = DiscriminatorType.STRING)
-public abstract class FileEntry implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Unique local database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- /**
- * Local (relative) path where file is stored.
- */
- @Column(columnDefinition = "TEXT")
- private String localPath;
-
- /**
- * Original name of the file.
- */
- private String originalFileName;
-
- /**
- * Is the file removed from databse.
- */
- private boolean removed = false;
-
- /**
- * Content of the file. If set to null it means it stored in filesystem.
- *
- * @see #localPath
- */
- private byte[] fileContent;
-
- /**
- * Constructor that copies data from the parameter.
- *
- * @param inputData
- * original object from which data will bbe copied
- */
- public FileEntry(FileEntry inputData) {
- setLocalPath(inputData.getLocalPath());
- setOriginalFileName(inputData.getOriginalFileName());
- setRemoved(inputData.isRemoved());
- if (inputData.getFileContent() != null) {
- setFileContent(inputData.getFileContent().clone());
- }
- }
-
- /**
- * Default constructor.
- */
- public FileEntry() {
- }
-
- /**
- * @return the localPath
- * @see #localPath
- */
- public String getLocalPath() {
- return localPath;
- }
-
- /**
- * @param localPath
- * the localPath to set
- * @see #localPath
- */
- public void setLocalPath(String localPath) {
- this.localPath = localPath;
- }
-
- /**
- * @return the id
- * @see #id
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
- /**
- * @return the removed
- * @see #removed
- */
- public boolean isRemoved() {
- return removed;
- }
-
- /**
- * @param removed
- * the removed to set
- * @see #removed
- */
- public void setRemoved(boolean removed) {
- this.removed = removed;
- }
-
- /**
- * @return the fileContent
- * @see #fileContent
- */
- public byte[] getFileContent() {
- return fileContent;
- }
-
- /**
- * @param fileContent
- * the fileContent to set
- * @see #fileContent
- */
- public void setFileContent(byte[] fileContent) {
- this.fileContent = fileContent;
- }
-
- /**
- * @return the originalFileName
- * @see #originalFileName
- */
- public String getOriginalFileName() {
- return originalFileName;
- }
-
- /**
- * @param originalFileName
- * the originalFileName to set
- * @see #originalFileName
- */
- public void setOriginalFileName(String originalFileName) {
- this.originalFileName = originalFileName;
- }
-}
+package lcsb.mapviewer.model.cache;
+
+import java.io.Serializable;
+
+import javax.persistence.Column;
+import javax.persistence.DiscriminatorColumn;
+import javax.persistence.DiscriminatorType;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.Inheritance;
+import javax.persistence.InheritanceType;
+import javax.persistence.Table;
+
+/**
+ * Database object representing file put in the system (it can be some cached
+ * file, or uploaded file). There are two ways of storing file. First is by
+ * storing the content in database directly (in the {@link #fileContent}
+ * field). Second way should be used for all big files - it stores content in
+ * the local file system (relative path is stored in {@link #localPath} field).
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "file_entry")
+@Inheritance(strategy = InheritanceType.SINGLE_TABLE)
+@DiscriminatorColumn(name = "file_type_db", discriminatorType = DiscriminatorType.STRING)
+public abstract class FileEntry implements Serializable {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Unique local database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * Local (relative) path where file is stored.
+ */
+ @Column(columnDefinition = "TEXT")
+ private String localPath;
+
+ /**
+ * Original name of the file.
+ */
+ private String originalFileName;
+
+ /**
+ * Is the file removed from databse.
+ */
+ private boolean removed = false;
+
+ /**
+ * Content of the file. If set to null it means it stored in filesystem.
+ *
+ * @see #localPath
+ */
+ private byte[] fileContent;
+
+ /**
+ * Constructor that copies data from the parameter.
+ *
+ * @param inputData
+ * original object from which data will bbe copied
+ */
+ public FileEntry(FileEntry inputData) {
+ setLocalPath(inputData.getLocalPath());
+ setOriginalFileName(inputData.getOriginalFileName());
+ setRemoved(inputData.isRemoved());
+ if (inputData.getFileContent() != null) {
+ setFileContent(inputData.getFileContent().clone());
+ }
+ }
+
+ /**
+ * Default constructor.
+ */
+ public FileEntry() {
+ }
+
+ /**
+ * @return the localPath
+ * @see #localPath
+ */
+ public String getLocalPath() {
+ return localPath;
+ }
+
+ /**
+ * @param localPath
+ * the localPath to set
+ * @see #localPath
+ */
+ public void setLocalPath(String localPath) {
+ this.localPath = localPath;
+ }
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ /**
+ * @return the removed
+ * @see #removed
+ */
+ public boolean isRemoved() {
+ return removed;
+ }
+
+ /**
+ * @param removed
+ * the removed to set
+ * @see #removed
+ */
+ public void setRemoved(boolean removed) {
+ this.removed = removed;
+ }
+
+ /**
+ * @return the fileContent
+ * @see #fileContent
+ */
+ public byte[] getFileContent() {
+ return fileContent;
+ }
+
+ /**
+ * @param fileContent
+ * the fileContent to set
+ * @see #fileContent
+ */
+ public void setFileContent(byte[] fileContent) {
+ this.fileContent = fileContent;
+ }
+
+ /**
+ * @return the originalFileName
+ * @see #originalFileName
+ */
+ public String getOriginalFileName() {
+ return originalFileName;
+ }
+
+ /**
+ * @param originalFileName
+ * the originalFileName to set
+ * @see #originalFileName
+ */
+ public void setOriginalFileName(String originalFileName) {
+ this.originalFileName = originalFileName;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/cache/UploadedFileEntry.java b/model/src/main/java/lcsb/mapviewer/model/cache/UploadedFileEntry.java
index acecea373d..05d024494f 100644
--- a/model/src/main/java/lcsb/mapviewer/model/cache/UploadedFileEntry.java
+++ b/model/src/main/java/lcsb/mapviewer/model/cache/UploadedFileEntry.java
@@ -1,68 +1,68 @@
-package lcsb.mapviewer.model.cache;
-
-import java.io.Serializable;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.ManyToOne;
-
-import lcsb.mapviewer.model.user.User;
-
-/**
- * Database object representing file uploaded into system.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("UPLOADED_FILE_ENTRY")
-public class UploadedFileEntry extends FileEntry implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Length of the file.
- */
- private long length;
-
- @ManyToOne(fetch = FetchType.LAZY)
- private User owner;
-
- /**
- * Default constructor.
- */
- public UploadedFileEntry() {
-
- }
-
- /**
- * Constructor that copies data from the parameter.
- *
- * @param original
- * original object from which data will bbe copied
- */
- public UploadedFileEntry(UploadedFileEntry original) {
- super(original);
- }
-
- public long getLength() {
- return length;
- }
-
- public void setLength(long length) {
- this.length = length;
- }
-
- public User getOwner() {
- return owner;
- }
-
- public void setOwner(User owner) {
- this.owner = owner;
- }
-
-}
+package lcsb.mapviewer.model.cache;
+
+import java.io.Serializable;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.ManyToOne;
+
+import lcsb.mapviewer.model.user.User;
+
+/**
+ * Database object representing file uploaded into system.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("UPLOADED_FILE_ENTRY")
+public class UploadedFileEntry extends FileEntry implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Length of the file.
+ */
+ private long length;
+
+ @ManyToOne(fetch = FetchType.LAZY)
+ private User owner;
+
+ /**
+ * Default constructor.
+ */
+ public UploadedFileEntry() {
+
+ }
+
+ /**
+ * Constructor that copies data from the parameter.
+ *
+ * @param original
+ * original object from which data will bbe copied
+ */
+ public UploadedFileEntry(UploadedFileEntry original) {
+ super(original);
+ }
+
+ public long getLength() {
+ return length;
+ }
+
+ public void setLength(long length) {
+ this.length = length;
+ }
+
+ public User getOwner() {
+ return owner;
+ }
+
+ public void setOwner(User owner) {
+ this.owner = owner;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/cache/package-info.java b/model/src/main/java/lcsb/mapviewer/model/cache/package-info.java
index 83ba3d1037..eeada7b7b0 100644
--- a/model/src/main/java/lcsb/mapviewer/model/cache/package-info.java
+++ b/model/src/main/java/lcsb/mapviewer/model/cache/package-info.java
@@ -1,5 +1,5 @@
-/**
- * Contains structures used for storing cached data.
- */
-package lcsb.mapviewer.model.cache;
-
+/**
+ * Contains structures used for storing cached data.
+ */
+package lcsb.mapviewer.model.cache;
+
diff --git a/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowType.java b/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowType.java
index 037437153f..509d773625 100644
--- a/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowType.java
@@ -1,101 +1,101 @@
-package lcsb.mapviewer.model.graphics;
-
-/**
- * Arrow types used in the graphics representation. Available types are:
- * <ul>
- * <li>{@link ArrowType#BLANK BLANK},</li>
- * <li>{@link ArrowType#BLANK_CROSSBAR BLANK_CROSSBAR},</li>
- * <li>{@link ArrowType#CIRCLE CIRCLE},</li>
- * <li>{@link ArrowType#CROSSBAR CROSSBAR},</li>
- * <li>{@link ArrowType#DIAMOND DIAMOND},</li>
- * <li>{@link ArrowType#FULL FULL},</li>
- * <li>{@link ArrowType#FULL_CROSSBAR FULL_CROSSBAR},</li>
- * <li>{@link ArrowType#NONE NONE},</li>
- * <li>{@link ArrowType#OPEN OPEN}.</li>
- * </ul>
- *
- * @author Piotr Gawron
- *
- */
-public enum ArrowType {
- // CHECKSTYLE:OFF
- /**
- * The arrow end that should look as an image bellow. <br/>
- * <br/>
- * <img alt="" src=
- * "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAEEAAAAUCAYAAADStFABAAAAVElEQVR42u3WsQoAIAhFUf//p21qM0miQd890NISXKQyA4B+/HJPMoIrxQgjbCox0ghBDJeNMD1IOcIhSHpAy1XVfTK+TwJ3Aq8D/wR+jFPDAHizAFMtRsiqJUUMAAAAAElFTkSuQmCC"
- * />
- */
- BLANK_CROSSBAR, //
- /**
- * The arrow end that should look as an image bellow. <br/>
- * <br/>
- * <img alt="" src=
- * "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAEEAAAAUCAYAAADStFABAAAARUlEQVR42u3WsQoAIAhAQf//p21oaQmMpuwOXBofUUYAvCcl2EdIEeb5OiJ0j3EaoWWQmwilGPnhuAneBL+DPcHGCFA1AN/ehXvm3UsqAAAAAElFTkSuQmCC"
- * />
- *
- */
- FULL_CROSSBAR, //
- /**
- * The arrow end that should look as an image bellow. <br/>
- * <br/>
- * <img alt="" src=
- * "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAEEAAAAUCAYAAADStFABAAAASElEQVR42u3UwQkAIAxD0ey/dL0oKAhW8GLzH3SAhLYSAAAwEX1sg8fgVMYSfGcuKNXib3Or6nYcC8luQsnTcH6Qcg8PAHilAdXavETyaCxKAAAAAElFTkSuQmCC"
- * />
- *
- */
- DIAMOND, //
- /**
- * The arrow end that should look as an image bellow. <br/>
- * <br/>
- * <img alt="" src=
- * "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAEEAAAAUCAYAAADStFABAAAATElEQVR42u3XMQ4AEBAFUfe/9ChEo5DVSPjzEgcwEVZrkvQHTDAikB6DKTkGq8TTwU5KEKoqMXh1nfrxZERv3jvB18E5wYnRv4N0RwevuDvTQl9v5wAAAABJRU5ErkJggg=="
- * />
- */
- BLANK, //
- /**
- * The arrow end that should look as an image bellow. <br/>
- * <br/>
- * <img alt="" src=
- * "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAEEAAAAUCAYAAADStFABAAAAMElEQVR42u3SQQ0AAAwCMfybZhK2/9oEAxcSAN6rBCKIIMIWoQ/nCRKIIIIIIgBXA1mQRrru0r/rAAAAAElFTkSuQmCC"
- * />
- *
- */
- CROSSBAR, //
- /**
- * The arrow end that should look as an image bellow. <br/>
- * <br/>
- * <img alt="" src=
- * "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAEEAAAAUCAYAAADStFABAAAASElEQVR42u3XgQkAIAzEwO6/9DtCVUQw5qALhIK2ShJMmuEH6NBDZBY1RFYRQ3wfIbtIIY5HyIvjJhjBCL4ORvDH6O3gFalLBns+vGCSjHRAAAAAAElFTkSuQmCC"
- * /> *
- */
- CIRCLE, //
- /**
- * The arrow end that should look as an image bellow. <br/>
- * <br/>
- * <img alt="" src=
- * "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAEEAAAAUCAYAAADStFABAAAANklEQVR42u3UMQ4AQAQEQP//tGuUCrmSmcQDbJYIAFbJGoTRhyEQgXyeSx4cTfATLK7ulgeYehEYVKxEPu3IAAAAAElFTkSuQmCC"
- * />
- */
- OPEN, //
- /**
- * The arrow end that should look as an image bellow. <br/>
- * <br/>
- * <img alt="" src=
- * "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAEEAAAAUCAYAAADStFABAAAAO0lEQVR42u3WsQ0AIAwDwey/tCloKF2TOykLvCLIDABfiQQ3wjsibI2RYkRoY2Th2ARvgt/BneBiBGgdPHh6hnF4gJ8AAAAASUVORK5CYII="
- * />
- */
- FULL, //
- /**
- * The arrow end that should look as an image bellow. <br/>
- * <br/>
- * <img alt="" src=
- * "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAEEAAAAUCAYAAADStFABAAAAIUlEQVR42u3DsQ0AAAgDoP7/tJ5QdyEhAQCAZh4GAOBqAUSYPMTcmIDAAAAAAElFTkSuQmCC"
- * />
- *
- */
- NONE
-
- // CHECKSTYLE:ON
-
-}
+package lcsb.mapviewer.model.graphics;
+
+/**
+ * Arrow types used in the graphics representation. Available types are:
+ * <ul>
+ * <li>{@link ArrowType#BLANK BLANK},</li>
+ * <li>{@link ArrowType#BLANK_CROSSBAR BLANK_CROSSBAR},</li>
+ * <li>{@link ArrowType#CIRCLE CIRCLE},</li>
+ * <li>{@link ArrowType#CROSSBAR CROSSBAR},</li>
+ * <li>{@link ArrowType#DIAMOND DIAMOND},</li>
+ * <li>{@link ArrowType#FULL FULL},</li>
+ * <li>{@link ArrowType#FULL_CROSSBAR FULL_CROSSBAR},</li>
+ * <li>{@link ArrowType#NONE NONE},</li>
+ * <li>{@link ArrowType#OPEN OPEN}.</li>
+ * </ul>
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum ArrowType {
+ // CHECKSTYLE:OFF
+ /**
+ * The arrow end that should look as an image bellow. <br/>
+ * <br/>
+ * <img alt="" src=
+ * "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAEEAAAAUCAYAAADStFABAAAAVElEQVR42u3WsQoAIAhFUf//p21qM0miQd890NISXKQyA4B+/HJPMoIrxQgjbCox0ghBDJeNMD1IOcIhSHpAy1XVfTK+TwJ3Aq8D/wR+jFPDAHizAFMtRsiqJUUMAAAAAElFTkSuQmCC"
+ * />
+ */
+ BLANK_CROSSBAR, //
+ /**
+ * The arrow end that should look as an image bellow. <br/>
+ * <br/>
+ * <img alt="" src=
+ * "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAEEAAAAUCAYAAADStFABAAAARUlEQVR42u3WsQoAIAhAQf//p21oaQmMpuwOXBofUUYAvCcl2EdIEeb5OiJ0j3EaoWWQmwilGPnhuAneBL+DPcHGCFA1AN/ehXvm3UsqAAAAAElFTkSuQmCC"
+ * />
+ *
+ */
+ FULL_CROSSBAR, //
+ /**
+ * The arrow end that should look as an image bellow. <br/>
+ * <br/>
+ * <img alt="" src=
+ * "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAEEAAAAUCAYAAADStFABAAAASElEQVR42u3UwQkAIAxD0ey/dL0oKAhW8GLzH3SAhLYSAAAwEX1sg8fgVMYSfGcuKNXib3Or6nYcC8luQsnTcH6Qcg8PAHilAdXavETyaCxKAAAAAElFTkSuQmCC"
+ * />
+ *
+ */
+ DIAMOND, //
+ /**
+ * The arrow end that should look as an image bellow. <br/>
+ * <br/>
+ * <img alt="" src=
+ * "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAEEAAAAUCAYAAADStFABAAAATElEQVR42u3XMQ4AEBAFUfe/9ChEo5DVSPjzEgcwEVZrkvQHTDAikB6DKTkGq8TTwU5KEKoqMXh1nfrxZERv3jvB18E5wYnRv4N0RwevuDvTQl9v5wAAAABJRU5ErkJggg=="
+ * />
+ */
+ BLANK, //
+ /**
+ * The arrow end that should look as an image bellow. <br/>
+ * <br/>
+ * <img alt="" src=
+ * "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAEEAAAAUCAYAAADStFABAAAAMElEQVR42u3SQQ0AAAwCMfybZhK2/9oEAxcSAN6rBCKIIMIWoQ/nCRKIIIIIIgBXA1mQRrru0r/rAAAAAElFTkSuQmCC"
+ * />
+ *
+ */
+ CROSSBAR, //
+ /**
+ * The arrow end that should look as an image bellow. <br/>
+ * <br/>
+ * <img alt="" src=
+ * "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAEEAAAAUCAYAAADStFABAAAASElEQVR42u3XgQkAIAzEwO6/9DtCVUQw5qALhIK2ShJMmuEH6NBDZBY1RFYRQ3wfIbtIIY5HyIvjJhjBCL4ORvDH6O3gFalLBns+vGCSjHRAAAAAAElFTkSuQmCC"
+ * /> *
+ */
+ CIRCLE, //
+ /**
+ * The arrow end that should look as an image bellow. <br/>
+ * <br/>
+ * <img alt="" src=
+ * "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAEEAAAAUCAYAAADStFABAAAANklEQVR42u3UMQ4AQAQEQP//tGuUCrmSmcQDbJYIAFbJGoTRhyEQgXyeSx4cTfATLK7ulgeYehEYVKxEPu3IAAAAAElFTkSuQmCC"
+ * />
+ */
+ OPEN, //
+ /**
+ * The arrow end that should look as an image bellow. <br/>
+ * <br/>
+ * <img alt="" src=
+ * "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAEEAAAAUCAYAAADStFABAAAAO0lEQVR42u3WsQ0AIAwDwey/tCloKF2TOykLvCLIDABfiQQ3wjsibI2RYkRoY2Th2ARvgt/BneBiBGgdPHh6hnF4gJ8AAAAASUVORK5CYII="
+ * />
+ */
+ FULL, //
+ /**
+ * The arrow end that should look as an image bellow. <br/>
+ * <br/>
+ * <img alt="" src=
+ * "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAEEAAAAUCAYAAADStFABAAAAIUlEQVR42u3DsQ0AAAgDoP7/tJ5QdyEhAQCAZh4GAOBqAUSYPMTcmIDAAAAAAElFTkSuQmCC"
+ * />
+ *
+ */
+ NONE
+
+ // CHECKSTYLE:ON
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowTypeData.java b/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowTypeData.java
index 9fac35e1c3..91ecadac86 100644
--- a/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowTypeData.java
+++ b/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowTypeData.java
@@ -1,184 +1,184 @@
-package lcsb.mapviewer.model.graphics;
-
-import java.io.Serializable;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-/**
- * This class define data for arrow ends.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-public class ArrowTypeData implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default angle of the arrow.
- */
- private static final double DEFAULT_ARROW_ANGLE = 0.875 * Math.PI;
-
- /**
- * Default length of the arrow.
- */
- private static final int DEFAULT_ARROW_LENGTH = 15;
-
- /**
- * Unique identifier in the database.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- /**
- * Type of the arrow.
- */
- private ArrowType arrowType;
-
- /**
- * Defines type of the line used to draw arrow end.
- */
- private LineType arrowLineType;
-
- /**
- * Defines length of the arrow head.
- */
- private double len;
-
- /**
- * Defines angle of the arrow head (when necessary).
- */
- private double angle;
-
- /**
- * Default constructor - uses default values.
- */
- public ArrowTypeData() {
- arrowType = ArrowType.NONE;
- arrowLineType = LineType.SOLID;
- len = DEFAULT_ARROW_LENGTH;
- angle = DEFAULT_ARROW_ANGLE;
- }
-
- /**
- * Constructor that creates object with the data copied from param object.
- *
- * @param param
- * object used for initialization of the data
- */
- public ArrowTypeData(ArrowTypeData param) {
- arrowType = param.arrowType;
- arrowLineType = param.arrowLineType;
- len = param.len;
- angle = param.angle;
- }
-
- /**
- * Creates a copy of the object.
- *
- * @return object copy
- */
- public ArrowTypeData copy() {
- if (this.getClass() == ArrowTypeData.class) {
- return new ArrowTypeData(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- /**
- * @return the id
- * @see #id
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
- /**
- * @return the arrowType
- * @see #arrowType
- */
- public ArrowType getArrowType() {
- return arrowType;
- }
-
- /**
- * @param arrowType
- * the arrowType to set
- * @see #arrowType
- */
- public void setArrowType(ArrowType arrowType) {
- this.arrowType = arrowType;
- }
-
- /**
- * @return the arrowLineType
- * @see #arrowLineType
- */
- public LineType getArrowLineType() {
- return arrowLineType;
- }
-
- /**
- * @param arrowLineType
- * the arrowLineType to set
- * @see #arrowLineType
- */
- public void setArrowLineType(LineType arrowLineType) {
- this.arrowLineType = arrowLineType;
- }
-
- /**
- * @return the len
- * @see #len
- */
- public double getLen() {
- return len;
- }
-
- /**
- * @param len
- * the len to set
- * @see #len
- */
- public void setLen(double len) {
- this.len = len;
- }
-
- /**
- * @return the angle
- * @see #angle
- */
- public double getAngle() {
- return angle;
- }
-
- /**
- * @param angle
- * the angle to set
- * @see #angle
- */
- public void setAngle(double angle) {
- this.angle = angle;
- }
-}
+package lcsb.mapviewer.model.graphics;
+
+import java.io.Serializable;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * This class define data for arrow ends.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+public class ArrowTypeData implements Serializable {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default angle of the arrow.
+ */
+ private static final double DEFAULT_ARROW_ANGLE = 0.875 * Math.PI;
+
+ /**
+ * Default length of the arrow.
+ */
+ private static final int DEFAULT_ARROW_LENGTH = 15;
+
+ /**
+ * Unique identifier in the database.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * Type of the arrow.
+ */
+ private ArrowType arrowType;
+
+ /**
+ * Defines type of the line used to draw arrow end.
+ */
+ private LineType arrowLineType;
+
+ /**
+ * Defines length of the arrow head.
+ */
+ private double len;
+
+ /**
+ * Defines angle of the arrow head (when necessary).
+ */
+ private double angle;
+
+ /**
+ * Default constructor - uses default values.
+ */
+ public ArrowTypeData() {
+ arrowType = ArrowType.NONE;
+ arrowLineType = LineType.SOLID;
+ len = DEFAULT_ARROW_LENGTH;
+ angle = DEFAULT_ARROW_ANGLE;
+ }
+
+ /**
+ * Constructor that creates object with the data copied from param object.
+ *
+ * @param param
+ * object used for initialization of the data
+ */
+ public ArrowTypeData(ArrowTypeData param) {
+ arrowType = param.arrowType;
+ arrowLineType = param.arrowLineType;
+ len = param.len;
+ angle = param.angle;
+ }
+
+ /**
+ * Creates a copy of the object.
+ *
+ * @return object copy
+ */
+ public ArrowTypeData copy() {
+ if (this.getClass() == ArrowTypeData.class) {
+ return new ArrowTypeData(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ /**
+ * @return the arrowType
+ * @see #arrowType
+ */
+ public ArrowType getArrowType() {
+ return arrowType;
+ }
+
+ /**
+ * @param arrowType
+ * the arrowType to set
+ * @see #arrowType
+ */
+ public void setArrowType(ArrowType arrowType) {
+ this.arrowType = arrowType;
+ }
+
+ /**
+ * @return the arrowLineType
+ * @see #arrowLineType
+ */
+ public LineType getArrowLineType() {
+ return arrowLineType;
+ }
+
+ /**
+ * @param arrowLineType
+ * the arrowLineType to set
+ * @see #arrowLineType
+ */
+ public void setArrowLineType(LineType arrowLineType) {
+ this.arrowLineType = arrowLineType;
+ }
+
+ /**
+ * @return the len
+ * @see #len
+ */
+ public double getLen() {
+ return len;
+ }
+
+ /**
+ * @param len
+ * the len to set
+ * @see #len
+ */
+ public void setLen(double len) {
+ this.len = len;
+ }
+
+ /**
+ * @return the angle
+ * @see #angle
+ */
+ public double getAngle() {
+ return angle;
+ }
+
+ /**
+ * @param angle
+ * the angle to set
+ * @see #angle
+ */
+ public void setAngle(double angle) {
+ this.angle = angle;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowTypeDataComparator.java b/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowTypeDataComparator.java
index 787d1a4e83..2586893335 100644
--- a/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowTypeDataComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowTypeDataComparator.java
@@ -1,71 +1,71 @@
-package lcsb.mapviewer.model.graphics;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.DoubleComparator;
-
-/**
- * This class implements comparator interface for ArrowTypeData. It compares the
- * content, but skip database identifier.
- *
- * @author Piotr Gawron
- *
- */
-public class ArrowTypeDataComparator extends Comparator<ArrowTypeData> {
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(PolylineDataComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public ArrowTypeDataComparator(double epsilon) {
- super(ArrowTypeData.class);
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public ArrowTypeDataComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected int internalCompare(ArrowTypeData arg0, ArrowTypeData arg1) {
- DoubleComparator doubleComparator = new DoubleComparator(epsilon);
-
- if (arg0.getArrowType().compareTo(arg1.getArrowType()) != 0) {
- logger.debug("Different arrow type: " + arg0.getArrowType() + ", " + arg1.getArrowType());
- return arg0.getArrowType().compareTo(arg1.getArrowType());
- }
-
- if (arg0.getArrowLineType().compareTo(arg1.getArrowLineType()) != 0) {
- logger.debug("Different arrow line type: " + arg0.getArrowLineType() + ", " + arg1.getArrowLineType());
- return arg0.getArrowLineType().compareTo(arg1.getArrowLineType());
- }
-
- if (doubleComparator.compare(arg0.getLen(), arg1.getLen()) != 0) {
- logger.debug("Different length: " + arg0.getLen() + ", " + arg1.getLen());
- return doubleComparator.compare(arg0.getLen(), arg1.getLen());
- }
-
- if (doubleComparator.compare(arg0.getAngle(), arg1.getAngle()) != 0) {
- logger.debug("Different angle: " + arg0.getAngle() + ", " + arg1.getAngle());
- return doubleComparator.compare(arg0.getAngle(), arg1.getAngle());
- }
- return 0;
- }
-
-}
+package lcsb.mapviewer.model.graphics;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.DoubleComparator;
+
+/**
+ * This class implements comparator interface for ArrowTypeData. It compares the
+ * content, but skip database identifier.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ArrowTypeDataComparator extends Comparator<ArrowTypeData> {
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(PolylineDataComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public ArrowTypeDataComparator(double epsilon) {
+ super(ArrowTypeData.class);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public ArrowTypeDataComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(ArrowTypeData arg0, ArrowTypeData arg1) {
+ DoubleComparator doubleComparator = new DoubleComparator(epsilon);
+
+ if (arg0.getArrowType().compareTo(arg1.getArrowType()) != 0) {
+ logger.debug("Different arrow type: " + arg0.getArrowType() + ", " + arg1.getArrowType());
+ return arg0.getArrowType().compareTo(arg1.getArrowType());
+ }
+
+ if (arg0.getArrowLineType().compareTo(arg1.getArrowLineType()) != 0) {
+ logger.debug("Different arrow line type: " + arg0.getArrowLineType() + ", " + arg1.getArrowLineType());
+ return arg0.getArrowLineType().compareTo(arg1.getArrowLineType());
+ }
+
+ if (doubleComparator.compare(arg0.getLen(), arg1.getLen()) != 0) {
+ logger.debug("Different length: " + arg0.getLen() + ", " + arg1.getLen());
+ return doubleComparator.compare(arg0.getLen(), arg1.getLen());
+ }
+
+ if (doubleComparator.compare(arg0.getAngle(), arg1.getAngle()) != 0) {
+ logger.debug("Different angle: " + arg0.getAngle() + ", " + arg1.getAngle());
+ return doubleComparator.compare(arg0.getAngle(), arg1.getAngle());
+ }
+ return 0;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/graphics/LineType.java b/model/src/main/java/lcsb/mapviewer/model/graphics/LineType.java
index f14d8a0f4b..3747dc907e 100644
--- a/model/src/main/java/lcsb/mapviewer/model/graphics/LineType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/graphics/LineType.java
@@ -1,133 +1,133 @@
-package lcsb.mapviewer.model.graphics;
-
-import java.awt.BasicStroke;
-import java.awt.Stroke;
-
-import lcsb.mapviewer.common.geometry.CompositeStroke;
-
-/**
- * Available types of lines in the system.
- *
- * @author Piotr Gawron
- *
- */
-public enum LineType {
- /**
- * Solid line.
- */
- SOLID(1),
-
- /**
- * Solid bold line.
- */
-
- SOLID_BOLD(3),
- /**
- * Dash-dot-dot line:
- *
- * <pre>
- * - . . - . . - . . - . .
- * </pre>
- */
-
- DASH_DOT_DOT(1, new float[] { 11.0f, 3.0f, 1.0f, 3.0f, 1.0f, 3.0f }),
- /**
- * Dash-dot line:
- *
- * <pre>
- * - . - . - . - . - . - . - .
- * </pre>
- */
- DASH_DOT(1, new float[] { 11.0f, 3.0f, 1.0f, 3.0f }),
-
- /**
- * Dashed line:
- *
- * <pre>
- * - - - - - - -
- * </pre>
- *
- * .
- */
- DASHED(1, new float[] { 8.0f, 8.0f }),
-
- /**
- * Dotted line:
- *
- * <pre>
- * . . . . . . . .
- * </pre>
- *
- * .
- */
- DOTTED(1, new float[] { 2.0f, 5.0f }),
-
- /**
- * Dashed and bold line:
- *
- * <pre>
- * - - - - - - -
- * </pre>
- *
- * .
- */
- DASHED_BOLD(3, new float[] { 8.0f, 8.0f }),
-
- /**
- * Double line.
- */
- DOUBLE(new CompositeStroke(new BasicStroke(10f), new BasicStroke(0.5f)));
-
- /**
- * Default miterlimit: "the limit to trim the miter join. The miterlimit must
- * be greater than or equal to 1.0f
- * " taken from <a href="http://docs.oracle.com
- * /javase/7/docs/api/java/awt/BasicStroke.html" >oracle webpage</a>
- */
- private static final float DEFAULT_MITERLIMIT = 10.0f;
-
- /**
- * {@link BasicStroke} defined for the line type.
- */
- private Stroke stroke;
-
- /**
- * Constructor with line width as a parameter.
- *
- * @param width
- * width of the line
- */
- LineType(float width) {
- this.stroke = new BasicStroke(width);
- }
-
- /**
- * Constructor for complex line types.
- *
- * @param stroke specific {@link Stroke} used for this line type
- */
- LineType(Stroke stroke) {
- this.stroke = stroke;
- }
-
- /**
- * Constructor with line width and pattern as a parameter.
- *
- * @param width
- * width of the line
- * @param pattern
- * pattern of the line
- */
- LineType(float width, float[] pattern) {
- this.stroke = new BasicStroke(width, BasicStroke.CAP_SQUARE, BasicStroke.JOIN_MITER, DEFAULT_MITERLIMIT, pattern, 0.0f);
- }
-
- /**
- * Return the {@link BasicStroke} for this line type.
- *
- * @return the {@link BasicStroke} for this line type
- */
- public Stroke getStroke() {
- return stroke;
- }
-}
+package lcsb.mapviewer.model.graphics;
+
+import java.awt.BasicStroke;
+import java.awt.Stroke;
+
+import lcsb.mapviewer.common.geometry.CompositeStroke;
+
+/**
+ * Available types of lines in the system.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum LineType {
+ /**
+ * Solid line.
+ */
+ SOLID(1),
+
+ /**
+ * Solid bold line.
+ */
+
+ SOLID_BOLD(3),
+ /**
+ * Dash-dot-dot line:
+ *
+ * <pre>
+ * - . . - . . - . . - . .
+ * </pre>
+ */
+
+ DASH_DOT_DOT(1, new float[] { 11.0f, 3.0f, 1.0f, 3.0f, 1.0f, 3.0f }),
+ /**
+ * Dash-dot line:
+ *
+ * <pre>
+ * - . - . - . - . - . - . - .
+ * </pre>
+ */
+ DASH_DOT(1, new float[] { 11.0f, 3.0f, 1.0f, 3.0f }),
+
+ /**
+ * Dashed line:
+ *
+ * <pre>
+ * - - - - - - -
+ * </pre>
+ *
+ * .
+ */
+ DASHED(1, new float[] { 8.0f, 8.0f }),
+
+ /**
+ * Dotted line:
+ *
+ * <pre>
+ * . . . . . . . .
+ * </pre>
+ *
+ * .
+ */
+ DOTTED(1, new float[] { 2.0f, 5.0f }),
+
+ /**
+ * Dashed and bold line:
+ *
+ * <pre>
+ * - - - - - - -
+ * </pre>
+ *
+ * .
+ */
+ DASHED_BOLD(3, new float[] { 8.0f, 8.0f }),
+
+ /**
+ * Double line.
+ */
+ DOUBLE(new CompositeStroke(new BasicStroke(10f), new BasicStroke(0.5f)));
+
+ /**
+ * Default miterlimit: "the limit to trim the miter join. The miterlimit must
+ * be greater than or equal to 1.0f
+ * " taken from <a href="http://docs.oracle.com
+ * /javase/7/docs/api/java/awt/BasicStroke.html" >oracle webpage</a>
+ */
+ private static final float DEFAULT_MITERLIMIT = 10.0f;
+
+ /**
+ * {@link BasicStroke} defined for the line type.
+ */
+ private Stroke stroke;
+
+ /**
+ * Constructor with line width as a parameter.
+ *
+ * @param width
+ * width of the line
+ */
+ LineType(float width) {
+ this.stroke = new BasicStroke(width);
+ }
+
+ /**
+ * Constructor for complex line types.
+ *
+ * @param stroke specific {@link Stroke} used for this line type
+ */
+ LineType(Stroke stroke) {
+ this.stroke = stroke;
+ }
+
+ /**
+ * Constructor with line width and pattern as a parameter.
+ *
+ * @param width
+ * width of the line
+ * @param pattern
+ * pattern of the line
+ */
+ LineType(float width, float[] pattern) {
+ this.stroke = new BasicStroke(width, BasicStroke.CAP_SQUARE, BasicStroke.JOIN_MITER, DEFAULT_MITERLIMIT, pattern, 0.0f);
+ }
+
+ /**
+ * Return the {@link BasicStroke} for this line type.
+ *
+ * @return the {@link BasicStroke} for this line type
+ */
+ public Stroke getStroke() {
+ return stroke;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineData.java b/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineData.java
index c4b59c816f..e22df7ef46 100644
--- a/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineData.java
+++ b/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineData.java
@@ -1,535 +1,535 @@
-package lcsb.mapviewer.model.graphics;
-
-import java.awt.Color;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.persistence.CollectionTable;
-import javax.persistence.Column;
-import javax.persistence.ElementCollection;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.OneToOne;
-
-import org.apache.log4j.Logger;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-import org.hibernate.annotations.IndexColumn;
-import org.hibernate.annotations.Type;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.common.geometry.PointTransformation;
-
-/**
- * This class represents general line structure. Line can contain several
- * segments. Beginning and the end of the line could be finished with the arrow.
- * There are also color and line width associated with the object.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-public class PolylineData implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Class used to perform some operation on points.
- */
- private static PointTransformation pt = new PointTransformation();
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(PolylineData.class);
-
- /**
- * Unique identifier in the database.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- /**
- * List of points that build the line.
- */
- @ElementCollection(fetch = FetchType.EAGER)
- @CollectionTable(name = "point_table", joinColumns = @JoinColumn(name = "idDb"))
- @IndexColumn(name = "idx")
- @Column(name = "point_val")
- @Type(type = "lcsb.mapviewer.persist.mapper.Point2DMapper")
- @Cascade({ CascadeType.ALL })
- private List<Point2D> points = new ArrayList<>();
-
- /**
- * Arrow at the beginning of the line.
- */
- @Cascade({ CascadeType.ALL })
- @OneToOne
- private ArrowTypeData beginAtd = new ArrowTypeData();
-
- /**
- * Arrow at the end of the line.
- */
- @Cascade({ CascadeType.ALL })
- @OneToOne
- private ArrowTypeData endAtd = new ArrowTypeData();
-
- /**
- * Width of the line.
- */
- private double width = 1;
-
- /**
- * Color of the line.
- */
- private Color color = Color.BLACK;
-
- /**
- * Type of the line (pattern used to draw it).
- */
- private LineType type = LineType.SOLID;
-
- /**
- * Default constructor for simple to points line.
- *
- * @param startPoint
- * start point of the line
- * @param endPoint
- * end point of the line
- */
- public PolylineData(Point2D startPoint, Point2D endPoint) {
- addPoint(startPoint);
- addPoint(endPoint);
- }
-
- /**
- * Default constructor.
- */
- public PolylineData() {
- }
-
- /**
- * Constructor that creates object initialized by the param line.
- *
- * @param param
- * parameter used for data initialization
- */
- public PolylineData(PolylineData param) {
- points = new ArrayList<Point2D>();
- for (Point2D point : param.getPoints()) {
- points.add(new Point2D.Double(point.getX(), point.getY()));
- }
- beginAtd = new ArrowTypeData(param.getBeginAtd());
- endAtd = new ArrowTypeData(param.getEndAtd());
- width = param.getWidth();
- color = param.getColor();
- type = param.getType();
- }
-
- /**
- * Creates line from the list of points.
- *
- * @param pointsList
- * list of points that represent the line
- */
- public PolylineData(List<Point2D> pointsList) {
- for (Point2D point2d : pointsList) {
- addPoint(point2d);
- }
- }
-
- /**
- * Adds a point to the line.
- *
- * @param point
- * point to add
- */
- public void addPoint(Point2D point) {
- if (!pt.isValidPoint(point)) {
- throw new InvalidArgumentException("Invalid coordinates: " + point);
- }
- points.add(point);
- }
-
- /**
- * Adds a point to the line at specific point (the rest will be shifted
- * accordingly).
- *
- * @param point
- * point to add
- * @param position
- * where the point should be inserted
- */
- public void addPoint(int position, Point2D point) {
- if (!pt.isValidPoint(point)) {
- throw new InvalidArgumentException("Invalid coordinates: " + point);
- }
- points.add(position, point);
- }
-
- /**
- * Set new coordinetas of the point inside line.
- *
- * @param position
- * which point should be changed
- * @param point
- * new point value
- */
- public void setPoint(int position, Point2D point) {
- if (!pt.isValidPoint(point)) {
- throw new InvalidArgumentException("Invalid coordinates (NaN is not accepted): " + point);
- }
- points.set(position, point);
- }
-
- /**
- * Returns all segment lines as a list of {@link Line2D} objects.
- *
- * @return list of segment lines
- */
- public List<Line2D> getLines() {
- List<Line2D> result = new ArrayList<Line2D>();
- if (points.size() > 1) {
- Point2D p1 = points.get(0);
-
- for (int i = 1; i < points.size(); i++) {
- Point2D p2 = points.get(i);
- Line2D line = new Line2D.Double(p1, p2);
- result.add(line);
- p1 = p2;
- }
- }
- return result;
- }
-
- /**
- * Return a line that correspond to the part of line.
- *
- * @param from
- * index of the point where line should start
- * @param to
- * index of the point where line should end
- * @return line that correspond to the part of line
- */
- public PolylineData getSubline(int from, int to) {
- PolylineData result = new PolylineData(this);
- result.setPoints(new ArrayList<Point2D>());
- for (int i = Math.max(from, 0); i < Math.min(to, points.size()); i++) {
- result.addPoint(new Point2D.Double(points.get(i).getX(), points.get(i).getY()));
- }
- return result;
- }
-
- /**
- * Sets the new value of the last point in the line.
- *
- * @param point
- * new value of the last point in the line
- */
- public void setEndPoint(Point2D point) {
- if (!pt.isValidPoint(point)) {
- throw new InvalidArgumentException("Invalid coordinates (NaN is not accepted): " + point);
- }
- points.set(points.size() - 1, point);
-
- }
-
- /**
- * Returns coordinates of the last point in the line.
- *
- * @return coordinates of the last point in the line
- */
- public Point2D getEndPoint() {
- return points.get(points.size() - 1);
- }
-
- /**
- * Transforms line representation into {@link GeneralPath} class.
- *
- * @return {@link GeneralPath} representation of line
- */
- public GeneralPath toGeneralPath() {
- GeneralPath path = new GeneralPath();
- Point2D p = points.get(0);
- path.moveTo(p.getX(), p.getY());
- for (int i = 1; i < points.size(); i++) {
- p = points.get(i);
- path.lineTo(p.getX(), p.getY());
- }
- return path;
- }
-
- /**
- * Trims the end of the line.
- *
- * @param distToTrim
- * distance by which end of line should be trimmed
- */
- public void trimEnd(double distToTrim) {
- Point2D last = points.get(points.size() - 1);
- Point2D last2 = points.get(points.size() - 2);
- double oldDist = last.distance(last2);
- if (oldDist <= distToTrim) {
- last.setLocation(last2);
- } else {
- double newDistr = oldDist - distToTrim;
- double ratio = newDistr / oldDist;
- double dx = last.getX() - last2.getX();
- double dy = last.getY() - last2.getY();
- dx *= ratio;
- dy *= ratio;
- last.setLocation(last2.getX() + dx, last2.getY() + dy);
- }
- }
-
- /**
- * Trims the begining of the line.
- *
- * @param distToTrim
- * distance by which beginning of line should be trimmed
- */
- public void trimBegin(double distToTrim) {
- Point2D last = points.get(0);
- Point2D last2 = points.get(1);
- double oldDist = last.distance(last2);
- if (oldDist <= distToTrim) {
- last.setLocation(last2);
- } else {
- double newDistr = oldDist - distToTrim;
- double ratio = newDistr / oldDist;
- double dx = last.getX() - last2.getX();
- double dy = last.getY() - last2.getY();
- dx *= ratio;
- dy *= ratio;
- last.setLocation(last2.getX() + dx, last2.getY() + dy);
- }
- }
-
- /**
- * Returns the object with reversed order of line.
- *
- * @return reversed line
- */
- public PolylineData reverse() {
- PolylineData result = new PolylineData(this);
- List<Point2D> points = new ArrayList<Point2D>();
- for (int i = getPoints().size() - 1; i >= 0; i--) {
- points.add(getPoints().get(i));
- }
- result.setPoints(points);
- result.setBeginAtd(getEndAtd());
- result.setEndAtd(getBeginAtd());
- return result;
- }
-
- /**
- * Returns length of the whole line.
- *
- * @return length of the line
- */
- public double length() {
- if (points.size() < 2) {
- return 0;
- }
- double dist = 0;
- Point2D point = points.get(0);
- for (int i = 1; i < points.size(); i++) {
- dist += point.distance(points.get(i));
- point = points.get(i);
- }
- return dist;
- }
-
- /**
- * Sets first point in the line.
- *
- * @param point
- * new first point in the line
- */
- public void setStartPoint(Point2D point) {
- if (!pt.isValidPoint(point)) {
- throw new InvalidArgumentException("Invalid coordinates: " + point);
- }
- points.set(0, point);
- }
-
- /**
- * Returns first point in the line.
- *
- * @return first point in the line
- */
- public Point2D getBeginPoint() {
- return points.get(0);
- }
-
- /**
- * @return the points
- * @see #points
- */
- public List<Point2D> getPoints() {
- return points;
- }
-
- /**
- * @param points
- * the points to set
- * @see #points
- */
- public void setPoints(List<Point2D> points) {
- for (Point2D point : points) {
- if (!pt.isValidPoint(point)) {
- throw new InvalidArgumentException("Invalid coordinates: " + point);
- }
- }
- this.points = points;
- }
-
- /**
- * @return the beginAtd
- * @see #beginAtd
- */
- public ArrowTypeData getBeginAtd() {
- return beginAtd;
- }
-
- /**
- * @param beginAtd
- * the beginAtd to set
- * @see #beginAtd
- */
- public void setBeginAtd(ArrowTypeData beginAtd) {
- this.beginAtd = beginAtd;
- }
-
- /**
- * @return the endAtd
- * @see #endAtd
- */
- public ArrowTypeData getEndAtd() {
- return endAtd;
- }
-
- /**
- * @param endAtd
- * the endAtd to set
- * @see #endAtd
- */
- public void setEndAtd(ArrowTypeData endAtd) {
- this.endAtd = endAtd;
- }
-
- /**
- * @return the width
- * @see #width
- */
- public double getWidth() {
- return width;
- }
-
- /**
- * @param width
- * the width to set
- * @see #width
- */
- public void setWidth(double width) {
- this.width = width;
- }
-
- /**
- * @return the color
- * @see #color
- */
- public Color getColor() {
- return color;
- }
-
- /**
- * @param color
- * the color to set
- * @see #color
- */
- public void setColor(Color color) {
- this.color = color;
- }
-
- /**
- * @return the type
- * @see #type
- */
- public LineType getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(LineType type) {
- this.type = type;
- }
-
- /**
- * @return the id
- * @see #id
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
- /**
- * @param string
- * the width to set
- * @see #width
- */
- public void setWidth(String string) {
- setWidth(Double.parseDouble(string));
- }
-
- /**
- * Prepares a copy of the object.
- *
- * @return copy of {@link PolylineData}
- */
- public PolylineData copy() {
- if (this.getClass().equals(PolylineData.class)) {
- return new PolylineData(this);
- } else {
- throw new NotImplementedException("Copy method for " + this.getClass() + " class not implemented.");
- }
- }
-
- @Override
- public String toString() {
- StringBuilder sb = new StringBuilder();
- sb.append("[" + this.getClass().getSimpleName() + "]: ");
- for (Point2D point : points) {
- sb.append(point.getX() + ", " + point.getY() + " ");
- }
- return sb.toString();
- }
-
-}
+package lcsb.mapviewer.model.graphics;
+
+import java.awt.Color;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.persistence.CollectionTable;
+import javax.persistence.Column;
+import javax.persistence.ElementCollection;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.OneToOne;
+
+import org.apache.log4j.Logger;
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+import org.hibernate.annotations.IndexColumn;
+import org.hibernate.annotations.Type;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.common.geometry.PointTransformation;
+
+/**
+ * This class represents general line structure. Line can contain several
+ * segments. Beginning and the end of the line could be finished with the arrow.
+ * There are also color and line width associated with the object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+public class PolylineData implements Serializable {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Class used to perform some operation on points.
+ */
+ private static PointTransformation pt = new PointTransformation();
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(PolylineData.class);
+
+ /**
+ * Unique identifier in the database.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * List of points that build the line.
+ */
+ @ElementCollection(fetch = FetchType.EAGER)
+ @CollectionTable(name = "point_table", joinColumns = @JoinColumn(name = "idDb"))
+ @IndexColumn(name = "idx")
+ @Column(name = "point_val")
+ @Type(type = "lcsb.mapviewer.persist.mapper.Point2DMapper")
+ @Cascade({ CascadeType.ALL })
+ private List<Point2D> points = new ArrayList<>();
+
+ /**
+ * Arrow at the beginning of the line.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToOne
+ private ArrowTypeData beginAtd = new ArrowTypeData();
+
+ /**
+ * Arrow at the end of the line.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToOne
+ private ArrowTypeData endAtd = new ArrowTypeData();
+
+ /**
+ * Width of the line.
+ */
+ private double width = 1;
+
+ /**
+ * Color of the line.
+ */
+ private Color color = Color.BLACK;
+
+ /**
+ * Type of the line (pattern used to draw it).
+ */
+ private LineType type = LineType.SOLID;
+
+ /**
+ * Default constructor for simple to points line.
+ *
+ * @param startPoint
+ * start point of the line
+ * @param endPoint
+ * end point of the line
+ */
+ public PolylineData(Point2D startPoint, Point2D endPoint) {
+ addPoint(startPoint);
+ addPoint(endPoint);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public PolylineData() {
+ }
+
+ /**
+ * Constructor that creates object initialized by the param line.
+ *
+ * @param param
+ * parameter used for data initialization
+ */
+ public PolylineData(PolylineData param) {
+ points = new ArrayList<Point2D>();
+ for (Point2D point : param.getPoints()) {
+ points.add(new Point2D.Double(point.getX(), point.getY()));
+ }
+ beginAtd = new ArrowTypeData(param.getBeginAtd());
+ endAtd = new ArrowTypeData(param.getEndAtd());
+ width = param.getWidth();
+ color = param.getColor();
+ type = param.getType();
+ }
+
+ /**
+ * Creates line from the list of points.
+ *
+ * @param pointsList
+ * list of points that represent the line
+ */
+ public PolylineData(List<Point2D> pointsList) {
+ for (Point2D point2d : pointsList) {
+ addPoint(point2d);
+ }
+ }
+
+ /**
+ * Adds a point to the line.
+ *
+ * @param point
+ * point to add
+ */
+ public void addPoint(Point2D point) {
+ if (!pt.isValidPoint(point)) {
+ throw new InvalidArgumentException("Invalid coordinates: " + point);
+ }
+ points.add(point);
+ }
+
+ /**
+ * Adds a point to the line at specific point (the rest will be shifted
+ * accordingly).
+ *
+ * @param point
+ * point to add
+ * @param position
+ * where the point should be inserted
+ */
+ public void addPoint(int position, Point2D point) {
+ if (!pt.isValidPoint(point)) {
+ throw new InvalidArgumentException("Invalid coordinates: " + point);
+ }
+ points.add(position, point);
+ }
+
+ /**
+ * Set new coordinetas of the point inside line.
+ *
+ * @param position
+ * which point should be changed
+ * @param point
+ * new point value
+ */
+ public void setPoint(int position, Point2D point) {
+ if (!pt.isValidPoint(point)) {
+ throw new InvalidArgumentException("Invalid coordinates (NaN is not accepted): " + point);
+ }
+ points.set(position, point);
+ }
+
+ /**
+ * Returns all segment lines as a list of {@link Line2D} objects.
+ *
+ * @return list of segment lines
+ */
+ public List<Line2D> getLines() {
+ List<Line2D> result = new ArrayList<Line2D>();
+ if (points.size() > 1) {
+ Point2D p1 = points.get(0);
+
+ for (int i = 1; i < points.size(); i++) {
+ Point2D p2 = points.get(i);
+ Line2D line = new Line2D.Double(p1, p2);
+ result.add(line);
+ p1 = p2;
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Return a line that correspond to the part of line.
+ *
+ * @param from
+ * index of the point where line should start
+ * @param to
+ * index of the point where line should end
+ * @return line that correspond to the part of line
+ */
+ public PolylineData getSubline(int from, int to) {
+ PolylineData result = new PolylineData(this);
+ result.setPoints(new ArrayList<Point2D>());
+ for (int i = Math.max(from, 0); i < Math.min(to, points.size()); i++) {
+ result.addPoint(new Point2D.Double(points.get(i).getX(), points.get(i).getY()));
+ }
+ return result;
+ }
+
+ /**
+ * Sets the new value of the last point in the line.
+ *
+ * @param point
+ * new value of the last point in the line
+ */
+ public void setEndPoint(Point2D point) {
+ if (!pt.isValidPoint(point)) {
+ throw new InvalidArgumentException("Invalid coordinates (NaN is not accepted): " + point);
+ }
+ points.set(points.size() - 1, point);
+
+ }
+
+ /**
+ * Returns coordinates of the last point in the line.
+ *
+ * @return coordinates of the last point in the line
+ */
+ public Point2D getEndPoint() {
+ return points.get(points.size() - 1);
+ }
+
+ /**
+ * Transforms line representation into {@link GeneralPath} class.
+ *
+ * @return {@link GeneralPath} representation of line
+ */
+ public GeneralPath toGeneralPath() {
+ GeneralPath path = new GeneralPath();
+ Point2D p = points.get(0);
+ path.moveTo(p.getX(), p.getY());
+ for (int i = 1; i < points.size(); i++) {
+ p = points.get(i);
+ path.lineTo(p.getX(), p.getY());
+ }
+ return path;
+ }
+
+ /**
+ * Trims the end of the line.
+ *
+ * @param distToTrim
+ * distance by which end of line should be trimmed
+ */
+ public void trimEnd(double distToTrim) {
+ Point2D last = points.get(points.size() - 1);
+ Point2D last2 = points.get(points.size() - 2);
+ double oldDist = last.distance(last2);
+ if (oldDist <= distToTrim) {
+ last.setLocation(last2);
+ } else {
+ double newDistr = oldDist - distToTrim;
+ double ratio = newDistr / oldDist;
+ double dx = last.getX() - last2.getX();
+ double dy = last.getY() - last2.getY();
+ dx *= ratio;
+ dy *= ratio;
+ last.setLocation(last2.getX() + dx, last2.getY() + dy);
+ }
+ }
+
+ /**
+ * Trims the begining of the line.
+ *
+ * @param distToTrim
+ * distance by which beginning of line should be trimmed
+ */
+ public void trimBegin(double distToTrim) {
+ Point2D last = points.get(0);
+ Point2D last2 = points.get(1);
+ double oldDist = last.distance(last2);
+ if (oldDist <= distToTrim) {
+ last.setLocation(last2);
+ } else {
+ double newDistr = oldDist - distToTrim;
+ double ratio = newDistr / oldDist;
+ double dx = last.getX() - last2.getX();
+ double dy = last.getY() - last2.getY();
+ dx *= ratio;
+ dy *= ratio;
+ last.setLocation(last2.getX() + dx, last2.getY() + dy);
+ }
+ }
+
+ /**
+ * Returns the object with reversed order of line.
+ *
+ * @return reversed line
+ */
+ public PolylineData reverse() {
+ PolylineData result = new PolylineData(this);
+ List<Point2D> points = new ArrayList<Point2D>();
+ for (int i = getPoints().size() - 1; i >= 0; i--) {
+ points.add(getPoints().get(i));
+ }
+ result.setPoints(points);
+ result.setBeginAtd(getEndAtd());
+ result.setEndAtd(getBeginAtd());
+ return result;
+ }
+
+ /**
+ * Returns length of the whole line.
+ *
+ * @return length of the line
+ */
+ public double length() {
+ if (points.size() < 2) {
+ return 0;
+ }
+ double dist = 0;
+ Point2D point = points.get(0);
+ for (int i = 1; i < points.size(); i++) {
+ dist += point.distance(points.get(i));
+ point = points.get(i);
+ }
+ return dist;
+ }
+
+ /**
+ * Sets first point in the line.
+ *
+ * @param point
+ * new first point in the line
+ */
+ public void setStartPoint(Point2D point) {
+ if (!pt.isValidPoint(point)) {
+ throw new InvalidArgumentException("Invalid coordinates: " + point);
+ }
+ points.set(0, point);
+ }
+
+ /**
+ * Returns first point in the line.
+ *
+ * @return first point in the line
+ */
+ public Point2D getBeginPoint() {
+ return points.get(0);
+ }
+
+ /**
+ * @return the points
+ * @see #points
+ */
+ public List<Point2D> getPoints() {
+ return points;
+ }
+
+ /**
+ * @param points
+ * the points to set
+ * @see #points
+ */
+ public void setPoints(List<Point2D> points) {
+ for (Point2D point : points) {
+ if (!pt.isValidPoint(point)) {
+ throw new InvalidArgumentException("Invalid coordinates: " + point);
+ }
+ }
+ this.points = points;
+ }
+
+ /**
+ * @return the beginAtd
+ * @see #beginAtd
+ */
+ public ArrowTypeData getBeginAtd() {
+ return beginAtd;
+ }
+
+ /**
+ * @param beginAtd
+ * the beginAtd to set
+ * @see #beginAtd
+ */
+ public void setBeginAtd(ArrowTypeData beginAtd) {
+ this.beginAtd = beginAtd;
+ }
+
+ /**
+ * @return the endAtd
+ * @see #endAtd
+ */
+ public ArrowTypeData getEndAtd() {
+ return endAtd;
+ }
+
+ /**
+ * @param endAtd
+ * the endAtd to set
+ * @see #endAtd
+ */
+ public void setEndAtd(ArrowTypeData endAtd) {
+ this.endAtd = endAtd;
+ }
+
+ /**
+ * @return the width
+ * @see #width
+ */
+ public double getWidth() {
+ return width;
+ }
+
+ /**
+ * @param width
+ * the width to set
+ * @see #width
+ */
+ public void setWidth(double width) {
+ this.width = width;
+ }
+
+ /**
+ * @return the color
+ * @see #color
+ */
+ public Color getColor() {
+ return color;
+ }
+
+ /**
+ * @param color
+ * the color to set
+ * @see #color
+ */
+ public void setColor(Color color) {
+ this.color = color;
+ }
+
+ /**
+ * @return the type
+ * @see #type
+ */
+ public LineType getType() {
+ return type;
+ }
+
+ /**
+ * @param type
+ * the type to set
+ * @see #type
+ */
+ public void setType(LineType type) {
+ this.type = type;
+ }
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ /**
+ * @param string
+ * the width to set
+ * @see #width
+ */
+ public void setWidth(String string) {
+ setWidth(Double.parseDouble(string));
+ }
+
+ /**
+ * Prepares a copy of the object.
+ *
+ * @return copy of {@link PolylineData}
+ */
+ public PolylineData copy() {
+ if (this.getClass().equals(PolylineData.class)) {
+ return new PolylineData(this);
+ } else {
+ throw new NotImplementedException("Copy method for " + this.getClass() + " class not implemented.");
+ }
+ }
+
+ @Override
+ public String toString() {
+ StringBuilder sb = new StringBuilder();
+ sb.append("[" + this.getClass().getSimpleName() + "]: ");
+ for (Point2D point : points) {
+ sb.append(point.getX() + ", " + point.getY() + " ");
+ }
+ return sb.toString();
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineDataComparator.java b/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineDataComparator.java
index 12e7bde45d..61b24f5548 100644
--- a/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineDataComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineDataComparator.java
@@ -1,109 +1,109 @@
-package lcsb.mapviewer.model.graphics;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.DoubleComparator;
-import lcsb.mapviewer.common.comparator.IntegerComparator;
-
-/**
- * This class implements comparator interface for {@link PolylineData}. It
- * compares the content, but skip database identifier.
- *
- * @author Piotr Gawron
- *
- */
-public class PolylineDataComparator extends Comparator<PolylineData> {
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(PolylineDataComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public PolylineDataComparator(double epsilon) {
- super(PolylineData.class, true);
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public PolylineDataComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected int internalCompare(PolylineData arg0, PolylineData arg1) {
- IntegerComparator integerComparator = new IntegerComparator();
- DoubleComparator doubleComparator = new DoubleComparator(epsilon);
- ArrowTypeDataComparator atdComparator = new ArrowTypeDataComparator(epsilon);
-
- int different1 = 0;
- int different2 = 0;
- for (int i = 1; i < arg0.getPoints().size(); i++) {
- if (arg0.getPoints().get(i).distance(arg0.getPoints().get(i - 1)) > Configuration.EPSILON) {
- different1++;
- }
- }
- for (int i = 1; i < arg1.getPoints().size(); i++) {
- if (arg1.getPoints().get(i).distance(arg1.getPoints().get(i - 1)) > Configuration.EPSILON) {
- different2++;
- }
- }
- if (integerComparator.compare(different1, different2) != 0) {
- logger.debug("Lines have different size: " + different1 + ", " + different2);
- return integerComparator.compare(arg0.getPoints().size(), arg1.getPoints().size());
- }
- // TODO this should be fixed
- // for (int i = 0; i < arg0.getPoints().size(); i++) {
- // if
- // (doubleComparator.compare(arg0.getPoints().get(i).distanceSq(arg1.getPoints().get(i)),
- // 0.0) != 0) {
- // logger.debug("Lines have different points: " + arg0.getPoints().get(i) +
- // ", " + arg1.getPoints().get(i));
- // return
- // doubleComparator.compare(arg0.getPoints().get(i).distanceSq(arg1.getPoints().get(i)),
- // 0.0);
- // }
- // }
-
- if (atdComparator.compare(arg0.getBeginAtd(), arg1.getBeginAtd()) != 0) {
- logger.debug("Lines have different begin adt: " + arg0.getBeginAtd() + ", " + arg1.getBeginAtd());
- return atdComparator.compare(arg0.getBeginAtd(), arg1.getBeginAtd());
- }
-
- if (atdComparator.compare(arg0.getEndAtd(), arg1.getEndAtd()) != 0) {
- logger.debug("Lines have different end adt: " + arg0.getEndAtd() + ", " + arg1.getEndAtd());
- return atdComparator.compare(arg0.getEndAtd(), arg1.getEndAtd());
- }
-
- if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
- logger.debug("Lines have different width: " + arg0.getWidth() + ", " + arg1.getWidth());
- return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
- }
-
- if (integerComparator.compare(arg0.getColor().getRGB(), arg1.getColor().getRGB()) != 0) {
- logger.debug("Lines have different color: " + arg0.getColor() + ", " + arg1.getColor());
- return integerComparator.compare(arg0.getColor().getRGB(), arg1.getColor().getRGB());
- }
-
- if (arg0.getType().compareTo(arg1.getType()) != 0) {
- logger.debug("Lines have different type: " + arg0.getType() + ", " + arg1.getType());
- return arg0.getType().compareTo(arg1.getType());
- }
-
- return 0;
- }
-
-}
+package lcsb.mapviewer.model.graphics;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.DoubleComparator;
+import lcsb.mapviewer.common.comparator.IntegerComparator;
+
+/**
+ * This class implements comparator interface for {@link PolylineData}. It
+ * compares the content, but skip database identifier.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class PolylineDataComparator extends Comparator<PolylineData> {
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(PolylineDataComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public PolylineDataComparator(double epsilon) {
+ super(PolylineData.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public PolylineDataComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(PolylineData arg0, PolylineData arg1) {
+ IntegerComparator integerComparator = new IntegerComparator();
+ DoubleComparator doubleComparator = new DoubleComparator(epsilon);
+ ArrowTypeDataComparator atdComparator = new ArrowTypeDataComparator(epsilon);
+
+ int different1 = 0;
+ int different2 = 0;
+ for (int i = 1; i < arg0.getPoints().size(); i++) {
+ if (arg0.getPoints().get(i).distance(arg0.getPoints().get(i - 1)) > Configuration.EPSILON) {
+ different1++;
+ }
+ }
+ for (int i = 1; i < arg1.getPoints().size(); i++) {
+ if (arg1.getPoints().get(i).distance(arg1.getPoints().get(i - 1)) > Configuration.EPSILON) {
+ different2++;
+ }
+ }
+ if (integerComparator.compare(different1, different2) != 0) {
+ logger.debug("Lines have different size: " + different1 + ", " + different2);
+ return integerComparator.compare(arg0.getPoints().size(), arg1.getPoints().size());
+ }
+ // TODO this should be fixed
+ // for (int i = 0; i < arg0.getPoints().size(); i++) {
+ // if
+ // (doubleComparator.compare(arg0.getPoints().get(i).distanceSq(arg1.getPoints().get(i)),
+ // 0.0) != 0) {
+ // logger.debug("Lines have different points: " + arg0.getPoints().get(i) +
+ // ", " + arg1.getPoints().get(i));
+ // return
+ // doubleComparator.compare(arg0.getPoints().get(i).distanceSq(arg1.getPoints().get(i)),
+ // 0.0);
+ // }
+ // }
+
+ if (atdComparator.compare(arg0.getBeginAtd(), arg1.getBeginAtd()) != 0) {
+ logger.debug("Lines have different begin adt: " + arg0.getBeginAtd() + ", " + arg1.getBeginAtd());
+ return atdComparator.compare(arg0.getBeginAtd(), arg1.getBeginAtd());
+ }
+
+ if (atdComparator.compare(arg0.getEndAtd(), arg1.getEndAtd()) != 0) {
+ logger.debug("Lines have different end adt: " + arg0.getEndAtd() + ", " + arg1.getEndAtd());
+ return atdComparator.compare(arg0.getEndAtd(), arg1.getEndAtd());
+ }
+
+ if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
+ logger.debug("Lines have different width: " + arg0.getWidth() + ", " + arg1.getWidth());
+ return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
+ }
+
+ if (integerComparator.compare(arg0.getColor().getRGB(), arg1.getColor().getRGB()) != 0) {
+ logger.debug("Lines have different color: " + arg0.getColor() + ", " + arg1.getColor());
+ return integerComparator.compare(arg0.getColor().getRGB(), arg1.getColor().getRGB());
+ }
+
+ if (arg0.getType().compareTo(arg1.getType()) != 0) {
+ logger.debug("Lines have different type: " + arg0.getType() + ", " + arg1.getType());
+ return arg0.getType().compareTo(arg1.getType());
+ }
+
+ return 0;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/graphics/package-info.java b/model/src/main/java/lcsb/mapviewer/model/graphics/package-info.java
index 1bbf7b7b8b..12c79169f4 100644
--- a/model/src/main/java/lcsb/mapviewer/model/graphics/package-info.java
+++ b/model/src/main/java/lcsb/mapviewer/model/graphics/package-info.java
@@ -1,6 +1,6 @@
-/**
- * Provides structures that represent graphical elements. The elements doesn't
- * have to belong to the map.
- */
-package lcsb.mapviewer.model.graphics;
-
+/**
+ * Provides structures that represent graphical elements. The elements doesn't
+ * have to belong to the map.
+ */
+package lcsb.mapviewer.model.graphics;
+
diff --git a/model/src/main/java/lcsb/mapviewer/model/log/GenericLog.java b/model/src/main/java/lcsb/mapviewer/model/log/GenericLog.java
index a0bb4fccee..0707e937a9 100644
--- a/model/src/main/java/lcsb/mapviewer/model/log/GenericLog.java
+++ b/model/src/main/java/lcsb/mapviewer/model/log/GenericLog.java
@@ -1,154 +1,154 @@
-package lcsb.mapviewer.model.log;
-
-import java.io.Serializable;
-import java.util.Calendar;
-
-import javax.persistence.Column;
-import javax.persistence.DiscriminatorColumn;
-import javax.persistence.DiscriminatorType;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Inheritance;
-import javax.persistence.InheritanceType;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-
-import lcsb.mapviewer.model.user.User;
-
-/**
- * Generic object representing log entry.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "log_table")
-@Inheritance(strategy = InheritanceType.SINGLE_TABLE)
-@DiscriminatorColumn(name = "log_type_db", discriminatorType = DiscriminatorType.STRING)
-@DiscriminatorValue("GENERIC_LOG")
-public abstract class GenericLog implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Unique database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- /**
- * Logged user responsible for the log event.
- */
- @ManyToOne(fetch = FetchType.LAZY)
- private User user;
-
- /**
- * Type of the logged event.
- */
- private LogType type;
-
- /**
- * Description with additional information.
- */
- private String description;
-
- /**
- * When the event took place.
- */
- private Calendar time;
-
- /**
- * @return the id
- * @see #id
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
- /**
- * @return the user
- * @see #user
- */
- public User getUser() {
- return user;
- }
-
- /**
- * @param user
- * the user to set
- * @see #user
- */
- public void setUser(User user) {
- this.user = user;
- }
-
- /**
- * @return the type
- * @see #type
- */
- public LogType getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(LogType type) {
- this.type = type;
- }
-
- /**
- * @return the description
- * @see #description
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * @param description
- * the description to set
- * @see #description
- */
- public void setDescription(String description) {
- this.description = description;
- }
-
- /**
- * @return the time
- * @see #time
- */
- public Calendar getTime() {
- return time;
- }
-
- /**
- * @param time
- * the time to set
- * @see #time
- */
- public void setTime(Calendar time) {
- this.time = time;
- }
-
-}
+package lcsb.mapviewer.model.log;
+
+import java.io.Serializable;
+import java.util.Calendar;
+
+import javax.persistence.Column;
+import javax.persistence.DiscriminatorColumn;
+import javax.persistence.DiscriminatorType;
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.Inheritance;
+import javax.persistence.InheritanceType;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+
+import lcsb.mapviewer.model.user.User;
+
+/**
+ * Generic object representing log entry.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "log_table")
+@Inheritance(strategy = InheritanceType.SINGLE_TABLE)
+@DiscriminatorColumn(name = "log_type_db", discriminatorType = DiscriminatorType.STRING)
+@DiscriminatorValue("GENERIC_LOG")
+public abstract class GenericLog implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Unique database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * Logged user responsible for the log event.
+ */
+ @ManyToOne(fetch = FetchType.LAZY)
+ private User user;
+
+ /**
+ * Type of the logged event.
+ */
+ private LogType type;
+
+ /**
+ * Description with additional information.
+ */
+ private String description;
+
+ /**
+ * When the event took place.
+ */
+ private Calendar time;
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ /**
+ * @return the user
+ * @see #user
+ */
+ public User getUser() {
+ return user;
+ }
+
+ /**
+ * @param user
+ * the user to set
+ * @see #user
+ */
+ public void setUser(User user) {
+ this.user = user;
+ }
+
+ /**
+ * @return the type
+ * @see #type
+ */
+ public LogType getType() {
+ return type;
+ }
+
+ /**
+ * @param type
+ * the type to set
+ * @see #type
+ */
+ public void setType(LogType type) {
+ this.type = type;
+ }
+
+ /**
+ * @return the description
+ * @see #description
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * @param description
+ * the description to set
+ * @see #description
+ */
+ public void setDescription(String description) {
+ this.description = description;
+ }
+
+ /**
+ * @return the time
+ * @see #time
+ */
+ public Calendar getTime() {
+ return time;
+ }
+
+ /**
+ * @param time
+ * the time to set
+ * @see #time
+ */
+ public void setTime(Calendar time) {
+ this.time = time;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/log/LogType.java b/model/src/main/java/lcsb/mapviewer/model/log/LogType.java
index 3fbcfceb0a..3521cc7678 100644
--- a/model/src/main/java/lcsb/mapviewer/model/log/LogType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/log/LogType.java
@@ -1,60 +1,60 @@
-package lcsb.mapviewer.model.log;
-
-/**
- * Types of log events.
- *
- * @author Piotr Gawron
- *
- */
-public enum LogType {
- /**
- * New data mining object was added to the map.
- */
- ADD_MISSING_CONNECTION,
-
- /**
- * Data mining object was removed from the map.
- */
- REMOVE_MISSING_CONNECTION,
-
- /**
- * User logged in.
- */
- USER_LOGIN,
-
- /**
- * User logged out.
- */
- USER_LOGOUT,
-
- /**
- * User was created.
- */
- USER_CREATED,
-
- /**
- * User was removed.
- */
- USER_REMOVED,
-
- /**
- * Map was created.
- */
- MAP_CREATED,
-
- /**
- * Map was removed.
- */
- MAP_REMOVED,
-
- /**
- * Custom layout was added.
- */
- LAYOUT_CREATED,
-
- /**
- * Custom layout was removed.
- */
- LAYOUT_REMOVED
-
-}
+package lcsb.mapviewer.model.log;
+
+/**
+ * Types of log events.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum LogType {
+ /**
+ * New data mining object was added to the map.
+ */
+ ADD_MISSING_CONNECTION,
+
+ /**
+ * Data mining object was removed from the map.
+ */
+ REMOVE_MISSING_CONNECTION,
+
+ /**
+ * User logged in.
+ */
+ USER_LOGIN,
+
+ /**
+ * User logged out.
+ */
+ USER_LOGOUT,
+
+ /**
+ * User was created.
+ */
+ USER_CREATED,
+
+ /**
+ * User was removed.
+ */
+ USER_REMOVED,
+
+ /**
+ * Map was created.
+ */
+ MAP_CREATED,
+
+ /**
+ * Map was removed.
+ */
+ MAP_REMOVED,
+
+ /**
+ * Custom layout was added.
+ */
+ LAYOUT_CREATED,
+
+ /**
+ * Custom layout was removed.
+ */
+ LAYOUT_REMOVED
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/log/ObjectLog.java b/model/src/main/java/lcsb/mapviewer/model/log/ObjectLog.java
index 1aef02d174..c56a478349 100644
--- a/model/src/main/java/lcsb/mapviewer/model/log/ObjectLog.java
+++ b/model/src/main/java/lcsb/mapviewer/model/log/ObjectLog.java
@@ -1,63 +1,63 @@
-package lcsb.mapviewer.model.log;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-/**
- * Log entry that has refernce to an object in the database.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("OBJECT_LOG")
-public class ObjectLog extends GenericLog {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Identifier of the referenced object in database.
- */
- private Integer objectId;
-
- /**
- * Class of the object that is referenced by this log entry.
- */
- private Class<?> tableName;
-
- /**
- * @return the objectId
- * @see #objectId
- */
- public Integer getObjectId() {
- return objectId;
- }
-
- /**
- * @param objectId
- * the objectId to set
- * @see #objectId
- */
- public void setObjectId(Integer objectId) {
- this.objectId = objectId;
- }
-
- /**
- * @return the tableName
- * @see #tableName
- */
- public Class<?> getTable() {
- return tableName;
- }
-
- /**
- * @param tableName
- * the tableName to set
- * @see #tableName
- */
- public void setTable(Class<?> tableName) {
- this.tableName = tableName;
- }
-}
+package lcsb.mapviewer.model.log;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+/**
+ * Log entry that has refernce to an object in the database.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("OBJECT_LOG")
+public class ObjectLog extends GenericLog {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Identifier of the referenced object in database.
+ */
+ private Integer objectId;
+
+ /**
+ * Class of the object that is referenced by this log entry.
+ */
+ private Class<?> tableName;
+
+ /**
+ * @return the objectId
+ * @see #objectId
+ */
+ public Integer getObjectId() {
+ return objectId;
+ }
+
+ /**
+ * @param objectId
+ * the objectId to set
+ * @see #objectId
+ */
+ public void setObjectId(Integer objectId) {
+ this.objectId = objectId;
+ }
+
+ /**
+ * @return the tableName
+ * @see #tableName
+ */
+ public Class<?> getTable() {
+ return tableName;
+ }
+
+ /**
+ * @param tableName
+ * the tableName to set
+ * @see #tableName
+ */
+ public void setTable(Class<?> tableName) {
+ this.tableName = tableName;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/log/SystemLog.java b/model/src/main/java/lcsb/mapviewer/model/log/SystemLog.java
index 52c939983a..e0162e53e1 100644
--- a/model/src/main/java/lcsb/mapviewer/model/log/SystemLog.java
+++ b/model/src/main/java/lcsb/mapviewer/model/log/SystemLog.java
@@ -1,20 +1,20 @@
-package lcsb.mapviewer.model.log;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-/**
- * General system log entry.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("SYSTEM_LOG")
-public class SystemLog extends GenericLog {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-}
+package lcsb.mapviewer.model.log;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+/**
+ * General system log entry.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("SYSTEM_LOG")
+public class SystemLog extends GenericLog {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/log/package-info.java b/model/src/main/java/lcsb/mapviewer/model/log/package-info.java
index aed68ab8f6..979acf8dc9 100644
--- a/model/src/main/java/lcsb/mapviewer/model/log/package-info.java
+++ b/model/src/main/java/lcsb/mapviewer/model/log/package-info.java
@@ -1,5 +1,5 @@
-/**
- * Provides structures used for loggin system events.
- */
-package lcsb.mapviewer.model.log;
-
+/**
+ * Provides structures used for loggin system events.
+ */
+package lcsb.mapviewer.model.log;
+
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java b/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java
index a54150fd8b..44f2935266 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java
@@ -1,201 +1,201 @@
-package lcsb.mapviewer.model.map;
-
-import java.io.Serializable;
-import java.util.Collection;
-import java.util.Comparator;
-import java.util.List;
-
-import lcsb.mapviewer.common.comparator.IntegerComparator;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * Interface that describes bio entity on the map (like Protein or Reaction).
- *
- * @author Piotr Gawron
- *
- */
-public interface BioEntity extends Serializable {
- Comparator<? super BioEntity> ID_COMPARATOR = new Comparator<BioEntity>() {
-
- @Override
- public int compare(BioEntity o1, BioEntity o2) {
- Integer id1 = null;
- Integer id2 = null;
- if (o1 != null) {
- id1 = o1.getId();
- if (o1 instanceof Reaction) {
- id1 *= -1;
- }
- }
- if (o2 != null) {
- id2 = o2.getId();
- if (o2 instanceof Reaction) {
- id2 *= -1;
- }
- }
- return new IntegerComparator().compare(id1, id2);
- }
- };
-
- /**
- * Returns list of {@link MiriamData annotations} for the object.
- *
- * @return list of {@link MiriamData annotations} for the object
- */
- Collection<MiriamData> getMiriamData();
-
- /**
- * Adds miriam annotations to the element.
- *
- * @param miriamData
- * set of miriam annotations to be added
- */
- void addMiriamData(Collection<MiriamData> miriamData);
-
- /**
- * Adds miriam annotation to the element.
- *
- * @param md
- * miriam annotation to be added
- */
- void addMiriamData(MiriamData md);
-
- /**
- * Returns the name of the object.
- *
- * @return the name of the object
- */
- String getName();
-
- /**
- * Returns notes about the object.
- *
- * @return notes about the object
- */
- String getNotes();
-
- /**
- * Sets notes about the object.
- *
- * @param notes
- * new notes
- */
- void setNotes(String notes);
-
- /**
- * Returns the symbol of the element.
- *
- * @return the symbol of the element
- */
- String getSymbol();
-
- /**
- * Sets symbol of the element.
- *
- * @param symbol
- * new symbol
- */
- void setSymbol(String symbol);
-
- /**
- * Get list of synonyms.
- *
- * @return list of synonyms
- */
- List<String> getSynonyms();
-
- /**
- * Sets list of synonyms to the element.
- *
- * @param synonyms
- * new list
- */
- void setSynonyms(List<String> synonyms);
-
- /**
- * Returns the abbreviation.
- *
- * @return the abbreviation
- */
- String getAbbreviation();
-
- /**
- * Sets abbreviation.
- *
- * @param abbreviation
- * new abbreviation
- */
- void setAbbreviation(String abbreviation);
-
- /**
- * Sets formula.
- *
- * @param formula
- * new formula
- */
- void setFormula(String formula);
-
- /**
- * Returns the formula.
- *
- * @return the formula
- */
- String getFormula();
-
- /**
- * Sets the name to the object.
- *
- * @param name
- * name of the object
- *
- */
- void setName(String name);
-
- /**
- * Returns database identifier of the object.
- *
- * @return database identifier of the object
- */
- int getId();
-
- /**
- * Return human readable {@link String} representing class.
- *
- * @return human readable {@link String} representing class
- */
- String getStringType();
-
- /**
- * Sets semantic zoom level visibility.
- *
- * @param zoomLevelVisibility
- * semantic zoom level visibility
- */
- void setVisibilityLevel(String zoomLevelVisibility);
-
- /**
- * Sets semantic zoom level visibility.
- *
- * @param zoomLevelVisibility
- * semantic zoom level visibility
- */
- void setVisibilityLevel(Integer zoomLevelVisibility);
-
- /**
- * Returns semantic zoom level visibility.
- *
- * @return semantic zoom level visibility
- */
- String getVisibilityLevel();
-
- /**
- * Returns the {@link Model} where BioEntity is located.
- *
- * @return the model
- */
- Model getModel();
-
- String getElementId();
-
-}
+package lcsb.mapviewer.model.map;
+
+import java.io.Serializable;
+import java.util.Collection;
+import java.util.Comparator;
+import java.util.List;
+
+import lcsb.mapviewer.common.comparator.IntegerComparator;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * Interface that describes bio entity on the map (like Protein or Reaction).
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface BioEntity extends Serializable {
+ Comparator<? super BioEntity> ID_COMPARATOR = new Comparator<BioEntity>() {
+
+ @Override
+ public int compare(BioEntity o1, BioEntity o2) {
+ Integer id1 = null;
+ Integer id2 = null;
+ if (o1 != null) {
+ id1 = o1.getId();
+ if (o1 instanceof Reaction) {
+ id1 *= -1;
+ }
+ }
+ if (o2 != null) {
+ id2 = o2.getId();
+ if (o2 instanceof Reaction) {
+ id2 *= -1;
+ }
+ }
+ return new IntegerComparator().compare(id1, id2);
+ }
+ };
+
+ /**
+ * Returns list of {@link MiriamData annotations} for the object.
+ *
+ * @return list of {@link MiriamData annotations} for the object
+ */
+ Collection<MiriamData> getMiriamData();
+
+ /**
+ * Adds miriam annotations to the element.
+ *
+ * @param miriamData
+ * set of miriam annotations to be added
+ */
+ void addMiriamData(Collection<MiriamData> miriamData);
+
+ /**
+ * Adds miriam annotation to the element.
+ *
+ * @param md
+ * miriam annotation to be added
+ */
+ void addMiriamData(MiriamData md);
+
+ /**
+ * Returns the name of the object.
+ *
+ * @return the name of the object
+ */
+ String getName();
+
+ /**
+ * Returns notes about the object.
+ *
+ * @return notes about the object
+ */
+ String getNotes();
+
+ /**
+ * Sets notes about the object.
+ *
+ * @param notes
+ * new notes
+ */
+ void setNotes(String notes);
+
+ /**
+ * Returns the symbol of the element.
+ *
+ * @return the symbol of the element
+ */
+ String getSymbol();
+
+ /**
+ * Sets symbol of the element.
+ *
+ * @param symbol
+ * new symbol
+ */
+ void setSymbol(String symbol);
+
+ /**
+ * Get list of synonyms.
+ *
+ * @return list of synonyms
+ */
+ List<String> getSynonyms();
+
+ /**
+ * Sets list of synonyms to the element.
+ *
+ * @param synonyms
+ * new list
+ */
+ void setSynonyms(List<String> synonyms);
+
+ /**
+ * Returns the abbreviation.
+ *
+ * @return the abbreviation
+ */
+ String getAbbreviation();
+
+ /**
+ * Sets abbreviation.
+ *
+ * @param abbreviation
+ * new abbreviation
+ */
+ void setAbbreviation(String abbreviation);
+
+ /**
+ * Sets formula.
+ *
+ * @param formula
+ * new formula
+ */
+ void setFormula(String formula);
+
+ /**
+ * Returns the formula.
+ *
+ * @return the formula
+ */
+ String getFormula();
+
+ /**
+ * Sets the name to the object.
+ *
+ * @param name
+ * name of the object
+ *
+ */
+ void setName(String name);
+
+ /**
+ * Returns database identifier of the object.
+ *
+ * @return database identifier of the object
+ */
+ int getId();
+
+ /**
+ * Return human readable {@link String} representing class.
+ *
+ * @return human readable {@link String} representing class
+ */
+ String getStringType();
+
+ /**
+ * Sets semantic zoom level visibility.
+ *
+ * @param zoomLevelVisibility
+ * semantic zoom level visibility
+ */
+ void setVisibilityLevel(String zoomLevelVisibility);
+
+ /**
+ * Sets semantic zoom level visibility.
+ *
+ * @param zoomLevelVisibility
+ * semantic zoom level visibility
+ */
+ void setVisibilityLevel(Integer zoomLevelVisibility);
+
+ /**
+ * Returns semantic zoom level visibility.
+ *
+ * @return semantic zoom level visibility
+ */
+ String getVisibilityLevel();
+
+ /**
+ * Returns the {@link Model} where BioEntity is located.
+ *
+ * @return the model
+ */
+ Model getModel();
+
+ String getElementId();
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/Comment.java b/model/src/main/java/lcsb/mapviewer/model/map/Comment.java
index 6e348820ca..bef4430dab 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/Comment.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/Comment.java
@@ -1,357 +1,357 @@
-package lcsb.mapviewer.model.map;
-
-import java.awt.geom.Point2D;
-import java.io.Serializable;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-
-import org.hibernate.annotations.Type;
-
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.user.User;
-
-/**
- * Class representing comments on the map.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "feedback")
-public class Comment implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Is the feedback removed.
- */
- private boolean deleted = false;
-
- /**
- * What was the reason of removal.
- */
- private String removeReason = "";
-
- /**
- * Unique database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- /**
- * Name of the user that insert this feedback.
- */
- private String name;
-
- /**
- * The model that was commented.
- */
- @ManyToOne(fetch = FetchType.LAZY)
- private ModelData model;
-
- /**
- * The model that was commented.
- */
- @ManyToOne(fetch = FetchType.LAZY)
- private ModelData submodel;
-
- /**
- * User who gave the feedback (if logged in).
- */
- @ManyToOne(fetch = FetchType.LAZY)
- private User user;
-
- /**
- * Email of the user who gave feedback.
- */
- private String email;
-
- /**
- * Content of the feedback.
- */
- @Column(columnDefinition = "TEXT")
- private String content;
-
- /**
- * Where on map the feedback is located.
- */
- @Type(type = "lcsb.mapviewer.persist.mapper.Point2DMapper")
- private Point2D coordinates;
-
- /**
- * If feedback is located on the element, what is the type of the element.
- */
- private Class<?> tableName;
-
- /**
- * If feedback is located on the element, what is the identifier of the element.
- */
- private Integer tableId;
-
- /**
- * @return the tableId
- * @see #tableId
- */
- public Integer getTableId() {
- return tableId;
- }
-
- /**
- * @param tableId
- * the tableId to set
- * @see #tableId
- */
- public void setTableId(Integer tableId) {
- this.tableId = tableId;
- }
-
- /**
- * @return the tableName
- * @see #tableName
- */
- public Class<?> getTableName() {
- return tableName;
- }
-
- /**
- * @param tableName
- * the tableName to set
- * @see #tableName
- */
- public void setTableName(Class<?> tableName) {
- this.tableName = tableName;
- }
-
- /**
- * @return the coordinates
- * @see #coordinates
- */
- public Point2D getCoordinates() {
- return coordinates;
- }
-
- /**
- * @param coordinates
- * the coordinates to set
- * @see #coordinates
- */
- public void setCoordinates(Point2D coordinates) {
- this.coordinates = coordinates;
- }
-
- /**
- * @return the content
- * @see #content
- */
- public String getContent() {
- return content;
- }
-
- /**
- * @param content
- * the content to set
- * @see #content
- */
- public void setContent(String content) {
- this.content = content;
- }
-
- /**
- * @return the email
- * @see #email
- */
- public String getEmail() {
- return email;
- }
-
- /**
- * @param email
- * the email to set
- * @see #email
- */
- public void setEmail(String email) {
- this.email = email;
- }
-
- /**
- * @return the user
- * @see #user
- */
- public User getUser() {
- return user;
- }
-
- /**
- * @param user
- * the user to set
- * @see #user
- */
- public void setUser(User user) {
- this.user = user;
- }
-
- /**
- * @return the model
- * @see #model
- */
- public ModelData getModelData() {
- return model;
- }
-
- /**
- * @param model
- * the model to set
- * @see #model
- */
- public void setModelData(ModelData model) {
- this.model = model;
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return the id
- * @see #id
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
- /**
- * @return the removeReason
- * @see #removeReason
- */
- public String getRemoveReason() {
- return removeReason;
- }
-
- /**
- * @param removeReason
- * the removeReason to set
- * @see #removeReason
- */
- public void setRemoveReason(String removeReason) {
- this.removeReason = removeReason;
- }
-
- /**
- * @return the deleted
- * @see #deleted
- */
- public boolean isDeleted() {
- return deleted;
- }
-
- /**
- * @param deleted
- * the deleted to set
- * @see #deleted
- */
- public void setDeleted(boolean deleted) {
- this.deleted = deleted;
- }
-
- /**
- * Determines if comment should be visible on the map.
- */
- private boolean pinned = false;
-
- /**
- * @return the pinned
- * @see #pinned
- */
- public boolean isPinned() {
- return pinned;
- }
-
- /**
- * @param pinned
- * the pinned to set
- * @see #pinned
- */
- public void setPinned(boolean pinned) {
- this.pinned = pinned;
- }
-
- /**
- * Sets model.
- *
- * @param model2
- * model to set
- */
- public void setModel(Model model2) {
- this.model = model2.getModelData();
- }
-
- /**
- * @return the submodel
- * @see #submodel
- */
- public ModelData getSubmodelData() {
- return submodel;
- }
-
- /**
- * @param submodel
- * the submodel to set
- * @see #submodel
- */
- public void setSubmodelData(ModelData submodel) {
- this.submodel = submodel;
- }
-
- /**
- * @param submodel
- * the submodel to set
- * @see #submodel
- */
- public void setSubmodel(Model submodel) {
- this.submodel = submodel.getModelData();
- }
-
- /**
- * @return the submodel
- * @see #submodel
- */
- public Model getSubmodel() {
- return this.submodel.getModel();
- }
-
-}
+package lcsb.mapviewer.model.map;
+
+import java.awt.geom.Point2D;
+import java.io.Serializable;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+
+import org.hibernate.annotations.Type;
+
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.user.User;
+
+/**
+ * Class representing comments on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "feedback")
+public class Comment implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Is the feedback removed.
+ */
+ private boolean deleted = false;
+
+ /**
+ * What was the reason of removal.
+ */
+ private String removeReason = "";
+
+ /**
+ * Unique database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * Name of the user that insert this feedback.
+ */
+ private String name;
+
+ /**
+ * The model that was commented.
+ */
+ @ManyToOne(fetch = FetchType.LAZY)
+ private ModelData model;
+
+ /**
+ * The model that was commented.
+ */
+ @ManyToOne(fetch = FetchType.LAZY)
+ private ModelData submodel;
+
+ /**
+ * User who gave the feedback (if logged in).
+ */
+ @ManyToOne(fetch = FetchType.LAZY)
+ private User user;
+
+ /**
+ * Email of the user who gave feedback.
+ */
+ private String email;
+
+ /**
+ * Content of the feedback.
+ */
+ @Column(columnDefinition = "TEXT")
+ private String content;
+
+ /**
+ * Where on map the feedback is located.
+ */
+ @Type(type = "lcsb.mapviewer.persist.mapper.Point2DMapper")
+ private Point2D coordinates;
+
+ /**
+ * If feedback is located on the element, what is the type of the element.
+ */
+ private Class<?> tableName;
+
+ /**
+ * If feedback is located on the element, what is the identifier of the element.
+ */
+ private Integer tableId;
+
+ /**
+ * @return the tableId
+ * @see #tableId
+ */
+ public Integer getTableId() {
+ return tableId;
+ }
+
+ /**
+ * @param tableId
+ * the tableId to set
+ * @see #tableId
+ */
+ public void setTableId(Integer tableId) {
+ this.tableId = tableId;
+ }
+
+ /**
+ * @return the tableName
+ * @see #tableName
+ */
+ public Class<?> getTableName() {
+ return tableName;
+ }
+
+ /**
+ * @param tableName
+ * the tableName to set
+ * @see #tableName
+ */
+ public void setTableName(Class<?> tableName) {
+ this.tableName = tableName;
+ }
+
+ /**
+ * @return the coordinates
+ * @see #coordinates
+ */
+ public Point2D getCoordinates() {
+ return coordinates;
+ }
+
+ /**
+ * @param coordinates
+ * the coordinates to set
+ * @see #coordinates
+ */
+ public void setCoordinates(Point2D coordinates) {
+ this.coordinates = coordinates;
+ }
+
+ /**
+ * @return the content
+ * @see #content
+ */
+ public String getContent() {
+ return content;
+ }
+
+ /**
+ * @param content
+ * the content to set
+ * @see #content
+ */
+ public void setContent(String content) {
+ this.content = content;
+ }
+
+ /**
+ * @return the email
+ * @see #email
+ */
+ public String getEmail() {
+ return email;
+ }
+
+ /**
+ * @param email
+ * the email to set
+ * @see #email
+ */
+ public void setEmail(String email) {
+ this.email = email;
+ }
+
+ /**
+ * @return the user
+ * @see #user
+ */
+ public User getUser() {
+ return user;
+ }
+
+ /**
+ * @param user
+ * the user to set
+ * @see #user
+ */
+ public void setUser(User user) {
+ this.user = user;
+ }
+
+ /**
+ * @return the model
+ * @see #model
+ */
+ public ModelData getModelData() {
+ return model;
+ }
+
+ /**
+ * @param model
+ * the model to set
+ * @see #model
+ */
+ public void setModelData(ModelData model) {
+ this.model = model;
+ }
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ /**
+ * @return the removeReason
+ * @see #removeReason
+ */
+ public String getRemoveReason() {
+ return removeReason;
+ }
+
+ /**
+ * @param removeReason
+ * the removeReason to set
+ * @see #removeReason
+ */
+ public void setRemoveReason(String removeReason) {
+ this.removeReason = removeReason;
+ }
+
+ /**
+ * @return the deleted
+ * @see #deleted
+ */
+ public boolean isDeleted() {
+ return deleted;
+ }
+
+ /**
+ * @param deleted
+ * the deleted to set
+ * @see #deleted
+ */
+ public void setDeleted(boolean deleted) {
+ this.deleted = deleted;
+ }
+
+ /**
+ * Determines if comment should be visible on the map.
+ */
+ private boolean pinned = false;
+
+ /**
+ * @return the pinned
+ * @see #pinned
+ */
+ public boolean isPinned() {
+ return pinned;
+ }
+
+ /**
+ * @param pinned
+ * the pinned to set
+ * @see #pinned
+ */
+ public void setPinned(boolean pinned) {
+ this.pinned = pinned;
+ }
+
+ /**
+ * Sets model.
+ *
+ * @param model2
+ * model to set
+ */
+ public void setModel(Model model2) {
+ this.model = model2.getModelData();
+ }
+
+ /**
+ * @return the submodel
+ * @see #submodel
+ */
+ public ModelData getSubmodelData() {
+ return submodel;
+ }
+
+ /**
+ * @param submodel
+ * the submodel to set
+ * @see #submodel
+ */
+ public void setSubmodelData(ModelData submodel) {
+ this.submodel = submodel;
+ }
+
+ /**
+ * @param submodel
+ * the submodel to set
+ * @see #submodel
+ */
+ public void setSubmodel(Model submodel) {
+ this.submodel = submodel.getModelData();
+ }
+
+ /**
+ * @return the submodel
+ * @see #submodel
+ */
+ public Model getSubmodel() {
+ return this.submodel.getModel();
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/ElementInFewParentsException.java b/model/src/main/java/lcsb/mapviewer/model/map/ElementInFewParentsException.java
index 3938eb8261..795ddbb7f8 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/ElementInFewParentsException.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/ElementInFewParentsException.java
@@ -1,24 +1,24 @@
-package lcsb.mapviewer.model.map;
-
-/**
- * Exception thrown when one element has more then one parent.
- *
- * @author Piotr Gawron
- *
- */
-public class ElementInFewParentsException extends Exception {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor with a message passed in the argument.
- *
- * @param message
- * text message of this exception
- */
- public ElementInFewParentsException(String message) {
- super(message);
- }
-}
+package lcsb.mapviewer.model.map;
+
+/**
+ * Exception thrown when one element has more then one parent.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ElementInFewParentsException extends Exception {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor with a message passed in the argument.
+ *
+ * @param message
+ * text message of this exception
+ */
+ public ElementInFewParentsException(String message) {
+ super(message);
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/InconsistentModelException.java b/model/src/main/java/lcsb/mapviewer/model/map/InconsistentModelException.java
index a823e1bf11..2cfa3c8905 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/InconsistentModelException.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/InconsistentModelException.java
@@ -1,28 +1,28 @@
-package lcsb.mapviewer.model.map;
-
-/**
- * Exception thrown when model is inconsistent.
- *
- * @author Piotr Gawron
- *
- */
-public class InconsistentModelException extends Exception {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor with a message passed in the argument.
- *
- * @param message
- * text message of this exception
- */
- public InconsistentModelException(String message) {
- super(message);
- }
-
- public InconsistentModelException(Exception e) {
- super(e);
- }
-}
+package lcsb.mapviewer.model.map;
+
+/**
+ * Exception thrown when model is inconsistent.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class InconsistentModelException extends Exception {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor with a message passed in the argument.
+ *
+ * @param message
+ * text message of this exception
+ */
+ public InconsistentModelException(String message) {
+ super(message);
+ }
+
+ public InconsistentModelException(Exception e) {
+ super(e);
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/MiriamData.java b/model/src/main/java/lcsb/mapviewer/model/map/MiriamData.java
index 6d66b971d4..e852b4fca2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamData.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamData.java
@@ -1,311 +1,311 @@
-package lcsb.mapviewer.model.map;
-
-import java.io.Serializable;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.EnumType;
-import javax.persistence.Enumerated;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Table;
-import javax.xml.bind.annotation.XmlRootElement;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-
-/**
- * Representation of a single species or reaction annotation. Miriam format is a
- * standard described <a href="http://www.ebi.ac.uk/miriam/main/">here</a>
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "miriam_data_table")
-@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
-@XmlRootElement
-public class MiriamData implements Comparable<MiriamData>, Serializable {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(MiriamData.class);
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Unique database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- /**
- * What is the connection between element and the annotation.
- */
- private MiriamRelationType relationType = null;
-
- /**
- * Type of database.
- */
- @Enumerated(EnumType.STRING)
- private MiriamType dataType;
-
- /**
- * Resource identifier in the database.
- */
- @Column(name = "resource")
- private String resource = "";
-
- /**
- * The annotator which created the miriam data or which
- * should be associated with it.
- */
- @Column(name = "annotator")
- private Class<?> annotator = null;
-
- /**
- * Default constructor.
- */
- public MiriamData() {
- super();
- }
-
- /**
- * Constructor that initialize the data by information from param.
- *
- * @param md
- * original miriam data object
- */
- public MiriamData(MiriamData md) {
- setRelationType(md.relationType);
- setDataType(md.dataType);
- setResource(md.resource);
- setAnnotator(md.annotator);
- }
-
- /**
- * Constructor that initialize the data by information from params.
- *
- * @param relationType
- * {@link #relationType}
- * @param mt
- * type of the miriam data (see: {@link MiriamType})
- * @param resource
- * {@link #resource}
- * @param annotator
- * {@link #annotator}
- *
- */
- public MiriamData(MiriamRelationType relationType, MiriamType mt, String resource, Class<?> annotator) {
- if (mt == null) {
- throw new InvalidArgumentException("MiriamType cannot be null");
- }
- if (relationType == null) {
- throw new InvalidArgumentException("MiriamRelationType cannot be null");
- }
- setRelationType(relationType);
- setDataType(mt);
- setResource(resource);
- setAnnotator(annotator);
- }
-
- /**
- * Constructor that initialize the data by information from params.
- *
- * @param relationType
- * {@link #relationType}
- * @param mt
- * type of the miriam data (see: {@link MiriamType})
- * @param resource
- * {@link #resource}
- */
- public MiriamData(MiriamRelationType relationType, MiriamType mt, String resource) {
- this(relationType, mt, resource, null);
- }
-
- /**
- * Constructor that initialize the data by information from params.
- *
- * @param mt
- * type of the miriam data (see: {@link MiriamType})
- * @param resource
- * {@link #resource}
- */
- public MiriamData(MiriamType mt, String resource, Class<?> annotator) {
- this(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, mt, resource, annotator);
- }
-
-
- /**
- * Constructor that initialize the data by information from params.
- *
- * @param mt
- * type of the miriam data (see: {@link MiriamType})
- * @param resource
- * {@link #resource}
- */
- public MiriamData(MiriamType mt, String resource) {
- this(mt, resource, null);
- }
-
- /**
- *
- * @return {@link #resource}
- */
- public String getResource() {
- return resource;
- }
-
- /**
- * @param identifier
- * string represents identifier.
- * @return {@link #resource}
- */
- public static String getIdFromIdentifier(String identifier) {
- if (identifier != null) {
- int index = identifier.indexOf(":");
- if (index != -1) {
- identifier = identifier.trim().substring(index + 1);
- }
- }
- return identifier;
- }
-
- /**
- * Sets new {@link #resource}.
- *
- * @param resource
- * new {@link #resource}
- */
- public void setResource(String resource) {
- if (resource == null) {
- this.resource = null;
- } else {
- this.resource = resource.replace("%3A", ":");
- }
- }
-
- @Override
- public boolean equals(Object aThat) {
- // check for self-comparison
- if (this == aThat) {
- return true;
- }
-
- // use instanceof instead of getClass here for two reasons
- // 1. if need be, it can match any supertype, and not just one class;
- // 2. it renders an explict check for "that == null" redundant, since
- // it does the check for null already - "null instanceof [type]" always
- // returns false. (See Effective Java by Joshua Bloch.)
- if (!(aThat instanceof MiriamData)) {
- return false;
- }
- // Alternative to the above line :
- // if ( aThat == null || aThat.getClass() != this.getClass() ) return false;
-
- // cast to native object is now safe
- MiriamData that = (MiriamData) aThat;
-
- // now a proper field-by-field evaluation can be made
- return this.compareTo(that) == 0;
- }
-
- @Override
- public int hashCode() {
- return (dataType + resource).hashCode();
- }
-
- @Override
- public int compareTo(MiriamData other) {
- String name = annotator != null ? annotator.getName() : "";
- String otherName = other.annotator != null ? other.annotator.getName() : "";
- return (dataType + ":" + resource + ":" + name).toLowerCase().compareTo((other.dataType + ":" + other.resource + ":" + otherName).toLowerCase());
- }
-
- /**
- * @return the id
- * @see #id
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
- /**
- * @return the dataType
- * @see #dataType
- */
- public MiriamType getDataType() {
- return dataType;
- }
-
- /**
- * @param dataType
- * the dataType to set
- * @see #dataType
- */
- public void setDataType(MiriamType dataType) {
- this.dataType = dataType;
- }
-
- /**
- * @return the relationType
- * @see #relationType
- */
- public MiriamRelationType getRelationType() {
- return relationType;
- }
-
- /**
- * @param relationType
- * the relationType to set
- * @see #relationType
- */
- public void setRelationType(MiriamRelationType relationType) {
- this.relationType = relationType;
- }
-
- /**
- *
- * @return {@link #annotator}
- */
- public Class<?> getAnnotator() {
- return annotator;
- }
-
- /**
- *
- * @param {@link #annotator}
- */
- public void setAnnotator(Class<?> annotator) {
- this.annotator = annotator;
- }
-
- @Override
- public String toString() {
- String annotatorClass = annotator != null ? ":" +annotator.getName() : "";
- if (relationType != null) {
- return "[" + relationType.getStringRepresentation() + "] " + dataType + ":" + resource + annotatorClass;
- } else {
- return "[UNKNOWN] " + dataType + ":" + resource + annotatorClass;
-
- }
- }
-}
+package lcsb.mapviewer.model.map;
+
+import java.io.Serializable;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.EnumType;
+import javax.persistence.Enumerated;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.Table;
+import javax.xml.bind.annotation.XmlRootElement;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+
+/**
+ * Representation of a single species or reaction annotation. Miriam format is a
+ * standard described <a href="http://www.ebi.ac.uk/miriam/main/">here</a>
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "miriam_data_table")
+@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
+@XmlRootElement
+public class MiriamData implements Comparable<MiriamData>, Serializable {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(MiriamData.class);
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Unique database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * What is the connection between element and the annotation.
+ */
+ private MiriamRelationType relationType = null;
+
+ /**
+ * Type of database.
+ */
+ @Enumerated(EnumType.STRING)
+ private MiriamType dataType;
+
+ /**
+ * Resource identifier in the database.
+ */
+ @Column(name = "resource")
+ private String resource = "";
+
+ /**
+ * The annotator which created the miriam data or which
+ * should be associated with it.
+ */
+ @Column(name = "annotator")
+ private Class<?> annotator = null;
+
+ /**
+ * Default constructor.
+ */
+ public MiriamData() {
+ super();
+ }
+
+ /**
+ * Constructor that initialize the data by information from param.
+ *
+ * @param md
+ * original miriam data object
+ */
+ public MiriamData(MiriamData md) {
+ setRelationType(md.relationType);
+ setDataType(md.dataType);
+ setResource(md.resource);
+ setAnnotator(md.annotator);
+ }
+
+ /**
+ * Constructor that initialize the data by information from params.
+ *
+ * @param relationType
+ * {@link #relationType}
+ * @param mt
+ * type of the miriam data (see: {@link MiriamType})
+ * @param resource
+ * {@link #resource}
+ * @param annotator
+ * {@link #annotator}
+ *
+ */
+ public MiriamData(MiriamRelationType relationType, MiriamType mt, String resource, Class<?> annotator) {
+ if (mt == null) {
+ throw new InvalidArgumentException("MiriamType cannot be null");
+ }
+ if (relationType == null) {
+ throw new InvalidArgumentException("MiriamRelationType cannot be null");
+ }
+ setRelationType(relationType);
+ setDataType(mt);
+ setResource(resource);
+ setAnnotator(annotator);
+ }
+
+ /**
+ * Constructor that initialize the data by information from params.
+ *
+ * @param relationType
+ * {@link #relationType}
+ * @param mt
+ * type of the miriam data (see: {@link MiriamType})
+ * @param resource
+ * {@link #resource}
+ */
+ public MiriamData(MiriamRelationType relationType, MiriamType mt, String resource) {
+ this(relationType, mt, resource, null);
+ }
+
+ /**
+ * Constructor that initialize the data by information from params.
+ *
+ * @param mt
+ * type of the miriam data (see: {@link MiriamType})
+ * @param resource
+ * {@link #resource}
+ */
+ public MiriamData(MiriamType mt, String resource, Class<?> annotator) {
+ this(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, mt, resource, annotator);
+ }
+
+
+ /**
+ * Constructor that initialize the data by information from params.
+ *
+ * @param mt
+ * type of the miriam data (see: {@link MiriamType})
+ * @param resource
+ * {@link #resource}
+ */
+ public MiriamData(MiriamType mt, String resource) {
+ this(mt, resource, null);
+ }
+
+ /**
+ *
+ * @return {@link #resource}
+ */
+ public String getResource() {
+ return resource;
+ }
+
+ /**
+ * @param identifier
+ * string represents identifier.
+ * @return {@link #resource}
+ */
+ public static String getIdFromIdentifier(String identifier) {
+ if (identifier != null) {
+ int index = identifier.indexOf(":");
+ if (index != -1) {
+ identifier = identifier.trim().substring(index + 1);
+ }
+ }
+ return identifier;
+ }
+
+ /**
+ * Sets new {@link #resource}.
+ *
+ * @param resource
+ * new {@link #resource}
+ */
+ public void setResource(String resource) {
+ if (resource == null) {
+ this.resource = null;
+ } else {
+ this.resource = resource.replace("%3A", ":");
+ }
+ }
+
+ @Override
+ public boolean equals(Object aThat) {
+ // check for self-comparison
+ if (this == aThat) {
+ return true;
+ }
+
+ // use instanceof instead of getClass here for two reasons
+ // 1. if need be, it can match any supertype, and not just one class;
+ // 2. it renders an explict check for "that == null" redundant, since
+ // it does the check for null already - "null instanceof [type]" always
+ // returns false. (See Effective Java by Joshua Bloch.)
+ if (!(aThat instanceof MiriamData)) {
+ return false;
+ }
+ // Alternative to the above line :
+ // if ( aThat == null || aThat.getClass() != this.getClass() ) return false;
+
+ // cast to native object is now safe
+ MiriamData that = (MiriamData) aThat;
+
+ // now a proper field-by-field evaluation can be made
+ return this.compareTo(that) == 0;
+ }
+
+ @Override
+ public int hashCode() {
+ return (dataType + resource).hashCode();
+ }
+
+ @Override
+ public int compareTo(MiriamData other) {
+ String name = annotator != null ? annotator.getName() : "";
+ String otherName = other.annotator != null ? other.annotator.getName() : "";
+ return (dataType + ":" + resource + ":" + name).toLowerCase().compareTo((other.dataType + ":" + other.resource + ":" + otherName).toLowerCase());
+ }
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ /**
+ * @return the dataType
+ * @see #dataType
+ */
+ public MiriamType getDataType() {
+ return dataType;
+ }
+
+ /**
+ * @param dataType
+ * the dataType to set
+ * @see #dataType
+ */
+ public void setDataType(MiriamType dataType) {
+ this.dataType = dataType;
+ }
+
+ /**
+ * @return the relationType
+ * @see #relationType
+ */
+ public MiriamRelationType getRelationType() {
+ return relationType;
+ }
+
+ /**
+ * @param relationType
+ * the relationType to set
+ * @see #relationType
+ */
+ public void setRelationType(MiriamRelationType relationType) {
+ this.relationType = relationType;
+ }
+
+ /**
+ *
+ * @return {@link #annotator}
+ */
+ public Class<?> getAnnotator() {
+ return annotator;
+ }
+
+ /**
+ *
+ * @param {@link #annotator}
+ */
+ public void setAnnotator(Class<?> annotator) {
+ this.annotator = annotator;
+ }
+
+ @Override
+ public String toString() {
+ String annotatorClass = annotator != null ? ":" +annotator.getName() : "";
+ if (relationType != null) {
+ return "[" + relationType.getStringRepresentation() + "] " + dataType + ":" + resource + annotatorClass;
+ } else {
+ return "[UNKNOWN] " + dataType + ":" + resource + annotatorClass;
+
+ }
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/MiriamRelationType.java b/model/src/main/java/lcsb/mapviewer/model/map/MiriamRelationType.java
index 5f400b9cc9..0ee468edb9 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamRelationType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamRelationType.java
@@ -1,112 +1,112 @@
-package lcsb.mapviewer.model.map;
-
-/**
- * Encodes list of biomodel qualifiers used for description in miriam
- * references. More information can be found <a
- * href="http://co.mbine.org/standards/qualifiers">here</a>.
- *
- * @author Piotr Gawron
- *
- */
-public enum MiriamRelationType {
-
- /**
- * Take a look <a href="http://co.mbine.org/standards/qualifiers">here</a>.
- */
- BQ_MODEL_IS("bqmodel:is"),
-
- /**
- * Take a look <a href="http://co.mbine.org/standards/qualifiers">here</a>.
- */
- BQ_MODEL_IS_DESCRIBED_BY("bqmodel:isDescribedBy"),
-
- /**
- * Take a look <a href="http://co.mbine.org/standards/qualifiers">here</a>.
- */
- BQ_BIOL_IS("bqbiol:is"),
-
- /**
- * Take a look <a href="http://co.mbine.org/standards/qualifiers">here</a>.
- */
- BQ_BIOL_HAS_PART("bqbiol:hasPart"),
-
- /**
- * Take a look <a href="http://co.mbine.org/standards/qualifiers">here</a>.
- */
- BQ_BIOL_IS_PART_OF("bqbiol:isPartOf"),
-
- /**
- * Take a look <a href="http://co.mbine.org/standards/qualifiers">here</a>.
- */
- BQ_BIOL_IS_VERSION_OF("bqbiol:isVersionOf"),
-
- /**
- * Take a look <a href="http://co.mbine.org/standards/qualifiers">here</a>.
- */
- BQ_BIOL_HAS_VERSION("bqbiol:hasVersion"),
-
- /**
- * Take a look <a href="http://co.mbine.org/standards/qualifiers">here</a>.
- */
- BQ_BIOL_IS_HOMOLOG_TO("bqbiol:isHomologTo"),
-
- /**
- * Take a look <a href="http://co.mbine.org/standards/qualifiers">here</a>.
- */
- BQ_BIOL_IS_DESCRIBED_BY("bqbiol:isDescribedBy"),
-
- /**
- * Take a look <a href="http://co.mbine.org/standards/qualifiers">here</a>.
- */
- BQ_BIOL_IS_ENCODED_BY("bqbiol:isEncodedBy"),
-
- /**
- * Take a look <a href="http://co.mbine.org/standards/qualifiers">here</a>.
- */
- BQ_BIOL_ENCODES("bqbiol:encodes"),
-
- /**
- * Take a look <a href="http://co.mbine.org/standards/qualifiers">here</a>.
- */
- BQ_BIOL_OCCURES("bqbiol:occures");
-
- /**
- * String representing relation. List of all possibilites can be found <a
- * href="http://co.mbine.org/standards/qualifiers">here</a>.
- */
- private String stringRepresentation;
-
- /**
- * Default constructor.
- *
- * @param stringRepresentation
- * {@link #stringRepresentation}
- */
- MiriamRelationType(String stringRepresentation) {
- this.stringRepresentation = stringRepresentation;
- }
-
- /**
- * @return the stringRepresentation
- * @see #stringRepresentation
- */
- public String getStringRepresentation() {
- return stringRepresentation;
- }
-
- /**
- * Returns {@link MiriamRelationType} associated with #stringRepresentation.
- *
- * @param string
- * #stringRepresentation
- * @return {@link MiriamRelationType} for given #stringRepresentation
- */
- public static MiriamRelationType getTypeByStringRepresentation(String string) {
- for (MiriamRelationType mrt : MiriamRelationType.values()) {
- if (mrt.getStringRepresentation().equalsIgnoreCase(string)) {
- return mrt;
- }
- }
- return null;
- }
-}
+package lcsb.mapviewer.model.map;
+
+/**
+ * Encodes list of biomodel qualifiers used for description in miriam
+ * references. More information can be found <a
+ * href="http://co.mbine.org/standards/qualifiers">here</a>.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum MiriamRelationType {
+
+ /**
+ * Take a look <a href="http://co.mbine.org/standards/qualifiers">here</a>.
+ */
+ BQ_MODEL_IS("bqmodel:is"),
+
+ /**
+ * Take a look <a href="http://co.mbine.org/standards/qualifiers">here</a>.
+ */
+ BQ_MODEL_IS_DESCRIBED_BY("bqmodel:isDescribedBy"),
+
+ /**
+ * Take a look <a href="http://co.mbine.org/standards/qualifiers">here</a>.
+ */
+ BQ_BIOL_IS("bqbiol:is"),
+
+ /**
+ * Take a look <a href="http://co.mbine.org/standards/qualifiers">here</a>.
+ */
+ BQ_BIOL_HAS_PART("bqbiol:hasPart"),
+
+ /**
+ * Take a look <a href="http://co.mbine.org/standards/qualifiers">here</a>.
+ */
+ BQ_BIOL_IS_PART_OF("bqbiol:isPartOf"),
+
+ /**
+ * Take a look <a href="http://co.mbine.org/standards/qualifiers">here</a>.
+ */
+ BQ_BIOL_IS_VERSION_OF("bqbiol:isVersionOf"),
+
+ /**
+ * Take a look <a href="http://co.mbine.org/standards/qualifiers">here</a>.
+ */
+ BQ_BIOL_HAS_VERSION("bqbiol:hasVersion"),
+
+ /**
+ * Take a look <a href="http://co.mbine.org/standards/qualifiers">here</a>.
+ */
+ BQ_BIOL_IS_HOMOLOG_TO("bqbiol:isHomologTo"),
+
+ /**
+ * Take a look <a href="http://co.mbine.org/standards/qualifiers">here</a>.
+ */
+ BQ_BIOL_IS_DESCRIBED_BY("bqbiol:isDescribedBy"),
+
+ /**
+ * Take a look <a href="http://co.mbine.org/standards/qualifiers">here</a>.
+ */
+ BQ_BIOL_IS_ENCODED_BY("bqbiol:isEncodedBy"),
+
+ /**
+ * Take a look <a href="http://co.mbine.org/standards/qualifiers">here</a>.
+ */
+ BQ_BIOL_ENCODES("bqbiol:encodes"),
+
+ /**
+ * Take a look <a href="http://co.mbine.org/standards/qualifiers">here</a>.
+ */
+ BQ_BIOL_OCCURES("bqbiol:occures");
+
+ /**
+ * String representing relation. List of all possibilites can be found <a
+ * href="http://co.mbine.org/standards/qualifiers">here</a>.
+ */
+ private String stringRepresentation;
+
+ /**
+ * Default constructor.
+ *
+ * @param stringRepresentation
+ * {@link #stringRepresentation}
+ */
+ MiriamRelationType(String stringRepresentation) {
+ this.stringRepresentation = stringRepresentation;
+ }
+
+ /**
+ * @return the stringRepresentation
+ * @see #stringRepresentation
+ */
+ public String getStringRepresentation() {
+ return stringRepresentation;
+ }
+
+ /**
+ * Returns {@link MiriamRelationType} associated with #stringRepresentation.
+ *
+ * @param string
+ * #stringRepresentation
+ * @return {@link MiriamRelationType} for given #stringRepresentation
+ */
+ public static MiriamRelationType getTypeByStringRepresentation(String string) {
+ for (MiriamRelationType mrt : MiriamRelationType.values()) {
+ if (mrt.getStringRepresentation().equalsIgnoreCase(string)) {
+ return mrt;
+ }
+ }
+ return null;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
index 910ab16ccb..bbb1df775f 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
@@ -1,736 +1,736 @@
-package lcsb.mapviewer.model.map;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Chemical;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Drug;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.Phenotype;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Rna;
-
-/**
- * Type of known miriam annotation.
- *
- * @author Piotr Gawron
- *
- */
-@SuppressWarnings("unchecked")
-public enum MiriamType {
-
- BiGG_COMPARTMENT("BiGG Compartment", //
- "http://bigg.ucsd.edu/compartments/", //
- new String[] { "urn:miriam:bigg.compartment" }, //
- new Class<?>[] {}, "MIR:00000555"), //
-
- BiGG_METABOLITE("BiGG Metabolite", //
- "http://bigg.ucsd.edu/universal/metabolites", //
- new String[] { "urn:miriam:bigg.metabolite" }, //
- new Class<?>[] {}, "MIR:00000556"), //
-
- BiGG_REACTIONS("BiGG Reaction", //
- "http://bigg.ucsd.edu/universal/reactions", //
- new String[] { "urn:miriam:bigg.reaction" }, //
- new Class<?>[] {}, "MIR:00000557"), //
-
- /**
- * Brenda enzyme database: http://www.brenda-enzymes.org.
- */
- BRENDA("BRENDA", //
- "http://www.brenda-enzymes.org", //
- new String[] { "urn:miriam:brenda" }, //
- new Class<?>[] {}, "MIR:00100101"), //
-
- /**
- * Chemical Abstracts Service database: http://commonchemistry.org.
- */
- CAS("Chemical Abstracts Service", //
- "http://commonchemistry.org", //
- new String[] { "urn:miriam:cas" }, //
- new Class<?>[] {}, "MIR:00000237"), //
-
- /**
- * The Carbohydrate-Active Enzyme (CAZy) database: http://www.cazy.org/.
- */
- CAZY("CAZy", //
- "http://commonchemistry.org", //
- new String[] { "urn:miriam:cazy" }, //
- new Class<?>[] {}, "MIR:00000195"), //
-
- /**
- * Consensus CDS: http://identifiers.org/ccds/.
- */
- CCDS("Consensus CDS", //
- "http://www.ncbi.nlm.nih.gov/CCDS/", //
- new String[] { "urn:miriam:ccds" }, //
- new Class<?>[] {}, "MIR:00000375"), //
-
- /**
- * Chebi database:
- * <a href = "http://www.ebi.ac.uk/chebi/">http://www.ebi.ac.uk/chebi/</a>.
- */
- CHEBI("Chebi", //
- "http://www.ebi.ac.uk/chebi/", //
- new String[] { "urn:miriam:obo.chebi", "urn:miriam:chebi" }, //
- new Class<?>[] { Chemical.class, Drug.class, }, "MIR:00000002", //
- new Class<?>[] { Chemical.class }), //
-
- /**
- * ChemSpider database:
- * <a href = "http://www.chemspider.com/">http://www.chemspider.com/</a>.
- */
- CHEMSPIDER("ChemSpider", //
- "http://www.chemspider.com//", //
- new String[] { "urn:miriam:chemspider" }, //
- new Class<?>[] {}, "MIR:00000138"), //
-
- /**
- * Chembl database: https://www.ebi.ac.uk/chembldb/.
- */
- CHEMBL_COMPOUND("ChEMBL", //
- "https://www.ebi.ac.uk/chembldb/", //
- new String[] { "urn:miriam:chembl.compound" }, //
- new Class<?>[] { Drug.class }, "MIR:00000084"), //
-
- /**
- * Target in chembl database: https://www.ebi.ac.uk/chembldb/.
- */
- CHEMBL_TARGET("ChEMBL target", //
- "https://www.ebi.ac.uk/chembldb/", //
- new String[] { "urn:miriam:chembl.target" }, //
- new Class<?>[] { Protein.class, Complex.class }, "MIR:00000085"), //
-
- /**
- * Clusters of Orthologous Groups: https://www.ncbi.nlm.nih.gov/COG/.
- */
- COG("Clusters of Orthologous Groups", //
- "https://www.ncbi.nlm.nih.gov/COG/", //
- new String[] { "urn:miriam:cogs" }, //
- new Class<?>[] { Reaction.class }, "MIR:00000296"), //
-
- /**
- * Digital Object Identifier: http://www.doi.org/.
- */
- DOI("Digital Object Identifier", //
- "http://www.doi.org/", //
- new String[] { "urn:miriam:doi" }, //
- new Class<?>[] { Reaction.class }, "MIR:00000019"), //
-
- /**
- * Drugbank database: http://www.drugbank.ca/.
- */
- DRUGBANK("DrugBank", //
- "http://www.drugbank.ca/", //
- new String[] { "urn:miriam:drugbank" }, //
- new Class<?>[] { Drug.class }, "MIR:00000102"), //
- /**
- * Drugbank targets: http://www.drugbank.ca/targets.
- */
- DRUGBANK_TARGET_V4("DrugBank Target v4", //
- "http://www.drugbank.ca/targets", //
- new String[] { "urn:miriam:drugbankv4.target" }, //
- new Class<?>[] {}, "MIR:00000528"), //
-
- /**
- * Enzyme Nomenclature: http://www.enzyme-database.org/.
- */
- EC("Enzyme Nomenclature", //
- "http://www.enzyme-database.org/", //
- new String[] { "urn:miriam:ec-code" }, //
- new Class<?>[] { Protein.class, Complex.class }, "MIR:00000004"), //
-
- /**
- * Ensembl: www.ensembl.org.
- */
- ENSEMBL("Ensembl", //
- "www.ensembl.org", //
- new String[] { "urn:miriam:ensembl" }, //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000003"), //
-
- /**
- * Ensembl Plants: http://plants.ensembl.org/.
- */
- ENSEMBL_PLANTS("Ensembl Plants", //
- "http://plants.ensembl.org/", //
- new String[] { "urn:miriam:ensembl.plant" }, //
- new Class<?>[] {}, "MIR:00000205"), //
-
- /**
- * Entrez Gene: http://www.ncbi.nlm.nih.gov/gene.
- */
- ENTREZ("Entrez Gene", //
- "http://www.ncbi.nlm.nih.gov/gene", //
- new String[] { "urn:miriam:ncbigene", "urn:miriam:entrez.gene" }, //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000069"), //
-
- /**
- * Gene Ontology: http://amigo.geneontology.org/amigo.
- */
- GO("Gene Ontology", //
- "http://amigo.geneontology.org/amigo", //
- new String[] { "urn:miriam:obo.go", "urn:miriam:go" }, //
- new Class<?>[] { Phenotype.class, Compartment.class, Complex.class }, "MIR:00000022"), //
-
- /**
- * HGNC: http://www.genenames.org.
- */
- HGNC("HGNC", //
- "http://www.genenames.org", //
- new String[] { "urn:miriam:hgnc" }, //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000080", //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }), //
-
- /**
- * HGNC symbol: http://www.genenames.org.
- */
- HGNC_SYMBOL("HGNC Symbol", //
- "http://www.genenames.org", //
- new String[] { "urn:miriam:hgnc.symbol" }, //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000362", //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }), //
-
- /**
- * HMDB: http://www.hmdb.ca/.
- */
- HMDB("HMDB", //
- "http://www.hmdb.ca/", //
- "urn:miriam:hmdb", //
- new Class<?>[] { Chemical.class, Drug.class, }, "MIR:00000051"), //
-
- /**
- * InterPro: http://www.ebi.ac.uk/interpro/.
- */
- INTERPRO("InterPro", //
- "http://www.ebi.ac.uk/interpro/", //
- new String[] { "urn:miriam:interpro" }, //
- new Class<?>[] { Protein.class, Complex.class }, "MIR:00000011"), //
-
- /**
- * KEGG Compound: http://www.genome.jp/kegg/ligand.html.
- */
- KEGG_COMPOUND("Kegg Compound", //
- "http://www.genome.jp/kegg/ligand.html", //
- "urn:miriam:kegg.compound", //
- new Class<?>[] { Chemical.class }, "MIR:00000013"), //
-
- /**
- * KEGG Genes: http://www.genome.jp/kegg/genes.html.
- */
- KEGG_GENES("Kegg Genes", //
- "http://www.genome.jp/kegg/genes.html", //
- new String[] { "urn:miriam:kegg.genes", "urn:miriam:kegg.genes:hsa" }, //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000070"), //
-
- /**
- * KEGG Orthology: http://www.genome.jp/kegg/ko.html.
- */
- KEGG_ORTHOLOGY("KEGG Orthology", //
- "http://www.genome.jp/kegg/ko.html", //
- new String[] { "urn:miriam:kegg.orthology" }, //
- new Class<?>[] {}, "MIR:00000116"), //
-
- /**
- * KEGG Pathway: http://www.genome.jp/kegg/pathway.html.
- */
- KEGG_PATHWAY("Kegg Pathway", //
- "http://www.genome.jp/kegg/pathway.html", //
- "urn:miriam:kegg.pathway", //
- new Class<?>[] { Reaction.class }, "MIR:00000012"), //
-
- /**
- * KEGG Reaction: http://www.genome.jp/kegg/reaction/.
- */
- KEGG_REACTION("Kegg Reaction", //
- "http://www.genome.jp/kegg/reaction/", //
- "urn:miriam:kegg.reaction", //
- new Class<?>[] { Reaction.class }, "MIR:00000014"), //
-
- /**
- * MeSH 2012: http://www.nlm.nih.gov/mesh/.
- */
- MESH_2012("MeSH 2012", //
- "http://www.nlm.nih.gov/mesh/", //
- new String[] { "urn:miriam:mesh.2012", "urn:miriam:mesh" }, //
- new Class<?>[] { Phenotype.class, Compartment.class, Complex.class }, "MIR:00000270"), //
-
- /**
- * miRBase Sequence: http://www.mirbase.org/.
- */
- MI_R_BASE_SEQUENCE("miRBase Sequence Database", //
- "http://www.mirbase.org/", //
- new String[] { "urn:miriam:mirbase" }, //
- new Class<?>[] {}, "MIR:00000078"), //
-
- /**
- * miRBase Mature Sequence: http://www.mirbase.org/.
- */
- MI_R_BASE_MATURE_SEQUENCE("miRBase Mature Sequence Database", //
- "http://www.mirbase.org/", //
- new String[] { "urn:miriam:mirbase.mature" }, //
- new Class<?>[] {}, "MIR:00000235"), //
-
- /**
- * miRTaRBase Mature Sequence: http://mirtarbase.mbc.nctu.edu.tw/.
- */
- MIR_TAR_BASE_MATURE_SEQUENCE("miRTarBase Mature Sequence Database", //
- "http://mirtarbase.mbc.nctu.edu.tw/", //
- new String[] { "urn:miriam:mirtarbase" }, //
- new Class<?>[] {}, "MIR:00100739"), //
-
- /**
- * Mouse Genome Database: http://www.informatics.jax.org/.
- */
- MGD("Mouse Genome Database", //
- "http://www.informatics.jax.org/", //
- new String[] { "urn:miriam:mgd" }, //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000037"), //
-
- /**
- * Online Mendelian Inheritance in Man: http://omim.org/.
- */
- OMIM("Online Mendelian Inheritance in Man", //
- "http://omim.org/", //
- new String[] { "urn:miriam:omim" }, //
- new Class<?>[] { Phenotype.class }, "MIR:00000016"), //
-
- /**
- * PANTHER Family: http://www.pantherdb.org/.
- */
- PANTHER("PANTHER Family", //
- "http://www.pantherdb.org/", //
- new String[] { "urn:miriam:panther.family", "urn:miriam:panther" }, //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000060"), //
-
- /**
- * PDB: http://www.pdbe.org/.
- */
- PDB("Protein Data Bank", //
- "http://www.pdbe.org/", //
- "urn:miriam:pdb", //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000020"),
-
- /**
- * Protein Family Database: http://pfam.xfam.org/.
- */
- PFAM("Protein Family Database", //
- "http://pfam.xfam.org//", //
- "urn:miriam:pfam", //
- new Class<?>[] {}, "MIR:00000028"), //
-
- /**
- * PharmGKB Pathways: http://www.pharmgkb.org/.
- */
- PHARM("PharmGKB Pathways", //
- "http://www.pharmgkb.org/", //
- "urn:miriam:pharmgkb.pathways", //
- new Class<?>[] {}, "MIR:00000089"), //
-
- /**
- * PubChem-compound: http://pubchem.ncbi.nlm.nih.gov/.
- */
- PUBCHEM("PubChem-compound", //
- "http://pubchem.ncbi.nlm.nih.gov/", //
- new String[] { "urn:miriam:pubchem.compound" }, //
- new Class<?>[] { Chemical.class }, "MIR:00000034", //
- new Class<?>[] { Chemical.class }), //
-
- /**
- * PubChem-substance: http://pubchem.ncbi.nlm.nih.gov/.
- */
- PUBCHEM_SUBSTANCE("PubChem-substance", //
- "http://pubchem.ncbi.nlm.nih.gov/", //
- new String[] { "urn:miriam:pubchem.substance" }, //
- new Class<?>[] { Chemical.class }, "MIR:00000033", //
- new Class<?>[] { Chemical.class }), //
-
- /**
- * PubMed: http://www.ncbi.nlm.nih.gov/PubMed/.
- */
- PUBMED("PubMed", //
- "http://www.ncbi.nlm.nih.gov/PubMed/", //
- new String[] { "urn:miriam:pubmed" }, //
- new Class<?>[] { BioEntity.class }, "MIR:00000015", //
- new Class<?>[] { Reaction.class }), //
-
- /**
- * Reactome: http://www.reactome.org/.
- */
- REACTOME("Reactome", //
- "http://www.reactome.org/", //
- "urn:miriam:reactome", //
- new Class<?>[] { Reaction.class }, "MIR:00000018"), //
-
- /**
- * RefSeq: http://www.ncbi.nlm.nih.gov/projects/RefSeq/.
- */
- REFSEQ("RefSeq", //
- "http://www.ncbi.nlm.nih.gov/projects/RefSeq/", //
- "urn:miriam:refseq", //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000039"),
-
- /**
- * Rhea: http://www.rhea-db.org/.
- */
- RHEA("Rhea", //
- "http://www.rhea-db.org/", //
- "urn:miriam:rhea", //
- new Class<?>[] { Reaction.class }, "MIR:00000082"),
-
- /**
- * SGD: http://www.yeastgenome.org/.
- */
- SGD("Saccharomyces Genome Database", //
- "http://www.yeastgenome.org/", //
- "urn:miriam:sgd", //
- new Class<?>[] {}, "MIR:00000023"),
-
- /**
- * STITCH: http://stitch.embl.de/.
- */
- STITCH("STITCH", //
- "http://stitch.embl.de/", //
- "urn:miriam:stitch", //
- new Class<?>[] {}, "MIR:00100343"),
-
- /**
- * STRING: http://string-db.org/.
- */
- STRING("STRING", //
- "http://string-db.org/", //
- "urn:miriam:string", //
- new Class<?>[] {}, "MIR:00000265"),
-
- /**
- * The Arabidopsis Information Resource (TAIR) maintains a database of genetic
- * and molecular biology data for the model higher plant Arabidopsis thaliana.
- * The name of a Locus is unique and used by TAIR, TIGR, and MIPS:
- * http://arabidopsis.org/index.jsp.
- */
- TAIR_LOCUS("TAIR Locus", //
- "http://arabidopsis.org/index.jsp", //
- "urn:miriam:tair.locus", //
- new Class<?>[] {}, "MIR:00000050"),
-
- /**
- * Taxonomy: http://www.ncbi.nlm.nih.gov/taxonomy/.
- */
- TAXONOMY("Taxonomy", //
- "http://www.ncbi.nlm.nih.gov/taxonomy/", //
- "urn:miriam:taxonomy", //
- new Class<?>[] {}, "MIR:00000006"),
- /**
- * Toxicogenomic: Chemical: http://ctdbase.org/detail.go.
- * http://ctdbase.org/detail.go
- */
- TOXICOGENOMIC_CHEMICAL("Toxicogenomic Chemical", //
- "http://ctdbase.org/", //
- "urn:miriam:ctd.chemical", //
- new Class<?>[] {}, "MIR:00000098"), //
-
- /**
- * UniGene: http://www.ncbi.nlm.nih.gov/unigene.
- */
- UNIGENE("UniGene", //
- "http://www.ncbi.nlm.nih.gov/unigene", //
- "urn:miriam:unigene", //
- new Class<?>[] {}, "MIR:00000346"),
-
- /**
- * Uniprot: http://www.uniprot.org/.
- */
- UNIPROT("Uniprot", //
- "http://www.uniprot.org/", //
- "urn:miriam:uniprot", //
- new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000005"),
-
- /**
- * UniProt Isoform: http://www.uniprot.org/.
- */
- UNIPROT_ISOFORM("UniProt Isoform", //
- "http://www.uniprot.org/", //
- "urn:miriam:uniprot.isoform", //
- new Class<?>[] { Protein.class }, "MIR:00000388"),
-
- /**
- * Unknown reference type...
- */
- UNKNOWN("Unknown", //
- null, //
- new String[] {}, //
- new Class<?>[] {}, null),
-
- /**
- * Wikidata: https://www.wikidata.org/.
- */
- WIKIDATA("Wikidata", //
- "https://www.wikidata.org/", //
- new String[] { "urn:miriam:wikidata" }, //
- new Class<?>[] {}, "MIR:00000549"), //
-
- /**
- * WikiPathways: http://www.wikipathways.org/.
- */
- WIKIPATHWAYS("WikiPathways", //
- "http://www.wikipathways.org/", //
- new String[] { "urn:miriam:wikipathways" }, //
- new Class<?>[] {}, "MIR:00000076"), //
-
- /**
- * Wikipedia: http://en.wikipedia.org/wiki/Main_Page.
- */
- WIKIPEDIA("Wikipedia (English)", //
- "http://en.wikipedia.org/wiki/Main_Page", // /
- new String[] { "urn:miriam:wikipedia.en" }, //
- new Class<?>[] {}, "MIR:00000384"),
-
- /**
- * WormBase: http://wormbase.bio2rdf.org/fct.
- */
- WORM_BASE("WormBase", //
- "http://wormbase.bio2rdf.org/fct", // /
- new String[] { "urn:miriam:wormbase" }, //
- new Class<?>[] {}, "MIR:00000027");
-
- /**
- * User friendly name.
- */
- private String commonName;
-
- /**
- * url to home page of given resource type.
- */
- private String dbHomepage;
-
- /**
- * Identifier of the database in miriam registry.
- */
- private String registryIdentifier;
-
- /**
- * Valid URIs to this resource.
- */
- private List<String> uris = new ArrayList<>();
-
- /**
- * Classes that can be annotated by this resource.
- */
- private List<Class<? extends BioEntity>> validClass = new ArrayList<>();
-
- /**
- * When class from this list is marked as "require at least one annotation" then
- * annotation of this type is valid.
- */
- private List<Class<? extends BioEntity>> requiredClass = new ArrayList<>();
-
- /**
- * Constructor that initialize enum object.
- *
- * @param dbHomePage
- * home page of the resource {@link #dbHomepage}
- * @param commonName
- * {@link #commonName}
- * @param uris
- * {@link #uris}
- * @param classes
- * {@link #validClass}
- * @param registryIdentifier
- * {@link #registryIdentifier}
- */
- MiriamType(String commonName, String dbHomePage, String[] uris, Class<?>[] classes, String registryIdentifier) {
- this(commonName, dbHomePage, uris, classes, registryIdentifier, new Class<?>[] {});
- }
-
- /**
- * Constructor that initialize enum object.
- *
- * @param dbHomePage
- * home page of the resource {@link #dbHomepage}
- * @param commonName
- * {@link #commonName}
- * @param uris
- * {@link #uris}
- * @param classes
- * {@link #validClass}
- * @param registryIdentifier
- * {@link #registryIdentifier}
- * @param requiredClasses
- * {@link #requiredClasses}
- */
- MiriamType(String commonName, String dbHomePage, String[] uris, Class<?>[] classes, String registryIdentifier,
- Class<?>[] requiredClasses) {
- this.commonName = commonName;
- this.dbHomepage = dbHomePage;
- for (String string : uris) {
- this.uris.add(string);
- }
- for (Class<?> clazz : classes) {
- this.validClass.add((Class<? extends BioEntity>) clazz);
- }
- for (Class<?> clazz : requiredClasses) {
- this.requiredClass.add((Class<? extends BioEntity>) clazz);
- }
- this.registryIdentifier = registryIdentifier;
- }
-
- /**
- * Constructor that initialize enum object.
- *
- * @param dbHomePage
- * home page of the resource {@link #dbHomepage}
- * @param commonName
- * {@link #commonName}
- * @param uri
- * one of {@link #uris}
- * @param registryIdentifier
- * {@link #registryIdentifier}
- * @param classes
- * {@link #validClass}
- */
- MiriamType(String commonName, String dbHomePage, String uri, Class<?>[] classes, String registryIdentifier) {
- this(commonName, dbHomePage, new String[] { uri }, classes, registryIdentifier);
- }
-
- /**
- *
- * @return {@link #commonName}
- */
- public String getCommonName() {
- return commonName;
- }
-
- /**
- *
- * @return {@link #uris}
- */
- public List<String> getUris() {
- return uris;
- }
-
- /**
- *
- * @return {@link #validClass}
- */
- public List<Class<? extends BioEntity>> getValidClass() {
- return validClass;
- }
-
- /**
- * Returns {@link MiriamType} associated with parameter uri address.
- *
- * @param uri
- * uri to check
- * @return {@link MiriamType} for given uri
- */
- public static MiriamType getTypeByUri(String uri) {
- for (MiriamType mt : MiriamType.values()) {
- for (String string : mt.getUris()) {
- if (string.equalsIgnoreCase(uri)) {
- return mt;
- }
- }
- }
- return null;
- }
-
- /**
- * @return the dbHomepage
- * @see #dbHomepage
- */
- public String getDbHomepage() {
- return dbHomepage;
- }
-
- /**
- * @return the registryIdentifier
- * @see #registryIdentifier
- */
- public String getRegistryIdentifier() {
- return registryIdentifier;
- }
-
- /**
- * @return the requiredClass
- * @see #requiredClass
- */
- public List<Class<? extends BioEntity>> getRequiredClass() {
- return requiredClass;
- }
-
- /**
- * Returns {@link MiriamType} associated with {@link #commonName}.
- *
- * @param string
- * {@link #commonName}
- * @return {@link MiriamType} for given name
- */
- public static MiriamType getTypeByCommonName(String string) {
- for (MiriamType mt : MiriamType.values()) {
- if (string.equalsIgnoreCase(mt.getCommonName())) {
- return mt;
- }
- }
- return null;
- }
-
- /**
- * Transforms identifier into {@link MiriamData}.
- *
- * @param generalIdentifier
- * identifier in the format NAME:IDENTIFIER. Where NAME is the name
- * from {@link MiriamType#commonName} and IDENTIFIER is resource
- * identifier.
- * @return {@link MiriamData} representing generalIdentifier, when identifier is
- * invalid InvalidArgumentException is thrown
- */
- public static MiriamData getMiriamDataFromIdentifier(String generalIdentifier) {
- int index = generalIdentifier.indexOf(":");
- if (index < 0) {
- throw new InvalidArgumentException("Identifier doesn't contain type");
- }
- String type = generalIdentifier.substring(0, index);
- String id = generalIdentifier.substring(index + 1);
- for (MiriamType mt : MiriamType.values()) {
- if (mt.getCommonName().equalsIgnoreCase(type)) {
- return new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, mt, id);
- }
- }
- throw new InvalidArgumentException("Unknown miriam type: " + type + " (id: " + id + ")");
- }
-
- /**
- * Creates {@link MiriamData} from miriam uri.
- *
- * @param miriamUri
- * miriam uri defining {@link MiriamData}
- * @return {@link MiriamData} from miriam uri
- */
- public static MiriamData getMiriamByUri(String miriamUri) {
- // this hack is due to CellDesigner issue (CellDesigner incorectly handle
- // with identifiers that have ":" inside resource ":" inside resource with
- // "%3A" and also the last ":"
- miriamUri = miriamUri.replace("%3A", ":");
-
- String foundUri = "";
- MiriamType foundType = null;
-
- for (MiriamType type : MiriamType.values()) {
- for (String uri : type.getUris()) {
- if (miriamUri.startsWith(uri + ":")) {
- if (uri.length() > foundUri.length()) {
- foundType = type;
- foundUri = uri;
- }
- }
- }
- }
- if (foundType != null) {
- return new MiriamData(foundType, miriamUri.substring(foundUri.length() + 1));
- }
- throw new InvalidArgumentException("Invalid miriam uri: " + miriamUri);
- }
-}
+package lcsb.mapviewer.model.map;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Chemical;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Drug;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+
+/**
+ * Type of known miriam annotation.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@SuppressWarnings("unchecked")
+public enum MiriamType {
+
+ BiGG_COMPARTMENT("BiGG Compartment", //
+ "http://bigg.ucsd.edu/compartments/", //
+ new String[] { "urn:miriam:bigg.compartment" }, //
+ new Class<?>[] {}, "MIR:00000555"), //
+
+ BiGG_METABOLITE("BiGG Metabolite", //
+ "http://bigg.ucsd.edu/universal/metabolites", //
+ new String[] { "urn:miriam:bigg.metabolite" }, //
+ new Class<?>[] {}, "MIR:00000556"), //
+
+ BiGG_REACTIONS("BiGG Reaction", //
+ "http://bigg.ucsd.edu/universal/reactions", //
+ new String[] { "urn:miriam:bigg.reaction" }, //
+ new Class<?>[] {}, "MIR:00000557"), //
+
+ /**
+ * Brenda enzyme database: http://www.brenda-enzymes.org.
+ */
+ BRENDA("BRENDA", //
+ "http://www.brenda-enzymes.org", //
+ new String[] { "urn:miriam:brenda" }, //
+ new Class<?>[] {}, "MIR:00100101"), //
+
+ /**
+ * Chemical Abstracts Service database: http://commonchemistry.org.
+ */
+ CAS("Chemical Abstracts Service", //
+ "http://commonchemistry.org", //
+ new String[] { "urn:miriam:cas" }, //
+ new Class<?>[] {}, "MIR:00000237"), //
+
+ /**
+ * The Carbohydrate-Active Enzyme (CAZy) database: http://www.cazy.org/.
+ */
+ CAZY("CAZy", //
+ "http://commonchemistry.org", //
+ new String[] { "urn:miriam:cazy" }, //
+ new Class<?>[] {}, "MIR:00000195"), //
+
+ /**
+ * Consensus CDS: http://identifiers.org/ccds/.
+ */
+ CCDS("Consensus CDS", //
+ "http://www.ncbi.nlm.nih.gov/CCDS/", //
+ new String[] { "urn:miriam:ccds" }, //
+ new Class<?>[] {}, "MIR:00000375"), //
+
+ /**
+ * Chebi database:
+ * <a href = "http://www.ebi.ac.uk/chebi/">http://www.ebi.ac.uk/chebi/</a>.
+ */
+ CHEBI("Chebi", //
+ "http://www.ebi.ac.uk/chebi/", //
+ new String[] { "urn:miriam:obo.chebi", "urn:miriam:chebi" }, //
+ new Class<?>[] { Chemical.class, Drug.class, }, "MIR:00000002", //
+ new Class<?>[] { Chemical.class }), //
+
+ /**
+ * ChemSpider database:
+ * <a href = "http://www.chemspider.com/">http://www.chemspider.com/</a>.
+ */
+ CHEMSPIDER("ChemSpider", //
+ "http://www.chemspider.com//", //
+ new String[] { "urn:miriam:chemspider" }, //
+ new Class<?>[] {}, "MIR:00000138"), //
+
+ /**
+ * Chembl database: https://www.ebi.ac.uk/chembldb/.
+ */
+ CHEMBL_COMPOUND("ChEMBL", //
+ "https://www.ebi.ac.uk/chembldb/", //
+ new String[] { "urn:miriam:chembl.compound" }, //
+ new Class<?>[] { Drug.class }, "MIR:00000084"), //
+
+ /**
+ * Target in chembl database: https://www.ebi.ac.uk/chembldb/.
+ */
+ CHEMBL_TARGET("ChEMBL target", //
+ "https://www.ebi.ac.uk/chembldb/", //
+ new String[] { "urn:miriam:chembl.target" }, //
+ new Class<?>[] { Protein.class, Complex.class }, "MIR:00000085"), //
+
+ /**
+ * Clusters of Orthologous Groups: https://www.ncbi.nlm.nih.gov/COG/.
+ */
+ COG("Clusters of Orthologous Groups", //
+ "https://www.ncbi.nlm.nih.gov/COG/", //
+ new String[] { "urn:miriam:cogs" }, //
+ new Class<?>[] { Reaction.class }, "MIR:00000296"), //
+
+ /**
+ * Digital Object Identifier: http://www.doi.org/.
+ */
+ DOI("Digital Object Identifier", //
+ "http://www.doi.org/", //
+ new String[] { "urn:miriam:doi" }, //
+ new Class<?>[] { Reaction.class }, "MIR:00000019"), //
+
+ /**
+ * Drugbank database: http://www.drugbank.ca/.
+ */
+ DRUGBANK("DrugBank", //
+ "http://www.drugbank.ca/", //
+ new String[] { "urn:miriam:drugbank" }, //
+ new Class<?>[] { Drug.class }, "MIR:00000102"), //
+ /**
+ * Drugbank targets: http://www.drugbank.ca/targets.
+ */
+ DRUGBANK_TARGET_V4("DrugBank Target v4", //
+ "http://www.drugbank.ca/targets", //
+ new String[] { "urn:miriam:drugbankv4.target" }, //
+ new Class<?>[] {}, "MIR:00000528"), //
+
+ /**
+ * Enzyme Nomenclature: http://www.enzyme-database.org/.
+ */
+ EC("Enzyme Nomenclature", //
+ "http://www.enzyme-database.org/", //
+ new String[] { "urn:miriam:ec-code" }, //
+ new Class<?>[] { Protein.class, Complex.class }, "MIR:00000004"), //
+
+ /**
+ * Ensembl: www.ensembl.org.
+ */
+ ENSEMBL("Ensembl", //
+ "www.ensembl.org", //
+ new String[] { "urn:miriam:ensembl" }, //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000003"), //
+
+ /**
+ * Ensembl Plants: http://plants.ensembl.org/.
+ */
+ ENSEMBL_PLANTS("Ensembl Plants", //
+ "http://plants.ensembl.org/", //
+ new String[] { "urn:miriam:ensembl.plant" }, //
+ new Class<?>[] {}, "MIR:00000205"), //
+
+ /**
+ * Entrez Gene: http://www.ncbi.nlm.nih.gov/gene.
+ */
+ ENTREZ("Entrez Gene", //
+ "http://www.ncbi.nlm.nih.gov/gene", //
+ new String[] { "urn:miriam:ncbigene", "urn:miriam:entrez.gene" }, //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000069"), //
+
+ /**
+ * Gene Ontology: http://amigo.geneontology.org/amigo.
+ */
+ GO("Gene Ontology", //
+ "http://amigo.geneontology.org/amigo", //
+ new String[] { "urn:miriam:obo.go", "urn:miriam:go" }, //
+ new Class<?>[] { Phenotype.class, Compartment.class, Complex.class }, "MIR:00000022"), //
+
+ /**
+ * HGNC: http://www.genenames.org.
+ */
+ HGNC("HGNC", //
+ "http://www.genenames.org", //
+ new String[] { "urn:miriam:hgnc" }, //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000080", //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }), //
+
+ /**
+ * HGNC symbol: http://www.genenames.org.
+ */
+ HGNC_SYMBOL("HGNC Symbol", //
+ "http://www.genenames.org", //
+ new String[] { "urn:miriam:hgnc.symbol" }, //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000362", //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }), //
+
+ /**
+ * HMDB: http://www.hmdb.ca/.
+ */
+ HMDB("HMDB", //
+ "http://www.hmdb.ca/", //
+ "urn:miriam:hmdb", //
+ new Class<?>[] { Chemical.class, Drug.class, }, "MIR:00000051"), //
+
+ /**
+ * InterPro: http://www.ebi.ac.uk/interpro/.
+ */
+ INTERPRO("InterPro", //
+ "http://www.ebi.ac.uk/interpro/", //
+ new String[] { "urn:miriam:interpro" }, //
+ new Class<?>[] { Protein.class, Complex.class }, "MIR:00000011"), //
+
+ /**
+ * KEGG Compound: http://www.genome.jp/kegg/ligand.html.
+ */
+ KEGG_COMPOUND("Kegg Compound", //
+ "http://www.genome.jp/kegg/ligand.html", //
+ "urn:miriam:kegg.compound", //
+ new Class<?>[] { Chemical.class }, "MIR:00000013"), //
+
+ /**
+ * KEGG Genes: http://www.genome.jp/kegg/genes.html.
+ */
+ KEGG_GENES("Kegg Genes", //
+ "http://www.genome.jp/kegg/genes.html", //
+ new String[] { "urn:miriam:kegg.genes", "urn:miriam:kegg.genes:hsa" }, //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000070"), //
+
+ /**
+ * KEGG Orthology: http://www.genome.jp/kegg/ko.html.
+ */
+ KEGG_ORTHOLOGY("KEGG Orthology", //
+ "http://www.genome.jp/kegg/ko.html", //
+ new String[] { "urn:miriam:kegg.orthology" }, //
+ new Class<?>[] {}, "MIR:00000116"), //
+
+ /**
+ * KEGG Pathway: http://www.genome.jp/kegg/pathway.html.
+ */
+ KEGG_PATHWAY("Kegg Pathway", //
+ "http://www.genome.jp/kegg/pathway.html", //
+ "urn:miriam:kegg.pathway", //
+ new Class<?>[] { Reaction.class }, "MIR:00000012"), //
+
+ /**
+ * KEGG Reaction: http://www.genome.jp/kegg/reaction/.
+ */
+ KEGG_REACTION("Kegg Reaction", //
+ "http://www.genome.jp/kegg/reaction/", //
+ "urn:miriam:kegg.reaction", //
+ new Class<?>[] { Reaction.class }, "MIR:00000014"), //
+
+ /**
+ * MeSH 2012: http://www.nlm.nih.gov/mesh/.
+ */
+ MESH_2012("MeSH 2012", //
+ "http://www.nlm.nih.gov/mesh/", //
+ new String[] { "urn:miriam:mesh.2012", "urn:miriam:mesh" }, //
+ new Class<?>[] { Phenotype.class, Compartment.class, Complex.class }, "MIR:00000270"), //
+
+ /**
+ * miRBase Sequence: http://www.mirbase.org/.
+ */
+ MI_R_BASE_SEQUENCE("miRBase Sequence Database", //
+ "http://www.mirbase.org/", //
+ new String[] { "urn:miriam:mirbase" }, //
+ new Class<?>[] {}, "MIR:00000078"), //
+
+ /**
+ * miRBase Mature Sequence: http://www.mirbase.org/.
+ */
+ MI_R_BASE_MATURE_SEQUENCE("miRBase Mature Sequence Database", //
+ "http://www.mirbase.org/", //
+ new String[] { "urn:miriam:mirbase.mature" }, //
+ new Class<?>[] {}, "MIR:00000235"), //
+
+ /**
+ * miRTaRBase Mature Sequence: http://mirtarbase.mbc.nctu.edu.tw/.
+ */
+ MIR_TAR_BASE_MATURE_SEQUENCE("miRTarBase Mature Sequence Database", //
+ "http://mirtarbase.mbc.nctu.edu.tw/", //
+ new String[] { "urn:miriam:mirtarbase" }, //
+ new Class<?>[] {}, "MIR:00100739"), //
+
+ /**
+ * Mouse Genome Database: http://www.informatics.jax.org/.
+ */
+ MGD("Mouse Genome Database", //
+ "http://www.informatics.jax.org/", //
+ new String[] { "urn:miriam:mgd" }, //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000037"), //
+
+ /**
+ * Online Mendelian Inheritance in Man: http://omim.org/.
+ */
+ OMIM("Online Mendelian Inheritance in Man", //
+ "http://omim.org/", //
+ new String[] { "urn:miriam:omim" }, //
+ new Class<?>[] { Phenotype.class }, "MIR:00000016"), //
+
+ /**
+ * PANTHER Family: http://www.pantherdb.org/.
+ */
+ PANTHER("PANTHER Family", //
+ "http://www.pantherdb.org/", //
+ new String[] { "urn:miriam:panther.family", "urn:miriam:panther" }, //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000060"), //
+
+ /**
+ * PDB: http://www.pdbe.org/.
+ */
+ PDB("Protein Data Bank", //
+ "http://www.pdbe.org/", //
+ "urn:miriam:pdb", //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000020"),
+
+ /**
+ * Protein Family Database: http://pfam.xfam.org/.
+ */
+ PFAM("Protein Family Database", //
+ "http://pfam.xfam.org//", //
+ "urn:miriam:pfam", //
+ new Class<?>[] {}, "MIR:00000028"), //
+
+ /**
+ * PharmGKB Pathways: http://www.pharmgkb.org/.
+ */
+ PHARM("PharmGKB Pathways", //
+ "http://www.pharmgkb.org/", //
+ "urn:miriam:pharmgkb.pathways", //
+ new Class<?>[] {}, "MIR:00000089"), //
+
+ /**
+ * PubChem-compound: http://pubchem.ncbi.nlm.nih.gov/.
+ */
+ PUBCHEM("PubChem-compound", //
+ "http://pubchem.ncbi.nlm.nih.gov/", //
+ new String[] { "urn:miriam:pubchem.compound" }, //
+ new Class<?>[] { Chemical.class }, "MIR:00000034", //
+ new Class<?>[] { Chemical.class }), //
+
+ /**
+ * PubChem-substance: http://pubchem.ncbi.nlm.nih.gov/.
+ */
+ PUBCHEM_SUBSTANCE("PubChem-substance", //
+ "http://pubchem.ncbi.nlm.nih.gov/", //
+ new String[] { "urn:miriam:pubchem.substance" }, //
+ new Class<?>[] { Chemical.class }, "MIR:00000033", //
+ new Class<?>[] { Chemical.class }), //
+
+ /**
+ * PubMed: http://www.ncbi.nlm.nih.gov/PubMed/.
+ */
+ PUBMED("PubMed", //
+ "http://www.ncbi.nlm.nih.gov/PubMed/", //
+ new String[] { "urn:miriam:pubmed" }, //
+ new Class<?>[] { BioEntity.class }, "MIR:00000015", //
+ new Class<?>[] { Reaction.class }), //
+
+ /**
+ * Reactome: http://www.reactome.org/.
+ */
+ REACTOME("Reactome", //
+ "http://www.reactome.org/", //
+ "urn:miriam:reactome", //
+ new Class<?>[] { Reaction.class }, "MIR:00000018"), //
+
+ /**
+ * RefSeq: http://www.ncbi.nlm.nih.gov/projects/RefSeq/.
+ */
+ REFSEQ("RefSeq", //
+ "http://www.ncbi.nlm.nih.gov/projects/RefSeq/", //
+ "urn:miriam:refseq", //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000039"),
+
+ /**
+ * Rhea: http://www.rhea-db.org/.
+ */
+ RHEA("Rhea", //
+ "http://www.rhea-db.org/", //
+ "urn:miriam:rhea", //
+ new Class<?>[] { Reaction.class }, "MIR:00000082"),
+
+ /**
+ * SGD: http://www.yeastgenome.org/.
+ */
+ SGD("Saccharomyces Genome Database", //
+ "http://www.yeastgenome.org/", //
+ "urn:miriam:sgd", //
+ new Class<?>[] {}, "MIR:00000023"),
+
+ /**
+ * STITCH: http://stitch.embl.de/.
+ */
+ STITCH("STITCH", //
+ "http://stitch.embl.de/", //
+ "urn:miriam:stitch", //
+ new Class<?>[] {}, "MIR:00100343"),
+
+ /**
+ * STRING: http://string-db.org/.
+ */
+ STRING("STRING", //
+ "http://string-db.org/", //
+ "urn:miriam:string", //
+ new Class<?>[] {}, "MIR:00000265"),
+
+ /**
+ * The Arabidopsis Information Resource (TAIR) maintains a database of genetic
+ * and molecular biology data for the model higher plant Arabidopsis thaliana.
+ * The name of a Locus is unique and used by TAIR, TIGR, and MIPS:
+ * http://arabidopsis.org/index.jsp.
+ */
+ TAIR_LOCUS("TAIR Locus", //
+ "http://arabidopsis.org/index.jsp", //
+ "urn:miriam:tair.locus", //
+ new Class<?>[] {}, "MIR:00000050"),
+
+ /**
+ * Taxonomy: http://www.ncbi.nlm.nih.gov/taxonomy/.
+ */
+ TAXONOMY("Taxonomy", //
+ "http://www.ncbi.nlm.nih.gov/taxonomy/", //
+ "urn:miriam:taxonomy", //
+ new Class<?>[] {}, "MIR:00000006"),
+ /**
+ * Toxicogenomic: Chemical: http://ctdbase.org/detail.go.
+ * http://ctdbase.org/detail.go
+ */
+ TOXICOGENOMIC_CHEMICAL("Toxicogenomic Chemical", //
+ "http://ctdbase.org/", //
+ "urn:miriam:ctd.chemical", //
+ new Class<?>[] {}, "MIR:00000098"), //
+
+ /**
+ * UniGene: http://www.ncbi.nlm.nih.gov/unigene.
+ */
+ UNIGENE("UniGene", //
+ "http://www.ncbi.nlm.nih.gov/unigene", //
+ "urn:miriam:unigene", //
+ new Class<?>[] {}, "MIR:00000346"),
+
+ /**
+ * Uniprot: http://www.uniprot.org/.
+ */
+ UNIPROT("Uniprot", //
+ "http://www.uniprot.org/", //
+ "urn:miriam:uniprot", //
+ new Class<?>[] { Protein.class, Gene.class, Rna.class }, "MIR:00000005"),
+
+ /**
+ * UniProt Isoform: http://www.uniprot.org/.
+ */
+ UNIPROT_ISOFORM("UniProt Isoform", //
+ "http://www.uniprot.org/", //
+ "urn:miriam:uniprot.isoform", //
+ new Class<?>[] { Protein.class }, "MIR:00000388"),
+
+ /**
+ * Unknown reference type...
+ */
+ UNKNOWN("Unknown", //
+ null, //
+ new String[] {}, //
+ new Class<?>[] {}, null),
+
+ /**
+ * Wikidata: https://www.wikidata.org/.
+ */
+ WIKIDATA("Wikidata", //
+ "https://www.wikidata.org/", //
+ new String[] { "urn:miriam:wikidata" }, //
+ new Class<?>[] {}, "MIR:00000549"), //
+
+ /**
+ * WikiPathways: http://www.wikipathways.org/.
+ */
+ WIKIPATHWAYS("WikiPathways", //
+ "http://www.wikipathways.org/", //
+ new String[] { "urn:miriam:wikipathways" }, //
+ new Class<?>[] {}, "MIR:00000076"), //
+
+ /**
+ * Wikipedia: http://en.wikipedia.org/wiki/Main_Page.
+ */
+ WIKIPEDIA("Wikipedia (English)", //
+ "http://en.wikipedia.org/wiki/Main_Page", // /
+ new String[] { "urn:miriam:wikipedia.en" }, //
+ new Class<?>[] {}, "MIR:00000384"),
+
+ /**
+ * WormBase: http://wormbase.bio2rdf.org/fct.
+ */
+ WORM_BASE("WormBase", //
+ "http://wormbase.bio2rdf.org/fct", // /
+ new String[] { "urn:miriam:wormbase" }, //
+ new Class<?>[] {}, "MIR:00000027");
+
+ /**
+ * User friendly name.
+ */
+ private String commonName;
+
+ /**
+ * url to home page of given resource type.
+ */
+ private String dbHomepage;
+
+ /**
+ * Identifier of the database in miriam registry.
+ */
+ private String registryIdentifier;
+
+ /**
+ * Valid URIs to this resource.
+ */
+ private List<String> uris = new ArrayList<>();
+
+ /**
+ * Classes that can be annotated by this resource.
+ */
+ private List<Class<? extends BioEntity>> validClass = new ArrayList<>();
+
+ /**
+ * When class from this list is marked as "require at least one annotation" then
+ * annotation of this type is valid.
+ */
+ private List<Class<? extends BioEntity>> requiredClass = new ArrayList<>();
+
+ /**
+ * Constructor that initialize enum object.
+ *
+ * @param dbHomePage
+ * home page of the resource {@link #dbHomepage}
+ * @param commonName
+ * {@link #commonName}
+ * @param uris
+ * {@link #uris}
+ * @param classes
+ * {@link #validClass}
+ * @param registryIdentifier
+ * {@link #registryIdentifier}
+ */
+ MiriamType(String commonName, String dbHomePage, String[] uris, Class<?>[] classes, String registryIdentifier) {
+ this(commonName, dbHomePage, uris, classes, registryIdentifier, new Class<?>[] {});
+ }
+
+ /**
+ * Constructor that initialize enum object.
+ *
+ * @param dbHomePage
+ * home page of the resource {@link #dbHomepage}
+ * @param commonName
+ * {@link #commonName}
+ * @param uris
+ * {@link #uris}
+ * @param classes
+ * {@link #validClass}
+ * @param registryIdentifier
+ * {@link #registryIdentifier}
+ * @param requiredClasses
+ * {@link #requiredClasses}
+ */
+ MiriamType(String commonName, String dbHomePage, String[] uris, Class<?>[] classes, String registryIdentifier,
+ Class<?>[] requiredClasses) {
+ this.commonName = commonName;
+ this.dbHomepage = dbHomePage;
+ for (String string : uris) {
+ this.uris.add(string);
+ }
+ for (Class<?> clazz : classes) {
+ this.validClass.add((Class<? extends BioEntity>) clazz);
+ }
+ for (Class<?> clazz : requiredClasses) {
+ this.requiredClass.add((Class<? extends BioEntity>) clazz);
+ }
+ this.registryIdentifier = registryIdentifier;
+ }
+
+ /**
+ * Constructor that initialize enum object.
+ *
+ * @param dbHomePage
+ * home page of the resource {@link #dbHomepage}
+ * @param commonName
+ * {@link #commonName}
+ * @param uri
+ * one of {@link #uris}
+ * @param registryIdentifier
+ * {@link #registryIdentifier}
+ * @param classes
+ * {@link #validClass}
+ */
+ MiriamType(String commonName, String dbHomePage, String uri, Class<?>[] classes, String registryIdentifier) {
+ this(commonName, dbHomePage, new String[] { uri }, classes, registryIdentifier);
+ }
+
+ /**
+ *
+ * @return {@link #commonName}
+ */
+ public String getCommonName() {
+ return commonName;
+ }
+
+ /**
+ *
+ * @return {@link #uris}
+ */
+ public List<String> getUris() {
+ return uris;
+ }
+
+ /**
+ *
+ * @return {@link #validClass}
+ */
+ public List<Class<? extends BioEntity>> getValidClass() {
+ return validClass;
+ }
+
+ /**
+ * Returns {@link MiriamType} associated with parameter uri address.
+ *
+ * @param uri
+ * uri to check
+ * @return {@link MiriamType} for given uri
+ */
+ public static MiriamType getTypeByUri(String uri) {
+ for (MiriamType mt : MiriamType.values()) {
+ for (String string : mt.getUris()) {
+ if (string.equalsIgnoreCase(uri)) {
+ return mt;
+ }
+ }
+ }
+ return null;
+ }
+
+ /**
+ * @return the dbHomepage
+ * @see #dbHomepage
+ */
+ public String getDbHomepage() {
+ return dbHomepage;
+ }
+
+ /**
+ * @return the registryIdentifier
+ * @see #registryIdentifier
+ */
+ public String getRegistryIdentifier() {
+ return registryIdentifier;
+ }
+
+ /**
+ * @return the requiredClass
+ * @see #requiredClass
+ */
+ public List<Class<? extends BioEntity>> getRequiredClass() {
+ return requiredClass;
+ }
+
+ /**
+ * Returns {@link MiriamType} associated with {@link #commonName}.
+ *
+ * @param string
+ * {@link #commonName}
+ * @return {@link MiriamType} for given name
+ */
+ public static MiriamType getTypeByCommonName(String string) {
+ for (MiriamType mt : MiriamType.values()) {
+ if (string.equalsIgnoreCase(mt.getCommonName())) {
+ return mt;
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Transforms identifier into {@link MiriamData}.
+ *
+ * @param generalIdentifier
+ * identifier in the format NAME:IDENTIFIER. Where NAME is the name
+ * from {@link MiriamType#commonName} and IDENTIFIER is resource
+ * identifier.
+ * @return {@link MiriamData} representing generalIdentifier, when identifier is
+ * invalid InvalidArgumentException is thrown
+ */
+ public static MiriamData getMiriamDataFromIdentifier(String generalIdentifier) {
+ int index = generalIdentifier.indexOf(":");
+ if (index < 0) {
+ throw new InvalidArgumentException("Identifier doesn't contain type");
+ }
+ String type = generalIdentifier.substring(0, index);
+ String id = generalIdentifier.substring(index + 1);
+ for (MiriamType mt : MiriamType.values()) {
+ if (mt.getCommonName().equalsIgnoreCase(type)) {
+ return new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, mt, id);
+ }
+ }
+ throw new InvalidArgumentException("Unknown miriam type: " + type + " (id: " + id + ")");
+ }
+
+ /**
+ * Creates {@link MiriamData} from miriam uri.
+ *
+ * @param miriamUri
+ * miriam uri defining {@link MiriamData}
+ * @return {@link MiriamData} from miriam uri
+ */
+ public static MiriamData getMiriamByUri(String miriamUri) {
+ // this hack is due to CellDesigner issue (CellDesigner incorectly handle
+ // with identifiers that have ":" inside resource ":" inside resource with
+ // "%3A" and also the last ":"
+ miriamUri = miriamUri.replace("%3A", ":");
+
+ String foundUri = "";
+ MiriamType foundType = null;
+
+ for (MiriamType type : MiriamType.values()) {
+ for (String uri : type.getUris()) {
+ if (miriamUri.startsWith(uri + ":")) {
+ if (uri.length() > foundUri.length()) {
+ foundType = type;
+ foundUri = uri;
+ }
+ }
+ }
+ }
+ if (foundType != null) {
+ return new MiriamData(foundType, miriamUri.substring(foundUri.length() + 1));
+ }
+ throw new InvalidArgumentException("Invalid miriam uri: " + miriamUri);
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/MiriamTypeNameComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/MiriamTypeNameComparator.java
index c7d9811884..d8ce7d1f5d 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamTypeNameComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamTypeNameComparator.java
@@ -1,23 +1,23 @@
-package lcsb.mapviewer.model.map;
-
-import lcsb.mapviewer.common.Comparator;
-
-/**
- * {@link Comparator} implementation for {@link MiriamType} that uses
- * {@link MiriamType#commonName} as a key to comparison.
- *
- * @author Piotr Gawron
- *
- */
-public class MiriamTypeNameComparator extends Comparator<MiriamType> {
-
- public MiriamTypeNameComparator() {
- super(MiriamType.class);
- }
-
- @Override
- protected int internalCompare(MiriamType arg0, MiriamType arg1) {
- return arg0.getCommonName().compareTo(arg1.getCommonName());
- }
-
-}
+package lcsb.mapviewer.model.map;
+
+import lcsb.mapviewer.common.Comparator;
+
+/**
+ * {@link Comparator} implementation for {@link MiriamType} that uses
+ * {@link MiriamType#commonName} as a key to comparison.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class MiriamTypeNameComparator extends Comparator<MiriamType> {
+
+ public MiriamTypeNameComparator() {
+ super(MiriamType.class);
+ }
+
+ @Override
+ protected int internalCompare(MiriamType arg0, MiriamType arg1) {
+ return arg0.getCommonName().compareTo(arg1.getCommonName());
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/OverviewImage.java b/model/src/main/java/lcsb/mapviewer/model/map/OverviewImage.java
index e837b18f77..ae22a55c8d 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/OverviewImage.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/OverviewImage.java
@@ -1,231 +1,231 @@
-package lcsb.mapviewer.model.map;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.ManyToOne;
-import javax.persistence.OneToMany;
-import javax.persistence.OrderBy;
-import javax.persistence.Table;
-
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.model.ModelData;
-
-/**
- * This class describes single image that overview the model. Images can create
- * hierarchical structure via {@link OverviewLink} (link can point to another
- * image). The idea is to have set of images that nicely represent biology and
- * map it into map via {@link OverviewModelLink}.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "overview_image_table")
-public class OverviewImage implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Unique database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- /**
- * The image belongs to this {@link Project}. Links can point to any
- * (sub)model in this project.
- */
- @ManyToOne(fetch = FetchType.LAZY, optional = false)
- private Project project;
-
- /**
- * Name of the file in file system that reresent this overview image.
- */
- private String filename;
-
- /**
- * Width of the image.
- */
- private Integer width;
-
- /**
- * Height of the image.
- */
- private Integer height;
-
- /**
- * List of links that should redirect from this image. They can refer to
- * another {@link OverviewImage} or {@link ModelData Model}.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(fetch = FetchType.EAGER, mappedBy = "overviewImage", orphanRemoval = true)
- @OrderBy("id")
- private List<OverviewLink> links = new ArrayList<>();
-
- /**
- * Default constructor.
- */
- public OverviewImage() {
-
- }
-
- /**
- * Default constructor with original {@link OverviewImage} as a source of
- * data.
- *
- * @param overviewImage
- * original {@link OverviewImage}
- */
- public OverviewImage(OverviewImage overviewImage) {
- this.setId(overviewImage.getId());
- this.setProject(overviewImage.getProject());
- this.setFilename(overviewImage.getFilename());
- this.setWidth(overviewImage.getWidth());
- this.setHeight(overviewImage.getHeight());
- for (OverviewLink ol : overviewImage.getLinks()) {
- this.addLink(ol.copy());
- }
- }
-
- /**
- * @return the filename
- * @see #filename
- */
- public String getFilename() {
- return filename;
- }
-
- /**
- * @param filename
- * the filename to set
- * @see #filename
- */
- public void setFilename(String filename) {
- this.filename = filename;
- }
-
- /**
- * @return the width
- * @see #width
- */
- public Integer getWidth() {
- return width;
- }
-
- /**
- * @param width
- * the width to set
- * @see #width
- */
- public void setWidth(Integer width) {
- this.width = width;
- }
-
- /**
- * @return the height
- * @see #height
- */
- public Integer getHeight() {
- return height;
- }
-
- /**
- * @param height
- * the height to set
- * @see #height
- */
- public void setHeight(Integer height) {
- this.height = height;
- }
-
- /**
- * @return the links
- * @see #links
- */
- public List<OverviewLink> getLinks() {
- return links;
- }
-
- /**
- * @param links
- * the links to set
- * @see #links
- */
- public void setLinks(List<OverviewLink> links) {
- this.links = links;
- }
-
- /**
- * @return the id
- * @see #id
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
- /**
- * Adds {@link OverviewLink link } to {@link #links}.
- *
- * @param oml
- * object to add
- */
- public void addLink(OverviewLink oml) {
- links.add(oml);
- oml.setOverviewImage(this);
- }
-
- /**
- * Creates a copy of the object.
- *
- * @return copy of the object
- */
- public OverviewImage copy() {
- if (this.getClass() == OverviewImage.class) {
- return new OverviewImage(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- /**
- * @return the project
- * @see #project
- */
- public Project getProject() {
- return project;
- }
-
- /**
- * @param project the project to set
- * @see #project
- */
- public void setProject(Project project) {
- this.project = project;
- }
-}
+package lcsb.mapviewer.model.map;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
+import javax.persistence.OrderBy;
+import javax.persistence.Table;
+
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.model.ModelData;
+
+/**
+ * This class describes single image that overview the model. Images can create
+ * hierarchical structure via {@link OverviewLink} (link can point to another
+ * image). The idea is to have set of images that nicely represent biology and
+ * map it into map via {@link OverviewModelLink}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "overview_image_table")
+public class OverviewImage implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Unique database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * The image belongs to this {@link Project}. Links can point to any
+ * (sub)model in this project.
+ */
+ @ManyToOne(fetch = FetchType.LAZY, optional = false)
+ private Project project;
+
+ /**
+ * Name of the file in file system that reresent this overview image.
+ */
+ private String filename;
+
+ /**
+ * Width of the image.
+ */
+ private Integer width;
+
+ /**
+ * Height of the image.
+ */
+ private Integer height;
+
+ /**
+ * List of links that should redirect from this image. They can refer to
+ * another {@link OverviewImage} or {@link ModelData Model}.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(fetch = FetchType.EAGER, mappedBy = "overviewImage", orphanRemoval = true)
+ @OrderBy("id")
+ private List<OverviewLink> links = new ArrayList<>();
+
+ /**
+ * Default constructor.
+ */
+ public OverviewImage() {
+
+ }
+
+ /**
+ * Default constructor with original {@link OverviewImage} as a source of
+ * data.
+ *
+ * @param overviewImage
+ * original {@link OverviewImage}
+ */
+ public OverviewImage(OverviewImage overviewImage) {
+ this.setId(overviewImage.getId());
+ this.setProject(overviewImage.getProject());
+ this.setFilename(overviewImage.getFilename());
+ this.setWidth(overviewImage.getWidth());
+ this.setHeight(overviewImage.getHeight());
+ for (OverviewLink ol : overviewImage.getLinks()) {
+ this.addLink(ol.copy());
+ }
+ }
+
+ /**
+ * @return the filename
+ * @see #filename
+ */
+ public String getFilename() {
+ return filename;
+ }
+
+ /**
+ * @param filename
+ * the filename to set
+ * @see #filename
+ */
+ public void setFilename(String filename) {
+ this.filename = filename;
+ }
+
+ /**
+ * @return the width
+ * @see #width
+ */
+ public Integer getWidth() {
+ return width;
+ }
+
+ /**
+ * @param width
+ * the width to set
+ * @see #width
+ */
+ public void setWidth(Integer width) {
+ this.width = width;
+ }
+
+ /**
+ * @return the height
+ * @see #height
+ */
+ public Integer getHeight() {
+ return height;
+ }
+
+ /**
+ * @param height
+ * the height to set
+ * @see #height
+ */
+ public void setHeight(Integer height) {
+ this.height = height;
+ }
+
+ /**
+ * @return the links
+ * @see #links
+ */
+ public List<OverviewLink> getLinks() {
+ return links;
+ }
+
+ /**
+ * @param links
+ * the links to set
+ * @see #links
+ */
+ public void setLinks(List<OverviewLink> links) {
+ this.links = links;
+ }
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ /**
+ * Adds {@link OverviewLink link } to {@link #links}.
+ *
+ * @param oml
+ * object to add
+ */
+ public void addLink(OverviewLink oml) {
+ links.add(oml);
+ oml.setOverviewImage(this);
+ }
+
+ /**
+ * Creates a copy of the object.
+ *
+ * @return copy of the object
+ */
+ public OverviewImage copy() {
+ if (this.getClass() == OverviewImage.class) {
+ return new OverviewImage(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ /**
+ * @return the project
+ * @see #project
+ */
+ public Project getProject() {
+ return project;
+ }
+
+ /**
+ * @param project the project to set
+ * @see #project
+ */
+ public void setProject(Project project) {
+ this.project = project;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/OverviewImageComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/OverviewImageComparator.java
index de8391c624..6dc3589c01 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/OverviewImageComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/OverviewImageComparator.java
@@ -1,98 +1,98 @@
-package lcsb.mapviewer.model.map;
-
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.IntegerComparator;
-import lcsb.mapviewer.common.comparator.StringComparator;
-
-/**
- * This class implements comparator interface for {@link OverviewImage}.
- *
- * @author Piotr Gawron
- *
- */
-public class OverviewImageComparator extends Comparator<OverviewImage> {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(OverviewImageComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public OverviewImageComparator(double epsilon) {
- super(OverviewImage.class);
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public OverviewImageComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected int internalCompare(OverviewImage arg0, OverviewImage arg1) {
- StringComparator stringComparator = new StringComparator();
-
- if (stringComparator.compare(arg0.getFilename(), arg1.getFilename()) != 0) {
- logger.debug("filename different: " + arg0.getFilename() + ", " + arg1.getFilename());
- return stringComparator.compare(arg0.getFilename(), arg1.getFilename());
- }
-
- IntegerComparator integerComparator = new IntegerComparator();
-
- if (integerComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
- logger.debug("width different: " + arg0.getWidth() + ", " + arg1.getWidth());
- return integerComparator.compare(arg0.getWidth(), arg1.getWidth());
- }
-
- if (integerComparator.compare(arg0.getHeight(), arg1.getHeight()) != 0) {
- logger.debug("height different: " + arg0.getHeight() + ", " + arg1.getHeight());
- return integerComparator.compare(arg0.getHeight(), arg1.getHeight());
- }
-
- if (compareLinks(arg0.getLinks(), arg1.getLinks()) != 0) {
- return compareLinks(arg0.getLinks(), arg1.getLinks());
- }
-
- return 0;
- }
-
- /**
- * Compare two list of {@link OverviewLink links}.
- *
- * @param links
- * first list to compare
- * @param links2
- * second list to compare
- * @return 0 if the list are identical, -1/1 otherwise
- */
- private int compareLinks(List<OverviewLink> links, List<OverviewLink> links2) {
- IntegerComparator integerComparator = new IntegerComparator();
- OverviewLinkComparator ovc = new OverviewLinkComparator(epsilon);
- if (integerComparator.compare(links.size(), links2.size()) != 0) {
- return integerComparator.compare(links.size(), links2.size());
- }
- for (int i = 0; i < links.size(); i++) {
- if (ovc.compare(links.get(i), links2.get(i)) != 0) {
- return ovc.compare(links.get(i), links2.get(i));
- }
- }
- return 0;
- }
-
-}
+package lcsb.mapviewer.model.map;
+
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.IntegerComparator;
+import lcsb.mapviewer.common.comparator.StringComparator;
+
+/**
+ * This class implements comparator interface for {@link OverviewImage}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class OverviewImageComparator extends Comparator<OverviewImage> {
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(OverviewImageComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public OverviewImageComparator(double epsilon) {
+ super(OverviewImage.class);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public OverviewImageComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(OverviewImage arg0, OverviewImage arg1) {
+ StringComparator stringComparator = new StringComparator();
+
+ if (stringComparator.compare(arg0.getFilename(), arg1.getFilename()) != 0) {
+ logger.debug("filename different: " + arg0.getFilename() + ", " + arg1.getFilename());
+ return stringComparator.compare(arg0.getFilename(), arg1.getFilename());
+ }
+
+ IntegerComparator integerComparator = new IntegerComparator();
+
+ if (integerComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
+ logger.debug("width different: " + arg0.getWidth() + ", " + arg1.getWidth());
+ return integerComparator.compare(arg0.getWidth(), arg1.getWidth());
+ }
+
+ if (integerComparator.compare(arg0.getHeight(), arg1.getHeight()) != 0) {
+ logger.debug("height different: " + arg0.getHeight() + ", " + arg1.getHeight());
+ return integerComparator.compare(arg0.getHeight(), arg1.getHeight());
+ }
+
+ if (compareLinks(arg0.getLinks(), arg1.getLinks()) != 0) {
+ return compareLinks(arg0.getLinks(), arg1.getLinks());
+ }
+
+ return 0;
+ }
+
+ /**
+ * Compare two list of {@link OverviewLink links}.
+ *
+ * @param links
+ * first list to compare
+ * @param links2
+ * second list to compare
+ * @return 0 if the list are identical, -1/1 otherwise
+ */
+ private int compareLinks(List<OverviewLink> links, List<OverviewLink> links2) {
+ IntegerComparator integerComparator = new IntegerComparator();
+ OverviewLinkComparator ovc = new OverviewLinkComparator(epsilon);
+ if (integerComparator.compare(links.size(), links2.size()) != 0) {
+ return integerComparator.compare(links.size(), links2.size());
+ }
+ for (int i = 0; i < links.size(); i++) {
+ if (ovc.compare(links.get(i), links2.get(i)) != 0) {
+ return ovc.compare(links.get(i), links2.get(i));
+ }
+ }
+ return 0;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/OverviewImageLink.java b/model/src/main/java/lcsb/mapviewer/model/map/OverviewImageLink.java
index 4610de7b60..c3a577f376 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/OverviewImageLink.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/OverviewImageLink.java
@@ -1,77 +1,77 @@
-package lcsb.mapviewer.model.map;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.ManyToOne;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-/**
- * Link used in {@link OverviewImage parent OverviewImage} to link it to
- * {@link OverviewImage child OverviewImage}.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("IMAGE_LINK")
-public class OverviewImageLink extends OverviewLink {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Child {@link OverviewImage} that can be reached via this link.
- */
- @ManyToOne(fetch = FetchType.LAZY, optional = false)
- private OverviewImage linkedOverviewImage;
-
- /**
- * Default constructor that copies object from the parameter.
- *
- * @param original
- * original object to be copied
- */
- public OverviewImageLink(OverviewImageLink original) {
- super(original);
- this.linkedOverviewImage = original.linkedOverviewImage;
-
- }
-
- /**
- * DEfault constructor.
- */
- public OverviewImageLink() {
- super();
- }
-
- /**
- * @return the linkedOverviewImage
- * @see #linkedOverviewImage
- */
- public OverviewImage getLinkedOverviewImage() {
- return linkedOverviewImage;
- }
-
- /**
- * @param linkedOverviewImage
- * the linkedOverviewImage to set
- * @see #linkedOverviewImage
- */
- public void setLinkedOverviewImage(OverviewImage linkedOverviewImage) {
- this.linkedOverviewImage = linkedOverviewImage;
- }
-
- @Override
- public OverviewImageLink copy() {
- if (this.getClass() == OverviewImageLink.class) {
- return new OverviewImageLink(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.ManyToOne;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * Link used in {@link OverviewImage parent OverviewImage} to link it to
+ * {@link OverviewImage child OverviewImage}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("IMAGE_LINK")
+public class OverviewImageLink extends OverviewLink {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Child {@link OverviewImage} that can be reached via this link.
+ */
+ @ManyToOne(fetch = FetchType.LAZY, optional = false)
+ private OverviewImage linkedOverviewImage;
+
+ /**
+ * Default constructor that copies object from the parameter.
+ *
+ * @param original
+ * original object to be copied
+ */
+ public OverviewImageLink(OverviewImageLink original) {
+ super(original);
+ this.linkedOverviewImage = original.linkedOverviewImage;
+
+ }
+
+ /**
+ * DEfault constructor.
+ */
+ public OverviewImageLink() {
+ super();
+ }
+
+ /**
+ * @return the linkedOverviewImage
+ * @see #linkedOverviewImage
+ */
+ public OverviewImage getLinkedOverviewImage() {
+ return linkedOverviewImage;
+ }
+
+ /**
+ * @param linkedOverviewImage
+ * the linkedOverviewImage to set
+ * @see #linkedOverviewImage
+ */
+ public void setLinkedOverviewImage(OverviewImage linkedOverviewImage) {
+ this.linkedOverviewImage = linkedOverviewImage;
+ }
+
+ @Override
+ public OverviewImageLink copy() {
+ if (this.getClass() == OverviewImageLink.class) {
+ return new OverviewImageLink(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/OverviewImageLinkComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/OverviewImageLinkComparator.java
index 8ffff6767c..bf94e0055c 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/OverviewImageLinkComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/OverviewImageLinkComparator.java
@@ -1,75 +1,75 @@
-package lcsb.mapviewer.model.map;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.IntegerComparator;
-
-/**
- * This class implements comparator interface for {@link OverviewImageLink}.
- *
- * @author Piotr Gawron
- *
- */
-public class OverviewImageLinkComparator extends Comparator<OverviewImageLink> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(OverviewImageLinkComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public OverviewImageLinkComparator(double epsilon) {
- super(OverviewImageLink.class);
- this.epsilon = epsilon;
- }
-
- @Override
- protected Comparator<?> getParentComparator() {
- return new OverviewLinkComparator(epsilon);
- }
-
- /**
- * Default constructor.
- */
- public OverviewImageLinkComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected int internalCompare(OverviewImageLink arg0, OverviewImageLink arg1) {
- int result = 0;
- IntegerComparator integerComparator = new IntegerComparator();
-
- if (arg0.getLinkedOverviewImage() == null) {
- if (arg1.getLinkedOverviewImage() == null) {
- result = 0;
- } else {
- result = 1;
- }
- } else if (arg1.getLinkedOverviewImage() == null) {
- result = -1;
- } else {
- result = integerComparator.compare(arg0.getLinkedOverviewImage().getId(), arg1.getLinkedOverviewImage().getId());
- }
-
- if (result != 0) {
- return result;
- }
-
- return 0;
-
- }
-
-}
+package lcsb.mapviewer.model.map;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.IntegerComparator;
+
+/**
+ * This class implements comparator interface for {@link OverviewImageLink}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class OverviewImageLinkComparator extends Comparator<OverviewImageLink> {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(OverviewImageLinkComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public OverviewImageLinkComparator(double epsilon) {
+ super(OverviewImageLink.class);
+ this.epsilon = epsilon;
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new OverviewLinkComparator(epsilon);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public OverviewImageLinkComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(OverviewImageLink arg0, OverviewImageLink arg1) {
+ int result = 0;
+ IntegerComparator integerComparator = new IntegerComparator();
+
+ if (arg0.getLinkedOverviewImage() == null) {
+ if (arg1.getLinkedOverviewImage() == null) {
+ result = 0;
+ } else {
+ result = 1;
+ }
+ } else if (arg1.getLinkedOverviewImage() == null) {
+ result = -1;
+ } else {
+ result = integerComparator.compare(arg0.getLinkedOverviewImage().getId(), arg1.getLinkedOverviewImage().getId());
+ }
+
+ if (result != 0) {
+ return result;
+ }
+
+ return 0;
+
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/OverviewLink.java b/model/src/main/java/lcsb/mapviewer/model/map/OverviewLink.java
index 33e949bd3a..bab1b93558 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/OverviewLink.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/OverviewLink.java
@@ -1,165 +1,165 @@
-package lcsb.mapviewer.model.map;
-
-import java.awt.geom.Point2D;
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.persistence.Column;
-import javax.persistence.DiscriminatorColumn;
-import javax.persistence.DiscriminatorType;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Inheritance;
-import javax.persistence.InheritanceType;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-
-/**
- * Abstract class representing link that connects {@link OverviewImage parent
- * OverviewImage} with some other piece of data. Right now there are two
- * implementations:
- * <ul>
- * <li> {@link OverviewImageLink} - connects to another {@link OverviewImageLink}
- * </li>
- * <li> {@link OverviewModelLink} - connects to a
- * {@link lcsb.mapviewer.model.map.model.Model Model}</li>
- * </ul>
- *
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "overview_link_table")
-@Inheritance(strategy = InheritanceType.SINGLE_TABLE)
-@DiscriminatorColumn(name = "link_type", discriminatorType = DiscriminatorType.STRING)
-@DiscriminatorValue("GENERIC_VIEW")
-public abstract class OverviewLink implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Unique identifier in the database.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- /**
- * Parent {@link OverviewImage} from which this link is outgoing.
- */
- @ManyToOne(fetch = FetchType.LAZY, optional = false)
- private OverviewImage overviewImage;
-
- /**
- * String representing polygon area on the image that should be clickable and
- * that corresponds to this link. This string should be space separated list
- * of coordinates. Example "10,10 20,20 100,0".
- */
- private String polygon;
-
- /**
- * Default constructor.
- */
- public OverviewLink() {
-
- }
-
- /**
- * Default constructor that creates a copy of the object from parameter.
- *
- * @param original
- * origianl object to copy
- */
- public OverviewLink(OverviewLink original) {
- this.id = original.id;
- this.overviewImage = original.overviewImage;
- this.polygon = original.polygon;
- }
-
- /**
- * @return the polygon
- * @see #polygon
- */
- public String getPolygon() {
- return polygon;
- }
-
- /**
- * @param polygon
- * the polygon to set
- * @see #polygon
- */
- public void setPolygon(String polygon) {
- this.polygon = polygon;
- }
-
- /**
- * Transforms {@link #polygon} into list of points.
- *
- * @return list of points representing {@link #polygon} area.
- */
- public List<Point2D> getPolygonCoordinates() {
- List<Point2D> coordinates = new ArrayList<Point2D>();
- String[] stringCoordinates = polygon.split(" ");
- for (String string : stringCoordinates) {
- String[] coord = string.split(",");
- Double x = Double.valueOf(coord[0]);
- Double y = Double.valueOf(coord[1]);
- Point2D point = new Point2D.Double(x, y);
- coordinates.add(point);
- }
- return coordinates;
- }
-
- /**
- * @return the overviewImage
- * @see #overviewImage
- */
- public OverviewImage getOverviewImage() {
- return overviewImage;
- }
-
- /**
- * @param overviewImage
- * the overviewImage to set
- * @see #overviewImage
- */
- public void setOverviewImage(OverviewImage overviewImage) {
- this.overviewImage = overviewImage;
- }
-
- /**
- * @return the id
- * @see #id
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
- /**
- * Copies the object and returns a copy.
- *
- * @return copy of the object
- */
- public abstract OverviewLink copy();
-
-}
+package lcsb.mapviewer.model.map;
+
+import java.awt.geom.Point2D;
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.persistence.Column;
+import javax.persistence.DiscriminatorColumn;
+import javax.persistence.DiscriminatorType;
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.Inheritance;
+import javax.persistence.InheritanceType;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+
+/**
+ * Abstract class representing link that connects {@link OverviewImage parent
+ * OverviewImage} with some other piece of data. Right now there are two
+ * implementations:
+ * <ul>
+ * <li> {@link OverviewImageLink} - connects to another {@link OverviewImageLink}
+ * </li>
+ * <li> {@link OverviewModelLink} - connects to a
+ * {@link lcsb.mapviewer.model.map.model.Model Model}</li>
+ * </ul>
+ *
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "overview_link_table")
+@Inheritance(strategy = InheritanceType.SINGLE_TABLE)
+@DiscriminatorColumn(name = "link_type", discriminatorType = DiscriminatorType.STRING)
+@DiscriminatorValue("GENERIC_VIEW")
+public abstract class OverviewLink implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Unique identifier in the database.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * Parent {@link OverviewImage} from which this link is outgoing.
+ */
+ @ManyToOne(fetch = FetchType.LAZY, optional = false)
+ private OverviewImage overviewImage;
+
+ /**
+ * String representing polygon area on the image that should be clickable and
+ * that corresponds to this link. This string should be space separated list
+ * of coordinates. Example "10,10 20,20 100,0".
+ */
+ private String polygon;
+
+ /**
+ * Default constructor.
+ */
+ public OverviewLink() {
+
+ }
+
+ /**
+ * Default constructor that creates a copy of the object from parameter.
+ *
+ * @param original
+ * origianl object to copy
+ */
+ public OverviewLink(OverviewLink original) {
+ this.id = original.id;
+ this.overviewImage = original.overviewImage;
+ this.polygon = original.polygon;
+ }
+
+ /**
+ * @return the polygon
+ * @see #polygon
+ */
+ public String getPolygon() {
+ return polygon;
+ }
+
+ /**
+ * @param polygon
+ * the polygon to set
+ * @see #polygon
+ */
+ public void setPolygon(String polygon) {
+ this.polygon = polygon;
+ }
+
+ /**
+ * Transforms {@link #polygon} into list of points.
+ *
+ * @return list of points representing {@link #polygon} area.
+ */
+ public List<Point2D> getPolygonCoordinates() {
+ List<Point2D> coordinates = new ArrayList<Point2D>();
+ String[] stringCoordinates = polygon.split(" ");
+ for (String string : stringCoordinates) {
+ String[] coord = string.split(",");
+ Double x = Double.valueOf(coord[0]);
+ Double y = Double.valueOf(coord[1]);
+ Point2D point = new Point2D.Double(x, y);
+ coordinates.add(point);
+ }
+ return coordinates;
+ }
+
+ /**
+ * @return the overviewImage
+ * @see #overviewImage
+ */
+ public OverviewImage getOverviewImage() {
+ return overviewImage;
+ }
+
+ /**
+ * @param overviewImage
+ * the overviewImage to set
+ * @see #overviewImage
+ */
+ public void setOverviewImage(OverviewImage overviewImage) {
+ this.overviewImage = overviewImage;
+ }
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ /**
+ * Copies the object and returns a copy.
+ *
+ * @return copy of the object
+ */
+ public abstract OverviewLink copy();
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/OverviewLinkComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/OverviewLinkComparator.java
index 6ea1cc68e5..da41e02372 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/OverviewLinkComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/OverviewLinkComparator.java
@@ -1,62 +1,62 @@
-package lcsb.mapviewer.model.map;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.StringComparator;
-
-/**
- * This class implements comparator interface for {@link OverviewLink}.
- *
- * @author Piotr Gawron
- *
- */
-public class OverviewLinkComparator extends Comparator<OverviewLink> {
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(OverviewLinkComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- @SuppressWarnings("unused")
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public OverviewLinkComparator(double epsilon) {
- super(OverviewLink.class, true);
- this.epsilon = epsilon;
- addSubClassComparator(new OverviewImageLinkComparator(epsilon));
- addSubClassComparator(new OverviewModelLinkComparator(epsilon));
- }
-
- /**
- * Default constructor.
- */
- public OverviewLinkComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected int internalCompare(OverviewLink arg0, OverviewLink arg1) {
-
- StringComparator stringComparator = new StringComparator();
-
- if (stringComparator.compare(arg0.getPolygon(), arg1.getPolygon()) != 0) {
- logger.debug("polygon different: " + arg0.getPolygon() + ", " + arg1.getPolygon());
- return stringComparator.compare(arg0.getPolygon(), arg1.getPolygon());
- }
-
- return 0;
-
- }
-
-}
+package lcsb.mapviewer.model.map;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.StringComparator;
+
+/**
+ * This class implements comparator interface for {@link OverviewLink}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class OverviewLinkComparator extends Comparator<OverviewLink> {
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(OverviewLinkComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ @SuppressWarnings("unused")
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public OverviewLinkComparator(double epsilon) {
+ super(OverviewLink.class, true);
+ this.epsilon = epsilon;
+ addSubClassComparator(new OverviewImageLinkComparator(epsilon));
+ addSubClassComparator(new OverviewModelLinkComparator(epsilon));
+ }
+
+ /**
+ * Default constructor.
+ */
+ public OverviewLinkComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(OverviewLink arg0, OverviewLink arg1) {
+
+ StringComparator stringComparator = new StringComparator();
+
+ if (stringComparator.compare(arg0.getPolygon(), arg1.getPolygon()) != 0) {
+ logger.debug("polygon different: " + arg0.getPolygon() + ", " + arg1.getPolygon());
+ return stringComparator.compare(arg0.getPolygon(), arg1.getPolygon());
+ }
+
+ return 0;
+
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/OverviewModelLink.java b/model/src/main/java/lcsb/mapviewer/model/map/OverviewModelLink.java
index b3ecb4f642..074874ae3e 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/OverviewModelLink.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/OverviewModelLink.java
@@ -1,181 +1,181 @@
-package lcsb.mapviewer.model.map;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.ManyToOne;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
-
-/**
- * Link used in {@link OverviewImage parent OverviewImage} to link it to
- * {@link ModelData (sub)model}.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("MODEL_LINK")
-public class OverviewModelLink extends OverviewLink {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Model to which this links is going.
- */
- @ManyToOne(fetch = FetchType.LAZY, optional = false)
- private ModelData linkedModel;
-
- /**
- * Zoom level at which model should be opened.
- */
- private Integer zoomLevel;
-
- /**
- * X coordinate on {@link #linkedModel} where this links point to.
- */
- private Integer xCoord;
-
- /**
- * Y coordinate on {@link #linkedModel} where this links point to.
- */
- private Integer yCoord;
-
- /**
- * Default constructor that creates copy of the parameter object.
- *
- * @param original
- * origianl object that will be copied to this one
- */
- public OverviewModelLink(OverviewModelLink original) {
- super(original);
- this.linkedModel = original.linkedModel;
- this.xCoord = original.xCoord;
- this.yCoord = original.yCoord;
- this.zoomLevel = original.zoomLevel;
- }
-
- /**
- * Default constructor.
- */
- public OverviewModelLink() {
- super();
- }
-
- /**
- * @return the model
- * @see #linkedModel
- */
- public ModelData getLinkedModel() {
- return linkedModel;
- }
-
- /**
- * @param model
- * the model to set
- * @see #linkedModel
- */
- public void setLinkedModel(Model model) {
- if (model != null) {
- this.linkedModel = model.getModelData();
- } else {
- this.linkedModel = null;
- }
- }
-
- @Override
- public OverviewModelLink copy() {
- if (this.getClass() == OverviewModelLink.class) {
- return new OverviewModelLink(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- /**
- * @return the zoomLevel
- * @see #zoomLevel
- */
- public Integer getZoomLevel() {
- return zoomLevel;
- }
-
- /**
- * @param zoomLevel
- * the zoomLevel to set
- * @see #zoomLevel
- */
- public void setZoomLevel(Integer zoomLevel) {
- this.zoomLevel = zoomLevel;
- }
-
- /**
- * @return the xCoord
- * @see #xCoord
- */
- public Integer getxCoord() {
- return xCoord;
- }
-
- /**
- * @param xCoord
- * the xCoord to set
- * @see #xCoord
- */
- public void setxCoord(Integer xCoord) {
- this.xCoord = xCoord;
- }
-
- /**
- * @return the yCoord
- * @see #yCoord
- */
- public Integer getyCoord() {
- return yCoord;
- }
-
- /**
- * @param yCoord
- * the yCoord to set
- * @see #yCoord
- */
- public void setyCoord(Integer yCoord) {
- this.yCoord = yCoord;
- }
-
- /**
- * Sets {@link #xCoord} value. Value will be trimmed to {@link Integer}.
- *
- * @param value
- * the xCoord to set
- * @see #xCoord
- */
- public void setxCoord(Double value) {
- if (value == null) {
- this.xCoord = null;
- } else {
- this.xCoord = value.intValue();
- }
- }
-
- /**
- * Sets {@link #yCoord} value. Value will be trimmed to {@link Integer}.
- *
- * @param value
- * the yCoord to set
- * @see #yCoord
- */
- public void setyCoord(Double value) {
- if (value == null) {
- this.yCoord = null;
- } else {
- this.yCoord = value.intValue();
- }
- }
-
-}
+package lcsb.mapviewer.model.map;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.ManyToOne;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+
+/**
+ * Link used in {@link OverviewImage parent OverviewImage} to link it to
+ * {@link ModelData (sub)model}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("MODEL_LINK")
+public class OverviewModelLink extends OverviewLink {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Model to which this links is going.
+ */
+ @ManyToOne(fetch = FetchType.LAZY, optional = false)
+ private ModelData linkedModel;
+
+ /**
+ * Zoom level at which model should be opened.
+ */
+ private Integer zoomLevel;
+
+ /**
+ * X coordinate on {@link #linkedModel} where this links point to.
+ */
+ private Integer xCoord;
+
+ /**
+ * Y coordinate on {@link #linkedModel} where this links point to.
+ */
+ private Integer yCoord;
+
+ /**
+ * Default constructor that creates copy of the parameter object.
+ *
+ * @param original
+ * origianl object that will be copied to this one
+ */
+ public OverviewModelLink(OverviewModelLink original) {
+ super(original);
+ this.linkedModel = original.linkedModel;
+ this.xCoord = original.xCoord;
+ this.yCoord = original.yCoord;
+ this.zoomLevel = original.zoomLevel;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public OverviewModelLink() {
+ super();
+ }
+
+ /**
+ * @return the model
+ * @see #linkedModel
+ */
+ public ModelData getLinkedModel() {
+ return linkedModel;
+ }
+
+ /**
+ * @param model
+ * the model to set
+ * @see #linkedModel
+ */
+ public void setLinkedModel(Model model) {
+ if (model != null) {
+ this.linkedModel = model.getModelData();
+ } else {
+ this.linkedModel = null;
+ }
+ }
+
+ @Override
+ public OverviewModelLink copy() {
+ if (this.getClass() == OverviewModelLink.class) {
+ return new OverviewModelLink(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ /**
+ * @return the zoomLevel
+ * @see #zoomLevel
+ */
+ public Integer getZoomLevel() {
+ return zoomLevel;
+ }
+
+ /**
+ * @param zoomLevel
+ * the zoomLevel to set
+ * @see #zoomLevel
+ */
+ public void setZoomLevel(Integer zoomLevel) {
+ this.zoomLevel = zoomLevel;
+ }
+
+ /**
+ * @return the xCoord
+ * @see #xCoord
+ */
+ public Integer getxCoord() {
+ return xCoord;
+ }
+
+ /**
+ * @param xCoord
+ * the xCoord to set
+ * @see #xCoord
+ */
+ public void setxCoord(Integer xCoord) {
+ this.xCoord = xCoord;
+ }
+
+ /**
+ * @return the yCoord
+ * @see #yCoord
+ */
+ public Integer getyCoord() {
+ return yCoord;
+ }
+
+ /**
+ * @param yCoord
+ * the yCoord to set
+ * @see #yCoord
+ */
+ public void setyCoord(Integer yCoord) {
+ this.yCoord = yCoord;
+ }
+
+ /**
+ * Sets {@link #xCoord} value. Value will be trimmed to {@link Integer}.
+ *
+ * @param value
+ * the xCoord to set
+ * @see #xCoord
+ */
+ public void setxCoord(Double value) {
+ if (value == null) {
+ this.xCoord = null;
+ } else {
+ this.xCoord = value.intValue();
+ }
+ }
+
+ /**
+ * Sets {@link #yCoord} value. Value will be trimmed to {@link Integer}.
+ *
+ * @param value
+ * the yCoord to set
+ * @see #yCoord
+ */
+ public void setyCoord(Double value) {
+ if (value == null) {
+ this.yCoord = null;
+ } else {
+ this.yCoord = value.intValue();
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/OverviewModelLinkComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/OverviewModelLinkComparator.java
index 7adb2b8647..3f2154797b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/OverviewModelLinkComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/OverviewModelLinkComparator.java
@@ -1,88 +1,88 @@
-package lcsb.mapviewer.model.map;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.IntegerComparator;
-
-/**
- * This class implements comparator interface for {@link OverviewModelLink}.
- *
- * @author Piotr Gawron
- *
- */
-public class OverviewModelLinkComparator extends Comparator<OverviewModelLink> {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(OverviewModelLinkComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public OverviewModelLinkComparator(double epsilon) {
- super(OverviewModelLink.class);
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public OverviewModelLinkComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- public Comparator<?> getParentComparator() {
- return new OverviewLinkComparator(epsilon);
- }
-
- @Override
- protected int internalCompare(OverviewModelLink arg0, OverviewModelLink arg1) {
- int result = 0;
- IntegerComparator integerComparator = new IntegerComparator();
- if (integerComparator.compare(arg0.getxCoord(), arg1.getxCoord()) != 0) {
- logger.debug("xCoord different: " + arg0.getxCoord() + ", " + arg1.getxCoord());
- return integerComparator.compare(arg0.getxCoord(), arg1.getxCoord());
- }
-
- if (integerComparator.compare(arg0.getyCoord(), arg1.getyCoord()) != 0) {
- logger.debug("yCoord different: " + arg0.getyCoord() + ", " + arg1.getyCoord());
- return integerComparator.compare(arg0.getyCoord(), arg1.getyCoord());
- }
-
- if (integerComparator.compare(arg0.getZoomLevel(), arg1.getZoomLevel()) != 0) {
- logger.debug("zoomLevel different: " + arg0.getZoomLevel() + ", " + arg1.getZoomLevel());
- return integerComparator.compare(arg0.getZoomLevel(), arg1.getZoomLevel());
- }
-
- if (arg0.getLinkedModel() == null) {
- if (arg1.getLinkedModel() == null) {
- result = 0;
- } else {
- result = 1;
- }
- } else if (arg1.getLinkedModel() == null) {
- result = -1;
- } else {
- result = integerComparator.compare(arg0.getLinkedModel().getId(), arg1.getLinkedModel().getId());
- }
-
- if (result != 0) {
- return result;
- }
-
- return 0;
-
- }
-
-}
+package lcsb.mapviewer.model.map;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.IntegerComparator;
+
+/**
+ * This class implements comparator interface for {@link OverviewModelLink}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class OverviewModelLinkComparator extends Comparator<OverviewModelLink> {
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(OverviewModelLinkComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public OverviewModelLinkComparator(double epsilon) {
+ super(OverviewModelLink.class);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public OverviewModelLinkComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ public Comparator<?> getParentComparator() {
+ return new OverviewLinkComparator(epsilon);
+ }
+
+ @Override
+ protected int internalCompare(OverviewModelLink arg0, OverviewModelLink arg1) {
+ int result = 0;
+ IntegerComparator integerComparator = new IntegerComparator();
+ if (integerComparator.compare(arg0.getxCoord(), arg1.getxCoord()) != 0) {
+ logger.debug("xCoord different: " + arg0.getxCoord() + ", " + arg1.getxCoord());
+ return integerComparator.compare(arg0.getxCoord(), arg1.getxCoord());
+ }
+
+ if (integerComparator.compare(arg0.getyCoord(), arg1.getyCoord()) != 0) {
+ logger.debug("yCoord different: " + arg0.getyCoord() + ", " + arg1.getyCoord());
+ return integerComparator.compare(arg0.getyCoord(), arg1.getyCoord());
+ }
+
+ if (integerComparator.compare(arg0.getZoomLevel(), arg1.getZoomLevel()) != 0) {
+ logger.debug("zoomLevel different: " + arg0.getZoomLevel() + ", " + arg1.getZoomLevel());
+ return integerComparator.compare(arg0.getZoomLevel(), arg1.getZoomLevel());
+ }
+
+ if (arg0.getLinkedModel() == null) {
+ if (arg1.getLinkedModel() == null) {
+ result = 0;
+ } else {
+ result = 1;
+ }
+ } else if (arg1.getLinkedModel() == null) {
+ result = -1;
+ } else {
+ result = integerComparator.compare(arg0.getLinkedModel().getId(), arg1.getLinkedModel().getId());
+ }
+
+ if (result != 0) {
+ return result;
+ }
+
+ return 0;
+
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/OverviewSearchLink.java b/model/src/main/java/lcsb/mapviewer/model/map/OverviewSearchLink.java
index cfe336aeb8..9d12d5a7d4 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/OverviewSearchLink.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/OverviewSearchLink.java
@@ -1,74 +1,74 @@
-package lcsb.mapviewer.model.map;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-/**
- * Link used in {@link OverviewImage parent OverviewImage} to link it to
- * {@link OverviewImage child OverviewImage}.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("SEARCH_LINK")
-public class OverviewSearchLink extends OverviewLink {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Results of this search query in the map will be a target for this link.
- */
- private String query;
-
- /**
- * Default constructor that copies object from the parameter.
- *
- * @param original
- * original object to be copied
- */
- public OverviewSearchLink(OverviewSearchLink original) {
- super(original);
- this.query = original.query;
-
- }
-
- /**
- * Default constructor.
- */
- public OverviewSearchLink() {
- super();
- }
-
- @Override
- public OverviewSearchLink copy() {
- if (this.getClass() == OverviewSearchLink.class) {
- return new OverviewSearchLink(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- /**
- * @return the query
- * @see #query
- */
- public String getQuery() {
- return query;
- }
-
- /**
- * @param query
- * the query to set
- * @see #query
- */
- public void setQuery(String query) {
- this.query = query;
- }
-
-}
+package lcsb.mapviewer.model.map;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * Link used in {@link OverviewImage parent OverviewImage} to link it to
+ * {@link OverviewImage child OverviewImage}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("SEARCH_LINK")
+public class OverviewSearchLink extends OverviewLink {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Results of this search query in the map will be a target for this link.
+ */
+ private String query;
+
+ /**
+ * Default constructor that copies object from the parameter.
+ *
+ * @param original
+ * original object to be copied
+ */
+ public OverviewSearchLink(OverviewSearchLink original) {
+ super(original);
+ this.query = original.query;
+
+ }
+
+ /**
+ * Default constructor.
+ */
+ public OverviewSearchLink() {
+ super();
+ }
+
+ @Override
+ public OverviewSearchLink copy() {
+ if (this.getClass() == OverviewSearchLink.class) {
+ return new OverviewSearchLink(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ /**
+ * @return the query
+ * @see #query
+ */
+ public String getQuery() {
+ return query;
+ }
+
+ /**
+ * @param query
+ * the query to set
+ * @see #query
+ */
+ public void setQuery(String query) {
+ this.query = query;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/SearchIndex.java b/model/src/main/java/lcsb/mapviewer/model/map/SearchIndex.java
index 584885c4f3..1de7115a90 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/SearchIndex.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/SearchIndex.java
@@ -1,188 +1,188 @@
-package lcsb.mapviewer.model.map;
-
-import java.io.Serializable;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * This class defines single search index for the element. Every element can
- * have few indexes. These indexes describes somehow elements. When the indexed
- * query match this index then element should be considered as a search result.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "search_index_table")
-public class SearchIndex implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(Element.class);
-
- /**
- * Database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- /**
- * Element to which index is assigned.
- */
- @ManyToOne
- private Element source;
-
- /**
- * Data of the index.
- */
- private String value;
-
- /**
- * Weight of the index. Lower values mean that index is less meaningfull.
- */
- private Integer weight;
-
- /**
- * Default constructor.
- */
- public SearchIndex() {
- }
-
- /**
- * Constructor that initialize index with weight and data.
- *
- * @param value
- * data of the index
- * @param weight
- * weight of the index
- */
- public SearchIndex(String value, int weight) {
- this.value = value;
- this.weight = weight;
- }
-
- /**
- * Constructor that initialize index with default weight and data.
- *
- * @param value
- * data of the index
- */
- public SearchIndex(String value) {
- this.value = value;
- this.weight = 1;
- }
-
- /**
- * Contructor that copies information from parameter.
- *
- * @param searchIndex
- * source of data initialization
- */
- public SearchIndex(SearchIndex searchIndex) {
- source = searchIndex.getSource();
- value = searchIndex.getValue();
- weight = searchIndex.getWeight();
- }
-
- /**
- * Creates object copy.
- *
- * @return copy of the object
- */
- public SearchIndex copy() {
- if (this.getClass() == SearchIndex.class) {
- return new SearchIndex(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- /**
- * @return the id
- * @see #id
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
- /**
- * @return the source
- * @see #source
- */
- public Element getSource() {
- return source;
- }
-
- /**
- * @param source
- * the source to set
- * @see #source
- */
- public void setSource(Element source) {
- this.source = source;
- }
-
- /**
- * @return the value
- * @see #value
- */
- public String getValue() {
- return value;
- }
-
- /**
- * @param value
- * the value to set
- * @see #value
- */
- public void setValue(String value) {
- this.value = value;
- }
-
- /**
- * @return the weight
- * @see #weight
- */
- public Integer getWeight() {
- return weight;
- }
-
- /**
- * @param weight
- * the weight to set
- * @see #weight
- */
- public void setWeight(Integer weight) {
- this.weight = weight;
- }
-
-}
+package lcsb.mapviewer.model.map;
+
+import java.io.Serializable;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * This class defines single search index for the element. Every element can
+ * have few indexes. These indexes describes somehow elements. When the indexed
+ * query match this index then element should be considered as a search result.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "search_index_table")
+public class SearchIndex implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(Element.class);
+
+ /**
+ * Database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * Element to which index is assigned.
+ */
+ @ManyToOne
+ private Element source;
+
+ /**
+ * Data of the index.
+ */
+ private String value;
+
+ /**
+ * Weight of the index. Lower values mean that index is less meaningfull.
+ */
+ private Integer weight;
+
+ /**
+ * Default constructor.
+ */
+ public SearchIndex() {
+ }
+
+ /**
+ * Constructor that initialize index with weight and data.
+ *
+ * @param value
+ * data of the index
+ * @param weight
+ * weight of the index
+ */
+ public SearchIndex(String value, int weight) {
+ this.value = value;
+ this.weight = weight;
+ }
+
+ /**
+ * Constructor that initialize index with default weight and data.
+ *
+ * @param value
+ * data of the index
+ */
+ public SearchIndex(String value) {
+ this.value = value;
+ this.weight = 1;
+ }
+
+ /**
+ * Contructor that copies information from parameter.
+ *
+ * @param searchIndex
+ * source of data initialization
+ */
+ public SearchIndex(SearchIndex searchIndex) {
+ source = searchIndex.getSource();
+ value = searchIndex.getValue();
+ weight = searchIndex.getWeight();
+ }
+
+ /**
+ * Creates object copy.
+ *
+ * @return copy of the object
+ */
+ public SearchIndex copy() {
+ if (this.getClass() == SearchIndex.class) {
+ return new SearchIndex(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ /**
+ * @return the source
+ * @see #source
+ */
+ public Element getSource() {
+ return source;
+ }
+
+ /**
+ * @param source
+ * the source to set
+ * @see #source
+ */
+ public void setSource(Element source) {
+ this.source = source;
+ }
+
+ /**
+ * @return the value
+ * @see #value
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * @param value
+ * the value to set
+ * @see #value
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ /**
+ * @return the weight
+ * @see #weight
+ */
+ public Integer getWeight() {
+ return weight;
+ }
+
+ /**
+ * @param weight
+ * the weight to set
+ * @see #weight
+ */
+ public void setWeight(Integer weight) {
+ this.weight = weight;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/compartment/BottomSquareCompartment.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/BottomSquareCompartment.java
index 7981046d40..f52c905817 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/compartment/BottomSquareCompartment.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/BottomSquareCompartment.java
@@ -1,79 +1,79 @@
-package lcsb.mapviewer.model.map.compartment;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.model.Model;
-
-/**
- * This class defines compartment that covers bottom part of the model up to
- * some border (the top is limited).
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("Bottom square Compartment")
-public class BottomSquareCompartment extends Compartment {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Constructor that creates an compartment with the new shape but takes the
- * reference data from the compartment given as parameter.
- *
- * @param original
- * orignal compartment where the data was kept
- * @param model
- * model object to which the compartment will be assigned
- */
- public BottomSquareCompartment(Compartment original, Model model) {
- super(original);
- setX(0.0);
- setWidth(model.getWidth() * 2);
- setY(0.0);
- setHeight(model.getHeight() * 2);
- }
-
- /**
- * Constructor that creates an compartment with the new shape and takes the
- * reference data from the compartment given as parameter.
- *
- * @param original
- * orignal compartment where the data was kept
- */
- public BottomSquareCompartment(Compartment original) {
- super(original);
- }
-
- /**
- * Empty constructor required by hibernate.
- */
- BottomSquareCompartment() {
- super();
- }
-
- /**
- * Default constructor.
- *
- * @param elementId
- * identifier of the compartment
- */
- public BottomSquareCompartment(String elementId) {
- setElementId(elementId);
- }
-
- @Override
- public BottomSquareCompartment copy() {
- if (this.getClass() == BottomSquareCompartment.class) {
- return new BottomSquareCompartment(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.compartment;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.model.Model;
+
+/**
+ * This class defines compartment that covers bottom part of the model up to
+ * some border (the top is limited).
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("Bottom square Compartment")
+public class BottomSquareCompartment extends Compartment {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Constructor that creates an compartment with the new shape but takes the
+ * reference data from the compartment given as parameter.
+ *
+ * @param original
+ * orignal compartment where the data was kept
+ * @param model
+ * model object to which the compartment will be assigned
+ */
+ public BottomSquareCompartment(Compartment original, Model model) {
+ super(original);
+ setX(0.0);
+ setWidth(model.getWidth() * 2);
+ setY(0.0);
+ setHeight(model.getHeight() * 2);
+ }
+
+ /**
+ * Constructor that creates an compartment with the new shape and takes the
+ * reference data from the compartment given as parameter.
+ *
+ * @param original
+ * orignal compartment where the data was kept
+ */
+ public BottomSquareCompartment(Compartment original) {
+ super(original);
+ }
+
+ /**
+ * Empty constructor required by hibernate.
+ */
+ BottomSquareCompartment() {
+ super();
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * identifier of the compartment
+ */
+ public BottomSquareCompartment(String elementId) {
+ setElementId(elementId);
+ }
+
+ @Override
+ public BottomSquareCompartment copy() {
+ if (this.getClass() == BottomSquareCompartment.class) {
+ return new BottomSquareCompartment(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/compartment/Compartment.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/Compartment.java
index bfba815afd..f5e35ab876 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/compartment/Compartment.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/Compartment.java
@@ -1,404 +1,404 @@
-package lcsb.mapviewer.model.map.compartment;
-
-import java.awt.Color;
-import java.awt.geom.Point2D;
-import java.util.HashSet;
-import java.util.Set;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.OneToMany;
-
-import org.apache.log4j.Logger;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-import org.hibernate.annotations.Type;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * This class defines compartment in the model.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("Compartment")
-public class Compartment extends Element {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default color of the compartment.
- */
- private static final Color DEFAULT_COLOR = Color.BLACK;
-
- /**
- * Default width of the inner compartment border.
- */
- private static final int DEFAULT_INNER_BORDER_WIDTH = 1;
-
- /**
- * Default width of the outer compartment border.
- */
- private static final int DEFAULT_OUTER_BORDER_WIDTH = 2;
-
- /**
- * Default thickness of compartment border.
- */
- private static final int DEFAULT_COMPARTMENT_THICKNESS = 12;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(Compartment.class);
-
- /**
- * Thickness of the compartment border.
- */
- private double thickness;
-
- /**
- * How thick should be the outer line of the compartment border.
- */
- private double outerWidth;
- /**
- * How thick should be the inner line of the compartment border.
- */
- private double innerWidth;
-
- /**
- * Describes where the description of the compartment lies.
- */
- @Type(type = "lcsb.mapviewer.persist.mapper.Point2DMapper")
- private Point2D namePoint = new Point2D.Double();
-
- /**
- * {@link Element Elements} that are directly inside this compartment.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(fetch = FetchType.EAGER, mappedBy = "compartment")
- private Set<Element> elements = new HashSet<>();
-
- /**
- * Constructor that creates a compartment which is initialized by the data from
- * the parameter object.
- *
- * @param original
- * object from which this object is initialized
- */
- public Compartment(Compartment original) {
- super(original);
- namePoint.setLocation(original.getNamePoint());
- thickness = original.thickness;
- outerWidth = original.outerWidth;
- innerWidth = original.innerWidth;
- for (Element element : original.elements) {
- addElement(element.copy());
- }
- }
-
- /**
- * Default constructor.
- */
- Compartment() {
- super();
- namePoint = new Point2D.Double(0, 0);
- thickness = DEFAULT_COMPARTMENT_THICKNESS;
- outerWidth = DEFAULT_OUTER_BORDER_WIDTH;
- innerWidth = DEFAULT_INNER_BORDER_WIDTH;
- setColor(DEFAULT_COLOR);
- }
-
- /**
- * Default constructor.
- *
- * @param elementId
- * identifier of the compartment
- */
- public Compartment(String elementId) {
- setElementId(elementId);
- }
-
- /**
- *
- * @param text
- * line thickness in String format
- */
- public void setLineThickness(String text) {
- try {
- thickness = Double.parseDouble(text);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid thickness format: " + text, e);
- }
- }
-
- /**
- *
- * @param text
- * outer line width in String format
- */
- public void setLineOuterWidth(String text) {
- try {
- outerWidth = Double.parseDouble(text);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid outerWidth format: " + text, e);
- }
- }
-
- /**
- *
- * @param text
- * inner line width in String format
- */
- public void setLineInnerWidth(String text) {
- try {
- innerWidth = Double.parseDouble(text);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid innerWidth format: " + text, e);
- }
- }
-
- /**
- * Add element into the compartment. In case element already exists in the
- * compartment {@link InvalidArgumentException} is thrown.
- *
- * @param elementToAdd
- * element that should be added
- */
- public void addElement(Element elementToAdd) {
- for (Element element : elements) {
- if (element.getElementId().equals(elementToAdd.getElementId())) {
- if (element.equals(elementToAdd)) {
- return;
- } else {
- throw new InvalidArgumentException("Element " + elementToAdd.getElementId()
- + " already on the list of compartment " + getElementId() + " children");
- }
- }
- }
- elements.add(elementToAdd);
- elementToAdd.setCompartment(this);
- }
-
- /**
- * Return set of all {@link Element elements} inside the compartment (not
- * necessary directly in the compartment).
- *
- * @return list of all elements in the compartment
- */
- public Set<Element> getAllSubElements() {
- Set<Element> result = new HashSet<>();
- result.addAll(getElements());
- for (Element subelement : getElements()) {
- if (subelement instanceof Compartment) {
- result.addAll(((Compartment) subelement).getAllSubElements());
- }
- }
-
- return result;
- }
-
- /**
- * Check if element given in the parameter has a common part with this
- * compartment. In case element2 lies inside complex the check with complex is
- * made.
- *
- * @param element2
- * element to be checked
- * @return true if the element2 cross this compartment, <code>false</code>
- * otherwise
- */
- public boolean cross(Element element2) {
- Set<Element> parents = new HashSet<>();
- // in case of elements in complexes we have to check if the top level
- // complex cross element
- if (element2 instanceof Species) {
- while (((Species) element2).getComplex() != null) {
- element2 = ((Species) element2).getComplex();
- if (parents.contains(element2)) {
- throw new InvalidStateException("Cycled nesting in complex parents: " + element2.getName());
- } else {
- parents.add(element2);
- }
- }
- }
-
- Point2D argumentTopLeftCorner = new Point2D.Double(element2.getX(), element2.getY());
- Point2D argumentBottomRightCorner = new Point2D.Double(element2.getX() + element2.getWidth(),
- element2.getY() + element2.getHeight());
-
- Point2D topLeftCorner = new Point2D.Double(getX(), getY());
- Point2D bottomRightCorner = new Point2D.Double(getX() + getWidth(), getY() + getHeight());
-
- return (argumentTopLeftCorner.getX() < bottomRightCorner.getX()
- && argumentTopLeftCorner.getY() < bottomRightCorner.getY()
- && argumentBottomRightCorner.getX() > topLeftCorner.getX()
- && argumentBottomRightCorner.getY() > topLeftCorner.getY());
-
- }
-
- /**
- * Checks if there is a species with the same name inside the compartment.
- *
- * @return <code>true</code> if there is {@link Species} with the same name
- * inside compartment, <code>false</code> otherwise
- */
- public boolean containsIdenticalSpecies() {
- for (Element innerElement : elements) {
- if (innerElement instanceof Species) {
- String name = innerElement.getName();
- if (name.equalsIgnoreCase(getName())) {
- return true;
- }
- }
- }
- return false;
- }
-
- /**
- * Creates a copy of this {@link Compartment}.
- *
- * @return copy of the object
- */
- public Compartment copy() {
- if (this.getClass() == Compartment.class) {
- return new Compartment(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- /**
- * Removes element from the {@link Compartment}.
- *
- * @param element
- * object to be removed
- */
- public void removeElement(Element element) {
- elements.remove(element);
- if (element.getCompartment() != null) {
- if (element.getCompartment() == this) {
- element.setCompartment(null);
- } else {
- logger.warn("Removing element from compartment that might not belong there");
- }
- }
- }
-
- /**
- * Set coordinate of the description point.
- *
- * @param x
- * x coordinate to be set
- * @param y
- * y coordinate to be set
- */
- public void setNamePoint(double x, double y) {
- setNamePoint(new Point2D.Double(x, y));
- }
-
- /**
- * @param elements
- * the elements to set
- */
- public void setElements(Set<Element> elements) {
- this.elements = elements;
- }
-
- /**
- * @return the thickness
- * @see #thickness
- */
- public double getThickness() {
- return thickness;
- }
-
- /**
- * @param thickness
- * the thickness to set
- * @see #thickness
- */
- public void setThickness(double thickness) {
- this.thickness = thickness;
- }
-
- /**
- * @return the outerWidth
- * @see #outerWidth
- */
- public double getOuterWidth() {
- return outerWidth;
- }
-
- /**
- * @param outerWidth
- * the outerWidth to set
- * @see #outerWidth
- */
- public void setOuterWidth(double outerWidth) {
- this.outerWidth = outerWidth;
- }
-
- /**
- * @return the innerWidth
- * @see #innerWidth
- */
- public double getInnerWidth() {
- return innerWidth;
- }
-
- /**
- * @param innerWidth
- * the innerWidth to set
- * @see #innerWidth
- */
- public void setInnerWidth(double innerWidth) {
- this.innerWidth = innerWidth;
- }
-
- /**
- * @return the namePoint
- * @see #namePoint
- */
- public Point2D getNamePoint() {
- return namePoint;
- }
-
- /**
- * @param namePoint
- * the namePoint to set
- * @see #namePoint
- */
- public void setNamePoint(Point2D namePoint) {
- this.namePoint = namePoint;
- }
-
- /**
- * @return the elements
- * @see #elements
- */
- public Set<Element> getElements() {
- return elements;
- }
-
- @Override
- public String getStringType() {
- return "Compartment";
- }
-
- public void removeElements(Set<Element> elements) {
- for (Element element : elements) {
- removeElement(element);
- }
- }
-
-}
+package lcsb.mapviewer.model.map.compartment;
+
+import java.awt.Color;
+import java.awt.geom.Point2D;
+import java.util.HashSet;
+import java.util.Set;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.OneToMany;
+
+import org.apache.log4j.Logger;
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+import org.hibernate.annotations.Type;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This class defines compartment in the model.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("Compartment")
+public class Compartment extends Element {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default color of the compartment.
+ */
+ private static final Color DEFAULT_COLOR = Color.BLACK;
+
+ /**
+ * Default width of the inner compartment border.
+ */
+ private static final int DEFAULT_INNER_BORDER_WIDTH = 1;
+
+ /**
+ * Default width of the outer compartment border.
+ */
+ private static final int DEFAULT_OUTER_BORDER_WIDTH = 2;
+
+ /**
+ * Default thickness of compartment border.
+ */
+ private static final int DEFAULT_COMPARTMENT_THICKNESS = 12;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(Compartment.class);
+
+ /**
+ * Thickness of the compartment border.
+ */
+ private double thickness;
+
+ /**
+ * How thick should be the outer line of the compartment border.
+ */
+ private double outerWidth;
+ /**
+ * How thick should be the inner line of the compartment border.
+ */
+ private double innerWidth;
+
+ /**
+ * Describes where the description of the compartment lies.
+ */
+ @Type(type = "lcsb.mapviewer.persist.mapper.Point2DMapper")
+ private Point2D namePoint = new Point2D.Double();
+
+ /**
+ * {@link Element Elements} that are directly inside this compartment.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(fetch = FetchType.EAGER, mappedBy = "compartment")
+ private Set<Element> elements = new HashSet<>();
+
+ /**
+ * Constructor that creates a compartment which is initialized by the data from
+ * the parameter object.
+ *
+ * @param original
+ * object from which this object is initialized
+ */
+ public Compartment(Compartment original) {
+ super(original);
+ namePoint.setLocation(original.getNamePoint());
+ thickness = original.thickness;
+ outerWidth = original.outerWidth;
+ innerWidth = original.innerWidth;
+ for (Element element : original.elements) {
+ addElement(element.copy());
+ }
+ }
+
+ /**
+ * Default constructor.
+ */
+ Compartment() {
+ super();
+ namePoint = new Point2D.Double(0, 0);
+ thickness = DEFAULT_COMPARTMENT_THICKNESS;
+ outerWidth = DEFAULT_OUTER_BORDER_WIDTH;
+ innerWidth = DEFAULT_INNER_BORDER_WIDTH;
+ setColor(DEFAULT_COLOR);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * identifier of the compartment
+ */
+ public Compartment(String elementId) {
+ setElementId(elementId);
+ }
+
+ /**
+ *
+ * @param text
+ * line thickness in String format
+ */
+ public void setLineThickness(String text) {
+ try {
+ thickness = Double.parseDouble(text);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid thickness format: " + text, e);
+ }
+ }
+
+ /**
+ *
+ * @param text
+ * outer line width in String format
+ */
+ public void setLineOuterWidth(String text) {
+ try {
+ outerWidth = Double.parseDouble(text);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid outerWidth format: " + text, e);
+ }
+ }
+
+ /**
+ *
+ * @param text
+ * inner line width in String format
+ */
+ public void setLineInnerWidth(String text) {
+ try {
+ innerWidth = Double.parseDouble(text);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid innerWidth format: " + text, e);
+ }
+ }
+
+ /**
+ * Add element into the compartment. In case element already exists in the
+ * compartment {@link InvalidArgumentException} is thrown.
+ *
+ * @param elementToAdd
+ * element that should be added
+ */
+ public void addElement(Element elementToAdd) {
+ for (Element element : elements) {
+ if (element.getElementId().equals(elementToAdd.getElementId())) {
+ if (element.equals(elementToAdd)) {
+ return;
+ } else {
+ throw new InvalidArgumentException("Element " + elementToAdd.getElementId()
+ + " already on the list of compartment " + getElementId() + " children");
+ }
+ }
+ }
+ elements.add(elementToAdd);
+ elementToAdd.setCompartment(this);
+ }
+
+ /**
+ * Return set of all {@link Element elements} inside the compartment (not
+ * necessary directly in the compartment).
+ *
+ * @return list of all elements in the compartment
+ */
+ public Set<Element> getAllSubElements() {
+ Set<Element> result = new HashSet<>();
+ result.addAll(getElements());
+ for (Element subelement : getElements()) {
+ if (subelement instanceof Compartment) {
+ result.addAll(((Compartment) subelement).getAllSubElements());
+ }
+ }
+
+ return result;
+ }
+
+ /**
+ * Check if element given in the parameter has a common part with this
+ * compartment. In case element2 lies inside complex the check with complex is
+ * made.
+ *
+ * @param element2
+ * element to be checked
+ * @return true if the element2 cross this compartment, <code>false</code>
+ * otherwise
+ */
+ public boolean cross(Element element2) {
+ Set<Element> parents = new HashSet<>();
+ // in case of elements in complexes we have to check if the top level
+ // complex cross element
+ if (element2 instanceof Species) {
+ while (((Species) element2).getComplex() != null) {
+ element2 = ((Species) element2).getComplex();
+ if (parents.contains(element2)) {
+ throw new InvalidStateException("Cycled nesting in complex parents: " + element2.getName());
+ } else {
+ parents.add(element2);
+ }
+ }
+ }
+
+ Point2D argumentTopLeftCorner = new Point2D.Double(element2.getX(), element2.getY());
+ Point2D argumentBottomRightCorner = new Point2D.Double(element2.getX() + element2.getWidth(),
+ element2.getY() + element2.getHeight());
+
+ Point2D topLeftCorner = new Point2D.Double(getX(), getY());
+ Point2D bottomRightCorner = new Point2D.Double(getX() + getWidth(), getY() + getHeight());
+
+ return (argumentTopLeftCorner.getX() < bottomRightCorner.getX()
+ && argumentTopLeftCorner.getY() < bottomRightCorner.getY()
+ && argumentBottomRightCorner.getX() > topLeftCorner.getX()
+ && argumentBottomRightCorner.getY() > topLeftCorner.getY());
+
+ }
+
+ /**
+ * Checks if there is a species with the same name inside the compartment.
+ *
+ * @return <code>true</code> if there is {@link Species} with the same name
+ * inside compartment, <code>false</code> otherwise
+ */
+ public boolean containsIdenticalSpecies() {
+ for (Element innerElement : elements) {
+ if (innerElement instanceof Species) {
+ String name = innerElement.getName();
+ if (name.equalsIgnoreCase(getName())) {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Creates a copy of this {@link Compartment}.
+ *
+ * @return copy of the object
+ */
+ public Compartment copy() {
+ if (this.getClass() == Compartment.class) {
+ return new Compartment(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ /**
+ * Removes element from the {@link Compartment}.
+ *
+ * @param element
+ * object to be removed
+ */
+ public void removeElement(Element element) {
+ elements.remove(element);
+ if (element.getCompartment() != null) {
+ if (element.getCompartment() == this) {
+ element.setCompartment(null);
+ } else {
+ logger.warn("Removing element from compartment that might not belong there");
+ }
+ }
+ }
+
+ /**
+ * Set coordinate of the description point.
+ *
+ * @param x
+ * x coordinate to be set
+ * @param y
+ * y coordinate to be set
+ */
+ public void setNamePoint(double x, double y) {
+ setNamePoint(new Point2D.Double(x, y));
+ }
+
+ /**
+ * @param elements
+ * the elements to set
+ */
+ public void setElements(Set<Element> elements) {
+ this.elements = elements;
+ }
+
+ /**
+ * @return the thickness
+ * @see #thickness
+ */
+ public double getThickness() {
+ return thickness;
+ }
+
+ /**
+ * @param thickness
+ * the thickness to set
+ * @see #thickness
+ */
+ public void setThickness(double thickness) {
+ this.thickness = thickness;
+ }
+
+ /**
+ * @return the outerWidth
+ * @see #outerWidth
+ */
+ public double getOuterWidth() {
+ return outerWidth;
+ }
+
+ /**
+ * @param outerWidth
+ * the outerWidth to set
+ * @see #outerWidth
+ */
+ public void setOuterWidth(double outerWidth) {
+ this.outerWidth = outerWidth;
+ }
+
+ /**
+ * @return the innerWidth
+ * @see #innerWidth
+ */
+ public double getInnerWidth() {
+ return innerWidth;
+ }
+
+ /**
+ * @param innerWidth
+ * the innerWidth to set
+ * @see #innerWidth
+ */
+ public void setInnerWidth(double innerWidth) {
+ this.innerWidth = innerWidth;
+ }
+
+ /**
+ * @return the namePoint
+ * @see #namePoint
+ */
+ public Point2D getNamePoint() {
+ return namePoint;
+ }
+
+ /**
+ * @param namePoint
+ * the namePoint to set
+ * @see #namePoint
+ */
+ public void setNamePoint(Point2D namePoint) {
+ this.namePoint = namePoint;
+ }
+
+ /**
+ * @return the elements
+ * @see #elements
+ */
+ public Set<Element> getElements() {
+ return elements;
+ }
+
+ @Override
+ public String getStringType() {
+ return "Compartment";
+ }
+
+ public void removeElements(Set<Element> elements) {
+ for (Element element : elements) {
+ removeElement(element);
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/compartment/CompartmentComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/CompartmentComparator.java
index 524cbddb45..51c6d1adeb 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/compartment/CompartmentComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/CompartmentComparator.java
@@ -1,119 +1,119 @@
-package lcsb.mapviewer.model.map.compartment;
-
-import java.util.HashMap;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.DoubleComparator;
-import lcsb.mapviewer.common.comparator.IntegerComparator;
-import lcsb.mapviewer.common.comparator.PointComparator;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.ElementComparator;
-
-/**
- * This class implements comparator interface for {@link Compartment} objects.
- *
- * @author Piotr Gawron
- *
- * @see Compartment
- *
- */
-public class CompartmentComparator extends Comparator<Compartment> {
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(CompartmentComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public CompartmentComparator(double epsilon) {
- super(Compartment.class);
- this.epsilon = epsilon;
- }
-
- protected Comparator<?> getParentComparator() {
- return new ElementComparator(epsilon);
- }
-
- /**
- * Default constructor.
- */
- public CompartmentComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected int internalCompare(Compartment arg0, Compartment arg1) {
- ElementComparator elementComparator = new ElementComparator(epsilon);
- DoubleComparator doubleComparator = new DoubleComparator(epsilon);
- IntegerComparator integerComparator = new IntegerComparator();
- PointComparator pointComparator = new PointComparator(epsilon);
-
- if (doubleComparator.compare(arg0.getThickness(), arg1.getThickness()) != 0) {
- logger.debug("Thickness different: " + arg0.getThickness() + ", " + arg1.getThickness());
- return doubleComparator.compare(arg0.getThickness(), arg1.getThickness());
- }
-
- if (doubleComparator.compare(arg0.getOuterWidth(), arg1.getOuterWidth()) != 0) {
- logger.debug("Outer width different: " + arg0.getOuterWidth() + ", " + arg1.getOuterWidth());
- return doubleComparator.compare(arg0.getOuterWidth(), arg1.getOuterWidth());
- }
-
- if (doubleComparator.compare(arg0.getInnerWidth(), arg1.getInnerWidth()) != 0) {
- logger.debug("Inner width different: " + arg0.getInnerWidth() + ", " + arg1.getInnerWidth());
- return doubleComparator.compare(arg0.getInnerWidth(), arg1.getInnerWidth());
- }
-
- if (pointComparator.compare(arg0.getNamePoint(), arg1.getNamePoint()) != 0) {
- logger.debug("NamePoint different: " + arg0.getNamePoint() + ", " + arg1.getNamePoint());
- return pointComparator.compare(arg0.getNamePoint(), arg1.getNamePoint());
- }
-
- if (integerComparator.compare(arg0.getElements().size(), arg1.getElements().size()) != 0) {
- logger.debug("Elements number different: " + arg0.getElements().size() + ", " + arg1.getElements().size());
- return integerComparator.compare(arg0.getElements().size(), arg1.getElements().size());
- }
-
- Map<String, Element> map1 = new HashMap<>();
- Map<String, Element> map2 = new HashMap<>();
-
- for (Element element : arg0.getElements()) {
- if (map1.get(element.getElementId()) != null) {
- throw new InvalidArgumentException("Few elements with the same id: " + element.getElementId());
- }
- map1.put(element.getElementId(), element);
- }
-
- for (Element element : arg1.getElements()) {
- if (map2.get(element.getElementId()) != null) {
- throw new InvalidArgumentException("Few elements with the same id: " + element.getElementId());
- }
- map2.put(element.getElementId(), element);
- }
-
- for (Element element : arg0.getElements()) {
- Element element2 = map2.get(element.getElementId());
- int status = elementComparator.compare(element, element2);
- if (status != 0) {
- logger.debug("Couldn't match element: " + element.getElementId() + ", " + element2);
- return status;
- }
- }
-
- return 0;
- }
-}
+package lcsb.mapviewer.model.map.compartment;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.DoubleComparator;
+import lcsb.mapviewer.common.comparator.IntegerComparator;
+import lcsb.mapviewer.common.comparator.PointComparator;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.ElementComparator;
+
+/**
+ * This class implements comparator interface for {@link Compartment} objects.
+ *
+ * @author Piotr Gawron
+ *
+ * @see Compartment
+ *
+ */
+public class CompartmentComparator extends Comparator<Compartment> {
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(CompartmentComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public CompartmentComparator(double epsilon) {
+ super(Compartment.class);
+ this.epsilon = epsilon;
+ }
+
+ protected Comparator<?> getParentComparator() {
+ return new ElementComparator(epsilon);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public CompartmentComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(Compartment arg0, Compartment arg1) {
+ ElementComparator elementComparator = new ElementComparator(epsilon);
+ DoubleComparator doubleComparator = new DoubleComparator(epsilon);
+ IntegerComparator integerComparator = new IntegerComparator();
+ PointComparator pointComparator = new PointComparator(epsilon);
+
+ if (doubleComparator.compare(arg0.getThickness(), arg1.getThickness()) != 0) {
+ logger.debug("Thickness different: " + arg0.getThickness() + ", " + arg1.getThickness());
+ return doubleComparator.compare(arg0.getThickness(), arg1.getThickness());
+ }
+
+ if (doubleComparator.compare(arg0.getOuterWidth(), arg1.getOuterWidth()) != 0) {
+ logger.debug("Outer width different: " + arg0.getOuterWidth() + ", " + arg1.getOuterWidth());
+ return doubleComparator.compare(arg0.getOuterWidth(), arg1.getOuterWidth());
+ }
+
+ if (doubleComparator.compare(arg0.getInnerWidth(), arg1.getInnerWidth()) != 0) {
+ logger.debug("Inner width different: " + arg0.getInnerWidth() + ", " + arg1.getInnerWidth());
+ return doubleComparator.compare(arg0.getInnerWidth(), arg1.getInnerWidth());
+ }
+
+ if (pointComparator.compare(arg0.getNamePoint(), arg1.getNamePoint()) != 0) {
+ logger.debug("NamePoint different: " + arg0.getNamePoint() + ", " + arg1.getNamePoint());
+ return pointComparator.compare(arg0.getNamePoint(), arg1.getNamePoint());
+ }
+
+ if (integerComparator.compare(arg0.getElements().size(), arg1.getElements().size()) != 0) {
+ logger.debug("Elements number different: " + arg0.getElements().size() + ", " + arg1.getElements().size());
+ return integerComparator.compare(arg0.getElements().size(), arg1.getElements().size());
+ }
+
+ Map<String, Element> map1 = new HashMap<>();
+ Map<String, Element> map2 = new HashMap<>();
+
+ for (Element element : arg0.getElements()) {
+ if (map1.get(element.getElementId()) != null) {
+ throw new InvalidArgumentException("Few elements with the same id: " + element.getElementId());
+ }
+ map1.put(element.getElementId(), element);
+ }
+
+ for (Element element : arg1.getElements()) {
+ if (map2.get(element.getElementId()) != null) {
+ throw new InvalidArgumentException("Few elements with the same id: " + element.getElementId());
+ }
+ map2.put(element.getElementId(), element);
+ }
+
+ for (Element element : arg0.getElements()) {
+ Element element2 = map2.get(element.getElementId());
+ int status = elementComparator.compare(element, element2);
+ if (status != 0) {
+ logger.debug("Couldn't match element: " + element.getElementId() + ", " + element2);
+ return status;
+ }
+ }
+
+ return 0;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/compartment/LeftSquareCompartment.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/LeftSquareCompartment.java
index a2136ad14c..876ebc656c 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/compartment/LeftSquareCompartment.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/LeftSquareCompartment.java
@@ -1,80 +1,80 @@
-package lcsb.mapviewer.model.map.compartment;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.model.Model;
-
-/**
- * This class defines compartment that covers left part of the model up to some
- * border on the right side.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("Left square Compartment")
-public class LeftSquareCompartment extends Compartment {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Empty constructor required by hibernate.
- */
- LeftSquareCompartment() {
- super();
- }
-
- /**
- * Constructor that creates a compartment with the new shape but takes the
- * reference data from the compartment given as parameter.
- *
- * @param original
- * orignal compartment where the data was kept
- * @param model
- * model object to which the compartment will be assigned
- */
-
- public LeftSquareCompartment(Compartment original, Model model) {
- super(original);
- setX(0.0);
- setWidth(model.getWidth() * 2);
- setY(0.0);
- setHeight(model.getHeight() * 2);
- }
-
- /**
- * Constructor that creates a compartment with the new shape and takes the
- * reference data from the compartment given as parameter.
- *
- * @param original
- * orignal compartment where the data was kept
- */
- public LeftSquareCompartment(LeftSquareCompartment original) {
- super(original);
- }
-
- /**
- * Default constructor.
- *
- * @param elementId
- * identifier of the compartment
- */
- public LeftSquareCompartment(String elementId) {
- setElementId(elementId);
- }
-
- @Override
- public LeftSquareCompartment copy() {
- if (this.getClass() == LeftSquareCompartment.class) {
- return new LeftSquareCompartment(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.compartment;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.model.Model;
+
+/**
+ * This class defines compartment that covers left part of the model up to some
+ * border on the right side.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("Left square Compartment")
+public class LeftSquareCompartment extends Compartment {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Empty constructor required by hibernate.
+ */
+ LeftSquareCompartment() {
+ super();
+ }
+
+ /**
+ * Constructor that creates a compartment with the new shape but takes the
+ * reference data from the compartment given as parameter.
+ *
+ * @param original
+ * orignal compartment where the data was kept
+ * @param model
+ * model object to which the compartment will be assigned
+ */
+
+ public LeftSquareCompartment(Compartment original, Model model) {
+ super(original);
+ setX(0.0);
+ setWidth(model.getWidth() * 2);
+ setY(0.0);
+ setHeight(model.getHeight() * 2);
+ }
+
+ /**
+ * Constructor that creates a compartment with the new shape and takes the
+ * reference data from the compartment given as parameter.
+ *
+ * @param original
+ * orignal compartment where the data was kept
+ */
+ public LeftSquareCompartment(LeftSquareCompartment original) {
+ super(original);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * identifier of the compartment
+ */
+ public LeftSquareCompartment(String elementId) {
+ setElementId(elementId);
+ }
+
+ @Override
+ public LeftSquareCompartment copy() {
+ if (this.getClass() == LeftSquareCompartment.class) {
+ return new LeftSquareCompartment(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/compartment/OvalCompartment.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/OvalCompartment.java
index 3dbbeab40d..8734071261 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/compartment/OvalCompartment.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/OvalCompartment.java
@@ -1,61 +1,61 @@
-package lcsb.mapviewer.model.map.compartment;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-/**
- * This class defines compartment with oval shape.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("Oval Compartment")
-public class OvalCompartment extends Compartment {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Empty constructor required by hibernate.
- */
- OvalCompartment() {
- super();
- }
-
- /**
- * Constructor that creates a compartment with the new shape and takes the
- * reference data from the compartment given as parameter.
- *
- * @param original
- * orignal compartment where the data was kept
- */
- public OvalCompartment(Compartment original) {
- super(original);
- }
-
- /**
- * Default constructor.
- *
- * @param elementId
- * identifier of the compartment
- */
- public OvalCompartment(String elementId) {
- super();
- setElementId(elementId);
- }
-
- @Override
- public OvalCompartment copy() {
- if (this.getClass() == OvalCompartment.class) {
- return new OvalCompartment(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.compartment;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * This class defines compartment with oval shape.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("Oval Compartment")
+public class OvalCompartment extends Compartment {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Empty constructor required by hibernate.
+ */
+ OvalCompartment() {
+ super();
+ }
+
+ /**
+ * Constructor that creates a compartment with the new shape and takes the
+ * reference data from the compartment given as parameter.
+ *
+ * @param original
+ * orignal compartment where the data was kept
+ */
+ public OvalCompartment(Compartment original) {
+ super(original);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * identifier of the compartment
+ */
+ public OvalCompartment(String elementId) {
+ super();
+ setElementId(elementId);
+ }
+
+ @Override
+ public OvalCompartment copy() {
+ if (this.getClass() == OvalCompartment.class) {
+ return new OvalCompartment(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/compartment/PathwayCompartment.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/PathwayCompartment.java
index 58fd5fadb6..369e81b1b7 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/compartment/PathwayCompartment.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/PathwayCompartment.java
@@ -1,60 +1,60 @@
-package lcsb.mapviewer.model.map.compartment;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-/**
- * Compartment that represents a pathway.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("Pathway Compartment")
-public class PathwayCompartment extends Compartment {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Empty constructor required by hibernate.
- */
- PathwayCompartment() {
- super();
- }
-
- /**
- * Default constructor.
- *
- * @param elementId
- * identifier of the compartment
- */
- public PathwayCompartment(String elementId) {
- super();
- setElementId(elementId);
- }
-
- /**
- * Constructor that intialize object with the data given in the parameter.
- *
- * @param original
- * data for initialization
- */
- public PathwayCompartment(PathwayCompartment original) {
- super(original);
- }
-
- @Override
- public PathwayCompartment copy() {
- if (this.getClass() == PathwayCompartment.class) {
- return new PathwayCompartment(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.compartment;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * Compartment that represents a pathway.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("Pathway Compartment")
+public class PathwayCompartment extends Compartment {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Empty constructor required by hibernate.
+ */
+ PathwayCompartment() {
+ super();
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * identifier of the compartment
+ */
+ public PathwayCompartment(String elementId) {
+ super();
+ setElementId(elementId);
+ }
+
+ /**
+ * Constructor that intialize object with the data given in the parameter.
+ *
+ * @param original
+ * data for initialization
+ */
+ public PathwayCompartment(PathwayCompartment original) {
+ super(original);
+ }
+
+ @Override
+ public PathwayCompartment copy() {
+ if (this.getClass() == PathwayCompartment.class) {
+ return new PathwayCompartment(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/compartment/RightSquareCompartment.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/RightSquareCompartment.java
index 5e257e5881..a83039cddd 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/compartment/RightSquareCompartment.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/RightSquareCompartment.java
@@ -1,102 +1,102 @@
-package lcsb.mapviewer.model.map.compartment;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.model.Model;
-
-/**
- * This class defines compartment that covers rightpart of the model up to some
- * border on the left side.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("Right square Compartment")
-public class RightSquareCompartment extends Compartment {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(RightSquareCompartment.class);
-
- /**
- * Empty constructor required by hibernate.
- */
- RightSquareCompartment() {
- super();
- }
-
- /**
- * Constructor that creates a compartment with the new shape but takes the
- * reference data from the compartment given as parameter.
- *
- * @param original
- * orignal compartment where the data was kept
- * @param model
- * model object to which the compartment will be assigned
- */
- public RightSquareCompartment(Compartment original, Model model) {
- super(original);
- setX(0.0);
- setWidth(model.getWidth() * 2);
- setY(0.0);
- setHeight(model.getHeight() * 2);
- }
-
- /**
- * Sets the CellDesigner point coordinates. In the implementation of
- * BottomSquare it should define left border.
- *
- * @param y
- * to be ignored
- * @param x
- * left border
- *
- */
- public void setPoint(String x, String y) {
- // set left border
- setX(x);
- setWidth(getWidth() - getX());
- }
-
- /**
- * Constructor that creates a compartment with the new shape and takes the
- * reference data from the compartment given as parameter.
- *
- * @param original
- * orignal compartment where the data was kept
- */
- public RightSquareCompartment(RightSquareCompartment original) {
- super(original);
- }
-
- /**
- * Default constructor.
- *
- * @param elementId
- * identifier of the compartment
- */
- public RightSquareCompartment(String elementId) {
- setElementId(elementId);
- }
-
- @Override
- public RightSquareCompartment copy() {
- if (this.getClass() == RightSquareCompartment.class) {
- return new RightSquareCompartment(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.compartment;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.model.Model;
+
+/**
+ * This class defines compartment that covers rightpart of the model up to some
+ * border on the left side.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("Right square Compartment")
+public class RightSquareCompartment extends Compartment {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(RightSquareCompartment.class);
+
+ /**
+ * Empty constructor required by hibernate.
+ */
+ RightSquareCompartment() {
+ super();
+ }
+
+ /**
+ * Constructor that creates a compartment with the new shape but takes the
+ * reference data from the compartment given as parameter.
+ *
+ * @param original
+ * orignal compartment where the data was kept
+ * @param model
+ * model object to which the compartment will be assigned
+ */
+ public RightSquareCompartment(Compartment original, Model model) {
+ super(original);
+ setX(0.0);
+ setWidth(model.getWidth() * 2);
+ setY(0.0);
+ setHeight(model.getHeight() * 2);
+ }
+
+ /**
+ * Sets the CellDesigner point coordinates. In the implementation of
+ * BottomSquare it should define left border.
+ *
+ * @param y
+ * to be ignored
+ * @param x
+ * left border
+ *
+ */
+ public void setPoint(String x, String y) {
+ // set left border
+ setX(x);
+ setWidth(getWidth() - getX());
+ }
+
+ /**
+ * Constructor that creates a compartment with the new shape and takes the
+ * reference data from the compartment given as parameter.
+ *
+ * @param original
+ * orignal compartment where the data was kept
+ */
+ public RightSquareCompartment(RightSquareCompartment original) {
+ super(original);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * identifier of the compartment
+ */
+ public RightSquareCompartment(String elementId) {
+ setElementId(elementId);
+ }
+
+ @Override
+ public RightSquareCompartment copy() {
+ if (this.getClass() == RightSquareCompartment.class) {
+ return new RightSquareCompartment(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/compartment/TopSquareCompartment.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/TopSquareCompartment.java
index 03dc161d9c..4e1b17f26f 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/compartment/TopSquareCompartment.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/TopSquareCompartment.java
@@ -1,80 +1,80 @@
-package lcsb.mapviewer.model.map.compartment;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.model.Model;
-
-/**
- * This class defines compartment that covers top part of the model up to some
- * border on the bottom.
- *
- * @author Piotr Gawron
- *
- */
-
-@Entity
-@DiscriminatorValue("Top square Compartment")
-public class TopSquareCompartment extends Compartment {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Empty constructor required by hibernate.
- */
- TopSquareCompartment() {
- super();
- }
-
- /**
- * Constructor that creates a compartment with the new shape but takes the
- * reference data from the compartment given as parameter.
- *
- * @param original
- * orignal compartment where the data was kept
- * @param model
- * model object to which the compartment will be assigned
- */
- public TopSquareCompartment(Compartment original, Model model) {
- super(original);
- setX(0.0);
- setWidth(model.getWidth() * 2);
- setY(0.0);
- setHeight(model.getHeight() * 2);
- }
-
- /**
- * Constructor that creates a compartment with the new shape and takes the
- * reference data from the compartment given as parameter.
- *
- * @param original
- * orignal compartment where the data was kept
- */
- public TopSquareCompartment(TopSquareCompartment original) {
- super(original);
- }
-
- /**
- * Default constructor.
- *
- * @param elementId
- * identifier of the compartment
- */
- public TopSquareCompartment(String elementId) {
- setElementId(elementId);
- }
-
- @Override
- public TopSquareCompartment copy() {
- if (this.getClass() == TopSquareCompartment.class) {
- return new TopSquareCompartment(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.compartment;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.model.Model;
+
+/**
+ * This class defines compartment that covers top part of the model up to some
+ * border on the bottom.
+ *
+ * @author Piotr Gawron
+ *
+ */
+
+@Entity
+@DiscriminatorValue("Top square Compartment")
+public class TopSquareCompartment extends Compartment {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Empty constructor required by hibernate.
+ */
+ TopSquareCompartment() {
+ super();
+ }
+
+ /**
+ * Constructor that creates a compartment with the new shape but takes the
+ * reference data from the compartment given as parameter.
+ *
+ * @param original
+ * orignal compartment where the data was kept
+ * @param model
+ * model object to which the compartment will be assigned
+ */
+ public TopSquareCompartment(Compartment original, Model model) {
+ super(original);
+ setX(0.0);
+ setWidth(model.getWidth() * 2);
+ setY(0.0);
+ setHeight(model.getHeight() * 2);
+ }
+
+ /**
+ * Constructor that creates a compartment with the new shape and takes the
+ * reference data from the compartment given as parameter.
+ *
+ * @param original
+ * orignal compartment where the data was kept
+ */
+ public TopSquareCompartment(TopSquareCompartment original) {
+ super(original);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * identifier of the compartment
+ */
+ public TopSquareCompartment(String elementId) {
+ setElementId(elementId);
+ }
+
+ @Override
+ public TopSquareCompartment copy() {
+ if (this.getClass() == TopSquareCompartment.class) {
+ return new TopSquareCompartment(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/compartment/package-info.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/package-info.java
index 9133cd1cfc..0d69d8005f 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/compartment/package-info.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/package-info.java
@@ -1,4 +1,4 @@
-/**
- * Contains structures used for compartment modeling.
- */
+/**
+ * Contains structures used for compartment modeling.
+ */
package lcsb.mapviewer.model.map.compartment;
\ No newline at end of file
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunction.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunction.java
index 1d94313a65..81e0564628 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunction.java
@@ -1,153 +1,153 @@
-package lcsb.mapviewer.model.map.kinetics;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.persistence.CollectionTable;
-import javax.persistence.Column;
-import javax.persistence.ElementCollection;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-import javax.xml.bind.annotation.XmlRootElement;
-
-import org.apache.log4j.Logger;
-import org.hibernate.annotations.IndexColumn;
-
-import lcsb.mapviewer.model.map.model.ModelData;
-
-/**
- * Representation of a single SBML function
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "sbml_function")
-@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
-@XmlRootElement
-public class SbmlFunction implements Serializable, SbmlArgument {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(SbmlFunction.class);
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Unique database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- private String functionId;
-
- private String name;
-
- @Column(columnDefinition = "TEXT")
- private String definition;
-
- @ElementCollection
- @CollectionTable(name = "sbml_function_arguments", joinColumns = @JoinColumn(name = "sbml_function_iddb"))
- @IndexColumn(name = "idx")
- @Column(name = "argument_name")
- private List<String> arguments = new ArrayList<>();
-
- /**
- * Map model object to which function belongs to.
- */
- @ManyToOne(fetch = FetchType.LAZY)
- private ModelData model;
-
- /**
- * Constructor required by hibernate.
- */
- SbmlFunction() {
- super();
- }
-
- public SbmlFunction(String functionId) {
- this.functionId = functionId;
- }
-
- public SbmlFunction(SbmlFunction original) {
- this.functionId = original.getFunctionId();
- this.definition = original.getDefinition();
- this.name = original.getName();
- for (String argument : original.getArguments()) {
- this.addArgument(argument);
- }
- }
-
- public String getFunctionId() {
- return functionId;
- }
-
- public void setFunctionId(String functionId) {
- this.functionId = functionId;
- }
-
- public String getName() {
- return name;
- }
-
- public void setName(String name) {
- this.name = name;
- }
-
- public List<String> getArguments() {
- return arguments;
- }
-
- public void setArguments(List<String> arguments) {
- this.arguments = arguments;
- }
-
- public String getDefinition() {
- return definition;
- }
-
- public void setDefinition(String definition) {
- this.definition = definition;
- }
-
- public void addArgument(String argument) {
- arguments.add(argument);
- }
-
- @Override
- public SbmlFunction copy() {
- return new SbmlFunction(this);
- }
-
- @Override
- public String getElementId() {
- return getFunctionId();
- }
-
- public ModelData getModel() {
- return model;
- }
-
- public void setModel(ModelData model) {
- this.model = model;
- }
-
- public int getId() {
- return id;
- }
-
-}
+package lcsb.mapviewer.model.map.kinetics;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.persistence.CollectionTable;
+import javax.persistence.Column;
+import javax.persistence.ElementCollection;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+import javax.xml.bind.annotation.XmlRootElement;
+
+import org.apache.log4j.Logger;
+import org.hibernate.annotations.IndexColumn;
+
+import lcsb.mapviewer.model.map.model.ModelData;
+
+/**
+ * Representation of a single SBML function
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "sbml_function")
+@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
+@XmlRootElement
+public class SbmlFunction implements Serializable, SbmlArgument {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(SbmlFunction.class);
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Unique database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ private String functionId;
+
+ private String name;
+
+ @Column(columnDefinition = "TEXT")
+ private String definition;
+
+ @ElementCollection
+ @CollectionTable(name = "sbml_function_arguments", joinColumns = @JoinColumn(name = "sbml_function_iddb"))
+ @IndexColumn(name = "idx")
+ @Column(name = "argument_name")
+ private List<String> arguments = new ArrayList<>();
+
+ /**
+ * Map model object to which function belongs to.
+ */
+ @ManyToOne(fetch = FetchType.LAZY)
+ private ModelData model;
+
+ /**
+ * Constructor required by hibernate.
+ */
+ SbmlFunction() {
+ super();
+ }
+
+ public SbmlFunction(String functionId) {
+ this.functionId = functionId;
+ }
+
+ public SbmlFunction(SbmlFunction original) {
+ this.functionId = original.getFunctionId();
+ this.definition = original.getDefinition();
+ this.name = original.getName();
+ for (String argument : original.getArguments()) {
+ this.addArgument(argument);
+ }
+ }
+
+ public String getFunctionId() {
+ return functionId;
+ }
+
+ public void setFunctionId(String functionId) {
+ this.functionId = functionId;
+ }
+
+ public String getName() {
+ return name;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ public List<String> getArguments() {
+ return arguments;
+ }
+
+ public void setArguments(List<String> arguments) {
+ this.arguments = arguments;
+ }
+
+ public String getDefinition() {
+ return definition;
+ }
+
+ public void setDefinition(String definition) {
+ this.definition = definition;
+ }
+
+ public void addArgument(String argument) {
+ arguments.add(argument);
+ }
+
+ @Override
+ public SbmlFunction copy() {
+ return new SbmlFunction(this);
+ }
+
+ @Override
+ public String getElementId() {
+ return getFunctionId();
+ }
+
+ public ModelData getModel() {
+ return model;
+ }
+
+ public void setModel(ModelData model) {
+ this.model = model;
+ }
+
+ public int getId() {
+ return id;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKinetics.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKinetics.java
index b0e12129b7..8206d2b122 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKinetics.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKinetics.java
@@ -1,205 +1,205 @@
-package lcsb.mapviewer.model.map.kinetics;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.JoinTable;
-import javax.persistence.ManyToMany;
-import javax.persistence.Table;
-import javax.xml.bind.annotation.XmlRootElement;
-
-import org.apache.log4j.Logger;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * Representation of a single SBML function
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "sbml_kinetics")
-@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
-@XmlRootElement
-public class SbmlKinetics implements Serializable {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(SbmlKinetics.class);
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- @Cascade({ CascadeType.ALL })
- @ManyToMany(fetch = FetchType.EAGER)
- @JoinTable(name = "kinetic_law_parameters", joinColumns = {
- @JoinColumn(name = "kinetic_law_id", referencedColumnName = "idDb", nullable = false, updatable = false) }, inverseJoinColumns = {
- @JoinColumn(name = "parameter_id", referencedColumnName = "idDb", nullable = true, updatable = true) })
- private Set<SbmlParameter> parameters = new HashSet<>();
-
- @Cascade({ CascadeType.ALL })
- @ManyToMany(fetch = FetchType.EAGER)
- @JoinTable(name = "kinetic_law_functions", joinColumns = {
- @JoinColumn(name = "kinetic_law_id", referencedColumnName = "idDb", nullable = false, updatable = false) }, inverseJoinColumns = {
- @JoinColumn(name = "function_id", referencedColumnName = "idDb", nullable = true, updatable = true) })
- private Set<SbmlFunction> functions = new HashSet<>();
-
- @Cascade({ CascadeType.ALL })
- @ManyToMany(fetch = FetchType.EAGER)
- @JoinTable(name = "kinetic_law_elements", joinColumns = {
- @JoinColumn(name = "kinetic_law_id", referencedColumnName = "idDb", nullable = false, updatable = false) }, inverseJoinColumns = {
- @JoinColumn(name = "element_id", referencedColumnName = "idDb", nullable = true, updatable = true) })
- private Set<Element> elements = new HashSet<>();
-
- /**
- * Unique database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- @Column(columnDefinition = "TEXT")
- private String definition;
-
- public SbmlKinetics(SbmlKinetics original) {
- this.definition = original.getDefinition();
- for (SbmlArgument argument : original.getArguments()) {
- addArgument(argument);
- }
- }
-
- public SbmlKinetics() {
- }
-
- public void addParameter(SbmlParameter parameter) {
- parameters.add(parameter);
- }
-
- public Set<SbmlParameter> getParameters() {
- return parameters;
- }
-
- public List<SbmlArgument> getArguments() {
- List<SbmlArgument> arguments = new ArrayList<>();
- arguments.addAll(parameters);
- arguments.addAll(elements);
- arguments.addAll(functions);
- return arguments;
- }
-
- public void addElement(Element element) {
- this.elements.add(element);
- }
-
- public String getDefinition() {
- return definition;
- }
-
- public void setDefinition(String definition) {
- this.definition = definition;
- }
-
- public void addElements(Set<Element> elements) {
- for (Element element : elements) {
- addElement(element);
- }
- }
-
- public void addParameters(Collection<SbmlParameter> parameters) {
- for (SbmlParameter parameter : parameters) {
- addParameter(parameter);
- }
-
- }
-
- public void addArguments(Collection<SbmlArgument> arguments) {
- for (SbmlArgument argument : arguments) {
- addArgument(argument);
- }
-
- }
-
- public void addArgument(SbmlArgument argument) {
- if (argument instanceof SbmlParameter) {
- addParameter((SbmlParameter) argument);
- } else if (argument instanceof SbmlFunction) {
- addFunction((SbmlFunction) argument);
- } else {
- addElement((Element) argument);
- }
-
- }
-
- public void addFunction(SbmlFunction argument) {
- functions.add(argument);
- }
-
- public SbmlParameter getParameterById(String id) {
- for (SbmlParameter parameter : parameters) {
- if (parameter.getParameterId().equals(id)) {
- return parameter;
- }
- }
- return null;
- }
-
- public Set<SbmlFunction> getFunctions() {
- return functions;
- }
-
- public Set<Element> getElements() {
- return elements;
- }
-
- public SbmlKinetics copy() {
- return new SbmlKinetics(this);
- }
-
- public void removeElement(Element elementToRemove) {
- elements.remove(elementToRemove);
- }
-
- public void removeArguments(Collection<SbmlArgument> arguments) {
- for (SbmlArgument sbmlArgument : arguments) {
- removeArgument(sbmlArgument);
- }
- }
-
- private void removeArgument(SbmlArgument argument) {
- if (argument instanceof SbmlParameter) {
- removeParameter((SbmlParameter) argument);
- } else if (argument instanceof SbmlFunction) {
- removeFunction((SbmlFunction) argument);
- } else {
- removeElement((Element) argument);
- }
- }
-
- private void removeFunction(SbmlFunction function) {
- functions.remove(function);
- }
-
- private void removeParameter(SbmlParameter parameter) {
- parameters.remove(parameter);
-
- }
-}
+package lcsb.mapviewer.model.map.kinetics;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.JoinTable;
+import javax.persistence.ManyToMany;
+import javax.persistence.Table;
+import javax.xml.bind.annotation.XmlRootElement;
+
+import org.apache.log4j.Logger;
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * Representation of a single SBML function
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "sbml_kinetics")
+@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
+@XmlRootElement
+public class SbmlKinetics implements Serializable {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(SbmlKinetics.class);
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ @Cascade({ CascadeType.ALL })
+ @ManyToMany(fetch = FetchType.EAGER)
+ @JoinTable(name = "kinetic_law_parameters", joinColumns = {
+ @JoinColumn(name = "kinetic_law_id", referencedColumnName = "idDb", nullable = false, updatable = false) }, inverseJoinColumns = {
+ @JoinColumn(name = "parameter_id", referencedColumnName = "idDb", nullable = true, updatable = true) })
+ private Set<SbmlParameter> parameters = new HashSet<>();
+
+ @Cascade({ CascadeType.ALL })
+ @ManyToMany(fetch = FetchType.EAGER)
+ @JoinTable(name = "kinetic_law_functions", joinColumns = {
+ @JoinColumn(name = "kinetic_law_id", referencedColumnName = "idDb", nullable = false, updatable = false) }, inverseJoinColumns = {
+ @JoinColumn(name = "function_id", referencedColumnName = "idDb", nullable = true, updatable = true) })
+ private Set<SbmlFunction> functions = new HashSet<>();
+
+ @Cascade({ CascadeType.ALL })
+ @ManyToMany(fetch = FetchType.EAGER)
+ @JoinTable(name = "kinetic_law_elements", joinColumns = {
+ @JoinColumn(name = "kinetic_law_id", referencedColumnName = "idDb", nullable = false, updatable = false) }, inverseJoinColumns = {
+ @JoinColumn(name = "element_id", referencedColumnName = "idDb", nullable = true, updatable = true) })
+ private Set<Element> elements = new HashSet<>();
+
+ /**
+ * Unique database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ @Column(columnDefinition = "TEXT")
+ private String definition;
+
+ public SbmlKinetics(SbmlKinetics original) {
+ this.definition = original.getDefinition();
+ for (SbmlArgument argument : original.getArguments()) {
+ addArgument(argument);
+ }
+ }
+
+ public SbmlKinetics() {
+ }
+
+ public void addParameter(SbmlParameter parameter) {
+ parameters.add(parameter);
+ }
+
+ public Set<SbmlParameter> getParameters() {
+ return parameters;
+ }
+
+ public List<SbmlArgument> getArguments() {
+ List<SbmlArgument> arguments = new ArrayList<>();
+ arguments.addAll(parameters);
+ arguments.addAll(elements);
+ arguments.addAll(functions);
+ return arguments;
+ }
+
+ public void addElement(Element element) {
+ this.elements.add(element);
+ }
+
+ public String getDefinition() {
+ return definition;
+ }
+
+ public void setDefinition(String definition) {
+ this.definition = definition;
+ }
+
+ public void addElements(Set<Element> elements) {
+ for (Element element : elements) {
+ addElement(element);
+ }
+ }
+
+ public void addParameters(Collection<SbmlParameter> parameters) {
+ for (SbmlParameter parameter : parameters) {
+ addParameter(parameter);
+ }
+
+ }
+
+ public void addArguments(Collection<SbmlArgument> arguments) {
+ for (SbmlArgument argument : arguments) {
+ addArgument(argument);
+ }
+
+ }
+
+ public void addArgument(SbmlArgument argument) {
+ if (argument instanceof SbmlParameter) {
+ addParameter((SbmlParameter) argument);
+ } else if (argument instanceof SbmlFunction) {
+ addFunction((SbmlFunction) argument);
+ } else {
+ addElement((Element) argument);
+ }
+
+ }
+
+ public void addFunction(SbmlFunction argument) {
+ functions.add(argument);
+ }
+
+ public SbmlParameter getParameterById(String id) {
+ for (SbmlParameter parameter : parameters) {
+ if (parameter.getParameterId().equals(id)) {
+ return parameter;
+ }
+ }
+ return null;
+ }
+
+ public Set<SbmlFunction> getFunctions() {
+ return functions;
+ }
+
+ public Set<Element> getElements() {
+ return elements;
+ }
+
+ public SbmlKinetics copy() {
+ return new SbmlKinetics(this);
+ }
+
+ public void removeElement(Element elementToRemove) {
+ elements.remove(elementToRemove);
+ }
+
+ public void removeArguments(Collection<SbmlArgument> arguments) {
+ for (SbmlArgument sbmlArgument : arguments) {
+ removeArgument(sbmlArgument);
+ }
+ }
+
+ private void removeArgument(SbmlArgument argument) {
+ if (argument instanceof SbmlParameter) {
+ removeParameter((SbmlParameter) argument);
+ } else if (argument instanceof SbmlFunction) {
+ removeFunction((SbmlFunction) argument);
+ } else {
+ removeElement((Element) argument);
+ }
+ }
+
+ private void removeFunction(SbmlFunction function) {
+ functions.remove(function);
+ }
+
+ private void removeParameter(SbmlParameter parameter) {
+ parameters.remove(parameter);
+
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKineticsComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKineticsComparator.java
index b0921f23a5..bba5d60139 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKineticsComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKineticsComparator.java
@@ -1,46 +1,46 @@
-package lcsb.mapviewer.model.map.kinetics;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.comparator.SetComparator;
-import lcsb.mapviewer.common.comparator.StringComparator;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.ElementComparator;
-
-public class SbmlKineticsComparator extends Comparator<SbmlKinetics> {
-
- Logger logger = Logger.getLogger(SbmlKineticsComparator.class);
-
- public SbmlKineticsComparator() {
- super(SbmlKinetics.class);
- }
-
- @Override
- protected int internalCompare(SbmlKinetics arg0, SbmlKinetics arg1) {
- SetComparator<SbmlFunction> functionComparator = new SetComparator<>(new SbmlFunctionComparator());
- if (functionComparator.compare(arg0.getFunctions(), arg1.getFunctions()) != 0) {
- logger.debug("Functions different");
- return functionComparator.compare(arg0.getFunctions(), arg1.getFunctions());
- }
- SetComparator<SbmlParameter> parameterComparator = new SetComparator<>(new SbmlParameterComparator());
- if (parameterComparator.compare(arg0.getParameters(), arg1.getParameters()) != 0) {
- logger.debug("Parameters different");
- return parameterComparator.compare(arg0.getParameters(), arg1.getParameters());
- }
- SetComparator<Element> elementComparator = new SetComparator<>(new ElementComparator());
- if (elementComparator.compare(arg0.getElements(), arg1.getElements()) != 0) {
- logger.debug("Elements different");
- return elementComparator.compare(arg0.getElements(), arg1.getElements());
- }
- StringComparator stringComparator = new StringComparator();
- if (stringComparator.compare(arg0.getDefinition(), arg1.getDefinition(), true) != 0) {
- logger.debug("Definition different");
- logger.debug(arg0.getDefinition());
- logger.debug(arg1.getDefinition());
- return stringComparator.compare(arg0.getDefinition(), arg1.getDefinition());
- }
- return 0;
- }
-
-}
+package lcsb.mapviewer.model.map.kinetics;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.comparator.SetComparator;
+import lcsb.mapviewer.common.comparator.StringComparator;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.ElementComparator;
+
+public class SbmlKineticsComparator extends Comparator<SbmlKinetics> {
+
+ Logger logger = Logger.getLogger(SbmlKineticsComparator.class);
+
+ public SbmlKineticsComparator() {
+ super(SbmlKinetics.class);
+ }
+
+ @Override
+ protected int internalCompare(SbmlKinetics arg0, SbmlKinetics arg1) {
+ SetComparator<SbmlFunction> functionComparator = new SetComparator<>(new SbmlFunctionComparator());
+ if (functionComparator.compare(arg0.getFunctions(), arg1.getFunctions()) != 0) {
+ logger.debug("Functions different");
+ return functionComparator.compare(arg0.getFunctions(), arg1.getFunctions());
+ }
+ SetComparator<SbmlParameter> parameterComparator = new SetComparator<>(new SbmlParameterComparator());
+ if (parameterComparator.compare(arg0.getParameters(), arg1.getParameters()) != 0) {
+ logger.debug("Parameters different");
+ return parameterComparator.compare(arg0.getParameters(), arg1.getParameters());
+ }
+ SetComparator<Element> elementComparator = new SetComparator<>(new ElementComparator());
+ if (elementComparator.compare(arg0.getElements(), arg1.getElements()) != 0) {
+ logger.debug("Elements different");
+ return elementComparator.compare(arg0.getElements(), arg1.getElements());
+ }
+ StringComparator stringComparator = new StringComparator();
+ if (stringComparator.compare(arg0.getDefinition(), arg1.getDefinition(), true) != 0) {
+ logger.debug("Definition different");
+ logger.debug(arg0.getDefinition());
+ logger.debug(arg1.getDefinition());
+ return stringComparator.compare(arg0.getDefinition(), arg1.getDefinition());
+ }
+ return 0;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlParameter.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlParameter.java
index aba446815c..586d5cdc4e 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlParameter.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlParameter.java
@@ -1,121 +1,121 @@
-package lcsb.mapviewer.model.map.kinetics;
-
-import java.io.Serializable;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-import javax.xml.bind.annotation.XmlRootElement;
-
-import org.apache.log4j.Logger;
-
-/**
- * Representation of a single SBML parameter
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "sbml_parameter")
-@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
-@XmlRootElement
-public class SbmlParameter implements Serializable, SbmlArgument {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(SbmlParameter.class);
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Unique database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- private String parameterId;
-
- private String name;
-
- private Double value;
-
- @ManyToOne()
- private SbmlUnit units;
-
- /**
- * Constructor required by hibernate.
- */
- SbmlParameter() {
- super();
- }
-
- public SbmlParameter(String parameterId) {
- this.parameterId = parameterId;
- }
-
- public SbmlParameter(SbmlParameter original) {
- this.parameterId = original.getParameterId();
- this.name = original.getName();
- this.value = original.getValue();
- this.units = original.getUnits();
- }
-
- public String getName() {
- return name;
- }
-
- public void setName(String name) {
- this.name = name;
- }
-
- public String getParameterId() {
- return parameterId;
- }
-
- public void setParameterId(String parameterId) {
- this.parameterId = parameterId;
- }
-
- public Double getValue() {
- return value;
- }
-
- public void setValue(Double value) {
- this.value = value;
- }
-
- public SbmlUnit getUnits() {
- return units;
- }
-
- public void setUnits(SbmlUnit units) {
- this.units = units;
-
- }
-
- @Override
- public SbmlParameter copy() {
- return new SbmlParameter(this);
- }
-
- @Override
- public String getElementId() {
- return getParameterId();
- }
-
- public int getId() {
- return id;
- }
-
-}
+package lcsb.mapviewer.model.map.kinetics;
+
+import java.io.Serializable;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+import javax.xml.bind.annotation.XmlRootElement;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Representation of a single SBML parameter
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "sbml_parameter")
+@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
+@XmlRootElement
+public class SbmlParameter implements Serializable, SbmlArgument {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(SbmlParameter.class);
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Unique database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ private String parameterId;
+
+ private String name;
+
+ private Double value;
+
+ @ManyToOne()
+ private SbmlUnit units;
+
+ /**
+ * Constructor required by hibernate.
+ */
+ SbmlParameter() {
+ super();
+ }
+
+ public SbmlParameter(String parameterId) {
+ this.parameterId = parameterId;
+ }
+
+ public SbmlParameter(SbmlParameter original) {
+ this.parameterId = original.getParameterId();
+ this.name = original.getName();
+ this.value = original.getValue();
+ this.units = original.getUnits();
+ }
+
+ public String getName() {
+ return name;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ public String getParameterId() {
+ return parameterId;
+ }
+
+ public void setParameterId(String parameterId) {
+ this.parameterId = parameterId;
+ }
+
+ public Double getValue() {
+ return value;
+ }
+
+ public void setValue(Double value) {
+ this.value = value;
+ }
+
+ public SbmlUnit getUnits() {
+ return units;
+ }
+
+ public void setUnits(SbmlUnit units) {
+ this.units = units;
+
+ }
+
+ @Override
+ public SbmlParameter copy() {
+ return new SbmlParameter(this);
+ }
+
+ @Override
+ public String getElementId() {
+ return getParameterId();
+ }
+
+ public int getId() {
+ return id;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnit.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnit.java
index 07c8f01aa9..df4f0a8fea 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnit.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnit.java
@@ -1,128 +1,128 @@
-package lcsb.mapviewer.model.map.kinetics;
-
-import java.io.Serializable;
-import java.util.HashSet;
-import java.util.Set;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.ManyToOne;
-import javax.persistence.OneToMany;
-import javax.persistence.Table;
-import javax.xml.bind.annotation.XmlRootElement;
-
-import org.apache.log4j.Logger;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-
-import lcsb.mapviewer.model.map.model.ModelData;
-
-/**
- * Representation of a single SBML unit
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "sbml_unit")
-@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
-@XmlRootElement
-public class SbmlUnit implements Serializable {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(SbmlUnit.class);
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Unique database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- private String unitId;
- private String name;
-
- @Cascade({ CascadeType.ALL })
- @OneToMany(mappedBy = "unit", orphanRemoval = true)
- private Set<SbmlUnitTypeFactor> unitTypeFactors = new HashSet<>();
-
- /**
- * Map model object to which unit belongs to.
- */
- @ManyToOne(fetch = FetchType.LAZY)
- private ModelData model;
-
- /**
- * Constructor required by hibernate.
- */
- SbmlUnit() {
- super();
- }
-
- public SbmlUnit(String unitId) {
- this.unitId = unitId;
- }
-
- public SbmlUnit(SbmlUnit sbmlUnit) {
- this(sbmlUnit.getUnitId());
- this.setName(sbmlUnit.getName());
- for (SbmlUnitTypeFactor factor : sbmlUnit.getUnitTypeFactors()) {
- this.addUnitTypeFactor(factor.copy());
- }
- }
-
- public String getUnitId() {
- return unitId;
- }
-
- public void setUnitId(String unitId) {
- this.unitId = unitId;
- }
-
- public String getName() {
- return name;
- }
-
- public void setName(String name) {
- this.name = name;
- }
-
- public void addUnitTypeFactor(SbmlUnitTypeFactor factor) {
- unitTypeFactors.add(factor);
- factor.setUnit(this);
- }
-
- public Set<SbmlUnitTypeFactor> getUnitTypeFactors() {
- return unitTypeFactors;
- }
-
- public ModelData getModel() {
- return model;
- }
-
- public void setModel(ModelData model) {
- this.model = model;
- }
-
- public SbmlUnit copy() {
- return new SbmlUnit(this);
- }
-
- public int getId() {
- return id;
- }
-
-}
+package lcsb.mapviewer.model.map.kinetics;
+
+import java.io.Serializable;
+import java.util.HashSet;
+import java.util.Set;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
+import javax.persistence.Table;
+import javax.xml.bind.annotation.XmlRootElement;
+
+import org.apache.log4j.Logger;
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+
+import lcsb.mapviewer.model.map.model.ModelData;
+
+/**
+ * Representation of a single SBML unit
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "sbml_unit")
+@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
+@XmlRootElement
+public class SbmlUnit implements Serializable {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(SbmlUnit.class);
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Unique database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ private String unitId;
+ private String name;
+
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(mappedBy = "unit", orphanRemoval = true)
+ private Set<SbmlUnitTypeFactor> unitTypeFactors = new HashSet<>();
+
+ /**
+ * Map model object to which unit belongs to.
+ */
+ @ManyToOne(fetch = FetchType.LAZY)
+ private ModelData model;
+
+ /**
+ * Constructor required by hibernate.
+ */
+ SbmlUnit() {
+ super();
+ }
+
+ public SbmlUnit(String unitId) {
+ this.unitId = unitId;
+ }
+
+ public SbmlUnit(SbmlUnit sbmlUnit) {
+ this(sbmlUnit.getUnitId());
+ this.setName(sbmlUnit.getName());
+ for (SbmlUnitTypeFactor factor : sbmlUnit.getUnitTypeFactors()) {
+ this.addUnitTypeFactor(factor.copy());
+ }
+ }
+
+ public String getUnitId() {
+ return unitId;
+ }
+
+ public void setUnitId(String unitId) {
+ this.unitId = unitId;
+ }
+
+ public String getName() {
+ return name;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ public void addUnitTypeFactor(SbmlUnitTypeFactor factor) {
+ unitTypeFactors.add(factor);
+ factor.setUnit(this);
+ }
+
+ public Set<SbmlUnitTypeFactor> getUnitTypeFactors() {
+ return unitTypeFactors;
+ }
+
+ public ModelData getModel() {
+ return model;
+ }
+
+ public void setModel(ModelData model) {
+ this.model = model;
+ }
+
+ public SbmlUnit copy() {
+ return new SbmlUnit(this);
+ }
+
+ public int getId() {
+ return id;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactor.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactor.java
index f1d6f1975b..8c4a7edf25 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactor.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactor.java
@@ -1,131 +1,131 @@
-package lcsb.mapviewer.model.map.kinetics;
-
-import java.io.Serializable;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.EnumType;
-import javax.persistence.Enumerated;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-import javax.xml.bind.annotation.XmlRootElement;
-
-import org.apache.log4j.Logger;
-
-/**
- * Representation of a single SBML unit factor. For example unit for velocity is
- * m/s. It means that we have two unit types here:
- * <ul>
- * <li>metre^1</li>
- * <li>second^-1</li>
- * </ul>
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "sbml_unit_factor")
-@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
-@XmlRootElement
-public class SbmlUnitTypeFactor implements Serializable {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(SbmlUnitTypeFactor.class);
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Unique database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- @Enumerated(EnumType.STRING)
- private SbmlUnitType unitType;
-
- private int exponent = 1;
- private int scale = 0;
- private double multiplier = 1.0;
-
- @ManyToOne(fetch = FetchType.LAZY)
- private SbmlUnit unit;
-
- /**
- * Constructor required by hibernate.
- */
- SbmlUnitTypeFactor() {
- super();
- }
-
- public SbmlUnitTypeFactor(SbmlUnitType unitType, int exponent, int scale, double multiplier) {
- this.unitType = unitType;
- this.exponent = exponent;
- this.scale = scale;
- this.multiplier = multiplier;
- }
-
- public SbmlUnitTypeFactor(SbmlUnitTypeFactor original) {
- this(original.getUnitType(), original.getExponent(), original.getScale(), original.getMultiplier());
- }
-
- public SbmlUnitType getUnitType() {
- return unitType;
- }
-
- public void setUnitType(SbmlUnitType unitType) {
- this.unitType = unitType;
- }
-
- public int getExponent() {
- return exponent;
- }
-
- public void setExponent(int exponent) {
- this.exponent = exponent;
- }
-
- public int getScale() {
- return scale;
- }
-
- public void setScale(int scale) {
- this.scale = scale;
- }
-
- public double getMultiplier() {
- return multiplier;
- }
-
- public void setMultiplier(double multiplier) {
- this.multiplier = multiplier;
- }
-
- public SbmlUnit getUnit() {
- return unit;
- }
-
- public void setUnit(SbmlUnit unit) {
- this.unit = unit;
- }
-
- public SbmlUnitTypeFactor copy() {
- return new SbmlUnitTypeFactor(this);
- }
-
- public int getId() {
- return id;
- }
-
-}
+package lcsb.mapviewer.model.map.kinetics;
+
+import java.io.Serializable;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.EnumType;
+import javax.persistence.Enumerated;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+import javax.xml.bind.annotation.XmlRootElement;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Representation of a single SBML unit factor. For example unit for velocity is
+ * m/s. It means that we have two unit types here:
+ * <ul>
+ * <li>metre^1</li>
+ * <li>second^-1</li>
+ * </ul>
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "sbml_unit_factor")
+@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
+@XmlRootElement
+public class SbmlUnitTypeFactor implements Serializable {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(SbmlUnitTypeFactor.class);
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Unique database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ @Enumerated(EnumType.STRING)
+ private SbmlUnitType unitType;
+
+ private int exponent = 1;
+ private int scale = 0;
+ private double multiplier = 1.0;
+
+ @ManyToOne(fetch = FetchType.LAZY)
+ private SbmlUnit unit;
+
+ /**
+ * Constructor required by hibernate.
+ */
+ SbmlUnitTypeFactor() {
+ super();
+ }
+
+ public SbmlUnitTypeFactor(SbmlUnitType unitType, int exponent, int scale, double multiplier) {
+ this.unitType = unitType;
+ this.exponent = exponent;
+ this.scale = scale;
+ this.multiplier = multiplier;
+ }
+
+ public SbmlUnitTypeFactor(SbmlUnitTypeFactor original) {
+ this(original.getUnitType(), original.getExponent(), original.getScale(), original.getMultiplier());
+ }
+
+ public SbmlUnitType getUnitType() {
+ return unitType;
+ }
+
+ public void setUnitType(SbmlUnitType unitType) {
+ this.unitType = unitType;
+ }
+
+ public int getExponent() {
+ return exponent;
+ }
+
+ public void setExponent(int exponent) {
+ this.exponent = exponent;
+ }
+
+ public int getScale() {
+ return scale;
+ }
+
+ public void setScale(int scale) {
+ this.scale = scale;
+ }
+
+ public double getMultiplier() {
+ return multiplier;
+ }
+
+ public void setMultiplier(double multiplier) {
+ this.multiplier = multiplier;
+ }
+
+ public SbmlUnit getUnit() {
+ return unit;
+ }
+
+ public void setUnit(SbmlUnit unit) {
+ this.unit = unit;
+ }
+
+ public SbmlUnitTypeFactor copy() {
+ return new SbmlUnitTypeFactor(this);
+ }
+
+ public int getId() {
+ return id;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/BlockDiagram.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/BlockDiagram.java
index c2190b9333..c0dec6dc38 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/BlockDiagram.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/BlockDiagram.java
@@ -1,19 +1,19 @@
-package lcsb.mapviewer.model.map.layout;
-
-import java.io.Serializable;
-
-
-/**
- * This model element is used by cell designer but don't know how... We ignore it
- *
- * @author Piotr Gawron
- *
- */
-public abstract class BlockDiagram implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
-}
+package lcsb.mapviewer.model.map.layout;
+
+import java.io.Serializable;
+
+
+/**
+ * This model element is used by cell designer but don't know how... We ignore it
+ *
+ * @author Piotr Gawron
+ *
+ */
+public abstract class BlockDiagram implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchema.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchema.java
index 53174c04f4..0c16a03410 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchema.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchema.java
@@ -1,403 +1,403 @@
-package lcsb.mapviewer.model.map.layout;
-
-import java.awt.Color;
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * Entry of coloring schema used for changing colors in the map. It allows to
- * identify some elements by use of the filters (by name, type, etc.) and
- * contains information about the color that should be assigned to the filter
- * elements.
- *
- * @author Piotr Gawron
- *
- */
-public abstract class ColorSchema implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Name of the {@link Element Element}. If null then this field will be skipped.
- */
- private String name = null;
-
- /**
- * Name of the {@link Model} to which this schema should be limited. If null
- * then this field will be skipped.
- */
- private String modelName = null;
-
- /**
- * Original identifier of the {@link BioEntity} to change the color.
- */
- private String elementId = null;
-
- /**
- * Should the direction of highlighted reaction be reversed.
- */
- private Boolean reverseReaction = null;
-
- /**
- * Width of the line in the reaction.
- */
- private Double lineWidth = null;
-
- /**
- * In which compartments (identified by name) the element can occur.
- */
- private List<String> compartments = new ArrayList<String>();
-
- /**
- * What types of element should be identified by this entry.
- */
- private List<Class<? extends Element>> types = new ArrayList<>();
-
- /**
- * Value (-1..1 range) that is assigned to filtered elements (it will be
- * transformed into color later on). Only one of the {@link #value} and
- * {@link #color} can be set.
- */
- private Double value = null;
-
- /**
- * Color that is assigned to filtered elements. Only one of the {@link #value}
- * and {@link #color} can be set.
- */
- private Color color = null;
-
- /**
- * Set of identifiers that filter the elements.
- */
- private Set<MiriamData> miriamData = new HashSet<>();
-
- /**
- * Number of elements matched by this entry.
- */
- private int matches = 0;
-
- /**
- * Short description of the entry.
- */
- private String description;
-
- /**
- * Default constructor.
- */
- protected ColorSchema() {
- }
-
- /**
- * Initializes object by copying data from the parameter.
- *
- * @param original
- * original object used for initialization
- */
- protected ColorSchema(ColorSchema original) {
- this.setName(original.getName());
- this.setElementId(original.getElementId());
- this.setReverseReaction(original.getReverseReaction());
- this.setLineWidth(original.getLineWidth());
- this.addCompartments(original.getCompartments());
- this.addTypes(original.getTypes());
- this.setValue(original.getValue());
- this.setColor(original.getColor());
- this.miriamData.addAll(original.getMiriamData());
- this.setMatches(original.getMatches());
- this.setDescription(original.getDescription());
- }
-
- /**
- * Adds class types to {@link #types} list.
- *
- * @param types2
- * list of classes to add
- */
- public void addTypes(List<Class<? extends Element>> types2) {
- for (Class<? extends Element> clazz : types2) {
- addType(clazz);
- }
- }
-
- /**
- * Adds compartment names to {@link #compartments} list.
- *
- * @param compartments2
- * elements to add
- */
- public void addCompartments(String[] compartments2) {
- for (String string : compartments2) {
- compartments.add(string);
- }
- }
-
- /**
- * Adds compartment names to {@link #compartments} list.
- *
- * @param compartments2
- * elements to add
- */
- public void addCompartments(Collection<String> compartments2) {
- for (String string : compartments2) {
- compartments.add(string);
- }
- }
-
- @Override
- public String toString() {
- StringBuilder result = new StringBuilder();
- result.append("[");
- if (name != null) {
- result.append(name + ",");
- }
- if (compartments.size() > 0) {
- result.append("(");
- for (String comp : compartments) {
- result.append(comp + ",");
- }
- result.append("),");
- }
- if (types.size() > 0) {
- result.append("(");
- for (Class<?> clazz : types) {
- result.append(clazz.getSimpleName() + ",");
- }
- result.append("),");
- }
- if (value != null) {
- result.append(value + ",");
- }
- if (color != null) {
- result.append(color + ",");
- }
- result.append(miriamData + ",");
-
- result.append(matches + "]");
- return result.toString();
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- if (name == null) {
- this.name = null;
- } else {
- this.name = name.trim();
- }
- }
-
- /**
- * @return the compartments
- * @see #compartments
- */
- public List<String> getCompartments() {
- return compartments;
- }
-
- /**
- * @param compartments
- * the compartments to set
- * @see #compartments
- */
- public void setCompartments(List<String> compartments) {
- this.compartments = compartments;
- }
-
- /**
- * @return the types
- * @see #types
- */
- public List<Class<? extends Element>> getTypes() {
- return types;
- }
-
- /**
- * @param types
- * the types to set
- * @see #types
- */
- public void setTypes(List<Class<? extends Element>> types) {
- this.types = types;
- }
-
- /**
- * @return the value
- * @see #value
- */
- public Double getValue() {
- return value;
- }
-
- /**
- * @param value
- * the value to set
- * @see #value
- */
- public void setValue(Double value) {
- this.value = value;
- }
-
- /**
- * @return the color
- * @see #color
- */
- public Color getColor() {
- return color;
- }
-
- /**
- * @param color
- * the color to set
- * @see #color
- */
- public void setColor(Color color) {
- this.color = color;
- }
-
- /**
- * @return the matches
- * @see #matches
- */
- public int getMatches() {
- return matches;
- }
-
- /**
- * @param matches
- * the matches to set
- * @see #matches
- */
- public void setMatches(int matches) {
- this.matches = matches;
- }
-
- /**
- * Adds identifier to {@link #miriamData} set.
- *
- */
- public void addMiriamData(MiriamData md) {
- miriamData.add(md);
- }
-
- /**
- * @return the lineWidth
- * @see #lineWidth
- */
- public Double getLineWidth() {
- return lineWidth;
- }
-
- /**
- * @param lineWidth
- * the lineWidth to set
- * @see #lineWidth
- */
- public void setLineWidth(Double lineWidth) {
- this.lineWidth = lineWidth;
- }
-
- /**
- * @return the reverseReaction
- * @see #reverseReaction
- */
- public Boolean getReverseReaction() {
- return reverseReaction;
- }
-
- /**
- * @param reverseReaction
- * the reverseReaction to set
- * @see #reverseReaction
- */
- public void setReverseReaction(Boolean reverseReaction) {
- this.reverseReaction = reverseReaction;
- }
-
- /**
- * Adds compartment name to {@link #compartments}.
- *
- * @param name
- * compartment name
- */
- public void addCompartment(String name) {
- compartments.add(name);
- }
-
- /**
- * Adds class type to {@link #types} list.
- *
- * @param clazz
- * class to add
- */
- public void addType(Class<? extends Element> clazz) {
- this.types.add(clazz);
- }
-
- /**
- * @return the description
- * @see #description
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * @param description
- * the description to set
- * @see #description
- */
- public void setDescription(String description) {
- this.description = description;
- }
-
- /**
- * Creates a copy of this object.
- *
- * @return copy of the object
- */
- public abstract ColorSchema copy();
-
- public String getModelName() {
- return modelName;
- }
-
- public void setModelName(String modelName) {
- this.modelName = modelName;
- }
-
- public String getElementId() {
- return elementId;
- }
-
- public void setElementId(String elementId) {
- this.elementId = elementId;
- }
-
- public Set<MiriamData> getMiriamData() {
- return miriamData;
- }
-
-}
+package lcsb.mapviewer.model.map.layout;
+
+import java.awt.Color;
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * Entry of coloring schema used for changing colors in the map. It allows to
+ * identify some elements by use of the filters (by name, type, etc.) and
+ * contains information about the color that should be assigned to the filter
+ * elements.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public abstract class ColorSchema implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Name of the {@link Element Element}. If null then this field will be skipped.
+ */
+ private String name = null;
+
+ /**
+ * Name of the {@link Model} to which this schema should be limited. If null
+ * then this field will be skipped.
+ */
+ private String modelName = null;
+
+ /**
+ * Original identifier of the {@link BioEntity} to change the color.
+ */
+ private String elementId = null;
+
+ /**
+ * Should the direction of highlighted reaction be reversed.
+ */
+ private Boolean reverseReaction = null;
+
+ /**
+ * Width of the line in the reaction.
+ */
+ private Double lineWidth = null;
+
+ /**
+ * In which compartments (identified by name) the element can occur.
+ */
+ private List<String> compartments = new ArrayList<String>();
+
+ /**
+ * What types of element should be identified by this entry.
+ */
+ private List<Class<? extends Element>> types = new ArrayList<>();
+
+ /**
+ * Value (-1..1 range) that is assigned to filtered elements (it will be
+ * transformed into color later on). Only one of the {@link #value} and
+ * {@link #color} can be set.
+ */
+ private Double value = null;
+
+ /**
+ * Color that is assigned to filtered elements. Only one of the {@link #value}
+ * and {@link #color} can be set.
+ */
+ private Color color = null;
+
+ /**
+ * Set of identifiers that filter the elements.
+ */
+ private Set<MiriamData> miriamData = new HashSet<>();
+
+ /**
+ * Number of elements matched by this entry.
+ */
+ private int matches = 0;
+
+ /**
+ * Short description of the entry.
+ */
+ private String description;
+
+ /**
+ * Default constructor.
+ */
+ protected ColorSchema() {
+ }
+
+ /**
+ * Initializes object by copying data from the parameter.
+ *
+ * @param original
+ * original object used for initialization
+ */
+ protected ColorSchema(ColorSchema original) {
+ this.setName(original.getName());
+ this.setElementId(original.getElementId());
+ this.setReverseReaction(original.getReverseReaction());
+ this.setLineWidth(original.getLineWidth());
+ this.addCompartments(original.getCompartments());
+ this.addTypes(original.getTypes());
+ this.setValue(original.getValue());
+ this.setColor(original.getColor());
+ this.miriamData.addAll(original.getMiriamData());
+ this.setMatches(original.getMatches());
+ this.setDescription(original.getDescription());
+ }
+
+ /**
+ * Adds class types to {@link #types} list.
+ *
+ * @param types2
+ * list of classes to add
+ */
+ public void addTypes(List<Class<? extends Element>> types2) {
+ for (Class<? extends Element> clazz : types2) {
+ addType(clazz);
+ }
+ }
+
+ /**
+ * Adds compartment names to {@link #compartments} list.
+ *
+ * @param compartments2
+ * elements to add
+ */
+ public void addCompartments(String[] compartments2) {
+ for (String string : compartments2) {
+ compartments.add(string);
+ }
+ }
+
+ /**
+ * Adds compartment names to {@link #compartments} list.
+ *
+ * @param compartments2
+ * elements to add
+ */
+ public void addCompartments(Collection<String> compartments2) {
+ for (String string : compartments2) {
+ compartments.add(string);
+ }
+ }
+
+ @Override
+ public String toString() {
+ StringBuilder result = new StringBuilder();
+ result.append("[");
+ if (name != null) {
+ result.append(name + ",");
+ }
+ if (compartments.size() > 0) {
+ result.append("(");
+ for (String comp : compartments) {
+ result.append(comp + ",");
+ }
+ result.append("),");
+ }
+ if (types.size() > 0) {
+ result.append("(");
+ for (Class<?> clazz : types) {
+ result.append(clazz.getSimpleName() + ",");
+ }
+ result.append("),");
+ }
+ if (value != null) {
+ result.append(value + ",");
+ }
+ if (color != null) {
+ result.append(color + ",");
+ }
+ result.append(miriamData + ",");
+
+ result.append(matches + "]");
+ return result.toString();
+ }
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ if (name == null) {
+ this.name = null;
+ } else {
+ this.name = name.trim();
+ }
+ }
+
+ /**
+ * @return the compartments
+ * @see #compartments
+ */
+ public List<String> getCompartments() {
+ return compartments;
+ }
+
+ /**
+ * @param compartments
+ * the compartments to set
+ * @see #compartments
+ */
+ public void setCompartments(List<String> compartments) {
+ this.compartments = compartments;
+ }
+
+ /**
+ * @return the types
+ * @see #types
+ */
+ public List<Class<? extends Element>> getTypes() {
+ return types;
+ }
+
+ /**
+ * @param types
+ * the types to set
+ * @see #types
+ */
+ public void setTypes(List<Class<? extends Element>> types) {
+ this.types = types;
+ }
+
+ /**
+ * @return the value
+ * @see #value
+ */
+ public Double getValue() {
+ return value;
+ }
+
+ /**
+ * @param value
+ * the value to set
+ * @see #value
+ */
+ public void setValue(Double value) {
+ this.value = value;
+ }
+
+ /**
+ * @return the color
+ * @see #color
+ */
+ public Color getColor() {
+ return color;
+ }
+
+ /**
+ * @param color
+ * the color to set
+ * @see #color
+ */
+ public void setColor(Color color) {
+ this.color = color;
+ }
+
+ /**
+ * @return the matches
+ * @see #matches
+ */
+ public int getMatches() {
+ return matches;
+ }
+
+ /**
+ * @param matches
+ * the matches to set
+ * @see #matches
+ */
+ public void setMatches(int matches) {
+ this.matches = matches;
+ }
+
+ /**
+ * Adds identifier to {@link #miriamData} set.
+ *
+ */
+ public void addMiriamData(MiriamData md) {
+ miriamData.add(md);
+ }
+
+ /**
+ * @return the lineWidth
+ * @see #lineWidth
+ */
+ public Double getLineWidth() {
+ return lineWidth;
+ }
+
+ /**
+ * @param lineWidth
+ * the lineWidth to set
+ * @see #lineWidth
+ */
+ public void setLineWidth(Double lineWidth) {
+ this.lineWidth = lineWidth;
+ }
+
+ /**
+ * @return the reverseReaction
+ * @see #reverseReaction
+ */
+ public Boolean getReverseReaction() {
+ return reverseReaction;
+ }
+
+ /**
+ * @param reverseReaction
+ * the reverseReaction to set
+ * @see #reverseReaction
+ */
+ public void setReverseReaction(Boolean reverseReaction) {
+ this.reverseReaction = reverseReaction;
+ }
+
+ /**
+ * Adds compartment name to {@link #compartments}.
+ *
+ * @param name
+ * compartment name
+ */
+ public void addCompartment(String name) {
+ compartments.add(name);
+ }
+
+ /**
+ * Adds class type to {@link #types} list.
+ *
+ * @param clazz
+ * class to add
+ */
+ public void addType(Class<? extends Element> clazz) {
+ this.types.add(clazz);
+ }
+
+ /**
+ * @return the description
+ * @see #description
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * @param description
+ * the description to set
+ * @see #description
+ */
+ public void setDescription(String description) {
+ this.description = description;
+ }
+
+ /**
+ * Creates a copy of this object.
+ *
+ * @return copy of the object
+ */
+ public abstract ColorSchema copy();
+
+ public String getModelName() {
+ return modelName;
+ }
+
+ public void setModelName(String modelName) {
+ this.modelName = modelName;
+ }
+
+ public String getElementId() {
+ return elementId;
+ }
+
+ public void setElementId(String elementId) {
+ this.elementId = elementId;
+ }
+
+ public Set<MiriamData> getMiriamData() {
+ return miriamData;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/ElementGroup.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/ElementGroup.java
index d3f3b0e78a..bcbd1a86d4 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/ElementGroup.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/ElementGroup.java
@@ -1,77 +1,77 @@
-package lcsb.mapviewer.model.map.layout;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * This model element is used by cell designer but we ignore it. Maybe it will
- * be usefull in the future.
- *
- * @author Piotr Gawron
- *
- */
-public class ElementGroup implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * String identifier of the group.
- */
- private String idGroup;
-
- /**
- * List of elements in the group.
- */
- private List<Element> elements = new ArrayList<>();
-
- /**
- * @return the idGroup
- * @see #idGroup
- */
- public String getIdGroup() {
- return idGroup;
- }
-
- /**
- * @param idGroup
- * the idGroup to set
- * @see #idGroup
- */
- public void setIdGroup(String idGroup) {
- this.idGroup = idGroup;
- }
-
- /**
- * @return the elements
- * @see #elements
- */
- public List<Element> getElements() {
- return elements;
- }
-
- /**
- * @param elements
- * the elements to set
- * @see #elements
- */
- public void setElements(List<Element> elements) {
- this.elements = elements;
- }
-
- /**
- * Add element to the group.
- *
- * @param element
- * object to add to the group
- */
- public void addElement(Element element) {
- elements.add(element);
- }
-
-}
+package lcsb.mapviewer.model.map.layout;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * This model element is used by cell designer but we ignore it. Maybe it will
+ * be usefull in the future.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ElementGroup implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * String identifier of the group.
+ */
+ private String idGroup;
+
+ /**
+ * List of elements in the group.
+ */
+ private List<Element> elements = new ArrayList<>();
+
+ /**
+ * @return the idGroup
+ * @see #idGroup
+ */
+ public String getIdGroup() {
+ return idGroup;
+ }
+
+ /**
+ * @param idGroup
+ * the idGroup to set
+ * @see #idGroup
+ */
+ public void setIdGroup(String idGroup) {
+ this.idGroup = idGroup;
+ }
+
+ /**
+ * @return the elements
+ * @see #elements
+ */
+ public List<Element> getElements() {
+ return elements;
+ }
+
+ /**
+ * @param elements
+ * the elements to set
+ * @see #elements
+ */
+ public void setElements(List<Element> elements) {
+ this.elements = elements;
+ }
+
+ /**
+ * Add element to the group.
+ *
+ * @param element
+ * object to add to the group
+ */
+ public void addElement(Element element) {
+ elements.add(element);
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/GeneVariation.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/GeneVariation.java
index 76eeee8ea9..ba4d3afd4a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/GeneVariation.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/GeneVariation.java
@@ -1,277 +1,277 @@
-package lcsb.mapviewer.model.map.layout;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.MiriamData;
-
-/**
- * Class describing single gene variation.
- *
- * @author Piotr Gawron
- *
- */
-public class GeneVariation implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Variation position in the genome.
- */
- private Long position;
-
- /**
- * Original dna (from the reference genome).
- */
- private String originalDna;
-
- /**
- * Alternative dna (suggested by the variant).
- */
- private String modifiedDna;
-
- /**
- * Contig where variant was observed.
- */
- private String contig;
-
- private String allelFrequency;
- private String variantIdentifier;
-
- /**
- * Reference genome type.
- */
- private ReferenceGenomeType referenceGenomeType;
-
- /**
- * Version of the reference genome.
- */
- private String referenceGenomeVersion;
-
- /**
- * List of references connected to this variant.
- */
- private List<MiriamData> references = new ArrayList<>();
-
- /**
- * Constructor that creates copy of the {@link GeneVariation}.
- *
- * @param original
- * original {@link GeneVariation}
- */
- protected GeneVariation(GeneVariation original) {
- this.setPosition(original.getPosition());
- this.setOriginalDna(original.getOriginalDna());
- this.setModifiedDna(original.getModifiedDna());
- this.setReferenceGenomeType(original.getReferenceGenomeType());
- this.setReferenceGenomeVersion(original.getReferenceGenomeVersion());
- this.addReferences(original.getReferences());
- this.setContig(original.getContig());
- this.setAllelFrequency(original.getAllelFrequency());
- this.setVariantIdentifier(original.getVariantIdentifier());
- }
-
- /**
- * Default constructor.
- */
- public GeneVariation() {
- }
-
- /**
- * Adds references.
- *
- * @param references
- * references to add
- * @see #references
- */
- private void addReferences(Collection<MiriamData> references) {
- for (MiriamData reference : references) {
- addReference(reference);
- }
- }
-
- /**
- * @return the position
- * @see #position
- */
- public Long getPosition() {
- return position;
- }
-
- /**
- * @param position
- * the position to set
- * @see #position
- */
- public void setPosition(Long position) {
- this.position = position;
- }
-
- /**
- * @return the originalDna
- * @see #originalDna
- */
- public String getOriginalDna() {
- return originalDna;
- }
-
- /**
- * @param originalDna
- * the originalDna to set
- * @see #originalDna
- */
- public void setOriginalDna(String originalDna) {
- this.originalDna = originalDna;
- }
-
- /**
- * @return the modifiedDna
- * @see #modifiedDna
- */
- public String getModifiedDna() {
- return modifiedDna;
- }
-
- /**
- * @param modifiedDna
- * the modifiedDna to set
- * @see #modifiedDna
- */
- public void setModifiedDna(String modifiedDna) {
- this.modifiedDna = modifiedDna;
- }
-
- /**
- * @return the referenceGenomeType
- * @see #referenceGenomeType
- */
- public ReferenceGenomeType getReferenceGenomeType() {
- return referenceGenomeType;
- }
-
- /**
- * @param referenceGenomeType
- * the referenceGenomeType to set
- * @see #referenceGenomeType
- */
- public void setReferenceGenomeType(ReferenceGenomeType referenceGenomeType) {
- this.referenceGenomeType = referenceGenomeType;
- }
-
- /**
- * @return the references
- * @see #references
- */
- public List<MiriamData> getReferences() {
- return references;
- }
-
- /**
- * @return the referenceGenomeVersion
- * @see #referenceGenomeVersion
- */
- public String getReferenceGenomeVersion() {
- return referenceGenomeVersion;
- }
-
- /**
- * @param referenceGenomeVersion
- * the referenceGenomeVersion to set
- * @see #referenceGenomeVersion
- */
- public void setReferenceGenomeVersion(String referenceGenomeVersion) {
- this.referenceGenomeVersion = referenceGenomeVersion;
- }
-
- /**
- * Adds reference.
- *
- * @param reference
- * reference to add
- * @see #references
- */
- public void addReference(MiriamData reference) {
- this.references.add(reference);
- }
-
- /**
- * Creates copy of the object.
- *
- * @return copy of the object
- */
- public GeneVariation copy() {
- if (this.getClass().equals(GeneVariation.class)) {
- return new GeneVariation(this);
- } else {
- throw new NotImplementedException("Copy method not implemented for class: " + this.getClass());
- }
- }
-
- /**
- * @return the contig
- * @see #contig
- */
- public String getContig() {
- return contig;
- }
-
- /**
- * @param contig
- * the contig to set
- * @see #contig
- */
- public void setContig(String contig) {
- this.contig = contig;
- }
-
- /**
- * Sets {@link #position}.
- *
- * @param position
- * new position value
- */
- public void setPosition(int position) {
- this.position = (long) position;
- }
-
- /**
- * @return the allelFrequency
- * @see #allelFrequency
- */
- public String getAllelFrequency() {
- return allelFrequency;
- }
-
- /**
- * @param allelFrequency
- * the allelFrequency to set
- * @see #allelFrequency
- */
- public void setAllelFrequency(String allelFrequency) {
- this.allelFrequency = allelFrequency;
- }
-
- /**
- * @return the variantIdentifier
- * @see #variantIdentifier
- */
- public String getVariantIdentifier() {
- return variantIdentifier;
- }
-
- /**
- * @param variantIdentifier
- * the variantIdentifier to set
- * @see #variantIdentifier
- */
- public void setVariantIdentifier(String variantIdentifier) {
- this.variantIdentifier = variantIdentifier;
- }
-
-}
+package lcsb.mapviewer.model.map.layout;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.MiriamData;
+
+/**
+ * Class describing single gene variation.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class GeneVariation implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Variation position in the genome.
+ */
+ private Long position;
+
+ /**
+ * Original dna (from the reference genome).
+ */
+ private String originalDna;
+
+ /**
+ * Alternative dna (suggested by the variant).
+ */
+ private String modifiedDna;
+
+ /**
+ * Contig where variant was observed.
+ */
+ private String contig;
+
+ private String allelFrequency;
+ private String variantIdentifier;
+
+ /**
+ * Reference genome type.
+ */
+ private ReferenceGenomeType referenceGenomeType;
+
+ /**
+ * Version of the reference genome.
+ */
+ private String referenceGenomeVersion;
+
+ /**
+ * List of references connected to this variant.
+ */
+ private List<MiriamData> references = new ArrayList<>();
+
+ /**
+ * Constructor that creates copy of the {@link GeneVariation}.
+ *
+ * @param original
+ * original {@link GeneVariation}
+ */
+ protected GeneVariation(GeneVariation original) {
+ this.setPosition(original.getPosition());
+ this.setOriginalDna(original.getOriginalDna());
+ this.setModifiedDna(original.getModifiedDna());
+ this.setReferenceGenomeType(original.getReferenceGenomeType());
+ this.setReferenceGenomeVersion(original.getReferenceGenomeVersion());
+ this.addReferences(original.getReferences());
+ this.setContig(original.getContig());
+ this.setAllelFrequency(original.getAllelFrequency());
+ this.setVariantIdentifier(original.getVariantIdentifier());
+ }
+
+ /**
+ * Default constructor.
+ */
+ public GeneVariation() {
+ }
+
+ /**
+ * Adds references.
+ *
+ * @param references
+ * references to add
+ * @see #references
+ */
+ private void addReferences(Collection<MiriamData> references) {
+ for (MiriamData reference : references) {
+ addReference(reference);
+ }
+ }
+
+ /**
+ * @return the position
+ * @see #position
+ */
+ public Long getPosition() {
+ return position;
+ }
+
+ /**
+ * @param position
+ * the position to set
+ * @see #position
+ */
+ public void setPosition(Long position) {
+ this.position = position;
+ }
+
+ /**
+ * @return the originalDna
+ * @see #originalDna
+ */
+ public String getOriginalDna() {
+ return originalDna;
+ }
+
+ /**
+ * @param originalDna
+ * the originalDna to set
+ * @see #originalDna
+ */
+ public void setOriginalDna(String originalDna) {
+ this.originalDna = originalDna;
+ }
+
+ /**
+ * @return the modifiedDna
+ * @see #modifiedDna
+ */
+ public String getModifiedDna() {
+ return modifiedDna;
+ }
+
+ /**
+ * @param modifiedDna
+ * the modifiedDna to set
+ * @see #modifiedDna
+ */
+ public void setModifiedDna(String modifiedDna) {
+ this.modifiedDna = modifiedDna;
+ }
+
+ /**
+ * @return the referenceGenomeType
+ * @see #referenceGenomeType
+ */
+ public ReferenceGenomeType getReferenceGenomeType() {
+ return referenceGenomeType;
+ }
+
+ /**
+ * @param referenceGenomeType
+ * the referenceGenomeType to set
+ * @see #referenceGenomeType
+ */
+ public void setReferenceGenomeType(ReferenceGenomeType referenceGenomeType) {
+ this.referenceGenomeType = referenceGenomeType;
+ }
+
+ /**
+ * @return the references
+ * @see #references
+ */
+ public List<MiriamData> getReferences() {
+ return references;
+ }
+
+ /**
+ * @return the referenceGenomeVersion
+ * @see #referenceGenomeVersion
+ */
+ public String getReferenceGenomeVersion() {
+ return referenceGenomeVersion;
+ }
+
+ /**
+ * @param referenceGenomeVersion
+ * the referenceGenomeVersion to set
+ * @see #referenceGenomeVersion
+ */
+ public void setReferenceGenomeVersion(String referenceGenomeVersion) {
+ this.referenceGenomeVersion = referenceGenomeVersion;
+ }
+
+ /**
+ * Adds reference.
+ *
+ * @param reference
+ * reference to add
+ * @see #references
+ */
+ public void addReference(MiriamData reference) {
+ this.references.add(reference);
+ }
+
+ /**
+ * Creates copy of the object.
+ *
+ * @return copy of the object
+ */
+ public GeneVariation copy() {
+ if (this.getClass().equals(GeneVariation.class)) {
+ return new GeneVariation(this);
+ } else {
+ throw new NotImplementedException("Copy method not implemented for class: " + this.getClass());
+ }
+ }
+
+ /**
+ * @return the contig
+ * @see #contig
+ */
+ public String getContig() {
+ return contig;
+ }
+
+ /**
+ * @param contig
+ * the contig to set
+ * @see #contig
+ */
+ public void setContig(String contig) {
+ this.contig = contig;
+ }
+
+ /**
+ * Sets {@link #position}.
+ *
+ * @param position
+ * new position value
+ */
+ public void setPosition(int position) {
+ this.position = (long) position;
+ }
+
+ /**
+ * @return the allelFrequency
+ * @see #allelFrequency
+ */
+ public String getAllelFrequency() {
+ return allelFrequency;
+ }
+
+ /**
+ * @param allelFrequency
+ * the allelFrequency to set
+ * @see #allelFrequency
+ */
+ public void setAllelFrequency(String allelFrequency) {
+ this.allelFrequency = allelFrequency;
+ }
+
+ /**
+ * @return the variantIdentifier
+ * @see #variantIdentifier
+ */
+ public String getVariantIdentifier() {
+ return variantIdentifier;
+ }
+
+ /**
+ * @param variantIdentifier
+ * the variantIdentifier to set
+ * @see #variantIdentifier
+ */
+ public void setVariantIdentifier(String variantIdentifier) {
+ this.variantIdentifier = variantIdentifier;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/GeneVariationColorSchema.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/GeneVariationColorSchema.java
index 35a4c11936..97bf6b2939 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/GeneVariationColorSchema.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/GeneVariationColorSchema.java
@@ -1,92 +1,92 @@
-package lcsb.mapviewer.model.map.layout;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-/**
- * Information about coloring element accoridng to genetic variation
- * information.
- *
- * @author Piotr Gawron
- *
- */
-public class GeneVariationColorSchema extends ColorSchema {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * List of {@link GeneVariation gene variations} used in this "coloring".
- */
- private List<GeneVariation> geneVariations = new ArrayList<>();
-
- /**
- * Default constructor.
- */
- public GeneVariationColorSchema() {
- }
-
- /**
- * Constructor that creates copy of the object.
- *
- * @param schema
- * original object from which data will be copied
- */
- public GeneVariationColorSchema(GeneVariationColorSchema schema) {
- super(schema);
- this.addGeneVariations(schema.getGeneVariations());
- }
-
- /**
- * Adds {@link GeneVariation gene variations} to {@link #geneVariations}.
- *
- * @param geneVariations2
- * collection of {@link GeneVariation} objects to add
- */
- public void addGeneVariations(Collection<GeneVariation> geneVariations2) {
- for (GeneVariation geneVariation : geneVariations2) {
- addGeneVariation(geneVariation.copy());
- }
- }
-
- @Override
- public GeneVariationColorSchema copy() {
- if (this.getClass().equals(GeneVariationColorSchema.class)) {
- return new GeneVariationColorSchema(this);
- } else {
- throw new NotImplementedException("Copy not implemented for class: " + this.getClass());
- }
- }
-
- /**
- * @return the geneVariations
- * @see #geneVariations
- */
- public List<GeneVariation> getGeneVariations() {
- return geneVariations;
- }
-
- /**
- * @param geneVariations
- * the geneVariations to set
- * @see #geneVariations
- */
- public void setGeneVariations(List<GeneVariation> geneVariations) {
- this.geneVariations = geneVariations;
- }
-
- /**
- * Adds {@link GeneVariation} to list gene variations.
- *
- * @param gv
- * object to add
- */
- public void addGeneVariation(GeneVariation gv) {
- this.geneVariations.add(gv);
- }
-}
+package lcsb.mapviewer.model.map.layout;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * Information about coloring element accoridng to genetic variation
+ * information.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class GeneVariationColorSchema extends ColorSchema {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * List of {@link GeneVariation gene variations} used in this "coloring".
+ */
+ private List<GeneVariation> geneVariations = new ArrayList<>();
+
+ /**
+ * Default constructor.
+ */
+ public GeneVariationColorSchema() {
+ }
+
+ /**
+ * Constructor that creates copy of the object.
+ *
+ * @param schema
+ * original object from which data will be copied
+ */
+ public GeneVariationColorSchema(GeneVariationColorSchema schema) {
+ super(schema);
+ this.addGeneVariations(schema.getGeneVariations());
+ }
+
+ /**
+ * Adds {@link GeneVariation gene variations} to {@link #geneVariations}.
+ *
+ * @param geneVariations2
+ * collection of {@link GeneVariation} objects to add
+ */
+ public void addGeneVariations(Collection<GeneVariation> geneVariations2) {
+ for (GeneVariation geneVariation : geneVariations2) {
+ addGeneVariation(geneVariation.copy());
+ }
+ }
+
+ @Override
+ public GeneVariationColorSchema copy() {
+ if (this.getClass().equals(GeneVariationColorSchema.class)) {
+ return new GeneVariationColorSchema(this);
+ } else {
+ throw new NotImplementedException("Copy not implemented for class: " + this.getClass());
+ }
+ }
+
+ /**
+ * @return the geneVariations
+ * @see #geneVariations
+ */
+ public List<GeneVariation> getGeneVariations() {
+ return geneVariations;
+ }
+
+ /**
+ * @param geneVariations
+ * the geneVariations to set
+ * @see #geneVariations
+ */
+ public void setGeneVariations(List<GeneVariation> geneVariations) {
+ this.geneVariations = geneVariations;
+ }
+
+ /**
+ * Adds {@link GeneVariation} to list gene variations.
+ *
+ * @param gv
+ * object to add
+ */
+ public void addGeneVariation(GeneVariation gv) {
+ this.geneVariations.add(gv);
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/GenericColorSchema.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/GenericColorSchema.java
index 48f38551d5..20f8d49e65 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/GenericColorSchema.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/GenericColorSchema.java
@@ -1,44 +1,44 @@
-package lcsb.mapviewer.model.map.layout;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-/**
- * Generic color schema used for visualization any data type.
- *
- * @author Piotr Gawron
- *
- */
-public class GenericColorSchema extends ColorSchema {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public GenericColorSchema() {
- }
-
- /**
- * Default constructor that copies data from parameter.
- *
- * @param original
- * origanl object from which data is copied
- */
- public GenericColorSchema(GenericColorSchema original) {
- super(original);
- }
-
- @Override
- public GenericColorSchema copy() {
- if (this.getClass().equals(GenericColorSchema.class)) {
- return new GenericColorSchema(this);
- } else {
- throw new NotImplementedException("Copy mechanism of class " + this.getClass() + " is not implemented");
- }
-
- }
-
-}
+package lcsb.mapviewer.model.map.layout;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * Generic color schema used for visualization any data type.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class GenericColorSchema extends ColorSchema {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public GenericColorSchema() {
+ }
+
+ /**
+ * Default constructor that copies data from parameter.
+ *
+ * @param original
+ * origanl object from which data is copied
+ */
+ public GenericColorSchema(GenericColorSchema original) {
+ super(original);
+ }
+
+ @Override
+ public GenericColorSchema copy() {
+ if (this.getClass().equals(GenericColorSchema.class)) {
+ return new GenericColorSchema(this);
+ } else {
+ throw new NotImplementedException("Copy mechanism of class " + this.getClass() + " is not implemented");
+ }
+
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/InvalidColorSchemaException.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/InvalidColorSchemaException.java
index d6cea25e2b..93208b5c94 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/InvalidColorSchemaException.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/InvalidColorSchemaException.java
@@ -1,48 +1,48 @@
-package lcsb.mapviewer.model.map.layout;
-
-/**
- * Exception that should be thrown when
- * {@link lcsb.mapviewer.model.map.layout.ColorSchema} is invalid.
- *
- * @author Piotr Gawron
- *
- */
-public class InvalidColorSchemaException extends Exception {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor with message passed in the argument.
- *
- * @param string
- * message of this exception
- */
- public InvalidColorSchemaException(String string) {
- super(string);
- }
-
- /**
- * Constructor with message and super exception passed in the argument.
- *
- * @param string
- * message of this exception
- * @param e
- * super exception that caused this
- */
- public InvalidColorSchemaException(String string, Exception e) {
- super(string, e);
- }
-
- /**
- * Constructor with exception passed in the argument.
- *
- * @param e
- * super exception that caused this
- */
- public InvalidColorSchemaException(Exception e) {
- super(e);
- }
-}
+package lcsb.mapviewer.model.map.layout;
+
+/**
+ * Exception that should be thrown when
+ * {@link lcsb.mapviewer.model.map.layout.ColorSchema} is invalid.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class InvalidColorSchemaException extends Exception {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor with message passed in the argument.
+ *
+ * @param string
+ * message of this exception
+ */
+ public InvalidColorSchemaException(String string) {
+ super(string);
+ }
+
+ /**
+ * Constructor with message and super exception passed in the argument.
+ *
+ * @param string
+ * message of this exception
+ * @param e
+ * super exception that caused this
+ */
+ public InvalidColorSchemaException(String string, Exception e) {
+ super(string, e);
+ }
+
+ /**
+ * Constructor with exception passed in the argument.
+ *
+ * @param e
+ * super exception that caused this
+ */
+ public InvalidColorSchemaException(Exception e) {
+ super(e);
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/LayoutComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/LayoutComparator.java
index 30055b47f7..edda7eb689 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/LayoutComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/LayoutComparator.java
@@ -1,58 +1,58 @@
-package lcsb.mapviewer.model.map.layout;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.BooleanComparator;
-import lcsb.mapviewer.common.comparator.StringComparator;
-
-/**
- * This class implements comparator interface for Layout.
- *
- * @author Piotr Gawron
- *
- */
-public class LayoutComparator extends Comparator<Layout> {
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- @SuppressWarnings("unused")
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public LayoutComparator(double epsilon) {
- super(Layout.class, true);
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public LayoutComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected int internalCompare(Layout arg0, Layout arg1) {
- StringComparator stringComparator = new StringComparator();
- BooleanComparator booleanComparator = new BooleanComparator();
- if (stringComparator.compare(arg0.getDirectory(), arg1.getDirectory()) != 0) {
- return stringComparator.compare(arg0.getDirectory(), arg1.getDirectory());
- }
- if (stringComparator.compare(arg0.getTitle(), arg1.getTitle()) != 0) {
- return stringComparator.compare(arg0.getTitle(), arg1.getTitle());
- }
-
- if (booleanComparator.compare(arg0.isHierarchicalView(), arg1.isHierarchicalView()) != 0) {
- return booleanComparator.compare(arg0.isHierarchicalView(), arg1.isHierarchicalView());
- }
-
- return 0;
- }
-
-}
+package lcsb.mapviewer.model.map.layout;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.BooleanComparator;
+import lcsb.mapviewer.common.comparator.StringComparator;
+
+/**
+ * This class implements comparator interface for Layout.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class LayoutComparator extends Comparator<Layout> {
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ @SuppressWarnings("unused")
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public LayoutComparator(double epsilon) {
+ super(Layout.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public LayoutComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(Layout arg0, Layout arg1) {
+ StringComparator stringComparator = new StringComparator();
+ BooleanComparator booleanComparator = new BooleanComparator();
+ if (stringComparator.compare(arg0.getDirectory(), arg1.getDirectory()) != 0) {
+ return stringComparator.compare(arg0.getDirectory(), arg1.getDirectory());
+ }
+ if (stringComparator.compare(arg0.getTitle(), arg1.getTitle()) != 0) {
+ return stringComparator.compare(arg0.getTitle(), arg1.getTitle());
+ }
+
+ if (booleanComparator.compare(arg0.isHierarchicalView(), arg1.isHierarchicalView()) != 0) {
+ return booleanComparator.compare(arg0.isHierarchicalView(), arg1.isHierarchicalView());
+ }
+
+ return 0;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/LayoutStatus.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/LayoutStatus.java
index 0943bedfaf..e47dcef76d 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/LayoutStatus.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/LayoutStatus.java
@@ -1,59 +1,59 @@
-package lcsb.mapviewer.model.map.layout;
-
-/**
- * Status available for the layouts (based on the processing progress).
- *
- * @author Piotr Gawron
- *
- */
-public enum LayoutStatus {
-
- /**
- * Default unknown status.
- */
- UNKNOWN("Unknown"),
-
- /**
- * Layout is not available.
- */
- NA("Not available"),
-
- /**
- * Layout is generating.
- */
- GENERATING("Generating"),
-
- /**
- * Layout is ready.
- */
- OK("OK"),
-
- /**
- * There was a problem during layout generation.
- */
- FAILURE("Failure");
-
- /**
- * Common name of the status.
- */
- private String commonName;
-
- /**
- *
- * @return {@link #commonName}
- */
- public String getCommonName() {
- return commonName;
- }
-
- /**
- * Default constructor.
- *
- * @param commonName
- * {@link #commonName}
- */
- LayoutStatus(String commonName) {
- this.commonName = commonName;
- }
-
-}
+package lcsb.mapviewer.model.map.layout;
+
+/**
+ * Status available for the layouts (based on the processing progress).
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum LayoutStatus {
+
+ /**
+ * Default unknown status.
+ */
+ UNKNOWN("Unknown"),
+
+ /**
+ * Layout is not available.
+ */
+ NA("Not available"),
+
+ /**
+ * Layout is generating.
+ */
+ GENERATING("Generating"),
+
+ /**
+ * Layout is ready.
+ */
+ OK("OK"),
+
+ /**
+ * There was a problem during layout generation.
+ */
+ FAILURE("Failure");
+
+ /**
+ * Common name of the status.
+ */
+ private String commonName;
+
+ /**
+ *
+ * @return {@link #commonName}
+ */
+ public String getCommonName() {
+ return commonName;
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param commonName
+ * {@link #commonName}
+ */
+ LayoutStatus(String commonName) {
+ this.commonName = commonName;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/ReferenceGenome.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/ReferenceGenome.java
index 11fdfcfa61..d9f39668f8 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/ReferenceGenome.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/ReferenceGenome.java
@@ -1,221 +1,221 @@
-package lcsb.mapviewer.model.map.layout;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.EnumType;
-import javax.persistence.Enumerated;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.OneToMany;
-import javax.persistence.OneToOne;
-import javax.persistence.OrderBy;
-import javax.persistence.Table;
-
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-
-import lcsb.mapviewer.model.map.MiriamData;
-
-/**
- * Reference genome describes data used as reference genome. This data is
- * obtained usually from exteral server, database. Right now we support only
- * .2bit file format.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "reference_genome")
-public class ReferenceGenome implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Unique local database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- /**
- * Organism for which the genome is provided.
- */
- @Cascade({ CascadeType.ALL })
- @OneToOne
- private MiriamData organism;
-
- /**
- * Type of reference genome. This describe source (database) from which
- * reference genome was taken.
- */
- @Enumerated(EnumType.STRING)
- private ReferenceGenomeType type;
-
- /**
- * Version of the reference genome (databases have different releases, this
- * string represent specific release of data).
- */
- private String version;
-
- /**
- * How much of the file we already downloaded.
- */
- private double downloadProgress;
-
- /**
- * Source url used to obtain data.
- */
- private String sourceUrl;
-
- /**
- * List of differente mappings to this genome. Reference genome is a string
- * containing nucleotides. However interpretation of these nucleotides is a
- * different thing. Many databases provides different mappings between genes
- * and genome (even for the same genome). Therefore we allow to have more gene
- * mappings.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(fetch = FetchType.EAGER, mappedBy = "referenceGenome", orphanRemoval = true)
- @OrderBy("id")
- private List<ReferenceGenomeGeneMapping> geneMapping = new ArrayList<>();
-
- /**
- * @return the type
- * @see #type
- */
- public ReferenceGenomeType getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(ReferenceGenomeType type) {
- this.type = type;
- }
-
- /**
- * @return the organism
- * @see #organism
- */
- public MiriamData getOrganism() {
- return organism;
- }
-
- /**
- * @param organism
- * the organism to set
- * @see #organism
- */
- public void setOrganism(MiriamData organism) {
- this.organism = organism;
- }
-
- /**
- * @return the version
- * @see #version
- */
- public String getVersion() {
- return version;
- }
-
- /**
- * @param version
- * the version to set
- * @see #version
- */
- public void setVersion(String version) {
- this.version = version;
- }
-
- /**
- * @return the sourceUrl
- * @see #sourceUrl
- */
- public String getSourceUrl() {
- return sourceUrl;
- }
-
- /**
- * @param sourceUrl
- * the sourceUrl to set
- * @see #sourceUrl
- */
- public void setSourceUrl(String sourceUrl) {
- this.sourceUrl = sourceUrl;
- }
-
- /**
- * @return the downloadProgress
- * @see #downloadProgress
- */
- public double getDownloadProgress() {
- return downloadProgress;
- }
-
- /**
- * @param downloadProgress
- * the downloadProgress to set
- * @see #downloadProgress
- */
- public void setDownloadProgress(double downloadProgress) {
- this.downloadProgress = downloadProgress;
- }
-
- /**
- * @return the id
- * @see #id
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
- /**
- * Adds {@link ReferenceGenomeGeneMapping gene mapping} to the reference
- * genome.
- *
- * @param mapping
- * mapping to add
- */
- public void addReferenceGenomeGeneMapping(ReferenceGenomeGeneMapping mapping) {
- geneMapping.add(mapping);
- mapping.setReferenceGenome(this);
- }
-
- /**
- * @return the geneMapping
- * @see #geneMapping
- */
- public List<ReferenceGenomeGeneMapping> getGeneMapping() {
- return geneMapping;
- }
-
- /**
- * @param geneMapping
- * the geneMapping to set
- * @see #geneMapping
- */
- public void setGeneMapping(List<ReferenceGenomeGeneMapping> geneMapping) {
- this.geneMapping = geneMapping;
- }
-}
+package lcsb.mapviewer.model.map.layout;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.EnumType;
+import javax.persistence.Enumerated;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.OneToMany;
+import javax.persistence.OneToOne;
+import javax.persistence.OrderBy;
+import javax.persistence.Table;
+
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+
+import lcsb.mapviewer.model.map.MiriamData;
+
+/**
+ * Reference genome describes data used as reference genome. This data is
+ * obtained usually from exteral server, database. Right now we support only
+ * .2bit file format.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "reference_genome")
+public class ReferenceGenome implements Serializable {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Unique local database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * Organism for which the genome is provided.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToOne
+ private MiriamData organism;
+
+ /**
+ * Type of reference genome. This describe source (database) from which
+ * reference genome was taken.
+ */
+ @Enumerated(EnumType.STRING)
+ private ReferenceGenomeType type;
+
+ /**
+ * Version of the reference genome (databases have different releases, this
+ * string represent specific release of data).
+ */
+ private String version;
+
+ /**
+ * How much of the file we already downloaded.
+ */
+ private double downloadProgress;
+
+ /**
+ * Source url used to obtain data.
+ */
+ private String sourceUrl;
+
+ /**
+ * List of differente mappings to this genome. Reference genome is a string
+ * containing nucleotides. However interpretation of these nucleotides is a
+ * different thing. Many databases provides different mappings between genes
+ * and genome (even for the same genome). Therefore we allow to have more gene
+ * mappings.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(fetch = FetchType.EAGER, mappedBy = "referenceGenome", orphanRemoval = true)
+ @OrderBy("id")
+ private List<ReferenceGenomeGeneMapping> geneMapping = new ArrayList<>();
+
+ /**
+ * @return the type
+ * @see #type
+ */
+ public ReferenceGenomeType getType() {
+ return type;
+ }
+
+ /**
+ * @param type
+ * the type to set
+ * @see #type
+ */
+ public void setType(ReferenceGenomeType type) {
+ this.type = type;
+ }
+
+ /**
+ * @return the organism
+ * @see #organism
+ */
+ public MiriamData getOrganism() {
+ return organism;
+ }
+
+ /**
+ * @param organism
+ * the organism to set
+ * @see #organism
+ */
+ public void setOrganism(MiriamData organism) {
+ this.organism = organism;
+ }
+
+ /**
+ * @return the version
+ * @see #version
+ */
+ public String getVersion() {
+ return version;
+ }
+
+ /**
+ * @param version
+ * the version to set
+ * @see #version
+ */
+ public void setVersion(String version) {
+ this.version = version;
+ }
+
+ /**
+ * @return the sourceUrl
+ * @see #sourceUrl
+ */
+ public String getSourceUrl() {
+ return sourceUrl;
+ }
+
+ /**
+ * @param sourceUrl
+ * the sourceUrl to set
+ * @see #sourceUrl
+ */
+ public void setSourceUrl(String sourceUrl) {
+ this.sourceUrl = sourceUrl;
+ }
+
+ /**
+ * @return the downloadProgress
+ * @see #downloadProgress
+ */
+ public double getDownloadProgress() {
+ return downloadProgress;
+ }
+
+ /**
+ * @param downloadProgress
+ * the downloadProgress to set
+ * @see #downloadProgress
+ */
+ public void setDownloadProgress(double downloadProgress) {
+ this.downloadProgress = downloadProgress;
+ }
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ /**
+ * Adds {@link ReferenceGenomeGeneMapping gene mapping} to the reference
+ * genome.
+ *
+ * @param mapping
+ * mapping to add
+ */
+ public void addReferenceGenomeGeneMapping(ReferenceGenomeGeneMapping mapping) {
+ geneMapping.add(mapping);
+ mapping.setReferenceGenome(this);
+ }
+
+ /**
+ * @return the geneMapping
+ * @see #geneMapping
+ */
+ public List<ReferenceGenomeGeneMapping> getGeneMapping() {
+ return geneMapping;
+ }
+
+ /**
+ * @param geneMapping
+ * the geneMapping to set
+ * @see #geneMapping
+ */
+ public void setGeneMapping(List<ReferenceGenomeGeneMapping> geneMapping) {
+ this.geneMapping = geneMapping;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/ReferenceGenomeGeneMapping.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/ReferenceGenomeGeneMapping.java
index fcd86b2a1a..20e25086e8 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/ReferenceGenomeGeneMapping.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/ReferenceGenomeGeneMapping.java
@@ -1,146 +1,146 @@
-package lcsb.mapviewer.model.map.layout;
-
-import java.io.Serializable;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-
-/**
- * This object defines information about mapping genes to gene. This data is
- * stored in external file (from some database, server, etc.). For now this file
- * should be in
- * <a href="https://genome.ucsc.edu/goldenpath/help/bigBed.html">big bed
- * format</a>.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "reference_genome_gene_mapping")
-public class ReferenceGenomeGeneMapping implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Unique local database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- /**
- * {@link ReferenceGenome Reference genome} for which gene mapping is
- * provided.
- */
- @ManyToOne(fetch = FetchType.LAZY)
- private ReferenceGenome referenceGenome;
-
- /**
- * Name of the mapping.
- */
- private String name;
-
- /**
- * Url to source file which provides mapping.
- */
- private String sourceUrl;
-
- /**
- * What is the progress of obtaining file.
- */
- private double downloadProgress;
-
- /**
- * @return the id
- * @see #id
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
- /**
- * @return the referenceGenome
- * @see #referenceGenome
- */
- public ReferenceGenome getReferenceGenome() {
- return referenceGenome;
- }
-
- /**
- * @param referenceGenome
- * the referenceGenome to set
- * @see #referenceGenome
- */
- public void setReferenceGenome(ReferenceGenome referenceGenome) {
- this.referenceGenome = referenceGenome;
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return the sourceUrl
- * @see #sourceUrl
- */
- public String getSourceUrl() {
- return sourceUrl;
- }
-
- /**
- * @param sourceUrl
- * the sourceUrl to set
- * @see #sourceUrl
- */
- public void setSourceUrl(String sourceUrl) {
- this.sourceUrl = sourceUrl;
- }
-
- /**
- * @return the downloadProgress
- * @see #downloadProgress
- */
- public double getDownloadProgress() {
- return downloadProgress;
- }
-
- /**
- * @param downloadProgress
- * the downloadProgress to set
- * @see #downloadProgress
- */
- public void setDownloadProgress(double downloadProgress) {
- this.downloadProgress = downloadProgress;
- }
-}
+package lcsb.mapviewer.model.map.layout;
+
+import java.io.Serializable;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+
+/**
+ * This object defines information about mapping genes to gene. This data is
+ * stored in external file (from some database, server, etc.). For now this file
+ * should be in
+ * <a href="https://genome.ucsc.edu/goldenpath/help/bigBed.html">big bed
+ * format</a>.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "reference_genome_gene_mapping")
+public class ReferenceGenomeGeneMapping implements Serializable {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Unique local database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * {@link ReferenceGenome Reference genome} for which gene mapping is
+ * provided.
+ */
+ @ManyToOne(fetch = FetchType.LAZY)
+ private ReferenceGenome referenceGenome;
+
+ /**
+ * Name of the mapping.
+ */
+ private String name;
+
+ /**
+ * Url to source file which provides mapping.
+ */
+ private String sourceUrl;
+
+ /**
+ * What is the progress of obtaining file.
+ */
+ private double downloadProgress;
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ /**
+ * @return the referenceGenome
+ * @see #referenceGenome
+ */
+ public ReferenceGenome getReferenceGenome() {
+ return referenceGenome;
+ }
+
+ /**
+ * @param referenceGenome
+ * the referenceGenome to set
+ * @see #referenceGenome
+ */
+ public void setReferenceGenome(ReferenceGenome referenceGenome) {
+ this.referenceGenome = referenceGenome;
+ }
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * @return the sourceUrl
+ * @see #sourceUrl
+ */
+ public String getSourceUrl() {
+ return sourceUrl;
+ }
+
+ /**
+ * @param sourceUrl
+ * the sourceUrl to set
+ * @see #sourceUrl
+ */
+ public void setSourceUrl(String sourceUrl) {
+ this.sourceUrl = sourceUrl;
+ }
+
+ /**
+ * @return the downloadProgress
+ * @see #downloadProgress
+ */
+ public double getDownloadProgress() {
+ return downloadProgress;
+ }
+
+ /**
+ * @param downloadProgress
+ * the downloadProgress to set
+ * @see #downloadProgress
+ */
+ public void setDownloadProgress(double downloadProgress) {
+ this.downloadProgress = downloadProgress;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/ReferenceGenomeType.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/ReferenceGenomeType.java
index 96341430f1..608d5a2247 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/ReferenceGenomeType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/ReferenceGenomeType.java
@@ -1,37 +1,37 @@
-package lcsb.mapviewer.model.map.layout;
-
-/**
- * Defines type of reference genome.
- *
- * @author Piotr Gawron
- *
- */
-public enum ReferenceGenomeType {
- /**
- * UCSC reference genome database.
- */
- UCSC("https://genome.ucsc.edu/");
-
- /**
- * Homepage of the reference genome database.
- */
- private String homepage;
-
- /**
- * Default constructor.
- *
- * @param homepage
- * {@link #homepage}
- */
- ReferenceGenomeType(String homepage) {
- this.homepage = homepage;
- }
-
- /**
- * @return the homepage
- * @see #homepage
- */
- public String getHomepage() {
- return homepage;
- }
-}
+package lcsb.mapviewer.model.map.layout;
+
+/**
+ * Defines type of reference genome.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum ReferenceGenomeType {
+ /**
+ * UCSC reference genome database.
+ */
+ UCSC("https://genome.ucsc.edu/");
+
+ /**
+ * Homepage of the reference genome database.
+ */
+ private String homepage;
+
+ /**
+ * Default constructor.
+ *
+ * @param homepage
+ * {@link #homepage}
+ */
+ ReferenceGenomeType(String homepage) {
+ this.homepage = homepage;
+ }
+
+ /**
+ * @return the homepage
+ * @see #homepage
+ */
+ public String getHomepage() {
+ return homepage;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/Layer.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/Layer.java
index 8e8592ab18..1a9237adff 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/Layer.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/Layer.java
@@ -1,401 +1,401 @@
-package lcsb.mapviewer.model.map.layout.graphics;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.ManyToOne;
-import javax.persistence.OneToMany;
-import javax.persistence.Table;
-
-import org.apache.log4j.Logger;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-import org.hibernate.annotations.IndexColumn;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.model.ModelData;
-
-/**
- * Object representing layer with additional graphics element (like, lines,
- * texts, etc.) in the model.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "layer_table")
-public class Layer implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(Layer.class);
-
- /**
- * Unique database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- /**
- * Layer identifier (unique in single model).
- */
- private String layerId;
-
- /**
- * Layer name.
- */
- private String name;
-
- /**
- * Is the layer visible.
- */
- private boolean visible;
-
- /**
- * Is the layer locekd (can be edited).
- */
- private boolean locked;
-
- /**
- * List of text objects on the layer.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(fetch = FetchType.EAGER)
- @IndexColumn(name = "idx")
- private List<LayerText> texts = new ArrayList<LayerText>();
-
- /**
- * List of line objects on the layer.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(fetch = FetchType.EAGER)
- @IndexColumn(name = "idx")
- private List<PolylineData> lines = new ArrayList<PolylineData>();
-
- /**
- * List of rectangle objects on the layer.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(fetch = FetchType.EAGER)
- @IndexColumn(name = "idx")
- private List<LayerRect> rectangles = new ArrayList<LayerRect>();
-
- /**
- * List of oval objects on the layer.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(fetch = FetchType.EAGER)
- @IndexColumn(name = "idx")
- private List<LayerOval> ovals = new ArrayList<LayerOval>();
-
- /**
- * ModelData to which layer belongs to.
- */
- @ManyToOne(fetch = FetchType.LAZY)
- private ModelData model;
-
- /**
- * Default constructor.
- */
- public Layer() {
- }
-
- /**
- * Constructor that copies data from the parameter.
- *
- * @param layer
- * from this paramter layer data will be copied
- */
- public Layer(Layer layer) {
- layerId = layer.getLayerId();
- name = layer.getName();
- visible = layer.isVisible();
- locked = layer.isLocked();
-
- for (LayerText lt : layer.getTexts()) {
- addLayerText(lt.copy());
- }
-
- for (PolylineData lt : layer.getLines()) {
- addLayerLine(lt.copy());
- }
-
- for (LayerRect lt : layer.getRectangles()) {
- addLayerRect(lt.copy());
- }
-
- for (LayerOval lt : layer.getOvals()) {
- addLayerOval(lt.copy());
- }
-
- model = layer.getModel();
- }
-
- /**
- * Makes copy of the layer.
- *
- * @return copy of the layer
- */
- public Layer copy() {
- if (this.getClass() == Layer.class) {
- return new Layer(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- /**
- * @return the model
- * @see #model
- */
- public ModelData getModel() {
- return model;
- }
-
- /**
- * @param model
- * the model to set
- * @see #model
- */
- public void setModel(ModelData model) {
- this.model = model;
- }
-
- /**
- * @return the ovals
- * @see #ovals
- */
- public List<LayerOval> getOvals() {
- return ovals;
- }
-
- /**
- * @param ovals
- * the ovals to set
- * @see #ovals
- */
- public void setOvals(List<LayerOval> ovals) {
- this.ovals = ovals;
- }
-
- /**
- * @return the rectangles
- * @see #rectangles
- */
- public List<LayerRect> getRectangles() {
- return rectangles;
- }
-
- /**
- * @param rectangles
- * the rectangles to set
- * @see #rectangles
- */
- public void setRectangles(List<LayerRect> rectangles) {
- this.rectangles = rectangles;
- }
-
- /**
- * @return the lines
- * @see #lines
- */
- public List<PolylineData> getLines() {
- return lines;
- }
-
- /**
- * @param lines
- * the lines to set
- * @see #lines
- */
- public void setLines(List<PolylineData> lines) {
- this.lines = lines;
- }
-
- /**
- * @return the texts
- * @see #texts
- */
- public List<LayerText> getTexts() {
- return texts;
- }
-
- /**
- * @param texts
- * the texts to set
- * @see #texts
- */
- public void setTexts(List<LayerText> texts) {
- this.texts = texts;
- }
-
- /**
- * @return the locked
- * @see #locked
- */
- public boolean isLocked() {
- return locked;
- }
-
- /**
- * @param locked
- * the locked to set
- * @see #locked
- */
- public void setLocked(boolean locked) {
- this.locked = locked;
- }
-
- /**
- * @return the visible
- * @see #visible
- */
- public boolean isVisible() {
- return visible;
- }
-
- /**
- * @param visible
- * the visible to set
- * @see #visible
- */
- public void setVisible(boolean visible) {
- this.visible = visible;
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * Sets locked param from the text input.
- *
- * @param param
- * text representing true/false
- * @see #locked
- */
- public void setLocked(String param) {
- locked = param.equalsIgnoreCase("TRUE");
- }
-
- /**
- * Sets visible param from the text input.
- *
- * @param param
- * text representing true/false
- * @see #visible
- */
- public void setVisible(String param) {
- visible = param.equalsIgnoreCase("TRUE");
- }
-
- /**
- * Adds text to the layer.
- *
- * @param layerText
- * text to add
- */
- public void addLayerText(LayerText layerText) {
- texts.add(layerText);
- }
-
- /**
- * Adds rectangle to the layer.
- *
- * @param layerRect
- * rectangle to add
- */
- public void addLayerRect(LayerRect layerRect) {
- rectangles.add(layerRect);
- }
-
- /**
- * Adds oval to the layer.
- *
- * @param layerOval
- * oval to add
- */
- public void addLayerOval(LayerOval layerOval) {
- ovals.add(layerOval);
- }
-
- /**
- * Adds line to the layer.
- *
- * @param layerLine
- * line to add
- */
- public void addLayerLine(PolylineData layerLine) {
- lines.add(layerLine);
- }
-
- /**
- * @return the layerId
- * @see #layerId
- */
- public String getLayerId() {
- return layerId;
- }
-
- /**
- * @param layerId
- * the layerId to set
- * @see #layerId
- */
- public void setLayerId(String layerId) {
- this.layerId = layerId;
- }
-
- /**
- * Adds lines to the layer.
- *
- * @param lines
- * lines to add
- */
- public void addLayerLines(Collection<PolylineData> lines) {
- for (PolylineData layerLine : lines) {
- addLayerLine(layerLine);
- }
- }
-
- /**
- * Removes {@link LayerText} from {@link Layer}.
- *
- * @param toRemove
- * object to remove
- */
- public void removeLayerText(LayerText toRemove) {
- texts.remove(toRemove);
- }
-}
+package lcsb.mapviewer.model.map.layout.graphics;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
+import javax.persistence.Table;
+
+import org.apache.log4j.Logger;
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+import org.hibernate.annotations.IndexColumn;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.model.ModelData;
+
+/**
+ * Object representing layer with additional graphics element (like, lines,
+ * texts, etc.) in the model.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "layer_table")
+public class Layer implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(Layer.class);
+
+ /**
+ * Unique database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * Layer identifier (unique in single model).
+ */
+ private String layerId;
+
+ /**
+ * Layer name.
+ */
+ private String name;
+
+ /**
+ * Is the layer visible.
+ */
+ private boolean visible;
+
+ /**
+ * Is the layer locekd (can be edited).
+ */
+ private boolean locked;
+
+ /**
+ * List of text objects on the layer.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(fetch = FetchType.EAGER)
+ @IndexColumn(name = "idx")
+ private List<LayerText> texts = new ArrayList<LayerText>();
+
+ /**
+ * List of line objects on the layer.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(fetch = FetchType.EAGER)
+ @IndexColumn(name = "idx")
+ private List<PolylineData> lines = new ArrayList<PolylineData>();
+
+ /**
+ * List of rectangle objects on the layer.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(fetch = FetchType.EAGER)
+ @IndexColumn(name = "idx")
+ private List<LayerRect> rectangles = new ArrayList<LayerRect>();
+
+ /**
+ * List of oval objects on the layer.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(fetch = FetchType.EAGER)
+ @IndexColumn(name = "idx")
+ private List<LayerOval> ovals = new ArrayList<LayerOval>();
+
+ /**
+ * ModelData to which layer belongs to.
+ */
+ @ManyToOne(fetch = FetchType.LAZY)
+ private ModelData model;
+
+ /**
+ * Default constructor.
+ */
+ public Layer() {
+ }
+
+ /**
+ * Constructor that copies data from the parameter.
+ *
+ * @param layer
+ * from this paramter layer data will be copied
+ */
+ public Layer(Layer layer) {
+ layerId = layer.getLayerId();
+ name = layer.getName();
+ visible = layer.isVisible();
+ locked = layer.isLocked();
+
+ for (LayerText lt : layer.getTexts()) {
+ addLayerText(lt.copy());
+ }
+
+ for (PolylineData lt : layer.getLines()) {
+ addLayerLine(lt.copy());
+ }
+
+ for (LayerRect lt : layer.getRectangles()) {
+ addLayerRect(lt.copy());
+ }
+
+ for (LayerOval lt : layer.getOvals()) {
+ addLayerOval(lt.copy());
+ }
+
+ model = layer.getModel();
+ }
+
+ /**
+ * Makes copy of the layer.
+ *
+ * @return copy of the layer
+ */
+ public Layer copy() {
+ if (this.getClass() == Layer.class) {
+ return new Layer(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ /**
+ * @return the model
+ * @see #model
+ */
+ public ModelData getModel() {
+ return model;
+ }
+
+ /**
+ * @param model
+ * the model to set
+ * @see #model
+ */
+ public void setModel(ModelData model) {
+ this.model = model;
+ }
+
+ /**
+ * @return the ovals
+ * @see #ovals
+ */
+ public List<LayerOval> getOvals() {
+ return ovals;
+ }
+
+ /**
+ * @param ovals
+ * the ovals to set
+ * @see #ovals
+ */
+ public void setOvals(List<LayerOval> ovals) {
+ this.ovals = ovals;
+ }
+
+ /**
+ * @return the rectangles
+ * @see #rectangles
+ */
+ public List<LayerRect> getRectangles() {
+ return rectangles;
+ }
+
+ /**
+ * @param rectangles
+ * the rectangles to set
+ * @see #rectangles
+ */
+ public void setRectangles(List<LayerRect> rectangles) {
+ this.rectangles = rectangles;
+ }
+
+ /**
+ * @return the lines
+ * @see #lines
+ */
+ public List<PolylineData> getLines() {
+ return lines;
+ }
+
+ /**
+ * @param lines
+ * the lines to set
+ * @see #lines
+ */
+ public void setLines(List<PolylineData> lines) {
+ this.lines = lines;
+ }
+
+ /**
+ * @return the texts
+ * @see #texts
+ */
+ public List<LayerText> getTexts() {
+ return texts;
+ }
+
+ /**
+ * @param texts
+ * the texts to set
+ * @see #texts
+ */
+ public void setTexts(List<LayerText> texts) {
+ this.texts = texts;
+ }
+
+ /**
+ * @return the locked
+ * @see #locked
+ */
+ public boolean isLocked() {
+ return locked;
+ }
+
+ /**
+ * @param locked
+ * the locked to set
+ * @see #locked
+ */
+ public void setLocked(boolean locked) {
+ this.locked = locked;
+ }
+
+ /**
+ * @return the visible
+ * @see #visible
+ */
+ public boolean isVisible() {
+ return visible;
+ }
+
+ /**
+ * @param visible
+ * the visible to set
+ * @see #visible
+ */
+ public void setVisible(boolean visible) {
+ this.visible = visible;
+ }
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * Sets locked param from the text input.
+ *
+ * @param param
+ * text representing true/false
+ * @see #locked
+ */
+ public void setLocked(String param) {
+ locked = param.equalsIgnoreCase("TRUE");
+ }
+
+ /**
+ * Sets visible param from the text input.
+ *
+ * @param param
+ * text representing true/false
+ * @see #visible
+ */
+ public void setVisible(String param) {
+ visible = param.equalsIgnoreCase("TRUE");
+ }
+
+ /**
+ * Adds text to the layer.
+ *
+ * @param layerText
+ * text to add
+ */
+ public void addLayerText(LayerText layerText) {
+ texts.add(layerText);
+ }
+
+ /**
+ * Adds rectangle to the layer.
+ *
+ * @param layerRect
+ * rectangle to add
+ */
+ public void addLayerRect(LayerRect layerRect) {
+ rectangles.add(layerRect);
+ }
+
+ /**
+ * Adds oval to the layer.
+ *
+ * @param layerOval
+ * oval to add
+ */
+ public void addLayerOval(LayerOval layerOval) {
+ ovals.add(layerOval);
+ }
+
+ /**
+ * Adds line to the layer.
+ *
+ * @param layerLine
+ * line to add
+ */
+ public void addLayerLine(PolylineData layerLine) {
+ lines.add(layerLine);
+ }
+
+ /**
+ * @return the layerId
+ * @see #layerId
+ */
+ public String getLayerId() {
+ return layerId;
+ }
+
+ /**
+ * @param layerId
+ * the layerId to set
+ * @see #layerId
+ */
+ public void setLayerId(String layerId) {
+ this.layerId = layerId;
+ }
+
+ /**
+ * Adds lines to the layer.
+ *
+ * @param lines
+ * lines to add
+ */
+ public void addLayerLines(Collection<PolylineData> lines) {
+ for (PolylineData layerLine : lines) {
+ addLayerLine(layerLine);
+ }
+ }
+
+ /**
+ * Removes {@link LayerText} from {@link Layer}.
+ *
+ * @param toRemove
+ * object to remove
+ */
+ public void removeLayerText(LayerText toRemove) {
+ texts.remove(toRemove);
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerComparator.java
index 222ab0a8f7..6a13ef28ed 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerComparator.java
@@ -1,131 +1,131 @@
-package lcsb.mapviewer.model.map.layout.graphics;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.BooleanComparator;
-import lcsb.mapviewer.common.comparator.IntegerComparator;
-import lcsb.mapviewer.common.comparator.StringComparator;
-import lcsb.mapviewer.model.graphics.PolylineDataComparator;
-
-/**
- * Comparator of {@link Layer} class.
- *
- * @author Piotr Gawron
- *
- *
- */
-public class LayerComparator extends Comparator<Layer> {
-
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(LayerComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public LayerComparator(double epsilon) {
- super(Layer.class, true);
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public LayerComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected int internalCompare(Layer arg0, Layer arg1) {
- StringComparator stringComparator = new StringComparator();
- BooleanComparator booleanComparator = new BooleanComparator();
- IntegerComparator integerComparator = new IntegerComparator();
-
- if (stringComparator.compare(arg0.getLayerId(), arg1.getLayerId()) != 0) {
- logger.debug("layer ids different: " + arg0.getLayerId() + ", " + arg1.getLayerId());
- return stringComparator.compare(arg0.getLayerId(), arg1.getLayerId());
- }
-
- if (stringComparator.compare(arg0.getName(), arg1.getName()) != 0) {
- logger.debug("layer name different: " + arg0.getName() + ", " + arg1.getName());
- return stringComparator.compare(arg0.getName(), arg1.getName());
- }
-
- if (booleanComparator.compare(arg0.isVisible(), arg1.isVisible()) != 0) {
- logger.debug("layer visibility different: " + arg0.isVisible() + ", " + arg1.isVisible());
- return booleanComparator.compare(arg0.isVisible(), arg1.isVisible());
- }
-
- if (booleanComparator.compare(arg0.isLocked(), arg1.isLocked()) != 0) {
- logger.debug("layer locked different: " + arg0.isLocked() + ", " + arg1.isLocked());
- return booleanComparator.compare(arg0.isLocked(), arg1.isLocked());
- }
-
- if (integerComparator.compare(arg0.getTexts().size(), arg1.getTexts().size()) != 0) {
- logger.debug("layer texts different: " + arg0.getTexts().size() + ", " + arg1.getTexts().size());
- return integerComparator.compare(arg0.getTexts().size(), arg1.getTexts().size());
- }
- if (integerComparator.compare(arg0.getLines().size(), arg1.getLines().size()) != 0) {
- logger.debug("layer lines different: " + arg0.getLines().size() + ", " + arg1.getLines().size());
- return integerComparator.compare(arg0.getLines().size(), arg1.getLines().size());
- }
- if (integerComparator.compare(arg0.getRectangles().size(), arg1.getRectangles().size()) != 0) {
- logger.debug("layer rectangles different: " + arg0.getRectangles().size() + ", " + arg1.getRectangles().size());
- return integerComparator.compare(arg0.getRectangles().size(), arg1.getRectangles().size());
- }
- if (integerComparator.compare(arg0.getOvals().size(), arg1.getOvals().size()) != 0) {
- logger.debug("layer ovals different: " + arg0.getOvals().size() + ", " + arg1.getOvals().size());
- return integerComparator.compare(arg0.getOvals().size(), arg1.getOvals().size());
- }
-
- LayerTextComparator textComparator = new LayerTextComparator(epsilon);
- for (int i = 0; i < arg0.getTexts().size(); i++) {
- int status = textComparator.compare(arg0.getTexts().get(i), arg1.getTexts().get(i));
- if (status != 0) {
- logger.debug("layer texts different");
- return status;
- }
- }
-
- LayerOvalComparator ovalComparator = new LayerOvalComparator(epsilon);
- for (int i = 0; i < arg0.getOvals().size(); i++) {
- int status = ovalComparator.compare(arg0.getOvals().get(i), arg1.getOvals().get(i));
- if (status != 0) {
- logger.debug("layer ovals different");
- return status;
- }
- }
-
- LayerRectComparator rectComparator = new LayerRectComparator(epsilon);
- for (int i = 0; i < arg0.getRectangles().size(); i++) {
- int status = rectComparator.compare(arg0.getRectangles().get(i), arg1.getRectangles().get(i));
- if (status != 0) {
- logger.debug("layer rectangles different ");
- return status;
- }
- }
-
- PolylineDataComparator lineComparator = new PolylineDataComparator(epsilon);
- for (int i = 0; i < arg0.getLines().size(); i++) {
- int status = lineComparator.compare(arg0.getLines().get(i), arg1.getLines().get(i));
- if (status != 0) {
- logger.debug("layer lines different ");
- return status;
- }
- }
-
- return 0;
- }
-
-}
+package lcsb.mapviewer.model.map.layout.graphics;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.BooleanComparator;
+import lcsb.mapviewer.common.comparator.IntegerComparator;
+import lcsb.mapviewer.common.comparator.StringComparator;
+import lcsb.mapviewer.model.graphics.PolylineDataComparator;
+
+/**
+ * Comparator of {@link Layer} class.
+ *
+ * @author Piotr Gawron
+ *
+ *
+ */
+public class LayerComparator extends Comparator<Layer> {
+
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(LayerComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public LayerComparator(double epsilon) {
+ super(Layer.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public LayerComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(Layer arg0, Layer arg1) {
+ StringComparator stringComparator = new StringComparator();
+ BooleanComparator booleanComparator = new BooleanComparator();
+ IntegerComparator integerComparator = new IntegerComparator();
+
+ if (stringComparator.compare(arg0.getLayerId(), arg1.getLayerId()) != 0) {
+ logger.debug("layer ids different: " + arg0.getLayerId() + ", " + arg1.getLayerId());
+ return stringComparator.compare(arg0.getLayerId(), arg1.getLayerId());
+ }
+
+ if (stringComparator.compare(arg0.getName(), arg1.getName()) != 0) {
+ logger.debug("layer name different: " + arg0.getName() + ", " + arg1.getName());
+ return stringComparator.compare(arg0.getName(), arg1.getName());
+ }
+
+ if (booleanComparator.compare(arg0.isVisible(), arg1.isVisible()) != 0) {
+ logger.debug("layer visibility different: " + arg0.isVisible() + ", " + arg1.isVisible());
+ return booleanComparator.compare(arg0.isVisible(), arg1.isVisible());
+ }
+
+ if (booleanComparator.compare(arg0.isLocked(), arg1.isLocked()) != 0) {
+ logger.debug("layer locked different: " + arg0.isLocked() + ", " + arg1.isLocked());
+ return booleanComparator.compare(arg0.isLocked(), arg1.isLocked());
+ }
+
+ if (integerComparator.compare(arg0.getTexts().size(), arg1.getTexts().size()) != 0) {
+ logger.debug("layer texts different: " + arg0.getTexts().size() + ", " + arg1.getTexts().size());
+ return integerComparator.compare(arg0.getTexts().size(), arg1.getTexts().size());
+ }
+ if (integerComparator.compare(arg0.getLines().size(), arg1.getLines().size()) != 0) {
+ logger.debug("layer lines different: " + arg0.getLines().size() + ", " + arg1.getLines().size());
+ return integerComparator.compare(arg0.getLines().size(), arg1.getLines().size());
+ }
+ if (integerComparator.compare(arg0.getRectangles().size(), arg1.getRectangles().size()) != 0) {
+ logger.debug("layer rectangles different: " + arg0.getRectangles().size() + ", " + arg1.getRectangles().size());
+ return integerComparator.compare(arg0.getRectangles().size(), arg1.getRectangles().size());
+ }
+ if (integerComparator.compare(arg0.getOvals().size(), arg1.getOvals().size()) != 0) {
+ logger.debug("layer ovals different: " + arg0.getOvals().size() + ", " + arg1.getOvals().size());
+ return integerComparator.compare(arg0.getOvals().size(), arg1.getOvals().size());
+ }
+
+ LayerTextComparator textComparator = new LayerTextComparator(epsilon);
+ for (int i = 0; i < arg0.getTexts().size(); i++) {
+ int status = textComparator.compare(arg0.getTexts().get(i), arg1.getTexts().get(i));
+ if (status != 0) {
+ logger.debug("layer texts different");
+ return status;
+ }
+ }
+
+ LayerOvalComparator ovalComparator = new LayerOvalComparator(epsilon);
+ for (int i = 0; i < arg0.getOvals().size(); i++) {
+ int status = ovalComparator.compare(arg0.getOvals().get(i), arg1.getOvals().get(i));
+ if (status != 0) {
+ logger.debug("layer ovals different");
+ return status;
+ }
+ }
+
+ LayerRectComparator rectComparator = new LayerRectComparator(epsilon);
+ for (int i = 0; i < arg0.getRectangles().size(); i++) {
+ int status = rectComparator.compare(arg0.getRectangles().get(i), arg1.getRectangles().get(i));
+ if (status != 0) {
+ logger.debug("layer rectangles different ");
+ return status;
+ }
+ }
+
+ PolylineDataComparator lineComparator = new PolylineDataComparator(epsilon);
+ for (int i = 0; i < arg0.getLines().size(); i++) {
+ int status = lineComparator.compare(arg0.getLines().get(i), arg1.getLines().get(i));
+ if (status != 0) {
+ logger.debug("layer lines different ");
+ return status;
+ }
+ }
+
+ return 0;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerOval.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerOval.java
index 7b8a629155..28f43d4492 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerOval.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerOval.java
@@ -1,262 +1,262 @@
-package lcsb.mapviewer.model.map.layout.graphics;
-
-import java.awt.Color;
-import java.io.Serializable;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-/**
- * This class describes ellipse in the layer.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-public class LayerOval implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(LayerOval.class);
-
- /**
- * Unique database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- /**
- * Color of the oval.
- */
- private Color color;
-
- /**
- * X coordinate of the top left ccorner of the ellipse.
- */
- private Double x = 0.0;
-
- /**
- * Y coordinate of the top left ccorner of the ellipse.
- */
- private Double y = 0.0;
-
- /**
- * Width of the ellipse.
- */
- private Double width = 0.0;
-
- /**
- * Height of the ellipse.
- */
- private Double height = 0.0;
-
- /**
- * Default constructor.
- */
- public LayerOval() {
-
- }
-
- /**
- * Constructor that copies data from the parameter.
- *
- * @param layerOval
- * from this paramter line data will be copied
- */
- public LayerOval(LayerOval layerOval) {
- this.color = layerOval.getColor();
- this.x = layerOval.getX();
- this.y = layerOval.getX();
- this.width = layerOval.getWidth();
- this.height = layerOval.getHeight();
- }
-
- /**
- * Set x from string containing double value.
- *
- * @param param
- * x of the line in text format
- */
- public void setX(String param) {
- try {
- x = Double.parseDouble(param);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid x value: " + param, e);
- }
- }
-
- /**
- * Set y from string containing double value.
- *
- * @param param
- * y of the line in text format
- */
- public void setY(String param) {
- try {
- y = Double.parseDouble(param);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid y value: " + param, e);
- }
- }
-
- /**
- * Set width from string containing double value.
- *
- * @param param
- * width of the line in text format
- */
- public void setWidth(String param) {
- try {
- width = Double.parseDouble(param);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid width value: " + param, e);
- }
- }
-
- /**
- * Set height from string containing double value.
- *
- * @param param
- * height of the line in text format
- */
- public void setHeight(String param) {
- try {
- height = Double.parseDouble(param);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid height value: " + param, e);
- }
- }
-
- /**
- * Prepares a copy of the object.
- *
- * @return copy of LayerOval
- */
- public LayerOval copy() {
- if (this.getClass() == LayerOval.class) {
- return new LayerOval(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- /**
- * @return the id
- * @see #id
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
- /**
- * @return the color
- * @see #color
- */
- public Color getColor() {
- return color;
- }
-
- /**
- * @param color
- * the color to set
- * @see #color
- */
- public void setColor(Color color) {
- this.color = color;
- }
-
- /**
- * @return the x
- * @see #x
- */
- public Double getX() {
- return x;
- }
-
- /**
- * @param x
- * the x to set
- * @see #x
- */
- public void setX(Double x) {
- this.x = x;
- }
-
- /**
- * @return the y
- * @see #y
- */
- public Double getY() {
- return y;
- }
-
- /**
- * @param y
- * the y to set
- * @see #y
- */
- public void setY(Double y) {
- this.y = y;
- }
-
- /**
- * @return the width
- * @see #width
- */
- public Double getWidth() {
- return width;
- }
-
- /**
- * @param width
- * the width to set
- * @see #width
- */
- public void setWidth(Double width) {
- this.width = width;
- }
-
- /**
- * @return the height
- * @see #height
- */
- public Double getHeight() {
- return height;
- }
-
- /**
- * @param height
- * the height to set
- * @see #height
- */
- public void setHeight(Double height) {
- this.height = height;
- }
-
-}
+package lcsb.mapviewer.model.map.layout.graphics;
+
+import java.awt.Color;
+import java.io.Serializable;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * This class describes ellipse in the layer.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+public class LayerOval implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(LayerOval.class);
+
+ /**
+ * Unique database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * Color of the oval.
+ */
+ private Color color;
+
+ /**
+ * X coordinate of the top left ccorner of the ellipse.
+ */
+ private Double x = 0.0;
+
+ /**
+ * Y coordinate of the top left ccorner of the ellipse.
+ */
+ private Double y = 0.0;
+
+ /**
+ * Width of the ellipse.
+ */
+ private Double width = 0.0;
+
+ /**
+ * Height of the ellipse.
+ */
+ private Double height = 0.0;
+
+ /**
+ * Default constructor.
+ */
+ public LayerOval() {
+
+ }
+
+ /**
+ * Constructor that copies data from the parameter.
+ *
+ * @param layerOval
+ * from this paramter line data will be copied
+ */
+ public LayerOval(LayerOval layerOval) {
+ this.color = layerOval.getColor();
+ this.x = layerOval.getX();
+ this.y = layerOval.getX();
+ this.width = layerOval.getWidth();
+ this.height = layerOval.getHeight();
+ }
+
+ /**
+ * Set x from string containing double value.
+ *
+ * @param param
+ * x of the line in text format
+ */
+ public void setX(String param) {
+ try {
+ x = Double.parseDouble(param);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid x value: " + param, e);
+ }
+ }
+
+ /**
+ * Set y from string containing double value.
+ *
+ * @param param
+ * y of the line in text format
+ */
+ public void setY(String param) {
+ try {
+ y = Double.parseDouble(param);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid y value: " + param, e);
+ }
+ }
+
+ /**
+ * Set width from string containing double value.
+ *
+ * @param param
+ * width of the line in text format
+ */
+ public void setWidth(String param) {
+ try {
+ width = Double.parseDouble(param);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid width value: " + param, e);
+ }
+ }
+
+ /**
+ * Set height from string containing double value.
+ *
+ * @param param
+ * height of the line in text format
+ */
+ public void setHeight(String param) {
+ try {
+ height = Double.parseDouble(param);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid height value: " + param, e);
+ }
+ }
+
+ /**
+ * Prepares a copy of the object.
+ *
+ * @return copy of LayerOval
+ */
+ public LayerOval copy() {
+ if (this.getClass() == LayerOval.class) {
+ return new LayerOval(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ /**
+ * @return the color
+ * @see #color
+ */
+ public Color getColor() {
+ return color;
+ }
+
+ /**
+ * @param color
+ * the color to set
+ * @see #color
+ */
+ public void setColor(Color color) {
+ this.color = color;
+ }
+
+ /**
+ * @return the x
+ * @see #x
+ */
+ public Double getX() {
+ return x;
+ }
+
+ /**
+ * @param x
+ * the x to set
+ * @see #x
+ */
+ public void setX(Double x) {
+ this.x = x;
+ }
+
+ /**
+ * @return the y
+ * @see #y
+ */
+ public Double getY() {
+ return y;
+ }
+
+ /**
+ * @param y
+ * the y to set
+ * @see #y
+ */
+ public void setY(Double y) {
+ this.y = y;
+ }
+
+ /**
+ * @return the width
+ * @see #width
+ */
+ public Double getWidth() {
+ return width;
+ }
+
+ /**
+ * @param width
+ * the width to set
+ * @see #width
+ */
+ public void setWidth(Double width) {
+ this.width = width;
+ }
+
+ /**
+ * @return the height
+ * @see #height
+ */
+ public Double getHeight() {
+ return height;
+ }
+
+ /**
+ * @param height
+ * the height to set
+ * @see #height
+ */
+ public void setHeight(Double height) {
+ this.height = height;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerOvalComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerOvalComparator.java
index 2ef01f855d..4e036b93c7 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerOvalComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerOvalComparator.java
@@ -1,68 +1,68 @@
-package lcsb.mapviewer.model.map.layout.graphics;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.ColorComparator;
-import lcsb.mapviewer.common.comparator.DoubleComparator;
-
-/**
- * Comparator of {@link LayerOval} class.
- *
- * @author Piotr Gawron
- *
- *
- */
-public class LayerOvalComparator extends Comparator<LayerOval> {
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public LayerOvalComparator(double epsilon) {
- super(LayerOval.class, true);
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public LayerOvalComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected int internalCompare(LayerOval arg0, LayerOval arg1) {
- DoubleComparator doubleComparator = new DoubleComparator(epsilon);
- ColorComparator colorComparator = new ColorComparator();
-
- if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
- return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
- }
-
- if (doubleComparator.compare(arg0.getHeight(), arg1.getHeight()) != 0) {
- return doubleComparator.compare(arg0.getHeight(), arg1.getHeight());
- }
-
- if (doubleComparator.compare(arg0.getX(), arg1.getX()) != 0) {
- return doubleComparator.compare(arg0.getX(), arg1.getX());
- }
-
- if (doubleComparator.compare(arg0.getY(), arg1.getY()) != 0) {
- return doubleComparator.compare(arg0.getY(), arg1.getY());
- }
-
- if (colorComparator.compare(arg0.getColor(), arg1.getColor()) != 0) {
- return colorComparator.compare(arg0.getColor(), arg1.getColor());
- }
-
- return 0;
- }
-
-}
+package lcsb.mapviewer.model.map.layout.graphics;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.ColorComparator;
+import lcsb.mapviewer.common.comparator.DoubleComparator;
+
+/**
+ * Comparator of {@link LayerOval} class.
+ *
+ * @author Piotr Gawron
+ *
+ *
+ */
+public class LayerOvalComparator extends Comparator<LayerOval> {
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public LayerOvalComparator(double epsilon) {
+ super(LayerOval.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public LayerOvalComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(LayerOval arg0, LayerOval arg1) {
+ DoubleComparator doubleComparator = new DoubleComparator(epsilon);
+ ColorComparator colorComparator = new ColorComparator();
+
+ if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
+ return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
+ }
+
+ if (doubleComparator.compare(arg0.getHeight(), arg1.getHeight()) != 0) {
+ return doubleComparator.compare(arg0.getHeight(), arg1.getHeight());
+ }
+
+ if (doubleComparator.compare(arg0.getX(), arg1.getX()) != 0) {
+ return doubleComparator.compare(arg0.getX(), arg1.getX());
+ }
+
+ if (doubleComparator.compare(arg0.getY(), arg1.getY()) != 0) {
+ return doubleComparator.compare(arg0.getY(), arg1.getY());
+ }
+
+ if (colorComparator.compare(arg0.getColor(), arg1.getColor()) != 0) {
+ return colorComparator.compare(arg0.getColor(), arg1.getColor());
+ }
+
+ return 0;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerRect.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerRect.java
index 566dd11fbe..5950e68801 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerRect.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerRect.java
@@ -1,245 +1,245 @@
-package lcsb.mapviewer.model.map.layout.graphics;
-
-import java.awt.Color;
-import java.io.Serializable;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-/**
- * This class describes rectangle in the layer.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-public class LayerRect implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(LayerRect.class);
-
- /**
- * Unique database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- /**
- * Color of the rectangle.
- */
- private Color color;
-
- /**
- * X coordinate of top left corner.
- */
- private Double x = 0.0;
-
- /**
- * Y coordinate of top left corner.
- */
- private Double y = 0.0;
-
- /**
- * Width of the rectangle.
- */
- private Double width = 0.0;
-
- /**
- * Height of the rectangle.
- */
- private Double height = 0.0;
-
- /**
- * Default constructor.
- */
- public LayerRect() {
-
- }
-
- /**
- * Constructor that copies data from the parameter.
- *
- * @param layerRect
- * from this paramter line data will be copied
- */
- public LayerRect(LayerRect layerRect) {
- color = layerRect.getColor();
- x = layerRect.getX();
- y = layerRect.getY();
- width = layerRect.getWidth();
- height = layerRect.getHeight();
- }
-
- /**
- * Set x from string containing double value.
- *
- * @param param
- * x of the line in text format
- */
- public void setX(String param) {
- try {
- x = Double.parseDouble(param);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid x value: " + param, e);
- }
- }
-
- /**
- * Set y from string containing double value.
- *
- * @param param
- * y of the line in text format
- */
- public void setY(String param) {
- try {
- y = Double.parseDouble(param);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid y value: " + param, e);
- }
- }
-
- /**
- * Set width from string containing double value.
- *
- * @param param
- * width of the line in text format
- */
- public void setWidth(String param) {
- try {
- width = Double.parseDouble(param);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid width value: " + param, e);
- }
- }
-
- /**
- * Set height from string containing double value.
- *
- * @param param
- * height of the line in text format
- */
- public void setHeight(String param) {
- try {
- height = Double.parseDouble(param);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid height value: " + param, e);
- }
- }
-
- /**
- * Prepares a copy of the object.
- *
- * @return copy of LayerRect
- */
- public LayerRect copy() {
- if (this.getClass() == LayerRect.class) {
- return new LayerRect(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- /**
- * @return the color
- * @see #color
- */
- public Color getColor() {
- return color;
- }
-
- /**
- * @param color
- * the color to set
- * @see #color
- */
- public void setColor(Color color) {
- this.color = color;
- }
-
- /**
- * @return the x
- * @see #x
- */
- public Double getX() {
- return x;
- }
-
- /**
- * @param x
- * the x to set
- * @see #x
- */
- public void setX(Double x) {
- this.x = x;
- }
-
- /**
- * @return the y
- * @see #y
- */
- public Double getY() {
- return y;
- }
-
- /**
- * @param y
- * the y to set
- * @see #y
- */
- public void setY(Double y) {
- this.y = y;
- }
-
- /**
- * @return the width
- * @see #width
- */
- public Double getWidth() {
- return width;
- }
-
- /**
- * @param width
- * the width to set
- * @see #width
- */
- public void setWidth(Double width) {
- this.width = width;
- }
-
- /**
- * @return the height
- * @see #height
- */
- public Double getHeight() {
- return height;
- }
-
- /**
- * @param height
- * the height to set
- * @see #height
- */
- public void setHeight(Double height) {
- this.height = height;
- }
-
-}
+package lcsb.mapviewer.model.map.layout.graphics;
+
+import java.awt.Color;
+import java.io.Serializable;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * This class describes rectangle in the layer.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+public class LayerRect implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(LayerRect.class);
+
+ /**
+ * Unique database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * Color of the rectangle.
+ */
+ private Color color;
+
+ /**
+ * X coordinate of top left corner.
+ */
+ private Double x = 0.0;
+
+ /**
+ * Y coordinate of top left corner.
+ */
+ private Double y = 0.0;
+
+ /**
+ * Width of the rectangle.
+ */
+ private Double width = 0.0;
+
+ /**
+ * Height of the rectangle.
+ */
+ private Double height = 0.0;
+
+ /**
+ * Default constructor.
+ */
+ public LayerRect() {
+
+ }
+
+ /**
+ * Constructor that copies data from the parameter.
+ *
+ * @param layerRect
+ * from this paramter line data will be copied
+ */
+ public LayerRect(LayerRect layerRect) {
+ color = layerRect.getColor();
+ x = layerRect.getX();
+ y = layerRect.getY();
+ width = layerRect.getWidth();
+ height = layerRect.getHeight();
+ }
+
+ /**
+ * Set x from string containing double value.
+ *
+ * @param param
+ * x of the line in text format
+ */
+ public void setX(String param) {
+ try {
+ x = Double.parseDouble(param);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid x value: " + param, e);
+ }
+ }
+
+ /**
+ * Set y from string containing double value.
+ *
+ * @param param
+ * y of the line in text format
+ */
+ public void setY(String param) {
+ try {
+ y = Double.parseDouble(param);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid y value: " + param, e);
+ }
+ }
+
+ /**
+ * Set width from string containing double value.
+ *
+ * @param param
+ * width of the line in text format
+ */
+ public void setWidth(String param) {
+ try {
+ width = Double.parseDouble(param);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid width value: " + param, e);
+ }
+ }
+
+ /**
+ * Set height from string containing double value.
+ *
+ * @param param
+ * height of the line in text format
+ */
+ public void setHeight(String param) {
+ try {
+ height = Double.parseDouble(param);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid height value: " + param, e);
+ }
+ }
+
+ /**
+ * Prepares a copy of the object.
+ *
+ * @return copy of LayerRect
+ */
+ public LayerRect copy() {
+ if (this.getClass() == LayerRect.class) {
+ return new LayerRect(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ /**
+ * @return the color
+ * @see #color
+ */
+ public Color getColor() {
+ return color;
+ }
+
+ /**
+ * @param color
+ * the color to set
+ * @see #color
+ */
+ public void setColor(Color color) {
+ this.color = color;
+ }
+
+ /**
+ * @return the x
+ * @see #x
+ */
+ public Double getX() {
+ return x;
+ }
+
+ /**
+ * @param x
+ * the x to set
+ * @see #x
+ */
+ public void setX(Double x) {
+ this.x = x;
+ }
+
+ /**
+ * @return the y
+ * @see #y
+ */
+ public Double getY() {
+ return y;
+ }
+
+ /**
+ * @param y
+ * the y to set
+ * @see #y
+ */
+ public void setY(Double y) {
+ this.y = y;
+ }
+
+ /**
+ * @return the width
+ * @see #width
+ */
+ public Double getWidth() {
+ return width;
+ }
+
+ /**
+ * @param width
+ * the width to set
+ * @see #width
+ */
+ public void setWidth(Double width) {
+ this.width = width;
+ }
+
+ /**
+ * @return the height
+ * @see #height
+ */
+ public Double getHeight() {
+ return height;
+ }
+
+ /**
+ * @param height
+ * the height to set
+ * @see #height
+ */
+ public void setHeight(Double height) {
+ this.height = height;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerRectComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerRectComparator.java
index b945ac9e01..d9c00d40bb 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerRectComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerRectComparator.java
@@ -1,68 +1,68 @@
-package lcsb.mapviewer.model.map.layout.graphics;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.ColorComparator;
-import lcsb.mapviewer.common.comparator.DoubleComparator;
-
-/**
- * Compparator of {@link LayerRect} class.
- *
- * @author Piotr Gawron
- *
- *
- */
-public class LayerRectComparator extends Comparator<LayerRect> {
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public LayerRectComparator(double epsilon) {
- super(LayerRect.class, true);
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public LayerRectComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected int internalCompare(LayerRect arg0, LayerRect arg1) {
- DoubleComparator doubleComparator = new DoubleComparator(epsilon);
- ColorComparator colorComparator = new ColorComparator();
-
- if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
- return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
- }
-
- if (doubleComparator.compare(arg0.getHeight(), arg1.getHeight()) != 0) {
- return doubleComparator.compare(arg0.getHeight(), arg1.getHeight());
- }
-
- if (doubleComparator.compare(arg0.getX(), arg1.getX()) != 0) {
- return doubleComparator.compare(arg0.getX(), arg1.getX());
- }
-
- if (doubleComparator.compare(arg0.getY(), arg1.getY()) != 0) {
- return doubleComparator.compare(arg0.getY(), arg1.getY());
- }
-
- if (colorComparator.compare(arg0.getColor(), arg1.getColor()) != 0) {
- return colorComparator.compare(arg0.getColor(), arg1.getColor());
- }
-
- return 0;
- }
-
-}
+package lcsb.mapviewer.model.map.layout.graphics;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.ColorComparator;
+import lcsb.mapviewer.common.comparator.DoubleComparator;
+
+/**
+ * Compparator of {@link LayerRect} class.
+ *
+ * @author Piotr Gawron
+ *
+ *
+ */
+public class LayerRectComparator extends Comparator<LayerRect> {
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public LayerRectComparator(double epsilon) {
+ super(LayerRect.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public LayerRectComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(LayerRect arg0, LayerRect arg1) {
+ DoubleComparator doubleComparator = new DoubleComparator(epsilon);
+ ColorComparator colorComparator = new ColorComparator();
+
+ if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
+ return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
+ }
+
+ if (doubleComparator.compare(arg0.getHeight(), arg1.getHeight()) != 0) {
+ return doubleComparator.compare(arg0.getHeight(), arg1.getHeight());
+ }
+
+ if (doubleComparator.compare(arg0.getX(), arg1.getX()) != 0) {
+ return doubleComparator.compare(arg0.getX(), arg1.getX());
+ }
+
+ if (doubleComparator.compare(arg0.getY(), arg1.getY()) != 0) {
+ return doubleComparator.compare(arg0.getY(), arg1.getY());
+ }
+
+ if (colorComparator.compare(arg0.getColor(), arg1.getColor()) != 0) {
+ return colorComparator.compare(arg0.getColor(), arg1.getColor());
+ }
+
+ return 0;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerText.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerText.java
index 618c63a857..3e7cf2269f 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerText.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerText.java
@@ -1,337 +1,337 @@
-package lcsb.mapviewer.model.map.layout.graphics;
-
-import java.awt.Color;
-import java.awt.geom.Rectangle2D;
-import java.io.Serializable;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-/**
- * This class describes single text in the layer.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-public class LayerText implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default font size of the text.
- */
- private static final double DEFAULT_LAYER_FONT_SIZE = 11.0;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(LayerText.class);
-
- /**
- * Unique database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- /**
- * Text color.
- */
- private Color color = Color.BLACK;
-
- /**
- * X coordinate of text start point.
- */
- private Double x = 0.0;
-
- /**
- * Y coordinate of text start point.
- */
- private Double y = 0.0;
-
- /**
- * Width of the rectangle where text is drawn.
- */
- private Double width = 0.0;
-
- /**
- * Height of the rectangle where text is drawn.
- */
- private Double height = 0.0;
-
- /**
- * Text.
- */
- private String notes;
-
- /**
- * Font size.
- */
- private Double fontSize = DEFAULT_LAYER_FONT_SIZE;
-
- /**
- * Default constructor.
- */
- public LayerText() {
-
- }
-
- /**
- * Default constructor.
- *
- * @param bound
- * bounds in which text is placed
- * @param text
- * {@link #notes text}
- */
- public LayerText(Rectangle2D bound, String text) {
- setX(bound.getX());
- setY(bound.getY());
- setWidth(bound.getWidth());
- setHeight(bound.getHeight());
- setNotes(text);
- }
-
- /**
- * Constructor that copies data from the parameter.
- *
- * @param layerText
- * from this paramter line data will be copied
- */
- public LayerText(LayerText layerText) {
- color = layerText.getColor();
- x = layerText.getX();
- y = layerText.getY();
- width = layerText.getWidth();
- height = layerText.getHeight();
- notes = layerText.getNotes();
- fontSize = layerText.getFontSize();
- }
-
- /**
- * Set x from string containing double value.
- *
- * @param param
- * x of the line in text format
- */
- public void setX(String param) {
- try {
- x = Double.parseDouble(param);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid x value: " + param, e);
- }
- }
-
- /**
- * Set y from string containing double value.
- *
- * @param param
- * y of the line in text format
- */
- public void setY(String param) {
- try {
- y = Double.parseDouble(param);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid y value: " + param, e);
- }
- }
-
- /**
- * Set width from string containing double value.
- *
- * @param param
- * width of the line in text format
- */
- public void setWidth(String param) {
- try {
- width = Double.parseDouble(param);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid width value: " + param, e);
- }
- }
-
- /**
- * Set height from string containing double value.
- *
- * @param param
- * height of the line in text format
- */
- public void setHeight(String param) {
- try {
- height = Double.parseDouble(param);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid height value: " + param, e);
- }
- }
-
- /**
- * Set font size from string containing double value.
- *
- * @param param
- * font size of the line in text format
- */
- public void setFontSize(String param) {
- try {
- fontSize = Double.parseDouble(param);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid fontSize value: " + param, e);
- }
-
- }
-
- /**
- * Prepares a copy of the object.
- *
- * @return copy of LayerText
- */
- public LayerText copy() {
- if (this.getClass() == LayerText.class) {
- return new LayerText(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- /**
- * @return the color
- * @see #color
- */
- public Color getColor() {
- return color;
- }
-
- /**
- * @param color
- * the color to set
- * @see #color
- */
- public void setColor(Color color) {
- this.color = color;
- }
-
- /**
- * @return the x
- * @see #x
- */
- public Double getX() {
- return x;
- }
-
- /**
- * @param x
- * the x to set
- * @see #x
- */
- public void setX(Double x) {
- this.x = x;
- }
-
- /**
- * @return the y
- * @see #y
- */
- public Double getY() {
- return y;
- }
-
- /**
- * @param y
- * the y to set
- * @see #y
- */
- public void setY(Double y) {
- this.y = y;
- }
-
- /**
- * @return the width
- * @see #width
- */
- public Double getWidth() {
- return width;
- }
-
- /**
- * @param width
- * the width to set
- * @see #width
- */
- public void setWidth(Double width) {
- this.width = width;
- }
-
- /**
- * @return the height
- * @see #height
- */
- public Double getHeight() {
- return height;
- }
-
- /**
- * @param height
- * the height to set
- * @see #height
- */
- public void setHeight(Double height) {
- this.height = height;
- }
-
- /**
- * @return the notes
- * @see #notes
- */
- public String getNotes() {
- return notes;
- }
-
- /**
- * @param notes
- * the notes to set
- * @see #notes
- */
- public void setNotes(String notes) {
- this.notes = notes;
- }
-
- /**
- * @return the fontSize
- * @see #fontSize
- */
- public Double getFontSize() {
- return fontSize;
- }
-
- /**
- * @param fontSize
- * the fontSize to set
- * @see #fontSize
- */
- public void setFontSize(Double fontSize) {
- this.fontSize = fontSize;
- }
-
- /**
- * Returns a rectangle that determines a rectangle border.
- *
- * @return rectangle border
- */
- public Rectangle2D getBorder() {
- return new Rectangle2D.Double(x, y, width, height);
- }
-
-}
+package lcsb.mapviewer.model.map.layout.graphics;
+
+import java.awt.Color;
+import java.awt.geom.Rectangle2D;
+import java.io.Serializable;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * This class describes single text in the layer.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+public class LayerText implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default font size of the text.
+ */
+ private static final double DEFAULT_LAYER_FONT_SIZE = 11.0;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(LayerText.class);
+
+ /**
+ * Unique database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * Text color.
+ */
+ private Color color = Color.BLACK;
+
+ /**
+ * X coordinate of text start point.
+ */
+ private Double x = 0.0;
+
+ /**
+ * Y coordinate of text start point.
+ */
+ private Double y = 0.0;
+
+ /**
+ * Width of the rectangle where text is drawn.
+ */
+ private Double width = 0.0;
+
+ /**
+ * Height of the rectangle where text is drawn.
+ */
+ private Double height = 0.0;
+
+ /**
+ * Text.
+ */
+ private String notes;
+
+ /**
+ * Font size.
+ */
+ private Double fontSize = DEFAULT_LAYER_FONT_SIZE;
+
+ /**
+ * Default constructor.
+ */
+ public LayerText() {
+
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param bound
+ * bounds in which text is placed
+ * @param text
+ * {@link #notes text}
+ */
+ public LayerText(Rectangle2D bound, String text) {
+ setX(bound.getX());
+ setY(bound.getY());
+ setWidth(bound.getWidth());
+ setHeight(bound.getHeight());
+ setNotes(text);
+ }
+
+ /**
+ * Constructor that copies data from the parameter.
+ *
+ * @param layerText
+ * from this paramter line data will be copied
+ */
+ public LayerText(LayerText layerText) {
+ color = layerText.getColor();
+ x = layerText.getX();
+ y = layerText.getY();
+ width = layerText.getWidth();
+ height = layerText.getHeight();
+ notes = layerText.getNotes();
+ fontSize = layerText.getFontSize();
+ }
+
+ /**
+ * Set x from string containing double value.
+ *
+ * @param param
+ * x of the line in text format
+ */
+ public void setX(String param) {
+ try {
+ x = Double.parseDouble(param);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid x value: " + param, e);
+ }
+ }
+
+ /**
+ * Set y from string containing double value.
+ *
+ * @param param
+ * y of the line in text format
+ */
+ public void setY(String param) {
+ try {
+ y = Double.parseDouble(param);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid y value: " + param, e);
+ }
+ }
+
+ /**
+ * Set width from string containing double value.
+ *
+ * @param param
+ * width of the line in text format
+ */
+ public void setWidth(String param) {
+ try {
+ width = Double.parseDouble(param);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid width value: " + param, e);
+ }
+ }
+
+ /**
+ * Set height from string containing double value.
+ *
+ * @param param
+ * height of the line in text format
+ */
+ public void setHeight(String param) {
+ try {
+ height = Double.parseDouble(param);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid height value: " + param, e);
+ }
+ }
+
+ /**
+ * Set font size from string containing double value.
+ *
+ * @param param
+ * font size of the line in text format
+ */
+ public void setFontSize(String param) {
+ try {
+ fontSize = Double.parseDouble(param);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid fontSize value: " + param, e);
+ }
+
+ }
+
+ /**
+ * Prepares a copy of the object.
+ *
+ * @return copy of LayerText
+ */
+ public LayerText copy() {
+ if (this.getClass() == LayerText.class) {
+ return new LayerText(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ /**
+ * @return the color
+ * @see #color
+ */
+ public Color getColor() {
+ return color;
+ }
+
+ /**
+ * @param color
+ * the color to set
+ * @see #color
+ */
+ public void setColor(Color color) {
+ this.color = color;
+ }
+
+ /**
+ * @return the x
+ * @see #x
+ */
+ public Double getX() {
+ return x;
+ }
+
+ /**
+ * @param x
+ * the x to set
+ * @see #x
+ */
+ public void setX(Double x) {
+ this.x = x;
+ }
+
+ /**
+ * @return the y
+ * @see #y
+ */
+ public Double getY() {
+ return y;
+ }
+
+ /**
+ * @param y
+ * the y to set
+ * @see #y
+ */
+ public void setY(Double y) {
+ this.y = y;
+ }
+
+ /**
+ * @return the width
+ * @see #width
+ */
+ public Double getWidth() {
+ return width;
+ }
+
+ /**
+ * @param width
+ * the width to set
+ * @see #width
+ */
+ public void setWidth(Double width) {
+ this.width = width;
+ }
+
+ /**
+ * @return the height
+ * @see #height
+ */
+ public Double getHeight() {
+ return height;
+ }
+
+ /**
+ * @param height
+ * the height to set
+ * @see #height
+ */
+ public void setHeight(Double height) {
+ this.height = height;
+ }
+
+ /**
+ * @return the notes
+ * @see #notes
+ */
+ public String getNotes() {
+ return notes;
+ }
+
+ /**
+ * @param notes
+ * the notes to set
+ * @see #notes
+ */
+ public void setNotes(String notes) {
+ this.notes = notes;
+ }
+
+ /**
+ * @return the fontSize
+ * @see #fontSize
+ */
+ public Double getFontSize() {
+ return fontSize;
+ }
+
+ /**
+ * @param fontSize
+ * the fontSize to set
+ * @see #fontSize
+ */
+ public void setFontSize(Double fontSize) {
+ this.fontSize = fontSize;
+ }
+
+ /**
+ * Returns a rectangle that determines a rectangle border.
+ *
+ * @return rectangle border
+ */
+ public Rectangle2D getBorder() {
+ return new Rectangle2D.Double(x, y, width, height);
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerTextComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerTextComparator.java
index d0371804ac..44870e9533 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerTextComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerTextComparator.java
@@ -1,78 +1,78 @@
-package lcsb.mapviewer.model.map.layout.graphics;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.ColorComparator;
-import lcsb.mapviewer.common.comparator.DoubleComparator;
-import lcsb.mapviewer.common.comparator.StringComparator;
-
-/**
- * Compparator of {@link LayerText} class.
- *
- * @author Piotr Gawron
- *
- *
- */
-public class LayerTextComparator extends Comparator<LayerText> {
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public LayerTextComparator(double epsilon) {
- super(LayerText.class, true);
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public LayerTextComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected int internalCompare(LayerText arg0, LayerText arg1) {
- DoubleComparator doubleComparator = new DoubleComparator(epsilon);
- StringComparator stringComparator = new StringComparator();
- ColorComparator colorComparator = new ColorComparator();
-
- if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
- return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
- }
-
- if (doubleComparator.compare(arg0.getHeight(), arg1.getHeight()) != 0) {
- return doubleComparator.compare(arg0.getHeight(), arg1.getHeight());
- }
-
- if (doubleComparator.compare(arg0.getX(), arg1.getX()) != 0) {
- return doubleComparator.compare(arg0.getX(), arg1.getX());
- }
-
- if (doubleComparator.compare(arg0.getY(), arg1.getY()) != 0) {
- return doubleComparator.compare(arg0.getY(), arg1.getY());
- }
-
- if (colorComparator.compare(arg0.getColor(), arg1.getColor()) != 0) {
- return colorComparator.compare(arg0.getColor(), arg1.getColor());
- }
-
- if (stringComparator.compare(arg0.getNotes(), arg1.getNotes()) != 0) {
- return stringComparator.compare(arg0.getNotes(), arg1.getNotes());
- }
-
- if (doubleComparator.compare(arg0.getFontSize(), arg1.getFontSize()) != 0) {
- return doubleComparator.compare(arg0.getFontSize(), arg1.getFontSize());
- }
-
- return 0;
- }
-
-}
+package lcsb.mapviewer.model.map.layout.graphics;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.ColorComparator;
+import lcsb.mapviewer.common.comparator.DoubleComparator;
+import lcsb.mapviewer.common.comparator.StringComparator;
+
+/**
+ * Compparator of {@link LayerText} class.
+ *
+ * @author Piotr Gawron
+ *
+ *
+ */
+public class LayerTextComparator extends Comparator<LayerText> {
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public LayerTextComparator(double epsilon) {
+ super(LayerText.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public LayerTextComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(LayerText arg0, LayerText arg1) {
+ DoubleComparator doubleComparator = new DoubleComparator(epsilon);
+ StringComparator stringComparator = new StringComparator();
+ ColorComparator colorComparator = new ColorComparator();
+
+ if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
+ return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
+ }
+
+ if (doubleComparator.compare(arg0.getHeight(), arg1.getHeight()) != 0) {
+ return doubleComparator.compare(arg0.getHeight(), arg1.getHeight());
+ }
+
+ if (doubleComparator.compare(arg0.getX(), arg1.getX()) != 0) {
+ return doubleComparator.compare(arg0.getX(), arg1.getX());
+ }
+
+ if (doubleComparator.compare(arg0.getY(), arg1.getY()) != 0) {
+ return doubleComparator.compare(arg0.getY(), arg1.getY());
+ }
+
+ if (colorComparator.compare(arg0.getColor(), arg1.getColor()) != 0) {
+ return colorComparator.compare(arg0.getColor(), arg1.getColor());
+ }
+
+ if (stringComparator.compare(arg0.getNotes(), arg1.getNotes()) != 0) {
+ return stringComparator.compare(arg0.getNotes(), arg1.getNotes());
+ }
+
+ if (doubleComparator.compare(arg0.getFontSize(), arg1.getFontSize()) != 0) {
+ return doubleComparator.compare(arg0.getFontSize(), arg1.getFontSize());
+ }
+
+ return 0;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/package-info.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/package-info.java
index d05f2be56d..97326a877f 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/package-info.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/package-info.java
@@ -1,6 +1,6 @@
-/**
- * Provides objects for additional layers with some graphical elements (like
- * lines, rectangles, etc.).
- */
-package lcsb.mapviewer.model.map.layout.graphics;
-
+/**
+ * Provides objects for additional layers with some graphical elements (like
+ * lines, rectangles, etc.).
+ */
+package lcsb.mapviewer.model.map.layout.graphics;
+
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/package-info.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/package-info.java
index c743dea905..2d03a51ab7 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/package-info.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/package-info.java
@@ -1,6 +1,6 @@
-/**
- * Provides data structures that stores information used for data visualization
- * of the map.
- */
-package lcsb.mapviewer.model.map.layout;
-
+/**
+ * Provides data structures that stores information used for data visualization
+ * of the map.
+ */
+package lcsb.mapviewer.model.map.layout;
+
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnection.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnection.java
index 20e56a9408..c3d5cf33d9 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnection.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnection.java
@@ -1,144 +1,144 @@
-package lcsb.mapviewer.model.map.model;
-
-import java.io.Serializable;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.ManyToOne;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * This class defines connection between {@link Element} and submap (submodel).
- * This means that single {@link Element} should be "expandable" into map
- * represented by {@link SubmodelConnection#submodel} object.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("ALIAS_SUBMODEL_LINK")
-public class ElementSubmodelConnection extends SubmodelConnection implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * From which {@link Element} this connection start.
- */
- @ManyToOne
- private Element fromElement;
-
- /**
- * This object defines reference element in submodel that represents central
- * (or identical) object in reference submodel.
- */
- @ManyToOne
- private Element toElement;
-
- /**
- * Default constructor that initialize some fields.
- *
- * @param submodel
- * {@link SubmodelConnection#submodel}
- * @param type
- * {@link SubmodelConnection#type}
- */
- public ElementSubmodelConnection(ModelData submodel, SubmodelType type) {
- super(submodel, type);
- }
-
- /**
- * Default constructor that initialize some fields.
- *
- * @param model
- * {@link SubmodelConnection#submodel}
- * @param type
- * {@link SubmodelConnection#type}
- */
- public ElementSubmodelConnection(Model model, SubmodelType type) {
- super(model.getModelData(), type);
- }
-
- /**
- * Default constructor.
- */
- public ElementSubmodelConnection() {
- }
-
- /**
- * Constructor that creates copy of the {@link ElementSubmodelConnection}
- * object.
- *
- * @param original
- * original object from which copy is prepared
- */
- public ElementSubmodelConnection(ElementSubmodelConnection original) {
- super(original);
- this.setFromElement(original.getFromElement());
- this.setToElement(original.getToElement());
- }
-
- /**
- * Default constructor that initialize some fields.
- *
- * @param submodel
- * {@link SubmodelConnection#submodel}
- * @param type
- * {@link SubmodelConnection#type}
- * @param name
- * {@link SubmodelConnection#name}
- */
- public ElementSubmodelConnection(Model submodel, SubmodelType type, String name) {
- super(submodel, type, name);
- }
-
- /**
- * @return the fromElement
- * @see #fromElement
- */
- public Element getFromElement() {
- return fromElement;
- }
-
- /**
- * @param fromElement
- * the fromElement to set
- * @see #fromElement
- */
- public void setFromElement(Element fromElement) {
- this.fromElement = fromElement;
- }
-
- /**
- * @return the toElement
- * @see #toElement
- */
- public Element getToElement() {
- return toElement;
- }
-
- /**
- * @param toElement
- * the toElement to set
- * @see #toElement
- */
- public void setToElement(Element toElement) {
- this.toElement = toElement;
- }
-
- @Override
- public ElementSubmodelConnection copy() {
- if (this.getClass() == ElementSubmodelConnection.class) {
- ElementSubmodelConnection result = new ElementSubmodelConnection();
- result.assignValuesFromOriginal(this);
- result.setFromElement(this.getFromElement());
- result.setToElement(this.getToElement());
- return result;
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-}
+package lcsb.mapviewer.model.map.model;
+
+import java.io.Serializable;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+import javax.persistence.ManyToOne;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * This class defines connection between {@link Element} and submap (submodel).
+ * This means that single {@link Element} should be "expandable" into map
+ * represented by {@link SubmodelConnection#submodel} object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("ALIAS_SUBMODEL_LINK")
+public class ElementSubmodelConnection extends SubmodelConnection implements Serializable {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * From which {@link Element} this connection start.
+ */
+ @ManyToOne
+ private Element fromElement;
+
+ /**
+ * This object defines reference element in submodel that represents central
+ * (or identical) object in reference submodel.
+ */
+ @ManyToOne
+ private Element toElement;
+
+ /**
+ * Default constructor that initialize some fields.
+ *
+ * @param submodel
+ * {@link SubmodelConnection#submodel}
+ * @param type
+ * {@link SubmodelConnection#type}
+ */
+ public ElementSubmodelConnection(ModelData submodel, SubmodelType type) {
+ super(submodel, type);
+ }
+
+ /**
+ * Default constructor that initialize some fields.
+ *
+ * @param model
+ * {@link SubmodelConnection#submodel}
+ * @param type
+ * {@link SubmodelConnection#type}
+ */
+ public ElementSubmodelConnection(Model model, SubmodelType type) {
+ super(model.getModelData(), type);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public ElementSubmodelConnection() {
+ }
+
+ /**
+ * Constructor that creates copy of the {@link ElementSubmodelConnection}
+ * object.
+ *
+ * @param original
+ * original object from which copy is prepared
+ */
+ public ElementSubmodelConnection(ElementSubmodelConnection original) {
+ super(original);
+ this.setFromElement(original.getFromElement());
+ this.setToElement(original.getToElement());
+ }
+
+ /**
+ * Default constructor that initialize some fields.
+ *
+ * @param submodel
+ * {@link SubmodelConnection#submodel}
+ * @param type
+ * {@link SubmodelConnection#type}
+ * @param name
+ * {@link SubmodelConnection#name}
+ */
+ public ElementSubmodelConnection(Model submodel, SubmodelType type, String name) {
+ super(submodel, type, name);
+ }
+
+ /**
+ * @return the fromElement
+ * @see #fromElement
+ */
+ public Element getFromElement() {
+ return fromElement;
+ }
+
+ /**
+ * @param fromElement
+ * the fromElement to set
+ * @see #fromElement
+ */
+ public void setFromElement(Element fromElement) {
+ this.fromElement = fromElement;
+ }
+
+ /**
+ * @return the toElement
+ * @see #toElement
+ */
+ public Element getToElement() {
+ return toElement;
+ }
+
+ /**
+ * @param toElement
+ * the toElement to set
+ * @see #toElement
+ */
+ public void setToElement(Element toElement) {
+ this.toElement = toElement;
+ }
+
+ @Override
+ public ElementSubmodelConnection copy() {
+ if (this.getClass() == ElementSubmodelConnection.class) {
+ ElementSubmodelConnection result = new ElementSubmodelConnection();
+ result.assignValuesFromOriginal(this);
+ result.setFromElement(this.getFromElement());
+ result.setToElement(this.getToElement());
+ return result;
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnectionComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnectionComparator.java
index 15f64f78e1..f1b7c20a8c 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnectionComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnectionComparator.java
@@ -1,81 +1,81 @@
-package lcsb.mapviewer.model.map.model;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.ElementComparator;
-
-/**
- * This class implements comparator interface for
- * {@link ElementSubmodelConnection}.
- *
- * @author Piotr Gawron
- *
- */
-public class ElementSubmodelConnectionComparator extends Comparator<ElementSubmodelConnection> {
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ElementSubmodelConnectionComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public ElementSubmodelConnectionComparator(double epsilon) {
- super(ElementSubmodelConnection.class);
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public ElementSubmodelConnectionComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected Comparator<?> getParentComparator() {
- return new SubmodelConnectionComparator(epsilon);
- }
-
- @Override
- protected int internalCompare(ElementSubmodelConnection arg0, ElementSubmodelConnection arg1) {
- ElementComparator elementComparator = new ElementComparator(epsilon);
- Element element1 = arg0.getFromElement();
- Element element2 = arg1.getFromElement();
- arg0.setFromElement(null);
- arg1.setFromElement(null);
- int status = elementComparator.compare(element1, element2);
- arg0.setFromElement(element1);
- arg1.setFromElement(element2);
- if (status != 0) {
- logger.debug("from element different: " + arg0.getFromElement() + ", " + arg1.getFromElement());
- return status;
- }
- element1 = arg0.getToElement();
- element2 = arg1.getToElement();
- arg0.setToElement(null);
- arg1.setToElement(null);
- status = elementComparator.compare(element1, element2);
- arg0.setToElement(element1);
- arg1.setToElement(element2);
- if (status != 0) {
- logger.debug("to element different: " + arg0.getToElement() + ", " + arg1.getToElement());
- return status;
- }
-
- return 0;
- }
-
-}
+package lcsb.mapviewer.model.map.model;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.ElementComparator;
+
+/**
+ * This class implements comparator interface for
+ * {@link ElementSubmodelConnection}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ElementSubmodelConnectionComparator extends Comparator<ElementSubmodelConnection> {
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ElementSubmodelConnectionComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public ElementSubmodelConnectionComparator(double epsilon) {
+ super(ElementSubmodelConnection.class);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public ElementSubmodelConnectionComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new SubmodelConnectionComparator(epsilon);
+ }
+
+ @Override
+ protected int internalCompare(ElementSubmodelConnection arg0, ElementSubmodelConnection arg1) {
+ ElementComparator elementComparator = new ElementComparator(epsilon);
+ Element element1 = arg0.getFromElement();
+ Element element2 = arg1.getFromElement();
+ arg0.setFromElement(null);
+ arg1.setFromElement(null);
+ int status = elementComparator.compare(element1, element2);
+ arg0.setFromElement(element1);
+ arg1.setFromElement(element2);
+ if (status != 0) {
+ logger.debug("from element different: " + arg0.getFromElement() + ", " + arg1.getFromElement());
+ return status;
+ }
+ element1 = arg0.getToElement();
+ element2 = arg1.getToElement();
+ arg0.setToElement(null);
+ arg1.setToElement(null);
+ status = elementComparator.compare(element1, element2);
+ arg0.setToElement(element1);
+ arg1.setToElement(element2);
+ if (status != 0) {
+ logger.debug("to element different: " + arg0.getToElement() + ", " + arg1.getToElement());
+ return status;
+ }
+
+ return 0;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelComparator.java
index 9a3ba6b6fb..4055779228 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelComparator.java
@@ -1,350 +1,350 @@
-package lcsb.mapviewer.model.map.model;
-
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.DoubleComparator;
-import lcsb.mapviewer.common.comparator.IntegerComparator;
-import lcsb.mapviewer.common.comparator.SetComparator;
-import lcsb.mapviewer.common.comparator.StringComparator;
-import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
-import lcsb.mapviewer.model.map.kinetics.SbmlFunctionComparator;
-import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
-import lcsb.mapviewer.model.map.kinetics.SbmlParameterComparator;
-import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
-import lcsb.mapviewer.model.map.kinetics.SbmlUnitComparator;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.LayoutComparator;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.layout.graphics.LayerComparator;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.ReactionComparator;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.ElementComparator;
-
-/**
- * Comparator for {@link Model} class.
- *
- * @author Piotr Gawron
- *
- */
-public class ModelComparator extends Comparator<Model> {
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(ModelComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public ModelComparator(double epsilon) {
- super(Model.class);
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public ModelComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected int internalCompare(Model arg0, Model arg1) {
- StringComparator stringComparator = new StringComparator();
- DoubleComparator doubleComparator = new DoubleComparator(epsilon);
- IntegerComparator integerComparator = new IntegerComparator();
-
- if (stringComparator.compare(arg0.getIdModel(), arg1.getIdModel()) != 0) {
- logger.debug("Id different: " + arg0.getIdModel() + ", " + arg1.getIdModel());
- return stringComparator.compare(arg0.getIdModel(), arg1.getIdModel());
- }
-
- if (stringComparator.compare(arg0.getName(), arg1.getName()) != 0) {
- logger.debug("Name different: " + arg0.getName() + ", " + arg1.getName());
- return stringComparator.compare(arg0.getName(), arg1.getName());
- }
-
- if (stringComparator.compare(arg0.getNotes(), arg1.getNotes(), true) != 0) {
- logger.debug(arg0.getNotes());
- logger.debug(arg1.getNotes());
- logger.debug("Notes different:\n" + arg0.getNotes() + "\n---\n" + arg1.getNotes() + "\n---");
- return stringComparator.compare(arg0.getNotes(), arg1.getNotes(), true);
- }
-
- if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
- logger.debug("Width different: " + arg0.getWidth() + ", " + arg1.getWidth());
- return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
- }
-
- if (doubleComparator.compare(arg0.getHeight(), arg1.getHeight()) != 0) {
- logger.debug("Height different: " + arg0.getHeight() + ", " + arg1.getHeight());
- return doubleComparator.compare(arg0.getHeight(), arg1.getHeight());
- }
-
- if (integerComparator.compare(arg0.getZoomLevels(), arg1.getZoomLevels()) != 0) {
- logger.debug("Zoom levels different: " + arg0.getZoomLevels() + ", " + arg1.getZoomLevels());
- return integerComparator.compare(arg0.getZoomLevels(), arg1.getZoomLevels());
- }
-
- if (integerComparator.compare(arg0.getTileSize(), arg1.getTileSize()) != 0) {
- logger.debug("Tile size different: " + arg0.getTileSize() + ", " + arg1.getTileSize());
- return integerComparator.compare(arg0.getTileSize(), arg1.getTileSize());
- }
-
- int status = compareElements(arg0.getElements(), arg1.getElements());
- if (status != 0) {
- logger.debug("Set of elements different");
- return status;
- }
-
- status = compareLayers(arg0.getLayers(), arg1.getLayers());
- if (status != 0) {
- logger.debug("Set of layers different");
- return status;
- }
-
- SetComparator<Reaction> reactionSetComparator = new SetComparator<>(new ReactionComparator(epsilon));
- status = reactionSetComparator.compare(arg0.getReactions(), arg1.getReactions());
- if (status != 0) {
- logger.debug("Set of reactions different");
- return status;
- }
-
- status = compareLayouts(arg0.getLayouts(), arg1.getLayouts());
- if (status != 0) {
- logger.debug("Set of layouts different");
- return status;
- }
-
- status = compareSubmodels(arg0.getSubmodelConnections(), arg1.getSubmodelConnections());
- if (status != 0) {
- logger.debug("Set of submodels different");
- return status;
- }
-
- SetComparator<SbmlUnit> unitSetComparator = new SetComparator<>(new SbmlUnitComparator());
- status = unitSetComparator.compare(arg0.getUnits(), arg1.getUnits());
- if (status != 0) {
- logger.debug("units different");
- return status;
- }
- SetComparator<SbmlFunction> functionSetComparator = new SetComparator<>(new SbmlFunctionComparator());
- status = functionSetComparator.compare(arg0.getFunctions(), arg1.getFunctions());
- if (status != 0) {
- logger.debug("functions different");
- return status;
- }
- SetComparator<SbmlParameter> parameterSetComparator = new SetComparator<>(new SbmlParameterComparator());
- status = parameterSetComparator.compare(arg0.getParameters(), arg1.getParameters());
- if (status != 0) {
- logger.debug("parameters different");
- return status;
- }
- return 0;
- }
-
- /**
- * Compares two sets of layers.
- *
- * @param layers
- * first set of layers
- * @param layers2
- * second set of layers
- * @return if sets are equal then returns 0. If they are different then -1/1 is
- * returned.
- */
- private int compareLayers(Set<Layer> layers, Set<Layer> layers2) {
- LayerComparator layerComparator = new LayerComparator(epsilon);
- for (Layer layer : layers) {
- boolean found = false;
- for (Layer layer2 : layers2) {
- if (layerComparator.compare(layer, layer2) == 0) {
- found = true;
- }
- }
- if (!found) {
- return 1;
- }
- }
- for (Layer layer : layers2) {
- boolean found = false;
- for (Layer layer2 : layers) {
- if (layerComparator.compare(layer, layer2) == 0) {
- found = true;
- }
- }
- if (!found) {
- return -1;
- }
- }
- return 0;
- }
-
- /**
- * Compares two sets of layouts.
- *
- * @param layouts
- * first set of layouts
- * @param layouts2
- * second set of layouts
- * @return if sets are equal then returns 0. If they are different then -1/1 is
- * returned.
- */
- private int compareLayouts(List<Layout> layouts, List<Layout> layouts2) {
- LayoutComparator layoutComparator = new LayoutComparator(epsilon);
- for (Layout layout : layouts) {
- boolean found = false;
- for (Layout layout2 : layouts2) {
- if (layoutComparator.compare(layout, layout2) == 0) {
- found = true;
- }
- }
- if (!found) {
- return 1;
- }
- }
- for (Layout layout : layouts2) {
- boolean found = false;
- for (Layout layout2 : layouts) {
- if (layoutComparator.compare(layout, layout2) == 0) {
- found = true;
- }
- }
- if (!found) {
- return -1;
- }
- }
- return 0;
- }
-
- /**
- * Compares two sets of elements.
- *
- * @param elements
- * first set of elements
- * @param elements2
- * second set of elements
- * @return if sets are equal then returns 0. If they are different then -1/1 is
- * returned.
- */
- private int compareElements(Set<Element> elements, Set<Element> elements2) {
- ElementComparator elementComparator = new ElementComparator(epsilon);
-
- Map<String, Element> map1 = new HashMap<>();
- Map<String, Element> map2 = new HashMap<>();
-
- if (elements.size() != elements2.size()) {
- logger.debug("Number of elements different: " + elements.size() + ", " + elements2.size());
- return ((Integer) elements.size()).compareTo(elements2.size());
- }
-
- for (Element element : elements) {
- map1.put(element.getElementId(), element);
- }
-
- for (Element element : elements2) {
- map2.put(element.getElementId(), element);
- }
-
- for (Element element : elements) {
- int status = elementComparator.compare(element, map2.get(element.getElementId()));
- if (status != 0) {
- logger
- .debug("Element doesn't have a match: " + element.getElementId() + ", " + map2.get(element.getElementId()));
- return status;
- }
- }
-
- for (Element element : elements2) {
- int status = elementComparator.compare(element, map1.get(element.getElementId()));
- if (status != 0) {
- logger
- .debug("Element doesn't have a match: " + element.getElementId() + ", " + map2.get(element.getElementId()));
- return status;
- }
- }
- return 0;
- }
-
- /**
- * Compares two collection of models.
- *
- * @param collection1
- * first collection to compare
- * @param collection2
- * second collection to compare
- * @return 0 if the collections are identical, -1/1 otherwise
- */
- private int compareSubmodels(Collection<ModelSubmodelConnection> collection1,
- Collection<ModelSubmodelConnection> collection2) {
- IntegerComparator integerComparator = new IntegerComparator();
- if (integerComparator.compare(collection1.size(), collection2.size()) != 0) {
- logger.debug("collection of submodels doesn't match: " + collection1.size() + ", " + collection2.size());
- return integerComparator.compare(collection1.size(), collection2.size());
- }
- ModelSubmodelConnectionComparator comparator = new ModelSubmodelConnectionComparator(epsilon);
- for (ModelSubmodelConnection submodel1 : collection1) {
- boolean found = false;
- for (ModelSubmodelConnection submodel2 : collection2) {
- ModelData parent1 = submodel1.getParentModel();
- submodel1.setParentModel((ModelData) null);
- ModelData parent2 = submodel2.getParentModel();
- submodel2.setParentModel((ModelData) null);
-
- if (comparator.compare(submodel1, submodel2) == 0) {
- found = true;
- }
- submodel1.setParentModel(parent1);
- submodel2.setParentModel(parent2);
- if (found) {
- break;
- }
- }
- if (!found) {
- logger.debug("collection of submodels doesn't match. " + submodel1 + " cannot be found in the second model");
- return 1;
- }
- }
-
- for (ModelSubmodelConnection submodel1 : collection2) {
- boolean found = false;
- for (ModelSubmodelConnection submodel2 : collection1) {
- ModelData parent1 = submodel1.getParentModel();
- submodel1.setParentModel((ModelData) null);
- ModelData parent2 = submodel2.getParentModel();
- submodel2.setParentModel((ModelData) null);
-
- if (comparator.compare(submodel1, submodel2) == 0) {
- found = true;
- }
- submodel1.setParentModel(parent1);
- submodel2.setParentModel(parent2);
- if (found) {
- break;
- }
- }
- if (!found) {
- logger.debug("collection of submodels doesn't match. " + submodel1 + " cannot be found in the first model");
- return -1;
- }
- }
-
- return 0;
- }
-}
+package lcsb.mapviewer.model.map.model;
+
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.DoubleComparator;
+import lcsb.mapviewer.common.comparator.IntegerComparator;
+import lcsb.mapviewer.common.comparator.SetComparator;
+import lcsb.mapviewer.common.comparator.StringComparator;
+import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
+import lcsb.mapviewer.model.map.kinetics.SbmlFunctionComparator;
+import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
+import lcsb.mapviewer.model.map.kinetics.SbmlParameterComparator;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnitComparator;
+import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.layout.LayoutComparator;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.layout.graphics.LayerComparator;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionComparator;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.ElementComparator;
+
+/**
+ * Comparator for {@link Model} class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ModelComparator extends Comparator<Model> {
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(ModelComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public ModelComparator(double epsilon) {
+ super(Model.class);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public ModelComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(Model arg0, Model arg1) {
+ StringComparator stringComparator = new StringComparator();
+ DoubleComparator doubleComparator = new DoubleComparator(epsilon);
+ IntegerComparator integerComparator = new IntegerComparator();
+
+ if (stringComparator.compare(arg0.getIdModel(), arg1.getIdModel()) != 0) {
+ logger.debug("Id different: " + arg0.getIdModel() + ", " + arg1.getIdModel());
+ return stringComparator.compare(arg0.getIdModel(), arg1.getIdModel());
+ }
+
+ if (stringComparator.compare(arg0.getName(), arg1.getName()) != 0) {
+ logger.debug("Name different: " + arg0.getName() + ", " + arg1.getName());
+ return stringComparator.compare(arg0.getName(), arg1.getName());
+ }
+
+ if (stringComparator.compare(arg0.getNotes(), arg1.getNotes(), true) != 0) {
+ logger.debug(arg0.getNotes());
+ logger.debug(arg1.getNotes());
+ logger.debug("Notes different:\n" + arg0.getNotes() + "\n---\n" + arg1.getNotes() + "\n---");
+ return stringComparator.compare(arg0.getNotes(), arg1.getNotes(), true);
+ }
+
+ if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
+ logger.debug("Width different: " + arg0.getWidth() + ", " + arg1.getWidth());
+ return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
+ }
+
+ if (doubleComparator.compare(arg0.getHeight(), arg1.getHeight()) != 0) {
+ logger.debug("Height different: " + arg0.getHeight() + ", " + arg1.getHeight());
+ return doubleComparator.compare(arg0.getHeight(), arg1.getHeight());
+ }
+
+ if (integerComparator.compare(arg0.getZoomLevels(), arg1.getZoomLevels()) != 0) {
+ logger.debug("Zoom levels different: " + arg0.getZoomLevels() + ", " + arg1.getZoomLevels());
+ return integerComparator.compare(arg0.getZoomLevels(), arg1.getZoomLevels());
+ }
+
+ if (integerComparator.compare(arg0.getTileSize(), arg1.getTileSize()) != 0) {
+ logger.debug("Tile size different: " + arg0.getTileSize() + ", " + arg1.getTileSize());
+ return integerComparator.compare(arg0.getTileSize(), arg1.getTileSize());
+ }
+
+ int status = compareElements(arg0.getElements(), arg1.getElements());
+ if (status != 0) {
+ logger.debug("Set of elements different");
+ return status;
+ }
+
+ status = compareLayers(arg0.getLayers(), arg1.getLayers());
+ if (status != 0) {
+ logger.debug("Set of layers different");
+ return status;
+ }
+
+ SetComparator<Reaction> reactionSetComparator = new SetComparator<>(new ReactionComparator(epsilon));
+ status = reactionSetComparator.compare(arg0.getReactions(), arg1.getReactions());
+ if (status != 0) {
+ logger.debug("Set of reactions different");
+ return status;
+ }
+
+ status = compareLayouts(arg0.getLayouts(), arg1.getLayouts());
+ if (status != 0) {
+ logger.debug("Set of layouts different");
+ return status;
+ }
+
+ status = compareSubmodels(arg0.getSubmodelConnections(), arg1.getSubmodelConnections());
+ if (status != 0) {
+ logger.debug("Set of submodels different");
+ return status;
+ }
+
+ SetComparator<SbmlUnit> unitSetComparator = new SetComparator<>(new SbmlUnitComparator());
+ status = unitSetComparator.compare(arg0.getUnits(), arg1.getUnits());
+ if (status != 0) {
+ logger.debug("units different");
+ return status;
+ }
+ SetComparator<SbmlFunction> functionSetComparator = new SetComparator<>(new SbmlFunctionComparator());
+ status = functionSetComparator.compare(arg0.getFunctions(), arg1.getFunctions());
+ if (status != 0) {
+ logger.debug("functions different");
+ return status;
+ }
+ SetComparator<SbmlParameter> parameterSetComparator = new SetComparator<>(new SbmlParameterComparator());
+ status = parameterSetComparator.compare(arg0.getParameters(), arg1.getParameters());
+ if (status != 0) {
+ logger.debug("parameters different");
+ return status;
+ }
+ return 0;
+ }
+
+ /**
+ * Compares two sets of layers.
+ *
+ * @param layers
+ * first set of layers
+ * @param layers2
+ * second set of layers
+ * @return if sets are equal then returns 0. If they are different then -1/1 is
+ * returned.
+ */
+ private int compareLayers(Set<Layer> layers, Set<Layer> layers2) {
+ LayerComparator layerComparator = new LayerComparator(epsilon);
+ for (Layer layer : layers) {
+ boolean found = false;
+ for (Layer layer2 : layers2) {
+ if (layerComparator.compare(layer, layer2) == 0) {
+ found = true;
+ }
+ }
+ if (!found) {
+ return 1;
+ }
+ }
+ for (Layer layer : layers2) {
+ boolean found = false;
+ for (Layer layer2 : layers) {
+ if (layerComparator.compare(layer, layer2) == 0) {
+ found = true;
+ }
+ }
+ if (!found) {
+ return -1;
+ }
+ }
+ return 0;
+ }
+
+ /**
+ * Compares two sets of layouts.
+ *
+ * @param layouts
+ * first set of layouts
+ * @param layouts2
+ * second set of layouts
+ * @return if sets are equal then returns 0. If they are different then -1/1 is
+ * returned.
+ */
+ private int compareLayouts(List<Layout> layouts, List<Layout> layouts2) {
+ LayoutComparator layoutComparator = new LayoutComparator(epsilon);
+ for (Layout layout : layouts) {
+ boolean found = false;
+ for (Layout layout2 : layouts2) {
+ if (layoutComparator.compare(layout, layout2) == 0) {
+ found = true;
+ }
+ }
+ if (!found) {
+ return 1;
+ }
+ }
+ for (Layout layout : layouts2) {
+ boolean found = false;
+ for (Layout layout2 : layouts) {
+ if (layoutComparator.compare(layout, layout2) == 0) {
+ found = true;
+ }
+ }
+ if (!found) {
+ return -1;
+ }
+ }
+ return 0;
+ }
+
+ /**
+ * Compares two sets of elements.
+ *
+ * @param elements
+ * first set of elements
+ * @param elements2
+ * second set of elements
+ * @return if sets are equal then returns 0. If they are different then -1/1 is
+ * returned.
+ */
+ private int compareElements(Set<Element> elements, Set<Element> elements2) {
+ ElementComparator elementComparator = new ElementComparator(epsilon);
+
+ Map<String, Element> map1 = new HashMap<>();
+ Map<String, Element> map2 = new HashMap<>();
+
+ if (elements.size() != elements2.size()) {
+ logger.debug("Number of elements different: " + elements.size() + ", " + elements2.size());
+ return ((Integer) elements.size()).compareTo(elements2.size());
+ }
+
+ for (Element element : elements) {
+ map1.put(element.getElementId(), element);
+ }
+
+ for (Element element : elements2) {
+ map2.put(element.getElementId(), element);
+ }
+
+ for (Element element : elements) {
+ int status = elementComparator.compare(element, map2.get(element.getElementId()));
+ if (status != 0) {
+ logger
+ .debug("Element doesn't have a match: " + element.getElementId() + ", " + map2.get(element.getElementId()));
+ return status;
+ }
+ }
+
+ for (Element element : elements2) {
+ int status = elementComparator.compare(element, map1.get(element.getElementId()));
+ if (status != 0) {
+ logger
+ .debug("Element doesn't have a match: " + element.getElementId() + ", " + map2.get(element.getElementId()));
+ return status;
+ }
+ }
+ return 0;
+ }
+
+ /**
+ * Compares two collection of models.
+ *
+ * @param collection1
+ * first collection to compare
+ * @param collection2
+ * second collection to compare
+ * @return 0 if the collections are identical, -1/1 otherwise
+ */
+ private int compareSubmodels(Collection<ModelSubmodelConnection> collection1,
+ Collection<ModelSubmodelConnection> collection2) {
+ IntegerComparator integerComparator = new IntegerComparator();
+ if (integerComparator.compare(collection1.size(), collection2.size()) != 0) {
+ logger.debug("collection of submodels doesn't match: " + collection1.size() + ", " + collection2.size());
+ return integerComparator.compare(collection1.size(), collection2.size());
+ }
+ ModelSubmodelConnectionComparator comparator = new ModelSubmodelConnectionComparator(epsilon);
+ for (ModelSubmodelConnection submodel1 : collection1) {
+ boolean found = false;
+ for (ModelSubmodelConnection submodel2 : collection2) {
+ ModelData parent1 = submodel1.getParentModel();
+ submodel1.setParentModel((ModelData) null);
+ ModelData parent2 = submodel2.getParentModel();
+ submodel2.setParentModel((ModelData) null);
+
+ if (comparator.compare(submodel1, submodel2) == 0) {
+ found = true;
+ }
+ submodel1.setParentModel(parent1);
+ submodel2.setParentModel(parent2);
+ if (found) {
+ break;
+ }
+ }
+ if (!found) {
+ logger.debug("collection of submodels doesn't match. " + submodel1 + " cannot be found in the second model");
+ return 1;
+ }
+ }
+
+ for (ModelSubmodelConnection submodel1 : collection2) {
+ boolean found = false;
+ for (ModelSubmodelConnection submodel2 : collection1) {
+ ModelData parent1 = submodel1.getParentModel();
+ submodel1.setParentModel((ModelData) null);
+ ModelData parent2 = submodel2.getParentModel();
+ submodel2.setParentModel((ModelData) null);
+
+ if (comparator.compare(submodel1, submodel2) == 0) {
+ found = true;
+ }
+ submodel1.setParentModel(parent1);
+ submodel2.setParentModel(parent2);
+ if (found) {
+ break;
+ }
+ }
+ if (!found) {
+ logger.debug("collection of submodels doesn't match. " + submodel1 + " cannot be found in the first model");
+ return -1;
+ }
+ }
+
+ return 0;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnection.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnection.java
index db3674b9e1..2638ad9a5a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnection.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnection.java
@@ -1,132 +1,132 @@
-package lcsb.mapviewer.model.map.model;
-
-import java.util.Comparator;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.ManyToOne;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-/**
- * This class defines connection between super-model (supermap) and sub-model
- * (submap).
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("MODEL_SUBMODEL_LINK")
-public class ModelSubmodelConnection extends SubmodelConnection {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- public static final Comparator<? super ModelSubmodelConnection> ID_COMPARATOR = new Comparator<ModelSubmodelConnection>() {
-
- @Override
- public int compare(ModelSubmodelConnection o1, ModelSubmodelConnection o2) {
- return o1.getId() - o2.getId();
- }
- };
-
- /**
- * Super (parent) model.
- */
- @ManyToOne(fetch = FetchType.LAZY)
- private ModelData parentModel;
-
- /**
- * Default constructor.
- */
- public ModelSubmodelConnection() {
-
- }
-
- /**
- * Default constructor that initialize some fields.
- *
- * @param submodel
- * {@link SubmodelConnection#submodel}
- * @param type
- * {@link SubmodelConnection#type}
- */
- public ModelSubmodelConnection(ModelData submodel, SubmodelType type) {
- super(submodel, type);
- }
-
- /**
- * Default constructor that initialize some fields.
- *
- * @param model
- * {@link SubmodelConnection#submodel}
- * @param type
- * {@link SubmodelConnection#type}
- */
- public ModelSubmodelConnection(Model model, SubmodelType type) {
- super(model.getModelData(), type);
- }
-
- /**
- * Constructor that creates copy of the {@link ModelSubmodelConnection} object.
- *
- * @param original
- * original object from which copy is prepared
- */
- public ModelSubmodelConnection(ModelSubmodelConnection original) {
- super(original);
- this.setParentModel(original.getParentModel());
- }
-
- /**
- * Default constructor that initialize some fields.
- *
- * @param submodel
- * {@link SubmodelConnection#submodel}
- * @param type
- * {@link SubmodelConnection#type}
- * @param name
- * {@link SubmodelConnection#name}
- */
- public ModelSubmodelConnection(Model submodel, SubmodelType type, String name) {
- super(submodel, type, name);
- }
-
- /**
- * @return the parentModel
- * @see #parentModel
- */
- public ModelData getParentModel() {
- return parentModel;
- }
-
- /**
- * @param parentModel
- * the parentModel to set
- * @see #parentModel
- */
- public void setParentModel(ModelData parentModel) {
- this.parentModel = parentModel;
- }
-
- /**
- * @param model
- * the parent model to set
- * @see #parentModel
- */
- public void setParentModel(Model model) {
- setParentModel(model.getModelData());
- }
-
- @Override
- public ModelSubmodelConnection copy() {
- if (this.getClass() == ModelSubmodelConnection.class) {
- return new ModelSubmodelConnection(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-}
+package lcsb.mapviewer.model.map.model;
+
+import java.util.Comparator;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.ManyToOne;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * This class defines connection between super-model (supermap) and sub-model
+ * (submap).
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("MODEL_SUBMODEL_LINK")
+public class ModelSubmodelConnection extends SubmodelConnection {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ public static final Comparator<? super ModelSubmodelConnection> ID_COMPARATOR = new Comparator<ModelSubmodelConnection>() {
+
+ @Override
+ public int compare(ModelSubmodelConnection o1, ModelSubmodelConnection o2) {
+ return o1.getId() - o2.getId();
+ }
+ };
+
+ /**
+ * Super (parent) model.
+ */
+ @ManyToOne(fetch = FetchType.LAZY)
+ private ModelData parentModel;
+
+ /**
+ * Default constructor.
+ */
+ public ModelSubmodelConnection() {
+
+ }
+
+ /**
+ * Default constructor that initialize some fields.
+ *
+ * @param submodel
+ * {@link SubmodelConnection#submodel}
+ * @param type
+ * {@link SubmodelConnection#type}
+ */
+ public ModelSubmodelConnection(ModelData submodel, SubmodelType type) {
+ super(submodel, type);
+ }
+
+ /**
+ * Default constructor that initialize some fields.
+ *
+ * @param model
+ * {@link SubmodelConnection#submodel}
+ * @param type
+ * {@link SubmodelConnection#type}
+ */
+ public ModelSubmodelConnection(Model model, SubmodelType type) {
+ super(model.getModelData(), type);
+ }
+
+ /**
+ * Constructor that creates copy of the {@link ModelSubmodelConnection} object.
+ *
+ * @param original
+ * original object from which copy is prepared
+ */
+ public ModelSubmodelConnection(ModelSubmodelConnection original) {
+ super(original);
+ this.setParentModel(original.getParentModel());
+ }
+
+ /**
+ * Default constructor that initialize some fields.
+ *
+ * @param submodel
+ * {@link SubmodelConnection#submodel}
+ * @param type
+ * {@link SubmodelConnection#type}
+ * @param name
+ * {@link SubmodelConnection#name}
+ */
+ public ModelSubmodelConnection(Model submodel, SubmodelType type, String name) {
+ super(submodel, type, name);
+ }
+
+ /**
+ * @return the parentModel
+ * @see #parentModel
+ */
+ public ModelData getParentModel() {
+ return parentModel;
+ }
+
+ /**
+ * @param parentModel
+ * the parentModel to set
+ * @see #parentModel
+ */
+ public void setParentModel(ModelData parentModel) {
+ this.parentModel = parentModel;
+ }
+
+ /**
+ * @param model
+ * the parent model to set
+ * @see #parentModel
+ */
+ public void setParentModel(Model model) {
+ setParentModel(model.getModelData());
+ }
+
+ @Override
+ public ModelSubmodelConnection copy() {
+ if (this.getClass() == ModelSubmodelConnection.class) {
+ return new ModelSubmodelConnection(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnectionComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnectionComparator.java
index f6dff4bdb9..40af213f72 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnectionComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnectionComparator.java
@@ -1,73 +1,73 @@
-package lcsb.mapviewer.model.map.model;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-
-/**
- * This class implements comparator interface for
- * {@link ModelSubmodelConnection}.
- *
- * @author Piotr Gawron
- *
- */
-public class ModelSubmodelConnectionComparator extends Comparator<ModelSubmodelConnection> {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ModelSubmodelConnectionComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public ModelSubmodelConnectionComparator(double epsilon) {
- super(ModelSubmodelConnection.class);
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public ModelSubmodelConnectionComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected Comparator<?> getParentComparator() {
- return new SubmodelConnectionComparator(epsilon);
- }
-
- @Override
- protected int internalCompare(ModelSubmodelConnection arg0, ModelSubmodelConnection arg1) {
- ModelComparator comparator = new ModelComparator(epsilon);
-
- if (arg0.getParentModel() != null && arg1.getParentModel() != null) {
- int status = comparator.compare(arg0.getParentModel().getModel(), arg1.getParentModel().getModel());
- if (status != 0) {
- logger.debug("Model different: " + arg0.getParentModel() + ", " + arg1.getParentModel());
- return status;
- }
- } else {
- if (arg0.getParentModel() != null) {
- logger.debug("Model different: " + arg0.getParentModel() + ", " + arg1.getParentModel());
- return -1;
- }
- if (arg1.getParentModel() != null) {
- logger.debug("Model different: " + arg0.getParentModel() + ", " + arg1.getParentModel());
- return 1;
- }
- }
-
- return 0;
- }
-
-}
+package lcsb.mapviewer.model.map.model;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+
+/**
+ * This class implements comparator interface for
+ * {@link ModelSubmodelConnection}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ModelSubmodelConnectionComparator extends Comparator<ModelSubmodelConnection> {
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ModelSubmodelConnectionComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public ModelSubmodelConnectionComparator(double epsilon) {
+ super(ModelSubmodelConnection.class);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public ModelSubmodelConnectionComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new SubmodelConnectionComparator(epsilon);
+ }
+
+ @Override
+ protected int internalCompare(ModelSubmodelConnection arg0, ModelSubmodelConnection arg1) {
+ ModelComparator comparator = new ModelComparator(epsilon);
+
+ if (arg0.getParentModel() != null && arg1.getParentModel() != null) {
+ int status = comparator.compare(arg0.getParentModel().getModel(), arg1.getParentModel().getModel());
+ if (status != 0) {
+ logger.debug("Model different: " + arg0.getParentModel() + ", " + arg1.getParentModel());
+ return status;
+ }
+ } else {
+ if (arg0.getParentModel() != null) {
+ logger.debug("Model different: " + arg0.getParentModel() + ", " + arg1.getParentModel());
+ return -1;
+ }
+ if (arg1.getParentModel() != null) {
+ logger.debug("Model different: " + arg0.getParentModel() + ", " + arg1.getParentModel());
+ return 1;
+ }
+ }
+
+ return 0;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelConnection.java b/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelConnection.java
index 5649101b08..0cfd620680 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelConnection.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelConnection.java
@@ -1,219 +1,219 @@
-package lcsb.mapviewer.model.map.model;
-
-import java.io.Serializable;
-
-import javax.persistence.Column;
-import javax.persistence.DiscriminatorColumn;
-import javax.persistence.DiscriminatorType;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Inheritance;
-import javax.persistence.InheritanceType;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-
-import org.apache.log4j.Logger;
-
-/**
- * This abstract class defines connection between models. It points to submodel
- * and describe type of the connection.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "submodel_connection_table")
-@Inheritance(strategy = InheritanceType.SINGLE_TABLE)
-@DiscriminatorColumn(name = "submodel_connections_type_db", discriminatorType = DiscriminatorType.STRING)
-@DiscriminatorValue("SUBMODEL_CONNECTION")
-public abstract class SubmodelConnection implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(SubmodelConnection.class);
-
- /**
- * Database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- /**
- * Sub model.
- */
- @ManyToOne(fetch = FetchType.LAZY, cascade = javax.persistence.CascadeType.ALL)
- private ModelData submodel;
- /**
- * Name of the connection.
- */
- private String name;
- /**
- * Type of the connection.
- */
- private SubmodelType type;
-
- /**
- * Default constructor.
- */
- public SubmodelConnection() {
- }
-
- /**
- * Default constructor that initialize some fields.
- *
- * @param submodel
- * {@link SubmodelConnection#submodel}
- * @param type
- * {@link SubmodelConnection#type}
- */
- public SubmodelConnection(ModelData submodel, SubmodelType type) {
- setSubmodel(submodel);
- setType(type);
- }
-
- /**
- * Constructor that creates copy of the {@link SubmodelConnection} object.
- *
- * @param original
- * original object from which copy is prepared
- */
- public SubmodelConnection(SubmodelConnection original) {
- setSubmodel(original.getSubmodel());
- setName(original.getName());
- setType(original.getType());
- }
-
- /**
- * Default constructor that initialize some fields.
- *
- * @param submodel
- * {@link SubmodelConnection#submodel}
- * @param type
- * {@link SubmodelConnection#type}
- * @param name
- * {@link SubmodelConnection#name}
- */
- public SubmodelConnection(Model submodel, SubmodelType type, String name) {
- setSubmodel(submodel);
- setName(name);
- setType(type);
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return the type
- * @see #type
- */
- public SubmodelType getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(SubmodelType type) {
- this.type = type;
- }
-
- /**
- * @return the submodel
- * @see #submodel
- */
- public ModelData getSubmodel() {
- return submodel;
- }
-
- /**
- * @param submodel
- * the submodel to set
- * @see #submodel
- */
- public void setSubmodel(ModelData submodel) {
- // sometimes we change submodel in the runtime (for instance when we do
- // create a copy), then we should clean information about connection from
- // both sides
- if (this.submodel != null) {
- this.submodel.getParentModels().remove(this);
- }
- this.submodel = submodel;
- submodel.getParentModels().add(this);
- }
-
- /**
- * @return the id
- * @see #id
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
- /**
- * Sets submodel to which this connection points to.
- *
- * @param submodel
- * submodel to set.
- * @see #submodel
- */
- public void setSubmodel(Model submodel) {
- setSubmodel(submodel.getModelData());
- }
-
- /**
- * Creates a copy of this object.
- *
- * @return copy of the object
- */
- public abstract SubmodelConnection copy();
-
- /**
- * This method assign values from the original model. It's different than
- * default constructor - doesn't interfere with the models.
- *
- * @param original original connection from which data is assigned
- */
- protected void assignValuesFromOriginal(SubmodelConnection original) {
- this.submodel = original.getSubmodel();
- this.name = original.getName();
- this.type = original.getType();
- }
-}
+package lcsb.mapviewer.model.map.model;
+
+import java.io.Serializable;
+
+import javax.persistence.Column;
+import javax.persistence.DiscriminatorColumn;
+import javax.persistence.DiscriminatorType;
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.Inheritance;
+import javax.persistence.InheritanceType;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+
+import org.apache.log4j.Logger;
+
+/**
+ * This abstract class defines connection between models. It points to submodel
+ * and describe type of the connection.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "submodel_connection_table")
+@Inheritance(strategy = InheritanceType.SINGLE_TABLE)
+@DiscriminatorColumn(name = "submodel_connections_type_db", discriminatorType = DiscriminatorType.STRING)
+@DiscriminatorValue("SUBMODEL_CONNECTION")
+public abstract class SubmodelConnection implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(SubmodelConnection.class);
+
+ /**
+ * Database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * Sub model.
+ */
+ @ManyToOne(fetch = FetchType.LAZY, cascade = javax.persistence.CascadeType.ALL)
+ private ModelData submodel;
+ /**
+ * Name of the connection.
+ */
+ private String name;
+ /**
+ * Type of the connection.
+ */
+ private SubmodelType type;
+
+ /**
+ * Default constructor.
+ */
+ public SubmodelConnection() {
+ }
+
+ /**
+ * Default constructor that initialize some fields.
+ *
+ * @param submodel
+ * {@link SubmodelConnection#submodel}
+ * @param type
+ * {@link SubmodelConnection#type}
+ */
+ public SubmodelConnection(ModelData submodel, SubmodelType type) {
+ setSubmodel(submodel);
+ setType(type);
+ }
+
+ /**
+ * Constructor that creates copy of the {@link SubmodelConnection} object.
+ *
+ * @param original
+ * original object from which copy is prepared
+ */
+ public SubmodelConnection(SubmodelConnection original) {
+ setSubmodel(original.getSubmodel());
+ setName(original.getName());
+ setType(original.getType());
+ }
+
+ /**
+ * Default constructor that initialize some fields.
+ *
+ * @param submodel
+ * {@link SubmodelConnection#submodel}
+ * @param type
+ * {@link SubmodelConnection#type}
+ * @param name
+ * {@link SubmodelConnection#name}
+ */
+ public SubmodelConnection(Model submodel, SubmodelType type, String name) {
+ setSubmodel(submodel);
+ setName(name);
+ setType(type);
+ }
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * @return the type
+ * @see #type
+ */
+ public SubmodelType getType() {
+ return type;
+ }
+
+ /**
+ * @param type
+ * the type to set
+ * @see #type
+ */
+ public void setType(SubmodelType type) {
+ this.type = type;
+ }
+
+ /**
+ * @return the submodel
+ * @see #submodel
+ */
+ public ModelData getSubmodel() {
+ return submodel;
+ }
+
+ /**
+ * @param submodel
+ * the submodel to set
+ * @see #submodel
+ */
+ public void setSubmodel(ModelData submodel) {
+ // sometimes we change submodel in the runtime (for instance when we do
+ // create a copy), then we should clean information about connection from
+ // both sides
+ if (this.submodel != null) {
+ this.submodel.getParentModels().remove(this);
+ }
+ this.submodel = submodel;
+ submodel.getParentModels().add(this);
+ }
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ /**
+ * Sets submodel to which this connection points to.
+ *
+ * @param submodel
+ * submodel to set.
+ * @see #submodel
+ */
+ public void setSubmodel(Model submodel) {
+ setSubmodel(submodel.getModelData());
+ }
+
+ /**
+ * Creates a copy of this object.
+ *
+ * @return copy of the object
+ */
+ public abstract SubmodelConnection copy();
+
+ /**
+ * This method assign values from the original model. It's different than
+ * default constructor - doesn't interfere with the models.
+ *
+ * @param original original connection from which data is assigned
+ */
+ protected void assignValuesFromOriginal(SubmodelConnection original) {
+ this.submodel = original.getSubmodel();
+ this.name = original.getName();
+ this.type = original.getType();
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparator.java
index 9fc00be432..4522733b94 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparator.java
@@ -1,101 +1,101 @@
-package lcsb.mapviewer.model.map.model;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.StringComparator;
-
-/**
- * This class implements comparator interface for {@link SubmodelConnection}. It
- * handles comparison of subclasses of {@link SubmodelConnection} class.
- *
- * @author Piotr Gawron
- *
- */
-public class SubmodelConnectionComparator extends Comparator<SubmodelConnection> {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(SubmodelConnection.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public SubmodelConnectionComparator(double epsilon) {
- super(SubmodelConnection.class, true);
- this.epsilon = epsilon;
- addSubClassComparator(new ModelSubmodelConnectionComparator(epsilon));
- addSubClassComparator(new ElementSubmodelConnectionComparator(epsilon));
- }
-
- /**
- * Default constructor.
- */
- public SubmodelConnectionComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected int internalCompare(SubmodelConnection arg0, SubmodelConnection arg1) {
- StringComparator stringComparator = new StringComparator();
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- if (stringComparator.compare(arg0.getName(), arg1.getName()) != 0) {
- logger.debug("Name different: " + arg0.getName() + ", " + arg1.getName());
- return stringComparator.compare(arg0.getName(), arg1.getName());
- }
-
- if (arg0.getType() == null && arg1.getType() != null) {
- logger.debug("Type different: " + arg0.getType() + ", " + arg1.getType());
- return -1;
- }
- if (arg0.getType() != null) {
- if (arg1.getType() == null) {
- logger.debug("Type different: " + arg0.getType() + ", " + arg1.getType());
- return -1;
- }
- if (arg0.getType().compareTo(arg1.getType()) != 0) {
- logger.debug("Type different: " + arg0.getType() + ", " + arg1.getType());
- return arg0.getType().compareTo(arg1.getType());
- }
- }
-
- ModelComparator modelComparator = new ModelComparator(epsilon);
- if (arg0.getSubmodel() != null && arg1.getSubmodel() != null) {
- int status = modelComparator.compare(arg0.getSubmodel().getModel(), arg1.getSubmodel().getModel());
- if (status != 0) {
- logger.debug("Model different: " + arg0.getSubmodel() + ", " + arg1.getSubmodel());
- return status;
- }
- } else {
- if (arg0.getSubmodel() != null) {
- logger.debug("Model different: " + arg0.getSubmodel() + ", " + arg1.getSubmodel());
- return 1;
- }
- if (arg1.getSubmodel() != null) {
- logger.debug("Model different: " + arg0.getSubmodel() + ", " + arg1.getSubmodel());
- return -1;
- }
- }
-
- return 0;
- }
-
-}
+package lcsb.mapviewer.model.map.model;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.StringComparator;
+
+/**
+ * This class implements comparator interface for {@link SubmodelConnection}. It
+ * handles comparison of subclasses of {@link SubmodelConnection} class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class SubmodelConnectionComparator extends Comparator<SubmodelConnection> {
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(SubmodelConnection.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public SubmodelConnectionComparator(double epsilon) {
+ super(SubmodelConnection.class, true);
+ this.epsilon = epsilon;
+ addSubClassComparator(new ModelSubmodelConnectionComparator(epsilon));
+ addSubClassComparator(new ElementSubmodelConnectionComparator(epsilon));
+ }
+
+ /**
+ * Default constructor.
+ */
+ public SubmodelConnectionComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(SubmodelConnection arg0, SubmodelConnection arg1) {
+ StringComparator stringComparator = new StringComparator();
+ if (arg0 == null) {
+ if (arg1 == null) {
+ return 0;
+ } else {
+ return 1;
+ }
+ } else if (arg1 == null) {
+ return -1;
+ }
+
+ if (stringComparator.compare(arg0.getName(), arg1.getName()) != 0) {
+ logger.debug("Name different: " + arg0.getName() + ", " + arg1.getName());
+ return stringComparator.compare(arg0.getName(), arg1.getName());
+ }
+
+ if (arg0.getType() == null && arg1.getType() != null) {
+ logger.debug("Type different: " + arg0.getType() + ", " + arg1.getType());
+ return -1;
+ }
+ if (arg0.getType() != null) {
+ if (arg1.getType() == null) {
+ logger.debug("Type different: " + arg0.getType() + ", " + arg1.getType());
+ return -1;
+ }
+ if (arg0.getType().compareTo(arg1.getType()) != 0) {
+ logger.debug("Type different: " + arg0.getType() + ", " + arg1.getType());
+ return arg0.getType().compareTo(arg1.getType());
+ }
+ }
+
+ ModelComparator modelComparator = new ModelComparator(epsilon);
+ if (arg0.getSubmodel() != null && arg1.getSubmodel() != null) {
+ int status = modelComparator.compare(arg0.getSubmodel().getModel(), arg1.getSubmodel().getModel());
+ if (status != 0) {
+ logger.debug("Model different: " + arg0.getSubmodel() + ", " + arg1.getSubmodel());
+ return status;
+ }
+ } else {
+ if (arg0.getSubmodel() != null) {
+ logger.debug("Model different: " + arg0.getSubmodel() + ", " + arg1.getSubmodel());
+ return 1;
+ }
+ if (arg1.getSubmodel() != null) {
+ logger.debug("Model different: " + arg0.getSubmodel() + ", " + arg1.getSubmodel());
+ return -1;
+ }
+ }
+
+ return 0;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelType.java b/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelType.java
index cb13eda18d..6573176d1f 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelType.java
@@ -1,46 +1,46 @@
-package lcsb.mapviewer.model.map.model;
-
-/**
- * Defines type of the connection between models (maps).
- *
- * @author Piotr Gawron
- *
- */
-public enum SubmodelType {
- /**
- * Downstream targets submap.
- */
- DOWNSTREAM_TARGETS("Downstream targets"),
-
- /**
- * Object that should be extended into pathway.
- */
- PATHWAY("Pathway"),
- /**
- * Unknown type.
- */
- UNKNOWN("Unknown");
-
- /**
- * Common name of the type.
- */
- private String commonName;
-
- /**
- * Default constructor.
- *
- * @param name
- * {@link #commonName}
- */
- SubmodelType(String name) {
- this.commonName = name;
- }
-
- /**
- * @return the commonName
- * @see #commonName
- */
- public String getCommonName() {
- return commonName;
- }
-}
+package lcsb.mapviewer.model.map.model;
+
+/**
+ * Defines type of the connection between models (maps).
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum SubmodelType {
+ /**
+ * Downstream targets submap.
+ */
+ DOWNSTREAM_TARGETS("Downstream targets"),
+
+ /**
+ * Object that should be extended into pathway.
+ */
+ PATHWAY("Pathway"),
+ /**
+ * Unknown type.
+ */
+ UNKNOWN("Unknown");
+
+ /**
+ * Common name of the type.
+ */
+ private String commonName;
+
+ /**
+ * Default constructor.
+ *
+ * @param name
+ * {@link #commonName}
+ */
+ SubmodelType(String name) {
+ this.commonName = name;
+ }
+
+ /**
+ * @return the commonName
+ * @see #commonName
+ */
+ public String getCommonName() {
+ return commonName;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/package-info.java b/model/src/main/java/lcsb/mapviewer/model/map/model/package-info.java
index 17d080bf79..7647ab8578 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/package-info.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/package-info.java
@@ -1,5 +1,5 @@
-/**
- * Contains map structures and structures used for connecting maps and submaps.
- */
-package lcsb.mapviewer.model.map.model;
-
+/**
+ * Contains map structures and structures used for connecting maps and submaps.
+ */
+package lcsb.mapviewer.model.map.model;
+
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Catalysis.java b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Catalysis.java
index f93e8502a9..a553dc82e1 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Catalysis.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Catalysis.java
@@ -1,61 +1,61 @@
-package lcsb.mapviewer.model.map.modifier;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * This class defines catalysis modifier in the reaction.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("CATALYSIS_MODIFIER")
-public class Catalysis extends Modifier {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public Catalysis() {
- super();
- }
-
- /**
- * Constructor that creates {@link Catalysis} modifier for given element.
- *
- * @param element
- * element object to which this modifier is assigned
- */
- public Catalysis(Element element) {
- super(element);
- }
-
- /**
- * Constructor that creates object with data taken from parameter catalysis.
- *
- * @param catalysis
- * object from which data are initialized
- */
- public Catalysis(Catalysis catalysis) {
- super(catalysis);
- }
-
- @Override
- public Catalysis copy() {
- if (this.getClass() == Catalysis.class) {
- return new Catalysis(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.modifier;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * This class defines catalysis modifier in the reaction.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("CATALYSIS_MODIFIER")
+public class Catalysis extends Modifier {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public Catalysis() {
+ super();
+ }
+
+ /**
+ * Constructor that creates {@link Catalysis} modifier for given element.
+ *
+ * @param element
+ * element object to which this modifier is assigned
+ */
+ public Catalysis(Element element) {
+ super(element);
+ }
+
+ /**
+ * Constructor that creates object with data taken from parameter catalysis.
+ *
+ * @param catalysis
+ * object from which data are initialized
+ */
+ public Catalysis(Catalysis catalysis) {
+ super(catalysis);
+ }
+
+ @Override
+ public Catalysis copy() {
+ if (this.getClass() == Catalysis.class) {
+ return new Catalysis(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Inhibition.java b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Inhibition.java
index 9079867dce..362594539b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Inhibition.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Inhibition.java
@@ -1,61 +1,61 @@
-package lcsb.mapviewer.model.map.modifier;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * This class defines inhibition modifier in the reaction.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("INHIBITION_MODIFIER")
-public class Inhibition extends Modifier {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public Inhibition() {
- super();
- }
-
- /**
- * Constructor that creates inhibition modifier for given element.
- *
- * @param element
- * element object to which this modifier is assigned
- */
- public Inhibition(Element element) {
- super(element);
- }
-
- /**
- * Constructor that creates object with data taken from parameter inhibition.
- *
- * @param inhibition
- * object from which data are initialized
- */
- public Inhibition(Inhibition inhibition) {
- super(inhibition);
- }
-
- @Override
- public Inhibition copy() {
- if (this.getClass() == Inhibition.class) {
- return new Inhibition(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.modifier;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * This class defines inhibition modifier in the reaction.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("INHIBITION_MODIFIER")
+public class Inhibition extends Modifier {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public Inhibition() {
+ super();
+ }
+
+ /**
+ * Constructor that creates inhibition modifier for given element.
+ *
+ * @param element
+ * element object to which this modifier is assigned
+ */
+ public Inhibition(Element element) {
+ super(element);
+ }
+
+ /**
+ * Constructor that creates object with data taken from parameter inhibition.
+ *
+ * @param inhibition
+ * object from which data are initialized
+ */
+ public Inhibition(Inhibition inhibition) {
+ super(inhibition);
+ }
+
+ @Override
+ public Inhibition copy() {
+ if (this.getClass() == Inhibition.class) {
+ return new Inhibition(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Modulation.java b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Modulation.java
index 6b29c11ffb..99ab59ce03 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Modulation.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Modulation.java
@@ -1,61 +1,61 @@
-package lcsb.mapviewer.model.map.modifier;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * This class defines modulation modifier in the reaction.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("MODULATION_MODIFIER")
-public class Modulation extends Modifier {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public Modulation() {
- super();
- }
-
- /**
- * Constructor that creates modulation modifier for given element.
- *
- * @param element
- * element object to which this modifier is assigned
- */
- public Modulation(Element element) {
- super(element);
- }
-
- /**
- * Constructor that creates object with data taken from parameter modulation.
- *
- * @param modulation
- * object from which data are initialized
- */
- public Modulation(Modulation modulation) {
- super(modulation);
- }
-
- @Override
- public Modulation copy() {
- if (this.getClass() == Modulation.class) {
- return new Modulation(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.modifier;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * This class defines modulation modifier in the reaction.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("MODULATION_MODIFIER")
+public class Modulation extends Modifier {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public Modulation() {
+ super();
+ }
+
+ /**
+ * Constructor that creates modulation modifier for given element.
+ *
+ * @param element
+ * element object to which this modifier is assigned
+ */
+ public Modulation(Element element) {
+ super(element);
+ }
+
+ /**
+ * Constructor that creates object with data taken from parameter modulation.
+ *
+ * @param modulation
+ * object from which data are initialized
+ */
+ public Modulation(Modulation modulation) {
+ super(modulation);
+ }
+
+ @Override
+ public Modulation copy() {
+ if (this.getClass() == Modulation.class) {
+ return new Modulation(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/modifier/PhysicalStimulation.java b/model/src/main/java/lcsb/mapviewer/model/map/modifier/PhysicalStimulation.java
index f7e40ddc45..e80792b412 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/modifier/PhysicalStimulation.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/modifier/PhysicalStimulation.java
@@ -1,62 +1,62 @@
-package lcsb.mapviewer.model.map.modifier;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * This class defines physical stimulation modifier in the reaction.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("PHYSICAL_STIMULATION_MODIFIER")
-public class PhysicalStimulation extends Modifier {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public PhysicalStimulation() {
- super();
- }
-
- /**
- * Constructor that creates physical stimulation modifier for given element.
- *
- * @param element
- * element object to which this modifier is assigned
- */
- public PhysicalStimulation(Element element) {
- super(element);
- }
-
- /**
- * Constructor that creates object with data taken from parameter physical
- * stimulation.
- *
- * @param physicalStimulation
- * object from which data are initialized
- */
- public PhysicalStimulation(PhysicalStimulation physicalStimulation) {
- super(physicalStimulation);
- }
-
- @Override
- public PhysicalStimulation copy() {
- if (this.getClass() == PhysicalStimulation.class) {
- return new PhysicalStimulation(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.modifier;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * This class defines physical stimulation modifier in the reaction.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("PHYSICAL_STIMULATION_MODIFIER")
+public class PhysicalStimulation extends Modifier {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public PhysicalStimulation() {
+ super();
+ }
+
+ /**
+ * Constructor that creates physical stimulation modifier for given element.
+ *
+ * @param element
+ * element object to which this modifier is assigned
+ */
+ public PhysicalStimulation(Element element) {
+ super(element);
+ }
+
+ /**
+ * Constructor that creates object with data taken from parameter physical
+ * stimulation.
+ *
+ * @param physicalStimulation
+ * object from which data are initialized
+ */
+ public PhysicalStimulation(PhysicalStimulation physicalStimulation) {
+ super(physicalStimulation);
+ }
+
+ @Override
+ public PhysicalStimulation copy() {
+ if (this.getClass() == PhysicalStimulation.class) {
+ return new PhysicalStimulation(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Trigger.java b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Trigger.java
index 66f653d6d5..8b2a441205 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/modifier/Trigger.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/modifier/Trigger.java
@@ -1,61 +1,61 @@
-package lcsb.mapviewer.model.map.modifier;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * This class defines trigger modifier in the reaction.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("TRIGGER_MODIFIER")
-public class Trigger extends Modifier {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public Trigger() {
- super();
- }
-
- /**
- * Constructor that creates trigger modifier for given element.
- *
- * @param element
- * element object to which this modifier is assigned
- */
- public Trigger(Element element) {
- super(element);
- }
-
- /**
- * Constructor that creates object with data taken from parameter trigger.
- *
- * @param trigger
- * object from which data are initialized
- */
- public Trigger(Trigger trigger) {
- super(trigger);
- }
-
- @Override
- public Trigger copy() {
- if (this.getClass() == Trigger.class) {
- return new Trigger(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.modifier;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * This class defines trigger modifier in the reaction.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("TRIGGER_MODIFIER")
+public class Trigger extends Modifier {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public Trigger() {
+ super();
+ }
+
+ /**
+ * Constructor that creates trigger modifier for given element.
+ *
+ * @param element
+ * element object to which this modifier is assigned
+ */
+ public Trigger(Element element) {
+ super(element);
+ }
+
+ /**
+ * Constructor that creates object with data taken from parameter trigger.
+ *
+ * @param trigger
+ * object from which data are initialized
+ */
+ public Trigger(Trigger trigger) {
+ super(trigger);
+ }
+
+ @Override
+ public Trigger copy() {
+ if (this.getClass() == Trigger.class) {
+ return new Trigger(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownCatalysis.java b/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownCatalysis.java
index fd299cb378..51dedcc61b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownCatalysis.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownCatalysis.java
@@ -1,62 +1,62 @@
-package lcsb.mapviewer.model.map.modifier;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * This class defines unknown catalysis modifier in the reaction.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("UNKNOWN_CATALYSIS_MODIFIER")
-public class UnknownCatalysis extends Modifier {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public UnknownCatalysis() {
- super();
- }
-
- /**
- * Constructor that creates unknown catalysis modifier for given element.
- *
- * @param element
- * element object to which this modifier is assigned
- */
- public UnknownCatalysis(Element element) {
- super(element);
- }
-
- /**
- * Constructor that creates object with data taken from parameter unknown
- * catalysis.
- *
- * @param unknownCatalysis
- * object from which data are initialized
- */
- public UnknownCatalysis(UnknownCatalysis unknownCatalysis) {
- super(unknownCatalysis);
- }
-
- @Override
- public UnknownCatalysis copy() {
- if (this.getClass() == UnknownCatalysis.class) {
- return new UnknownCatalysis(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.modifier;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * This class defines unknown catalysis modifier in the reaction.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("UNKNOWN_CATALYSIS_MODIFIER")
+public class UnknownCatalysis extends Modifier {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public UnknownCatalysis() {
+ super();
+ }
+
+ /**
+ * Constructor that creates unknown catalysis modifier for given element.
+ *
+ * @param element
+ * element object to which this modifier is assigned
+ */
+ public UnknownCatalysis(Element element) {
+ super(element);
+ }
+
+ /**
+ * Constructor that creates object with data taken from parameter unknown
+ * catalysis.
+ *
+ * @param unknownCatalysis
+ * object from which data are initialized
+ */
+ public UnknownCatalysis(UnknownCatalysis unknownCatalysis) {
+ super(unknownCatalysis);
+ }
+
+ @Override
+ public UnknownCatalysis copy() {
+ if (this.getClass() == UnknownCatalysis.class) {
+ return new UnknownCatalysis(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownInhibition.java b/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownInhibition.java
index 65d97ab656..0f7a1fb3a2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownInhibition.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/modifier/UnknownInhibition.java
@@ -1,62 +1,62 @@
-package lcsb.mapviewer.model.map.modifier;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * This class defines unknown inhibition modifier in the reaction.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("UNKNOWN_INHIBITION_MODIFIER")
-public class UnknownInhibition extends Modifier {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public UnknownInhibition() {
- super();
- }
-
- /**
- * Constructor that creates unknown inhibition modifier for given and element.
- *
- * @param element
- * element object to which this modifier is assigned
- */
- public UnknownInhibition(Element element) {
- super(element);
- }
-
- /**
- * Constructor that creates object with data taken from parameter unknown
- * inhibition.
- *
- * @param unknownInhibition
- * object from which data are initialized
- */
- public UnknownInhibition(UnknownInhibition unknownInhibition) {
- super(unknownInhibition);
- }
-
- @Override
- public UnknownInhibition copy() {
- if (this.getClass() == UnknownInhibition.class) {
- return new UnknownInhibition(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.modifier;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * This class defines unknown inhibition modifier in the reaction.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("UNKNOWN_INHIBITION_MODIFIER")
+public class UnknownInhibition extends Modifier {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public UnknownInhibition() {
+ super();
+ }
+
+ /**
+ * Constructor that creates unknown inhibition modifier for given and element.
+ *
+ * @param element
+ * element object to which this modifier is assigned
+ */
+ public UnknownInhibition(Element element) {
+ super(element);
+ }
+
+ /**
+ * Constructor that creates object with data taken from parameter unknown
+ * inhibition.
+ *
+ * @param unknownInhibition
+ * object from which data are initialized
+ */
+ public UnknownInhibition(UnknownInhibition unknownInhibition) {
+ super(unknownInhibition);
+ }
+
+ @Override
+ public UnknownInhibition copy() {
+ if (this.getClass() == UnknownInhibition.class) {
+ return new UnknownInhibition(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/modifier/package-info.java b/model/src/main/java/lcsb/mapviewer/model/map/modifier/package-info.java
index 6f03d37da6..b5520bf31f 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/modifier/package-info.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/modifier/package-info.java
@@ -1,6 +1,6 @@
-/**
- * Provides data structure for
- * {@link lcsb.mapviewer.model.map.reaction.Reaction Reaction} modifier.
- */
-package lcsb.mapviewer.model.map.modifier;
-
+/**
+ * Provides data structure for
+ * {@link lcsb.mapviewer.model.map.reaction.Reaction Reaction} modifier.
+ */
+package lcsb.mapviewer.model.map.modifier;
+
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/package-info.java b/model/src/main/java/lcsb/mapviewer/model/map/package-info.java
index cc4d791654..902c25f151 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/package-info.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/package-info.java
@@ -1,7 +1,7 @@
-/**
- * Contains structures used for map modeling. The most important class
- * representing model is {@link lcsb.mapviewer.model.map.model.Model}. All other
- * class represents fields or elements of the model (or model elements).
- */
-package lcsb.mapviewer.model.map;
-
+/**
+ * Contains structures used for map modeling. The most important class
+ * representing model is {@link lcsb.mapviewer.model.map.model.Model}. All other
+ * class represents fields or elements of the model (or model elements).
+ */
+package lcsb.mapviewer.model.map;
+
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/AbstractNode.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/AbstractNode.java
index e55a046e15..dfa685ad3b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/AbstractNode.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/AbstractNode.java
@@ -1,182 +1,182 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import java.io.Serializable;
-
-import javax.persistence.Column;
-import javax.persistence.DiscriminatorColumn;
-import javax.persistence.DiscriminatorType;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Inheritance;
-import javax.persistence.InheritanceType;
-import javax.persistence.ManyToOne;
-import javax.persistence.OneToOne;
-import javax.persistence.Table;
-
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-
-import lcsb.mapviewer.model.graphics.PolylineData;
-
-/**
- * This class defines abstract node of the reaction. By the design there are two
- * main classes of nodes (that are extended further):
- * <ul>
- * <li>end nodes with linked elements
- * {@link lcsb.mapviewer.model.map.reaction.ReactionNode ReactionNode} - defines
- * what elements participate in the reaction and in what role (product,
- * reactant)</li>
- * <li>operator nodes {@link lcsb.mapviewer.model.map.reaction.NodeOperator
- * NodeOperator} - defines relation between different participants of the
- * reaction (and operator, split/dissociation, etc.)</li>
- * </ul>
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "node_table")
-@Inheritance(strategy = InheritanceType.SINGLE_TABLE)
-@DiscriminatorColumn(name = "node_type_db", discriminatorType = DiscriminatorType.STRING)
-@DiscriminatorValue("GENERIC_NODE")
-public abstract class AbstractNode implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- /**
- * This object define the node that is next in the schema (in the flow from
- * reactants to products). In case the node is terminal product this object is
- * set to null.
- */
- @ManyToOne
- private NodeOperator nodeOperatorForInput = null;
-
- /**
- * This object define the node that is before in the schema (in the flow from
- * reactants to products). In case the node is reactant this object is set to
- * null.
- */
- @ManyToOne
- private NodeOperator nodeOperatorForOutput = null;
-
- /**
- * Reaction object where this node is located.
- */
- @ManyToOne
- private Reaction reaction = null;
-
- /**
- * Line that represent this node in graphical representation.
- */
- @Cascade({ CascadeType.ALL })
- @OneToOne(fetch = FetchType.EAGER)
- private PolylineData line;
-
- /**
- * Default constructor.
- */
- public AbstractNode() {
-
- }
-
- /**
- * Constructor that copies the data from the original node in the parameter.
- *
- * @param node
- * original node based on which this one will be created
- */
- public AbstractNode(AbstractNode node) {
- this.reaction = node.reaction;
- this.line = new PolylineData(node.getLine());
- }
-
- /**
- * @return the reaction
- * @see #reaction
- */
- public Reaction getReaction() {
- return reaction;
- }
-
- /**
- * @param reaction
- * the reaction to set
- * @see #reaction
- */
- public void setReaction(Reaction reaction) {
- this.reaction = reaction;
- }
-
- /**
- * @return the line
- * @see #line
- */
- public PolylineData getLine() {
- return line;
- }
-
- /**
- * @param line
- * the line to set
- * @see #line
- */
- public void setLine(PolylineData line) {
- this.line = line;
- }
-
- /**
- * Creates a copy of the object.
- *
- * @return copy of the object
- */
- public abstract AbstractNode copy();
-
- /**
- * @return the nodeOperatorForInput
- * @see #nodeOperatorForInput
- */
- public NodeOperator getNodeOperatorForInput() {
- return nodeOperatorForInput;
- }
-
- /**
- * @param nodeOperatorForInput
- * the nodeOperatorForInput to set
- * @see #nodeOperatorForInput
- */
- public void setNodeOperatorForInput(NodeOperator nodeOperatorForInput) {
- this.nodeOperatorForInput = nodeOperatorForInput;
- }
-
- /**
- * @return the nodeOperatorForOutput
- * @see #nodeOperatorForOutput
- */
- public NodeOperator getNodeOperatorForOutput() {
- return nodeOperatorForOutput;
- }
-
- /**
- * @param nodeOperatorForOutput
- * the nodeOperatorForOutput to set
- * @see #nodeOperatorForOutput
- */
- public void setNodeOperatorForOutput(NodeOperator nodeOperatorForOutput) {
- this.nodeOperatorForOutput = nodeOperatorForOutput;
- }
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import java.io.Serializable;
+
+import javax.persistence.Column;
+import javax.persistence.DiscriminatorColumn;
+import javax.persistence.DiscriminatorType;
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.Inheritance;
+import javax.persistence.InheritanceType;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToOne;
+import javax.persistence.Table;
+
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+
+import lcsb.mapviewer.model.graphics.PolylineData;
+
+/**
+ * This class defines abstract node of the reaction. By the design there are two
+ * main classes of nodes (that are extended further):
+ * <ul>
+ * <li>end nodes with linked elements
+ * {@link lcsb.mapviewer.model.map.reaction.ReactionNode ReactionNode} - defines
+ * what elements participate in the reaction and in what role (product,
+ * reactant)</li>
+ * <li>operator nodes {@link lcsb.mapviewer.model.map.reaction.NodeOperator
+ * NodeOperator} - defines relation between different participants of the
+ * reaction (and operator, split/dissociation, etc.)</li>
+ * </ul>
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "node_table")
+@Inheritance(strategy = InheritanceType.SINGLE_TABLE)
+@DiscriminatorColumn(name = "node_type_db", discriminatorType = DiscriminatorType.STRING)
+@DiscriminatorValue("GENERIC_NODE")
+public abstract class AbstractNode implements Serializable {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * This object define the node that is next in the schema (in the flow from
+ * reactants to products). In case the node is terminal product this object is
+ * set to null.
+ */
+ @ManyToOne
+ private NodeOperator nodeOperatorForInput = null;
+
+ /**
+ * This object define the node that is before in the schema (in the flow from
+ * reactants to products). In case the node is reactant this object is set to
+ * null.
+ */
+ @ManyToOne
+ private NodeOperator nodeOperatorForOutput = null;
+
+ /**
+ * Reaction object where this node is located.
+ */
+ @ManyToOne
+ private Reaction reaction = null;
+
+ /**
+ * Line that represent this node in graphical representation.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToOne(fetch = FetchType.EAGER)
+ private PolylineData line;
+
+ /**
+ * Default constructor.
+ */
+ public AbstractNode() {
+
+ }
+
+ /**
+ * Constructor that copies the data from the original node in the parameter.
+ *
+ * @param node
+ * original node based on which this one will be created
+ */
+ public AbstractNode(AbstractNode node) {
+ this.reaction = node.reaction;
+ this.line = new PolylineData(node.getLine());
+ }
+
+ /**
+ * @return the reaction
+ * @see #reaction
+ */
+ public Reaction getReaction() {
+ return reaction;
+ }
+
+ /**
+ * @param reaction
+ * the reaction to set
+ * @see #reaction
+ */
+ public void setReaction(Reaction reaction) {
+ this.reaction = reaction;
+ }
+
+ /**
+ * @return the line
+ * @see #line
+ */
+ public PolylineData getLine() {
+ return line;
+ }
+
+ /**
+ * @param line
+ * the line to set
+ * @see #line
+ */
+ public void setLine(PolylineData line) {
+ this.line = line;
+ }
+
+ /**
+ * Creates a copy of the object.
+ *
+ * @return copy of the object
+ */
+ public abstract AbstractNode copy();
+
+ /**
+ * @return the nodeOperatorForInput
+ * @see #nodeOperatorForInput
+ */
+ public NodeOperator getNodeOperatorForInput() {
+ return nodeOperatorForInput;
+ }
+
+ /**
+ * @param nodeOperatorForInput
+ * the nodeOperatorForInput to set
+ * @see #nodeOperatorForInput
+ */
+ public void setNodeOperatorForInput(NodeOperator nodeOperatorForInput) {
+ this.nodeOperatorForInput = nodeOperatorForInput;
+ }
+
+ /**
+ * @return the nodeOperatorForOutput
+ * @see #nodeOperatorForOutput
+ */
+ public NodeOperator getNodeOperatorForOutput() {
+ return nodeOperatorForOutput;
+ }
+
+ /**
+ * @param nodeOperatorForOutput
+ * the nodeOperatorForOutput to set
+ * @see #nodeOperatorForOutput
+ */
+ public void setNodeOperatorForOutput(NodeOperator nodeOperatorForOutput) {
+ this.nodeOperatorForOutput = nodeOperatorForOutput;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/AbstractNodeComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/AbstractNodeComparator.java
index b68812bfd9..411ce324e2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/AbstractNodeComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/AbstractNodeComparator.java
@@ -1,57 +1,57 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.model.graphics.PolylineDataComparator;
-
-/**
- * This class implements comparator interface for AbstractNode. It also handles
- * comparison of subclasses of AbstractNode class.
- *
- * @author Piotr Gawron
- *
- */
-public class AbstractNodeComparator extends Comparator<AbstractNode> {
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(AbstractNodeComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public AbstractNodeComparator(double epsilon) {
- super(AbstractNode.class, true);
- this.epsilon = epsilon;
- addSubClassComparator(new NodeOperatorComparator(epsilon));
- addSubClassComparator(new ReactionNodeComparator(epsilon));
- }
-
- /**
- * Default constructor.
- */
- public AbstractNodeComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected int internalCompare(AbstractNode arg0, AbstractNode arg1) {
- PolylineDataComparator pdComparator = new PolylineDataComparator(epsilon);
- if (pdComparator.compare(arg0.getLine(), arg1.getLine()) != 0) {
- logger.debug("Different lines: " + arg0.getLine() + ", " + arg1.getLine());
- return pdComparator.compare(arg0.getLine(), arg1.getLine());
- }
- return 0;
- }
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.model.graphics.PolylineDataComparator;
+
+/**
+ * This class implements comparator interface for AbstractNode. It also handles
+ * comparison of subclasses of AbstractNode class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class AbstractNodeComparator extends Comparator<AbstractNode> {
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(AbstractNodeComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public AbstractNodeComparator(double epsilon) {
+ super(AbstractNode.class, true);
+ this.epsilon = epsilon;
+ addSubClassComparator(new NodeOperatorComparator(epsilon));
+ addSubClassComparator(new ReactionNodeComparator(epsilon));
+ }
+
+ /**
+ * Default constructor.
+ */
+ public AbstractNodeComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(AbstractNode arg0, AbstractNode arg1) {
+ PolylineDataComparator pdComparator = new PolylineDataComparator(epsilon);
+ if (pdComparator.compare(arg0.getLine(), arg1.getLine()) != 0) {
+ logger.debug("Different lines: " + arg0.getLine() + ", " + arg1.getLine());
+ return pdComparator.compare(arg0.getLine(), arg1.getLine());
+ }
+ return 0;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/AndOperator.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/AndOperator.java
index 77daea75ea..8fde0ea87e 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/AndOperator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/AndOperator.java
@@ -1,67 +1,67 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-/**
- * Class representing "and operator" between two or more nodes in the reaction.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("AND_OPERATOR_NODE")
-public class AndOperator extends NodeOperator {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(AndOperator.class);
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param operator
- * parent operator from which we copy data
- */
- public AndOperator(AndOperator operator) {
- super(operator);
- }
-
- /**
- * Default constructor.
- */
- public AndOperator() {
- super();
- }
-
- @Override
- public String getOperatorText() {
- return "&";
- }
-
- @Override
- public String getSBGNOperatorText() {
- return "AND";
- }
-
- @Override
- public AndOperator copy() {
- if (this.getClass() == AndOperator.class) {
- return new AndOperator(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * Class representing "and operator" between two or more nodes in the reaction.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("AND_OPERATOR_NODE")
+public class AndOperator extends NodeOperator {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(AndOperator.class);
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param operator
+ * parent operator from which we copy data
+ */
+ public AndOperator(AndOperator operator) {
+ super(operator);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public AndOperator() {
+ super();
+ }
+
+ @Override
+ public String getOperatorText() {
+ return "&";
+ }
+
+ @Override
+ public String getSBGNOperatorText() {
+ return "AND";
+ }
+
+ @Override
+ public AndOperator copy() {
+ if (this.getClass() == AndOperator.class) {
+ return new AndOperator(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/AssociationOperator.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/AssociationOperator.java
index e8bc4d7f7e..fcdea08a0e 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/AssociationOperator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/AssociationOperator.java
@@ -1,64 +1,64 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-/**
- * Class representing operator between two input nodes in
- * {@link lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction
- * HeterodimerAssociationReaction}.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("ASSOCIATION_OPERATOR_NODE")
-public class AssociationOperator extends NodeOperator {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(AssociationOperator.class);
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param operator
- * parent operator from which we copy data
- */
- public AssociationOperator(AssociationOperator operator) {
- super(operator);
- }
-
- /**
- * Default constructor.
- */
- public AssociationOperator() {
- super();
- }
-
- @Override
- public String getOperatorText() {
- return "&";
- }
-
- @Override
- public AssociationOperator copy() {
- if (this.getClass() == AssociationOperator.class) {
- return new AssociationOperator(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * Class representing operator between two input nodes in
+ * {@link lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction
+ * HeterodimerAssociationReaction}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("ASSOCIATION_OPERATOR_NODE")
+public class AssociationOperator extends NodeOperator {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(AssociationOperator.class);
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param operator
+ * parent operator from which we copy data
+ */
+ public AssociationOperator(AssociationOperator operator) {
+ super(operator);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public AssociationOperator() {
+ super();
+ }
+
+ @Override
+ public String getOperatorText() {
+ return "&";
+ }
+
+ @Override
+ public AssociationOperator copy() {
+ if (this.getClass() == AssociationOperator.class) {
+ return new AssociationOperator(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/DissociationOperator.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/DissociationOperator.java
index 5bd1b190c6..6453ede8c1 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/DissociationOperator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/DissociationOperator.java
@@ -1,63 +1,63 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-/**
- * Class representing "dissociation operator" of one node into two or more nodes
- * in the reaction (in the product part of the reaction).
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("DISSOCIATION_OPERATOR_NODE")
-public class DissociationOperator extends NodeOperator {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(DissociationOperator.class);
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param operator
- * parent operator from which we copy data
- */
- public DissociationOperator(DissociationOperator operator) {
- super(operator);
- }
-
- /**
- * Default constructor.
- */
- public DissociationOperator() {
- super();
- }
-
- @Override
- public String getOperatorText() {
- return "â—‹";
- }
-
- @Override
- public DissociationOperator copy() {
- if (this.getClass() == DissociationOperator.class) {
- return new DissociationOperator(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * Class representing "dissociation operator" of one node into two or more nodes
+ * in the reaction (in the product part of the reaction).
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("DISSOCIATION_OPERATOR_NODE")
+public class DissociationOperator extends NodeOperator {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(DissociationOperator.class);
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param operator
+ * parent operator from which we copy data
+ */
+ public DissociationOperator(DissociationOperator operator) {
+ super(operator);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public DissociationOperator() {
+ super();
+ }
+
+ @Override
+ public String getOperatorText() {
+ return "â—‹";
+ }
+
+ @Override
+ public DissociationOperator copy() {
+ if (this.getClass() == DissociationOperator.class) {
+ return new DissociationOperator(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Modifier.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Modifier.java
index 39d96b497b..5527d7a4e2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Modifier.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Modifier.java
@@ -1,64 +1,64 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * Represents modifier (ie. catalyst) in the {@link Reaction}. It is an
- * implementation of more general {@link ReactionNode} class which describes the
- * node.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("MODIFIER_NODE")
-public class Modifier extends ReactionNode {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- protected Modifier() {
- super();
- }
-
- /**
- * Constructor that creates modifier for given {@link Species}. These
- * elements reference to the objects in the
- * {@link lcsb.mapviewer.model.map.model.db.model.map.Model Model} that
- * represents this modifier.
- *
- * @param element
- * element that represent this modifier
- */
- public Modifier(Element element) {
- super(element);
- }
-
- /**
- * Constructor that initialize the modifier with data from parameter.
- *
- * @param original
- * original modifier used for data initialization
- */
- protected Modifier(Modifier original) {
- super(original);
- }
-
- @Override
- public Modifier copy() {
- if (this.getClass() == Modifier.class) {
- return new Modifier(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * Represents modifier (ie. catalyst) in the {@link Reaction}. It is an
+ * implementation of more general {@link ReactionNode} class which describes the
+ * node.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("MODIFIER_NODE")
+public class Modifier extends ReactionNode {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ protected Modifier() {
+ super();
+ }
+
+ /**
+ * Constructor that creates modifier for given {@link Species}. These
+ * elements reference to the objects in the
+ * {@link lcsb.mapviewer.model.map.model.db.model.map.Model Model} that
+ * represents this modifier.
+ *
+ * @param element
+ * element that represent this modifier
+ */
+ public Modifier(Element element) {
+ super(element);
+ }
+
+ /**
+ * Constructor that initialize the modifier with data from parameter.
+ *
+ * @param original
+ * original modifier used for data initialization
+ */
+ protected Modifier(Modifier original) {
+ super(original);
+ }
+
+ @Override
+ public Modifier copy() {
+ if (this.getClass() == Modifier.class) {
+ return new Modifier(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/NandOperator.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/NandOperator.java
index f0d4490514..bc88d04dbd 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/NandOperator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/NandOperator.java
@@ -1,62 +1,62 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-/**
- * Class representing "not and operator" between two or more nodes in the
- * reaction.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("NAND_OPERATOR_NODE")
-public class NandOperator extends NodeOperator {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(NandOperator.class);
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param operator
- * parent operator from which we copy data
- */
- public NandOperator(NandOperator operator) {
- super(operator);
- }
-
- /**
- * Default constructor.
- */
- public NandOperator() {
- super();
- }
-
- @Override
- public String getOperatorText() {
- return "~";
- }
-
- @Override
- public NandOperator copy() {
- if (this.getClass() == NandOperator.class) {
- return new NandOperator(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * Class representing "not and operator" between two or more nodes in the
+ * reaction.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("NAND_OPERATOR_NODE")
+public class NandOperator extends NodeOperator {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(NandOperator.class);
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param operator
+ * parent operator from which we copy data
+ */
+ public NandOperator(NandOperator operator) {
+ super(operator);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public NandOperator() {
+ super();
+ }
+
+ @Override
+ public String getOperatorText() {
+ return "~";
+ }
+
+ @Override
+ public NandOperator copy() {
+ if (this.getClass() == NandOperator.class) {
+ return new NandOperator(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/NodeOperator.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/NodeOperator.java
index 3db88e3c77..e340714aee 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/NodeOperator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/NodeOperator.java
@@ -1,264 +1,264 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.OneToMany;
-import javax.persistence.OrderBy;
-
-import org.apache.log4j.Logger;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-
-/**
- * One of two known types of nodes in the {@link Reaction}. It describes
- * relation between two (or more) nodes in the reaction. There are few types of
- * relations that are implemented:
- * <ul>
- * <li>{@link AndOperator} - when the output node is a result of logic "and
- * operator" between two or more input nodes</li>
- * <li>{@link AssociationOperator} - when the output node is a result of logic
- * "and operator" between two or more input nodes</li>
- * <li>{@link DissociationOperator} - when two (or more) output nodes is a
- * result of dissociation of the input</li>
- * <li>{@link NandOperator} - when the output node is a result of logic "nand
- * operator" between two or more input nodes</li>
- * <li>{@link OrOperator} - when the output node is a result of logic "or
- * operator" between two or more input nodes</li>
- * <li>{@link SplitOperator} - when two (or more) output nodes is a result of
- * spliting (dissociation???) of the input</li>
- * <li>{@link TruncationOperator} - when the output nodes are a result of
- * truncation of the input. As a result we will get truncated node and the
- * reminder part.</li>
- * <li>{@link UnknownOperator} - when the output node is a result of logic
- * operator between two or more input nodes, but the logic is unknown</li>
- * </ul>
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("GENERIC_OPERATOR_NODE")
-public abstract class NodeOperator extends AbstractNode {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(NodeOperator.class);
-
- /**
- * List of input nodes.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(fetch = FetchType.EAGER, mappedBy = "nodeOperatorForInput")
- @OrderBy("id")
- private List<AbstractNode> inputs = new ArrayList<>();
-
- /**
- * List of output nodes.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(fetch = FetchType.EAGER, mappedBy = "nodeOperatorForOutput")
- @OrderBy("id")
- private List<AbstractNode> outputs = new ArrayList<>();
-
- /**
- * Default constructor.
- */
- public NodeOperator() {
- }
-
- /**
- * Creates operator using the data from the original operator in the parameter.
- *
- * @param operator
- * original operator from which data is initialized
- */
- public NodeOperator(NodeOperator operator) {
- super(operator);
-
- for (AbstractNode node : operator.getInputs()) {
- addInput(node);
- }
- for (AbstractNode node : operator.getOutputs()) {
- addOutput(node);
- }
- }
-
- /**
- * Adds input node.
- *
- * @param node
- * node to add
- */
- public void addInput(AbstractNode node) {
- node.setNodeOperatorForInput(this);
- if (inputs.contains(node)) {
- throw new InvalidArgumentException("Node already on the list: " + node);
- }
- inputs.add(node);
- }
-
- /**
- * Adds set of inputs.
- *
- * @param newInputs
- * set of input nodes to add
- */
- public void addInputs(Collection<? extends AbstractNode> newInputs) {
- for (AbstractNode input : newInputs) {
- addInput(input);
- }
- }
-
- /**
- * Checks if the operator connects several inputs to one output.
- *
- * @return <code>true</code> if the operator connects several inputs to one
- * output, <code>false</code> otherwise
- */
- public boolean isReactantOperator() {
- for (AbstractNode node : inputs) {
- if (node instanceof Reactant) {
- return true;
- }
- if (node instanceof NodeOperator) {
- if (((NodeOperator) node).isReactantOperator()) {
- return true;
- }
- }
-
- }
- return false;
- }
-
- /**
- * Adds output to the operator.
- *
- * @param node
- * output node to add
- */
- public void addOutput(AbstractNode node) {
- node.setNodeOperatorForOutput(this);
- if (outputs.contains(node)) {
- throw new InvalidArgumentException("Node already on the list: " + node);
- }
- outputs.add(node);
- }
-
- /**
- * Checks if the operator connects one input to several outputs.
- *
- * @return <code>true</code> if the operator connects one input to several
- * outputs, <code>false</code> otherwise
- */
- public boolean isProductOperator() {
- for (AbstractNode node : outputs) {
- if (node instanceof Product) {
- return true;
- }
- if (node instanceof NodeOperator) {
- if (((NodeOperator) node).isProductOperator()) {
- return true;
- }
- }
- }
- return false;
- }
-
- /**
- * Returns one character length description of the operator.
- *
- * @return one character length description of the operator
- */
- public abstract String getOperatorText();
-
- /**
- * Returns SBGN description of the operator.
- *
- * @return SBGN description of the operator
- */
- public String getSBGNOperatorText() {
- return getOperatorText();
- }
-
- /**
- * Checks if the operator connects several inputs (that are modifiers) to one
- * output.
- *
- * @return <code>true</code> if the operator connects several inputs (that are
- * modifiers) to one output, <code>false</code> otherwise
- */
- public boolean isModifierOperator() {
- for (AbstractNode node : inputs) {
- if (node instanceof Modifier) {
- return true;
- }
- if (node instanceof NodeOperator) {
- if (((NodeOperator) node).isModifierOperator()) {
- return true;
- }
- }
- }
- return false;
- }
-
- /**
- * Adds outputs to the operator.
- *
- * @param newOutputs
- * output nodes to add
- */
- public void addOutputs(Collection<? extends AbstractNode> newOutputs) {
- for (AbstractNode output : newOutputs) {
- addOutput(output);
- }
- }
-
- /**
- * @return the inputs
- * @see #inputs
- */
- public List<AbstractNode> getInputs() {
- return inputs;
- }
-
- /**
- * @param inputs
- * the inputs to set
- * @see #inputs
- */
- public void setInputs(List<AbstractNode> inputs) {
- this.inputs = inputs;
- }
-
- /**
- * @return the outputs
- * @see #outputs
- */
- public List<AbstractNode> getOutputs() {
- return outputs;
- }
-
- /**
- * @param outputs
- * the outputs to set
- * @see #outputs
- */
- public void setOutputs(List<AbstractNode> outputs) {
- this.outputs = outputs;
- }
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.OneToMany;
+import javax.persistence.OrderBy;
+
+import org.apache.log4j.Logger;
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+
+/**
+ * One of two known types of nodes in the {@link Reaction}. It describes
+ * relation between two (or more) nodes in the reaction. There are few types of
+ * relations that are implemented:
+ * <ul>
+ * <li>{@link AndOperator} - when the output node is a result of logic "and
+ * operator" between two or more input nodes</li>
+ * <li>{@link AssociationOperator} - when the output node is a result of logic
+ * "and operator" between two or more input nodes</li>
+ * <li>{@link DissociationOperator} - when two (or more) output nodes is a
+ * result of dissociation of the input</li>
+ * <li>{@link NandOperator} - when the output node is a result of logic "nand
+ * operator" between two or more input nodes</li>
+ * <li>{@link OrOperator} - when the output node is a result of logic "or
+ * operator" between two or more input nodes</li>
+ * <li>{@link SplitOperator} - when two (or more) output nodes is a result of
+ * spliting (dissociation???) of the input</li>
+ * <li>{@link TruncationOperator} - when the output nodes are a result of
+ * truncation of the input. As a result we will get truncated node and the
+ * reminder part.</li>
+ * <li>{@link UnknownOperator} - when the output node is a result of logic
+ * operator between two or more input nodes, but the logic is unknown</li>
+ * </ul>
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("GENERIC_OPERATOR_NODE")
+public abstract class NodeOperator extends AbstractNode {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(NodeOperator.class);
+
+ /**
+ * List of input nodes.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(fetch = FetchType.EAGER, mappedBy = "nodeOperatorForInput")
+ @OrderBy("id")
+ private List<AbstractNode> inputs = new ArrayList<>();
+
+ /**
+ * List of output nodes.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(fetch = FetchType.EAGER, mappedBy = "nodeOperatorForOutput")
+ @OrderBy("id")
+ private List<AbstractNode> outputs = new ArrayList<>();
+
+ /**
+ * Default constructor.
+ */
+ public NodeOperator() {
+ }
+
+ /**
+ * Creates operator using the data from the original operator in the parameter.
+ *
+ * @param operator
+ * original operator from which data is initialized
+ */
+ public NodeOperator(NodeOperator operator) {
+ super(operator);
+
+ for (AbstractNode node : operator.getInputs()) {
+ addInput(node);
+ }
+ for (AbstractNode node : operator.getOutputs()) {
+ addOutput(node);
+ }
+ }
+
+ /**
+ * Adds input node.
+ *
+ * @param node
+ * node to add
+ */
+ public void addInput(AbstractNode node) {
+ node.setNodeOperatorForInput(this);
+ if (inputs.contains(node)) {
+ throw new InvalidArgumentException("Node already on the list: " + node);
+ }
+ inputs.add(node);
+ }
+
+ /**
+ * Adds set of inputs.
+ *
+ * @param newInputs
+ * set of input nodes to add
+ */
+ public void addInputs(Collection<? extends AbstractNode> newInputs) {
+ for (AbstractNode input : newInputs) {
+ addInput(input);
+ }
+ }
+
+ /**
+ * Checks if the operator connects several inputs to one output.
+ *
+ * @return <code>true</code> if the operator connects several inputs to one
+ * output, <code>false</code> otherwise
+ */
+ public boolean isReactantOperator() {
+ for (AbstractNode node : inputs) {
+ if (node instanceof Reactant) {
+ return true;
+ }
+ if (node instanceof NodeOperator) {
+ if (((NodeOperator) node).isReactantOperator()) {
+ return true;
+ }
+ }
+
+ }
+ return false;
+ }
+
+ /**
+ * Adds output to the operator.
+ *
+ * @param node
+ * output node to add
+ */
+ public void addOutput(AbstractNode node) {
+ node.setNodeOperatorForOutput(this);
+ if (outputs.contains(node)) {
+ throw new InvalidArgumentException("Node already on the list: " + node);
+ }
+ outputs.add(node);
+ }
+
+ /**
+ * Checks if the operator connects one input to several outputs.
+ *
+ * @return <code>true</code> if the operator connects one input to several
+ * outputs, <code>false</code> otherwise
+ */
+ public boolean isProductOperator() {
+ for (AbstractNode node : outputs) {
+ if (node instanceof Product) {
+ return true;
+ }
+ if (node instanceof NodeOperator) {
+ if (((NodeOperator) node).isProductOperator()) {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Returns one character length description of the operator.
+ *
+ * @return one character length description of the operator
+ */
+ public abstract String getOperatorText();
+
+ /**
+ * Returns SBGN description of the operator.
+ *
+ * @return SBGN description of the operator
+ */
+ public String getSBGNOperatorText() {
+ return getOperatorText();
+ }
+
+ /**
+ * Checks if the operator connects several inputs (that are modifiers) to one
+ * output.
+ *
+ * @return <code>true</code> if the operator connects several inputs (that are
+ * modifiers) to one output, <code>false</code> otherwise
+ */
+ public boolean isModifierOperator() {
+ for (AbstractNode node : inputs) {
+ if (node instanceof Modifier) {
+ return true;
+ }
+ if (node instanceof NodeOperator) {
+ if (((NodeOperator) node).isModifierOperator()) {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Adds outputs to the operator.
+ *
+ * @param newOutputs
+ * output nodes to add
+ */
+ public void addOutputs(Collection<? extends AbstractNode> newOutputs) {
+ for (AbstractNode output : newOutputs) {
+ addOutput(output);
+ }
+ }
+
+ /**
+ * @return the inputs
+ * @see #inputs
+ */
+ public List<AbstractNode> getInputs() {
+ return inputs;
+ }
+
+ /**
+ * @param inputs
+ * the inputs to set
+ * @see #inputs
+ */
+ public void setInputs(List<AbstractNode> inputs) {
+ this.inputs = inputs;
+ }
+
+ /**
+ * @return the outputs
+ * @see #outputs
+ */
+ public List<AbstractNode> getOutputs() {
+ return outputs;
+ }
+
+ /**
+ * @param outputs
+ * the outputs to set
+ * @see #outputs
+ */
+ public void setOutputs(List<AbstractNode> outputs) {
+ this.outputs = outputs;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/NodeOperatorComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/NodeOperatorComparator.java
index cbe96d3692..b8ca13c0f6 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/NodeOperatorComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/NodeOperatorComparator.java
@@ -1,101 +1,101 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.IntegerComparator;
-
-/**
- * This class implements comparator interface for {@link NodeOperator}. It also
- * handles comparison of subclasses of {@link NodeOperator} class.
- *
- *
- * @author Piotr Gawron
- *
- */
-public class NodeOperatorComparator extends Comparator<NodeOperator> {
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(NodeOperatorComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public NodeOperatorComparator(double epsilon) {
- super(NodeOperator.class);
- this.epsilon = epsilon;
- }
-
- protected Comparator<?> getParentComparator() {
- return new AbstractNodeComparator(epsilon);
- }
-
- /**
- * Default constructor.
- */
- public NodeOperatorComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected int internalCompare(NodeOperator arg0, NodeOperator arg1) {
- AbstractNodeComparator anComparator = new AbstractNodeComparator(epsilon);
-
- IntegerComparator integerComparator = new IntegerComparator();
-
- if (integerComparator.compare(arg0.getInputs().size(), arg1.getInputs().size()) != 0) {
- logger.debug("Different input size: " + arg0.getInputs().size() + ", " + arg1.getInputs().size());
- return integerComparator.compare(arg0.getInputs().size(), arg1.getInputs().size());
- }
- if (integerComparator.compare(arg0.getOutputs().size(), arg1.getOutputs().size()) != 0) {
- logger.debug("Different output size: " + arg0.getOutputs().size() + ", " + arg1.getOutputs().size());
- return integerComparator.compare(arg0.getOutputs().size(), arg1.getOutputs().size());
- }
-
- for (int i = 0; i < arg0.getInputs().size(); i++) {
- AbstractNode node1 = arg0.getInputs().get(i);
- int status = -1;
- for (int j = 0; j < arg1.getInputs().size(); j++) {
- AbstractNode node2 = arg1.getInputs().get(j);
- int tmpStatus = anComparator.compare(node1, node2);
- if (tmpStatus == 0) {
- status = 0;
- break;
- }
- }
- if (status != 0) {
- logger.debug("Can't find match in inputs.");
- return status;
- }
- }
- for (int i = 0; i < arg0.getOutputs().size(); i++) {
- AbstractNode node1 = arg0.getOutputs().get(i);
- int status = -1;
- for (int j = 0; j < arg1.getOutputs().size(); j++) {
- AbstractNode node2 = arg1.getOutputs().get(j);
- int tmpStatus = anComparator.compare(node1, node2);
- if (tmpStatus == 0) {
- status = 0;
- break;
- }
- }
- if (status != 0) {
- logger.debug("Can't find match in outputs.");
- return status;
- }
- }
-
- return 0;
- }
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.IntegerComparator;
+
+/**
+ * This class implements comparator interface for {@link NodeOperator}. It also
+ * handles comparison of subclasses of {@link NodeOperator} class.
+ *
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class NodeOperatorComparator extends Comparator<NodeOperator> {
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(NodeOperatorComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public NodeOperatorComparator(double epsilon) {
+ super(NodeOperator.class);
+ this.epsilon = epsilon;
+ }
+
+ protected Comparator<?> getParentComparator() {
+ return new AbstractNodeComparator(epsilon);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public NodeOperatorComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(NodeOperator arg0, NodeOperator arg1) {
+ AbstractNodeComparator anComparator = new AbstractNodeComparator(epsilon);
+
+ IntegerComparator integerComparator = new IntegerComparator();
+
+ if (integerComparator.compare(arg0.getInputs().size(), arg1.getInputs().size()) != 0) {
+ logger.debug("Different input size: " + arg0.getInputs().size() + ", " + arg1.getInputs().size());
+ return integerComparator.compare(arg0.getInputs().size(), arg1.getInputs().size());
+ }
+ if (integerComparator.compare(arg0.getOutputs().size(), arg1.getOutputs().size()) != 0) {
+ logger.debug("Different output size: " + arg0.getOutputs().size() + ", " + arg1.getOutputs().size());
+ return integerComparator.compare(arg0.getOutputs().size(), arg1.getOutputs().size());
+ }
+
+ for (int i = 0; i < arg0.getInputs().size(); i++) {
+ AbstractNode node1 = arg0.getInputs().get(i);
+ int status = -1;
+ for (int j = 0; j < arg1.getInputs().size(); j++) {
+ AbstractNode node2 = arg1.getInputs().get(j);
+ int tmpStatus = anComparator.compare(node1, node2);
+ if (tmpStatus == 0) {
+ status = 0;
+ break;
+ }
+ }
+ if (status != 0) {
+ logger.debug("Can't find match in inputs.");
+ return status;
+ }
+ }
+ for (int i = 0; i < arg0.getOutputs().size(); i++) {
+ AbstractNode node1 = arg0.getOutputs().get(i);
+ int status = -1;
+ for (int j = 0; j < arg1.getOutputs().size(); j++) {
+ AbstractNode node2 = arg1.getOutputs().get(j);
+ int tmpStatus = anComparator.compare(node1, node2);
+ if (tmpStatus == 0) {
+ status = 0;
+ break;
+ }
+ }
+ if (status != 0) {
+ logger.debug("Can't find match in outputs.");
+ return status;
+ }
+ }
+
+ return 0;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/OrOperator.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/OrOperator.java
index 7995a1572d..267fab63a6 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/OrOperator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/OrOperator.java
@@ -1,68 +1,68 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-/**
- * Class representing boolean "or operator" between two or more nodes in the
- * reaction.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("OR_OPERATOR_NODE")
-public class OrOperator extends NodeOperator {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(OrOperator.class);
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param operator
- * parent operator from which we copy data
- */
- public OrOperator(OrOperator operator) {
- super(operator);
- }
-
- /**
- * Default constructor.
- */
- public OrOperator() {
- super();
- }
-
- @Override
- public String getOperatorText() {
- return "|";
- }
-
- @Override
- public String getSBGNOperatorText() {
- return "OR";
- }
-
- @Override
- public OrOperator copy() {
- if (this.getClass() == OrOperator.class) {
- return new OrOperator(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * Class representing boolean "or operator" between two or more nodes in the
+ * reaction.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("OR_OPERATOR_NODE")
+public class OrOperator extends NodeOperator {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(OrOperator.class);
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param operator
+ * parent operator from which we copy data
+ */
+ public OrOperator(OrOperator operator) {
+ super(operator);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public OrOperator() {
+ super();
+ }
+
+ @Override
+ public String getOperatorText() {
+ return "|";
+ }
+
+ @Override
+ public String getSBGNOperatorText() {
+ return "OR";
+ }
+
+ @Override
+ public OrOperator copy() {
+ if (this.getClass() == OrOperator.class) {
+ return new OrOperator(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Product.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Product.java
index 7513f79195..63bb09a4df 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Product.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Product.java
@@ -1,63 +1,63 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * Represents product of the reaction (in the reaction).
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("PRODUCT_NODE")
-public class Product extends ReactionNode {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public Product() {
- super();
- }
-
- /**
- * Constructor that creates product for given {@link Species}. These
- * elements reference to the objects in the
- * {@link lcsb.mapviewer.model.map.model.db.model.map.Model Model} that
- * represents this product.
- *
- * @param element
- * element that represent this product
- */
- public Product(Species element) {
- super(element);
- }
-
- /**
- * Constructor that initialize the product with data from parameter.
- *
- * @param original
- * original product used for data initalization
- */
- protected Product(Product original) {
- super(original);
- }
-
- @Override
- public Product copy() {
- if (this.getClass() == Product.class) {
- return new Product(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * Represents product of the reaction (in the reaction).
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("PRODUCT_NODE")
+public class Product extends ReactionNode {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public Product() {
+ super();
+ }
+
+ /**
+ * Constructor that creates product for given {@link Species}. These
+ * elements reference to the objects in the
+ * {@link lcsb.mapviewer.model.map.model.db.model.map.Model Model} that
+ * represents this product.
+ *
+ * @param element
+ * element that represent this product
+ */
+ public Product(Species element) {
+ super(element);
+ }
+
+ /**
+ * Constructor that initialize the product with data from parameter.
+ *
+ * @param original
+ * original product used for data initalization
+ */
+ protected Product(Product original) {
+ super(original);
+ }
+
+ @Override
+ public Product copy() {
+ if (this.getClass() == Product.class) {
+ return new Product(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reactant.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reactant.java
index 4484a4bc15..ab8024ae03 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reactant.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reactant.java
@@ -1,62 +1,62 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * Represents reactant of the reaction.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("REACTANT_NODE")
-public class Reactant extends ReactionNode {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public Reactant() {
- super();
- }
-
- /**
- * Constructor that creates reactant for a given {@link Species}. These
- * elements reference to the objects in the
- * {@link lcsb.mapviewer.model.map.model.db.model.map.Model Model} that
- * represents this reactant.
- *
- * @param element
- * element that represent this reactant
- */
- public Reactant(Species element) {
- super(element);
- }
-
- /**
- * Constructor that initialize the reactant with data from parameter.
- *
- * @param original
- * original reactant used for data initalization
- */
- public Reactant(Reactant original) {
- super(original);
- }
-
- @Override
- public Reactant copy() {
- if (this.getClass() == Reactant.class) {
- return new Reactant(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * Represents reactant of the reaction.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("REACTANT_NODE")
+public class Reactant extends ReactionNode {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public Reactant() {
+ super();
+ }
+
+ /**
+ * Constructor that creates reactant for a given {@link Species}. These
+ * elements reference to the objects in the
+ * {@link lcsb.mapviewer.model.map.model.db.model.map.Model Model} that
+ * represents this reactant.
+ *
+ * @param element
+ * element that represent this reactant
+ */
+ public Reactant(Species element) {
+ super(element);
+ }
+
+ /**
+ * Constructor that initialize the reactant with data from parameter.
+ *
+ * @param original
+ * original reactant used for data initalization
+ */
+ public Reactant(Reactant original) {
+ super(original);
+ }
+
+ @Override
+ public Reactant copy() {
+ if (this.getClass() == Reactant.class) {
+ return new Reactant(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
index 84d23941b6..4b3ff344ca 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
@@ -1,892 +1,892 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Comparator;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import javax.persistence.CollectionTable;
-import javax.persistence.Column;
-import javax.persistence.DiscriminatorColumn;
-import javax.persistence.DiscriminatorType;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.ElementCollection;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Inheritance;
-import javax.persistence.InheritanceType;
-import javax.persistence.JoinColumn;
-import javax.persistence.JoinTable;
-import javax.persistence.ManyToMany;
-import javax.persistence.ManyToOne;
-import javax.persistence.OneToMany;
-import javax.persistence.OneToOne;
-import javax.persistence.OrderBy;
-import javax.persistence.Table;
-import javax.xml.bind.annotation.XmlTransient;
-
-import org.apache.log4j.Logger;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-import org.hibernate.annotations.IndexColumn;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.common.geometry.LineTransformation;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.map.reaction.type.ReactionRect;
-import lcsb.mapviewer.model.map.reaction.type.ReducedNotation;
-import lcsb.mapviewer.model.map.reaction.type.TwoProductReactionInterface;
-import lcsb.mapviewer.model.map.reaction.type.TwoReactantReactionInterface;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * This class describes reaction in the {@link Model}. Every reaction consists
- * of set of participants (nodes):
- * <ul>
- * <li>{@link Reactant reactants},</li>
- * <li>{@link Product products},</li>
- * <li>{@link Modifier modifiers}.</li>
- * </ul>
- * These nodes are connected using {@link NodeOperator operators} that define
- * relation among them.<br/>
- * <br/>
- * There are also other fields that describes reaction (like {@link #reversible}
- * , {@link #kineticLaw}, etc.).<br/>
- * <br/>
- * This class is general and shouldn't be used (except during initialization).
- * There are few extensions of this class (in sub-package:
- * {@link lcsb.mapviewer.model.map.reaction.type type}) that defines specific
- * reaction type.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "reaction_table")
-@Inheritance(strategy = InheritanceType.SINGLE_TABLE)
-@DiscriminatorColumn(name = "reaction_type_db", discriminatorType = DiscriminatorType.STRING)
-@DiscriminatorValue("GENERIC_REACTION")
-public class Reaction implements BioEntity {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Comparator of reactions that compare them using {@link #idReaction
- * identifier} as a key.
- */
- public static final Comparator<Reaction> ID_COMPARATOR = new Comparator<Reaction>() {
- @Override
- public int compare(Reaction reaction1, Reaction reaction2) {
- return reaction1.getIdReaction().compareTo(reaction2.getIdReaction());
- }
- };
-
- /**
- * Default class logger.
- */
-
- private static Logger logger = Logger.getLogger(Reaction.class.getName());
-
- /**
- * Unique database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- /**
- * List of {@link AbstractNode nodes} in the reaction.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(mappedBy = "reaction")
- @OrderBy("id")
- private List<AbstractNode> nodes = new ArrayList<>();
-
- /**
- * Description of the reaction.
- */
- @Column(name = "notes", columnDefinition = "TEXT")
- private String notes = "";
-
- /**
- * Identifier of the reaction. Unique in the {@link Model}.
- */
- private String idReaction = "";
-
- /**
- * Name of the reaction.
- */
- private String name = "";
-
- /**
- * Is the reaction reversible.
- */
- private boolean reversible = false;
-
- /**
- * Symbol of the reaction (RECON).
- */
- private String symbol = null;
-
- /**
- * Abbreviation of the reaction (RECON).
- */
- private String abbreviation = null;
-
- /**
- * Formula (RECON).
- */
- private String formula = null;
-
- /**
- * Mechanical confidence score (RECON).
- */
- private Integer mechanicalConfidenceScore = null;
-
- /**
- * Lower bound (RECON).
- */
- private Double lowerBound = null;
-
- /**
- * Upper bound (RECON).
- */
- private Double upperBound = null;
-
- /**
- * Subsystem (RECON).
- */
- private String subsystem = null;
-
- /**
- * Gene protein reaction (RECON).
- */
- private String geneProteinReaction = null;
-
- /**
- * Zoom level visibility for semantic zooming.
- */
- private String visibilityLevel = "";
-
- /**
- * Lists of all synonyms used for describing this element.
- */
- @ElementCollection
- @CollectionTable(name = "reaction_synonyms", joinColumns = @JoinColumn(name = "idDb"))
- @Column(name = "synonym")
- @IndexColumn(name = "idx")
- @Cascade({ org.hibernate.annotations.CascadeType.ALL })
- private List<String> synonyms = new ArrayList<>();
-
- /**
- * Set of annotations (references to external resources) that describe this
- * reaction.
- */
- @Cascade({ CascadeType.ALL })
- @ManyToMany(fetch = FetchType.EAGER)
- @JoinTable(name = "reaction_miriam", joinColumns = {
- @JoinColumn(name = "reaction_id", referencedColumnName = "idDb", nullable = false, updatable = false) }, inverseJoinColumns = {
- @JoinColumn(name = "miriam_id", referencedColumnName = "idDb", nullable = true, updatable = true) })
- private Set<MiriamData> miriamDataSet = new HashSet<>();
-
- /**
- * ModelData where reaction is placed.
- */
- @ManyToOne(fetch = FetchType.LAZY)
- private ModelData model;
-
- @Cascade({ CascadeType.ALL })
- @OneToOne
- private SbmlKinetics kinetics;
-
- /**
- * Default constructor.
- */
- public Reaction() {
- }
-
- /**
- * Creates reaction based on the information from the reaction passed as
- * parameter.
- *
- * @param original
- * original reaction
- */
- public Reaction(Reaction original) {
- // don't copy nodes - reactions refers to this objects (maybe it should be
- // refactored)
- for (AbstractNode node : original.getNodes()) {
- addNode(node);
- }
-
- notes = original.getNotes();
- idReaction = original.getIdReaction();
- name = original.getName();
- reversible = original.reversible;
- miriamDataSet = new HashSet<>();
- for (MiriamData md : original.getMiriamData()) {
- miriamDataSet.add(new MiriamData(md));
- }
-
- symbol = original.getSymbol();
- abbreviation = original.getAbbreviation();
- formula = original.getFormula();
- mechanicalConfidenceScore = original.getMechanicalConfidenceScore();
- lowerBound = original.getLowerBound();
- upperBound = original.getUpperBound();
- subsystem = original.getSubsystem();
- geneProteinReaction = original.getGeneProteinReaction();
- synonyms = new ArrayList<>();
- for (String synonym : original.getSynonyms()) {
- synonyms.add(synonym);
- }
- setVisibilityLevel(original.getVisibilityLevel());
- if (original.getKinetics() != null) {
- setKinetics(original.getKinetics().copy());
- }
-
- }
-
- public Reaction(String reactionId) {
- setIdReaction(reactionId);
- }
-
- /**
- * Adds node to the reaction.
- *
- * @param node
- * node to add
- */
- public void addNode(AbstractNode node) {
- node.setReaction(this);
- nodes.add(node);
- }
-
- /**
- * Adds reactant.
- *
- * @param reactant
- * reactant to add
- */
- public void addReactant(Reactant reactant) {
- addNode(reactant);
- }
-
- /**
- * Adds product.
- *
- * @param product
- * product to add
- */
- public void addProduct(Product product) {
- addNode(product);
- }
-
- /**
- * Adds modifier.
- *
- * @param modifier
- * modifier to add
- */
- public void addModifier(Modifier modifier) {
- addNode(modifier);
- }
-
- /**
- * Returns list of reaction products.
- *
- * @return list of products
- */
- public List<Product> getProducts() {
- List<Product> result = new ArrayList<>();
- for (AbstractNode node : nodes) {
- if (node instanceof Product) {
- result.add((Product) node);
- }
- }
- return result;
- }
-
- /**
- * Returns list of reaction reactants.
- *
- * @return list of reactants
- */
- public List<Reactant> getReactants() {
- List<Reactant> result = new ArrayList<>();
- for (AbstractNode node : nodes) {
- if (node instanceof Reactant) {
- result.add((Reactant) node);
- }
- }
- return result;
- }
-
- /**
- * Returns list of reaction modifiers.
- *
- * @return list of modifiers
- */
- public List<Modifier> getModifiers() {
- List<Modifier> result = new ArrayList<Modifier>();
- for (AbstractNode node : nodes) {
- if (node instanceof Modifier) {
- result.add((Modifier) node);
- }
- }
- return result;
- }
-
- /**
- * This method return the minimum distance from the reaction representation (all
- * lines which describe reaction) and point given as a parameter.
- *
- * @param point
- * from where we look for the shortest possible distance
- *
- * @return the shortest possible distance from this reaction and point
- */
- public double getDistanceFromPoint(Point2D point) {
- LineTransformation lt = new LineTransformation();
- double dist = Double.MAX_VALUE;
- List<Line2D> lines = getLines();
- for (Line2D line : lines) {
- double d2 = lt.distBetweenPointAndLineSegment(line, point);
- if (d2 < dist) {
- dist = d2;
- }
- }
- return dist;
- }
-
- /**
- * Return list of all lines in the reaction that describe it.
- *
- * @return list of all lines that describes every connection in the rection
- */
- public List<Line2D> getLines() {
- List<Line2D> result = new ArrayList<Line2D>();
- for (AbstractNode node : nodes) {
- result.addAll(node.getLine().getLines());
- }
- return result;
- }
-
- /**
- * Returns point on the reaction that is as close as possible to the given
- * parameter point.
- *
- * @param point
- * parameter point to which results will be as close as possible
- * @return the closest point to the parameter point that is placed on the
- * reaction
- */
- public Point2D getClosestPointTo(Point2D point) {
- LineTransformation lt = new LineTransformation();
- double dist = Double.MAX_VALUE;
- List<Line2D> lines = getLines();
- Point2D result = null;
- for (Line2D line : lines) {
- double d2 = lt.distBetweenPointAndLineSegment(line, point);
- if (d2 < dist) {
- dist = d2;
- result = lt.closestPointOnSegmentLineToPoint(line, point);
- }
- }
- return result;
- }
-
- /**
- * Returns short string describing type of the reaction.
- *
- * @return short string describing type of the reaction
- */
- public String getStringType() {
- return "Generic Reaction";
- }
-
- @Override
- public String getVisibilityLevel() {
- return visibilityLevel;
- }
-
- @Override
- public void setVisibilityLevel(String visibilityLevel) {
- this.visibilityLevel = visibilityLevel;
- }
-
- /**
- * Returns list of nodes (producst+rectants+modifiers) in the reaction.
- *
- * @return list of nodes (producst+rectants+modifiers) in the reaction
- */
- public List<ReactionNode> getReactionNodes() {
- List<ReactionNode> result = new ArrayList<ReactionNode>();
- for (AbstractNode node : nodes) {
- if (node instanceof ReactionNode) {
- result.add((ReactionNode) node);
- }
- }
- return result;
- }
-
- /**
- * Returns central line of the reaction. Central line is the line that separates
- * inputs from outputs.
- *
- * @return central line of the reaction
- */
- public Line2D getCenterLine() {
- Product product = getProducts().get(0);
- Reactant reactant = getReactants().get(0);
-
- Point2D startPoint = reactant.getLine().getPoints().get(reactant.getLine().getPoints().size() - 2);
- Point2D endPoint = product.getLine().getPoints().get(1);
-
- if (this instanceof TwoReactantReactionInterface) {
-
- NodeOperator firstOperator = null;
-
- for (NodeOperator operator : getOperators()) {
- if (operator.isReactantOperator() && firstOperator == null) {
- firstOperator = operator;
- }
- }
- if (firstOperator != null) {
- startPoint = firstOperator.getLine().getPoints().get(firstOperator.getLine().getPoints().size() - 2);
- }
- } else if (this instanceof TwoProductReactionInterface) {
-
- NodeOperator firstOperator = null;
-
- for (NodeOperator operator : getOperators()) {
- if (operator.isProductOperator() && firstOperator == null) {
- firstOperator = operator;
- }
- }
- if (firstOperator != null) {
- endPoint = firstOperator.getLine().getPoints().get(firstOperator.getLine().getPoints().size() - 2);
- }
- } else if (this instanceof ReducedNotation) {
- startPoint = reactant.getLine().getEndPoint();
- endPoint = product.getLine().getBeginPoint();
- }
-
- return new Line2D.Double(startPoint, endPoint);
- }
-
- /**
- * Removes modifier.
- *
- * @param modifier
- * modifier to remove
- */
- public void removeModifier(Modifier modifier) {
- nodes.remove(modifier);
- }
-
- /**
- * Removes {@link AbstractNode}.
- *
- * @param node
- * node to remove
- */
- public void removeNode(AbstractNode node) {
- nodes.remove(node);
- }
-
- /**
- * Returns {@link ReactionRect} object that defines a small object that should
- * be drawn on the central line of the reaction.
- *
- * @return {@link ReactionRect} object that defines a small object that should
- * be drawn on the central line of the reaction
- */
- public ReactionRect getReactionRect() {
- return null;
- }
-
- /**
- * Returns central point of the reaction - point on central line (see:
- * {@link #getCenterLine()}). This point determines one of the points where
- * modifiers are attached.
- *
- * @return central point of the reaction
- */
- public Point2D getCenterPoint() {
- Line2D line2D = getCenterLine();
- return new Point2D.Double((line2D.getX1() + line2D.getX2()) / 2, (line2D.getY1() + line2D.getY2()) / 2);
- }
-
- /**
- * Check if one of the nodes reference to the element.
- *
- * @param element
- * element to be checked
- * @return <code>true</code> if element is part of the reaction,
- * <code>false</code> otherwise
- */
- public boolean containsElement(Element element) {
- for (ReactionNode node : getReactionNodes()) {
- if (node.getElement().equals(element)) {
- return true;
- }
- }
- return false;
- }
-
- /**
- * Creates copy of the reaction.
- *
- * @return copy of the reaction
- */
- public Reaction copy() {
- if (this.getClass() == Reaction.class) {
- return new Reaction(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- /**
- * Returns list of all {@link NodeOperator operators}.
- *
- * @return list of all {@link NodeOperator operators}
- */
- public List<NodeOperator> getOperators() {
- List<NodeOperator> result = new ArrayList<NodeOperator>();
- for (AbstractNode node : getNodes()) {
- if (node instanceof NodeOperator) {
- result.add((NodeOperator) node);
- }
- }
- return result;
- }
-
- /**
- * @return the id
- * @see #id
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
- /**
- * @return the nodes
- * @see #nodes
- */
- public List<AbstractNode> getNodes() {
- return nodes;
- }
-
- /**
- * @param nodes
- * the nodes to set
- * @see #nodes
- */
- public void setNodes(List<AbstractNode> nodes) {
- this.nodes = nodes;
- }
-
- @Override
- public String getNotes() {
- return notes;
- }
-
- @Override
- public void setNotes(String notes) {
- this.notes = notes;
- }
-
- /**
- * @return the idReaction
- * @see #idReaction
- */
- public String getIdReaction() {
- return idReaction;
- }
-
- @Override
- public String getElementId() {
- return getIdReaction();
- }
-
- /**
- * @param idReaction
- * the idReaction to set
- * @see #idReaction
- */
- public void setIdReaction(String idReaction) {
- this.idReaction = idReaction;
- }
-
- @Override
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return the reversible
- * @see #reversible
- */
- public boolean isReversible() {
- return reversible;
- }
-
- /**
- * @param reversible
- * the reversible to set
- * @see #reversible
- */
- public void setReversible(boolean reversible) {
- this.reversible = reversible;
- }
-
- @Override
- public Set<MiriamData> getMiriamData() {
- return miriamDataSet;
- }
-
- @Override
- public void addMiriamData(Collection<MiriamData> miriamData) {
- for (MiriamData md : miriamData) {
- addMiriamData(md);
- }
- }
-
- /**
- * @return the model
- * @see #model
- */
- public ModelData getModelData() {
- return model;
- }
-
- /**
- * @param model
- * the model to set
- * @see #model
- */
- public void setModelData(ModelData model) {
- this.model = model;
- }
-
- @Override
- public void addMiriamData(MiriamData md) {
- if (this.miriamDataSet.contains(md)) {
- logger.warn("Miriam data (" + md.getDataType() + ": " + md.getResource() + ") for " + getIdReaction()
- + " already exists. Ignoring...");
- } else {
- this.miriamDataSet.add(md);
- }
- }
-
- /**
- * Sets model where the reaction is located.
- *
- * @param model2
- * model where the reaction is located
- */
- public void setModel(Model model2) {
- this.model = model2.getModelData();
- }
-
- @XmlTransient
- @Override
- public Model getModel() {
- return model.getModel();
- }
-
- @Override
- public String getSymbol() {
- return symbol;
- }
-
- @Override
- public void setSymbol(String symbol) {
- this.symbol = symbol;
- }
-
- @Override
- public String getAbbreviation() {
- return abbreviation;
- }
-
- @Override
- public void setAbbreviation(String abbreviation) {
- this.abbreviation = abbreviation;
- }
-
- @Override
- public String getFormula() {
- return formula;
- }
-
- @Override
- public void setFormula(String formula) {
- this.formula = formula;
- }
-
- /**
- * @return the mechanicalConfidenceScore
- * @see #mechanicalConfidenceScore
- */
- public Integer getMechanicalConfidenceScore() {
- return mechanicalConfidenceScore;
- }
-
- /**
- * @param mechanicalConfidenceScore
- * the mechanicalConfidenceScore to set
- * @see #mechanicalConfidenceScore
- */
- public void setMechanicalConfidenceScore(Integer mechanicalConfidenceScore) {
- this.mechanicalConfidenceScore = mechanicalConfidenceScore;
- }
-
- /**
- * @return the lowerBound
- * @see #lowerBound
- */
- public Double getLowerBound() {
- return lowerBound;
- }
-
- /**
- * @param lowerBound
- * the lowerBound to set
- * @see #lowerBound
- */
- public void setLowerBound(Double lowerBound) {
- this.lowerBound = lowerBound;
- }
-
- /**
- * @return the upperBound
- * @see #upperBound
- */
- public Double getUpperBound() {
- return upperBound;
- }
-
- /**
- * @param upperBound
- * the upperBound to set
- * @see #upperBound
- */
- public void setUpperBound(Double upperBound) {
- this.upperBound = upperBound;
- }
-
- /**
- * @return the subsystem
- * @see #subsystem
- */
- public String getSubsystem() {
- return subsystem;
- }
-
- /**
- * @param subsystem
- * the subsystem to set
- * @see #subsystem
- */
- public void setSubsystem(String subsystem) {
- this.subsystem = subsystem;
- }
-
- /**
- * @return the geneProteinReaction
- * @see #geneProteinReaction
- */
- public String getGeneProteinReaction() {
- return geneProteinReaction;
- }
-
- /**
- * @param geneProteinReaction
- * the geneProteinReaction to set
- * @see #geneProteinReaction
- */
- public void setGeneProteinReaction(String geneProteinReaction) {
- this.geneProteinReaction = geneProteinReaction;
- }
-
- /**
- * @return the synonyms
- * @see #synonyms
- */
- public List<String> getSynonyms() {
- return synonyms;
- }
-
- /**
- * @param synonyms
- * the synonyms to set
- * @see #synonyms
- */
- public void setSynonyms(List<String> synonyms) {
- this.synonyms = synonyms;
- }
-
- /**
- * Adds synonym to the {@link #synonyms}.
- *
- * @param synonym
- * new synonym to add
- */
- public void addSynonym(String synonym) {
- this.synonyms.add(synonym);
- }
-
- @Override
- public void setVisibilityLevel(Integer zoomLevelVisibility) {
- if (zoomLevelVisibility == null) {
- this.visibilityLevel = null;
- } else {
- this.visibilityLevel = zoomLevelVisibility + "";
- }
-
- }
-
- public SbmlKinetics getKinetics() {
- return kinetics;
- }
-
- public void setKinetics(SbmlKinetics kinetics) {
- this.kinetics = kinetics;
- }
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Comparator;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import javax.persistence.CollectionTable;
+import javax.persistence.Column;
+import javax.persistence.DiscriminatorColumn;
+import javax.persistence.DiscriminatorType;
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.ElementCollection;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.Inheritance;
+import javax.persistence.InheritanceType;
+import javax.persistence.JoinColumn;
+import javax.persistence.JoinTable;
+import javax.persistence.ManyToMany;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
+import javax.persistence.OneToOne;
+import javax.persistence.OrderBy;
+import javax.persistence.Table;
+import javax.xml.bind.annotation.XmlTransient;
+
+import org.apache.log4j.Logger;
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+import org.hibernate.annotations.IndexColumn;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.common.geometry.LineTransformation;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.reaction.type.ReactionRect;
+import lcsb.mapviewer.model.map.reaction.type.ReducedNotation;
+import lcsb.mapviewer.model.map.reaction.type.TwoProductReactionInterface;
+import lcsb.mapviewer.model.map.reaction.type.TwoReactantReactionInterface;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * This class describes reaction in the {@link Model}. Every reaction consists
+ * of set of participants (nodes):
+ * <ul>
+ * <li>{@link Reactant reactants},</li>
+ * <li>{@link Product products},</li>
+ * <li>{@link Modifier modifiers}.</li>
+ * </ul>
+ * These nodes are connected using {@link NodeOperator operators} that define
+ * relation among them.<br/>
+ * <br/>
+ * There are also other fields that describes reaction (like {@link #reversible}
+ * , {@link #kineticLaw}, etc.).<br/>
+ * <br/>
+ * This class is general and shouldn't be used (except during initialization).
+ * There are few extensions of this class (in sub-package:
+ * {@link lcsb.mapviewer.model.map.reaction.type type}) that defines specific
+ * reaction type.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "reaction_table")
+@Inheritance(strategy = InheritanceType.SINGLE_TABLE)
+@DiscriminatorColumn(name = "reaction_type_db", discriminatorType = DiscriminatorType.STRING)
+@DiscriminatorValue("GENERIC_REACTION")
+public class Reaction implements BioEntity {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Comparator of reactions that compare them using {@link #idReaction
+ * identifier} as a key.
+ */
+ public static final Comparator<Reaction> ID_COMPARATOR = new Comparator<Reaction>() {
+ @Override
+ public int compare(Reaction reaction1, Reaction reaction2) {
+ return reaction1.getIdReaction().compareTo(reaction2.getIdReaction());
+ }
+ };
+
+ /**
+ * Default class logger.
+ */
+
+ private static Logger logger = Logger.getLogger(Reaction.class.getName());
+
+ /**
+ * Unique database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * List of {@link AbstractNode nodes} in the reaction.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(mappedBy = "reaction")
+ @OrderBy("id")
+ private List<AbstractNode> nodes = new ArrayList<>();
+
+ /**
+ * Description of the reaction.
+ */
+ @Column(name = "notes", columnDefinition = "TEXT")
+ private String notes = "";
+
+ /**
+ * Identifier of the reaction. Unique in the {@link Model}.
+ */
+ private String idReaction = "";
+
+ /**
+ * Name of the reaction.
+ */
+ private String name = "";
+
+ /**
+ * Is the reaction reversible.
+ */
+ private boolean reversible = false;
+
+ /**
+ * Symbol of the reaction (RECON).
+ */
+ private String symbol = null;
+
+ /**
+ * Abbreviation of the reaction (RECON).
+ */
+ private String abbreviation = null;
+
+ /**
+ * Formula (RECON).
+ */
+ private String formula = null;
+
+ /**
+ * Mechanical confidence score (RECON).
+ */
+ private Integer mechanicalConfidenceScore = null;
+
+ /**
+ * Lower bound (RECON).
+ */
+ private Double lowerBound = null;
+
+ /**
+ * Upper bound (RECON).
+ */
+ private Double upperBound = null;
+
+ /**
+ * Subsystem (RECON).
+ */
+ private String subsystem = null;
+
+ /**
+ * Gene protein reaction (RECON).
+ */
+ private String geneProteinReaction = null;
+
+ /**
+ * Zoom level visibility for semantic zooming.
+ */
+ private String visibilityLevel = "";
+
+ /**
+ * Lists of all synonyms used for describing this element.
+ */
+ @ElementCollection
+ @CollectionTable(name = "reaction_synonyms", joinColumns = @JoinColumn(name = "idDb"))
+ @Column(name = "synonym")
+ @IndexColumn(name = "idx")
+ @Cascade({ org.hibernate.annotations.CascadeType.ALL })
+ private List<String> synonyms = new ArrayList<>();
+
+ /**
+ * Set of annotations (references to external resources) that describe this
+ * reaction.
+ */
+ @Cascade({ CascadeType.ALL })
+ @ManyToMany(fetch = FetchType.EAGER)
+ @JoinTable(name = "reaction_miriam", joinColumns = {
+ @JoinColumn(name = "reaction_id", referencedColumnName = "idDb", nullable = false, updatable = false) }, inverseJoinColumns = {
+ @JoinColumn(name = "miriam_id", referencedColumnName = "idDb", nullable = true, updatable = true) })
+ private Set<MiriamData> miriamDataSet = new HashSet<>();
+
+ /**
+ * ModelData where reaction is placed.
+ */
+ @ManyToOne(fetch = FetchType.LAZY)
+ private ModelData model;
+
+ @Cascade({ CascadeType.ALL })
+ @OneToOne
+ private SbmlKinetics kinetics;
+
+ /**
+ * Default constructor.
+ */
+ public Reaction() {
+ }
+
+ /**
+ * Creates reaction based on the information from the reaction passed as
+ * parameter.
+ *
+ * @param original
+ * original reaction
+ */
+ public Reaction(Reaction original) {
+ // don't copy nodes - reactions refers to this objects (maybe it should be
+ // refactored)
+ for (AbstractNode node : original.getNodes()) {
+ addNode(node);
+ }
+
+ notes = original.getNotes();
+ idReaction = original.getIdReaction();
+ name = original.getName();
+ reversible = original.reversible;
+ miriamDataSet = new HashSet<>();
+ for (MiriamData md : original.getMiriamData()) {
+ miriamDataSet.add(new MiriamData(md));
+ }
+
+ symbol = original.getSymbol();
+ abbreviation = original.getAbbreviation();
+ formula = original.getFormula();
+ mechanicalConfidenceScore = original.getMechanicalConfidenceScore();
+ lowerBound = original.getLowerBound();
+ upperBound = original.getUpperBound();
+ subsystem = original.getSubsystem();
+ geneProteinReaction = original.getGeneProteinReaction();
+ synonyms = new ArrayList<>();
+ for (String synonym : original.getSynonyms()) {
+ synonyms.add(synonym);
+ }
+ setVisibilityLevel(original.getVisibilityLevel());
+ if (original.getKinetics() != null) {
+ setKinetics(original.getKinetics().copy());
+ }
+
+ }
+
+ public Reaction(String reactionId) {
+ setIdReaction(reactionId);
+ }
+
+ /**
+ * Adds node to the reaction.
+ *
+ * @param node
+ * node to add
+ */
+ public void addNode(AbstractNode node) {
+ node.setReaction(this);
+ nodes.add(node);
+ }
+
+ /**
+ * Adds reactant.
+ *
+ * @param reactant
+ * reactant to add
+ */
+ public void addReactant(Reactant reactant) {
+ addNode(reactant);
+ }
+
+ /**
+ * Adds product.
+ *
+ * @param product
+ * product to add
+ */
+ public void addProduct(Product product) {
+ addNode(product);
+ }
+
+ /**
+ * Adds modifier.
+ *
+ * @param modifier
+ * modifier to add
+ */
+ public void addModifier(Modifier modifier) {
+ addNode(modifier);
+ }
+
+ /**
+ * Returns list of reaction products.
+ *
+ * @return list of products
+ */
+ public List<Product> getProducts() {
+ List<Product> result = new ArrayList<>();
+ for (AbstractNode node : nodes) {
+ if (node instanceof Product) {
+ result.add((Product) node);
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Returns list of reaction reactants.
+ *
+ * @return list of reactants
+ */
+ public List<Reactant> getReactants() {
+ List<Reactant> result = new ArrayList<>();
+ for (AbstractNode node : nodes) {
+ if (node instanceof Reactant) {
+ result.add((Reactant) node);
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Returns list of reaction modifiers.
+ *
+ * @return list of modifiers
+ */
+ public List<Modifier> getModifiers() {
+ List<Modifier> result = new ArrayList<Modifier>();
+ for (AbstractNode node : nodes) {
+ if (node instanceof Modifier) {
+ result.add((Modifier) node);
+ }
+ }
+ return result;
+ }
+
+ /**
+ * This method return the minimum distance from the reaction representation (all
+ * lines which describe reaction) and point given as a parameter.
+ *
+ * @param point
+ * from where we look for the shortest possible distance
+ *
+ * @return the shortest possible distance from this reaction and point
+ */
+ public double getDistanceFromPoint(Point2D point) {
+ LineTransformation lt = new LineTransformation();
+ double dist = Double.MAX_VALUE;
+ List<Line2D> lines = getLines();
+ for (Line2D line : lines) {
+ double d2 = lt.distBetweenPointAndLineSegment(line, point);
+ if (d2 < dist) {
+ dist = d2;
+ }
+ }
+ return dist;
+ }
+
+ /**
+ * Return list of all lines in the reaction that describe it.
+ *
+ * @return list of all lines that describes every connection in the rection
+ */
+ public List<Line2D> getLines() {
+ List<Line2D> result = new ArrayList<Line2D>();
+ for (AbstractNode node : nodes) {
+ result.addAll(node.getLine().getLines());
+ }
+ return result;
+ }
+
+ /**
+ * Returns point on the reaction that is as close as possible to the given
+ * parameter point.
+ *
+ * @param point
+ * parameter point to which results will be as close as possible
+ * @return the closest point to the parameter point that is placed on the
+ * reaction
+ */
+ public Point2D getClosestPointTo(Point2D point) {
+ LineTransformation lt = new LineTransformation();
+ double dist = Double.MAX_VALUE;
+ List<Line2D> lines = getLines();
+ Point2D result = null;
+ for (Line2D line : lines) {
+ double d2 = lt.distBetweenPointAndLineSegment(line, point);
+ if (d2 < dist) {
+ dist = d2;
+ result = lt.closestPointOnSegmentLineToPoint(line, point);
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Returns short string describing type of the reaction.
+ *
+ * @return short string describing type of the reaction
+ */
+ public String getStringType() {
+ return "Generic Reaction";
+ }
+
+ @Override
+ public String getVisibilityLevel() {
+ return visibilityLevel;
+ }
+
+ @Override
+ public void setVisibilityLevel(String visibilityLevel) {
+ this.visibilityLevel = visibilityLevel;
+ }
+
+ /**
+ * Returns list of nodes (producst+rectants+modifiers) in the reaction.
+ *
+ * @return list of nodes (producst+rectants+modifiers) in the reaction
+ */
+ public List<ReactionNode> getReactionNodes() {
+ List<ReactionNode> result = new ArrayList<ReactionNode>();
+ for (AbstractNode node : nodes) {
+ if (node instanceof ReactionNode) {
+ result.add((ReactionNode) node);
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Returns central line of the reaction. Central line is the line that separates
+ * inputs from outputs.
+ *
+ * @return central line of the reaction
+ */
+ public Line2D getCenterLine() {
+ Product product = getProducts().get(0);
+ Reactant reactant = getReactants().get(0);
+
+ Point2D startPoint = reactant.getLine().getPoints().get(reactant.getLine().getPoints().size() - 2);
+ Point2D endPoint = product.getLine().getPoints().get(1);
+
+ if (this instanceof TwoReactantReactionInterface) {
+
+ NodeOperator firstOperator = null;
+
+ for (NodeOperator operator : getOperators()) {
+ if (operator.isReactantOperator() && firstOperator == null) {
+ firstOperator = operator;
+ }
+ }
+ if (firstOperator != null) {
+ startPoint = firstOperator.getLine().getPoints().get(firstOperator.getLine().getPoints().size() - 2);
+ }
+ } else if (this instanceof TwoProductReactionInterface) {
+
+ NodeOperator firstOperator = null;
+
+ for (NodeOperator operator : getOperators()) {
+ if (operator.isProductOperator() && firstOperator == null) {
+ firstOperator = operator;
+ }
+ }
+ if (firstOperator != null) {
+ endPoint = firstOperator.getLine().getPoints().get(firstOperator.getLine().getPoints().size() - 2);
+ }
+ } else if (this instanceof ReducedNotation) {
+ startPoint = reactant.getLine().getEndPoint();
+ endPoint = product.getLine().getBeginPoint();
+ }
+
+ return new Line2D.Double(startPoint, endPoint);
+ }
+
+ /**
+ * Removes modifier.
+ *
+ * @param modifier
+ * modifier to remove
+ */
+ public void removeModifier(Modifier modifier) {
+ nodes.remove(modifier);
+ }
+
+ /**
+ * Removes {@link AbstractNode}.
+ *
+ * @param node
+ * node to remove
+ */
+ public void removeNode(AbstractNode node) {
+ nodes.remove(node);
+ }
+
+ /**
+ * Returns {@link ReactionRect} object that defines a small object that should
+ * be drawn on the central line of the reaction.
+ *
+ * @return {@link ReactionRect} object that defines a small object that should
+ * be drawn on the central line of the reaction
+ */
+ public ReactionRect getReactionRect() {
+ return null;
+ }
+
+ /**
+ * Returns central point of the reaction - point on central line (see:
+ * {@link #getCenterLine()}). This point determines one of the points where
+ * modifiers are attached.
+ *
+ * @return central point of the reaction
+ */
+ public Point2D getCenterPoint() {
+ Line2D line2D = getCenterLine();
+ return new Point2D.Double((line2D.getX1() + line2D.getX2()) / 2, (line2D.getY1() + line2D.getY2()) / 2);
+ }
+
+ /**
+ * Check if one of the nodes reference to the element.
+ *
+ * @param element
+ * element to be checked
+ * @return <code>true</code> if element is part of the reaction,
+ * <code>false</code> otherwise
+ */
+ public boolean containsElement(Element element) {
+ for (ReactionNode node : getReactionNodes()) {
+ if (node.getElement().equals(element)) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Creates copy of the reaction.
+ *
+ * @return copy of the reaction
+ */
+ public Reaction copy() {
+ if (this.getClass() == Reaction.class) {
+ return new Reaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ /**
+ * Returns list of all {@link NodeOperator operators}.
+ *
+ * @return list of all {@link NodeOperator operators}
+ */
+ public List<NodeOperator> getOperators() {
+ List<NodeOperator> result = new ArrayList<NodeOperator>();
+ for (AbstractNode node : getNodes()) {
+ if (node instanceof NodeOperator) {
+ result.add((NodeOperator) node);
+ }
+ }
+ return result;
+ }
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ /**
+ * @return the nodes
+ * @see #nodes
+ */
+ public List<AbstractNode> getNodes() {
+ return nodes;
+ }
+
+ /**
+ * @param nodes
+ * the nodes to set
+ * @see #nodes
+ */
+ public void setNodes(List<AbstractNode> nodes) {
+ this.nodes = nodes;
+ }
+
+ @Override
+ public String getNotes() {
+ return notes;
+ }
+
+ @Override
+ public void setNotes(String notes) {
+ this.notes = notes;
+ }
+
+ /**
+ * @return the idReaction
+ * @see #idReaction
+ */
+ public String getIdReaction() {
+ return idReaction;
+ }
+
+ @Override
+ public String getElementId() {
+ return getIdReaction();
+ }
+
+ /**
+ * @param idReaction
+ * the idReaction to set
+ * @see #idReaction
+ */
+ public void setIdReaction(String idReaction) {
+ this.idReaction = idReaction;
+ }
+
+ @Override
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * @return the reversible
+ * @see #reversible
+ */
+ public boolean isReversible() {
+ return reversible;
+ }
+
+ /**
+ * @param reversible
+ * the reversible to set
+ * @see #reversible
+ */
+ public void setReversible(boolean reversible) {
+ this.reversible = reversible;
+ }
+
+ @Override
+ public Set<MiriamData> getMiriamData() {
+ return miriamDataSet;
+ }
+
+ @Override
+ public void addMiriamData(Collection<MiriamData> miriamData) {
+ for (MiriamData md : miriamData) {
+ addMiriamData(md);
+ }
+ }
+
+ /**
+ * @return the model
+ * @see #model
+ */
+ public ModelData getModelData() {
+ return model;
+ }
+
+ /**
+ * @param model
+ * the model to set
+ * @see #model
+ */
+ public void setModelData(ModelData model) {
+ this.model = model;
+ }
+
+ @Override
+ public void addMiriamData(MiriamData md) {
+ if (this.miriamDataSet.contains(md)) {
+ logger.warn("Miriam data (" + md.getDataType() + ": " + md.getResource() + ") for " + getIdReaction()
+ + " already exists. Ignoring...");
+ } else {
+ this.miriamDataSet.add(md);
+ }
+ }
+
+ /**
+ * Sets model where the reaction is located.
+ *
+ * @param model2
+ * model where the reaction is located
+ */
+ public void setModel(Model model2) {
+ this.model = model2.getModelData();
+ }
+
+ @XmlTransient
+ @Override
+ public Model getModel() {
+ return model.getModel();
+ }
+
+ @Override
+ public String getSymbol() {
+ return symbol;
+ }
+
+ @Override
+ public void setSymbol(String symbol) {
+ this.symbol = symbol;
+ }
+
+ @Override
+ public String getAbbreviation() {
+ return abbreviation;
+ }
+
+ @Override
+ public void setAbbreviation(String abbreviation) {
+ this.abbreviation = abbreviation;
+ }
+
+ @Override
+ public String getFormula() {
+ return formula;
+ }
+
+ @Override
+ public void setFormula(String formula) {
+ this.formula = formula;
+ }
+
+ /**
+ * @return the mechanicalConfidenceScore
+ * @see #mechanicalConfidenceScore
+ */
+ public Integer getMechanicalConfidenceScore() {
+ return mechanicalConfidenceScore;
+ }
+
+ /**
+ * @param mechanicalConfidenceScore
+ * the mechanicalConfidenceScore to set
+ * @see #mechanicalConfidenceScore
+ */
+ public void setMechanicalConfidenceScore(Integer mechanicalConfidenceScore) {
+ this.mechanicalConfidenceScore = mechanicalConfidenceScore;
+ }
+
+ /**
+ * @return the lowerBound
+ * @see #lowerBound
+ */
+ public Double getLowerBound() {
+ return lowerBound;
+ }
+
+ /**
+ * @param lowerBound
+ * the lowerBound to set
+ * @see #lowerBound
+ */
+ public void setLowerBound(Double lowerBound) {
+ this.lowerBound = lowerBound;
+ }
+
+ /**
+ * @return the upperBound
+ * @see #upperBound
+ */
+ public Double getUpperBound() {
+ return upperBound;
+ }
+
+ /**
+ * @param upperBound
+ * the upperBound to set
+ * @see #upperBound
+ */
+ public void setUpperBound(Double upperBound) {
+ this.upperBound = upperBound;
+ }
+
+ /**
+ * @return the subsystem
+ * @see #subsystem
+ */
+ public String getSubsystem() {
+ return subsystem;
+ }
+
+ /**
+ * @param subsystem
+ * the subsystem to set
+ * @see #subsystem
+ */
+ public void setSubsystem(String subsystem) {
+ this.subsystem = subsystem;
+ }
+
+ /**
+ * @return the geneProteinReaction
+ * @see #geneProteinReaction
+ */
+ public String getGeneProteinReaction() {
+ return geneProteinReaction;
+ }
+
+ /**
+ * @param geneProteinReaction
+ * the geneProteinReaction to set
+ * @see #geneProteinReaction
+ */
+ public void setGeneProteinReaction(String geneProteinReaction) {
+ this.geneProteinReaction = geneProteinReaction;
+ }
+
+ /**
+ * @return the synonyms
+ * @see #synonyms
+ */
+ public List<String> getSynonyms() {
+ return synonyms;
+ }
+
+ /**
+ * @param synonyms
+ * the synonyms to set
+ * @see #synonyms
+ */
+ public void setSynonyms(List<String> synonyms) {
+ this.synonyms = synonyms;
+ }
+
+ /**
+ * Adds synonym to the {@link #synonyms}.
+ *
+ * @param synonym
+ * new synonym to add
+ */
+ public void addSynonym(String synonym) {
+ this.synonyms.add(synonym);
+ }
+
+ @Override
+ public void setVisibilityLevel(Integer zoomLevelVisibility) {
+ if (zoomLevelVisibility == null) {
+ this.visibilityLevel = null;
+ } else {
+ this.visibilityLevel = zoomLevelVisibility + "";
+ }
+
+ }
+
+ public SbmlKinetics getKinetics() {
+ return kinetics;
+ }
+
+ public void setKinetics(SbmlKinetics kinetics) {
+ this.kinetics = kinetics;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java
index 856ed07348..4b0334265a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java
@@ -1,187 +1,187 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import java.util.HashSet;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.BooleanComparator;
-import lcsb.mapviewer.common.comparator.DoubleComparator;
-import lcsb.mapviewer.common.comparator.IntegerComparator;
-import lcsb.mapviewer.common.comparator.StringComparator;
-import lcsb.mapviewer.common.comparator.StringListComparator;
-import lcsb.mapviewer.common.comparator.StringSetComparator;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.kinetics.SbmlKineticsComparator;
-
-/**
- * This class implements comparator interface for {@link Reaction}.
- *
- * @author Piotr Gawron
- *
- */
-public class ReactionComparator extends Comparator<Reaction> {
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(ReactionComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public ReactionComparator(double epsilon) {
- super(Reaction.class);
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public ReactionComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected int internalCompare(Reaction arg0, Reaction arg1) {
- StringComparator stringComparator = new StringComparator();
- BooleanComparator booleanComparator = new BooleanComparator();
- AbstractNodeComparator aNodeComparator = new AbstractNodeComparator(epsilon);
-
- if (stringComparator.compare(arg0.getName(), arg1.getName()) != 0) {
- logger.debug("Name different: " + arg0.getName() + ", " + arg1.getName());
- return stringComparator.compare(arg0.getName(), arg1.getName());
- }
-
- if (stringComparator.compare(arg0.getNotes().trim(), arg1.getNotes().trim()) != 0) {
- logger.debug("Notes different: " + arg0.getNotes() + ", " + arg1.getNotes());
- return stringComparator.compare(arg0.getNotes(), arg1.getNotes());
- }
-
- if (stringComparator.compare(arg0.getIdReaction(), arg1.getIdReaction()) != 0) {
- logger.debug("IdReaction different: " + arg0.getIdReaction() + ", " + arg1.getIdReaction());
- return stringComparator.compare(arg0.getIdReaction(), arg1.getIdReaction());
- }
-
- if (booleanComparator.compare(arg0.isReversible(), arg1.isReversible()) != 0) {
- logger.debug("Reversible different: " + arg0.isReversible() + ", " + arg1.isReversible());
- return booleanComparator.compare(arg0.isReversible(), arg1.isReversible());
- }
-
- if (stringComparator.compare(arg0.getSymbol(), arg1.getSymbol()) != 0) {
- logger.debug("Symbol different: " + arg0.getSymbol() + ", " + arg1.getSymbol());
- return stringComparator.compare(arg0.getSymbol(), arg1.getSymbol());
- }
- if (stringComparator.compare(arg0.getAbbreviation(), arg1.getAbbreviation()) != 0) {
- logger.debug("abbreviation different: " + arg0.getAbbreviation() + ", " + arg1.getAbbreviation());
- return stringComparator.compare(arg0.getAbbreviation(), arg1.getAbbreviation());
- }
- if (stringComparator.compare(arg0.getFormula(), arg1.getFormula()) != 0) {
- logger.debug("Formula different: " + arg0.getFormula() + ", " + arg1.getFormula());
- return stringComparator.compare(arg0.getFormula(), arg1.getFormula());
- }
- if (stringComparator.compare(arg0.getSubsystem(), arg1.getSubsystem()) != 0) {
- logger.debug("Subsystem different: " + arg0.getSubsystem() + ", " + arg1.getSubsystem());
- return stringComparator.compare(arg0.getSubsystem(), arg1.getSubsystem());
- }
- if (stringComparator.compare(arg0.getGeneProteinReaction(), arg1.getGeneProteinReaction()) != 0) {
- logger.debug(
- "GeneProteinReaction different: " + arg0.getGeneProteinReaction() + ", " + arg1.getGeneProteinReaction());
- return stringComparator.compare(arg0.getGeneProteinReaction(), arg1.getGeneProteinReaction());
- }
- if (stringComparator.compare(arg0.getVisibilityLevel(), arg1.getVisibilityLevel()) != 0) {
- logger.debug("SemanticZoomLevelVisibility different: \"" + arg0.getVisibilityLevel() + "\", \""
- + arg1.getVisibilityLevel() + "\"");
- return stringComparator.compare(arg0.getVisibilityLevel(), arg1.getVisibilityLevel());
- }
-
- IntegerComparator integerComparator = new IntegerComparator();
-
- if (integerComparator.compare(arg0.getMechanicalConfidenceScore(), arg1.getMechanicalConfidenceScore()) != 0) {
- logger.debug("MechanicalConfidenceScore different: " + arg0.getMechanicalConfidenceScore() + ", "
- + arg1.getMechanicalConfidenceScore());
- return integerComparator.compare(arg0.getMechanicalConfidenceScore(), arg1.getMechanicalConfidenceScore());
- }
-
- DoubleComparator doubleComparator = new DoubleComparator(epsilon);
- if (doubleComparator.compare(arg0.getLowerBound(), arg1.getLowerBound()) != 0) {
- logger.debug("LowerBound different: " + arg0.getLowerBound() + ", " + arg1.getLowerBound());
- return doubleComparator.compare(arg0.getLowerBound(), arg1.getLowerBound());
- }
- if (doubleComparator.compare(arg0.getUpperBound(), arg1.getUpperBound()) != 0) {
- logger.debug("UpperBound different: " + arg0.getUpperBound() + ", " + arg1.getUpperBound());
- return doubleComparator.compare(arg0.getUpperBound(), arg1.getUpperBound());
- }
-
- StringListComparator stringListComparator = new StringListComparator();
-
- if (stringListComparator.compare(arg0.getSynonyms(), arg1.getSynonyms()) != 0) {
- logger.debug("Synonyms dataset different");
- return stringListComparator.compare(arg0.getSynonyms(), arg1.getSynonyms());
- }
-
- Set<String> hashCode1 = new HashSet<String>();
- Set<String> hashCode2 = new HashSet<String>();
-
- for (MiriamData md : arg0.getMiriamData()) {
- String hash = md.getRelationType() + " " + md.getDataType() + " " + md.getResource();
- hashCode1.add(hash);
- }
-
- for (MiriamData md : arg1.getMiriamData()) {
- String hash = md.getRelationType() + " " + md.getDataType() + " " + md.getResource();
- hashCode2.add(hash);
- }
-
- StringSetComparator stringSetComparator = new StringSetComparator();
- if (stringSetComparator.compare(hashCode1, hashCode2) != 0) {
- logger.debug("Miriam dataset different");
- return stringSetComparator.compare(hashCode1, hashCode2);
- }
-
- if (arg0.getNodes().size() != arg1.getNodes().size()) {
- logger.debug("Different number of nodes: " + arg0.getNodes().size() + ", " + arg1.getNodes().size());
- return ((Integer) arg0.getNodes().size()).compareTo(arg1.getNodes().size());
- }
-
- for (int i = 0; i < arg0.getNodes().size(); i++) {
- AbstractNode node0 = arg0.getNodes().get(i);
- int status = -1;
- for (int j = 0; j < arg1.getNodes().size(); j++) {
- int tmpStatus = aNodeComparator.compare(node0, arg1.getNodes().get(j));
- if (tmpStatus == 0) {
- status = 0;
- break;
- }
- }
- if (status != 0) {
- String debugMessage = "Can't find matching node for: " + node0.getClass().getSimpleName();
- if (node0 instanceof ReactionNode) {
- debugMessage += " [" + ((ReactionNode) node0).getElement().getElementId() + "]";
- }
-
- logger.debug(debugMessage);
- return status;
- }
- }
-
- SbmlKineticsComparator kineticsComparator = new SbmlKineticsComparator();
- if (kineticsComparator.compare(arg0.getKinetics(), arg1.getKinetics()) != 0) {
- logger.debug("Kinetics different");
- logger.debug(arg0.getKinetics());
- logger.debug(arg1.getKinetics());
- return kineticsComparator.compare(arg0.getKinetics(), arg1.getKinetics());
- }
- return 0;
- }
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.BooleanComparator;
+import lcsb.mapviewer.common.comparator.DoubleComparator;
+import lcsb.mapviewer.common.comparator.IntegerComparator;
+import lcsb.mapviewer.common.comparator.StringComparator;
+import lcsb.mapviewer.common.comparator.StringListComparator;
+import lcsb.mapviewer.common.comparator.StringSetComparator;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.kinetics.SbmlKineticsComparator;
+
+/**
+ * This class implements comparator interface for {@link Reaction}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ReactionComparator extends Comparator<Reaction> {
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(ReactionComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public ReactionComparator(double epsilon) {
+ super(Reaction.class);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public ReactionComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(Reaction arg0, Reaction arg1) {
+ StringComparator stringComparator = new StringComparator();
+ BooleanComparator booleanComparator = new BooleanComparator();
+ AbstractNodeComparator aNodeComparator = new AbstractNodeComparator(epsilon);
+
+ if (stringComparator.compare(arg0.getName(), arg1.getName()) != 0) {
+ logger.debug("Name different: " + arg0.getName() + ", " + arg1.getName());
+ return stringComparator.compare(arg0.getName(), arg1.getName());
+ }
+
+ if (stringComparator.compare(arg0.getNotes().trim(), arg1.getNotes().trim()) != 0) {
+ logger.debug("Notes different: " + arg0.getNotes() + ", " + arg1.getNotes());
+ return stringComparator.compare(arg0.getNotes(), arg1.getNotes());
+ }
+
+ if (stringComparator.compare(arg0.getIdReaction(), arg1.getIdReaction()) != 0) {
+ logger.debug("IdReaction different: " + arg0.getIdReaction() + ", " + arg1.getIdReaction());
+ return stringComparator.compare(arg0.getIdReaction(), arg1.getIdReaction());
+ }
+
+ if (booleanComparator.compare(arg0.isReversible(), arg1.isReversible()) != 0) {
+ logger.debug("Reversible different: " + arg0.isReversible() + ", " + arg1.isReversible());
+ return booleanComparator.compare(arg0.isReversible(), arg1.isReversible());
+ }
+
+ if (stringComparator.compare(arg0.getSymbol(), arg1.getSymbol()) != 0) {
+ logger.debug("Symbol different: " + arg0.getSymbol() + ", " + arg1.getSymbol());
+ return stringComparator.compare(arg0.getSymbol(), arg1.getSymbol());
+ }
+ if (stringComparator.compare(arg0.getAbbreviation(), arg1.getAbbreviation()) != 0) {
+ logger.debug("abbreviation different: " + arg0.getAbbreviation() + ", " + arg1.getAbbreviation());
+ return stringComparator.compare(arg0.getAbbreviation(), arg1.getAbbreviation());
+ }
+ if (stringComparator.compare(arg0.getFormula(), arg1.getFormula()) != 0) {
+ logger.debug("Formula different: " + arg0.getFormula() + ", " + arg1.getFormula());
+ return stringComparator.compare(arg0.getFormula(), arg1.getFormula());
+ }
+ if (stringComparator.compare(arg0.getSubsystem(), arg1.getSubsystem()) != 0) {
+ logger.debug("Subsystem different: " + arg0.getSubsystem() + ", " + arg1.getSubsystem());
+ return stringComparator.compare(arg0.getSubsystem(), arg1.getSubsystem());
+ }
+ if (stringComparator.compare(arg0.getGeneProteinReaction(), arg1.getGeneProteinReaction()) != 0) {
+ logger.debug(
+ "GeneProteinReaction different: " + arg0.getGeneProteinReaction() + ", " + arg1.getGeneProteinReaction());
+ return stringComparator.compare(arg0.getGeneProteinReaction(), arg1.getGeneProteinReaction());
+ }
+ if (stringComparator.compare(arg0.getVisibilityLevel(), arg1.getVisibilityLevel()) != 0) {
+ logger.debug("SemanticZoomLevelVisibility different: \"" + arg0.getVisibilityLevel() + "\", \""
+ + arg1.getVisibilityLevel() + "\"");
+ return stringComparator.compare(arg0.getVisibilityLevel(), arg1.getVisibilityLevel());
+ }
+
+ IntegerComparator integerComparator = new IntegerComparator();
+
+ if (integerComparator.compare(arg0.getMechanicalConfidenceScore(), arg1.getMechanicalConfidenceScore()) != 0) {
+ logger.debug("MechanicalConfidenceScore different: " + arg0.getMechanicalConfidenceScore() + ", "
+ + arg1.getMechanicalConfidenceScore());
+ return integerComparator.compare(arg0.getMechanicalConfidenceScore(), arg1.getMechanicalConfidenceScore());
+ }
+
+ DoubleComparator doubleComparator = new DoubleComparator(epsilon);
+ if (doubleComparator.compare(arg0.getLowerBound(), arg1.getLowerBound()) != 0) {
+ logger.debug("LowerBound different: " + arg0.getLowerBound() + ", " + arg1.getLowerBound());
+ return doubleComparator.compare(arg0.getLowerBound(), arg1.getLowerBound());
+ }
+ if (doubleComparator.compare(arg0.getUpperBound(), arg1.getUpperBound()) != 0) {
+ logger.debug("UpperBound different: " + arg0.getUpperBound() + ", " + arg1.getUpperBound());
+ return doubleComparator.compare(arg0.getUpperBound(), arg1.getUpperBound());
+ }
+
+ StringListComparator stringListComparator = new StringListComparator();
+
+ if (stringListComparator.compare(arg0.getSynonyms(), arg1.getSynonyms()) != 0) {
+ logger.debug("Synonyms dataset different");
+ return stringListComparator.compare(arg0.getSynonyms(), arg1.getSynonyms());
+ }
+
+ Set<String> hashCode1 = new HashSet<String>();
+ Set<String> hashCode2 = new HashSet<String>();
+
+ for (MiriamData md : arg0.getMiriamData()) {
+ String hash = md.getRelationType() + " " + md.getDataType() + " " + md.getResource();
+ hashCode1.add(hash);
+ }
+
+ for (MiriamData md : arg1.getMiriamData()) {
+ String hash = md.getRelationType() + " " + md.getDataType() + " " + md.getResource();
+ hashCode2.add(hash);
+ }
+
+ StringSetComparator stringSetComparator = new StringSetComparator();
+ if (stringSetComparator.compare(hashCode1, hashCode2) != 0) {
+ logger.debug("Miriam dataset different");
+ return stringSetComparator.compare(hashCode1, hashCode2);
+ }
+
+ if (arg0.getNodes().size() != arg1.getNodes().size()) {
+ logger.debug("Different number of nodes: " + arg0.getNodes().size() + ", " + arg1.getNodes().size());
+ return ((Integer) arg0.getNodes().size()).compareTo(arg1.getNodes().size());
+ }
+
+ for (int i = 0; i < arg0.getNodes().size(); i++) {
+ AbstractNode node0 = arg0.getNodes().get(i);
+ int status = -1;
+ for (int j = 0; j < arg1.getNodes().size(); j++) {
+ int tmpStatus = aNodeComparator.compare(node0, arg1.getNodes().get(j));
+ if (tmpStatus == 0) {
+ status = 0;
+ break;
+ }
+ }
+ if (status != 0) {
+ String debugMessage = "Can't find matching node for: " + node0.getClass().getSimpleName();
+ if (node0 instanceof ReactionNode) {
+ debugMessage += " [" + ((ReactionNode) node0).getElement().getElementId() + "]";
+ }
+
+ logger.debug(debugMessage);
+ return status;
+ }
+ }
+
+ SbmlKineticsComparator kineticsComparator = new SbmlKineticsComparator();
+ if (kineticsComparator.compare(arg0.getKinetics(), arg1.getKinetics()) != 0) {
+ logger.debug("Kinetics different");
+ logger.debug(arg0.getKinetics());
+ logger.debug(arg1.getKinetics());
+ return kineticsComparator.compare(arg0.getKinetics(), arg1.getKinetics());
+ }
+ return 0;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionNode.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionNode.java
index 2f51aa9cc3..93320c63e4 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionNode.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionNode.java
@@ -1,95 +1,95 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.ManyToOne;
-
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * One of two known types of nodes in the {@link Reaction}. It defines input or
- * output element of the reaction in the map model. {@link #element} define
- * which element on the map correspond to this node. There are three known
- * subclasses:
- * <ul>
- * <li>{@link Reactant} - input of the reaction,</li>
- * <li>{@link Product} - output of the reaction,</li>
- * <li>{@link Modifier} - some modifier of the reaction.</li>
- * </ul>
- *
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("GENERIC_REACTION_NODE")
-public abstract class ReactionNode extends AbstractNode {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- private Double stoichiometry = null;
-
- /**
- * {@link Element} that represents this node in the model.
- */
- @ManyToOne
- private Element element;
-
- /**
- * Default constructor.
- */
- protected ReactionNode() {
- super();
- }
-
- /**
- * Constructor that creates a copy of the object in the parameter.
- *
- * @param node
- * original node
- */
- protected ReactionNode(ReactionNode node) {
- super(node);
- this.element = node.getElement();
- this.stoichiometry = node.getStoichiometry();
- }
-
- /**
- * Constructor that creates node for given {@link #element}.
- *
- * @param element
- * {@link Element} to which this node refer to
- */
- public ReactionNode(Element element) {
- this.element = element;
- }
-
- /**
- * @return the element
- * @see #element
- */
- public Element getElement() {
- return element;
- }
-
- /**
- * @param element
- * the element to set
- * @see #element
- */
- public void setElement(Element element) {
- this.element = element;
- }
-
- public Double getStoichiometry() {
- return stoichiometry;
- }
-
- public void setStoichiometry(Double stoichiometry) {
- this.stoichiometry = stoichiometry;
- }
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+import javax.persistence.ManyToOne;
+
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * One of two known types of nodes in the {@link Reaction}. It defines input or
+ * output element of the reaction in the map model. {@link #element} define
+ * which element on the map correspond to this node. There are three known
+ * subclasses:
+ * <ul>
+ * <li>{@link Reactant} - input of the reaction,</li>
+ * <li>{@link Product} - output of the reaction,</li>
+ * <li>{@link Modifier} - some modifier of the reaction.</li>
+ * </ul>
+ *
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("GENERIC_REACTION_NODE")
+public abstract class ReactionNode extends AbstractNode {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ private Double stoichiometry = null;
+
+ /**
+ * {@link Element} that represents this node in the model.
+ */
+ @ManyToOne
+ private Element element;
+
+ /**
+ * Default constructor.
+ */
+ protected ReactionNode() {
+ super();
+ }
+
+ /**
+ * Constructor that creates a copy of the object in the parameter.
+ *
+ * @param node
+ * original node
+ */
+ protected ReactionNode(ReactionNode node) {
+ super(node);
+ this.element = node.getElement();
+ this.stoichiometry = node.getStoichiometry();
+ }
+
+ /**
+ * Constructor that creates node for given {@link #element}.
+ *
+ * @param element
+ * {@link Element} to which this node refer to
+ */
+ public ReactionNode(Element element) {
+ this.element = element;
+ }
+
+ /**
+ * @return the element
+ * @see #element
+ */
+ public Element getElement() {
+ return element;
+ }
+
+ /**
+ * @param element
+ * the element to set
+ * @see #element
+ */
+ public void setElement(Element element) {
+ this.element = element;
+ }
+
+ public Double getStoichiometry() {
+ return stoichiometry;
+ }
+
+ public void setStoichiometry(Double stoichiometry) {
+ this.stoichiometry = stoichiometry;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionNodeComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionNodeComparator.java
index 63ed196dc8..cd7a401e8c 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionNodeComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionNodeComparator.java
@@ -1,76 +1,76 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.DoubleComparator;
-import lcsb.mapviewer.model.map.species.ElementComparator;
-
-/**
- * This class implements comparator interface for {@link ReactionNode}. It also
- * handles comparison of subclasses of {@link ReactionNode} class.
- *
- *
- * @author Piotr Gawron
- *
- */
-public class ReactionNodeComparator extends Comparator<ReactionNode> {
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(ReactionNodeComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- private DoubleComparator doubleComparator;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public ReactionNodeComparator(double epsilon) {
- super(ReactionNode.class);
- this.epsilon = epsilon;
- this.doubleComparator = new DoubleComparator(epsilon);
- }
-
- protected Comparator<?> getParentComparator() {
- return new AbstractNodeComparator(epsilon);
- }
-
- /**
- * Default constructor.
- */
- public ReactionNodeComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected int internalCompare(ReactionNode arg0, ReactionNode arg1) {
- AbstractNodeComparator anComparator = new AbstractNodeComparator(epsilon);
- ElementComparator elementComparator = new ElementComparator(epsilon);
-
- int result = anComparator.internalCompare(arg0, arg1);
- if (result != 0) {
- return result;
- }
-
- if (elementComparator.compare(arg0.getElement(), arg1.getElement()) != 0) {
- logger.debug("Element different");
- return elementComparator.compare(arg0.getElement(), arg1.getElement());
- }
-
- if (doubleComparator.compare(arg0.getStoichiometry(), arg1.getStoichiometry()) != 0) {
- logger.debug("Stoichiometry different");
- return doubleComparator.compare(arg0.getStoichiometry(), arg1.getStoichiometry());
- }
-
- return 0;
- }
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.DoubleComparator;
+import lcsb.mapviewer.model.map.species.ElementComparator;
+
+/**
+ * This class implements comparator interface for {@link ReactionNode}. It also
+ * handles comparison of subclasses of {@link ReactionNode} class.
+ *
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ReactionNodeComparator extends Comparator<ReactionNode> {
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(ReactionNodeComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ private DoubleComparator doubleComparator;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public ReactionNodeComparator(double epsilon) {
+ super(ReactionNode.class);
+ this.epsilon = epsilon;
+ this.doubleComparator = new DoubleComparator(epsilon);
+ }
+
+ protected Comparator<?> getParentComparator() {
+ return new AbstractNodeComparator(epsilon);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public ReactionNodeComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(ReactionNode arg0, ReactionNode arg1) {
+ AbstractNodeComparator anComparator = new AbstractNodeComparator(epsilon);
+ ElementComparator elementComparator = new ElementComparator(epsilon);
+
+ int result = anComparator.internalCompare(arg0, arg1);
+ if (result != 0) {
+ return result;
+ }
+
+ if (elementComparator.compare(arg0.getElement(), arg1.getElement()) != 0) {
+ logger.debug("Element different");
+ return elementComparator.compare(arg0.getElement(), arg1.getElement());
+ }
+
+ if (doubleComparator.compare(arg0.getStoichiometry(), arg1.getStoichiometry()) != 0) {
+ logger.debug("Stoichiometry different");
+ return doubleComparator.compare(arg0.getStoichiometry(), arg1.getStoichiometry());
+ }
+
+ return 0;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/SplitOperator.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/SplitOperator.java
index 1599fee579..4ebb08b866 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/SplitOperator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/SplitOperator.java
@@ -1,63 +1,63 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-/**
- * Class representing "split operator" (dissociation???) of one node into two or
- * more nodes in the reaction (in the product part of the reaction).
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("SPLIT_OPERATOR_NODE")
-public class SplitOperator extends NodeOperator {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(SplitOperator.class);
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param operator
- * parent operator from which we copy data
- */
- public SplitOperator(SplitOperator operator) {
- super(operator);
- }
-
- /**
- * Default constructor.
- */
- public SplitOperator() {
- super();
- }
-
- @Override
- public String getOperatorText() {
- return "";
- }
-
- @Override
- public SplitOperator copy() {
- if (this.getClass() == SplitOperator.class) {
- return new SplitOperator(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * Class representing "split operator" (dissociation???) of one node into two or
+ * more nodes in the reaction (in the product part of the reaction).
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("SPLIT_OPERATOR_NODE")
+public class SplitOperator extends NodeOperator {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(SplitOperator.class);
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param operator
+ * parent operator from which we copy data
+ */
+ public SplitOperator(SplitOperator operator) {
+ super(operator);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public SplitOperator() {
+ super();
+ }
+
+ @Override
+ public String getOperatorText() {
+ return "";
+ }
+
+ @Override
+ public SplitOperator copy() {
+ if (this.getClass() == SplitOperator.class) {
+ return new SplitOperator(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/TruncationOperator.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/TruncationOperator.java
index 1408e838dc..a9c96692b8 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/TruncationOperator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/TruncationOperator.java
@@ -1,63 +1,63 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-/**
- * Class representing "truncation operator" of one node into two nodes in the
- * reaction.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("TRUNCATION_OPERATOR_NODE")
-public class TruncationOperator extends NodeOperator {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(TruncationOperator.class);
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param operator
- * parent operator from which we copy data
- */
- public TruncationOperator(TruncationOperator operator) {
- super(operator);
- }
-
- /**
- * Default constructor.
- */
- public TruncationOperator() {
- super();
- }
-
- @Override
- public String getOperatorText() {
- return "";
- }
-
- @Override
- public TruncationOperator copy() {
- if (this.getClass() == TruncationOperator.class) {
- return new TruncationOperator(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * Class representing "truncation operator" of one node into two nodes in the
+ * reaction.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("TRUNCATION_OPERATOR_NODE")
+public class TruncationOperator extends NodeOperator {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(TruncationOperator.class);
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param operator
+ * parent operator from which we copy data
+ */
+ public TruncationOperator(TruncationOperator operator) {
+ super(operator);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public TruncationOperator() {
+ super();
+ }
+
+ @Override
+ public String getOperatorText() {
+ return "";
+ }
+
+ @Override
+ public TruncationOperator copy() {
+ if (this.getClass() == TruncationOperator.class) {
+ return new TruncationOperator(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/UnknownOperator.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/UnknownOperator.java
index 15d2b75fdf..01f80e6d22 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/UnknownOperator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/UnknownOperator.java
@@ -1,63 +1,63 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-/**
- * Class representing boolean, but unknown operator between two or more nodes in
- * the reaction.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("UNKNOWN_OPERATOR_NODE")
-public class UnknownOperator extends NodeOperator {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(UnknownOperator.class);
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param operator
- * parent operator from which we copy data
- */
- public UnknownOperator(UnknownOperator operator) {
- super(operator);
- }
-
- /**
- * Default constructor.
- */
- public UnknownOperator() {
- super();
- }
-
- @Override
- public String getOperatorText() {
- return "?";
- }
-
- @Override
- public UnknownOperator copy() {
- if (this.getClass() == UnknownOperator.class) {
- return new UnknownOperator(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * Class representing boolean, but unknown operator between two or more nodes in
+ * the reaction.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("UNKNOWN_OPERATOR_NODE")
+public class UnknownOperator extends NodeOperator {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(UnknownOperator.class);
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param operator
+ * parent operator from which we copy data
+ */
+ public UnknownOperator(UnknownOperator operator) {
+ super(operator);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public UnknownOperator() {
+ super();
+ }
+
+ @Override
+ public String getOperatorText() {
+ return "?";
+ }
+
+ @Override
+ public UnknownOperator copy() {
+ if (this.getClass() == UnknownOperator.class) {
+ return new UnknownOperator(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/package-info.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/package-info.java
index 800b2e9848..bd371e82b9 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/package-info.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/package-info.java
@@ -1,12 +1,12 @@
-/**
- * Contains structures used for modeling reactions. Main class representing
- * reaction is {@link lcsb.mapviewer.model.map.reaction.Reaction Reaction}.
- * It is extended by several different types of reactions that were put in the
- * {@link lcsb.mapviewer.model.map.reaction.type type} sub-package.
- *
- * Every reaction contains set of nodes that extend
- * {@link lcsb.mapviewer.model.map.reaction.AbstractNode AbstractNode} class.
- *
- */
-package lcsb.mapviewer.model.map.reaction;
-
+/**
+ * Contains structures used for modeling reactions. Main class representing
+ * reaction is {@link lcsb.mapviewer.model.map.reaction.Reaction Reaction}.
+ * It is extended by several different types of reactions that were put in the
+ * {@link lcsb.mapviewer.model.map.reaction.type type} sub-package.
+ *
+ * Every reaction contains set of nodes that extend
+ * {@link lcsb.mapviewer.model.map.reaction.AbstractNode AbstractNode} class.
+ *
+ */
+package lcsb.mapviewer.model.map.reaction;
+
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/BooleanLogicGateReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/BooleanLogicGateReaction.java
index e7aa3cacad..11b21885b1 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/BooleanLogicGateReaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/BooleanLogicGateReaction.java
@@ -1,73 +1,73 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * This class defines a reaction that as an input contains at least one boolean
- * gate. This type was defined by CellDesigner.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("BOOLEAN_LOGIC_GATE")
-public class BooleanLogicGateReaction extends Reaction implements TwoReactantReactionInterface {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public BooleanLogicGateReaction() {
- super();
- }
-
- /**
- * Constructor that makes new reaction based on the data from reaction in the
- * parameter.
- *
- * @param result
- * original reaction
- */
- public BooleanLogicGateReaction(Reaction result) {
- super(result);
- if (result.getProducts().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to Boolean logic gate: number of products must be greater than 0");
- }
- if (result.getReactants().size() < 2) {
- throw new InvalidArgumentException("Reaction cannot be transformed to Boolean logic gate: number of reactants must be greater than 1");
- }
- }
-
- @Override
- public String getStringType() {
- return "Boolean logic gate";
- }
-
- @Override
- public ReactionRect getReactionRect() {
- return null;
- }
-
- /**
- * Prepares a copy of the reaction.
- *
- * @return copy of the reaction
- */
- public BooleanLogicGateReaction copy() {
- if (this.getClass() == BooleanLogicGateReaction.class) {
- return new BooleanLogicGateReaction(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a reaction that as an input contains at least one boolean
+ * gate. This type was defined by CellDesigner.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("BOOLEAN_LOGIC_GATE")
+public class BooleanLogicGateReaction extends Reaction implements TwoReactantReactionInterface {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public BooleanLogicGateReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that makes new reaction based on the data from reaction in the
+ * parameter.
+ *
+ * @param result
+ * original reaction
+ */
+ public BooleanLogicGateReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to Boolean logic gate: number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 2) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to Boolean logic gate: number of reactants must be greater than 1");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Boolean logic gate";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return null;
+ }
+
+ /**
+ * Prepares a copy of the reaction.
+ *
+ * @return copy of the reaction
+ */
+ public BooleanLogicGateReaction copy() {
+ if (this.getClass() == BooleanLogicGateReaction.class) {
+ return new BooleanLogicGateReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/CatalysisReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/CatalysisReaction.java
index a226aeed7a..7b3f12d864 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/CatalysisReaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/CatalysisReaction.java
@@ -1,67 +1,67 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * This class defines a standard CellDesigner catalysis reaction.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("CATALYSIS_REACTION")
-public class CatalysisReaction extends Reaction implements SimpleReactionInterface, ModifierReactionNotation {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public CatalysisReaction() {
- super();
- }
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param result
- * parent reaction from which we copy data
- */
- public CatalysisReaction(Reaction result) {
- super(result);
- if (result.getProducts().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
- }
- if (result.getReactants().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
- }
- }
-
- @Override
- public String getStringType() {
- return "Catalysis";
- }
-
- @Override
- public ReactionRect getReactionRect() {
- return null;
- }
-
- @Override
- public CatalysisReaction copy() {
- if (this.getClass() == CatalysisReaction.class) {
- return new CatalysisReaction(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner catalysis reaction.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("CATALYSIS_REACTION")
+public class CatalysisReaction extends Reaction implements SimpleReactionInterface, ModifierReactionNotation {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public CatalysisReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public CatalysisReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Catalysis";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return null;
+ }
+
+ @Override
+ public CatalysisReaction copy() {
+ if (this.getClass() == CatalysisReaction.class) {
+ return new CatalysisReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/DissociationReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/DissociationReaction.java
index 605e0d29d8..143318f1b0 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/DissociationReaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/DissociationReaction.java
@@ -1,68 +1,68 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * This class defines a standard CellDesigner dissociation. It must have at
- * least one reactant and two products.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("DISSOCIATION_REACTION")
-public class DissociationReaction extends Reaction implements TwoProductReactionInterface {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public DissociationReaction() {
- super();
- }
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param result
- * parent reaction from which we copy data
- */
- public DissociationReaction(Reaction result) {
- super(result);
- if (result.getProducts().size() < 2) {
- throw new InvalidArgumentException("Reaction cannot be transformed to dissociation: number of products must be greater than 1");
- }
- if (result.getReactants().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to dissociation: number of reactants must be greater than 0");
- }
- }
-
- @Override
- public String getStringType() {
- return "Dissociation";
- }
-
- @Override
- public ReactionRect getReactionRect() {
- return ReactionRect.RECT_EMPTY;
- }
-
- @Override
- public DissociationReaction copy() {
- if (this.getClass() == DissociationReaction.class) {
- return new DissociationReaction(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner dissociation. It must have at
+ * least one reactant and two products.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("DISSOCIATION_REACTION")
+public class DissociationReaction extends Reaction implements TwoProductReactionInterface {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public DissociationReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public DissociationReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 2) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to dissociation: number of products must be greater than 1");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to dissociation: number of reactants must be greater than 0");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Dissociation";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return ReactionRect.RECT_EMPTY;
+ }
+
+ @Override
+ public DissociationReaction copy() {
+ if (this.getClass() == DissociationReaction.class) {
+ return new DissociationReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/HeterodimerAssociationReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/HeterodimerAssociationReaction.java
index 4fc072de29..a75d40b6ed 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/HeterodimerAssociationReaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/HeterodimerAssociationReaction.java
@@ -1,68 +1,68 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * This class defines a standard CellDesigner dissociation. It must have at
- * least two reactants and one product.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("HETERODIMER_REACTION")
-public class HeterodimerAssociationReaction extends Reaction implements TwoReactantReactionInterface {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public HeterodimerAssociationReaction() {
- super();
- }
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param result
- * parent reaction from which we copy data
- */
- public HeterodimerAssociationReaction(Reaction result) {
- super(result);
- if (result.getProducts().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to heterodimer association: number of products must be greater than 0");
- }
- if (result.getReactants().size() < 2) {
- throw new InvalidArgumentException("Reaction cannot be transformed to heterodimer association: number of reactants must be greater than 1");
- }
- }
-
- @Override
- public String getStringType() {
- return "Heterodimer association";
- }
-
- @Override
- public ReactionRect getReactionRect() {
- return ReactionRect.RECT_EMPTY;
- }
-
- @Override
- public HeterodimerAssociationReaction copy() {
- if (this.getClass() == HeterodimerAssociationReaction.class) {
- return new HeterodimerAssociationReaction(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner dissociation. It must have at
+ * least two reactants and one product.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("HETERODIMER_REACTION")
+public class HeterodimerAssociationReaction extends Reaction implements TwoReactantReactionInterface {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public HeterodimerAssociationReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public HeterodimerAssociationReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to heterodimer association: number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 2) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to heterodimer association: number of reactants must be greater than 1");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Heterodimer association";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return ReactionRect.RECT_EMPTY;
+ }
+
+ @Override
+ public HeterodimerAssociationReaction copy() {
+ if (this.getClass() == HeterodimerAssociationReaction.class) {
+ return new HeterodimerAssociationReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/InhibitionReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/InhibitionReaction.java
index f44a73ee55..13ef9e3409 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/InhibitionReaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/InhibitionReaction.java
@@ -1,67 +1,67 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * This class defines a standard CellDesigner inhibition reaction.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("INHIBITION_REACTION")
-public class InhibitionReaction extends Reaction implements SimpleReactionInterface, ModifierReactionNotation {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public InhibitionReaction() {
- super();
- }
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param result
- * parent reaction from which we copy data
- */
- public InhibitionReaction(Reaction result) {
- super(result);
- if (result.getProducts().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
- }
- if (result.getReactants().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
- }
- }
-
- @Override
- public String getStringType() {
- return "Inhibition";
- }
-
- @Override
- public ReactionRect getReactionRect() {
- return null;
- }
-
- @Override
- public InhibitionReaction copy() {
- if (this.getClass() == InhibitionReaction.class) {
- return new InhibitionReaction(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner inhibition reaction.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("INHIBITION_REACTION")
+public class InhibitionReaction extends Reaction implements SimpleReactionInterface, ModifierReactionNotation {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public InhibitionReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public InhibitionReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Inhibition";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return null;
+ }
+
+ @Override
+ public InhibitionReaction copy() {
+ if (this.getClass() == InhibitionReaction.class) {
+ return new InhibitionReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/KnownTransitionOmittedReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/KnownTransitionOmittedReaction.java
index 63509f34b1..72a15ae6de 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/KnownTransitionOmittedReaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/KnownTransitionOmittedReaction.java
@@ -1,68 +1,68 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * This class defines a standard CellDesigner knwon transition omitted reaction.
- * It must have at least one reactant and one product.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("KNOWN_TRANSITION_OMMITED")
-public class KnownTransitionOmittedReaction extends Reaction implements SimpleReactionInterface {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public KnownTransitionOmittedReaction() {
- super();
- }
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param result
- * parent reaction from which we copy data
- */
- public KnownTransitionOmittedReaction(Reaction result) {
- super(result);
- if (result.getProducts().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
- }
- if (result.getReactants().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
- }
- }
-
- @Override
- public String getStringType() {
- return "Known transition omitted";
- }
-
- @Override
- public ReactionRect getReactionRect() {
- return ReactionRect.RECT_SLASH;
- }
-
- @Override
- public KnownTransitionOmittedReaction copy() {
- if (this.getClass() == KnownTransitionOmittedReaction.class) {
- return new KnownTransitionOmittedReaction(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner knwon transition omitted reaction.
+ * It must have at least one reactant and one product.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("KNOWN_TRANSITION_OMMITED")
+public class KnownTransitionOmittedReaction extends Reaction implements SimpleReactionInterface {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public KnownTransitionOmittedReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public KnownTransitionOmittedReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Known transition omitted";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return ReactionRect.RECT_SLASH;
+ }
+
+ @Override
+ public KnownTransitionOmittedReaction copy() {
+ if (this.getClass() == KnownTransitionOmittedReaction.class) {
+ return new KnownTransitionOmittedReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ModifierReactionNotation.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ModifierReactionNotation.java
index 1dcafec54c..b8e38dfbaa 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ModifierReactionNotation.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ModifierReactionNotation.java
@@ -1,15 +1,15 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import lcsb.mapviewer.model.map.species.Phenotype;
-
-/**
- * Interface used for marking {@link lcsb.mapviewer.model.map.reaction.Reaction
- * Reaction} extensions that implements something that should be modifier but is
- * a reaction to {@link Phenotype}.
- *
- * @author Piotr Gawron
- *
- */
-public interface ModifierReactionNotation {
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import lcsb.mapviewer.model.map.species.Phenotype;
+
+/**
+ * Interface used for marking {@link lcsb.mapviewer.model.map.reaction.Reaction
+ * Reaction} extensions that implements something that should be modifier but is
+ * a reaction to {@link Phenotype}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface ModifierReactionNotation {
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ModulationReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ModulationReaction.java
index 7c007cf614..79f3dc1ea7 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ModulationReaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ModulationReaction.java
@@ -1,67 +1,67 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * This class defines a standard CellDesigner modulation reaction.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("MODULATION_REACTION")
-public class ModulationReaction extends Reaction implements SimpleReactionInterface, ModifierReactionNotation {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public ModulationReaction() {
- super();
- }
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param result
- * parent reaction from which we copy data
- */
- public ModulationReaction(Reaction result) {
- super(result);
- if (result.getProducts().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
- }
- if (result.getReactants().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
- }
- }
-
- @Override
- public String getStringType() {
- return "Modulation";
- }
-
- @Override
- public ReactionRect getReactionRect() {
- return null;
- }
-
- @Override
- public ModulationReaction copy() {
- if (this.getClass() == ModulationReaction.class) {
- return new ModulationReaction(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner modulation reaction.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("MODULATION_REACTION")
+public class ModulationReaction extends Reaction implements SimpleReactionInterface, ModifierReactionNotation {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public ModulationReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public ModulationReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Modulation";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return null;
+ }
+
+ @Override
+ public ModulationReaction copy() {
+ if (this.getClass() == ModulationReaction.class) {
+ return new ModulationReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/NegativeInfluenceReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/NegativeInfluenceReaction.java
index 55292119e6..4fa4dc0868 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/NegativeInfluenceReaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/NegativeInfluenceReaction.java
@@ -1,68 +1,68 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * This class defines a standard CellDesigner negative influence reaction. It
- * must have at least one reactant and one product.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("NEGATIVE_INFLUENCE_REACTION")
-public class NegativeInfluenceReaction extends Reaction implements SimpleReactionInterface, ReducedNotation {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public NegativeInfluenceReaction() {
- super();
- }
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param result
- * parent reaction from which we copy data
- */
- public NegativeInfluenceReaction(Reaction result) {
- super(result);
- if (result.getProducts().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
- }
- if (result.getReactants().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
- }
- }
-
- @Override
- public String getStringType() {
- return "Negative influence";
- }
-
- @Override
- public ReactionRect getReactionRect() {
- return null;
- }
-
- @Override
- public NegativeInfluenceReaction copy() {
- if (this.getClass() == NegativeInfluenceReaction.class) {
- return new NegativeInfluenceReaction(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner negative influence reaction. It
+ * must have at least one reactant and one product.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("NEGATIVE_INFLUENCE_REACTION")
+public class NegativeInfluenceReaction extends Reaction implements SimpleReactionInterface, ReducedNotation {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public NegativeInfluenceReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public NegativeInfluenceReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Negative influence";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return null;
+ }
+
+ @Override
+ public NegativeInfluenceReaction copy() {
+ if (this.getClass() == NegativeInfluenceReaction.class) {
+ return new NegativeInfluenceReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/PhysicalStimulationReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/PhysicalStimulationReaction.java
index 99a5b46e13..6346a32fba 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/PhysicalStimulationReaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/PhysicalStimulationReaction.java
@@ -1,67 +1,67 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * This class defines a standard CellDesigner physical stimulation reaction.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("PHYSICAL_STIMULATION_REACTION")
-public class PhysicalStimulationReaction extends Reaction implements SimpleReactionInterface, ModifierReactionNotation {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public PhysicalStimulationReaction() {
- super();
- }
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param result
- * parent reaction from which we copy data
- */
- public PhysicalStimulationReaction(Reaction result) {
- super(result);
- if (result.getProducts().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
- }
- if (result.getReactants().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
- }
- }
-
- @Override
- public String getStringType() {
- return "Physical stimulation";
- }
-
- @Override
- public ReactionRect getReactionRect() {
- return null;
- }
-
- @Override
- public PhysicalStimulationReaction copy() {
- if (this.getClass() == PhysicalStimulationReaction.class) {
- return new PhysicalStimulationReaction(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner physical stimulation reaction.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("PHYSICAL_STIMULATION_REACTION")
+public class PhysicalStimulationReaction extends Reaction implements SimpleReactionInterface, ModifierReactionNotation {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public PhysicalStimulationReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public PhysicalStimulationReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Physical stimulation";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return null;
+ }
+
+ @Override
+ public PhysicalStimulationReaction copy() {
+ if (this.getClass() == PhysicalStimulationReaction.class) {
+ return new PhysicalStimulationReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/PositiveInfluenceReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/PositiveInfluenceReaction.java
index 088c32a1ed..aaebd013f6 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/PositiveInfluenceReaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/PositiveInfluenceReaction.java
@@ -1,68 +1,68 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * This class defines a standard CellDesigner positive influence reaction. It
- * must have at least one reactant and one product.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("POSITIVE_INFLUENCE_REACTION")
-public class PositiveInfluenceReaction extends Reaction implements SimpleReactionInterface, ReducedNotation {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public PositiveInfluenceReaction() {
- super();
- }
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param result
- * parent reaction from which we copy data
- */
- public PositiveInfluenceReaction(Reaction result) {
- super(result);
- if (result.getProducts().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
- }
- if (result.getReactants().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
- }
- }
-
- @Override
- public String getStringType() {
- return "Positive influence";
- }
-
- @Override
- public ReactionRect getReactionRect() {
- return null;
- }
-
- @Override
- public PositiveInfluenceReaction copy() {
- if (this.getClass() == PositiveInfluenceReaction.class) {
- return new PositiveInfluenceReaction(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner positive influence reaction. It
+ * must have at least one reactant and one product.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("POSITIVE_INFLUENCE_REACTION")
+public class PositiveInfluenceReaction extends Reaction implements SimpleReactionInterface, ReducedNotation {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public PositiveInfluenceReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public PositiveInfluenceReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Positive influence";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return null;
+ }
+
+ @Override
+ public PositiveInfluenceReaction copy() {
+ if (this.getClass() == PositiveInfluenceReaction.class) {
+ return new PositiveInfluenceReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ReactionRect.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ReactionRect.java
index 807e0be16f..fe7207565f 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ReactionRect.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ReactionRect.java
@@ -1,53 +1,53 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-/**
- * This enum describes inside of the central rectangle in the reaction.
- *
- * @author Piotr Gawron
- *
- */
-public enum ReactionRect {
-
- /**
- * Double slashed inside.
- */
- RECT_SLASH("//"),
-
- /**
- * Question mark (something is unknonw).
- */
- RECT_QUESTION("?"),
-
- /**
- * Thunderbolt should be drawn.
- */
- RECT_BOLT(""),
-
- /**
- * Empty inside.
- */
- RECT_EMPTY("");
-
- /**
- * Text drawn in the inside of the rectangle.
- */
- private String text;
-
- /**
- * Default constructor that initilized the text inside a spicific type of
- * rectangle.
- *
- * @param text text describing inside
- */
- ReactionRect(String text) {
- this.text = text;
- }
-
- /**
- * @return the text
- * @see #text
- */
- public String getText() {
- return text;
- }
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+/**
+ * This enum describes inside of the central rectangle in the reaction.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum ReactionRect {
+
+ /**
+ * Double slashed inside.
+ */
+ RECT_SLASH("//"),
+
+ /**
+ * Question mark (something is unknonw).
+ */
+ RECT_QUESTION("?"),
+
+ /**
+ * Thunderbolt should be drawn.
+ */
+ RECT_BOLT(""),
+
+ /**
+ * Empty inside.
+ */
+ RECT_EMPTY("");
+
+ /**
+ * Text drawn in the inside of the rectangle.
+ */
+ private String text;
+
+ /**
+ * Default constructor that initilized the text inside a spicific type of
+ * rectangle.
+ *
+ * @param text text describing inside
+ */
+ ReactionRect(String text) {
+ this.text = text;
+ }
+
+ /**
+ * @return the text
+ * @see #text
+ */
+ public String getText() {
+ return text;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ReducedModulationReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ReducedModulationReaction.java
index a10c04d092..c4de178bb2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ReducedModulationReaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ReducedModulationReaction.java
@@ -1,68 +1,68 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * This class defines a standard CellDesigner reduced modulation reaction. It
- * must have at least one reactant and one product.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("REDUCED_MODULATION_REACTION")
-public class ReducedModulationReaction extends Reaction implements SimpleReactionInterface, ReducedNotation {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public ReducedModulationReaction() {
- super();
- }
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param result
- * parent reaction from which we copy data
- */
- public ReducedModulationReaction(Reaction result) {
- super(result);
- if (result.getProducts().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
- }
- if (result.getReactants().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
- }
- }
-
- @Override
- public String getStringType() {
- return "Reduced modulation";
- }
-
- @Override
- public ReactionRect getReactionRect() {
- return null;
- }
-
- @Override
- public ReducedModulationReaction copy() {
- if (this.getClass() == ReducedModulationReaction.class) {
- return new ReducedModulationReaction(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner reduced modulation reaction. It
+ * must have at least one reactant and one product.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("REDUCED_MODULATION_REACTION")
+public class ReducedModulationReaction extends Reaction implements SimpleReactionInterface, ReducedNotation {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public ReducedModulationReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public ReducedModulationReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Reduced modulation";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return null;
+ }
+
+ @Override
+ public ReducedModulationReaction copy() {
+ if (this.getClass() == ReducedModulationReaction.class) {
+ return new ReducedModulationReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ReducedNotation.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ReducedNotation.java
index f0b5da8973..dba363883e 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ReducedNotation.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ReducedNotation.java
@@ -1,15 +1,15 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-/**
- *
- * Interface used for marking {@link lcsb.mapviewer.model.map.reaction.Reaction
- * Reaction} extensions that implements reduced notation in CellDesigner. These
- * classes should have more than one reactant and product and cannot have any
- * modifiers.
- *
- * @author Piotr Gawron
- *
- */
-public interface ReducedNotation {
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+/**
+ *
+ * Interface used for marking {@link lcsb.mapviewer.model.map.reaction.Reaction
+ * Reaction} extensions that implements reduced notation in CellDesigner. These
+ * classes should have more than one reactant and product and cannot have any
+ * modifiers.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface ReducedNotation {
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ReducedPhysicalStimulationReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ReducedPhysicalStimulationReaction.java
index df09816a83..79df181d36 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ReducedPhysicalStimulationReaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ReducedPhysicalStimulationReaction.java
@@ -1,68 +1,68 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * This class defines a standard CellDesigner reduced physical stimulation
- * reaction. It must have at least one reactant and one product.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("REDUCED_PHYSICAL_STIMULATION")
-public class ReducedPhysicalStimulationReaction extends Reaction implements SimpleReactionInterface, ReducedNotation {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public ReducedPhysicalStimulationReaction() {
- super();
- }
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param result
- * parent reaction from which we copy data
- */
- public ReducedPhysicalStimulationReaction(Reaction result) {
- super(result);
- if (result.getProducts().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
- }
- if (result.getReactants().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
- }
- }
-
- @Override
- public String getStringType() {
- return "Reduced physical stimulation";
- }
-
- @Override
- public ReactionRect getReactionRect() {
- return null;
- }
-
- @Override
- public ReducedPhysicalStimulationReaction copy() {
- if (this.getClass() == ReducedPhysicalStimulationReaction.class) {
- return new ReducedPhysicalStimulationReaction(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner reduced physical stimulation
+ * reaction. It must have at least one reactant and one product.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("REDUCED_PHYSICAL_STIMULATION")
+public class ReducedPhysicalStimulationReaction extends Reaction implements SimpleReactionInterface, ReducedNotation {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public ReducedPhysicalStimulationReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public ReducedPhysicalStimulationReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Reduced physical stimulation";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return null;
+ }
+
+ @Override
+ public ReducedPhysicalStimulationReaction copy() {
+ if (this.getClass() == ReducedPhysicalStimulationReaction.class) {
+ return new ReducedPhysicalStimulationReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ReducedTriggerReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ReducedTriggerReaction.java
index 862eddc6d2..889c430049 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ReducedTriggerReaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ReducedTriggerReaction.java
@@ -1,68 +1,68 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * This class defines a standard CellDesigner reduced trigger reaction. It must have at
- * least one reactant and one product.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("REDUCED_TRIGGER_REACTION")
-public class ReducedTriggerReaction extends Reaction implements SimpleReactionInterface, ReducedNotation {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public ReducedTriggerReaction() {
- super();
- }
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param result
- * parent reaction from which we copy data
- */
- public ReducedTriggerReaction(Reaction result) {
- super(result);
- if (result.getProducts().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
- }
- if (result.getReactants().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
- }
- }
-
- @Override
- public String getStringType() {
- return "Reduced trigger";
- }
-
- @Override
- public ReactionRect getReactionRect() {
- return null;
- }
-
- @Override
- public ReducedTriggerReaction copy() {
- if (this.getClass() == ReducedTriggerReaction.class) {
- return new ReducedTriggerReaction(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner reduced trigger reaction. It must have at
+ * least one reactant and one product.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("REDUCED_TRIGGER_REACTION")
+public class ReducedTriggerReaction extends Reaction implements SimpleReactionInterface, ReducedNotation {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public ReducedTriggerReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public ReducedTriggerReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Reduced trigger";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return null;
+ }
+
+ @Override
+ public ReducedTriggerReaction copy() {
+ if (this.getClass() == ReducedTriggerReaction.class) {
+ return new ReducedTriggerReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/SimpleReactionInterface.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/SimpleReactionInterface.java
index 82e5f36fdd..d9447d9c84 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/SimpleReactionInterface.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/SimpleReactionInterface.java
@@ -1,12 +1,12 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-/**
- * This interface is only a marker which points out the type of reaction deigned
- * in CD.
- *
- * @author Piotr Gawron
- *
- */
-public interface SimpleReactionInterface {
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+/**
+ * This interface is only a marker which points out the type of reaction deigned
+ * in CD.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface SimpleReactionInterface {
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/StateTransitionReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/StateTransitionReaction.java
index 0993d4c26c..5882c3eac3 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/StateTransitionReaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/StateTransitionReaction.java
@@ -1,67 +1,67 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * This class defines a standard CellDesigner state transition reaction. It must
- * have at least one reactant and one product.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("STATE_TRANSITION_REACTION")
-public class StateTransitionReaction extends Reaction implements SimpleReactionInterface {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public StateTransitionReaction() {
- super();
- }
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param result
- * parent reaction from which we copy data
- */
- public StateTransitionReaction(Reaction result) {
- super(result);
- if (result.getProducts().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
- }
- if (result.getReactants().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
- }
- }
-
- @Override
- public String getStringType() {
- return "State transition";
- }
-
- @Override
- public ReactionRect getReactionRect() {
- return ReactionRect.RECT_EMPTY;
- }
-
- @Override
- public StateTransitionReaction copy() {
- if (this.getClass() == StateTransitionReaction.class) {
- return new StateTransitionReaction(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner state transition reaction. It must
+ * have at least one reactant and one product.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("STATE_TRANSITION_REACTION")
+public class StateTransitionReaction extends Reaction implements SimpleReactionInterface {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public StateTransitionReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public StateTransitionReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "State transition";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return ReactionRect.RECT_EMPTY;
+ }
+
+ @Override
+ public StateTransitionReaction copy() {
+ if (this.getClass() == StateTransitionReaction.class) {
+ return new StateTransitionReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TranscriptionReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TranscriptionReaction.java
index 9b247b5e34..81e595033a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TranscriptionReaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TranscriptionReaction.java
@@ -1,67 +1,67 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * This class defines a standard CellDesigner transcription reaction. It must
- * have at least one reactant and one product.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("TRANSCRIPTION_REACTION")
-public class TranscriptionReaction extends Reaction implements SimpleReactionInterface {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public TranscriptionReaction() {
- super();
- }
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param result
- * parent reaction from which we copy data
- */
- public TranscriptionReaction(Reaction result) {
- super(result);
- if (result.getProducts().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
- }
- if (result.getReactants().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
- }
- }
-
- @Override
- public String getStringType() {
- return "Transcription";
- }
-
- @Override
- public ReactionRect getReactionRect() {
- return ReactionRect.RECT_EMPTY;
- }
-
- @Override
- public TranscriptionReaction copy() {
- if (this.getClass() == TranscriptionReaction.class) {
- return new TranscriptionReaction(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner transcription reaction. It must
+ * have at least one reactant and one product.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("TRANSCRIPTION_REACTION")
+public class TranscriptionReaction extends Reaction implements SimpleReactionInterface {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public TranscriptionReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public TranscriptionReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Transcription";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return ReactionRect.RECT_EMPTY;
+ }
+
+ @Override
+ public TranscriptionReaction copy() {
+ if (this.getClass() == TranscriptionReaction.class) {
+ return new TranscriptionReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TranslationReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TranslationReaction.java
index 08a36d5252..85a736dbec 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TranslationReaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TranslationReaction.java
@@ -1,68 +1,68 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * This class defines a standard CellDesigner translation reaction. It must have
- * at least one reactant and one product.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("TRANSLATION_REACTION")
-public class TranslationReaction extends Reaction implements SimpleReactionInterface {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public TranslationReaction() {
- super();
- }
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param result
- * parent reaction from which we copy data
- */
- public TranslationReaction(Reaction result) {
- super(result);
- if (result.getProducts().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
- }
- if (result.getReactants().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
- }
- }
-
- @Override
- public String getStringType() {
- return "Translation";
- }
-
- @Override
- public ReactionRect getReactionRect() {
- return ReactionRect.RECT_EMPTY;
- }
-
- @Override
- public TranslationReaction copy() {
- if (this.getClass() == TranslationReaction.class) {
- return new TranslationReaction(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner translation reaction. It must have
+ * at least one reactant and one product.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("TRANSLATION_REACTION")
+public class TranslationReaction extends Reaction implements SimpleReactionInterface {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public TranslationReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public TranslationReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Translation";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return ReactionRect.RECT_EMPTY;
+ }
+
+ @Override
+ public TranslationReaction copy() {
+ if (this.getClass() == TranslationReaction.class) {
+ return new TranslationReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TransportReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TransportReaction.java
index 4d107c09f9..8793fdedf3 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TransportReaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TransportReaction.java
@@ -1,74 +1,74 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * This class defines a standard CellDesigner transport reaction. It must have
- * at least one reactant and one product.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("TRANSPORT_REACTION")
-public class TransportReaction extends Reaction implements SimpleReactionInterface {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public TransportReaction() {
- super();
- }
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param result
- * parent reaction from which we copy data
- */
- public TransportReaction(Reaction result) {
- super(result);
- if (result.getProducts().size() < 1) {
- throw new InvalidArgumentException(
- "Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
- }
- if (result.getReactants().size() < 1) {
- throw new InvalidArgumentException(
- "Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
- }
- }
-
- public TransportReaction(String reactionId) {
- super(reactionId);
- }
-
- @Override
- public String getStringType() {
- return "Transport";
- }
-
- @Override
- public ReactionRect getReactionRect() {
- return ReactionRect.RECT_EMPTY;
- }
-
- @Override
- public TransportReaction copy() {
- if (this.getClass() == TransportReaction.class) {
- return new TransportReaction(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner transport reaction. It must have
+ * at least one reactant and one product.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("TRANSPORT_REACTION")
+public class TransportReaction extends Reaction implements SimpleReactionInterface {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public TransportReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public TransportReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException(
+ "Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException(
+ "Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
+ }
+ }
+
+ public TransportReaction(String reactionId) {
+ super(reactionId);
+ }
+
+ @Override
+ public String getStringType() {
+ return "Transport";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return ReactionRect.RECT_EMPTY;
+ }
+
+ @Override
+ public TransportReaction copy() {
+ if (this.getClass() == TransportReaction.class) {
+ return new TransportReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TriggerReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TriggerReaction.java
index ca7575dde6..14c91e8ac6 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TriggerReaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TriggerReaction.java
@@ -1,67 +1,67 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * This class defines a standard CellDesigner trigger reaction.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("TRIGGER_REACTION")
-public class TriggerReaction extends Reaction implements SimpleReactionInterface, ModifierReactionNotation {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public TriggerReaction() {
- super();
- }
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param result
- * parent reaction from which we copy data
- */
- public TriggerReaction(Reaction result) {
- super(result);
- if (result.getProducts().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
- }
- if (result.getReactants().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
- }
- }
-
- @Override
- public String getStringType() {
- return "Trigger";
- }
-
- @Override
- public ReactionRect getReactionRect() {
- return null;
- }
-
- @Override
- public TriggerReaction copy() {
- if (this.getClass() == TriggerReaction.class) {
- return new TriggerReaction(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner trigger reaction.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("TRIGGER_REACTION")
+public class TriggerReaction extends Reaction implements SimpleReactionInterface, ModifierReactionNotation {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public TriggerReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public TriggerReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Trigger";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return null;
+ }
+
+ @Override
+ public TriggerReaction copy() {
+ if (this.getClass() == TriggerReaction.class) {
+ return new TriggerReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TruncationReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TruncationReaction.java
index 353744559a..7ece41cc5b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TruncationReaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TruncationReaction.java
@@ -1,68 +1,68 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * This class defines a standard CellDesigner truncation reaction. It must have
- * at least one reactant and two products.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("TRUNCATION_REACTION_REACTION")
-public class TruncationReaction extends Reaction implements TwoProductReactionInterface {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public TruncationReaction() {
- super();
- }
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param result
- * parent reaction from which we copy data
- */
- public TruncationReaction(Reaction result) {
- super(result);
- if (result.getProducts().size() < 2) {
- throw new InvalidArgumentException("Reaction cannot be transformed to truncation: number of products must be greater than 1");
- }
- if (result.getReactants().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to truncation: number of reactants must be greater than 0");
- }
- }
-
- @Override
- public String getStringType() {
- return "Truncation";
- }
-
- @Override
- public ReactionRect getReactionRect() {
- return ReactionRect.RECT_BOLT;
- }
-
- @Override
- public TruncationReaction copy() {
- if (this.getClass() == TruncationReaction.class) {
- return new TruncationReaction(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner truncation reaction. It must have
+ * at least one reactant and two products.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("TRUNCATION_REACTION_REACTION")
+public class TruncationReaction extends Reaction implements TwoProductReactionInterface {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public TruncationReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public TruncationReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 2) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to truncation: number of products must be greater than 1");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to truncation: number of reactants must be greater than 0");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Truncation";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return ReactionRect.RECT_BOLT;
+ }
+
+ @Override
+ public TruncationReaction copy() {
+ if (this.getClass() == TruncationReaction.class) {
+ return new TruncationReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TwoProductReactionInterface.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TwoProductReactionInterface.java
index 47d583012b..bf86c3bd18 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TwoProductReactionInterface.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TwoProductReactionInterface.java
@@ -1,12 +1,12 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-/**
- * This interface is only a marker which points out the type of reaction deigned
- * in CD.
- *
- * @author Piotr Gawron
- *
- */
-public interface TwoProductReactionInterface {
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+/**
+ * This interface is only a marker which points out the type of reaction deigned
+ * in CD.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface TwoProductReactionInterface {
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TwoReactantReactionInterface.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TwoReactantReactionInterface.java
index e94556e416..e64b90f898 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TwoReactantReactionInterface.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TwoReactantReactionInterface.java
@@ -1,12 +1,12 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-/**
- * This interface is only a marker which points out the type of reaction deigned
- * in CD.
- *
- * @author Piotr Gawron
- *
- */
-public interface TwoReactantReactionInterface {
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+/**
+ * This interface is only a marker which points out the type of reaction deigned
+ * in CD.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface TwoReactantReactionInterface {
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownCatalysisReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownCatalysisReaction.java
index bce08d8bc1..fba63f4bd9 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownCatalysisReaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownCatalysisReaction.java
@@ -1,67 +1,67 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * This class defines a standard CellDesigner unknown catalysis reaction.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("UNKNOWN_CATALYSIS_REACTION")
-public class UnknownCatalysisReaction extends Reaction implements SimpleReactionInterface, ModifierReactionNotation {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public UnknownCatalysisReaction() {
- super();
- }
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param result
- * parent reaction from which we copy data
- */
- public UnknownCatalysisReaction(Reaction result) {
- super(result);
- if (result.getProducts().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
- }
- if (result.getReactants().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
- }
- }
-
- @Override
- public String getStringType() {
- return "Unknown catalysis";
- }
-
- @Override
- public ReactionRect getReactionRect() {
- return null;
- }
-
- @Override
- public UnknownCatalysisReaction copy() {
- if (this.getClass() == UnknownCatalysisReaction.class) {
- return new UnknownCatalysisReaction(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner unknown catalysis reaction.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("UNKNOWN_CATALYSIS_REACTION")
+public class UnknownCatalysisReaction extends Reaction implements SimpleReactionInterface, ModifierReactionNotation {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public UnknownCatalysisReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public UnknownCatalysisReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Unknown catalysis";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return null;
+ }
+
+ @Override
+ public UnknownCatalysisReaction copy() {
+ if (this.getClass() == UnknownCatalysisReaction.class) {
+ return new UnknownCatalysisReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownInhibitionReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownInhibitionReaction.java
index 42c4d6ad99..e0ebd2ceaa 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownInhibitionReaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownInhibitionReaction.java
@@ -1,67 +1,67 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * This class defines a standard CellDesigner unknown inhibition reaction.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("UNKNOWN_INHIBITION_REACTION")
-public class UnknownInhibitionReaction extends Reaction implements SimpleReactionInterface, ModifierReactionNotation {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public UnknownInhibitionReaction() {
- super();
- }
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param result
- * parent reaction from which we copy data
- */
- public UnknownInhibitionReaction(Reaction result) {
- super(result);
- if (result.getProducts().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
- }
- if (result.getReactants().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
- }
- }
-
- @Override
- public String getStringType() {
- return "Unknown inhibition";
- }
-
- @Override
- public ReactionRect getReactionRect() {
- return null;
- }
-
- @Override
- public UnknownInhibitionReaction copy() {
- if (this.getClass() == UnknownInhibitionReaction.class) {
- return new UnknownInhibitionReaction(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner unknown inhibition reaction.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("UNKNOWN_INHIBITION_REACTION")
+public class UnknownInhibitionReaction extends Reaction implements SimpleReactionInterface, ModifierReactionNotation {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public UnknownInhibitionReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public UnknownInhibitionReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Unknown inhibition";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return null;
+ }
+
+ @Override
+ public UnknownInhibitionReaction copy() {
+ if (this.getClass() == UnknownInhibitionReaction.class) {
+ return new UnknownInhibitionReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownNegativeInfluenceReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownNegativeInfluenceReaction.java
index 93a0bceed5..3215aed989 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownNegativeInfluenceReaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownNegativeInfluenceReaction.java
@@ -1,68 +1,68 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * This class defines a standard CellDesigner unknown negative influence
- * reaction. It must have at least one reactant and one product.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("UNKNOWN_NEGATIVE_INFLUENCE")
-public class UnknownNegativeInfluenceReaction extends Reaction implements SimpleReactionInterface, ReducedNotation {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public UnknownNegativeInfluenceReaction() {
- super();
- }
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param result
- * parent reaction from which we copy data
- */
- public UnknownNegativeInfluenceReaction(Reaction result) {
- super(result);
- if (result.getProducts().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
- }
- if (result.getReactants().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
- }
- }
-
- @Override
- public String getStringType() {
- return "Unknown negative influence";
- }
-
- @Override
- public ReactionRect getReactionRect() {
- return null;
- }
-
- @Override
- public UnknownNegativeInfluenceReaction copy() {
- if (this.getClass() == UnknownNegativeInfluenceReaction.class) {
- return new UnknownNegativeInfluenceReaction(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner unknown negative influence
+ * reaction. It must have at least one reactant and one product.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("UNKNOWN_NEGATIVE_INFLUENCE")
+public class UnknownNegativeInfluenceReaction extends Reaction implements SimpleReactionInterface, ReducedNotation {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public UnknownNegativeInfluenceReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public UnknownNegativeInfluenceReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Unknown negative influence";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return null;
+ }
+
+ @Override
+ public UnknownNegativeInfluenceReaction copy() {
+ if (this.getClass() == UnknownNegativeInfluenceReaction.class) {
+ return new UnknownNegativeInfluenceReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownPositiveInfluenceReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownPositiveInfluenceReaction.java
index 1e48cc05b8..a48d2fa6a2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownPositiveInfluenceReaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownPositiveInfluenceReaction.java
@@ -1,67 +1,67 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * This class defines a standard CellDesigner unknown positive influence
- * reaction. It must have at least one reactant and one product.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("UNKNOWN_POSITIVE_INFLUENCE")
-public class UnknownPositiveInfluenceReaction extends Reaction implements SimpleReactionInterface, ReducedNotation {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public UnknownPositiveInfluenceReaction() {
- super();
- }
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param result
- * parent reaction from which we copy data
- */
- public UnknownPositiveInfluenceReaction(Reaction result) {
- super(result);
- if (result.getProducts().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
- }
- if (result.getReactants().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
- }
- }
-
- @Override
- public String getStringType() {
- return "Unknown positive influence";
- }
-
- @Override
- public ReactionRect getReactionRect() {
- return null;
- }
-
- @Override
- public UnknownPositiveInfluenceReaction copy() {
- if (this.getClass() == UnknownPositiveInfluenceReaction.class) {
- return new UnknownPositiveInfluenceReaction(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner unknown positive influence
+ * reaction. It must have at least one reactant and one product.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("UNKNOWN_POSITIVE_INFLUENCE")
+public class UnknownPositiveInfluenceReaction extends Reaction implements SimpleReactionInterface, ReducedNotation {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public UnknownPositiveInfluenceReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public UnknownPositiveInfluenceReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Unknown positive influence";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return null;
+ }
+
+ @Override
+ public UnknownPositiveInfluenceReaction copy() {
+ if (this.getClass() == UnknownPositiveInfluenceReaction.class) {
+ return new UnknownPositiveInfluenceReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownReducedModulationReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownReducedModulationReaction.java
index bddf42c923..33dc07d0e6 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownReducedModulationReaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownReducedModulationReaction.java
@@ -1,68 +1,68 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * This class defines a standard CellDesigner unknown reduced modulation
- * reaction. It must have at least one reactant and one product.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("U_REDUCED_MODULATION")
-public class UnknownReducedModulationReaction extends Reaction implements SimpleReactionInterface, ReducedNotation {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public UnknownReducedModulationReaction() {
- super();
- }
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param result
- * parent reaction from which we copy data
- */
- public UnknownReducedModulationReaction(Reaction result) {
- super(result);
- if (result.getProducts().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
- }
- if (result.getReactants().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
- }
- }
-
- @Override
- public String getStringType() {
- return "Unknown reduced modulation";
- }
-
- @Override
- public ReactionRect getReactionRect() {
- return null;
- }
-
- @Override
- public UnknownReducedModulationReaction copy() {
- if (this.getClass() == UnknownReducedModulationReaction.class) {
- return new UnknownReducedModulationReaction(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner unknown reduced modulation
+ * reaction. It must have at least one reactant and one product.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("U_REDUCED_MODULATION")
+public class UnknownReducedModulationReaction extends Reaction implements SimpleReactionInterface, ReducedNotation {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public UnknownReducedModulationReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public UnknownReducedModulationReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Unknown reduced modulation";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return null;
+ }
+
+ @Override
+ public UnknownReducedModulationReaction copy() {
+ if (this.getClass() == UnknownReducedModulationReaction.class) {
+ return new UnknownReducedModulationReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownReducedPhysicalStimulationReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownReducedPhysicalStimulationReaction.java
index 793b876079..938b2fbe20 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownReducedPhysicalStimulationReaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownReducedPhysicalStimulationReaction.java
@@ -1,68 +1,68 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * This class defines a standard CellDesigner unknown reduced physical
- * stimulation reaction. It must have at least one reactant and one product.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("U_REDUCED_PHYSICAL_STIM")
-public class UnknownReducedPhysicalStimulationReaction extends Reaction implements SimpleReactionInterface, ReducedNotation {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public UnknownReducedPhysicalStimulationReaction() {
- super();
- }
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param result
- * parent reaction from which we copy data
- */
- public UnknownReducedPhysicalStimulationReaction(Reaction result) {
- super(result);
- if (result.getProducts().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
- }
- if (result.getReactants().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
- }
- }
-
- @Override
- public String getStringType() {
- return "Unknown reduced physical stimulation";
- }
-
- @Override
- public ReactionRect getReactionRect() {
- return null;
- }
-
- @Override
- public UnknownReducedPhysicalStimulationReaction copy() {
- if (this.getClass() == UnknownReducedPhysicalStimulationReaction.class) {
- return new UnknownReducedPhysicalStimulationReaction(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner unknown reduced physical
+ * stimulation reaction. It must have at least one reactant and one product.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("U_REDUCED_PHYSICAL_STIM")
+public class UnknownReducedPhysicalStimulationReaction extends Reaction implements SimpleReactionInterface, ReducedNotation {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public UnknownReducedPhysicalStimulationReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public UnknownReducedPhysicalStimulationReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Unknown reduced physical stimulation";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return null;
+ }
+
+ @Override
+ public UnknownReducedPhysicalStimulationReaction copy() {
+ if (this.getClass() == UnknownReducedPhysicalStimulationReaction.class) {
+ return new UnknownReducedPhysicalStimulationReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownReducedTriggerReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownReducedTriggerReaction.java
index 00d3529fcc..6c34124301 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownReducedTriggerReaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownReducedTriggerReaction.java
@@ -1,68 +1,68 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * This class defines a standard CellDesigner unknown reduced trigger reaction.
- * It must have at least one reactant and one product.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("U_REDUCED_TRIGGER")
-public class UnknownReducedTriggerReaction extends Reaction implements SimpleReactionInterface, ReducedNotation {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public UnknownReducedTriggerReaction() {
- super();
- }
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param result
- * parent reaction from which we copy data
- */
- public UnknownReducedTriggerReaction(Reaction result) {
- super(result);
- if (result.getProducts().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
- }
- if (result.getReactants().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
- }
- }
-
- @Override
- public String getStringType() {
- return "Unknown reduced trigger";
- }
-
- @Override
- public ReactionRect getReactionRect() {
- return null;
- }
-
- @Override
- public UnknownReducedTriggerReaction copy() {
- if (this.getClass() == UnknownReducedTriggerReaction.class) {
- return new UnknownReducedTriggerReaction(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner unknown reduced trigger reaction.
+ * It must have at least one reactant and one product.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("U_REDUCED_TRIGGER")
+public class UnknownReducedTriggerReaction extends Reaction implements SimpleReactionInterface, ReducedNotation {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public UnknownReducedTriggerReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public UnknownReducedTriggerReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Unknown reduced trigger";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return null;
+ }
+
+ @Override
+ public UnknownReducedTriggerReaction copy() {
+ if (this.getClass() == UnknownReducedTriggerReaction.class) {
+ return new UnknownReducedTriggerReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownTransitionReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownTransitionReaction.java
index 8aa4e08538..da95f840e6 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownTransitionReaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownTransitionReaction.java
@@ -1,68 +1,68 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * This class defines a standard CellDesigner unknown transition reaction. It
- * must have at least one reactant and one product.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("UNKNOWN_TRANSITION_REACTION")
-public class UnknownTransitionReaction extends Reaction implements SimpleReactionInterface {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- */
- public UnknownTransitionReaction() {
- super();
- }
-
- /**
- * Constructor that copies data from the parameter given in the argument.
- *
- * @param result
- * parent reaction from which we copy data
- */
- public UnknownTransitionReaction(Reaction result) {
- super(result);
- if (result.getProducts().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
- }
- if (result.getReactants().size() < 1) {
- throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
- }
- }
-
- @Override
- public String getStringType() {
- return "Unknown transition";
- }
-
- @Override
- public ReactionRect getReactionRect() {
- return ReactionRect.RECT_QUESTION;
- }
-
- @Override
- public UnknownTransitionReaction copy() {
- if (this.getClass() == UnknownTransitionReaction.class) {
- return new UnknownTransitionReaction(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner unknown transition reaction. It
+ * must have at least one reactant and one product.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("UNKNOWN_TRANSITION_REACTION")
+public class UnknownTransitionReaction extends Reaction implements SimpleReactionInterface {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public UnknownTransitionReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public UnknownTransitionReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Unknown transition";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return ReactionRect.RECT_QUESTION;
+ }
+
+ @Override
+ public UnknownTransitionReaction copy() {
+ if (this.getClass() == UnknownTransitionReaction.class) {
+ return new UnknownTransitionReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/package-info.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/package-info.java
index 110fd06b37..806f1943bb 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/package-info.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/package-info.java
@@ -1,6 +1,6 @@
-/**
- * This package contains all types of reactions that are allowed in the system
- * (maybe it should be transformed to a kind of enum...).
- */
-package lcsb.mapviewer.model.map.reaction.type;
-
+/**
+ * This package contains all types of reactions that are allowed in the system
+ * (maybe it should be transformed to a kind of enum...).
+ */
+package lcsb.mapviewer.model.map.reaction.type;
+
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparator.java
index 65f2b00630..c81aa87861 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparator.java
@@ -1,79 +1,79 @@
-package lcsb.mapviewer.model.map.species;
-
-import java.util.HashSet;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.StringSetComparator;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-
-/**
- * Comparator class used for comparing {@link AntisenseRna} objects.
- *
- * @author Piotr Gawron
- *
- */
-public class AntisenseRnaComparator extends Comparator<AntisenseRna> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(AntisenseRnaComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public AntisenseRnaComparator(double epsilon) {
- super(AntisenseRna.class, true);
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public AntisenseRnaComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected Comparator<?> getParentComparator() {
- return new SpeciesComparator(epsilon);
- }
-
- @Override
- protected int internalCompare(AntisenseRna arg0, AntisenseRna arg1) {
- StringSetComparator stringSetComparator = new StringSetComparator();
-
- Set<String> set1 = new HashSet<>();
- Set<String> set2 = new HashSet<>();
-
- for (ModificationResidue region : arg0.getRegions()) {
- set1.add(region.toString());
- }
-
- for (ModificationResidue region : arg1.getRegions()) {
- set2.add(region.toString());
- }
-
- if (stringSetComparator.compare(set1, set2) != 0) {
- logger.debug(set1);
- logger.debug(set2);
- logger.debug("Regions mismatch");
- return stringSetComparator.compare(set1, set2);
- }
-
- return 0;
- }
-}
+package lcsb.mapviewer.model.map.species;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.StringSetComparator;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+
+/**
+ * Comparator class used for comparing {@link AntisenseRna} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class AntisenseRnaComparator extends Comparator<AntisenseRna> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(AntisenseRnaComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public AntisenseRnaComparator(double epsilon) {
+ super(AntisenseRna.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public AntisenseRnaComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new SpeciesComparator(epsilon);
+ }
+
+ @Override
+ protected int internalCompare(AntisenseRna arg0, AntisenseRna arg1) {
+ StringSetComparator stringSetComparator = new StringSetComparator();
+
+ Set<String> set1 = new HashSet<>();
+ Set<String> set2 = new HashSet<>();
+
+ for (ModificationResidue region : arg0.getRegions()) {
+ set1.add(region.toString());
+ }
+
+ for (ModificationResidue region : arg1.getRegions()) {
+ set2.add(region.toString());
+ }
+
+ if (stringSetComparator.compare(set1, set2) != 0) {
+ logger.debug(set1);
+ logger.debug(set2);
+ logger.debug("Regions mismatch");
+ return stringSetComparator.compare(set1, set2);
+ }
+
+ return 0;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Chemical.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Chemical.java
index bec1401d70..2c3a2bfbd6 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Chemical.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Chemical.java
@@ -1,116 +1,116 @@
-package lcsb.mapviewer.model.map.species;
-
-import javax.persistence.Column;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-/**
- * Entity representing chemical element on the map.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("CHEMICAL_ALIAS")
-public abstract class Chemical extends Species {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * <a href=
- * "http://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system"
- * >Smiles</a> parameter for the chemical.
- */
- @Column(name = "smiles", columnDefinition = "TEXT")
- private String smiles;
-
- /**
- * <a href= "http://en.wikipedia.org/wiki/International_Chemical_Identifier" >
- * InChI</a> parameter for the chemical.
- */
-
- @Column(name = "inchi", columnDefinition = "TEXT")
- private String inChI;
-
- /**
- * <a href=
- * "http://en.wikipedia.org/wiki/International_Chemical_Identifier#InChIKey" >
- * InChIKey</a> parameter for the chemical.
- */
-
- private String inChIKey;
-
- /**
- * Empty constructor required by hibernate.
- */
- Chemical() {
- }
-
- /**
- * Constructor that creates a copy of the element given in the parameter.
- *
- * @param original
- * original object that will be used for creating copy
- */
- public Chemical(Chemical original) {
- super(original);
- smiles = original.getSmiles();
- inChI = original.getInChI();
- inChIKey = original.getInChIKey();
- }
-
- /**
- * @return the inChIKey
- * @see #inChIKey
- */
- public String getInChIKey() {
- return inChIKey;
- }
-
- /**
- * @param inChIKey
- * the inChIKey to set
- * @see #inChIKey
- */
- public void setInChIKey(String inChIKey) {
- this.inChIKey = inChIKey;
- }
-
- /**
- * @return the inChI
- * @see #inChI
- */
- public String getInChI() {
- return inChI;
- }
-
- /**
- * @param inChI
- * the inChI to set
- * @see #inChI
- */
- public void setInChI(String inChI) {
- this.inChI = inChI;
- }
-
- /**
- * @return the smiles
- * @see #smiles
- */
- public String getSmiles() {
- return smiles;
- }
-
- /**
- * @param smiles
- * the smiles to set
- * @see #smiles
- */
- public void setSmiles(String smiles) {
- this.smiles = smiles;
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import javax.persistence.Column;
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+/**
+ * Entity representing chemical element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("CHEMICAL_ALIAS")
+public abstract class Chemical extends Species {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * <a href=
+ * "http://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system"
+ * >Smiles</a> parameter for the chemical.
+ */
+ @Column(name = "smiles", columnDefinition = "TEXT")
+ private String smiles;
+
+ /**
+ * <a href= "http://en.wikipedia.org/wiki/International_Chemical_Identifier" >
+ * InChI</a> parameter for the chemical.
+ */
+
+ @Column(name = "inchi", columnDefinition = "TEXT")
+ private String inChI;
+
+ /**
+ * <a href=
+ * "http://en.wikipedia.org/wiki/International_Chemical_Identifier#InChIKey" >
+ * InChIKey</a> parameter for the chemical.
+ */
+
+ private String inChIKey;
+
+ /**
+ * Empty constructor required by hibernate.
+ */
+ Chemical() {
+ }
+
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
+ public Chemical(Chemical original) {
+ super(original);
+ smiles = original.getSmiles();
+ inChI = original.getInChI();
+ inChIKey = original.getInChIKey();
+ }
+
+ /**
+ * @return the inChIKey
+ * @see #inChIKey
+ */
+ public String getInChIKey() {
+ return inChIKey;
+ }
+
+ /**
+ * @param inChIKey
+ * the inChIKey to set
+ * @see #inChIKey
+ */
+ public void setInChIKey(String inChIKey) {
+ this.inChIKey = inChIKey;
+ }
+
+ /**
+ * @return the inChI
+ * @see #inChI
+ */
+ public String getInChI() {
+ return inChI;
+ }
+
+ /**
+ * @param inChI
+ * the inChI to set
+ * @see #inChI
+ */
+ public void setInChI(String inChI) {
+ this.inChI = inChI;
+ }
+
+ /**
+ * @return the smiles
+ * @see #smiles
+ */
+ public String getSmiles() {
+ return smiles;
+ }
+
+ /**
+ * @param smiles
+ * the smiles to set
+ * @see #smiles
+ */
+ public void setSmiles(String smiles) {
+ this.smiles = smiles;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ChemicalComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ChemicalComparator.java
index 14601f6a0f..89cde448fe 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ChemicalComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ChemicalComparator.java
@@ -1,73 +1,73 @@
-package lcsb.mapviewer.model.map.species;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.StringComparator;
-
-/**
- * Comparator class used for comparing {@link Chemical} objects.
- *
- * @author Piotr Gawron
- *
- */
-public class ChemicalComparator extends Comparator<Chemical> {
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ChemicalComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public ChemicalComparator(double epsilon) {
- super(Chemical.class, true);
- this.epsilon = epsilon;
- addSubClassComparator(new IonComparator(epsilon));
- addSubClassComparator(new SimpleMoleculeComparator(epsilon));
- }
-
- @Override
- protected Comparator<?> getParentComparator() {
- return new SpeciesComparator(epsilon);
- }
-
- /**
- * Default constructor.
- */
- public ChemicalComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected int internalCompare(Chemical arg0, Chemical arg1) {
- StringComparator stringComparator = new StringComparator();
-
- if (stringComparator.compare(arg0.getSmiles(), arg1.getSmiles()) != 0) {
- logger.debug("Smiles different: " + arg0.getSmiles() + ", " + arg1.getSmiles());
- return stringComparator.compare(arg0.getSmiles(), arg1.getSmiles());
- }
-
- if (stringComparator.compare(arg0.getInChIKey(), arg1.getInChIKey()) != 0) {
- logger.debug("InChIKey different: " + arg0.getInChIKey() + ", " + arg1.getInChIKey());
- return stringComparator.compare(arg0.getInChIKey(), arg1.getInChIKey());
- }
-
- if (stringComparator.compare(arg0.getInChI(), arg1.getInChI()) != 0) {
- logger.debug("InChI different: " + arg0.getInChI() + ", " + arg1.getInChI());
- return stringComparator.compare(arg0.getInChI(), arg1.getInChI());
- }
-
- return 0;
- }
-}
+package lcsb.mapviewer.model.map.species;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.StringComparator;
+
+/**
+ * Comparator class used for comparing {@link Chemical} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ChemicalComparator extends Comparator<Chemical> {
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ChemicalComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public ChemicalComparator(double epsilon) {
+ super(Chemical.class, true);
+ this.epsilon = epsilon;
+ addSubClassComparator(new IonComparator(epsilon));
+ addSubClassComparator(new SimpleMoleculeComparator(epsilon));
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new SpeciesComparator(epsilon);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public ChemicalComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(Chemical arg0, Chemical arg1) {
+ StringComparator stringComparator = new StringComparator();
+
+ if (stringComparator.compare(arg0.getSmiles(), arg1.getSmiles()) != 0) {
+ logger.debug("Smiles different: " + arg0.getSmiles() + ", " + arg1.getSmiles());
+ return stringComparator.compare(arg0.getSmiles(), arg1.getSmiles());
+ }
+
+ if (stringComparator.compare(arg0.getInChIKey(), arg1.getInChIKey()) != 0) {
+ logger.debug("InChIKey different: " + arg0.getInChIKey() + ", " + arg1.getInChIKey());
+ return stringComparator.compare(arg0.getInChIKey(), arg1.getInChIKey());
+ }
+
+ if (stringComparator.compare(arg0.getInChI(), arg1.getInChI()) != 0) {
+ logger.debug("InChI different: " + arg0.getInChI() + ", " + arg1.getInChI());
+ return stringComparator.compare(arg0.getInChI(), arg1.getInChI());
+ }
+
+ return 0;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Complex.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Complex.java
index c1320b9e93..3d9ae6ba31 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Complex.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Complex.java
@@ -1,199 +1,199 @@
-package lcsb.mapviewer.model.map.species;
-
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.OneToMany;
-
-import org.apache.log4j.Logger;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-/**
- * Class that represents complex in the model. Complex elements contain
- * subelements.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("Complex")
-public class Complex extends Species {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(Complex.class);
-
- /**
- * List of elements that are in this complex (only elements that lies there
- * directly).
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(fetch = FetchType.EAGER, mappedBy = "complex")
- private List<Species> elements = new ArrayList<>();
-
- /**
- * State of the complex species.
- */
- private String structuralState = null;
-
- /**
- * Empty constructor required by hibernate.
- */
- Complex() {
- super();
- }
-
- /**
- * Constructor that creates object initialized by the object given in the
- * parameter.
- *
- * @param original
- * original complex used for initialization
- */
- public Complex(Complex original) {
- super(original);
-
- for (Species element : original.getElements()) {
- addSpecies(element.copy());
- }
- this.structuralState = original.getStructuralState();
- }
-
- /**
- * Default constructor.
- *
- * @param elementId
- * uniqe (within model) element identifier
- */
- public Complex(String elementId) {
- super(elementId);
- }
-
- /**
- * Adds {@link Species} to the complex.
- *
- * @param species
- * object to add
- */
- public void addSpecies(Species species) {
- boolean contains = false;
- for (Species element2 : elements) {
- if (species.getElementId().equals(element2.getElementId())) {
- contains = true;
- }
-
- }
- if (!contains) {
- elements.add(species);
- species.setComplex(this);
- }
- }
-
- /**
- * Returns list of elements.
- *
- * @return list of element inside complex
- */
- public List<Species> getElements() {
- return elements;
- }
-
- /**
- * Returns list of all {@link Species} that lies inside complex (direct and
- * undirect).
- *
- * @return list of all {@link Species} inside {@link Complex}
- */
- public List<Species> getAllChildren() {
- List<Species> result = new ArrayList<>();
- result.addAll(elements);
- for (Species species : elements) {
- if (species instanceof Complex) {
- result.addAll(((Complex) species).getAllChildren());
- }
- }
- return result;
- }
-
- @Override
- public Complex copy() {
- if (this.getClass() == Complex.class) {
- return new Complex(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
-
- }
-
- /**
- * Removes {@link Species} from the complex.
- *
- * @param element
- * object to remove
- */
- public void removeElement(Species element) {
- elements.remove(element);
- if (element.getComplex() != null) {
- if (element.getComplex() == this) {
- element.setComplex(null);
- } else {
- logger.warn("Removing element from complex that probably doesn't belong there");
- }
- }
- }
-
- /**
- * @return the structuralState
- * @see #structuralState
- */
- public String getStructuralState() {
- return structuralState;
- }
-
- /**
- * @param structuralState
- * the structuralState to set
- * @see #structuralState
- */
- public void setStructuralState(String structuralState) {
- this.structuralState = structuralState;
- }
-
- /**
- * Returns all children and subchildren elements for this element. Only non
- * {@link Complex} children will be returned.
- *
- * @return all children and subchildren elements for this element
- */
- public Set<Species> getAllSimpleChildren() {
- Set<Species> result = new HashSet<>();
- for (Species element : getElements()) {
- if (element instanceof Complex) {
- result.addAll(((Complex) element).getAllSimpleChildren());
- } else {
- result.add(element);
- }
- }
- return result;
- }
-
- @Override
- public String getStringType() {
- return "Complex";
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.OneToMany;
+
+import org.apache.log4j.Logger;
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * Class that represents complex in the model. Complex elements contain
+ * subelements.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("Complex")
+public class Complex extends Species {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(Complex.class);
+
+ /**
+ * List of elements that are in this complex (only elements that lies there
+ * directly).
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(fetch = FetchType.EAGER, mappedBy = "complex")
+ private List<Species> elements = new ArrayList<>();
+
+ /**
+ * State of the complex species.
+ */
+ private String structuralState = null;
+
+ /**
+ * Empty constructor required by hibernate.
+ */
+ Complex() {
+ super();
+ }
+
+ /**
+ * Constructor that creates object initialized by the object given in the
+ * parameter.
+ *
+ * @param original
+ * original complex used for initialization
+ */
+ public Complex(Complex original) {
+ super(original);
+
+ for (Species element : original.getElements()) {
+ addSpecies(element.copy());
+ }
+ this.structuralState = original.getStructuralState();
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * uniqe (within model) element identifier
+ */
+ public Complex(String elementId) {
+ super(elementId);
+ }
+
+ /**
+ * Adds {@link Species} to the complex.
+ *
+ * @param species
+ * object to add
+ */
+ public void addSpecies(Species species) {
+ boolean contains = false;
+ for (Species element2 : elements) {
+ if (species.getElementId().equals(element2.getElementId())) {
+ contains = true;
+ }
+
+ }
+ if (!contains) {
+ elements.add(species);
+ species.setComplex(this);
+ }
+ }
+
+ /**
+ * Returns list of elements.
+ *
+ * @return list of element inside complex
+ */
+ public List<Species> getElements() {
+ return elements;
+ }
+
+ /**
+ * Returns list of all {@link Species} that lies inside complex (direct and
+ * undirect).
+ *
+ * @return list of all {@link Species} inside {@link Complex}
+ */
+ public List<Species> getAllChildren() {
+ List<Species> result = new ArrayList<>();
+ result.addAll(elements);
+ for (Species species : elements) {
+ if (species instanceof Complex) {
+ result.addAll(((Complex) species).getAllChildren());
+ }
+ }
+ return result;
+ }
+
+ @Override
+ public Complex copy() {
+ if (this.getClass() == Complex.class) {
+ return new Complex(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+
+ }
+
+ /**
+ * Removes {@link Species} from the complex.
+ *
+ * @param element
+ * object to remove
+ */
+ public void removeElement(Species element) {
+ elements.remove(element);
+ if (element.getComplex() != null) {
+ if (element.getComplex() == this) {
+ element.setComplex(null);
+ } else {
+ logger.warn("Removing element from complex that probably doesn't belong there");
+ }
+ }
+ }
+
+ /**
+ * @return the structuralState
+ * @see #structuralState
+ */
+ public String getStructuralState() {
+ return structuralState;
+ }
+
+ /**
+ * @param structuralState
+ * the structuralState to set
+ * @see #structuralState
+ */
+ public void setStructuralState(String structuralState) {
+ this.structuralState = structuralState;
+ }
+
+ /**
+ * Returns all children and subchildren elements for this element. Only non
+ * {@link Complex} children will be returned.
+ *
+ * @return all children and subchildren elements for this element
+ */
+ public Set<Species> getAllSimpleChildren() {
+ Set<Species> result = new HashSet<>();
+ for (Species element : getElements()) {
+ if (element instanceof Complex) {
+ result.addAll(((Complex) element).getAllSimpleChildren());
+ } else {
+ result.add(element);
+ }
+ }
+ return result;
+ }
+
+ @Override
+ public String getStringType() {
+ return "Complex";
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ComplexComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ComplexComparator.java
index b452ec2cea..ccfe3537aa 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ComplexComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ComplexComparator.java
@@ -1,100 +1,100 @@
-package lcsb.mapviewer.model.map.species;
-
-import java.util.HashMap;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.IntegerComparator;
-import lcsb.mapviewer.common.comparator.StringComparator;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-
-/**
- * This class implements comparator interface for {@link Complex}.
- *
- * @author Piotr Gawron
- *
- */
-public class ComplexComparator extends Comparator<Complex> {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ComplexComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public ComplexComparator(double epsilon) {
- super(Complex.class, true);
- this.epsilon = epsilon;
- }
-
- @Override
- protected Comparator<?> getParentComparator() {
- return new SpeciesComparator(epsilon);
- }
-
- /**
- * Default constructor.
- */
- public ComplexComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected int internalCompare(Complex arg0, Complex arg1) {
- ElementComparator elementComparator = new ElementComparator(epsilon);
- IntegerComparator integerComparator = new IntegerComparator();
-
- if (integerComparator.compare(arg0.getElements().size(), arg1.getElements().size()) != 0) {
- logger.debug("children elements size different: " + arg0.getElements().size() + ", " + arg1.getElements().size());
- return integerComparator.compare(arg0.getElements().size(), arg1.getElements().size());
- }
-
- Map<String, Element> map1 = new HashMap<>();
- Map<String, Element> map2 = new HashMap<>();
-
- for (Element element : arg0.getElements()) {
- if (map1.get(element.getElementId()) != null) {
- throw new InvalidArgumentException("Few elements with the same id: " + element.getElementId());
- }
- map1.put(element.getElementId(), element);
- }
-
- for (Element element : arg1.getElements()) {
- if (map2.get(element.getElementId()) != null) {
- throw new InvalidArgumentException("Few elements with the same id: " + element.getElementId());
- }
- map2.put(element.getElementId(), element);
- }
-
- for (Element element : arg0.getElements()) {
- Element element2 = map2.get(element.getElementId());
- int status = elementComparator.compare(element, element2);
- if (status != 0) {
- logger.debug("child doesn't have a match: " + element.getElementId());
- return status;
- }
- }
-
- StringComparator stringComparator = new StringComparator();
-
- if (stringComparator.compare(arg0.getStructuralState(), arg1.getStructuralState()) != 0) {
- logger
- .debug("Species structuralState different: " + arg0.getStructuralState() + ", " + arg1.getStructuralState());
- return stringComparator.compare(arg0.getStructuralState(), arg1.getStructuralState());
- }
-
- return 0;
- }
-}
+package lcsb.mapviewer.model.map.species;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.IntegerComparator;
+import lcsb.mapviewer.common.comparator.StringComparator;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+
+/**
+ * This class implements comparator interface for {@link Complex}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ComplexComparator extends Comparator<Complex> {
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ComplexComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public ComplexComparator(double epsilon) {
+ super(Complex.class, true);
+ this.epsilon = epsilon;
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new SpeciesComparator(epsilon);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public ComplexComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(Complex arg0, Complex arg1) {
+ ElementComparator elementComparator = new ElementComparator(epsilon);
+ IntegerComparator integerComparator = new IntegerComparator();
+
+ if (integerComparator.compare(arg0.getElements().size(), arg1.getElements().size()) != 0) {
+ logger.debug("children elements size different: " + arg0.getElements().size() + ", " + arg1.getElements().size());
+ return integerComparator.compare(arg0.getElements().size(), arg1.getElements().size());
+ }
+
+ Map<String, Element> map1 = new HashMap<>();
+ Map<String, Element> map2 = new HashMap<>();
+
+ for (Element element : arg0.getElements()) {
+ if (map1.get(element.getElementId()) != null) {
+ throw new InvalidArgumentException("Few elements with the same id: " + element.getElementId());
+ }
+ map1.put(element.getElementId(), element);
+ }
+
+ for (Element element : arg1.getElements()) {
+ if (map2.get(element.getElementId()) != null) {
+ throw new InvalidArgumentException("Few elements with the same id: " + element.getElementId());
+ }
+ map2.put(element.getElementId(), element);
+ }
+
+ for (Element element : arg0.getElements()) {
+ Element element2 = map2.get(element.getElementId());
+ int status = elementComparator.compare(element, element2);
+ if (status != 0) {
+ logger.debug("child doesn't have a match: " + element.getElementId());
+ return status;
+ }
+ }
+
+ StringComparator stringComparator = new StringComparator();
+
+ if (stringComparator.compare(arg0.getStructuralState(), arg1.getStructuralState()) != 0) {
+ logger
+ .debug("Species structuralState different: " + arg0.getStructuralState() + ", " + arg1.getStructuralState());
+ return stringComparator.compare(arg0.getStructuralState(), arg1.getStructuralState());
+ }
+
+ return 0;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Degraded.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Degraded.java
index d030136fce..a9706c0dd9 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Degraded.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Degraded.java
@@ -1,62 +1,62 @@
-package lcsb.mapviewer.model.map.species;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-/**
- * Entity representing degraded element on the map.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("DEGRADED_ALIAS")
-public class Degraded extends Species {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Empty constructor required by hibernate.
- */
- Degraded() {
- }
-
- /**
- * Constructor that creates a copy of the element given in the parameter.
- *
- * @param original
- * original object that will be used for creating copy
- */
- public Degraded(Degraded original) {
- super(original);
- }
-
- /**
- * Default constructor.
- *
- * @param elementId
- * uniqe (within model) element identifier
- */
- public Degraded(String elementId) {
- super.setElementId(elementId);
- }
-
- @Override
- public Degraded copy() {
- if (this.getClass() == Degraded.class) {
- return new Degraded(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- @Override
- public String getStringType() {
- return "Degraded";
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * Entity representing degraded element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("DEGRADED_ALIAS")
+public class Degraded extends Species {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Empty constructor required by hibernate.
+ */
+ Degraded() {
+ }
+
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
+ public Degraded(Degraded original) {
+ super(original);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * uniqe (within model) element identifier
+ */
+ public Degraded(String elementId) {
+ super.setElementId(elementId);
+ }
+
+ @Override
+ public Degraded copy() {
+ if (this.getClass() == Degraded.class) {
+ return new Degraded(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Degraded";
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/DegradedComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/DegradedComparator.java
index 51333b2e03..0f578f4414 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/DegradedComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/DegradedComparator.java
@@ -1,54 +1,54 @@
-package lcsb.mapviewer.model.map.species;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-
-/**
- * Comparator class used for comparing {@link Degraded} objects.
- *
- * @author Piotr Gawron
- *
- */
-public class DegradedComparator extends Comparator<Degraded> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(DegradedComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public DegradedComparator(double epsilon) {
- super(Degraded.class, true);
- this.epsilon = epsilon;
- }
-
- @Override
- protected Comparator<?> getParentComparator() {
- return new SpeciesComparator(epsilon);
- }
-
- /**
- * Default constructor.
- */
- public DegradedComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected int internalCompare(Degraded arg0, Degraded arg1) {
- return 0;
- }
-}
+package lcsb.mapviewer.model.map.species;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+
+/**
+ * Comparator class used for comparing {@link Degraded} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class DegradedComparator extends Comparator<Degraded> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(DegradedComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public DegradedComparator(double epsilon) {
+ super(Degraded.class, true);
+ this.epsilon = epsilon;
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new SpeciesComparator(epsilon);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public DegradedComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(Degraded arg0, Degraded arg1) {
+ return 0;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Drug.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Drug.java
index aec5c847fd..f5ba5e8df1 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Drug.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Drug.java
@@ -1,63 +1,63 @@
-package lcsb.mapviewer.model.map.species;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-/**
- * Entity representing drug element on the map.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("DRUG_ALIAS")
-public class Drug extends Species {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Empty constructor required by hibernate.
- */
- Drug() {
- }
-
- /**
- * Constructor that creates a copy of the element given in the parameter.
- *
- * @param original
- * original object that will be used for creating copy
- */
- public Drug(Drug original) {
- super(original);
- }
-
- /**
- * Default constructor.
- *
- * @param elementId
- * uniqe (within model) element identifier
- */
- public Drug(String elementId) {
- setElementId(elementId);
- }
-
- @Override
- public Drug copy() {
- if (this.getClass() == Drug.class) {
- return new Drug(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- @Override
- public String getStringType() {
- return "Drug";
- }
-
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * Entity representing drug element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("DRUG_ALIAS")
+public class Drug extends Species {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Empty constructor required by hibernate.
+ */
+ Drug() {
+ }
+
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
+ public Drug(Drug original) {
+ super(original);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * uniqe (within model) element identifier
+ */
+ public Drug(String elementId) {
+ setElementId(elementId);
+ }
+
+ @Override
+ public Drug copy() {
+ if (this.getClass() == Drug.class) {
+ return new Drug(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Drug";
+ }
+
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/DrugComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/DrugComparator.java
index 7f0173f5f4..f1d068a965 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/DrugComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/DrugComparator.java
@@ -1,54 +1,54 @@
-package lcsb.mapviewer.model.map.species;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-
-/**
- * Comparator class used for comparing {@link Drug} objects.
- *
- * @author Piotr Gawron
- *
- */
-public class DrugComparator extends Comparator<Drug> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(DrugComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public DrugComparator(double epsilon) {
- super(Drug.class, true);
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public DrugComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected Comparator<?> getParentComparator() {
- return new SpeciesComparator(epsilon);
- }
-
- @Override
- protected int internalCompare(Drug arg0, Drug arg1) {
- return 0;
- }
-}
+package lcsb.mapviewer.model.map.species;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+
+/**
+ * Comparator class used for comparing {@link Drug} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class DrugComparator extends Comparator<Drug> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(DrugComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public DrugComparator(double epsilon) {
+ super(Drug.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public DrugComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new SpeciesComparator(epsilon);
+ }
+
+ @Override
+ protected int internalCompare(Drug arg0, Drug arg1) {
+ return 0;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java
index 7a985fc597..aef04ac56d 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java
@@ -1,202 +1,202 @@
-package lcsb.mapviewer.model.map.species;
-
-import java.util.HashSet;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.ColorComparator;
-import lcsb.mapviewer.common.comparator.DoubleComparator;
-import lcsb.mapviewer.common.comparator.StringComparator;
-import lcsb.mapviewer.common.comparator.StringListComparator;
-import lcsb.mapviewer.common.comparator.StringSetComparator;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.compartment.CompartmentComparator;
-import lcsb.mapviewer.model.map.model.ElementSubmodelConnectionComparator;
-
-/**
- * Comparator class used for comparing {@link Element} objects.
- *
- * @author Piotr Gawron
- *
- */
-public class ElementComparator extends Comparator<Element> {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ElementComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public ElementComparator(double epsilon) {
- super(Element.class, true);
- this.epsilon = epsilon;
- addSubClassComparator(new ComplexComparator(epsilon));
- addSubClassComparator(new CompartmentComparator(epsilon));
- addSubClassComparator(new SpeciesComparator(epsilon));
- }
-
- /**
- * Default constructor.
- */
- public ElementComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected int internalCompare(Element arg0, Element arg1) {
- if (arg0 == null) {
- if (arg1 == null) {
- return 0;
- } else {
- return 1;
- }
- } else if (arg1 == null) {
- return -1;
- }
-
- StringComparator stringComparator = new StringComparator();
- ColorComparator colorComparator = new ColorComparator();
- DoubleComparator doubleComparator = new DoubleComparator(epsilon);
-
- if (stringComparator.compare(arg0.getElementId(), arg1.getElementId()) != 0) {
- logger.debug("ElementId different: " + arg0.getElementId() + ", " + arg1.getElementId());
- return stringComparator.compare(arg0.getElementId(), arg1.getElementId());
- }
-
- if (doubleComparator.compare(arg0.getX(), arg1.getX()) != 0) {
- logger.debug("X different: " + arg0.getX() + ", " + arg1.getX());
- return doubleComparator.compare(arg0.getX(), arg1.getX());
- }
-
- if (doubleComparator.compare(arg0.getY(), arg1.getY()) != 0) {
- logger.debug("Y different: " + arg0.getY() + ", " + arg1.getY());
- return doubleComparator.compare(arg0.getY(), arg1.getY());
- }
-
- if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
- logger.debug("Width different: " + arg0.getWidth() + ", " + arg1.getWidth());
- return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
- }
-
- if (doubleComparator.compare(arg0.getHeight(), arg1.getHeight()) != 0) {
- logger.debug("Height different: " + arg0.getHeight() + ", " + arg1.getHeight());
- return doubleComparator.compare(arg0.getHeight(), arg1.getHeight());
- }
-
- if (doubleComparator.compare(arg0.getFontSize(), arg1.getFontSize()) != 0) {
- logger.debug("Font size different: " + arg0.getFontSize() + ", " + arg1.getFontSize());
- return doubleComparator.compare(arg0.getFontSize(), arg1.getFontSize());
- }
-
- if (stringComparator.compare(arg0.getVisibilityLevel(), arg1.getVisibilityLevel()) != 0) {
- logger.debug("Visibility level different: " + arg0.getVisibilityLevel() + ", " + arg1.getVisibilityLevel());
- return stringComparator.compare(arg0.getVisibilityLevel(), arg1.getVisibilityLevel());
- }
-
- if (colorComparator.compare(arg0.getColor(), arg1.getColor()) != 0) {
- logger.debug("Color different: " + arg0.getColor() + ", " + arg1.getColor());
- return colorComparator.compare(arg0.getColor(), arg1.getColor());
- }
-
- // this should be somehow modified, because it can create a situation where
- // comparison will fall into infinite loop (in cyclic submodels)
- ElementSubmodelConnectionComparator ascc = new ElementSubmodelConnectionComparator(epsilon);
- int status = ascc.compare(arg0.getSubmodel(), arg1.getSubmodel());
- if (status != 0) {
- logger.debug("Element submodel different: " + arg0.getSubmodel() + ", " + arg1.getSubmodel());
- return status;
- }
-
- if (stringComparator.compare(arg0.getName(), arg1.getName()) != 0) {
- logger.debug("Name different: " + arg0.getName() + ", " + arg1.getName());
- return stringComparator.compare(arg0.getName(), arg1.getName());
- }
-
- if (stringComparator.compare(arg0.getNotes(), arg1.getNotes(), true) != 0) {
- logger.debug("notes different: \n\"" + arg0.getNotes() + "\"\n\"" + arg1.getNotes() + "\"");
- return stringComparator.compare(arg0.getNotes(), arg1.getNotes());
- }
-
- if (stringComparator.compare(arg0.getSymbol(), arg1.getSymbol()) != 0) {
- logger.debug("symbol different: \"" + arg0.getSymbol() + "\", \"" + arg1.getSymbol() + "\"");
- return stringComparator.compare(arg0.getSymbol(), arg1.getSymbol());
- }
-
- if (stringComparator.compare(arg0.getFullName(), arg1.getFullName()) != 0) {
- logger.debug("full name different: \"" + arg0.getFullName() + "\", \"" + arg1.getFullName() + "\"");
- return stringComparator.compare(arg0.getFullName(), arg1.getFullName());
- }
-
- if (stringComparator.compare(arg0.getAbbreviation(), arg1.getAbbreviation()) != 0) {
- logger.debug("Abbreviation different: \"" + arg0.getAbbreviation() + "\", \"" + arg1.getAbbreviation() + "\"");
- return stringComparator.compare(arg0.getAbbreviation(), arg1.getAbbreviation());
- }
-
- if (stringComparator.compare(arg0.getFormula(), arg1.getFormula()) != 0) {
- logger.debug("formula different: \"" + arg0.getFormula() + "\", \"" + arg1.getFormula() + "\"");
- return stringComparator.compare(arg0.getFormula(), arg1.getFormula());
- }
-
- StringSetComparator stringSetComparator = new StringSetComparator();
- StringListComparator stringListComparator = new StringListComparator();
-
- if (stringListComparator.compare(arg0.getSynonyms(), arg1.getSynonyms()) != 0) {
- logger.debug("List of synonyms different");
- return stringListComparator.compare(arg0.getSynonyms(), arg1.getSynonyms());
- }
-
- if (stringListComparator.compare(arg0.getFormerSymbols(), arg1.getFormerSymbols()) != 0) {
- logger.debug("List of former symbols different");
- return stringListComparator.compare(arg0.getFormerSymbols(), arg1.getFormerSymbols());
- }
-
- Set<String> hashCode1 = new HashSet<>();
- Set<String> hashCode2 = new HashSet<>();
-
- if (arg0.getMiriamData().size() != arg1.getMiriamData().size()) {
- logger.debug(
- "different number of annotations: " + arg0.getMiriamData().size() + ", " + arg1.getMiriamData().size());
- return ((Integer) arg0.getMiriamData().size()).compareTo(arg1.getMiriamData().size());
- }
-
- for (MiriamData md : arg0.getMiriamData()) {
- String hash = md.getRelationType() + " " + md.getDataType() + " " + md.getResource();
- hashCode1.add(hash);
- }
-
- for (MiriamData md : arg1.getMiriamData()) {
- String hash = md.getRelationType() + " " + md.getDataType() + " " + md.getResource();
- hashCode2.add(hash);
- }
-
- if (stringSetComparator.compare(hashCode1, hashCode2) != 0) {
- logger.debug("different annotations: ");
- logger.debug("A:");
- for (String string : hashCode1) {
- logger.debug("|" + string + "|");
- }
- logger.debug("B:");
- for (String string : hashCode2) {
- logger.debug("|" + string + "|");
- }
- logger.debug("--");
- return stringSetComparator.compare(hashCode1, hashCode2);
-
- }
-
- return 0;
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.ColorComparator;
+import lcsb.mapviewer.common.comparator.DoubleComparator;
+import lcsb.mapviewer.common.comparator.StringComparator;
+import lcsb.mapviewer.common.comparator.StringListComparator;
+import lcsb.mapviewer.common.comparator.StringSetComparator;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.compartment.CompartmentComparator;
+import lcsb.mapviewer.model.map.model.ElementSubmodelConnectionComparator;
+
+/**
+ * Comparator class used for comparing {@link Element} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ElementComparator extends Comparator<Element> {
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ElementComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public ElementComparator(double epsilon) {
+ super(Element.class, true);
+ this.epsilon = epsilon;
+ addSubClassComparator(new ComplexComparator(epsilon));
+ addSubClassComparator(new CompartmentComparator(epsilon));
+ addSubClassComparator(new SpeciesComparator(epsilon));
+ }
+
+ /**
+ * Default constructor.
+ */
+ public ElementComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(Element arg0, Element arg1) {
+ if (arg0 == null) {
+ if (arg1 == null) {
+ return 0;
+ } else {
+ return 1;
+ }
+ } else if (arg1 == null) {
+ return -1;
+ }
+
+ StringComparator stringComparator = new StringComparator();
+ ColorComparator colorComparator = new ColorComparator();
+ DoubleComparator doubleComparator = new DoubleComparator(epsilon);
+
+ if (stringComparator.compare(arg0.getElementId(), arg1.getElementId()) != 0) {
+ logger.debug("ElementId different: " + arg0.getElementId() + ", " + arg1.getElementId());
+ return stringComparator.compare(arg0.getElementId(), arg1.getElementId());
+ }
+
+ if (doubleComparator.compare(arg0.getX(), arg1.getX()) != 0) {
+ logger.debug("X different: " + arg0.getX() + ", " + arg1.getX());
+ return doubleComparator.compare(arg0.getX(), arg1.getX());
+ }
+
+ if (doubleComparator.compare(arg0.getY(), arg1.getY()) != 0) {
+ logger.debug("Y different: " + arg0.getY() + ", " + arg1.getY());
+ return doubleComparator.compare(arg0.getY(), arg1.getY());
+ }
+
+ if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
+ logger.debug("Width different: " + arg0.getWidth() + ", " + arg1.getWidth());
+ return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
+ }
+
+ if (doubleComparator.compare(arg0.getHeight(), arg1.getHeight()) != 0) {
+ logger.debug("Height different: " + arg0.getHeight() + ", " + arg1.getHeight());
+ return doubleComparator.compare(arg0.getHeight(), arg1.getHeight());
+ }
+
+ if (doubleComparator.compare(arg0.getFontSize(), arg1.getFontSize()) != 0) {
+ logger.debug("Font size different: " + arg0.getFontSize() + ", " + arg1.getFontSize());
+ return doubleComparator.compare(arg0.getFontSize(), arg1.getFontSize());
+ }
+
+ if (stringComparator.compare(arg0.getVisibilityLevel(), arg1.getVisibilityLevel()) != 0) {
+ logger.debug("Visibility level different: " + arg0.getVisibilityLevel() + ", " + arg1.getVisibilityLevel());
+ return stringComparator.compare(arg0.getVisibilityLevel(), arg1.getVisibilityLevel());
+ }
+
+ if (colorComparator.compare(arg0.getColor(), arg1.getColor()) != 0) {
+ logger.debug("Color different: " + arg0.getColor() + ", " + arg1.getColor());
+ return colorComparator.compare(arg0.getColor(), arg1.getColor());
+ }
+
+ // this should be somehow modified, because it can create a situation where
+ // comparison will fall into infinite loop (in cyclic submodels)
+ ElementSubmodelConnectionComparator ascc = new ElementSubmodelConnectionComparator(epsilon);
+ int status = ascc.compare(arg0.getSubmodel(), arg1.getSubmodel());
+ if (status != 0) {
+ logger.debug("Element submodel different: " + arg0.getSubmodel() + ", " + arg1.getSubmodel());
+ return status;
+ }
+
+ if (stringComparator.compare(arg0.getName(), arg1.getName()) != 0) {
+ logger.debug("Name different: " + arg0.getName() + ", " + arg1.getName());
+ return stringComparator.compare(arg0.getName(), arg1.getName());
+ }
+
+ if (stringComparator.compare(arg0.getNotes(), arg1.getNotes(), true) != 0) {
+ logger.debug("notes different: \n\"" + arg0.getNotes() + "\"\n\"" + arg1.getNotes() + "\"");
+ return stringComparator.compare(arg0.getNotes(), arg1.getNotes());
+ }
+
+ if (stringComparator.compare(arg0.getSymbol(), arg1.getSymbol()) != 0) {
+ logger.debug("symbol different: \"" + arg0.getSymbol() + "\", \"" + arg1.getSymbol() + "\"");
+ return stringComparator.compare(arg0.getSymbol(), arg1.getSymbol());
+ }
+
+ if (stringComparator.compare(arg0.getFullName(), arg1.getFullName()) != 0) {
+ logger.debug("full name different: \"" + arg0.getFullName() + "\", \"" + arg1.getFullName() + "\"");
+ return stringComparator.compare(arg0.getFullName(), arg1.getFullName());
+ }
+
+ if (stringComparator.compare(arg0.getAbbreviation(), arg1.getAbbreviation()) != 0) {
+ logger.debug("Abbreviation different: \"" + arg0.getAbbreviation() + "\", \"" + arg1.getAbbreviation() + "\"");
+ return stringComparator.compare(arg0.getAbbreviation(), arg1.getAbbreviation());
+ }
+
+ if (stringComparator.compare(arg0.getFormula(), arg1.getFormula()) != 0) {
+ logger.debug("formula different: \"" + arg0.getFormula() + "\", \"" + arg1.getFormula() + "\"");
+ return stringComparator.compare(arg0.getFormula(), arg1.getFormula());
+ }
+
+ StringSetComparator stringSetComparator = new StringSetComparator();
+ StringListComparator stringListComparator = new StringListComparator();
+
+ if (stringListComparator.compare(arg0.getSynonyms(), arg1.getSynonyms()) != 0) {
+ logger.debug("List of synonyms different");
+ return stringListComparator.compare(arg0.getSynonyms(), arg1.getSynonyms());
+ }
+
+ if (stringListComparator.compare(arg0.getFormerSymbols(), arg1.getFormerSymbols()) != 0) {
+ logger.debug("List of former symbols different");
+ return stringListComparator.compare(arg0.getFormerSymbols(), arg1.getFormerSymbols());
+ }
+
+ Set<String> hashCode1 = new HashSet<>();
+ Set<String> hashCode2 = new HashSet<>();
+
+ if (arg0.getMiriamData().size() != arg1.getMiriamData().size()) {
+ logger.debug(
+ "different number of annotations: " + arg0.getMiriamData().size() + ", " + arg1.getMiriamData().size());
+ return ((Integer) arg0.getMiriamData().size()).compareTo(arg1.getMiriamData().size());
+ }
+
+ for (MiriamData md : arg0.getMiriamData()) {
+ String hash = md.getRelationType() + " " + md.getDataType() + " " + md.getResource();
+ hashCode1.add(hash);
+ }
+
+ for (MiriamData md : arg1.getMiriamData()) {
+ String hash = md.getRelationType() + " " + md.getDataType() + " " + md.getResource();
+ hashCode2.add(hash);
+ }
+
+ if (stringSetComparator.compare(hashCode1, hashCode2) != 0) {
+ logger.debug("different annotations: ");
+ logger.debug("A:");
+ for (String string : hashCode1) {
+ logger.debug("|" + string + "|");
+ }
+ logger.debug("B:");
+ for (String string : hashCode2) {
+ logger.debug("|" + string + "|");
+ }
+ logger.debug("--");
+ return stringSetComparator.compare(hashCode1, hashCode2);
+
+ }
+
+ return 0;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/GeneComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/GeneComparator.java
index 95aa3b734f..0f982bc630 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/GeneComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/GeneComparator.java
@@ -1,80 +1,80 @@
-package lcsb.mapviewer.model.map.species;
-
-import java.util.HashSet;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.StringSetComparator;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-
-/**
- * Comparator class used for comparing {@link Gene} objects.
- *
- * @author Piotr Gawron
- *
- */
-public class GeneComparator extends Comparator<Gene> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(GeneComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public GeneComparator(double epsilon) {
- super(Gene.class, true);
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public GeneComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected Comparator<?> getParentComparator() {
- return new SpeciesComparator(epsilon);
- }
-
- @Override
- protected int internalCompare(Gene arg0, Gene arg1) {
- StringSetComparator stringSetComparator = new StringSetComparator();
-
- Set<String> set1 = new HashSet<>();
- Set<String> set2 = new HashSet<>();
-
- for (ModificationResidue region : arg0.getModificationResidues()) {
- set1.add(region.toString());
- }
-
- for (ModificationResidue region : arg1.getModificationResidues()) {
- set2.add(region.toString());
- }
-
- if (stringSetComparator.compare(set1, set2) != 0) {
- logger.debug(set1);
- logger.debug(set2);
- logger.debug("Different modifications");
- logger.debug("---");
- return stringSetComparator.compare(set1, set2);
- }
-
- return 0;
- }
-}
+package lcsb.mapviewer.model.map.species;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.StringSetComparator;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+
+/**
+ * Comparator class used for comparing {@link Gene} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class GeneComparator extends Comparator<Gene> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(GeneComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public GeneComparator(double epsilon) {
+ super(Gene.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public GeneComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new SpeciesComparator(epsilon);
+ }
+
+ @Override
+ protected int internalCompare(Gene arg0, Gene arg1) {
+ StringSetComparator stringSetComparator = new StringSetComparator();
+
+ Set<String> set1 = new HashSet<>();
+ Set<String> set2 = new HashSet<>();
+
+ for (ModificationResidue region : arg0.getModificationResidues()) {
+ set1.add(region.toString());
+ }
+
+ for (ModificationResidue region : arg1.getModificationResidues()) {
+ set2.add(region.toString());
+ }
+
+ if (stringSetComparator.compare(set1, set2) != 0) {
+ logger.debug(set1);
+ logger.debug(set2);
+ logger.debug("Different modifications");
+ logger.debug("---");
+ return stringSetComparator.compare(set1, set2);
+ }
+
+ return 0;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProtein.java b/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProtein.java
index d3b1db81c7..ee2b3e1d31 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProtein.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProtein.java
@@ -1,58 +1,58 @@
-package lcsb.mapviewer.model.map.species;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-/**
- * Entity representing generic protein element on the map.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("GENERIC_PROTEIN_ALIAS")
-public class GenericProtein extends Protein {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Empty constructor required by hibernate.
- */
- GenericProtein() {
- }
-
- /**
- * Default constructor.
- *
- * @param elementId
- * unique (within model) element identifier
- */
- public GenericProtein(String elementId) {
- super(elementId);
- }
-
- /**
- * Constructor that creates a copy of the element given in the parameter.
- *
- * @param original
- * original object that will be used for creating copy
- */
- public GenericProtein(GenericProtein original) {
- super(original);
- }
-
- @Override
- public GenericProtein copy() {
- if (this.getClass() == GenericProtein.class) {
- return new GenericProtein(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * Entity representing generic protein element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("GENERIC_PROTEIN_ALIAS")
+public class GenericProtein extends Protein {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Empty constructor required by hibernate.
+ */
+ GenericProtein() {
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * unique (within model) element identifier
+ */
+ public GenericProtein(String elementId) {
+ super(elementId);
+ }
+
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
+ public GenericProtein(GenericProtein original) {
+ super(original);
+ }
+
+ @Override
+ public GenericProtein copy() {
+ if (this.getClass() == GenericProtein.class) {
+ return new GenericProtein(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProteinComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProteinComparator.java
index 694a41e8d6..a87f3855e2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProteinComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/GenericProteinComparator.java
@@ -1,54 +1,54 @@
-package lcsb.mapviewer.model.map.species;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-
-/**
- * Comparator class used for comparing {@link GenericProtein} objects.
- *
- * @author Piotr Gawron
- *
- */
-public class GenericProteinComparator extends Comparator<GenericProtein> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(GenericProteinComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public GenericProteinComparator(double epsilon) {
- super(GenericProtein.class, true);
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public GenericProteinComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected Comparator<?> getParentComparator() {
- return new ProteinComparator(epsilon);
- }
-
- @Override
- protected int internalCompare(GenericProtein arg0, GenericProtein arg1) {
- return 0;
- }
-}
+package lcsb.mapviewer.model.map.species;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+
+/**
+ * Comparator class used for comparing {@link GenericProtein} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class GenericProteinComparator extends Comparator<GenericProtein> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(GenericProteinComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public GenericProteinComparator(double epsilon) {
+ super(GenericProtein.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public GenericProteinComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new ProteinComparator(epsilon);
+ }
+
+ @Override
+ protected int internalCompare(GenericProtein arg0, GenericProtein arg1) {
+ return 0;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Ion.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Ion.java
index 8170a7890e..9e41b20e1a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Ion.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Ion.java
@@ -1,64 +1,64 @@
-package lcsb.mapviewer.model.map.species;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-/**
- * Entity representing ion element on the map.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("ION_ALIAS")
-public class Ion extends Chemical {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Empty constructor required by hibernate.
- */
- Ion() {
- }
-
- /**
- * Constructor that creates a copy of the element given in the parameter.
- *
- * @param original
- * original object that will be used for creating copy
- */
- public Ion(Ion original) {
- super(original);
- }
-
- /**
- * Default constructor.
- *
- * @param elementId
- * uniqe (within model) element identifier
- */
- public Ion(String elementId) {
- setElementId(elementId);
- }
-
- @Override
- public Ion copy() {
- if (this.getClass() == Ion.class) {
- return new Ion(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- @Override
- public String getStringType() {
- return "Ion";
- }
-
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * Entity representing ion element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("ION_ALIAS")
+public class Ion extends Chemical {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Empty constructor required by hibernate.
+ */
+ Ion() {
+ }
+
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
+ public Ion(Ion original) {
+ super(original);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * uniqe (within model) element identifier
+ */
+ public Ion(String elementId) {
+ setElementId(elementId);
+ }
+
+ @Override
+ public Ion copy() {
+ if (this.getClass() == Ion.class) {
+ return new Ion(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Ion";
+ }
+
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProtein.java b/model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProtein.java
index 95225bc76e..5a628feedd 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProtein.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProtein.java
@@ -1,58 +1,58 @@
-package lcsb.mapviewer.model.map.species;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-/**
- * Entity representing ion channel protein element on the map.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("ION_CHANNEL_PROTEIN_ALIAS")
-public class IonChannelProtein extends Protein {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Empty constructor required by hibernate.
- */
- IonChannelProtein() {
- }
-
- /**
- * Constructor that creates a copy of the element given in the parameter.
- *
- * @param original
- * original object that will be used for creating copy
- */
- public IonChannelProtein(IonChannelProtein original) {
- super(original);
- }
-
- /**
- * Default constructor.
- *
- * @param elementId
- * uniqe (within model) element identifier
- */
- public IonChannelProtein(String elementId) {
- setElementId(elementId);
- }
-
- @Override
- public IonChannelProtein copy() {
- if (this.getClass() == IonChannelProtein.class) {
- return new IonChannelProtein(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * Entity representing ion channel protein element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("ION_CHANNEL_PROTEIN_ALIAS")
+public class IonChannelProtein extends Protein {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Empty constructor required by hibernate.
+ */
+ IonChannelProtein() {
+ }
+
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
+ public IonChannelProtein(IonChannelProtein original) {
+ super(original);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * uniqe (within model) element identifier
+ */
+ public IonChannelProtein(String elementId) {
+ setElementId(elementId);
+ }
+
+ @Override
+ public IonChannelProtein copy() {
+ if (this.getClass() == IonChannelProtein.class) {
+ return new IonChannelProtein(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProteinComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProteinComparator.java
index 3fead0056f..6006187ed1 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProteinComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/IonChannelProteinComparator.java
@@ -1,54 +1,54 @@
-package lcsb.mapviewer.model.map.species;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-
-/**
- * Comparator class used for comparing {@link IonChannelProtein} objects.
- *
- * @author Piotr Gawron
- *
- */
-public class IonChannelProteinComparator extends Comparator<IonChannelProtein> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(IonChannelProteinComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public IonChannelProteinComparator(double epsilon) {
- super(IonChannelProtein.class, true);
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public IonChannelProteinComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected Comparator<?> getParentComparator() {
- return new ProteinComparator(epsilon);
- }
-
- @Override
- protected int internalCompare(IonChannelProtein arg0, IonChannelProtein arg1) {
- return 0;
- }
-}
+package lcsb.mapviewer.model.map.species;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+
+/**
+ * Comparator class used for comparing {@link IonChannelProtein} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class IonChannelProteinComparator extends Comparator<IonChannelProtein> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(IonChannelProteinComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public IonChannelProteinComparator(double epsilon) {
+ super(IonChannelProtein.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public IonChannelProteinComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new ProteinComparator(epsilon);
+ }
+
+ @Override
+ protected int internalCompare(IonChannelProtein arg0, IonChannelProtein arg1) {
+ return 0;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/IonComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/IonComparator.java
index d1a1f8ec3b..63126506ac 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/IonComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/IonComparator.java
@@ -1,54 +1,54 @@
-package lcsb.mapviewer.model.map.species;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-
-/**
- * Comparator class used for comparing {@link Ion} objects.
- *
- * @author Piotr Gawron
- *
- */
-public class IonComparator extends Comparator<Ion> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(IonComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public IonComparator(double epsilon) {
- super(Ion.class, true);
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public IonComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected Comparator<?> getParentComparator() {
- return new ChemicalComparator(epsilon);
- }
-
- @Override
- protected int internalCompare(Ion arg0, Ion arg1) {
- return 0;
- }
-}
+package lcsb.mapviewer.model.map.species;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+
+/**
+ * Comparator class used for comparing {@link Ion} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class IonComparator extends Comparator<Ion> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(IonComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public IonComparator(double epsilon) {
+ super(Ion.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public IonComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new ChemicalComparator(epsilon);
+ }
+
+ @Override
+ protected int internalCompare(Ion arg0, Ion arg1) {
+ return 0;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Phenotype.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Phenotype.java
index 58634bdeee..0f130d7816 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Phenotype.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Phenotype.java
@@ -1,64 +1,64 @@
-package lcsb.mapviewer.model.map.species;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-/**
- * Entity representing phenotype element on the map.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("PHENTOYPE_ALIAS")
-public class Phenotype extends Species {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Empty constructor required by hibernate.
- */
- Phenotype() {
- }
-
- /**
- * Constructor that creates a copy of the element given in the parameter.
- *
- * @param original
- * original object that will be used for creating copy
- */
- public Phenotype(Phenotype original) {
- super(original);
- }
-
- /**
- * Default constructor.
- *
- * @param elementId
- * uniqe (within model) element identifier
- */
- public Phenotype(String elementId) {
- setElementId(elementId);
- }
-
- @Override
- public Phenotype copy() {
- if (this.getClass() == Phenotype.class) {
- return new Phenotype(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- @Override
- public String getStringType() {
- return "Phenotype";
- }
-
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * Entity representing phenotype element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("PHENTOYPE_ALIAS")
+public class Phenotype extends Species {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Empty constructor required by hibernate.
+ */
+ Phenotype() {
+ }
+
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
+ public Phenotype(Phenotype original) {
+ super(original);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * uniqe (within model) element identifier
+ */
+ public Phenotype(String elementId) {
+ setElementId(elementId);
+ }
+
+ @Override
+ public Phenotype copy() {
+ if (this.getClass() == Phenotype.class) {
+ return new Phenotype(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Phenotype";
+ }
+
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/PhenotypeComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/PhenotypeComparator.java
index 93be641239..c0a199ca92 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/PhenotypeComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/PhenotypeComparator.java
@@ -1,55 +1,55 @@
-package lcsb.mapviewer.model.map.species;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-
-/**
- * Comparator class used for comparing {@link Phenotype} objects.
- *
- * @author Piotr Gawron
- *
- */
-public class PhenotypeComparator extends Comparator<Phenotype> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(PhenotypeComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public PhenotypeComparator(double epsilon) {
- super(Phenotype.class, true);
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public PhenotypeComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected Comparator<?> getParentComparator() {
- return new SpeciesComparator(epsilon);
- }
-
-
- @Override
- protected int internalCompare(Phenotype arg0, Phenotype arg1) {
- return 0;
- }
-}
+package lcsb.mapviewer.model.map.species;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+
+/**
+ * Comparator class used for comparing {@link Phenotype} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class PhenotypeComparator extends Comparator<Phenotype> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(PhenotypeComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public PhenotypeComparator(double epsilon) {
+ super(Phenotype.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public PhenotypeComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new SpeciesComparator(epsilon);
+ }
+
+
+ @Override
+ protected int internalCompare(Phenotype arg0, Phenotype arg1) {
+ return 0;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Protein.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Protein.java
index 8f4cf0ecf0..c49a439a52 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Protein.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Protein.java
@@ -1,125 +1,125 @@
-package lcsb.mapviewer.model.map.species;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.OneToMany;
-
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-import org.hibernate.annotations.LazyCollection;
-import org.hibernate.annotations.LazyCollectionOption;
-
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-
-/**
- * Entity representing protein element on the map.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("PROTEIN_ALIAS")
-public abstract class Protein extends Species {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * State of the protein.
- */
- private String structuralState = null;
-
- /**
- * List of modifications for the Protein.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(mappedBy = "species", orphanRemoval = true)
- @LazyCollection(LazyCollectionOption.FALSE)
- private List<ModificationResidue> modificationResidues = new ArrayList<>();
-
- /**
- * Empty constructor required by hibernate.
- */
- Protein() {
- }
-
- /**
- * Constructor that creates a copy of the element given in the parameter.
- *
- * @param original
- * original object that will be used for creating copy
- */
- protected Protein(Protein original) {
- super(original);
- this.structuralState = original.getStructuralState();
- for (ModificationResidue mr : original.getModificationResidues()) {
- addModificationResidue(mr.copy());
- }
- }
-
- /**
- * Default constructor.
- *
- * @param elementId
- * unique (within model) element identifier
- */
- protected Protein(String elementId) {
- super(elementId);
- }
-
- /**
- * Adds modification to the protein.
- *
- * @param modificationResidue
- * modification to add
- */
- public void addModificationResidue(ModificationResidue modificationResidue) {
- modificationResidues.add(modificationResidue);
- modificationResidue.setSpecies(this);
- }
-
- /**
- * @return the modificationResidues
- * @see #modificationResidues
- */
- public List<ModificationResidue> getModificationResidues() {
- return modificationResidues;
- }
-
- /**
- * @param modificationResidues
- * the modificationResidues to set
- * @see #modificationResidues
- */
- public void setModificationResidues(List<ModificationResidue> modificationResidues) {
- this.modificationResidues = modificationResidues;
- }
-
- /**
- * @return the structuralState
- * @see #structuralState
- */
- public String getStructuralState() {
- return structuralState;
- }
-
- /**
- * @param structuralState
- * the structuralState to set
- * @see #structuralState
- */
- public void setStructuralState(String structuralState) {
- this.structuralState = structuralState;
- }
-
- @Override
- public String getStringType() {
- return "Protein";
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+import javax.persistence.OneToMany;
+
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+import org.hibernate.annotations.LazyCollection;
+import org.hibernate.annotations.LazyCollectionOption;
+
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+
+/**
+ * Entity representing protein element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("PROTEIN_ALIAS")
+public abstract class Protein extends Species {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * State of the protein.
+ */
+ private String structuralState = null;
+
+ /**
+ * List of modifications for the Protein.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(mappedBy = "species", orphanRemoval = true)
+ @LazyCollection(LazyCollectionOption.FALSE)
+ private List<ModificationResidue> modificationResidues = new ArrayList<>();
+
+ /**
+ * Empty constructor required by hibernate.
+ */
+ Protein() {
+ }
+
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
+ protected Protein(Protein original) {
+ super(original);
+ this.structuralState = original.getStructuralState();
+ for (ModificationResidue mr : original.getModificationResidues()) {
+ addModificationResidue(mr.copy());
+ }
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * unique (within model) element identifier
+ */
+ protected Protein(String elementId) {
+ super(elementId);
+ }
+
+ /**
+ * Adds modification to the protein.
+ *
+ * @param modificationResidue
+ * modification to add
+ */
+ public void addModificationResidue(ModificationResidue modificationResidue) {
+ modificationResidues.add(modificationResidue);
+ modificationResidue.setSpecies(this);
+ }
+
+ /**
+ * @return the modificationResidues
+ * @see #modificationResidues
+ */
+ public List<ModificationResidue> getModificationResidues() {
+ return modificationResidues;
+ }
+
+ /**
+ * @param modificationResidues
+ * the modificationResidues to set
+ * @see #modificationResidues
+ */
+ public void setModificationResidues(List<ModificationResidue> modificationResidues) {
+ this.modificationResidues = modificationResidues;
+ }
+
+ /**
+ * @return the structuralState
+ * @see #structuralState
+ */
+ public String getStructuralState() {
+ return structuralState;
+ }
+
+ /**
+ * @param structuralState
+ * the structuralState to set
+ * @see #structuralState
+ */
+ public void setStructuralState(String structuralState) {
+ this.structuralState = structuralState;
+ }
+
+ @Override
+ public String getStringType() {
+ return "Protein";
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java
index 976ef785d5..5deb711e15 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java
@@ -1,89 +1,89 @@
-package lcsb.mapviewer.model.map.species;
-
-import java.util.HashSet;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.StringComparator;
-import lcsb.mapviewer.common.comparator.StringSetComparator;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-
-/**
- * Comparator class used for comparing {@link Protein} objects.
- *
- * @author Piotr Gawron
- *
- */
-public class ProteinComparator extends Comparator<Protein> {
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ProteinComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public ProteinComparator(double epsilon) {
- super(Protein.class, true);
- this.epsilon = epsilon;
- addSubClassComparator(new GenericProteinComparator(epsilon));
- addSubClassComparator(new IonChannelProteinComparator(epsilon));
- addSubClassComparator(new ReceptorProteinComparator(epsilon));
- addSubClassComparator(new TruncatedProteinComparator(epsilon));
- }
-
- /**
- * Default constructor.
- */
- public ProteinComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected Comparator<?> getParentComparator() {
- return new SpeciesComparator(epsilon);
- }
-
- @Override
- protected int internalCompare(Protein arg0, Protein arg1) {
- StringComparator stringComparator = new StringComparator();
- StringSetComparator stringSetComparator = new StringSetComparator();
-
- if (stringComparator.compare(arg0.getStructuralState(), arg1.getStructuralState()) != 0) {
- logger.debug("structural state different: " + arg0.getStructuralState() + ", " + arg1.getStructuralState());
- return stringComparator.compare(arg0.getStructuralState(), arg1.getStructuralState());
- }
-
- Set<String> set1 = new HashSet<>();
- Set<String> set2 = new HashSet<>();
-
- for (ModificationResidue region : arg0.getModificationResidues()) {
- set1.add(region.toString());
- }
-
- for (ModificationResidue region : arg1.getModificationResidues()) {
- set2.add(region.toString());
- }
-
- if (stringSetComparator.compare(set1, set2) != 0) {
- logger.debug(set1);
- logger.debug(set2);
- logger.debug("modification residues different");
- return stringSetComparator.compare(set1, set2);
- }
-
- return 0;
- }
-}
+package lcsb.mapviewer.model.map.species;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.StringComparator;
+import lcsb.mapviewer.common.comparator.StringSetComparator;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+
+/**
+ * Comparator class used for comparing {@link Protein} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ProteinComparator extends Comparator<Protein> {
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ProteinComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public ProteinComparator(double epsilon) {
+ super(Protein.class, true);
+ this.epsilon = epsilon;
+ addSubClassComparator(new GenericProteinComparator(epsilon));
+ addSubClassComparator(new IonChannelProteinComparator(epsilon));
+ addSubClassComparator(new ReceptorProteinComparator(epsilon));
+ addSubClassComparator(new TruncatedProteinComparator(epsilon));
+ }
+
+ /**
+ * Default constructor.
+ */
+ public ProteinComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new SpeciesComparator(epsilon);
+ }
+
+ @Override
+ protected int internalCompare(Protein arg0, Protein arg1) {
+ StringComparator stringComparator = new StringComparator();
+ StringSetComparator stringSetComparator = new StringSetComparator();
+
+ if (stringComparator.compare(arg0.getStructuralState(), arg1.getStructuralState()) != 0) {
+ logger.debug("structural state different: " + arg0.getStructuralState() + ", " + arg1.getStructuralState());
+ return stringComparator.compare(arg0.getStructuralState(), arg1.getStructuralState());
+ }
+
+ Set<String> set1 = new HashSet<>();
+ Set<String> set2 = new HashSet<>();
+
+ for (ModificationResidue region : arg0.getModificationResidues()) {
+ set1.add(region.toString());
+ }
+
+ for (ModificationResidue region : arg1.getModificationResidues()) {
+ set2.add(region.toString());
+ }
+
+ if (stringSetComparator.compare(set1, set2) != 0) {
+ logger.debug(set1);
+ logger.debug(set2);
+ logger.debug("modification residues different");
+ return stringSetComparator.compare(set1, set2);
+ }
+
+ return 0;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProtein.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProtein.java
index 89aa61cf12..8e0043ab07 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProtein.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProtein.java
@@ -1,57 +1,57 @@
-package lcsb.mapviewer.model.map.species;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-/**
- * Entity representing receptor protein element on the map.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("RECEPTOR_PROTEIN_ALIAS")
-public class ReceptorProtein extends Protein {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Empty constructor required by hibernate.
- */
- ReceptorProtein() {
- }
-
- /**
- * Constructor that creates a copy of the element given in the parameter.
- *
- * @param original
- * original object that will be used for creating copy
- */
- public ReceptorProtein(ReceptorProtein original) {
- super(original);
- }
-
- /**
- * Default constructor.
- *
- * @param elementId
- * uniqe (within model) element identifier
- */
- public ReceptorProtein(String elementId) {
- super(elementId);
- }
-
- @Override
- public ReceptorProtein copy() {
- if (this.getClass() == ReceptorProtein.class) {
- return new ReceptorProtein(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * Entity representing receptor protein element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("RECEPTOR_PROTEIN_ALIAS")
+public class ReceptorProtein extends Protein {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Empty constructor required by hibernate.
+ */
+ ReceptorProtein() {
+ }
+
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
+ public ReceptorProtein(ReceptorProtein original) {
+ super(original);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * uniqe (within model) element identifier
+ */
+ public ReceptorProtein(String elementId) {
+ super(elementId);
+ }
+
+ @Override
+ public ReceptorProtein copy() {
+ if (this.getClass() == ReceptorProtein.class) {
+ return new ReceptorProtein(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProteinComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProteinComparator.java
index 8fef3d5d0c..36472b445e 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProteinComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ReceptorProteinComparator.java
@@ -1,54 +1,54 @@
-package lcsb.mapviewer.model.map.species;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-
-/**
- * Comparator class used for comparing {@link ReceptorProtein} objects.
- *
- * @author Piotr Gawron
- *
- */
-public class ReceptorProteinComparator extends Comparator<ReceptorProtein> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(ReceptorProteinComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public ReceptorProteinComparator(double epsilon) {
- super(ReceptorProtein.class, true);
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public ReceptorProteinComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected Comparator<?> getParentComparator() {
- return new ProteinComparator(epsilon);
- }
-
- @Override
- protected int internalCompare(ReceptorProtein arg0, ReceptorProtein arg1) {
- return 0;
- }
-}
+package lcsb.mapviewer.model.map.species;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+
+/**
+ * Comparator class used for comparing {@link ReceptorProtein} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ReceptorProteinComparator extends Comparator<ReceptorProtein> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(ReceptorProteinComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public ReceptorProteinComparator(double epsilon) {
+ super(ReceptorProtein.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public ReceptorProteinComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new ProteinComparator(epsilon);
+ }
+
+ @Override
+ protected int internalCompare(ReceptorProtein arg0, ReceptorProtein arg1) {
+ return 0;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/RnaComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/RnaComparator.java
index 34efa599e5..f8ffa614af 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/RnaComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/RnaComparator.java
@@ -1,79 +1,79 @@
-package lcsb.mapviewer.model.map.species;
-
-import java.util.HashSet;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.StringSetComparator;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-
-/**
- * Comparator class used for comparing {@link Rna} objects.
- *
- * @author Piotr Gawron
- *
- */
-public class RnaComparator extends Comparator<Rna> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(RnaComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public RnaComparator(double epsilon) {
- super(Rna.class, true);
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public RnaComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected Comparator<?> getParentComparator() {
- return new SpeciesComparator(epsilon);
- }
-
- @Override
- protected int internalCompare(Rna arg0, Rna arg1) {
- StringSetComparator stringSetComparator = new StringSetComparator();
-
- Set<String> set1 = new HashSet<>();
- Set<String> set2 = new HashSet<>();
-
- for (ModificationResidue region : arg0.getRegions()) {
- set1.add(region.toString());
- }
-
- for (ModificationResidue region : arg1.getRegions()) {
- set2.add(region.toString());
- }
-
- if (stringSetComparator.compare(set1, set2) != 0) {
- logger.debug("Regions different");
- logger.debug(set1);
- logger.debug(set2);
- return stringSetComparator.compare(set1, set2);
- }
-
- return 0;
- }
-}
+package lcsb.mapviewer.model.map.species;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.StringSetComparator;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+
+/**
+ * Comparator class used for comparing {@link Rna} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class RnaComparator extends Comparator<Rna> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(RnaComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public RnaComparator(double epsilon) {
+ super(Rna.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public RnaComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new SpeciesComparator(epsilon);
+ }
+
+ @Override
+ protected int internalCompare(Rna arg0, Rna arg1) {
+ StringSetComparator stringSetComparator = new StringSetComparator();
+
+ Set<String> set1 = new HashSet<>();
+ Set<String> set2 = new HashSet<>();
+
+ for (ModificationResidue region : arg0.getRegions()) {
+ set1.add(region.toString());
+ }
+
+ for (ModificationResidue region : arg1.getRegions()) {
+ set2.add(region.toString());
+ }
+
+ if (stringSetComparator.compare(set1, set2) != 0) {
+ logger.debug("Regions different");
+ logger.debug(set1);
+ logger.debug(set2);
+ return stringSetComparator.compare(set1, set2);
+ }
+
+ return 0;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMolecule.java b/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMolecule.java
index 37f9f9fbcb..d535c4dcc8 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMolecule.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMolecule.java
@@ -1,64 +1,64 @@
-package lcsb.mapviewer.model.map.species;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-/**
- * Entity representing simple molecule element on the map.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("SIMPLE_MOLECULE_ALIAS")
-public class SimpleMolecule extends Chemical {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Empty constructor required by hibernate.
- */
- SimpleMolecule() {
- }
-
- /**
- * Constructor that creates a copy of the element given in the parameter.
- *
- * @param original
- * original object that will be used for creating copy
- */
- public SimpleMolecule(SimpleMolecule original) {
- super(original);
- }
-
- /**
- * Default constructor.
- *
- * @param elementId
- * uniqe (within model) element identifier
- */
- public SimpleMolecule(String elementId) {
- setElementId(elementId);
- }
-
- @Override
- public SimpleMolecule copy() {
- if (this.getClass() == SimpleMolecule.class) {
- return new SimpleMolecule(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- @Override
- public String getStringType() {
- return "Simple molecule";
- }
-
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * Entity representing simple molecule element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("SIMPLE_MOLECULE_ALIAS")
+public class SimpleMolecule extends Chemical {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Empty constructor required by hibernate.
+ */
+ SimpleMolecule() {
+ }
+
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
+ public SimpleMolecule(SimpleMolecule original) {
+ super(original);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * uniqe (within model) element identifier
+ */
+ public SimpleMolecule(String elementId) {
+ setElementId(elementId);
+ }
+
+ @Override
+ public SimpleMolecule copy() {
+ if (this.getClass() == SimpleMolecule.class) {
+ return new SimpleMolecule(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Simple molecule";
+ }
+
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparator.java
index ef10a99608..22c1716164 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparator.java
@@ -1,54 +1,54 @@
-package lcsb.mapviewer.model.map.species;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-
-/**
- * Comparator class used for comparing {@link SimpleMolecule} objects.
- *
- * @author Piotr Gawron
- *
- */
-public class SimpleMoleculeComparator extends Comparator<SimpleMolecule> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(SimpleMoleculeComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public SimpleMoleculeComparator(double epsilon) {
- super(SimpleMolecule.class, true);
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public SimpleMoleculeComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected Comparator<?> getParentComparator() {
- return new ChemicalComparator(epsilon);
- }
-
- @Override
- protected int internalCompare(SimpleMolecule arg0, SimpleMolecule arg1) {
- return 0;
- }
-}
+package lcsb.mapviewer.model.map.species;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+
+/**
+ * Comparator class used for comparing {@link SimpleMolecule} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class SimpleMoleculeComparator extends Comparator<SimpleMolecule> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(SimpleMoleculeComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public SimpleMoleculeComparator(double epsilon) {
+ super(SimpleMolecule.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public SimpleMoleculeComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new ChemicalComparator(epsilon);
+ }
+
+ @Override
+ protected int internalCompare(SimpleMolecule arg0, SimpleMolecule arg1) {
+ return 0;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java
index d3c9189cab..8990825e01 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java
@@ -1,487 +1,487 @@
-package lcsb.mapviewer.model.map.species;
-
-import java.util.HashSet;
-import java.util.Set;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.EnumType;
-import javax.persistence.Enumerated;
-import javax.persistence.FetchType;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.OneToMany;
-
-import org.apache.log4j.Logger;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-
-import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
-import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
-import lcsb.mapviewer.model.map.species.field.UniprotRecord;
-
-/**
- * Structure used for representing information about single element.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("Species")
-public abstract class Species extends Element {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(Species.class);
-
- /**
- * Is the element active.
- */
- private Boolean activity;
-
- /**
- * Width of the element border.
- */
- private Double lineWidth;
-
- /**
- * State of the element visualization (should the inside be presented in details
- * or not). TODO this should be transformed into enum
- */
- private String state;
-
- /**
- * State (free text describing element in some way) of the element is split into
- * {@link #statePrefix prefix} and {@link #stateLabel label}. This value
- * represent the first part of the state.
- */
- private String statePrefix;
-
- /**
- * State (free text describing element in some way) of the element is split into
- * {@link #statePrefix prefix} and {@link #stateLabel label}. This value
- * represent the second part of the state.
- */
- private String stateLabel;
-
- /**
- * Complex to which this element belongs to. Null if such complex doesn't exist.
- */
- @ManyToOne
- @Cascade({ CascadeType.ALL })
- @JoinColumn(name = "idcomplexdb")
- private Complex complex;
-
- /**
- * Initial amount of species.
- */
- private Double initialAmount = null;
-
- /**
- * Charge of the species.
- */
- private Integer charge = null;
-
- /**
- * Initial concentration of species.
- */
- private Double initialConcentration = null;
-
- /**
- * Is only substance units allowed.
- */
- private Boolean onlySubstanceUnits = null;
-
- /**
- * How many dimers are in this species.
- */
- private int homodimer = 1;
-
- /**
- * Position on the compartment.
- */
- @Enumerated(EnumType.STRING)
- private PositionToCompartment positionToCompartment = null;
-
- /**
- * Is species hypothetical.
- */
- private Boolean hypothetical = null;
-
- /**
- * List of uniprot records which are associated with this species.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(fetch = FetchType.EAGER, mappedBy = "species", orphanRemoval = true)
- private Set<UniprotRecord> uniprots = new HashSet<>();
-
- private Boolean boundaryCondition;
-
- private Boolean constant;
-
- @Enumerated(EnumType.STRING)
- private SbmlUnitType substanceUnits;
-
- /**
- * Constructor that set element identifier.
- *
- * @param elementId
- * {@link Element#elementId}
- */
- public Species(String elementId) {
- this();
- setElementId(elementId);
- setName(elementId);
- }
-
- /**
- * Empty constructor required by hibernate.
- */
- Species() {
- super();
- activity = false;
- lineWidth = 1.0;
- state = "usual";
- }
-
- /**
- * Constructor that initializes data with the information given in the
- * parameter.
- *
- * @param original
- * object from which data will be initialized
- */
- protected Species(Species original) {
- super(original);
- activity = original.getActivity();
- lineWidth = original.getLineWidth();
- state = original.getState();
-
- complex = original.getComplex();
- stateLabel = original.getStateLabel();
- statePrefix = original.getStatePrefix();
-
- initialAmount = original.getInitialAmount();
- charge = original.getCharge();
- initialConcentration = original.getInitialConcentration();
- onlySubstanceUnits = original.getOnlySubstanceUnits();
- homodimer = original.getHomodimer();
- positionToCompartment = original.getPositionToCompartment();
- hypothetical = original.getHypothetical();
- boundaryCondition = original.getBoundaryCondition();
- constant = original.getConstant();
- substanceUnits = original.getSubstanceUnits();
-
- uniprots = original.getUniprots();
-
- // don't copy reaction nodes
- }
-
- /**
- * @return the activity
- * @see #activity
- */
- public Boolean getActivity() {
- return activity;
- }
-
- /**
- * @param activity
- * the activity to set
- * @see #activity
- */
- public void setActivity(Boolean activity) {
- this.activity = activity;
- }
-
- /**
- * @return the lineWidth
- * @see #lineWidth
- */
- public Double getLineWidth() {
- return lineWidth;
- }
-
- /**
- * @param lineWidth
- * the lineWidth to set
- * @see #lineWidth
- */
- public void setLineWidth(Double lineWidth) {
- this.lineWidth = lineWidth;
- }
-
- /**
- * @return the state
- * @see #state
- */
- public String getState() {
- return state;
- }
-
- /**
- * @param state
- * the state to set
- * @see #state
- */
- public void setState(String state) {
- this.state = state;
- }
-
- /**
- * @return the complex
- * @see #complex
- */
- public Complex getComplex() {
- return complex;
- }
-
- /**
- * @param complex
- * the complex to set
- * @see #complex
- */
- public void setComplex(Complex complex) {
- this.complex = complex;
- }
-
- /**
- * @return the statePrefix
- * @see #statePrefix
- */
- public String getStatePrefix() {
- return statePrefix;
- }
-
- /**
- * @param statePrefix
- * the statePrefix to set
- * @see #statePrefix
- */
- public void setStatePrefix(String statePrefix) {
- this.statePrefix = statePrefix;
- }
-
- /**
- * @return the stateLabel
- * @see #stateLabel
- */
- public String getStateLabel() {
- return stateLabel;
- }
-
- /**
- * @param stateLabel
- * the stateLabel to set
- * @see #stateLabel
- */
- public void setStateLabel(String stateLabel) {
- this.stateLabel = stateLabel;
- }
-
- @Override
- public abstract Species copy();
-
- /**
- * @return the initialAmount
- * @see #initialAmount
- */
- public Double getInitialAmount() {
- return initialAmount;
- }
-
- /**
- * @param initialAmount
- * the initialAmount to set
- * @see #initialAmount
- */
- public void setInitialAmount(Double initialAmount) {
- this.initialAmount = initialAmount;
- }
-
- /**
- * @return the charge
- * @see #charge
- */
- public Integer getCharge() {
- return charge;
- }
-
- /**
- * @param charge
- * the charge to set
- * @see #charge
- */
- public void setCharge(Integer charge) {
- this.charge = charge;
- }
-
- /**
- * @return the initialConcentration
- * @see #initialConcentration
- */
- public Double getInitialConcentration() {
- return initialConcentration;
- }
-
- /**
- * @param initialConcentration
- * the initialConcentration to set
- * @see #initialConcentration
- */
- public void setInitialConcentration(Double initialConcentration) {
- this.initialConcentration = initialConcentration;
- }
-
- /**
- * @return the onlySubstanceUnits
- * @see #onlySubstanceUnits
- */
- public Boolean getOnlySubstanceUnits() {
- return onlySubstanceUnits;
- }
-
- /**
- * @param onlySubstanceUnits
- * the onlySubstanceUnits to set
- * @see #onlySubstanceUnits
- */
- public void setOnlySubstanceUnits(Boolean onlySubstanceUnits) {
- this.onlySubstanceUnits = onlySubstanceUnits;
- }
-
- /**
- * @return the homodimer
- * @see #homodimer
- */
- public int getHomodimer() {
- return homodimer;
- }
-
- /**
- * @param homodimer
- * the homodimer to set
- * @see #homodimer
- */
- public void setHomodimer(int homodimer) {
- this.homodimer = homodimer;
- }
-
- /**
- * @return the positionToCompartment
- * @see #positionToCompartment
- */
- public PositionToCompartment getPositionToCompartment() {
- return positionToCompartment;
- }
-
- /**
- * @param positionToCompartment
- * the positionToCompartment to set
- * @see #positionToCompartment
- */
- public void setPositionToCompartment(PositionToCompartment positionToCompartment) {
- this.positionToCompartment = positionToCompartment;
- }
-
- /**
- * @return the hypothetical
- * @see #hypothetical
- */
- public Boolean getHypothetical() {
- return hypothetical;
- }
-
- /**
- * @param uniprots
- * set of uniprot records for this species
- * @see #uniprots
- */
- public void setUniprots(Set<UniprotRecord> uniprots) {
- this.uniprots = uniprots;
- }
-
- /**
- * @return the uniprot
- * @see #uniprots
- */
- public Set<UniprotRecord> getUniprots() {
- return uniprots;
- }
-
- /**
- * @param hypothetical
- * the hypothetical to set
- * @see #hypothetical
- */
- public void setHypothetical(Boolean hypothetical) {
- this.hypothetical = hypothetical;
- }
-
- /**
- * @return the onlySubstanceUnits
- * @see #onlySubstanceUnits
- */
- public Boolean hasOnlySubstanceUnits() {
- return onlySubstanceUnits;
- }
-
- /**
- * Is species hypothetical or not.
- *
- * @return <code>true</code> if species is hypothetical, <code>false</code>
- * otherwise
- */
- public boolean isHypothetical() {
- if (hypothetical == null) {
- return false;
- }
- return hypothetical;
- }
-
- public boolean isBoundaryCondition() {
- if (boundaryCondition == null) {
- return false;
- }
- return boundaryCondition;
- }
-
- public Boolean getBoundaryCondition() {
- return boundaryCondition;
- }
-
- public void setBoundaryCondition(Boolean boundaryCondition) {
- this.boundaryCondition = boundaryCondition;
- }
-
- public boolean isConstant() {
- if (constant == null) {
- return false;
- }
- return constant;
- }
-
- public Boolean getConstant() {
- return constant;
- }
-
- public SbmlUnitType getSubstanceUnits() {
- return substanceUnits;
- }
-
- public void setConstant(Boolean constant) {
- this.constant = constant;
- }
-
- public void setSubstanceUnits(SbmlUnitType substanceUnits) {
- this.substanceUnits = substanceUnits;
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+import javax.persistence.EnumType;
+import javax.persistence.Enumerated;
+import javax.persistence.FetchType;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
+
+import org.apache.log4j.Logger;
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+
+import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
+import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
+import lcsb.mapviewer.model.map.species.field.UniprotRecord;
+
+/**
+ * Structure used for representing information about single element.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("Species")
+public abstract class Species extends Element {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(Species.class);
+
+ /**
+ * Is the element active.
+ */
+ private Boolean activity;
+
+ /**
+ * Width of the element border.
+ */
+ private Double lineWidth;
+
+ /**
+ * State of the element visualization (should the inside be presented in details
+ * or not). TODO this should be transformed into enum
+ */
+ private String state;
+
+ /**
+ * State (free text describing element in some way) of the element is split into
+ * {@link #statePrefix prefix} and {@link #stateLabel label}. This value
+ * represent the first part of the state.
+ */
+ private String statePrefix;
+
+ /**
+ * State (free text describing element in some way) of the element is split into
+ * {@link #statePrefix prefix} and {@link #stateLabel label}. This value
+ * represent the second part of the state.
+ */
+ private String stateLabel;
+
+ /**
+ * Complex to which this element belongs to. Null if such complex doesn't exist.
+ */
+ @ManyToOne
+ @Cascade({ CascadeType.ALL })
+ @JoinColumn(name = "idcomplexdb")
+ private Complex complex;
+
+ /**
+ * Initial amount of species.
+ */
+ private Double initialAmount = null;
+
+ /**
+ * Charge of the species.
+ */
+ private Integer charge = null;
+
+ /**
+ * Initial concentration of species.
+ */
+ private Double initialConcentration = null;
+
+ /**
+ * Is only substance units allowed.
+ */
+ private Boolean onlySubstanceUnits = null;
+
+ /**
+ * How many dimers are in this species.
+ */
+ private int homodimer = 1;
+
+ /**
+ * Position on the compartment.
+ */
+ @Enumerated(EnumType.STRING)
+ private PositionToCompartment positionToCompartment = null;
+
+ /**
+ * Is species hypothetical.
+ */
+ private Boolean hypothetical = null;
+
+ /**
+ * List of uniprot records which are associated with this species.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(fetch = FetchType.EAGER, mappedBy = "species", orphanRemoval = true)
+ private Set<UniprotRecord> uniprots = new HashSet<>();
+
+ private Boolean boundaryCondition;
+
+ private Boolean constant;
+
+ @Enumerated(EnumType.STRING)
+ private SbmlUnitType substanceUnits;
+
+ /**
+ * Constructor that set element identifier.
+ *
+ * @param elementId
+ * {@link Element#elementId}
+ */
+ public Species(String elementId) {
+ this();
+ setElementId(elementId);
+ setName(elementId);
+ }
+
+ /**
+ * Empty constructor required by hibernate.
+ */
+ Species() {
+ super();
+ activity = false;
+ lineWidth = 1.0;
+ state = "usual";
+ }
+
+ /**
+ * Constructor that initializes data with the information given in the
+ * parameter.
+ *
+ * @param original
+ * object from which data will be initialized
+ */
+ protected Species(Species original) {
+ super(original);
+ activity = original.getActivity();
+ lineWidth = original.getLineWidth();
+ state = original.getState();
+
+ complex = original.getComplex();
+ stateLabel = original.getStateLabel();
+ statePrefix = original.getStatePrefix();
+
+ initialAmount = original.getInitialAmount();
+ charge = original.getCharge();
+ initialConcentration = original.getInitialConcentration();
+ onlySubstanceUnits = original.getOnlySubstanceUnits();
+ homodimer = original.getHomodimer();
+ positionToCompartment = original.getPositionToCompartment();
+ hypothetical = original.getHypothetical();
+ boundaryCondition = original.getBoundaryCondition();
+ constant = original.getConstant();
+ substanceUnits = original.getSubstanceUnits();
+
+ uniprots = original.getUniprots();
+
+ // don't copy reaction nodes
+ }
+
+ /**
+ * @return the activity
+ * @see #activity
+ */
+ public Boolean getActivity() {
+ return activity;
+ }
+
+ /**
+ * @param activity
+ * the activity to set
+ * @see #activity
+ */
+ public void setActivity(Boolean activity) {
+ this.activity = activity;
+ }
+
+ /**
+ * @return the lineWidth
+ * @see #lineWidth
+ */
+ public Double getLineWidth() {
+ return lineWidth;
+ }
+
+ /**
+ * @param lineWidth
+ * the lineWidth to set
+ * @see #lineWidth
+ */
+ public void setLineWidth(Double lineWidth) {
+ this.lineWidth = lineWidth;
+ }
+
+ /**
+ * @return the state
+ * @see #state
+ */
+ public String getState() {
+ return state;
+ }
+
+ /**
+ * @param state
+ * the state to set
+ * @see #state
+ */
+ public void setState(String state) {
+ this.state = state;
+ }
+
+ /**
+ * @return the complex
+ * @see #complex
+ */
+ public Complex getComplex() {
+ return complex;
+ }
+
+ /**
+ * @param complex
+ * the complex to set
+ * @see #complex
+ */
+ public void setComplex(Complex complex) {
+ this.complex = complex;
+ }
+
+ /**
+ * @return the statePrefix
+ * @see #statePrefix
+ */
+ public String getStatePrefix() {
+ return statePrefix;
+ }
+
+ /**
+ * @param statePrefix
+ * the statePrefix to set
+ * @see #statePrefix
+ */
+ public void setStatePrefix(String statePrefix) {
+ this.statePrefix = statePrefix;
+ }
+
+ /**
+ * @return the stateLabel
+ * @see #stateLabel
+ */
+ public String getStateLabel() {
+ return stateLabel;
+ }
+
+ /**
+ * @param stateLabel
+ * the stateLabel to set
+ * @see #stateLabel
+ */
+ public void setStateLabel(String stateLabel) {
+ this.stateLabel = stateLabel;
+ }
+
+ @Override
+ public abstract Species copy();
+
+ /**
+ * @return the initialAmount
+ * @see #initialAmount
+ */
+ public Double getInitialAmount() {
+ return initialAmount;
+ }
+
+ /**
+ * @param initialAmount
+ * the initialAmount to set
+ * @see #initialAmount
+ */
+ public void setInitialAmount(Double initialAmount) {
+ this.initialAmount = initialAmount;
+ }
+
+ /**
+ * @return the charge
+ * @see #charge
+ */
+ public Integer getCharge() {
+ return charge;
+ }
+
+ /**
+ * @param charge
+ * the charge to set
+ * @see #charge
+ */
+ public void setCharge(Integer charge) {
+ this.charge = charge;
+ }
+
+ /**
+ * @return the initialConcentration
+ * @see #initialConcentration
+ */
+ public Double getInitialConcentration() {
+ return initialConcentration;
+ }
+
+ /**
+ * @param initialConcentration
+ * the initialConcentration to set
+ * @see #initialConcentration
+ */
+ public void setInitialConcentration(Double initialConcentration) {
+ this.initialConcentration = initialConcentration;
+ }
+
+ /**
+ * @return the onlySubstanceUnits
+ * @see #onlySubstanceUnits
+ */
+ public Boolean getOnlySubstanceUnits() {
+ return onlySubstanceUnits;
+ }
+
+ /**
+ * @param onlySubstanceUnits
+ * the onlySubstanceUnits to set
+ * @see #onlySubstanceUnits
+ */
+ public void setOnlySubstanceUnits(Boolean onlySubstanceUnits) {
+ this.onlySubstanceUnits = onlySubstanceUnits;
+ }
+
+ /**
+ * @return the homodimer
+ * @see #homodimer
+ */
+ public int getHomodimer() {
+ return homodimer;
+ }
+
+ /**
+ * @param homodimer
+ * the homodimer to set
+ * @see #homodimer
+ */
+ public void setHomodimer(int homodimer) {
+ this.homodimer = homodimer;
+ }
+
+ /**
+ * @return the positionToCompartment
+ * @see #positionToCompartment
+ */
+ public PositionToCompartment getPositionToCompartment() {
+ return positionToCompartment;
+ }
+
+ /**
+ * @param positionToCompartment
+ * the positionToCompartment to set
+ * @see #positionToCompartment
+ */
+ public void setPositionToCompartment(PositionToCompartment positionToCompartment) {
+ this.positionToCompartment = positionToCompartment;
+ }
+
+ /**
+ * @return the hypothetical
+ * @see #hypothetical
+ */
+ public Boolean getHypothetical() {
+ return hypothetical;
+ }
+
+ /**
+ * @param uniprots
+ * set of uniprot records for this species
+ * @see #uniprots
+ */
+ public void setUniprots(Set<UniprotRecord> uniprots) {
+ this.uniprots = uniprots;
+ }
+
+ /**
+ * @return the uniprot
+ * @see #uniprots
+ */
+ public Set<UniprotRecord> getUniprots() {
+ return uniprots;
+ }
+
+ /**
+ * @param hypothetical
+ * the hypothetical to set
+ * @see #hypothetical
+ */
+ public void setHypothetical(Boolean hypothetical) {
+ this.hypothetical = hypothetical;
+ }
+
+ /**
+ * @return the onlySubstanceUnits
+ * @see #onlySubstanceUnits
+ */
+ public Boolean hasOnlySubstanceUnits() {
+ return onlySubstanceUnits;
+ }
+
+ /**
+ * Is species hypothetical or not.
+ *
+ * @return <code>true</code> if species is hypothetical, <code>false</code>
+ * otherwise
+ */
+ public boolean isHypothetical() {
+ if (hypothetical == null) {
+ return false;
+ }
+ return hypothetical;
+ }
+
+ public boolean isBoundaryCondition() {
+ if (boundaryCondition == null) {
+ return false;
+ }
+ return boundaryCondition;
+ }
+
+ public Boolean getBoundaryCondition() {
+ return boundaryCondition;
+ }
+
+ public void setBoundaryCondition(Boolean boundaryCondition) {
+ this.boundaryCondition = boundaryCondition;
+ }
+
+ public boolean isConstant() {
+ if (constant == null) {
+ return false;
+ }
+ return constant;
+ }
+
+ public Boolean getConstant() {
+ return constant;
+ }
+
+ public SbmlUnitType getSubstanceUnits() {
+ return substanceUnits;
+ }
+
+ public void setConstant(Boolean constant) {
+ this.constant = constant;
+ }
+
+ public void setSubstanceUnits(SbmlUnitType substanceUnits) {
+ this.substanceUnits = substanceUnits;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/SpeciesComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/SpeciesComparator.java
index 1b1dac99bb..00dac7285a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/SpeciesComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/SpeciesComparator.java
@@ -1,157 +1,157 @@
-package lcsb.mapviewer.model.map.species;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.BooleanComparator;
-import lcsb.mapviewer.common.comparator.DoubleComparator;
-import lcsb.mapviewer.common.comparator.EnumComparator;
-import lcsb.mapviewer.common.comparator.IntegerComparator;
-import lcsb.mapviewer.common.comparator.StringComparator;
-
-/**
- * Comparator class used for comparing {@link Species} objects.
- *
- * @author Piotr Gawron
- *
- */
-public class SpeciesComparator extends Comparator<Species> {
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(SpeciesComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public SpeciesComparator(double epsilon) {
- super(Species.class, true);
- this.epsilon = epsilon;
- addSubClassComparator(new AntisenseRnaComparator(epsilon));
- addSubClassComparator(new ChemicalComparator(epsilon));
- addSubClassComparator(new ComplexComparator(epsilon));
- addSubClassComparator(new DegradedComparator(epsilon));
- addSubClassComparator(new DrugComparator(epsilon));
- addSubClassComparator(new GeneComparator(epsilon));
- addSubClassComparator(new PhenotypeComparator(epsilon));
- addSubClassComparator(new ProteinComparator(epsilon));
- addSubClassComparator(new RnaComparator(epsilon));
- addSubClassComparator(new UnknownComparator(epsilon));
- }
-
- /**
- * Default constructor.
- */
- public SpeciesComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected int internalCompare(Species arg0, Species arg1) {
- ElementComparator elementComparator = new ElementComparator(epsilon);
- int result = elementComparator.internalCompare(arg0, arg1);
- if (result != 0) {
- return result;
- }
-
- DoubleComparator doubleComparator = new DoubleComparator(epsilon);
- BooleanComparator booleanComparator = new BooleanComparator();
- IntegerComparator integerComparator = new IntegerComparator();
-
- if (booleanComparator.compare(arg0.getActivity(), arg1.getActivity()) != 0) {
- logger.debug("activity different: " + arg0.getActivity() + ", " + arg1.getActivity());
- return booleanComparator.compare(arg0.getActivity(), arg1.getActivity());
- }
-
- if (doubleComparator.compare(arg0.getLineWidth(), arg1.getLineWidth()) != 0) {
- logger.debug("line width different: " + arg0.getLineWidth() + ", " + arg1.getLineWidth());
- return doubleComparator.compare(arg0.getLineWidth(), arg1.getLineWidth());
- }
- StringComparator stringComparator = new StringComparator();
- if (stringComparator.compare(arg0.getStateLabel(), arg1.getStateLabel()) != 0) {
- logger.debug("state label different: " + arg0.getStateLabel() + ", " + arg1.getStateLabel());
- return stringComparator.compare(arg0.getStateLabel(), arg1.getStateLabel());
- }
-
- if (stringComparator.compare(arg0.getStatePrefix(), arg1.getStatePrefix()) != 0) {
- logger.debug("state prefix different: " + arg0.getStatePrefix() + ", " + arg1.getStatePrefix());
- return stringComparator.compare(arg0.getStatePrefix(), arg1.getStatePrefix());
- }
-
- if (doubleComparator.compare(arg0.getInitialAmount(), arg1.getInitialAmount()) != 0) {
- logger.debug("Initial amount different: " + arg0.getInitialAmount() + ", " + arg1.getInitialAmount());
- return doubleComparator.compare(arg0.getInitialAmount(), arg1.getInitialAmount());
- }
-
- if (integerComparator.compare(arg0.getCharge(), arg1.getCharge()) != 0) {
- logger.debug("Charge different: " + arg0.getCharge() + ", " + arg1.getCharge());
- return integerComparator.compare(arg0.getCharge(), arg1.getCharge());
- }
-
- if (integerComparator.compare(arg0.getHomodimer(), arg1.getHomodimer()) != 0) {
- logger.debug("Homodimer different: " + arg0.getHomodimer() + ", " + arg1.getHomodimer());
- return integerComparator.compare(arg0.getHomodimer(), arg1.getHomodimer());
- }
-
- if (doubleComparator.compare(arg0.getInitialConcentration(), arg1.getInitialConcentration()) != 0) {
- logger.debug(
- "Initial concentration different: " + arg0.getInitialConcentration() + ", " + arg1.getInitialConcentration());
- return doubleComparator.compare(arg0.getInitialConcentration(), arg1.getInitialConcentration());
- }
-
- if (booleanComparator.compare(arg0.hasOnlySubstanceUnits(), arg1.hasOnlySubstanceUnits()) != 0) {
- logger
- .debug("OnlySubstanceUnits different: " + arg0.hasOnlySubstanceUnits() + ", " + arg1.hasOnlySubstanceUnits());
- return booleanComparator.compare(arg0.hasOnlySubstanceUnits(), arg1.hasOnlySubstanceUnits());
- }
-
- if (arg0.getPositionToCompartment() != null || arg1.getPositionToCompartment() != null) {
- Integer pos0 = null;
- Integer pos1 = null;
- if (arg0.getPositionToCompartment() != null) {
- pos0 = arg0.getPositionToCompartment().ordinal();
- }
- if (arg1.getPositionToCompartment() != null) {
- pos1 = arg1.getPositionToCompartment().ordinal();
- }
- if (integerComparator.compare(pos0, pos1) != 0) {
- logger.debug("PositionToCompartment different: \"" + arg0.getPositionToCompartment() + "\", \""
- + arg1.getPositionToCompartment() + "\"");
- return integerComparator.compare(pos0, pos1);
- }
- }
-
- if (booleanComparator.compare(arg0.isHypothetical(), arg1.isHypothetical()) != 0) {
- logger.debug("Hypothetical different: \"" + arg0.isHypothetical() + "\", \"" + arg1.isHypothetical() + "\"");
- return booleanComparator.compare(arg0.isHypothetical(), arg1.isHypothetical());
- }
-
- if (booleanComparator.compare(arg0.isConstant(), arg1.isConstant()) != 0) {
- logger.debug("Constant different: \"" + arg0.isConstant() + "\", \"" + arg1.isConstant() + "\"");
- return booleanComparator.compare(arg0.isConstant(), arg1.isConstant());
- }
-
- if (booleanComparator.compare(arg0.isBoundaryCondition(), arg1.isBoundaryCondition()) != 0) {
- logger.debug("BoundaryCondition different: \"" + arg0.isBoundaryCondition() + "\", \"" + arg1.isBoundaryCondition() + "\"");
- return booleanComparator.compare(arg0.isBoundaryCondition(), arg1.isBoundaryCondition());
- }
-
- EnumComparator enumComparator = new EnumComparator();
- if (enumComparator.compare(arg0.getSubstanceUnits(), arg1.getSubstanceUnits()) != 0) {
- logger.debug("SubstanceUnits different: \"" + arg0.getSubstanceUnits() + "\", \"" + arg1.getSubstanceUnits() + "\"");
- return enumComparator.compare(arg0.getSubstanceUnits(), arg1.getSubstanceUnits());
- }
-
- return 0;
- }
-}
+package lcsb.mapviewer.model.map.species;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.BooleanComparator;
+import lcsb.mapviewer.common.comparator.DoubleComparator;
+import lcsb.mapviewer.common.comparator.EnumComparator;
+import lcsb.mapviewer.common.comparator.IntegerComparator;
+import lcsb.mapviewer.common.comparator.StringComparator;
+
+/**
+ * Comparator class used for comparing {@link Species} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class SpeciesComparator extends Comparator<Species> {
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(SpeciesComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public SpeciesComparator(double epsilon) {
+ super(Species.class, true);
+ this.epsilon = epsilon;
+ addSubClassComparator(new AntisenseRnaComparator(epsilon));
+ addSubClassComparator(new ChemicalComparator(epsilon));
+ addSubClassComparator(new ComplexComparator(epsilon));
+ addSubClassComparator(new DegradedComparator(epsilon));
+ addSubClassComparator(new DrugComparator(epsilon));
+ addSubClassComparator(new GeneComparator(epsilon));
+ addSubClassComparator(new PhenotypeComparator(epsilon));
+ addSubClassComparator(new ProteinComparator(epsilon));
+ addSubClassComparator(new RnaComparator(epsilon));
+ addSubClassComparator(new UnknownComparator(epsilon));
+ }
+
+ /**
+ * Default constructor.
+ */
+ public SpeciesComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(Species arg0, Species arg1) {
+ ElementComparator elementComparator = new ElementComparator(epsilon);
+ int result = elementComparator.internalCompare(arg0, arg1);
+ if (result != 0) {
+ return result;
+ }
+
+ DoubleComparator doubleComparator = new DoubleComparator(epsilon);
+ BooleanComparator booleanComparator = new BooleanComparator();
+ IntegerComparator integerComparator = new IntegerComparator();
+
+ if (booleanComparator.compare(arg0.getActivity(), arg1.getActivity()) != 0) {
+ logger.debug("activity different: " + arg0.getActivity() + ", " + arg1.getActivity());
+ return booleanComparator.compare(arg0.getActivity(), arg1.getActivity());
+ }
+
+ if (doubleComparator.compare(arg0.getLineWidth(), arg1.getLineWidth()) != 0) {
+ logger.debug("line width different: " + arg0.getLineWidth() + ", " + arg1.getLineWidth());
+ return doubleComparator.compare(arg0.getLineWidth(), arg1.getLineWidth());
+ }
+ StringComparator stringComparator = new StringComparator();
+ if (stringComparator.compare(arg0.getStateLabel(), arg1.getStateLabel()) != 0) {
+ logger.debug("state label different: " + arg0.getStateLabel() + ", " + arg1.getStateLabel());
+ return stringComparator.compare(arg0.getStateLabel(), arg1.getStateLabel());
+ }
+
+ if (stringComparator.compare(arg0.getStatePrefix(), arg1.getStatePrefix()) != 0) {
+ logger.debug("state prefix different: " + arg0.getStatePrefix() + ", " + arg1.getStatePrefix());
+ return stringComparator.compare(arg0.getStatePrefix(), arg1.getStatePrefix());
+ }
+
+ if (doubleComparator.compare(arg0.getInitialAmount(), arg1.getInitialAmount()) != 0) {
+ logger.debug("Initial amount different: " + arg0.getInitialAmount() + ", " + arg1.getInitialAmount());
+ return doubleComparator.compare(arg0.getInitialAmount(), arg1.getInitialAmount());
+ }
+
+ if (integerComparator.compare(arg0.getCharge(), arg1.getCharge()) != 0) {
+ logger.debug("Charge different: " + arg0.getCharge() + ", " + arg1.getCharge());
+ return integerComparator.compare(arg0.getCharge(), arg1.getCharge());
+ }
+
+ if (integerComparator.compare(arg0.getHomodimer(), arg1.getHomodimer()) != 0) {
+ logger.debug("Homodimer different: " + arg0.getHomodimer() + ", " + arg1.getHomodimer());
+ return integerComparator.compare(arg0.getHomodimer(), arg1.getHomodimer());
+ }
+
+ if (doubleComparator.compare(arg0.getInitialConcentration(), arg1.getInitialConcentration()) != 0) {
+ logger.debug(
+ "Initial concentration different: " + arg0.getInitialConcentration() + ", " + arg1.getInitialConcentration());
+ return doubleComparator.compare(arg0.getInitialConcentration(), arg1.getInitialConcentration());
+ }
+
+ if (booleanComparator.compare(arg0.hasOnlySubstanceUnits(), arg1.hasOnlySubstanceUnits()) != 0) {
+ logger
+ .debug("OnlySubstanceUnits different: " + arg0.hasOnlySubstanceUnits() + ", " + arg1.hasOnlySubstanceUnits());
+ return booleanComparator.compare(arg0.hasOnlySubstanceUnits(), arg1.hasOnlySubstanceUnits());
+ }
+
+ if (arg0.getPositionToCompartment() != null || arg1.getPositionToCompartment() != null) {
+ Integer pos0 = null;
+ Integer pos1 = null;
+ if (arg0.getPositionToCompartment() != null) {
+ pos0 = arg0.getPositionToCompartment().ordinal();
+ }
+ if (arg1.getPositionToCompartment() != null) {
+ pos1 = arg1.getPositionToCompartment().ordinal();
+ }
+ if (integerComparator.compare(pos0, pos1) != 0) {
+ logger.debug("PositionToCompartment different: \"" + arg0.getPositionToCompartment() + "\", \""
+ + arg1.getPositionToCompartment() + "\"");
+ return integerComparator.compare(pos0, pos1);
+ }
+ }
+
+ if (booleanComparator.compare(arg0.isHypothetical(), arg1.isHypothetical()) != 0) {
+ logger.debug("Hypothetical different: \"" + arg0.isHypothetical() + "\", \"" + arg1.isHypothetical() + "\"");
+ return booleanComparator.compare(arg0.isHypothetical(), arg1.isHypothetical());
+ }
+
+ if (booleanComparator.compare(arg0.isConstant(), arg1.isConstant()) != 0) {
+ logger.debug("Constant different: \"" + arg0.isConstant() + "\", \"" + arg1.isConstant() + "\"");
+ return booleanComparator.compare(arg0.isConstant(), arg1.isConstant());
+ }
+
+ if (booleanComparator.compare(arg0.isBoundaryCondition(), arg1.isBoundaryCondition()) != 0) {
+ logger.debug("BoundaryCondition different: \"" + arg0.isBoundaryCondition() + "\", \"" + arg1.isBoundaryCondition() + "\"");
+ return booleanComparator.compare(arg0.isBoundaryCondition(), arg1.isBoundaryCondition());
+ }
+
+ EnumComparator enumComparator = new EnumComparator();
+ if (enumComparator.compare(arg0.getSubstanceUnits(), arg1.getSubstanceUnits()) != 0) {
+ logger.debug("SubstanceUnits different: \"" + arg0.getSubstanceUnits() + "\", \"" + arg1.getSubstanceUnits() + "\"");
+ return enumComparator.compare(arg0.getSubstanceUnits(), arg1.getSubstanceUnits());
+ }
+
+ return 0;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProtein.java b/model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProtein.java
index 2d487478b4..6dd5521353 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProtein.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProtein.java
@@ -1,57 +1,57 @@
-package lcsb.mapviewer.model.map.species;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-/**
- * Entity representing truncated protein element on the map.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("TRUNCATED_PROTEIN_ALIAS")
-public class TruncatedProtein extends Protein {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Empty constructor required by hibernate.
- */
- TruncatedProtein() {
- }
-
- /**
- * Constructor that creates a copy of the element given in the parameter.
- *
- * @param original
- * original object that will be used for creating copy
- */
- public TruncatedProtein(TruncatedProtein original) {
- super(original);
- }
-
- /**
- * Default constructor.
- *
- * @param elementId
- * uniqe (within model) element identifier
- */
- public TruncatedProtein(String elementId) {
- super(elementId);
- }
-
- @Override
- public TruncatedProtein copy() {
- if (this.getClass() == TruncatedProtein.class) {
- return new TruncatedProtein(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * Entity representing truncated protein element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("TRUNCATED_PROTEIN_ALIAS")
+public class TruncatedProtein extends Protein {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Empty constructor required by hibernate.
+ */
+ TruncatedProtein() {
+ }
+
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
+ public TruncatedProtein(TruncatedProtein original) {
+ super(original);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * uniqe (within model) element identifier
+ */
+ public TruncatedProtein(String elementId) {
+ super(elementId);
+ }
+
+ @Override
+ public TruncatedProtein copy() {
+ if (this.getClass() == TruncatedProtein.class) {
+ return new TruncatedProtein(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProteinComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProteinComparator.java
index e05a1edf0e..952e69e4e2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProteinComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/TruncatedProteinComparator.java
@@ -1,54 +1,54 @@
-package lcsb.mapviewer.model.map.species;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-
-/**
- * Comparator class used for comparing {@link TruncatedProtein} objects.
- *
- * @author Piotr Gawron
- *
- */
-public class TruncatedProteinComparator extends Comparator<TruncatedProtein> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(TruncatedProteinComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public TruncatedProteinComparator(double epsilon) {
- super(TruncatedProtein.class, true);
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public TruncatedProteinComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected Comparator<?> getParentComparator() {
- return new ProteinComparator(epsilon);
- }
-
- @Override
- protected int internalCompare(TruncatedProtein arg0, TruncatedProtein arg1) {
- return 0;
- }
-}
+package lcsb.mapviewer.model.map.species;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+
+/**
+ * Comparator class used for comparing {@link TruncatedProtein} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class TruncatedProteinComparator extends Comparator<TruncatedProtein> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(TruncatedProteinComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public TruncatedProteinComparator(double epsilon) {
+ super(TruncatedProtein.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public TruncatedProteinComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new ProteinComparator(epsilon);
+ }
+
+ @Override
+ protected int internalCompare(TruncatedProtein arg0, TruncatedProtein arg1) {
+ return 0;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Unknown.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Unknown.java
index d475d6de9d..bb261edd81 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Unknown.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Unknown.java
@@ -1,63 +1,63 @@
-package lcsb.mapviewer.model.map.species;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-/**
- * Entity representing unknown element on the map.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("UNKNOWN_ALIAS")
-public class Unknown extends Species {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Empty constructor required by hibernate.
- */
- Unknown() {
- }
-
- /**
- * Constructor that creates a copy of the element given in the parameter.
- *
- * @param original
- * original object that will be used for creating copy
- */
- public Unknown(Unknown original) {
- super(original);
- }
-
- /**
- * Default constructor.
- *
- * @param elementId
- * uniqe (within model) element identifier
- */
- public Unknown(String elementId) {
- setElementId(elementId);
- }
-
- @Override
- public Unknown copy() {
- if (this.getClass() == Unknown.class) {
- return new Unknown(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- @Override
- public String getStringType() {
- return "Unknown";
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+/**
+ * Entity representing unknown element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("UNKNOWN_ALIAS")
+public class Unknown extends Species {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Empty constructor required by hibernate.
+ */
+ Unknown() {
+ }
+
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
+ public Unknown(Unknown original) {
+ super(original);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * uniqe (within model) element identifier
+ */
+ public Unknown(String elementId) {
+ setElementId(elementId);
+ }
+
+ @Override
+ public Unknown copy() {
+ if (this.getClass() == Unknown.class) {
+ return new Unknown(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Unknown";
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/UnknownComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/UnknownComparator.java
index 1c45054aea..bbc83d06f9 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/UnknownComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/UnknownComparator.java
@@ -1,54 +1,54 @@
-package lcsb.mapviewer.model.map.species;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Comparator;
-import lcsb.mapviewer.common.Configuration;
-
-/**
- * Comparator class used for comparing {@link Unknown} objects.
- *
- * @author Piotr Gawron
- *
- */
-public class UnknownComparator extends Comparator<Unknown> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(UnknownComparator.class);
-
- /**
- * Epsilon value used for comparison of doubles.
- */
- private double epsilon;
-
- /**
- * Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
- */
- public UnknownComparator(double epsilon) {
- super(Unknown.class, true);
- this.epsilon = epsilon;
- }
-
- /**
- * Default constructor.
- */
- public UnknownComparator() {
- this(Configuration.EPSILON);
- }
-
- @Override
- protected Comparator<?> getParentComparator() {
- return new SpeciesComparator(epsilon);
- }
-
- @Override
- protected int internalCompare(Unknown arg0, Unknown arg1) {
- return 0;
- }
-}
+package lcsb.mapviewer.model.map.species;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+
+/**
+ * Comparator class used for comparing {@link Unknown} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class UnknownComparator extends Comparator<Unknown> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(UnknownComparator.class);
+
+ /**
+ * Epsilon value used for comparison of doubles.
+ */
+ private double epsilon;
+
+ /**
+ * Constructor that requires {@link #epsilon} parameter.
+ *
+ * @param epsilon
+ * {@link #epsilon}
+ */
+ public UnknownComparator(double epsilon) {
+ super(Unknown.class, true);
+ this.epsilon = epsilon;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public UnknownComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected Comparator<?> getParentComparator() {
+ return new SpeciesComparator(epsilon);
+ }
+
+ @Override
+ protected int internalCompare(Unknown arg0, Unknown arg1) {
+ return 0;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/PositionToCompartment.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/PositionToCompartment.java
index b03ba01d97..2d1a26e2a6 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/PositionToCompartment.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/PositionToCompartment.java
@@ -1,77 +1,77 @@
-package lcsb.mapviewer.model.map.species.field;
-
-/**
- * Defines possible position of
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.Species} on
- * {@link lcsb.mapviewer.model.map.agregator.converter.model.celldesigner.structure.Compartment}
- * .
- *
- * @author Piotr Gawron
- *
- */
-public enum PositionToCompartment {
-
- /**
- * Species is inside compartment.
- */
- INSIDE("inside"),
-
- /**
- * Species is inside the border.
- */
- INSIDE_OF_MEMBRANE("insideOfMembrane"),
-
- /**
- * Species is crossing the border.
- */
- TRANSMEMBRANE("transmembrane"),
-
- /**
- * Species is on outer border of compartment.
- */
- OUTER_SURFACE("outerSurface"),
-
- /**
- * Species is on inner border of compartment.
- */
- INNER_SURFACE("innerSurface");
-
- /**
- * String representing the position.
- */
- private String stringName;
-
- /**
- * Default constructor.
- *
- * @param stringName
- * {@link #stringName}
- */
- PositionToCompartment(String stringName) {
- this.stringName = stringName;
- }
-
- /**
- * @return the stringName
- * @see #stringName
- */
- public String getStringName() {
- return stringName;
- }
-
- /**
- * Returns {@link PositionToCompartment} based on the {@link #stringName}.
- *
- * @param string
- * {@link #stringName}
- * @return {@link PositionToCompartment} based on the {@link #stringName}
- */
- public static PositionToCompartment getByString(String string) {
- for (PositionToCompartment pos : PositionToCompartment.values()) {
- if (pos.getStringName().equalsIgnoreCase(string)) {
- return pos;
- }
- }
- return null;
- }
-}
+package lcsb.mapviewer.model.map.species.field;
+
+/**
+ * Defines possible position of
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.Species} on
+ * {@link lcsb.mapviewer.model.map.agregator.converter.model.celldesigner.structure.Compartment}
+ * .
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum PositionToCompartment {
+
+ /**
+ * Species is inside compartment.
+ */
+ INSIDE("inside"),
+
+ /**
+ * Species is inside the border.
+ */
+ INSIDE_OF_MEMBRANE("insideOfMembrane"),
+
+ /**
+ * Species is crossing the border.
+ */
+ TRANSMEMBRANE("transmembrane"),
+
+ /**
+ * Species is on outer border of compartment.
+ */
+ OUTER_SURFACE("outerSurface"),
+
+ /**
+ * Species is on inner border of compartment.
+ */
+ INNER_SURFACE("innerSurface");
+
+ /**
+ * String representing the position.
+ */
+ private String stringName;
+
+ /**
+ * Default constructor.
+ *
+ * @param stringName
+ * {@link #stringName}
+ */
+ PositionToCompartment(String stringName) {
+ this.stringName = stringName;
+ }
+
+ /**
+ * @return the stringName
+ * @see #stringName
+ */
+ public String getStringName() {
+ return stringName;
+ }
+
+ /**
+ * Returns {@link PositionToCompartment} based on the {@link #stringName}.
+ *
+ * @param string
+ * {@link #stringName}
+ * @return {@link PositionToCompartment} based on the {@link #stringName}
+ */
+ public static PositionToCompartment getByString(String string) {
+ for (PositionToCompartment pos : PositionToCompartment.values()) {
+ if (pos.getStringName().equalsIgnoreCase(string)) {
+ return pos;
+ }
+ }
+ return null;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/package-info.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/package-info.java
index 2a4ed87d92..7ef3bd99b0 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/package-info.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/package-info.java
@@ -1,7 +1,7 @@
-/**
- * Provides data structure for complicated
- * {@link lcsb.mapviewer.model.map.species.Species Species} implementation.
- * These structures contain some additional structural information about
- * elements.
- */
+/**
+ * Provides data structure for complicated
+ * {@link lcsb.mapviewer.model.map.species.Species Species} implementation.
+ * These structures contain some additional structural information about
+ * elements.
+ */
package lcsb.mapviewer.model.map.species.field;
\ No newline at end of file
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/package-info.java b/model/src/main/java/lcsb/mapviewer/model/map/species/package-info.java
index b4478e672a..fdc9d28cd5 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/package-info.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/package-info.java
@@ -1,10 +1,10 @@
-/**
- * Provides data structure for elements on the map. The generic class from which
- * all element classes inherit data is
- * {@link lcsb.mapviewer.db.model.map.species.Element Element}. However, for
- * species there is another class that inherits from this class:
- * {@link lcsb.mapviewer.model.map.species.Species}. The package also contains
- * comparators for these elements that compare the data of the structures, but
- * ignore database-related information (like identifiers).
- */
+/**
+ * Provides data structure for elements on the map. The generic class from which
+ * all element classes inherit data is
+ * {@link lcsb.mapviewer.db.model.map.species.Element Element}. However, for
+ * species there is another class that inherits from this class:
+ * {@link lcsb.mapviewer.model.map.species.Species}. The package also contains
+ * comparators for these elements that compare the data of the structures, but
+ * ignore database-related information (like identifiers).
+ */
package lcsb.mapviewer.model.map.species;
\ No newline at end of file
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/statistics/SearchHistory.java b/model/src/main/java/lcsb/mapviewer/model/map/statistics/SearchHistory.java
index d45cbdebdf..bc9dd821a6 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/statistics/SearchHistory.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/statistics/SearchHistory.java
@@ -1,169 +1,169 @@
-package lcsb.mapviewer.model.map.statistics;
-
-import java.io.Serializable;
-import java.util.Calendar;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Table;
-
-/**
- * This object describe single search event entry. It's used for gathering some
- * statistics about system usage.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "history_table")
-public class SearchHistory implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Unique database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- /**
- * Query entered by the user.
- */
- @Column(nullable = false)
- private String query;
-
- /**
- * Name of the project where user performed search. (It cannot be id, because
- * event after map is removed we want to store statistics).
- */
- private String map;
-
- /**
- * When the event occurred.
- */
- @Column(nullable = false)
- private Calendar timestamp = Calendar.getInstance();
-
- /**
- * Type of the search event.
- */
- @Column(nullable = false)
- private SearchType type;
-
- /**
- * Client ip address.
- */
- @Column(nullable = false)
- private String ipAddress;
-
- /**
- * @return the id
- * @see #id
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
- /**
- * @return the query
- * @see #query
- */
- public String getQuery() {
- return query;
- }
-
- /**
- * @param query
- * the query to set
- * @see #query
- */
- public void setQuery(String query) {
- this.query = query;
- }
-
- /**
- * @return the map
- * @see #map
- */
- public String getMap() {
- return map;
- }
-
- /**
- * @param map
- * the map to set
- * @see #map
- */
- public void setMap(String map) {
- this.map = map;
- }
-
- /**
- * @return the timestamp
- * @see #timestamp
- */
- public Calendar getTimestamp() {
- return timestamp;
- }
-
- /**
- * @param timestamp
- * the timestamp to set
- * @see #timestamp
- */
- public void setTimestamp(Calendar timestamp) {
- this.timestamp = timestamp;
- }
-
- /**
- * @return the type
- * @see #type
- */
- public SearchType getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(SearchType type) {
- this.type = type;
- }
-
- /**
- * @return the ipAddress
- * @see #ipAddress
- */
- public String getIpAddress() {
- return ipAddress;
- }
-
- /**
- * @param ipAddress
- * the ipAddress to set
- * @see #ipAddress
- */
- public void setIpAddress(String ipAddress) {
- this.ipAddress = ipAddress;
- }
-
-}
+package lcsb.mapviewer.model.map.statistics;
+
+import java.io.Serializable;
+import java.util.Calendar;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.Table;
+
+/**
+ * This object describe single search event entry. It's used for gathering some
+ * statistics about system usage.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "history_table")
+public class SearchHistory implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Unique database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * Query entered by the user.
+ */
+ @Column(nullable = false)
+ private String query;
+
+ /**
+ * Name of the project where user performed search. (It cannot be id, because
+ * event after map is removed we want to store statistics).
+ */
+ private String map;
+
+ /**
+ * When the event occurred.
+ */
+ @Column(nullable = false)
+ private Calendar timestamp = Calendar.getInstance();
+
+ /**
+ * Type of the search event.
+ */
+ @Column(nullable = false)
+ private SearchType type;
+
+ /**
+ * Client ip address.
+ */
+ @Column(nullable = false)
+ private String ipAddress;
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ /**
+ * @return the query
+ * @see #query
+ */
+ public String getQuery() {
+ return query;
+ }
+
+ /**
+ * @param query
+ * the query to set
+ * @see #query
+ */
+ public void setQuery(String query) {
+ this.query = query;
+ }
+
+ /**
+ * @return the map
+ * @see #map
+ */
+ public String getMap() {
+ return map;
+ }
+
+ /**
+ * @param map
+ * the map to set
+ * @see #map
+ */
+ public void setMap(String map) {
+ this.map = map;
+ }
+
+ /**
+ * @return the timestamp
+ * @see #timestamp
+ */
+ public Calendar getTimestamp() {
+ return timestamp;
+ }
+
+ /**
+ * @param timestamp
+ * the timestamp to set
+ * @see #timestamp
+ */
+ public void setTimestamp(Calendar timestamp) {
+ this.timestamp = timestamp;
+ }
+
+ /**
+ * @return the type
+ * @see #type
+ */
+ public SearchType getType() {
+ return type;
+ }
+
+ /**
+ * @param type
+ * the type to set
+ * @see #type
+ */
+ public void setType(SearchType type) {
+ this.type = type;
+ }
+
+ /**
+ * @return the ipAddress
+ * @see #ipAddress
+ */
+ public String getIpAddress() {
+ return ipAddress;
+ }
+
+ /**
+ * @param ipAddress
+ * the ipAddress to set
+ * @see #ipAddress
+ */
+ public void setIpAddress(String ipAddress) {
+ this.ipAddress = ipAddress;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/statistics/SearchType.java b/model/src/main/java/lcsb/mapviewer/model/map/statistics/SearchType.java
index 63081775d1..26afa5c6dd 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/statistics/SearchType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/statistics/SearchType.java
@@ -1,29 +1,29 @@
-package lcsb.mapviewer.model.map.statistics;
-
-/**
- * Enum that defines types of {@link SearchHistory} entry.
- *
- * @author Piotr Gawron
- *
- */
-public enum SearchType {
- /**
- * General search event.
- */
- GENERAL,
-
- /**
- * Drug search event.
- */
- DRUG,
-
- /**
- * Chemical search event.
- */
- CHEMICAL,
-
- /**
- * Mi RNA search event.
- */
- MI_RNA
-}
+package lcsb.mapviewer.model.map.statistics;
+
+/**
+ * Enum that defines types of {@link SearchHistory} entry.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum SearchType {
+ /**
+ * General search event.
+ */
+ GENERAL,
+
+ /**
+ * Drug search event.
+ */
+ DRUG,
+
+ /**
+ * Chemical search event.
+ */
+ CHEMICAL,
+
+ /**
+ * Mi RNA search event.
+ */
+ MI_RNA
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/statistics/package-info.java b/model/src/main/java/lcsb/mapviewer/model/map/statistics/package-info.java
index 5fbd7532ae..c1e9adffde 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/statistics/package-info.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/statistics/package-info.java
@@ -1,5 +1,5 @@
-/**
- * Provides data structure for statistics about the usage of the map.
- */
-package lcsb.mapviewer.model.map.statistics;
-
+/**
+ * Provides data structure for statistics about the usage of the map.
+ */
+package lcsb.mapviewer.model.map.statistics;
+
diff --git a/model/src/main/java/lcsb/mapviewer/model/package-info.java b/model/src/main/java/lcsb/mapviewer/model/package-info.java
index 41042bf466..76cf68c54a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/package-info.java
+++ b/model/src/main/java/lcsb/mapviewer/model/package-info.java
@@ -1,21 +1,21 @@
-/**
- * Contains structures used for modeling. They are designed to be stored in the
- * database. Package is divided into several functional subpackages:
- * <ul>
- * <li>graphics - where graphical structures are defined (not connected to the
- * model)</li>
- * <li>log - where log entries of the systems are defined</li>
- * <li>map - where map model is defined (
- * {@link lcsb.mapviewer.model.map.model.Model Model} is the main structure in this
- * package)</li>
- * <li>cache (former reactome) - where cache structure is defined</li>
- * <li>user - structure for user definition is kept there</li>
- * </ul>
- * <br/>
- * The main structure is {@link lcsb.mapviewer.model.Project}. It defines
- * single project that exists in the system. Signle project can contain few map
- * {@link lcsb.mapviewer.model.map.model.Model models} (few different versions of
- * the map).
- */
-package lcsb.mapviewer.model;
-
+/**
+ * Contains structures used for modeling. They are designed to be stored in the
+ * database. Package is divided into several functional subpackages:
+ * <ul>
+ * <li>graphics - where graphical structures are defined (not connected to the
+ * model)</li>
+ * <li>log - where log entries of the systems are defined</li>
+ * <li>map - where map model is defined (
+ * {@link lcsb.mapviewer.model.map.model.Model Model} is the main structure in this
+ * package)</li>
+ * <li>cache (former reactome) - where cache structure is defined</li>
+ * <li>user - structure for user definition is kept there</li>
+ * </ul>
+ * <br/>
+ * The main structure is {@link lcsb.mapviewer.model.Project}. It defines
+ * single project that exists in the system. Signle project can contain few map
+ * {@link lcsb.mapviewer.model.map.model.Model models} (few different versions of
+ * the map).
+ */
+package lcsb.mapviewer.model;
+
diff --git a/model/src/main/java/lcsb/mapviewer/model/plugin/Plugin.java b/model/src/main/java/lcsb/mapviewer/model/plugin/Plugin.java
index 22a9d41741..1edbfbbe12 100644
--- a/model/src/main/java/lcsb/mapviewer/model/plugin/Plugin.java
+++ b/model/src/main/java/lcsb/mapviewer/model/plugin/Plugin.java
@@ -1,113 +1,113 @@
-package lcsb.mapviewer.model.plugin;
-
-import java.io.Serializable;
-import java.util.Comparator;
-import java.util.HashSet;
-import java.util.Set;
-
-import javax.persistence.CollectionTable;
-import javax.persistence.Column;
-import javax.persistence.ElementCollection;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.Table;
-
-import lcsb.mapviewer.common.comparator.IntegerComparator;
-
-/**
- * Meta data of the plugin used in the system.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "plugin_table")
-public class Plugin implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- public static final Comparator<? super Plugin> ID_COMPARATOR = new Comparator<Plugin>() {
-
- @Override
- public int compare(Plugin o1, Plugin o2) {
- return new IntegerComparator().compare(o1.getId(), o2.getId());
- }
- };
-
- /**
- * Unique database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- /**
- * Hash of the plugin code used as identifier to distinguish between plugins.
- */
- private String hash;
-
- /**
- * Name of the plugin.
- */
- private String name;
-
- /**
- * Version of the plugin.
- */
- private String version;
-
- /**
- * List of urls from which plugin can be downloaded.
- */
- @ElementCollection
- @CollectionTable(name = "plugin_urls", joinColumns = @JoinColumn(name = "plugin_iddb"))
- @Column(name = "url")
- private Set<String> urls = new HashSet<>();
-
- public String getHash() {
- return hash;
- }
-
- public void setHash(String hash) {
- this.hash = hash;
- }
-
- public Set<String> getUrls() {
- return urls;
- }
-
- public void setUrls(Set<String> urls) {
- this.urls = urls;
- }
-
- public String getName() {
- return name;
- }
-
- public void setName(String name) {
- this.name = name;
- }
-
- public String getVersion() {
- return version;
- }
-
- public void setVersion(String version) {
- this.version = version;
- }
-
- public int getId() {
- return id;
- }
-
- public void setId(int id) {
- this.id = id;
- }
-}
+package lcsb.mapviewer.model.plugin;
+
+import java.io.Serializable;
+import java.util.Comparator;
+import java.util.HashSet;
+import java.util.Set;
+
+import javax.persistence.CollectionTable;
+import javax.persistence.Column;
+import javax.persistence.ElementCollection;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.Table;
+
+import lcsb.mapviewer.common.comparator.IntegerComparator;
+
+/**
+ * Meta data of the plugin used in the system.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "plugin_table")
+public class Plugin implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ public static final Comparator<? super Plugin> ID_COMPARATOR = new Comparator<Plugin>() {
+
+ @Override
+ public int compare(Plugin o1, Plugin o2) {
+ return new IntegerComparator().compare(o1.getId(), o2.getId());
+ }
+ };
+
+ /**
+ * Unique database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * Hash of the plugin code used as identifier to distinguish between plugins.
+ */
+ private String hash;
+
+ /**
+ * Name of the plugin.
+ */
+ private String name;
+
+ /**
+ * Version of the plugin.
+ */
+ private String version;
+
+ /**
+ * List of urls from which plugin can be downloaded.
+ */
+ @ElementCollection
+ @CollectionTable(name = "plugin_urls", joinColumns = @JoinColumn(name = "plugin_iddb"))
+ @Column(name = "url")
+ private Set<String> urls = new HashSet<>();
+
+ public String getHash() {
+ return hash;
+ }
+
+ public void setHash(String hash) {
+ this.hash = hash;
+ }
+
+ public Set<String> getUrls() {
+ return urls;
+ }
+
+ public void setUrls(Set<String> urls) {
+ this.urls = urls;
+ }
+
+ public String getName() {
+ return name;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ public String getVersion() {
+ return version;
+ }
+
+ public void setVersion(String version) {
+ this.version = version;
+ }
+
+ public int getId() {
+ return id;
+ }
+
+ public void setId(int id) {
+ this.id = id;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/plugin/PluginDataEntry.java b/model/src/main/java/lcsb/mapviewer/model/plugin/PluginDataEntry.java
index 3f661f5284..5a8588d7ad 100644
--- a/model/src/main/java/lcsb/mapviewer/model/plugin/PluginDataEntry.java
+++ b/model/src/main/java/lcsb/mapviewer/model/plugin/PluginDataEntry.java
@@ -1,90 +1,90 @@
-package lcsb.mapviewer.model.plugin;
-
-import java.io.Serializable;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-
-import lcsb.mapviewer.model.user.User;
-
-/**
- * Single entry of data stored by the plugin.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "plugin_data_entry")
-public class PluginDataEntry implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Unique database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- @ManyToOne(fetch = FetchType.LAZY, optional = true)
- private User user;
-
- @ManyToOne(fetch = FetchType.LAZY, optional = false)
- private Plugin plugin;
-
- @Column(name = "entry_key", nullable = false)
- private String key;
-
- @Column(name = "entry_value", nullable = false)
- private String value;
-
- public int getId() {
- return id;
- }
-
- public void setId(int id) {
- this.id = id;
- }
-
- public User getUser() {
- return user;
- }
-
- public void setUser(User user) {
- this.user = user;
- }
-
- public Plugin getPlugin() {
- return plugin;
- }
-
- public void setPlugin(Plugin plugin) {
- this.plugin = plugin;
- }
-
- public String getKey() {
- return key;
- }
-
- public void setKey(String key) {
- this.key = key;
- }
-
- public String getValue() {
- return value;
- }
-
- public void setValue(String value) {
- this.value = value;
- }
-}
+package lcsb.mapviewer.model.plugin;
+
+import java.io.Serializable;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+
+import lcsb.mapviewer.model.user.User;
+
+/**
+ * Single entry of data stored by the plugin.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "plugin_data_entry")
+public class PluginDataEntry implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Unique database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ @ManyToOne(fetch = FetchType.LAZY, optional = true)
+ private User user;
+
+ @ManyToOne(fetch = FetchType.LAZY, optional = false)
+ private Plugin plugin;
+
+ @Column(name = "entry_key", nullable = false)
+ private String key;
+
+ @Column(name = "entry_value", nullable = false)
+ private String value;
+
+ public int getId() {
+ return id;
+ }
+
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ public User getUser() {
+ return user;
+ }
+
+ public void setUser(User user) {
+ this.user = user;
+ }
+
+ public Plugin getPlugin() {
+ return plugin;
+ }
+
+ public void setPlugin(Plugin plugin) {
+ this.plugin = plugin;
+ }
+
+ public String getKey() {
+ return key;
+ }
+
+ public void setKey(String key) {
+ this.key = key;
+ }
+
+ public String getValue() {
+ return value;
+ }
+
+ public void setValue(String value) {
+ this.value = value;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/BasicPrivilege.java b/model/src/main/java/lcsb/mapviewer/model/user/BasicPrivilege.java
index 7da82d48c5..04f34a6ca0 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/BasicPrivilege.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/BasicPrivilege.java
@@ -1,183 +1,183 @@
-package lcsb.mapviewer.model.user;
-
-import java.io.Serializable;
-import java.util.Comparator;
-
-import javax.persistence.Column;
-import javax.persistence.DiscriminatorColumn;
-import javax.persistence.DiscriminatorType;
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.EnumType;
-import javax.persistence.Enumerated;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Inheritance;
-import javax.persistence.InheritanceType;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-
-import lcsb.mapviewer.common.comparator.IntegerComparator;
-
-/**
- * Class that defines user privilege. Privilege has an access level (typically 0,
- * 1 value), type of the privilege and user reference.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "privilege_table")
-@Inheritance(strategy = InheritanceType.SINGLE_TABLE)
-@DiscriminatorColumn(name = "privilege_class_type_db", discriminatorType = DiscriminatorType.STRING)
-@DiscriminatorValue("BASIC_PRIVILEGE")
-public class BasicPrivilege implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- public static final Comparator<? super BasicPrivilege> ID_COMPARATOR = new Comparator<BasicPrivilege>() {
-
- @Override
- public int compare(BasicPrivilege o1, BasicPrivilege o2) {
- return new IntegerComparator().compare(o1.getId(), o2.getId());
- }
- };
-
- /**
- * Unique identifier in the database.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- /**
- * Which user this privilege concerns.
- */
- @ManyToOne(fetch = FetchType.LAZY)
- private User user;
-
- /**
- * Type of the privilege.
- */
- @Enumerated(EnumType.STRING)
- private PrivilegeType type;
-
- /**
- * Access level of the privilege. By default 0 means that user doesn't have
- * privilege and value greater than 0 means that user has privilege. It's
- * possible to implement different behaviour for different level values.
- */
- private int level;
-
- /**
- * Constructor that initialize the privilege with given data.
- *
- * @param level
- * level on which the privilege is set
- * @param type
- * type of the privilege
- * @param user
- * user for which this privilege is set
- */
- public BasicPrivilege(int level, PrivilegeType type, User user) {
- this.level = level;
- this.type = type;
- this.user = user;
- }
-
- /**
- * Default constructor.
- */
- public BasicPrivilege() {
- }
-
- /**
- * Checks if the privilege is with the same type as privilege given in the
- * parameter.
- *
- * @param privilege
- * other privilege to compare
- * @return <code>true</code> if privilege is of the same type as an argument,
- * <code>false</code> otherwise
- */
- public boolean equalsPrivilege(BasicPrivilege privilege) {
- if (privilege == null) {
- return false;
- }
- return type.equals(privilege.getType());
- }
-
- /**
- * @return the id
- * @see #id
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
- /**
- * @return the user
- * @see #user
- */
- public User getUser() {
- return user;
- }
-
- /**
- * @param user
- * the user to set
- * @see #user
- */
- public void setUser(User user) {
- this.user = user;
- }
-
- /**
- * @return the type
- * @see #type
- */
- public PrivilegeType getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(PrivilegeType type) {
- this.type = type;
- }
-
- /**
- * @return the level
- * @see #level
- */
- public int getLevel() {
- return level;
- }
-
- /**
- * @param level
- * the level to set
- * @see #level
- */
- public void setLevel(int level) {
- this.level = level;
- }
-}
+package lcsb.mapviewer.model.user;
+
+import java.io.Serializable;
+import java.util.Comparator;
+
+import javax.persistence.Column;
+import javax.persistence.DiscriminatorColumn;
+import javax.persistence.DiscriminatorType;
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+import javax.persistence.EnumType;
+import javax.persistence.Enumerated;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.Inheritance;
+import javax.persistence.InheritanceType;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+
+import lcsb.mapviewer.common.comparator.IntegerComparator;
+
+/**
+ * Class that defines user privilege. Privilege has an access level (typically 0,
+ * 1 value), type of the privilege and user reference.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "privilege_table")
+@Inheritance(strategy = InheritanceType.SINGLE_TABLE)
+@DiscriminatorColumn(name = "privilege_class_type_db", discriminatorType = DiscriminatorType.STRING)
+@DiscriminatorValue("BASIC_PRIVILEGE")
+public class BasicPrivilege implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ public static final Comparator<? super BasicPrivilege> ID_COMPARATOR = new Comparator<BasicPrivilege>() {
+
+ @Override
+ public int compare(BasicPrivilege o1, BasicPrivilege o2) {
+ return new IntegerComparator().compare(o1.getId(), o2.getId());
+ }
+ };
+
+ /**
+ * Unique identifier in the database.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * Which user this privilege concerns.
+ */
+ @ManyToOne(fetch = FetchType.LAZY)
+ private User user;
+
+ /**
+ * Type of the privilege.
+ */
+ @Enumerated(EnumType.STRING)
+ private PrivilegeType type;
+
+ /**
+ * Access level of the privilege. By default 0 means that user doesn't have
+ * privilege and value greater than 0 means that user has privilege. It's
+ * possible to implement different behaviour for different level values.
+ */
+ private int level;
+
+ /**
+ * Constructor that initialize the privilege with given data.
+ *
+ * @param level
+ * level on which the privilege is set
+ * @param type
+ * type of the privilege
+ * @param user
+ * user for which this privilege is set
+ */
+ public BasicPrivilege(int level, PrivilegeType type, User user) {
+ this.level = level;
+ this.type = type;
+ this.user = user;
+ }
+
+ /**
+ * Default constructor.
+ */
+ public BasicPrivilege() {
+ }
+
+ /**
+ * Checks if the privilege is with the same type as privilege given in the
+ * parameter.
+ *
+ * @param privilege
+ * other privilege to compare
+ * @return <code>true</code> if privilege is of the same type as an argument,
+ * <code>false</code> otherwise
+ */
+ public boolean equalsPrivilege(BasicPrivilege privilege) {
+ if (privilege == null) {
+ return false;
+ }
+ return type.equals(privilege.getType());
+ }
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ /**
+ * @return the user
+ * @see #user
+ */
+ public User getUser() {
+ return user;
+ }
+
+ /**
+ * @param user
+ * the user to set
+ * @see #user
+ */
+ public void setUser(User user) {
+ this.user = user;
+ }
+
+ /**
+ * @return the type
+ * @see #type
+ */
+ public PrivilegeType getType() {
+ return type;
+ }
+
+ /**
+ * @param type
+ * the type to set
+ * @see #type
+ */
+ public void setType(PrivilegeType type) {
+ this.type = type;
+ }
+
+ /**
+ * @return the level
+ * @see #level
+ */
+ public int getLevel() {
+ return level;
+ }
+
+ /**
+ * @param level
+ * the level to set
+ * @see #level
+ */
+ public void setLevel(int level) {
+ this.level = level;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementEditType.java b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementEditType.java
index 3199cf8921..b2576ba60c 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementEditType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementEditType.java
@@ -1,55 +1,55 @@
-package lcsb.mapviewer.model.user;
-
-/**
- * Defines how the {@link ConfigurationElementType} should be edited (what kind
- * of values we are storing).
- *
- * @author Piotr Gawron
- *
- */
-public enum ConfigurationElementEditType {
- /**
- * Double value.
- */
- DOUBLE,
-
- /**
- * Integer value.
- */
- INTEGER,
-
- /**
- * String value.
- */
- STRING,
-
- /**
- * Multiple line text value.
- */
- TEXT,
-
- /**
- * Color value (for color picker).
- */
- COLOR,
-
- /**
- * Url value.
- */
- URL,
-
- /**
- * Email value.
- */
- EMAIL,
-
- /**
- * Password value.
- */
- PASSWORD,
-
- /**
- * True/false value.
- */
- BOOLEAN,
-}
+package lcsb.mapviewer.model.user;
+
+/**
+ * Defines how the {@link ConfigurationElementType} should be edited (what kind
+ * of values we are storing).
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum ConfigurationElementEditType {
+ /**
+ * Double value.
+ */
+ DOUBLE,
+
+ /**
+ * Integer value.
+ */
+ INTEGER,
+
+ /**
+ * String value.
+ */
+ STRING,
+
+ /**
+ * Multiple line text value.
+ */
+ TEXT,
+
+ /**
+ * Color value (for color picker).
+ */
+ COLOR,
+
+ /**
+ * Url value.
+ */
+ URL,
+
+ /**
+ * Email value.
+ */
+ EMAIL,
+
+ /**
+ * Password value.
+ */
+ PASSWORD,
+
+ /**
+ * True/false value.
+ */
+ BOOLEAN,
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementTypeGroup.java b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementTypeGroup.java
index 6ca381ccc8..bb7417e9c7 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementTypeGroup.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementTypeGroup.java
@@ -1,26 +1,26 @@
-package lcsb.mapviewer.model.user;
-
-public enum ConfigurationElementTypeGroup {
- EMAIL_NOTIFICATION("Email notification details"), //
- DEFAULT_USER_PRIVILEGES("Default user privileges"), //
- LEGEND_AND_LOGO("Legend and logo"), //
- OVERLAYS("Overlays"), //
- POINT_AND_CLICK("Point and click"), //
- SERVER_CONFIGURATION("Server configuration"),//
- LDAP_CONFIGURATION("LDAP configuration"),//
-
- ;
- private String commonName;
-
- ConfigurationElementTypeGroup(String commonName) {
- this.commonName = commonName;
- }
-
- public String getCommonName() {
- return commonName;
- }
-
- public void setCommonName(String commonName) {
- this.commonName = commonName;
- }
-}
+package lcsb.mapviewer.model.user;
+
+public enum ConfigurationElementTypeGroup {
+ EMAIL_NOTIFICATION("Email notification details"), //
+ DEFAULT_USER_PRIVILEGES("Default user privileges"), //
+ LEGEND_AND_LOGO("Legend and logo"), //
+ OVERLAYS("Overlays"), //
+ POINT_AND_CLICK("Point and click"), //
+ SERVER_CONFIGURATION("Server configuration"),//
+ LDAP_CONFIGURATION("LDAP configuration"),//
+
+ ;
+ private String commonName;
+
+ ConfigurationElementTypeGroup(String commonName) {
+ this.commonName = commonName;
+ }
+
+ public String getCommonName() {
+ return commonName;
+ }
+
+ public void setCommonName(String commonName) {
+ this.commonName = commonName;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationOption.java b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationOption.java
index 50a348a66b..2d12ff2709 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationOption.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/ConfigurationOption.java
@@ -1,96 +1,96 @@
-package lcsb.mapviewer.model.user;
-
-import java.io.Serializable;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.Table;
-
-/**
- * This class represents one configurable parameter of the system.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "configuration_table")
-public class ConfigurationOption implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Unique identifier in the database.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- /**
- * Type of the configuration element.
- */
- private ConfigurationElementType type;
-
- /**
- * What is the value of the configuration parameter.
- */
- private String value;
-
- /**
- * @return the id
- * @see #id
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
- /**
- * @return the type
- * @see #type
- */
- public ConfigurationElementType getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(ConfigurationElementType type) {
- this.type = type;
- }
-
- /**
- * @return the value
- * @see #value
- */
- public String getValue() {
- return value;
- }
-
- /**
- * @param value
- * the value to set
- * @see #value
- */
- public void setValue(String value) {
- this.value = value;
- }
-
-}
+package lcsb.mapviewer.model.user;
+
+import java.io.Serializable;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.Table;
+
+/**
+ * This class represents one configurable parameter of the system.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "configuration_table")
+public class ConfigurationOption implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Unique identifier in the database.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * Type of the configuration element.
+ */
+ private ConfigurationElementType type;
+
+ /**
+ * What is the value of the configuration parameter.
+ */
+ private String value;
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ /**
+ * @return the type
+ * @see #type
+ */
+ public ConfigurationElementType getType() {
+ return type;
+ }
+
+ /**
+ * @param type
+ * the type to set
+ * @see #type
+ */
+ public void setType(ConfigurationElementType type) {
+ this.type = type;
+ }
+
+ /**
+ * @return the value
+ * @see #value
+ */
+ public String getValue() {
+ return value;
+ }
+
+ /**
+ * @param value
+ * the value to set
+ * @see #value
+ */
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/ObjectPrivilege.java b/model/src/main/java/lcsb/mapviewer/model/user/ObjectPrivilege.java
index d50a7fbf86..085b035727 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/ObjectPrivilege.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/ObjectPrivilege.java
@@ -1,99 +1,99 @@
-package lcsb.mapviewer.model.user;
-
-import java.io.Serializable;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-
-import lcsb.mapviewer.common.ObjectUtils;
-import lcsb.mapviewer.common.comparator.IntegerComparator;
-
-/**
- * This class extends {@link BasicPrivilege} class which define typical user
- * privilege. The extension introduces specific object in the model to which
- * privilege is given.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("OBJECT_PRIVILEGE")
-public class ObjectPrivilege extends BasicPrivilege implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Identifier of the object connected to this privilege.
- */
- private Integer idObject;
-
- /**
- * Constructor that initialize data with the information given in the
- * parameters.
- *
- * @param object
- * object connected to this privilege
- * @param level
- * access level
- * @param type
- * type of the privilege
- * @param user
- * user who has this privilege
- */
- public ObjectPrivilege(Object object, int level, PrivilegeType type, User user) {
- super(level, type, user);
- if (object != null) {
- idObject = ObjectUtils.getIdOfObject(object);
- }
- }
-
- /**
- * Default constructor.
- */
- public ObjectPrivilege() {
- }
-
- @Override
- public boolean equalsPrivilege(BasicPrivilege privilege) {
- if (privilege == null) {
- return false;
- }
- if (privilege instanceof ObjectPrivilege) {
- IntegerComparator integerComparator = new IntegerComparator();
- return super.equalsPrivilege(privilege)
- && integerComparator.compare(idObject, ((ObjectPrivilege) privilege).getIdObject()) == 0;
- } else {
- return false;
- }
- }
-
- /**
- * @return the idObject
- * @see #idObject
- */
- public Integer getIdObject() {
- return idObject;
- }
-
- /**
- * @param idObject
- * the idObject to set
- * @see #idObject
- */
- public void setIdObject(Integer idObject) {
- this.idObject = idObject;
- }
-
- /**
- * @param idObject
- * the idObject to set
- * @see #idObject
- */
- public void setIdObject(String idObject) {
- this.idObject = Integer.valueOf(idObject);
- }
-
-}
+package lcsb.mapviewer.model.user;
+
+import java.io.Serializable;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.ObjectUtils;
+import lcsb.mapviewer.common.comparator.IntegerComparator;
+
+/**
+ * This class extends {@link BasicPrivilege} class which define typical user
+ * privilege. The extension introduces specific object in the model to which
+ * privilege is given.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("OBJECT_PRIVILEGE")
+public class ObjectPrivilege extends BasicPrivilege implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Identifier of the object connected to this privilege.
+ */
+ private Integer idObject;
+
+ /**
+ * Constructor that initialize data with the information given in the
+ * parameters.
+ *
+ * @param object
+ * object connected to this privilege
+ * @param level
+ * access level
+ * @param type
+ * type of the privilege
+ * @param user
+ * user who has this privilege
+ */
+ public ObjectPrivilege(Object object, int level, PrivilegeType type, User user) {
+ super(level, type, user);
+ if (object != null) {
+ idObject = ObjectUtils.getIdOfObject(object);
+ }
+ }
+
+ /**
+ * Default constructor.
+ */
+ public ObjectPrivilege() {
+ }
+
+ @Override
+ public boolean equalsPrivilege(BasicPrivilege privilege) {
+ if (privilege == null) {
+ return false;
+ }
+ if (privilege instanceof ObjectPrivilege) {
+ IntegerComparator integerComparator = new IntegerComparator();
+ return super.equalsPrivilege(privilege)
+ && integerComparator.compare(idObject, ((ObjectPrivilege) privilege).getIdObject()) == 0;
+ } else {
+ return false;
+ }
+ }
+
+ /**
+ * @return the idObject
+ * @see #idObject
+ */
+ public Integer getIdObject() {
+ return idObject;
+ }
+
+ /**
+ * @param idObject
+ * the idObject to set
+ * @see #idObject
+ */
+ public void setIdObject(Integer idObject) {
+ this.idObject = idObject;
+ }
+
+ /**
+ * @param idObject
+ * the idObject to set
+ * @see #idObject
+ */
+ public void setIdObject(String idObject) {
+ this.idObject = Integer.valueOf(idObject);
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/PrivilegeType.java b/model/src/main/java/lcsb/mapviewer/model/user/PrivilegeType.java
index b214a50ab8..c341163adf 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/PrivilegeType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/PrivilegeType.java
@@ -1,151 +1,151 @@
-package lcsb.mapviewer.model.user;
-
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.layout.Layout;
-
-/**
- * Defines types of privileges in the system.
- *
- * @author Piotr Gawron
- *
- */
-public enum PrivilegeType {
-
- /**
- * User can browse project.
- */
- VIEW_PROJECT(ObjectPrivilege.class, Project.class, "View project"),
-
- /**
- * User can add project.
- */
- ADD_MAP(BasicPrivilege.class, null, "Add project"),
-
- /**
- * User can edit comments in the project.
- */
- EDIT_COMMENTS_PROJECT(ObjectPrivilege.class, Project.class, "Manage comments"),
-
- /**
- * User can manage projects.
- */
- PROJECT_MANAGEMENT(BasicPrivilege.class, null, "Map management"),
-
- /**
- * User can manage users.
- */
- USER_MANAGEMENT(BasicPrivilege.class, null, "User management"),
-
- /**
- * User can have custom layouts (access level defines how many).
- */
- CUSTOM_LAYOUTS(BasicPrivilege.class, null, "Custom overlays", true),
-
- /**
- * User can view non-public layout.
- */
- LAYOUT_VIEW(ObjectPrivilege.class, Layout.class, "View overlay"),
-
- /**
- * User can manage configuration.
- */
- CONFIGURATION_MANAGE(BasicPrivilege.class, null, "Manage configuration"),
-
- /**
- * User can manage layouts of all users in the project.
- */
- LAYOUT_MANAGEMENT(ObjectPrivilege.class, Project.class, "Manage overlays"), //
-
- /**
- * User can manage reference genomes.
- */
- MANAGE_GENOMES(BasicPrivilege.class, null, "Manage genomes");
-
- /**
- * Type of privilege (basic or privilege to the object).
- */
- private Class<? extends BasicPrivilege> privilegeClassType;
-
- /**
- * Type of the object to which privilege refers.
- */
- private Class<?> privilegeObjectType;
-
- /**
- * Name of the privilege.
- */
- private String commonName;
-
- /**
- * Is the privilege numeric.
- */
- private boolean numeric = false;
-
- /**
- * Constructor that initialize enum with data.
- *
- * @param privilegeClazz
- * {@link #privilegeClassType}
- * @param objectClazz
- * {@link #privilegeObjectType}
- * @param commonName
- * {@link #commonName}
- */
- PrivilegeType(Class<? extends BasicPrivilege> privilegeClazz, Class<?> objectClazz, String commonName) {
- this.privilegeClassType = privilegeClazz;
- this.privilegeObjectType = objectClazz;
- this.commonName = commonName;
- }
-
- /**
- * Constructor that initialize enum with data.
- *
- * @param privilegeClazz
- * {@link #privilegeClassType}
- * @param objectClazz
- * {@link #privilegeObjectType}
- * @param commonName
- * {@link #commonName}
- * @param numeric
- * {@link #numeric}
- */
- PrivilegeType(Class<? extends BasicPrivilege> privilegeClazz, Class<?> objectClazz, String commonName,
- boolean numeric) {
- this.privilegeClassType = privilegeClazz;
- this.privilegeObjectType = objectClazz;
- this.commonName = commonName;
- this.numeric = true;
- }
-
- /**
- *
- * @return {@link #privilegeClassType}
- */
- public Class<? extends BasicPrivilege> getPrivilegeClassType() {
- return privilegeClassType;
- }
-
- /**
- *
- * @return {@link #privilegeObjectType}
- */
- public Class<?> getPrivilegeObjectType() {
- return privilegeObjectType;
- }
-
- /**
- *
- * @return {@link #commonName}
- */
- public String getCommonName() {
- return commonName;
- }
-
- /**
- *
- * @return {@link #numeric}
- */
- public boolean isNumeric() {
- return numeric;
- }
-}
+package lcsb.mapviewer.model.user;
+
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.layout.Layout;
+
+/**
+ * Defines types of privileges in the system.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum PrivilegeType {
+
+ /**
+ * User can browse project.
+ */
+ VIEW_PROJECT(ObjectPrivilege.class, Project.class, "View project"),
+
+ /**
+ * User can add project.
+ */
+ ADD_MAP(BasicPrivilege.class, null, "Add project"),
+
+ /**
+ * User can edit comments in the project.
+ */
+ EDIT_COMMENTS_PROJECT(ObjectPrivilege.class, Project.class, "Manage comments"),
+
+ /**
+ * User can manage projects.
+ */
+ PROJECT_MANAGEMENT(BasicPrivilege.class, null, "Map management"),
+
+ /**
+ * User can manage users.
+ */
+ USER_MANAGEMENT(BasicPrivilege.class, null, "User management"),
+
+ /**
+ * User can have custom layouts (access level defines how many).
+ */
+ CUSTOM_LAYOUTS(BasicPrivilege.class, null, "Custom overlays", true),
+
+ /**
+ * User can view non-public layout.
+ */
+ LAYOUT_VIEW(ObjectPrivilege.class, Layout.class, "View overlay"),
+
+ /**
+ * User can manage configuration.
+ */
+ CONFIGURATION_MANAGE(BasicPrivilege.class, null, "Manage configuration"),
+
+ /**
+ * User can manage layouts of all users in the project.
+ */
+ LAYOUT_MANAGEMENT(ObjectPrivilege.class, Project.class, "Manage overlays"), //
+
+ /**
+ * User can manage reference genomes.
+ */
+ MANAGE_GENOMES(BasicPrivilege.class, null, "Manage genomes");
+
+ /**
+ * Type of privilege (basic or privilege to the object).
+ */
+ private Class<? extends BasicPrivilege> privilegeClassType;
+
+ /**
+ * Type of the object to which privilege refers.
+ */
+ private Class<?> privilegeObjectType;
+
+ /**
+ * Name of the privilege.
+ */
+ private String commonName;
+
+ /**
+ * Is the privilege numeric.
+ */
+ private boolean numeric = false;
+
+ /**
+ * Constructor that initialize enum with data.
+ *
+ * @param privilegeClazz
+ * {@link #privilegeClassType}
+ * @param objectClazz
+ * {@link #privilegeObjectType}
+ * @param commonName
+ * {@link #commonName}
+ */
+ PrivilegeType(Class<? extends BasicPrivilege> privilegeClazz, Class<?> objectClazz, String commonName) {
+ this.privilegeClassType = privilegeClazz;
+ this.privilegeObjectType = objectClazz;
+ this.commonName = commonName;
+ }
+
+ /**
+ * Constructor that initialize enum with data.
+ *
+ * @param privilegeClazz
+ * {@link #privilegeClassType}
+ * @param objectClazz
+ * {@link #privilegeObjectType}
+ * @param commonName
+ * {@link #commonName}
+ * @param numeric
+ * {@link #numeric}
+ */
+ PrivilegeType(Class<? extends BasicPrivilege> privilegeClazz, Class<?> objectClazz, String commonName,
+ boolean numeric) {
+ this.privilegeClassType = privilegeClazz;
+ this.privilegeObjectType = objectClazz;
+ this.commonName = commonName;
+ this.numeric = true;
+ }
+
+ /**
+ *
+ * @return {@link #privilegeClassType}
+ */
+ public Class<? extends BasicPrivilege> getPrivilegeClassType() {
+ return privilegeClassType;
+ }
+
+ /**
+ *
+ * @return {@link #privilegeObjectType}
+ */
+ public Class<?> getPrivilegeObjectType() {
+ return privilegeObjectType;
+ }
+
+ /**
+ *
+ * @return {@link #commonName}
+ */
+ public String getCommonName() {
+ return commonName;
+ }
+
+ /**
+ *
+ * @return {@link #numeric}
+ */
+ public boolean isNumeric() {
+ return numeric;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/User.java b/model/src/main/java/lcsb/mapviewer/model/user/User.java
index 59c480f3c8..d9b997d4f8 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/User.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/User.java
@@ -1,416 +1,416 @@
-package lcsb.mapviewer.model.user;
-
-import java.awt.Color;
-import java.io.Serializable;
-import java.util.Calendar;
-import java.util.Comparator;
-import java.util.HashSet;
-import java.util.Set;
-
-import javax.persistence.CascadeType;
-import javax.persistence.CollectionTable;
-import javax.persistence.Column;
-import javax.persistence.ElementCollection;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.OneToMany;
-import javax.persistence.OneToOne;
-import javax.persistence.Table;
-
-import org.hibernate.annotations.Cascade;
-
-import lcsb.mapviewer.common.comparator.StringComparator;
-
-/**
- * Class representing user.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "user_table")
-public class User implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- public static final Comparator<? super User> LOGIN_COMPARATOR = new Comparator<User>() {
-
- @Override
- public int compare(User o1, User o2) {
- String login1 = null;
- String login2 = null;
- if (o1 != null) {
- login1 = o1.getLogin();
- }
- if (o2 != null) {
- login2 = o2.getLogin();
- }
- return new StringComparator().compare(login1, login2);
- }
- };
-
- /**
- * Unique identifier in the database.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private Integer id;
-
- /**
- * User login.
- */
- private String login;
-
- /**
- * Password in encrypted form. For the encryption PasswordEncoder spring bean is
- * used.
- */
- private String cryptedPassword;
-
- /**
- * Name of the user.
- */
- private String name;
-
- /**
- * Family name of the user.
- */
- private String surname;
-
- /**
- * Email address of the user.
- */
- private String email;
-
- /**
- * User defined color overriding system
- * {@link ConfigurationElementType#MIN_COLOR_VAL}. Used for coloring minimum
- * values in overlays.
- */
- private Color minColor;
-
- /**
- * User defined color overriding system
- * {@link ConfigurationElementType#MAX_COLOR_VAL}. Used for coloring maximum
- * values in overlays.
- */
- private Color maxColor;
-
- /**
- * User defined color overriding system
- * {@link ConfigurationElementType#NEUTRAL_COLOR_VAL}. Used for coloring neutral
- * values (0) in overlays.
- */
- private Color neutralColor;
-
- /**
- * User defined color overriding system
- * {@link ConfigurationElementType#SIMPLE_COLOR_VAL}. Used for coloring overlays
- * without values and colors.
- */
- private Color simpleColor;
-
- /**
- * Is the user removed.
- */
- private boolean removed = false;
-
- /**
- * User is connected to LDAP directory.
- */
- private boolean connectedToLdap = false;
-
- @Column(name = "terms_of_use_consent")
- private boolean termsOfUseConsent = false;
-
- @ElementCollection(fetch = FetchType.EAGER)
- @CollectionTable(name = "user_terms_of_use_consent", joinColumns = @JoinColumn(name = "user_iddb"))
- @Column(name = "date")
- @Cascade({ org.hibernate.annotations.CascadeType.ALL })
- private Set<Calendar> termsOfUseConsentDates = new HashSet<>();
-
- /**
- * Set of user privileges.
- */
- @OneToMany(fetch = FetchType.EAGER, mappedBy = "user", orphanRemoval = true, cascade = CascadeType.ALL)
- private Set<BasicPrivilege> privileges = new HashSet<>();
-
- /**
- * Default annotations schema used by this user.
- */
- @OneToOne(cascade = CascadeType.ALL)
- @JoinColumn(nullable = true)
- private UserAnnotationSchema annotationSchema;
-
- /**
- * Default constructor.
- */
- public User() {
- }
-
- /**
- * Adds privilege to the user.
- *
- * @param privilege
- * privilege to add
- */
- public void addPrivilege(BasicPrivilege privilege) {
- privileges.add(privilege);
- }
-
- /**
- * @return the id
- * @see #id
- */
- public Integer getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(Integer id) {
- this.id = id;
- }
-
- /**
- * @return the login
- * @see #login
- */
- public String getLogin() {
- return login;
- }
-
- /**
- * @param login
- * the login to set
- * @see #login
- */
- public void setLogin(String login) {
- this.login = login;
- }
-
- /**
- * @return the cryptedPassword
- * @see #cryptedPassword
- */
- public String getCryptedPassword() {
- return cryptedPassword;
- }
-
- /**
- * @param cryptedPassword
- * the cryptedPassword to set
- * @see #cryptedPassword
- */
- public void setCryptedPassword(String cryptedPassword) {
- this.cryptedPassword = cryptedPassword;
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return the surname
- * @see #surname
- */
- public String getSurname() {
- return surname;
- }
-
- /**
- * @param surname
- * the surname to set
- * @see #surname
- */
- public void setSurname(String surname) {
- this.surname = surname;
- }
-
- /**
- * @return the email
- * @see #email
- */
- public String getEmail() {
- return email;
- }
-
- /**
- * @param email
- * the email to set
- * @see #email
- */
- public void setEmail(String email) {
- this.email = email;
- }
-
- /**
- * @return the privileges
- * @see #privileges
- */
- public Set<BasicPrivilege> getPrivileges() {
- return privileges;
- }
-
- /**
- * @param privileges
- * the privileges to set
- * @see #privileges
- */
- public void setPrivileges(Set<BasicPrivilege> privileges) {
- this.privileges = privileges;
- }
-
- /**
- * @return the removed
- * @see #removed
- */
- public boolean isRemoved() {
- return removed;
- }
-
- /**
- * @param removed
- * the removed to set
- * @see #removed
- */
- public void setRemoved(boolean removed) {
- this.removed = removed;
- }
-
- /**
- * @return the annotationSchema
- * @see #annotationSchema
- */
- public UserAnnotationSchema getAnnotationSchema() {
- return annotationSchema;
- }
-
- /**
- * @param annotationSchema
- * the annotationSchema to set
- * @see #annotationSchema
- */
- public void setAnnotationSchema(UserAnnotationSchema annotationSchema) {
- this.annotationSchema = annotationSchema;
- if (!this.equals(annotationSchema.getUser())) {
- annotationSchema.setUser(this);
- }
- }
-
- @Override
- public String toString() {
- return "[" + this.getClass().getSimpleName() + "] " + getName() + " " + getSurname();
- }
-
- /**
- * @return the minColor
- * @see #minColor
- */
- public Color getMinColor() {
- return minColor;
- }
-
- /**
- * @param minColor
- * the minColor to set
- * @see #minColor
- */
- public void setMinColor(Color minColor) {
- this.minColor = minColor;
- }
-
- /**
- * @return the maxColor
- * @see #maxColor
- */
- public Color getMaxColor() {
- return maxColor;
- }
-
- /**
- * @param maxColor
- * the maxColor to set
- * @see #maxColor
- */
- public void setMaxColor(Color maxColor) {
- this.maxColor = maxColor;
- }
-
- /**
- * @return the simpleColor
- * @see #simpleColor
- */
- public Color getSimpleColor() {
- return simpleColor;
- }
-
- /**
- * @param simpleColor
- * the simpleColor to set
- * @see #simpleColor
- */
- public void setSimpleColor(Color simpleColor) {
- this.simpleColor = simpleColor;
- }
-
- public Color getNeutralColor() {
- return neutralColor;
- }
-
- public void setNeutralColor(Color neutralColor) {
- this.neutralColor = neutralColor;
- }
-
- public boolean isTermsOfUseConsent() {
- return termsOfUseConsent;
- }
-
- public void setTermsOfUseConsent(boolean termsOfUseConsent) {
- if (!this.termsOfUseConsent && termsOfUseConsent) {
- this.getTermsOfUseConsentDates().add(Calendar.getInstance());
- }
- this.termsOfUseConsent = termsOfUseConsent;
- }
-
- public boolean isConnectedToLdap() {
- return connectedToLdap;
- }
-
- public void setConnectedToLdap(boolean connectedToLdap) {
- this.connectedToLdap = connectedToLdap;
- }
-
- public Set<Calendar> getTermsOfUseConsentDates() {
- return termsOfUseConsentDates;
- }
-
- public void setTermsOfUseConsentDates(Set<Calendar> termsOfUseConsentDates) {
- this.termsOfUseConsentDates = termsOfUseConsentDates;
- }
-
-}
+package lcsb.mapviewer.model.user;
+
+import java.awt.Color;
+import java.io.Serializable;
+import java.util.Calendar;
+import java.util.Comparator;
+import java.util.HashSet;
+import java.util.Set;
+
+import javax.persistence.CascadeType;
+import javax.persistence.CollectionTable;
+import javax.persistence.Column;
+import javax.persistence.ElementCollection;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.OneToMany;
+import javax.persistence.OneToOne;
+import javax.persistence.Table;
+
+import org.hibernate.annotations.Cascade;
+
+import lcsb.mapviewer.common.comparator.StringComparator;
+
+/**
+ * Class representing user.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "user_table")
+public class User implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ public static final Comparator<? super User> LOGIN_COMPARATOR = new Comparator<User>() {
+
+ @Override
+ public int compare(User o1, User o2) {
+ String login1 = null;
+ String login2 = null;
+ if (o1 != null) {
+ login1 = o1.getLogin();
+ }
+ if (o2 != null) {
+ login2 = o2.getLogin();
+ }
+ return new StringComparator().compare(login1, login2);
+ }
+ };
+
+ /**
+ * Unique identifier in the database.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private Integer id;
+
+ /**
+ * User login.
+ */
+ private String login;
+
+ /**
+ * Password in encrypted form. For the encryption PasswordEncoder spring bean is
+ * used.
+ */
+ private String cryptedPassword;
+
+ /**
+ * Name of the user.
+ */
+ private String name;
+
+ /**
+ * Family name of the user.
+ */
+ private String surname;
+
+ /**
+ * Email address of the user.
+ */
+ private String email;
+
+ /**
+ * User defined color overriding system
+ * {@link ConfigurationElementType#MIN_COLOR_VAL}. Used for coloring minimum
+ * values in overlays.
+ */
+ private Color minColor;
+
+ /**
+ * User defined color overriding system
+ * {@link ConfigurationElementType#MAX_COLOR_VAL}. Used for coloring maximum
+ * values in overlays.
+ */
+ private Color maxColor;
+
+ /**
+ * User defined color overriding system
+ * {@link ConfigurationElementType#NEUTRAL_COLOR_VAL}. Used for coloring neutral
+ * values (0) in overlays.
+ */
+ private Color neutralColor;
+
+ /**
+ * User defined color overriding system
+ * {@link ConfigurationElementType#SIMPLE_COLOR_VAL}. Used for coloring overlays
+ * without values and colors.
+ */
+ private Color simpleColor;
+
+ /**
+ * Is the user removed.
+ */
+ private boolean removed = false;
+
+ /**
+ * User is connected to LDAP directory.
+ */
+ private boolean connectedToLdap = false;
+
+ @Column(name = "terms_of_use_consent")
+ private boolean termsOfUseConsent = false;
+
+ @ElementCollection(fetch = FetchType.EAGER)
+ @CollectionTable(name = "user_terms_of_use_consent", joinColumns = @JoinColumn(name = "user_iddb"))
+ @Column(name = "date")
+ @Cascade({ org.hibernate.annotations.CascadeType.ALL })
+ private Set<Calendar> termsOfUseConsentDates = new HashSet<>();
+
+ /**
+ * Set of user privileges.
+ */
+ @OneToMany(fetch = FetchType.EAGER, mappedBy = "user", orphanRemoval = true, cascade = CascadeType.ALL)
+ private Set<BasicPrivilege> privileges = new HashSet<>();
+
+ /**
+ * Default annotations schema used by this user.
+ */
+ @OneToOne(cascade = CascadeType.ALL)
+ @JoinColumn(nullable = true)
+ private UserAnnotationSchema annotationSchema;
+
+ /**
+ * Default constructor.
+ */
+ public User() {
+ }
+
+ /**
+ * Adds privilege to the user.
+ *
+ * @param privilege
+ * privilege to add
+ */
+ public void addPrivilege(BasicPrivilege privilege) {
+ privileges.add(privilege);
+ }
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public Integer getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(Integer id) {
+ this.id = id;
+ }
+
+ /**
+ * @return the login
+ * @see #login
+ */
+ public String getLogin() {
+ return login;
+ }
+
+ /**
+ * @param login
+ * the login to set
+ * @see #login
+ */
+ public void setLogin(String login) {
+ this.login = login;
+ }
+
+ /**
+ * @return the cryptedPassword
+ * @see #cryptedPassword
+ */
+ public String getCryptedPassword() {
+ return cryptedPassword;
+ }
+
+ /**
+ * @param cryptedPassword
+ * the cryptedPassword to set
+ * @see #cryptedPassword
+ */
+ public void setCryptedPassword(String cryptedPassword) {
+ this.cryptedPassword = cryptedPassword;
+ }
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * @return the surname
+ * @see #surname
+ */
+ public String getSurname() {
+ return surname;
+ }
+
+ /**
+ * @param surname
+ * the surname to set
+ * @see #surname
+ */
+ public void setSurname(String surname) {
+ this.surname = surname;
+ }
+
+ /**
+ * @return the email
+ * @see #email
+ */
+ public String getEmail() {
+ return email;
+ }
+
+ /**
+ * @param email
+ * the email to set
+ * @see #email
+ */
+ public void setEmail(String email) {
+ this.email = email;
+ }
+
+ /**
+ * @return the privileges
+ * @see #privileges
+ */
+ public Set<BasicPrivilege> getPrivileges() {
+ return privileges;
+ }
+
+ /**
+ * @param privileges
+ * the privileges to set
+ * @see #privileges
+ */
+ public void setPrivileges(Set<BasicPrivilege> privileges) {
+ this.privileges = privileges;
+ }
+
+ /**
+ * @return the removed
+ * @see #removed
+ */
+ public boolean isRemoved() {
+ return removed;
+ }
+
+ /**
+ * @param removed
+ * the removed to set
+ * @see #removed
+ */
+ public void setRemoved(boolean removed) {
+ this.removed = removed;
+ }
+
+ /**
+ * @return the annotationSchema
+ * @see #annotationSchema
+ */
+ public UserAnnotationSchema getAnnotationSchema() {
+ return annotationSchema;
+ }
+
+ /**
+ * @param annotationSchema
+ * the annotationSchema to set
+ * @see #annotationSchema
+ */
+ public void setAnnotationSchema(UserAnnotationSchema annotationSchema) {
+ this.annotationSchema = annotationSchema;
+ if (!this.equals(annotationSchema.getUser())) {
+ annotationSchema.setUser(this);
+ }
+ }
+
+ @Override
+ public String toString() {
+ return "[" + this.getClass().getSimpleName() + "] " + getName() + " " + getSurname();
+ }
+
+ /**
+ * @return the minColor
+ * @see #minColor
+ */
+ public Color getMinColor() {
+ return minColor;
+ }
+
+ /**
+ * @param minColor
+ * the minColor to set
+ * @see #minColor
+ */
+ public void setMinColor(Color minColor) {
+ this.minColor = minColor;
+ }
+
+ /**
+ * @return the maxColor
+ * @see #maxColor
+ */
+ public Color getMaxColor() {
+ return maxColor;
+ }
+
+ /**
+ * @param maxColor
+ * the maxColor to set
+ * @see #maxColor
+ */
+ public void setMaxColor(Color maxColor) {
+ this.maxColor = maxColor;
+ }
+
+ /**
+ * @return the simpleColor
+ * @see #simpleColor
+ */
+ public Color getSimpleColor() {
+ return simpleColor;
+ }
+
+ /**
+ * @param simpleColor
+ * the simpleColor to set
+ * @see #simpleColor
+ */
+ public void setSimpleColor(Color simpleColor) {
+ this.simpleColor = simpleColor;
+ }
+
+ public Color getNeutralColor() {
+ return neutralColor;
+ }
+
+ public void setNeutralColor(Color neutralColor) {
+ this.neutralColor = neutralColor;
+ }
+
+ public boolean isTermsOfUseConsent() {
+ return termsOfUseConsent;
+ }
+
+ public void setTermsOfUseConsent(boolean termsOfUseConsent) {
+ if (!this.termsOfUseConsent && termsOfUseConsent) {
+ this.getTermsOfUseConsentDates().add(Calendar.getInstance());
+ }
+ this.termsOfUseConsent = termsOfUseConsent;
+ }
+
+ public boolean isConnectedToLdap() {
+ return connectedToLdap;
+ }
+
+ public void setConnectedToLdap(boolean connectedToLdap) {
+ this.connectedToLdap = connectedToLdap;
+ }
+
+ public Set<Calendar> getTermsOfUseConsentDates() {
+ return termsOfUseConsentDates;
+ }
+
+ public void setTermsOfUseConsentDates(Set<Calendar> termsOfUseConsentDates) {
+ this.termsOfUseConsentDates = termsOfUseConsentDates;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/UserAnnotationSchema.java b/model/src/main/java/lcsb/mapviewer/model/user/UserAnnotationSchema.java
index afe8badee0..11dfdeafeb 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/UserAnnotationSchema.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/UserAnnotationSchema.java
@@ -1,540 +1,540 @@
-package lcsb.mapviewer.model.user;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.OneToMany;
-import javax.persistence.OneToOne;
-import javax.persistence.OrderBy;
-import javax.persistence.Table;
-import javax.persistence.Transient;
-
-import org.apache.log4j.Logger;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.MiriamType;
-
-/**
- * Annotation schema used by the user. It contains information about annotators
- * used by the user. Which annotations are valid/required for given object
- * types.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "user_annotation_schema_table")
-public class UserAnnotationSchema implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @Transient
- private final transient Logger logger = Logger.getLogger(UserAnnotationSchema.class);
-
- /**
- * Unique identifier in the database.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private Integer id;
-
- /**
- * {@link User} for which annotation schema is defined.
- */
- @OneToOne
- private User user;
-
- /**
- * Should the miriam types be validated?
- */
- private Boolean validateMiriamTypes = false;
-
- private Boolean annotateModel = false;
-
- private Boolean cacheData = false;
-
- private Boolean autoResizeMap = true;
-
- private Boolean semanticZooming = false;
- private Boolean semanticZoomContainsMultipleOverlays = false;
-
- /**
- * Should map be visualized as sbgn?
- */
- private Boolean sbgnFormat = false;
-
- /**
- * Should the default view be network (if not then it will be pathways and
- * compartments)?
- */
- private Boolean networkLayoutAsDefault = false;
-
- /**
- * List of class annotators for specific object types.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(mappedBy = "annotationSchema")
- @OrderBy("id")
- private List<UserClassAnnotators> classAnnotators = new ArrayList<>();
-
- /**
- * List of class annotators params.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(mappedBy = "annotationSchema")
- @OrderBy("id")
- private List<UserAnnotatorsParam> annotatorsParams = new ArrayList<>();
-
- /**
- * List of valid annotations for given object type.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(mappedBy = "annotationSchema")
- @OrderBy("id")
- private List<UserClassValidAnnotations> classValidAnnotators = new ArrayList<>();
-
- /**
- * List of required annotations for given object type.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(mappedBy = "annotationSchema")
- @OrderBy("id")
- private List<UserClassRequiredAnnotations> classRequiredAnnotators = new ArrayList<>();
-
- @Cascade({ CascadeType.ALL })
- @OneToMany(mappedBy = "annotationSchema")
- private Set<UserGuiPreference> guiPreferences = new HashSet<>();
-
- /**
- * @return the user
- * @see #user
- */
- public User getUser() {
- return user;
- }
-
- /**
- * @param user
- * the user to set
- * @see #user
- */
- public void setUser(User user) {
- this.user = user;
- }
-
- /**
- * @return the validateMiriamTypes
- * @see #validateMiriamTypes
- */
- public Boolean getValidateMiriamTypes() {
- return validateMiriamTypes;
- }
-
- /**
- * @param validateMiriamTypes
- * the validateMiriamTypes to set
- * @see #validateMiriamTypes
- */
- public void setValidateMiriamTypes(Boolean validateMiriamTypes) {
- this.validateMiriamTypes = validateMiriamTypes;
- }
-
- /**
- * @return the classAnnotators
- * @see #classAnnotators
- */
- public List<UserClassAnnotators> getClassAnnotators() {
- return classAnnotators;
- }
-
- /**
- * @param classAnnotators
- * the classAnnotators to set
- * @see #classAnnotators
- */
- public void setClassAnnotators(List<UserClassAnnotators> classAnnotators) {
- this.classAnnotators = classAnnotators;
- }
-
- /**
- * @return the annotatorsParams
- */
- public List<UserAnnotatorsParam> getAnnotatorsParams() {
- return annotatorsParams;
- }
-
- /**
- * @param annotatorsParams
- * the annotatorsParams to set
- */
- public void setAnnotatorsParams(List<UserAnnotatorsParam> annotatorsParams) {
- this.annotatorsParams = annotatorsParams;
- }
-
- /**
- * @return the classValidAnnotators
- * @see #classValidAnnotators
- */
- public List<UserClassValidAnnotations> getClassValidAnnotators() {
- return classValidAnnotators;
- }
-
- /**
- * @param classValidAnnotators
- * the classValidAnnotators to set
- * @see #classValidAnnotators
- */
- public void setClassValidAnnotators(List<UserClassValidAnnotations> classValidAnnotators) {
- this.classValidAnnotators = classValidAnnotators;
- }
-
- /**
- * Adds (or updates) {@link UserClassAnnotators class annotator} information to
- * {@link #classAnnotators}.
- *
- * @param ca
- * object to add/update
- */
- public void addClassAnnotator(UserClassAnnotators ca) {
- if (ca.getClassName() == null) {
- throw new InvalidArgumentException("Class name cannot be null");
- }
- boolean replaced = false;
- for (int i = 0; i < this.classAnnotators.size(); i++) {
- UserClassAnnotators annotators = this.classAnnotators.get(i);
- if (annotators.getClassName().equals(ca.getClassName())) {
- annotators.setAnnotationSchema(null);
- this.classAnnotators.set(i, ca);
- replaced = true;
- }
- }
- if (!replaced) {
- classAnnotators.add(ca);
- }
- ca.setAnnotationSchema(this);
- }
-
- /**
- * Adds (or updates) {@link UserAnnotatorsParam} information to
- * {@link #annotatorsParams}.
- *
- * @param ap
- * object to add/update
- */
- public void addAnnotatorParam(UserAnnotatorsParam ap) {
- if (ap.getAnnotatorClassName() == null) {
- throw new InvalidArgumentException("Class name cannot be null");
- }
- if (ap.getParamName() == null) {
- throw new InvalidArgumentException("Parameter name cannot be null");
- }
- if (ap.getParamValue() == null) {
- throw new InvalidArgumentException("Parameter value cannot be null");
- }
-
- for (int i = 0; i < this.annotatorsParams.size(); i++) {
- UserAnnotatorsParam params = this.annotatorsParams.get(i);
- if (params.getAnnotatorClassName().equals(ap.getAnnotatorClassName())
- && params.getParamName().equals(ap.getParamName())) {
- this.annotatorsParams.get(i).setParamValue(ap.getParamValue());
- return;
- }
- }
-
- ap.setAnnotationSchema(this);
- this.annotatorsParams.add(ap);
- }
-
- /**
- * Adds (or updates) {@link UserClassValidAnnotations valid annotation}
- * information to {@link #classValidAnnotators}.
- *
- * @param cva
- * object to add/update
- */
- public void addClassValidAnnotations(UserClassValidAnnotations cva) {
- if (cva.getClassName() == null) {
- throw new InvalidArgumentException("Class name cannot be null");
- }
- boolean replaced = false;
- for (int i = 0; i < this.classValidAnnotators.size(); i++) {
- UserClassValidAnnotations annotators = this.classValidAnnotators.get(i);
- if (annotators.getClassName().equals(cva.getClassName())) {
- annotators.setAnnotationSchema(null);
- this.classValidAnnotators.set(i, cva);
- replaced = true;
- }
- }
- if (!replaced) {
- classValidAnnotators.add(cva);
- }
- cva.setAnnotationSchema(this);
- }
-
- /**
- * Returns list of annotators for given object type.
- *
- * @param clazz
- * type of object
- * @return list of annotators names
- */
- public List<String> getAnnotatorsForClass(Class<?> clazz) {
- List<String> result = new ArrayList<String>();
- for (UserClassAnnotators ca : classAnnotators) {
- if (ca.getClassName().equals(clazz.getCanonicalName())) {
- result = ca.getAnnotators();
- }
- }
- return result;
- }
-
- /**
- * Return list of valid annotation types for given class.
- *
- * @param clazz
- * type of the object for which result is returned
- * @return list of valid annotation types
- */
- public Collection<MiriamType> getValidAnnotations(Class<?> clazz) {
- for (UserClassValidAnnotations cva : classValidAnnotators) {
- if (cva.getClassName().equals(clazz.getCanonicalName())) {
- return cva.getValidMiriamTypes();
- }
- }
- return new ArrayList<MiriamType>();
- }
-
- /**
- * Return list of required annotation types for given class.
- *
- * @param clazz
- * type of the object for which result is returned
- * @return list of requried annotation types
- */
- public Collection<MiriamType> getRequiredAnnotations(Class<?> clazz) {
- for (UserClassRequiredAnnotations cva : classRequiredAnnotators) {
- if (cva.getClassName().equals(clazz.getCanonicalName())) {
- return cva.getRequiredMiriamTypes();
- }
- }
- return new ArrayList<MiriamType>();
- }
-
- public boolean requiresAtLeastOneAnnotation(Class<?> clazz) {
- for (UserClassRequiredAnnotations cva : classRequiredAnnotators) {
- if (cva.getClassName().equals(clazz.getCanonicalName())) {
- return cva.getRequireAtLeastOneAnnotation();
- }
- }
- return false;
- }
-
- /**
- * @return the classRequiredAnnotators
- * @see #classRequiredAnnotators
- */
- public List<UserClassRequiredAnnotations> getClassRequiredAnnotators() {
- return classRequiredAnnotators;
- }
-
- /**
- * @param classRequiredAnnotators
- * the classRequiredAnnotators to set
- * @see #classRequiredAnnotators
- */
- public void setClassRequiredAnnotators(List<UserClassRequiredAnnotations> classRequiredAnnotators) {
- this.classRequiredAnnotators = classRequiredAnnotators;
- }
-
- /**
- * Adds (or updates) {@link UserClassRequiredAnnotations required annotation}
- * information to {@link #classRequiredAnnotators}.
- *
- * @param cra
- * object to add/update
- */
- public void addClassRequiredAnnotations(UserClassRequiredAnnotations cra) {
- if (cra.getClassName() == null) {
- throw new InvalidArgumentException("Class name cannot be null");
- }
- boolean replaced = false;
- for (int i = 0; i < this.classRequiredAnnotators.size(); i++) {
- UserClassRequiredAnnotations annotators = this.classRequiredAnnotators.get(i);
- if (annotators.getClassName().equals(cra.getClassName())) {
- annotators.setAnnotationSchema(null);
- this.classRequiredAnnotators.set(i, cra);
- replaced = true;
- }
- }
- if (!replaced) {
- this.classRequiredAnnotators.add(cra);
- }
- cra.setAnnotationSchema(this);
- }
-
- /**
- * @return the sbgnFormat
- * @see #sbgnFormat
- */
- public Boolean getSbgnFormat() {
- return sbgnFormat;
- }
-
- /**
- * @param sbgnFormat
- * the sbgnFormat to set
- * @see #sbgnFormat
- */
- public void setSbgnFormat(Boolean sbgnFormat) {
- this.sbgnFormat = sbgnFormat;
- }
-
- /**
- * @return the networkLayoutAsDefault
- * @see #networkLayoutAsDefault
- */
- public Boolean getNetworkLayoutAsDefault() {
- return networkLayoutAsDefault;
- }
-
- /**
- * @param networkLayoutAsDefault
- * the networkLayoutAsDefault to set
- * @see #networkLayoutAsDefault
- */
- public void setNetworkLayoutAsDefault(Boolean networkLayoutAsDefault) {
- this.networkLayoutAsDefault = networkLayoutAsDefault;
- }
-
- /**
- * @return the annotateModel
- * @see #annotateModel
- */
- public Boolean getAnnotateModel() {
- return annotateModel;
- }
-
- /**
- * @param annotateModel
- * the annotateModel to set
- * @see #annotateModel
- */
- public void setAnnotateModel(Boolean annotateModel) {
- this.annotateModel = annotateModel;
- }
-
- /**
- * @return the cacheData
- * @see #cacheData
- */
- public Boolean getCacheData() {
- return cacheData;
- }
-
- /**
- * @param cacheData
- * the cacheData to set
- * @see #cacheData
- */
- public void setCacheData(Boolean cacheData) {
- this.cacheData = cacheData;
- }
-
- /**
- * @return the autoResizeMap
- * @see #autoResizeMap
- */
- public Boolean getAutoResizeMap() {
- return autoResizeMap;
- }
-
- /**
- * @param autoResizeMap
- * the autoResizeMap to set
- * @see #autoResizeMap
- */
- public void setAutoResizeMap(Boolean autoResizeMap) {
- this.autoResizeMap = autoResizeMap;
- }
-
- /**
- * @return the semanticZooming
- * @see #semanticZooming
- */
- public Boolean getSemanticZooming() {
- return semanticZooming;
- }
-
- /**
- * @param semanticZooming
- * the semanticZooming to set
- * @see #semanticZooming
- */
- public void setSemanticZooming(Boolean semanticZooming) {
- this.semanticZooming = semanticZooming;
- }
-
- public Set<UserGuiPreference> getGuiPreferences() {
- return guiPreferences;
- }
-
- public void addGuiPreference(UserGuiPreference option) {
- boolean updated = false;
- for (UserGuiPreference userOption : guiPreferences) {
- if (userOption.getKey().equals(option.getKey())) {
- userOption.setValue(option.getValue());
- updated = true;
- }
- }
- if (!updated) {
- guiPreferences.add(option);
- option.setAnnotationSchema(this);
- }
- }
-
- public UserGuiPreference getGuiPreference(String key) {
- for (UserGuiPreference userOption : guiPreferences) {
- if (userOption.getKey().equals(key)) {
- return userOption;
- }
- }
- return null;
- }
-
- public void setGuiPreference(String key, String value) {
- UserGuiPreference option = getGuiPreference(key);
- if (option == null) {
- option = new UserGuiPreference();
- option.setKey(key);
- addGuiPreference(option);
- }
- option.setValue(value);
- }
-
- public Boolean getSemanticZoomContainsMultipleOverlays() {
- return semanticZoomContainsMultipleOverlays;
- }
-
- public void setSemanticZoomContainsMultipleOverlays(Boolean semanticZoomContainsMultipleOverlays) {
- this.semanticZoomContainsMultipleOverlays = semanticZoomContainsMultipleOverlays;
- }
-
-}
+package lcsb.mapviewer.model.user;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.OneToMany;
+import javax.persistence.OneToOne;
+import javax.persistence.OrderBy;
+import javax.persistence.Table;
+import javax.persistence.Transient;
+
+import org.apache.log4j.Logger;
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.MiriamType;
+
+/**
+ * Annotation schema used by the user. It contains information about annotators
+ * used by the user. Which annotations are valid/required for given object
+ * types.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "user_annotation_schema_table")
+public class UserAnnotationSchema implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @Transient
+ private final transient Logger logger = Logger.getLogger(UserAnnotationSchema.class);
+
+ /**
+ * Unique identifier in the database.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private Integer id;
+
+ /**
+ * {@link User} for which annotation schema is defined.
+ */
+ @OneToOne
+ private User user;
+
+ /**
+ * Should the miriam types be validated?
+ */
+ private Boolean validateMiriamTypes = false;
+
+ private Boolean annotateModel = false;
+
+ private Boolean cacheData = false;
+
+ private Boolean autoResizeMap = true;
+
+ private Boolean semanticZooming = false;
+ private Boolean semanticZoomContainsMultipleOverlays = false;
+
+ /**
+ * Should map be visualized as sbgn?
+ */
+ private Boolean sbgnFormat = false;
+
+ /**
+ * Should the default view be network (if not then it will be pathways and
+ * compartments)?
+ */
+ private Boolean networkLayoutAsDefault = false;
+
+ /**
+ * List of class annotators for specific object types.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(mappedBy = "annotationSchema")
+ @OrderBy("id")
+ private List<UserClassAnnotators> classAnnotators = new ArrayList<>();
+
+ /**
+ * List of class annotators params.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(mappedBy = "annotationSchema")
+ @OrderBy("id")
+ private List<UserAnnotatorsParam> annotatorsParams = new ArrayList<>();
+
+ /**
+ * List of valid annotations for given object type.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(mappedBy = "annotationSchema")
+ @OrderBy("id")
+ private List<UserClassValidAnnotations> classValidAnnotators = new ArrayList<>();
+
+ /**
+ * List of required annotations for given object type.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(mappedBy = "annotationSchema")
+ @OrderBy("id")
+ private List<UserClassRequiredAnnotations> classRequiredAnnotators = new ArrayList<>();
+
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(mappedBy = "annotationSchema")
+ private Set<UserGuiPreference> guiPreferences = new HashSet<>();
+
+ /**
+ * @return the user
+ * @see #user
+ */
+ public User getUser() {
+ return user;
+ }
+
+ /**
+ * @param user
+ * the user to set
+ * @see #user
+ */
+ public void setUser(User user) {
+ this.user = user;
+ }
+
+ /**
+ * @return the validateMiriamTypes
+ * @see #validateMiriamTypes
+ */
+ public Boolean getValidateMiriamTypes() {
+ return validateMiriamTypes;
+ }
+
+ /**
+ * @param validateMiriamTypes
+ * the validateMiriamTypes to set
+ * @see #validateMiriamTypes
+ */
+ public void setValidateMiriamTypes(Boolean validateMiriamTypes) {
+ this.validateMiriamTypes = validateMiriamTypes;
+ }
+
+ /**
+ * @return the classAnnotators
+ * @see #classAnnotators
+ */
+ public List<UserClassAnnotators> getClassAnnotators() {
+ return classAnnotators;
+ }
+
+ /**
+ * @param classAnnotators
+ * the classAnnotators to set
+ * @see #classAnnotators
+ */
+ public void setClassAnnotators(List<UserClassAnnotators> classAnnotators) {
+ this.classAnnotators = classAnnotators;
+ }
+
+ /**
+ * @return the annotatorsParams
+ */
+ public List<UserAnnotatorsParam> getAnnotatorsParams() {
+ return annotatorsParams;
+ }
+
+ /**
+ * @param annotatorsParams
+ * the annotatorsParams to set
+ */
+ public void setAnnotatorsParams(List<UserAnnotatorsParam> annotatorsParams) {
+ this.annotatorsParams = annotatorsParams;
+ }
+
+ /**
+ * @return the classValidAnnotators
+ * @see #classValidAnnotators
+ */
+ public List<UserClassValidAnnotations> getClassValidAnnotators() {
+ return classValidAnnotators;
+ }
+
+ /**
+ * @param classValidAnnotators
+ * the classValidAnnotators to set
+ * @see #classValidAnnotators
+ */
+ public void setClassValidAnnotators(List<UserClassValidAnnotations> classValidAnnotators) {
+ this.classValidAnnotators = classValidAnnotators;
+ }
+
+ /**
+ * Adds (or updates) {@link UserClassAnnotators class annotator} information to
+ * {@link #classAnnotators}.
+ *
+ * @param ca
+ * object to add/update
+ */
+ public void addClassAnnotator(UserClassAnnotators ca) {
+ if (ca.getClassName() == null) {
+ throw new InvalidArgumentException("Class name cannot be null");
+ }
+ boolean replaced = false;
+ for (int i = 0; i < this.classAnnotators.size(); i++) {
+ UserClassAnnotators annotators = this.classAnnotators.get(i);
+ if (annotators.getClassName().equals(ca.getClassName())) {
+ annotators.setAnnotationSchema(null);
+ this.classAnnotators.set(i, ca);
+ replaced = true;
+ }
+ }
+ if (!replaced) {
+ classAnnotators.add(ca);
+ }
+ ca.setAnnotationSchema(this);
+ }
+
+ /**
+ * Adds (or updates) {@link UserAnnotatorsParam} information to
+ * {@link #annotatorsParams}.
+ *
+ * @param ap
+ * object to add/update
+ */
+ public void addAnnotatorParam(UserAnnotatorsParam ap) {
+ if (ap.getAnnotatorClassName() == null) {
+ throw new InvalidArgumentException("Class name cannot be null");
+ }
+ if (ap.getParamName() == null) {
+ throw new InvalidArgumentException("Parameter name cannot be null");
+ }
+ if (ap.getParamValue() == null) {
+ throw new InvalidArgumentException("Parameter value cannot be null");
+ }
+
+ for (int i = 0; i < this.annotatorsParams.size(); i++) {
+ UserAnnotatorsParam params = this.annotatorsParams.get(i);
+ if (params.getAnnotatorClassName().equals(ap.getAnnotatorClassName())
+ && params.getParamName().equals(ap.getParamName())) {
+ this.annotatorsParams.get(i).setParamValue(ap.getParamValue());
+ return;
+ }
+ }
+
+ ap.setAnnotationSchema(this);
+ this.annotatorsParams.add(ap);
+ }
+
+ /**
+ * Adds (or updates) {@link UserClassValidAnnotations valid annotation}
+ * information to {@link #classValidAnnotators}.
+ *
+ * @param cva
+ * object to add/update
+ */
+ public void addClassValidAnnotations(UserClassValidAnnotations cva) {
+ if (cva.getClassName() == null) {
+ throw new InvalidArgumentException("Class name cannot be null");
+ }
+ boolean replaced = false;
+ for (int i = 0; i < this.classValidAnnotators.size(); i++) {
+ UserClassValidAnnotations annotators = this.classValidAnnotators.get(i);
+ if (annotators.getClassName().equals(cva.getClassName())) {
+ annotators.setAnnotationSchema(null);
+ this.classValidAnnotators.set(i, cva);
+ replaced = true;
+ }
+ }
+ if (!replaced) {
+ classValidAnnotators.add(cva);
+ }
+ cva.setAnnotationSchema(this);
+ }
+
+ /**
+ * Returns list of annotators for given object type.
+ *
+ * @param clazz
+ * type of object
+ * @return list of annotators names
+ */
+ public List<String> getAnnotatorsForClass(Class<?> clazz) {
+ List<String> result = new ArrayList<String>();
+ for (UserClassAnnotators ca : classAnnotators) {
+ if (ca.getClassName().equals(clazz.getCanonicalName())) {
+ result = ca.getAnnotators();
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Return list of valid annotation types for given class.
+ *
+ * @param clazz
+ * type of the object for which result is returned
+ * @return list of valid annotation types
+ */
+ public Collection<MiriamType> getValidAnnotations(Class<?> clazz) {
+ for (UserClassValidAnnotations cva : classValidAnnotators) {
+ if (cva.getClassName().equals(clazz.getCanonicalName())) {
+ return cva.getValidMiriamTypes();
+ }
+ }
+ return new ArrayList<MiriamType>();
+ }
+
+ /**
+ * Return list of required annotation types for given class.
+ *
+ * @param clazz
+ * type of the object for which result is returned
+ * @return list of requried annotation types
+ */
+ public Collection<MiriamType> getRequiredAnnotations(Class<?> clazz) {
+ for (UserClassRequiredAnnotations cva : classRequiredAnnotators) {
+ if (cva.getClassName().equals(clazz.getCanonicalName())) {
+ return cva.getRequiredMiriamTypes();
+ }
+ }
+ return new ArrayList<MiriamType>();
+ }
+
+ public boolean requiresAtLeastOneAnnotation(Class<?> clazz) {
+ for (UserClassRequiredAnnotations cva : classRequiredAnnotators) {
+ if (cva.getClassName().equals(clazz.getCanonicalName())) {
+ return cva.getRequireAtLeastOneAnnotation();
+ }
+ }
+ return false;
+ }
+
+ /**
+ * @return the classRequiredAnnotators
+ * @see #classRequiredAnnotators
+ */
+ public List<UserClassRequiredAnnotations> getClassRequiredAnnotators() {
+ return classRequiredAnnotators;
+ }
+
+ /**
+ * @param classRequiredAnnotators
+ * the classRequiredAnnotators to set
+ * @see #classRequiredAnnotators
+ */
+ public void setClassRequiredAnnotators(List<UserClassRequiredAnnotations> classRequiredAnnotators) {
+ this.classRequiredAnnotators = classRequiredAnnotators;
+ }
+
+ /**
+ * Adds (or updates) {@link UserClassRequiredAnnotations required annotation}
+ * information to {@link #classRequiredAnnotators}.
+ *
+ * @param cra
+ * object to add/update
+ */
+ public void addClassRequiredAnnotations(UserClassRequiredAnnotations cra) {
+ if (cra.getClassName() == null) {
+ throw new InvalidArgumentException("Class name cannot be null");
+ }
+ boolean replaced = false;
+ for (int i = 0; i < this.classRequiredAnnotators.size(); i++) {
+ UserClassRequiredAnnotations annotators = this.classRequiredAnnotators.get(i);
+ if (annotators.getClassName().equals(cra.getClassName())) {
+ annotators.setAnnotationSchema(null);
+ this.classRequiredAnnotators.set(i, cra);
+ replaced = true;
+ }
+ }
+ if (!replaced) {
+ this.classRequiredAnnotators.add(cra);
+ }
+ cra.setAnnotationSchema(this);
+ }
+
+ /**
+ * @return the sbgnFormat
+ * @see #sbgnFormat
+ */
+ public Boolean getSbgnFormat() {
+ return sbgnFormat;
+ }
+
+ /**
+ * @param sbgnFormat
+ * the sbgnFormat to set
+ * @see #sbgnFormat
+ */
+ public void setSbgnFormat(Boolean sbgnFormat) {
+ this.sbgnFormat = sbgnFormat;
+ }
+
+ /**
+ * @return the networkLayoutAsDefault
+ * @see #networkLayoutAsDefault
+ */
+ public Boolean getNetworkLayoutAsDefault() {
+ return networkLayoutAsDefault;
+ }
+
+ /**
+ * @param networkLayoutAsDefault
+ * the networkLayoutAsDefault to set
+ * @see #networkLayoutAsDefault
+ */
+ public void setNetworkLayoutAsDefault(Boolean networkLayoutAsDefault) {
+ this.networkLayoutAsDefault = networkLayoutAsDefault;
+ }
+
+ /**
+ * @return the annotateModel
+ * @see #annotateModel
+ */
+ public Boolean getAnnotateModel() {
+ return annotateModel;
+ }
+
+ /**
+ * @param annotateModel
+ * the annotateModel to set
+ * @see #annotateModel
+ */
+ public void setAnnotateModel(Boolean annotateModel) {
+ this.annotateModel = annotateModel;
+ }
+
+ /**
+ * @return the cacheData
+ * @see #cacheData
+ */
+ public Boolean getCacheData() {
+ return cacheData;
+ }
+
+ /**
+ * @param cacheData
+ * the cacheData to set
+ * @see #cacheData
+ */
+ public void setCacheData(Boolean cacheData) {
+ this.cacheData = cacheData;
+ }
+
+ /**
+ * @return the autoResizeMap
+ * @see #autoResizeMap
+ */
+ public Boolean getAutoResizeMap() {
+ return autoResizeMap;
+ }
+
+ /**
+ * @param autoResizeMap
+ * the autoResizeMap to set
+ * @see #autoResizeMap
+ */
+ public void setAutoResizeMap(Boolean autoResizeMap) {
+ this.autoResizeMap = autoResizeMap;
+ }
+
+ /**
+ * @return the semanticZooming
+ * @see #semanticZooming
+ */
+ public Boolean getSemanticZooming() {
+ return semanticZooming;
+ }
+
+ /**
+ * @param semanticZooming
+ * the semanticZooming to set
+ * @see #semanticZooming
+ */
+ public void setSemanticZooming(Boolean semanticZooming) {
+ this.semanticZooming = semanticZooming;
+ }
+
+ public Set<UserGuiPreference> getGuiPreferences() {
+ return guiPreferences;
+ }
+
+ public void addGuiPreference(UserGuiPreference option) {
+ boolean updated = false;
+ for (UserGuiPreference userOption : guiPreferences) {
+ if (userOption.getKey().equals(option.getKey())) {
+ userOption.setValue(option.getValue());
+ updated = true;
+ }
+ }
+ if (!updated) {
+ guiPreferences.add(option);
+ option.setAnnotationSchema(this);
+ }
+ }
+
+ public UserGuiPreference getGuiPreference(String key) {
+ for (UserGuiPreference userOption : guiPreferences) {
+ if (userOption.getKey().equals(key)) {
+ return userOption;
+ }
+ }
+ return null;
+ }
+
+ public void setGuiPreference(String key, String value) {
+ UserGuiPreference option = getGuiPreference(key);
+ if (option == null) {
+ option = new UserGuiPreference();
+ option.setKey(key);
+ addGuiPreference(option);
+ }
+ option.setValue(value);
+ }
+
+ public Boolean getSemanticZoomContainsMultipleOverlays() {
+ return semanticZoomContainsMultipleOverlays;
+ }
+
+ public void setSemanticZoomContainsMultipleOverlays(Boolean semanticZoomContainsMultipleOverlays) {
+ this.semanticZoomContainsMultipleOverlays = semanticZoomContainsMultipleOverlays;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/UserClassAnnotators.java b/model/src/main/java/lcsb/mapviewer/model/user/UserClassAnnotators.java
index d0d7f2753a..de1b067eeb 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/UserClassAnnotators.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/UserClassAnnotators.java
@@ -1,175 +1,175 @@
-package lcsb.mapviewer.model.user;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import javax.persistence.CollectionTable;
-import javax.persistence.Column;
-import javax.persistence.ElementCollection;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-
-import org.hibernate.annotations.IndexColumn;
-
-/**
- * This class defines set of default class annotatators for a single class type
- * that are used by a user.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "class_annotator_table")
-public class UserClassAnnotators implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Unique identifier in the database.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private Integer id;
-
- /**
- * {@link UserAnnotationSchema} that defines which user is using this set of
- * annotators.
- */
- @ManyToOne
- private UserAnnotationSchema annotationSchema;
-
- /**
- * Class for which this set of annotators is defined.
- */
- private String className;
-
- /**
- * List of strings defining set of annotators (canonical class names).
- */
- @ElementCollection
- @CollectionTable(name = "class_annotator_annotators_table", joinColumns = @JoinColumn(name = "class_annotator_iddb"))
- @IndexColumn(name = "idx")
- @Column(name = "annotator_name")
- private List<String> annotators = new ArrayList<>();
-
- /**
- * Default constructor.
- */
- public UserClassAnnotators() {
-
- }
-
- /**
- * Default constructor.
- *
- * @param objectClass
- * {@link #className}
- * @param annotators
- * {@link #annotators}
- */
- public UserClassAnnotators(Class<?> objectClass, Collection<String> annotators) {
- setClassName(objectClass);
- for (String className : annotators) {
- this.annotators.add(className);
- }
- }
-
- /**
- * @return the id
- * @see #id
- */
- public Integer getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(Integer id) {
- this.id = id;
- }
-
- /**
- * @return the annotationSchema
- * @see #annotationSchema
- */
- public UserAnnotationSchema getAnnotationSchema() {
- return annotationSchema;
- }
-
- /**
- * @param annotationSchema
- * the annotationSchema to set
- * @see #annotationSchema
- */
- public void setAnnotationSchema(UserAnnotationSchema annotationSchema) {
- this.annotationSchema = annotationSchema;
- }
-
- /**
- * @return the className
- * @see #className
- */
- public String getClassName() {
- return className;
- }
-
- /**
- * @param className
- * the className to set
- * @see #className
- */
- public void setClassName(String className) {
- this.className = className;
- }
-
- /**
- * @return the annotators
- * @see #annotators
- */
- public List<String> getAnnotators() {
- return annotators;
- }
-
- /**
- * @param annotators
- * the annotators to set
- * @see #annotators
- */
- public void setAnnotators(List<String> annotators) {
- this.annotators = annotators;
- }
-
- /**
- * Sets {@link #className}.
- *
- * @param clazz
- * new {@link #className} value
- */
- public void setClassName(Class<?> clazz) {
- setClassName(clazz.getCanonicalName());
- }
-
- /**
- * Adds annotator to {@link #annotators list of annotators}.
- *
- * @param clazz
- * object to add
- */
- public void addAnnotator(Class<?> clazz) {
- annotators.add(clazz.getCanonicalName());
- }
-}
+package lcsb.mapviewer.model.user;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import javax.persistence.CollectionTable;
+import javax.persistence.Column;
+import javax.persistence.ElementCollection;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+
+import org.hibernate.annotations.IndexColumn;
+
+/**
+ * This class defines set of default class annotatators for a single class type
+ * that are used by a user.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "class_annotator_table")
+public class UserClassAnnotators implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Unique identifier in the database.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private Integer id;
+
+ /**
+ * {@link UserAnnotationSchema} that defines which user is using this set of
+ * annotators.
+ */
+ @ManyToOne
+ private UserAnnotationSchema annotationSchema;
+
+ /**
+ * Class for which this set of annotators is defined.
+ */
+ private String className;
+
+ /**
+ * List of strings defining set of annotators (canonical class names).
+ */
+ @ElementCollection
+ @CollectionTable(name = "class_annotator_annotators_table", joinColumns = @JoinColumn(name = "class_annotator_iddb"))
+ @IndexColumn(name = "idx")
+ @Column(name = "annotator_name")
+ private List<String> annotators = new ArrayList<>();
+
+ /**
+ * Default constructor.
+ */
+ public UserClassAnnotators() {
+
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param objectClass
+ * {@link #className}
+ * @param annotators
+ * {@link #annotators}
+ */
+ public UserClassAnnotators(Class<?> objectClass, Collection<String> annotators) {
+ setClassName(objectClass);
+ for (String className : annotators) {
+ this.annotators.add(className);
+ }
+ }
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public Integer getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(Integer id) {
+ this.id = id;
+ }
+
+ /**
+ * @return the annotationSchema
+ * @see #annotationSchema
+ */
+ public UserAnnotationSchema getAnnotationSchema() {
+ return annotationSchema;
+ }
+
+ /**
+ * @param annotationSchema
+ * the annotationSchema to set
+ * @see #annotationSchema
+ */
+ public void setAnnotationSchema(UserAnnotationSchema annotationSchema) {
+ this.annotationSchema = annotationSchema;
+ }
+
+ /**
+ * @return the className
+ * @see #className
+ */
+ public String getClassName() {
+ return className;
+ }
+
+ /**
+ * @param className
+ * the className to set
+ * @see #className
+ */
+ public void setClassName(String className) {
+ this.className = className;
+ }
+
+ /**
+ * @return the annotators
+ * @see #annotators
+ */
+ public List<String> getAnnotators() {
+ return annotators;
+ }
+
+ /**
+ * @param annotators
+ * the annotators to set
+ * @see #annotators
+ */
+ public void setAnnotators(List<String> annotators) {
+ this.annotators = annotators;
+ }
+
+ /**
+ * Sets {@link #className}.
+ *
+ * @param clazz
+ * new {@link #className} value
+ */
+ public void setClassName(Class<?> clazz) {
+ setClassName(clazz.getCanonicalName());
+ }
+
+ /**
+ * Adds annotator to {@link #annotators list of annotators}.
+ *
+ * @param clazz
+ * object to add
+ */
+ public void addAnnotator(Class<?> clazz) {
+ annotators.add(clazz.getCanonicalName());
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/UserClassRequiredAnnotations.java b/model/src/main/java/lcsb/mapviewer/model/user/UserClassRequiredAnnotations.java
index 31665d2109..1f4a573027 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/UserClassRequiredAnnotations.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/UserClassRequiredAnnotations.java
@@ -1,230 +1,230 @@
-package lcsb.mapviewer.model.user;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import javax.persistence.Column;
-import javax.persistence.ElementCollection;
-import javax.persistence.Entity;
-import javax.persistence.EnumType;
-import javax.persistence.Enumerated;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.JoinTable;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-import javax.persistence.Transient;
-
-import org.apache.log4j.Logger;
-import org.hibernate.annotations.IndexColumn;
-
-import lcsb.mapviewer.model.map.MiriamType;
-
-/**
- * Defines set of required {@link MiriamType annotations} for a given object
- * type.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "class_required_annotation_table")
-public class UserClassRequiredAnnotations implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Defdault class logger.
- */
- @Transient
- private final transient Logger logger = Logger.getLogger(UserClassRequiredAnnotations.class);
-
- /**
- * Unique identifier in the database.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private Integer id;
-
- /**
- * {@link UserAnnotationSchema} in which this set of required
- * {@link MiriamType annotations} is used.
- */
- @ManyToOne
- private UserAnnotationSchema annotationSchema;
-
- /**
- * Name of the class for which this set is defined.
- */
- private String className;
-
- /**
- * Are the annotations required?
- */
- private Boolean requireAtLeastOneAnnotation;
-
- /**
- * One of this annotations will be required if
- * {@link #requireAtLeastOneAnnotation} is set.
- */
- @ElementCollection
- @JoinTable(name = "class_required_annotation_miriam_type_table", joinColumns = @JoinColumn(name = "class_required_annotation_iddb"))
- @Column(name = "miriam_type_name", nullable = false)
- @IndexColumn(name = "idx")
- @Enumerated(EnumType.STRING)
- private List<MiriamType> requiredMiriamTypes = new ArrayList<>();
-
- /**
- * Default constructor.
- */
- public UserClassRequiredAnnotations() {
-
- }
-
- /**
- * Default constructor.
- *
- * @param clazz
- * {@link #className}
- * @param miriamTypes
- * {@link #requiredMiriamTypes}
- */
- public UserClassRequiredAnnotations(Class<?> clazz, Collection<MiriamType> miriamTypes) {
- setClassName(clazz);
- if (miriamTypes != null) {
- setRequireAtLeastOneAnnotation(true);
- this.requiredMiriamTypes.addAll(miriamTypes);
- } else {
- setRequireAtLeastOneAnnotation(false);
- }
- }
-
- /**
- * Default constructor.
- *
- * @param clazz
- * {@link #className}
- * @param miriamTypes
- * {@link #requiredMiriamTypes}
- */
- public UserClassRequiredAnnotations(Class<?> clazz, MiriamType[] miriamTypes) {
- setClassName(clazz);
- for (MiriamType miriamType : miriamTypes) {
- this.requiredMiriamTypes.add(miriamType);
- }
- setRequireAtLeastOneAnnotation(miriamTypes.length > 0);
- }
-
- /**
- * @return the className
- * @see #className
- */
- public String getClassName() {
- return className;
- }
-
- /**
- * @param className
- * the className to set
- * @see #className
- */
- public void setClassName(String className) {
- this.className = className;
- }
-
- /**
- * @return the id
- * @see #id
- */
- public Integer getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(Integer id) {
- this.id = id;
- }
-
- /**
- * Sets {@link #className}.
- *
- * @param clazz
- * new {@link #className} value
- */
- public void setClassName(Class<?> clazz) {
- setClassName(clazz.getCanonicalName());
- }
-
- /**
- * Adds a type into {@link #requiredMiriamTypes list of required annotations}.
- *
- * @param miriamType
- * object to add
- */
- public void addRequiredMiriamType(MiriamType miriamType) {
- requiredMiriamTypes.add(miriamType);
- }
-
- /**
- * @return the annotationSchema
- * @see #annotationSchema
- */
- public UserAnnotationSchema getAnnotationSchema() {
- return annotationSchema;
- }
-
- /**
- * @param annotationSchema
- * the annotationSchema to set
- * @see #annotationSchema
- */
- public void setAnnotationSchema(UserAnnotationSchema annotationSchema) {
- this.annotationSchema = annotationSchema;
- }
-
- /**
- * @return the requiredMiriamTypes
- * @see #requiredMiriamTypes
- */
- public List<MiriamType> getRequiredMiriamTypes() {
- return requiredMiriamTypes;
- }
-
- /**
- * @param requiredMiriamTypes
- * the requiredMiriamTypes to set
- * @see #requiredMiriamTypes
- */
- public void setRequiredMiriamTypes(List<MiriamType> requiredMiriamTypes) {
- this.requiredMiriamTypes = requiredMiriamTypes;
- }
-
- /**
- * @return the requireAtLestOneAnnotation
- * @see #requireAtLeastOneAnnotation
- */
- public Boolean getRequireAtLeastOneAnnotation() {
- return requireAtLeastOneAnnotation;
- }
-
- /**
- * @param requireAtLeastOneAnnotation
- * the requireAtLestOneAnnotation to set
- * @see #requireAtLeastOneAnnotation
- */
- public void setRequireAtLeastOneAnnotation(Boolean requireAtLeastOneAnnotation) {
- this.requireAtLeastOneAnnotation = requireAtLeastOneAnnotation;
- }
-}
+package lcsb.mapviewer.model.user;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import javax.persistence.Column;
+import javax.persistence.ElementCollection;
+import javax.persistence.Entity;
+import javax.persistence.EnumType;
+import javax.persistence.Enumerated;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.JoinTable;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+import javax.persistence.Transient;
+
+import org.apache.log4j.Logger;
+import org.hibernate.annotations.IndexColumn;
+
+import lcsb.mapviewer.model.map.MiriamType;
+
+/**
+ * Defines set of required {@link MiriamType annotations} for a given object
+ * type.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "class_required_annotation_table")
+public class UserClassRequiredAnnotations implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Defdault class logger.
+ */
+ @Transient
+ private final transient Logger logger = Logger.getLogger(UserClassRequiredAnnotations.class);
+
+ /**
+ * Unique identifier in the database.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private Integer id;
+
+ /**
+ * {@link UserAnnotationSchema} in which this set of required
+ * {@link MiriamType annotations} is used.
+ */
+ @ManyToOne
+ private UserAnnotationSchema annotationSchema;
+
+ /**
+ * Name of the class for which this set is defined.
+ */
+ private String className;
+
+ /**
+ * Are the annotations required?
+ */
+ private Boolean requireAtLeastOneAnnotation;
+
+ /**
+ * One of this annotations will be required if
+ * {@link #requireAtLeastOneAnnotation} is set.
+ */
+ @ElementCollection
+ @JoinTable(name = "class_required_annotation_miriam_type_table", joinColumns = @JoinColumn(name = "class_required_annotation_iddb"))
+ @Column(name = "miriam_type_name", nullable = false)
+ @IndexColumn(name = "idx")
+ @Enumerated(EnumType.STRING)
+ private List<MiriamType> requiredMiriamTypes = new ArrayList<>();
+
+ /**
+ * Default constructor.
+ */
+ public UserClassRequiredAnnotations() {
+
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param clazz
+ * {@link #className}
+ * @param miriamTypes
+ * {@link #requiredMiriamTypes}
+ */
+ public UserClassRequiredAnnotations(Class<?> clazz, Collection<MiriamType> miriamTypes) {
+ setClassName(clazz);
+ if (miriamTypes != null) {
+ setRequireAtLeastOneAnnotation(true);
+ this.requiredMiriamTypes.addAll(miriamTypes);
+ } else {
+ setRequireAtLeastOneAnnotation(false);
+ }
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param clazz
+ * {@link #className}
+ * @param miriamTypes
+ * {@link #requiredMiriamTypes}
+ */
+ public UserClassRequiredAnnotations(Class<?> clazz, MiriamType[] miriamTypes) {
+ setClassName(clazz);
+ for (MiriamType miriamType : miriamTypes) {
+ this.requiredMiriamTypes.add(miriamType);
+ }
+ setRequireAtLeastOneAnnotation(miriamTypes.length > 0);
+ }
+
+ /**
+ * @return the className
+ * @see #className
+ */
+ public String getClassName() {
+ return className;
+ }
+
+ /**
+ * @param className
+ * the className to set
+ * @see #className
+ */
+ public void setClassName(String className) {
+ this.className = className;
+ }
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public Integer getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(Integer id) {
+ this.id = id;
+ }
+
+ /**
+ * Sets {@link #className}.
+ *
+ * @param clazz
+ * new {@link #className} value
+ */
+ public void setClassName(Class<?> clazz) {
+ setClassName(clazz.getCanonicalName());
+ }
+
+ /**
+ * Adds a type into {@link #requiredMiriamTypes list of required annotations}.
+ *
+ * @param miriamType
+ * object to add
+ */
+ public void addRequiredMiriamType(MiriamType miriamType) {
+ requiredMiriamTypes.add(miriamType);
+ }
+
+ /**
+ * @return the annotationSchema
+ * @see #annotationSchema
+ */
+ public UserAnnotationSchema getAnnotationSchema() {
+ return annotationSchema;
+ }
+
+ /**
+ * @param annotationSchema
+ * the annotationSchema to set
+ * @see #annotationSchema
+ */
+ public void setAnnotationSchema(UserAnnotationSchema annotationSchema) {
+ this.annotationSchema = annotationSchema;
+ }
+
+ /**
+ * @return the requiredMiriamTypes
+ * @see #requiredMiriamTypes
+ */
+ public List<MiriamType> getRequiredMiriamTypes() {
+ return requiredMiriamTypes;
+ }
+
+ /**
+ * @param requiredMiriamTypes
+ * the requiredMiriamTypes to set
+ * @see #requiredMiriamTypes
+ */
+ public void setRequiredMiriamTypes(List<MiriamType> requiredMiriamTypes) {
+ this.requiredMiriamTypes = requiredMiriamTypes;
+ }
+
+ /**
+ * @return the requireAtLestOneAnnotation
+ * @see #requireAtLeastOneAnnotation
+ */
+ public Boolean getRequireAtLeastOneAnnotation() {
+ return requireAtLeastOneAnnotation;
+ }
+
+ /**
+ * @param requireAtLeastOneAnnotation
+ * the requireAtLestOneAnnotation to set
+ * @see #requireAtLeastOneAnnotation
+ */
+ public void setRequireAtLeastOneAnnotation(Boolean requireAtLeastOneAnnotation) {
+ this.requireAtLeastOneAnnotation = requireAtLeastOneAnnotation;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/UserClassValidAnnotations.java b/model/src/main/java/lcsb/mapviewer/model/user/UserClassValidAnnotations.java
index 636492bf37..4eea94c30d 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/UserClassValidAnnotations.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/UserClassValidAnnotations.java
@@ -1,192 +1,192 @@
-package lcsb.mapviewer.model.user;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import javax.persistence.Column;
-import javax.persistence.ElementCollection;
-import javax.persistence.Entity;
-import javax.persistence.EnumType;
-import javax.persistence.Enumerated;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.JoinTable;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-
-import lcsb.mapviewer.model.map.MiriamType;
-
-import org.hibernate.annotations.IndexColumn;
-
-/**
- * Defines set of valid {@link MiriamType annotations} for a given object type.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "class_valid_annotation_table")
-public class UserClassValidAnnotations implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Unique identifier in the database.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private Integer id;
-
- /**
- * {@link UserAnnotationSchema} in which this set of valid {@link MiriamType
- * annotations} is used.
- */
- @ManyToOne
- private UserAnnotationSchema annotationSchema;
-
- /**
- * Name of the class for which this set is defined.
- */
- private String className;
-
- /**
- * List of annotations that are valid.
- */
- @ElementCollection
- @JoinTable(name = "class_valid_annotation_miriam_type_table", joinColumns = @JoinColumn(name = "class_valid_annotation_iddb"))
- @Column(name = "miriam_type_name", nullable = false)
- @IndexColumn(name = "idx")
- @Enumerated(EnumType.STRING)
- private List<MiriamType> validMiriamTypes = new ArrayList<>();
-
- /**
- * Default constructor.
- */
- public UserClassValidAnnotations() {
-
- }
-
- /**
- * Default constructor.
- *
- * @param clazz
- * {@link #className}
- * @param miriamTypes
- * {@link #validMiriamTypes}
- */
- public UserClassValidAnnotations(Class<?> clazz, Collection<MiriamType> miriamTypes) {
- setClassName(clazz);
- this.validMiriamTypes.addAll(miriamTypes);
- }
-
- /**
- * Default constructor.
- *
- * @param clazz
- * {@link #className}
- * @param miriamTypes
- * {@link #validMiriamTypes}
- */
- public UserClassValidAnnotations(Class<?> clazz, MiriamType[] miriamTypes) {
- setClassName(clazz);
- for (MiriamType miriamType : miriamTypes) {
- this.validMiriamTypes.add(miriamType);
- }
- }
-
- /**
- * @return the validMiriamTypes
- * @see #validMiriamTypes
- */
- public List<MiriamType> getValidMiriamTypes() {
- return validMiriamTypes;
- }
-
- /**
- * @param validMiriamTypes
- * the validMiriamTypes to set
- * @see #validMiriamTypes
- */
- public void setValidMiriamTypes(List<MiriamType> validMiriamTypes) {
- this.validMiriamTypes = validMiriamTypes;
- }
-
- /**
- * @return the className
- * @see #className
- */
- public String getClassName() {
- return className;
- }
-
- /**
- * @param className
- * the className to set
- * @see #className
- */
- public void setClassName(String className) {
- this.className = className;
- }
-
- /**
- * @return the id
- * @see #id
- */
- public Integer getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(Integer id) {
- this.id = id;
- }
-
- /**
- * Sets {@link #className} value.
- *
- * @param clazz
- * new {@link #className} value
- */
- public void setClassName(Class<?> clazz) {
- setClassName(clazz.getCanonicalName());
- }
-
- /**
- * Adds new valid annotation to {@link #validMiriamTypes}.
- *
- * @param miriamType
- * obejct to add
- */
- public void addValidMiriamType(MiriamType miriamType) {
- validMiriamTypes.add(miriamType);
- }
-
- /**
- * @return the annotationSchema
- * @see #annotationSchema
- */
- public UserAnnotationSchema getAnnotationSchema() {
- return annotationSchema;
- }
-
- /**
- * @param annotationSchema
- * the annotationSchema to set
- * @see #annotationSchema
- */
- public void setAnnotationSchema(UserAnnotationSchema annotationSchema) {
- this.annotationSchema = annotationSchema;
- }
-}
+package lcsb.mapviewer.model.user;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import javax.persistence.Column;
+import javax.persistence.ElementCollection;
+import javax.persistence.Entity;
+import javax.persistence.EnumType;
+import javax.persistence.Enumerated;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.JoinTable;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+
+import lcsb.mapviewer.model.map.MiriamType;
+
+import org.hibernate.annotations.IndexColumn;
+
+/**
+ * Defines set of valid {@link MiriamType annotations} for a given object type.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "class_valid_annotation_table")
+public class UserClassValidAnnotations implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Unique identifier in the database.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private Integer id;
+
+ /**
+ * {@link UserAnnotationSchema} in which this set of valid {@link MiriamType
+ * annotations} is used.
+ */
+ @ManyToOne
+ private UserAnnotationSchema annotationSchema;
+
+ /**
+ * Name of the class for which this set is defined.
+ */
+ private String className;
+
+ /**
+ * List of annotations that are valid.
+ */
+ @ElementCollection
+ @JoinTable(name = "class_valid_annotation_miriam_type_table", joinColumns = @JoinColumn(name = "class_valid_annotation_iddb"))
+ @Column(name = "miriam_type_name", nullable = false)
+ @IndexColumn(name = "idx")
+ @Enumerated(EnumType.STRING)
+ private List<MiriamType> validMiriamTypes = new ArrayList<>();
+
+ /**
+ * Default constructor.
+ */
+ public UserClassValidAnnotations() {
+
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param clazz
+ * {@link #className}
+ * @param miriamTypes
+ * {@link #validMiriamTypes}
+ */
+ public UserClassValidAnnotations(Class<?> clazz, Collection<MiriamType> miriamTypes) {
+ setClassName(clazz);
+ this.validMiriamTypes.addAll(miriamTypes);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param clazz
+ * {@link #className}
+ * @param miriamTypes
+ * {@link #validMiriamTypes}
+ */
+ public UserClassValidAnnotations(Class<?> clazz, MiriamType[] miriamTypes) {
+ setClassName(clazz);
+ for (MiriamType miriamType : miriamTypes) {
+ this.validMiriamTypes.add(miriamType);
+ }
+ }
+
+ /**
+ * @return the validMiriamTypes
+ * @see #validMiriamTypes
+ */
+ public List<MiriamType> getValidMiriamTypes() {
+ return validMiriamTypes;
+ }
+
+ /**
+ * @param validMiriamTypes
+ * the validMiriamTypes to set
+ * @see #validMiriamTypes
+ */
+ public void setValidMiriamTypes(List<MiriamType> validMiriamTypes) {
+ this.validMiriamTypes = validMiriamTypes;
+ }
+
+ /**
+ * @return the className
+ * @see #className
+ */
+ public String getClassName() {
+ return className;
+ }
+
+ /**
+ * @param className
+ * the className to set
+ * @see #className
+ */
+ public void setClassName(String className) {
+ this.className = className;
+ }
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public Integer getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(Integer id) {
+ this.id = id;
+ }
+
+ /**
+ * Sets {@link #className} value.
+ *
+ * @param clazz
+ * new {@link #className} value
+ */
+ public void setClassName(Class<?> clazz) {
+ setClassName(clazz.getCanonicalName());
+ }
+
+ /**
+ * Adds new valid annotation to {@link #validMiriamTypes}.
+ *
+ * @param miriamType
+ * obejct to add
+ */
+ public void addValidMiriamType(MiriamType miriamType) {
+ validMiriamTypes.add(miriamType);
+ }
+
+ /**
+ * @return the annotationSchema
+ * @see #annotationSchema
+ */
+ public UserAnnotationSchema getAnnotationSchema() {
+ return annotationSchema;
+ }
+
+ /**
+ * @param annotationSchema
+ * the annotationSchema to set
+ * @see #annotationSchema
+ */
+ public void setAnnotationSchema(UserAnnotationSchema annotationSchema) {
+ this.annotationSchema = annotationSchema;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/package-info.java b/model/src/main/java/lcsb/mapviewer/model/user/package-info.java
index b78a85bd5c..d5dd86f858 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/package-info.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/package-info.java
@@ -1,5 +1,5 @@
-/**
- * Contains structures used for modeling users, privileges, etc.
- */
-package lcsb.mapviewer.model.user;
-
+/**
+ * Contains structures used for modeling users, privileges, etc.
+ */
+package lcsb.mapviewer.model.user;
+
diff --git a/model/src/main/java/lcsb/mapviewer/modelutils/map/ClassNameComparator.java b/model/src/main/java/lcsb/mapviewer/modelutils/map/ClassNameComparator.java
index e20dd7678d..0f93ec51d7 100644
--- a/model/src/main/java/lcsb/mapviewer/modelutils/map/ClassNameComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/modelutils/map/ClassNameComparator.java
@@ -1,18 +1,18 @@
-package lcsb.mapviewer.modelutils.map;
-
-import java.util.Comparator;
-
-/**
- * Class used to compare classes using class names (SimpleName).
- *
- * @author Piotr Gawron
- *
- */
-public class ClassNameComparator implements Comparator<Class<?>> {
-
- @Override
- public int compare(Class<?> o1, Class<?> o2) {
- return o1.getSimpleName().compareTo(o2.getSimpleName());
- }
-
-}
+package lcsb.mapviewer.modelutils.map;
+
+import java.util.Comparator;
+
+/**
+ * Class used to compare classes using class names (SimpleName).
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ClassNameComparator implements Comparator<Class<?>> {
+
+ @Override
+ public int compare(Class<?> o1, Class<?> o2) {
+ return o1.getSimpleName().compareTo(o2.getSimpleName());
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/modelutils/map/ClassTreeNode.java b/model/src/main/java/lcsb/mapviewer/modelutils/map/ClassTreeNode.java
index f8ef4eff9e..b482eb5ffa 100644
--- a/model/src/main/java/lcsb/mapviewer/modelutils/map/ClassTreeNode.java
+++ b/model/src/main/java/lcsb/mapviewer/modelutils/map/ClassTreeNode.java
@@ -1,154 +1,154 @@
-package lcsb.mapviewer.modelutils.map;
-
-import java.lang.reflect.InvocationTargetException;
-import java.util.ArrayList;
-import java.util.List;
-
-import javassist.Modifier;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-/**
- * This class is used to represent inheritance hierarchy of classes.
- *
- * @author Piotr Gawron
- *
- */
-public class ClassTreeNode {
-
- /**
- * Origial class.
- */
- private Class<?> clazz;
-
- /**
- * Children classes.
- */
- private List<ClassTreeNode> children;
-
- /**
- * Parent node.
- */
- private ClassTreeNode parent;
-
- /**
- * Name used to present this class.
- */
- private String commonName;
-
- /**
- * Additional data in the node.
- */
- private Object data;
-
- /**
- * Default constructor.
- *
- * @param class1
- * class that should be put in this node
- */
- public ClassTreeNode(Class<?> class1) {
- this.clazz = class1;
- this.children = new ArrayList<>();
- this.commonName = class1.getSimpleName();
- if (!Modifier.isAbstract(clazz.getModifiers())) {
- try {
- if (Reaction.class.isAssignableFrom(clazz)) {
- this.commonName = ((BioEntity) (clazz.getDeclaredConstructor().newInstance())).getStringType();
- } else {
- this.commonName = ((BioEntity) (clazz.getDeclaredConstructor(String.class).newInstance("id"))).getStringType();
- }
- } catch (InstantiationException | IllegalAccessException | IllegalArgumentException | InvocationTargetException | NoSuchMethodException
- | SecurityException e) {
- }
- }
-
- this.data = null;
- }
-
- /**
- * @return the clazz
- * @see #clazz
- */
- public Class<?> getClazz() {
- return clazz;
- }
-
- /**
- * @param clazz
- * the clazz to set
- * @see #clazz
- */
- public void setClazz(Class<?> clazz) {
- this.clazz = clazz;
- }
-
- /**
- * @return the children
- * @see #children
- */
- public List<ClassTreeNode> getChildren() {
- return children;
- }
-
- /**
- * @param children
- * the children to set
- * @see #children
- */
- public void setChildren(List<ClassTreeNode> children) {
- this.children = children;
- }
-
- /**
- * @return the commonName
- * @see #commonName
- */
- public String getCommonName() {
- return commonName;
- }
-
- /**
- * @param commonName
- * the commonName to set
- * @see #commonName
- */
- public void setCommonName(String commonName) {
- this.commonName = commonName;
- }
-
- /**
- * @return the data
- * @see #data
- */
- public Object getData() {
- return data;
- }
-
- /**
- * @param data
- * the data to set
- * @see #data
- */
- public void setData(Object data) {
- this.data = data;
- }
-
- /**
- * @return the parent
- * @see #parent
- */
- public ClassTreeNode getParent() {
- return parent;
- }
-
- /**
- * @param parent
- * the parent to set
- * @see #parent
- */
- public void setParent(ClassTreeNode parent) {
- this.parent = parent;
- }
-
-}
+package lcsb.mapviewer.modelutils.map;
+
+import java.lang.reflect.InvocationTargetException;
+import java.util.ArrayList;
+import java.util.List;
+
+import javassist.Modifier;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class is used to represent inheritance hierarchy of classes.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ClassTreeNode {
+
+ /**
+ * Origial class.
+ */
+ private Class<?> clazz;
+
+ /**
+ * Children classes.
+ */
+ private List<ClassTreeNode> children;
+
+ /**
+ * Parent node.
+ */
+ private ClassTreeNode parent;
+
+ /**
+ * Name used to present this class.
+ */
+ private String commonName;
+
+ /**
+ * Additional data in the node.
+ */
+ private Object data;
+
+ /**
+ * Default constructor.
+ *
+ * @param class1
+ * class that should be put in this node
+ */
+ public ClassTreeNode(Class<?> class1) {
+ this.clazz = class1;
+ this.children = new ArrayList<>();
+ this.commonName = class1.getSimpleName();
+ if (!Modifier.isAbstract(clazz.getModifiers())) {
+ try {
+ if (Reaction.class.isAssignableFrom(clazz)) {
+ this.commonName = ((BioEntity) (clazz.getDeclaredConstructor().newInstance())).getStringType();
+ } else {
+ this.commonName = ((BioEntity) (clazz.getDeclaredConstructor(String.class).newInstance("id"))).getStringType();
+ }
+ } catch (InstantiationException | IllegalAccessException | IllegalArgumentException | InvocationTargetException | NoSuchMethodException
+ | SecurityException e) {
+ }
+ }
+
+ this.data = null;
+ }
+
+ /**
+ * @return the clazz
+ * @see #clazz
+ */
+ public Class<?> getClazz() {
+ return clazz;
+ }
+
+ /**
+ * @param clazz
+ * the clazz to set
+ * @see #clazz
+ */
+ public void setClazz(Class<?> clazz) {
+ this.clazz = clazz;
+ }
+
+ /**
+ * @return the children
+ * @see #children
+ */
+ public List<ClassTreeNode> getChildren() {
+ return children;
+ }
+
+ /**
+ * @param children
+ * the children to set
+ * @see #children
+ */
+ public void setChildren(List<ClassTreeNode> children) {
+ this.children = children;
+ }
+
+ /**
+ * @return the commonName
+ * @see #commonName
+ */
+ public String getCommonName() {
+ return commonName;
+ }
+
+ /**
+ * @param commonName
+ * the commonName to set
+ * @see #commonName
+ */
+ public void setCommonName(String commonName) {
+ this.commonName = commonName;
+ }
+
+ /**
+ * @return the data
+ * @see #data
+ */
+ public Object getData() {
+ return data;
+ }
+
+ /**
+ * @param data
+ * the data to set
+ * @see #data
+ */
+ public void setData(Object data) {
+ this.data = data;
+ }
+
+ /**
+ * @return the parent
+ * @see #parent
+ */
+ public ClassTreeNode getParent() {
+ return parent;
+ }
+
+ /**
+ * @param parent
+ * the parent to set
+ * @see #parent
+ */
+ public void setParent(ClassTreeNode parent) {
+ this.parent = parent;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/modelutils/map/ClassTreeNodeNameComparator.java b/model/src/main/java/lcsb/mapviewer/modelutils/map/ClassTreeNodeNameComparator.java
index fdcd4b9c8f..0b775750cd 100644
--- a/model/src/main/java/lcsb/mapviewer/modelutils/map/ClassTreeNodeNameComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/modelutils/map/ClassTreeNodeNameComparator.java
@@ -1,25 +1,25 @@
-package lcsb.mapviewer.modelutils.map;
-
-import java.util.Comparator;
-
-import lcsb.mapviewer.common.comparator.StringComparator;
-
-/**
- * Name {@link Comparator} for {@link ClassTreeNode} class.
- *
- * @author Piotr Gawron
- *
- */
-public class ClassTreeNodeNameComparator implements Comparator<ClassTreeNode> {
-
- /**
- * String comparator used for comparison (it's null safe).
- */
- private StringComparator stringComparator = new StringComparator();
-
- @Override
- public int compare(ClassTreeNode o1, ClassTreeNode o2) {
- return stringComparator.compare(o1.getCommonName(), o2.getCommonName());
- }
-
-}
+package lcsb.mapviewer.modelutils.map;
+
+import java.util.Comparator;
+
+import lcsb.mapviewer.common.comparator.StringComparator;
+
+/**
+ * Name {@link Comparator} for {@link ClassTreeNode} class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ClassTreeNodeNameComparator implements Comparator<ClassTreeNode> {
+
+ /**
+ * String comparator used for comparison (it's null safe).
+ */
+ private StringComparator stringComparator = new StringComparator();
+
+ @Override
+ public int compare(ClassTreeNode o1, ClassTreeNode o2) {
+ return stringComparator.compare(o1.getCommonName(), o2.getCommonName());
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/modelutils/map/package-info.java b/model/src/main/java/lcsb/mapviewer/modelutils/map/package-info.java
index a1062823ae..1e96e287fb 100644
--- a/model/src/main/java/lcsb/mapviewer/modelutils/map/package-info.java
+++ b/model/src/main/java/lcsb/mapviewer/modelutils/map/package-info.java
@@ -1,5 +1,5 @@
-/**
- * Contains util classe for map modeling structures.
- */
-package lcsb.mapviewer.modelutils.map;
-
+/**
+ * Contains util classe for map modeling structures.
+ */
+package lcsb.mapviewer.modelutils.map;
+
diff --git a/model/src/test/java/lcsb/mapviewer/AllTests.java b/model/src/test/java/lcsb/mapviewer/AllTests.java
index cfbbd296b9..60ea0c795e 100644
--- a/model/src/test/java/lcsb/mapviewer/AllTests.java
+++ b/model/src/test/java/lcsb/mapviewer/AllTests.java
@@ -1,16 +1,16 @@
-package lcsb.mapviewer;
-
-import lcsb.mapviewer.model.AllModelTests;
-import lcsb.mapviewer.modelutils.map.AllMapUtilTests;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AllModelTests.class, //
- AllMapUtilTests.class,//
-})
-public class AllTests {
-
-}
+package lcsb.mapviewer;
+
+import lcsb.mapviewer.model.AllModelTests;
+import lcsb.mapviewer.modelutils.map.AllMapUtilTests;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AllModelTests.class, //
+ AllMapUtilTests.class,//
+})
+public class AllTests {
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/ModelTestFunctions.java b/model/src/test/java/lcsb/mapviewer/ModelTestFunctions.java
index a99c4fe2df..fc9832424e 100644
--- a/model/src/test/java/lcsb/mapviewer/ModelTestFunctions.java
+++ b/model/src/test/java/lcsb/mapviewer/ModelTestFunctions.java
@@ -1,32 +1,32 @@
-package lcsb.mapviewer;
-
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.apache.log4j.spi.LoggingEvent;
-import org.junit.After;
-import org.junit.Before;
-
-import lcsb.mapviewer.common.EventStorageLoggerAppender;
-
-public class ModelTestFunctions {
-
- private EventStorageLoggerAppender appender;
-
- @Before
- public final void _setUp() throws Exception {
- Logger.getRootLogger().removeAppender(appender);
- appender = new EventStorageLoggerAppender();
- Logger.getRootLogger().addAppender(appender);
- }
-
- @After
- public final void _tearDown() throws Exception {
- Logger.getRootLogger().removeAppender(appender);
- }
-
- protected List<LoggingEvent> getWarnings() {
- return appender.getWarnings();
- }
-
-}
+package lcsb.mapviewer;
+
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.apache.log4j.spi.LoggingEvent;
+import org.junit.After;
+import org.junit.Before;
+
+import lcsb.mapviewer.common.EventStorageLoggerAppender;
+
+public class ModelTestFunctions {
+
+ private EventStorageLoggerAppender appender;
+
+ @Before
+ public final void _setUp() throws Exception {
+ Logger.getRootLogger().removeAppender(appender);
+ appender = new EventStorageLoggerAppender();
+ Logger.getRootLogger().addAppender(appender);
+ }
+
+ @After
+ public final void _tearDown() throws Exception {
+ Logger.getRootLogger().removeAppender(appender);
+ }
+
+ protected List<LoggingEvent> getWarnings() {
+ return appender.getWarnings();
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/AllModelTests.java b/model/src/test/java/lcsb/mapviewer/model/AllModelTests.java
index bd4e35c210..9387ffa40a 100644
--- a/model/src/test/java/lcsb/mapviewer/model/AllModelTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/AllModelTests.java
@@ -1,24 +1,24 @@
-package lcsb.mapviewer.model;
-
-import lcsb.mapviewer.model.cache.AllCacheTests;
-import lcsb.mapviewer.model.graphics.AllGraphicsTests;
-import lcsb.mapviewer.model.log.AllLogTests;
-import lcsb.mapviewer.model.map.AllMapTests;
-import lcsb.mapviewer.model.user.AllUserTests;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AllCacheTests.class, //
- AllGraphicsTests.class, //
- AllLogTests.class, //
- AllMapTests.class, //
- AllUserTests.class, //
- ProjectStatusTest.class, //
- ProjectTest.class,//
-})
-public class AllModelTests {
-
-}
+package lcsb.mapviewer.model;
+
+import lcsb.mapviewer.model.cache.AllCacheTests;
+import lcsb.mapviewer.model.graphics.AllGraphicsTests;
+import lcsb.mapviewer.model.log.AllLogTests;
+import lcsb.mapviewer.model.map.AllMapTests;
+import lcsb.mapviewer.model.user.AllUserTests;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AllCacheTests.class, //
+ AllGraphicsTests.class, //
+ AllLogTests.class, //
+ AllMapTests.class, //
+ AllUserTests.class, //
+ ProjectStatusTest.class, //
+ ProjectTest.class,//
+})
+public class AllModelTests {
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/ProjectStatusTest.java b/model/src/test/java/lcsb/mapviewer/model/ProjectStatusTest.java
index 3a966d4e01..0d4cdcdfeb 100644
--- a/model/src/test/java/lcsb/mapviewer/model/ProjectStatusTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/ProjectStatusTest.java
@@ -1,30 +1,30 @@
-package lcsb.mapviewer.model;
-
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ProjectStatusTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testValidValues() {
- for (ProjectStatus type : ProjectStatus.values()) {
- assertNotNull(type);
-
- // for coverage tests
- ProjectStatus.valueOf(type.name());
- type.toString();
- }
- }
-
-}
+package lcsb.mapviewer.model;
+
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ProjectStatusTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testValidValues() {
+ for (ProjectStatus type : ProjectStatus.values()) {
+ assertNotNull(type);
+
+ // for coverage tests
+ ProjectStatus.valueOf(type.name());
+ type.toString();
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/ProjectTest.java b/model/src/test/java/lcsb/mapviewer/model/ProjectTest.java
index dcbadd0b48..9b9cfa9cff 100644
--- a/model/src/test/java/lcsb/mapviewer/model/ProjectTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/ProjectTest.java
@@ -1,261 +1,261 @@
-package lcsb.mapviewer.model;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.apache.log4j.Logger;
-import org.apache.log4j.spi.LoggingEvent;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.EventStorageLoggerAppender;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.cache.UploadedFileEntry;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-
-public class ProjectTest {
- Logger logger = Logger.getLogger(ProjectTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new Project());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProject() {
- try {
- Project project = new Project("str");
- assertNotNull(project);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddModel() {
- try {
- Model model = new ModelFullIndexed(null);
- Model model2 = new ModelFullIndexed(null);
- Project project = new Project();
- assertEquals(0, project.getModels().size());
- project.addModel(model);
- assertEquals(1, project.getModels().size());
- project.addModel(model);
- assertEquals(1, project.getModels().size());
- project.addModel(model2.getModelData());
- assertEquals(2, project.getModels().size());
- project.removeModel(model2.getModelData());
- assertEquals(1, project.getModels().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- MiriamData organism = new MiriamData();
- int id = 5;
- String projectId = "str";
- ProjectStatus status = ProjectStatus.ANNOTATING;
- double progress = 4.5;
- Set<ModelData> models = new HashSet<>();
- String errors = "eerStr";
- String directory = "dir";
- String name = "name3";
- MiriamData disease = new MiriamData();
- Project project = new Project("str");
- boolean sbgn = true;
-
- project.setSbgnFormat(sbgn);
- assertEquals(sbgn, project.isSbgnFormat());
-
- project.setId(id);
- assertEquals(id, project.getId());
-
- project.setProjectId(projectId);
- assertEquals(projectId, project.getProjectId());
-
- project.setStatus(status);
- assertEquals(status, project.getStatus());
-
- project.setProgress(progress);
- assertEquals(progress, project.getProgress(), Configuration.EPSILON);
-
- project.setModels(models);
- assertEquals(models, project.getModels());
-
- project.setErrors(errors);
- assertEquals(errors, project.getErrors());
-
- project.setDirectory(directory);
- assertEquals(directory, project.getDirectory());
-
- project.setName(name);
- assertEquals(name, project.getName());
-
- project.setDisease(disease);
- assertEquals(disease, project.getDisease());
-
- UploadedFileEntry entry = new UploadedFileEntry() ;
- project.setInputData(entry );
- assertEquals(entry , project.getInputData());
-
- project.setOrganism(organism);
- assertEquals(organism, project.getOrganism());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddCreationWarning() {
- try {
- Project md = new Project();
- md.addWarning("text\ntext");
-
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddCreationWarning2() {
- try {
- Project md = new Project();
- md.addWarning("");
- List<String> warnings = md.getWarnings();
- assertEquals(0, warnings.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddCreationWarning3() {
- try {
- Project md = new Project();
- md.addWarning("xqw");
- List<String> warnings = md.getWarnings();
- assertEquals(1, warnings.size());
- assertEquals("xqw", warnings.get(0));
-
- md.addWarning("WER");
- warnings = md.getWarnings();
- assertEquals(2, warnings.size());
- assertEquals("WER", warnings.get(1));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddCreationWarnings() {
- try {
- List<String> warnings = new ArrayList<>();
- warnings.add("xqw");
- warnings.add("aso");
- warnings.add("");
- Project project = new Project();
- project.addWarnings(warnings);
-
- project.addWarning("WER");
- warnings = project.getWarnings();
- assertEquals(3, warnings.size());
- assertEquals("aso", warnings.get(1));
-
- project.addWarnings(warnings);
- warnings = project.getWarnings();
- assertEquals(6, warnings.size());
- assertEquals("aso", warnings.get(1));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddCreationWarnings2() {
- try {
- List<String> warnings = new ArrayList<>();
- warnings.add("xqw\nwer\nt");
- Project md = new Project();
- md.addWarnings(warnings);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddCreationWarnings3() {
- try {
- List<String> warnings = new ArrayList<>();
- Project md = new Project();
- md.addWarnings(warnings);
- assertEquals(0, md.getWarnings().size());
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddLoggingInfo() {
- try {
- Project project = new Project();
- EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
- logger.addAppender(appender);
- logger.warn("test");
- logger.warn("test2");
- LoggingEvent event = appender.getWarnings().get(0);
- appender.getWarnings().add(new LoggingEvent("St", event.getLogger(), null, new Object(), null));
- logger.removeAppender(appender);
-
- project.addLoggingInfo(appender);
- assertEquals(2, project.getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.apache.log4j.Logger;
+import org.apache.log4j.spi.LoggingEvent;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.EventStorageLoggerAppender;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+
+public class ProjectTest {
+ Logger logger = Logger.getLogger(ProjectTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new Project());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProject() {
+ try {
+ Project project = new Project("str");
+ assertNotNull(project);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddModel() {
+ try {
+ Model model = new ModelFullIndexed(null);
+ Model model2 = new ModelFullIndexed(null);
+ Project project = new Project();
+ assertEquals(0, project.getModels().size());
+ project.addModel(model);
+ assertEquals(1, project.getModels().size());
+ project.addModel(model);
+ assertEquals(1, project.getModels().size());
+ project.addModel(model2.getModelData());
+ assertEquals(2, project.getModels().size());
+ project.removeModel(model2.getModelData());
+ assertEquals(1, project.getModels().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ MiriamData organism = new MiriamData();
+ int id = 5;
+ String projectId = "str";
+ ProjectStatus status = ProjectStatus.ANNOTATING;
+ double progress = 4.5;
+ Set<ModelData> models = new HashSet<>();
+ String errors = "eerStr";
+ String directory = "dir";
+ String name = "name3";
+ MiriamData disease = new MiriamData();
+ Project project = new Project("str");
+ boolean sbgn = true;
+
+ project.setSbgnFormat(sbgn);
+ assertEquals(sbgn, project.isSbgnFormat());
+
+ project.setId(id);
+ assertEquals(id, project.getId());
+
+ project.setProjectId(projectId);
+ assertEquals(projectId, project.getProjectId());
+
+ project.setStatus(status);
+ assertEquals(status, project.getStatus());
+
+ project.setProgress(progress);
+ assertEquals(progress, project.getProgress(), Configuration.EPSILON);
+
+ project.setModels(models);
+ assertEquals(models, project.getModels());
+
+ project.setErrors(errors);
+ assertEquals(errors, project.getErrors());
+
+ project.setDirectory(directory);
+ assertEquals(directory, project.getDirectory());
+
+ project.setName(name);
+ assertEquals(name, project.getName());
+
+ project.setDisease(disease);
+ assertEquals(disease, project.getDisease());
+
+ UploadedFileEntry entry = new UploadedFileEntry() ;
+ project.setInputData(entry );
+ assertEquals(entry , project.getInputData());
+
+ project.setOrganism(organism);
+ assertEquals(organism, project.getOrganism());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddCreationWarning() {
+ try {
+ Project md = new Project();
+ md.addWarning("text\ntext");
+
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddCreationWarning2() {
+ try {
+ Project md = new Project();
+ md.addWarning("");
+ List<String> warnings = md.getWarnings();
+ assertEquals(0, warnings.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddCreationWarning3() {
+ try {
+ Project md = new Project();
+ md.addWarning("xqw");
+ List<String> warnings = md.getWarnings();
+ assertEquals(1, warnings.size());
+ assertEquals("xqw", warnings.get(0));
+
+ md.addWarning("WER");
+ warnings = md.getWarnings();
+ assertEquals(2, warnings.size());
+ assertEquals("WER", warnings.get(1));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddCreationWarnings() {
+ try {
+ List<String> warnings = new ArrayList<>();
+ warnings.add("xqw");
+ warnings.add("aso");
+ warnings.add("");
+ Project project = new Project();
+ project.addWarnings(warnings);
+
+ project.addWarning("WER");
+ warnings = project.getWarnings();
+ assertEquals(3, warnings.size());
+ assertEquals("aso", warnings.get(1));
+
+ project.addWarnings(warnings);
+ warnings = project.getWarnings();
+ assertEquals(6, warnings.size());
+ assertEquals("aso", warnings.get(1));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddCreationWarnings2() {
+ try {
+ List<String> warnings = new ArrayList<>();
+ warnings.add("xqw\nwer\nt");
+ Project md = new Project();
+ md.addWarnings(warnings);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddCreationWarnings3() {
+ try {
+ List<String> warnings = new ArrayList<>();
+ Project md = new Project();
+ md.addWarnings(warnings);
+ assertEquals(0, md.getWarnings().size());
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddLoggingInfo() {
+ try {
+ Project project = new Project();
+ EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
+ logger.addAppender(appender);
+ logger.warn("test");
+ logger.warn("test2");
+ LoggingEvent event = appender.getWarnings().get(0);
+ appender.getWarnings().add(new LoggingEvent("St", event.getLogger(), null, new Object(), null));
+ logger.removeAppender(appender);
+
+ project.addLoggingInfo(appender);
+ assertEquals(2, project.getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/cache/AllCacheTests.java b/model/src/test/java/lcsb/mapviewer/model/cache/AllCacheTests.java
index bb1c289b23..063c947872 100644
--- a/model/src/test/java/lcsb/mapviewer/model/cache/AllCacheTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/cache/AllCacheTests.java
@@ -1,16 +1,16 @@
-package lcsb.mapviewer.model.cache;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ BigFileEntryTest.class, //
- CacheQueryTest.class, //
- CacheTypeTest.class,//
- UploadedFileEntryTest.class,//
-
-})
-public class AllCacheTests {
-
-}
+package lcsb.mapviewer.model.cache;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ BigFileEntryTest.class, //
+ CacheQueryTest.class, //
+ CacheTypeTest.class,//
+ UploadedFileEntryTest.class,//
+
+})
+public class AllCacheTests {
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/cache/BigFileEntryTest.java b/model/src/test/java/lcsb/mapviewer/model/cache/BigFileEntryTest.java
index bd0b87cc24..08e0eb2353 100644
--- a/model/src/test/java/lcsb/mapviewer/model/cache/BigFileEntryTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/cache/BigFileEntryTest.java
@@ -1,66 +1,66 @@
-package lcsb.mapviewer.model.cache;
-
-import static org.junit.Assert.assertEquals;
-
-import java.util.Calendar;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class BigFileEntryTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetters() {
- try {
- Calendar downloadDate = Calendar.getInstance();
- int id = 120;
- double downloadProgress = 4.6;
- long downloadThreadId = 6;
- String localPath = "C:/";
- boolean removed = true;
- String url = "www.google.com";
- String filename = "tmp";
- byte[] content = new byte[] { 1, 2 };
-
- BigFileEntry element = new BigFileEntry();
- element.setDownloadDate(downloadDate);
- element.setDownloadProgress(downloadProgress);
- element.setDownloadThreadId(downloadThreadId);
- element.setId(id);
- element.setLocalPath(localPath);
- element.setRemoved(removed);
- element.setUrl(url);
- element.setOriginalFileName(filename);
- element.setFileContent(content);
-
- assertEquals(downloadDate, element.getDownloadDate());
- assertEquals((Double) downloadProgress, element.getDownloadProgress());
- assertEquals((Long) downloadThreadId, element.getDownloadThreadId());
- assertEquals(id, element.getId());
- assertEquals(localPath, element.getLocalPath());
- assertEquals(removed, element.isRemoved());
- assertEquals(url, element.getUrl());
- assertEquals(content, element.getFileContent());
- assertEquals(filename, element.getOriginalFileName());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.cache;
+
+import static org.junit.Assert.assertEquals;
+
+import java.util.Calendar;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class BigFileEntryTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ Calendar downloadDate = Calendar.getInstance();
+ int id = 120;
+ double downloadProgress = 4.6;
+ long downloadThreadId = 6;
+ String localPath = "C:/";
+ boolean removed = true;
+ String url = "www.google.com";
+ String filename = "tmp";
+ byte[] content = new byte[] { 1, 2 };
+
+ BigFileEntry element = new BigFileEntry();
+ element.setDownloadDate(downloadDate);
+ element.setDownloadProgress(downloadProgress);
+ element.setDownloadThreadId(downloadThreadId);
+ element.setId(id);
+ element.setLocalPath(localPath);
+ element.setRemoved(removed);
+ element.setUrl(url);
+ element.setOriginalFileName(filename);
+ element.setFileContent(content);
+
+ assertEquals(downloadDate, element.getDownloadDate());
+ assertEquals((Double) downloadProgress, element.getDownloadProgress());
+ assertEquals((Long) downloadThreadId, element.getDownloadThreadId());
+ assertEquals(id, element.getId());
+ assertEquals(localPath, element.getLocalPath());
+ assertEquals(removed, element.isRemoved());
+ assertEquals(url, element.getUrl());
+ assertEquals(content, element.getFileContent());
+ assertEquals(filename, element.getOriginalFileName());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/cache/CacheQueryTest.java b/model/src/test/java/lcsb/mapviewer/model/cache/CacheQueryTest.java
index 89a305b561..ce9a2d4a94 100644
--- a/model/src/test/java/lcsb/mapviewer/model/cache/CacheQueryTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/cache/CacheQueryTest.java
@@ -1,69 +1,69 @@
-package lcsb.mapviewer.model.cache;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-
-import java.util.Calendar;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class CacheQueryTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new CacheQuery());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- Calendar expires = Calendar.getInstance();
- expires.add(Calendar.DATE, 1);
- Calendar accessed = Calendar.getInstance();
- accessed.add(Calendar.DATE, 10);
- int id = 120;
- String query = "query1";
- int type = 34;
- int type2 = 45;
- String value = "val";
- CacheType ctype = new CacheType();
- ctype.setId(type2);
-
- CacheQuery cq = new CacheQuery();
- cq.setAccessed(accessed);
- assertTrue(accessed.equals(cq.getAccessed()));
- cq.setExpires(expires);
- assertTrue(expires.equals(cq.getExpires()));
- cq.setId(id);
- assertEquals(id, cq.getId());
- cq.setQuery(query);
- assertEquals(query, cq.getQuery());
- cq.setType(ctype);
- assertEquals((Integer) type2, cq.getType());
- cq.setType(type);
- assertEquals((Integer) type, cq.getType());
- cq.setValue(value);
- assertEquals(value, cq.getValue());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.cache;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.util.Calendar;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class CacheQueryTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new CacheQuery());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ Calendar expires = Calendar.getInstance();
+ expires.add(Calendar.DATE, 1);
+ Calendar accessed = Calendar.getInstance();
+ accessed.add(Calendar.DATE, 10);
+ int id = 120;
+ String query = "query1";
+ int type = 34;
+ int type2 = 45;
+ String value = "val";
+ CacheType ctype = new CacheType();
+ ctype.setId(type2);
+
+ CacheQuery cq = new CacheQuery();
+ cq.setAccessed(accessed);
+ assertTrue(accessed.equals(cq.getAccessed()));
+ cq.setExpires(expires);
+ assertTrue(expires.equals(cq.getExpires()));
+ cq.setId(id);
+ assertEquals(id, cq.getId());
+ cq.setQuery(query);
+ assertEquals(query, cq.getQuery());
+ cq.setType(ctype);
+ assertEquals((Integer) type2, cq.getType());
+ cq.setType(type);
+ assertEquals((Integer) type, cq.getType());
+ cq.setValue(value);
+ assertEquals(value, cq.getValue());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/cache/CacheTypeTest.java b/model/src/test/java/lcsb/mapviewer/model/cache/CacheTypeTest.java
index a9ccdc9666..fe634b21ce 100644
--- a/model/src/test/java/lcsb/mapviewer/model/cache/CacheTypeTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/cache/CacheTypeTest.java
@@ -1,50 +1,50 @@
-package lcsb.mapviewer.model.cache;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class CacheTypeTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new CacheType());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- int id = 4;
- int validity = 12;
- String className = "cname";
- CacheType ct = new CacheType();
- ct.setId(id);
- ct.setClassName(className);
- ct.setValidity(validity);
- assertEquals(id, ct.getId());
- assertEquals(className, ct.getClassName());
- assertEquals(validity, ct.getValidity());
- assertNotNull(ct.toString());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.cache;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class CacheTypeTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new CacheType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ int id = 4;
+ int validity = 12;
+ String className = "cname";
+ CacheType ct = new CacheType();
+ ct.setId(id);
+ ct.setClassName(className);
+ ct.setValidity(validity);
+ assertEquals(id, ct.getId());
+ assertEquals(className, ct.getClassName());
+ assertEquals(validity, ct.getValidity());
+ assertNotNull(ct.toString());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/cache/UploadedFileEntryTest.java b/model/src/test/java/lcsb/mapviewer/model/cache/UploadedFileEntryTest.java
index 54f7f5f75f..ed6588fe62 100644
--- a/model/src/test/java/lcsb/mapviewer/model/cache/UploadedFileEntryTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/cache/UploadedFileEntryTest.java
@@ -1,33 +1,33 @@
-package lcsb.mapviewer.model.cache;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class UploadedFileEntryTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new UploadedFileEntry());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.cache;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class UploadedFileEntryTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new UploadedFileEntry());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/graphics/AllGraphicsTests.java b/model/src/test/java/lcsb/mapviewer/model/graphics/AllGraphicsTests.java
index e1aa276dc7..a17a49b09b 100644
--- a/model/src/test/java/lcsb/mapviewer/model/graphics/AllGraphicsTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/graphics/AllGraphicsTests.java
@@ -1,18 +1,18 @@
-package lcsb.mapviewer.model.graphics;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ ArrowTypeDataComparatorTest.class, //
- ArrowTypeDataTest.class, //
- ArrowTypeTest.class, //
- LineTypeTest.class, //
- PolylineDataTest.class, //
- PolylineDataComparatorTest.class,//
-
-})
-public class AllGraphicsTests {
-
-}
+package lcsb.mapviewer.model.graphics;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ ArrowTypeDataComparatorTest.class, //
+ ArrowTypeDataTest.class, //
+ ArrowTypeTest.class, //
+ LineTypeTest.class, //
+ PolylineDataTest.class, //
+ PolylineDataComparatorTest.class,//
+
+})
+public class AllGraphicsTests {
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/graphics/ArrowTypeDataComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/graphics/ArrowTypeDataComparatorTest.java
index dd7e91768e..1a15ccf54c 100644
--- a/model/src/test/java/lcsb/mapviewer/model/graphics/ArrowTypeDataComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/graphics/ArrowTypeDataComparatorTest.java
@@ -1,72 +1,72 @@
-package lcsb.mapviewer.model.graphics;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ArrowTypeDataComparatorTest {
- ArrowTypeDataComparator comparator = new ArrowTypeDataComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testCompareEquals() {
- try {
- assertEquals(0, comparator.compare(null, null));
- assertEquals(0, comparator.compare(new ArrowTypeData(), new ArrowTypeData()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCompareDifferent() {
- try {
- assertTrue(comparator.compare(new ArrowTypeData(), null) != 0);
- assertTrue(comparator.compare(null, new ArrowTypeData()) != 0);
- assertTrue(comparator.compare(new ArrowTypeData() {
- private static final long serialVersionUID = 1L;
- }, new ArrowTypeData()) != 0);
-
- ArrowTypeData atd1 = new ArrowTypeData();
- ArrowTypeData atd2 = new ArrowTypeData();
-
- atd1.setArrowType(ArrowType.CROSSBAR);
- assertTrue(comparator.compare(atd1, atd2)!=0);
-
- atd1 = new ArrowTypeData();
- atd2 = new ArrowTypeData();
-
- atd1.setArrowLineType(LineType.DOUBLE);
- assertTrue(comparator.compare(atd1, atd2)!=0);
-
- atd1 = new ArrowTypeData();
- atd2 = new ArrowTypeData();
-
- atd1.setLen(2.0);
- assertTrue(comparator.compare(atd1, atd2)!=0);
-
-
- atd1 = new ArrowTypeData();
- atd2 = new ArrowTypeData();
-
- atd1.setAngle(3.4);
- assertTrue(comparator.compare(atd1, atd2)!=0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.graphics;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ArrowTypeDataComparatorTest {
+ ArrowTypeDataComparator comparator = new ArrowTypeDataComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testCompareEquals() {
+ try {
+ assertEquals(0, comparator.compare(null, null));
+ assertEquals(0, comparator.compare(new ArrowTypeData(), new ArrowTypeData()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCompareDifferent() {
+ try {
+ assertTrue(comparator.compare(new ArrowTypeData(), null) != 0);
+ assertTrue(comparator.compare(null, new ArrowTypeData()) != 0);
+ assertTrue(comparator.compare(new ArrowTypeData() {
+ private static final long serialVersionUID = 1L;
+ }, new ArrowTypeData()) != 0);
+
+ ArrowTypeData atd1 = new ArrowTypeData();
+ ArrowTypeData atd2 = new ArrowTypeData();
+
+ atd1.setArrowType(ArrowType.CROSSBAR);
+ assertTrue(comparator.compare(atd1, atd2)!=0);
+
+ atd1 = new ArrowTypeData();
+ atd2 = new ArrowTypeData();
+
+ atd1.setArrowLineType(LineType.DOUBLE);
+ assertTrue(comparator.compare(atd1, atd2)!=0);
+
+ atd1 = new ArrowTypeData();
+ atd2 = new ArrowTypeData();
+
+ atd1.setLen(2.0);
+ assertTrue(comparator.compare(atd1, atd2)!=0);
+
+
+ atd1 = new ArrowTypeData();
+ atd2 = new ArrowTypeData();
+
+ atd1.setAngle(3.4);
+ assertTrue(comparator.compare(atd1, atd2)!=0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/graphics/ArrowTypeDataTest.java b/model/src/test/java/lcsb/mapviewer/model/graphics/ArrowTypeDataTest.java
index 274720d480..7127d2f882 100644
--- a/model/src/test/java/lcsb/mapviewer/model/graphics/ArrowTypeDataTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/graphics/ArrowTypeDataTest.java
@@ -1,79 +1,79 @@
-package lcsb.mapviewer.model.graphics;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class ArrowTypeDataTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new ArrowTypeData());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- ArrowTypeData original = new ArrowTypeData();
- ArrowTypeData degraded = original.copy();
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- ArrowTypeData original = new ArrowTypeData();
- int id = 29;
-
- original.setId(id);
- assertEquals(id, original.getId());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new ArrowTypeData() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.graphics;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class ArrowTypeDataTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new ArrowTypeData());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ ArrowTypeData original = new ArrowTypeData();
+ ArrowTypeData degraded = original.copy();
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ ArrowTypeData original = new ArrowTypeData();
+ int id = 29;
+
+ original.setId(id);
+ assertEquals(id, original.getId());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new ArrowTypeData() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/graphics/ArrowTypeTest.java b/model/src/test/java/lcsb/mapviewer/model/graphics/ArrowTypeTest.java
index 9fbee6020e..d8701436b3 100644
--- a/model/src/test/java/lcsb/mapviewer/model/graphics/ArrowTypeTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/graphics/ArrowTypeTest.java
@@ -1,29 +1,29 @@
-package lcsb.mapviewer.model.graphics;
-
-import static org.junit.Assert.*;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ArrowTypeTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testValidValues() {
- for (ArrowType type : ArrowType.values()) {
- assertNotNull(type);
-
- // for coverage tests
- ArrowType.valueOf(type.toString());
- }
- }
-
-}
+package lcsb.mapviewer.model.graphics;
+
+import static org.junit.Assert.*;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ArrowTypeTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testValidValues() {
+ for (ArrowType type : ArrowType.values()) {
+ assertNotNull(type);
+
+ // for coverage tests
+ ArrowType.valueOf(type.toString());
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/graphics/LineTypeTest.java b/model/src/test/java/lcsb/mapviewer/model/graphics/LineTypeTest.java
index 8bb7702d1e..8d16c8f510 100644
--- a/model/src/test/java/lcsb/mapviewer/model/graphics/LineTypeTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/graphics/LineTypeTest.java
@@ -1,30 +1,30 @@
-package lcsb.mapviewer.model.graphics;
-
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class LineTypeTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testValidValues() {
- for (LineType type : LineType.values()) {
- assertNotNull(type);
- assertNotNull(type.getStroke());
-
- // for coverage tests
- LineType.valueOf(type.toString());
- }
- }
-
-}
+package lcsb.mapviewer.model.graphics;
+
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class LineTypeTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testValidValues() {
+ for (LineType type : LineType.values()) {
+ assertNotNull(type);
+ assertNotNull(type.getStroke());
+
+ // for coverage tests
+ LineType.valueOf(type.toString());
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/graphics/PolylineDataComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/graphics/PolylineDataComparatorTest.java
index 2348b1ca8c..4abcb430fd 100644
--- a/model/src/test/java/lcsb/mapviewer/model/graphics/PolylineDataComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/graphics/PolylineDataComparatorTest.java
@@ -1,112 +1,112 @@
-package lcsb.mapviewer.model.graphics;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.awt.Color;
-import java.awt.geom.Point2D;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class PolylineDataComparatorTest {
-
- PolylineDataComparator comparator = new PolylineDataComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- PolylineData pd1 = new PolylineData();
- PolylineData pd2 = new PolylineData();
- assertEquals(0, comparator.compare(pd1, pd2));
- assertEquals(0, comparator.compare(null, null));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid() {
- try {
- class Tmp extends PolylineData {
- private static final long serialVersionUID = 1L;
- }
- Tmp pd1 = new Tmp();
- Tmp pd2 = new Tmp();
- comparator.compare(pd1, pd2);
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent() {
- try {
- PolylineData pd1 = new PolylineData();
- PolylineData pd2 = new PolylineData();
-
- assertTrue(comparator.compare(pd2, null) != 0);
- assertTrue(comparator.compare(null, pd1) != 0);
-
- pd1 = new PolylineData();
- pd2 = new PolylineData();
- pd2.addPoint(new Point2D.Double(1, 2));
- pd2.addPoint(new Point2D.Double(1, 3));
- assertTrue(comparator.compare(pd1, pd2) != 0);
- assertTrue(comparator.compare(pd2, pd1) != 0);
-
- pd1 = new PolylineData();
- pd2 = new PolylineData();
- ArrowTypeData atd = new ArrowTypeData();
- atd.setLen(34);
- pd2.setBeginAtd(atd);
- assertTrue(comparator.compare(pd1, pd2) != 0);
- assertTrue(comparator.compare(pd2, pd1) != 0);
-
- pd1 = new PolylineData();
- pd2 = new PolylineData();
- atd = new ArrowTypeData();
- atd.setLen(34);
- pd2.setEndAtd(atd);
- assertTrue(comparator.compare(pd1, pd2) != 0);
- assertTrue(comparator.compare(pd2, pd1) != 0);
-
- pd1 = new PolylineData();
- pd2 = new PolylineData();
- pd2.setColor(Color.BLUE);
- assertTrue(comparator.compare(pd1, pd2) != 0);
- assertTrue(comparator.compare(pd2, pd1) != 0);
-
- pd1 = new PolylineData();
- pd2 = new PolylineData();
- pd2.setType(LineType.DASHED);
- assertTrue(comparator.compare(pd1, pd2) != 0);
- assertTrue(comparator.compare(pd2, pd1) != 0);
-
- assertTrue(comparator.compare(pd2, new PolylineData() {
- private static final long serialVersionUID = 1L;
- }) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.graphics;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.awt.Color;
+import java.awt.geom.Point2D;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class PolylineDataComparatorTest {
+
+ PolylineDataComparator comparator = new PolylineDataComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ PolylineData pd1 = new PolylineData();
+ PolylineData pd2 = new PolylineData();
+ assertEquals(0, comparator.compare(pd1, pd2));
+ assertEquals(0, comparator.compare(null, null));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid() {
+ try {
+ class Tmp extends PolylineData {
+ private static final long serialVersionUID = 1L;
+ }
+ Tmp pd1 = new Tmp();
+ Tmp pd2 = new Tmp();
+ comparator.compare(pd1, pd2);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ PolylineData pd1 = new PolylineData();
+ PolylineData pd2 = new PolylineData();
+
+ assertTrue(comparator.compare(pd2, null) != 0);
+ assertTrue(comparator.compare(null, pd1) != 0);
+
+ pd1 = new PolylineData();
+ pd2 = new PolylineData();
+ pd2.addPoint(new Point2D.Double(1, 2));
+ pd2.addPoint(new Point2D.Double(1, 3));
+ assertTrue(comparator.compare(pd1, pd2) != 0);
+ assertTrue(comparator.compare(pd2, pd1) != 0);
+
+ pd1 = new PolylineData();
+ pd2 = new PolylineData();
+ ArrowTypeData atd = new ArrowTypeData();
+ atd.setLen(34);
+ pd2.setBeginAtd(atd);
+ assertTrue(comparator.compare(pd1, pd2) != 0);
+ assertTrue(comparator.compare(pd2, pd1) != 0);
+
+ pd1 = new PolylineData();
+ pd2 = new PolylineData();
+ atd = new ArrowTypeData();
+ atd.setLen(34);
+ pd2.setEndAtd(atd);
+ assertTrue(comparator.compare(pd1, pd2) != 0);
+ assertTrue(comparator.compare(pd2, pd1) != 0);
+
+ pd1 = new PolylineData();
+ pd2 = new PolylineData();
+ pd2.setColor(Color.BLUE);
+ assertTrue(comparator.compare(pd1, pd2) != 0);
+ assertTrue(comparator.compare(pd2, pd1) != 0);
+
+ pd1 = new PolylineData();
+ pd2 = new PolylineData();
+ pd2.setType(LineType.DASHED);
+ assertTrue(comparator.compare(pd1, pd2) != 0);
+ assertTrue(comparator.compare(pd2, pd1) != 0);
+
+ assertTrue(comparator.compare(pd2, new PolylineData() {
+ private static final long serialVersionUID = 1L;
+ }) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/graphics/PolylineDataTest.java b/model/src/test/java/lcsb/mapviewer/model/graphics/PolylineDataTest.java
index ffde78d536..2acb342d6c 100644
--- a/model/src/test/java/lcsb/mapviewer/model/graphics/PolylineDataTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/graphics/PolylineDataTest.java
@@ -1,421 +1,421 @@
-package lcsb.mapviewer.model.graphics;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.awt.Color;
-import java.awt.geom.AffineTransform;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class PolylineDataTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testConstructor() throws Exception {
- try {
- PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
- assertNotNull(pd);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor2() throws Exception {
- try {
- PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
- PolylineData pd2 = new PolylineData(pd);
- assertNotNull(pd2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor3() throws Exception {
- try {
- List<Point2D> points = new ArrayList<>();
- points.add(new Point2D.Double(1, 1));
- points.add(new Point2D.Double(5, 1));
- points.add(new Point2D.Double(5, 5));
- PolylineData pd2 = new PolylineData(points);
- assertNotNull(pd2);
- assertEquals(points.size(), pd2.getPoints().size());
- assertEquals(8, pd2.length(), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddPoint() throws Exception {
- try {
- PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
- pd.addPoint(0, new Point2D.Double(-10, -10));
- assertEquals(3, pd.getPoints().size());
- assertTrue(pd.getPoints().get(0).getX() < 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddInvalidPoint() throws Exception {
- try {
- PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
- pd.addPoint(0, new Point2D.Double(Double.NEGATIVE_INFINITY, -10));
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetPoint() throws Exception {
- try {
- PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
- pd.setPoint(0, new Point2D.Double(-10, -10));
- assertEquals(2, pd.getPoints().size());
- assertTrue(pd.getPoints().get(0).getX() < 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetInvalidPoint() throws Exception {
- try {
- PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
- pd.setPoint(0, new Point2D.Double(Double.NEGATIVE_INFINITY, -10));
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetLines() throws Exception {
- try {
- List<Point2D> points = new ArrayList<>();
- points.add(new Point2D.Double(1, 1));
- points.add(new Point2D.Double(5, 1));
- points.add(new Point2D.Double(5, 5));
- PolylineData pd2 = new PolylineData(points);
- assertEquals(2, pd2.getLines().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvaliArgument() throws Exception {
- try {
- new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, Double.NaN));
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new PolylineData());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetSubline() throws Exception {
- try {
- List<Point2D> points = new ArrayList<>();
- points.add(new Point2D.Double(1, 1));
- points.add(new Point2D.Double(5, 1));
- points.add(new Point2D.Double(5, 5));
- PolylineData pd = new PolylineData(points);
- PolylineData pd2 = pd.getSubline(0, 2);
- assertNotNull(pd2);
- assertEquals(2, pd2.getPoints().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetEndPoint() throws Exception {
- try {
- PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
- pd.setEndPoint(new Point2D.Double(-10, -10));
- assertEquals(2, pd.getPoints().size());
- assertTrue(pd.getEndPoint().getX() < 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetInvalidEndPoint() throws Exception {
- try {
- PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
- pd.setEndPoint(new Point2D.Double(Double.NEGATIVE_INFINITY, -10));
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetStartPoint() throws Exception {
- try {
- PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
- pd.setStartPoint(new Point2D.Double(-10, -10));
- assertEquals(2, pd.getPoints().size());
- assertTrue(pd.getBeginPoint().getX() < 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetInvalidStartPoint() throws Exception {
- try {
- PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
- pd.setStartPoint(new Point2D.Double(Double.NEGATIVE_INFINITY, -10));
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToGeneralPath() throws Exception {
- try {
- List<Point2D> points = new ArrayList<>();
- points.add(new Point2D.Double(1, 1));
- points.add(new Point2D.Double(5, 1));
- points.add(new Point2D.Double(5, 5));
- PolylineData pd = new PolylineData(points);
- GeneralPath gp = pd.toGeneralPath();
- PathIterator pi = gp.getPathIterator(new AffineTransform());
- int count = 0;
- while (!pi.isDone()) {
- count++;
- pi.next();
- }
- assertEquals(3, count);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testTrimEnd() throws Exception {
- try {
- List<Point2D> points = new ArrayList<>();
- points.add(new Point2D.Double(1, 1));
- points.add(new Point2D.Double(11, 1));
- PolylineData pd = new PolylineData(points);
- pd.trimEnd(3);
-
- assertEquals(8, pd.getEndPoint().getX(), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testTrimBegin() throws Exception {
- try {
- List<Point2D> points = new ArrayList<>();
- points.add(new Point2D.Double(1, 1));
- points.add(new Point2D.Double(11, 1));
- PolylineData pd = new PolylineData(points);
- pd.trimBegin(3);
-
- assertEquals(4, pd.getPoints().get(0).getX(), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testTrimEnd2() throws Exception {
- try {
- List<Point2D> points = new ArrayList<>();
- points.add(new Point2D.Double(1, 1));
- points.add(new Point2D.Double(11, 1));
- PolylineData pd = new PolylineData(points);
- pd.trimEnd(30);
-
- assertEquals(1, pd.getEndPoint().getX(), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testTrimBegin2() throws Exception {
- try {
- List<Point2D> points = new ArrayList<>();
- points.add(new Point2D.Double(1, 1));
- points.add(new Point2D.Double(11, 1));
- PolylineData pd = new PolylineData(points);
- pd.trimBegin(30);
-
- assertEquals(11, pd.getPoints().get(0).getX(), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReverse() throws Exception {
- try {
- List<Point2D> points = new ArrayList<>();
- points.add(new Point2D.Double(1, 1));
- points.add(new Point2D.Double(11, 1));
- PolylineData pd = new PolylineData(points);
- PolylineData pd2 = pd.reverse();
- assertTrue(pd.getBeginPoint().distance(pd2.getEndPoint()) <= Configuration.EPSILON);
- assertTrue(pd2.getBeginPoint().distance(pd.getEndPoint()) <= Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testEmptyLength() throws Exception {
- try {
- PolylineData pd = new PolylineData();
- pd.addPoint(new Point2D.Double(0, 0));
- assertEquals(0, pd.length(), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetInvalidPoints() throws Exception {
- try {
- List<Point2D> points = new ArrayList<>();
- points.add(new Point2D.Double(Double.NEGATIVE_INFINITY, -10));
- PolylineData pd = new PolylineData();
- pd.setPoints(points);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() throws Exception {
- try {
- PolylineData pd = new PolylineData();
- Color color = Color.BLACK;
- LineType type = LineType.DASH_DOT;
- String strWidth = "12";
- double width = 12.0;
- int id = 3;
- pd.setColor(color);
- pd.setId(id);
- pd.setType(type);
- pd.setWidth(strWidth);
-
- assertEquals(id, pd.getId());
- assertEquals(color, pd.getColor());
- assertEquals(width, pd.getWidth(), Configuration.EPSILON);
- assertEquals(type, pd.getType());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSimpleCopy() throws Exception {
- try {
- PolylineData pd = new PolylineData();
- PolylineData pd2 = pd.copy();
-
- assertNotNull(pd2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() throws Exception {
- try {
- PolylineData pd = new PolylineData() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- };
- pd.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.graphics;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.awt.Color;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class PolylineDataTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testConstructor() throws Exception {
+ try {
+ PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
+ assertNotNull(pd);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor2() throws Exception {
+ try {
+ PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
+ PolylineData pd2 = new PolylineData(pd);
+ assertNotNull(pd2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor3() throws Exception {
+ try {
+ List<Point2D> points = new ArrayList<>();
+ points.add(new Point2D.Double(1, 1));
+ points.add(new Point2D.Double(5, 1));
+ points.add(new Point2D.Double(5, 5));
+ PolylineData pd2 = new PolylineData(points);
+ assertNotNull(pd2);
+ assertEquals(points.size(), pd2.getPoints().size());
+ assertEquals(8, pd2.length(), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddPoint() throws Exception {
+ try {
+ PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
+ pd.addPoint(0, new Point2D.Double(-10, -10));
+ assertEquals(3, pd.getPoints().size());
+ assertTrue(pd.getPoints().get(0).getX() < 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddInvalidPoint() throws Exception {
+ try {
+ PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
+ pd.addPoint(0, new Point2D.Double(Double.NEGATIVE_INFINITY, -10));
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetPoint() throws Exception {
+ try {
+ PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
+ pd.setPoint(0, new Point2D.Double(-10, -10));
+ assertEquals(2, pd.getPoints().size());
+ assertTrue(pd.getPoints().get(0).getX() < 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetInvalidPoint() throws Exception {
+ try {
+ PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
+ pd.setPoint(0, new Point2D.Double(Double.NEGATIVE_INFINITY, -10));
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetLines() throws Exception {
+ try {
+ List<Point2D> points = new ArrayList<>();
+ points.add(new Point2D.Double(1, 1));
+ points.add(new Point2D.Double(5, 1));
+ points.add(new Point2D.Double(5, 5));
+ PolylineData pd2 = new PolylineData(points);
+ assertEquals(2, pd2.getLines().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvaliArgument() throws Exception {
+ try {
+ new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, Double.NaN));
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new PolylineData());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetSubline() throws Exception {
+ try {
+ List<Point2D> points = new ArrayList<>();
+ points.add(new Point2D.Double(1, 1));
+ points.add(new Point2D.Double(5, 1));
+ points.add(new Point2D.Double(5, 5));
+ PolylineData pd = new PolylineData(points);
+ PolylineData pd2 = pd.getSubline(0, 2);
+ assertNotNull(pd2);
+ assertEquals(2, pd2.getPoints().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetEndPoint() throws Exception {
+ try {
+ PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
+ pd.setEndPoint(new Point2D.Double(-10, -10));
+ assertEquals(2, pd.getPoints().size());
+ assertTrue(pd.getEndPoint().getX() < 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetInvalidEndPoint() throws Exception {
+ try {
+ PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
+ pd.setEndPoint(new Point2D.Double(Double.NEGATIVE_INFINITY, -10));
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetStartPoint() throws Exception {
+ try {
+ PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
+ pd.setStartPoint(new Point2D.Double(-10, -10));
+ assertEquals(2, pd.getPoints().size());
+ assertTrue(pd.getBeginPoint().getX() < 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetInvalidStartPoint() throws Exception {
+ try {
+ PolylineData pd = new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10));
+ pd.setStartPoint(new Point2D.Double(Double.NEGATIVE_INFINITY, -10));
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToGeneralPath() throws Exception {
+ try {
+ List<Point2D> points = new ArrayList<>();
+ points.add(new Point2D.Double(1, 1));
+ points.add(new Point2D.Double(5, 1));
+ points.add(new Point2D.Double(5, 5));
+ PolylineData pd = new PolylineData(points);
+ GeneralPath gp = pd.toGeneralPath();
+ PathIterator pi = gp.getPathIterator(new AffineTransform());
+ int count = 0;
+ while (!pi.isDone()) {
+ count++;
+ pi.next();
+ }
+ assertEquals(3, count);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTrimEnd() throws Exception {
+ try {
+ List<Point2D> points = new ArrayList<>();
+ points.add(new Point2D.Double(1, 1));
+ points.add(new Point2D.Double(11, 1));
+ PolylineData pd = new PolylineData(points);
+ pd.trimEnd(3);
+
+ assertEquals(8, pd.getEndPoint().getX(), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTrimBegin() throws Exception {
+ try {
+ List<Point2D> points = new ArrayList<>();
+ points.add(new Point2D.Double(1, 1));
+ points.add(new Point2D.Double(11, 1));
+ PolylineData pd = new PolylineData(points);
+ pd.trimBegin(3);
+
+ assertEquals(4, pd.getPoints().get(0).getX(), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTrimEnd2() throws Exception {
+ try {
+ List<Point2D> points = new ArrayList<>();
+ points.add(new Point2D.Double(1, 1));
+ points.add(new Point2D.Double(11, 1));
+ PolylineData pd = new PolylineData(points);
+ pd.trimEnd(30);
+
+ assertEquals(1, pd.getEndPoint().getX(), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTrimBegin2() throws Exception {
+ try {
+ List<Point2D> points = new ArrayList<>();
+ points.add(new Point2D.Double(1, 1));
+ points.add(new Point2D.Double(11, 1));
+ PolylineData pd = new PolylineData(points);
+ pd.trimBegin(30);
+
+ assertEquals(11, pd.getPoints().get(0).getX(), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReverse() throws Exception {
+ try {
+ List<Point2D> points = new ArrayList<>();
+ points.add(new Point2D.Double(1, 1));
+ points.add(new Point2D.Double(11, 1));
+ PolylineData pd = new PolylineData(points);
+ PolylineData pd2 = pd.reverse();
+ assertTrue(pd.getBeginPoint().distance(pd2.getEndPoint()) <= Configuration.EPSILON);
+ assertTrue(pd2.getBeginPoint().distance(pd.getEndPoint()) <= Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testEmptyLength() throws Exception {
+ try {
+ PolylineData pd = new PolylineData();
+ pd.addPoint(new Point2D.Double(0, 0));
+ assertEquals(0, pd.length(), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetInvalidPoints() throws Exception {
+ try {
+ List<Point2D> points = new ArrayList<>();
+ points.add(new Point2D.Double(Double.NEGATIVE_INFINITY, -10));
+ PolylineData pd = new PolylineData();
+ pd.setPoints(points);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() throws Exception {
+ try {
+ PolylineData pd = new PolylineData();
+ Color color = Color.BLACK;
+ LineType type = LineType.DASH_DOT;
+ String strWidth = "12";
+ double width = 12.0;
+ int id = 3;
+ pd.setColor(color);
+ pd.setId(id);
+ pd.setType(type);
+ pd.setWidth(strWidth);
+
+ assertEquals(id, pd.getId());
+ assertEquals(color, pd.getColor());
+ assertEquals(width, pd.getWidth(), Configuration.EPSILON);
+ assertEquals(type, pd.getType());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSimpleCopy() throws Exception {
+ try {
+ PolylineData pd = new PolylineData();
+ PolylineData pd2 = pd.copy();
+
+ assertNotNull(pd2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() throws Exception {
+ try {
+ PolylineData pd = new PolylineData() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ };
+ pd.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/log/AllLogTests.java b/model/src/test/java/lcsb/mapviewer/model/log/AllLogTests.java
index 8ac37dc1f1..9c2ae5c6d3 100644
--- a/model/src/test/java/lcsb/mapviewer/model/log/AllLogTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/log/AllLogTests.java
@@ -1,14 +1,14 @@
-package lcsb.mapviewer.model.log;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ LogTypeTest.class, //
- ObjectLogTest.class, //
- SystemLogTest.class //
-})
-public class AllLogTests {
-
-}
+package lcsb.mapviewer.model.log;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ LogTypeTest.class, //
+ ObjectLogTest.class, //
+ SystemLogTest.class //
+})
+public class AllLogTests {
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/log/LogTypeTest.java b/model/src/test/java/lcsb/mapviewer/model/log/LogTypeTest.java
index 743855cb5e..a1f6925281 100644
--- a/model/src/test/java/lcsb/mapviewer/model/log/LogTypeTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/log/LogTypeTest.java
@@ -1,29 +1,29 @@
-package lcsb.mapviewer.model.log;
-
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class LogTypeTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testValidValues() {
- for (LogType type : LogType.values()) {
- assertNotNull(type);
-
- // for coverage tests
- LogType.valueOf(type.toString());
- }
- }
-
-}
+package lcsb.mapviewer.model.log;
+
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class LogTypeTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testValidValues() {
+ for (LogType type : LogType.values()) {
+ assertNotNull(type);
+
+ // for coverage tests
+ LogType.valueOf(type.toString());
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/log/ObjectLogTest.java b/model/src/test/java/lcsb/mapviewer/model/log/ObjectLogTest.java
index 882666ad11..ca0f9f8f3e 100644
--- a/model/src/test/java/lcsb/mapviewer/model/log/ObjectLogTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/log/ObjectLogTest.java
@@ -1,65 +1,65 @@
-package lcsb.mapviewer.model.log;
-
-import static org.junit.Assert.assertEquals;
-
-import java.util.Calendar;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.user.User;
-
-public class ObjectLogTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new ObjectLog());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- ObjectLog log = new ObjectLog();
- String description = "qwe";
- int id = 20;
- int objectId = 21;
- Calendar time = Calendar.getInstance();
- Class<?> tableName = Object.class;
- LogType type = LogType.ADD_MISSING_CONNECTION;
- User user = new User();
- log.setDescription(description);
- log.setId(id);
- log.setObjectId(objectId);
- log.setTime(time);
- log.setTable(tableName);
- log.setType(type);
- log.setUser(user);
-
- assertEquals(description,log.getDescription());
- assertEquals(id,log.getId());
- assertEquals((Integer)objectId,log.getObjectId());
- assertEquals(time,log.getTime());
- assertEquals(tableName,log.getTable());
- assertEquals(type,log.getType());
- assertEquals(user,log.getUser());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.log;
+
+import static org.junit.Assert.assertEquals;
+
+import java.util.Calendar;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.user.User;
+
+public class ObjectLogTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new ObjectLog());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ ObjectLog log = new ObjectLog();
+ String description = "qwe";
+ int id = 20;
+ int objectId = 21;
+ Calendar time = Calendar.getInstance();
+ Class<?> tableName = Object.class;
+ LogType type = LogType.ADD_MISSING_CONNECTION;
+ User user = new User();
+ log.setDescription(description);
+ log.setId(id);
+ log.setObjectId(objectId);
+ log.setTime(time);
+ log.setTable(tableName);
+ log.setType(type);
+ log.setUser(user);
+
+ assertEquals(description,log.getDescription());
+ assertEquals(id,log.getId());
+ assertEquals((Integer)objectId,log.getObjectId());
+ assertEquals(time,log.getTime());
+ assertEquals(tableName,log.getTable());
+ assertEquals(type,log.getType());
+ assertEquals(user,log.getUser());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/log/SystemLogTest.java b/model/src/test/java/lcsb/mapviewer/model/log/SystemLogTest.java
index 0de26cceed..d555b5a184 100644
--- a/model/src/test/java/lcsb/mapviewer/model/log/SystemLogTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/log/SystemLogTest.java
@@ -1,27 +1,27 @@
-package lcsb.mapviewer.model.log;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class SystemLogTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new SystemLog());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.log;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class SystemLogTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new SystemLog());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/AllMapTests.java b/model/src/test/java/lcsb/mapviewer/model/map/AllMapTests.java
index 4a625e304c..5f78c6bd33 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/AllMapTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/AllMapTests.java
@@ -1,49 +1,49 @@
-package lcsb.mapviewer.model.map;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-import lcsb.mapviewer.model.map.compartment.AllCompartmentTests;
-import lcsb.mapviewer.model.map.kinetics.AllKineticsTests;
-import lcsb.mapviewer.model.map.layout.AllLayoutTests;
-import lcsb.mapviewer.model.map.layout.graphics.AllGraphicsTests;
-import lcsb.mapviewer.model.map.model.AllModelTests;
-import lcsb.mapviewer.model.map.modifier.AllModifierTests;
-import lcsb.mapviewer.model.map.reaction.AllReactionTests;
-import lcsb.mapviewer.model.map.species.AllSpeciesTests;
-import lcsb.mapviewer.model.map.statistics.AllStatisticsTests;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AllCompartmentTests.class, //
- ElementInFewParentsExceptionTest.class, //
- AllGraphicsTests.class, //
- AllKineticsTests.class, //
- AllLayoutTests.class, //
- AllModelTests.class, //
- AllModifierTests.class, //
- AllReactionTests.class, //
- AllSpeciesTests.class, //
- AllStatisticsTests.class, //
- CommentTest.class, //
- InconsistentModelExceptionTest.class, //
- LayoutComparatorTest.class, //
- MiriamDataTest.class, //
- MiriamRelationTypeTest.class, //
- MiriamTypeTest.class, //
- MiriamTypeNameComparatorTest.class, //
- OverviewImageComparatorTest.class, //
- OverviewImageLinkComparatorTest.class, //
- OverviewImageLinkTest.class, //
- OverviewImageTest.class, //
- OverviewLinkComparatorTest.class, //
- OverviewLinkTest.class, //
- OverviewModelLinkComparatorTest.class, //
- OverviewModelLinkTest.class, //
- OverviewSearchLinkTest.class, //
- SearchIndexTest.class,//
-})
-
-public class AllMapTests {
-
-}
+package lcsb.mapviewer.model.map;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+import lcsb.mapviewer.model.map.compartment.AllCompartmentTests;
+import lcsb.mapviewer.model.map.kinetics.AllKineticsTests;
+import lcsb.mapviewer.model.map.layout.AllLayoutTests;
+import lcsb.mapviewer.model.map.layout.graphics.AllGraphicsTests;
+import lcsb.mapviewer.model.map.model.AllModelTests;
+import lcsb.mapviewer.model.map.modifier.AllModifierTests;
+import lcsb.mapviewer.model.map.reaction.AllReactionTests;
+import lcsb.mapviewer.model.map.species.AllSpeciesTests;
+import lcsb.mapviewer.model.map.statistics.AllStatisticsTests;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AllCompartmentTests.class, //
+ ElementInFewParentsExceptionTest.class, //
+ AllGraphicsTests.class, //
+ AllKineticsTests.class, //
+ AllLayoutTests.class, //
+ AllModelTests.class, //
+ AllModifierTests.class, //
+ AllReactionTests.class, //
+ AllSpeciesTests.class, //
+ AllStatisticsTests.class, //
+ CommentTest.class, //
+ InconsistentModelExceptionTest.class, //
+ LayoutComparatorTest.class, //
+ MiriamDataTest.class, //
+ MiriamRelationTypeTest.class, //
+ MiriamTypeTest.class, //
+ MiriamTypeNameComparatorTest.class, //
+ OverviewImageComparatorTest.class, //
+ OverviewImageLinkComparatorTest.class, //
+ OverviewImageLinkTest.class, //
+ OverviewImageTest.class, //
+ OverviewLinkComparatorTest.class, //
+ OverviewLinkTest.class, //
+ OverviewModelLinkComparatorTest.class, //
+ OverviewModelLinkTest.class, //
+ OverviewSearchLinkTest.class, //
+ SearchIndexTest.class,//
+})
+
+public class AllMapTests {
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/CommentTest.java b/model/src/test/java/lcsb/mapviewer/model/map/CommentTest.java
index d44b3e1ad9..65bdb2a74a 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/CommentTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/CommentTest.java
@@ -1,90 +1,90 @@
-package lcsb.mapviewer.model.map;
-
-import static org.junit.Assert.assertEquals;
-
-import java.awt.geom.Point2D;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.user.User;
-
-public class CommentTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new Comment());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- Comment comment = new Comment();
- String content = "c";
- Point2D.Double coordinates = new Point2D.Double(1, 2);
- String email = "a";
- boolean deleted = true;
- int id = 85;
- Model model = new ModelFullIndexed(null);
- String name = "n";
- boolean pinned = true;
- String removeReason = "rr";
- Model submodel = new ModelFullIndexed(null);
- Integer tableId = 5;
- Class<?> tableName = Object.class;
- User user = new User();
-
- comment.setContent(content);
- assertEquals(content, comment.getContent());
- comment.setCoordinates(coordinates);
- assertEquals(coordinates, comment.getCoordinates());
- comment.setDeleted(deleted);
- assertEquals(deleted, comment.isDeleted());
- comment.setEmail(email);
- assertEquals(email, comment.getEmail());
- comment.setId(id);
- assertEquals(id, comment.getId());
- comment.setModel(model);
- assertEquals(model, comment.getModelData().getModel());
- comment.setModelData(model.getModelData());
- assertEquals(model.getModelData(), comment.getModelData());
- comment.setName(name);
- assertEquals(name, comment.getName());
- comment.setPinned(pinned);
- assertEquals(pinned, comment.isPinned());
- comment.setRemoveReason(removeReason);
- assertEquals(removeReason, comment.getRemoveReason());
- comment.setSubmodel(submodel);
- assertEquals(submodel, comment.getSubmodel());
- comment.setSubmodelData(submodel.getModelData());
- assertEquals(submodel.getModelData(), comment.getSubmodelData());
- comment.setTableId(tableId);
- assertEquals(tableId, comment.getTableId());
- comment.setTableName(tableName);
- assertEquals(tableName, comment.getTableName());
- comment.setUser(user);
- assertEquals(user, comment.getUser());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.map;
+
+import static org.junit.Assert.assertEquals;
+
+import java.awt.geom.Point2D;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.user.User;
+
+public class CommentTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new Comment());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ Comment comment = new Comment();
+ String content = "c";
+ Point2D.Double coordinates = new Point2D.Double(1, 2);
+ String email = "a";
+ boolean deleted = true;
+ int id = 85;
+ Model model = new ModelFullIndexed(null);
+ String name = "n";
+ boolean pinned = true;
+ String removeReason = "rr";
+ Model submodel = new ModelFullIndexed(null);
+ Integer tableId = 5;
+ Class<?> tableName = Object.class;
+ User user = new User();
+
+ comment.setContent(content);
+ assertEquals(content, comment.getContent());
+ comment.setCoordinates(coordinates);
+ assertEquals(coordinates, comment.getCoordinates());
+ comment.setDeleted(deleted);
+ assertEquals(deleted, comment.isDeleted());
+ comment.setEmail(email);
+ assertEquals(email, comment.getEmail());
+ comment.setId(id);
+ assertEquals(id, comment.getId());
+ comment.setModel(model);
+ assertEquals(model, comment.getModelData().getModel());
+ comment.setModelData(model.getModelData());
+ assertEquals(model.getModelData(), comment.getModelData());
+ comment.setName(name);
+ assertEquals(name, comment.getName());
+ comment.setPinned(pinned);
+ assertEquals(pinned, comment.isPinned());
+ comment.setRemoveReason(removeReason);
+ assertEquals(removeReason, comment.getRemoveReason());
+ comment.setSubmodel(submodel);
+ assertEquals(submodel, comment.getSubmodel());
+ comment.setSubmodelData(submodel.getModelData());
+ assertEquals(submodel.getModelData(), comment.getSubmodelData());
+ comment.setTableId(tableId);
+ assertEquals(tableId, comment.getTableId());
+ comment.setTableName(tableName);
+ assertEquals(tableName, comment.getTableName());
+ comment.setUser(user);
+ assertEquals(user, comment.getUser());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/ElementInFewParentsExceptionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/ElementInFewParentsExceptionTest.java
index 5d4cb523ac..ab1f0f351f 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/ElementInFewParentsExceptionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/ElementInFewParentsExceptionTest.java
@@ -1,28 +1,28 @@
-package lcsb.mapviewer.model.map;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ElementInFewParentsExceptionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new ElementInFewParentsException(""));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ElementInFewParentsExceptionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new ElementInFewParentsException(""));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/InconsistentModelExceptionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/InconsistentModelExceptionTest.java
index 22c1b1ec38..604387471b 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/InconsistentModelExceptionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/InconsistentModelExceptionTest.java
@@ -1,28 +1,28 @@
-package lcsb.mapviewer.model.map;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class InconsistentModelExceptionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new InconsistentModelException(""));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class InconsistentModelExceptionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new InconsistentModelException(""));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/LayoutComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/LayoutComparatorTest.java
index b42cb22632..c50fe1a559 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/LayoutComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/LayoutComparatorTest.java
@@ -1,139 +1,139 @@
-package lcsb.mapviewer.model.map;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.LayoutComparator;
-
-public class LayoutComparatorTest {
- LayoutComparator comparator = new LayoutComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- Layout layout1 = getLayout();
- Layout layout2 = getLayout();
-
- assertEquals(0, comparator.compare(new Layout(), new Layout()));
- assertEquals(0, comparator.compare(layout1, layout2));
- assertEquals(0, comparator.compare(layout1, layout1));
- assertEquals(0, comparator.compare(null, null));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
- private Layout getLayout() {
- Layout layout = new Layout();
- layout.setDirectory("dirrr");
- layout.setTitle("title");
- return layout;
- }
-
- @Test
- public void testDifferent() {
- try {
- Layout layout1 = getLayout();
- Layout layout2 = getLayout();
-
- assertTrue(comparator.compare(layout1, new Layout()) != 0);
-
- assertTrue(comparator.compare(layout1, null) != 0);
- assertTrue(comparator.compare(null, layout1) != 0);
-
- layout1 = getLayout();
- layout2 = getLayout();
-
- layout1.setDirectory("ASDsaD");
-
- assertTrue(comparator.compare(layout1, layout2) != 0);
- assertTrue(comparator.compare(layout2, layout1) != 0);
-
- layout1 = getLayout();
- layout2 = getLayout();
-
- layout1.setTitle("ASDsaD");
-
- assertTrue(comparator.compare(layout1, layout2) != 0);
- assertTrue(comparator.compare(layout2, layout1) != 0);
-
- layout1 = getLayout();
- layout2 = getLayout();
-
- layout1.setHierarchicalView(true);
-
- assertTrue(comparator.compare(layout1, layout2) != 0);
- assertTrue(comparator.compare(layout2, layout1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
- @Test
- public void testDifferent2() {
- try {
- class Tmp extends Layout {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }
- ;
-
- Layout layout1 = new Tmp();
- Layout layout2 = new Layout();
-
- assertTrue(comparator.compare(layout1, layout2) != 0);
- assertTrue(comparator.compare(layout2, layout1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
- @Test
- public void testInvalid() {
- try {
- class Tmp extends Layout {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }
- ;
-
- Layout layout1 = new Tmp();
- Layout layout2 = new Tmp();
-
- comparator.compare(layout1, layout2);
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
-}
+package lcsb.mapviewer.model.map;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.layout.LayoutComparator;
+
+public class LayoutComparatorTest {
+ LayoutComparator comparator = new LayoutComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ Layout layout1 = getLayout();
+ Layout layout2 = getLayout();
+
+ assertEquals(0, comparator.compare(new Layout(), new Layout()));
+ assertEquals(0, comparator.compare(layout1, layout2));
+ assertEquals(0, comparator.compare(layout1, layout1));
+ assertEquals(0, comparator.compare(null, null));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+ private Layout getLayout() {
+ Layout layout = new Layout();
+ layout.setDirectory("dirrr");
+ layout.setTitle("title");
+ return layout;
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ Layout layout1 = getLayout();
+ Layout layout2 = getLayout();
+
+ assertTrue(comparator.compare(layout1, new Layout()) != 0);
+
+ assertTrue(comparator.compare(layout1, null) != 0);
+ assertTrue(comparator.compare(null, layout1) != 0);
+
+ layout1 = getLayout();
+ layout2 = getLayout();
+
+ layout1.setDirectory("ASDsaD");
+
+ assertTrue(comparator.compare(layout1, layout2) != 0);
+ assertTrue(comparator.compare(layout2, layout1) != 0);
+
+ layout1 = getLayout();
+ layout2 = getLayout();
+
+ layout1.setTitle("ASDsaD");
+
+ assertTrue(comparator.compare(layout1, layout2) != 0);
+ assertTrue(comparator.compare(layout2, layout1) != 0);
+
+ layout1 = getLayout();
+ layout2 = getLayout();
+
+ layout1.setHierarchicalView(true);
+
+ assertTrue(comparator.compare(layout1, layout2) != 0);
+ assertTrue(comparator.compare(layout2, layout1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+ @Test
+ public void testDifferent2() {
+ try {
+ class Tmp extends Layout {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }
+ ;
+
+ Layout layout1 = new Tmp();
+ Layout layout2 = new Layout();
+
+ assertTrue(comparator.compare(layout1, layout2) != 0);
+ assertTrue(comparator.compare(layout2, layout1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+ @Test
+ public void testInvalid() {
+ try {
+ class Tmp extends Layout {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }
+ ;
+
+ Layout layout1 = new Tmp();
+ Layout layout2 = new Tmp();
+
+ comparator.compare(layout1, layout2);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/MiriamDataTest.java b/model/src/test/java/lcsb/mapviewer/model/map/MiriamDataTest.java
index 8e9668360d..a8dca2f41f 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/MiriamDataTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/MiriamDataTest.java
@@ -1,135 +1,135 @@
-package lcsb.mapviewer.model.map;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-
-public class MiriamDataTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new MiriamData());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidConstructor1() {
- try {
- new MiriamData(null, null);
- fail("Exception expection");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidConstructor2() {
- try {
- new MiriamData(null, MiriamType.CAS, null);
- fail("Exception expection");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetIdFromIdentifier() {
- try {
- assertEquals("id", MiriamData.getIdFromIdentifier("name:id"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- int id = 6;
- MiriamData md = new MiriamData();
- md.setResource(null);
- assertNull(md.getResource());
-
- md.setId(id);
- assertEquals(id, md.getId());
-
- md.setAnnotator(this.getClass());
- assertEquals(this.getClass(), md.getAnnotator());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToString() {
- try {
- assertNotNull(new MiriamData().toString());
- assertNotNull(new MiriamData(MiriamType.CAS, "a").toString());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testEqual() {
- try {
- MiriamData md = new MiriamData();
- assertFalse(md.equals(new Object()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCompareTo() {
- try {
- MiriamData md = new MiriamData();
- assertTrue(md.compareTo(new MiriamData(MiriamType.CAS, "a")) != 0);
-
- MiriamData md1 = new MiriamData(MiriamType.CAS, "a");
- MiriamData md2 = new MiriamData(MiriamType.CAS, "a");
- assertTrue(md1.compareTo(md2) == 0);
-
- md1.setAnnotator(Integer.class);
- assertTrue(md1.compareTo(md2) != 0);
-
- md2.setAnnotator(Integer.class);
- assertTrue(md1.compareTo(md2) == 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.map;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+
+public class MiriamDataTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new MiriamData());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidConstructor1() {
+ try {
+ new MiriamData(null, null);
+ fail("Exception expection");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidConstructor2() {
+ try {
+ new MiriamData(null, MiriamType.CAS, null);
+ fail("Exception expection");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetIdFromIdentifier() {
+ try {
+ assertEquals("id", MiriamData.getIdFromIdentifier("name:id"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ int id = 6;
+ MiriamData md = new MiriamData();
+ md.setResource(null);
+ assertNull(md.getResource());
+
+ md.setId(id);
+ assertEquals(id, md.getId());
+
+ md.setAnnotator(this.getClass());
+ assertEquals(this.getClass(), md.getAnnotator());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToString() {
+ try {
+ assertNotNull(new MiriamData().toString());
+ assertNotNull(new MiriamData(MiriamType.CAS, "a").toString());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testEqual() {
+ try {
+ MiriamData md = new MiriamData();
+ assertFalse(md.equals(new Object()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCompareTo() {
+ try {
+ MiriamData md = new MiriamData();
+ assertTrue(md.compareTo(new MiriamData(MiriamType.CAS, "a")) != 0);
+
+ MiriamData md1 = new MiriamData(MiriamType.CAS, "a");
+ MiriamData md2 = new MiriamData(MiriamType.CAS, "a");
+ assertTrue(md1.compareTo(md2) == 0);
+
+ md1.setAnnotator(Integer.class);
+ assertTrue(md1.compareTo(md2) != 0);
+
+ md2.setAnnotator(Integer.class);
+ assertTrue(md1.compareTo(md2) == 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/MiriamRelationTypeTest.java b/model/src/test/java/lcsb/mapviewer/model/map/MiriamRelationTypeTest.java
index 0e7d84d3dc..17e609addf 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/MiriamRelationTypeTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/MiriamRelationTypeTest.java
@@ -1,38 +1,38 @@
-package lcsb.mapviewer.model.map;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class MiriamRelationTypeTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testValidValues() {
- for (MiriamRelationType type : MiriamRelationType.values()) {
- assertNotNull(type);
-
- // for coverage tests
- MiriamRelationType.valueOf(type.toString());
- assertNotNull(type.getStringRepresentation());
-
- }
- }
-
- @Test
- public void testGetTypeByString() {
- assertNull(MiriamRelationType.getTypeByStringRepresentation("DSfsdfs"));
- assertNotNull(MiriamRelationType.getTypeByStringRepresentation("bqbiol:occures"));
- }
-
-}
+package lcsb.mapviewer.model.map;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class MiriamRelationTypeTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testValidValues() {
+ for (MiriamRelationType type : MiriamRelationType.values()) {
+ assertNotNull(type);
+
+ // for coverage tests
+ MiriamRelationType.valueOf(type.toString());
+ assertNotNull(type.getStringRepresentation());
+
+ }
+ }
+
+ @Test
+ public void testGetTypeByString() {
+ assertNull(MiriamRelationType.getTypeByStringRepresentation("DSfsdfs"));
+ assertNotNull(MiriamRelationType.getTypeByStringRepresentation("bqbiol:occures"));
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/MiriamTypeNameComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/MiriamTypeNameComparatorTest.java
index b2d2bfb9f1..8dba860590 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/MiriamTypeNameComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/MiriamTypeNameComparatorTest.java
@@ -1,46 +1,46 @@
-package lcsb.mapviewer.model.map;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class MiriamTypeNameComparatorTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testCompareNulls() {
- try {
- MiriamTypeNameComparator comparator = new MiriamTypeNameComparator();
- assertEquals(0, comparator.compare(null, null));
- assertTrue(comparator.compare(null, MiriamType.CAS) != 0);
- assertTrue(comparator.compare(MiriamType.CAS, null) != 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCompare() {
- try {
- MiriamTypeNameComparator comparator = new MiriamTypeNameComparator();
- assertTrue(comparator.compare(MiriamType.CHEBI, MiriamType.CAS) < 0);
- assertTrue(comparator.compare(MiriamType.CAS, MiriamType.CHEBI) > 0);
- assertTrue(comparator.compare(MiriamType.CAS, MiriamType.CAS) == 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class MiriamTypeNameComparatorTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testCompareNulls() {
+ try {
+ MiriamTypeNameComparator comparator = new MiriamTypeNameComparator();
+ assertEquals(0, comparator.compare(null, null));
+ assertTrue(comparator.compare(null, MiriamType.CAS) != 0);
+ assertTrue(comparator.compare(MiriamType.CAS, null) != 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCompare() {
+ try {
+ MiriamTypeNameComparator comparator = new MiriamTypeNameComparator();
+ assertTrue(comparator.compare(MiriamType.CHEBI, MiriamType.CAS) < 0);
+ assertTrue(comparator.compare(MiriamType.CAS, MiriamType.CHEBI) > 0);
+ assertTrue(comparator.compare(MiriamType.CAS, MiriamType.CAS) == 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/MiriamTypeTest.java b/model/src/test/java/lcsb/mapviewer/model/map/MiriamTypeTest.java
index ec19ddedcb..75aad77291 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/MiriamTypeTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/MiriamTypeTest.java
@@ -1,136 +1,136 @@
-package lcsb.mapviewer.model.map;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.util.HashMap;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-
-public class MiriamTypeTest {
- Logger logger = Logger.getLogger(MiriamDataTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testIdUniqness() {
- try {
- Map<String, MiriamType> ids = new HashMap<>();
- for (MiriamType mt : MiriamType.values()) {
- assertNull(mt.getCommonName() + " doesn't have a unique key", ids.get(mt.getRegistryIdentifier()));
- ids.put(mt.getRegistryIdentifier(), mt);
-
- // coverage tests
- assertNotNull(MiriamType.valueOf(mt.name()));
- assertNotNull(mt.getUris());
- assertNotNull(mt.getValidClass());
- assertNotNull(mt.getRequiredClass());
- if (mt != MiriamType.UNKNOWN) {
- assertNotNull("No homepage for: " + mt, mt.getDbHomepage());
- }
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetMiriamDataFromIdentifier() {
- MiriamData md = MiriamType.getMiriamDataFromIdentifier("HGNC Symbol:SNCA");
- assertEquals(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"), md);
- }
-
- @Test
- public void testGetMiriamDataFromInvalidIdentifier() {
- try {
- MiriamType.getMiriamDataFromIdentifier("xyz:SNCA");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- }
- }
-
- @Test
- public void testGetMiriamDataFromInvalidIdentifier2() {
- try {
- MiriamType.getMiriamDataFromIdentifier("xyz");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- }
- }
-
- @Test
- public void testTypeByUri() {
- assertNotNull(MiriamType.getTypeByUri("urn:miriam:cas"));
- assertNull(MiriamType.getTypeByUri("xyz"));
- }
-
- @Test
- public void testTypeByCommonName() {
- assertNotNull(MiriamType.getTypeByCommonName("Consensus CDS"));
- assertNull(MiriamType.getTypeByCommonName("xyz"));
- }
-
- @Test
- public void testGetMiriamByUri1() throws Exception {
- try {
- MiriamData md = MiriamType.getMiriamByUri("urn:miriam:panther.family:PTHR19384:SF5");
- assertTrue(new MiriamData(MiriamType.PANTHER, "PTHR19384:SF5").equals(md));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetMiriamByUri2() throws Exception {
- try {
- MiriamData md = MiriamType.getMiriamByUri("urn:miriam:panther.family:PTHR19384%3ASF5");
- assertTrue(new MiriamData(MiriamType.PANTHER, "PTHR19384:SF5").equals(md));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetMiriamByUri3() throws Exception {
- try {
- MiriamData md = MiriamType.getMiriamByUri("urn:miriam:panther.family%3APTHR19384%3ASF5");
- assertTrue(new MiriamData(MiriamType.PANTHER, "PTHR19384:SF5").equals(md));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetMiriamByInvalidUri() throws Exception {
- try {
- MiriamType.getMiriamByUri("invalid_uri");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+
+public class MiriamTypeTest {
+ Logger logger = Logger.getLogger(MiriamDataTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testIdUniqness() {
+ try {
+ Map<String, MiriamType> ids = new HashMap<>();
+ for (MiriamType mt : MiriamType.values()) {
+ assertNull(mt.getCommonName() + " doesn't have a unique key", ids.get(mt.getRegistryIdentifier()));
+ ids.put(mt.getRegistryIdentifier(), mt);
+
+ // coverage tests
+ assertNotNull(MiriamType.valueOf(mt.name()));
+ assertNotNull(mt.getUris());
+ assertNotNull(mt.getValidClass());
+ assertNotNull(mt.getRequiredClass());
+ if (mt != MiriamType.UNKNOWN) {
+ assertNotNull("No homepage for: " + mt, mt.getDbHomepage());
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetMiriamDataFromIdentifier() {
+ MiriamData md = MiriamType.getMiriamDataFromIdentifier("HGNC Symbol:SNCA");
+ assertEquals(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"), md);
+ }
+
+ @Test
+ public void testGetMiriamDataFromInvalidIdentifier() {
+ try {
+ MiriamType.getMiriamDataFromIdentifier("xyz:SNCA");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ }
+ }
+
+ @Test
+ public void testGetMiriamDataFromInvalidIdentifier2() {
+ try {
+ MiriamType.getMiriamDataFromIdentifier("xyz");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ }
+ }
+
+ @Test
+ public void testTypeByUri() {
+ assertNotNull(MiriamType.getTypeByUri("urn:miriam:cas"));
+ assertNull(MiriamType.getTypeByUri("xyz"));
+ }
+
+ @Test
+ public void testTypeByCommonName() {
+ assertNotNull(MiriamType.getTypeByCommonName("Consensus CDS"));
+ assertNull(MiriamType.getTypeByCommonName("xyz"));
+ }
+
+ @Test
+ public void testGetMiriamByUri1() throws Exception {
+ try {
+ MiriamData md = MiriamType.getMiriamByUri("urn:miriam:panther.family:PTHR19384:SF5");
+ assertTrue(new MiriamData(MiriamType.PANTHER, "PTHR19384:SF5").equals(md));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetMiriamByUri2() throws Exception {
+ try {
+ MiriamData md = MiriamType.getMiriamByUri("urn:miriam:panther.family:PTHR19384%3ASF5");
+ assertTrue(new MiriamData(MiriamType.PANTHER, "PTHR19384:SF5").equals(md));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetMiriamByUri3() throws Exception {
+ try {
+ MiriamData md = MiriamType.getMiriamByUri("urn:miriam:panther.family%3APTHR19384%3ASF5");
+ assertTrue(new MiriamData(MiriamType.PANTHER, "PTHR19384:SF5").equals(md));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetMiriamByInvalidUri() throws Exception {
+ try {
+ MiriamType.getMiriamByUri("invalid_uri");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/OverviewImageComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/OverviewImageComparatorTest.java
index e61c0b1c82..7bbbc7a1bc 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/OverviewImageComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/OverviewImageComparatorTest.java
@@ -1,92 +1,92 @@
-package lcsb.mapviewer.model.map;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class OverviewImageComparatorTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEqual() throws Exception {
- try {
- OverviewImageComparator oic = new OverviewImageComparator();
-
- OverviewImage oi = new OverviewImage();
- OverviewImage oi2 = new OverviewImage();
-
- assertEquals(0, oic.compare(oi, oi2));
- assertEquals(0, oic.compare(null, null));
-
- oi.addLink(new OverviewImageLink());
- oi2.addLink(new OverviewImageLink());
- assertEquals(0, oic.compare(oi, oi2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent() throws Exception {
- try {
- OverviewImageComparator oic = new OverviewImageComparator();
-
- OverviewImage oi = new OverviewImage();
-
- OverviewImage oi2 = new OverviewImage();
- oi2.setFilename("x");
-
- assertTrue(0 != oic.compare(oi, oi2));
-
- oi2 = new OverviewImage();
- oi2.setHeight(1);
-
- assertTrue(0 != oic.compare(oi, oi2));
-
- oi2 = new OverviewImage();
- oi2.setWidth(2);
- ;
-
- assertTrue(0 != oic.compare(oi, oi2));
-
- oi2 = new OverviewImage();
- oi2.addLink(new OverviewModelLink());
-
- assertTrue(0 != oic.compare(oi, oi2));
-
- assertTrue(0 != oic.compare(oi, null));
- assertTrue(0 != oic.compare(null, oi2));
-
- assertTrue(0 != oic.compare(new OverviewImage() {
- private static final long serialVersionUID = 1L;
- }, oi2));
-
- oi = new OverviewImage();
- oi2 = new OverviewImage();
- OverviewImageLink link= new OverviewImageLink();
- link.setPolygon("1,1");
- oi.addLink(link);
- link= new OverviewImageLink();
- link.setPolygon("1,2");
- oi2.addLink(link);
-
- assertTrue(0 != oic.compare(oi, oi2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class OverviewImageComparatorTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEqual() throws Exception {
+ try {
+ OverviewImageComparator oic = new OverviewImageComparator();
+
+ OverviewImage oi = new OverviewImage();
+ OverviewImage oi2 = new OverviewImage();
+
+ assertEquals(0, oic.compare(oi, oi2));
+ assertEquals(0, oic.compare(null, null));
+
+ oi.addLink(new OverviewImageLink());
+ oi2.addLink(new OverviewImageLink());
+ assertEquals(0, oic.compare(oi, oi2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent() throws Exception {
+ try {
+ OverviewImageComparator oic = new OverviewImageComparator();
+
+ OverviewImage oi = new OverviewImage();
+
+ OverviewImage oi2 = new OverviewImage();
+ oi2.setFilename("x");
+
+ assertTrue(0 != oic.compare(oi, oi2));
+
+ oi2 = new OverviewImage();
+ oi2.setHeight(1);
+
+ assertTrue(0 != oic.compare(oi, oi2));
+
+ oi2 = new OverviewImage();
+ oi2.setWidth(2);
+ ;
+
+ assertTrue(0 != oic.compare(oi, oi2));
+
+ oi2 = new OverviewImage();
+ oi2.addLink(new OverviewModelLink());
+
+ assertTrue(0 != oic.compare(oi, oi2));
+
+ assertTrue(0 != oic.compare(oi, null));
+ assertTrue(0 != oic.compare(null, oi2));
+
+ assertTrue(0 != oic.compare(new OverviewImage() {
+ private static final long serialVersionUID = 1L;
+ }, oi2));
+
+ oi = new OverviewImage();
+ oi2 = new OverviewImage();
+ OverviewImageLink link= new OverviewImageLink();
+ link.setPolygon("1,1");
+ oi.addLink(link);
+ link= new OverviewImageLink();
+ link.setPolygon("1,2");
+ oi2.addLink(link);
+
+ assertTrue(0 != oic.compare(oi, oi2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/OverviewImageLinkComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/OverviewImageLinkComparatorTest.java
index 9e8cd81472..858b560e52 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/OverviewImageLinkComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/OverviewImageLinkComparatorTest.java
@@ -1,97 +1,97 @@
-package lcsb.mapviewer.model.map;
-
-import static org.junit.Assert.*;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class OverviewImageLinkComparatorTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEqual() throws Exception {
- try {
- OverviewImageLinkComparator oic = new OverviewImageLinkComparator();
-
- OverviewImageLink oi = new OverviewImageLink();
- OverviewImageLink oi2 = new OverviewImageLink();
-
- assertEquals(0, oic.compare(oi, oi2));
- assertEquals(0, oic.compare(null, null));
-
- oi2.setLinkedOverviewImage(new OverviewImage());
- oi.setLinkedOverviewImage(new OverviewImage());
- assertEquals(0, oic.compare(oi, oi2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent() throws Exception {
- try {
- OverviewImageLinkComparator oic = new OverviewImageLinkComparator();
-
- OverviewImageLink oi = new OverviewImageLink();
-
- OverviewImageLink oi2 = new OverviewImageLink();
- oi2.setLinkedOverviewImage(new OverviewImage());
-
- assertTrue(0 != oic.compare(oi, oi2));
- assertTrue(0 != oic.compare(oi2, oi));
-
- oi2 = new OverviewImageLink();
- oi2.setLinkedOverviewImage(new OverviewImage());
-
- assertTrue(0 != oic.compare(oi, oi2));
- assertTrue(0 != oic.compare(oi2, oi));
-
- oi2 = new OverviewImageLink();
- oi2.setPolygon("AS");
-
- assertTrue(0 != oic.compare(oi, oi2));
- assertTrue(0 != oic.compare(oi, null));
- assertTrue(0 != oic.compare(null, oi2));
- assertTrue(0 != oic.compare(new OverviewImageLink() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }, oi2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferentPolygon() throws Exception {
- try {
- OverviewImageLinkComparator comparator = new OverviewImageLinkComparator();
-
- OverviewImageLink iml1 = new OverviewImageLink();
- OverviewImageLink iml2 = new OverviewImageLink();
- iml2.setPolygon("1,2");
-
- assertTrue(0 != comparator.compare(iml1, iml2));
- assertTrue(0 != comparator.compare(iml2, iml1));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map;
+
+import static org.junit.Assert.*;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class OverviewImageLinkComparatorTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEqual() throws Exception {
+ try {
+ OverviewImageLinkComparator oic = new OverviewImageLinkComparator();
+
+ OverviewImageLink oi = new OverviewImageLink();
+ OverviewImageLink oi2 = new OverviewImageLink();
+
+ assertEquals(0, oic.compare(oi, oi2));
+ assertEquals(0, oic.compare(null, null));
+
+ oi2.setLinkedOverviewImage(new OverviewImage());
+ oi.setLinkedOverviewImage(new OverviewImage());
+ assertEquals(0, oic.compare(oi, oi2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent() throws Exception {
+ try {
+ OverviewImageLinkComparator oic = new OverviewImageLinkComparator();
+
+ OverviewImageLink oi = new OverviewImageLink();
+
+ OverviewImageLink oi2 = new OverviewImageLink();
+ oi2.setLinkedOverviewImage(new OverviewImage());
+
+ assertTrue(0 != oic.compare(oi, oi2));
+ assertTrue(0 != oic.compare(oi2, oi));
+
+ oi2 = new OverviewImageLink();
+ oi2.setLinkedOverviewImage(new OverviewImage());
+
+ assertTrue(0 != oic.compare(oi, oi2));
+ assertTrue(0 != oic.compare(oi2, oi));
+
+ oi2 = new OverviewImageLink();
+ oi2.setPolygon("AS");
+
+ assertTrue(0 != oic.compare(oi, oi2));
+ assertTrue(0 != oic.compare(oi, null));
+ assertTrue(0 != oic.compare(null, oi2));
+ assertTrue(0 != oic.compare(new OverviewImageLink() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }, oi2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferentPolygon() throws Exception {
+ try {
+ OverviewImageLinkComparator comparator = new OverviewImageLinkComparator();
+
+ OverviewImageLink iml1 = new OverviewImageLink();
+ OverviewImageLink iml2 = new OverviewImageLink();
+ iml2.setPolygon("1,2");
+
+ assertTrue(0 != comparator.compare(iml1, iml2));
+ assertTrue(0 != comparator.compare(iml2, iml1));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/OverviewImageLinkTest.java b/model/src/test/java/lcsb/mapviewer/model/map/OverviewImageLinkTest.java
index f78fd125dd..5fbc342400 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/OverviewImageLinkTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/OverviewImageLinkTest.java
@@ -1,63 +1,63 @@
-package lcsb.mapviewer.model.map;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class OverviewImageLinkTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new OverviewImageLink());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- OverviewImageLink original = new OverviewImageLink();
- OverviewImageLink degraded = original.copy();
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new OverviewImageLink() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class OverviewImageLinkTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new OverviewImageLink());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ OverviewImageLink original = new OverviewImageLink();
+ OverviewImageLink degraded = original.copy();
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new OverviewImageLink() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/OverviewImageTest.java b/model/src/test/java/lcsb/mapviewer/model/map/OverviewImageTest.java
index 3b712fd29e..eccd4f9b06 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/OverviewImageTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/OverviewImageTest.java
@@ -1,82 +1,82 @@
-package lcsb.mapviewer.model.map;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class OverviewImageTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new OverviewImage());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- OverviewImage original = new OverviewImage();
- original.addLink(new OverviewImageLink());
- OverviewImage degraded = original.copy();
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetters() {
- try {
- OverviewImage original = new OverviewImage();
- List<OverviewLink> links = new ArrayList<>();
- original.setLinks(links);
-
- assertEquals(links, original.getLinks());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new OverviewImage() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class OverviewImageTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new OverviewImage());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ OverviewImage original = new OverviewImage();
+ original.addLink(new OverviewImageLink());
+ OverviewImage degraded = original.copy();
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetters() {
+ try {
+ OverviewImage original = new OverviewImage();
+ List<OverviewLink> links = new ArrayList<>();
+ original.setLinks(links);
+
+ assertEquals(links, original.getLinks());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new OverviewImage() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/OverviewLinkComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/OverviewLinkComparatorTest.java
index a328f37ae6..ccd5ca3c3f 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/OverviewLinkComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/OverviewLinkComparatorTest.java
@@ -1,93 +1,93 @@
-package lcsb.mapviewer.model.map;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-
-public class OverviewLinkComparatorTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEqual() throws Exception {
- try {
- OverviewLinkComparator omlc = new OverviewLinkComparator();
-
- OverviewModelLink oml = new OverviewModelLink();
- OverviewModelLink oml2 = new OverviewModelLink();
-
- assertEquals(0, omlc.compare(oml, oml2));
- assertEquals(0, omlc.compare(null, null));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid() throws Exception {
- try {
- class Tmp extends OverviewLink {
- private static final long serialVersionUID = 1L;
-
- @Override
- public OverviewLink copy() {
- return null;
- }
- }
- ;
- OverviewLinkComparator omlc = new OverviewLinkComparator();
-
- OverviewLink oml = new Tmp();
- OverviewLink oml2 = new Tmp();
-
- omlc.compare(oml, oml2);
-
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent() throws Exception {
- try {
- OverviewLinkComparator omlc = new OverviewLinkComparator();
-
- OverviewModelLink oml = new OverviewModelLink();
- OverviewImageLink iml = new OverviewImageLink();
-
- assertTrue(0 != omlc.compare(oml, iml));
- assertTrue(0 != omlc.compare(oml, null));
- assertTrue(0 != omlc.compare(null, iml));
-
- oml = new OverviewModelLink();
- OverviewModelLink oml2 = new OverviewModelLink();
- oml2.setLinkedModel(new ModelFullIndexed(new ModelData()));
-
- assertTrue(0 != omlc.compare(oml, oml2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+
+public class OverviewLinkComparatorTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEqual() throws Exception {
+ try {
+ OverviewLinkComparator omlc = new OverviewLinkComparator();
+
+ OverviewModelLink oml = new OverviewModelLink();
+ OverviewModelLink oml2 = new OverviewModelLink();
+
+ assertEquals(0, omlc.compare(oml, oml2));
+ assertEquals(0, omlc.compare(null, null));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid() throws Exception {
+ try {
+ class Tmp extends OverviewLink {
+ private static final long serialVersionUID = 1L;
+
+ @Override
+ public OverviewLink copy() {
+ return null;
+ }
+ }
+ ;
+ OverviewLinkComparator omlc = new OverviewLinkComparator();
+
+ OverviewLink oml = new Tmp();
+ OverviewLink oml2 = new Tmp();
+
+ omlc.compare(oml, oml2);
+
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent() throws Exception {
+ try {
+ OverviewLinkComparator omlc = new OverviewLinkComparator();
+
+ OverviewModelLink oml = new OverviewModelLink();
+ OverviewImageLink iml = new OverviewImageLink();
+
+ assertTrue(0 != omlc.compare(oml, iml));
+ assertTrue(0 != omlc.compare(oml, null));
+ assertTrue(0 != omlc.compare(null, iml));
+
+ oml = new OverviewModelLink();
+ OverviewModelLink oml2 = new OverviewModelLink();
+ oml2.setLinkedModel(new ModelFullIndexed(new ModelData()));
+
+ assertTrue(0 != omlc.compare(oml, oml2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/OverviewLinkTest.java b/model/src/test/java/lcsb/mapviewer/model/map/OverviewLinkTest.java
index 68f045d706..7287d170cb 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/OverviewLinkTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/OverviewLinkTest.java
@@ -1,73 +1,73 @@
-package lcsb.mapviewer.model.map;
-
-import static org.junit.Assert.assertEquals;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class OverviewLinkTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetPolygonCoord() {
- try {
- OverviewLink link = new OverviewLink() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- @Override
- public OverviewLink copy() {
- // TODO Auto-generated method stub
- return null;
- }
- };
- String polygon = "1,1 2,2 4,0";
- link.setPolygon(polygon);
- assertEquals(3, link.getPolygonCoordinates().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- OverviewLink link = new OverviewLink() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- @Override
- public OverviewLink copy() {
- // TODO Auto-generated method stub
- return null;
- }
- };
- OverviewImage image= new OverviewImage();
- int id = 309;
- link.setOverviewImage(image);
- link.setId(id);
-
- assertEquals(image, link.getOverviewImage());
- assertEquals(id, link.getId());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map;
+
+import static org.junit.Assert.assertEquals;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class OverviewLinkTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetPolygonCoord() {
+ try {
+ OverviewLink link = new OverviewLink() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ @Override
+ public OverviewLink copy() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+ };
+ String polygon = "1,1 2,2 4,0";
+ link.setPolygon(polygon);
+ assertEquals(3, link.getPolygonCoordinates().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ OverviewLink link = new OverviewLink() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ @Override
+ public OverviewLink copy() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+ };
+ OverviewImage image= new OverviewImage();
+ int id = 309;
+ link.setOverviewImage(image);
+ link.setId(id);
+
+ assertEquals(image, link.getOverviewImage());
+ assertEquals(id, link.getId());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/OverviewModelLinkComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/OverviewModelLinkComparatorTest.java
index b060511d70..38b6e3b8a6 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/OverviewModelLinkComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/OverviewModelLinkComparatorTest.java
@@ -1,107 +1,107 @@
-package lcsb.mapviewer.model.map;
-
-import static org.junit.Assert.*;
-
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class OverviewModelLinkComparatorTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEqual() throws Exception {
- try {
- OverviewModelLinkComparator oic = new OverviewModelLinkComparator();
-
- OverviewModelLink oi = new OverviewModelLink();
- OverviewModelLink oi2 = new OverviewModelLink();
-
- assertEquals(0, oic.compare(oi, oi2));
- assertEquals(0, oic.compare(null, null));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent() throws Exception {
- try {
- OverviewModelLinkComparator oic = new OverviewModelLinkComparator();
-
- OverviewModelLink oi = new OverviewModelLink();
-
- OverviewModelLink oi2 = new OverviewModelLink();
- oi2.setLinkedModel(new ModelFullIndexed(null));
-
- assertTrue(0 != oic.compare(oi, oi2));
- assertTrue(0 != oic.compare(oi2, oi));
- assertTrue(0 != oic.compare(oi, null));
- assertTrue(0 != oic.compare(null, oi2));
-
- Model model = new ModelFullIndexed(null);
- model.setId(1);
- oi.setLinkedModel(model);
- assertTrue(0 != oic.compare(oi, oi2));
-
- oi2 = new OverviewModelLink();
- oi2.setPolygon("AS");
-
- assertTrue(0 != oic.compare(oi, oi2));
-
- oi2 = new OverviewModelLink();
- oi2.setxCoord(12);
-
- assertTrue(0 != oic.compare(oi, oi2));
-
- oi2 = new OverviewModelLink();
- oi2.setyCoord(13);
-
- assertTrue(0 != oic.compare(oi, oi2));
-
- oi2 = new OverviewModelLink();
- oi2.setZoomLevel(345);
-
- assertTrue(0 != oic.compare(oi, oi2));
-
- assertTrue(0 != oic.compare(oi, new OverviewModelLink() {
- private static final long serialVersionUID = 1L;
- }));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferentPolygon() throws Exception {
- try {
- OverviewModelLinkComparator comparator = new OverviewModelLinkComparator();
-
- OverviewModelLink iml1 = new OverviewModelLink();
- OverviewModelLink iml2 = new OverviewModelLink();
- iml2.setPolygon("1,2");
-
- assertTrue(0 != comparator.compare(iml1, iml2));
- assertTrue(0 != comparator.compare(iml2, iml1));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map;
+
+import static org.junit.Assert.*;
+
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class OverviewModelLinkComparatorTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEqual() throws Exception {
+ try {
+ OverviewModelLinkComparator oic = new OverviewModelLinkComparator();
+
+ OverviewModelLink oi = new OverviewModelLink();
+ OverviewModelLink oi2 = new OverviewModelLink();
+
+ assertEquals(0, oic.compare(oi, oi2));
+ assertEquals(0, oic.compare(null, null));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent() throws Exception {
+ try {
+ OverviewModelLinkComparator oic = new OverviewModelLinkComparator();
+
+ OverviewModelLink oi = new OverviewModelLink();
+
+ OverviewModelLink oi2 = new OverviewModelLink();
+ oi2.setLinkedModel(new ModelFullIndexed(null));
+
+ assertTrue(0 != oic.compare(oi, oi2));
+ assertTrue(0 != oic.compare(oi2, oi));
+ assertTrue(0 != oic.compare(oi, null));
+ assertTrue(0 != oic.compare(null, oi2));
+
+ Model model = new ModelFullIndexed(null);
+ model.setId(1);
+ oi.setLinkedModel(model);
+ assertTrue(0 != oic.compare(oi, oi2));
+
+ oi2 = new OverviewModelLink();
+ oi2.setPolygon("AS");
+
+ assertTrue(0 != oic.compare(oi, oi2));
+
+ oi2 = new OverviewModelLink();
+ oi2.setxCoord(12);
+
+ assertTrue(0 != oic.compare(oi, oi2));
+
+ oi2 = new OverviewModelLink();
+ oi2.setyCoord(13);
+
+ assertTrue(0 != oic.compare(oi, oi2));
+
+ oi2 = new OverviewModelLink();
+ oi2.setZoomLevel(345);
+
+ assertTrue(0 != oic.compare(oi, oi2));
+
+ assertTrue(0 != oic.compare(oi, new OverviewModelLink() {
+ private static final long serialVersionUID = 1L;
+ }));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferentPolygon() throws Exception {
+ try {
+ OverviewModelLinkComparator comparator = new OverviewModelLinkComparator();
+
+ OverviewModelLink iml1 = new OverviewModelLink();
+ OverviewModelLink iml2 = new OverviewModelLink();
+ iml2.setPolygon("1,2");
+
+ assertTrue(0 != comparator.compare(iml1, iml2));
+ assertTrue(0 != comparator.compare(iml2, iml1));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/OverviewModelLinkTest.java b/model/src/test/java/lcsb/mapviewer/model/map/OverviewModelLinkTest.java
index f9ef8d37ad..f2044c6d78 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/OverviewModelLinkTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/OverviewModelLinkTest.java
@@ -1,98 +1,98 @@
-package lcsb.mapviewer.model.map;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class OverviewModelLinkTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new OverviewModelLink());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- OverviewModelLink link = new OverviewModelLink(new OverviewModelLink());
- assertNotNull(link);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetters() {
- try {
- OverviewModelLink link = new OverviewModelLink();
- link.setLinkedModel(null);
- assertNull(link.getLinkedModel());
-
- link.setxCoord(2.0);
- link.setyCoord(3.0);
-
- assertEquals((Integer) 2, link.getxCoord());
- assertEquals((Integer) 3, link.getyCoord());
-
- link.setxCoord((Double) null);
- link.setyCoord((Double) null);
- assertNull(link.getxCoord());
- assertNull(link.getyCoord());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- OverviewModelLink degraded = new OverviewModelLink().copy();
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new OverviewModelLink() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class OverviewModelLinkTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new OverviewModelLink());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ OverviewModelLink link = new OverviewModelLink(new OverviewModelLink());
+ assertNotNull(link);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetters() {
+ try {
+ OverviewModelLink link = new OverviewModelLink();
+ link.setLinkedModel(null);
+ assertNull(link.getLinkedModel());
+
+ link.setxCoord(2.0);
+ link.setyCoord(3.0);
+
+ assertEquals((Integer) 2, link.getxCoord());
+ assertEquals((Integer) 3, link.getyCoord());
+
+ link.setxCoord((Double) null);
+ link.setyCoord((Double) null);
+ assertNull(link.getxCoord());
+ assertNull(link.getyCoord());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ OverviewModelLink degraded = new OverviewModelLink().copy();
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new OverviewModelLink() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/OverviewSearchLinkTest.java b/model/src/test/java/lcsb/mapviewer/model/map/OverviewSearchLinkTest.java
index 2d9b9e0ad0..58f77f773d 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/OverviewSearchLinkTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/OverviewSearchLinkTest.java
@@ -1,87 +1,87 @@
-package lcsb.mapviewer.model.map;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class OverviewSearchLinkTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new OverviewSearchLink());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- OverviewSearchLink osl = new OverviewSearchLink(new OverviewSearchLink());
- assertNotNull(osl);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- OverviewSearchLink osl = new OverviewSearchLink(new OverviewSearchLink());
- String query = "st";
- osl.setQuery(query);
- assertEquals(query, osl.getQuery());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- OverviewSearchLink degraded = new OverviewSearchLink().copy();
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new OverviewSearchLink() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class OverviewSearchLinkTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new OverviewSearchLink());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ OverviewSearchLink osl = new OverviewSearchLink(new OverviewSearchLink());
+ assertNotNull(osl);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ OverviewSearchLink osl = new OverviewSearchLink(new OverviewSearchLink());
+ String query = "st";
+ osl.setQuery(query);
+ assertEquals(query, osl.getQuery());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ OverviewSearchLink degraded = new OverviewSearchLink().copy();
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new OverviewSearchLink() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/SearchIndexTest.java b/model/src/test/java/lcsb/mapviewer/model/map/SearchIndexTest.java
index d9be1175f5..fbae6bb1b4 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/SearchIndexTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/SearchIndexTest.java
@@ -1,128 +1,128 @@
-package lcsb.mapviewer.model.map;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.SearchIndex;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Gene;
-
-public class SearchIndexTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new SearchIndex());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- SearchIndex index = new SearchIndex("str", 2);
- assertEquals("str", index.getValue());
- assertEquals((Integer) 2, index.getWeight());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor2() {
- try {
- SearchIndex index = new SearchIndex("str");
- assertEquals("str", index.getValue());
- assertEquals((Integer) 1, index.getWeight());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor3() {
- try {
- SearchIndex index = new SearchIndex("str");
- SearchIndex index2 = new SearchIndex(index);
- assertNotNull(index2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- SearchIndex aRna = new SearchIndex().copy();
- assertNotNull(aRna);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopyInvalid() {
- try {
- new SearchIndex() {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- int id = 54;
- int weight = 8;
- String value = "val5";
- Element element = new Gene("gene_id");
-
- SearchIndex index = new SearchIndex();
- index.setId(id);
- assertEquals(id, index.getId());
-
- index.setValue(value);
- assertEquals(value, index.getValue());
-
- index.setSource(element);
- assertEquals(element, index.getSource());
-
- index.setWeight(weight);
- assertEquals((Integer) weight, index.getWeight());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.SearchIndex;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Gene;
+
+public class SearchIndexTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new SearchIndex());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ SearchIndex index = new SearchIndex("str", 2);
+ assertEquals("str", index.getValue());
+ assertEquals((Integer) 2, index.getWeight());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor2() {
+ try {
+ SearchIndex index = new SearchIndex("str");
+ assertEquals("str", index.getValue());
+ assertEquals((Integer) 1, index.getWeight());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor3() {
+ try {
+ SearchIndex index = new SearchIndex("str");
+ SearchIndex index2 = new SearchIndex(index);
+ assertNotNull(index2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ SearchIndex aRna = new SearchIndex().copy();
+ assertNotNull(aRna);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyInvalid() {
+ try {
+ new SearchIndex() {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ int id = 54;
+ int weight = 8;
+ String value = "val5";
+ Element element = new Gene("gene_id");
+
+ SearchIndex index = new SearchIndex();
+ index.setId(id);
+ assertEquals(id, index.getId());
+
+ index.setValue(value);
+ assertEquals(value, index.getValue());
+
+ index.setSource(element);
+ assertEquals(element, index.getSource());
+
+ index.setWeight(weight);
+ assertEquals((Integer) weight, index.getWeight());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/compartment/AllCompartmentTests.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/AllCompartmentTests.java
index 0c68c92a16..abad8d91d0 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/compartment/AllCompartmentTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/AllCompartmentTests.java
@@ -1,20 +1,20 @@
-package lcsb.mapviewer.model.map.compartment;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ BottomSquareCompartmentTest.class, //
- CompartmentComparatorTest.class, //
- CompartmentTest.class, //
- LeftSquareCompartmentTest.class, //
- OvalCompartmentTest.class, //
- PathwayCompartmentTest.class, //
- RightSquareCompartmentTest.class, //
- SquareCompartmentTest.class, //
- TopSquareCompartmentTest.class, //
-})
-public class AllCompartmentTests {
-
-}
+package lcsb.mapviewer.model.map.compartment;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ BottomSquareCompartmentTest.class, //
+ CompartmentComparatorTest.class, //
+ CompartmentTest.class, //
+ LeftSquareCompartmentTest.class, //
+ OvalCompartmentTest.class, //
+ PathwayCompartmentTest.class, //
+ RightSquareCompartmentTest.class, //
+ SquareCompartmentTest.class, //
+ TopSquareCompartmentTest.class, //
+})
+public class AllCompartmentTests {
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/compartment/BottomSquareCompartmentTest.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/BottomSquareCompartmentTest.java
index 3651565a4d..f993b717f5 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/compartment/BottomSquareCompartmentTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/BottomSquareCompartmentTest.java
@@ -1,95 +1,95 @@
-package lcsb.mapviewer.model.map.compartment;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-
-public class BottomSquareCompartmentTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new BottomSquareCompartment());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- BottomSquareCompartment compartment = new BottomSquareCompartment(new Compartment());
- assertNotNull(compartment);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor3() {
- try {
- BottomSquareCompartment compartment = new BottomSquareCompartment("id");
- assertNotNull(compartment);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor2() {
- try {
- Model model = new ModelFullIndexed(null);
- model.setWidth(1);
- model.setHeight(1);
- BottomSquareCompartment compartment = new BottomSquareCompartment(new Compartment(), model);
- assertNotNull(compartment);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- BottomSquareCompartment compartment = new BottomSquareCompartment().copy();
- assertNotNull(compartment);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- BottomSquareCompartment compartment = Mockito.spy(BottomSquareCompartment.class);
- compartment.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.map.compartment;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+
+public class BottomSquareCompartmentTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new BottomSquareCompartment());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ BottomSquareCompartment compartment = new BottomSquareCompartment(new Compartment());
+ assertNotNull(compartment);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor3() {
+ try {
+ BottomSquareCompartment compartment = new BottomSquareCompartment("id");
+ assertNotNull(compartment);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor2() {
+ try {
+ Model model = new ModelFullIndexed(null);
+ model.setWidth(1);
+ model.setHeight(1);
+ BottomSquareCompartment compartment = new BottomSquareCompartment(new Compartment(), model);
+ assertNotNull(compartment);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ BottomSquareCompartment compartment = new BottomSquareCompartment().copy();
+ assertNotNull(compartment);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ BottomSquareCompartment compartment = Mockito.spy(BottomSquareCompartment.class);
+ compartment.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentComparatorTest.java
index 535233b7c0..35f4d3ed3f 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentComparatorTest.java
@@ -1,222 +1,222 @@
-package lcsb.mapviewer.model.map.compartment;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.awt.Color;
-import java.awt.geom.Point2D;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class CompartmentComparatorTest {
-
- Logger logger = Logger.getLogger(CompartmentComparatorTest.class);
-
- CompartmentComparator comparator = new CompartmentComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- Compartment compartment1 = createCompartment();
- Compartment compartment2 = createCompartment();
-
- assertEquals(0, comparator.compare(compartment1, compartment2));
-
- assertEquals(0, comparator.compare(null, null));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent2() {
- try {
- Compartment compartment = createCompartment();
-
- assertTrue(comparator.compare(compartment, new PathwayCompartment()) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid() {
- try {
- Compartment compartment1 = createCompartment();
- Compartment compartment2 = createCompartment();
-
- GenericProtein protein = new GenericProtein("1");
- compartment1.getElements().add(protein);
- protein = new GenericProtein("1");
- compartment1.getElements().add(protein);
-
- compartment2.getElements().add(new GenericProtein("b"));
- compartment2.getElements().add(new GenericProtein("a"));
-
- comparator.compare(compartment1, compartment2);
- fail("Exception expected");
-
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid2() {
- try {
- Compartment compartment1 = createCompartment();
- Compartment compartment2 = createCompartment();
-
- Species protein = new GenericProtein("1");
- compartment1.getElements().add(protein);
- protein = new GenericProtein("1");
- compartment1.getElements().add(protein);
-
- compartment2.getElements().add(new GenericProtein("A"));
- compartment2.getElements().add(new GenericProtein("B"));
-
- comparator.compare(compartment2, compartment1);
- fail("Exception expected");
-
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private Compartment createCompartment() {
- Compartment result = new Compartment();
-
- result.setElementId("asd");
- result.setX(12.0);
- result.setY(123.0);
- result.setWidth(4);
- result.setHeight(5);
- result.setFontSize(9.0);
- result.setColor(Color.BLUE);
- result.setVisibilityLevel("14");
- result.setThickness(998);
- result.setOuterWidth(45);
- result.setInnerWidth(65);
- result.setNamePoint(new Point2D.Double(9, 2));
-
- GenericProtein protein = new GenericProtein("S");
- protein.setName("a");
- result.addElement(protein);
-
- return result;
- }
-
- @Test
- public void testDifferentElementList() {
- Compartment compartment1 = createCompartment();
- Compartment compartment2 = createCompartment();
-
- compartment1.addElement(new GenericProtein("idd"));
-
- assertTrue(comparator.compare(compartment1, compartment2) != 0);
- assertTrue(comparator.compare(compartment2, compartment1) != 0);
- }
-
- @Test
- public void testDifferentElementId() {
- Compartment compartment1 = createCompartment();
- Compartment compartment2 = createCompartment();
-
- compartment1.setElementId("tmp");
-
- assertTrue(comparator.compare(compartment1, compartment2) != 0);
- assertTrue(comparator.compare(compartment2, compartment1) != 0);
- }
-
- @Test
- public void testDifferent() {
- try {
- Compartment compartment1 = createCompartment();
- Compartment compartment2 = createCompartment();
-
- assertTrue(comparator.compare(compartment1, null) != 0);
- assertTrue(comparator.compare(null, compartment1) != 0);
-
- compartment1 = createCompartment();
- compartment2 = createCompartment();
-
- compartment1.setThickness(11111);
-
- assertTrue(comparator.compare(compartment1, compartment2) != 0);
- assertTrue(comparator.compare(compartment2, compartment1) != 0);
-
- compartment1 = createCompartment();
- compartment2 = createCompartment();
-
- compartment1.setNamePoint(new Point2D.Double(9, 999));
-
- assertTrue(comparator.compare(compartment1, compartment2) != 0);
- assertTrue(comparator.compare(compartment2, compartment1) != 0);
-
- compartment1 = createCompartment();
- compartment2 = createCompartment();
-
- compartment1.getElements().iterator().next().setElementId("bnu");
-
- assertTrue(comparator.compare(compartment1, compartment2) != 0);
- assertTrue(comparator.compare(compartment2, compartment1) != 0);
-
- compartment1 = createCompartment();
- compartment2 = createCompartment();
-
- Species species = (Species) compartment1.getElements().iterator().next();
- species.setName("new namne");
-
- assertTrue(comparator.compare(compartment1, compartment2) != 0);
- assertTrue(comparator.compare(compartment2, compartment1) != 0);
-
- compartment1 = createCompartment();
- compartment2 = createCompartment();
-
- compartment1.setOuterWidth(2);
-
- assertTrue(comparator.compare(compartment1, compartment2) != 0);
- assertTrue(comparator.compare(compartment2, compartment1) != 0);
-
- compartment1 = createCompartment();
- compartment2 = createCompartment();
-
- compartment1.setInnerWidth(2);
-
- assertTrue(comparator.compare(compartment1, compartment2) != 0);
- assertTrue(comparator.compare(compartment2, compartment1) != 0);
-
- compartment1 = createCompartment();
- compartment2 = createCompartment();
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.compartment;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.awt.Color;
+import java.awt.geom.Point2D;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class CompartmentComparatorTest {
+
+ Logger logger = Logger.getLogger(CompartmentComparatorTest.class);
+
+ CompartmentComparator comparator = new CompartmentComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ Compartment compartment1 = createCompartment();
+ Compartment compartment2 = createCompartment();
+
+ assertEquals(0, comparator.compare(compartment1, compartment2));
+
+ assertEquals(0, comparator.compare(null, null));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent2() {
+ try {
+ Compartment compartment = createCompartment();
+
+ assertTrue(comparator.compare(compartment, new PathwayCompartment()) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid() {
+ try {
+ Compartment compartment1 = createCompartment();
+ Compartment compartment2 = createCompartment();
+
+ GenericProtein protein = new GenericProtein("1");
+ compartment1.getElements().add(protein);
+ protein = new GenericProtein("1");
+ compartment1.getElements().add(protein);
+
+ compartment2.getElements().add(new GenericProtein("b"));
+ compartment2.getElements().add(new GenericProtein("a"));
+
+ comparator.compare(compartment1, compartment2);
+ fail("Exception expected");
+
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid2() {
+ try {
+ Compartment compartment1 = createCompartment();
+ Compartment compartment2 = createCompartment();
+
+ Species protein = new GenericProtein("1");
+ compartment1.getElements().add(protein);
+ protein = new GenericProtein("1");
+ compartment1.getElements().add(protein);
+
+ compartment2.getElements().add(new GenericProtein("A"));
+ compartment2.getElements().add(new GenericProtein("B"));
+
+ comparator.compare(compartment2, compartment1);
+ fail("Exception expected");
+
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Compartment createCompartment() {
+ Compartment result = new Compartment();
+
+ result.setElementId("asd");
+ result.setX(12.0);
+ result.setY(123.0);
+ result.setWidth(4);
+ result.setHeight(5);
+ result.setFontSize(9.0);
+ result.setColor(Color.BLUE);
+ result.setVisibilityLevel("14");
+ result.setThickness(998);
+ result.setOuterWidth(45);
+ result.setInnerWidth(65);
+ result.setNamePoint(new Point2D.Double(9, 2));
+
+ GenericProtein protein = new GenericProtein("S");
+ protein.setName("a");
+ result.addElement(protein);
+
+ return result;
+ }
+
+ @Test
+ public void testDifferentElementList() {
+ Compartment compartment1 = createCompartment();
+ Compartment compartment2 = createCompartment();
+
+ compartment1.addElement(new GenericProtein("idd"));
+
+ assertTrue(comparator.compare(compartment1, compartment2) != 0);
+ assertTrue(comparator.compare(compartment2, compartment1) != 0);
+ }
+
+ @Test
+ public void testDifferentElementId() {
+ Compartment compartment1 = createCompartment();
+ Compartment compartment2 = createCompartment();
+
+ compartment1.setElementId("tmp");
+
+ assertTrue(comparator.compare(compartment1, compartment2) != 0);
+ assertTrue(comparator.compare(compartment2, compartment1) != 0);
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ Compartment compartment1 = createCompartment();
+ Compartment compartment2 = createCompartment();
+
+ assertTrue(comparator.compare(compartment1, null) != 0);
+ assertTrue(comparator.compare(null, compartment1) != 0);
+
+ compartment1 = createCompartment();
+ compartment2 = createCompartment();
+
+ compartment1.setThickness(11111);
+
+ assertTrue(comparator.compare(compartment1, compartment2) != 0);
+ assertTrue(comparator.compare(compartment2, compartment1) != 0);
+
+ compartment1 = createCompartment();
+ compartment2 = createCompartment();
+
+ compartment1.setNamePoint(new Point2D.Double(9, 999));
+
+ assertTrue(comparator.compare(compartment1, compartment2) != 0);
+ assertTrue(comparator.compare(compartment2, compartment1) != 0);
+
+ compartment1 = createCompartment();
+ compartment2 = createCompartment();
+
+ compartment1.getElements().iterator().next().setElementId("bnu");
+
+ assertTrue(comparator.compare(compartment1, compartment2) != 0);
+ assertTrue(comparator.compare(compartment2, compartment1) != 0);
+
+ compartment1 = createCompartment();
+ compartment2 = createCompartment();
+
+ Species species = (Species) compartment1.getElements().iterator().next();
+ species.setName("new namne");
+
+ assertTrue(comparator.compare(compartment1, compartment2) != 0);
+ assertTrue(comparator.compare(compartment2, compartment1) != 0);
+
+ compartment1 = createCompartment();
+ compartment2 = createCompartment();
+
+ compartment1.setOuterWidth(2);
+
+ assertTrue(comparator.compare(compartment1, compartment2) != 0);
+ assertTrue(comparator.compare(compartment2, compartment1) != 0);
+
+ compartment1 = createCompartment();
+ compartment2 = createCompartment();
+
+ compartment1.setInnerWidth(2);
+
+ assertTrue(comparator.compare(compartment1, compartment2) != 0);
+ assertTrue(comparator.compare(compartment2, compartment1) != 0);
+
+ compartment1 = createCompartment();
+ compartment2 = createCompartment();
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentTest.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentTest.java
index bbe1ad98aa..47229fe199 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentTest.java
@@ -1,414 +1,414 @@
-package lcsb.mapviewer.model.map.compartment;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.util.HashSet;
-import java.util.Set;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class CompartmentTest {
- Logger logger = Logger.getLogger(CompartmentTest.class);
-
- int identifierCounter = 1;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testCross() throws Exception {
- try {
- Model model = createCrossModel();
- Element ldhb1 = model.getElementByElementId("sa1115");
- Element ldhb2 = model.getElementByElementId("sa1117");
- Element ldhb3 = model.getElementByElementId("sa1119");
- Element ldhb4 = model.getElementByElementId("sa1121");
-
- Compartment cytosol = (Compartment) model.getElementByElementId("ca1");
-
- assertTrue(cytosol.cross(ldhb1));
- assertTrue(cytosol.cross(ldhb2));
- assertTrue(cytosol.cross(ldhb3));
- assertTrue(cytosol.cross(ldhb4));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCrossException() throws Exception {
- try {
- Compartment compartment = new Compartment();
- Complex complex = new Complex("idd");
- complex.setComplex(complex);
- compartment.cross(complex);
-
- fail("Exception epxected");
- } catch (InvalidStateException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCross2() throws Exception {
- try {
- Compartment compartment = new Compartment();
- compartment.setX(10.0);
- compartment.setY(10.0);
- compartment.setWidth(10.0);
- compartment.setHeight(10.0);
- Complex complex = new Complex("idd");
- complex.setWidth(10.0);
- complex.setHeight(10.0);
- complex.setX(5.0);
- complex.setY(5.0);
- assertTrue(compartment.cross(complex));
-
- complex.setX(15.0);
- complex.setY(5.0);
- assertTrue(compartment.cross(complex));
-
- complex.setX(5.0);
- complex.setY(15.0);
- assertTrue(compartment.cross(complex));
-
- complex.setX(15.0);
- complex.setY(15.0);
- assertTrue(compartment.cross(complex));
-
- complex.setWidth(100.0);
- complex.setHeight(100.0);
- complex.setX(-110.0);
- complex.setY(-10.0);
- assertFalse(compartment.cross(complex));
-
- complex.setX(-10.0);
- complex.setY(-110.0);
- assertFalse(compartment.cross(complex));
-
- complex.setX(40.0);
- complex.setY(-10.0);
- assertFalse(compartment.cross(complex));
-
- complex.setX(-10.0);
- complex.setY(40.0);
- assertFalse(compartment.cross(complex));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testContainsIdenticalSpecies() throws Exception {
- try {
- Compartment compartment = new Compartment();
-
- compartment.setName("AS");
-
- assertFalse(compartment.containsIdenticalSpecies());
-
- Species species = new GenericProtein("idd");
- species.setName("AS");
-
- compartment.addElement(species);
-
- assertTrue(compartment.containsIdenticalSpecies());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDoesntContainsIdenticalSpecies() throws Exception {
- try {
- Compartment compartment = new Compartment();
-
- compartment.setName("AS");
-
- Species species = new GenericProtein("idd");
- species.setName("not identical name");
-
- compartment.addElement(species);
-
- assertFalse(compartment.containsIdenticalSpecies());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private Model createCrossModel() {
- Model model = new ModelFullIndexed(null);
- model.addElement(new Compartment("default"));
-
- model.addElement(createSpecies(3264.8333333333335, 7517.75, 86.0, 46.0, "sa1115"));
- model.addElement(createSpecies(3267.6666666666665, 7438.75, 80.0, 40.0, "sa1117"));
- model.addElement(createSpecies(3261.6666666666665, 7600.75, 92.0, 52.0, "sa1119"));
- model.addElement(createSpecies(3203.666666666667, 7687.75, 98.0, 58.0, "sa1121"));
-
- Species species = createSpecies(7817.714285714286, 11287.642857142859, 80.0, 40.0, "sa1422");
- Species species2 = createSpecies(8224.964285714286, 11241.392857142859, 80.0, 40.0, "sa1419");
- Complex complex = createComplex(7804.714285714286, 11182.642857142859, 112.0, 172.0, "csa152");
- complex.addSpecies(species);
- complex.addSpecies(species2);
- species.setComplex(complex);
- species2.setComplex(complex);
-
- model.addElement(species);
- model.addElement(species2);
- model.addElement(complex);
-
- model.addElement(createCompartment(1380.0, 416.0, 15893.0, 10866.0, "ca1"));
- return model;
- }
-
- private Compartment createCompartment(double x, double y, double width, double height, String elementId) {
- Compartment compartment = new Compartment(elementId);
- compartment.setElementId(elementId);
- compartment.setX(x);
- compartment.setY(y);
- compartment.setWidth(width);
- compartment.setHeight(height);
- return compartment;
- }
-
- private Species createSpecies(double x, double y, double width, double height, String elementId) {
- SimpleMolecule simpleMolecule = new SimpleMolecule(elementId);
- simpleMolecule.setX(x);
- simpleMolecule.setY(y);
- simpleMolecule.setWidth(width);
- simpleMolecule.setHeight(height);
- return simpleMolecule;
- }
-
- private Complex createComplex(double x, double y, double width, double height, String elementId) {
- Complex complex = new Complex(elementId);
- complex.setX(x);
- complex.setY(y);
- complex.setWidth(width);
- complex.setHeight(height);
- return complex;
- }
-
- @Test
- public void testCrossWithComplexElements() throws Exception {
- try {
- Model model = createCrossModel();
- Element ldhb1 = model.getElementByElementId("sa1422");
- Element ldhb2 = model.getElementByElementId("sa1419");
-
- Compartment cytosol = (Compartment) model.getElementByElementId("ca1");
-
- assertTrue(cytosol.cross(ldhb1));
- assertTrue(cytosol.cross(ldhb2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new Compartment());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Compartment compartment = new Compartment();
- compartment.addElement(new GenericProtein("idd"));
- Compartment copy = new Compartment(compartment);
- assertNotNull(copy);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- Compartment compartment = new Compartment();
- String invalidVal = "a1.6";
- String val = "1.6";
- Double dVal = 1.6;
-
- compartment.setLineThickness(val);
- compartment.setLineOuterWidth(val);
- compartment.setLineInnerWidth(val);
-
- assertEquals(dVal, compartment.getThickness(), Configuration.EPSILON);
- assertEquals(dVal, compartment.getOuterWidth(), Configuration.EPSILON);
- assertEquals(dVal, compartment.getInnerWidth(), Configuration.EPSILON);
-
- try {
- compartment.setLineThickness(invalidVal);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- try {
- compartment.setLineOuterWidth(invalidVal);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- try {
- compartment.setLineInnerWidth(invalidVal);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
-
- compartment.setNamePoint(2, 3);
- assertEquals(0, compartment.getNamePoint().distance(2, 3), Configuration.EPSILON);
-
- Set<Element> elements = new HashSet<>();
-
- compartment.setElements(elements);
- assertEquals(elements, compartment.getElements());
-
- assertNotNull(compartment.getStringType());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddElement() {
- try {
- Compartment compartment = new Compartment();
-
- Species child = new GenericProtein("id");
-
- compartment.addElement(child);
- compartment.addElement(child);
-
- assertEquals(1, compartment.getElements().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddInvalidElement() {
- try {
- Compartment compartment = new Compartment();
-
- Species child = new GenericProtein("id");
- Species child2 = new GenericProtein("id");
-
- compartment.addElement(child);
- compartment.addElement(child2);
-
- fail("Exception expected");
-
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAllElements() {
- try {
- Compartment compartment = new Compartment();
-
- Species child = new GenericProtein("id");
- Compartment child2 = new Compartment();
- child2.addElement(child);
- compartment.addElement(child2);
-
- assertEquals(2, compartment.getAllSubElements().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- Compartment degraded = new Compartment().copy();
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRemoveElement() {
- try {
- Compartment comp = new Compartment();
- Species protein = new GenericProtein("idd");
- comp.addElement(protein);
- protein.setCompartment(new Compartment());
-
- comp.removeElement(protein);
-
- assertEquals(0, comp.getElements().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- Compartment compartment = Mockito.spy(Compartment.class);
- compartment.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.compartment;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class CompartmentTest {
+ Logger logger = Logger.getLogger(CompartmentTest.class);
+
+ int identifierCounter = 1;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testCross() throws Exception {
+ try {
+ Model model = createCrossModel();
+ Element ldhb1 = model.getElementByElementId("sa1115");
+ Element ldhb2 = model.getElementByElementId("sa1117");
+ Element ldhb3 = model.getElementByElementId("sa1119");
+ Element ldhb4 = model.getElementByElementId("sa1121");
+
+ Compartment cytosol = (Compartment) model.getElementByElementId("ca1");
+
+ assertTrue(cytosol.cross(ldhb1));
+ assertTrue(cytosol.cross(ldhb2));
+ assertTrue(cytosol.cross(ldhb3));
+ assertTrue(cytosol.cross(ldhb4));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCrossException() throws Exception {
+ try {
+ Compartment compartment = new Compartment();
+ Complex complex = new Complex("idd");
+ complex.setComplex(complex);
+ compartment.cross(complex);
+
+ fail("Exception epxected");
+ } catch (InvalidStateException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCross2() throws Exception {
+ try {
+ Compartment compartment = new Compartment();
+ compartment.setX(10.0);
+ compartment.setY(10.0);
+ compartment.setWidth(10.0);
+ compartment.setHeight(10.0);
+ Complex complex = new Complex("idd");
+ complex.setWidth(10.0);
+ complex.setHeight(10.0);
+ complex.setX(5.0);
+ complex.setY(5.0);
+ assertTrue(compartment.cross(complex));
+
+ complex.setX(15.0);
+ complex.setY(5.0);
+ assertTrue(compartment.cross(complex));
+
+ complex.setX(5.0);
+ complex.setY(15.0);
+ assertTrue(compartment.cross(complex));
+
+ complex.setX(15.0);
+ complex.setY(15.0);
+ assertTrue(compartment.cross(complex));
+
+ complex.setWidth(100.0);
+ complex.setHeight(100.0);
+ complex.setX(-110.0);
+ complex.setY(-10.0);
+ assertFalse(compartment.cross(complex));
+
+ complex.setX(-10.0);
+ complex.setY(-110.0);
+ assertFalse(compartment.cross(complex));
+
+ complex.setX(40.0);
+ complex.setY(-10.0);
+ assertFalse(compartment.cross(complex));
+
+ complex.setX(-10.0);
+ complex.setY(40.0);
+ assertFalse(compartment.cross(complex));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testContainsIdenticalSpecies() throws Exception {
+ try {
+ Compartment compartment = new Compartment();
+
+ compartment.setName("AS");
+
+ assertFalse(compartment.containsIdenticalSpecies());
+
+ Species species = new GenericProtein("idd");
+ species.setName("AS");
+
+ compartment.addElement(species);
+
+ assertTrue(compartment.containsIdenticalSpecies());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDoesntContainsIdenticalSpecies() throws Exception {
+ try {
+ Compartment compartment = new Compartment();
+
+ compartment.setName("AS");
+
+ Species species = new GenericProtein("idd");
+ species.setName("not identical name");
+
+ compartment.addElement(species);
+
+ assertFalse(compartment.containsIdenticalSpecies());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Model createCrossModel() {
+ Model model = new ModelFullIndexed(null);
+ model.addElement(new Compartment("default"));
+
+ model.addElement(createSpecies(3264.8333333333335, 7517.75, 86.0, 46.0, "sa1115"));
+ model.addElement(createSpecies(3267.6666666666665, 7438.75, 80.0, 40.0, "sa1117"));
+ model.addElement(createSpecies(3261.6666666666665, 7600.75, 92.0, 52.0, "sa1119"));
+ model.addElement(createSpecies(3203.666666666667, 7687.75, 98.0, 58.0, "sa1121"));
+
+ Species species = createSpecies(7817.714285714286, 11287.642857142859, 80.0, 40.0, "sa1422");
+ Species species2 = createSpecies(8224.964285714286, 11241.392857142859, 80.0, 40.0, "sa1419");
+ Complex complex = createComplex(7804.714285714286, 11182.642857142859, 112.0, 172.0, "csa152");
+ complex.addSpecies(species);
+ complex.addSpecies(species2);
+ species.setComplex(complex);
+ species2.setComplex(complex);
+
+ model.addElement(species);
+ model.addElement(species2);
+ model.addElement(complex);
+
+ model.addElement(createCompartment(1380.0, 416.0, 15893.0, 10866.0, "ca1"));
+ return model;
+ }
+
+ private Compartment createCompartment(double x, double y, double width, double height, String elementId) {
+ Compartment compartment = new Compartment(elementId);
+ compartment.setElementId(elementId);
+ compartment.setX(x);
+ compartment.setY(y);
+ compartment.setWidth(width);
+ compartment.setHeight(height);
+ return compartment;
+ }
+
+ private Species createSpecies(double x, double y, double width, double height, String elementId) {
+ SimpleMolecule simpleMolecule = new SimpleMolecule(elementId);
+ simpleMolecule.setX(x);
+ simpleMolecule.setY(y);
+ simpleMolecule.setWidth(width);
+ simpleMolecule.setHeight(height);
+ return simpleMolecule;
+ }
+
+ private Complex createComplex(double x, double y, double width, double height, String elementId) {
+ Complex complex = new Complex(elementId);
+ complex.setX(x);
+ complex.setY(y);
+ complex.setWidth(width);
+ complex.setHeight(height);
+ return complex;
+ }
+
+ @Test
+ public void testCrossWithComplexElements() throws Exception {
+ try {
+ Model model = createCrossModel();
+ Element ldhb1 = model.getElementByElementId("sa1422");
+ Element ldhb2 = model.getElementByElementId("sa1419");
+
+ Compartment cytosol = (Compartment) model.getElementByElementId("ca1");
+
+ assertTrue(cytosol.cross(ldhb1));
+ assertTrue(cytosol.cross(ldhb2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new Compartment());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Compartment compartment = new Compartment();
+ compartment.addElement(new GenericProtein("idd"));
+ Compartment copy = new Compartment(compartment);
+ assertNotNull(copy);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ Compartment compartment = new Compartment();
+ String invalidVal = "a1.6";
+ String val = "1.6";
+ Double dVal = 1.6;
+
+ compartment.setLineThickness(val);
+ compartment.setLineOuterWidth(val);
+ compartment.setLineInnerWidth(val);
+
+ assertEquals(dVal, compartment.getThickness(), Configuration.EPSILON);
+ assertEquals(dVal, compartment.getOuterWidth(), Configuration.EPSILON);
+ assertEquals(dVal, compartment.getInnerWidth(), Configuration.EPSILON);
+
+ try {
+ compartment.setLineThickness(invalidVal);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ try {
+ compartment.setLineOuterWidth(invalidVal);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ try {
+ compartment.setLineInnerWidth(invalidVal);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+
+ compartment.setNamePoint(2, 3);
+ assertEquals(0, compartment.getNamePoint().distance(2, 3), Configuration.EPSILON);
+
+ Set<Element> elements = new HashSet<>();
+
+ compartment.setElements(elements);
+ assertEquals(elements, compartment.getElements());
+
+ assertNotNull(compartment.getStringType());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddElement() {
+ try {
+ Compartment compartment = new Compartment();
+
+ Species child = new GenericProtein("id");
+
+ compartment.addElement(child);
+ compartment.addElement(child);
+
+ assertEquals(1, compartment.getElements().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddInvalidElement() {
+ try {
+ Compartment compartment = new Compartment();
+
+ Species child = new GenericProtein("id");
+ Species child2 = new GenericProtein("id");
+
+ compartment.addElement(child);
+ compartment.addElement(child2);
+
+ fail("Exception expected");
+
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAllElements() {
+ try {
+ Compartment compartment = new Compartment();
+
+ Species child = new GenericProtein("id");
+ Compartment child2 = new Compartment();
+ child2.addElement(child);
+ compartment.addElement(child2);
+
+ assertEquals(2, compartment.getAllSubElements().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ Compartment degraded = new Compartment().copy();
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRemoveElement() {
+ try {
+ Compartment comp = new Compartment();
+ Species protein = new GenericProtein("idd");
+ comp.addElement(protein);
+ protein.setCompartment(new Compartment());
+
+ comp.removeElement(protein);
+
+ assertEquals(0, comp.getElements().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ Compartment compartment = Mockito.spy(Compartment.class);
+ compartment.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/compartment/LeftSquareCompartmentTest.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/LeftSquareCompartmentTest.java
index c50d5fa465..0237ebeaba 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/compartment/LeftSquareCompartmentTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/LeftSquareCompartmentTest.java
@@ -1,96 +1,96 @@
-package lcsb.mapviewer.model.map.compartment;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-
-public class LeftSquareCompartmentTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new LeftSquareCompartment());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- LeftSquareCompartment compartment = new LeftSquareCompartment(new LeftSquareCompartment());
- assertNotNull(compartment);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor3() {
- try {
- LeftSquareCompartment compartment = new LeftSquareCompartment("id");
- assertNotNull(compartment);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor2() {
- try {
- Model model = new ModelFullIndexed(null);
- model.setWidth(1);
- model.setHeight(1);
- LeftSquareCompartment compartment = new LeftSquareCompartment(new Compartment(), model);
- assertNotNull(compartment);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- LeftSquareCompartment compartment = new LeftSquareCompartment().copy();
- assertNotNull(compartment);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- LeftSquareCompartment compartment = Mockito.spy(LeftSquareCompartment.class);
- compartment.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.compartment;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+
+public class LeftSquareCompartmentTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new LeftSquareCompartment());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ LeftSquareCompartment compartment = new LeftSquareCompartment(new LeftSquareCompartment());
+ assertNotNull(compartment);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor3() {
+ try {
+ LeftSquareCompartment compartment = new LeftSquareCompartment("id");
+ assertNotNull(compartment);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor2() {
+ try {
+ Model model = new ModelFullIndexed(null);
+ model.setWidth(1);
+ model.setHeight(1);
+ LeftSquareCompartment compartment = new LeftSquareCompartment(new Compartment(), model);
+ assertNotNull(compartment);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ LeftSquareCompartment compartment = new LeftSquareCompartment().copy();
+ assertNotNull(compartment);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ LeftSquareCompartment compartment = Mockito.spy(LeftSquareCompartment.class);
+ compartment.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/compartment/OvalCompartmentTest.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/OvalCompartmentTest.java
index e4f7886231..d403f5f575 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/compartment/OvalCompartmentTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/OvalCompartmentTest.java
@@ -1,71 +1,71 @@
-package lcsb.mapviewer.model.map.compartment;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class OvalCompartmentTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new OvalCompartment());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- OvalCompartment original = new OvalCompartment();
- OvalCompartment copy = new OvalCompartment(original);
- assertNotNull(copy);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- OvalCompartment original = new OvalCompartment();
- OvalCompartment copy = original.copy();
- assertNotNull(copy);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- OvalCompartment compartment = Mockito.spy(OvalCompartment.class);
- compartment.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.compartment;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class OvalCompartmentTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new OvalCompartment());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ OvalCompartment original = new OvalCompartment();
+ OvalCompartment copy = new OvalCompartment(original);
+ assertNotNull(copy);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ OvalCompartment original = new OvalCompartment();
+ OvalCompartment copy = original.copy();
+ assertNotNull(copy);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ OvalCompartment compartment = Mockito.spy(OvalCompartment.class);
+ compartment.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/compartment/PathwayCompartmentTest.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/PathwayCompartmentTest.java
index eb1b298228..32f1d578f4 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/compartment/PathwayCompartmentTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/PathwayCompartmentTest.java
@@ -1,90 +1,90 @@
-package lcsb.mapviewer.model.map.compartment;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.compartment.CompartmentComparator;
-import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
-
-public class PathwayCompartmentTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void test() throws Exception {
- try {
- CompartmentComparator comparator = new CompartmentComparator();
- Compartment pathway = new PathwayCompartment("id");
- Compartment copy = pathway.copy();
-
- assertEquals(0, comparator.compare(pathway, copy));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new PathwayCompartment("id"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- PathwayCompartment pathway = new PathwayCompartment("id");
- String title = "tit27";
- pathway.setName(title);
- assertEquals(title, pathway.getName());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- PathwayCompartment comp = Mockito.spy(PathwayCompartment.class);
- comp.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- PathwayCompartment degraded = new PathwayCompartment("id").copy();
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.compartment;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.CompartmentComparator;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
+
+public class PathwayCompartmentTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void test() throws Exception {
+ try {
+ CompartmentComparator comparator = new CompartmentComparator();
+ Compartment pathway = new PathwayCompartment("id");
+ Compartment copy = pathway.copy();
+
+ assertEquals(0, comparator.compare(pathway, copy));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new PathwayCompartment("id"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ PathwayCompartment pathway = new PathwayCompartment("id");
+ String title = "tit27";
+ pathway.setName(title);
+ assertEquals(title, pathway.getName());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ PathwayCompartment comp = Mockito.spy(PathwayCompartment.class);
+ comp.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ PathwayCompartment degraded = new PathwayCompartment("id").copy();
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/compartment/RightSquareCompartmentTest.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/RightSquareCompartmentTest.java
index bfcb69f605..26fe88ef30 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/compartment/RightSquareCompartmentTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/RightSquareCompartmentTest.java
@@ -1,109 +1,109 @@
-package lcsb.mapviewer.model.map.compartment;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-
-public class RightSquareCompartmentTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new RightSquareCompartment());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- RightSquareCompartment compartment = new RightSquareCompartment(new RightSquareCompartment());
- assertNotNull(compartment);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor3() {
- try {
- RightSquareCompartment compartment = new RightSquareCompartment("id");
- assertNotNull(compartment);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor2() {
- try {
- Model model = new ModelFullIndexed(null);
- model.setWidth(1);
- model.setHeight(1);
- RightSquareCompartment compartment = new RightSquareCompartment(new Compartment(), model);
- assertNotNull(compartment);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- RightSquareCompartment compartment = new RightSquareCompartment().copy();
- assertNotNull(compartment);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetPoint() {
- try {
- RightSquareCompartment compartment = new RightSquareCompartment();
- compartment.setPoint("10", "10");
- assertTrue(compartment.getWidth() < 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- RightSquareCompartment compartment = Mockito.spy(RightSquareCompartment.class);
- compartment.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.compartment;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+
+public class RightSquareCompartmentTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new RightSquareCompartment());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ RightSquareCompartment compartment = new RightSquareCompartment(new RightSquareCompartment());
+ assertNotNull(compartment);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor3() {
+ try {
+ RightSquareCompartment compartment = new RightSquareCompartment("id");
+ assertNotNull(compartment);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor2() {
+ try {
+ Model model = new ModelFullIndexed(null);
+ model.setWidth(1);
+ model.setHeight(1);
+ RightSquareCompartment compartment = new RightSquareCompartment(new Compartment(), model);
+ assertNotNull(compartment);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ RightSquareCompartment compartment = new RightSquareCompartment().copy();
+ assertNotNull(compartment);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetPoint() {
+ try {
+ RightSquareCompartment compartment = new RightSquareCompartment();
+ compartment.setPoint("10", "10");
+ assertTrue(compartment.getWidth() < 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ RightSquareCompartment compartment = Mockito.spy(RightSquareCompartment.class);
+ compartment.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/compartment/TopSquareCompartmentTest.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/TopSquareCompartmentTest.java
index fe002f67b3..6b56de409e 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/compartment/TopSquareCompartmentTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/TopSquareCompartmentTest.java
@@ -1,100 +1,100 @@
-package lcsb.mapviewer.model.map.compartment;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.compartment.TopSquareCompartment;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-
-public class TopSquareCompartmentTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new TopSquareCompartment());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
- @Test
- public void testConstructor1() {
- try {
- TopSquareCompartment compartment = new TopSquareCompartment(new TopSquareCompartment());
- assertNotNull(compartment);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor3() {
- try {
- TopSquareCompartment compartment = new TopSquareCompartment("id");
- assertNotNull(compartment);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor2() {
- try {
- Model model = new ModelFullIndexed(null);
- model.setWidth(1);
- model.setHeight(1);
- TopSquareCompartment compartment = new TopSquareCompartment(new Compartment(), model);
- assertNotNull(compartment);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- TopSquareCompartment compartment = new TopSquareCompartment().copy();
- assertNotNull(compartment);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- TopSquareCompartment compartment = Mockito.spy(TopSquareCompartment.class);
- compartment.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
-}
+package lcsb.mapviewer.model.map.compartment;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.TopSquareCompartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+
+public class TopSquareCompartmentTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new TopSquareCompartment());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
+ @Test
+ public void testConstructor1() {
+ try {
+ TopSquareCompartment compartment = new TopSquareCompartment(new TopSquareCompartment());
+ assertNotNull(compartment);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor3() {
+ try {
+ TopSquareCompartment compartment = new TopSquareCompartment("id");
+ assertNotNull(compartment);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor2() {
+ try {
+ Model model = new ModelFullIndexed(null);
+ model.setWidth(1);
+ model.setHeight(1);
+ TopSquareCompartment compartment = new TopSquareCompartment(new Compartment(), model);
+ assertNotNull(compartment);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ TopSquareCompartment compartment = new TopSquareCompartment().copy();
+ assertNotNull(compartment);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ TopSquareCompartment compartment = Mockito.spy(TopSquareCompartment.class);
+ compartment.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/AllLayoutTests.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/AllLayoutTests.java
index 10a1e3535a..0d89ca417c 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/AllLayoutTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/AllLayoutTests.java
@@ -1,25 +1,25 @@
-package lcsb.mapviewer.model.map.layout;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-import lcsb.mapviewer.model.map.layout.graphics.AllGraphicsTests;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AllGraphicsTests.class, //
- ColorSchemaTest.class, //
- ElementGroupTest.class, //
- GenericColorSchemaTest.class, //
- GeneVariationTest.class, //
- GeneVariationColorSchemaTest.class, //
- InvalidColorSchemaExceptionTest.class, //
- LayoutStatusTest.class, //
- LayoutTest.class, //
- ReferenceGenomeGeneMappingTest.class, //
- ReferenceGenomeTest.class, //
- ReferenceGenomeTypeTest.class,//
-})
-public class AllLayoutTests {
-
-}
+package lcsb.mapviewer.model.map.layout;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+import lcsb.mapviewer.model.map.layout.graphics.AllGraphicsTests;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AllGraphicsTests.class, //
+ ColorSchemaTest.class, //
+ ElementGroupTest.class, //
+ GenericColorSchemaTest.class, //
+ GeneVariationTest.class, //
+ GeneVariationColorSchemaTest.class, //
+ InvalidColorSchemaExceptionTest.class, //
+ LayoutStatusTest.class, //
+ LayoutTest.class, //
+ ReferenceGenomeGeneMappingTest.class, //
+ ReferenceGenomeTest.class, //
+ ReferenceGenomeTypeTest.class,//
+})
+public class AllLayoutTests {
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/ColorSchemaTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/ColorSchemaTest.java
index 1f58992fcf..6aa5af479e 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/ColorSchemaTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/ColorSchemaTest.java
@@ -1,147 +1,147 @@
-package lcsb.mapviewer.model.map.layout;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class ColorSchemaTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSetGetters() throws Exception {
- try {
- ColorSchema cs = new GenericColorSchema();
- List<String> compartments = new ArrayList<>();
- List<Class<? extends Element>> types = new ArrayList<>();
- String name = "S";
- int matches = 79;
- Double lineWidth = 5.89;
- String reactionIdentifier = "re id";
- Boolean reverseReaction = true;
-
- cs.setName(name);
- assertEquals(name, cs.getName());
-
- cs.setCompartments(compartments);
- assertEquals(compartments, cs.getCompartments());
-
- cs.setTypes(types);
- assertEquals(types, cs.getTypes());
-
- cs.setMatches(matches);
- assertEquals(matches, cs.getMatches());
-
- cs.setLineWidth(lineWidth);
- assertEquals(lineWidth, cs.getLineWidth());
-
- cs.setElementId(reactionIdentifier);
- assertEquals(reactionIdentifier, cs.getElementId());
-
- cs.setReverseReaction(reverseReaction);
- assertEquals(reverseReaction, cs.getReverseReaction());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToString() throws Exception {
- try {
- ColorSchema cs = new GenericColorSchema();
- assertNotNull(cs.toString());
- cs.setName("gene name");
- cs.addCompartment("A");
- cs.addType(Species.class);
- cs.setValue(1.2);
- cs.setColor(Color.BLACK);
- cs.addMiriamData(new MiriamData(MiriamType.CAS, "X"));
- assertNotNull(cs.toString());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddCompartments() throws Exception {
- try {
- ColorSchema cs = new GenericColorSchema();
- cs.addCompartments(new String[] { "a", "b" });
- assertEquals(2, cs.getCompartments().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddCompartments2() throws Exception {
- try {
- ColorSchema cs = new GenericColorSchema();
- List<String> compartments = new ArrayList<>();
- compartments.add("a");
- compartments.add("b");
- cs.addCompartments(compartments);
- assertEquals(2, cs.getCompartments().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddIdentifgierColumns() throws Exception {
- try {
- MiriamData generalIdentifier = new MiriamData();
- ColorSchema cs = new GenericColorSchema();
- List<Pair<MiriamType, String>> compartments = new ArrayList<>();
- compartments.add(new Pair<MiriamType, String>(MiriamType.CAS, "x"));
- cs.addMiriamData(generalIdentifier);
-
- assertEquals(1, cs.getMiriamData().size());
- assertEquals(generalIdentifier, cs.getMiriamData().iterator().next());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddTypes() throws Exception {
- try {
- ColorSchema cs = new GenericColorSchema();
- List<Class<? extends Element>> compartments = new ArrayList<>();
- compartments.add(Species.class);
- compartments.add(Protein.class);
- cs.addTypes(compartments);
- assertEquals(2, cs.getTypes().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.layout;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class ColorSchemaTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSetGetters() throws Exception {
+ try {
+ ColorSchema cs = new GenericColorSchema();
+ List<String> compartments = new ArrayList<>();
+ List<Class<? extends Element>> types = new ArrayList<>();
+ String name = "S";
+ int matches = 79;
+ Double lineWidth = 5.89;
+ String reactionIdentifier = "re id";
+ Boolean reverseReaction = true;
+
+ cs.setName(name);
+ assertEquals(name, cs.getName());
+
+ cs.setCompartments(compartments);
+ assertEquals(compartments, cs.getCompartments());
+
+ cs.setTypes(types);
+ assertEquals(types, cs.getTypes());
+
+ cs.setMatches(matches);
+ assertEquals(matches, cs.getMatches());
+
+ cs.setLineWidth(lineWidth);
+ assertEquals(lineWidth, cs.getLineWidth());
+
+ cs.setElementId(reactionIdentifier);
+ assertEquals(reactionIdentifier, cs.getElementId());
+
+ cs.setReverseReaction(reverseReaction);
+ assertEquals(reverseReaction, cs.getReverseReaction());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToString() throws Exception {
+ try {
+ ColorSchema cs = new GenericColorSchema();
+ assertNotNull(cs.toString());
+ cs.setName("gene name");
+ cs.addCompartment("A");
+ cs.addType(Species.class);
+ cs.setValue(1.2);
+ cs.setColor(Color.BLACK);
+ cs.addMiriamData(new MiriamData(MiriamType.CAS, "X"));
+ assertNotNull(cs.toString());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddCompartments() throws Exception {
+ try {
+ ColorSchema cs = new GenericColorSchema();
+ cs.addCompartments(new String[] { "a", "b" });
+ assertEquals(2, cs.getCompartments().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddCompartments2() throws Exception {
+ try {
+ ColorSchema cs = new GenericColorSchema();
+ List<String> compartments = new ArrayList<>();
+ compartments.add("a");
+ compartments.add("b");
+ cs.addCompartments(compartments);
+ assertEquals(2, cs.getCompartments().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddIdentifgierColumns() throws Exception {
+ try {
+ MiriamData generalIdentifier = new MiriamData();
+ ColorSchema cs = new GenericColorSchema();
+ List<Pair<MiriamType, String>> compartments = new ArrayList<>();
+ compartments.add(new Pair<MiriamType, String>(MiriamType.CAS, "x"));
+ cs.addMiriamData(generalIdentifier);
+
+ assertEquals(1, cs.getMiriamData().size());
+ assertEquals(generalIdentifier, cs.getMiriamData().iterator().next());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddTypes() throws Exception {
+ try {
+ ColorSchema cs = new GenericColorSchema();
+ List<Class<? extends Element>> compartments = new ArrayList<>();
+ compartments.add(Species.class);
+ compartments.add(Protein.class);
+ cs.addTypes(compartments);
+ assertEquals(2, cs.getTypes().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/ElementGroupTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/ElementGroupTest.java
index b8673bb117..5c8e121c54 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/ElementGroupTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/ElementGroupTest.java
@@ -1,66 +1,66 @@
-package lcsb.mapviewer.model.map.layout;
-
-import static org.junit.Assert.assertEquals;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.map.layout.ElementGroup;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-
-public class ElementGroupTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new ElementGroup());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- ElementGroup group = new ElementGroup();
- String idGroup = "str";
- List<Element> elements = new ArrayList<>();
-
- group.setIdGroup(idGroup);
- group.setElements(elements);
-
- assertEquals(idGroup, group.getIdGroup());
- assertEquals(elements, group.getElements());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddElement() {
- try {
- ElementGroup group = new ElementGroup();
- group.addElement(new GenericProtein("id"));
- assertEquals(1, group.getElements().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.map.layout;
+
+import static org.junit.Assert.assertEquals;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.map.layout.ElementGroup;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+
+public class ElementGroupTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new ElementGroup());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ ElementGroup group = new ElementGroup();
+ String idGroup = "str";
+ List<Element> elements = new ArrayList<>();
+
+ group.setIdGroup(idGroup);
+ group.setElements(elements);
+
+ assertEquals(idGroup, group.getIdGroup());
+ assertEquals(elements, group.getElements());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddElement() {
+ try {
+ ElementGroup group = new ElementGroup();
+ group.addElement(new GenericProtein("id"));
+ assertEquals(1, group.getElements().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/GeneVariationColorSchemaTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/GeneVariationColorSchemaTest.java
index e7dc2f79b4..da6babd624 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/GeneVariationColorSchemaTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/GeneVariationColorSchemaTest.java
@@ -1,124 +1,124 @@
-package lcsb.mapviewer.model.map.layout;
-
-import static org.junit.Assert.*;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class GeneVariationColorSchemaTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new GeneVariationColorSchema());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- GeneVariationColorSchema schema = new GeneVariationColorSchema();
- schema.setDescription("desc");
- GeneVariationColorSchema copy = new GeneVariationColorSchema(schema);
- assertEquals("desc", copy.getDescription());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- GeneVariationColorSchema schema = new GeneVariationColorSchema();
- schema.setDescription("desc");
- GeneVariationColorSchema copy = schema.copy();
-
- assertEquals("desc", copy.getDescription());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
-
- List<GeneVariation> geneVariations = new ArrayList<>();
-
- GeneVariationColorSchema schema = new GeneVariationColorSchema();
- schema.setGeneVariations(geneVariations);
-
- assertEquals(geneVariations, schema.getGeneVariations());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddGeneVariations() {
- try {
-
- List<GeneVariation> geneVariations = new ArrayList<>();
- geneVariations.add(new GeneVariation());
-
- GeneVariationColorSchema schema = new GeneVariationColorSchema();
- schema.addGeneVariations(geneVariations);
-
- assertEquals(1, schema.getGeneVariations().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- GeneVariationColorSchema schema = new GeneVariationColorSchema() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- };
- schema.copy();
- fail("Exception expected");
-
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.layout;
+
+import static org.junit.Assert.*;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class GeneVariationColorSchemaTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new GeneVariationColorSchema());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ GeneVariationColorSchema schema = new GeneVariationColorSchema();
+ schema.setDescription("desc");
+ GeneVariationColorSchema copy = new GeneVariationColorSchema(schema);
+ assertEquals("desc", copy.getDescription());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ GeneVariationColorSchema schema = new GeneVariationColorSchema();
+ schema.setDescription("desc");
+ GeneVariationColorSchema copy = schema.copy();
+
+ assertEquals("desc", copy.getDescription());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+
+ List<GeneVariation> geneVariations = new ArrayList<>();
+
+ GeneVariationColorSchema schema = new GeneVariationColorSchema();
+ schema.setGeneVariations(geneVariations);
+
+ assertEquals(geneVariations, schema.getGeneVariations());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddGeneVariations() {
+ try {
+
+ List<GeneVariation> geneVariations = new ArrayList<>();
+ geneVariations.add(new GeneVariation());
+
+ GeneVariationColorSchema schema = new GeneVariationColorSchema();
+ schema.addGeneVariations(geneVariations);
+
+ assertEquals(1, schema.getGeneVariations().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ GeneVariationColorSchema schema = new GeneVariationColorSchema() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ };
+ schema.copy();
+ fail("Exception expected");
+
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/GeneVariationTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/GeneVariationTest.java
index f0c15a3242..6474d485b9 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/GeneVariationTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/GeneVariationTest.java
@@ -1,101 +1,101 @@
-package lcsb.mapviewer.model.map.layout;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.fail;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.MiriamData;
-
-public class GeneVariationTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetters() throws Exception {
- try {
- String modifiedDna = "str";
-
- int position = 12;
-
- GeneVariation gv = new GeneVariation();
-
- gv.setModifiedDna(modifiedDna);
- assertEquals(modifiedDna, gv.getModifiedDna());
-
- gv.setPosition(position);
-
- assertEquals((long) position, (long) gv.getPosition());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddReference() throws Exception {
- try {
- GeneVariation gv = new GeneVariation();
- gv.addReference(new MiriamData());
- assertEquals(1, gv.getReferences().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() throws Exception {
- try {
- String modifiedDna = "str";
-
- GeneVariation gv = new GeneVariation();
-
- gv.setModifiedDna(modifiedDna);
- gv.addReference(new MiriamData());
-
- GeneVariation copy = gv.copy();
-
- assertEquals(gv.getModifiedDna(), copy.getModifiedDna());
- assertEquals(1, copy.getReferences().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() throws Exception {
- try {
- GeneVariation gv = new GeneVariation() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- };
-
- gv.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.layout;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.MiriamData;
+
+public class GeneVariationTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetters() throws Exception {
+ try {
+ String modifiedDna = "str";
+
+ int position = 12;
+
+ GeneVariation gv = new GeneVariation();
+
+ gv.setModifiedDna(modifiedDna);
+ assertEquals(modifiedDna, gv.getModifiedDna());
+
+ gv.setPosition(position);
+
+ assertEquals((long) position, (long) gv.getPosition());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddReference() throws Exception {
+ try {
+ GeneVariation gv = new GeneVariation();
+ gv.addReference(new MiriamData());
+ assertEquals(1, gv.getReferences().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() throws Exception {
+ try {
+ String modifiedDna = "str";
+
+ GeneVariation gv = new GeneVariation();
+
+ gv.setModifiedDna(modifiedDna);
+ gv.addReference(new MiriamData());
+
+ GeneVariation copy = gv.copy();
+
+ assertEquals(gv.getModifiedDna(), copy.getModifiedDna());
+ assertEquals(1, copy.getReferences().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() throws Exception {
+ try {
+ GeneVariation gv = new GeneVariation() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ };
+
+ gv.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/GenericColorSchemaTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/GenericColorSchemaTest.java
index e855e26768..02c2315dc8 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/GenericColorSchemaTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/GenericColorSchemaTest.java
@@ -1,81 +1,81 @@
-package lcsb.mapviewer.model.map.layout;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class GenericColorSchemaTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new GenericColorSchema());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- GenericColorSchema schema = new GenericColorSchema();
- schema.setDescription("desc");
- GenericColorSchema copy = new GenericColorSchema(schema);
- assertEquals("desc", copy.getDescription());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- GenericColorSchema schema = new GenericColorSchema();
- schema.setDescription("desc");
- GenericColorSchema copy = schema.copy();
-
- assertEquals("desc", copy.getDescription());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- GenericColorSchema schema = new GenericColorSchema() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- };
- schema.copy();
- fail("Exception expected");
-
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.map.layout;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class GenericColorSchemaTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new GenericColorSchema());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ GenericColorSchema schema = new GenericColorSchema();
+ schema.setDescription("desc");
+ GenericColorSchema copy = new GenericColorSchema(schema);
+ assertEquals("desc", copy.getDescription());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ GenericColorSchema schema = new GenericColorSchema();
+ schema.setDescription("desc");
+ GenericColorSchema copy = schema.copy();
+
+ assertEquals("desc", copy.getDescription());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ GenericColorSchema schema = new GenericColorSchema() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ };
+ schema.copy();
+ fail("Exception expected");
+
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/InvalidColorSchemaExceptionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/InvalidColorSchemaExceptionTest.java
index 4d3126561d..24130c2591 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/InvalidColorSchemaExceptionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/InvalidColorSchemaExceptionTest.java
@@ -1,57 +1,57 @@
-package lcsb.mapviewer.model.map.layout;
-
-import static org.junit.Assert.*;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class InvalidColorSchemaExceptionTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new InvalidColorSchemaException("x"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- Exception e = new InvalidColorSchemaException(new Exception());
- assertNotNull(e);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor2() {
- try {
- Exception e = new InvalidColorSchemaException("message", new Exception());
- assertNotNull(e);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.layout;
+
+import static org.junit.Assert.*;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class InvalidColorSchemaExceptionTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new InvalidColorSchemaException("x"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ Exception e = new InvalidColorSchemaException(new Exception());
+ assertNotNull(e);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor2() {
+ try {
+ Exception e = new InvalidColorSchemaException("message", new Exception());
+ assertNotNull(e);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/LayoutStatusTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/LayoutStatusTest.java
index 624b3f47ae..7517897fd9 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/LayoutStatusTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/LayoutStatusTest.java
@@ -1,30 +1,30 @@
-package lcsb.mapviewer.model.map.layout;
-
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class LayoutStatusTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testValidValues() {
- for (LayoutStatus type : LayoutStatus.values()) {
- assertNotNull(type);
-
- // for coverage tests
- LayoutStatus.valueOf(type.toString());
- assertNotNull(type.getCommonName());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.layout;
+
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class LayoutStatusTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testValidValues() {
+ for (LayoutStatus type : LayoutStatus.values()) {
+ assertNotNull(type);
+
+ // for coverage tests
+ LayoutStatus.valueOf(type.toString());
+ assertNotNull(type.getCommonName());
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/LayoutTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/LayoutTest.java
index 10f0c19abd..4a4633fb86 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/LayoutTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/LayoutTest.java
@@ -1,181 +1,181 @@
-package lcsb.mapviewer.model.map.layout;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.fail;
-
-import java.util.HashSet;
-import java.util.Set;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.cache.UploadedFileEntry;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-
-public class LayoutTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new Layout());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- String title = "TIT";
- String dir = "TIT";
- boolean publicL = true;
- Layout layout = new Layout(title, dir, publicL);
- assertEquals(title, layout.getTitle());
- assertEquals(dir, layout.getDirectory());
- assertEquals(publicL, layout.isPublicLayout());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor2() {
- try {
- String title = "TIT";
- String dir = "TIT";
- boolean publicL = true;
- Layout layout = new Layout(title, dir, publicL);
- Layout layout2 = new Layout(layout);
- assertNotNull(layout2);
- UploadedFileEntry fileEntry = new UploadedFileEntry();
- fileEntry.setFileContent(new byte[] {});
-
- layout.setInputData(fileEntry);
- Layout layout3 = new Layout(layout);
- assertNotNull(layout3);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithOrder() {
- try {
- boolean publicL = true;
- Layout overlay1 = new Layout(null, null, publicL);
- overlay1.setOrderIndex(12);
- Layout overlay2 = new Layout(overlay1);
- assertEquals(overlay1.getOrderIndex(), overlay2.getOrderIndex());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- String title = "TIT";
- String dir = "TIT";
- boolean publicL = true;
- Layout layout = new Layout(title, dir, publicL);
- Layout layout2 = layout.copy();
- assertNotNull(layout2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- Layout layout = new Layout() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- };
- layout.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- ModelFullIndexed model = new ModelFullIndexed(null);
- Set<Layout> layouts = new HashSet<>();
- boolean hierarchicalView = false;
- boolean publicLayout = true;
- int id = 62;
- String description = "qds";
- String directory = "vcccv";
- String title = "tit";
- LayoutStatus status = LayoutStatus.FAILURE;
- double progress = 1.6;
- UploadedFileEntry inputData = new UploadedFileEntry();
- Layout parentLayout = new Layout();
- Layout layout = new Layout();
- layout.setHierarchicalView(hierarchicalView);
- assertEquals(hierarchicalView, layout.isHierarchicalView());
- layout.setId(id);
- assertEquals(id, layout.getId());
- layout.setDescription(description);
- assertEquals(description, layout.getDescription());
- layout.setDirectory(directory);
- assertEquals(directory, layout.getDirectory());
- layout.setTitle(title);
- assertEquals(title, layout.getTitle());
- layout.setModel((ModelData) null);
- assertNull(layout.getModel());
- layout.setCreator(null);
- assertNull(layout.getCreator());
- layout.setStatus(status);
- assertEquals(status, layout.getStatus());
- layout.setProgress(progress);
- assertEquals(progress, layout.getProgress(), Configuration.EPSILON);
- layout.setInputData(inputData);
- assertEquals(inputData, layout.getInputData());
- layout.setParentLayout(parentLayout);
- assertEquals(parentLayout, layout.getParentLayout());
- layout.setPublicLayout(publicLayout);
- assertEquals(publicLayout, layout.isPublicLayout());
-
- layout.setLayouts(layouts);
- assertEquals(layouts, layout.getLayouts());
- layout.addLayout(parentLayout);
- assertEquals(1, layouts.size());
- layout.setModel(model);
- assertEquals(model.getModelData(), layout.getModel());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.layout;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.fail;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+
+public class LayoutTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new Layout());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ String title = "TIT";
+ String dir = "TIT";
+ boolean publicL = true;
+ Layout layout = new Layout(title, dir, publicL);
+ assertEquals(title, layout.getTitle());
+ assertEquals(dir, layout.getDirectory());
+ assertEquals(publicL, layout.isPublicLayout());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor2() {
+ try {
+ String title = "TIT";
+ String dir = "TIT";
+ boolean publicL = true;
+ Layout layout = new Layout(title, dir, publicL);
+ Layout layout2 = new Layout(layout);
+ assertNotNull(layout2);
+ UploadedFileEntry fileEntry = new UploadedFileEntry();
+ fileEntry.setFileContent(new byte[] {});
+
+ layout.setInputData(fileEntry);
+ Layout layout3 = new Layout(layout);
+ assertNotNull(layout3);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructorWithOrder() {
+ try {
+ boolean publicL = true;
+ Layout overlay1 = new Layout(null, null, publicL);
+ overlay1.setOrderIndex(12);
+ Layout overlay2 = new Layout(overlay1);
+ assertEquals(overlay1.getOrderIndex(), overlay2.getOrderIndex());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ String title = "TIT";
+ String dir = "TIT";
+ boolean publicL = true;
+ Layout layout = new Layout(title, dir, publicL);
+ Layout layout2 = layout.copy();
+ assertNotNull(layout2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ Layout layout = new Layout() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ };
+ layout.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ ModelFullIndexed model = new ModelFullIndexed(null);
+ Set<Layout> layouts = new HashSet<>();
+ boolean hierarchicalView = false;
+ boolean publicLayout = true;
+ int id = 62;
+ String description = "qds";
+ String directory = "vcccv";
+ String title = "tit";
+ LayoutStatus status = LayoutStatus.FAILURE;
+ double progress = 1.6;
+ UploadedFileEntry inputData = new UploadedFileEntry();
+ Layout parentLayout = new Layout();
+ Layout layout = new Layout();
+ layout.setHierarchicalView(hierarchicalView);
+ assertEquals(hierarchicalView, layout.isHierarchicalView());
+ layout.setId(id);
+ assertEquals(id, layout.getId());
+ layout.setDescription(description);
+ assertEquals(description, layout.getDescription());
+ layout.setDirectory(directory);
+ assertEquals(directory, layout.getDirectory());
+ layout.setTitle(title);
+ assertEquals(title, layout.getTitle());
+ layout.setModel((ModelData) null);
+ assertNull(layout.getModel());
+ layout.setCreator(null);
+ assertNull(layout.getCreator());
+ layout.setStatus(status);
+ assertEquals(status, layout.getStatus());
+ layout.setProgress(progress);
+ assertEquals(progress, layout.getProgress(), Configuration.EPSILON);
+ layout.setInputData(inputData);
+ assertEquals(inputData, layout.getInputData());
+ layout.setParentLayout(parentLayout);
+ assertEquals(parentLayout, layout.getParentLayout());
+ layout.setPublicLayout(publicLayout);
+ assertEquals(publicLayout, layout.isPublicLayout());
+
+ layout.setLayouts(layouts);
+ assertEquals(layouts, layout.getLayouts());
+ layout.addLayout(parentLayout);
+ assertEquals(1, layouts.size());
+ layout.setModel(model);
+ assertEquals(model.getModelData(), layout.getModel());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/ReferenceGenomeGeneMappingTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/ReferenceGenomeGeneMappingTest.java
index a3f9bd8ea7..48aa9f1695 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/ReferenceGenomeGeneMappingTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/ReferenceGenomeGeneMappingTest.java
@@ -1,54 +1,54 @@
-package lcsb.mapviewer.model.map.layout;
-
-import static org.junit.Assert.assertEquals;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.ModelTestFunctions;
-import lcsb.mapviewer.common.Configuration;
-
-public class ReferenceGenomeGeneMappingTest extends ModelTestFunctions {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetters() {
- try {
- int id = 96;
- ReferenceGenome genome = new ReferenceGenome();
- String name = "test_name_97";
- String url = "http://some.url/";
- double progress = 4;
-
- ReferenceGenomeGeneMapping mapping = new ReferenceGenomeGeneMapping();
- mapping.setId(id);
- mapping.setReferenceGenome(genome);
- mapping.setName(name);
- mapping.setSourceUrl(url);
- mapping.setDownloadProgress(progress);
-
- assertEquals(genome, mapping.getReferenceGenome());
- assertEquals(name, mapping.getName());
- assertEquals(url, mapping.getSourceUrl());
- assertEquals(progress, mapping.getDownloadProgress(), Configuration.EPSILON);
- assertEquals(id, mapping.getId());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.layout;
+
+import static org.junit.Assert.assertEquals;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.ModelTestFunctions;
+import lcsb.mapviewer.common.Configuration;
+
+public class ReferenceGenomeGeneMappingTest extends ModelTestFunctions {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ int id = 96;
+ ReferenceGenome genome = new ReferenceGenome();
+ String name = "test_name_97";
+ String url = "http://some.url/";
+ double progress = 4;
+
+ ReferenceGenomeGeneMapping mapping = new ReferenceGenomeGeneMapping();
+ mapping.setId(id);
+ mapping.setReferenceGenome(genome);
+ mapping.setName(name);
+ mapping.setSourceUrl(url);
+ mapping.setDownloadProgress(progress);
+
+ assertEquals(genome, mapping.getReferenceGenome());
+ assertEquals(name, mapping.getName());
+ assertEquals(url, mapping.getSourceUrl());
+ assertEquals(progress, mapping.getDownloadProgress(), Configuration.EPSILON);
+ assertEquals(id, mapping.getId());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/ReferenceGenomeTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/ReferenceGenomeTest.java
index 9195a401a8..d1416e065c 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/ReferenceGenomeTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/ReferenceGenomeTest.java
@@ -1,89 +1,89 @@
-package lcsb.mapviewer.model.map.layout;
-
-import static org.junit.Assert.*;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-
-public class ReferenceGenomeTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new ReferenceGenome());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddReferenceGenomeGeneMapping() {
- try {
- ReferenceGenome genome = new ReferenceGenome();
- assertEquals(0, genome.getGeneMapping().size());
- genome.addReferenceGenomeGeneMapping(new ReferenceGenomeGeneMapping());
- assertEquals(1, genome.getGeneMapping().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- int id = 16;
- MiriamData organism = new MiriamData(MiriamType.TAXONOMY, "9606");
- ReferenceGenomeType type = ReferenceGenomeType.UCSC;
- String version = "hg19";
- double downloadProgress = 3.0;
- String sourceUrl = "google.pl";
- List<ReferenceGenomeGeneMapping> geneMapping = new ArrayList<>();
-
- ReferenceGenome genome = new ReferenceGenome();
-
- genome.setDownloadProgress(downloadProgress);
- genome.setId(id);
- genome.setOrganism(organism);
- genome.setSourceUrl(sourceUrl);
- genome.setType(type);
- genome.setVersion(version);
- genome.setGeneMapping(geneMapping);
-
- assertEquals(downloadProgress, genome.getDownloadProgress(), Configuration.EPSILON);
- assertEquals(id, genome.getId());
- assertEquals(organism, genome.getOrganism());
- assertEquals(sourceUrl, genome.getSourceUrl());
- assertEquals(type, genome.getType());
- assertEquals(version, genome.getVersion());
- assertEquals(geneMapping, genome.getGeneMapping());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.layout;
+
+import static org.junit.Assert.*;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+
+public class ReferenceGenomeTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new ReferenceGenome());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddReferenceGenomeGeneMapping() {
+ try {
+ ReferenceGenome genome = new ReferenceGenome();
+ assertEquals(0, genome.getGeneMapping().size());
+ genome.addReferenceGenomeGeneMapping(new ReferenceGenomeGeneMapping());
+ assertEquals(1, genome.getGeneMapping().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ int id = 16;
+ MiriamData organism = new MiriamData(MiriamType.TAXONOMY, "9606");
+ ReferenceGenomeType type = ReferenceGenomeType.UCSC;
+ String version = "hg19";
+ double downloadProgress = 3.0;
+ String sourceUrl = "google.pl";
+ List<ReferenceGenomeGeneMapping> geneMapping = new ArrayList<>();
+
+ ReferenceGenome genome = new ReferenceGenome();
+
+ genome.setDownloadProgress(downloadProgress);
+ genome.setId(id);
+ genome.setOrganism(organism);
+ genome.setSourceUrl(sourceUrl);
+ genome.setType(type);
+ genome.setVersion(version);
+ genome.setGeneMapping(geneMapping);
+
+ assertEquals(downloadProgress, genome.getDownloadProgress(), Configuration.EPSILON);
+ assertEquals(id, genome.getId());
+ assertEquals(organism, genome.getOrganism());
+ assertEquals(sourceUrl, genome.getSourceUrl());
+ assertEquals(type, genome.getType());
+ assertEquals(version, genome.getVersion());
+ assertEquals(geneMapping, genome.getGeneMapping());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/ReferenceGenomeTypeTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/ReferenceGenomeTypeTest.java
index cbd1a60cea..1b4c5c817b 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/ReferenceGenomeTypeTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/ReferenceGenomeTypeTest.java
@@ -1,35 +1,35 @@
-package lcsb.mapviewer.model.map.layout;
-
-import static org.junit.Assert.*;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ReferenceGenomeTypeTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testValidValues() {
- for (ReferenceGenomeType type : ReferenceGenomeType.values()) {
- assertNotNull(type);
-
- // for coverage tests
- ReferenceGenomeType.valueOf(type.toString());
- assertNotNull(type.getHomepage());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.layout;
+
+import static org.junit.Assert.*;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ReferenceGenomeTypeTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testValidValues() {
+ for (ReferenceGenomeType type : ReferenceGenomeType.values()) {
+ assertNotNull(type);
+
+ // for coverage tests
+ ReferenceGenomeType.valueOf(type.toString());
+ assertNotNull(type.getHomepage());
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/AllGraphicsTests.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/AllGraphicsTests.java
index f36fb4312e..7901cc401a 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/AllGraphicsTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/AllGraphicsTests.java
@@ -1,19 +1,19 @@
-package lcsb.mapviewer.model.map.layout.graphics;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ LayerComparatorTest.class,//
- LayerOvalComparatorTest.class,//
- LayerOvalTest.class,//
- LayerRectComparatorTest.class,//
- LayerRectTest.class,//
- LayerTest.class,//
- LayerTextComparatorTest.class,//
- LayerTextTest.class,//
-})
-public class AllGraphicsTests {
-
-}
+package lcsb.mapviewer.model.map.layout.graphics;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ LayerComparatorTest.class,//
+ LayerOvalComparatorTest.class,//
+ LayerOvalTest.class,//
+ LayerRectComparatorTest.class,//
+ LayerRectTest.class,//
+ LayerTest.class,//
+ LayerTextComparatorTest.class,//
+ LayerTextTest.class,//
+})
+public class AllGraphicsTests {
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerComparatorTest.java
index 1ff30dfbc7..f99db67d57 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerComparatorTest.java
@@ -1,200 +1,200 @@
-package lcsb.mapviewer.model.map.layout.graphics;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.graphics.PolylineData;
-
-public class LayerComparatorTest {
- LayerComparator comparator = new LayerComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- Layer layer1 = getLayer();
- Layer layer2 = getLayer();
-
- assertEquals(0, comparator.compare(new Layer(), new Layer()));
- assertEquals(0, comparator.compare(layer1, layer2));
- assertEquals(0, comparator.compare(layer1, layer1));
- assertEquals(0, comparator.compare(null, null));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
- @Test
- public void testInvalid() {
- try {
- class Tmp extends Layer {
- private static final long serialVersionUID = 1L;
- }
- ;
- Tmp layer1 = new Tmp();
- Tmp layer2 = new Tmp();
-
- comparator.compare(layer1, layer2);
- fail("Exception expected");
- } catch (NotImplementedException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
- private Layer getLayer() {
- Layer layer = new Layer();
-
- layer.setLayerId("A");
- layer.setName("B");
- layer.setVisible(true);
- layer.setLocked(true);
-
- PolylineData line = new PolylineData();
- layer.addLayerLine(line);
-
- LayerText text = new LayerText();
- text.setWidth(32.1);
- text.setNotes("SAda");
- layer.addLayerText(text);
-
- LayerRect rect = new LayerRect();
- rect.setHeight(4.3);
- layer.addLayerRect(rect);
-
- LayerOval oval = new LayerOval();
- oval.setX(12.0);
- layer.addLayerOval(oval);
-
- return layer;
- }
-
- @Test
- public void testDifferent() throws Exception {
- try {
- Layer layer1 = getLayer();
- Layer layer2 = getLayer();
-
- assertTrue(comparator.compare(layer1, new Layer()) != 0);
-
- assertTrue(comparator.compare(layer1, null) != 0);
- assertTrue(comparator.compare(null, layer1) != 0);
- assertTrue(comparator.compare(layer1, new Layer() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }) != 0);
-
- layer1 = getLayer();
- layer2 = getLayer();
-
- layer1.setName("ASdasdas");
-
- assertTrue(comparator.compare(layer1, layer2) != 0);
- assertTrue(comparator.compare(layer2, layer1) != 0);
-
- layer1 = getLayer();
- layer2 = getLayer();
-
- layer1.getLines().add(new PolylineData());
-
- assertTrue(comparator.compare(layer1, layer2) != 0);
- assertTrue(comparator.compare(layer2, layer1) != 0);
-
- layer1 = getLayer();
- layer2 = getLayer();
-
- layer1.getLines().get(0).setWidth(654);
-
- assertTrue(comparator.compare(layer1, layer2) != 0);
- assertTrue(comparator.compare(layer2, layer1) != 0);
-
- layer1 = getLayer();
- layer2 = getLayer();
-
- layer1.getOvals().add(new LayerOval());
-
- assertTrue(comparator.compare(layer1, layer2) != 0);
- assertTrue(comparator.compare(layer2, layer1) != 0);
-
- layer1 = getLayer();
- layer2 = getLayer();
-
- layer1.getOvals().get(0).setWidth("654");
-
- assertTrue(comparator.compare(layer1, layer2) != 0);
- assertTrue(comparator.compare(layer2, layer1) != 0);
-
- layer1 = getLayer();
- layer2 = getLayer();
-
- layer1.getRectangles().add(new LayerRect());
-
- assertTrue(comparator.compare(layer1, layer2) != 0);
- assertTrue(comparator.compare(layer2, layer1) != 0);
-
- layer1 = getLayer();
- layer2 = getLayer();
-
- layer1.getRectangles().get(0).setWidth("654");
-
- assertTrue(comparator.compare(layer1, layer2) != 0);
- assertTrue(comparator.compare(layer2, layer1) != 0);
-
- layer1 = getLayer();
- layer2 = getLayer();
-
- layer1.getTexts().add(new LayerText());
-
- assertTrue(comparator.compare(layer1, layer2) != 0);
- assertTrue(comparator.compare(layer2, layer1) != 0);
-
- layer1 = getLayer();
- layer2 = getLayer();
-
- layer1.getTexts().get(0).setWidth("654");
-
- assertTrue(comparator.compare(layer1, layer2) != 0);
- assertTrue(comparator.compare(layer2, layer1) != 0);
-
- layer1 = getLayer();
- layer2 = getLayer();
-
- layer1.setVisible(false);
-
- assertTrue(comparator.compare(layer1, layer2) != 0);
- assertTrue(comparator.compare(layer2, layer1) != 0);
-
- layer1 = getLayer();
- layer2 = getLayer();
-
- layer1.setLocked(false);
-
- assertTrue(comparator.compare(layer1, layer2) != 0);
- assertTrue(comparator.compare(layer2, layer1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.map.layout.graphics;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+
+public class LayerComparatorTest {
+ LayerComparator comparator = new LayerComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ Layer layer1 = getLayer();
+ Layer layer2 = getLayer();
+
+ assertEquals(0, comparator.compare(new Layer(), new Layer()));
+ assertEquals(0, comparator.compare(layer1, layer2));
+ assertEquals(0, comparator.compare(layer1, layer1));
+ assertEquals(0, comparator.compare(null, null));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+ @Test
+ public void testInvalid() {
+ try {
+ class Tmp extends Layer {
+ private static final long serialVersionUID = 1L;
+ }
+ ;
+ Tmp layer1 = new Tmp();
+ Tmp layer2 = new Tmp();
+
+ comparator.compare(layer1, layer2);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+ private Layer getLayer() {
+ Layer layer = new Layer();
+
+ layer.setLayerId("A");
+ layer.setName("B");
+ layer.setVisible(true);
+ layer.setLocked(true);
+
+ PolylineData line = new PolylineData();
+ layer.addLayerLine(line);
+
+ LayerText text = new LayerText();
+ text.setWidth(32.1);
+ text.setNotes("SAda");
+ layer.addLayerText(text);
+
+ LayerRect rect = new LayerRect();
+ rect.setHeight(4.3);
+ layer.addLayerRect(rect);
+
+ LayerOval oval = new LayerOval();
+ oval.setX(12.0);
+ layer.addLayerOval(oval);
+
+ return layer;
+ }
+
+ @Test
+ public void testDifferent() throws Exception {
+ try {
+ Layer layer1 = getLayer();
+ Layer layer2 = getLayer();
+
+ assertTrue(comparator.compare(layer1, new Layer()) != 0);
+
+ assertTrue(comparator.compare(layer1, null) != 0);
+ assertTrue(comparator.compare(null, layer1) != 0);
+ assertTrue(comparator.compare(layer1, new Layer() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }) != 0);
+
+ layer1 = getLayer();
+ layer2 = getLayer();
+
+ layer1.setName("ASdasdas");
+
+ assertTrue(comparator.compare(layer1, layer2) != 0);
+ assertTrue(comparator.compare(layer2, layer1) != 0);
+
+ layer1 = getLayer();
+ layer2 = getLayer();
+
+ layer1.getLines().add(new PolylineData());
+
+ assertTrue(comparator.compare(layer1, layer2) != 0);
+ assertTrue(comparator.compare(layer2, layer1) != 0);
+
+ layer1 = getLayer();
+ layer2 = getLayer();
+
+ layer1.getLines().get(0).setWidth(654);
+
+ assertTrue(comparator.compare(layer1, layer2) != 0);
+ assertTrue(comparator.compare(layer2, layer1) != 0);
+
+ layer1 = getLayer();
+ layer2 = getLayer();
+
+ layer1.getOvals().add(new LayerOval());
+
+ assertTrue(comparator.compare(layer1, layer2) != 0);
+ assertTrue(comparator.compare(layer2, layer1) != 0);
+
+ layer1 = getLayer();
+ layer2 = getLayer();
+
+ layer1.getOvals().get(0).setWidth("654");
+
+ assertTrue(comparator.compare(layer1, layer2) != 0);
+ assertTrue(comparator.compare(layer2, layer1) != 0);
+
+ layer1 = getLayer();
+ layer2 = getLayer();
+
+ layer1.getRectangles().add(new LayerRect());
+
+ assertTrue(comparator.compare(layer1, layer2) != 0);
+ assertTrue(comparator.compare(layer2, layer1) != 0);
+
+ layer1 = getLayer();
+ layer2 = getLayer();
+
+ layer1.getRectangles().get(0).setWidth("654");
+
+ assertTrue(comparator.compare(layer1, layer2) != 0);
+ assertTrue(comparator.compare(layer2, layer1) != 0);
+
+ layer1 = getLayer();
+ layer2 = getLayer();
+
+ layer1.getTexts().add(new LayerText());
+
+ assertTrue(comparator.compare(layer1, layer2) != 0);
+ assertTrue(comparator.compare(layer2, layer1) != 0);
+
+ layer1 = getLayer();
+ layer2 = getLayer();
+
+ layer1.getTexts().get(0).setWidth("654");
+
+ assertTrue(comparator.compare(layer1, layer2) != 0);
+ assertTrue(comparator.compare(layer2, layer1) != 0);
+
+ layer1 = getLayer();
+ layer2 = getLayer();
+
+ layer1.setVisible(false);
+
+ assertTrue(comparator.compare(layer1, layer2) != 0);
+ assertTrue(comparator.compare(layer2, layer1) != 0);
+
+ layer1 = getLayer();
+ layer2 = getLayer();
+
+ layer1.setLocked(false);
+
+ assertTrue(comparator.compare(layer1, layer2) != 0);
+ assertTrue(comparator.compare(layer2, layer1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerOvalComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerOvalComparatorTest.java
index 787a9c6471..468210ea8e 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerOvalComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerOvalComparatorTest.java
@@ -1,142 +1,142 @@
-package lcsb.mapviewer.model.map.layout.graphics;
-
-import static org.junit.Assert.*;
-
-import java.awt.Color;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class LayerOvalComparatorTest {
- LayerOvalComparator comparator = new LayerOvalComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- LayerOval layer1 = getLayerOval();
- LayerOval layer2 = getLayerOval();
-
- assertEquals(0, comparator.compare(new LayerOval(), new LayerOval()));
- assertEquals(0, comparator.compare(layer1, layer2));
- assertEquals(0, comparator.compare(layer1, layer1));
- assertEquals(0, comparator.compare(null,null));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
- private LayerOval getLayerOval() {
-
- LayerOval line = new LayerOval();
- line.setColor(Color.YELLOW);
- line.setWidth(4.3);
-
-
- return line;
- }
-
- @Test
- public void testDifferent() {
- try {
- LayerOval layer1 = getLayerOval();
- LayerOval layer2 = getLayerOval();
-
- assertTrue(comparator.compare(layer1, new LayerOval())!=0);
-
- assertTrue(comparator.compare(layer1, null)!=0);
- assertTrue(comparator.compare(null,layer1)!=0);
-
- layer1 = getLayerOval();
- layer2 = getLayerOval();
-
- layer1.setColor(Color.GREEN);
-
- assertTrue(comparator.compare(layer1, layer2)!=0);
- assertTrue(comparator.compare(layer2, layer1)!=0);
-
- layer1 = getLayerOval();
- layer2 = getLayerOval();
-
- layer1.setHeight(78.0);
-
- assertTrue(comparator.compare(layer1, layer2)!=0);
- assertTrue(comparator.compare(layer2, layer1)!=0);
-
- layer1 = getLayerOval();
- layer2 = getLayerOval();
-
- layer1.setHeight(1.2);
-
- assertTrue(comparator.compare(layer1, layer2)!=0);
- assertTrue(comparator.compare(layer2, layer1)!=0);
-
- layer1 = getLayerOval();
- layer2 = getLayerOval();
-
- layer1.setX(33.4);
-
- assertTrue(comparator.compare(layer1, layer2)!=0);
- assertTrue(comparator.compare(layer2, layer1)!=0);
-
- layer1 = getLayerOval();
- layer2 = getLayerOval();
-
- layer1.setY(33.4);
-
- assertTrue(comparator.compare(layer1, layer2)!=0);
- assertTrue(comparator.compare(layer2, layer1)!=0);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
- @Test
- public void testDifferent2() {
- try {
- LayerOval layer1 = getLayerOval();
-
- assertTrue(comparator.compare(layer1, new LayerOval() {
- private static final long serialVersionUID = 1L;
- }) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
- @Test
- public void testInvalid() {
- try {
- class Tmp extends LayerOval {
- private static final long serialVersionUID = 1L;
- }
- Tmp layer1 = new Tmp();
- Tmp layer2 = new Tmp();
-
- comparator.compare(layer1, layer2);
- fail("Exception expected");
-
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
-}
+package lcsb.mapviewer.model.map.layout.graphics;
+
+import static org.junit.Assert.*;
+
+import java.awt.Color;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class LayerOvalComparatorTest {
+ LayerOvalComparator comparator = new LayerOvalComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ LayerOval layer1 = getLayerOval();
+ LayerOval layer2 = getLayerOval();
+
+ assertEquals(0, comparator.compare(new LayerOval(), new LayerOval()));
+ assertEquals(0, comparator.compare(layer1, layer2));
+ assertEquals(0, comparator.compare(layer1, layer1));
+ assertEquals(0, comparator.compare(null,null));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+ private LayerOval getLayerOval() {
+
+ LayerOval line = new LayerOval();
+ line.setColor(Color.YELLOW);
+ line.setWidth(4.3);
+
+
+ return line;
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ LayerOval layer1 = getLayerOval();
+ LayerOval layer2 = getLayerOval();
+
+ assertTrue(comparator.compare(layer1, new LayerOval())!=0);
+
+ assertTrue(comparator.compare(layer1, null)!=0);
+ assertTrue(comparator.compare(null,layer1)!=0);
+
+ layer1 = getLayerOval();
+ layer2 = getLayerOval();
+
+ layer1.setColor(Color.GREEN);
+
+ assertTrue(comparator.compare(layer1, layer2)!=0);
+ assertTrue(comparator.compare(layer2, layer1)!=0);
+
+ layer1 = getLayerOval();
+ layer2 = getLayerOval();
+
+ layer1.setHeight(78.0);
+
+ assertTrue(comparator.compare(layer1, layer2)!=0);
+ assertTrue(comparator.compare(layer2, layer1)!=0);
+
+ layer1 = getLayerOval();
+ layer2 = getLayerOval();
+
+ layer1.setHeight(1.2);
+
+ assertTrue(comparator.compare(layer1, layer2)!=0);
+ assertTrue(comparator.compare(layer2, layer1)!=0);
+
+ layer1 = getLayerOval();
+ layer2 = getLayerOval();
+
+ layer1.setX(33.4);
+
+ assertTrue(comparator.compare(layer1, layer2)!=0);
+ assertTrue(comparator.compare(layer2, layer1)!=0);
+
+ layer1 = getLayerOval();
+ layer2 = getLayerOval();
+
+ layer1.setY(33.4);
+
+ assertTrue(comparator.compare(layer1, layer2)!=0);
+ assertTrue(comparator.compare(layer2, layer1)!=0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+ @Test
+ public void testDifferent2() {
+ try {
+ LayerOval layer1 = getLayerOval();
+
+ assertTrue(comparator.compare(layer1, new LayerOval() {
+ private static final long serialVersionUID = 1L;
+ }) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+ @Test
+ public void testInvalid() {
+ try {
+ class Tmp extends LayerOval {
+ private static final long serialVersionUID = 1L;
+ }
+ Tmp layer1 = new Tmp();
+ Tmp layer2 = new Tmp();
+
+ comparator.compare(layer1, layer2);
+ fail("Exception expected");
+
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerOvalTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerOvalTest.java
index ca1e4f6651..ee96a805c2 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerOvalTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerOvalTest.java
@@ -1,165 +1,165 @@
-package lcsb.mapviewer.model.map.layout.graphics;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.fail;
-
-import java.awt.Color;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class LayerOvalTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new LayerOval());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- LayerOval layerOval = new LayerOval();
-
- LayerOval copy = new LayerOval(layerOval);
-
- assertNotNull(copy);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- LayerOval copy = new LayerOval().copy();
-
- assertNotNull(copy);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new LayerOval() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
-
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- LayerOval oval = new LayerOval();
-
- String yParam = "1.2";
- Double y = 1.2;
-
- String xParam = "2.2";
- Double x = 2.2;
-
- String widthParam = "10.2";
- Double width = 10.2;
-
- String heightParam = "72.2";
- Double height = 72.2;
-
- String invalidNumberStr = "xxd";
-
- int id = 52;
- Color color = Color.BLACK;
-
- oval.setY(yParam);
- assertEquals(y, oval.getY(), Configuration.EPSILON);
- try {
- oval.setY(invalidNumberStr);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- oval.setY((Double) null);
- assertNull(oval.getY());
- oval.setY(y);
- assertEquals(y, oval.getY(), Configuration.EPSILON);
-
- oval.setX(xParam);
- assertEquals(x, oval.getX(), Configuration.EPSILON);
- try {
- oval.setX(invalidNumberStr);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- oval.setX((Double) null);
- assertNull(oval.getX());
- oval.setX(x);
- assertEquals(x, oval.getX(), Configuration.EPSILON);
-
- oval.setWidth(widthParam);
- assertEquals(width, oval.getWidth(), Configuration.EPSILON);
- try {
- oval.setWidth(invalidNumberStr);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- oval.setWidth((Double) null);
- assertNull(oval.getWidth());
- oval.setWidth(width);
- assertEquals(width, oval.getWidth(), Configuration.EPSILON);
-
- oval.setHeight(heightParam);
- assertEquals(height, oval.getHeight(), Configuration.EPSILON);
- try {
- oval.setHeight(invalidNumberStr);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- oval.setHeight((Double) null);
- assertNull(oval.getHeight());
- oval.setHeight(height);
- assertEquals(height, oval.getHeight(), Configuration.EPSILON);
-
- oval.setId(id);
- assertEquals(id, oval.getId());
- oval.setColor(color);
- assertEquals(color, oval.getColor());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.layout.graphics;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.fail;
+
+import java.awt.Color;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class LayerOvalTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new LayerOval());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ LayerOval layerOval = new LayerOval();
+
+ LayerOval copy = new LayerOval(layerOval);
+
+ assertNotNull(copy);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ LayerOval copy = new LayerOval().copy();
+
+ assertNotNull(copy);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new LayerOval() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ LayerOval oval = new LayerOval();
+
+ String yParam = "1.2";
+ Double y = 1.2;
+
+ String xParam = "2.2";
+ Double x = 2.2;
+
+ String widthParam = "10.2";
+ Double width = 10.2;
+
+ String heightParam = "72.2";
+ Double height = 72.2;
+
+ String invalidNumberStr = "xxd";
+
+ int id = 52;
+ Color color = Color.BLACK;
+
+ oval.setY(yParam);
+ assertEquals(y, oval.getY(), Configuration.EPSILON);
+ try {
+ oval.setY(invalidNumberStr);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ oval.setY((Double) null);
+ assertNull(oval.getY());
+ oval.setY(y);
+ assertEquals(y, oval.getY(), Configuration.EPSILON);
+
+ oval.setX(xParam);
+ assertEquals(x, oval.getX(), Configuration.EPSILON);
+ try {
+ oval.setX(invalidNumberStr);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ oval.setX((Double) null);
+ assertNull(oval.getX());
+ oval.setX(x);
+ assertEquals(x, oval.getX(), Configuration.EPSILON);
+
+ oval.setWidth(widthParam);
+ assertEquals(width, oval.getWidth(), Configuration.EPSILON);
+ try {
+ oval.setWidth(invalidNumberStr);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ oval.setWidth((Double) null);
+ assertNull(oval.getWidth());
+ oval.setWidth(width);
+ assertEquals(width, oval.getWidth(), Configuration.EPSILON);
+
+ oval.setHeight(heightParam);
+ assertEquals(height, oval.getHeight(), Configuration.EPSILON);
+ try {
+ oval.setHeight(invalidNumberStr);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ oval.setHeight((Double) null);
+ assertNull(oval.getHeight());
+ oval.setHeight(height);
+ assertEquals(height, oval.getHeight(), Configuration.EPSILON);
+
+ oval.setId(id);
+ assertEquals(id, oval.getId());
+ oval.setColor(color);
+ assertEquals(color, oval.getColor());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerRectComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerRectComparatorTest.java
index bacc8c201e..e3a3ebe5d9 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerRectComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerRectComparatorTest.java
@@ -1,141 +1,141 @@
-package lcsb.mapviewer.model.map.layout.graphics;
-
-import static org.junit.Assert.*;
-
-import java.awt.Color;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class LayerRectComparatorTest {
- LayerRectComparator comparator = new LayerRectComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- LayerRect layer1 = getLayerRect();
- LayerRect layer2 = getLayerRect();
-
- assertEquals(0, comparator.compare(new LayerRect(), new LayerRect()));
- assertEquals(0, comparator.compare(layer1, layer2));
- assertEquals(0, comparator.compare(layer1, layer1));
- assertEquals(0, comparator.compare(null,null));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
- private LayerRect getLayerRect() {
-
- LayerRect line = new LayerRect();
- line.setColor(Color.YELLOW);
- line.setWidth(4.3);
-
-
- return line;
- }
-
- @Test
- public void testDifferent() {
- try {
- LayerRect layer1 = getLayerRect();
- LayerRect layer2 = getLayerRect();
-
- assertTrue(comparator.compare(layer1, new LayerRect())!=0);
-
- assertTrue(comparator.compare(layer1, null)!=0);
- assertTrue(comparator.compare(null,layer1)!=0);
-
- layer1 = getLayerRect();
- layer2 = getLayerRect();
-
- layer1.setColor(Color.GREEN);
-
- assertTrue(comparator.compare(layer1, layer2)!=0);
- assertTrue(comparator.compare(layer2, layer1)!=0);
-
- layer1 = getLayerRect();
- layer2 = getLayerRect();
-
- layer1.setHeight("23");
-
- assertTrue(comparator.compare(layer1, layer2)!=0);
- assertTrue(comparator.compare(layer2, layer1)!=0);
-
- layer1 = getLayerRect();
- layer2 = getLayerRect();
-
- layer1.setHeight(1.2);
-
- assertTrue(comparator.compare(layer1, layer2)!=0);
- assertTrue(comparator.compare(layer2, layer1)!=0);
-
- layer1 = getLayerRect();
- layer2 = getLayerRect();
-
- layer1.setX(33.4);
-
- assertTrue(comparator.compare(layer1, layer2)!=0);
- assertTrue(comparator.compare(layer2, layer1)!=0);
-
- layer1 = getLayerRect();
- layer2 = getLayerRect();
-
- layer1.setY(33.4);
-
- assertTrue(comparator.compare(layer1, layer2)!=0);
- assertTrue(comparator.compare(layer2, layer1)!=0);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
- @Test
- public void testDifferent2() {
- try {
- LayerRect layer1 = getLayerRect();
-
- assertTrue(comparator.compare(layer1, new LayerRect() {
- private static final long serialVersionUID = 1L;
- }) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
- @Test
- public void testInvalid() {
- try {
- class Tmp extends LayerRect {
- private static final long serialVersionUID = 1L;
- }
- Tmp layer1 = new Tmp();
- Tmp layer2 = new Tmp();
-
- comparator.compare(layer1, layer2);
- fail("Exception expected");
-
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
-}
+package lcsb.mapviewer.model.map.layout.graphics;
+
+import static org.junit.Assert.*;
+
+import java.awt.Color;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class LayerRectComparatorTest {
+ LayerRectComparator comparator = new LayerRectComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ LayerRect layer1 = getLayerRect();
+ LayerRect layer2 = getLayerRect();
+
+ assertEquals(0, comparator.compare(new LayerRect(), new LayerRect()));
+ assertEquals(0, comparator.compare(layer1, layer2));
+ assertEquals(0, comparator.compare(layer1, layer1));
+ assertEquals(0, comparator.compare(null,null));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+ private LayerRect getLayerRect() {
+
+ LayerRect line = new LayerRect();
+ line.setColor(Color.YELLOW);
+ line.setWidth(4.3);
+
+
+ return line;
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ LayerRect layer1 = getLayerRect();
+ LayerRect layer2 = getLayerRect();
+
+ assertTrue(comparator.compare(layer1, new LayerRect())!=0);
+
+ assertTrue(comparator.compare(layer1, null)!=0);
+ assertTrue(comparator.compare(null,layer1)!=0);
+
+ layer1 = getLayerRect();
+ layer2 = getLayerRect();
+
+ layer1.setColor(Color.GREEN);
+
+ assertTrue(comparator.compare(layer1, layer2)!=0);
+ assertTrue(comparator.compare(layer2, layer1)!=0);
+
+ layer1 = getLayerRect();
+ layer2 = getLayerRect();
+
+ layer1.setHeight("23");
+
+ assertTrue(comparator.compare(layer1, layer2)!=0);
+ assertTrue(comparator.compare(layer2, layer1)!=0);
+
+ layer1 = getLayerRect();
+ layer2 = getLayerRect();
+
+ layer1.setHeight(1.2);
+
+ assertTrue(comparator.compare(layer1, layer2)!=0);
+ assertTrue(comparator.compare(layer2, layer1)!=0);
+
+ layer1 = getLayerRect();
+ layer2 = getLayerRect();
+
+ layer1.setX(33.4);
+
+ assertTrue(comparator.compare(layer1, layer2)!=0);
+ assertTrue(comparator.compare(layer2, layer1)!=0);
+
+ layer1 = getLayerRect();
+ layer2 = getLayerRect();
+
+ layer1.setY(33.4);
+
+ assertTrue(comparator.compare(layer1, layer2)!=0);
+ assertTrue(comparator.compare(layer2, layer1)!=0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+ @Test
+ public void testDifferent2() {
+ try {
+ LayerRect layer1 = getLayerRect();
+
+ assertTrue(comparator.compare(layer1, new LayerRect() {
+ private static final long serialVersionUID = 1L;
+ }) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+ @Test
+ public void testInvalid() {
+ try {
+ class Tmp extends LayerRect {
+ private static final long serialVersionUID = 1L;
+ }
+ Tmp layer1 = new Tmp();
+ Tmp layer2 = new Tmp();
+
+ comparator.compare(layer1, layer2);
+ fail("Exception expected");
+
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerRectTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerRectTest.java
index 1f7021155c..ed02f6ef57 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerRectTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerRectTest.java
@@ -1,162 +1,162 @@
-package lcsb.mapviewer.model.map.layout.graphics;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.fail;
-
-import java.awt.Color;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class LayerRectTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new LayerRect());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- LayerRect layerRect = new LayerRect();
-
- LayerRect copy = new LayerRect(layerRect);
-
- assertNotNull(copy);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- LayerRect copy = new LayerRect().copy();
-
- assertNotNull(copy);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new LayerRect() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
-
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- LayerRect rect = new LayerRect();
-
- String yParam = "1.2";
- Double y = 1.2;
-
- String xParam = "2.2";
- Double x = 2.2;
-
- String widthParam = "10.2";
- Double width = 10.2;
-
- String heightParam = "72.2";
- Double height = 72.2;
-
- String invalidNumberStr = "xxd";
-
- Color color = Color.BLACK;
-
- rect.setY(yParam);
- assertEquals(y, rect.getY(), Configuration.EPSILON);
- try {
- rect.setY(invalidNumberStr);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- rect.setY((Double) null);
- assertNull(rect.getY());
- rect.setY(y);
- assertEquals(y, rect.getY(), Configuration.EPSILON);
-
- rect.setX(xParam);
- assertEquals(x, rect.getX(), Configuration.EPSILON);
- try {
- rect.setX(invalidNumberStr);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- rect.setX((Double) null);
- assertNull(rect.getX());
- rect.setX(x);
- assertEquals(x, rect.getX(), Configuration.EPSILON);
-
- rect.setWidth(widthParam);
- assertEquals(width, rect.getWidth(), Configuration.EPSILON);
- try {
- rect.setWidth(invalidNumberStr);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- rect.setWidth((Double) null);
- assertNull(rect.getWidth());
- rect.setWidth(width);
- assertEquals(width, rect.getWidth(), Configuration.EPSILON);
-
- rect.setHeight(heightParam);
- assertEquals(height, rect.getHeight(), Configuration.EPSILON);
- try {
- rect.setHeight(invalidNumberStr);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- rect.setHeight((Double) null);
- assertNull(rect.getHeight());
- rect.setHeight(height);
- assertEquals(height, rect.getHeight(), Configuration.EPSILON);
-
- rect.setColor(color);
- assertEquals(color, rect.getColor());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.layout.graphics;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.fail;
+
+import java.awt.Color;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class LayerRectTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new LayerRect());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ LayerRect layerRect = new LayerRect();
+
+ LayerRect copy = new LayerRect(layerRect);
+
+ assertNotNull(copy);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ LayerRect copy = new LayerRect().copy();
+
+ assertNotNull(copy);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new LayerRect() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ LayerRect rect = new LayerRect();
+
+ String yParam = "1.2";
+ Double y = 1.2;
+
+ String xParam = "2.2";
+ Double x = 2.2;
+
+ String widthParam = "10.2";
+ Double width = 10.2;
+
+ String heightParam = "72.2";
+ Double height = 72.2;
+
+ String invalidNumberStr = "xxd";
+
+ Color color = Color.BLACK;
+
+ rect.setY(yParam);
+ assertEquals(y, rect.getY(), Configuration.EPSILON);
+ try {
+ rect.setY(invalidNumberStr);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ rect.setY((Double) null);
+ assertNull(rect.getY());
+ rect.setY(y);
+ assertEquals(y, rect.getY(), Configuration.EPSILON);
+
+ rect.setX(xParam);
+ assertEquals(x, rect.getX(), Configuration.EPSILON);
+ try {
+ rect.setX(invalidNumberStr);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ rect.setX((Double) null);
+ assertNull(rect.getX());
+ rect.setX(x);
+ assertEquals(x, rect.getX(), Configuration.EPSILON);
+
+ rect.setWidth(widthParam);
+ assertEquals(width, rect.getWidth(), Configuration.EPSILON);
+ try {
+ rect.setWidth(invalidNumberStr);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ rect.setWidth((Double) null);
+ assertNull(rect.getWidth());
+ rect.setWidth(width);
+ assertEquals(width, rect.getWidth(), Configuration.EPSILON);
+
+ rect.setHeight(heightParam);
+ assertEquals(height, rect.getHeight(), Configuration.EPSILON);
+ try {
+ rect.setHeight(invalidNumberStr);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ rect.setHeight((Double) null);
+ assertNull(rect.getHeight());
+ rect.setHeight(height);
+ assertEquals(height, rect.getHeight(), Configuration.EPSILON);
+
+ rect.setColor(color);
+ assertEquals(color, rect.getColor());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerTest.java
index 93d729255b..c1eb42b89a 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerTest.java
@@ -1,158 +1,158 @@
-package lcsb.mapviewer.model.map.layout.graphics;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.model.ModelData;
-
-public class LayerTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new Layer());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Layer layer = new Layer();
- layer.addLayerText(new LayerText());
- layer.addLayerLine(new PolylineData());
- layer.addLayerRect(new LayerRect());
- layer.addLayerOval(new LayerOval());
- Layer copy = new Layer(layer);
-
- assertNotNull(copy);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- Layer degraded = new Layer().copy();
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetters() {
- try {
- Layer layer = new Layer().copy();
-
- ModelData model = new ModelData();
- List<LayerOval> ovals = new ArrayList<>();
- List<LayerRect> rectangles = new ArrayList<>();
- List<PolylineData> lines = new ArrayList<>();
- List<LayerText> texts= new ArrayList<>();
-
- boolean locked = true;
- boolean visible = true;
- String name = "sdtr";
- String layerId = "id";
-
- layer.setModel(model);
- layer.setOvals(ovals);
- layer.setTexts(texts);
- layer.setRectangles(rectangles);
- layer.setLines(lines);
- layer.setLocked(locked);
- layer.setVisible(visible);
- layer.setName(name);
- layer.setLayerId(layerId);
-
- assertEquals(model, layer.getModel());
- assertEquals(ovals, layer.getOvals());
- assertEquals(rectangles, layer.getRectangles());
- assertEquals(lines, layer.getLines());
- assertEquals(texts, layer.getTexts());
- assertEquals(locked, layer.isLocked());
- assertEquals(name, layer.getName());
- assertEquals(visible, layer.isVisible());
- assertEquals(layerId, layer.getLayerId());
-
- layer.setLocked("FALSE");
- layer.setVisible("FALSE");
-
- assertFalse(layer.isLocked());
- assertFalse(layer.isVisible());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new Layer() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRemoveLayerText() {
- try {
- Layer layer = new Layer();
- layer.removeLayerText(new LayerText());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddLines() {
- try {
- Layer layer = new Layer();
- List<PolylineData> lines = new ArrayList<>();
- lines.add(new PolylineData());
- layer.addLayerLines(lines);
- assertEquals(1, layer.getLines().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.layout.graphics;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.model.ModelData;
+
+public class LayerTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new Layer());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Layer layer = new Layer();
+ layer.addLayerText(new LayerText());
+ layer.addLayerLine(new PolylineData());
+ layer.addLayerRect(new LayerRect());
+ layer.addLayerOval(new LayerOval());
+ Layer copy = new Layer(layer);
+
+ assertNotNull(copy);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ Layer degraded = new Layer().copy();
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetters() {
+ try {
+ Layer layer = new Layer().copy();
+
+ ModelData model = new ModelData();
+ List<LayerOval> ovals = new ArrayList<>();
+ List<LayerRect> rectangles = new ArrayList<>();
+ List<PolylineData> lines = new ArrayList<>();
+ List<LayerText> texts= new ArrayList<>();
+
+ boolean locked = true;
+ boolean visible = true;
+ String name = "sdtr";
+ String layerId = "id";
+
+ layer.setModel(model);
+ layer.setOvals(ovals);
+ layer.setTexts(texts);
+ layer.setRectangles(rectangles);
+ layer.setLines(lines);
+ layer.setLocked(locked);
+ layer.setVisible(visible);
+ layer.setName(name);
+ layer.setLayerId(layerId);
+
+ assertEquals(model, layer.getModel());
+ assertEquals(ovals, layer.getOvals());
+ assertEquals(rectangles, layer.getRectangles());
+ assertEquals(lines, layer.getLines());
+ assertEquals(texts, layer.getTexts());
+ assertEquals(locked, layer.isLocked());
+ assertEquals(name, layer.getName());
+ assertEquals(visible, layer.isVisible());
+ assertEquals(layerId, layer.getLayerId());
+
+ layer.setLocked("FALSE");
+ layer.setVisible("FALSE");
+
+ assertFalse(layer.isLocked());
+ assertFalse(layer.isVisible());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new Layer() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRemoveLayerText() {
+ try {
+ Layer layer = new Layer();
+ layer.removeLayerText(new LayerText());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddLines() {
+ try {
+ Layer layer = new Layer();
+ List<PolylineData> lines = new ArrayList<>();
+ lines.add(new PolylineData());
+ layer.addLayerLines(lines);
+ assertEquals(1, layer.getLines().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerTextComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerTextComparatorTest.java
index 5ef880bc4d..ad94f9b49a 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerTextComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerTextComparatorTest.java
@@ -1,151 +1,151 @@
-package lcsb.mapviewer.model.map.layout.graphics;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.awt.Color;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class LayerTextComparatorTest {
- LayerTextComparator comparator = new LayerTextComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- LayerText layer1 = getLayerText();
- LayerText layer2 = getLayerText();
-
- assertEquals(0, comparator.compare(new LayerText(), new LayerText()));
- assertEquals(0, comparator.compare(layer1, layer2));
- assertEquals(0, comparator.compare(layer1, layer1));
- assertEquals(0, comparator.compare(null, null));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
- @Test
- public void testDifferent2() {
- try {
- LayerText layer1 = getLayerText();
-
- assertTrue(comparator.compare(layer1, new LayerText() {
- private static final long serialVersionUID = 1L;
- }) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
- @Test
- public void testInvalid() {
- try {
- class Tmp extends LayerText {
- private static final long serialVersionUID = 1L;
- }
- Tmp layer1 = new Tmp();
- Tmp layer2 = new Tmp();
-
- comparator.compare(layer1, layer2);
-
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
- private LayerText getLayerText() {
-
- LayerText line = new LayerText();
- line.setColor(Color.YELLOW);
- line.setNotes(":asd");
- line.setFontSize(4.3);
-
- return line;
- }
-
- @Test
- public void testDifferent() {
- try {
- LayerText layer1 = getLayerText();
- LayerText layer2 = getLayerText();
-
- assertTrue(comparator.compare(layer1, new LayerText()) != 0);
-
- assertTrue(comparator.compare(layer1, null) != 0);
- assertTrue(comparator.compare(null, layer1) != 0);
-
- layer1 = getLayerText();
- layer2 = getLayerText();
-
- layer1.setColor(Color.GREEN);
-
- assertTrue(comparator.compare(layer1, layer2) != 0);
- assertTrue(comparator.compare(layer2, layer1) != 0);
-
- layer1 = getLayerText();
- layer2 = getLayerText();
-
- layer1.setNotes("asd");
-
- assertTrue(comparator.compare(layer1, layer2) != 0);
- assertTrue(comparator.compare(layer2, layer1) != 0);
-
- layer1 = getLayerText();
- layer2 = getLayerText();
-
- layer1.setHeight(1.2);
-
- assertTrue(comparator.compare(layer1, layer2) != 0);
- assertTrue(comparator.compare(layer2, layer1) != 0);
-
- layer1 = getLayerText();
- layer2 = getLayerText();
-
- layer1.setX(33.4);
-
- assertTrue(comparator.compare(layer1, layer2) != 0);
- assertTrue(comparator.compare(layer2, layer1) != 0);
-
- layer1 = getLayerText();
- layer2 = getLayerText();
-
- layer1.setY(33.4);
-
- assertTrue(comparator.compare(layer1, layer2) != 0);
- assertTrue(comparator.compare(layer2, layer1) != 0);
-
- layer1 = getLayerText();
- layer2 = getLayerText();
-
- layer1.setFontSize(64.1);
-
- assertTrue(comparator.compare(layer1, layer2) != 0);
- assertTrue(comparator.compare(layer2, layer1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-}
+package lcsb.mapviewer.model.map.layout.graphics;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.awt.Color;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class LayerTextComparatorTest {
+ LayerTextComparator comparator = new LayerTextComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ LayerText layer1 = getLayerText();
+ LayerText layer2 = getLayerText();
+
+ assertEquals(0, comparator.compare(new LayerText(), new LayerText()));
+ assertEquals(0, comparator.compare(layer1, layer2));
+ assertEquals(0, comparator.compare(layer1, layer1));
+ assertEquals(0, comparator.compare(null, null));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+ @Test
+ public void testDifferent2() {
+ try {
+ LayerText layer1 = getLayerText();
+
+ assertTrue(comparator.compare(layer1, new LayerText() {
+ private static final long serialVersionUID = 1L;
+ }) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+ @Test
+ public void testInvalid() {
+ try {
+ class Tmp extends LayerText {
+ private static final long serialVersionUID = 1L;
+ }
+ Tmp layer1 = new Tmp();
+ Tmp layer2 = new Tmp();
+
+ comparator.compare(layer1, layer2);
+
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+ private LayerText getLayerText() {
+
+ LayerText line = new LayerText();
+ line.setColor(Color.YELLOW);
+ line.setNotes(":asd");
+ line.setFontSize(4.3);
+
+ return line;
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ LayerText layer1 = getLayerText();
+ LayerText layer2 = getLayerText();
+
+ assertTrue(comparator.compare(layer1, new LayerText()) != 0);
+
+ assertTrue(comparator.compare(layer1, null) != 0);
+ assertTrue(comparator.compare(null, layer1) != 0);
+
+ layer1 = getLayerText();
+ layer2 = getLayerText();
+
+ layer1.setColor(Color.GREEN);
+
+ assertTrue(comparator.compare(layer1, layer2) != 0);
+ assertTrue(comparator.compare(layer2, layer1) != 0);
+
+ layer1 = getLayerText();
+ layer2 = getLayerText();
+
+ layer1.setNotes("asd");
+
+ assertTrue(comparator.compare(layer1, layer2) != 0);
+ assertTrue(comparator.compare(layer2, layer1) != 0);
+
+ layer1 = getLayerText();
+ layer2 = getLayerText();
+
+ layer1.setHeight(1.2);
+
+ assertTrue(comparator.compare(layer1, layer2) != 0);
+ assertTrue(comparator.compare(layer2, layer1) != 0);
+
+ layer1 = getLayerText();
+ layer2 = getLayerText();
+
+ layer1.setX(33.4);
+
+ assertTrue(comparator.compare(layer1, layer2) != 0);
+ assertTrue(comparator.compare(layer2, layer1) != 0);
+
+ layer1 = getLayerText();
+ layer2 = getLayerText();
+
+ layer1.setY(33.4);
+
+ assertTrue(comparator.compare(layer1, layer2) != 0);
+ assertTrue(comparator.compare(layer2, layer1) != 0);
+
+ layer1 = getLayerText();
+ layer2 = getLayerText();
+
+ layer1.setFontSize(64.1);
+
+ assertTrue(comparator.compare(layer1, layer2) != 0);
+ assertTrue(comparator.compare(layer2, layer1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerTextTest.java b/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerTextTest.java
index efa18368f5..a9bd36d8da 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerTextTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/layout/graphics/LayerTextTest.java
@@ -1,196 +1,196 @@
-package lcsb.mapviewer.model.map.layout.graphics;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.fail;
-
-import java.awt.geom.Rectangle2D;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class LayerTextTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new LayerText());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- LayerText layerText = new LayerText();
-
- LayerText copy = new LayerText(layerText);
-
- assertNotNull(copy);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor2() {
- try {
-
- LayerText copy = new LayerText(new Rectangle2D.Double(), "text");
-
- assertNotNull(copy);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- LayerText copy = new LayerText().copy();
-
- assertNotNull(copy);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new LayerText() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
-
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetBorder() {
- try {
- LayerText copy = new LayerText().copy();
- assertNotNull(copy.getBorder());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- LayerText text = new LayerText();
-
- String yParam = "1.2";
- Double y = 1.2;
-
- String xParam = "2.2";
- Double x = 2.2;
-
- String widthParam = "10.2";
- Double width = 10.2;
-
- String heightParam = "72.2";
- Double height = 72.2;
-
- String fontSizeParam = "5.0";
- Double fontSize = 5.0;
-
- String invalidNumberStr = "xxd";
-
- text.setY(yParam);
- assertEquals(y, text.getY(), Configuration.EPSILON);
- try {
- text.setY(invalidNumberStr);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- assertEquals(y, text.getY(), Configuration.EPSILON);
- text.setY((Double) null);
- assertNull(text.getY());
- text.setY(y);
- assertEquals(y, text.getY(), Configuration.EPSILON);
-
- text.setX(xParam);
- assertEquals(x, text.getX(), Configuration.EPSILON);
- try {
- text.setX(invalidNumberStr);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- text.setX((Double) null);
- assertNull(text.getX());
- text.setX(x);
- assertEquals(x, text.getX(), Configuration.EPSILON);
-
- text.setFontSize(fontSizeParam);
- assertEquals(fontSize, text.getFontSize(), Configuration.EPSILON);
- try {
- text.setFontSize(invalidNumberStr);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- text.setFontSize((Double) null);
- assertNull(text.getFontSize());
- text.setFontSize(fontSize);
- assertEquals(fontSize, text.getFontSize(), Configuration.EPSILON);
-
- text.setWidth(widthParam);
- assertEquals(width, text.getWidth(), Configuration.EPSILON);
- try {
- text.setWidth(invalidNumberStr);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- text.setWidth((Double) null);
- assertNull(text.getWidth());
- text.setWidth(width);
- assertEquals(width, text.getWidth(), Configuration.EPSILON);
-
- text.setHeight(heightParam);
- assertEquals(height, text.getHeight(), Configuration.EPSILON);
- try {
- text.setHeight(invalidNumberStr);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- text.setHeight((Double) null);
- assertNull(text.getHeight());
- text.setHeight(height);
- assertEquals(height, text.getHeight(), Configuration.EPSILON);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.map.layout.graphics;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.fail;
+
+import java.awt.geom.Rectangle2D;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class LayerTextTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new LayerText());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ LayerText layerText = new LayerText();
+
+ LayerText copy = new LayerText(layerText);
+
+ assertNotNull(copy);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor2() {
+ try {
+
+ LayerText copy = new LayerText(new Rectangle2D.Double(), "text");
+
+ assertNotNull(copy);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ LayerText copy = new LayerText().copy();
+
+ assertNotNull(copy);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new LayerText() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetBorder() {
+ try {
+ LayerText copy = new LayerText().copy();
+ assertNotNull(copy.getBorder());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ LayerText text = new LayerText();
+
+ String yParam = "1.2";
+ Double y = 1.2;
+
+ String xParam = "2.2";
+ Double x = 2.2;
+
+ String widthParam = "10.2";
+ Double width = 10.2;
+
+ String heightParam = "72.2";
+ Double height = 72.2;
+
+ String fontSizeParam = "5.0";
+ Double fontSize = 5.0;
+
+ String invalidNumberStr = "xxd";
+
+ text.setY(yParam);
+ assertEquals(y, text.getY(), Configuration.EPSILON);
+ try {
+ text.setY(invalidNumberStr);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ assertEquals(y, text.getY(), Configuration.EPSILON);
+ text.setY((Double) null);
+ assertNull(text.getY());
+ text.setY(y);
+ assertEquals(y, text.getY(), Configuration.EPSILON);
+
+ text.setX(xParam);
+ assertEquals(x, text.getX(), Configuration.EPSILON);
+ try {
+ text.setX(invalidNumberStr);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ text.setX((Double) null);
+ assertNull(text.getX());
+ text.setX(x);
+ assertEquals(x, text.getX(), Configuration.EPSILON);
+
+ text.setFontSize(fontSizeParam);
+ assertEquals(fontSize, text.getFontSize(), Configuration.EPSILON);
+ try {
+ text.setFontSize(invalidNumberStr);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ text.setFontSize((Double) null);
+ assertNull(text.getFontSize());
+ text.setFontSize(fontSize);
+ assertEquals(fontSize, text.getFontSize(), Configuration.EPSILON);
+
+ text.setWidth(widthParam);
+ assertEquals(width, text.getWidth(), Configuration.EPSILON);
+ try {
+ text.setWidth(invalidNumberStr);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ text.setWidth((Double) null);
+ assertNull(text.getWidth());
+ text.setWidth(width);
+ assertEquals(width, text.getWidth(), Configuration.EPSILON);
+
+ text.setHeight(heightParam);
+ assertEquals(height, text.getHeight(), Configuration.EPSILON);
+ try {
+ text.setHeight(invalidNumberStr);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ text.setHeight((Double) null);
+ assertNull(text.getHeight());
+ text.setHeight(height);
+ assertEquals(height, text.getHeight(), Configuration.EPSILON);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/AllModelTests.java b/model/src/test/java/lcsb/mapviewer/model/map/model/AllModelTests.java
index b111535413..52fe9455b4 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/AllModelTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/AllModelTests.java
@@ -1,21 +1,21 @@
-package lcsb.mapviewer.model.map.model;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ ElementSubmodelConnectionComparatorTest.class, //
- ElementSubmodelConnectionTest.class, //
- ModelComparatorTest.class, //
- ModelDataTest.class, //
- ModelFullIndexedTest.class, //
- ModelSubmodelConnectionComparatorTest.class, //
- ModelSubmodelConnectionTest.class, //
- ModelTest.class, //
- SubmodelConnectionComparatorTest.class,//
- SubmodelTypeTest.class,//
-})
-public class AllModelTests {
-
-}
+package lcsb.mapviewer.model.map.model;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ ElementSubmodelConnectionComparatorTest.class, //
+ ElementSubmodelConnectionTest.class, //
+ ModelComparatorTest.class, //
+ ModelDataTest.class, //
+ ModelFullIndexedTest.class, //
+ ModelSubmodelConnectionComparatorTest.class, //
+ ModelSubmodelConnectionTest.class, //
+ ModelTest.class, //
+ SubmodelConnectionComparatorTest.class,//
+ SubmodelTypeTest.class,//
+})
+public class AllModelTests {
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnectionComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnectionComparatorTest.java
index 742f507357..8207eade06 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnectionComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnectionComparatorTest.java
@@ -1,129 +1,129 @@
-package lcsb.mapviewer.model.map.model;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.Color;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-
-public class ElementSubmodelConnectionComparatorTest {
-
- ElementSubmodelConnectionComparator comparator = new ElementSubmodelConnectionComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() throws Exception {
- try {
- ElementSubmodelConnection connectionA = createConnection();
- ElementSubmodelConnection connectionB = createConnection();
-
- assertEquals(0, comparator.compare(new ElementSubmodelConnection(), new ElementSubmodelConnection()));
- assertEquals(0, comparator.compare(connectionA, connectionB));
- assertEquals(0, comparator.compare(connectionA, connectionA));
- assertEquals(0, comparator.compare(null, null));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent() throws Exception {
- try {
- ElementSubmodelConnection connectionA = createConnection();
- ElementSubmodelConnection connectionB = createConnection();
-
- assertTrue(comparator.compare(null, connectionB) != 0);
- assertTrue(comparator.compare(connectionA, null) != 0);
-
- connectionA.setFromElement(null);
- assertTrue(comparator.compare(connectionA, connectionB) != 0);
- assertTrue(comparator.compare(connectionB, connectionA) != 0);
-
- connectionA = createConnection();
- connectionB = createConnection();
-
- connectionA.getFromElement().setWidth(1234567);
-
- assertTrue(comparator.compare(connectionA, connectionB) != 0);
- assertTrue(comparator.compare(connectionB, connectionA) != 0);
-
- connectionA = createConnection();
- connectionB = createConnection();
-
- connectionA.setToElement(null);
- assertTrue(comparator.compare(connectionA, connectionB) != 0);
- assertTrue(comparator.compare(connectionB, connectionA) != 0);
-
- connectionA = createConnection();
- connectionB = createConnection();
-
- connectionA.getToElement().setWidth(1234567);
-
- assertTrue(comparator.compare(connectionA, connectionB) != 0);
- assertTrue(comparator.compare(connectionB, connectionA) != 0);
-
- assertTrue(comparator.compare(connectionB, new ElementSubmodelConnection() {
- private static final long serialVersionUID = 1L;
- }) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private Model getModel() {
- Model model = new ModelFullIndexed(null);
-
- model.setNotes("Some description");
- GenericProtein protein = new GenericProtein("A");
- protein.setName("ad");
- model.addElement(protein);
-
- GenericProtein protein2 = new GenericProtein("a_id");
- protein2.setName("ad");
- model.addElement(protein2);
-
- model.addElement(new Compartment("default"));
-
- Layer layer = new Layer();
- layer.setName("layer name");
- model.addLayer(layer);
-
- model.addReaction(new Reaction());
- return model;
- }
-
- private ElementSubmodelConnection createConnection() {
- ElementSubmodelConnection result = new ElementSubmodelConnection(getModel(), SubmodelType.DOWNSTREAM_TARGETS);
- result.setName("name A");
- result.setFromElement(createElement());
- result.setToElement(createElement());
- return result;
- }
-
- private Element createElement() {
- Element protein = new GenericProtein("protein_id");
- protein.setColor(Color.BLACK);
- return protein;
- }
-
-}
+package lcsb.mapviewer.model.map.model;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.awt.Color;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+
+public class ElementSubmodelConnectionComparatorTest {
+
+ ElementSubmodelConnectionComparator comparator = new ElementSubmodelConnectionComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() throws Exception {
+ try {
+ ElementSubmodelConnection connectionA = createConnection();
+ ElementSubmodelConnection connectionB = createConnection();
+
+ assertEquals(0, comparator.compare(new ElementSubmodelConnection(), new ElementSubmodelConnection()));
+ assertEquals(0, comparator.compare(connectionA, connectionB));
+ assertEquals(0, comparator.compare(connectionA, connectionA));
+ assertEquals(0, comparator.compare(null, null));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent() throws Exception {
+ try {
+ ElementSubmodelConnection connectionA = createConnection();
+ ElementSubmodelConnection connectionB = createConnection();
+
+ assertTrue(comparator.compare(null, connectionB) != 0);
+ assertTrue(comparator.compare(connectionA, null) != 0);
+
+ connectionA.setFromElement(null);
+ assertTrue(comparator.compare(connectionA, connectionB) != 0);
+ assertTrue(comparator.compare(connectionB, connectionA) != 0);
+
+ connectionA = createConnection();
+ connectionB = createConnection();
+
+ connectionA.getFromElement().setWidth(1234567);
+
+ assertTrue(comparator.compare(connectionA, connectionB) != 0);
+ assertTrue(comparator.compare(connectionB, connectionA) != 0);
+
+ connectionA = createConnection();
+ connectionB = createConnection();
+
+ connectionA.setToElement(null);
+ assertTrue(comparator.compare(connectionA, connectionB) != 0);
+ assertTrue(comparator.compare(connectionB, connectionA) != 0);
+
+ connectionA = createConnection();
+ connectionB = createConnection();
+
+ connectionA.getToElement().setWidth(1234567);
+
+ assertTrue(comparator.compare(connectionA, connectionB) != 0);
+ assertTrue(comparator.compare(connectionB, connectionA) != 0);
+
+ assertTrue(comparator.compare(connectionB, new ElementSubmodelConnection() {
+ private static final long serialVersionUID = 1L;
+ }) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Model getModel() {
+ Model model = new ModelFullIndexed(null);
+
+ model.setNotes("Some description");
+ GenericProtein protein = new GenericProtein("A");
+ protein.setName("ad");
+ model.addElement(protein);
+
+ GenericProtein protein2 = new GenericProtein("a_id");
+ protein2.setName("ad");
+ model.addElement(protein2);
+
+ model.addElement(new Compartment("default"));
+
+ Layer layer = new Layer();
+ layer.setName("layer name");
+ model.addLayer(layer);
+
+ model.addReaction(new Reaction());
+ return model;
+ }
+
+ private ElementSubmodelConnection createConnection() {
+ ElementSubmodelConnection result = new ElementSubmodelConnection(getModel(), SubmodelType.DOWNSTREAM_TARGETS);
+ result.setName("name A");
+ result.setFromElement(createElement());
+ result.setToElement(createElement());
+ return result;
+ }
+
+ private Element createElement() {
+ Element protein = new GenericProtein("protein_id");
+ protein.setColor(Color.BLACK);
+ return protein;
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnectionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnectionTest.java
index 941aeb1dff..ee58dfbe8d 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnectionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnectionTest.java
@@ -1,94 +1,94 @@
-package lcsb.mapviewer.model.map.model;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class ElementSubmodelConnectionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new ElementSubmodelConnection());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- ElementSubmodelConnection connection = new ElementSubmodelConnection(new ModelData(), SubmodelType.DOWNSTREAM_TARGETS);
- assertNotNull(connection);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor2() {
- try {
- ElementSubmodelConnection connection = new ElementSubmodelConnection(new ElementSubmodelConnection(new ModelData(), SubmodelType.DOWNSTREAM_TARGETS));
- assertNotNull(connection);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor3() {
- try {
- ElementSubmodelConnection connection = new ElementSubmodelConnection(new ModelFullIndexed(null), SubmodelType.DOWNSTREAM_TARGETS, "sd");
- assertNotNull(connection);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- ElementSubmodelConnection connection = new ElementSubmodelConnection().copy();
- assertNotNull(connection);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new ElementSubmodelConnection() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.map.model;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class ElementSubmodelConnectionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new ElementSubmodelConnection());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ ElementSubmodelConnection connection = new ElementSubmodelConnection(new ModelData(), SubmodelType.DOWNSTREAM_TARGETS);
+ assertNotNull(connection);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor2() {
+ try {
+ ElementSubmodelConnection connection = new ElementSubmodelConnection(new ElementSubmodelConnection(new ModelData(), SubmodelType.DOWNSTREAM_TARGETS));
+ assertNotNull(connection);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor3() {
+ try {
+ ElementSubmodelConnection connection = new ElementSubmodelConnection(new ModelFullIndexed(null), SubmodelType.DOWNSTREAM_TARGETS, "sd");
+ assertNotNull(connection);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ ElementSubmodelConnection connection = new ElementSubmodelConnection().copy();
+ assertNotNull(connection);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new ElementSubmodelConnection() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelComparatorTest.java
index 0e0f2321a0..5c2641dc1a 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelComparatorTest.java
@@ -1,426 +1,426 @@
-package lcsb.mapviewer.model.map.model;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-import static org.mockito.Mockito.when;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class ModelComparatorTest {
- Logger logger = Logger.getLogger(ModelComparatorTest.class);
-
- ModelComparator comparator = new ModelComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- Model model1 = getModel();
- Model model2 = getModel();
-
- assertEquals(0, comparator.compare(new ModelFullIndexed(null), new ModelFullIndexed(null)));
- assertEquals(0, comparator.compare(model1, model2));
- assertEquals(0, comparator.compare(model1, model1));
- assertEquals(0, comparator.compare(null, null));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
- @Test
- public void testDifferent2() {
- try {
- Model model1 = getModel();
- Model model2 = Mockito.mock(Model.class);
-
- assertTrue(comparator.compare(model1, model2) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent3() {
- try {
- Model model1 = getModel();
- Model model2 = getModel();
-
- Compartment compartment = new PathwayCompartment("1");
- Compartment compartment2 = new PathwayCompartment("12");
- model1.addElement(compartment);
- model1.addElement(compartment2);
-
- compartment = new PathwayCompartment("1");
- compartment2 = new PathwayCompartment("12");
- model2.addElement(compartment);
- model2.addElement(compartment2);
- compartment2.setElementId("1");
-
- assertTrue(comparator.compare(model1, model2) != 0);
- assertTrue(comparator.compare(model2, model1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferentReactionsInReactionSet() {
- try {
- Model model1 = getModel();
- Model model2 = getModel();
-
- Reaction reaction1 = new Reaction();
- Reaction reaction2 = new Reaction();
- Reaction reaction3 = new Reaction();
- Reaction reaction4 = new Reaction();
- reaction1.setIdReaction("a");
- reaction2.setIdReaction("b");
- reaction3.setIdReaction("a");
- reaction4.setIdReaction("b");
-
- model1.addReaction(reaction1);
- model1.addReaction(reaction2);
- model2.addReaction(reaction3);
- model2.addReaction(reaction4);
-
- reaction2.setIdReaction("a");
-
- assertTrue(comparator.compare(model1, model2) != 0);
- assertTrue(comparator.compare(model2, model1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferentReactionSet() {
- try {
- Model model1 = getModel();
- Model model2 = getModel();
-
- model1.addReaction(new TransportReaction("id"));
-
- assertTrue(comparator.compare(model1, model2) != 0);
- assertTrue(comparator.compare(model2, model1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid() {
- try {
- Model model1 = getModel();
- Model model2 = getModel();
-
- Species mockSpecies = Mockito.mock(Species.class);
- when(mockSpecies.getElementId()).thenReturn("1");
- model1.addElement(mockSpecies);
-
- model2.addElement(mockSpecies);
-
- try {
- comparator.compare(model1, model2);
- fail("Exception expected");
-
- } catch (NotImplementedException e) {
-
- }
- try {
- comparator.compare(model2, model1);
- fail("Exception expected");
-
- } catch (NotImplementedException e) {
-
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent() throws Exception {
- try {
- Model model1 = getModel();
- Model model2 = getModel();
-
- assertTrue(comparator.compare(model1, new ModelFullIndexed(null)) != 0);
- assertTrue(comparator.compare(model1, null) != 0);
- assertTrue(comparator.compare(null, model1) != 0);
-
- model1 = getModel();
- model2 = getModel();
-
- model1.setNotes("ASDsaD");
-
- assertTrue(comparator.compare(model1, model2) != 0);
- assertTrue(comparator.compare(model2, model1) != 0);
-
- model1 = getModel();
- model2 = getModel();
-
- GenericProtein protein = new GenericProtein("SAd");
-
- model1.addElement(protein);
-
- assertTrue(comparator.compare(model1, model2) != 0);
- assertTrue(comparator.compare(model2, model1) != 0);
-
- model1 = getModel();
- model2 = getModel();
-
- model1.getElements().iterator().next().setElementId("sdfsd");
-
- assertTrue(comparator.compare(model1, model2) != 0);
- assertTrue(comparator.compare(model2, model1) != 0);
-
- model1 = getModel();
- model2 = getModel();
-
- model1.addElement(new Compartment("unk_id"));
-
- assertTrue(comparator.compare(model1, model2) != 0);
- assertTrue(comparator.compare(model2, model1) != 0);
-
- model1 = getModel();
- model2 = getModel();
-
- model1.getElementByElementId("default").setName("tmpxx");
-
- assertTrue(comparator.compare(model1, model2) != 0);
- assertTrue(comparator.compare(model2, model1) != 0);
-
- model1 = getModel();
- model2 = getModel();
-
- model1.addLayer(new Layer());
-
- assertTrue(comparator.compare(model1, model2) != 0);
- assertTrue(comparator.compare(model2, model1) != 0);
-
- model1 = getModel();
- model2 = getModel();
-
- model1.getLayers().iterator().next().setName("buu");
-
- assertTrue(comparator.compare(model1, model2) != 0);
- assertTrue(comparator.compare(model2, model1) != 0);
-
- model1 = getModel();
- model2 = getModel();
-
- model1.addElement(new GenericProtein("ASdas"));
-
- assertTrue(comparator.compare(model1, model2) != 0);
- assertTrue(comparator.compare(model2, model1) != 0);
-
- model1 = getModel();
- model2 = getModel();
-
- model1.getElements().iterator().next()
- .addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_HAS_PART, MiriamType.CHEBI, "c"));
-
- assertTrue(comparator.compare(model1, model2) != 0);
- assertTrue(comparator.compare(model2, model1) != 0);
-
- model1 = getModel();
- model2 = getModel();
-
- model1.getReactions().iterator().next().setName("dsf");
-
- assertTrue(comparator.compare(model1, model2) != 0);
- assertTrue(comparator.compare(model2, model1) != 0);
-
- model1 = getModel();
- model2 = getModel();
-
- model1.setIdModel("asdsdasd");
-
- assertTrue(comparator.compare(model1, model2) != 0);
- assertTrue(comparator.compare(model2, model1) != 0);
-
- model1 = getModel();
- model2 = getModel();
-
- model1.setWidth(123);
-
- assertTrue(comparator.compare(model1, model2) != 0);
- assertTrue(comparator.compare(model2, model1) != 0);
-
- model1 = getModel();
- model2 = getModel();
-
- model1.setHeight(636);
-
- assertTrue(comparator.compare(model1, model2) != 0);
- assertTrue(comparator.compare(model2, model1) != 0);
-
- model1 = getModel();
- model2 = getModel();
-
- model1.setZoomLevels(1);
-
- assertTrue(comparator.compare(model1, model2) != 0);
- assertTrue(comparator.compare(model2, model1) != 0);
-
- model1 = getModel();
- model2 = getModel();
-
- model1.setTileSize(129);
-
- assertTrue(comparator.compare(model1, model2) != 0);
- assertTrue(comparator.compare(model2, model1) != 0);
-
- model1 = getModel();
- model2 = getModel();
-
- model1.addLayout(new Layout());
-
- assertTrue(comparator.compare(model1, model2) != 0);
- assertTrue(comparator.compare(model2, model1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private Model getModel() {
- Model model = new ModelFullIndexed(null);
- model.setNotes("Some description");
- GenericProtein protein = new GenericProtein("a_id");
- protein.setName("ad");
-
- model.addElement(protein);
-
- model.addElement(new Compartment("default"));
-
- Layer layer = new Layer();
- layer.setName("layer name");
- model.addLayer(layer);
-
- model.addLayout(new Layout("1", "2", true));
-
- model.addReaction(new Reaction());
- return model;
- }
-
- @Test
- public void testCompareSubmodels() throws Exception {
- try {
- Model model1 = getModel();
- Model model2 = getModel();
-
- Model model3 = getModel();
-
- ModelSubmodelConnection submodelA = new ModelSubmodelConnection(model3, SubmodelType.DOWNSTREAM_TARGETS);
-
- model1.addSubmodelConnection(submodelA);
-
- assertTrue(comparator.compare(model1, model2) != 0);
- assertTrue(comparator.compare(model2, model1) != 0);
-
- Model model4 = getModel();
-
- ModelSubmodelConnection submodelB = new ModelSubmodelConnection(model4, SubmodelType.DOWNSTREAM_TARGETS);
-
- model2.addSubmodelConnection(submodelB);
-
- assertTrue(comparator.compare(model1, model2) == 0);
-
- submodelB.setName("A");
-
- assertTrue(comparator.compare(model1, model2) != 0);
- assertTrue(comparator.compare(model2, model1) != 0);
-
- submodelB.setName(null);
- assertTrue(comparator.compare(model1, model2) == 0);
-
- model4.setNotes("ASdasdhsjkadhask");
- assertTrue(comparator.compare(model1, model2) != 0);
- assertTrue(comparator.compare(model2, model1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCompareSubmodels2() throws Exception {
- try {
- Model model1 = getModel();
- Model model2 = getModel();
-
- model1.addSubmodelConnection(new ModelSubmodelConnection(getModel(), SubmodelType.DOWNSTREAM_TARGETS));
- model1.addSubmodelConnection(new ModelSubmodelConnection(getModel(), SubmodelType.DOWNSTREAM_TARGETS));
-
- model2.addSubmodelConnection(new ModelSubmodelConnection(getModel(), SubmodelType.DOWNSTREAM_TARGETS));
- model2.addSubmodelConnection(new ModelSubmodelConnection(getModel(), SubmodelType.PATHWAY));
-
- assertTrue(comparator.compare(model1, model2) != 0);
- assertTrue(comparator.compare(model2, model1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCompareName() throws Exception {
- try {
- Model model1 = getModel();
- Model model2 = getModel();
- model1.setName("ASD");
- assertTrue(comparator.compare(model1, model2) != 0);
- assertTrue(comparator.compare(model2, model1) != 0);
- model2.setName("A");
- assertTrue(comparator.compare(model1, model2) != 0);
- assertTrue(comparator.compare(model2, model1) != 0);
- model1.setName("A");
- assertEquals(0, comparator.compare(model1, model2));
- assertEquals(0, comparator.compare(model2, model1));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.model;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import static org.mockito.Mockito.when;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
+import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class ModelComparatorTest {
+ Logger logger = Logger.getLogger(ModelComparatorTest.class);
+
+ ModelComparator comparator = new ModelComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ Model model1 = getModel();
+ Model model2 = getModel();
+
+ assertEquals(0, comparator.compare(new ModelFullIndexed(null), new ModelFullIndexed(null)));
+ assertEquals(0, comparator.compare(model1, model2));
+ assertEquals(0, comparator.compare(model1, model1));
+ assertEquals(0, comparator.compare(null, null));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+ @Test
+ public void testDifferent2() {
+ try {
+ Model model1 = getModel();
+ Model model2 = Mockito.mock(Model.class);
+
+ assertTrue(comparator.compare(model1, model2) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent3() {
+ try {
+ Model model1 = getModel();
+ Model model2 = getModel();
+
+ Compartment compartment = new PathwayCompartment("1");
+ Compartment compartment2 = new PathwayCompartment("12");
+ model1.addElement(compartment);
+ model1.addElement(compartment2);
+
+ compartment = new PathwayCompartment("1");
+ compartment2 = new PathwayCompartment("12");
+ model2.addElement(compartment);
+ model2.addElement(compartment2);
+ compartment2.setElementId("1");
+
+ assertTrue(comparator.compare(model1, model2) != 0);
+ assertTrue(comparator.compare(model2, model1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferentReactionsInReactionSet() {
+ try {
+ Model model1 = getModel();
+ Model model2 = getModel();
+
+ Reaction reaction1 = new Reaction();
+ Reaction reaction2 = new Reaction();
+ Reaction reaction3 = new Reaction();
+ Reaction reaction4 = new Reaction();
+ reaction1.setIdReaction("a");
+ reaction2.setIdReaction("b");
+ reaction3.setIdReaction("a");
+ reaction4.setIdReaction("b");
+
+ model1.addReaction(reaction1);
+ model1.addReaction(reaction2);
+ model2.addReaction(reaction3);
+ model2.addReaction(reaction4);
+
+ reaction2.setIdReaction("a");
+
+ assertTrue(comparator.compare(model1, model2) != 0);
+ assertTrue(comparator.compare(model2, model1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferentReactionSet() {
+ try {
+ Model model1 = getModel();
+ Model model2 = getModel();
+
+ model1.addReaction(new TransportReaction("id"));
+
+ assertTrue(comparator.compare(model1, model2) != 0);
+ assertTrue(comparator.compare(model2, model1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid() {
+ try {
+ Model model1 = getModel();
+ Model model2 = getModel();
+
+ Species mockSpecies = Mockito.mock(Species.class);
+ when(mockSpecies.getElementId()).thenReturn("1");
+ model1.addElement(mockSpecies);
+
+ model2.addElement(mockSpecies);
+
+ try {
+ comparator.compare(model1, model2);
+ fail("Exception expected");
+
+ } catch (NotImplementedException e) {
+
+ }
+ try {
+ comparator.compare(model2, model1);
+ fail("Exception expected");
+
+ } catch (NotImplementedException e) {
+
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent() throws Exception {
+ try {
+ Model model1 = getModel();
+ Model model2 = getModel();
+
+ assertTrue(comparator.compare(model1, new ModelFullIndexed(null)) != 0);
+ assertTrue(comparator.compare(model1, null) != 0);
+ assertTrue(comparator.compare(null, model1) != 0);
+
+ model1 = getModel();
+ model2 = getModel();
+
+ model1.setNotes("ASDsaD");
+
+ assertTrue(comparator.compare(model1, model2) != 0);
+ assertTrue(comparator.compare(model2, model1) != 0);
+
+ model1 = getModel();
+ model2 = getModel();
+
+ GenericProtein protein = new GenericProtein("SAd");
+
+ model1.addElement(protein);
+
+ assertTrue(comparator.compare(model1, model2) != 0);
+ assertTrue(comparator.compare(model2, model1) != 0);
+
+ model1 = getModel();
+ model2 = getModel();
+
+ model1.getElements().iterator().next().setElementId("sdfsd");
+
+ assertTrue(comparator.compare(model1, model2) != 0);
+ assertTrue(comparator.compare(model2, model1) != 0);
+
+ model1 = getModel();
+ model2 = getModel();
+
+ model1.addElement(new Compartment("unk_id"));
+
+ assertTrue(comparator.compare(model1, model2) != 0);
+ assertTrue(comparator.compare(model2, model1) != 0);
+
+ model1 = getModel();
+ model2 = getModel();
+
+ model1.getElementByElementId("default").setName("tmpxx");
+
+ assertTrue(comparator.compare(model1, model2) != 0);
+ assertTrue(comparator.compare(model2, model1) != 0);
+
+ model1 = getModel();
+ model2 = getModel();
+
+ model1.addLayer(new Layer());
+
+ assertTrue(comparator.compare(model1, model2) != 0);
+ assertTrue(comparator.compare(model2, model1) != 0);
+
+ model1 = getModel();
+ model2 = getModel();
+
+ model1.getLayers().iterator().next().setName("buu");
+
+ assertTrue(comparator.compare(model1, model2) != 0);
+ assertTrue(comparator.compare(model2, model1) != 0);
+
+ model1 = getModel();
+ model2 = getModel();
+
+ model1.addElement(new GenericProtein("ASdas"));
+
+ assertTrue(comparator.compare(model1, model2) != 0);
+ assertTrue(comparator.compare(model2, model1) != 0);
+
+ model1 = getModel();
+ model2 = getModel();
+
+ model1.getElements().iterator().next()
+ .addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_HAS_PART, MiriamType.CHEBI, "c"));
+
+ assertTrue(comparator.compare(model1, model2) != 0);
+ assertTrue(comparator.compare(model2, model1) != 0);
+
+ model1 = getModel();
+ model2 = getModel();
+
+ model1.getReactions().iterator().next().setName("dsf");
+
+ assertTrue(comparator.compare(model1, model2) != 0);
+ assertTrue(comparator.compare(model2, model1) != 0);
+
+ model1 = getModel();
+ model2 = getModel();
+
+ model1.setIdModel("asdsdasd");
+
+ assertTrue(comparator.compare(model1, model2) != 0);
+ assertTrue(comparator.compare(model2, model1) != 0);
+
+ model1 = getModel();
+ model2 = getModel();
+
+ model1.setWidth(123);
+
+ assertTrue(comparator.compare(model1, model2) != 0);
+ assertTrue(comparator.compare(model2, model1) != 0);
+
+ model1 = getModel();
+ model2 = getModel();
+
+ model1.setHeight(636);
+
+ assertTrue(comparator.compare(model1, model2) != 0);
+ assertTrue(comparator.compare(model2, model1) != 0);
+
+ model1 = getModel();
+ model2 = getModel();
+
+ model1.setZoomLevels(1);
+
+ assertTrue(comparator.compare(model1, model2) != 0);
+ assertTrue(comparator.compare(model2, model1) != 0);
+
+ model1 = getModel();
+ model2 = getModel();
+
+ model1.setTileSize(129);
+
+ assertTrue(comparator.compare(model1, model2) != 0);
+ assertTrue(comparator.compare(model2, model1) != 0);
+
+ model1 = getModel();
+ model2 = getModel();
+
+ model1.addLayout(new Layout());
+
+ assertTrue(comparator.compare(model1, model2) != 0);
+ assertTrue(comparator.compare(model2, model1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Model getModel() {
+ Model model = new ModelFullIndexed(null);
+ model.setNotes("Some description");
+ GenericProtein protein = new GenericProtein("a_id");
+ protein.setName("ad");
+
+ model.addElement(protein);
+
+ model.addElement(new Compartment("default"));
+
+ Layer layer = new Layer();
+ layer.setName("layer name");
+ model.addLayer(layer);
+
+ model.addLayout(new Layout("1", "2", true));
+
+ model.addReaction(new Reaction());
+ return model;
+ }
+
+ @Test
+ public void testCompareSubmodels() throws Exception {
+ try {
+ Model model1 = getModel();
+ Model model2 = getModel();
+
+ Model model3 = getModel();
+
+ ModelSubmodelConnection submodelA = new ModelSubmodelConnection(model3, SubmodelType.DOWNSTREAM_TARGETS);
+
+ model1.addSubmodelConnection(submodelA);
+
+ assertTrue(comparator.compare(model1, model2) != 0);
+ assertTrue(comparator.compare(model2, model1) != 0);
+
+ Model model4 = getModel();
+
+ ModelSubmodelConnection submodelB = new ModelSubmodelConnection(model4, SubmodelType.DOWNSTREAM_TARGETS);
+
+ model2.addSubmodelConnection(submodelB);
+
+ assertTrue(comparator.compare(model1, model2) == 0);
+
+ submodelB.setName("A");
+
+ assertTrue(comparator.compare(model1, model2) != 0);
+ assertTrue(comparator.compare(model2, model1) != 0);
+
+ submodelB.setName(null);
+ assertTrue(comparator.compare(model1, model2) == 0);
+
+ model4.setNotes("ASdasdhsjkadhask");
+ assertTrue(comparator.compare(model1, model2) != 0);
+ assertTrue(comparator.compare(model2, model1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCompareSubmodels2() throws Exception {
+ try {
+ Model model1 = getModel();
+ Model model2 = getModel();
+
+ model1.addSubmodelConnection(new ModelSubmodelConnection(getModel(), SubmodelType.DOWNSTREAM_TARGETS));
+ model1.addSubmodelConnection(new ModelSubmodelConnection(getModel(), SubmodelType.DOWNSTREAM_TARGETS));
+
+ model2.addSubmodelConnection(new ModelSubmodelConnection(getModel(), SubmodelType.DOWNSTREAM_TARGETS));
+ model2.addSubmodelConnection(new ModelSubmodelConnection(getModel(), SubmodelType.PATHWAY));
+
+ assertTrue(comparator.compare(model1, model2) != 0);
+ assertTrue(comparator.compare(model2, model1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCompareName() throws Exception {
+ try {
+ Model model1 = getModel();
+ Model model2 = getModel();
+ model1.setName("ASD");
+ assertTrue(comparator.compare(model1, model2) != 0);
+ assertTrue(comparator.compare(model2, model1) != 0);
+ model2.setName("A");
+ assertTrue(comparator.compare(model1, model2) != 0);
+ assertTrue(comparator.compare(model2, model1) != 0);
+ model1.setName("A");
+ assertEquals(0, comparator.compare(model1, model2));
+ assertEquals(0, comparator.compare(model2, model1));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelDataTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelDataTest.java
index f41ccdc4d8..1a8e06175b 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelDataTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelDataTest.java
@@ -1,301 +1,301 @@
-package lcsb.mapviewer.model.map.model;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.fail;
-
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.OverviewImage;
-import lcsb.mapviewer.model.map.layout.BlockDiagram;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-
-public class ModelDataTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new ModelData());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddElements() {
- try {
- ModelData md = new ModelData();
- List<Element> elements = new ArrayList<>();
- elements.add(new GenericProtein("unk_id"));
- md.addElements(elements);
- assertEquals(1, md.getElements().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddReactions() {
- try {
- ModelData md = new ModelData();
- List<Reaction> reactions = new ArrayList<>();
- reactions.add(new Reaction());
- md.addReactions(reactions);
- assertEquals(1, md.getReactions().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddLayers() {
- try {
- ModelData md = new ModelData();
- List<Layer> layers = new ArrayList<>();
- layers.add(new Layer());
- md.addLayers(layers);
- assertEquals(1, md.getLayers().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddElementGroup() {
- try {
- ModelData md = new ModelData();
- md.addElementGroup(null);
- // not implemented for now
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddBlockDiagram() {
- try {
- ModelData md = new ModelData();
- md.addBlockDiagream(new BlockDiagram() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- });
- // not implemented for now
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddRemoveLayout() {
- try {
- ModelData md = new ModelData();
- Layout l = new Layout();
- l.setId(3);
- md.addLayout(l);
- assertEquals(1, md.getLayouts().size());
- md.removeLayout(new Layout());
- assertEquals(1, md.getLayouts().size());
- md.removeLayout(l);
- assertEquals(0, md.getLayouts().size());
- md.addLayout(0, l);
- assertEquals(1, md.getLayouts().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRemoveElement1() {
- try {
- ModelData md = new ModelData();
- md.removeElement(null);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRemoveElement2() {
- try {
- ModelData md = new ModelData();
- md.removeElement(new GenericProtein("unk_id"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRemoveElement3() {
- try {
- ModelData md = new ModelData();
- Element protein = new GenericProtein("unk_id");
- md.addElement(protein);
- assertEquals(1, md.getElements().size());
- md.removeElement(protein);
- assertEquals(0, md.getElements().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRemoveReaction2() {
- try {
- ModelData md = new ModelData();
- md.removeReaction(new Reaction());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRemoveReaction3() {
- try {
- ModelData md = new ModelData();
- Reaction reaction = new Reaction();
- md.addReaction(reaction);
- assertEquals(1, md.getReactions().size());
- md.removeReaction(reaction);
- assertEquals(0, md.getReactions().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddSubmodel() {
- try {
- ModelData md = new ModelData();
- md.addSubmodel(new ModelSubmodelConnection());
- assertEquals(1, md.getSubmodels().size());
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- ModelData md = new ModelData();
- Set<Element> elements = new HashSet<>();
- List<Layout> layouts = new ArrayList<>();
- Set<Layer> layers = new HashSet<>();
- Set<Reaction> reactions = new HashSet<>();
- Set<SubmodelConnection> parents = new HashSet<>();
- List<OverviewImage> overviewImages = new ArrayList<>();
- overviewImages.add(new OverviewImage());
- Integer id = 95;
- int width = 2;
- Double widthDouble = 2.0;
- int height = 29;
- int zoomLevels = 3;
- int tileSize = 512;
- String modelId = "modId";
- String notes = "nOT";
- String name = "n_ma";
- Double heightDouble = 29.0;
- Project project = new Project();
- Calendar creationDate = Calendar.getInstance();
-
- Model model = new ModelFullIndexed(null);
-
- md.setId(id);
- assertEquals(id, md.getId());
-
- md.setElements(elements);
- assertEquals(elements, md.getElements());
-
- md.setProject(project);
- assertEquals(project, md.getProject());
-
- md.setCreationDate(creationDate);
- assertEquals(creationDate, md.getCreationDate());
-
- md.setLayouts(layouts);
- assertEquals(layouts, md.getLayouts());
-
- md.setWidth(width);
- assertEquals(widthDouble, md.getWidth(), Configuration.EPSILON);
-
- md.setHeight(height);
- assertEquals(heightDouble, md.getHeight(), Configuration.EPSILON);
-
- md.setZoomLevels(zoomLevels);
- assertEquals(zoomLevels, md.getZoomLevels());
-
- md.setTileSize(tileSize);
- assertEquals(tileSize, md.getTileSize());
-
- md.setIdModel(modelId);
- assertEquals(modelId, md.getIdModel());
-
- md.setNotes(notes);
- assertEquals(notes, md.getNotes());
-
- md.setName(name);
- assertEquals(name, md.getName());
-
- md.setModel(null);
- assertNull(md.getModel());
- md.setModel(model);
- assertEquals(model, md.getModel());
-
- md.setLayers(layers);
- assertEquals(layers, md.getLayers());
-
- md.setReactions(reactions);
- assertEquals(reactions, md.getReactions());
-
- md.setParentModels(parents);
- assertEquals(parents, md.getParentModels());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.map.model;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.fail;
+
+import java.util.ArrayList;
+import java.util.Calendar;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.OverviewImage;
+import lcsb.mapviewer.model.map.layout.BlockDiagram;
+import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+
+public class ModelDataTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new ModelData());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddElements() {
+ try {
+ ModelData md = new ModelData();
+ List<Element> elements = new ArrayList<>();
+ elements.add(new GenericProtein("unk_id"));
+ md.addElements(elements);
+ assertEquals(1, md.getElements().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddReactions() {
+ try {
+ ModelData md = new ModelData();
+ List<Reaction> reactions = new ArrayList<>();
+ reactions.add(new Reaction());
+ md.addReactions(reactions);
+ assertEquals(1, md.getReactions().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddLayers() {
+ try {
+ ModelData md = new ModelData();
+ List<Layer> layers = new ArrayList<>();
+ layers.add(new Layer());
+ md.addLayers(layers);
+ assertEquals(1, md.getLayers().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddElementGroup() {
+ try {
+ ModelData md = new ModelData();
+ md.addElementGroup(null);
+ // not implemented for now
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddBlockDiagram() {
+ try {
+ ModelData md = new ModelData();
+ md.addBlockDiagream(new BlockDiagram() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ });
+ // not implemented for now
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddRemoveLayout() {
+ try {
+ ModelData md = new ModelData();
+ Layout l = new Layout();
+ l.setId(3);
+ md.addLayout(l);
+ assertEquals(1, md.getLayouts().size());
+ md.removeLayout(new Layout());
+ assertEquals(1, md.getLayouts().size());
+ md.removeLayout(l);
+ assertEquals(0, md.getLayouts().size());
+ md.addLayout(0, l);
+ assertEquals(1, md.getLayouts().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRemoveElement1() {
+ try {
+ ModelData md = new ModelData();
+ md.removeElement(null);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRemoveElement2() {
+ try {
+ ModelData md = new ModelData();
+ md.removeElement(new GenericProtein("unk_id"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRemoveElement3() {
+ try {
+ ModelData md = new ModelData();
+ Element protein = new GenericProtein("unk_id");
+ md.addElement(protein);
+ assertEquals(1, md.getElements().size());
+ md.removeElement(protein);
+ assertEquals(0, md.getElements().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRemoveReaction2() {
+ try {
+ ModelData md = new ModelData();
+ md.removeReaction(new Reaction());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRemoveReaction3() {
+ try {
+ ModelData md = new ModelData();
+ Reaction reaction = new Reaction();
+ md.addReaction(reaction);
+ assertEquals(1, md.getReactions().size());
+ md.removeReaction(reaction);
+ assertEquals(0, md.getReactions().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddSubmodel() {
+ try {
+ ModelData md = new ModelData();
+ md.addSubmodel(new ModelSubmodelConnection());
+ assertEquals(1, md.getSubmodels().size());
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ ModelData md = new ModelData();
+ Set<Element> elements = new HashSet<>();
+ List<Layout> layouts = new ArrayList<>();
+ Set<Layer> layers = new HashSet<>();
+ Set<Reaction> reactions = new HashSet<>();
+ Set<SubmodelConnection> parents = new HashSet<>();
+ List<OverviewImage> overviewImages = new ArrayList<>();
+ overviewImages.add(new OverviewImage());
+ Integer id = 95;
+ int width = 2;
+ Double widthDouble = 2.0;
+ int height = 29;
+ int zoomLevels = 3;
+ int tileSize = 512;
+ String modelId = "modId";
+ String notes = "nOT";
+ String name = "n_ma";
+ Double heightDouble = 29.0;
+ Project project = new Project();
+ Calendar creationDate = Calendar.getInstance();
+
+ Model model = new ModelFullIndexed(null);
+
+ md.setId(id);
+ assertEquals(id, md.getId());
+
+ md.setElements(elements);
+ assertEquals(elements, md.getElements());
+
+ md.setProject(project);
+ assertEquals(project, md.getProject());
+
+ md.setCreationDate(creationDate);
+ assertEquals(creationDate, md.getCreationDate());
+
+ md.setLayouts(layouts);
+ assertEquals(layouts, md.getLayouts());
+
+ md.setWidth(width);
+ assertEquals(widthDouble, md.getWidth(), Configuration.EPSILON);
+
+ md.setHeight(height);
+ assertEquals(heightDouble, md.getHeight(), Configuration.EPSILON);
+
+ md.setZoomLevels(zoomLevels);
+ assertEquals(zoomLevels, md.getZoomLevels());
+
+ md.setTileSize(tileSize);
+ assertEquals(tileSize, md.getTileSize());
+
+ md.setIdModel(modelId);
+ assertEquals(modelId, md.getIdModel());
+
+ md.setNotes(notes);
+ assertEquals(notes, md.getNotes());
+
+ md.setName(name);
+ assertEquals(name, md.getName());
+
+ md.setModel(null);
+ assertNull(md.getModel());
+ md.setModel(model);
+ assertEquals(model, md.getModel());
+
+ md.setLayers(layers);
+ assertEquals(layers, md.getLayers());
+
+ md.setReactions(reactions);
+ assertEquals(reactions, md.getReactions());
+
+ md.setParentModels(parents);
+ assertEquals(parents, md.getParentModels());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnectionComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnectionComparatorTest.java
index daeeda9fcc..d20df8137c 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnectionComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnectionComparatorTest.java
@@ -1,110 +1,110 @@
-package lcsb.mapviewer.model.map.model;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class ModelSubmodelConnectionComparatorTest {
-
- ModelSubmodelConnectionComparator comparator = new ModelSubmodelConnectionComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() throws Exception {
- try {
- ModelSubmodelConnection connectionA = createConnection();
- ModelSubmodelConnection connectionB = createConnection();
-
- assertEquals(0, comparator.compare(new ModelSubmodelConnection(), new ModelSubmodelConnection()));
- assertEquals(0, comparator.compare(connectionA, connectionB));
- assertEquals(0, comparator.compare(connectionA, connectionA));
- assertEquals(0, comparator.compare(null, null));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent() throws Exception {
- try {
- ModelSubmodelConnection connectionA = createConnection();
- ModelSubmodelConnection connectionB = createConnection();
-
- assertTrue(comparator.compare(null, connectionB) != 0);
- assertTrue(comparator.compare(connectionA, null) != 0);
-
- connectionA.getParentModel().setNotes("QQWECS");
- assertTrue(comparator.compare(connectionA, connectionB) != 0);
- assertTrue(comparator.compare(connectionB, connectionA) != 0);
-
- connectionA = createConnection();
- connectionB = createConnection();
-
- connectionA.setParentModel((ModelData) null);
-
- assertTrue(comparator.compare(connectionA, connectionB) != 0);
- assertTrue(comparator.compare(connectionB, connectionA) != 0);
-
- connectionA = createConnection();
- connectionB = createConnection();
-
- connectionA.setType(SubmodelType.UNKNOWN);
-
- assertTrue(comparator.compare(connectionA, connectionB) != 0);
- assertTrue(comparator.compare(connectionB, connectionA) != 0);
-
- assertTrue(comparator.compare(connectionB, new ModelSubmodelConnection() {
- private static final long serialVersionUID = 1L;
- }) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private Model getModel() {
- Model model = new ModelFullIndexed(null);
-
- model.setNotes("Some description");
-
- Species species = new GenericProtein("a_id");
- species.setName("ad");
- model.addElement(species);
-
- model.addElement(new Compartment("default"));
-
- Layer layer = new Layer();
- layer.setName("layer name");
- model.addLayer(layer);
-
- model.addReaction(new Reaction());
- return model;
- }
-
- private ModelSubmodelConnection createConnection() {
- ModelSubmodelConnection result = new ModelSubmodelConnection(getModel(), SubmodelType.DOWNSTREAM_TARGETS);
- result.setName("name A");
- result.setParentModel(getModel());
- return result;
- }
-
-}
+package lcsb.mapviewer.model.map.model;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class ModelSubmodelConnectionComparatorTest {
+
+ ModelSubmodelConnectionComparator comparator = new ModelSubmodelConnectionComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() throws Exception {
+ try {
+ ModelSubmodelConnection connectionA = createConnection();
+ ModelSubmodelConnection connectionB = createConnection();
+
+ assertEquals(0, comparator.compare(new ModelSubmodelConnection(), new ModelSubmodelConnection()));
+ assertEquals(0, comparator.compare(connectionA, connectionB));
+ assertEquals(0, comparator.compare(connectionA, connectionA));
+ assertEquals(0, comparator.compare(null, null));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent() throws Exception {
+ try {
+ ModelSubmodelConnection connectionA = createConnection();
+ ModelSubmodelConnection connectionB = createConnection();
+
+ assertTrue(comparator.compare(null, connectionB) != 0);
+ assertTrue(comparator.compare(connectionA, null) != 0);
+
+ connectionA.getParentModel().setNotes("QQWECS");
+ assertTrue(comparator.compare(connectionA, connectionB) != 0);
+ assertTrue(comparator.compare(connectionB, connectionA) != 0);
+
+ connectionA = createConnection();
+ connectionB = createConnection();
+
+ connectionA.setParentModel((ModelData) null);
+
+ assertTrue(comparator.compare(connectionA, connectionB) != 0);
+ assertTrue(comparator.compare(connectionB, connectionA) != 0);
+
+ connectionA = createConnection();
+ connectionB = createConnection();
+
+ connectionA.setType(SubmodelType.UNKNOWN);
+
+ assertTrue(comparator.compare(connectionA, connectionB) != 0);
+ assertTrue(comparator.compare(connectionB, connectionA) != 0);
+
+ assertTrue(comparator.compare(connectionB, new ModelSubmodelConnection() {
+ private static final long serialVersionUID = 1L;
+ }) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Model getModel() {
+ Model model = new ModelFullIndexed(null);
+
+ model.setNotes("Some description");
+
+ Species species = new GenericProtein("a_id");
+ species.setName("ad");
+ model.addElement(species);
+
+ model.addElement(new Compartment("default"));
+
+ Layer layer = new Layer();
+ layer.setName("layer name");
+ model.addLayer(layer);
+
+ model.addReaction(new Reaction());
+ return model;
+ }
+
+ private ModelSubmodelConnection createConnection() {
+ ModelSubmodelConnection result = new ModelSubmodelConnection(getModel(), SubmodelType.DOWNSTREAM_TARGETS);
+ result.setName("name A");
+ result.setParentModel(getModel());
+ return result;
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnectionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnectionTest.java
index a81b8062dc..5652e39481 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnectionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelSubmodelConnectionTest.java
@@ -1,102 +1,102 @@
-package lcsb.mapviewer.model.map.model;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class ModelSubmodelConnectionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new ModelSubmodelConnection());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- ModelSubmodelConnection connection = new ModelSubmodelConnection(new ModelFullIndexed(null), SubmodelType.DOWNSTREAM_TARGETS, "str");
- ModelSubmodelConnection connection2 = new ModelSubmodelConnection(connection);
- assertNotNull(connection2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor2() {
- try {
- ModelSubmodelConnection connection = new ModelSubmodelConnection(new ModelFullIndexed(null), SubmodelType.DOWNSTREAM_TARGETS, "str");
-
- assertNotNull(connection);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- ModelSubmodelConnection connection = new ModelSubmodelConnection(new ModelFullIndexed(null), SubmodelType.DOWNSTREAM_TARGETS, "str");
- ModelSubmodelConnection degraded = connection.copy();
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- ModelSubmodelConnection connection = new ModelSubmodelConnection(new ModelFullIndexed(null), SubmodelType.DOWNSTREAM_TARGETS, "str");
-
- int id = 30;
- connection.setId(id);
- assertEquals(id, connection.getId());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new ModelSubmodelConnection() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.model;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class ModelSubmodelConnectionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new ModelSubmodelConnection());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ ModelSubmodelConnection connection = new ModelSubmodelConnection(new ModelFullIndexed(null), SubmodelType.DOWNSTREAM_TARGETS, "str");
+ ModelSubmodelConnection connection2 = new ModelSubmodelConnection(connection);
+ assertNotNull(connection2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor2() {
+ try {
+ ModelSubmodelConnection connection = new ModelSubmodelConnection(new ModelFullIndexed(null), SubmodelType.DOWNSTREAM_TARGETS, "str");
+
+ assertNotNull(connection);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ ModelSubmodelConnection connection = new ModelSubmodelConnection(new ModelFullIndexed(null), SubmodelType.DOWNSTREAM_TARGETS, "str");
+ ModelSubmodelConnection degraded = connection.copy();
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ ModelSubmodelConnection connection = new ModelSubmodelConnection(new ModelFullIndexed(null), SubmodelType.DOWNSTREAM_TARGETS, "str");
+
+ int id = 30;
+ connection.setId(id);
+ assertEquals(id, connection.getId());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new ModelSubmodelConnection() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparatorTest.java
index e4598a4f02..df1ff90e5b 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparatorTest.java
@@ -1,189 +1,189 @@
-package lcsb.mapviewer.model.map.model;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class SubmodelConnectionComparatorTest {
-
- SubmodelConnectionComparator comparator = new SubmodelConnectionComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() throws Exception {
- try {
- SubmodelConnection connectionA = createConnection();
- SubmodelConnection connectionB = createConnection();
-
- assertEquals(0, comparator.compare(new ElementSubmodelConnection(), new ElementSubmodelConnection()));
- assertEquals(0, comparator.compare(new ModelSubmodelConnection(), new ModelSubmodelConnection()));
- assertEquals(0, comparator.compare(connectionA, connectionB));
- assertEquals(0, comparator.compare(connectionA, connectionA));
- assertEquals(0, comparator.compare(null, null));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid() throws Exception {
- try {
- class Tmp extends SubmodelConnection {
- private static final long serialVersionUID = 1L;
-
- @Override
- public SubmodelConnection copy() {
- return null;
- }
- }
- ;
- Tmp connectionA = new Tmp();
- Tmp connectionB = new Tmp();
-
- comparator.compare(connectionA, connectionB);
- comparator.compare(connectionA, connectionA);
-
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInternal() throws Exception {
- try {
- SubmodelConnection connectionA = createConnection();
- SubmodelConnection connectionB = createConnection();
-
- assertTrue(comparator.internalCompare(null, connectionB) != 0);
- assertTrue(comparator.internalCompare(connectionA, null) != 0);
- assertEquals(0, comparator.internalCompare(null, null));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent() throws Exception {
- try {
- SubmodelConnection connectionA = createConnection();
- SubmodelConnection connectionB = createConnection();
-
- assertTrue(comparator.compare(null, connectionB) != 0);
- assertTrue(comparator.compare(connectionA, null) != 0);
-
- connectionA.setName("AA");
- assertTrue(comparator.compare(connectionA, connectionB) != 0);
- assertTrue(comparator.compare(connectionB, connectionA) != 0);
-
- connectionA = createConnection();
- connectionB = createConnection();
-
- connectionA.setType(null);
-
- assertTrue(comparator.compare(connectionA, connectionB) != 0);
- assertTrue(comparator.compare(connectionB, connectionA) != 0);
-
- connectionA = createConnection();
- connectionB = createConnection();
-
- connectionA.setType(SubmodelType.PATHWAY);
-
- assertTrue(comparator.compare(connectionA, connectionB) != 0);
- assertTrue(comparator.compare(connectionB, connectionA) != 0);
-
- connectionA = createConnection();
- connectionB = createConnection();
-
- connectionA.getSubmodel().setNotes("ASD acd");
-
- assertTrue(comparator.compare(connectionA, connectionB) != 0);
- assertTrue(comparator.compare(connectionB, connectionA) != 0);
-
- connectionA = createConnection();
- connectionB = createConnection();
- connectionB.setSubmodel(new ModelFullIndexed(null));
- assertTrue(comparator.compare(connectionA, connectionB) != 0);
- assertTrue(comparator.compare(connectionB, connectionA) != 0);
-
- assertTrue(comparator.compare(connectionB, new SubmodelConnection() {
- private static final long serialVersionUID = 1L;
-
- @Override
- public SubmodelConnection copy() {
- return null;
- }
- }) != 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent2() throws Exception {
- try {
- ElementSubmodelConnection connectionA = new ElementSubmodelConnection();
- ElementSubmodelConnection connectionB = new ElementSubmodelConnection();
-
- connectionB.setSubmodel(new ModelFullIndexed(null));
- assertTrue(comparator.compare(connectionA, connectionB) != 0);
- assertTrue(comparator.compare(connectionB, connectionA) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private Model getModel() {
- Model model = new ModelFullIndexed(null);
-
- model.setNotes("Some description");
-
- Species protein = new GenericProtein("a_id");
- protein.setName("ad");
- protein.setElementId("a_id");
- model.addElement(protein);
-
- model.addElement(new Compartment("default"));
-
- Layer layer = new Layer();
- layer.setName("layer name");
- model.addLayer(layer);
-
- model.addReaction(new Reaction());
- return model;
- }
-
- private ElementSubmodelConnection createConnection() {
- ElementSubmodelConnection result = new ElementSubmodelConnection(getModel(), SubmodelType.DOWNSTREAM_TARGETS);
- result.setName("name A");
- return result;
- }
-
-}
+package lcsb.mapviewer.model.map.model;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class SubmodelConnectionComparatorTest {
+
+ SubmodelConnectionComparator comparator = new SubmodelConnectionComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() throws Exception {
+ try {
+ SubmodelConnection connectionA = createConnection();
+ SubmodelConnection connectionB = createConnection();
+
+ assertEquals(0, comparator.compare(new ElementSubmodelConnection(), new ElementSubmodelConnection()));
+ assertEquals(0, comparator.compare(new ModelSubmodelConnection(), new ModelSubmodelConnection()));
+ assertEquals(0, comparator.compare(connectionA, connectionB));
+ assertEquals(0, comparator.compare(connectionA, connectionA));
+ assertEquals(0, comparator.compare(null, null));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid() throws Exception {
+ try {
+ class Tmp extends SubmodelConnection {
+ private static final long serialVersionUID = 1L;
+
+ @Override
+ public SubmodelConnection copy() {
+ return null;
+ }
+ }
+ ;
+ Tmp connectionA = new Tmp();
+ Tmp connectionB = new Tmp();
+
+ comparator.compare(connectionA, connectionB);
+ comparator.compare(connectionA, connectionA);
+
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInternal() throws Exception {
+ try {
+ SubmodelConnection connectionA = createConnection();
+ SubmodelConnection connectionB = createConnection();
+
+ assertTrue(comparator.internalCompare(null, connectionB) != 0);
+ assertTrue(comparator.internalCompare(connectionA, null) != 0);
+ assertEquals(0, comparator.internalCompare(null, null));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent() throws Exception {
+ try {
+ SubmodelConnection connectionA = createConnection();
+ SubmodelConnection connectionB = createConnection();
+
+ assertTrue(comparator.compare(null, connectionB) != 0);
+ assertTrue(comparator.compare(connectionA, null) != 0);
+
+ connectionA.setName("AA");
+ assertTrue(comparator.compare(connectionA, connectionB) != 0);
+ assertTrue(comparator.compare(connectionB, connectionA) != 0);
+
+ connectionA = createConnection();
+ connectionB = createConnection();
+
+ connectionA.setType(null);
+
+ assertTrue(comparator.compare(connectionA, connectionB) != 0);
+ assertTrue(comparator.compare(connectionB, connectionA) != 0);
+
+ connectionA = createConnection();
+ connectionB = createConnection();
+
+ connectionA.setType(SubmodelType.PATHWAY);
+
+ assertTrue(comparator.compare(connectionA, connectionB) != 0);
+ assertTrue(comparator.compare(connectionB, connectionA) != 0);
+
+ connectionA = createConnection();
+ connectionB = createConnection();
+
+ connectionA.getSubmodel().setNotes("ASD acd");
+
+ assertTrue(comparator.compare(connectionA, connectionB) != 0);
+ assertTrue(comparator.compare(connectionB, connectionA) != 0);
+
+ connectionA = createConnection();
+ connectionB = createConnection();
+ connectionB.setSubmodel(new ModelFullIndexed(null));
+ assertTrue(comparator.compare(connectionA, connectionB) != 0);
+ assertTrue(comparator.compare(connectionB, connectionA) != 0);
+
+ assertTrue(comparator.compare(connectionB, new SubmodelConnection() {
+ private static final long serialVersionUID = 1L;
+
+ @Override
+ public SubmodelConnection copy() {
+ return null;
+ }
+ }) != 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent2() throws Exception {
+ try {
+ ElementSubmodelConnection connectionA = new ElementSubmodelConnection();
+ ElementSubmodelConnection connectionB = new ElementSubmodelConnection();
+
+ connectionB.setSubmodel(new ModelFullIndexed(null));
+ assertTrue(comparator.compare(connectionA, connectionB) != 0);
+ assertTrue(comparator.compare(connectionB, connectionA) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Model getModel() {
+ Model model = new ModelFullIndexed(null);
+
+ model.setNotes("Some description");
+
+ Species protein = new GenericProtein("a_id");
+ protein.setName("ad");
+ protein.setElementId("a_id");
+ model.addElement(protein);
+
+ model.addElement(new Compartment("default"));
+
+ Layer layer = new Layer();
+ layer.setName("layer name");
+ model.addLayer(layer);
+
+ model.addReaction(new Reaction());
+ return model;
+ }
+
+ private ElementSubmodelConnection createConnection() {
+ ElementSubmodelConnection result = new ElementSubmodelConnection(getModel(), SubmodelType.DOWNSTREAM_TARGETS);
+ result.setName("name A");
+ return result;
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/SubmodelTypeTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/SubmodelTypeTest.java
index ed6ab6d99b..202a2f1996 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/SubmodelTypeTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/SubmodelTypeTest.java
@@ -1,30 +1,30 @@
-package lcsb.mapviewer.model.map.model;
-
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class SubmodelTypeTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testValidValues() {
- for (SubmodelType type : SubmodelType.values()) {
- assertNotNull(type);
-
- // for coverage tests
- SubmodelType.valueOf(type.toString());
- assertNotNull(type.getCommonName());
- }
- }
-
-}
+package lcsb.mapviewer.model.map.model;
+
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class SubmodelTypeTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testValidValues() {
+ for (SubmodelType type : SubmodelType.values()) {
+ assertNotNull(type);
+
+ // for coverage tests
+ SubmodelType.valueOf(type.toString());
+ assertNotNull(type.getCommonName());
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/modifier/AllModifierTests.java b/model/src/test/java/lcsb/mapviewer/model/map/modifier/AllModifierTests.java
index 81e5da29c4..f6ec478388 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/modifier/AllModifierTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/modifier/AllModifierTests.java
@@ -1,18 +1,18 @@
-package lcsb.mapviewer.model.map.modifier;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ CatalysisTest.class, //
- InhibitionTest.class, //
- ModulationTest.class, //
- PhysicalStimulationTest.class, //
- TriggerTest.class, //
- UnknownCatalysisTest.class,//
- UnknownInhibitionTest.class,//
-})
-public class AllModifierTests {
-
-}
+package lcsb.mapviewer.model.map.modifier;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ CatalysisTest.class, //
+ InhibitionTest.class, //
+ ModulationTest.class, //
+ PhysicalStimulationTest.class, //
+ TriggerTest.class, //
+ UnknownCatalysisTest.class,//
+ UnknownInhibitionTest.class,//
+})
+public class AllModifierTests {
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/modifier/CatalysisTest.java b/model/src/test/java/lcsb/mapviewer/model/map/modifier/CatalysisTest.java
index 661fa42125..44222b739e 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/modifier/CatalysisTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/modifier/CatalysisTest.java
@@ -1,84 +1,84 @@
-package lcsb.mapviewer.model.map.modifier;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-
-public class CatalysisTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new Catalysis());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Catalysis modifier = new Catalysis(new AntisenseRna("unk_id"));
- assertNotNull(modifier);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor2() {
- try {
- Catalysis modifier = new Catalysis(new AntisenseRna("unk_id"));
- modifier.setLine(new PolylineData());
- Catalysis modifier2 = new Catalysis(modifier);
- assertNotNull(modifier2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- Catalysis modifier = new Catalysis(new AntisenseRna("unk_id"));
- modifier.setLine(new PolylineData());
- Catalysis modifier2 = modifier.copy();
- assertNotNull(modifier2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopyInvalid() {
- try {
- Mockito.mock(Catalysis.class, Mockito.CALLS_REAL_METHODS).copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.map.modifier;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+
+public class CatalysisTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new Catalysis());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Catalysis modifier = new Catalysis(new AntisenseRna("unk_id"));
+ assertNotNull(modifier);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor2() {
+ try {
+ Catalysis modifier = new Catalysis(new AntisenseRna("unk_id"));
+ modifier.setLine(new PolylineData());
+ Catalysis modifier2 = new Catalysis(modifier);
+ assertNotNull(modifier2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ Catalysis modifier = new Catalysis(new AntisenseRna("unk_id"));
+ modifier.setLine(new PolylineData());
+ Catalysis modifier2 = modifier.copy();
+ assertNotNull(modifier2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyInvalid() {
+ try {
+ Mockito.mock(Catalysis.class, Mockito.CALLS_REAL_METHODS).copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/modifier/InhibitionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/modifier/InhibitionTest.java
index b33292c49c..c02610ebf6 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/modifier/InhibitionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/modifier/InhibitionTest.java
@@ -1,85 +1,85 @@
-package lcsb.mapviewer.model.map.modifier;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-
-public class InhibitionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new Inhibition());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Inhibition modifier = new Inhibition(new GenericProtein("unk_id"));
- assertNotNull(modifier);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor2() {
- try {
- Inhibition modifier = new Inhibition(new GenericProtein("unk_id"));
- modifier.setLine(new PolylineData());
- Inhibition modifier2 = new Inhibition(modifier);
- assertNotNull(modifier2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- Inhibition modifier = new Inhibition(new GenericProtein("unk_id"));
- modifier.setLine(new PolylineData());
- Inhibition modifier2 = modifier.copy();
- assertNotNull(modifier2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopyInvalid() {
- try {
- Mockito.mock(Inhibition.class, Mockito.CALLS_REAL_METHODS).copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.modifier;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+
+public class InhibitionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new Inhibition());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Inhibition modifier = new Inhibition(new GenericProtein("unk_id"));
+ assertNotNull(modifier);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor2() {
+ try {
+ Inhibition modifier = new Inhibition(new GenericProtein("unk_id"));
+ modifier.setLine(new PolylineData());
+ Inhibition modifier2 = new Inhibition(modifier);
+ assertNotNull(modifier2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ Inhibition modifier = new Inhibition(new GenericProtein("unk_id"));
+ modifier.setLine(new PolylineData());
+ Inhibition modifier2 = modifier.copy();
+ assertNotNull(modifier2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyInvalid() {
+ try {
+ Mockito.mock(Inhibition.class, Mockito.CALLS_REAL_METHODS).copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/modifier/ModulationTest.java b/model/src/test/java/lcsb/mapviewer/model/map/modifier/ModulationTest.java
index 626ae7b4a6..22341eec88 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/modifier/ModulationTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/modifier/ModulationTest.java
@@ -1,85 +1,85 @@
-package lcsb.mapviewer.model.map.modifier;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-
-public class ModulationTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new Modulation());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Modulation modifier = new Modulation(new GenericProtein("unk_id"));
- assertNotNull(modifier);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor2() {
- try {
- Modulation modifier = new Modulation(new GenericProtein("unk_id"));
- modifier.setLine(new PolylineData());
- Modulation modifier2 = new Modulation(modifier);
- assertNotNull(modifier2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopyInvalid() {
- try {
- Mockito.mock(Modulation.class, Mockito.CALLS_REAL_METHODS).copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- Modulation modifier = new Modulation(new GenericProtein("unk_id"));
- modifier.setLine(new PolylineData());
- Modulation modifier2 = modifier.copy();
- assertNotNull(modifier2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.modifier;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+
+public class ModulationTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new Modulation());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Modulation modifier = new Modulation(new GenericProtein("unk_id"));
+ assertNotNull(modifier);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor2() {
+ try {
+ Modulation modifier = new Modulation(new GenericProtein("unk_id"));
+ modifier.setLine(new PolylineData());
+ Modulation modifier2 = new Modulation(modifier);
+ assertNotNull(modifier2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyInvalid() {
+ try {
+ Mockito.mock(Modulation.class, Mockito.CALLS_REAL_METHODS).copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ Modulation modifier = new Modulation(new GenericProtein("unk_id"));
+ modifier.setLine(new PolylineData());
+ Modulation modifier2 = modifier.copy();
+ assertNotNull(modifier2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/modifier/PhysicalStimulationTest.java b/model/src/test/java/lcsb/mapviewer/model/map/modifier/PhysicalStimulationTest.java
index 29821f55d0..29ae6503fa 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/modifier/PhysicalStimulationTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/modifier/PhysicalStimulationTest.java
@@ -1,85 +1,85 @@
-package lcsb.mapviewer.model.map.modifier;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-
-public class PhysicalStimulationTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new PhysicalStimulation());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- PhysicalStimulation modifier = new PhysicalStimulation(new GenericProtein("unk_id"));
- assertNotNull(modifier);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor2() {
- try {
- PhysicalStimulation modifier = new PhysicalStimulation(new GenericProtein("unk_id"));
- modifier.setLine(new PolylineData());
- PhysicalStimulation modifier2 = new PhysicalStimulation(modifier);
- assertNotNull(modifier2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopyInvalid() {
- try {
- Mockito.mock(PhysicalStimulation.class, Mockito.CALLS_REAL_METHODS).copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- PhysicalStimulation modifier = new PhysicalStimulation(new GenericProtein("unk_id"));
- modifier.setLine(new PolylineData());
- PhysicalStimulation modifier2 = modifier.copy();
- assertNotNull(modifier2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.modifier;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+
+public class PhysicalStimulationTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new PhysicalStimulation());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ PhysicalStimulation modifier = new PhysicalStimulation(new GenericProtein("unk_id"));
+ assertNotNull(modifier);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor2() {
+ try {
+ PhysicalStimulation modifier = new PhysicalStimulation(new GenericProtein("unk_id"));
+ modifier.setLine(new PolylineData());
+ PhysicalStimulation modifier2 = new PhysicalStimulation(modifier);
+ assertNotNull(modifier2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyInvalid() {
+ try {
+ Mockito.mock(PhysicalStimulation.class, Mockito.CALLS_REAL_METHODS).copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ PhysicalStimulation modifier = new PhysicalStimulation(new GenericProtein("unk_id"));
+ modifier.setLine(new PolylineData());
+ PhysicalStimulation modifier2 = modifier.copy();
+ assertNotNull(modifier2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/modifier/TriggerTest.java b/model/src/test/java/lcsb/mapviewer/model/map/modifier/TriggerTest.java
index d6b71b5fda..48e1a908df 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/modifier/TriggerTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/modifier/TriggerTest.java
@@ -1,85 +1,85 @@
-package lcsb.mapviewer.model.map.modifier;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-
-public class TriggerTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new Trigger());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Trigger modifier = new Trigger(new GenericProtein("unk_id"));
- assertNotNull(modifier);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor2() {
- try {
- Trigger modifier = new Trigger(new GenericProtein("unk_id"));
- modifier.setLine(new PolylineData());
- Trigger modifier2 = new Trigger(modifier);
- assertNotNull(modifier2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- Trigger modifier = new Trigger(new GenericProtein("unk_id"));
- modifier.setLine(new PolylineData());
- Trigger modifier2 = modifier.copy();
- assertNotNull(modifier2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopyInvalid() {
- try {
- Mockito.mock(Trigger.class, Mockito.CALLS_REAL_METHODS).copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.modifier;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+
+public class TriggerTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new Trigger());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Trigger modifier = new Trigger(new GenericProtein("unk_id"));
+ assertNotNull(modifier);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor2() {
+ try {
+ Trigger modifier = new Trigger(new GenericProtein("unk_id"));
+ modifier.setLine(new PolylineData());
+ Trigger modifier2 = new Trigger(modifier);
+ assertNotNull(modifier2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ Trigger modifier = new Trigger(new GenericProtein("unk_id"));
+ modifier.setLine(new PolylineData());
+ Trigger modifier2 = modifier.copy();
+ assertNotNull(modifier2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyInvalid() {
+ try {
+ Mockito.mock(Trigger.class, Mockito.CALLS_REAL_METHODS).copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/modifier/UnknownCatalysisTest.java b/model/src/test/java/lcsb/mapviewer/model/map/modifier/UnknownCatalysisTest.java
index 31c679e2bf..9d66e7e47b 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/modifier/UnknownCatalysisTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/modifier/UnknownCatalysisTest.java
@@ -1,85 +1,85 @@
-package lcsb.mapviewer.model.map.modifier;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-
-public class UnknownCatalysisTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new UnknownCatalysis());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- UnknownCatalysis modifier = new UnknownCatalysis(new GenericProtein("unk_id"));
- assertNotNull(modifier);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor2() {
- try {
- UnknownCatalysis modifier = new UnknownCatalysis(new GenericProtein("unk_id"));
- modifier.setLine(new PolylineData());
- UnknownCatalysis modifier2 = new UnknownCatalysis(modifier);
- assertNotNull(modifier2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- UnknownCatalysis modifier = new UnknownCatalysis(new GenericProtein("unk_id"));
- modifier.setLine(new PolylineData());
- UnknownCatalysis modifier2 = modifier.copy();
- assertNotNull(modifier2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopyInvalid() {
- try {
- Mockito.mock(UnknownCatalysis.class, Mockito.CALLS_REAL_METHODS).copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.modifier;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+
+public class UnknownCatalysisTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new UnknownCatalysis());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ UnknownCatalysis modifier = new UnknownCatalysis(new GenericProtein("unk_id"));
+ assertNotNull(modifier);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor2() {
+ try {
+ UnknownCatalysis modifier = new UnknownCatalysis(new GenericProtein("unk_id"));
+ modifier.setLine(new PolylineData());
+ UnknownCatalysis modifier2 = new UnknownCatalysis(modifier);
+ assertNotNull(modifier2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ UnknownCatalysis modifier = new UnknownCatalysis(new GenericProtein("unk_id"));
+ modifier.setLine(new PolylineData());
+ UnknownCatalysis modifier2 = modifier.copy();
+ assertNotNull(modifier2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyInvalid() {
+ try {
+ Mockito.mock(UnknownCatalysis.class, Mockito.CALLS_REAL_METHODS).copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/modifier/UnknownInhibitionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/modifier/UnknownInhibitionTest.java
index 33de793ebd..dab8c5099f 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/modifier/UnknownInhibitionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/modifier/UnknownInhibitionTest.java
@@ -1,85 +1,85 @@
-package lcsb.mapviewer.model.map.modifier;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-
-public class UnknownInhibitionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new UnknownInhibition());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- UnknownInhibition modifier = new UnknownInhibition(new GenericProtein("unk_id"));
- assertNotNull(modifier);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor2() {
- try {
- UnknownInhibition modifier = new UnknownInhibition(new GenericProtein("unk_id"));
- modifier.setLine(new PolylineData());
- UnknownInhibition modifier2 = new UnknownInhibition(modifier);
- assertNotNull(modifier2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- UnknownInhibition modifier = new UnknownInhibition(new GenericProtein("unk_id"));
- modifier.setLine(new PolylineData());
- UnknownInhibition modifier2 = modifier.copy();
- assertNotNull(modifier2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopyInvalid() {
- try {
- Mockito.mock(UnknownInhibition.class, Mockito.CALLS_REAL_METHODS).copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.modifier;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+
+public class UnknownInhibitionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new UnknownInhibition());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ UnknownInhibition modifier = new UnknownInhibition(new GenericProtein("unk_id"));
+ assertNotNull(modifier);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor2() {
+ try {
+ UnknownInhibition modifier = new UnknownInhibition(new GenericProtein("unk_id"));
+ modifier.setLine(new PolylineData());
+ UnknownInhibition modifier2 = new UnknownInhibition(modifier);
+ assertNotNull(modifier2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ UnknownInhibition modifier = new UnknownInhibition(new GenericProtein("unk_id"));
+ modifier.setLine(new PolylineData());
+ UnknownInhibition modifier2 = modifier.copy();
+ assertNotNull(modifier2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyInvalid() {
+ try {
+ Mockito.mock(UnknownInhibition.class, Mockito.CALLS_REAL_METHODS).copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/AbstractNodeComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/AbstractNodeComparatorTest.java
index d8e2ed5174..917b58d35d 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/AbstractNodeComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/AbstractNodeComparatorTest.java
@@ -1,52 +1,52 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class AbstractNodeComparatorTest {
-
- AbstractNodeComparator comparator = new AbstractNodeComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test(expected = NotImplementedException.class)
- public void testCompareException() {
- comparator.compare(Mockito.mock(AbstractNode.class, Mockito.CALLS_REAL_METHODS),
- Mockito.mock(AbstractNode.class, Mockito.CALLS_REAL_METHODS));
- }
-
- @Test
- public void testCompareOk() {
- try {
- assertEquals(0, comparator.compare(new AndOperator(), new AndOperator()));
- assertEquals(0, comparator.compare(null, null));
- } catch (Exception e) {
- e.printStackTrace();
- }
- }
-
- @Test
- public void testDifferent() {
- try {
- assertTrue(comparator.compare(new AndOperator(), null) != 0);
- assertTrue(comparator.compare(null, new AndOperator()) != 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class AbstractNodeComparatorTest {
+
+ AbstractNodeComparator comparator = new AbstractNodeComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test(expected = NotImplementedException.class)
+ public void testCompareException() {
+ comparator.compare(Mockito.mock(AbstractNode.class, Mockito.CALLS_REAL_METHODS),
+ Mockito.mock(AbstractNode.class, Mockito.CALLS_REAL_METHODS));
+ }
+
+ @Test
+ public void testCompareOk() {
+ try {
+ assertEquals(0, comparator.compare(new AndOperator(), new AndOperator()));
+ assertEquals(0, comparator.compare(null, null));
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ assertTrue(comparator.compare(new AndOperator(), null) != 0);
+ assertTrue(comparator.compare(null, new AndOperator()) != 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/AllReactionTests.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/AllReactionTests.java
index adb267fb6b..99a848941d 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/AllReactionTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/AllReactionTests.java
@@ -1,31 +1,31 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import lcsb.mapviewer.model.map.reaction.type.AllReactionTypeTests;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AbstractNodeComparatorTest.class, //
- AllReactionTypeTests.class,//
- AndOperatorTest.class, //
- AssociationOperatorTest.class, //
- DissociationOperatorTest.class, //
- ModifierTest.class,//
- NandOperatorTest.class, //
- NodeOperatorComparatorTest.class, //
- NodeOperatorTest.class, //
- OrOperatorTest.class, //
- ProductTest.class, //
- ReactantTest.class,//
- ReactionComparatorTest.class, //
- ReactionNodeComparatorTest.class, //
- ReactionTest.class, //
- SplitOperatorTest.class,//
- TruncationOperatorTest.class, //
- UnknownOperatorTest.class,//
-})
-public class AllReactionTests {
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import lcsb.mapviewer.model.map.reaction.type.AllReactionTypeTests;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AbstractNodeComparatorTest.class, //
+ AllReactionTypeTests.class,//
+ AndOperatorTest.class, //
+ AssociationOperatorTest.class, //
+ DissociationOperatorTest.class, //
+ ModifierTest.class,//
+ NandOperatorTest.class, //
+ NodeOperatorComparatorTest.class, //
+ NodeOperatorTest.class, //
+ OrOperatorTest.class, //
+ ProductTest.class, //
+ ReactantTest.class,//
+ ReactionComparatorTest.class, //
+ ReactionNodeComparatorTest.class, //
+ ReactionTest.class, //
+ SplitOperatorTest.class,//
+ TruncationOperatorTest.class, //
+ UnknownOperatorTest.class,//
+})
+public class AllReactionTests {
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/AndOperatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/AndOperatorTest.java
index 4afb1e447a..3673aecbf7 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/AndOperatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/AndOperatorTest.java
@@ -1,100 +1,100 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.graphics.PolylineData;
-
-public class AndOperatorTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new AndOperator());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- AndOperator op = new AndOperator();
- op.setLine(new PolylineData());
- AndOperator operator = new AndOperator(op);
- assertNotNull(operator);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- AndOperator operator = new AndOperator();
- assertFalse("".equals(new AndOperator().getSBGNOperatorText()));
- assertFalse("".equals(operator.getOperatorText()));
-
- NodeOperator nodeOperatorForInput = new AndOperator();
- NodeOperator nodeOperatorForOutput = new AndOperator();
-
- Reaction reaction = new Reaction();
-
- operator.setReaction(reaction);
- operator.setNodeOperatorForInput(nodeOperatorForInput);
- operator.setNodeOperatorForOutput(nodeOperatorForOutput);
-
- assertEquals(reaction, operator.getReaction());
- assertEquals(nodeOperatorForInput, operator.getNodeOperatorForInput());
- assertEquals(nodeOperatorForOutput, operator.getNodeOperatorForOutput());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy1() {
- try {
- AndOperator op = new AndOperator();
- op.setLine(new PolylineData());
- AndOperator operator = op.copy();
- assertNotNull(operator);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy2() {
- try {
- Mockito.mock(AndOperator.class, Mockito.CALLS_REAL_METHODS).copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+
+public class AndOperatorTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new AndOperator());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ AndOperator op = new AndOperator();
+ op.setLine(new PolylineData());
+ AndOperator operator = new AndOperator(op);
+ assertNotNull(operator);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ AndOperator operator = new AndOperator();
+ assertFalse("".equals(new AndOperator().getSBGNOperatorText()));
+ assertFalse("".equals(operator.getOperatorText()));
+
+ NodeOperator nodeOperatorForInput = new AndOperator();
+ NodeOperator nodeOperatorForOutput = new AndOperator();
+
+ Reaction reaction = new Reaction();
+
+ operator.setReaction(reaction);
+ operator.setNodeOperatorForInput(nodeOperatorForInput);
+ operator.setNodeOperatorForOutput(nodeOperatorForOutput);
+
+ assertEquals(reaction, operator.getReaction());
+ assertEquals(nodeOperatorForInput, operator.getNodeOperatorForInput());
+ assertEquals(nodeOperatorForOutput, operator.getNodeOperatorForOutput());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy1() {
+ try {
+ AndOperator op = new AndOperator();
+ op.setLine(new PolylineData());
+ AndOperator operator = op.copy();
+ assertNotNull(operator);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy2() {
+ try {
+ Mockito.mock(AndOperator.class, Mockito.CALLS_REAL_METHODS).copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/AssociationOperatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/AssociationOperatorTest.java
index 2c2fd35775..7e1867e0b2 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/AssociationOperatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/AssociationOperatorTest.java
@@ -1,85 +1,85 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.graphics.PolylineData;
-
-public class AssociationOperatorTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new AssociationOperator());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- AssociationOperator op = new AssociationOperator();
- op.setLine(new PolylineData());
- AssociationOperator operator = new AssociationOperator(op);
- assertNotNull(operator);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- assertFalse("".equals(new AssociationOperator().getSBGNOperatorText()));
- assertFalse("".equals(new AssociationOperator().getOperatorText()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy1() {
- try {
- AssociationOperator op = new AssociationOperator();
- op.setLine(new PolylineData());
- AssociationOperator operator = op.copy();
- assertNotNull(operator);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy2() {
- try {
- Mockito.mock(AssociationOperator.class, Mockito.CALLS_REAL_METHODS).copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+
+public class AssociationOperatorTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new AssociationOperator());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ AssociationOperator op = new AssociationOperator();
+ op.setLine(new PolylineData());
+ AssociationOperator operator = new AssociationOperator(op);
+ assertNotNull(operator);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ assertFalse("".equals(new AssociationOperator().getSBGNOperatorText()));
+ assertFalse("".equals(new AssociationOperator().getOperatorText()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy1() {
+ try {
+ AssociationOperator op = new AssociationOperator();
+ op.setLine(new PolylineData());
+ AssociationOperator operator = op.copy();
+ assertNotNull(operator);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy2() {
+ try {
+ Mockito.mock(AssociationOperator.class, Mockito.CALLS_REAL_METHODS).copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/DissociationOperatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/DissociationOperatorTest.java
index b548feb6dd..32e7603167 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/DissociationOperatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/DissociationOperatorTest.java
@@ -1,85 +1,85 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.graphics.PolylineData;
-
-public class DissociationOperatorTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new DissociationOperator());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- DissociationOperator op = new DissociationOperator();
- op.setLine(new PolylineData());
- DissociationOperator operator = new DissociationOperator(op);
- assertNotNull(operator);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- assertFalse("".equals(new DissociationOperator().getSBGNOperatorText()));
- assertFalse("".equals(new DissociationOperator().getOperatorText()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy1() {
- try {
- DissociationOperator op = new DissociationOperator();
- op.setLine(new PolylineData());
- DissociationOperator operator = op.copy();
- assertNotNull(operator);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy2() {
- try {
- Mockito.mock(DissociationOperator.class, Mockito.CALLS_REAL_METHODS).copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+
+public class DissociationOperatorTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new DissociationOperator());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ DissociationOperator op = new DissociationOperator();
+ op.setLine(new PolylineData());
+ DissociationOperator operator = new DissociationOperator(op);
+ assertNotNull(operator);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ assertFalse("".equals(new DissociationOperator().getSBGNOperatorText()));
+ assertFalse("".equals(new DissociationOperator().getOperatorText()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy1() {
+ try {
+ DissociationOperator op = new DissociationOperator();
+ op.setLine(new PolylineData());
+ DissociationOperator operator = op.copy();
+ assertNotNull(operator);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy2() {
+ try {
+ Mockito.mock(DissociationOperator.class, Mockito.CALLS_REAL_METHODS).copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ModifierTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ModifierTest.java
index bf8bfdeb93..d99344c118 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ModifierTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ModifierTest.java
@@ -1,73 +1,73 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.graphics.PolylineData;
-
-public class ModifierTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new Modifier());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Modifier original = new Modifier();
- original.setLine(new PolylineData());
- Modifier modifier = new Modifier(original);
- assertNotNull(modifier);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- Modifier original = new Modifier();
- original.setLine(new PolylineData());
- Modifier modifier = original.copy();
- assertNotNull(modifier);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- Mockito.mock(Modifier.class, Mockito.CALLS_REAL_METHODS).copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+
+public class ModifierTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new Modifier());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Modifier original = new Modifier();
+ original.setLine(new PolylineData());
+ Modifier modifier = new Modifier(original);
+ assertNotNull(modifier);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ Modifier original = new Modifier();
+ original.setLine(new PolylineData());
+ Modifier modifier = original.copy();
+ assertNotNull(modifier);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ Mockito.mock(Modifier.class, Mockito.CALLS_REAL_METHODS).copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/NandOperatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/NandOperatorTest.java
index 091ee853ba..943434f3a0 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/NandOperatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/NandOperatorTest.java
@@ -1,85 +1,85 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.graphics.PolylineData;
-
-public class NandOperatorTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new NandOperator());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- NandOperator op = new NandOperator();
- op.setLine(new PolylineData());
- NandOperator operator = new NandOperator(op);
- assertNotNull(operator);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- assertFalse("".equals(new NandOperator().getSBGNOperatorText()));
- assertFalse("".equals(new NandOperator().getOperatorText()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy1() {
- try {
- NandOperator op = new NandOperator();
- op.setLine(new PolylineData());
- NandOperator operator = op.copy();
- assertNotNull(operator);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy2() {
- try {
- Mockito.mock(NandOperator.class, Mockito.CALLS_REAL_METHODS).copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+
+public class NandOperatorTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new NandOperator());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ NandOperator op = new NandOperator();
+ op.setLine(new PolylineData());
+ NandOperator operator = new NandOperator(op);
+ assertNotNull(operator);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ assertFalse("".equals(new NandOperator().getSBGNOperatorText()));
+ assertFalse("".equals(new NandOperator().getOperatorText()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy1() {
+ try {
+ NandOperator op = new NandOperator();
+ op.setLine(new PolylineData());
+ NandOperator operator = op.copy();
+ assertNotNull(operator);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy2() {
+ try {
+ Mockito.mock(NandOperator.class, Mockito.CALLS_REAL_METHODS).copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/NodeOperatorComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/NodeOperatorComparatorTest.java
index e7e4afecb4..df23bf8087 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/NodeOperatorComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/NodeOperatorComparatorTest.java
@@ -1,156 +1,156 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.geom.Point2D;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class NodeOperatorComparatorTest {
-
- NodeOperatorComparator comparator = new NodeOperatorComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- assertEquals(0, comparator.compare(new AndOperator(), new AndOperator()));
-
- NodeOperator operator1 = createNodeOperator();
- NodeOperator operator2 = createNodeOperator();
-
- assertEquals(0, comparator.compare(operator1, operator2));
-
- assertEquals(0, comparator.compare(operator1, operator1));
-
- assertEquals(0, comparator.compare(null, null));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferentElement() {
- NodeOperator operator1 = createNodeOperator();
- NodeOperator operator2 = createNodeOperator();
-
- Reactant reactant = (Reactant) operator1.getInputs().get(0);
- reactant.setElement(new GenericProtein("id666"));
- assertTrue(comparator.compare(operator1, operator2) != 0);
- assertTrue(comparator.compare(operator2, operator1) != 0);
- }
-
- @Test
- public void testDifferent() {
- try {
- NodeOperator operator1 = createNodeOperator();
- NodeOperator operator2 = createNodeOperator();
-
- operator1.getLine().addPoint(new Point2D.Double(1, 1));
- assertTrue(comparator.compare(operator1, operator2) != 0);
- assertTrue(comparator.compare(operator2, operator1) != 0);
-
- operator1 = createNodeOperator();
- operator2 = createNodeOperator();
-
- operator1.addInput(new Reactant());
- assertTrue(comparator.compare(operator1, operator2) != 0);
- assertTrue(comparator.compare(operator2, operator1) != 0);
-
- operator1 = createNodeOperator();
- operator2 = createNodeOperator();
-
- operator1.addOutput(new Product());
- assertTrue(comparator.compare(operator1, operator2) != 0);
- assertTrue(comparator.compare(operator2, operator1) != 0);
-
- operator1 = createNodeOperator();
- operator2 = createNodeOperator();
-
- Product product = (Product) operator1.getOutputs().get(0);
- product.setElement(new GenericProtein("id666"));
- assertTrue(comparator.compare(operator1, operator2) != 0);
- assertTrue(comparator.compare(operator2, operator1) != 0);
-
- operator1 = createNodeOperator();
- operator2 = createNodeOperator();
-
- Reactant reactant = (Reactant) operator1.getInputs().get(0);
- reactant.getElement().setName("bla");
- assertTrue(comparator.compare(operator1, operator2) != 0);
- assertTrue(comparator.compare(operator2, operator1) != 0);
-
- assertTrue(comparator.compare(null, operator1) != 0);
- assertTrue(comparator.compare(operator2, null) != 0);
-
- assertTrue(comparator.compare(operator2, new OrOperator()) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private NodeOperator createNodeOperator() {
- AndOperator result = new AndOperator();
-
- Species protein0 = new GenericProtein("id0");
- protein0.setName("protein a");
- protein0.setX(12.0);
- protein0.setY(1.0);
- protein0.setWidth(2.0);
- protein0.setHeight(3.0);
-
- Product product = new Product(protein0);
-
- result.addOutput(product);
-
- Species protein1 = new GenericProtein("id1");
- protein1.setName("protein b");
- protein1.setX(120.0);
- protein1.setY(10.0);
- protein1.setWidth(20.0);
- protein1.setHeight(30.0);
-
- Reactant reactant = new Reactant(protein1);
-
- result.addInput(reactant);
-
- Species protein2 = new Gene("id2");
- protein2.setName("gene b");
- protein2.setX(320.0);
- protein2.setY(30.0);
- protein2.setWidth(30.0);
- protein2.setHeight(40.0);
-
- Modifier modifier = new Modifier(protein2);
-
- result.addInput(modifier);
-
- PolylineData pd = new PolylineData();
- pd.addPoint(new Point2D.Double(1, 2));
- pd.addPoint(new Point2D.Double(1, 22));
- pd.addPoint(new Point2D.Double(10, 22));
- result.setLine(pd);
-
- return result;
- }
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.awt.geom.Point2D;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class NodeOperatorComparatorTest {
+
+ NodeOperatorComparator comparator = new NodeOperatorComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ assertEquals(0, comparator.compare(new AndOperator(), new AndOperator()));
+
+ NodeOperator operator1 = createNodeOperator();
+ NodeOperator operator2 = createNodeOperator();
+
+ assertEquals(0, comparator.compare(operator1, operator2));
+
+ assertEquals(0, comparator.compare(operator1, operator1));
+
+ assertEquals(0, comparator.compare(null, null));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferentElement() {
+ NodeOperator operator1 = createNodeOperator();
+ NodeOperator operator2 = createNodeOperator();
+
+ Reactant reactant = (Reactant) operator1.getInputs().get(0);
+ reactant.setElement(new GenericProtein("id666"));
+ assertTrue(comparator.compare(operator1, operator2) != 0);
+ assertTrue(comparator.compare(operator2, operator1) != 0);
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ NodeOperator operator1 = createNodeOperator();
+ NodeOperator operator2 = createNodeOperator();
+
+ operator1.getLine().addPoint(new Point2D.Double(1, 1));
+ assertTrue(comparator.compare(operator1, operator2) != 0);
+ assertTrue(comparator.compare(operator2, operator1) != 0);
+
+ operator1 = createNodeOperator();
+ operator2 = createNodeOperator();
+
+ operator1.addInput(new Reactant());
+ assertTrue(comparator.compare(operator1, operator2) != 0);
+ assertTrue(comparator.compare(operator2, operator1) != 0);
+
+ operator1 = createNodeOperator();
+ operator2 = createNodeOperator();
+
+ operator1.addOutput(new Product());
+ assertTrue(comparator.compare(operator1, operator2) != 0);
+ assertTrue(comparator.compare(operator2, operator1) != 0);
+
+ operator1 = createNodeOperator();
+ operator2 = createNodeOperator();
+
+ Product product = (Product) operator1.getOutputs().get(0);
+ product.setElement(new GenericProtein("id666"));
+ assertTrue(comparator.compare(operator1, operator2) != 0);
+ assertTrue(comparator.compare(operator2, operator1) != 0);
+
+ operator1 = createNodeOperator();
+ operator2 = createNodeOperator();
+
+ Reactant reactant = (Reactant) operator1.getInputs().get(0);
+ reactant.getElement().setName("bla");
+ assertTrue(comparator.compare(operator1, operator2) != 0);
+ assertTrue(comparator.compare(operator2, operator1) != 0);
+
+ assertTrue(comparator.compare(null, operator1) != 0);
+ assertTrue(comparator.compare(operator2, null) != 0);
+
+ assertTrue(comparator.compare(operator2, new OrOperator()) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private NodeOperator createNodeOperator() {
+ AndOperator result = new AndOperator();
+
+ Species protein0 = new GenericProtein("id0");
+ protein0.setName("protein a");
+ protein0.setX(12.0);
+ protein0.setY(1.0);
+ protein0.setWidth(2.0);
+ protein0.setHeight(3.0);
+
+ Product product = new Product(protein0);
+
+ result.addOutput(product);
+
+ Species protein1 = new GenericProtein("id1");
+ protein1.setName("protein b");
+ protein1.setX(120.0);
+ protein1.setY(10.0);
+ protein1.setWidth(20.0);
+ protein1.setHeight(30.0);
+
+ Reactant reactant = new Reactant(protein1);
+
+ result.addInput(reactant);
+
+ Species protein2 = new Gene("id2");
+ protein2.setName("gene b");
+ protein2.setX(320.0);
+ protein2.setY(30.0);
+ protein2.setWidth(30.0);
+ protein2.setHeight(40.0);
+
+ Modifier modifier = new Modifier(protein2);
+
+ result.addInput(modifier);
+
+ PolylineData pd = new PolylineData();
+ pd.addPoint(new Point2D.Double(1, 2));
+ pd.addPoint(new Point2D.Double(1, 22));
+ pd.addPoint(new Point2D.Double(10, 22));
+ result.setLine(pd);
+
+ return result;
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/NodeOperatorMock.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/NodeOperatorMock.java
index 39f4a8ded9..73a6e2ee50 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/NodeOperatorMock.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/NodeOperatorMock.java
@@ -1,30 +1,30 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class NodeOperatorMock extends NodeOperator {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- public NodeOperatorMock(NodeOperator operator) {
- super(operator);
- }
-
- public NodeOperatorMock() {
- super();
- }
-
- @Override
- public String getOperatorText() {
- return "mock string";
- }
-
- @Override
- public AbstractNode copy() {
- throw new NotImplementedException();
- }
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class NodeOperatorMock extends NodeOperator {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ public NodeOperatorMock(NodeOperator operator) {
+ super(operator);
+ }
+
+ public NodeOperatorMock() {
+ super();
+ }
+
+ @Override
+ public String getOperatorText() {
+ return "mock string";
+ }
+
+ @Override
+ public AbstractNode copy() {
+ throw new NotImplementedException();
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/NodeOperatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/NodeOperatorTest.java
index 5cb9896c1a..de27fe0cce 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/NodeOperatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/NodeOperatorTest.java
@@ -1,210 +1,210 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.graphics.PolylineData;
-
-public class NodeOperatorTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testConstructor() {
- try {
- NodeOperator operator = new NodeOperatorMock();
- NodeOperator operator2 = new NodeOperatorMock();
- NodeOperator operator3 = new NodeOperatorMock();
- operator.addInput(operator2);
- operator.addOutput(operator3);
- operator.setLine(new PolylineData());
-
- NodeOperator result = new NodeOperatorMock(operator);
- assertEquals(1, result.getInputs().size());
- assertEquals(1, result.getOutputs().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testAddInput() {
- try {
- NodeOperator operator = new NodeOperatorMock();
- NodeOperator operator2 = new NodeOperatorMock();
- operator.addInput(operator2);
- assertEquals(1, operator.getInputs().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testAddInputs() {
- try {
- NodeOperator operator = new NodeOperatorMock();
- NodeOperator operator2 = new NodeOperatorMock();
- List<NodeOperator> list = new ArrayList<>();
- list.add(operator2);
- operator.addInputs(list);
- assertEquals(1, operator.getInputs().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testAddInput2() {
- try {
- NodeOperator operator = new NodeOperatorMock();
- NodeOperator operator2 = new NodeOperatorMock();
- operator.addInput(operator2);
- operator.addInput(operator2);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testIsReactantOperator() {
- try {
- NodeOperator operator = new NodeOperatorMock();
- assertFalse(operator.isReactantOperator());
-
- AndOperator op1 = new AndOperator();
- operator.addInput(op1);
- assertFalse(operator.isReactantOperator());
-
- op1.addInput(new Reactant());
- assertTrue(operator.isReactantOperator());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testAddOutputs() {
- try {
- NodeOperator operator = new NodeOperatorMock();
- NodeOperator operator2 = new NodeOperatorMock();
- List<NodeOperator> list = new ArrayList<>();
- list.add(operator2);
- operator.addOutputs(list);
- assertEquals(1, operator.getOutputs().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testAddOutput2() {
- try {
- NodeOperator operator = new NodeOperatorMock();
- NodeOperator operator2 = new NodeOperatorMock();
- operator.addOutput(operator2);
- operator.addOutput(operator2);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testIsProductOperator() {
- try {
- NodeOperator operator = new NodeOperatorMock();
- assertFalse(operator.isReactantOperator());
-
- AndOperator op1 = new AndOperator();
- operator.addInput(op1);
- assertFalse(operator.isProductOperator());
-
- op1.addInput(new Reactant());
- assertFalse(operator.isProductOperator());
-
- SplitOperator op2 = new SplitOperator();
- operator.addOutput(op2);
- assertFalse(operator.isProductOperator());
-
- op2.addOutput(new Product());
- assertTrue(operator.isProductOperator());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetters() {
- try {
- NodeOperator operator = new NodeOperatorMock();
- assertNotNull(operator.getSBGNOperatorText());
- List<AbstractNode> inputs = new ArrayList<>();
- List<AbstractNode> outputs = new ArrayList<>();
- operator.setInputs(inputs);
- operator.setOutputs(outputs);
- assertEquals(inputs, operator.getInputs());
- assertEquals(outputs, operator.getOutputs());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testIsModifierOperator() {
- try {
- NodeOperator operator = new NodeOperatorMock();
- assertFalse(operator.isReactantOperator());
-
- AndOperator op1 = new AndOperator();
- operator.addInput(op1);
- assertFalse(operator.isModifierOperator());
-
- op1.addInput(new Modifier());
- assertTrue(operator.isModifierOperator());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+
+public class NodeOperatorTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ NodeOperator operator = new NodeOperatorMock();
+ NodeOperator operator2 = new NodeOperatorMock();
+ NodeOperator operator3 = new NodeOperatorMock();
+ operator.addInput(operator2);
+ operator.addOutput(operator3);
+ operator.setLine(new PolylineData());
+
+ NodeOperator result = new NodeOperatorMock(operator);
+ assertEquals(1, result.getInputs().size());
+ assertEquals(1, result.getOutputs().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testAddInput() {
+ try {
+ NodeOperator operator = new NodeOperatorMock();
+ NodeOperator operator2 = new NodeOperatorMock();
+ operator.addInput(operator2);
+ assertEquals(1, operator.getInputs().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testAddInputs() {
+ try {
+ NodeOperator operator = new NodeOperatorMock();
+ NodeOperator operator2 = new NodeOperatorMock();
+ List<NodeOperator> list = new ArrayList<>();
+ list.add(operator2);
+ operator.addInputs(list);
+ assertEquals(1, operator.getInputs().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testAddInput2() {
+ try {
+ NodeOperator operator = new NodeOperatorMock();
+ NodeOperator operator2 = new NodeOperatorMock();
+ operator.addInput(operator2);
+ operator.addInput(operator2);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testIsReactantOperator() {
+ try {
+ NodeOperator operator = new NodeOperatorMock();
+ assertFalse(operator.isReactantOperator());
+
+ AndOperator op1 = new AndOperator();
+ operator.addInput(op1);
+ assertFalse(operator.isReactantOperator());
+
+ op1.addInput(new Reactant());
+ assertTrue(operator.isReactantOperator());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testAddOutputs() {
+ try {
+ NodeOperator operator = new NodeOperatorMock();
+ NodeOperator operator2 = new NodeOperatorMock();
+ List<NodeOperator> list = new ArrayList<>();
+ list.add(operator2);
+ operator.addOutputs(list);
+ assertEquals(1, operator.getOutputs().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testAddOutput2() {
+ try {
+ NodeOperator operator = new NodeOperatorMock();
+ NodeOperator operator2 = new NodeOperatorMock();
+ operator.addOutput(operator2);
+ operator.addOutput(operator2);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testIsProductOperator() {
+ try {
+ NodeOperator operator = new NodeOperatorMock();
+ assertFalse(operator.isReactantOperator());
+
+ AndOperator op1 = new AndOperator();
+ operator.addInput(op1);
+ assertFalse(operator.isProductOperator());
+
+ op1.addInput(new Reactant());
+ assertFalse(operator.isProductOperator());
+
+ SplitOperator op2 = new SplitOperator();
+ operator.addOutput(op2);
+ assertFalse(operator.isProductOperator());
+
+ op2.addOutput(new Product());
+ assertTrue(operator.isProductOperator());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ NodeOperator operator = new NodeOperatorMock();
+ assertNotNull(operator.getSBGNOperatorText());
+ List<AbstractNode> inputs = new ArrayList<>();
+ List<AbstractNode> outputs = new ArrayList<>();
+ operator.setInputs(inputs);
+ operator.setOutputs(outputs);
+ assertEquals(inputs, operator.getInputs());
+ assertEquals(outputs, operator.getOutputs());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testIsModifierOperator() {
+ try {
+ NodeOperator operator = new NodeOperatorMock();
+ assertFalse(operator.isReactantOperator());
+
+ AndOperator op1 = new AndOperator();
+ operator.addInput(op1);
+ assertFalse(operator.isModifierOperator());
+
+ op1.addInput(new Modifier());
+ assertTrue(operator.isModifierOperator());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/OrOperatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/OrOperatorTest.java
index 2b74c38dfe..23a13dcc51 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/OrOperatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/OrOperatorTest.java
@@ -1,85 +1,85 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.graphics.PolylineData;
-
-public class OrOperatorTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new OrOperator());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- OrOperator op = new OrOperator();
- op.setLine(new PolylineData());
- OrOperator operator = new OrOperator(op);
- assertNotNull(operator);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- assertFalse("".equals(new OrOperator().getSBGNOperatorText()));
- assertFalse("".equals(new OrOperator().getOperatorText()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy1() {
- try {
- OrOperator op = new OrOperator();
- op.setLine(new PolylineData());
- OrOperator operator = op.copy();
- assertNotNull(operator);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy2() {
- try {
- Mockito.mock(OrOperator.class, Mockito.CALLS_REAL_METHODS).copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+
+public class OrOperatorTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new OrOperator());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ OrOperator op = new OrOperator();
+ op.setLine(new PolylineData());
+ OrOperator operator = new OrOperator(op);
+ assertNotNull(operator);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ assertFalse("".equals(new OrOperator().getSBGNOperatorText()));
+ assertFalse("".equals(new OrOperator().getOperatorText()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy1() {
+ try {
+ OrOperator op = new OrOperator();
+ op.setLine(new PolylineData());
+ OrOperator operator = op.copy();
+ assertNotNull(operator);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy2() {
+ try {
+ Mockito.mock(OrOperator.class, Mockito.CALLS_REAL_METHODS).copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ProductTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ProductTest.java
index 4f2e47b2e3..900bd6c5b1 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ProductTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ProductTest.java
@@ -1,72 +1,72 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.graphics.PolylineData;
-
-public class ProductTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new Product());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Product original = new Product();
- original.setLine(new PolylineData());
- Product product = new Product(original);
- assertNotNull(product);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- Product original = new Product();
- original.setLine(new PolylineData());
- Product product = original.copy();
- assertNotNull(product);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- Mockito.mock(Product.class, Mockito.CALLS_REAL_METHODS).copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+
+public class ProductTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new Product());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Product original = new Product();
+ original.setLine(new PolylineData());
+ Product product = new Product(original);
+ assertNotNull(product);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ Product original = new Product();
+ original.setLine(new PolylineData());
+ Product product = original.copy();
+ assertNotNull(product);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ Mockito.mock(Product.class, Mockito.CALLS_REAL_METHODS).copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactantTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactantTest.java
index 59c7379efb..0cc12001ac 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactantTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactantTest.java
@@ -1,73 +1,73 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.graphics.PolylineData;
-
-public class ReactantTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new Reactant());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Reactant original = new Reactant();
- original.setLine(new PolylineData());
- Reactant reactant = new Reactant(original);
- assertNotNull(reactant);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- Reactant original = new Reactant();
- original.setLine(new PolylineData());
- Reactant reactant = original.copy();
- assertNotNull(reactant);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- Mockito.mock(Reactant.class, Mockito.CALLS_REAL_METHODS).copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+
+public class ReactantTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new Reactant());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Reactant original = new Reactant();
+ original.setLine(new PolylineData());
+ Reactant reactant = new Reactant(original);
+ assertNotNull(reactant);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ Reactant original = new Reactant();
+ original.setLine(new PolylineData());
+ Reactant reactant = original.copy();
+ assertNotNull(reactant);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ Mockito.mock(Reactant.class, Mockito.CALLS_REAL_METHODS).copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionComparatorTest.java
index 06403a2233..271edc6538 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionComparatorTest.java
@@ -1,298 +1,298 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.geom.Point2D;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
-import lcsb.mapviewer.model.map.modifier.Catalysis;
-import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
-import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.Unknown;
-
-public class ReactionComparatorTest {
-
- ReactionComparator comparator = new ReactionComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- Reaction reaction1 = createReaction();
- Reaction reaction2 = createReaction();
- assertEquals(0, comparator.compare(reaction1, reaction2));
- assertEquals(0, comparator.compare(reaction2, reaction1));
- assertEquals(0, comparator.compare(reaction1, reaction1));
- assertEquals(0, comparator.compare(null, null));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent3() {
- try {
- Reaction reaction1 = createReaction();
- Reaction reaction2 = createReaction();
-
- reaction1.setNotes("a");
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.setIdReaction("a");
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.setSymbol("a");
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.setFormula("a");
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.setSubsystem("a");
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.setGeneProteinReaction("a");
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.setMechanicalConfidenceScore(1);
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.setLowerBound(1.2);
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.setUpperBound(4.3);
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.addSynonym("syn");
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.addNode(new AndOperator());
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent4() {
- try {
- Reaction reaction1 = createReaction();
- Reaction reaction2 = createReaction();
-
- reaction1.addNode(new AndOperator());
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent2() {
- try {
- Reaction reaction1 = createReaction();
- assertTrue(comparator.compare(reaction1, null) != 0);
- assertTrue(comparator.compare(null, reaction1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent() {
- try {
-
- assertTrue(comparator.compare(new TransportReaction(), new StateTransitionReaction()) != 0);
-
- Reaction reaction1 = createReaction();
- Reaction reaction2 = createReaction();
-
- reaction1.setReversible(true);
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.addModifier(new Modifier());
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.getModifiers().get(0).getElement().setElementId("dfshkj");
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.addReactant(new Reactant());
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.getReactants().get(0).getElement().setElementId("dfshkj");
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.addProduct(new Product());
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.getProducts().get(0).getElement().setElementId("dfshkj");
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.getOperators().get(0).getLine().addPoint(new Point2D.Double(2, 2));
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
- reaction1.getMiriamData().add(new MiriamData(MiriamRelationType.BQ_BIOL_ENCODES, MiriamType.UNKNOWN, "c"));
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private Reaction createReaction() {
- Reaction reaction = new Reaction();
- Species protein = new GenericProtein("id1");
- protein.setName("ASD");
- Reactant reactant = new Reactant(protein);
-
- Species protein2 = new GenericProtein("id2");
- protein2.setName("ASD2");
- Reactant reactant2 = new Reactant(protein2);
-
- Species simpleMolecule = new SimpleMolecule("id3");
- simpleMolecule.setName("mol");
- Product product = new Product(simpleMolecule);
-
- Species unknown = new Unknown("id4");
- unknown.setName("unk");
- Modifier modifier = new Catalysis(unknown);
-
- AndOperator operator = new AndOperator();
- operator.setLine(new PolylineData(new Point2D.Double(2, 2), new Point2D.Double(4, 4)));
- operator.addInput(reactant);
- operator.addInput(reactant2);
-
- reaction.addModifier(modifier);
- reaction.addReactant(reactant);
- reaction.addReactant(reactant2);
- reaction.addProduct(product);
- reaction.addNode(operator);
- return reaction;
- }
-
- @Test
- public void testDifferentNewFields() throws Exception {
- try {
- Reaction reaction1 = createReaction();
- Reaction reaction2 = createReaction();
- reaction2.setAbbreviation("ABRR");
-
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferentKinetics() {
- Reaction reaction1 = createReaction();
- Reaction reaction2 = createReaction();
-
- reaction1.setKinetics(new SbmlKinetics());
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
- }
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.awt.geom.Point2D;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
+import lcsb.mapviewer.model.map.modifier.Catalysis;
+import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
+import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.Unknown;
+
+public class ReactionComparatorTest {
+
+ ReactionComparator comparator = new ReactionComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ Reaction reaction1 = createReaction();
+ Reaction reaction2 = createReaction();
+ assertEquals(0, comparator.compare(reaction1, reaction2));
+ assertEquals(0, comparator.compare(reaction2, reaction1));
+ assertEquals(0, comparator.compare(reaction1, reaction1));
+ assertEquals(0, comparator.compare(null, null));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent3() {
+ try {
+ Reaction reaction1 = createReaction();
+ Reaction reaction2 = createReaction();
+
+ reaction1.setNotes("a");
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.setIdReaction("a");
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.setSymbol("a");
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.setFormula("a");
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.setSubsystem("a");
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.setGeneProteinReaction("a");
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.setMechanicalConfidenceScore(1);
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.setLowerBound(1.2);
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.setUpperBound(4.3);
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.addSynonym("syn");
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.addNode(new AndOperator());
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent4() {
+ try {
+ Reaction reaction1 = createReaction();
+ Reaction reaction2 = createReaction();
+
+ reaction1.addNode(new AndOperator());
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent2() {
+ try {
+ Reaction reaction1 = createReaction();
+ assertTrue(comparator.compare(reaction1, null) != 0);
+ assertTrue(comparator.compare(null, reaction1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+
+ assertTrue(comparator.compare(new TransportReaction(), new StateTransitionReaction()) != 0);
+
+ Reaction reaction1 = createReaction();
+ Reaction reaction2 = createReaction();
+
+ reaction1.setReversible(true);
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.addModifier(new Modifier());
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.getModifiers().get(0).getElement().setElementId("dfshkj");
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.addReactant(new Reactant());
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.getReactants().get(0).getElement().setElementId("dfshkj");
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.addProduct(new Product());
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.getProducts().get(0).getElement().setElementId("dfshkj");
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.getOperators().get(0).getLine().addPoint(new Point2D.Double(2, 2));
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction1 = createReaction();
+ reaction2 = createReaction();
+
+ reaction1.getMiriamData().add(new MiriamData(MiriamRelationType.BQ_BIOL_ENCODES, MiriamType.UNKNOWN, "c"));
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Reaction createReaction() {
+ Reaction reaction = new Reaction();
+ Species protein = new GenericProtein("id1");
+ protein.setName("ASD");
+ Reactant reactant = new Reactant(protein);
+
+ Species protein2 = new GenericProtein("id2");
+ protein2.setName("ASD2");
+ Reactant reactant2 = new Reactant(protein2);
+
+ Species simpleMolecule = new SimpleMolecule("id3");
+ simpleMolecule.setName("mol");
+ Product product = new Product(simpleMolecule);
+
+ Species unknown = new Unknown("id4");
+ unknown.setName("unk");
+ Modifier modifier = new Catalysis(unknown);
+
+ AndOperator operator = new AndOperator();
+ operator.setLine(new PolylineData(new Point2D.Double(2, 2), new Point2D.Double(4, 4)));
+ operator.addInput(reactant);
+ operator.addInput(reactant2);
+
+ reaction.addModifier(modifier);
+ reaction.addReactant(reactant);
+ reaction.addReactant(reactant2);
+ reaction.addProduct(product);
+ reaction.addNode(operator);
+ return reaction;
+ }
+
+ @Test
+ public void testDifferentNewFields() throws Exception {
+ try {
+ Reaction reaction1 = createReaction();
+ Reaction reaction2 = createReaction();
+ reaction2.setAbbreviation("ABRR");
+
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferentKinetics() {
+ Reaction reaction1 = createReaction();
+ Reaction reaction2 = createReaction();
+
+ reaction1.setKinetics(new SbmlKinetics());
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionNodeComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionNodeComparatorTest.java
index c15449fd50..2b2f878ba9 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionNodeComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionNodeComparatorTest.java
@@ -1,137 +1,137 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.geom.Point2D;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class ReactionNodeComparatorTest {
-
- ReactionNodeComparator comparator = new ReactionNodeComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- assertEquals(0, comparator.compare(new Modifier(), new Modifier()));
-
- ReactionNode operator1 = createNodeOperator();
- ReactionNode operator2 = createNodeOperator();
-
- assertEquals(0, comparator.compare(operator1, operator2));
-
- assertEquals(0, comparator.compare(operator1, operator1));
-
- assertEquals(0, comparator.compare(null, null));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent() {
- try {
- ReactionNode operator1 = createNodeOperator();
- ReactionNode operator2 = createNodeOperator();
-
- operator1.getLine().addPoint(new Point2D.Double(1, 1));
- assertTrue(comparator.compare(operator1, operator2) != 0);
- assertTrue(comparator.compare(operator2, operator1) != 0);
-
- operator1 = createNodeOperator();
- operator2 = createNodeOperator();
-
- operator1 = new Product();
- assertTrue(comparator.compare(operator1, operator2) != 0);
- assertTrue(comparator.compare(operator2, operator1) != 0);
-
- operator1 = createNodeOperator();
- operator2 = createNodeOperator();
-
- operator1 = new Reactant();
- assertTrue(comparator.compare(operator1, operator2) != 0);
- assertTrue(comparator.compare(operator2, operator1) != 0);
-
- operator1 = createNodeOperator();
- operator2 = createNodeOperator();
-
- operator1.setElement(new GenericProtein("new_id"));
- assertTrue(comparator.compare(operator1, operator2) != 0);
- assertTrue(comparator.compare(operator2, operator1) != 0);
-
- operator1 = createNodeOperator();
- operator2 = createNodeOperator();
-
- operator1.getElement().setName("bla");
- assertTrue(comparator.compare(operator1, operator2) != 0);
- assertTrue(comparator.compare(operator2, operator1) != 0);
-
- assertTrue(comparator.compare(null, operator1) != 0);
- assertTrue(comparator.compare(operator2, null) != 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private ReactionNode createNodeOperator() {
-
- Species species = new Gene("id_1");
- species.setName("gene b");
- species.setX(320.0);
- species.setY(30.0);
- species.setWidth(30.0);
- species.setHeight(40.0);
-
- Modifier modifier = new Modifier(species);
-
- PolylineData pd = new PolylineData();
- pd.addPoint(new Point2D.Double(1, 2));
- pd.addPoint(new Point2D.Double(1, 21));
- pd.addPoint(new Point2D.Double(11, 2));
- modifier.setLine(pd);
-
- return modifier;
- }
-
- @Test
- public void testDifferentStoichiometry() {
- try {
- ReactionNode operator1 = createNodeOperator();
- ReactionNode operator2 = createNodeOperator();
-
- operator1.setStoichiometry(2.0);
-
- assertTrue(0 != comparator.compare(operator1, operator2));
- assertTrue(0 != comparator.compare(operator2, operator1));
-
- operator1.setStoichiometry(3.0);
-
- assertTrue(0 != comparator.compare(operator1, operator2));
- assertTrue(0 != comparator.compare(operator2, operator1));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.awt.geom.Point2D;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class ReactionNodeComparatorTest {
+
+ ReactionNodeComparator comparator = new ReactionNodeComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ assertEquals(0, comparator.compare(new Modifier(), new Modifier()));
+
+ ReactionNode operator1 = createNodeOperator();
+ ReactionNode operator2 = createNodeOperator();
+
+ assertEquals(0, comparator.compare(operator1, operator2));
+
+ assertEquals(0, comparator.compare(operator1, operator1));
+
+ assertEquals(0, comparator.compare(null, null));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ ReactionNode operator1 = createNodeOperator();
+ ReactionNode operator2 = createNodeOperator();
+
+ operator1.getLine().addPoint(new Point2D.Double(1, 1));
+ assertTrue(comparator.compare(operator1, operator2) != 0);
+ assertTrue(comparator.compare(operator2, operator1) != 0);
+
+ operator1 = createNodeOperator();
+ operator2 = createNodeOperator();
+
+ operator1 = new Product();
+ assertTrue(comparator.compare(operator1, operator2) != 0);
+ assertTrue(comparator.compare(operator2, operator1) != 0);
+
+ operator1 = createNodeOperator();
+ operator2 = createNodeOperator();
+
+ operator1 = new Reactant();
+ assertTrue(comparator.compare(operator1, operator2) != 0);
+ assertTrue(comparator.compare(operator2, operator1) != 0);
+
+ operator1 = createNodeOperator();
+ operator2 = createNodeOperator();
+
+ operator1.setElement(new GenericProtein("new_id"));
+ assertTrue(comparator.compare(operator1, operator2) != 0);
+ assertTrue(comparator.compare(operator2, operator1) != 0);
+
+ operator1 = createNodeOperator();
+ operator2 = createNodeOperator();
+
+ operator1.getElement().setName("bla");
+ assertTrue(comparator.compare(operator1, operator2) != 0);
+ assertTrue(comparator.compare(operator2, operator1) != 0);
+
+ assertTrue(comparator.compare(null, operator1) != 0);
+ assertTrue(comparator.compare(operator2, null) != 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private ReactionNode createNodeOperator() {
+
+ Species species = new Gene("id_1");
+ species.setName("gene b");
+ species.setX(320.0);
+ species.setY(30.0);
+ species.setWidth(30.0);
+ species.setHeight(40.0);
+
+ Modifier modifier = new Modifier(species);
+
+ PolylineData pd = new PolylineData();
+ pd.addPoint(new Point2D.Double(1, 2));
+ pd.addPoint(new Point2D.Double(1, 21));
+ pd.addPoint(new Point2D.Double(11, 2));
+ modifier.setLine(pd);
+
+ return modifier;
+ }
+
+ @Test
+ public void testDifferentStoichiometry() {
+ try {
+ ReactionNode operator1 = createNodeOperator();
+ ReactionNode operator2 = createNodeOperator();
+
+ operator1.setStoichiometry(2.0);
+
+ assertTrue(0 != comparator.compare(operator1, operator2));
+ assertTrue(0 != comparator.compare(operator2, operator1));
+
+ operator1.setStoichiometry(3.0);
+
+ assertTrue(0 != comparator.compare(operator1, operator2));
+ assertTrue(0 != comparator.compare(operator2, operator1));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java
index 844daf3a55..54ebb5cff9 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java
@@ -1,428 +1,428 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.ModelTestFunctions;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
-import lcsb.mapviewer.model.map.kinetics.SbmlKineticsComparator;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.modifier.Catalysis;
-import lcsb.mapviewer.model.map.reaction.type.DissociationReaction;
-import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class ReactionTest extends ModelTestFunctions {
-
- Logger logger = Logger.getLogger(ReactantTest.class);
-
- private Species species;
-
- @Before
- public void setUp() throws Exception {
- species = new GenericProtein("sa1");
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testContainsElement() {
- try {
- Reaction reaction = new Reaction();
- assertFalse(reaction.containsElement(species));
- Modifier modifier = new Catalysis(species);
- reaction.addModifier(modifier);
- assertTrue(reaction.containsElement(species));
- assertFalse(reaction.containsElement(new GenericProtein("id")));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testComparator() {
- try {
- Reaction reaction1 = new Reaction();
- reaction1.setIdReaction("2");
- Reaction reaction2 = new Reaction();
- reaction2.setIdReaction("1");
- Reaction reaction3 = new Reaction();
- reaction3.setIdReaction("3");
- List<Reaction> reactions = new ArrayList<>();
- reactions.add(reaction1);
- reactions.add(reaction2);
- reactions.add(reaction3);
- Collections.sort(reactions, Reaction.ID_COMPARATOR);
- assertEquals(reaction2, reactions.get(0));
- assertEquals(reaction1, reactions.get(1));
- assertEquals(reaction3, reactions.get(2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Reaction reaction1 = new Reaction();
- reaction1.addMiriamData(new MiriamData());
- reaction1.addSynonym("s");
- Reaction reaction2 = new Reaction(reaction1);
-
- assertEquals(1, reaction2.getMiriamData().size());
- assertEquals(1, reaction2.getSynonyms().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetDistanceFromPoint() {
- try {
- Reaction reaction1 = new Reaction();
- Reactant reactant = new Reactant();
- PolylineData line = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(2.0, 0.0));
- reactant.setLine(line);
- reaction1.addReactant(reactant);
-
- assertEquals(0.0, reaction1.getDistanceFromPoint(new Point2D.Double(0.0, 0.0)), Configuration.EPSILON);
- assertEquals(0.0, reaction1.getDistanceFromPoint(new Point2D.Double(1.0, 0.0)), Configuration.EPSILON);
- assertEquals(1.0, reaction1.getDistanceFromPoint(new Point2D.Double(1.0, 1.0)), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetClosestPointTo() {
- try {
- Reaction reaction1 = new Reaction();
- Reactant reactant = new Reactant();
- PolylineData line = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(2.0, 0.0));
- reactant.setLine(line);
- reaction1.addReactant(reactant);
-
- assertEquals(0.0,
- reaction1.getClosestPointTo(new Point2D.Double(0.0, 0.0)).distance(new Point2D.Double(0.0, 0.0)),
- Configuration.EPSILON);
- assertEquals(0.0,
- reaction1.getClosestPointTo(new Point2D.Double(1.0, 0.0)).distance(new Point2D.Double(1.0, 0.0)),
- Configuration.EPSILON);
- assertEquals(0.0,
- reaction1.getClosestPointTo(new Point2D.Double(1.0, 1.0)).distance(new Point2D.Double(1.0, 0.0)),
- Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddMiriam() {
- try {
- Reaction reaction1 = new Reaction();
-
- MiriamData md = new MiriamData(MiriamType.CAS, "1");
- reaction1.addMiriamData(md);
-
- assertEquals(1, reaction1.getMiriamData().size());
-
- reaction1.addMiriamData(md);
- assertEquals(1, reaction1.getMiriamData().size());
- assertEquals(1, getWarnings().size());
-
- List<MiriamData> list = new ArrayList<>();
- list.add(md);
-
- reaction1.addMiriamData(list);
- assertEquals(2, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- Reaction reaction1 = new Reaction();
-
- assertNotNull(reaction1.getStringType());
- assertNull(reaction1.getReactionRect());
-
- int id = 61;
- List<AbstractNode> nodes = new ArrayList<>();
- String notes = "dfp";
-
- ModelData data = new ModelData();
- Model model = new ModelFullIndexed(data);
- String symbol = "sybm";
- String formula = "form";
- Integer mechanicalConfidenceScore = 9908;
- Double lowerBound = 9.2;
- Double upperBound = 9.2;
- String subsystem = "ssyst";
- String geneProteinReaction = "GPR";
- List<String> synonyms = new ArrayList<>();
-
- reaction1.setId(id);
- reaction1.setNodes(nodes);
- reaction1.setNotes(notes);
- reaction1.setModel(model);
- assertEquals(model, reaction1.getModel());
- reaction1.setModelData(data);
- assertEquals(data, reaction1.getModelData());
- reaction1.setSymbol(symbol);
- assertEquals(symbol, reaction1.getSymbol());
- reaction1.setFormula(formula);
- assertEquals(formula, reaction1.getFormula());
- reaction1.setMechanicalConfidenceScore(mechanicalConfidenceScore);
- assertEquals(mechanicalConfidenceScore, reaction1.getMechanicalConfidenceScore());
- reaction1.setLowerBound(lowerBound);
- assertEquals(lowerBound, reaction1.getLowerBound());
- reaction1.setUpperBound(upperBound);
- assertEquals(upperBound, reaction1.getUpperBound());
- reaction1.setSubsystem(subsystem);
- assertEquals(subsystem, reaction1.getSubsystem());
- reaction1.setGeneProteinReaction(geneProteinReaction);
- assertEquals(geneProteinReaction, reaction1.getGeneProteinReaction());
- reaction1.setSynonyms(synonyms);
- assertEquals(synonyms, reaction1.getSynonyms());
-
- assertEquals(id, reaction1.getId());
- assertEquals(nodes, reaction1.getNodes());
- assertEquals(notes, reaction1.getNotes());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testVisibilityLevel() {
- try {
- Reaction reaction1 = new Reaction();
- assertEquals("", reaction1.getVisibilityLevel());
-
- reaction1.setVisibilityLevel(1);
- assertEquals("1", reaction1.getVisibilityLevel());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetCenterLine() {
- try {
- Reaction reaction1 = new Reaction();
-
- Reactant reactant = new Reactant();
- PolylineData line1 = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(0.0, 1.0));
- reactant.setLine(line1);
- reaction1.addReactant(reactant);
-
- Product product = new Product();
- PolylineData line2 = new PolylineData(new Point2D.Double(0.0, 2.0), new Point2D.Double(4.0, 0.0));
- product.setLine(line2);
- reaction1.addProduct(product);
-
- Line2D line = reaction1.getCenterLine();
- assertEquals(4.0, line.getP1().distance(line.getP2()), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetCenterPoint() {
- try {
- Reaction reaction1 = new Reaction();
-
- Reactant reactant = new Reactant();
- PolylineData line1 = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(0.0, 1.0));
- reactant.setLine(line1);
- reaction1.addReactant(reactant);
-
- Product product = new Product();
- PolylineData line2 = new PolylineData(new Point2D.Double(0.0, 2.0), new Point2D.Double(4.0, 0.0));
- product.setLine(line2);
- reaction1.addProduct(product);
-
- assertEquals(0.0, reaction1.getCenterPoint().distance(new Point2D.Double(2.0, 0.0)), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetCenterLine2() {
- try {
- Reaction reaction1 = new HeterodimerAssociationReaction();
-
- Reactant reactant = new Reactant();
- PolylineData line1 = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(0.0, 1.0));
- reactant.setLine(line1);
- reaction1.addReactant(reactant);
-
- Reactant reactant2 = new Reactant();
- PolylineData line3 = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(0.0, 1.0));
- reactant2.setLine(line3);
- reaction1.addReactant(reactant2);
- AndOperator operator = new AndOperator();
- operator.addInput(reactant);
- operator.addInput(reactant2);
- PolylineData line4 = new PolylineData(new Point2D.Double(10.0, 0.0), new Point2D.Double(11.0, 11.0));
- operator.setLine(line4);
- reaction1.addNode(operator);
-
- Product product = new Product();
- PolylineData line2 = new PolylineData(new Point2D.Double(0.0, 2.0), new Point2D.Double(4.0, 0.0));
- product.setLine(line2);
- reaction1.addProduct(product);
-
- Line2D line = reaction1.getCenterLine();
- assertEquals(6.0, line.getP1().distance(line.getP2()), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetCenterLine3() {
- try {
- Reaction reaction1 = new DissociationReaction();
-
- Reactant reactant = new Reactant();
- PolylineData line1 = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(0.0, 1.0));
- reactant.setLine(line1);
- reaction1.addReactant(reactant);
-
- Product product = new Product();
- PolylineData line2 = new PolylineData(new Point2D.Double(0.0, 2.0), new Point2D.Double(4.0, 0.0));
- product.setLine(line2);
- reaction1.addProduct(product);
-
- Product product2 = new Product();
- PolylineData line3 = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(0.0, 1.0));
- product2.setLine(line3);
- reaction1.addProduct(product2);
- SplitOperator operator = new SplitOperator();
- operator.addOutput(product);
- operator.addOutput(product2);
- PolylineData line4 = new PolylineData(new Point2D.Double(10.0, 0.0), new Point2D.Double(11.0, 0.0));
- operator.setLine(line4);
- reaction1.addNode(operator);
-
- Line2D line = reaction1.getCenterLine();
- assertEquals(10.0, line.getP1().distance(line.getP2()), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new Reaction());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRemoveModifier() {
- try {
- Reaction reaction = new Reaction();
- Modifier modifier = new Modifier();
- reaction.addModifier(modifier);
- assertEquals(1, reaction.getModifiers().size());
- reaction.removeModifier(modifier);
- assertEquals(0, reaction.getModifiers().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- Reaction original = new Reaction();
- Reaction copy = original.copy();
- assertNotNull(copy);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopyWithKinetics() {
- try {
- Reaction original = new Reaction();
- original.setKinetics(new SbmlKinetics());
- Reaction copy = original.copy();
- SbmlKineticsComparator kineticsComparator = new SbmlKineticsComparator();
- assertEquals(0, kineticsComparator.compare(original.getKinetics(), copy.getKinetics()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new Reaction() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.ModelTestFunctions;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
+import lcsb.mapviewer.model.map.kinetics.SbmlKineticsComparator;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.modifier.Catalysis;
+import lcsb.mapviewer.model.map.reaction.type.DissociationReaction;
+import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class ReactionTest extends ModelTestFunctions {
+
+ Logger logger = Logger.getLogger(ReactantTest.class);
+
+ private Species species;
+
+ @Before
+ public void setUp() throws Exception {
+ species = new GenericProtein("sa1");
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testContainsElement() {
+ try {
+ Reaction reaction = new Reaction();
+ assertFalse(reaction.containsElement(species));
+ Modifier modifier = new Catalysis(species);
+ reaction.addModifier(modifier);
+ assertTrue(reaction.containsElement(species));
+ assertFalse(reaction.containsElement(new GenericProtein("id")));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testComparator() {
+ try {
+ Reaction reaction1 = new Reaction();
+ reaction1.setIdReaction("2");
+ Reaction reaction2 = new Reaction();
+ reaction2.setIdReaction("1");
+ Reaction reaction3 = new Reaction();
+ reaction3.setIdReaction("3");
+ List<Reaction> reactions = new ArrayList<>();
+ reactions.add(reaction1);
+ reactions.add(reaction2);
+ reactions.add(reaction3);
+ Collections.sort(reactions, Reaction.ID_COMPARATOR);
+ assertEquals(reaction2, reactions.get(0));
+ assertEquals(reaction1, reactions.get(1));
+ assertEquals(reaction3, reactions.get(2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Reaction reaction1 = new Reaction();
+ reaction1.addMiriamData(new MiriamData());
+ reaction1.addSynonym("s");
+ Reaction reaction2 = new Reaction(reaction1);
+
+ assertEquals(1, reaction2.getMiriamData().size());
+ assertEquals(1, reaction2.getSynonyms().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetDistanceFromPoint() {
+ try {
+ Reaction reaction1 = new Reaction();
+ Reactant reactant = new Reactant();
+ PolylineData line = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(2.0, 0.0));
+ reactant.setLine(line);
+ reaction1.addReactant(reactant);
+
+ assertEquals(0.0, reaction1.getDistanceFromPoint(new Point2D.Double(0.0, 0.0)), Configuration.EPSILON);
+ assertEquals(0.0, reaction1.getDistanceFromPoint(new Point2D.Double(1.0, 0.0)), Configuration.EPSILON);
+ assertEquals(1.0, reaction1.getDistanceFromPoint(new Point2D.Double(1.0, 1.0)), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetClosestPointTo() {
+ try {
+ Reaction reaction1 = new Reaction();
+ Reactant reactant = new Reactant();
+ PolylineData line = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(2.0, 0.0));
+ reactant.setLine(line);
+ reaction1.addReactant(reactant);
+
+ assertEquals(0.0,
+ reaction1.getClosestPointTo(new Point2D.Double(0.0, 0.0)).distance(new Point2D.Double(0.0, 0.0)),
+ Configuration.EPSILON);
+ assertEquals(0.0,
+ reaction1.getClosestPointTo(new Point2D.Double(1.0, 0.0)).distance(new Point2D.Double(1.0, 0.0)),
+ Configuration.EPSILON);
+ assertEquals(0.0,
+ reaction1.getClosestPointTo(new Point2D.Double(1.0, 1.0)).distance(new Point2D.Double(1.0, 0.0)),
+ Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddMiriam() {
+ try {
+ Reaction reaction1 = new Reaction();
+
+ MiriamData md = new MiriamData(MiriamType.CAS, "1");
+ reaction1.addMiriamData(md);
+
+ assertEquals(1, reaction1.getMiriamData().size());
+
+ reaction1.addMiriamData(md);
+ assertEquals(1, reaction1.getMiriamData().size());
+ assertEquals(1, getWarnings().size());
+
+ List<MiriamData> list = new ArrayList<>();
+ list.add(md);
+
+ reaction1.addMiriamData(list);
+ assertEquals(2, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ Reaction reaction1 = new Reaction();
+
+ assertNotNull(reaction1.getStringType());
+ assertNull(reaction1.getReactionRect());
+
+ int id = 61;
+ List<AbstractNode> nodes = new ArrayList<>();
+ String notes = "dfp";
+
+ ModelData data = new ModelData();
+ Model model = new ModelFullIndexed(data);
+ String symbol = "sybm";
+ String formula = "form";
+ Integer mechanicalConfidenceScore = 9908;
+ Double lowerBound = 9.2;
+ Double upperBound = 9.2;
+ String subsystem = "ssyst";
+ String geneProteinReaction = "GPR";
+ List<String> synonyms = new ArrayList<>();
+
+ reaction1.setId(id);
+ reaction1.setNodes(nodes);
+ reaction1.setNotes(notes);
+ reaction1.setModel(model);
+ assertEquals(model, reaction1.getModel());
+ reaction1.setModelData(data);
+ assertEquals(data, reaction1.getModelData());
+ reaction1.setSymbol(symbol);
+ assertEquals(symbol, reaction1.getSymbol());
+ reaction1.setFormula(formula);
+ assertEquals(formula, reaction1.getFormula());
+ reaction1.setMechanicalConfidenceScore(mechanicalConfidenceScore);
+ assertEquals(mechanicalConfidenceScore, reaction1.getMechanicalConfidenceScore());
+ reaction1.setLowerBound(lowerBound);
+ assertEquals(lowerBound, reaction1.getLowerBound());
+ reaction1.setUpperBound(upperBound);
+ assertEquals(upperBound, reaction1.getUpperBound());
+ reaction1.setSubsystem(subsystem);
+ assertEquals(subsystem, reaction1.getSubsystem());
+ reaction1.setGeneProteinReaction(geneProteinReaction);
+ assertEquals(geneProteinReaction, reaction1.getGeneProteinReaction());
+ reaction1.setSynonyms(synonyms);
+ assertEquals(synonyms, reaction1.getSynonyms());
+
+ assertEquals(id, reaction1.getId());
+ assertEquals(nodes, reaction1.getNodes());
+ assertEquals(notes, reaction1.getNotes());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testVisibilityLevel() {
+ try {
+ Reaction reaction1 = new Reaction();
+ assertEquals("", reaction1.getVisibilityLevel());
+
+ reaction1.setVisibilityLevel(1);
+ assertEquals("1", reaction1.getVisibilityLevel());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetCenterLine() {
+ try {
+ Reaction reaction1 = new Reaction();
+
+ Reactant reactant = new Reactant();
+ PolylineData line1 = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(0.0, 1.0));
+ reactant.setLine(line1);
+ reaction1.addReactant(reactant);
+
+ Product product = new Product();
+ PolylineData line2 = new PolylineData(new Point2D.Double(0.0, 2.0), new Point2D.Double(4.0, 0.0));
+ product.setLine(line2);
+ reaction1.addProduct(product);
+
+ Line2D line = reaction1.getCenterLine();
+ assertEquals(4.0, line.getP1().distance(line.getP2()), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetCenterPoint() {
+ try {
+ Reaction reaction1 = new Reaction();
+
+ Reactant reactant = new Reactant();
+ PolylineData line1 = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(0.0, 1.0));
+ reactant.setLine(line1);
+ reaction1.addReactant(reactant);
+
+ Product product = new Product();
+ PolylineData line2 = new PolylineData(new Point2D.Double(0.0, 2.0), new Point2D.Double(4.0, 0.0));
+ product.setLine(line2);
+ reaction1.addProduct(product);
+
+ assertEquals(0.0, reaction1.getCenterPoint().distance(new Point2D.Double(2.0, 0.0)), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetCenterLine2() {
+ try {
+ Reaction reaction1 = new HeterodimerAssociationReaction();
+
+ Reactant reactant = new Reactant();
+ PolylineData line1 = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(0.0, 1.0));
+ reactant.setLine(line1);
+ reaction1.addReactant(reactant);
+
+ Reactant reactant2 = new Reactant();
+ PolylineData line3 = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(0.0, 1.0));
+ reactant2.setLine(line3);
+ reaction1.addReactant(reactant2);
+ AndOperator operator = new AndOperator();
+ operator.addInput(reactant);
+ operator.addInput(reactant2);
+ PolylineData line4 = new PolylineData(new Point2D.Double(10.0, 0.0), new Point2D.Double(11.0, 11.0));
+ operator.setLine(line4);
+ reaction1.addNode(operator);
+
+ Product product = new Product();
+ PolylineData line2 = new PolylineData(new Point2D.Double(0.0, 2.0), new Point2D.Double(4.0, 0.0));
+ product.setLine(line2);
+ reaction1.addProduct(product);
+
+ Line2D line = reaction1.getCenterLine();
+ assertEquals(6.0, line.getP1().distance(line.getP2()), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetCenterLine3() {
+ try {
+ Reaction reaction1 = new DissociationReaction();
+
+ Reactant reactant = new Reactant();
+ PolylineData line1 = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(0.0, 1.0));
+ reactant.setLine(line1);
+ reaction1.addReactant(reactant);
+
+ Product product = new Product();
+ PolylineData line2 = new PolylineData(new Point2D.Double(0.0, 2.0), new Point2D.Double(4.0, 0.0));
+ product.setLine(line2);
+ reaction1.addProduct(product);
+
+ Product product2 = new Product();
+ PolylineData line3 = new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(0.0, 1.0));
+ product2.setLine(line3);
+ reaction1.addProduct(product2);
+ SplitOperator operator = new SplitOperator();
+ operator.addOutput(product);
+ operator.addOutput(product2);
+ PolylineData line4 = new PolylineData(new Point2D.Double(10.0, 0.0), new Point2D.Double(11.0, 0.0));
+ operator.setLine(line4);
+ reaction1.addNode(operator);
+
+ Line2D line = reaction1.getCenterLine();
+ assertEquals(10.0, line.getP1().distance(line.getP2()), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new Reaction());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRemoveModifier() {
+ try {
+ Reaction reaction = new Reaction();
+ Modifier modifier = new Modifier();
+ reaction.addModifier(modifier);
+ assertEquals(1, reaction.getModifiers().size());
+ reaction.removeModifier(modifier);
+ assertEquals(0, reaction.getModifiers().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ Reaction original = new Reaction();
+ Reaction copy = original.copy();
+ assertNotNull(copy);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyWithKinetics() {
+ try {
+ Reaction original = new Reaction();
+ original.setKinetics(new SbmlKinetics());
+ Reaction copy = original.copy();
+ SbmlKineticsComparator kineticsComparator = new SbmlKineticsComparator();
+ assertEquals(0, kineticsComparator.compare(original.getKinetics(), copy.getKinetics()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new Reaction() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/SplitOperatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/SplitOperatorTest.java
index 83c1ca3545..63d17b64cf 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/SplitOperatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/SplitOperatorTest.java
@@ -1,84 +1,84 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.graphics.PolylineData;
-
-public class SplitOperatorTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new SplitOperator());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- SplitOperator op = new SplitOperator();
- op.setLine(new PolylineData());
- SplitOperator operator = new SplitOperator(op);
- assertNotNull(operator);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- assertNotNull(new SplitOperator().getSBGNOperatorText());
- assertNotNull(new SplitOperator().getOperatorText());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy1() {
- try {
- SplitOperator op = new SplitOperator();
- op.setLine(new PolylineData());
- SplitOperator operator = op.copy();
- assertNotNull(operator);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy2() {
- try {
- Mockito.mock(SplitOperator.class, Mockito.CALLS_REAL_METHODS).copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+
+public class SplitOperatorTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new SplitOperator());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ SplitOperator op = new SplitOperator();
+ op.setLine(new PolylineData());
+ SplitOperator operator = new SplitOperator(op);
+ assertNotNull(operator);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ assertNotNull(new SplitOperator().getSBGNOperatorText());
+ assertNotNull(new SplitOperator().getOperatorText());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy1() {
+ try {
+ SplitOperator op = new SplitOperator();
+ op.setLine(new PolylineData());
+ SplitOperator operator = op.copy();
+ assertNotNull(operator);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy2() {
+ try {
+ Mockito.mock(SplitOperator.class, Mockito.CALLS_REAL_METHODS).copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/TruncationOperatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/TruncationOperatorTest.java
index 544f27738f..5e30099cc9 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/TruncationOperatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/TruncationOperatorTest.java
@@ -1,84 +1,84 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.graphics.PolylineData;
-
-public class TruncationOperatorTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new TruncationOperator());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- TruncationOperator op = new TruncationOperator();
- op.setLine(new PolylineData());
- TruncationOperator operator = new TruncationOperator(op);
- assertNotNull(operator);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- assertNotNull(new TruncationOperator().getSBGNOperatorText());
- assertNotNull(new TruncationOperator().getOperatorText());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy1() {
- try {
- TruncationOperator op = new TruncationOperator();
- op.setLine(new PolylineData());
- TruncationOperator operator = op.copy();
- assertNotNull(operator);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy2() {
- try {
- Mockito.mock(TruncationOperator.class, Mockito.CALLS_REAL_METHODS).copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+
+public class TruncationOperatorTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new TruncationOperator());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ TruncationOperator op = new TruncationOperator();
+ op.setLine(new PolylineData());
+ TruncationOperator operator = new TruncationOperator(op);
+ assertNotNull(operator);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ assertNotNull(new TruncationOperator().getSBGNOperatorText());
+ assertNotNull(new TruncationOperator().getOperatorText());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy1() {
+ try {
+ TruncationOperator op = new TruncationOperator();
+ op.setLine(new PolylineData());
+ TruncationOperator operator = op.copy();
+ assertNotNull(operator);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy2() {
+ try {
+ Mockito.mock(TruncationOperator.class, Mockito.CALLS_REAL_METHODS).copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/UnknownOperatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/UnknownOperatorTest.java
index 62bf1fdc82..046b15620f 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/UnknownOperatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/UnknownOperatorTest.java
@@ -1,85 +1,85 @@
-package lcsb.mapviewer.model.map.reaction;
-
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.graphics.PolylineData;
-
-public class UnknownOperatorTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new UnknownOperator());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- UnknownOperator op = new UnknownOperator();
- op.setLine(new PolylineData());
- UnknownOperator operator = new UnknownOperator(op);
- assertNotNull(operator);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- assertFalse("".equals(new UnknownOperator().getSBGNOperatorText()));
- assertFalse("".equals(new UnknownOperator().getOperatorText()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy1() {
- try {
- UnknownOperator op = new UnknownOperator();
- op.setLine(new PolylineData());
- UnknownOperator operator = op.copy();
- assertNotNull(operator);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy2() {
- try {
- Mockito.mock(UnknownOperator.class, Mockito.CALLS_REAL_METHODS).copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction;
+
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+
+public class UnknownOperatorTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new UnknownOperator());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ UnknownOperator op = new UnknownOperator();
+ op.setLine(new PolylineData());
+ UnknownOperator operator = new UnknownOperator(op);
+ assertNotNull(operator);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ assertFalse("".equals(new UnknownOperator().getSBGNOperatorText()));
+ assertFalse("".equals(new UnknownOperator().getOperatorText()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy1() {
+ try {
+ UnknownOperator op = new UnknownOperator();
+ op.setLine(new PolylineData());
+ UnknownOperator operator = op.copy();
+ assertNotNull(operator);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy2() {
+ try {
+ Mockito.mock(UnknownOperator.class, Mockito.CALLS_REAL_METHODS).copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/AllReactionTypeTests.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/AllReactionTypeTests.java
index 814c337da8..f0a8d101d1 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/AllReactionTypeTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/AllReactionTypeTests.java
@@ -1,32 +1,32 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ BooleanLogicGateReactionTest.class, //
- DissociationReactionTest.class, //
- HeterodimerAssociationReactionTest.class, //
- KnownTransitionOmittedReactionTest.class, //
- NegativeInfluenceReactionTest.class, //
- PositiveInfluenceReactionTest.class, //
- ReactionRectTest.class, //
- ReducedModulationReactionTest.class, //
- ReducedPhysicalStimulationReactionTest.class, //
- ReducedTriggerReactionTest.class, //
- StateTransitionReactionTest.class, //
- TranscriptionReactionTest.class, //
- TranslationReactionTest.class, //
- TransportReactionTest.class, //
- TruncationReactionTest.class, //
- UnknownNegativeInfluenceReactionTest.class, //
- UnknownPositiveInfluenceReactionTest.class, //
- UnknownReducedModulationReactionTest.class, //
- UnknownReducedPhysicalStimulationReactionTest.class, //
- UnknownReducedTriggerReactionTest.class, //
- UnknownTransitionReactionTest.class, //
-})
-public class AllReactionTypeTests {
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ BooleanLogicGateReactionTest.class, //
+ DissociationReactionTest.class, //
+ HeterodimerAssociationReactionTest.class, //
+ KnownTransitionOmittedReactionTest.class, //
+ NegativeInfluenceReactionTest.class, //
+ PositiveInfluenceReactionTest.class, //
+ ReactionRectTest.class, //
+ ReducedModulationReactionTest.class, //
+ ReducedPhysicalStimulationReactionTest.class, //
+ ReducedTriggerReactionTest.class, //
+ StateTransitionReactionTest.class, //
+ TranscriptionReactionTest.class, //
+ TranslationReactionTest.class, //
+ TransportReactionTest.class, //
+ TruncationReactionTest.class, //
+ UnknownNegativeInfluenceReactionTest.class, //
+ UnknownPositiveInfluenceReactionTest.class, //
+ UnknownReducedModulationReactionTest.class, //
+ UnknownReducedPhysicalStimulationReactionTest.class, //
+ UnknownReducedTriggerReactionTest.class, //
+ UnknownTransitionReactionTest.class, //
+})
+public class AllReactionTypeTests {
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/BooleanLogicGateReactionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/BooleanLogicGateReactionTest.java
index c6294b0d89..faba3e776b 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/BooleanLogicGateReactionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/BooleanLogicGateReactionTest.java
@@ -1,128 +1,128 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-public class BooleanLogicGateReactionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new BooleanLogicGateReaction());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- Reaction reaction = new BooleanLogicGateReaction();
- assertNotNull(reaction.getStringType());
- assertNull(reaction.getReactionRect());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg() {
- try {
- Reaction reaction = new Reaction();
- new BooleanLogicGateReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg2() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- new BooleanLogicGateReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- reaction.addReactant(new Reactant());
- reaction.addReactant(new Reactant());
- BooleanLogicGateReaction validReaction = new BooleanLogicGateReaction(reaction);
- assertNotNull(validReaction);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- BooleanLogicGateReaction original = new BooleanLogicGateReaction();
- original.addProduct(new Product());
- original.addReactant(new Reactant());
- original.addReactant(new Reactant());
- BooleanLogicGateReaction product = original.copy();
- assertNotNull(product);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new BooleanLogicGateReaction() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+public class BooleanLogicGateReactionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new BooleanLogicGateReaction());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ Reaction reaction = new BooleanLogicGateReaction();
+ assertNotNull(reaction.getStringType());
+ assertNull(reaction.getReactionRect());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructorWithInvalidArg() {
+ try {
+ Reaction reaction = new Reaction();
+ new BooleanLogicGateReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructorWithInvalidArg2() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ new BooleanLogicGateReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ reaction.addReactant(new Reactant());
+ reaction.addReactant(new Reactant());
+ BooleanLogicGateReaction validReaction = new BooleanLogicGateReaction(reaction);
+ assertNotNull(validReaction);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ BooleanLogicGateReaction original = new BooleanLogicGateReaction();
+ original.addProduct(new Product());
+ original.addReactant(new Reactant());
+ original.addReactant(new Reactant());
+ BooleanLogicGateReaction product = original.copy();
+ assertNotNull(product);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new BooleanLogicGateReaction() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/DissociationReactionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/DissociationReactionTest.java
index 4dac799b4b..7823cbe2be 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/DissociationReactionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/DissociationReactionTest.java
@@ -1,129 +1,129 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-public class DissociationReactionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new DissociationReaction());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
- @Test
- public void testGetters() {
- try {
- Reaction reaction = new DissociationReaction();
- assertNotNull(reaction.getStringType());
- assertNotNull(reaction.getReactionRect());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg() {
- try {
- Reaction reaction = new Reaction();
- new DissociationReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg2() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- reaction.addProduct(new Product());
- new DissociationReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- reaction.addProduct(new Product());
- reaction.addReactant(new Reactant());
- DissociationReaction validReaction = new DissociationReaction(reaction);
- assertNotNull(validReaction);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- DissociationReaction original = new DissociationReaction();
- original.addProduct(new Product());
- original.addProduct(new Product());
- original.addReactant(new Reactant());
- DissociationReaction product = original.copy();
- assertNotNull(product);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new DissociationReaction() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+public class DissociationReactionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new DissociationReaction());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
+ @Test
+ public void testGetters() {
+ try {
+ Reaction reaction = new DissociationReaction();
+ assertNotNull(reaction.getStringType());
+ assertNotNull(reaction.getReactionRect());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructorWithInvalidArg() {
+ try {
+ Reaction reaction = new Reaction();
+ new DissociationReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructorWithInvalidArg2() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ reaction.addProduct(new Product());
+ new DissociationReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ reaction.addProduct(new Product());
+ reaction.addReactant(new Reactant());
+ DissociationReaction validReaction = new DissociationReaction(reaction);
+ assertNotNull(validReaction);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ DissociationReaction original = new DissociationReaction();
+ original.addProduct(new Product());
+ original.addProduct(new Product());
+ original.addReactant(new Reactant());
+ DissociationReaction product = original.copy();
+ assertNotNull(product);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new DissociationReaction() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/HeterodimerAssociationReactionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/HeterodimerAssociationReactionTest.java
index 6ef2739021..081b14e376 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/HeterodimerAssociationReactionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/HeterodimerAssociationReactionTest.java
@@ -1,127 +1,127 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-public class HeterodimerAssociationReactionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new HeterodimerAssociationReaction());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- Reaction reaction = new HeterodimerAssociationReaction();
- assertNotNull(reaction.getStringType());
- assertNotNull(reaction.getReactionRect());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg() {
- try {
- Reaction reaction = new Reaction();
- new HeterodimerAssociationReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg2() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- new HeterodimerAssociationReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- reaction.addReactant(new Reactant());
- reaction.addReactant(new Reactant());
- HeterodimerAssociationReaction validReaction = new HeterodimerAssociationReaction(reaction);
- assertNotNull(validReaction);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- HeterodimerAssociationReaction original = new HeterodimerAssociationReaction();
- original.addProduct(new Product());
- original.addReactant(new Reactant());
- original.addReactant(new Reactant());
- HeterodimerAssociationReaction product = original.copy();
- assertNotNull(product);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new HeterodimerAssociationReaction() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+public class HeterodimerAssociationReactionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new HeterodimerAssociationReaction());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ Reaction reaction = new HeterodimerAssociationReaction();
+ assertNotNull(reaction.getStringType());
+ assertNotNull(reaction.getReactionRect());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructorWithInvalidArg() {
+ try {
+ Reaction reaction = new Reaction();
+ new HeterodimerAssociationReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructorWithInvalidArg2() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ new HeterodimerAssociationReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ reaction.addReactant(new Reactant());
+ reaction.addReactant(new Reactant());
+ HeterodimerAssociationReaction validReaction = new HeterodimerAssociationReaction(reaction);
+ assertNotNull(validReaction);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ HeterodimerAssociationReaction original = new HeterodimerAssociationReaction();
+ original.addProduct(new Product());
+ original.addReactant(new Reactant());
+ original.addReactant(new Reactant());
+ HeterodimerAssociationReaction product = original.copy();
+ assertNotNull(product);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new HeterodimerAssociationReaction() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/KnownTransitionOmittedReactionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/KnownTransitionOmittedReactionTest.java
index 6e51c5f1c4..40c862a73c 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/KnownTransitionOmittedReactionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/KnownTransitionOmittedReactionTest.java
@@ -1,127 +1,127 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-public class KnownTransitionOmittedReactionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new KnownTransitionOmittedReaction());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg() {
- try {
- Reaction reaction = new Reaction();
- new KnownTransitionOmittedReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg2() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- new KnownTransitionOmittedReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- reaction.addReactant(new Reactant());
- KnownTransitionOmittedReaction validReaction = new KnownTransitionOmittedReaction(reaction);
- assertNotNull(validReaction);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- KnownTransitionOmittedReaction original = new KnownTransitionOmittedReaction();
- original.addProduct(new Product());
- original.addReactant(new Reactant());
- original.addReactant(new Reactant());
- KnownTransitionOmittedReaction product = original.copy();
- assertNotNull(product);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new KnownTransitionOmittedReaction() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- KnownTransitionOmittedReaction original = new KnownTransitionOmittedReaction();
- assertNotNull(original.getReactionRect());
- assertNotNull(original.getStringType());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+public class KnownTransitionOmittedReactionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new KnownTransitionOmittedReaction());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructorWithInvalidArg() {
+ try {
+ Reaction reaction = new Reaction();
+ new KnownTransitionOmittedReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructorWithInvalidArg2() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ new KnownTransitionOmittedReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ reaction.addReactant(new Reactant());
+ KnownTransitionOmittedReaction validReaction = new KnownTransitionOmittedReaction(reaction);
+ assertNotNull(validReaction);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ KnownTransitionOmittedReaction original = new KnownTransitionOmittedReaction();
+ original.addProduct(new Product());
+ original.addReactant(new Reactant());
+ original.addReactant(new Reactant());
+ KnownTransitionOmittedReaction product = original.copy();
+ assertNotNull(product);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new KnownTransitionOmittedReaction() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ KnownTransitionOmittedReaction original = new KnownTransitionOmittedReaction();
+ assertNotNull(original.getReactionRect());
+ assertNotNull(original.getStringType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/NegativeInfluenceReactionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/NegativeInfluenceReactionTest.java
index f55de0127b..b869884437 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/NegativeInfluenceReactionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/NegativeInfluenceReactionTest.java
@@ -1,127 +1,127 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-public class NegativeInfluenceReactionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new NegativeInfluenceReaction());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg() {
- try {
- Reaction reaction = new Reaction();
- new NegativeInfluenceReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg2() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- new NegativeInfluenceReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- reaction.addReactant(new Reactant());
- NegativeInfluenceReaction validReaction = new NegativeInfluenceReaction(reaction);
- assertNotNull(validReaction);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- NegativeInfluenceReaction original = new NegativeInfluenceReaction();
- original.addProduct(new Product());
- original.addReactant(new Reactant());
- original.addReactant(new Reactant());
- NegativeInfluenceReaction product = original.copy();
- assertNotNull(product);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new NegativeInfluenceReaction() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- NegativeInfluenceReaction original = new NegativeInfluenceReaction();
- assertNull(original.getReactionRect());
- assertNotNull(original.getStringType());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+public class NegativeInfluenceReactionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new NegativeInfluenceReaction());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructorWithInvalidArg() {
+ try {
+ Reaction reaction = new Reaction();
+ new NegativeInfluenceReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructorWithInvalidArg2() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ new NegativeInfluenceReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ reaction.addReactant(new Reactant());
+ NegativeInfluenceReaction validReaction = new NegativeInfluenceReaction(reaction);
+ assertNotNull(validReaction);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ NegativeInfluenceReaction original = new NegativeInfluenceReaction();
+ original.addProduct(new Product());
+ original.addReactant(new Reactant());
+ original.addReactant(new Reactant());
+ NegativeInfluenceReaction product = original.copy();
+ assertNotNull(product);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new NegativeInfluenceReaction() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ NegativeInfluenceReaction original = new NegativeInfluenceReaction();
+ assertNull(original.getReactionRect());
+ assertNotNull(original.getStringType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/PositiveInfluenceReactionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/PositiveInfluenceReactionTest.java
index eeeec1ee35..2bf2f72bf7 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/PositiveInfluenceReactionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/PositiveInfluenceReactionTest.java
@@ -1,127 +1,127 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-public class PositiveInfluenceReactionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new PositiveInfluenceReaction());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg() {
- try {
- Reaction reaction = new Reaction();
- new PositiveInfluenceReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg2() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- new PositiveInfluenceReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- reaction.addReactant(new Reactant());
- PositiveInfluenceReaction validReaction = new PositiveInfluenceReaction(reaction);
- assertNotNull(validReaction);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- PositiveInfluenceReaction original = new PositiveInfluenceReaction();
- original.addProduct(new Product());
- original.addReactant(new Reactant());
- original.addReactant(new Reactant());
- PositiveInfluenceReaction product = original.copy();
- assertNotNull(product);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new PositiveInfluenceReaction() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- PositiveInfluenceReaction original = new PositiveInfluenceReaction();
- assertNull(original.getReactionRect());
- assertNotNull(original.getStringType());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+public class PositiveInfluenceReactionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new PositiveInfluenceReaction());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructorWithInvalidArg() {
+ try {
+ Reaction reaction = new Reaction();
+ new PositiveInfluenceReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructorWithInvalidArg2() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ new PositiveInfluenceReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ reaction.addReactant(new Reactant());
+ PositiveInfluenceReaction validReaction = new PositiveInfluenceReaction(reaction);
+ assertNotNull(validReaction);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ PositiveInfluenceReaction original = new PositiveInfluenceReaction();
+ original.addProduct(new Product());
+ original.addReactant(new Reactant());
+ original.addReactant(new Reactant());
+ PositiveInfluenceReaction product = original.copy();
+ assertNotNull(product);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new PositiveInfluenceReaction() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ PositiveInfluenceReaction original = new PositiveInfluenceReaction();
+ assertNull(original.getReactionRect());
+ assertNotNull(original.getStringType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/ReactionRectTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/ReactionRectTest.java
index 63e8933ed6..7c4de9b4b3 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/ReactionRectTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/ReactionRectTest.java
@@ -1,29 +1,29 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ReactionRectTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testValidValues() {
- for (ReactionRect type : ReactionRect.values()) {
- assertNotNull(type);
-
- // for coverage tests
- ReactionRect.valueOf(type.toString());
- assertNotNull(type.getText());
- }
- }
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ReactionRectTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testValidValues() {
+ for (ReactionRect type : ReactionRect.values()) {
+ assertNotNull(type);
+
+ // for coverage tests
+ ReactionRect.valueOf(type.toString());
+ assertNotNull(type.getText());
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/ReducedModulationReactionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/ReducedModulationReactionTest.java
index ce31b446ad..162baa4aad 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/ReducedModulationReactionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/ReducedModulationReactionTest.java
@@ -1,126 +1,126 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-public class ReducedModulationReactionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new ReducedModulationReaction());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void testConstructorWithInvalidArg() {
- try {
- Reaction reaction = new Reaction();
- new ReducedModulationReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg2() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- new ReducedModulationReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- reaction.addReactant(new Reactant());
- ReducedModulationReaction validReaction = new ReducedModulationReaction(reaction);
- assertNotNull(validReaction);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- ReducedModulationReaction original = new ReducedModulationReaction();
- original.addProduct(new Product());
- original.addReactant(new Reactant());
- original.addReactant(new Reactant());
- ReducedModulationReaction product = original.copy();
- assertNotNull(product);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new ReducedModulationReaction() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
- @Test
- public void testGetters() {
- try {
- ReducedModulationReaction original = new ReducedModulationReaction();
- assertNull(original.getReactionRect());
- assertNotNull(original.getStringType());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+public class ReducedModulationReactionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new ReducedModulationReaction());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void testConstructorWithInvalidArg() {
+ try {
+ Reaction reaction = new Reaction();
+ new ReducedModulationReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructorWithInvalidArg2() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ new ReducedModulationReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ reaction.addReactant(new Reactant());
+ ReducedModulationReaction validReaction = new ReducedModulationReaction(reaction);
+ assertNotNull(validReaction);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ ReducedModulationReaction original = new ReducedModulationReaction();
+ original.addProduct(new Product());
+ original.addReactant(new Reactant());
+ original.addReactant(new Reactant());
+ ReducedModulationReaction product = original.copy();
+ assertNotNull(product);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new ReducedModulationReaction() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
+ @Test
+ public void testGetters() {
+ try {
+ ReducedModulationReaction original = new ReducedModulationReaction();
+ assertNull(original.getReactionRect());
+ assertNotNull(original.getStringType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/ReducedPhysicalStimulationReactionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/ReducedPhysicalStimulationReactionTest.java
index a4ef55d6f6..bb4eff01d5 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/ReducedPhysicalStimulationReactionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/ReducedPhysicalStimulationReactionTest.java
@@ -1,126 +1,126 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-public class ReducedPhysicalStimulationReactionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new ReducedPhysicalStimulationReaction());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void testConstructorWithInvalidArg() {
- try {
- Reaction reaction = new Reaction();
- new ReducedPhysicalStimulationReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg2() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- new ReducedPhysicalStimulationReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- reaction.addReactant(new Reactant());
- ReducedPhysicalStimulationReaction validReaction = new ReducedPhysicalStimulationReaction(reaction);
- assertNotNull(validReaction);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- ReducedPhysicalStimulationReaction original = new ReducedPhysicalStimulationReaction();
- original.addProduct(new Product());
- original.addReactant(new Reactant());
- original.addReactant(new Reactant());
- ReducedPhysicalStimulationReaction product = original.copy();
- assertNotNull(product);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new ReducedPhysicalStimulationReaction() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
- @Test
- public void testGetters() {
- try {
- ReducedPhysicalStimulationReaction original = new ReducedPhysicalStimulationReaction();
- assertNull(original.getReactionRect());
- assertNotNull(original.getStringType());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+public class ReducedPhysicalStimulationReactionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new ReducedPhysicalStimulationReaction());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void testConstructorWithInvalidArg() {
+ try {
+ Reaction reaction = new Reaction();
+ new ReducedPhysicalStimulationReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructorWithInvalidArg2() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ new ReducedPhysicalStimulationReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ reaction.addReactant(new Reactant());
+ ReducedPhysicalStimulationReaction validReaction = new ReducedPhysicalStimulationReaction(reaction);
+ assertNotNull(validReaction);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ ReducedPhysicalStimulationReaction original = new ReducedPhysicalStimulationReaction();
+ original.addProduct(new Product());
+ original.addReactant(new Reactant());
+ original.addReactant(new Reactant());
+ ReducedPhysicalStimulationReaction product = original.copy();
+ assertNotNull(product);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new ReducedPhysicalStimulationReaction() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
+ @Test
+ public void testGetters() {
+ try {
+ ReducedPhysicalStimulationReaction original = new ReducedPhysicalStimulationReaction();
+ assertNull(original.getReactionRect());
+ assertNotNull(original.getStringType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/ReducedTriggerReactionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/ReducedTriggerReactionTest.java
index 20f99a0d41..53955053d7 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/ReducedTriggerReactionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/ReducedTriggerReactionTest.java
@@ -1,126 +1,126 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-public class ReducedTriggerReactionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new ReducedTriggerReaction());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void testConstructorWithInvalidArg() {
- try {
- Reaction reaction = new Reaction();
- new ReducedTriggerReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg2() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- new ReducedTriggerReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- reaction.addReactant(new Reactant());
- ReducedTriggerReaction validReaction = new ReducedTriggerReaction(reaction);
- assertNotNull(validReaction);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- ReducedTriggerReaction original = new ReducedTriggerReaction();
- original.addProduct(new Product());
- original.addReactant(new Reactant());
- original.addReactant(new Reactant());
- ReducedTriggerReaction product = original.copy();
- assertNotNull(product);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new ReducedTriggerReaction() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
- @Test
- public void testGetters() {
- try {
- ReducedTriggerReaction original = new ReducedTriggerReaction();
- assertNull(original.getReactionRect());
- assertNotNull(original.getStringType());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+public class ReducedTriggerReactionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new ReducedTriggerReaction());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void testConstructorWithInvalidArg() {
+ try {
+ Reaction reaction = new Reaction();
+ new ReducedTriggerReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructorWithInvalidArg2() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ new ReducedTriggerReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ reaction.addReactant(new Reactant());
+ ReducedTriggerReaction validReaction = new ReducedTriggerReaction(reaction);
+ assertNotNull(validReaction);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ ReducedTriggerReaction original = new ReducedTriggerReaction();
+ original.addProduct(new Product());
+ original.addReactant(new Reactant());
+ original.addReactant(new Reactant());
+ ReducedTriggerReaction product = original.copy();
+ assertNotNull(product);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new ReducedTriggerReaction() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
+ @Test
+ public void testGetters() {
+ try {
+ ReducedTriggerReaction original = new ReducedTriggerReaction();
+ assertNull(original.getReactionRect());
+ assertNotNull(original.getStringType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/StateTransitionReactionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/StateTransitionReactionTest.java
index 8e058b420f..9e63bf2ac4 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/StateTransitionReactionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/StateTransitionReactionTest.java
@@ -1,125 +1,125 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-public class StateTransitionReactionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new StateTransitionReaction());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void testConstructorWithInvalidArg() {
- try {
- Reaction reaction = new Reaction();
- new StateTransitionReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg2() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- new StateTransitionReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- reaction.addReactant(new Reactant());
- StateTransitionReaction validReaction = new StateTransitionReaction(reaction);
- assertNotNull(validReaction);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- StateTransitionReaction original = new StateTransitionReaction();
- original.addProduct(new Product());
- original.addReactant(new Reactant());
- original.addReactant(new Reactant());
- StateTransitionReaction product = original.copy();
- assertNotNull(product);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new StateTransitionReaction() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
- @Test
- public void testGetters() {
- try {
- StateTransitionReaction original = new StateTransitionReaction();
- assertNotNull(original.getReactionRect());
- assertNotNull(original.getStringType());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+public class StateTransitionReactionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new StateTransitionReaction());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void testConstructorWithInvalidArg() {
+ try {
+ Reaction reaction = new Reaction();
+ new StateTransitionReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructorWithInvalidArg2() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ new StateTransitionReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ reaction.addReactant(new Reactant());
+ StateTransitionReaction validReaction = new StateTransitionReaction(reaction);
+ assertNotNull(validReaction);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ StateTransitionReaction original = new StateTransitionReaction();
+ original.addProduct(new Product());
+ original.addReactant(new Reactant());
+ original.addReactant(new Reactant());
+ StateTransitionReaction product = original.copy();
+ assertNotNull(product);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new StateTransitionReaction() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
+ @Test
+ public void testGetters() {
+ try {
+ StateTransitionReaction original = new StateTransitionReaction();
+ assertNotNull(original.getReactionRect());
+ assertNotNull(original.getStringType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/TranscriptionReactionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/TranscriptionReactionTest.java
index 30f8276b9b..7fb334aa6f 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/TranscriptionReactionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/TranscriptionReactionTest.java
@@ -1,125 +1,125 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-public class TranscriptionReactionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new TranscriptionReaction());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void testConstructorWithInvalidArg() {
- try {
- Reaction reaction = new Reaction();
- new TranscriptionReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg2() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- new TranscriptionReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- reaction.addReactant(new Reactant());
- TranscriptionReaction validReaction = new TranscriptionReaction(reaction);
- assertNotNull(validReaction);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- TranscriptionReaction original = new TranscriptionReaction();
- original.addProduct(new Product());
- original.addReactant(new Reactant());
- original.addReactant(new Reactant());
- TranscriptionReaction product = original.copy();
- assertNotNull(product);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new TranscriptionReaction() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
- @Test
- public void testGetters() {
- try {
- TranscriptionReaction original = new TranscriptionReaction();
- assertNotNull(original.getReactionRect());
- assertNotNull(original.getStringType());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+public class TranscriptionReactionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new TranscriptionReaction());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void testConstructorWithInvalidArg() {
+ try {
+ Reaction reaction = new Reaction();
+ new TranscriptionReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructorWithInvalidArg2() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ new TranscriptionReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ reaction.addReactant(new Reactant());
+ TranscriptionReaction validReaction = new TranscriptionReaction(reaction);
+ assertNotNull(validReaction);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ TranscriptionReaction original = new TranscriptionReaction();
+ original.addProduct(new Product());
+ original.addReactant(new Reactant());
+ original.addReactant(new Reactant());
+ TranscriptionReaction product = original.copy();
+ assertNotNull(product);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new TranscriptionReaction() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
+ @Test
+ public void testGetters() {
+ try {
+ TranscriptionReaction original = new TranscriptionReaction();
+ assertNotNull(original.getReactionRect());
+ assertNotNull(original.getStringType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/TranslationReactionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/TranslationReactionTest.java
index a03e4c7a3a..58f0741cf9 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/TranslationReactionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/TranslationReactionTest.java
@@ -1,125 +1,125 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-public class TranslationReactionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new TranslationReaction());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void testConstructorWithInvalidArg() {
- try {
- Reaction reaction = new Reaction();
- new TranslationReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg2() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- new TranslationReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- reaction.addReactant(new Reactant());
- TranslationReaction validReaction = new TranslationReaction(reaction);
- assertNotNull(validReaction);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- TranslationReaction original = new TranslationReaction();
- original.addProduct(new Product());
- original.addReactant(new Reactant());
- original.addReactant(new Reactant());
- TranslationReaction product = original.copy();
- assertNotNull(product);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new TranslationReaction() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
- @Test
- public void testGetters() {
- try {
- TranslationReaction original = new TranslationReaction();
- assertNotNull(original.getReactionRect());
- assertNotNull(original.getStringType());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+public class TranslationReactionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new TranslationReaction());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void testConstructorWithInvalidArg() {
+ try {
+ Reaction reaction = new Reaction();
+ new TranslationReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructorWithInvalidArg2() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ new TranslationReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ reaction.addReactant(new Reactant());
+ TranslationReaction validReaction = new TranslationReaction(reaction);
+ assertNotNull(validReaction);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ TranslationReaction original = new TranslationReaction();
+ original.addProduct(new Product());
+ original.addReactant(new Reactant());
+ original.addReactant(new Reactant());
+ TranslationReaction product = original.copy();
+ assertNotNull(product);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new TranslationReaction() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
+ @Test
+ public void testGetters() {
+ try {
+ TranslationReaction original = new TranslationReaction();
+ assertNotNull(original.getReactionRect());
+ assertNotNull(original.getStringType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/TransportReactionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/TransportReactionTest.java
index a1efd630fa..1620cc2b66 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/TransportReactionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/TransportReactionTest.java
@@ -1,126 +1,126 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-public class TransportReactionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new TransportReaction());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg() {
- try {
- Reaction reaction = new Reaction();
- new TransportReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg2() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- new TransportReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- reaction.addReactant(new Reactant());
- TransportReaction validReaction = new TransportReaction(reaction);
- assertNotNull(validReaction);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- TransportReaction original = new TransportReaction();
- original.addProduct(new Product());
- original.addReactant(new Reactant());
- original.addReactant(new Reactant());
- TransportReaction product = original.copy();
- assertNotNull(product);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new TransportReaction() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
- @Test
- public void testGetters() {
- try {
- TransportReaction original = new TransportReaction();
- assertNotNull(original.getReactionRect());
- assertNotNull(original.getStringType());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+public class TransportReactionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new TransportReaction());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructorWithInvalidArg() {
+ try {
+ Reaction reaction = new Reaction();
+ new TransportReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructorWithInvalidArg2() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ new TransportReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ reaction.addReactant(new Reactant());
+ TransportReaction validReaction = new TransportReaction(reaction);
+ assertNotNull(validReaction);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ TransportReaction original = new TransportReaction();
+ original.addProduct(new Product());
+ original.addReactant(new Reactant());
+ original.addReactant(new Reactant());
+ TransportReaction product = original.copy();
+ assertNotNull(product);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new TransportReaction() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
+ @Test
+ public void testGetters() {
+ try {
+ TransportReaction original = new TransportReaction();
+ assertNotNull(original.getReactionRect());
+ assertNotNull(original.getStringType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/TruncationReactionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/TruncationReactionTest.java
index 5e8091a9e9..21a47429b4 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/TruncationReactionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/TruncationReactionTest.java
@@ -1,127 +1,127 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-public class TruncationReactionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new TruncationReaction());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void testConstructorWithInvalidArg() {
- try {
- Reaction reaction = new Reaction();
- new TruncationReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg2() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- reaction.addProduct(new Product());
- new TruncationReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- reaction.addProduct(new Product());
- reaction.addReactant(new Reactant());
- TruncationReaction validReaction = new TruncationReaction(reaction);
- assertNotNull(validReaction);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- TruncationReaction original = new TruncationReaction();
- original.addProduct(new Product());
- original.addProduct(new Product());
- original.addReactant(new Reactant());
- TruncationReaction product = original.copy();
- assertNotNull(product);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new TruncationReaction() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- Reaction reaction = new TruncationReaction();
- assertNotNull(reaction.getStringType());
- assertNotNull(reaction.getReactionRect());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+public class TruncationReactionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new TruncationReaction());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void testConstructorWithInvalidArg() {
+ try {
+ Reaction reaction = new Reaction();
+ new TruncationReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructorWithInvalidArg2() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ reaction.addProduct(new Product());
+ new TruncationReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ reaction.addProduct(new Product());
+ reaction.addReactant(new Reactant());
+ TruncationReaction validReaction = new TruncationReaction(reaction);
+ assertNotNull(validReaction);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ TruncationReaction original = new TruncationReaction();
+ original.addProduct(new Product());
+ original.addProduct(new Product());
+ original.addReactant(new Reactant());
+ TruncationReaction product = original.copy();
+ assertNotNull(product);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new TruncationReaction() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ Reaction reaction = new TruncationReaction();
+ assertNotNull(reaction.getStringType());
+ assertNotNull(reaction.getReactionRect());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/UnknownNegativeInfluenceReactionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/UnknownNegativeInfluenceReactionTest.java
index ec5a8eb907..0ad2061f23 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/UnknownNegativeInfluenceReactionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/UnknownNegativeInfluenceReactionTest.java
@@ -1,126 +1,126 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-public class UnknownNegativeInfluenceReactionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new UnknownNegativeInfluenceReaction());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void testConstructorWithInvalidArg() {
- try {
- Reaction reaction = new Reaction();
- new UnknownNegativeInfluenceReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg2() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- new UnknownNegativeInfluenceReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- reaction.addReactant(new Reactant());
- UnknownNegativeInfluenceReaction validReaction = new UnknownNegativeInfluenceReaction(reaction);
- assertNotNull(validReaction);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- UnknownNegativeInfluenceReaction original = new UnknownNegativeInfluenceReaction();
- original.addProduct(new Product());
- original.addReactant(new Reactant());
- original.addReactant(new Reactant());
- UnknownNegativeInfluenceReaction product = original.copy();
- assertNotNull(product);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new UnknownNegativeInfluenceReaction() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
- @Test
- public void testGetters() {
- try {
- UnknownNegativeInfluenceReaction original = new UnknownNegativeInfluenceReaction();
- assertNull(original.getReactionRect());
- assertNotNull(original.getStringType());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+public class UnknownNegativeInfluenceReactionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new UnknownNegativeInfluenceReaction());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void testConstructorWithInvalidArg() {
+ try {
+ Reaction reaction = new Reaction();
+ new UnknownNegativeInfluenceReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructorWithInvalidArg2() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ new UnknownNegativeInfluenceReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ reaction.addReactant(new Reactant());
+ UnknownNegativeInfluenceReaction validReaction = new UnknownNegativeInfluenceReaction(reaction);
+ assertNotNull(validReaction);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ UnknownNegativeInfluenceReaction original = new UnknownNegativeInfluenceReaction();
+ original.addProduct(new Product());
+ original.addReactant(new Reactant());
+ original.addReactant(new Reactant());
+ UnknownNegativeInfluenceReaction product = original.copy();
+ assertNotNull(product);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new UnknownNegativeInfluenceReaction() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
+ @Test
+ public void testGetters() {
+ try {
+ UnknownNegativeInfluenceReaction original = new UnknownNegativeInfluenceReaction();
+ assertNull(original.getReactionRect());
+ assertNotNull(original.getStringType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/UnknownPositiveInfluenceReactionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/UnknownPositiveInfluenceReactionTest.java
index aa9de353a8..9901b46018 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/UnknownPositiveInfluenceReactionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/UnknownPositiveInfluenceReactionTest.java
@@ -1,126 +1,126 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-public class UnknownPositiveInfluenceReactionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new UnknownPositiveInfluenceReaction());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void testConstructorWithInvalidArg() {
- try {
- Reaction reaction = new Reaction();
- new UnknownPositiveInfluenceReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg2() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- new UnknownPositiveInfluenceReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- reaction.addReactant(new Reactant());
- UnknownPositiveInfluenceReaction validReaction = new UnknownPositiveInfluenceReaction(reaction);
- assertNotNull(validReaction);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- UnknownPositiveInfluenceReaction original = new UnknownPositiveInfluenceReaction();
- original.addProduct(new Product());
- original.addReactant(new Reactant());
- original.addReactant(new Reactant());
- UnknownPositiveInfluenceReaction product = original.copy();
- assertNotNull(product);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new UnknownPositiveInfluenceReaction() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
- @Test
- public void testGetters() {
- try {
- UnknownPositiveInfluenceReaction original = new UnknownPositiveInfluenceReaction();
- assertNull(original.getReactionRect());
- assertNotNull(original.getStringType());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+public class UnknownPositiveInfluenceReactionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new UnknownPositiveInfluenceReaction());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void testConstructorWithInvalidArg() {
+ try {
+ Reaction reaction = new Reaction();
+ new UnknownPositiveInfluenceReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructorWithInvalidArg2() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ new UnknownPositiveInfluenceReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ reaction.addReactant(new Reactant());
+ UnknownPositiveInfluenceReaction validReaction = new UnknownPositiveInfluenceReaction(reaction);
+ assertNotNull(validReaction);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ UnknownPositiveInfluenceReaction original = new UnknownPositiveInfluenceReaction();
+ original.addProduct(new Product());
+ original.addReactant(new Reactant());
+ original.addReactant(new Reactant());
+ UnknownPositiveInfluenceReaction product = original.copy();
+ assertNotNull(product);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new UnknownPositiveInfluenceReaction() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
+ @Test
+ public void testGetters() {
+ try {
+ UnknownPositiveInfluenceReaction original = new UnknownPositiveInfluenceReaction();
+ assertNull(original.getReactionRect());
+ assertNotNull(original.getStringType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/UnknownReducedModulationReactionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/UnknownReducedModulationReactionTest.java
index 6d60187878..136833568f 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/UnknownReducedModulationReactionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/UnknownReducedModulationReactionTest.java
@@ -1,126 +1,126 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-public class UnknownReducedModulationReactionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new UnknownReducedModulationReaction());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void testConstructorWithInvalidArg() {
- try {
- Reaction reaction = new Reaction();
- new UnknownReducedModulationReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg2() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- new UnknownReducedModulationReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- reaction.addReactant(new Reactant());
- UnknownReducedModulationReaction validReaction = new UnknownReducedModulationReaction(reaction);
- assertNotNull(validReaction);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- UnknownReducedModulationReaction original = new UnknownReducedModulationReaction();
- original.addProduct(new Product());
- original.addReactant(new Reactant());
- original.addReactant(new Reactant());
- UnknownReducedModulationReaction product = original.copy();
- assertNotNull(product);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new UnknownReducedModulationReaction() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
- @Test
- public void testGetters() {
- try {
- UnknownReducedModulationReaction original = new UnknownReducedModulationReaction();
- assertNull(original.getReactionRect());
- assertNotNull(original.getStringType());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+public class UnknownReducedModulationReactionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new UnknownReducedModulationReaction());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void testConstructorWithInvalidArg() {
+ try {
+ Reaction reaction = new Reaction();
+ new UnknownReducedModulationReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructorWithInvalidArg2() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ new UnknownReducedModulationReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ reaction.addReactant(new Reactant());
+ UnknownReducedModulationReaction validReaction = new UnknownReducedModulationReaction(reaction);
+ assertNotNull(validReaction);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ UnknownReducedModulationReaction original = new UnknownReducedModulationReaction();
+ original.addProduct(new Product());
+ original.addReactant(new Reactant());
+ original.addReactant(new Reactant());
+ UnknownReducedModulationReaction product = original.copy();
+ assertNotNull(product);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new UnknownReducedModulationReaction() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
+ @Test
+ public void testGetters() {
+ try {
+ UnknownReducedModulationReaction original = new UnknownReducedModulationReaction();
+ assertNull(original.getReactionRect());
+ assertNotNull(original.getStringType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/UnknownReducedPhysicalStimulationReactionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/UnknownReducedPhysicalStimulationReactionTest.java
index cf1b3970dd..f011daf484 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/UnknownReducedPhysicalStimulationReactionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/UnknownReducedPhysicalStimulationReactionTest.java
@@ -1,126 +1,126 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-public class UnknownReducedPhysicalStimulationReactionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new UnknownReducedPhysicalStimulationReaction());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void testConstructorWithInvalidArg() {
- try {
- Reaction reaction = new Reaction();
- new UnknownReducedPhysicalStimulationReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg2() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- new UnknownReducedPhysicalStimulationReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- reaction.addReactant(new Reactant());
- UnknownReducedPhysicalStimulationReaction validReaction = new UnknownReducedPhysicalStimulationReaction(reaction);
- assertNotNull(validReaction);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- UnknownReducedPhysicalStimulationReaction original = new UnknownReducedPhysicalStimulationReaction();
- original.addProduct(new Product());
- original.addReactant(new Reactant());
- original.addReactant(new Reactant());
- UnknownReducedPhysicalStimulationReaction product = original.copy();
- assertNotNull(product);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new UnknownReducedPhysicalStimulationReaction() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
- @Test
- public void testGetters() {
- try {
- UnknownReducedPhysicalStimulationReaction original = new UnknownReducedPhysicalStimulationReaction();
- assertNull(original.getReactionRect());
- assertNotNull(original.getStringType());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+public class UnknownReducedPhysicalStimulationReactionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new UnknownReducedPhysicalStimulationReaction());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void testConstructorWithInvalidArg() {
+ try {
+ Reaction reaction = new Reaction();
+ new UnknownReducedPhysicalStimulationReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructorWithInvalidArg2() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ new UnknownReducedPhysicalStimulationReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ reaction.addReactant(new Reactant());
+ UnknownReducedPhysicalStimulationReaction validReaction = new UnknownReducedPhysicalStimulationReaction(reaction);
+ assertNotNull(validReaction);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ UnknownReducedPhysicalStimulationReaction original = new UnknownReducedPhysicalStimulationReaction();
+ original.addProduct(new Product());
+ original.addReactant(new Reactant());
+ original.addReactant(new Reactant());
+ UnknownReducedPhysicalStimulationReaction product = original.copy();
+ assertNotNull(product);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new UnknownReducedPhysicalStimulationReaction() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
+ @Test
+ public void testGetters() {
+ try {
+ UnknownReducedPhysicalStimulationReaction original = new UnknownReducedPhysicalStimulationReaction();
+ assertNull(original.getReactionRect());
+ assertNotNull(original.getStringType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/UnknownReducedTriggerReactionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/UnknownReducedTriggerReactionTest.java
index 0b94040b7b..92877a42b4 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/UnknownReducedTriggerReactionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/UnknownReducedTriggerReactionTest.java
@@ -1,126 +1,126 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-public class UnknownReducedTriggerReactionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new UnknownReducedTriggerReaction());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void testConstructorWithInvalidArg() {
- try {
- Reaction reaction = new Reaction();
- new UnknownReducedTriggerReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg2() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- new UnknownReducedTriggerReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- reaction.addReactant(new Reactant());
- UnknownReducedTriggerReaction validReaction = new UnknownReducedTriggerReaction(reaction);
- assertNotNull(validReaction);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- UnknownReducedTriggerReaction original = new UnknownReducedTriggerReaction();
- original.addProduct(new Product());
- original.addReactant(new Reactant());
- original.addReactant(new Reactant());
- UnknownReducedTriggerReaction product = original.copy();
- assertNotNull(product);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new UnknownReducedTriggerReaction() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
- @Test
- public void testGetters() {
- try {
- UnknownReducedTriggerReaction original = new UnknownReducedTriggerReaction();
- assertNull(original.getReactionRect());
- assertNotNull(original.getStringType());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+public class UnknownReducedTriggerReactionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new UnknownReducedTriggerReaction());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void testConstructorWithInvalidArg() {
+ try {
+ Reaction reaction = new Reaction();
+ new UnknownReducedTriggerReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructorWithInvalidArg2() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ new UnknownReducedTriggerReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ reaction.addReactant(new Reactant());
+ UnknownReducedTriggerReaction validReaction = new UnknownReducedTriggerReaction(reaction);
+ assertNotNull(validReaction);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ UnknownReducedTriggerReaction original = new UnknownReducedTriggerReaction();
+ original.addProduct(new Product());
+ original.addReactant(new Reactant());
+ original.addReactant(new Reactant());
+ UnknownReducedTriggerReaction product = original.copy();
+ assertNotNull(product);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new UnknownReducedTriggerReaction() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
+ @Test
+ public void testGetters() {
+ try {
+ UnknownReducedTriggerReaction original = new UnknownReducedTriggerReaction();
+ assertNull(original.getReactionRect());
+ assertNotNull(original.getStringType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/UnknownTransitionReactionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/UnknownTransitionReactionTest.java
index f720ec44dd..278e02ce73 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/UnknownTransitionReactionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/type/UnknownTransitionReactionTest.java
@@ -1,126 +1,126 @@
-package lcsb.mapviewer.model.map.reaction.type;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-public class UnknownTransitionReactionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new UnknownTransitionReaction());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg() {
- try {
- Reaction reaction = new Reaction();
- new UnknownTransitionReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructorWithInvalidArg2() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- new UnknownTransitionReaction(reaction);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Reaction reaction = new Reaction();
- reaction.addProduct(new Product());
- reaction.addReactant(new Reactant());
- UnknownTransitionReaction validReaction = new UnknownTransitionReaction(reaction);
- assertNotNull(validReaction);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
- @Test
- public void testCopy() {
- try {
- UnknownTransitionReaction original = new UnknownTransitionReaction();
- original.addProduct(new Product());
- original.addReactant(new Reactant());
- original.addReactant(new Reactant());
- UnknownTransitionReaction product = original.copy();
- assertNotNull(product);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- new UnknownTransitionReaction() {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
- }.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- UnknownTransitionReaction original = new UnknownTransitionReaction();
- assertNotNull(original.getReactionRect());
- assertNotNull(original.getStringType());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.map.reaction.type;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+public class UnknownTransitionReactionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new UnknownTransitionReaction());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructorWithInvalidArg() {
+ try {
+ Reaction reaction = new Reaction();
+ new UnknownTransitionReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructorWithInvalidArg2() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ new UnknownTransitionReaction(reaction);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.addProduct(new Product());
+ reaction.addReactant(new Reactant());
+ UnknownTransitionReaction validReaction = new UnknownTransitionReaction(reaction);
+ assertNotNull(validReaction);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+
+ @Test
+ public void testCopy() {
+ try {
+ UnknownTransitionReaction original = new UnknownTransitionReaction();
+ original.addProduct(new Product());
+ original.addReactant(new Reactant());
+ original.addReactant(new Reactant());
+ UnknownTransitionReaction product = original.copy();
+ assertNotNull(product);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ new UnknownTransitionReaction() {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+ }.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ UnknownTransitionReaction original = new UnknownTransitionReaction();
+ assertNotNull(original.getReactionRect());
+ assertNotNull(original.getStringType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/AllSpeciesTests.java b/model/src/test/java/lcsb/mapviewer/model/map/species/AllSpeciesTests.java
index 7d9ef9c87c..6bdf056efd 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/AllSpeciesTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/AllSpeciesTests.java
@@ -1,49 +1,49 @@
-package lcsb.mapviewer.model.map.species;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-import lcsb.mapviewer.model.map.species.field.AllFieldTests;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AllFieldTests.class, //
- AntisenseRnaComparatorTest.class, //
- AntisenseRnaTest.class, //
- ChemicalComparatorTest.class, //
- ComplexComparatorTest.class, //
- ComplexTest.class, //
- DegradedComparatorTest.class, //
- DegradedTest.class, //
- DrugComparatorTest.class, //
- DrugTest.class, //
- ElementComparatorTest.class, //
- ElementTest.class, //
- GeneComparatorTest.class, //
- GenericProteinComparatorTest.class, //
- GenericProteinTest.class, //
- GeneTest.class, //
- IonChannelProteinTest.class, //
- IonChannelProteinComparatorTest.class, //
- IonComparatorTest.class, //
- IonTest.class, //
- PhenotypeComparatorTest.class, //
- PhenotypeTest.class, //
- ProteinComparatorTest.class, //
- ProteinTest.class, //
- ReceptorProteinTest.class, //
- ReceptorProteinComparatorTest.class, //
- RnaComparatorTest.class, //
- RnaTest.class, //
- SimpleMoleculeComparatorTest.class, //
- SimpleMoleculeTest.class, //
- SpeciesComparatorTest.class, //
- SpeciesTest.class, //
- TruncatedProteinTest.class, //
- TruncatedProteinComparatorTest.class, //
- UnknownComparatorTest.class, //
- UnknownTest.class, //
-})
-public class AllSpeciesTests {
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+import lcsb.mapviewer.model.map.species.field.AllFieldTests;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AllFieldTests.class, //
+ AntisenseRnaComparatorTest.class, //
+ AntisenseRnaTest.class, //
+ ChemicalComparatorTest.class, //
+ ComplexComparatorTest.class, //
+ ComplexTest.class, //
+ DegradedComparatorTest.class, //
+ DegradedTest.class, //
+ DrugComparatorTest.class, //
+ DrugTest.class, //
+ ElementComparatorTest.class, //
+ ElementTest.class, //
+ GeneComparatorTest.class, //
+ GenericProteinComparatorTest.class, //
+ GenericProteinTest.class, //
+ GeneTest.class, //
+ IonChannelProteinTest.class, //
+ IonChannelProteinComparatorTest.class, //
+ IonComparatorTest.class, //
+ IonTest.class, //
+ PhenotypeComparatorTest.class, //
+ PhenotypeTest.class, //
+ ProteinComparatorTest.class, //
+ ProteinTest.class, //
+ ReceptorProteinTest.class, //
+ ReceptorProteinComparatorTest.class, //
+ RnaComparatorTest.class, //
+ RnaTest.class, //
+ SimpleMoleculeComparatorTest.class, //
+ SimpleMoleculeTest.class, //
+ SpeciesComparatorTest.class, //
+ SpeciesTest.class, //
+ TruncatedProteinTest.class, //
+ TruncatedProteinComparatorTest.class, //
+ UnknownComparatorTest.class, //
+ UnknownTest.class, //
+})
+public class AllSpeciesTests {
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparatorTest.java
index c601f66be9..3df395f239 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparatorTest.java
@@ -1,95 +1,95 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.awt.geom.Point2D;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.field.CodingRegion;
-
-public class AntisenseRnaComparatorTest {
-
- AntisenseRnaComparator comparator = new AntisenseRnaComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- AntisenseRna aRna1 = createAntisenseRna();
- AntisenseRna aRna2 = createAntisenseRna();
-
- assertEquals(0, comparator.compare(aRna1, aRna1));
-
- assertEquals(0, comparator.compare(aRna1, aRna2));
- assertEquals(0, comparator.compare(aRna2, aRna1));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- @Test
- public void testDifferent() {
- try {
- AntisenseRna aRna1 = createAntisenseRna();
- AntisenseRna aRna2 = createAntisenseRna();
- aRna1.getRegions().get(0).setName("bla");
- assertTrue(comparator.compare(aRna1, aRna2) != 0);
- assertTrue(comparator.compare(aRna2, aRna1) != 0);
-
- aRna1 = createAntisenseRna();
- aRna2 = createAntisenseRna();
- aRna1.getRegions().clear();
- assertTrue(comparator.compare(aRna1, aRna2) != 0);
- assertTrue(comparator.compare(aRna2, aRna1) != 0);
-
- aRna1 = createAntisenseRna();
- aRna2 = createAntisenseRna();
- assertTrue(comparator.compare(null, aRna2) != 0);
- assertTrue(comparator.compare(aRna2, null) != 0);
- assertTrue(comparator.compare(null, null) == 0);
-
- AntisenseRna unknown = createAntisenseRna();
- unknown.setName("n");
- assertTrue(comparator.compare(unknown, aRna2) != 0);
-
- assertTrue(comparator.compare(unknown, Mockito.mock(AntisenseRna.class)) != 0);
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- public AntisenseRna createAntisenseRna() {
- AntisenseRna result = new AntisenseRna();
-
- CodingRegion region1 = new CodingRegion();
- result.addRegion(region1);
- region1.setIdModificationResidue("a");
- region1.setName("name");
- region1.setPosition(new Point2D.Double(0, 1));
- region1.setWidth(2);
- return result;
- }
-
- @Test(expected = NotImplementedException.class)
- public void testInvalid() {
- AntisenseRna element = Mockito.mock(AntisenseRna.class);
- comparator.compare(element, element);
- }
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.awt.geom.Point2D;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.field.CodingRegion;
+
+public class AntisenseRnaComparatorTest {
+
+ AntisenseRnaComparator comparator = new AntisenseRnaComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ AntisenseRna aRna1 = createAntisenseRna();
+ AntisenseRna aRna2 = createAntisenseRna();
+
+ assertEquals(0, comparator.compare(aRna1, aRna1));
+
+ assertEquals(0, comparator.compare(aRna1, aRna2));
+ assertEquals(0, comparator.compare(aRna2, aRna1));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ AntisenseRna aRna1 = createAntisenseRna();
+ AntisenseRna aRna2 = createAntisenseRna();
+ aRna1.getRegions().get(0).setName("bla");
+ assertTrue(comparator.compare(aRna1, aRna2) != 0);
+ assertTrue(comparator.compare(aRna2, aRna1) != 0);
+
+ aRna1 = createAntisenseRna();
+ aRna2 = createAntisenseRna();
+ aRna1.getRegions().clear();
+ assertTrue(comparator.compare(aRna1, aRna2) != 0);
+ assertTrue(comparator.compare(aRna2, aRna1) != 0);
+
+ aRna1 = createAntisenseRna();
+ aRna2 = createAntisenseRna();
+ assertTrue(comparator.compare(null, aRna2) != 0);
+ assertTrue(comparator.compare(aRna2, null) != 0);
+ assertTrue(comparator.compare(null, null) == 0);
+
+ AntisenseRna unknown = createAntisenseRna();
+ unknown.setName("n");
+ assertTrue(comparator.compare(unknown, aRna2) != 0);
+
+ assertTrue(comparator.compare(unknown, Mockito.mock(AntisenseRna.class)) != 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ public AntisenseRna createAntisenseRna() {
+ AntisenseRna result = new AntisenseRna();
+
+ CodingRegion region1 = new CodingRegion();
+ result.addRegion(region1);
+ region1.setIdModificationResidue("a");
+ region1.setName("name");
+ region1.setPosition(new Point2D.Double(0, 1));
+ region1.setWidth(2);
+ return result;
+ }
+
+ @Test(expected = NotImplementedException.class)
+ public void testInvalid() {
+ AntisenseRna element = Mockito.mock(AntisenseRna.class);
+ comparator.compare(element, element);
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ChemicalComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ChemicalComparatorTest.java
index ccf0fe04d0..9599938630 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ChemicalComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ChemicalComparatorTest.java
@@ -1,74 +1,74 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class ChemicalComparatorTest {
-
- ChemicalComparator comparator = new ChemicalComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- Chemical drug1 = createChemical();
- Chemical drug2 = createChemical();
-
- assertEquals(0, comparator.compare(drug1, drug1));
-
- assertEquals(0, comparator.compare(drug1, drug2));
- assertEquals(0, comparator.compare(drug2, drug1));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- @Test
- public void testDifferent() {
- try {
- Chemical drug2 = createChemical();
- assertTrue(comparator.compare(null, drug2) != 0);
- assertTrue(comparator.compare(drug2, null) != 0);
- assertTrue(comparator.compare(null, null) == 0);
-
- Chemical drug = createChemical();
- drug.setName("n");
- assertTrue(comparator.compare(drug, drug2) != 0);
-
- assertTrue(comparator.compare(drug, Mockito.mock(Chemical.class)) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- public Chemical createChemical() {
- Chemical result = new Ion();
- return result;
- }
-
- @Test(expected = NotImplementedException.class)
- public void testInvalid() {
- Chemical object = Mockito.mock(Chemical.class);
- comparator.compare(object, object);
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class ChemicalComparatorTest {
+
+ ChemicalComparator comparator = new ChemicalComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ Chemical drug1 = createChemical();
+ Chemical drug2 = createChemical();
+
+ assertEquals(0, comparator.compare(drug1, drug1));
+
+ assertEquals(0, comparator.compare(drug1, drug2));
+ assertEquals(0, comparator.compare(drug2, drug1));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ Chemical drug2 = createChemical();
+ assertTrue(comparator.compare(null, drug2) != 0);
+ assertTrue(comparator.compare(drug2, null) != 0);
+ assertTrue(comparator.compare(null, null) == 0);
+
+ Chemical drug = createChemical();
+ drug.setName("n");
+ assertTrue(comparator.compare(drug, drug2) != 0);
+
+ assertTrue(comparator.compare(drug, Mockito.mock(Chemical.class)) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ public Chemical createChemical() {
+ Chemical result = new Ion();
+ return result;
+ }
+
+ @Test(expected = NotImplementedException.class)
+ public void testInvalid() {
+ Chemical object = Mockito.mock(Chemical.class);
+ comparator.compare(object, object);
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexComparatorTest.java
index 227e981367..b7d0182c13 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexComparatorTest.java
@@ -1,383 +1,383 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-import static org.mockito.Mockito.when;
-
-import java.awt.Color;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class ComplexComparatorTest {
-
- Logger logger = Logger.getLogger(ComplexComparatorTest.class);
- ComplexComparator comparator = new ComplexComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- Complex complex1 = createComplex2();
- Complex complex2 = createComplex2();
-
- assertEquals(0, comparator.compare(complex1, complex2));
-
- assertEquals(0, comparator.compare(null, null));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private Complex createComplex2() {
- Complex result = new Complex();
- result.setName("complex");
-
- result.setElementId("asd");
- result.setX(12.0);
- result.setY(123.0);
- result.setWidth(4);
- result.setHeight(5);
- result.setFontSize(9.0);
- result.setColor(Color.BLUE);
- result.setVisibilityLevel("14");
-
- Species protein = new GenericProtein("S");
- protein.setName("a");
- result.addSpecies(protein);
-
- return result;
- }
-
- @Test
- public void testDifferent() {
- try {
- Complex complex1 = createComplex2();
- Complex complex2 = createComplex2();
-
- assertTrue(comparator.compare(complex1, null) != 0);
- assertTrue(comparator.compare(null, complex1) != 0);
-
- complex1 = createComplex2();
- complex2 = createComplex2();
-
- complex1.setElementId("tmp");
-
- assertTrue(comparator.compare(complex1, complex2) != 0);
- assertTrue(comparator.compare(complex2, complex1) != 0);
-
- complex1 = createComplex2();
- complex2 = createComplex2();
-
- complex1.addSpecies(new GenericProtein("id"));
-
- assertTrue(comparator.compare(complex1, complex2) != 0);
- assertTrue(comparator.compare(complex2, complex1) != 0);
-
- complex1 = createComplex2();
- complex2 = createComplex2();
-
- complex1.getElements().iterator().next().setElementId("bnu");
-
- assertTrue(comparator.compare(complex1, complex2) != 0);
- assertTrue(comparator.compare(complex2, complex1) != 0);
-
- complex1 = createComplex2();
- complex2 = createComplex2();
-
- Species species = (Species) complex1.getElements().iterator().next();
- species.setName("new namne");
-
- assertTrue(comparator.compare(complex1, complex2) != 0);
- assertTrue(comparator.compare(complex2, complex1) != 0);
-
- complex1 = createComplex2();
- complex2 = createComplex2();
-
- complex1.setName("new namne");
-
- assertTrue(comparator.compare(complex1, complex2) != 0);
- assertTrue(comparator.compare(complex2, complex1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid() {
- try {
- Complex complex1 = createComplex2();
- Complex complex2 = createComplex2();
-
- GenericProtein protein = new GenericProtein("1");
- complex1.getElements().add(protein);
- protein = new GenericProtein("1");
- complex1.getElements().add(protein);
-
- complex2.getElements().add(new GenericProtein("b"));
- complex2.getElements().add(new GenericProtein("a"));
-
- comparator.compare(complex1, complex2);
- fail("Exception expected");
-
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test(expected = NotImplementedException.class)
- public void testInvalid3() {
- Complex invalidComplex = Mockito.mock(Complex.class);
-
- comparator.compare(invalidComplex, invalidComplex);
-
- }
-
- @Test
- public void testInvalid2() {
- try {
- Complex complex1 = createComplex2();
- Complex complex2 = createComplex2();
-
- Species protein = new GenericProtein("1");
- complex1.getElements().add(protein);
- protein = new GenericProtein("1");
- complex1.getElements().add(protein);
-
- complex2.getElements().add(new GenericProtein("A"));
- complex2.getElements().add(new GenericProtein("B"));
-
- comparator.compare(complex2, complex1);
- fail("Exception expected");
-
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testEquals2() {
- try {
- Complex complex1 = createComplex();
- Complex complex2 = createComplex();
-
- assertEquals(0, comparator.compare(complex1, complex1));
-
- assertEquals(0, comparator.compare(complex1, complex2));
- assertEquals(0, comparator.compare(complex2, complex1));
-
- complex2.addSpecies(new GenericProtein("test"));
- complex1.addSpecies(new GenericProtein("test"));
- assertEquals(0, comparator.compare(complex1, complex2));
- assertEquals(0, comparator.compare(complex2, complex1));
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- @Test
- public void testInvalidComp2() throws Exception {
- try {
- Complex complex1 = createComplex();
- Complex complex2 = createComplex();
-
- Species mock = Mockito.mock(Species.class);
- when(mock.getElementId()).thenReturn("id");
- complex1.addSpecies(mock);
- complex2.addSpecies(mock);
- comparator.compare(complex1, complex2);
- comparator.compare(complex2, complex1);
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testInvalidComp3() throws Exception {
- try {
- Complex complex1 = createComplex();
- Complex complex2 = createComplex();
- GenericProtein c = new GenericProtein("test");
- complex2.addSpecies(c);
- complex1.addSpecies(new GenericProtein("test"));
- Species mock = Mockito.mock(Species.class);
- when(mock.getElementId()).thenReturn("id");
- complex1.addSpecies(mock);
- complex2.addSpecies(mock);
- comparator.compare(complex2, complex1);
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testDifferent5() throws Exception {
- try {
- Complex complex1 = createComplex();
- Complex complex2 = createComplex();
- complex1.setHomodimer(123);
- assertTrue(comparator.compare(complex1, complex2) != 0);
- assertTrue(comparator.compare(complex2, complex1) != 0);
-
- complex1 = createComplex();
- complex2 = createComplex();
- complex1.getElements().iterator().next().setNotes("bla");
- assertTrue(comparator.compare(complex1, complex2) != 0);
- assertTrue(comparator.compare(complex2, complex1) != 0);
-
- complex1 = createComplex();
- complex2 = createComplex();
- complex1.getElements().clear();
- assertTrue(comparator.compare(complex1, complex2) != 0);
- assertTrue(comparator.compare(complex2, complex1) != 0);
-
- complex1 = createComplex();
- complex2 = createComplex();
- assertTrue(comparator.compare(null, complex2) != 0);
- assertTrue(comparator.compare(complex2, null) != 0);
- assertTrue(comparator.compare(null, null) == 0);
-
- complex1 = createComplex();
- complex2 = createComplex();
- Complex child = (Complex) complex1.getElements().iterator().next();
- child.getElements().iterator().next().setNotes("grand child notes");
- assertTrue(comparator.compare(complex1, complex2) != 0);
- assertTrue(comparator.compare(complex2, complex1) != 0);
-
- complex1 = createComplex();
- complex2 = createComplex();
- Protein prot = new GenericProtein();
- prot.setElementId("test");
- complex1.addSpecies(prot);
- assertTrue(comparator.compare(complex1, complex2) != 0);
- assertTrue(comparator.compare(complex2, complex1) != 0);
-
- complex1 = createComplex();
- complex2 = createComplex();
- complex1.setStructuralState("str");
- assertTrue(comparator.compare(complex1, complex2) != 0);
- assertTrue(comparator.compare(complex2, complex1) != 0);
-
- assertTrue(comparator.compare(new Complex(), Mockito.mock(Complex.class)) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent3() throws Exception {
- try {
- Complex complex1 = createComplex();
- Complex complex2 = createComplex();
- GenericProtein prot = new GenericProtein();
- prot.setElementId("test");
- complex1.addSpecies(prot);
- prot = new GenericProtein();
- prot.setElementId("test2");
- complex2.addSpecies(prot);
- assertTrue(comparator.compare(complex1, complex2) != 0);
- assertTrue(comparator.compare(complex2, complex1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent4() throws Exception {
- try {
- Complex complex1 = createComplex();
- Complex complex2 = createComplex();
- GenericProtein c = new GenericProtein("test");
- c.setName("a");
- complex2.addSpecies(c);
- complex2.addSpecies(new GenericProtein("test"));
- c.setName("");
-
- complex1.addSpecies(new GenericProtein("test"));
- GenericProtein d = new GenericProtein("test2");
- d.setName("a");
- complex1.addSpecies(d);
- assertTrue(comparator.compare(complex1, complex2) != 0);
- assertTrue(comparator.compare(complex2, complex1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent2() throws Exception {
- try {
- Complex complex1 = createComplex();
- Complex complex2 = createComplex();
- GenericProtein comp = new GenericProtein("test");
- comp.setFullName("X");
- complex1.addSpecies(comp);
- complex2.addSpecies(new GenericProtein("test"));
- assertTrue(comparator.compare(complex1, complex2) != 0);
- assertTrue(comparator.compare(complex2, complex1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- public Complex createComplex() {
- Complex result = new Complex();
-
- result.setHypothetical(true);
- result.setHomodimer(3);
-
- Complex child = new Complex();
- result.addSpecies(child);
- child.setCharge(12);
- child.setName("buu");
- child.setNotes("hey, hi, hello");
-
- Complex grandChild = new Complex();
- child.addSpecies(grandChild);
- child.setCharge(123);
- child.setName("buus");
- child.setNotes("hey, hi, hello !!");
-
- return result;
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import static org.mockito.Mockito.when;
+
+import java.awt.Color;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class ComplexComparatorTest {
+
+ Logger logger = Logger.getLogger(ComplexComparatorTest.class);
+ ComplexComparator comparator = new ComplexComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ Complex complex1 = createComplex2();
+ Complex complex2 = createComplex2();
+
+ assertEquals(0, comparator.compare(complex1, complex2));
+
+ assertEquals(0, comparator.compare(null, null));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Complex createComplex2() {
+ Complex result = new Complex();
+ result.setName("complex");
+
+ result.setElementId("asd");
+ result.setX(12.0);
+ result.setY(123.0);
+ result.setWidth(4);
+ result.setHeight(5);
+ result.setFontSize(9.0);
+ result.setColor(Color.BLUE);
+ result.setVisibilityLevel("14");
+
+ Species protein = new GenericProtein("S");
+ protein.setName("a");
+ result.addSpecies(protein);
+
+ return result;
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ Complex complex1 = createComplex2();
+ Complex complex2 = createComplex2();
+
+ assertTrue(comparator.compare(complex1, null) != 0);
+ assertTrue(comparator.compare(null, complex1) != 0);
+
+ complex1 = createComplex2();
+ complex2 = createComplex2();
+
+ complex1.setElementId("tmp");
+
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
+
+ complex1 = createComplex2();
+ complex2 = createComplex2();
+
+ complex1.addSpecies(new GenericProtein("id"));
+
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
+
+ complex1 = createComplex2();
+ complex2 = createComplex2();
+
+ complex1.getElements().iterator().next().setElementId("bnu");
+
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
+
+ complex1 = createComplex2();
+ complex2 = createComplex2();
+
+ Species species = (Species) complex1.getElements().iterator().next();
+ species.setName("new namne");
+
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
+
+ complex1 = createComplex2();
+ complex2 = createComplex2();
+
+ complex1.setName("new namne");
+
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid() {
+ try {
+ Complex complex1 = createComplex2();
+ Complex complex2 = createComplex2();
+
+ GenericProtein protein = new GenericProtein("1");
+ complex1.getElements().add(protein);
+ protein = new GenericProtein("1");
+ complex1.getElements().add(protein);
+
+ complex2.getElements().add(new GenericProtein("b"));
+ complex2.getElements().add(new GenericProtein("a"));
+
+ comparator.compare(complex1, complex2);
+ fail("Exception expected");
+
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test(expected = NotImplementedException.class)
+ public void testInvalid3() {
+ Complex invalidComplex = Mockito.mock(Complex.class);
+
+ comparator.compare(invalidComplex, invalidComplex);
+
+ }
+
+ @Test
+ public void testInvalid2() {
+ try {
+ Complex complex1 = createComplex2();
+ Complex complex2 = createComplex2();
+
+ Species protein = new GenericProtein("1");
+ complex1.getElements().add(protein);
+ protein = new GenericProtein("1");
+ complex1.getElements().add(protein);
+
+ complex2.getElements().add(new GenericProtein("A"));
+ complex2.getElements().add(new GenericProtein("B"));
+
+ comparator.compare(complex2, complex1);
+ fail("Exception expected");
+
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testEquals2() {
+ try {
+ Complex complex1 = createComplex();
+ Complex complex2 = createComplex();
+
+ assertEquals(0, comparator.compare(complex1, complex1));
+
+ assertEquals(0, comparator.compare(complex1, complex2));
+ assertEquals(0, comparator.compare(complex2, complex1));
+
+ complex2.addSpecies(new GenericProtein("test"));
+ complex1.addSpecies(new GenericProtein("test"));
+ assertEquals(0, comparator.compare(complex1, complex2));
+ assertEquals(0, comparator.compare(complex2, complex1));
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ @Test
+ public void testInvalidComp2() throws Exception {
+ try {
+ Complex complex1 = createComplex();
+ Complex complex2 = createComplex();
+
+ Species mock = Mockito.mock(Species.class);
+ when(mock.getElementId()).thenReturn("id");
+ complex1.addSpecies(mock);
+ complex2.addSpecies(mock);
+ comparator.compare(complex1, complex2);
+ comparator.compare(complex2, complex1);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testInvalidComp3() throws Exception {
+ try {
+ Complex complex1 = createComplex();
+ Complex complex2 = createComplex();
+ GenericProtein c = new GenericProtein("test");
+ complex2.addSpecies(c);
+ complex1.addSpecies(new GenericProtein("test"));
+ Species mock = Mockito.mock(Species.class);
+ when(mock.getElementId()).thenReturn("id");
+ complex1.addSpecies(mock);
+ complex2.addSpecies(mock);
+ comparator.compare(complex2, complex1);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testDifferent5() throws Exception {
+ try {
+ Complex complex1 = createComplex();
+ Complex complex2 = createComplex();
+ complex1.setHomodimer(123);
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
+
+ complex1 = createComplex();
+ complex2 = createComplex();
+ complex1.getElements().iterator().next().setNotes("bla");
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
+
+ complex1 = createComplex();
+ complex2 = createComplex();
+ complex1.getElements().clear();
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
+
+ complex1 = createComplex();
+ complex2 = createComplex();
+ assertTrue(comparator.compare(null, complex2) != 0);
+ assertTrue(comparator.compare(complex2, null) != 0);
+ assertTrue(comparator.compare(null, null) == 0);
+
+ complex1 = createComplex();
+ complex2 = createComplex();
+ Complex child = (Complex) complex1.getElements().iterator().next();
+ child.getElements().iterator().next().setNotes("grand child notes");
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
+
+ complex1 = createComplex();
+ complex2 = createComplex();
+ Protein prot = new GenericProtein();
+ prot.setElementId("test");
+ complex1.addSpecies(prot);
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
+
+ complex1 = createComplex();
+ complex2 = createComplex();
+ complex1.setStructuralState("str");
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
+
+ assertTrue(comparator.compare(new Complex(), Mockito.mock(Complex.class)) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent3() throws Exception {
+ try {
+ Complex complex1 = createComplex();
+ Complex complex2 = createComplex();
+ GenericProtein prot = new GenericProtein();
+ prot.setElementId("test");
+ complex1.addSpecies(prot);
+ prot = new GenericProtein();
+ prot.setElementId("test2");
+ complex2.addSpecies(prot);
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent4() throws Exception {
+ try {
+ Complex complex1 = createComplex();
+ Complex complex2 = createComplex();
+ GenericProtein c = new GenericProtein("test");
+ c.setName("a");
+ complex2.addSpecies(c);
+ complex2.addSpecies(new GenericProtein("test"));
+ c.setName("");
+
+ complex1.addSpecies(new GenericProtein("test"));
+ GenericProtein d = new GenericProtein("test2");
+ d.setName("a");
+ complex1.addSpecies(d);
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent2() throws Exception {
+ try {
+ Complex complex1 = createComplex();
+ Complex complex2 = createComplex();
+ GenericProtein comp = new GenericProtein("test");
+ comp.setFullName("X");
+ complex1.addSpecies(comp);
+ complex2.addSpecies(new GenericProtein("test"));
+ assertTrue(comparator.compare(complex1, complex2) != 0);
+ assertTrue(comparator.compare(complex2, complex1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ public Complex createComplex() {
+ Complex result = new Complex();
+
+ result.setHypothetical(true);
+ result.setHomodimer(3);
+
+ Complex child = new Complex();
+ result.addSpecies(child);
+ child.setCharge(12);
+ child.setName("buu");
+ child.setNotes("hey, hi, hello");
+
+ Complex grandChild = new Complex();
+ child.addSpecies(grandChild);
+ child.setCharge(123);
+ child.setName("buus");
+ child.setNotes("hey, hi, hello !!");
+
+ return result;
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexTest.java
index 6e10c57191..1af1ed5d4c 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexTest.java
@@ -1,181 +1,181 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.ModelTestFunctions;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class ComplexTest extends ModelTestFunctions {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new Complex());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- Complex complex = new Complex();
- complex.addSpecies(new GenericProtein());
- Complex copy = new Complex(complex);
- assertNotNull(copy);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddElement() {
- try {
- Complex complex = new Complex();
- Species species = new GenericProtein("id1");
- complex.addSpecies(species);
- assertEquals(1, complex.getAllChildren().size());
- complex.addSpecies(species);
- assertEquals(1, complex.getAllChildren().size());
- Species protein2 = new GenericProtein("s");
- complex.addSpecies(protein2);
- assertEquals(2, complex.getAllChildren().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAllChildren() {
- try {
- Complex complex = new Complex();
-
- complex.addSpecies(new GenericProtein("1"));
- Complex complex2 = new Complex("c3");
- complex2.addSpecies(new GenericProtein("2"));
- complex2.addSpecies(new GenericProtein("4"));
-
- complex.addSpecies(complex2);
-
- assertEquals(4, complex.getAllChildren().size());
- assertEquals(2, complex.getElements().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRemoveElement() {
- try {
- Complex complex = new Complex();
-
- Species protein = new GenericProtein("1");
- complex.addSpecies(protein);
- complex.addSpecies(new GenericProtein("2"));
- complex.addSpecies(new GenericProtein("4"));
-
- assertEquals(3, complex.getElements().size());
- complex.removeElement(protein);
- assertEquals(2, complex.getElements().size());
- complex.removeElement(protein);
- assertEquals(2, complex.getElements().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRemoveNonExistingElement() {
- try {
- Complex complex = new Complex();
- Complex complex2 = new Complex();
-
- Species protein = new GenericProtein("1");
- protein.setComplex(complex2);
- complex.removeElement(protein);
-
- assertEquals(1, super.getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- Complex original = new Complex();
- Complex copy = original.copy();
- assertNotNull(copy);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- Complex original = new Complex();
- assertNotNull(original.getStringType());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAllSimpleChildren() {
- try {
- Complex child = new Complex();
- child.addSpecies(new GenericProtein("id2"));
- Complex original = new Complex();
- original.addSpecies(child);
- original.addSpecies(new Complex());
- original.addSpecies(new GenericProtein("id"));
- assertEquals(2, original.getAllSimpleChildren().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- Complex object = Mockito.spy(Complex.class);
- object.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.ModelTestFunctions;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class ComplexTest extends ModelTestFunctions {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new Complex());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ Complex complex = new Complex();
+ complex.addSpecies(new GenericProtein());
+ Complex copy = new Complex(complex);
+ assertNotNull(copy);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddElement() {
+ try {
+ Complex complex = new Complex();
+ Species species = new GenericProtein("id1");
+ complex.addSpecies(species);
+ assertEquals(1, complex.getAllChildren().size());
+ complex.addSpecies(species);
+ assertEquals(1, complex.getAllChildren().size());
+ Species protein2 = new GenericProtein("s");
+ complex.addSpecies(protein2);
+ assertEquals(2, complex.getAllChildren().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAllChildren() {
+ try {
+ Complex complex = new Complex();
+
+ complex.addSpecies(new GenericProtein("1"));
+ Complex complex2 = new Complex("c3");
+ complex2.addSpecies(new GenericProtein("2"));
+ complex2.addSpecies(new GenericProtein("4"));
+
+ complex.addSpecies(complex2);
+
+ assertEquals(4, complex.getAllChildren().size());
+ assertEquals(2, complex.getElements().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRemoveElement() {
+ try {
+ Complex complex = new Complex();
+
+ Species protein = new GenericProtein("1");
+ complex.addSpecies(protein);
+ complex.addSpecies(new GenericProtein("2"));
+ complex.addSpecies(new GenericProtein("4"));
+
+ assertEquals(3, complex.getElements().size());
+ complex.removeElement(protein);
+ assertEquals(2, complex.getElements().size());
+ complex.removeElement(protein);
+ assertEquals(2, complex.getElements().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRemoveNonExistingElement() {
+ try {
+ Complex complex = new Complex();
+ Complex complex2 = new Complex();
+
+ Species protein = new GenericProtein("1");
+ protein.setComplex(complex2);
+ complex.removeElement(protein);
+
+ assertEquals(1, super.getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ Complex original = new Complex();
+ Complex copy = original.copy();
+ assertNotNull(copy);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ Complex original = new Complex();
+ assertNotNull(original.getStringType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAllSimpleChildren() {
+ try {
+ Complex child = new Complex();
+ child.addSpecies(new GenericProtein("id2"));
+ Complex original = new Complex();
+ original.addSpecies(child);
+ original.addSpecies(new Complex());
+ original.addSpecies(new GenericProtein("id"));
+ assertEquals(2, original.getAllSimpleChildren().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ Complex object = Mockito.spy(Complex.class);
+ object.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/DegradedComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/DegradedComparatorTest.java
index e21a9162f1..9a9ed82eeb 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/DegradedComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/DegradedComparatorTest.java
@@ -1,83 +1,83 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class DegradedComparatorTest {
-
- DegradedComparator comparator = new DegradedComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- Degraded degraded1 = createDegraded();
- Degraded degraded2 = createDegraded();
-
- assertEquals(0, comparator.compare(degraded1, degraded1));
-
- assertEquals(0, comparator.compare(degraded1, degraded2));
- assertEquals(0, comparator.compare(degraded2, degraded1));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- @Test
- public void testDifferent() {
- try {
- Degraded degraded1 = createDegraded();
- Degraded degraded2 = createDegraded();
- degraded1 = createDegraded();
- degraded2 = createDegraded();
- degraded1.setCharge(54);
- assertTrue(comparator.compare(degraded1, degraded2) != 0);
- assertTrue(comparator.compare(degraded2, degraded1) != 0);
-
- degraded1 = createDegraded();
- degraded2 = createDegraded();
- assertTrue(comparator.compare(null, degraded2) != 0);
- assertTrue(comparator.compare(degraded2, null) != 0);
- assertTrue(comparator.compare(null, null) == 0);
-
- Degraded degraded = createDegraded();
- degraded.setName("n");
- assertTrue(comparator.compare(degraded, degraded1) != 0);
-
- assertTrue(comparator.compare(degraded, Mockito.mock(Degraded.class)) != 0);
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- public Degraded createDegraded() {
- Degraded result = new Degraded();
- result.setCharge(12);
- return result;
- }
-
- @Test(expected = NotImplementedException.class)
- public void testInvalid() {
- Degraded object = Mockito.mock(Degraded.class);
-
- comparator.compare(object, object);
- }
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class DegradedComparatorTest {
+
+ DegradedComparator comparator = new DegradedComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ Degraded degraded1 = createDegraded();
+ Degraded degraded2 = createDegraded();
+
+ assertEquals(0, comparator.compare(degraded1, degraded1));
+
+ assertEquals(0, comparator.compare(degraded1, degraded2));
+ assertEquals(0, comparator.compare(degraded2, degraded1));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ Degraded degraded1 = createDegraded();
+ Degraded degraded2 = createDegraded();
+ degraded1 = createDegraded();
+ degraded2 = createDegraded();
+ degraded1.setCharge(54);
+ assertTrue(comparator.compare(degraded1, degraded2) != 0);
+ assertTrue(comparator.compare(degraded2, degraded1) != 0);
+
+ degraded1 = createDegraded();
+ degraded2 = createDegraded();
+ assertTrue(comparator.compare(null, degraded2) != 0);
+ assertTrue(comparator.compare(degraded2, null) != 0);
+ assertTrue(comparator.compare(null, null) == 0);
+
+ Degraded degraded = createDegraded();
+ degraded.setName("n");
+ assertTrue(comparator.compare(degraded, degraded1) != 0);
+
+ assertTrue(comparator.compare(degraded, Mockito.mock(Degraded.class)) != 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ public Degraded createDegraded() {
+ Degraded result = new Degraded();
+ result.setCharge(12);
+ return result;
+ }
+
+ @Test(expected = NotImplementedException.class)
+ public void testInvalid() {
+ Degraded object = Mockito.mock(Degraded.class);
+
+ comparator.compare(object, object);
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/DegradedTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/DegradedTest.java
index b41fdde8f4..49e886ebf5 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/DegradedTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/DegradedTest.java
@@ -1,80 +1,80 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class DegradedTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new Degraded());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- Degraded degraded = new Degraded("");
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- Degraded degraded = new Degraded(new Degraded());
- assertNotNull(degraded.getStringType());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- Degraded degraded = new Degraded().copy();
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- Degraded object = Mockito.spy(Degraded.class);
- object.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class DegradedTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new Degraded());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ Degraded degraded = new Degraded("");
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ Degraded degraded = new Degraded(new Degraded());
+ assertNotNull(degraded.getStringType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ Degraded degraded = new Degraded().copy();
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ Degraded object = Mockito.spy(Degraded.class);
+ object.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/DrugComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/DrugComparatorTest.java
index 266e2dcb24..2351016ea2 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/DrugComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/DrugComparatorTest.java
@@ -1,75 +1,75 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class DrugComparatorTest {
-
- DrugComparator comparator = new DrugComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- Drug drug1 = createDrug();
- Drug drug2 = createDrug();
-
- assertEquals(0, comparator.compare(drug1, drug1));
-
- assertEquals(0, comparator.compare(drug1, drug2));
- assertEquals(0, comparator.compare(drug2, drug1));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- @Test
- public void testDifferent() {
- try {
- Drug drug2 = createDrug();
- assertTrue(comparator.compare(null, drug2) != 0);
- assertTrue(comparator.compare(drug2, null) != 0);
- assertTrue(comparator.compare(null, null) == 0);
-
- Drug drug = createDrug();
- drug.setName("n");
- assertTrue(comparator.compare(drug, drug2) != 0);
-
- assertTrue(comparator.compare(drug, Mockito.mock(Drug.class)) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- public Drug createDrug() {
- Drug result = new Drug();
- return result;
- }
-
- @Test(expected = NotImplementedException.class)
- public void testInvalid() {
- Drug object = Mockito.mock(Drug.class);
-
- comparator.compare(object, object);
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class DrugComparatorTest {
+
+ DrugComparator comparator = new DrugComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ Drug drug1 = createDrug();
+ Drug drug2 = createDrug();
+
+ assertEquals(0, comparator.compare(drug1, drug1));
+
+ assertEquals(0, comparator.compare(drug1, drug2));
+ assertEquals(0, comparator.compare(drug2, drug1));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ Drug drug2 = createDrug();
+ assertTrue(comparator.compare(null, drug2) != 0);
+ assertTrue(comparator.compare(drug2, null) != 0);
+ assertTrue(comparator.compare(null, null) == 0);
+
+ Drug drug = createDrug();
+ drug.setName("n");
+ assertTrue(comparator.compare(drug, drug2) != 0);
+
+ assertTrue(comparator.compare(drug, Mockito.mock(Drug.class)) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ public Drug createDrug() {
+ Drug result = new Drug();
+ return result;
+ }
+
+ @Test(expected = NotImplementedException.class)
+ public void testInvalid() {
+ Drug object = Mockito.mock(Drug.class);
+
+ comparator.compare(object, object);
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/DrugTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/DrugTest.java
index bb1dd2c8b5..1bebe8771b 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/DrugTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/DrugTest.java
@@ -1,80 +1,80 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class DrugTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new Drug());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- Drug degraded = new Drug("");
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- Drug degraded = new Drug(new Drug());
- assertNotNull(degraded.getStringType());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- Drug degraded = new Drug().copy();
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- Drug drug = Mockito.spy(Drug.class);
- drug.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class DrugTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new Drug());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ Drug degraded = new Drug("");
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ Drug degraded = new Drug(new Drug());
+ assertNotNull(degraded.getStringType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ Drug degraded = new Drug().copy();
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ Drug drug = Mockito.spy(Drug.class);
+ drug.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ElementComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ElementComparatorTest.java
index 19058bdb84..b4bc5fde03 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ElementComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ElementComparatorTest.java
@@ -1,321 +1,321 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.awt.Color;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.InvalidClassException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.model.SubmodelType;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
-
-public class ElementComparatorTest {
-
- ElementComparator comparator = new ElementComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testCompareException() throws Exception {
- try {
- comparator.compare(Mockito.mock(Element.class), Mockito.mock(Element.class));
-
- fail("Exception should occur");
- } catch (NotImplementedException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent() throws Exception {
- try {
- assertTrue(comparator.compare(new GenericProtein("id2"), new GenericProtein("id1")) != 0);
-
- assertTrue(comparator.compare(null, new GenericProtein()) != 0);
- assertTrue(comparator.compare(new GenericProtein(), null) != 0);
- assertTrue(comparator.compare(new GenericProtein(), new Complex()) != 0);
-
- Species sa1 = new GenericProtein("id2");
- Species sa2 = new GenericProtein("id2");
- sa2.setX(2);
- assertTrue(comparator.compare(sa1, sa2) != 0);
-
- sa1 = new GenericProtein("id2");
- sa2 = new GenericProtein("id2");
- sa2.setY(2);
- assertTrue(comparator.compare(sa1, sa2) != 0);
-
- sa1 = new GenericProtein("id2");
- sa2 = new GenericProtein("id2");
- sa2.setHeight(2);
- assertTrue(comparator.compare(sa1, sa2) != 0);
-
- sa1 = new GenericProtein("id2");
- sa2 = new GenericProtein("id2");
- sa2.setFontSize(2);
- assertTrue(comparator.compare(sa1, sa2) != 0);
-
- sa1 = new GenericProtein("id2");
- sa2 = new GenericProtein("id2");
- sa2.setColor(Color.BLUE);
- assertTrue(comparator.compare(sa1, sa2) != 0);
-
- sa1 = new GenericProtein("id2");
- sa2 = new GenericProtein("id2");
- sa2.setVisibilityLevel(6);
- assertTrue(comparator.compare(sa1, sa2) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCompareSubmodel() throws Exception {
- try {
- Element element1 = createElement();
- Element element2 = createElement();
- assertEquals(0, comparator.compare(element1, element2));
-
- element1.setSubmodel(null);
- assertTrue(comparator.compare(element1, element2) != 0);
- assertTrue(comparator.compare(element2, element1) != 0);
-
- element1 = createElement();
- element2 = createElement();
-
- element1.getSubmodel().setName("Na");
-
- assertTrue(comparator.compare(element1, element2) != 0);
- assertTrue(comparator.compare(element2, element1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private Element createElement() {
- Element result = new GenericProtein("id2");
- ElementSubmodelConnection submodel = new ElementSubmodelConnection(getModel(), SubmodelType.DOWNSTREAM_TARGETS);
- result.setSubmodel(submodel);
- return result;
- }
-
- private Model getModel() {
- Model model = new ModelFullIndexed(null);
-
- model.setNotes("Some description");
- GenericProtein protein = new GenericProtein("A");
- protein.setName("ad");
- model.addElement(protein);
-
- Protein protein2 = new GenericProtein("a_id");
- protein2.setName("ad");
- model.addElement(protein2);
-
- model.addElement(new Compartment("default"));
-
- Layer layer = new Layer();
- layer.setName("layer name");
- model.addLayer(layer);
-
- model.addReaction(new Reaction());
- return model;
- }
-
- @Test
- public void testException() {
- try {
- Element el = Mockito.mock(Element.class);
- comparator.compare(el, el);
-
- fail("Exception should occur");
- } catch (NotImplementedException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInternalCompare() {
- try {
- SimpleMolecule species1 = createSimpleMolecule();
- assertTrue(comparator.internalCompare(species1, null) != 0);
- assertTrue(comparator.internalCompare(null, species1) != 0);
-
- assertEquals(0, comparator.internalCompare(null, null));
-
- } catch (InvalidClassException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent2() {
- try {
- SimpleMolecule species1 = createSimpleMolecule();
- SimpleMolecule species2 = createSimpleMolecule();
-
- species1.setCharge(99);
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.setHomodimer(233);
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.setFormula("a");
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.setElementId("");
- species1.setElementId("ASD");
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.setNotes("ASD");
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.setPositionToCompartment(PositionToCompartment.INSIDE);
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.getMiriamData().clear();
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.getMiriamData().iterator().next().setRelationType(MiriamRelationType.BQ_BIOL_HAS_PART);
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.addMiriamData(new MiriamData());
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- assertTrue(comparator.compare(species1, null) != 0);
- assertTrue(comparator.compare(null, species1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unkowne exception");
- }
- }
-
- @Test
- public void testDifferentNewFields() throws Exception {
- try {
- SimpleMolecule species1 = createSimpleMolecule();
- SimpleMolecule species2 = createSimpleMolecule();
-
- species1.setSymbol("some symbol");
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
-
- species1.setFullName("some symbol");
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
-
- species1.getSynonyms().add("asd");
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
-
- species1.getFormerSymbols().add("asd");
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- public SimpleMolecule createSimpleMolecule() {
- SimpleMolecule result = new SimpleMolecule("id");
- result.setHomodimer(12);
- result.setName("id");
- result.setInitialAmount(12.0);
- result.setCharge(13);
- result.setInitialConcentration(14.0);
- result.setOnlySubstanceUnits(true);
- result.setPositionToCompartment(PositionToCompartment.TRANSMEMBRANE);
- result.setNotes("id");
- MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, "c");
- result.addMiriamData(md);
- return result;
- }
-
- @Test
- public void testDifferentNewReconFields() throws Exception {
- try {
- SimpleMolecule element1 = createSimpleMolecule();
-
- SimpleMolecule element2 = createSimpleMolecule();
- element2.setAbbreviation("ABRR");
-
- assertTrue(comparator.compare(element1, element2) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.awt.Color;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.InvalidClassException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.model.SubmodelType;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
+
+public class ElementComparatorTest {
+
+ ElementComparator comparator = new ElementComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testCompareException() throws Exception {
+ try {
+ comparator.compare(Mockito.mock(Element.class), Mockito.mock(Element.class));
+
+ fail("Exception should occur");
+ } catch (NotImplementedException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent() throws Exception {
+ try {
+ assertTrue(comparator.compare(new GenericProtein("id2"), new GenericProtein("id1")) != 0);
+
+ assertTrue(comparator.compare(null, new GenericProtein()) != 0);
+ assertTrue(comparator.compare(new GenericProtein(), null) != 0);
+ assertTrue(comparator.compare(new GenericProtein(), new Complex()) != 0);
+
+ Species sa1 = new GenericProtein("id2");
+ Species sa2 = new GenericProtein("id2");
+ sa2.setX(2);
+ assertTrue(comparator.compare(sa1, sa2) != 0);
+
+ sa1 = new GenericProtein("id2");
+ sa2 = new GenericProtein("id2");
+ sa2.setY(2);
+ assertTrue(comparator.compare(sa1, sa2) != 0);
+
+ sa1 = new GenericProtein("id2");
+ sa2 = new GenericProtein("id2");
+ sa2.setHeight(2);
+ assertTrue(comparator.compare(sa1, sa2) != 0);
+
+ sa1 = new GenericProtein("id2");
+ sa2 = new GenericProtein("id2");
+ sa2.setFontSize(2);
+ assertTrue(comparator.compare(sa1, sa2) != 0);
+
+ sa1 = new GenericProtein("id2");
+ sa2 = new GenericProtein("id2");
+ sa2.setColor(Color.BLUE);
+ assertTrue(comparator.compare(sa1, sa2) != 0);
+
+ sa1 = new GenericProtein("id2");
+ sa2 = new GenericProtein("id2");
+ sa2.setVisibilityLevel(6);
+ assertTrue(comparator.compare(sa1, sa2) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCompareSubmodel() throws Exception {
+ try {
+ Element element1 = createElement();
+ Element element2 = createElement();
+ assertEquals(0, comparator.compare(element1, element2));
+
+ element1.setSubmodel(null);
+ assertTrue(comparator.compare(element1, element2) != 0);
+ assertTrue(comparator.compare(element2, element1) != 0);
+
+ element1 = createElement();
+ element2 = createElement();
+
+ element1.getSubmodel().setName("Na");
+
+ assertTrue(comparator.compare(element1, element2) != 0);
+ assertTrue(comparator.compare(element2, element1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Element createElement() {
+ Element result = new GenericProtein("id2");
+ ElementSubmodelConnection submodel = new ElementSubmodelConnection(getModel(), SubmodelType.DOWNSTREAM_TARGETS);
+ result.setSubmodel(submodel);
+ return result;
+ }
+
+ private Model getModel() {
+ Model model = new ModelFullIndexed(null);
+
+ model.setNotes("Some description");
+ GenericProtein protein = new GenericProtein("A");
+ protein.setName("ad");
+ model.addElement(protein);
+
+ Protein protein2 = new GenericProtein("a_id");
+ protein2.setName("ad");
+ model.addElement(protein2);
+
+ model.addElement(new Compartment("default"));
+
+ Layer layer = new Layer();
+ layer.setName("layer name");
+ model.addLayer(layer);
+
+ model.addReaction(new Reaction());
+ return model;
+ }
+
+ @Test
+ public void testException() {
+ try {
+ Element el = Mockito.mock(Element.class);
+ comparator.compare(el, el);
+
+ fail("Exception should occur");
+ } catch (NotImplementedException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInternalCompare() {
+ try {
+ SimpleMolecule species1 = createSimpleMolecule();
+ assertTrue(comparator.internalCompare(species1, null) != 0);
+ assertTrue(comparator.internalCompare(null, species1) != 0);
+
+ assertEquals(0, comparator.internalCompare(null, null));
+
+ } catch (InvalidClassException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent2() {
+ try {
+ SimpleMolecule species1 = createSimpleMolecule();
+ SimpleMolecule species2 = createSimpleMolecule();
+
+ species1.setCharge(99);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.setHomodimer(233);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.setFormula("a");
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.setElementId("");
+ species1.setElementId("ASD");
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.setNotes("ASD");
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.setPositionToCompartment(PositionToCompartment.INSIDE);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.getMiriamData().clear();
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.getMiriamData().iterator().next().setRelationType(MiriamRelationType.BQ_BIOL_HAS_PART);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.addMiriamData(new MiriamData());
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ assertTrue(comparator.compare(species1, null) != 0);
+ assertTrue(comparator.compare(null, species1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unkowne exception");
+ }
+ }
+
+ @Test
+ public void testDifferentNewFields() throws Exception {
+ try {
+ SimpleMolecule species1 = createSimpleMolecule();
+ SimpleMolecule species2 = createSimpleMolecule();
+
+ species1.setSymbol("some symbol");
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+
+ species1.setFullName("some symbol");
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+
+ species1.getSynonyms().add("asd");
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+
+ species1.getFormerSymbols().add("asd");
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ public SimpleMolecule createSimpleMolecule() {
+ SimpleMolecule result = new SimpleMolecule("id");
+ result.setHomodimer(12);
+ result.setName("id");
+ result.setInitialAmount(12.0);
+ result.setCharge(13);
+ result.setInitialConcentration(14.0);
+ result.setOnlySubstanceUnits(true);
+ result.setPositionToCompartment(PositionToCompartment.TRANSMEMBRANE);
+ result.setNotes("id");
+ MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, "c");
+ result.addMiriamData(md);
+ return result;
+ }
+
+ @Test
+ public void testDifferentNewReconFields() throws Exception {
+ try {
+ SimpleMolecule element1 = createSimpleMolecule();
+
+ SimpleMolecule element2 = createSimpleMolecule();
+ element2.setAbbreviation("ABRR");
+
+ assertTrue(comparator.compare(element1, element2) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ElementTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ElementTest.java
index 540521afd2..62a8b5829d 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ElementTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ElementTest.java
@@ -1,404 +1,404 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.ModelTestFunctions;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.SearchIndex;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.layout.graphics.LayerText;
-import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-
-public class ElementTest extends ModelTestFunctions {
-
- private static double EPSILON = Configuration.EPSILON;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testDistance1() {
- Species species = new GenericProtein();
- species.setWidth(10);
- species.setHeight(20);
- species.setX(100.0);
- species.setY(200.0);
- double distance = species.getDistanceFromPoint(species.getCenter());
- assertEquals(0, distance, EPSILON);
- }
-
- @Test
- public void testDistance2() {
- Species species = new GenericProtein();
- species.setWidth(10);
- species.setHeight(20);
- species.setX(100.0);
- species.setY(200.0);
- double distance = species.getDistanceFromPoint(new Point2D.Double(100, 205));
- assertEquals(0, distance, EPSILON);
- }
-
- @Test
- public void testDistance6() {
- Species species = new GenericProtein();
- species.setWidth(10);
- species.setHeight(20);
- species.setX(100.0);
- species.setY(200.0);
- double distance = species.getDistanceFromPoint(new Point2D.Double(105, 95));
- assertEquals(105, distance, EPSILON);
- }
-
- @Test
- public void testDistance3() {
- Species species = new GenericProtein();
- species.setWidth(10);
- species.setHeight(20);
- species.setX(100.0);
- species.setY(200.0);
- double distance = species.getDistanceFromPoint(new Point2D.Double(50, 205));
- assertEquals(50, distance, EPSILON);
- }
-
- @Test
- public void testDistance4() {
- Species species = new GenericProtein();
- species.setWidth(10);
- species.setHeight(20);
- species.setX(100.0);
- species.setY(200.0);
- double distance = species.getDistanceFromPoint(new Point2D.Double(120, 230));
- assertEquals(Math.sqrt(200), distance, EPSILON);
- }
-
- @Test
- public void testConstructor() {
- try {
- GenericProtein protein = new GenericProtein();
- protein.addSearchIndex(new SearchIndex());
- protein.setSubmodel(new ElementSubmodelConnection());
- Element copy = new GenericProtein(protein);
- assertNotNull(copy);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testIncreaseBorder() {
- try {
- Species protein = new GenericProtein();
- assertEquals(0.0, protein.getSize(), Configuration.EPSILON);
- protein.increaseBorder(2);
- assertEquals(16.0, protein.getSize(), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- Element element = new GenericProtein();
- Double nullDouble = null;
- String xStr = "1.2";
- Double x = 1.2;
- String yStr = "1.3";
- Double y = 1.3;
- String fontSizeStr = "5.0";
- Double fontSize = 5.0;
- int fontSizeInt = 5;
- String widthStr = "3.0";
- Double width = 3.0;
- String heightStr = "4.0";
- Double height = 4.0;
- ModelData modelData = new ModelData();
- Set<MiriamData> miriamData = new HashSet<>();
- Compartment compartment = new Compartment("idd");
- int id = 72;
- String transparencyLevel = "2";
- Model model = new ModelFullIndexed(modelData);
- List<SearchIndex> indexes = new ArrayList<>();
- indexes.add(new SearchIndex());
-
- element.setMiriamData(miriamData);
- assertEquals(miriamData, element.getMiriamData());
-
- element.setX(xStr);
- assertEquals(x, element.getX(), Configuration.EPSILON);
- element.setX(nullDouble);
- assertNull(element.getX());
- element.setX(x);
- assertEquals(x, element.getX(), Configuration.EPSILON);
-
- element.setY(yStr);
- assertEquals(y, element.getY(), Configuration.EPSILON);
- element.setY(nullDouble);
- assertNull(element.getY());
- element.setY(y);
- assertEquals(y, element.getY(), Configuration.EPSILON);
-
- element.setFontSize(fontSizeStr);
- assertEquals(fontSize, element.getFontSize(), Configuration.EPSILON);
- element.setFontSize(nullDouble);
- assertNull(element.getFontSize());
- element.setFontSize(fontSize);
- assertEquals(fontSize, element.getFontSize(), Configuration.EPSILON);
- element.setFontSize(nullDouble);
- assertNull(element.getFontSize());
- element.setFontSize(fontSizeInt);
- assertEquals(fontSize, element.getFontSize(), Configuration.EPSILON);
-
- element.setWidth(widthStr);
- assertEquals(width, element.getWidth(), Configuration.EPSILON);
- element.setWidth(nullDouble);
- assertNull(element.getWidth());
- element.setWidth(width);
- assertEquals(width, element.getWidth(), Configuration.EPSILON);
- try {
- element.setWidth("as");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
-
- element.setHeight(heightStr);
- assertEquals(height, element.getHeight(), Configuration.EPSILON);
- element.setHeight(nullDouble);
- assertNull(element.getHeight());
- element.setHeight(height);
- assertEquals(height, element.getHeight(), Configuration.EPSILON);
- try {
- element.setHeight("as");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
-
- element.setCompartment(compartment);
- assertEquals(compartment, element.getCompartment());
- element.setId(id);
- assertEquals(id, element.getId());
- element.setTransparencyLevel(transparencyLevel);
- assertEquals(transparencyLevel, element.getTransparencyLevel());
- element.setModel(model);
- assertEquals(model, element.getModel());
- element.setModelData(modelData);
- assertEquals(modelData, element.getModelData());
- element.setSearchIndexes(indexes);
- assertEquals(indexes, element.getSearchIndexes());
-
- assertNotNull(element.getBorder());
-
- element = Mockito.spy(Element.class);
- List<String> synonyms = new ArrayList<>();
- List<String> formerSymbols = new ArrayList<>();
- String formula = "some_form";
-
- element.setSynonyms(synonyms);
- element.setFormerSymbols(formerSymbols);
- element.setModel(model);
- element.setFormula(formula);
-
- assertEquals(synonyms, element.getSynonyms());
- assertEquals(formerSymbols, element.getFormerSymbols());
- assertEquals(model.getModelData(), element.getModelData());
- assertEquals(formula, element.getFormula());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testContainsElement() {
- try {
- Species element = new GenericProtein();
- element.setWidth(100);
- element.setHeight(100);
- Species element2 = new GenericProtein();
- element2.setX(-2);
- element2.setY(-2);
- element2.setWidth(100);
- element2.setHeight(100);
-
- assertTrue(element.contains(element2));
- element2.setX(2);
- element2.setY(2);
- assertTrue(element.contains(element2));
- element2.setX(-2);
- element2.setY(2);
- assertTrue(element.contains(element2));
- element2.setX(2);
- element2.setY(-2);
- assertTrue(element.contains(element2));
-
- element2.setX(-2);
- element2.setY(-2);
- element2.setWidth(200);
- element2.setHeight(200);
- assertFalse(element.contains(element2));
-
- Compartment compartment = new Compartment("idd");
- compartment.setX(2);
- compartment.setY(2);
- compartment.setWidth(10);
- compartment.setHeight(100);
- assertFalse(element.contains(compartment));
-
- compartment.setWidth(100);
- compartment.setHeight(10);
- assertFalse(element.contains(compartment));
-
- compartment.setWidth(10);
- compartment.setHeight(10);
- assertTrue(element.contains(compartment));
-
- compartment.setWidth(100);
- compartment.setHeight(100);
- compartment.setX(-2);
- compartment.setY(2);
- assertFalse(element.contains(compartment));
- compartment.setX(2);
- compartment.setY(-2);
- assertFalse(element.contains(compartment));
- compartment.setX(-2);
- compartment.setY(-2);
- assertFalse(element.contains(compartment));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testContainsLayerText() {
- try {
- Species protein = new GenericProtein();
- protein.setWidth(100);
- protein.setHeight(100);
- LayerText layerText = new LayerText();
- layerText.setX(2.0);
- layerText.setY(2.0);
- layerText.setWidth(100.0);
- layerText.setHeight(100.0);
-
- assertFalse(protein.contains(layerText));
- layerText.setWidth(10.0);
- layerText.setHeight(10.0);
- assertTrue(protein.contains(layerText));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddMiriamCollection() {
- try {
- List<MiriamData> list = new ArrayList<>();
- list.add(new MiriamData(MiriamType.CAS, "1"));
- list.add(new MiriamData(MiriamType.CAS, "1"));
- Element element = Mockito.spy(Element.class);
- element.addMiriamData(list);
- assertEquals(1, element.getMiriamData().size());
- assertEquals(1, getWarnings().size());
-
- element.addMiriamData(list);
- assertEquals(3, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetNotes() {
- try {
- Element element = Mockito.spy(Element.class);
- element.setNotes("</html>");
- fail("Exception epxected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddSynonym() {
- try {
- Element element = Mockito.spy(Element.class);
- List<String> synonyms = new ArrayList<>();
- synonyms.add("syn");
- element.addSynonyms(synonyms);
- element.addSynonym("syn2");
- assertEquals("syn", element.getSynonyms().get(0));
- StringBuilder sb = new StringBuilder();
- for (int i = 0; i < 300; i++) {
- sb.append("a");
- }
- String syn = sb.toString();
- synonyms = new ArrayList<>();
- synonyms.add(syn);
- element.addSynonyms(synonyms);
- assertFalse(syn.equals(element.getSynonyms().get(1)));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddFormerSymbols() {
- try {
- Element element = Mockito.spy(Element.class);
- List<String> formerSymbols = new ArrayList<>();
- formerSymbols.add("symbol");
- element.addFormerSymbols(formerSymbols);
- element.addFormerSymbol("symbol2");
- assertEquals("symbol", element.getFormerSymbols().get(0));
- StringBuilder sb = new StringBuilder();
- for (int i = 0; i < 300; i++) {
- sb.append("a");
- }
- String syn = sb.toString();
- formerSymbols = new ArrayList<>();
- formerSymbols.add(syn);
- element.addFormerSymbols(formerSymbols);
- assertFalse(syn.equals(element.getFormerSymbols().get(1)));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.ModelTestFunctions;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.SearchIndex;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.layout.graphics.LayerText;
+import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+
+public class ElementTest extends ModelTestFunctions {
+
+ private static double EPSILON = Configuration.EPSILON;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testDistance1() {
+ Species species = new GenericProtein();
+ species.setWidth(10);
+ species.setHeight(20);
+ species.setX(100.0);
+ species.setY(200.0);
+ double distance = species.getDistanceFromPoint(species.getCenter());
+ assertEquals(0, distance, EPSILON);
+ }
+
+ @Test
+ public void testDistance2() {
+ Species species = new GenericProtein();
+ species.setWidth(10);
+ species.setHeight(20);
+ species.setX(100.0);
+ species.setY(200.0);
+ double distance = species.getDistanceFromPoint(new Point2D.Double(100, 205));
+ assertEquals(0, distance, EPSILON);
+ }
+
+ @Test
+ public void testDistance6() {
+ Species species = new GenericProtein();
+ species.setWidth(10);
+ species.setHeight(20);
+ species.setX(100.0);
+ species.setY(200.0);
+ double distance = species.getDistanceFromPoint(new Point2D.Double(105, 95));
+ assertEquals(105, distance, EPSILON);
+ }
+
+ @Test
+ public void testDistance3() {
+ Species species = new GenericProtein();
+ species.setWidth(10);
+ species.setHeight(20);
+ species.setX(100.0);
+ species.setY(200.0);
+ double distance = species.getDistanceFromPoint(new Point2D.Double(50, 205));
+ assertEquals(50, distance, EPSILON);
+ }
+
+ @Test
+ public void testDistance4() {
+ Species species = new GenericProtein();
+ species.setWidth(10);
+ species.setHeight(20);
+ species.setX(100.0);
+ species.setY(200.0);
+ double distance = species.getDistanceFromPoint(new Point2D.Double(120, 230));
+ assertEquals(Math.sqrt(200), distance, EPSILON);
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ GenericProtein protein = new GenericProtein();
+ protein.addSearchIndex(new SearchIndex());
+ protein.setSubmodel(new ElementSubmodelConnection());
+ Element copy = new GenericProtein(protein);
+ assertNotNull(copy);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testIncreaseBorder() {
+ try {
+ Species protein = new GenericProtein();
+ assertEquals(0.0, protein.getSize(), Configuration.EPSILON);
+ protein.increaseBorder(2);
+ assertEquals(16.0, protein.getSize(), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ Element element = new GenericProtein();
+ Double nullDouble = null;
+ String xStr = "1.2";
+ Double x = 1.2;
+ String yStr = "1.3";
+ Double y = 1.3;
+ String fontSizeStr = "5.0";
+ Double fontSize = 5.0;
+ int fontSizeInt = 5;
+ String widthStr = "3.0";
+ Double width = 3.0;
+ String heightStr = "4.0";
+ Double height = 4.0;
+ ModelData modelData = new ModelData();
+ Set<MiriamData> miriamData = new HashSet<>();
+ Compartment compartment = new Compartment("idd");
+ int id = 72;
+ String transparencyLevel = "2";
+ Model model = new ModelFullIndexed(modelData);
+ List<SearchIndex> indexes = new ArrayList<>();
+ indexes.add(new SearchIndex());
+
+ element.setMiriamData(miriamData);
+ assertEquals(miriamData, element.getMiriamData());
+
+ element.setX(xStr);
+ assertEquals(x, element.getX(), Configuration.EPSILON);
+ element.setX(nullDouble);
+ assertNull(element.getX());
+ element.setX(x);
+ assertEquals(x, element.getX(), Configuration.EPSILON);
+
+ element.setY(yStr);
+ assertEquals(y, element.getY(), Configuration.EPSILON);
+ element.setY(nullDouble);
+ assertNull(element.getY());
+ element.setY(y);
+ assertEquals(y, element.getY(), Configuration.EPSILON);
+
+ element.setFontSize(fontSizeStr);
+ assertEquals(fontSize, element.getFontSize(), Configuration.EPSILON);
+ element.setFontSize(nullDouble);
+ assertNull(element.getFontSize());
+ element.setFontSize(fontSize);
+ assertEquals(fontSize, element.getFontSize(), Configuration.EPSILON);
+ element.setFontSize(nullDouble);
+ assertNull(element.getFontSize());
+ element.setFontSize(fontSizeInt);
+ assertEquals(fontSize, element.getFontSize(), Configuration.EPSILON);
+
+ element.setWidth(widthStr);
+ assertEquals(width, element.getWidth(), Configuration.EPSILON);
+ element.setWidth(nullDouble);
+ assertNull(element.getWidth());
+ element.setWidth(width);
+ assertEquals(width, element.getWidth(), Configuration.EPSILON);
+ try {
+ element.setWidth("as");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+
+ element.setHeight(heightStr);
+ assertEquals(height, element.getHeight(), Configuration.EPSILON);
+ element.setHeight(nullDouble);
+ assertNull(element.getHeight());
+ element.setHeight(height);
+ assertEquals(height, element.getHeight(), Configuration.EPSILON);
+ try {
+ element.setHeight("as");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+
+ element.setCompartment(compartment);
+ assertEquals(compartment, element.getCompartment());
+ element.setId(id);
+ assertEquals(id, element.getId());
+ element.setTransparencyLevel(transparencyLevel);
+ assertEquals(transparencyLevel, element.getTransparencyLevel());
+ element.setModel(model);
+ assertEquals(model, element.getModel());
+ element.setModelData(modelData);
+ assertEquals(modelData, element.getModelData());
+ element.setSearchIndexes(indexes);
+ assertEquals(indexes, element.getSearchIndexes());
+
+ assertNotNull(element.getBorder());
+
+ element = Mockito.spy(Element.class);
+ List<String> synonyms = new ArrayList<>();
+ List<String> formerSymbols = new ArrayList<>();
+ String formula = "some_form";
+
+ element.setSynonyms(synonyms);
+ element.setFormerSymbols(formerSymbols);
+ element.setModel(model);
+ element.setFormula(formula);
+
+ assertEquals(synonyms, element.getSynonyms());
+ assertEquals(formerSymbols, element.getFormerSymbols());
+ assertEquals(model.getModelData(), element.getModelData());
+ assertEquals(formula, element.getFormula());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testContainsElement() {
+ try {
+ Species element = new GenericProtein();
+ element.setWidth(100);
+ element.setHeight(100);
+ Species element2 = new GenericProtein();
+ element2.setX(-2);
+ element2.setY(-2);
+ element2.setWidth(100);
+ element2.setHeight(100);
+
+ assertTrue(element.contains(element2));
+ element2.setX(2);
+ element2.setY(2);
+ assertTrue(element.contains(element2));
+ element2.setX(-2);
+ element2.setY(2);
+ assertTrue(element.contains(element2));
+ element2.setX(2);
+ element2.setY(-2);
+ assertTrue(element.contains(element2));
+
+ element2.setX(-2);
+ element2.setY(-2);
+ element2.setWidth(200);
+ element2.setHeight(200);
+ assertFalse(element.contains(element2));
+
+ Compartment compartment = new Compartment("idd");
+ compartment.setX(2);
+ compartment.setY(2);
+ compartment.setWidth(10);
+ compartment.setHeight(100);
+ assertFalse(element.contains(compartment));
+
+ compartment.setWidth(100);
+ compartment.setHeight(10);
+ assertFalse(element.contains(compartment));
+
+ compartment.setWidth(10);
+ compartment.setHeight(10);
+ assertTrue(element.contains(compartment));
+
+ compartment.setWidth(100);
+ compartment.setHeight(100);
+ compartment.setX(-2);
+ compartment.setY(2);
+ assertFalse(element.contains(compartment));
+ compartment.setX(2);
+ compartment.setY(-2);
+ assertFalse(element.contains(compartment));
+ compartment.setX(-2);
+ compartment.setY(-2);
+ assertFalse(element.contains(compartment));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testContainsLayerText() {
+ try {
+ Species protein = new GenericProtein();
+ protein.setWidth(100);
+ protein.setHeight(100);
+ LayerText layerText = new LayerText();
+ layerText.setX(2.0);
+ layerText.setY(2.0);
+ layerText.setWidth(100.0);
+ layerText.setHeight(100.0);
+
+ assertFalse(protein.contains(layerText));
+ layerText.setWidth(10.0);
+ layerText.setHeight(10.0);
+ assertTrue(protein.contains(layerText));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddMiriamCollection() {
+ try {
+ List<MiriamData> list = new ArrayList<>();
+ list.add(new MiriamData(MiriamType.CAS, "1"));
+ list.add(new MiriamData(MiriamType.CAS, "1"));
+ Element element = Mockito.spy(Element.class);
+ element.addMiriamData(list);
+ assertEquals(1, element.getMiriamData().size());
+ assertEquals(1, getWarnings().size());
+
+ element.addMiriamData(list);
+ assertEquals(3, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetNotes() {
+ try {
+ Element element = Mockito.spy(Element.class);
+ element.setNotes("</html>");
+ fail("Exception epxected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddSynonym() {
+ try {
+ Element element = Mockito.spy(Element.class);
+ List<String> synonyms = new ArrayList<>();
+ synonyms.add("syn");
+ element.addSynonyms(synonyms);
+ element.addSynonym("syn2");
+ assertEquals("syn", element.getSynonyms().get(0));
+ StringBuilder sb = new StringBuilder();
+ for (int i = 0; i < 300; i++) {
+ sb.append("a");
+ }
+ String syn = sb.toString();
+ synonyms = new ArrayList<>();
+ synonyms.add(syn);
+ element.addSynonyms(synonyms);
+ assertFalse(syn.equals(element.getSynonyms().get(1)));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddFormerSymbols() {
+ try {
+ Element element = Mockito.spy(Element.class);
+ List<String> formerSymbols = new ArrayList<>();
+ formerSymbols.add("symbol");
+ element.addFormerSymbols(formerSymbols);
+ element.addFormerSymbol("symbol2");
+ assertEquals("symbol", element.getFormerSymbols().get(0));
+ StringBuilder sb = new StringBuilder();
+ for (int i = 0; i < 300; i++) {
+ sb.append("a");
+ }
+ String syn = sb.toString();
+ formerSymbols = new ArrayList<>();
+ formerSymbols.add(syn);
+ element.addFormerSymbols(formerSymbols);
+ assertFalse(syn.equals(element.getFormerSymbols().get(1)));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/GenericProteinComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/GenericProteinComparatorTest.java
index 08c34c0b73..aa378d8cdd 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/GenericProteinComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/GenericProteinComparatorTest.java
@@ -1,84 +1,84 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class GenericProteinComparatorTest {
-
- GenericProteinComparator comparator = new GenericProteinComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- GenericProtein drug1 = createGenericProtein();
- GenericProtein drug2 = createGenericProtein();
-
- assertEquals(0, comparator.compare(drug1, drug1));
-
- assertEquals(0, comparator.compare(drug1, drug2));
- assertEquals(0, comparator.compare(drug2, drug1));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- @Test
- public void testDifferent() {
- try {
- GenericProtein drug2 = createGenericProtein();
- assertTrue(comparator.compare(null, drug2) != 0);
- assertTrue(comparator.compare(drug2, null) != 0);
- assertTrue(comparator.compare(null, null) == 0);
-
- GenericProtein drug = createGenericProtein();
- drug.setName("n");
- assertTrue(comparator.compare(drug, drug2) != 0);
-
- assertTrue(comparator.compare(drug, Mockito.mock(GenericProtein.class)) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- public GenericProtein createGenericProtein() {
- GenericProtein result = new GenericProtein();
- return result;
- }
-
- @Test
- public void testInvalid() {
- try {
- GenericProtein object = Mockito.mock(GenericProtein.class);
-
- comparator.compare(object, object);
-
- fail("Exception expected");
- } catch (NotImplementedException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class GenericProteinComparatorTest {
+
+ GenericProteinComparator comparator = new GenericProteinComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ GenericProtein drug1 = createGenericProtein();
+ GenericProtein drug2 = createGenericProtein();
+
+ assertEquals(0, comparator.compare(drug1, drug1));
+
+ assertEquals(0, comparator.compare(drug1, drug2));
+ assertEquals(0, comparator.compare(drug2, drug1));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ GenericProtein drug2 = createGenericProtein();
+ assertTrue(comparator.compare(null, drug2) != 0);
+ assertTrue(comparator.compare(drug2, null) != 0);
+ assertTrue(comparator.compare(null, null) == 0);
+
+ GenericProtein drug = createGenericProtein();
+ drug.setName("n");
+ assertTrue(comparator.compare(drug, drug2) != 0);
+
+ assertTrue(comparator.compare(drug, Mockito.mock(GenericProtein.class)) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ public GenericProtein createGenericProtein() {
+ GenericProtein result = new GenericProtein();
+ return result;
+ }
+
+ @Test
+ public void testInvalid() {
+ try {
+ GenericProtein object = Mockito.mock(GenericProtein.class);
+
+ comparator.compare(object, object);
+
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/GenericProteinTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/GenericProteinTest.java
index 213f7baefc..addbd76893 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/GenericProteinTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/GenericProteinTest.java
@@ -1,68 +1,68 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class GenericProteinTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new GenericProtein());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- GenericProtein species = new GenericProtein("");
- assertNotNull(species);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy1() {
- try {
- GenericProtein species = new GenericProtein(new GenericProtein()).copy();
- assertNotNull(species);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy2() {
- try {
- GenericProtein protein = Mockito.spy(GenericProtein.class);
- protein.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class GenericProteinTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new GenericProtein());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ GenericProtein species = new GenericProtein("");
+ assertNotNull(species);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy1() {
+ try {
+ GenericProtein species = new GenericProtein(new GenericProtein()).copy();
+ assertNotNull(species);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy2() {
+ try {
+ GenericProtein protein = Mockito.spy(GenericProtein.class);
+ protein.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/IonChannelProteinComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/IonChannelProteinComparatorTest.java
index b1aae7f059..36795950ca 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/IonChannelProteinComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/IonChannelProteinComparatorTest.java
@@ -1,84 +1,84 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class IonChannelProteinComparatorTest {
-
- IonChannelProteinComparator comparator = new IonChannelProteinComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- IonChannelProtein drug1 = createIonChannelProtein();
- IonChannelProtein drug2 = createIonChannelProtein();
-
- assertEquals(0, comparator.compare(drug1, drug1));
-
- assertEquals(0, comparator.compare(drug1, drug2));
- assertEquals(0, comparator.compare(drug2, drug1));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- @Test
- public void testDifferent() {
- try {
- IonChannelProtein drug2 = createIonChannelProtein();
- assertTrue(comparator.compare(null, drug2) != 0);
- assertTrue(comparator.compare(drug2, null) != 0);
- assertTrue(comparator.compare(null, null) == 0);
-
- IonChannelProtein drug = createIonChannelProtein();
- drug.setName("n");
- assertTrue(comparator.compare(drug, drug2) != 0);
-
- assertTrue(comparator.compare(drug, Mockito.mock(IonChannelProtein.class)) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- public IonChannelProtein createIonChannelProtein() {
- IonChannelProtein result = new IonChannelProtein();
- return result;
- }
-
- @Test
- public void testInvalid() {
- try {
- IonChannelProtein object = Mockito.mock(IonChannelProtein.class);
-
- comparator.compare(object, object);
-
- fail("Exception expected");
- } catch (NotImplementedException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class IonChannelProteinComparatorTest {
+
+ IonChannelProteinComparator comparator = new IonChannelProteinComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ IonChannelProtein drug1 = createIonChannelProtein();
+ IonChannelProtein drug2 = createIonChannelProtein();
+
+ assertEquals(0, comparator.compare(drug1, drug1));
+
+ assertEquals(0, comparator.compare(drug1, drug2));
+ assertEquals(0, comparator.compare(drug2, drug1));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ IonChannelProtein drug2 = createIonChannelProtein();
+ assertTrue(comparator.compare(null, drug2) != 0);
+ assertTrue(comparator.compare(drug2, null) != 0);
+ assertTrue(comparator.compare(null, null) == 0);
+
+ IonChannelProtein drug = createIonChannelProtein();
+ drug.setName("n");
+ assertTrue(comparator.compare(drug, drug2) != 0);
+
+ assertTrue(comparator.compare(drug, Mockito.mock(IonChannelProtein.class)) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ public IonChannelProtein createIonChannelProtein() {
+ IonChannelProtein result = new IonChannelProtein();
+ return result;
+ }
+
+ @Test
+ public void testInvalid() {
+ try {
+ IonChannelProtein object = Mockito.mock(IonChannelProtein.class);
+
+ comparator.compare(object, object);
+
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/IonChannelProteinTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/IonChannelProteinTest.java
index abbd65bbb6..1008ea19e5 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/IonChannelProteinTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/IonChannelProteinTest.java
@@ -1,69 +1,69 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class IonChannelProteinTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new IonChannelProtein());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- IonChannelProtein species = new IonChannelProtein(new IonChannelProtein());
- assertNotNull(species);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy1() {
- try {
- IonChannelProtein species = new IonChannelProtein("id").copy();
- assertNotNull(species);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy2() {
- try {
- IonChannelProtein protein = Mockito.spy(IonChannelProtein.class);
- protein.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class IonChannelProteinTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new IonChannelProtein());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ IonChannelProtein species = new IonChannelProtein(new IonChannelProtein());
+ assertNotNull(species);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy1() {
+ try {
+ IonChannelProtein species = new IonChannelProtein("id").copy();
+ assertNotNull(species);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy2() {
+ try {
+ IonChannelProtein protein = Mockito.spy(IonChannelProtein.class);
+ protein.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/IonComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/IonComparatorTest.java
index 8163f74c76..ede0274d62 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/IonComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/IonComparatorTest.java
@@ -1,83 +1,83 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class IonComparatorTest {
-
- IonComparator comparator = new IonComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- Ion ion1 = createIon();
- Ion ion2 = createIon();
-
- assertEquals(0, comparator.compare(ion1, ion1));
-
- assertEquals(0, comparator.compare(ion1, ion2));
- assertEquals(0, comparator.compare(ion2, ion1));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Ione exception occurred");
- }
- }
-
- @Test
- public void testDifferent() {
- try {
- Ion ion2 = createIon();
- assertTrue(comparator.compare(null, ion2) != 0);
- assertTrue(comparator.compare(ion2, null) != 0);
- assertTrue(comparator.compare(null, null) == 0);
-
- Ion ion = createIon();
- ion.setName("n");
- assertTrue(comparator.compare(ion, ion2) != 0);
-
- assertTrue(comparator.compare(ion, Mockito.mock(Ion.class)) != 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- public Ion createIon() {
- Ion result = new Ion();
- return result;
- }
-
- @Test
- public void testInvalid() {
- try {
- Ion object = Mockito.mock(Ion.class);
-
- comparator.compare(object, object);
-
- fail("Exception expected");
- } catch (NotImplementedException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class IonComparatorTest {
+
+ IonComparator comparator = new IonComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ Ion ion1 = createIon();
+ Ion ion2 = createIon();
+
+ assertEquals(0, comparator.compare(ion1, ion1));
+
+ assertEquals(0, comparator.compare(ion1, ion2));
+ assertEquals(0, comparator.compare(ion2, ion1));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Ione exception occurred");
+ }
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ Ion ion2 = createIon();
+ assertTrue(comparator.compare(null, ion2) != 0);
+ assertTrue(comparator.compare(ion2, null) != 0);
+ assertTrue(comparator.compare(null, null) == 0);
+
+ Ion ion = createIon();
+ ion.setName("n");
+ assertTrue(comparator.compare(ion, ion2) != 0);
+
+ assertTrue(comparator.compare(ion, Mockito.mock(Ion.class)) != 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ public Ion createIon() {
+ Ion result = new Ion();
+ return result;
+ }
+
+ @Test
+ public void testInvalid() {
+ try {
+ Ion object = Mockito.mock(Ion.class);
+
+ comparator.compare(object, object);
+
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/IonTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/IonTest.java
index dd3a5ace78..50c4174cd6 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/IonTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/IonTest.java
@@ -1,80 +1,80 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class IonTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new Ion());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- Ion degraded = new Ion(new Ion());
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- Ion degraded = new Ion("id");
- assertNotNull(degraded.getStringType());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- Ion degraded = new Ion().copy();
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- Ion ion = Mockito.spy(Ion.class);
- ion.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class IonTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new Ion());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ Ion degraded = new Ion(new Ion());
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ Ion degraded = new Ion("id");
+ assertNotNull(degraded.getStringType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ Ion degraded = new Ion().copy();
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ Ion ion = Mockito.spy(Ion.class);
+ ion.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/PhenotypeComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/PhenotypeComparatorTest.java
index 8d0db8a144..b97c906278 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/PhenotypeComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/PhenotypeComparatorTest.java
@@ -1,86 +1,86 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class PhenotypeComparatorTest {
-
- PhenotypeComparator comparator = new PhenotypeComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- Phenotype phenotype1 = createPhenotype();
- Phenotype phenotype2 = createPhenotype();
-
- assertEquals(0, comparator.compare(phenotype1, phenotype1));
-
- assertEquals(0, comparator.compare(phenotype1, phenotype2));
- assertEquals(0, comparator.compare(phenotype2, phenotype1));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- @Test
- public void testInvalid() {
- try {
- Phenotype phenotype1 = Mockito.mock(Phenotype.class);
-
- comparator.compare(phenotype1, phenotype1);
-
- fail("Exception expected");
- } catch (NotImplementedException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- @Test
- public void testDifferent() {
- try {
- Phenotype phenotype2 = createPhenotype();
- assertTrue(comparator.compare(null, phenotype2) != 0);
- assertTrue(comparator.compare(phenotype2, null) != 0);
- assertTrue(comparator.compare(null, null) == 0);
-
- assertTrue(comparator.compare(phenotype2, Mockito.mock(Phenotype.class)) != 0);
-
- Phenotype phenotype = createPhenotype();
- phenotype2 = createPhenotype();
- phenotype.setName("n");
- assertTrue(comparator.compare(phenotype, phenotype2) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- public Phenotype createPhenotype() {
- Phenotype result = new Phenotype();
-
- return result;
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class PhenotypeComparatorTest {
+
+ PhenotypeComparator comparator = new PhenotypeComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ Phenotype phenotype1 = createPhenotype();
+ Phenotype phenotype2 = createPhenotype();
+
+ assertEquals(0, comparator.compare(phenotype1, phenotype1));
+
+ assertEquals(0, comparator.compare(phenotype1, phenotype2));
+ assertEquals(0, comparator.compare(phenotype2, phenotype1));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ @Test
+ public void testInvalid() {
+ try {
+ Phenotype phenotype1 = Mockito.mock(Phenotype.class);
+
+ comparator.compare(phenotype1, phenotype1);
+
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ Phenotype phenotype2 = createPhenotype();
+ assertTrue(comparator.compare(null, phenotype2) != 0);
+ assertTrue(comparator.compare(phenotype2, null) != 0);
+ assertTrue(comparator.compare(null, null) == 0);
+
+ assertTrue(comparator.compare(phenotype2, Mockito.mock(Phenotype.class)) != 0);
+
+ Phenotype phenotype = createPhenotype();
+ phenotype2 = createPhenotype();
+ phenotype.setName("n");
+ assertTrue(comparator.compare(phenotype, phenotype2) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ public Phenotype createPhenotype() {
+ Phenotype result = new Phenotype();
+
+ return result;
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/PhenotypeTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/PhenotypeTest.java
index 5342df9a7d..acfd986657 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/PhenotypeTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/PhenotypeTest.java
@@ -1,94 +1,94 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class PhenotypeTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new Phenotype());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- Phenotype original = new Phenotype();
- Phenotype copy = new Phenotype(original);
- assertNotNull(copy);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor2() {
- try {
- String id = "idd";
- Phenotype copy = new Phenotype(id);
- assertEquals(id, copy.getElementId());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- Phenotype copy = new Phenotype("id");
- assertNotNull(copy.getStringType());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- Phenotype degraded = new Phenotype().copy();
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- Phenotype phenotype = Mockito.spy(Phenotype.class);
- phenotype.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class PhenotypeTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new Phenotype());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ Phenotype original = new Phenotype();
+ Phenotype copy = new Phenotype(original);
+ assertNotNull(copy);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor2() {
+ try {
+ String id = "idd";
+ Phenotype copy = new Phenotype(id);
+ assertEquals(id, copy.getElementId());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ Phenotype copy = new Phenotype("id");
+ assertNotNull(copy.getStringType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ Phenotype degraded = new Phenotype().copy();
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ Phenotype phenotype = Mockito.spy(Phenotype.class);
+ phenotype.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ReceptorProteinComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ReceptorProteinComparatorTest.java
index 29c5801d47..f5906304ec 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ReceptorProteinComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ReceptorProteinComparatorTest.java
@@ -1,84 +1,84 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class ReceptorProteinComparatorTest {
-
- ReceptorProteinComparator comparator = new ReceptorProteinComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- ReceptorProtein drug1 = createReceptorProtein();
- ReceptorProtein drug2 = createReceptorProtein();
-
- assertEquals(0, comparator.compare(drug1, drug1));
-
- assertEquals(0, comparator.compare(drug1, drug2));
- assertEquals(0, comparator.compare(drug2, drug1));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- @Test
- public void testDifferent() {
- try {
- ReceptorProtein drug2 = createReceptorProtein();
- assertTrue(comparator.compare(null, drug2) != 0);
- assertTrue(comparator.compare(drug2, null) != 0);
- assertTrue(comparator.compare(null, null) == 0);
-
- ReceptorProtein drug = createReceptorProtein();
- drug.setName("n");
- assertTrue(comparator.compare(drug, drug2) != 0);
-
- assertTrue(comparator.compare(drug, Mockito.mock(ReceptorProtein.class)) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- public ReceptorProtein createReceptorProtein() {
- ReceptorProtein result = new ReceptorProtein();
- return result;
- }
-
- @Test
- public void testInvalid() {
- try {
- ReceptorProtein object = Mockito.mock(ReceptorProtein.class);
-
- comparator.compare(object, object);
-
- fail("Exception expected");
- } catch (NotImplementedException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class ReceptorProteinComparatorTest {
+
+ ReceptorProteinComparator comparator = new ReceptorProteinComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ ReceptorProtein drug1 = createReceptorProtein();
+ ReceptorProtein drug2 = createReceptorProtein();
+
+ assertEquals(0, comparator.compare(drug1, drug1));
+
+ assertEquals(0, comparator.compare(drug1, drug2));
+ assertEquals(0, comparator.compare(drug2, drug1));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ ReceptorProtein drug2 = createReceptorProtein();
+ assertTrue(comparator.compare(null, drug2) != 0);
+ assertTrue(comparator.compare(drug2, null) != 0);
+ assertTrue(comparator.compare(null, null) == 0);
+
+ ReceptorProtein drug = createReceptorProtein();
+ drug.setName("n");
+ assertTrue(comparator.compare(drug, drug2) != 0);
+
+ assertTrue(comparator.compare(drug, Mockito.mock(ReceptorProtein.class)) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ public ReceptorProtein createReceptorProtein() {
+ ReceptorProtein result = new ReceptorProtein();
+ return result;
+ }
+
+ @Test
+ public void testInvalid() {
+ try {
+ ReceptorProtein object = Mockito.mock(ReceptorProtein.class);
+
+ comparator.compare(object, object);
+
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ReceptorProteinTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ReceptorProteinTest.java
index 7b8a84dab4..a220ae88ca 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ReceptorProteinTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ReceptorProteinTest.java
@@ -1,69 +1,69 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class ReceptorProteinTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new ReceptorProtein());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- ReceptorProtein species = new ReceptorProtein(new ReceptorProtein());
- assertNotNull(species);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy1() {
- try {
- ReceptorProtein species = new ReceptorProtein("id").copy();
- assertNotNull(species);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy2() {
- try {
- ReceptorProtein protein = Mockito.spy(ReceptorProtein.class);
- protein.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class ReceptorProteinTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new ReceptorProtein());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ ReceptorProtein species = new ReceptorProtein(new ReceptorProtein());
+ assertNotNull(species);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy1() {
+ try {
+ ReceptorProtein species = new ReceptorProtein("id").copy();
+ assertNotNull(species);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy2() {
+ try {
+ ReceptorProtein protein = Mockito.spy(ReceptorProtein.class);
+ protein.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparatorTest.java
index b696a4286f..12f7612191 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/SimpleMoleculeComparatorTest.java
@@ -1,121 +1,121 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class SimpleMoleculeComparatorTest {
-
- SimpleMoleculeComparator comparator = new SimpleMoleculeComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- SimpleMolecule simpleMolecule1 = createSimpleMolecule();
- SimpleMolecule simpleMolecule2 = createSimpleMolecule();
-
- assertEquals(0, comparator.compare(simpleMolecule1, simpleMolecule1));
-
- assertEquals(0, comparator.compare(simpleMolecule1, simpleMolecule2));
- assertEquals(0, comparator.compare(simpleMolecule2, simpleMolecule1));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- @Test
- public void testDifferent() {
- try {
- SimpleMolecule simpleMolecule1 = createSimpleMolecule();
- SimpleMolecule simpleMolecule2 = createSimpleMolecule();
- simpleMolecule1.setHomodimer(3);
- assertTrue(comparator.compare(simpleMolecule1, simpleMolecule2) != 0);
- assertTrue(comparator.compare(simpleMolecule2, simpleMolecule1) != 0);
-
- simpleMolecule1 = createSimpleMolecule();
- simpleMolecule2 = createSimpleMolecule();
- simpleMolecule1.setName("as");
- assertTrue(comparator.compare(simpleMolecule1, simpleMolecule2) != 0);
- assertTrue(comparator.compare(simpleMolecule2, simpleMolecule1) != 0);
-
- simpleMolecule1 = createSimpleMolecule();
- simpleMolecule2 = createSimpleMolecule();
- simpleMolecule1.setInChIKey("as");
- assertTrue(comparator.compare(simpleMolecule1, simpleMolecule2) != 0);
- assertTrue(comparator.compare(simpleMolecule2, simpleMolecule1) != 0);
-
- simpleMolecule1 = createSimpleMolecule();
- simpleMolecule2 = createSimpleMolecule();
- assertTrue(comparator.compare(null, simpleMolecule2) != 0);
- assertTrue(comparator.compare(simpleMolecule2, null) != 0);
- assertTrue(comparator.compare(null, null) == 0);
-
- assertTrue(comparator.compare(simpleMolecule1, Mockito.mock(SimpleMolecule.class)) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid() {
- try {
- SimpleMolecule simpleMolecule1 = Mockito.mock(SimpleMolecule.class);
- comparator.compare(simpleMolecule1, simpleMolecule1);
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferentNewFields() throws Exception {
- try {
- SimpleMolecule species1 = createSimpleMolecule();
- SimpleMolecule species2 = createSimpleMolecule();
-
- species1.setSmiles("some symbol");
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
-
- species1.setInChI("some inchi");
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- public SimpleMolecule createSimpleMolecule() {
- SimpleMolecule result = new SimpleMolecule();
- result.setHomodimer(12);
-
- return result;
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class SimpleMoleculeComparatorTest {
+
+ SimpleMoleculeComparator comparator = new SimpleMoleculeComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ SimpleMolecule simpleMolecule1 = createSimpleMolecule();
+ SimpleMolecule simpleMolecule2 = createSimpleMolecule();
+
+ assertEquals(0, comparator.compare(simpleMolecule1, simpleMolecule1));
+
+ assertEquals(0, comparator.compare(simpleMolecule1, simpleMolecule2));
+ assertEquals(0, comparator.compare(simpleMolecule2, simpleMolecule1));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ SimpleMolecule simpleMolecule1 = createSimpleMolecule();
+ SimpleMolecule simpleMolecule2 = createSimpleMolecule();
+ simpleMolecule1.setHomodimer(3);
+ assertTrue(comparator.compare(simpleMolecule1, simpleMolecule2) != 0);
+ assertTrue(comparator.compare(simpleMolecule2, simpleMolecule1) != 0);
+
+ simpleMolecule1 = createSimpleMolecule();
+ simpleMolecule2 = createSimpleMolecule();
+ simpleMolecule1.setName("as");
+ assertTrue(comparator.compare(simpleMolecule1, simpleMolecule2) != 0);
+ assertTrue(comparator.compare(simpleMolecule2, simpleMolecule1) != 0);
+
+ simpleMolecule1 = createSimpleMolecule();
+ simpleMolecule2 = createSimpleMolecule();
+ simpleMolecule1.setInChIKey("as");
+ assertTrue(comparator.compare(simpleMolecule1, simpleMolecule2) != 0);
+ assertTrue(comparator.compare(simpleMolecule2, simpleMolecule1) != 0);
+
+ simpleMolecule1 = createSimpleMolecule();
+ simpleMolecule2 = createSimpleMolecule();
+ assertTrue(comparator.compare(null, simpleMolecule2) != 0);
+ assertTrue(comparator.compare(simpleMolecule2, null) != 0);
+ assertTrue(comparator.compare(null, null) == 0);
+
+ assertTrue(comparator.compare(simpleMolecule1, Mockito.mock(SimpleMolecule.class)) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid() {
+ try {
+ SimpleMolecule simpleMolecule1 = Mockito.mock(SimpleMolecule.class);
+ comparator.compare(simpleMolecule1, simpleMolecule1);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferentNewFields() throws Exception {
+ try {
+ SimpleMolecule species1 = createSimpleMolecule();
+ SimpleMolecule species2 = createSimpleMolecule();
+
+ species1.setSmiles("some symbol");
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+
+ species1.setInChI("some inchi");
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ public SimpleMolecule createSimpleMolecule() {
+ SimpleMolecule result = new SimpleMolecule();
+ result.setHomodimer(12);
+
+ return result;
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/SimpleMoleculeTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/SimpleMoleculeTest.java
index 65d2709d38..e238e10b50 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/SimpleMoleculeTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/SimpleMoleculeTest.java
@@ -1,80 +1,80 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class SimpleMoleculeTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new SimpleMolecule());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- SimpleMolecule degraded = new SimpleMolecule("id");
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- SimpleMolecule degraded = new SimpleMolecule(new SimpleMolecule());
- assertNotNull(degraded.getStringType());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- SimpleMolecule degraded = new SimpleMolecule().copy();
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- SimpleMolecule simpleMolecule = Mockito.spy(SimpleMolecule.class);
- simpleMolecule.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class SimpleMoleculeTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new SimpleMolecule());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ SimpleMolecule degraded = new SimpleMolecule("id");
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ SimpleMolecule degraded = new SimpleMolecule(new SimpleMolecule());
+ assertNotNull(degraded.getStringType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ SimpleMolecule degraded = new SimpleMolecule().copy();
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ SimpleMolecule simpleMolecule = Mockito.spy(SimpleMolecule.class);
+ simpleMolecule.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesComparatorTest.java
index 66931eb816..898e00b37a 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesComparatorTest.java
@@ -1,313 +1,313 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import java.awt.Color;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
-import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
-
-public class SpeciesComparatorTest {
-
- SpeciesComparator comparator = new SpeciesComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- Species species1 = createSpecies();
- Species species2 = createSpecies();
-
- assertEquals(0, comparator.compare(species1, species2));
-
- assertEquals(0, comparator.compare(null, null));
-
- assertEquals(0, comparator.compare(new Complex(), new Complex()));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCompareInvalid() {
- try {
-
- Species speciesMock = Mockito.mock(Species.class);
- comparator.compare(speciesMock, speciesMock);
- fail("Exception expected");
-
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unkowne exception");
- }
- }
-
- private Species createSpecies() {
- GenericProtein result = new GenericProtein();
- result.setName("a");
-
- result.setElementId("asd");
- result.setX(12.0);
- result.setY(123.0);
- result.setWidth(4);
- result.setHeight(5);
- result.setFontSize(9.0);
- result.setColor(Color.BLUE);
- result.setVisibilityLevel(14);
- result.setStateLabel("123");
- result.setStatePrefix("1234");
-
- return result;
- }
-
- @Test
- public void testDifferent() throws Exception {
- try {
- Species species1 = createSpecies();
- Species species2 = createSpecies();
-
- assertTrue(comparator.compare(species1, null) != 0);
- assertTrue(comparator.compare(null, species1) != 0);
-
- assertTrue(comparator.compare(new Complex(), species1) != 0);
-
- species1 = createSpecies();
- species2 = createSpecies();
-
- species1.setElementId("tmp");
-
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSpecies();
- species2 = createSpecies();
-
- species1.setStateLabel("tmp");
-
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSpecies();
- species2 = createSpecies();
-
- species1.setStatePrefix("tmp");
-
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSpecies();
- species2 = createSpecies();
-
- species1.setName("new namne");
-
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSpecies();
- species2 = createSpecies();
-
- species1.setActivity(true);
-
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSpecies();
- species2 = createSpecies();
-
- species1.setLineWidth(453.75);
-
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testException() {
- try {
- Species mock = Mockito.mock(Species.class);
- comparator.compare(mock, mock);
-
- fail("Exception expected");
- } catch (NotImplementedException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testEquals2() {
- try {
- SimpleMolecule species1 = createSimpleMolecule();
- SimpleMolecule species2 = createSimpleMolecule();
- assertEquals(0, comparator.compare(species1, species2));
-
- assertEquals(0, comparator.compare(null, null));
-
- assertEquals(0, comparator.compare(new AntisenseRna(), new AntisenseRna()));
- assertEquals(0, comparator.compare(new Degraded(), new Degraded()));
- assertEquals(0, comparator.compare(new Drug(), new Drug()));
- assertEquals(0, comparator.compare(new Ion(), new Ion()));
- assertEquals(0, comparator.compare(new Phenotype(), new Phenotype()));
- assertEquals(0, comparator.compare(new Rna(), new Rna()));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDifferent2() {
- try {
- SimpleMolecule species1 = createSimpleMolecule();
- SimpleMolecule species2 = createSimpleMolecule();
-
- species1.setCharge(99);
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
- assertTrue(comparator.compare(null, species1) != 0);
- assertTrue(comparator.compare(species1, null) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.setHomodimer(1233);
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.setElementId("");
- species1.setElementId("ASD");
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.setNotes("ASD");
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.setPositionToCompartment(PositionToCompartment.TRANSMEMBRANE);
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.getMiriamData().clear();
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.setInitialAmount(4.0);
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.setInitialConcentration(4.0);
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.setOnlySubstanceUnits(false);
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.setHypothetical(true);
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.getMiriamData().iterator().next().setRelationType(MiriamRelationType.BQ_BIOL_IS);
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- species1 = createSimpleMolecule();
- species2 = createSimpleMolecule();
- species1.addMiriamData(new MiriamData());
- assertTrue(comparator.compare(species1, species2) != 0);
- assertTrue(comparator.compare(species2, species1) != 0);
-
- assertTrue(comparator.compare(new Rna(), new Drug()) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unkowne exception");
- }
- }
-
- public SimpleMolecule createSimpleMolecule() {
- SimpleMolecule result = new SimpleMolecule();
- result.setHomodimer(12);
- result.setElementId("id");
- result.setName("id");
- result.setInitialAmount(12.0);
- result.setCharge(13);
- result.setInitialConcentration(14.0);
- result.setOnlySubstanceUnits(true);
- result.setPositionToCompartment(PositionToCompartment.INSIDE);
- result.setNotes("id");
- MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.UNKNOWN, "c");
- result.addMiriamData(md);
- return result;
- }
-
- @Test
- public void testDifferentConstant() {
- SimpleMolecule species1 = createSimpleMolecule();
- SimpleMolecule species2 = createSimpleMolecule();
- species1.setConstant(true);
- assertTrue(0 != comparator.compare(species1, species2));
- }
-
- @Test
- public void testDifferentBoundaryCondition() {
- SimpleMolecule species1 = createSimpleMolecule();
- SimpleMolecule species2 = createSimpleMolecule();
- species1.setBoundaryCondition(true);
- assertTrue(0 != comparator.compare(species1, species2));
- }
-
- @Test
- public void testDifferentSubstanceUnits() {
- SimpleMolecule species1 = createSimpleMolecule();
- SimpleMolecule species2 = createSimpleMolecule();
- species1.setSubstanceUnits(SbmlUnitType.HERTZ);
- assertTrue(0 != comparator.compare(species1, species2));
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.awt.Color;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
+import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
+
+public class SpeciesComparatorTest {
+
+ SpeciesComparator comparator = new SpeciesComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ Species species1 = createSpecies();
+ Species species2 = createSpecies();
+
+ assertEquals(0, comparator.compare(species1, species2));
+
+ assertEquals(0, comparator.compare(null, null));
+
+ assertEquals(0, comparator.compare(new Complex(), new Complex()));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCompareInvalid() {
+ try {
+
+ Species speciesMock = Mockito.mock(Species.class);
+ comparator.compare(speciesMock, speciesMock);
+ fail("Exception expected");
+
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unkowne exception");
+ }
+ }
+
+ private Species createSpecies() {
+ GenericProtein result = new GenericProtein();
+ result.setName("a");
+
+ result.setElementId("asd");
+ result.setX(12.0);
+ result.setY(123.0);
+ result.setWidth(4);
+ result.setHeight(5);
+ result.setFontSize(9.0);
+ result.setColor(Color.BLUE);
+ result.setVisibilityLevel(14);
+ result.setStateLabel("123");
+ result.setStatePrefix("1234");
+
+ return result;
+ }
+
+ @Test
+ public void testDifferent() throws Exception {
+ try {
+ Species species1 = createSpecies();
+ Species species2 = createSpecies();
+
+ assertTrue(comparator.compare(species1, null) != 0);
+ assertTrue(comparator.compare(null, species1) != 0);
+
+ assertTrue(comparator.compare(new Complex(), species1) != 0);
+
+ species1 = createSpecies();
+ species2 = createSpecies();
+
+ species1.setElementId("tmp");
+
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSpecies();
+ species2 = createSpecies();
+
+ species1.setStateLabel("tmp");
+
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSpecies();
+ species2 = createSpecies();
+
+ species1.setStatePrefix("tmp");
+
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSpecies();
+ species2 = createSpecies();
+
+ species1.setName("new namne");
+
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSpecies();
+ species2 = createSpecies();
+
+ species1.setActivity(true);
+
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSpecies();
+ species2 = createSpecies();
+
+ species1.setLineWidth(453.75);
+
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testException() {
+ try {
+ Species mock = Mockito.mock(Species.class);
+ comparator.compare(mock, mock);
+
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testEquals2() {
+ try {
+ SimpleMolecule species1 = createSimpleMolecule();
+ SimpleMolecule species2 = createSimpleMolecule();
+ assertEquals(0, comparator.compare(species1, species2));
+
+ assertEquals(0, comparator.compare(null, null));
+
+ assertEquals(0, comparator.compare(new AntisenseRna(), new AntisenseRna()));
+ assertEquals(0, comparator.compare(new Degraded(), new Degraded()));
+ assertEquals(0, comparator.compare(new Drug(), new Drug()));
+ assertEquals(0, comparator.compare(new Ion(), new Ion()));
+ assertEquals(0, comparator.compare(new Phenotype(), new Phenotype()));
+ assertEquals(0, comparator.compare(new Rna(), new Rna()));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDifferent2() {
+ try {
+ SimpleMolecule species1 = createSimpleMolecule();
+ SimpleMolecule species2 = createSimpleMolecule();
+
+ species1.setCharge(99);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+ assertTrue(comparator.compare(null, species1) != 0);
+ assertTrue(comparator.compare(species1, null) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.setHomodimer(1233);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.setElementId("");
+ species1.setElementId("ASD");
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.setNotes("ASD");
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.setPositionToCompartment(PositionToCompartment.TRANSMEMBRANE);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.getMiriamData().clear();
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.setInitialAmount(4.0);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.setInitialConcentration(4.0);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.setOnlySubstanceUnits(false);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.setHypothetical(true);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.getMiriamData().iterator().next().setRelationType(MiriamRelationType.BQ_BIOL_IS);
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+ species1.addMiriamData(new MiriamData());
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ assertTrue(comparator.compare(new Rna(), new Drug()) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unkowne exception");
+ }
+ }
+
+ public SimpleMolecule createSimpleMolecule() {
+ SimpleMolecule result = new SimpleMolecule();
+ result.setHomodimer(12);
+ result.setElementId("id");
+ result.setName("id");
+ result.setInitialAmount(12.0);
+ result.setCharge(13);
+ result.setInitialConcentration(14.0);
+ result.setOnlySubstanceUnits(true);
+ result.setPositionToCompartment(PositionToCompartment.INSIDE);
+ result.setNotes("id");
+ MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.UNKNOWN, "c");
+ result.addMiriamData(md);
+ return result;
+ }
+
+ @Test
+ public void testDifferentConstant() {
+ SimpleMolecule species1 = createSimpleMolecule();
+ SimpleMolecule species2 = createSimpleMolecule();
+ species1.setConstant(true);
+ assertTrue(0 != comparator.compare(species1, species2));
+ }
+
+ @Test
+ public void testDifferentBoundaryCondition() {
+ SimpleMolecule species1 = createSimpleMolecule();
+ SimpleMolecule species2 = createSimpleMolecule();
+ species1.setBoundaryCondition(true);
+ assertTrue(0 != comparator.compare(species1, species2));
+ }
+
+ @Test
+ public void testDifferentSubstanceUnits() {
+ SimpleMolecule species1 = createSimpleMolecule();
+ SimpleMolecule species2 = createSimpleMolecule();
+ species1.setSubstanceUnits(SbmlUnitType.HERTZ);
+ assertTrue(0 != comparator.compare(species1, species2));
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesTest.java
index 0282160cc3..a492d7aa9a 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesTest.java
@@ -1,34 +1,34 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertEquals;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class SpeciesTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetter() {
- try {
- Species species = new GenericProtein("id");
- String state = "as";
- species.setState(state);
-
- assertEquals(state, species.getState());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class SpeciesTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetter() {
+ try {
+ Species species = new GenericProtein("id");
+ String state = "as";
+ species.setState(state);
+
+ assertEquals(state, species.getState());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/TruncatedProteinComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/TruncatedProteinComparatorTest.java
index 8c81b8f89f..8495fd04c2 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/TruncatedProteinComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/TruncatedProteinComparatorTest.java
@@ -1,84 +1,84 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class TruncatedProteinComparatorTest {
-
- TruncatedProteinComparator comparator = new TruncatedProteinComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- TruncatedProtein drug1 = createTruncatedProtein();
- TruncatedProtein drug2 = createTruncatedProtein();
-
- assertEquals(0, comparator.compare(drug1, drug1));
-
- assertEquals(0, comparator.compare(drug1, drug2));
- assertEquals(0, comparator.compare(drug2, drug1));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- @Test
- public void testDifferent() {
- try {
- TruncatedProtein drug2 = createTruncatedProtein();
- assertTrue(comparator.compare(null, drug2) != 0);
- assertTrue(comparator.compare(drug2, null) != 0);
- assertTrue(comparator.compare(null, null) == 0);
-
- TruncatedProtein drug = createTruncatedProtein();
- drug.setName("n");
- assertTrue(comparator.compare(drug, drug2) != 0);
-
- assertTrue(comparator.compare(drug, Mockito.mock(TruncatedProtein.class)) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- public TruncatedProtein createTruncatedProtein() {
- TruncatedProtein result = new TruncatedProtein();
- return result;
- }
-
- @Test
- public void testInvalid() {
- try {
- TruncatedProtein object = Mockito.mock(TruncatedProtein.class);
-
- comparator.compare(object, object);
-
- fail("Exception expected");
- } catch (NotImplementedException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class TruncatedProteinComparatorTest {
+
+ TruncatedProteinComparator comparator = new TruncatedProteinComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ TruncatedProtein drug1 = createTruncatedProtein();
+ TruncatedProtein drug2 = createTruncatedProtein();
+
+ assertEquals(0, comparator.compare(drug1, drug1));
+
+ assertEquals(0, comparator.compare(drug1, drug2));
+ assertEquals(0, comparator.compare(drug2, drug1));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ TruncatedProtein drug2 = createTruncatedProtein();
+ assertTrue(comparator.compare(null, drug2) != 0);
+ assertTrue(comparator.compare(drug2, null) != 0);
+ assertTrue(comparator.compare(null, null) == 0);
+
+ TruncatedProtein drug = createTruncatedProtein();
+ drug.setName("n");
+ assertTrue(comparator.compare(drug, drug2) != 0);
+
+ assertTrue(comparator.compare(drug, Mockito.mock(TruncatedProtein.class)) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ public TruncatedProtein createTruncatedProtein() {
+ TruncatedProtein result = new TruncatedProtein();
+ return result;
+ }
+
+ @Test
+ public void testInvalid() {
+ try {
+ TruncatedProtein object = Mockito.mock(TruncatedProtein.class);
+
+ comparator.compare(object, object);
+
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/TruncatedProteinTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/TruncatedProteinTest.java
index 1150dc7a2d..c67c4db57e 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/TruncatedProteinTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/TruncatedProteinTest.java
@@ -1,69 +1,69 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class TruncatedProteinTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new TruncatedProtein());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- TruncatedProtein species = new TruncatedProtein(new TruncatedProtein());
- assertNotNull(species);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy1() {
- try {
- TruncatedProtein species = new TruncatedProtein("id").copy();
- assertNotNull(species);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy2() {
- try {
- TruncatedProtein protein = Mockito.spy(TruncatedProtein.class);
- protein.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class TruncatedProteinTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new TruncatedProtein());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ TruncatedProtein species = new TruncatedProtein(new TruncatedProtein());
+ assertNotNull(species);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy1() {
+ try {
+ TruncatedProtein species = new TruncatedProtein("id").copy();
+ assertNotNull(species);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy2() {
+ try {
+ TruncatedProtein protein = Mockito.spy(TruncatedProtein.class);
+ protein.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/UnknownComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/UnknownComparatorTest.java
index fbc4809cd9..e0fe9a859d 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/UnknownComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/UnknownComparatorTest.java
@@ -1,84 +1,84 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class UnknownComparatorTest {
-
- UnknownComparator comparator = new UnknownComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- Unknown aRna1 = createUnknown();
- Unknown aRna2 = createUnknown();
-
- assertEquals(0, comparator.compare(aRna1, aRna1));
-
- assertEquals(0, comparator.compare(aRna1, aRna2));
- assertEquals(0, comparator.compare(aRna2, aRna1));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- @Test
- public void testDifferent() {
- try {
- Unknown unknown2 = createUnknown();
- assertTrue(comparator.compare(null, unknown2) != 0);
- assertTrue(comparator.compare(unknown2, null) != 0);
- assertTrue(comparator.compare(null, null) == 0);
-
- Unknown unknown = createUnknown();
- unknown.setName("n");
- assertTrue(comparator.compare(unknown, unknown2) != 0);
-
- assertTrue(comparator.compare(unknown, Mockito.mock(Unknown.class)) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- public Unknown createUnknown() {
- Unknown result = new Unknown();
- return result;
- }
-
- @Test
- public void testInvalid() {
- try {
- Unknown object = Mockito.mock(Unknown.class);
-
- comparator.compare(object, object);
-
- fail("Exception expected");
- } catch (NotImplementedException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class UnknownComparatorTest {
+
+ UnknownComparator comparator = new UnknownComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ Unknown aRna1 = createUnknown();
+ Unknown aRna2 = createUnknown();
+
+ assertEquals(0, comparator.compare(aRna1, aRna1));
+
+ assertEquals(0, comparator.compare(aRna1, aRna2));
+ assertEquals(0, comparator.compare(aRna2, aRna1));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ Unknown unknown2 = createUnknown();
+ assertTrue(comparator.compare(null, unknown2) != 0);
+ assertTrue(comparator.compare(unknown2, null) != 0);
+ assertTrue(comparator.compare(null, null) == 0);
+
+ Unknown unknown = createUnknown();
+ unknown.setName("n");
+ assertTrue(comparator.compare(unknown, unknown2) != 0);
+
+ assertTrue(comparator.compare(unknown, Mockito.mock(Unknown.class)) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ public Unknown createUnknown() {
+ Unknown result = new Unknown();
+ return result;
+ }
+
+ @Test
+ public void testInvalid() {
+ try {
+ Unknown object = Mockito.mock(Unknown.class);
+
+ comparator.compare(object, object);
+
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/UnknownTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/UnknownTest.java
index 5dc8c9566d..591ac886f1 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/UnknownTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/UnknownTest.java
@@ -1,80 +1,80 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-
-public class UnknownTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new Unknown());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- Unknown degraded = new Unknown(new Unknown());
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- Unknown degraded = new Unknown("id");
- assertNotNull(degraded.getStringType());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- Unknown degraded = new Unknown().copy();
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- Unknown object = Mockito.spy(Unknown.class);
- object.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+public class UnknownTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new Unknown());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ Unknown degraded = new Unknown(new Unknown());
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ Unknown degraded = new Unknown("id");
+ assertNotNull(degraded.getStringType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ Unknown degraded = new Unknown().copy();
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ Unknown object = Mockito.spy(Unknown.class);
+ object.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/field/AllFieldTests.java b/model/src/test/java/lcsb/mapviewer/model/map/species/field/AllFieldTests.java
index ccfe28648a..afde73415e 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/field/AllFieldTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/field/AllFieldTests.java
@@ -1,18 +1,18 @@
-package lcsb.mapviewer.model.map.species.field;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ CodingRegionTest.class, //
- ModificationStateTest.class, //
- ResidueTest.class, //
- PositionToCompartmentTest.class, //
- ProteinBindingDomainTest.class,//
- StructureTest.class,//
- UniprotRecordTest.class,//
-})
-public class AllFieldTests {
-
-}
+package lcsb.mapviewer.model.map.species.field;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ CodingRegionTest.class, //
+ ModificationStateTest.class, //
+ ResidueTest.class, //
+ PositionToCompartmentTest.class, //
+ ProteinBindingDomainTest.class,//
+ StructureTest.class,//
+ UniprotRecordTest.class,//
+})
+public class AllFieldTests {
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/field/ModificationStateTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/field/ModificationStateTest.java
index 8867d157f8..3de4dbaae7 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/field/ModificationStateTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/field/ModificationStateTest.java
@@ -1,40 +1,40 @@
-package lcsb.mapviewer.model.map.species.field;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.map.species.field.ModificationState;
-
-public class ModificationStateTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testValidValues() {
- for (ModificationState type : ModificationState.values()) {
- assertNotNull(type);
-
- // for coverage tests
- ModificationState.valueOf(type.toString());
- assertNotNull(type.getFullName());
- assertNotNull(type.getAbbreviation());
- }
- }
-
- @Test
- public void testGetByName() {
- assertNull(ModificationState.getByName("Adasd"));
- assertNotNull(ModificationState.getByName("protonated"));
- }
-
-}
+package lcsb.mapviewer.model.map.species.field;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+
+public class ModificationStateTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testValidValues() {
+ for (ModificationState type : ModificationState.values()) {
+ assertNotNull(type);
+
+ // for coverage tests
+ ModificationState.valueOf(type.toString());
+ assertNotNull(type.getFullName());
+ assertNotNull(type.getAbbreviation());
+ }
+ }
+
+ @Test
+ public void testGetByName() {
+ assertNull(ModificationState.getByName("Adasd"));
+ assertNotNull(ModificationState.getByName("protonated"));
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/field/PositionToCompartmentTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/field/PositionToCompartmentTest.java
index 5ddadcaac7..dabb973bd6 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/field/PositionToCompartmentTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/field/PositionToCompartmentTest.java
@@ -1,39 +1,39 @@
-package lcsb.mapviewer.model.map.species.field;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
-
-public class PositionToCompartmentTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testValidValues() {
- for (PositionToCompartment type : PositionToCompartment.values()) {
- assertNotNull(type);
- assertNotNull(type.getStringName());
-
- // for coverage tests
- PositionToCompartment.valueOf(type.toString());
- }
- }
-
- @Test
- public void testGetByString() {
- assertNotNull(PositionToCompartment.getByString("insideOfMembrane"));
- assertNull(PositionToCompartment.getByString("insideOfasdasdas"));
- }
-
-}
+package lcsb.mapviewer.model.map.species.field;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
+
+public class PositionToCompartmentTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testValidValues() {
+ for (PositionToCompartment type : PositionToCompartment.values()) {
+ assertNotNull(type);
+ assertNotNull(type.getStringName());
+
+ // for coverage tests
+ PositionToCompartment.valueOf(type.toString());
+ }
+ }
+
+ @Test
+ public void testGetByString() {
+ assertNotNull(PositionToCompartment.getByString("insideOfMembrane"));
+ assertNull(PositionToCompartment.getByString("insideOfasdasdas"));
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/statistics/AllStatisticsTests.java b/model/src/test/java/lcsb/mapviewer/model/map/statistics/AllStatisticsTests.java
index b059c1fd94..278b07f38d 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/statistics/AllStatisticsTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/statistics/AllStatisticsTests.java
@@ -1,13 +1,13 @@
-package lcsb.mapviewer.model.map.statistics;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ SearchHistoryTest.class, //
- SearchTypeTest.class,//
-})
-public class AllStatisticsTests {
-
-}
+package lcsb.mapviewer.model.map.statistics;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ SearchHistoryTest.class, //
+ SearchTypeTest.class,//
+})
+public class AllStatisticsTests {
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/statistics/SearchHistoryTest.java b/model/src/test/java/lcsb/mapviewer/model/map/statistics/SearchHistoryTest.java
index a1eff9d1da..bbbda64dde 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/statistics/SearchHistoryTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/statistics/SearchHistoryTest.java
@@ -1,63 +1,63 @@
-package lcsb.mapviewer.model.map.statistics;
-
-import static org.junit.Assert.assertEquals;
-
-import java.util.Calendar;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class SearchHistoryTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new SearchHistory());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- SearchHistory sh = new SearchHistory();
-
- int id = 60;
- String query = "q";
- String map = "e";
- Calendar timestamp = Calendar.getInstance();
- SearchType type = SearchType.DRUG;
- String ipAddress = "3.4";
-
- sh.setId(id);
- sh.setQuery(query);
- sh.setMap(map);
- sh.setTimestamp(timestamp);
- sh.setType(type);
- sh.setIpAddress(ipAddress);
-
- assertEquals(id, sh.getId());
- assertEquals(query, sh.getQuery());
- assertEquals(map, sh.getMap());
- assertEquals(timestamp, sh.getTimestamp());
- assertEquals(type, sh.getType());
- assertEquals(ipAddress, sh.getIpAddress());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.map.statistics;
+
+import static org.junit.Assert.assertEquals;
+
+import java.util.Calendar;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class SearchHistoryTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new SearchHistory());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ SearchHistory sh = new SearchHistory();
+
+ int id = 60;
+ String query = "q";
+ String map = "e";
+ Calendar timestamp = Calendar.getInstance();
+ SearchType type = SearchType.DRUG;
+ String ipAddress = "3.4";
+
+ sh.setId(id);
+ sh.setQuery(query);
+ sh.setMap(map);
+ sh.setTimestamp(timestamp);
+ sh.setType(type);
+ sh.setIpAddress(ipAddress);
+
+ assertEquals(id, sh.getId());
+ assertEquals(query, sh.getQuery());
+ assertEquals(map, sh.getMap());
+ assertEquals(timestamp, sh.getTimestamp());
+ assertEquals(type, sh.getType());
+ assertEquals(ipAddress, sh.getIpAddress());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/statistics/SearchTypeTest.java b/model/src/test/java/lcsb/mapviewer/model/map/statistics/SearchTypeTest.java
index cacbcc2ff7..0d0ed2796f 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/statistics/SearchTypeTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/statistics/SearchTypeTest.java
@@ -1,28 +1,28 @@
-package lcsb.mapviewer.model.map.statistics;
-
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class SearchTypeTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testValidValues() {
- for (SearchType type : SearchType.values()) {
- assertNotNull(type);
-
- // for coverage tests
- SearchType.valueOf(type.toString());
- }
- }
-}
+package lcsb.mapviewer.model.map.statistics;
+
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class SearchTypeTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testValidValues() {
+ for (SearchType type : SearchType.values()) {
+ assertNotNull(type);
+
+ // for coverage tests
+ SearchType.valueOf(type.toString());
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/user/AllUserTests.java b/model/src/test/java/lcsb/mapviewer/model/user/AllUserTests.java
index db80b08b4f..11d59b900b 100644
--- a/model/src/test/java/lcsb/mapviewer/model/user/AllUserTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/user/AllUserTests.java
@@ -1,22 +1,22 @@
-package lcsb.mapviewer.model.user;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ BasicPrivilegeTest.class, //
- ConfigurationElementTypeTest.class, //
- ConfigurationElementEditTypeTest.class, //
- ConfigurationTest.class, //
- ObjectPrivilegeTest.class, //
- PrivilegeTypeTest.class, //
- UserAnnotationSchemaTest.class, //
- UserClassAnnotatorsTest.class, //
- UserClassRequiredAnnotationsTest.class, //
- UserClassValidAnnotationsTest.class, //
- UserTest.class,//
-})
-public class AllUserTests {
-
-}
+package lcsb.mapviewer.model.user;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ BasicPrivilegeTest.class, //
+ ConfigurationElementTypeTest.class, //
+ ConfigurationElementEditTypeTest.class, //
+ ConfigurationTest.class, //
+ ObjectPrivilegeTest.class, //
+ PrivilegeTypeTest.class, //
+ UserAnnotationSchemaTest.class, //
+ UserClassAnnotatorsTest.class, //
+ UserClassRequiredAnnotationsTest.class, //
+ UserClassValidAnnotationsTest.class, //
+ UserTest.class,//
+})
+public class AllUserTests {
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/user/BasicPrivilegeTest.java b/model/src/test/java/lcsb/mapviewer/model/user/BasicPrivilegeTest.java
index c34bee4c76..8a226413bb 100644
--- a/model/src/test/java/lcsb/mapviewer/model/user/BasicPrivilegeTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/user/BasicPrivilegeTest.java
@@ -1,65 +1,65 @@
-package lcsb.mapviewer.model.user;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class BasicPrivilegeTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new BasicPrivilege());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- BasicPrivilege privilege = new BasicPrivilege();
- int id = 25;
- int level = 26;
- PrivilegeType type = PrivilegeType.ADD_MAP;
- User user = new User();
-
- privilege.setId(id);
- privilege.setLevel(level);
- privilege.setType(type);
- privilege.setUser(user);
-
- assertEquals(id, privilege.getId());
- assertEquals(level, privilege.getLevel());
- assertEquals(type, privilege.getType());
- assertEquals(user, privilege.getUser());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testEqualsPrivilege() {
- try {
- BasicPrivilege privilege = new BasicPrivilege();
- assertFalse(privilege.equalsPrivilege(null));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.user;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class BasicPrivilegeTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new BasicPrivilege());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ BasicPrivilege privilege = new BasicPrivilege();
+ int id = 25;
+ int level = 26;
+ PrivilegeType type = PrivilegeType.ADD_MAP;
+ User user = new User();
+
+ privilege.setId(id);
+ privilege.setLevel(level);
+ privilege.setType(type);
+ privilege.setUser(user);
+
+ assertEquals(id, privilege.getId());
+ assertEquals(level, privilege.getLevel());
+ assertEquals(type, privilege.getType());
+ assertEquals(user, privilege.getUser());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testEqualsPrivilege() {
+ try {
+ BasicPrivilege privilege = new BasicPrivilege();
+ assertFalse(privilege.equalsPrivilege(null));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/user/ConfigurationElementEditTypeTest.java b/model/src/test/java/lcsb/mapviewer/model/user/ConfigurationElementEditTypeTest.java
index 839105c1d0..39d37832c9 100644
--- a/model/src/test/java/lcsb/mapviewer/model/user/ConfigurationElementEditTypeTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/user/ConfigurationElementEditTypeTest.java
@@ -1,31 +1,31 @@
-package lcsb.mapviewer.model.user;
-
-import static org.junit.Assert.*;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ConfigurationElementEditTypeTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testValues() {
- for (ConfigurationElementEditType type: ConfigurationElementEditType.values()){
- assertNotNull(ConfigurationElementEditType.valueOf(type.toString()));
- }
- }
-
-}
+package lcsb.mapviewer.model.user;
+
+import static org.junit.Assert.*;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ConfigurationElementEditTypeTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testValues() {
+ for (ConfigurationElementEditType type: ConfigurationElementEditType.values()){
+ assertNotNull(ConfigurationElementEditType.valueOf(type.toString()));
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/user/ConfigurationElementTypeTest.java b/model/src/test/java/lcsb/mapviewer/model/user/ConfigurationElementTypeTest.java
index 0624e5daf6..2c9d683b50 100644
--- a/model/src/test/java/lcsb/mapviewer/model/user/ConfigurationElementTypeTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/user/ConfigurationElementTypeTest.java
@@ -1,31 +1,31 @@
-package lcsb.mapviewer.model.user;
-
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ConfigurationElementTypeTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testValidValues() {
- for (ConfigurationElementType type : ConfigurationElementType.values()) {
- assertNotNull(type);
-
- // for coverage tests
- ConfigurationElementType.valueOf(type.toString());
- assertNotNull(type.getCommonName());
- assertNotNull(type.getDefaultValue());
- assertNotNull(type.getEditType());
- }
- }
-}
+package lcsb.mapviewer.model.user;
+
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ConfigurationElementTypeTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testValidValues() {
+ for (ConfigurationElementType type : ConfigurationElementType.values()) {
+ assertNotNull(type);
+
+ // for coverage tests
+ ConfigurationElementType.valueOf(type.toString());
+ assertNotNull(type.getCommonName());
+ assertNotNull(type.getDefaultValue());
+ assertNotNull(type.getEditType());
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/user/ConfigurationTest.java b/model/src/test/java/lcsb/mapviewer/model/user/ConfigurationTest.java
index 11e52d9c0e..554afa44ce 100644
--- a/model/src/test/java/lcsb/mapviewer/model/user/ConfigurationTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/user/ConfigurationTest.java
@@ -1,49 +1,49 @@
-package lcsb.mapviewer.model.user;
-
-import static org.junit.Assert.assertEquals;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ConfigurationTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new ConfigurationOption());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- ConfigurationOption conf = new ConfigurationOption();
- int id = 81;
- ConfigurationElementType type = ConfigurationElementType.DEFAULT_MAP;
- String value = "a.val";
- conf.setId(id);
- assertEquals(id, conf.getId());
- conf.setType(type);
- assertEquals(type, conf.getType());
- conf.setValue(value);
- assertEquals(value, conf.getValue());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.user;
+
+import static org.junit.Assert.assertEquals;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ConfigurationTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new ConfigurationOption());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ ConfigurationOption conf = new ConfigurationOption();
+ int id = 81;
+ ConfigurationElementType type = ConfigurationElementType.DEFAULT_MAP;
+ String value = "a.val";
+ conf.setId(id);
+ assertEquals(id, conf.getId());
+ conf.setType(type);
+ assertEquals(type, conf.getType());
+ conf.setValue(value);
+ assertEquals(value, conf.getValue());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/user/ObjectPrivilegeTest.java b/model/src/test/java/lcsb/mapviewer/model/user/ObjectPrivilegeTest.java
index 90869f31f2..3820cdc171 100644
--- a/model/src/test/java/lcsb/mapviewer/model/user/ObjectPrivilegeTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/user/ObjectPrivilegeTest.java
@@ -1,113 +1,113 @@
-package lcsb.mapviewer.model.user;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.Project;
-
-public class ObjectPrivilegeTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new ObjectPrivilege());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructror() {
- try {
- Integer id = 12;
- Project project = new Project();
- project.setId(id);
- ObjectPrivilege privilege = new ObjectPrivilege(project, 1, PrivilegeType.VIEW_PROJECT, new User());
- assertEquals(id, privilege.getIdObject());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- String idStr = "12";
- Integer id = 12;
- ObjectPrivilege privilege = new ObjectPrivilege();
- privilege.setIdObject(idStr);
- assertEquals(id, privilege.getIdObject());
- privilege.setIdObject((Integer) null);
- assertNull(privilege.getIdObject());
- privilege.setIdObject(id);
- assertEquals(id, privilege.getIdObject());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testEqualsPrivilege() {
- try {
- ObjectPrivilege privilege = new ObjectPrivilege();
- privilege.setType(PrivilegeType.ADD_MAP);
- assertFalse(privilege.equalsPrivilege(null));
- assertFalse(privilege.equalsPrivilege(new BasicPrivilege()));
-
- privilege.setIdObject(2);
- ObjectPrivilege privilege2 = new ObjectPrivilege();
- privilege2.setIdObject(3);
- privilege2.setType(PrivilegeType.ADD_MAP);
- assertFalse(privilege.equalsPrivilege(privilege2));
-
- privilege2.setIdObject(3);
- privilege2.setType(PrivilegeType.CONFIGURATION_MANAGE);
- assertFalse(privilege.equalsPrivilege(privilege2));
-
- privilege2.setIdObject(2);
- privilege2.setType(PrivilegeType.ADD_MAP);
- assertTrue(privilege.equalsPrivilege(privilege2));
-
- privilege.setIdObject((Integer) null);
- assertFalse(privilege.equalsPrivilege(privilege2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testEqualsWithEmptyObjectId() {
- try {
- ObjectPrivilege privilege = new ObjectPrivilege();
- privilege.setType(PrivilegeType.ADD_MAP);
- privilege.setIdObject((Integer) null);
-
- ObjectPrivilege privilege2 = new ObjectPrivilege();
- privilege2.setType(PrivilegeType.ADD_MAP);
- privilege2.setIdObject((Integer) null);
- assertTrue(privilege.equalsPrivilege(privilege2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.user;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.Project;
+
+public class ObjectPrivilegeTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new ObjectPrivilege());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructror() {
+ try {
+ Integer id = 12;
+ Project project = new Project();
+ project.setId(id);
+ ObjectPrivilege privilege = new ObjectPrivilege(project, 1, PrivilegeType.VIEW_PROJECT, new User());
+ assertEquals(id, privilege.getIdObject());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ String idStr = "12";
+ Integer id = 12;
+ ObjectPrivilege privilege = new ObjectPrivilege();
+ privilege.setIdObject(idStr);
+ assertEquals(id, privilege.getIdObject());
+ privilege.setIdObject((Integer) null);
+ assertNull(privilege.getIdObject());
+ privilege.setIdObject(id);
+ assertEquals(id, privilege.getIdObject());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testEqualsPrivilege() {
+ try {
+ ObjectPrivilege privilege = new ObjectPrivilege();
+ privilege.setType(PrivilegeType.ADD_MAP);
+ assertFalse(privilege.equalsPrivilege(null));
+ assertFalse(privilege.equalsPrivilege(new BasicPrivilege()));
+
+ privilege.setIdObject(2);
+ ObjectPrivilege privilege2 = new ObjectPrivilege();
+ privilege2.setIdObject(3);
+ privilege2.setType(PrivilegeType.ADD_MAP);
+ assertFalse(privilege.equalsPrivilege(privilege2));
+
+ privilege2.setIdObject(3);
+ privilege2.setType(PrivilegeType.CONFIGURATION_MANAGE);
+ assertFalse(privilege.equalsPrivilege(privilege2));
+
+ privilege2.setIdObject(2);
+ privilege2.setType(PrivilegeType.ADD_MAP);
+ assertTrue(privilege.equalsPrivilege(privilege2));
+
+ privilege.setIdObject((Integer) null);
+ assertFalse(privilege.equalsPrivilege(privilege2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testEqualsWithEmptyObjectId() {
+ try {
+ ObjectPrivilege privilege = new ObjectPrivilege();
+ privilege.setType(PrivilegeType.ADD_MAP);
+ privilege.setIdObject((Integer) null);
+
+ ObjectPrivilege privilege2 = new ObjectPrivilege();
+ privilege2.setType(PrivilegeType.ADD_MAP);
+ privilege2.setIdObject((Integer) null);
+ assertTrue(privilege.equalsPrivilege(privilege2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/user/PrivilegeTypeTest.java b/model/src/test/java/lcsb/mapviewer/model/user/PrivilegeTypeTest.java
index b872138a09..d9b3476b9c 100644
--- a/model/src/test/java/lcsb/mapviewer/model/user/PrivilegeTypeTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/user/PrivilegeTypeTest.java
@@ -1,34 +1,34 @@
-package lcsb.mapviewer.model.user;
-
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class PrivilegeTypeTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testValidValues() {
- for (PrivilegeType type : PrivilegeType.values()) {
- assertNotNull(type);
-
- // for coverage tests
- PrivilegeType.valueOf(type.toString());
- assertNotNull(type.getCommonName());
- assertNotNull(type.getPrivilegeClassType());
- type.getPrivilegeObjectType();
- type.isNumeric();
-
- }
- }
-
-}
+package lcsb.mapviewer.model.user;
+
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class PrivilegeTypeTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testValidValues() {
+ for (PrivilegeType type : PrivilegeType.values()) {
+ assertNotNull(type);
+
+ // for coverage tests
+ PrivilegeType.valueOf(type.toString());
+ assertNotNull(type.getCommonName());
+ assertNotNull(type.getPrivilegeClassType());
+ type.getPrivilegeObjectType();
+ type.isNumeric();
+
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/user/UserAnnotationSchemaTest.java b/model/src/test/java/lcsb/mapviewer/model/user/UserAnnotationSchemaTest.java
index c7da866bd3..97e467672b 100644
--- a/model/src/test/java/lcsb/mapviewer/model/user/UserAnnotationSchemaTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/user/UserAnnotationSchemaTest.java
@@ -1,232 +1,232 @@
-package lcsb.mapviewer.model.user;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.fail;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.MiriamType;
-
-public class UserAnnotationSchemaTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testAddClassAnnotator() throws Exception {
- try {
- UserAnnotationSchema annotationSchema = new UserAnnotationSchema();
- UserClassAnnotators ca = new UserClassAnnotators(String.class, new ArrayList<String>());
- UserClassAnnotators ca2 = new UserClassAnnotators(String.class, new ArrayList<String>());
- annotationSchema.addClassAnnotator(ca);
- annotationSchema.addClassAnnotator(ca2);
- assertEquals(1, annotationSchema.getClassAnnotators().size());
- assertEquals(ca2.getAnnotators(), annotationSchema.getAnnotatorsForClass(String.class));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidAddClassAnnotator() throws Exception {
- try {
- UserAnnotationSchema annotationSchema = new UserAnnotationSchema();
- UserClassAnnotators ca = new UserClassAnnotators(String.class, new ArrayList<String>());
- ca.setClassName((String) null);
- annotationSchema.addClassAnnotator(ca);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddClassRequiredAnnotations() throws Exception {
- try {
- UserAnnotationSchema annotationSchema = new UserAnnotationSchema();
- UserClassRequiredAnnotations cra = new UserClassRequiredAnnotations(String.class, new ArrayList<MiriamType>());
- UserClassRequiredAnnotations cra2 = new UserClassRequiredAnnotations(String.class, new ArrayList<MiriamType>());
- annotationSchema.addClassRequiredAnnotations(cra);
- annotationSchema.addClassRequiredAnnotations(cra2);
- assertEquals(1, annotationSchema.getClassRequiredAnnotators().size());
- assertEquals(cra2, annotationSchema.getClassRequiredAnnotators().get(0));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddInvalidClassRequiredAnnotations() throws Exception {
- try {
- UserAnnotationSchema annotationSchema = new UserAnnotationSchema();
- UserClassRequiredAnnotations cra = new UserClassRequiredAnnotations(String.class, new ArrayList<MiriamType>());
- cra.setClassName((String) null);
-
- annotationSchema.addClassRequiredAnnotations(cra);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddClassValidAnnotations() throws Exception {
- try {
- UserAnnotationSchema annotationSchema = new UserAnnotationSchema();
- UserClassValidAnnotations cva = new UserClassValidAnnotations(String.class, new ArrayList<MiriamType>());
- UserClassValidAnnotations cva2 = new UserClassValidAnnotations(String.class, new ArrayList<MiriamType>());
- annotationSchema.addClassValidAnnotations(cva);
- annotationSchema.addClassValidAnnotations(cva2);
- assertEquals(1, annotationSchema.getClassValidAnnotators().size());
- assertEquals(cva2, annotationSchema.getClassValidAnnotators().get(0));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetValidAnnotations() throws Exception {
- try {
- UserAnnotationSchema annotationSchema = new UserAnnotationSchema();
- List<MiriamType> list = new ArrayList<>();
- list.add(MiriamType.CAS);
- UserClassValidAnnotations cva = new UserClassValidAnnotations(String.class, list);
- annotationSchema.addClassValidAnnotations(cva);
- assertEquals(1, annotationSchema.getValidAnnotations(String.class).size());
- assertEquals(0, annotationSchema.getValidAnnotations(Integer.class).size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetRequiredAnnotations() throws Exception {
- try {
- UserAnnotationSchema annotationSchema = new UserAnnotationSchema();
- List<MiriamType> list = new ArrayList<>();
- list.add(MiriamType.CAS);
- UserClassRequiredAnnotations cva = new UserClassRequiredAnnotations(String.class, list);
- annotationSchema.addClassRequiredAnnotations(cva);
- assertEquals(1, annotationSchema.getRequiredAnnotations(String.class).size());
- assertEquals(0, annotationSchema.getRequiredAnnotations(Integer.class).size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddInvalidClassValidAnnotations() throws Exception {
- try {
- UserAnnotationSchema annotationSchema = new UserAnnotationSchema();
- UserClassValidAnnotations cva = new UserClassValidAnnotations(String.class, new ArrayList<MiriamType>());
- cva.setClassName((String) null);
-
- annotationSchema.addClassValidAnnotations(cva);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddGuiPreference() throws Exception {
- try {
- UserAnnotationSchema annotationSchema = new UserAnnotationSchema();
-
- annotationSchema.addGuiPreference(new UserGuiPreference());
- assertEquals(1, annotationSchema.getGuiPreferences().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddGuiPreferenceWithDuplicateKey() throws Exception {
- try {
- UserAnnotationSchema annotationSchema = new UserAnnotationSchema();
- UserGuiPreference preference1 = new UserGuiPreference();
- preference1.setKey("test");
- preference1.setValue("value");
- annotationSchema.addGuiPreference(preference1);
- UserGuiPreference preference2 = new UserGuiPreference();
- preference2.setKey("test");
- preference2.setValue("new value");
- annotationSchema.addGuiPreference(preference2);
- assertEquals(1, annotationSchema.getGuiPreferences().size());
- assertEquals("new value", annotationSchema.getGuiPreferences().iterator().next().getValue());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new UserAnnotationSchema());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- UserAnnotationSchema uas = new UserAnnotationSchema();
- Boolean validateMiriamTypes = true;
- List<UserClassAnnotators> classAnnotators = new ArrayList<>();
- List<UserClassValidAnnotations> classValidAnnotators = new ArrayList<>();
- List<UserClassRequiredAnnotations> classRequiredAnnotators = new ArrayList<>();
- User user = new User();
-
- Boolean sbgnFormat = true;
- Boolean networkLayoutAsDefault = true;
-
- uas.setValidateMiriamTypes(validateMiriamTypes);
- uas.setClassAnnotators(classAnnotators);
- uas.setClassValidAnnotators(classValidAnnotators);
- uas.setClassRequiredAnnotators(classRequiredAnnotators);
- uas.setSbgnFormat(sbgnFormat);
- uas.setNetworkLayoutAsDefault(networkLayoutAsDefault);
- uas.setUser(user);
-
- assertEquals(validateMiriamTypes, uas.getValidateMiriamTypes());
- assertEquals(classAnnotators, uas.getClassAnnotators());
- assertEquals(classValidAnnotators, uas.getClassValidAnnotators());
- assertEquals(classRequiredAnnotators, uas.getClassRequiredAnnotators());
- assertEquals(sbgnFormat, uas.getSbgnFormat());
- assertEquals(networkLayoutAsDefault, uas.getNetworkLayoutAsDefault());
- assertEquals(user, uas.getUser());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.user;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.fail;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.MiriamType;
+
+public class UserAnnotationSchemaTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testAddClassAnnotator() throws Exception {
+ try {
+ UserAnnotationSchema annotationSchema = new UserAnnotationSchema();
+ UserClassAnnotators ca = new UserClassAnnotators(String.class, new ArrayList<String>());
+ UserClassAnnotators ca2 = new UserClassAnnotators(String.class, new ArrayList<String>());
+ annotationSchema.addClassAnnotator(ca);
+ annotationSchema.addClassAnnotator(ca2);
+ assertEquals(1, annotationSchema.getClassAnnotators().size());
+ assertEquals(ca2.getAnnotators(), annotationSchema.getAnnotatorsForClass(String.class));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidAddClassAnnotator() throws Exception {
+ try {
+ UserAnnotationSchema annotationSchema = new UserAnnotationSchema();
+ UserClassAnnotators ca = new UserClassAnnotators(String.class, new ArrayList<String>());
+ ca.setClassName((String) null);
+ annotationSchema.addClassAnnotator(ca);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddClassRequiredAnnotations() throws Exception {
+ try {
+ UserAnnotationSchema annotationSchema = new UserAnnotationSchema();
+ UserClassRequiredAnnotations cra = new UserClassRequiredAnnotations(String.class, new ArrayList<MiriamType>());
+ UserClassRequiredAnnotations cra2 = new UserClassRequiredAnnotations(String.class, new ArrayList<MiriamType>());
+ annotationSchema.addClassRequiredAnnotations(cra);
+ annotationSchema.addClassRequiredAnnotations(cra2);
+ assertEquals(1, annotationSchema.getClassRequiredAnnotators().size());
+ assertEquals(cra2, annotationSchema.getClassRequiredAnnotators().get(0));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddInvalidClassRequiredAnnotations() throws Exception {
+ try {
+ UserAnnotationSchema annotationSchema = new UserAnnotationSchema();
+ UserClassRequiredAnnotations cra = new UserClassRequiredAnnotations(String.class, new ArrayList<MiriamType>());
+ cra.setClassName((String) null);
+
+ annotationSchema.addClassRequiredAnnotations(cra);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddClassValidAnnotations() throws Exception {
+ try {
+ UserAnnotationSchema annotationSchema = new UserAnnotationSchema();
+ UserClassValidAnnotations cva = new UserClassValidAnnotations(String.class, new ArrayList<MiriamType>());
+ UserClassValidAnnotations cva2 = new UserClassValidAnnotations(String.class, new ArrayList<MiriamType>());
+ annotationSchema.addClassValidAnnotations(cva);
+ annotationSchema.addClassValidAnnotations(cva2);
+ assertEquals(1, annotationSchema.getClassValidAnnotators().size());
+ assertEquals(cva2, annotationSchema.getClassValidAnnotators().get(0));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetValidAnnotations() throws Exception {
+ try {
+ UserAnnotationSchema annotationSchema = new UserAnnotationSchema();
+ List<MiriamType> list = new ArrayList<>();
+ list.add(MiriamType.CAS);
+ UserClassValidAnnotations cva = new UserClassValidAnnotations(String.class, list);
+ annotationSchema.addClassValidAnnotations(cva);
+ assertEquals(1, annotationSchema.getValidAnnotations(String.class).size());
+ assertEquals(0, annotationSchema.getValidAnnotations(Integer.class).size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetRequiredAnnotations() throws Exception {
+ try {
+ UserAnnotationSchema annotationSchema = new UserAnnotationSchema();
+ List<MiriamType> list = new ArrayList<>();
+ list.add(MiriamType.CAS);
+ UserClassRequiredAnnotations cva = new UserClassRequiredAnnotations(String.class, list);
+ annotationSchema.addClassRequiredAnnotations(cva);
+ assertEquals(1, annotationSchema.getRequiredAnnotations(String.class).size());
+ assertEquals(0, annotationSchema.getRequiredAnnotations(Integer.class).size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddInvalidClassValidAnnotations() throws Exception {
+ try {
+ UserAnnotationSchema annotationSchema = new UserAnnotationSchema();
+ UserClassValidAnnotations cva = new UserClassValidAnnotations(String.class, new ArrayList<MiriamType>());
+ cva.setClassName((String) null);
+
+ annotationSchema.addClassValidAnnotations(cva);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddGuiPreference() throws Exception {
+ try {
+ UserAnnotationSchema annotationSchema = new UserAnnotationSchema();
+
+ annotationSchema.addGuiPreference(new UserGuiPreference());
+ assertEquals(1, annotationSchema.getGuiPreferences().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddGuiPreferenceWithDuplicateKey() throws Exception {
+ try {
+ UserAnnotationSchema annotationSchema = new UserAnnotationSchema();
+ UserGuiPreference preference1 = new UserGuiPreference();
+ preference1.setKey("test");
+ preference1.setValue("value");
+ annotationSchema.addGuiPreference(preference1);
+ UserGuiPreference preference2 = new UserGuiPreference();
+ preference2.setKey("test");
+ preference2.setValue("new value");
+ annotationSchema.addGuiPreference(preference2);
+ assertEquals(1, annotationSchema.getGuiPreferences().size());
+ assertEquals("new value", annotationSchema.getGuiPreferences().iterator().next().getValue());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new UserAnnotationSchema());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ UserAnnotationSchema uas = new UserAnnotationSchema();
+ Boolean validateMiriamTypes = true;
+ List<UserClassAnnotators> classAnnotators = new ArrayList<>();
+ List<UserClassValidAnnotations> classValidAnnotators = new ArrayList<>();
+ List<UserClassRequiredAnnotations> classRequiredAnnotators = new ArrayList<>();
+ User user = new User();
+
+ Boolean sbgnFormat = true;
+ Boolean networkLayoutAsDefault = true;
+
+ uas.setValidateMiriamTypes(validateMiriamTypes);
+ uas.setClassAnnotators(classAnnotators);
+ uas.setClassValidAnnotators(classValidAnnotators);
+ uas.setClassRequiredAnnotators(classRequiredAnnotators);
+ uas.setSbgnFormat(sbgnFormat);
+ uas.setNetworkLayoutAsDefault(networkLayoutAsDefault);
+ uas.setUser(user);
+
+ assertEquals(validateMiriamTypes, uas.getValidateMiriamTypes());
+ assertEquals(classAnnotators, uas.getClassAnnotators());
+ assertEquals(classValidAnnotators, uas.getClassValidAnnotators());
+ assertEquals(classRequiredAnnotators, uas.getClassRequiredAnnotators());
+ assertEquals(sbgnFormat, uas.getSbgnFormat());
+ assertEquals(networkLayoutAsDefault, uas.getNetworkLayoutAsDefault());
+ assertEquals(user, uas.getUser());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/user/UserClassAnnotatorsTest.java b/model/src/test/java/lcsb/mapviewer/model/user/UserClassAnnotatorsTest.java
index c704efc4bc..27a06d7cce 100644
--- a/model/src/test/java/lcsb/mapviewer/model/user/UserClassAnnotatorsTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/user/UserClassAnnotatorsTest.java
@@ -1,71 +1,71 @@
-package lcsb.mapviewer.model.user;
-
-import static org.junit.Assert.assertEquals;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class UserClassAnnotatorsTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new UserClassAnnotators());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- List<String> list = new ArrayList<>();
- list.add("test");
- UserClassAnnotators uca = new UserClassAnnotators(String.class,list);
-
- assertEquals(1,uca.getAnnotators().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void testGetters() {
- try {
- UserClassAnnotators uca = new UserClassAnnotators();
- Integer id = 26;
- UserAnnotationSchema annotationSchema = new UserAnnotationSchema();
- List<String> annotators = new ArrayList<>();
- Class<?> clazz = String.class;
-
- uca.setId(id);
- uca.setAnnotationSchema(annotationSchema);
- uca.setAnnotators(annotators);
- uca.addAnnotator(clazz);
-
- assertEquals(id, uca.getId());
- assertEquals(annotationSchema, uca.getAnnotationSchema());
- assertEquals(annotators, uca.getAnnotators());
- assertEquals(clazz.getCanonicalName(), uca.getAnnotators().get(0));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.user;
+
+import static org.junit.Assert.assertEquals;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class UserClassAnnotatorsTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new UserClassAnnotators());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ List<String> list = new ArrayList<>();
+ list.add("test");
+ UserClassAnnotators uca = new UserClassAnnotators(String.class,list);
+
+ assertEquals(1,uca.getAnnotators().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void testGetters() {
+ try {
+ UserClassAnnotators uca = new UserClassAnnotators();
+ Integer id = 26;
+ UserAnnotationSchema annotationSchema = new UserAnnotationSchema();
+ List<String> annotators = new ArrayList<>();
+ Class<?> clazz = String.class;
+
+ uca.setId(id);
+ uca.setAnnotationSchema(annotationSchema);
+ uca.setAnnotators(annotators);
+ uca.addAnnotator(clazz);
+
+ assertEquals(id, uca.getId());
+ assertEquals(annotationSchema, uca.getAnnotationSchema());
+ assertEquals(annotators, uca.getAnnotators());
+ assertEquals(clazz.getCanonicalName(), uca.getAnnotators().get(0));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/user/UserClassRequiredAnnotationsTest.java b/model/src/test/java/lcsb/mapviewer/model/user/UserClassRequiredAnnotationsTest.java
index 0c35b87210..367d4d3fd0 100644
--- a/model/src/test/java/lcsb/mapviewer/model/user/UserClassRequiredAnnotationsTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/user/UserClassRequiredAnnotationsTest.java
@@ -1,97 +1,97 @@
-package lcsb.mapviewer.model.user;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.map.MiriamType;
-
-public class UserClassRequiredAnnotationsTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new UserClassRequiredAnnotations());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- UserClassRequiredAnnotations obj = new UserClassRequiredAnnotations();
- Integer id= 24;
- List<MiriamType> requiredMiriamTypes = new ArrayList<>();
- Boolean requireAtLestOneAnnotation = true;
- UserAnnotationSchema annotationSchema = new UserAnnotationSchema();
-
- obj.setId(id);
- obj.setRequiredMiriamTypes(requiredMiriamTypes);
- obj.setRequireAtLeastOneAnnotation(requireAtLestOneAnnotation);
- obj.setAnnotationSchema(annotationSchema);
-
- assertEquals(id, obj.getId());
- assertEquals(requiredMiriamTypes, obj.getRequiredMiriamTypes());
- assertEquals(requireAtLestOneAnnotation, obj.getRequireAtLeastOneAnnotation());
-
- assertEquals(annotationSchema, obj.getAnnotationSchema());
-
- obj.addRequiredMiriamType(MiriamType.CCDS);
- assertEquals(1,obj.getRequiredMiriamTypes().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- UserClassRequiredAnnotations obj = new UserClassRequiredAnnotations(String.class,(Collection<MiriamType>)null);
- assertFalse(obj.getRequireAtLeastOneAnnotation());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor2() {
- try {
- UserClassRequiredAnnotations obj = new UserClassRequiredAnnotations(String.class,new MiriamType[]{MiriamType.CAS});
- assertTrue(obj.getRequireAtLeastOneAnnotation());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void testConstructor3() {
- try {
- UserClassRequiredAnnotations obj = new UserClassRequiredAnnotations(String.class,new MiriamType[]{});
- assertFalse(obj.getRequireAtLeastOneAnnotation());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.user;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.map.MiriamType;
+
+public class UserClassRequiredAnnotationsTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new UserClassRequiredAnnotations());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ UserClassRequiredAnnotations obj = new UserClassRequiredAnnotations();
+ Integer id= 24;
+ List<MiriamType> requiredMiriamTypes = new ArrayList<>();
+ Boolean requireAtLestOneAnnotation = true;
+ UserAnnotationSchema annotationSchema = new UserAnnotationSchema();
+
+ obj.setId(id);
+ obj.setRequiredMiriamTypes(requiredMiriamTypes);
+ obj.setRequireAtLeastOneAnnotation(requireAtLestOneAnnotation);
+ obj.setAnnotationSchema(annotationSchema);
+
+ assertEquals(id, obj.getId());
+ assertEquals(requiredMiriamTypes, obj.getRequiredMiriamTypes());
+ assertEquals(requireAtLestOneAnnotation, obj.getRequireAtLeastOneAnnotation());
+
+ assertEquals(annotationSchema, obj.getAnnotationSchema());
+
+ obj.addRequiredMiriamType(MiriamType.CCDS);
+ assertEquals(1,obj.getRequiredMiriamTypes().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ UserClassRequiredAnnotations obj = new UserClassRequiredAnnotations(String.class,(Collection<MiriamType>)null);
+ assertFalse(obj.getRequireAtLeastOneAnnotation());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor2() {
+ try {
+ UserClassRequiredAnnotations obj = new UserClassRequiredAnnotations(String.class,new MiriamType[]{MiriamType.CAS});
+ assertTrue(obj.getRequireAtLeastOneAnnotation());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void testConstructor3() {
+ try {
+ UserClassRequiredAnnotations obj = new UserClassRequiredAnnotations(String.class,new MiriamType[]{});
+ assertFalse(obj.getRequireAtLeastOneAnnotation());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/user/UserClassValidAnnotationsTest.java b/model/src/test/java/lcsb/mapviewer/model/user/UserClassValidAnnotationsTest.java
index 29e55642e6..a53c5c0f51 100644
--- a/model/src/test/java/lcsb/mapviewer/model/user/UserClassValidAnnotationsTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/user/UserClassValidAnnotationsTest.java
@@ -1,80 +1,80 @@
-package lcsb.mapviewer.model.user;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.map.MiriamType;
-
-public class UserClassValidAnnotationsTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new UserClassValidAnnotations());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- UserClassValidAnnotations usva = new UserClassValidAnnotations(Object.class, new MiriamType[] { MiriamType.CAS });
- assertNotNull(usva);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- UserClassValidAnnotations usva = new UserClassValidAnnotations();
- List<MiriamType> validMiriamTypes = new ArrayList<>();
- UserAnnotationSchema schema = new UserAnnotationSchema();
- Integer id = 69;
- usva.setValidMiriamTypes(validMiriamTypes);
- assertEquals(validMiriamTypes, usva.getValidMiriamTypes());
- usva.setId(id);
- assertEquals(id, usva.getId());
- usva.setAnnotationSchema(schema);
- assertEquals(schema, usva.getAnnotationSchema());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddValidMiriamType() {
- try {
- UserClassValidAnnotations usva = new UserClassValidAnnotations();
- usva.addValidMiriamType(MiriamType.CAS);
- assertTrue(usva.getValidMiriamTypes().contains(MiriamType.CAS));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.user;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.map.MiriamType;
+
+public class UserClassValidAnnotationsTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new UserClassValidAnnotations());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ UserClassValidAnnotations usva = new UserClassValidAnnotations(Object.class, new MiriamType[] { MiriamType.CAS });
+ assertNotNull(usva);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ UserClassValidAnnotations usva = new UserClassValidAnnotations();
+ List<MiriamType> validMiriamTypes = new ArrayList<>();
+ UserAnnotationSchema schema = new UserAnnotationSchema();
+ Integer id = 69;
+ usva.setValidMiriamTypes(validMiriamTypes);
+ assertEquals(validMiriamTypes, usva.getValidMiriamTypes());
+ usva.setId(id);
+ assertEquals(id, usva.getId());
+ usva.setAnnotationSchema(schema);
+ assertEquals(schema, usva.getAnnotationSchema());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddValidMiriamType() {
+ try {
+ UserClassValidAnnotations usva = new UserClassValidAnnotations();
+ usva.addValidMiriamType(MiriamType.CAS);
+ assertTrue(usva.getValidMiriamTypes().contains(MiriamType.CAS));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/user/UserTest.java b/model/src/test/java/lcsb/mapviewer/model/user/UserTest.java
index e2638d3efa..863536f39f 100644
--- a/model/src/test/java/lcsb/mapviewer/model/user/UserTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/user/UserTest.java
@@ -1,111 +1,111 @@
-package lcsb.mapviewer.model.user;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-
-import java.awt.Color;
-import java.util.HashSet;
-import java.util.Set;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class UserTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new User());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToString() {
- try {
- assertNotNull(new User().toString());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddPrivilege() {
- try {
- User user = new User();
- user.addPrivilege(new BasicPrivilege());
- assertEquals(1, user.getPrivileges().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- User user = new User();
- int id = 737;
- String login = "log 54";
- String cryptedPassword = "pa";
- String name = "ccr";
- String email= "a.a@pl.pl";
- String surname = "cccv";
- Set<BasicPrivilege> privileges = new HashSet<>();
- boolean removed = true;
- UserAnnotationSchema annotationSchema = new UserAnnotationSchema();
- Color minColor = Color.BLACK;
- Color maxColor = Color.BLUE;
-
- user.setMaxColor(maxColor);
- assertEquals(maxColor, user.getMaxColor());
-
- user.setMinColor(minColor);
- assertEquals(minColor, user.getMinColor());
-
- user.setId(id);
- assertEquals((Integer)id, user.getId());
-
- user.setLogin(login);
- assertEquals(login, user.getLogin());
-
- user.setCryptedPassword(cryptedPassword);
- assertEquals(cryptedPassword, user.getCryptedPassword());
-
- user.setName(name);
- assertEquals(name, user.getName());
-
- user.setSurname(surname);
- assertEquals(surname, user.getSurname());
-
- user.setPrivileges(privileges);
- assertEquals(privileges, user.getPrivileges());
-
- user.setRemoved(removed);
- assertEquals(removed, user.isRemoved());
-
- user.setEmail(email);
- assertEquals(email, user.getEmail());
-
- user.setAnnotationSchema(annotationSchema);
- assertEquals(annotationSchema, user.getAnnotationSchema());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.model.user;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import java.awt.Color;
+import java.util.HashSet;
+import java.util.Set;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class UserTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new User());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToString() {
+ try {
+ assertNotNull(new User().toString());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddPrivilege() {
+ try {
+ User user = new User();
+ user.addPrivilege(new BasicPrivilege());
+ assertEquals(1, user.getPrivileges().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ User user = new User();
+ int id = 737;
+ String login = "log 54";
+ String cryptedPassword = "pa";
+ String name = "ccr";
+ String email= "a.a@pl.pl";
+ String surname = "cccv";
+ Set<BasicPrivilege> privileges = new HashSet<>();
+ boolean removed = true;
+ UserAnnotationSchema annotationSchema = new UserAnnotationSchema();
+ Color minColor = Color.BLACK;
+ Color maxColor = Color.BLUE;
+
+ user.setMaxColor(maxColor);
+ assertEquals(maxColor, user.getMaxColor());
+
+ user.setMinColor(minColor);
+ assertEquals(minColor, user.getMinColor());
+
+ user.setId(id);
+ assertEquals((Integer)id, user.getId());
+
+ user.setLogin(login);
+ assertEquals(login, user.getLogin());
+
+ user.setCryptedPassword(cryptedPassword);
+ assertEquals(cryptedPassword, user.getCryptedPassword());
+
+ user.setName(name);
+ assertEquals(name, user.getName());
+
+ user.setSurname(surname);
+ assertEquals(surname, user.getSurname());
+
+ user.setPrivileges(privileges);
+ assertEquals(privileges, user.getPrivileges());
+
+ user.setRemoved(removed);
+ assertEquals(removed, user.isRemoved());
+
+ user.setEmail(email);
+ assertEquals(email, user.getEmail());
+
+ user.setAnnotationSchema(annotationSchema);
+ assertEquals(annotationSchema, user.getAnnotationSchema());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/model/src/test/java/lcsb/mapviewer/modelutils/map/AllMapUtilTests.java b/model/src/test/java/lcsb/mapviewer/modelutils/map/AllMapUtilTests.java
index 39b4cc031b..6e4837f4a5 100644
--- a/model/src/test/java/lcsb/mapviewer/modelutils/map/AllMapUtilTests.java
+++ b/model/src/test/java/lcsb/mapviewer/modelutils/map/AllMapUtilTests.java
@@ -1,14 +1,14 @@
-package lcsb.mapviewer.modelutils.map;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ ClassTreeNodeTest.class, //
- ElementUtilsTest.class, //
- RequireAnnotationMapTest.class, //
-})
-public class AllMapUtilTests {
-
-}
+package lcsb.mapviewer.modelutils.map;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ ClassTreeNodeTest.class, //
+ ElementUtilsTest.class, //
+ RequireAnnotationMapTest.class, //
+})
+public class AllMapUtilTests {
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/modelutils/map/ClassTreeNodeTest.java b/model/src/test/java/lcsb/mapviewer/modelutils/map/ClassTreeNodeTest.java
index 5ef9e5a72a..db90ccf768 100644
--- a/model/src/test/java/lcsb/mapviewer/modelutils/map/ClassTreeNodeTest.java
+++ b/model/src/test/java/lcsb/mapviewer/modelutils/map/ClassTreeNodeTest.java
@@ -1,43 +1,43 @@
-package lcsb.mapviewer.modelutils.map;
-
-import static org.junit.Assert.assertEquals;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ClassTreeNodeTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSetters() {
- try {
- ClassTreeNode node = new ClassTreeNode(Object.class);
- Class<?> clazz = String.class;
- List<ClassTreeNode> children = new ArrayList<>();
- String commonName= "test";
- node.setClazz(clazz);
- node.setChildren(children);
- node.setCommonName(commonName);
-
- assertEquals(clazz, node.getClazz());
- assertEquals(children, node.getChildren());
- assertEquals(commonName, node.getCommonName());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.modelutils.map;
+
+import static org.junit.Assert.assertEquals;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ClassTreeNodeTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSetters() {
+ try {
+ ClassTreeNode node = new ClassTreeNode(Object.class);
+ Class<?> clazz = String.class;
+ List<ClassTreeNode> children = new ArrayList<>();
+ String commonName= "test";
+ node.setClazz(clazz);
+ node.setChildren(children);
+ node.setCommonName(commonName);
+
+ assertEquals(clazz, node.getClazz());
+ assertEquals(children, node.getChildren());
+ assertEquals(commonName, node.getCommonName());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/modelutils/map/RequireAnnotationMapTest.java b/model/src/test/java/lcsb/mapviewer/modelutils/map/RequireAnnotationMapTest.java
index e90a4446bb..9c30c4cea4 100644
--- a/model/src/test/java/lcsb/mapviewer/modelutils/map/RequireAnnotationMapTest.java
+++ b/model/src/test/java/lcsb/mapviewer/modelutils/map/RequireAnnotationMapTest.java
@@ -1,29 +1,29 @@
-package lcsb.mapviewer.modelutils.map;
-
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class RequireAnnotationMapTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testValidValues() {
- for (RequireAnnotationMap type : RequireAnnotationMap.values()) {
- assertNotNull(type);
-
- // for coverage tests
- RequireAnnotationMap.valueOf(type.toString());
- }
- }
-
-}
+package lcsb.mapviewer.modelutils.map;
+
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class RequireAnnotationMapTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testValidValues() {
+ for (RequireAnnotationMap type : RequireAnnotationMap.values()) {
+ assertNotNull(type);
+
+ // for coverage tests
+ RequireAnnotationMap.valueOf(type.toString());
+ }
+ }
+
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/Activator.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/Activator.java
index 819b9c9353..e08ed1dfa0 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/Activator.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/Activator.java
@@ -1,34 +1,34 @@
-package lcsb.mapviewer.wikipathway;
-
-import org.osgi.framework.BundleActivator;
-import org.osgi.framework.BundleContext;
-import org.pathvisio.desktop.plugin.Plugin;
-
-/**
- * Bundle activator of plugin. Responsible for registering bundle and cleaning
- * during finishing.
- *
- * @author Piotr Gawron
- *
- */
-
-public class Activator implements BundleActivator {
-
- /**
- * CellDesigner plugin for pathvisio.
- */
- private ImportExport plugin;
-
- @Override
- public void start(BundleContext context) throws Exception {
- plugin = new ImportExport();
- context.registerService(Plugin.class.getName(), plugin, null);
- }
-
- @Override
- public void stop(BundleContext context) throws Exception {
- if (plugin != null) {
- plugin.done();
- }
- }
-}
+package lcsb.mapviewer.wikipathway;
+
+import org.osgi.framework.BundleActivator;
+import org.osgi.framework.BundleContext;
+import org.pathvisio.desktop.plugin.Plugin;
+
+/**
+ * Bundle activator of plugin. Responsible for registering bundle and cleaning
+ * during finishing.
+ *
+ * @author Piotr Gawron
+ *
+ */
+
+public class Activator implements BundleActivator {
+
+ /**
+ * CellDesigner plugin for pathvisio.
+ */
+ private ImportExport plugin;
+
+ @Override
+ public void start(BundleContext context) throws Exception {
+ plugin = new ImportExport();
+ context.registerService(Plugin.class.getName(), plugin, null);
+ }
+
+ @Override
+ public void stop(BundleContext context) throws Exception {
+ if (plugin != null) {
+ plugin.done();
+ }
+ }
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/ImportExport.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/ImportExport.java
index 31511781b9..c9ee0be1fe 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/ImportExport.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/ImportExport.java
@@ -1,221 +1,221 @@
-package lcsb.mapviewer.wikipathway;
-
-import java.io.ByteArrayInputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.InputStream;
-import java.io.PrintWriter;
-import java.nio.charset.StandardCharsets;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Properties;
-
-import org.apache.log4j.Logger;
-import org.apache.log4j.PropertyConfigurator;
-import org.apache.log4j.spi.LoggingEvent;
-import org.pathvisio.core.model.ConverterException;
-import org.pathvisio.core.model.Pathway;
-import org.pathvisio.core.model.PathwayExporter;
-import org.pathvisio.core.model.PathwayImporter;
-import org.pathvisio.desktop.PvDesktop;
-import org.pathvisio.desktop.plugin.Plugin;
-
-import lcsb.mapviewer.common.EventStorageLoggerAppender;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
-import lcsb.mapviewer.wikipathway.XML.ModelToGPML;
-
-/**
- * Pathvisio plugin that allows to import/export CellDesigner file.
- *
- * @author Piotr Gawron
- *
- */
-public class ImportExport implements Plugin {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ImportExport.class);
- /**
- * List of extensions supported by import plugin.
- */
- private final String[] importExtensions = new String[] { "xml" };
- /**
- * List of extensions supported by export plugin.
- */
- private final String[] exportExtensions = new String[] { "cell" };
-
- @Override
- public void init(PvDesktop desktop) {
- try {
- Properties props = new Properties();
- props.load(new FileInputStream("log4j.properties"));
- PropertyConfigurator.configure(props);
- } catch (Exception e) {
- e.printStackTrace();
- }
- ExportCellDesigner exportPlugin = new ExportCellDesigner();
- ImportCellDesigner importPlugin = new ImportCellDesigner();
- desktop.getSwingEngine().getEngine().addPathwayImporter(importPlugin);
- desktop.getSwingEngine().getEngine().addPathwayExporter(exportPlugin);
- }
-
- @Override
- public void done() {
- }
-
- /**
- * Implementation of {@link PathwayExporter} that allows PathVisio to import
- * from CellDesigner xml file.
- *
- * @author Piotr Gawron
- *
- */
- protected class ImportCellDesigner implements PathwayImporter {
-
- /**
- * List of warnings that occured during conversion.
- */
- private List<LoggingEvent> warnings = new ArrayList<>();
-
- /**
- * Default constructor.
- */
- public ImportCellDesigner() {
- }
-
- @Override
- public String[] getExtensions() {
- return importExtensions;
- }
-
- @Override
- public String getName() {
- return "CellDesigner";
- }
-
- @Override
- public Pathway doImport(File file) throws ConverterException {
- EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
- try {
- Logger.getRootLogger().addAppender(appender);
- Pathway pathway = new Pathway();
- String fileName = file.getPath();
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- Model model = (Model) parser.createModel(new ConverterParams().filename(fileName).sizeAutoAdjust(false));
- String tmp = new ModelToGPML().getGPML(model);
- InputStream stream = new ByteArrayInputStream(tmp.getBytes(StandardCharsets.UTF_8));
- Boolean validate = false;
- pathway.readFromXml(stream, validate);
-
- Logger.getRootLogger().removeAppender(appender);
- warnings.addAll(appender.getWarnings());
- return pathway;
- } catch (Exception e) {
- logger.error(e, e);
- throw new ConverterException(e);
- } finally {
- Logger.getRootLogger().removeAppender(appender);
- }
- }
-
- @Override
- public boolean isCorrectType(File arg0) {
- return true;
- }
-
- @Override
- public List<String> getWarnings() {
- List<String> result = new ArrayList<>();
- for (LoggingEvent event : warnings) {
- if (event.getMessage() instanceof String) {
- result.add((String) event.getMessage());
- }
- }
- return result;
- }
- }
-
- /**
- * Implementation of {@link PathwayExporter} that allows PathVisio to export
- * into CellDesigner xml file.
- *
- * @author Piotr Gawron
- *
- */
- protected class ExportCellDesigner implements PathwayExporter {
-
- /**
- * {@link Model} that was created using this {@link PathwayExporter}.
- */
- private Model model = null;
-
- /**
- * List of export warnings.
- */
- private List<String> warnings = new ArrayList<>();
-
- @Override
- public String[] getExtensions() {
- return exportExtensions;
- }
-
- @Override
- public String getName() {
- return "CellDesigner";
- }
-
- @Override
- public List<String> getWarnings() {
- return warnings;
- }
-
- @Override
- public void doExport(File file, Pathway pathway) throws ConverterException {
- EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
- try {
- Logger.getRootLogger().addAppender(appender);
- pathway.writeToXml(new File("tmp.gpml"), false);
- model = new GPMLToModel().getModel("tmp.gpml");
-
- Logger.getRootLogger().removeAppender(appender);
- warnings = createWarnings(appender);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model);
- PrintWriter writer = new PrintWriter(file.getPath(), "UTF-8");
- writer.println(xml);
- writer.close();
-
- warnings.add("Please manually change extension of saved file from .cell to .xml");
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw new ConverterException(e);
- } finally {
- Logger.getRootLogger().removeAppender(appender);
- }
- }
-
- /**
- * Creates list of warnings from log4j appender data.
- *
- * @param appender
- * appender with the logs
- * @return list of warnings from log4j appender data
- */
- private List<String> createWarnings(EventStorageLoggerAppender appender) {
- List<String> warnings = new ArrayList<>();
- for (LoggingEvent event : appender.getWarnings()) {
- if (event.getMessage() instanceof String) {
- warnings.add(((String) event.getMessage()).replaceAll("\n", "_NEW_LINE_"));
- } else {
- logger.warn("Unknown message class: " + event.getClass());
- }
- }
- return warnings;
- }
- }
-}
+package lcsb.mapviewer.wikipathway;
+
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.InputStream;
+import java.io.PrintWriter;
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Properties;
+
+import org.apache.log4j.Logger;
+import org.apache.log4j.PropertyConfigurator;
+import org.apache.log4j.spi.LoggingEvent;
+import org.pathvisio.core.model.ConverterException;
+import org.pathvisio.core.model.Pathway;
+import org.pathvisio.core.model.PathwayExporter;
+import org.pathvisio.core.model.PathwayImporter;
+import org.pathvisio.desktop.PvDesktop;
+import org.pathvisio.desktop.plugin.Plugin;
+
+import lcsb.mapviewer.common.EventStorageLoggerAppender;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
+import lcsb.mapviewer.wikipathway.XML.ModelToGPML;
+
+/**
+ * Pathvisio plugin that allows to import/export CellDesigner file.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ImportExport implements Plugin {
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ImportExport.class);
+ /**
+ * List of extensions supported by import plugin.
+ */
+ private final String[] importExtensions = new String[] { "xml" };
+ /**
+ * List of extensions supported by export plugin.
+ */
+ private final String[] exportExtensions = new String[] { "cell" };
+
+ @Override
+ public void init(PvDesktop desktop) {
+ try {
+ Properties props = new Properties();
+ props.load(new FileInputStream("log4j.properties"));
+ PropertyConfigurator.configure(props);
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ ExportCellDesigner exportPlugin = new ExportCellDesigner();
+ ImportCellDesigner importPlugin = new ImportCellDesigner();
+ desktop.getSwingEngine().getEngine().addPathwayImporter(importPlugin);
+ desktop.getSwingEngine().getEngine().addPathwayExporter(exportPlugin);
+ }
+
+ @Override
+ public void done() {
+ }
+
+ /**
+ * Implementation of {@link PathwayExporter} that allows PathVisio to import
+ * from CellDesigner xml file.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ protected class ImportCellDesigner implements PathwayImporter {
+
+ /**
+ * List of warnings that occured during conversion.
+ */
+ private List<LoggingEvent> warnings = new ArrayList<>();
+
+ /**
+ * Default constructor.
+ */
+ public ImportCellDesigner() {
+ }
+
+ @Override
+ public String[] getExtensions() {
+ return importExtensions;
+ }
+
+ @Override
+ public String getName() {
+ return "CellDesigner";
+ }
+
+ @Override
+ public Pathway doImport(File file) throws ConverterException {
+ EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
+ try {
+ Logger.getRootLogger().addAppender(appender);
+ Pathway pathway = new Pathway();
+ String fileName = file.getPath();
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ Model model = (Model) parser.createModel(new ConverterParams().filename(fileName).sizeAutoAdjust(false));
+ String tmp = new ModelToGPML().getGPML(model);
+ InputStream stream = new ByteArrayInputStream(tmp.getBytes(StandardCharsets.UTF_8));
+ Boolean validate = false;
+ pathway.readFromXml(stream, validate);
+
+ Logger.getRootLogger().removeAppender(appender);
+ warnings.addAll(appender.getWarnings());
+ return pathway;
+ } catch (Exception e) {
+ logger.error(e, e);
+ throw new ConverterException(e);
+ } finally {
+ Logger.getRootLogger().removeAppender(appender);
+ }
+ }
+
+ @Override
+ public boolean isCorrectType(File arg0) {
+ return true;
+ }
+
+ @Override
+ public List<String> getWarnings() {
+ List<String> result = new ArrayList<>();
+ for (LoggingEvent event : warnings) {
+ if (event.getMessage() instanceof String) {
+ result.add((String) event.getMessage());
+ }
+ }
+ return result;
+ }
+ }
+
+ /**
+ * Implementation of {@link PathwayExporter} that allows PathVisio to export
+ * into CellDesigner xml file.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ protected class ExportCellDesigner implements PathwayExporter {
+
+ /**
+ * {@link Model} that was created using this {@link PathwayExporter}.
+ */
+ private Model model = null;
+
+ /**
+ * List of export warnings.
+ */
+ private List<String> warnings = new ArrayList<>();
+
+ @Override
+ public String[] getExtensions() {
+ return exportExtensions;
+ }
+
+ @Override
+ public String getName() {
+ return "CellDesigner";
+ }
+
+ @Override
+ public List<String> getWarnings() {
+ return warnings;
+ }
+
+ @Override
+ public void doExport(File file, Pathway pathway) throws ConverterException {
+ EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
+ try {
+ Logger.getRootLogger().addAppender(appender);
+ pathway.writeToXml(new File("tmp.gpml"), false);
+ model = new GPMLToModel().getModel("tmp.gpml");
+
+ Logger.getRootLogger().removeAppender(appender);
+ warnings = createWarnings(appender);
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model);
+ PrintWriter writer = new PrintWriter(file.getPath(), "UTF-8");
+ writer.println(xml);
+ writer.close();
+
+ warnings.add("Please manually change extension of saved file from .cell to .xml");
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw new ConverterException(e);
+ } finally {
+ Logger.getRootLogger().removeAppender(appender);
+ }
+ }
+
+ /**
+ * Creates list of warnings from log4j appender data.
+ *
+ * @param appender
+ * appender with the logs
+ * @return list of warnings from log4j appender data
+ */
+ private List<String> createWarnings(EventStorageLoggerAppender appender) {
+ List<String> warnings = new ArrayList<>();
+ for (LoggingEvent event : appender.getWarnings()) {
+ if (event.getMessage() instanceof String) {
+ warnings.add(((String) event.getMessage()).replaceAll("\n", "_NEW_LINE_"));
+ } else {
+ logger.warn("Unknown message class: " + event.getClass());
+ }
+ }
+ return warnings;
+ }
+ }
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/BiopaxParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/BiopaxParser.java
index 18be5df81c..c9e669f18d 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/BiopaxParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/BiopaxParser.java
@@ -1,264 +1,264 @@
-package lcsb.mapviewer.wikipathway.XML;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import lcsb.mapviewer.common.XmlParser;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.wikipathway.model.biopax.BiopaxData;
-import lcsb.mapviewer.wikipathway.model.biopax.BiopaxOpenControlledVocabulary;
-import lcsb.mapviewer.wikipathway.model.biopax.BiopaxPublication;
-
-/**
- * Parser of Biopax data from the gpml file.
- *
- * @author Piotr Gawron
- *
- */
-public class BiopaxParser extends XmlParser {
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(BiopaxParser.class);
-
- /**
- * Hash used for next {@link BiopaxPublication} processed by parser.
- */
- private Integer hash = 1;
-
- /**
- * Mapping between {@link MiriamData} and hash value.
- */
- private Map<MiriamData, String> miriamHash = new HashMap<>();
-
- /**
- * Creates data structure from biopax xml node.
- *
- * @param biopax
- * xml node
- * @return {@link BiopaxData} structure containing biopax data
- */
- public BiopaxData parse(Node biopax) {
- BiopaxData result = new BiopaxData();
- NodeList nodes = biopax.getChildNodes();
- for (int i = 0; i < nodes.getLength(); i++) {
- Node node = nodes.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if ("bp:PublicationXref".equalsIgnoreCase(node.getNodeName())) {
- BiopaxPublication publication = parsePublication(node);
- if (publication.getId() == null || publication.getId().isEmpty()) {
- logger.warn("No pubmed identifier defined for publication: title: " + publication.getTitle());
- }
- result.addPublication(publication);
- } else if ("bp:openControlledVocabulary".equalsIgnoreCase(node.getNodeName())) {
- result.addOpenControlledVocabulary(parseOpenControlledVocabulary(node));
- } else {
- logger.warn("Unknown biopax node: " + node.getNodeName());
- }
- }
- }
- return result;
- }
-
- /**
- * Method which parse biopax vocabulary xml node.
- *
- * @param biopaxNode
- * xml node
- * @return {@link BiopaxOpenControlledVocabulary}
- */
- private BiopaxOpenControlledVocabulary parseOpenControlledVocabulary(Node biopaxNode) {
- BiopaxOpenControlledVocabulary result = new BiopaxOpenControlledVocabulary();
- NodeList nodes = biopaxNode.getChildNodes();
-
- for (int i = 0; i < nodes.getLength(); i++) {
- Node node = nodes.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if ("bp:ID".equalsIgnoreCase(node.getNodeName())) {
- result.setId(node.getTextContent());
- } else if ("bp:TERM".equalsIgnoreCase(node.getNodeName())) {
- result.setTerm(node.getTextContent());
- } else if ("bp:Ontology".equalsIgnoreCase(node.getNodeName())) {
- result.setOntology(node.getTextContent());
- } else {
- logger.warn("Unknown biopax node: " + node.getNodeName());
- }
- }
- }
- return result;
- }
-
- /**
- * Method which parse biopax publication xml node.
- *
- * @param publication
- * xml node
- * @return {@link BiopaxPublication}
- */
- protected BiopaxPublication parsePublication(Node publication) {
- BiopaxPublication result = new BiopaxPublication();
- NodeList nodes = publication.getChildNodes();
-
- result.setReferenceId(getNodeAttr("rdf:id", publication));
- for (int i = 0; i < nodes.getLength(); i++) {
- Node node = nodes.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if ("bp:ID".equalsIgnoreCase(node.getNodeName())) {
- result.setId(node.getTextContent());
- } else if ("bp:DB".equalsIgnoreCase(node.getNodeName())) {
- result.setDb(node.getTextContent());
- } else if ("bp:TITLE".equalsIgnoreCase(node.getNodeName())) {
- result.setTitle(node.getTextContent());
- } else if ("bp:SOURCE".equalsIgnoreCase(node.getNodeName())) {
- result.setSource(node.getTextContent());
- } else if ("bp:YEAR".equalsIgnoreCase(node.getNodeName())) {
- result.setYear(node.getTextContent());
- } else if ("bp:AUTHORS".equalsIgnoreCase(node.getNodeName())) {
- result.setAuthors(node.getTextContent());
- } else {
- logger.warn("Unknown biopax node: " + node.getNodeName());
- }
- }
- }
- return result;
- }
-
- /**
- * Returns xml string representing biopax reference to set of
- * {@link MiriamData} form parameters.
- *
- * @param miriamData
- * set of {@link MiriamData} for which we want to obtain biopax
- * references
- * @return xml string representing biopax reference to set of
- * {@link MiriamData} form parameters. Only references to
- * {@link MiriamType#PUBMED} are included.
- */
- public String toReferenceXml(Set<MiriamData> miriamData) {
- StringBuilder sb = new StringBuilder("");
- for (MiriamData md : miriamData) {
- if (md.getDataType().equals(MiriamType.PUBMED)) {
- sb.append("<BiopaxRef>" + getHash(md) + "</BiopaxRef>\n");
- }
- }
- return sb.toString();
- }
-
- /**
- * Returns unique hash for the {@link MiriamData} that can be used as a key in
- * Biopax xml.
- *
- * @param md
- * {@link MiriamData} for which we want to have unique hash value
- * @return unique hash for the {@link MiriamData} that can be used as a key in
- * Biopax xml
- */
- private String getHash(MiriamData md) {
- if (miriamHash.get(md) == null) {
- miriamHash.put(md, "ann" + hash);
- hash++;
- }
- return miriamHash.get(md);
- }
-
- /**
- * Converts collection of {@link MiriamData} into an xml {@link String}
- * representing this collection as a biopax data.
- *
- * @param miriamData
- * collection of {@link MiriamData}
- * @return xml {@link String} representing this collection as a biopax data
- */
- public String toXml(Collection<MiriamData> miriamData) {
- StringBuilder sb = new StringBuilder("");
- sb.append("<Biopax>\n");
- for (MiriamData md : miriamData) {
- if (md.getDataType().equals(MiriamType.PUBMED)) {
- sb.append(toXml(md));
- }
- }
- sb.append("</Biopax>\n");
-
- return sb.toString();
- }
-
- /**
- * Converts {@link MiriamData} into xml string in biopax format.
- *
- * @param md
- * {@link MiriamData} to transform
- * @return xml string in biopax format representing {@link MiriamData}
- */
- public String toXml(MiriamData md) {
- StringBuilder sb = new StringBuilder();
- sb.append(
- "<bp:PublicationXref xmlns:bp=\"http://www.biopax.org/release/biopax-level3.owl#\" "
- + "xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" rdf:id=\"" + getHash(md) + "\">\n");
- sb.append(" <bp:ID rdf:datatype=\"http://www.w3.org/2001/XMLSchema#string\">" + md.getResource() + "</bp:ID>\n");
- sb.append(" <bp:DB rdf:datatype=\"http://www.w3.org/2001/XMLSchema#string\">PubMed</bp:DB>\n");
- sb.append("</bp:PublicationXref>\n");
- return sb.toString();
- }
-
- /**
- * Creates {@link MiriamData annotation} from {@link BiopaxPublication}.
- *
- * @param publication
- * input biopax structure
- * @return {@link MiriamData annotation}
- */
- protected MiriamData createMiriamData(BiopaxPublication publication) {
- if ("PubMed".equals(publication.getDb())) {
- if (publication.getId() == null || publication.getId().equals("")) {
- return null;
- } else {
- return new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, publication.getId());
- }
- } else {
- throw new InvalidArgumentException("Unknown biopax database: " + publication.getDb());
- }
- }
-
- /**
- * Returns list of {@link MiriamData} that are refernced in {@link BiopaxData}
- * with identifier given in biopaxReference.
- *
- * @param biopaxData
- * {@link BiopaxData} where annotations are stored
- * @param biopaxReference
- * list of refrences (to data in {@link BiopaxData}) that we want to
- * convert into {@link MiriamData}
- * @return list of {@link MiriamData} that are refernced in {@link BiopaxData}
- * with identifier given in biopaxReference.
- */
- public Collection<MiriamData> getMiriamData(BiopaxData biopaxData, List<String> biopaxReference) {
- List<MiriamData> result = new ArrayList<>();
- for (String string : biopaxReference) {
- BiopaxPublication bp = biopaxData.getPublicationByReference(string);
- if (bp != null) {
- MiriamData md = createMiriamData(bp);
- if (md != null) {
- result.add(md);
- } else {
- logger.warn("[" + string + "]\tBiopax publication is invalid.");
- }
- } else {
- logger.warn("[" + string + "]\tBiopax publication doesn't exist.");
- }
- }
- return result;
- }
-
-}
+package lcsb.mapviewer.wikipathway.XML;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.wikipathway.model.biopax.BiopaxData;
+import lcsb.mapviewer.wikipathway.model.biopax.BiopaxOpenControlledVocabulary;
+import lcsb.mapviewer.wikipathway.model.biopax.BiopaxPublication;
+
+/**
+ * Parser of Biopax data from the gpml file.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class BiopaxParser extends XmlParser {
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(BiopaxParser.class);
+
+ /**
+ * Hash used for next {@link BiopaxPublication} processed by parser.
+ */
+ private Integer hash = 1;
+
+ /**
+ * Mapping between {@link MiriamData} and hash value.
+ */
+ private Map<MiriamData, String> miriamHash = new HashMap<>();
+
+ /**
+ * Creates data structure from biopax xml node.
+ *
+ * @param biopax
+ * xml node
+ * @return {@link BiopaxData} structure containing biopax data
+ */
+ public BiopaxData parse(Node biopax) {
+ BiopaxData result = new BiopaxData();
+ NodeList nodes = biopax.getChildNodes();
+ for (int i = 0; i < nodes.getLength(); i++) {
+ Node node = nodes.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if ("bp:PublicationXref".equalsIgnoreCase(node.getNodeName())) {
+ BiopaxPublication publication = parsePublication(node);
+ if (publication.getId() == null || publication.getId().isEmpty()) {
+ logger.warn("No pubmed identifier defined for publication: title: " + publication.getTitle());
+ }
+ result.addPublication(publication);
+ } else if ("bp:openControlledVocabulary".equalsIgnoreCase(node.getNodeName())) {
+ result.addOpenControlledVocabulary(parseOpenControlledVocabulary(node));
+ } else {
+ logger.warn("Unknown biopax node: " + node.getNodeName());
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Method which parse biopax vocabulary xml node.
+ *
+ * @param biopaxNode
+ * xml node
+ * @return {@link BiopaxOpenControlledVocabulary}
+ */
+ private BiopaxOpenControlledVocabulary parseOpenControlledVocabulary(Node biopaxNode) {
+ BiopaxOpenControlledVocabulary result = new BiopaxOpenControlledVocabulary();
+ NodeList nodes = biopaxNode.getChildNodes();
+
+ for (int i = 0; i < nodes.getLength(); i++) {
+ Node node = nodes.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if ("bp:ID".equalsIgnoreCase(node.getNodeName())) {
+ result.setId(node.getTextContent());
+ } else if ("bp:TERM".equalsIgnoreCase(node.getNodeName())) {
+ result.setTerm(node.getTextContent());
+ } else if ("bp:Ontology".equalsIgnoreCase(node.getNodeName())) {
+ result.setOntology(node.getTextContent());
+ } else {
+ logger.warn("Unknown biopax node: " + node.getNodeName());
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Method which parse biopax publication xml node.
+ *
+ * @param publication
+ * xml node
+ * @return {@link BiopaxPublication}
+ */
+ protected BiopaxPublication parsePublication(Node publication) {
+ BiopaxPublication result = new BiopaxPublication();
+ NodeList nodes = publication.getChildNodes();
+
+ result.setReferenceId(getNodeAttr("rdf:id", publication));
+ for (int i = 0; i < nodes.getLength(); i++) {
+ Node node = nodes.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if ("bp:ID".equalsIgnoreCase(node.getNodeName())) {
+ result.setId(node.getTextContent());
+ } else if ("bp:DB".equalsIgnoreCase(node.getNodeName())) {
+ result.setDb(node.getTextContent());
+ } else if ("bp:TITLE".equalsIgnoreCase(node.getNodeName())) {
+ result.setTitle(node.getTextContent());
+ } else if ("bp:SOURCE".equalsIgnoreCase(node.getNodeName())) {
+ result.setSource(node.getTextContent());
+ } else if ("bp:YEAR".equalsIgnoreCase(node.getNodeName())) {
+ result.setYear(node.getTextContent());
+ } else if ("bp:AUTHORS".equalsIgnoreCase(node.getNodeName())) {
+ result.setAuthors(node.getTextContent());
+ } else {
+ logger.warn("Unknown biopax node: " + node.getNodeName());
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Returns xml string representing biopax reference to set of
+ * {@link MiriamData} form parameters.
+ *
+ * @param miriamData
+ * set of {@link MiriamData} for which we want to obtain biopax
+ * references
+ * @return xml string representing biopax reference to set of
+ * {@link MiriamData} form parameters. Only references to
+ * {@link MiriamType#PUBMED} are included.
+ */
+ public String toReferenceXml(Set<MiriamData> miriamData) {
+ StringBuilder sb = new StringBuilder("");
+ for (MiriamData md : miriamData) {
+ if (md.getDataType().equals(MiriamType.PUBMED)) {
+ sb.append("<BiopaxRef>" + getHash(md) + "</BiopaxRef>\n");
+ }
+ }
+ return sb.toString();
+ }
+
+ /**
+ * Returns unique hash for the {@link MiriamData} that can be used as a key in
+ * Biopax xml.
+ *
+ * @param md
+ * {@link MiriamData} for which we want to have unique hash value
+ * @return unique hash for the {@link MiriamData} that can be used as a key in
+ * Biopax xml
+ */
+ private String getHash(MiriamData md) {
+ if (miriamHash.get(md) == null) {
+ miriamHash.put(md, "ann" + hash);
+ hash++;
+ }
+ return miriamHash.get(md);
+ }
+
+ /**
+ * Converts collection of {@link MiriamData} into an xml {@link String}
+ * representing this collection as a biopax data.
+ *
+ * @param miriamData
+ * collection of {@link MiriamData}
+ * @return xml {@link String} representing this collection as a biopax data
+ */
+ public String toXml(Collection<MiriamData> miriamData) {
+ StringBuilder sb = new StringBuilder("");
+ sb.append("<Biopax>\n");
+ for (MiriamData md : miriamData) {
+ if (md.getDataType().equals(MiriamType.PUBMED)) {
+ sb.append(toXml(md));
+ }
+ }
+ sb.append("</Biopax>\n");
+
+ return sb.toString();
+ }
+
+ /**
+ * Converts {@link MiriamData} into xml string in biopax format.
+ *
+ * @param md
+ * {@link MiriamData} to transform
+ * @return xml string in biopax format representing {@link MiriamData}
+ */
+ public String toXml(MiriamData md) {
+ StringBuilder sb = new StringBuilder();
+ sb.append(
+ "<bp:PublicationXref xmlns:bp=\"http://www.biopax.org/release/biopax-level3.owl#\" "
+ + "xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" rdf:id=\"" + getHash(md) + "\">\n");
+ sb.append(" <bp:ID rdf:datatype=\"http://www.w3.org/2001/XMLSchema#string\">" + md.getResource() + "</bp:ID>\n");
+ sb.append(" <bp:DB rdf:datatype=\"http://www.w3.org/2001/XMLSchema#string\">PubMed</bp:DB>\n");
+ sb.append("</bp:PublicationXref>\n");
+ return sb.toString();
+ }
+
+ /**
+ * Creates {@link MiriamData annotation} from {@link BiopaxPublication}.
+ *
+ * @param publication
+ * input biopax structure
+ * @return {@link MiriamData annotation}
+ */
+ protected MiriamData createMiriamData(BiopaxPublication publication) {
+ if ("PubMed".equals(publication.getDb())) {
+ if (publication.getId() == null || publication.getId().equals("")) {
+ return null;
+ } else {
+ return new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, publication.getId());
+ }
+ } else {
+ throw new InvalidArgumentException("Unknown biopax database: " + publication.getDb());
+ }
+ }
+
+ /**
+ * Returns list of {@link MiriamData} that are refernced in {@link BiopaxData}
+ * with identifier given in biopaxReference.
+ *
+ * @param biopaxData
+ * {@link BiopaxData} where annotations are stored
+ * @param biopaxReference
+ * list of refrences (to data in {@link BiopaxData}) that we want to
+ * convert into {@link MiriamData}
+ * @return list of {@link MiriamData} that are refernced in {@link BiopaxData}
+ * with identifier given in biopaxReference.
+ */
+ public Collection<MiriamData> getMiriamData(BiopaxData biopaxData, List<String> biopaxReference) {
+ List<MiriamData> result = new ArrayList<>();
+ for (String string : biopaxReference) {
+ BiopaxPublication bp = biopaxData.getPublicationByReference(string);
+ if (bp != null) {
+ MiriamData md = createMiriamData(bp);
+ if (md != null) {
+ result.add(md);
+ } else {
+ logger.warn("[" + string + "]\tBiopax publication is invalid.");
+ }
+ } else {
+ logger.warn("[" + string + "]\tBiopax publication doesn't exist.");
+ }
+ }
+ return result;
+ }
+
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/CyclicEdgeException.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/CyclicEdgeException.java
index 3c8d715639..46ad82cf91 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/CyclicEdgeException.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/CyclicEdgeException.java
@@ -1,38 +1,38 @@
-package lcsb.mapviewer.wikipathway.XML;
-
-import lcsb.mapviewer.converter.ConverterException;
-
-/**
- * Exception that shold be thrown when edges create a cycle. Consider an example
- * which has three edges:
- * <ul>
- * <li>edge_A - starts in edge_B and ends in some protein,</li>
- * <li>edge_B - starts in edge_C and ends in some protein,</li>
- * <li>edge_C - starts in edge_A and ends in some protein,</li>
- * </ul>
- * During resolving how it should be maintained there are two options - either
- * merge it (but in more complex example it's almost impossible to do it
- * properly) or report an errow. This exception will be thrown in such
- * situations.
- *
- * @author Piotr Gawron
- *
- */
-public class CyclicEdgeException extends ConverterException {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor with message passed in the argument.
- *
- * @param string
- * message of this exception
- */
- public CyclicEdgeException(String string) {
- super(string);
- }
-
-}
+package lcsb.mapviewer.wikipathway.XML;
+
+import lcsb.mapviewer.converter.ConverterException;
+
+/**
+ * Exception that shold be thrown when edges create a cycle. Consider an example
+ * which has three edges:
+ * <ul>
+ * <li>edge_A - starts in edge_B and ends in some protein,</li>
+ * <li>edge_B - starts in edge_C and ends in some protein,</li>
+ * <li>edge_C - starts in edge_A and ends in some protein,</li>
+ * </ul>
+ * During resolving how it should be maintained there are two options - either
+ * merge it (but in more complex example it's almost impossible to do it
+ * properly) or report an errow. This exception will be thrown in such
+ * situations.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CyclicEdgeException extends ConverterException {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor with message passed in the argument.
+ *
+ * @param string
+ * message of this exception
+ */
+ public CyclicEdgeException(String string) {
+ super(string);
+ }
+
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/DataNodeParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/DataNodeParser.java
index b9a02d90b9..16a6b3b717 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/DataNodeParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/DataNodeParser.java
@@ -1,200 +1,200 @@
-package lcsb.mapviewer.wikipathway.XML;
-
-import java.awt.geom.Rectangle2D;
-import java.util.Collection;
-
-import org.apache.log4j.Logger;
-import org.w3c.dom.Element;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.ConverterException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.wikipathway.model.DataNode;
-import lcsb.mapviewer.wikipathway.model.GpmlLineType;
-import lcsb.mapviewer.wikipathway.model.UnknownTypeException;
-
-/**
- * Parser class that creates {@link DataNode} objects from Xml {@link Element
- * node}.
- *
- * @author Piotr Gawron
- *
- */
-public class DataNodeParser extends GraphicalPathwayElementParser<DataNode> {
-
- /**
- * Default claass logger.
- */
- private final Logger logger = Logger.getLogger(DataNodeParser.class);
-
- /**
- * PArser used to process references.
- */
- private final ReferenceParser referenceParser = new ReferenceParser();
-
- @Override
- public DataNode parse(Element eElement) throws UnknownTypeException {
- if (!eElement.getNodeName().equals("DataNode")) {
- throw new InvalidArgumentException(ShapeParser.class.getSimpleName() + " can parse only DataNode xml nodes");
- }
- DataNode node = new DataNode(eElement.getAttribute("GraphId"));
-
- for (Pair<String, String> entry : getAttributes(eElement)) {
- switch (entry.getLeft()) {
- case ("GraphId"):
- break;
- case ("TextLabel"):
- node.setTextLabel(entry.getRight());
- break;
- case ("GroupRef"):
- node.setGroupRef(entry.getRight());
- break;
- case ("Type"):
- node.setType(entry.getRight());
- break;
- default:
- logger.warn("Unknown attribute of " + eElement.getNodeName() + " node: " + entry.getLeft());
- break;
- }
- }
-
- NodeList tmpList = eElement.getChildNodes();
- for (int j = 0; j < tmpList.getLength(); j++) {
- Node tmpNode = tmpList.item(j);
- if (tmpNode.getNodeType() == Node.ELEMENT_NODE) {
- Element eTmp = (Element) tmpNode;
- switch (eTmp.getNodeName()) {
- case ("Comment"):
- node.addComment(eTmp.getTextContent());
- break;
- case ("BiopaxRef"):
- node.addBiopaxReference(eTmp.getTextContent());
- break;
- case ("Xref"):
- MiriamData data = referenceParser.parse(eTmp);
- if (data != null) {
- node.addReference(data);
- }
- break;
- case ("Graphics"):
- parseGraphics(eTmp, node);
- break;
- case ("Attribute"):
- parseAttribute(eTmp, node);
- break;
- default:
- logger.warn("Unknown sub-node of " + eElement.getNodeName() + " node: " + eTmp.getNodeName());
- break;
- }
- }
- }
-
- return node;
- }
-
- /**
- * Parse graphics xml node in the shape node.
- *
- * @param eTmp
- * xml node with graphics
- * @param shape
- * shape where data should be added
- * @throws UnknownTypeException
- * thrown when node contains unknown types
- */
- private void parseGraphics(Element eTmp, DataNode shape) throws UnknownTypeException {
- Double centerX = null;
- Double centerY = null;
- Double width = null;
- Double height = null;
- for (Pair<String, String> entry : getAttributes(eTmp)) {
- if (!parseCommonGraphicAttributes(shape, entry)) {
- switch (entry.getLeft()) {
- case ("CenterX"):
- centerX = Double.valueOf(entry.getRight());
- break;
- case ("CenterY"):
- centerY = Double.valueOf(entry.getRight());
- break;
- case ("Width"):
- width = Double.valueOf(entry.getRight());
- break;
- case ("Height"):
- height = Double.valueOf(entry.getRight());
- break;
- case ("ShapeType"):
- shape.setType(entry.getRight());
- break;
- case ("Color"):
- shape.setColor(hexStringToColor(entry.getRight()));
- break;
- case ("FillColor"):
- shape.setFillColor(hexStringToColor(entry.getRight()));
- break;
- case ("ZOrder"):
- shape.setzOrder(Integer.valueOf(entry.getRight()));
- break;
- case ("LineStyle"):
- shape.setLineType(GpmlLineType.getByGpmlName(entry.getRight()).getCorrespondingGlobalLineType());
- break;
- case ("FontSize"):
- shape.setFontSize(Double.valueOf(entry.getRight()));
- break;
- case ("FontWeight"):
- shape.setFontWeight(entry.getRight());
- break;
- case ("Valign"):
- shape.setvAlign(entry.getRight());
- break;
- default:
- logger.warn("Unknown attribute of " + eTmp.getNodeName() + " node: " + entry.getLeft());
- break;
- }
- }
- }
- shape.setRectangle(new Rectangle2D.Double(centerX - width / 2, centerY - height / 2, width, height));
- }
-
- /**
- * Method that parses {@link DataNode} xml attribute.
- *
- * @param eTmp
- * xml node with attribute
- * @param shape
- * shape where data should be added
- */
- private void parseAttribute(Element eTmp, DataNode shape) {
- String key = eTmp.getAttribute("Key");
- String value = eTmp.getAttribute("Value");
- switch (key) {
- case ("org.pathvisio.model.BackpageHead"):
- // it's deprecated in PathVisio so we can skip it
- break;
- case ("org.pathvisio.model.GenMAPP-Xref"):
- // skip it when it's empty
- if (!value.isEmpty()) {
- logger.warn(shape.getWarningPrefix() + "Unknown attribute of node. Key: " + key + "; value: " + value);
- break;
- }
- break;
- default:
- logger.warn(shape.getWarningPrefix() + "Unknown attribute of node. Key: " + key + "; value: " + value);
- break;
- }
- }
-
- @Override
- public String toXml(DataNode node) throws ConverterException {
- throw new NotImplementedException();
- }
-
- @Override
- public String toXml(Collection<DataNode> list) throws ConverterException {
- throw new NotImplementedException();
- }
-
-}
+package lcsb.mapviewer.wikipathway.XML;
+
+import java.awt.geom.Rectangle2D;
+import java.util.Collection;
+
+import org.apache.log4j.Logger;
+import org.w3c.dom.Element;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.wikipathway.model.DataNode;
+import lcsb.mapviewer.wikipathway.model.GpmlLineType;
+import lcsb.mapviewer.wikipathway.model.UnknownTypeException;
+
+/**
+ * Parser class that creates {@link DataNode} objects from Xml {@link Element
+ * node}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class DataNodeParser extends GraphicalPathwayElementParser<DataNode> {
+
+ /**
+ * Default claass logger.
+ */
+ private final Logger logger = Logger.getLogger(DataNodeParser.class);
+
+ /**
+ * PArser used to process references.
+ */
+ private final ReferenceParser referenceParser = new ReferenceParser();
+
+ @Override
+ public DataNode parse(Element eElement) throws UnknownTypeException {
+ if (!eElement.getNodeName().equals("DataNode")) {
+ throw new InvalidArgumentException(ShapeParser.class.getSimpleName() + " can parse only DataNode xml nodes");
+ }
+ DataNode node = new DataNode(eElement.getAttribute("GraphId"));
+
+ for (Pair<String, String> entry : getAttributes(eElement)) {
+ switch (entry.getLeft()) {
+ case ("GraphId"):
+ break;
+ case ("TextLabel"):
+ node.setTextLabel(entry.getRight());
+ break;
+ case ("GroupRef"):
+ node.setGroupRef(entry.getRight());
+ break;
+ case ("Type"):
+ node.setType(entry.getRight());
+ break;
+ default:
+ logger.warn("Unknown attribute of " + eElement.getNodeName() + " node: " + entry.getLeft());
+ break;
+ }
+ }
+
+ NodeList tmpList = eElement.getChildNodes();
+ for (int j = 0; j < tmpList.getLength(); j++) {
+ Node tmpNode = tmpList.item(j);
+ if (tmpNode.getNodeType() == Node.ELEMENT_NODE) {
+ Element eTmp = (Element) tmpNode;
+ switch (eTmp.getNodeName()) {
+ case ("Comment"):
+ node.addComment(eTmp.getTextContent());
+ break;
+ case ("BiopaxRef"):
+ node.addBiopaxReference(eTmp.getTextContent());
+ break;
+ case ("Xref"):
+ MiriamData data = referenceParser.parse(eTmp);
+ if (data != null) {
+ node.addReference(data);
+ }
+ break;
+ case ("Graphics"):
+ parseGraphics(eTmp, node);
+ break;
+ case ("Attribute"):
+ parseAttribute(eTmp, node);
+ break;
+ default:
+ logger.warn("Unknown sub-node of " + eElement.getNodeName() + " node: " + eTmp.getNodeName());
+ break;
+ }
+ }
+ }
+
+ return node;
+ }
+
+ /**
+ * Parse graphics xml node in the shape node.
+ *
+ * @param eTmp
+ * xml node with graphics
+ * @param shape
+ * shape where data should be added
+ * @throws UnknownTypeException
+ * thrown when node contains unknown types
+ */
+ private void parseGraphics(Element eTmp, DataNode shape) throws UnknownTypeException {
+ Double centerX = null;
+ Double centerY = null;
+ Double width = null;
+ Double height = null;
+ for (Pair<String, String> entry : getAttributes(eTmp)) {
+ if (!parseCommonGraphicAttributes(shape, entry)) {
+ switch (entry.getLeft()) {
+ case ("CenterX"):
+ centerX = Double.valueOf(entry.getRight());
+ break;
+ case ("CenterY"):
+ centerY = Double.valueOf(entry.getRight());
+ break;
+ case ("Width"):
+ width = Double.valueOf(entry.getRight());
+ break;
+ case ("Height"):
+ height = Double.valueOf(entry.getRight());
+ break;
+ case ("ShapeType"):
+ shape.setType(entry.getRight());
+ break;
+ case ("Color"):
+ shape.setColor(hexStringToColor(entry.getRight()));
+ break;
+ case ("FillColor"):
+ shape.setFillColor(hexStringToColor(entry.getRight()));
+ break;
+ case ("ZOrder"):
+ shape.setzOrder(Integer.valueOf(entry.getRight()));
+ break;
+ case ("LineStyle"):
+ shape.setLineType(GpmlLineType.getByGpmlName(entry.getRight()).getCorrespondingGlobalLineType());
+ break;
+ case ("FontSize"):
+ shape.setFontSize(Double.valueOf(entry.getRight()));
+ break;
+ case ("FontWeight"):
+ shape.setFontWeight(entry.getRight());
+ break;
+ case ("Valign"):
+ shape.setvAlign(entry.getRight());
+ break;
+ default:
+ logger.warn("Unknown attribute of " + eTmp.getNodeName() + " node: " + entry.getLeft());
+ break;
+ }
+ }
+ }
+ shape.setRectangle(new Rectangle2D.Double(centerX - width / 2, centerY - height / 2, width, height));
+ }
+
+ /**
+ * Method that parses {@link DataNode} xml attribute.
+ *
+ * @param eTmp
+ * xml node with attribute
+ * @param shape
+ * shape where data should be added
+ */
+ private void parseAttribute(Element eTmp, DataNode shape) {
+ String key = eTmp.getAttribute("Key");
+ String value = eTmp.getAttribute("Value");
+ switch (key) {
+ case ("org.pathvisio.model.BackpageHead"):
+ // it's deprecated in PathVisio so we can skip it
+ break;
+ case ("org.pathvisio.model.GenMAPP-Xref"):
+ // skip it when it's empty
+ if (!value.isEmpty()) {
+ logger.warn(shape.getWarningPrefix() + "Unknown attribute of node. Key: " + key + "; value: " + value);
+ break;
+ }
+ break;
+ default:
+ logger.warn(shape.getWarningPrefix() + "Unknown attribute of node. Key: " + key + "; value: " + value);
+ break;
+ }
+ }
+
+ @Override
+ public String toXml(DataNode node) throws ConverterException {
+ throw new NotImplementedException();
+ }
+
+ @Override
+ public String toXml(Collection<DataNode> list) throws ConverterException {
+ throw new NotImplementedException();
+ }
+
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeLineParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeLineParser.java
index b573f26c44..92feeb4c0b 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeLineParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeLineParser.java
@@ -1,92 +1,92 @@
-package lcsb.mapviewer.wikipathway.XML;
-
-import java.util.Collection;
-
-import org.apache.log4j.Logger;
-import org.w3c.dom.Element;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.ConverterException;
-import lcsb.mapviewer.wikipathway.model.Edge;
-
-/**
- * Parser class that creates {@link Edge} objects from Xml {@link Element node}.
- * However the xml node is not typica edge node , but line node.
- *
- * @author Piotr Gawron
- *
- */
-public class EdgeLineParser extends ElementGpmlParser<Edge> {
-
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(EdgeLineParser.class);
-
- /**
- * Parser used to parse typical {@link Edge} xml nodes.
- */
- private final EdgeParser edgeParser = new EdgeParser();
-
- /**
- * Creates {@link Edge} from xml line node.
- *
- * @return {@link Edge} from xml node
- * @throws ConverterException
- */
- @Override
- public Edge parse(Element eElement) throws ConverterException {
- if (!eElement.getNodeName().equals("GraphicalLine")) {
- throw new InvalidArgumentException(ShapeParser.class.getSimpleName() + " can parse only GraphicalLine xml nodes. But " + eElement.getNodeName());
- }
- Edge line = edgeParser.createEmpty();
- NodeList nodes = eElement.getChildNodes();
- for (Pair<String, String> entry : getAttributes(eElement)) {
- switch (entry.getLeft()) {
- case ("GraphId"):
- line.setGraphId(entry.getRight());
- break;
- case ("GroupRef"):
- line.setGroupRef(entry.getRight());
- break;
- default:
- logger.warn("Unknown attribute of " + eElement.getNodeName() + " node: " + entry.getLeft());
- }
- }
-
- for (int i = 0; i < nodes.getLength(); i++) {
- Node node = nodes.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- Element eTmp = (Element) node;
- switch (node.getNodeName()) {
- case ("Graphics"):
- edgeParser.parseGraphics(line, (Element) node);
- break;
- case ("BiopaxRef"):
- line.addBiopaxReference(eTmp.getTextContent());
- break;
- case ("Comment"):
- line.addComment(eTmp.getTextContent());
- break;
- default:
- logger.warn("Unknown node in line: " + node.getNodeName());
- }
- }
- }
- return line;
- }
-
- @Override
- public String toXml(Edge node) throws ConverterException {
- throw new NotImplementedException();
- }
-
- @Override
- public String toXml(Collection<Edge> list) throws ConverterException {
- throw new NotImplementedException();
- }
-}
+package lcsb.mapviewer.wikipathway.XML;
+
+import java.util.Collection;
+
+import org.apache.log4j.Logger;
+import org.w3c.dom.Element;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.wikipathway.model.Edge;
+
+/**
+ * Parser class that creates {@link Edge} objects from Xml {@link Element node}.
+ * However the xml node is not typica edge node , but line node.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class EdgeLineParser extends ElementGpmlParser<Edge> {
+
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(EdgeLineParser.class);
+
+ /**
+ * Parser used to parse typical {@link Edge} xml nodes.
+ */
+ private final EdgeParser edgeParser = new EdgeParser();
+
+ /**
+ * Creates {@link Edge} from xml line node.
+ *
+ * @return {@link Edge} from xml node
+ * @throws ConverterException
+ */
+ @Override
+ public Edge parse(Element eElement) throws ConverterException {
+ if (!eElement.getNodeName().equals("GraphicalLine")) {
+ throw new InvalidArgumentException(ShapeParser.class.getSimpleName() + " can parse only GraphicalLine xml nodes. But " + eElement.getNodeName());
+ }
+ Edge line = edgeParser.createEmpty();
+ NodeList nodes = eElement.getChildNodes();
+ for (Pair<String, String> entry : getAttributes(eElement)) {
+ switch (entry.getLeft()) {
+ case ("GraphId"):
+ line.setGraphId(entry.getRight());
+ break;
+ case ("GroupRef"):
+ line.setGroupRef(entry.getRight());
+ break;
+ default:
+ logger.warn("Unknown attribute of " + eElement.getNodeName() + " node: " + entry.getLeft());
+ }
+ }
+
+ for (int i = 0; i < nodes.getLength(); i++) {
+ Node node = nodes.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ Element eTmp = (Element) node;
+ switch (node.getNodeName()) {
+ case ("Graphics"):
+ edgeParser.parseGraphics(line, (Element) node);
+ break;
+ case ("BiopaxRef"):
+ line.addBiopaxReference(eTmp.getTextContent());
+ break;
+ case ("Comment"):
+ line.addComment(eTmp.getTextContent());
+ break;
+ default:
+ logger.warn("Unknown node in line: " + node.getNodeName());
+ }
+ }
+ }
+ return line;
+ }
+
+ @Override
+ public String toXml(Edge node) throws ConverterException {
+ throw new NotImplementedException();
+ }
+
+ @Override
+ public String toXml(Collection<Edge> list) throws ConverterException {
+ throw new NotImplementedException();
+ }
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeParser.java
index 3cd2c16ebe..5c367ccade 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeParser.java
@@ -1,579 +1,579 @@
-package lcsb.mapviewer.wikipathway.XML;
-
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.w3c.dom.Element;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.ConverterException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.wikipathway.model.Direction;
-import lcsb.mapviewer.wikipathway.model.Edge;
-import lcsb.mapviewer.wikipathway.model.GpmlLineConnectorType;
-import lcsb.mapviewer.wikipathway.model.GpmlLineType;
-import lcsb.mapviewer.wikipathway.model.PointData;
-import lcsb.mapviewer.wikipathway.model.UnknownTypeException;
-
-/**
- * Parser class that creates {@link Edge} objects from Xml {@link Element node}.
- *
- * @author Piotr Gawron
- *
- */
-public class EdgeParser extends ElementGpmlParser<Edge> {
-
- /**
- * Parser used for extracting {@link lcsb.mapviewer.model.map.MiriamData
- * references} from GPML model.
- */
- private ReferenceParser referenceParser = new ReferenceParser();
-
- /**
- * Parser used for extracting {@link PointData points} from GPML xml nodes.
- */
- private PointDataParser pointParser = new PointDataParser();
-
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(EdgeParser.class);
-
- /**
- * First id value used for generating identifiers during conversion.
- */
- private static final int INITIAL_ID_VALUE = 10000;
-
- /**
- * This is default lenght of lines when lines are drawn in
- * {@link GpmlLineConnectorType#ELBOW} mode, but without specifing
- * coordinates.
- */
- private static final double DEFAULT_DISTNACE = 20;
-
- /**
- * Counter used for generating identifiers if identifiers aren't provided by
- * the gpml model.
- */
- private static int idCounter = INITIAL_ID_VALUE;
-
- /**
- * This function get new id for interactions that don't have id.
- *
- * @return String - new id
- */
- private String getNewId() {
- idCounter++;
- return "id" + idCounter;
- }
-
- /**
- * Creates {@link Edge} from xml node.
- *
- * @return {@link Edge} from xml node
- * @throws ConverterException
- * thrown when there is a problem with parsing edge
- */
- @Override
- public Edge parse(Element eElement) throws ConverterException {
-
- String graphId = eElement.getAttribute("GraphId");
- if (graphId == null || graphId.equals("")) {
- graphId = getNewId();
- }
- Edge edge = new Edge(graphId);
-
- for (Pair<String, String> entry : getAttributes(eElement)) {
- switch (entry.getLeft()) {
- case ("GraphId"):
- break;
- case ("GroupRef"):
- edge.setGroupRef(entry.getRight());
- break;
- default:
- logger.warn("Unknown attribute of " + eElement.getNodeName() + " node: " + entry.getLeft());
- break;
- }
- }
-
- NodeList nodes = eElement.getChildNodes();
- boolean graphicsParsed = false;
- for (int i = 0; i < nodes.getLength(); i++) {
- Node node = nodes.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- Element element = (Element) node;
- switch (node.getNodeName()) {
- // references (annotations)
- case ("Xref"):
- MiriamData md = referenceParser.parse(element);
- if (md != null) {
- edge.addReference(md);
- }
- break;
- case ("Comment"):
- edge.addComment(node.getTextContent());
- break;
- // references (annotations)
- case ("BiopaxRef"):
- edge.getBiopaxReferences().add(node.getTextContent());
- break;
- case ("Graphics"):
- graphicsParsed = true;
- parseGraphics(edge, element);
- break;
- case ("Attribute"):
- parseAttribute(element, edge);
- break;
- default:
- logger.warn(edge.getWarningPrefix() + "Unknown edge node: " + node.getNodeName() + ".");
- break;
- }
- }
- }
- if (!graphicsParsed) {
- throw new ConverterException(edge.getWarningPrefix() + "No Graphics information found for edge.");
- }
- return edge;
- }
-
- /**
- * Parses graphics xml node that is part of edge xml node.
- *
- * @param edge
- * edge which is parsed
- * @param graphicsNode
- * xml node
- * @throws ConverterException
- * thrown when data for the edge is invalid
- */
- protected void parseGraphics(Edge edge, Element graphicsNode) throws ConverterException {
- List<Element> points = new ArrayList<Element>();
- List<Element> anchors = new ArrayList<Element>();
-
- GpmlLineConnectorType connectorType = GpmlLineConnectorType.STRAIGHT;
-
- for (Pair<String, String> entry : getAttributes(graphicsNode)) {
- switch (entry.getLeft()) {
- case ("ConnectorType"):
- connectorType = GpmlLineConnectorType.getByGpmlName(entry.getRight());
- break;
- case ("LineThickness"):
- // line thicknes
- edge.getLine().setWidth(entry.getRight());
- break;
- case ("LineStyle"):
- // line type
- GpmlLineType lineType = GpmlLineType.getByGpmlName(entry.getRight());
- edge.getLine().setType(lineType.getCorrespondingGlobalLineType());
- break;
- case ("ZOrder"):
- edge.setzOrder(Integer.valueOf(entry.getRight()));
- break;
- case ("Color"):
- // graphics color
- edge.setColor(hexStringToColor(entry.getRight()));
- break;
- default:
- logger.warn("Unknown attribute of " + graphicsNode.getNodeName() + " node: " + entry.getLeft());
- break;
- }
- }
-
- NodeList nodes;
- nodes = graphicsNode.getChildNodes();
- for (int i = 0; i < nodes.getLength(); i++) {
- Node node = nodes.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if ("Point".equalsIgnoreCase(node.getNodeName())) {
- points.add((Element) node);
- } else if ("Anchor".equalsIgnoreCase(node.getNodeName())) {
- anchors.add((Element) node);
- } else {
- logger.warn(edge.getWarningPrefix() + "Unknown graphics edge node: " + node.getNodeName() + ".");
- }
- }
- }
-
- // lines
-
- List<PointData> pointDataList = new ArrayList<>();
-
- for (int j = 0; j < points.size(); j++) {
- Node point = points.get(j);
- PointData pointData = pointParser.parse((Element) point);
-
- pointDataList.add(pointData);
- if (j == 0 && pointData.hasGraphRef()) {
- edge.setStart(pointData.getGraphRef());
- }
- if (j == points.size() - 1 && pointData.hasGraphRef()) {
- edge.setEnd(pointData.getGraphRef());
- }
-
- edge.setType(pointData.getType());
- }
-
- edge.getLine().setPoints(getPoints(edge.getWarningPrefix(), pointDataList, connectorType));
- if (edge.getLine().getPoints().size() < 2) {
- throw new ConverterException(edge.getWarningPrefix() + "Contains too less points. At least two points are required in a line.");
- }
- double lineLength = 0;
- for (Line2D line : edge.getLine().getLines()) {
- lineLength += line.getP1().distance(line.getP2());
- }
- if (lineLength <= Configuration.EPSILON) {
- throw new ConverterException(edge.getWarningPrefix() + "Line cannot have 0 length.");
- }
-
- // anchors
- for (Element anchor : anchors) {
- String anchorId = anchor.getAttribute("GraphId");
- String position = anchor.getAttribute("Position");
- if (anchorId != null && !anchorId.isEmpty()) {
- edge.addAnchor(anchorId);
- // if our edge is not connected from at first point but we have anchor
- // there, then set this anchor there (so we could merge it later on)
- if (edge.getStart() == null && "0.0".equals(position)) {
- edge.setStart(anchorId);
- }
- // if our edge is not connected from at last point but we have anchor
- // there, then set this anchor there (so we could merge it later on)
- if (edge.getEnd() == null && "1.0".equals(position)) {
- edge.setEnd(anchorId);
- }
- }
- }
- }
-
- /**
- * This method transforms list of {@link PointData points} from gpml xml into
- * list of standard {@link Point2D points}.
- *
- * @param warningPrefix
- * prefix that should be used for warnings
- * @param pointDataList
- * list of points from gpml format
- * @param connectorType
- * {@link GpmlLineConnectorType type} defining how points are
- * connected in gpml format
- * @return list of standard {@link Point2D points} obtained from input data
- * @throws UnknownGpmlLineConnectorTypeException
- * thrown when {@link GpmlLineConnectorType type} is unknown
- * @throws InvalidElbowConnectorException
- * thrown when input data define invalid line
- * @throws UnknownTypeException
- * throw when connector type is invalid
- */
- private List<Point2D> getPoints(String warningPrefix, List<PointData> pointDataList, GpmlLineConnectorType connectorType)
- throws InvalidElbowConnectorException, UnknownTypeException {
- List<Point2D> result = new ArrayList<>();
- switch (connectorType) {
- // line is a list of perpendicular segments
- case ELBOW:
- Direction from = pointDataList.get(0).getDirection();
- Direction to = pointDataList.get(pointDataList.size() - 1).getDirection();
-
- if (from == null) {
- from = Direction.WEST;
- }
- if (to == null) {
- to = Direction.EAST;
- }
-
- // how many segments do we have
- int lines = computeNumberOfPerpendicularSegments(warningPrefix, pointDataList.get(0), pointDataList.get(pointDataList.size() - 1));
- // now we know how many segments should be i the line
-
- // if segments are defined in the input the it's easy
- if (lines == pointDataList.size()) {
- List<Point2D> points = new ArrayList<>();
- for (PointData pd : pointDataList) {
- points.add(pd.toPoint());
- }
- result = preparePerpendicularLines(from, points);
-
- // if we know how many segments should be in the line, but we have
- // only first and last point
- // then we need to add missing points (some default behaviour).
- } else if (pointDataList.size() == 2) {
- List<Point2D> points = new ArrayList<>();
- points.add(pointDataList.get(0).toPoint());
- points.add(pointDataList.get(1).toPoint());
- // add middle point
- points.add(1, computeDefaultPoint(from, points.get(0)));
- // CHECKSTYLE:OFF
- // if something is still missing then add defult beginning line
- if (lines > 3) {
- points.add(2, computeDefaultPoint(to, points.get(2)));
- }
- // if something is still missing then add defult end line
- if (lines > 4) {
- double x = (points.get(1).getX() + points.get(2).getX()) / 2;
- double y = (points.get(1).getY() + points.get(2).getY()) / 2;
- points.add(2, new Point2D.Double(x, y));
- }
- // if something is still missing then there is something terrible
- // wrong
- if (lines > 5) {
- throw new InvalidElbowConnectorException(warningPrefix + " Line with connector type " + connectorType + " contains too many segments: " + lines);
- }
- // CHECKSTYLE:ON
-
- // and now transform the points into perpendicular segments
- result = preparePerpendicularLines(from, points);
-
- // if number of expectred segments is lower than number of defined
- // segments then we probably missed something, let's assume that in
- // gpml file the data is correct and parse it
- } else if (pointDataList.size() > lines) {
- List<Point2D> points = new ArrayList<>();
- for (PointData pd : pointDataList) {
- points.add(pd.toPoint());
- }
- result = preparePerpendicularLines(from, points);
-
- // if number of expectred segments is different than number of defined
- // segments then something is wrong
- } else {
- throw new InvalidElbowConnectorException(
- warningPrefix + "Don't know how to prepare lines. " + connectorType + " contains invalid number of points: " + pointDataList.size()
- + ". Expected: " + lines);
- }
-
- break;
-
- // if line is straight then pass input points into the output
- case STRAIGHT:
- for (PointData pointData : pointDataList) {
- result.add(pointData.toPoint());
- }
- break;
- // if line is segmented then pass input points into the output
- case SEGMENTED:
- for (PointData pointData : pointDataList) {
- result.add(pointData.toPoint());
- }
- break;
- // if line is curved then inform user that we don't support it and create
- // a default one
- case CURVED:
- logger.warn(warningPrefix + "Curved connections are not supported.");
- for (PointData pointData : pointDataList) {
- result.add(pointData.toPoint());
- }
- break;
- default:
- throw new UnknownTypeException(warningPrefix + "Connector type is not supported: " + connectorType);
- }
- return result;
- }
-
- /**
- * Method that computes number of perpendicular lines that should connect
- * start point with the end point.
- *
- * @param warningPrefix
- * string used as a prefix for warnings/errors
- * @param start
- * starting point
- * @param end
- * end point
- * @return number of perpendicular lines that should connect start point with
- * the end point
- * @throws InvalidElbowConnectorException
- * thrown when output cannot be computed because input data is
- * invalid
- */
- private int computeNumberOfPerpendicularSegments(String warningPrefix, PointData start, PointData end) throws InvalidElbowConnectorException {
- Point2D fromPoint = start.toPoint();
- Point2D toPoint = end.toPoint();
-
- Direction from = start.getDirection();
- if (from == null) {
- from = Direction.WEST;
- }
- Direction to = end.getDirection();
- if (to == null) {
- to = Direction.EAST;
- }
-
- // result (2 is the minimu)
- int lines = 2;
-
- // if line starts and ends i nthe same axis then number of segments
- // should be at least3
- if (from.getAxis().equals(to.getAxis())) {
- lines++;
- }
-
- // if they are not starting and ending in the same direction (for
- // instance they both start from NORTH)
- // then check if some addition lines are needed
- if (!from.equals(to)) {
- int addition = 0;
- // check if begining requires additional lines because the end is
- // overlapping the beginning
- switch (from) {
- case EAST:
- if (fromPoint.getX() >= toPoint.getX()) {
- addition = 2;
- }
- break;
- case WEST:
- if (fromPoint.getX() <= toPoint.getX()) {
- addition = 2;
- }
- break;
- case NORTH:
- if (fromPoint.getY() <= toPoint.getY()) {
- addition = 2;
- }
- break;
- case SOUTH:
- if (fromPoint.getY() >= toPoint.getY()) {
- addition = 2;
- }
- break;
- default:
- throw new InvalidElbowConnectorException(warningPrefix + "Unknown direction: " + from);
- }
- // check if emdrequires additional lines because the beginning is
- // overlapping end part
- switch (to) {
- case EAST:
- if (fromPoint.getX() <= toPoint.getX()) {
- addition = 2;
- }
- break;
- case WEST:
- if (fromPoint.getX() >= toPoint.getX()) {
- addition = 2;
- }
- break;
- case NORTH:
- if (fromPoint.getY() >= toPoint.getY()) {
- addition = 2;
- }
- break;
- case SOUTH:
- if (fromPoint.getY() <= toPoint.getY()) {
- addition = 2;
- }
- break;
- default:
- throw new InvalidElbowConnectorException(warningPrefix + "Unknown direction: " + from);
- }
- lines += addition;
- }
- return lines;
- }
-
- /**
- * Creates point that defines default perpendicular line from input point.
- *
- * @param from
- * direction from which point is connected
- * @param original
- * point from where we want to have a line
- * @return point that defines default perpendicular line from input point
- */
- private Point2D computeDefaultPoint(Direction from, Point2D original) {
- switch (from) {
- case NORTH:
- return new Point2D.Double(original.getX(), original.getY() - DEFAULT_DISTNACE);
- case SOUTH:
- return new Point2D.Double(original.getX(), original.getY() + DEFAULT_DISTNACE);
- case EAST:
- return new Point2D.Double(original.getX() + DEFAULT_DISTNACE, original.getY());
- case WEST:
- return new Point2D.Double(original.getX() - DEFAULT_DISTNACE, original.getY());
- default:
- throw new InvalidStateException("Unknown direction: " + from);
- }
- }
-
- /**
- * Creates perpendicular lines going through all input points.
- *
- * @param from
- * in which direction should go the first line
- * @param points
- * set of points through which perpendicular line should go
- * @return perpendicular lines going through all input points
- */
- private List<Point2D> preparePerpendicularLines(Direction from, List<Point2D> points) {
- List<Point2D> result = new ArrayList<>();
- result.add(points.get(0));
- Point2D lastPoint = points.get(0);
- for (int i = 1; i < points.size(); i++) {
- Point2D point = points.get(i);
- switch (from.getAxis()) {
- case NORTH_SOUTH:
- result.add(new Point2D.Double(lastPoint.getX(), point.getY()));
- break;
- case EAST_WEST:
- result.add(new Point2D.Double(point.getX(), lastPoint.getY()));
- break;
- default:
- throw new InvalidStateException("Unknown direction axis: " + from.getAxis());
- }
- lastPoint = result.get(i);
- from = from.nextClockwiseDirection();
- }
- result.add(points.get(points.size() - 1));
- return result;
- }
-
- /**
- * Creates new {@link Edge} object with unique identifier.
- *
- * @return new {@link Edge} object with unique identifier
- */
- public Edge createEmpty() {
- return new Edge(getNewId());
- }
-
- /**
- * Method that parses {@link Edge} xml attribute.
- *
- * @param eTmp
- * xml node with attribute
- * @param edge
- * edge where data should be added
- */
- private void parseAttribute(Element eTmp, Edge edge) {
- String key = eTmp.getAttribute("Key");
- String value = eTmp.getAttribute("Value");
- switch (key) {
- case ("org.pathvisio.core.ds"):
- // skip for now (no idea what des it mean)
- break;
- case ("org.pathvisio.core.id"):
- // skip for now (no idea what des it mean)
- break;
- default:
- logger.warn(edge.getWarningPrefix() + "Unknown attribute of node. Key: " + key + "; value: " + value);
- break;
- }
- }
-
- @Override
- public String toXml(Edge node) throws ConverterException {
- throw new NotImplementedException();
- }
-
- @Override
- public String toXml(Collection<Edge> list) throws ConverterException {
- throw new NotImplementedException();
- }
-
-}
+package lcsb.mapviewer.wikipathway.XML;
+
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.w3c.dom.Element;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.wikipathway.model.Direction;
+import lcsb.mapviewer.wikipathway.model.Edge;
+import lcsb.mapviewer.wikipathway.model.GpmlLineConnectorType;
+import lcsb.mapviewer.wikipathway.model.GpmlLineType;
+import lcsb.mapviewer.wikipathway.model.PointData;
+import lcsb.mapviewer.wikipathway.model.UnknownTypeException;
+
+/**
+ * Parser class that creates {@link Edge} objects from Xml {@link Element node}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class EdgeParser extends ElementGpmlParser<Edge> {
+
+ /**
+ * Parser used for extracting {@link lcsb.mapviewer.model.map.MiriamData
+ * references} from GPML model.
+ */
+ private ReferenceParser referenceParser = new ReferenceParser();
+
+ /**
+ * Parser used for extracting {@link PointData points} from GPML xml nodes.
+ */
+ private PointDataParser pointParser = new PointDataParser();
+
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(EdgeParser.class);
+
+ /**
+ * First id value used for generating identifiers during conversion.
+ */
+ private static final int INITIAL_ID_VALUE = 10000;
+
+ /**
+ * This is default lenght of lines when lines are drawn in
+ * {@link GpmlLineConnectorType#ELBOW} mode, but without specifing
+ * coordinates.
+ */
+ private static final double DEFAULT_DISTNACE = 20;
+
+ /**
+ * Counter used for generating identifiers if identifiers aren't provided by
+ * the gpml model.
+ */
+ private static int idCounter = INITIAL_ID_VALUE;
+
+ /**
+ * This function get new id for interactions that don't have id.
+ *
+ * @return String - new id
+ */
+ private String getNewId() {
+ idCounter++;
+ return "id" + idCounter;
+ }
+
+ /**
+ * Creates {@link Edge} from xml node.
+ *
+ * @return {@link Edge} from xml node
+ * @throws ConverterException
+ * thrown when there is a problem with parsing edge
+ */
+ @Override
+ public Edge parse(Element eElement) throws ConverterException {
+
+ String graphId = eElement.getAttribute("GraphId");
+ if (graphId == null || graphId.equals("")) {
+ graphId = getNewId();
+ }
+ Edge edge = new Edge(graphId);
+
+ for (Pair<String, String> entry : getAttributes(eElement)) {
+ switch (entry.getLeft()) {
+ case ("GraphId"):
+ break;
+ case ("GroupRef"):
+ edge.setGroupRef(entry.getRight());
+ break;
+ default:
+ logger.warn("Unknown attribute of " + eElement.getNodeName() + " node: " + entry.getLeft());
+ break;
+ }
+ }
+
+ NodeList nodes = eElement.getChildNodes();
+ boolean graphicsParsed = false;
+ for (int i = 0; i < nodes.getLength(); i++) {
+ Node node = nodes.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ Element element = (Element) node;
+ switch (node.getNodeName()) {
+ // references (annotations)
+ case ("Xref"):
+ MiriamData md = referenceParser.parse(element);
+ if (md != null) {
+ edge.addReference(md);
+ }
+ break;
+ case ("Comment"):
+ edge.addComment(node.getTextContent());
+ break;
+ // references (annotations)
+ case ("BiopaxRef"):
+ edge.getBiopaxReferences().add(node.getTextContent());
+ break;
+ case ("Graphics"):
+ graphicsParsed = true;
+ parseGraphics(edge, element);
+ break;
+ case ("Attribute"):
+ parseAttribute(element, edge);
+ break;
+ default:
+ logger.warn(edge.getWarningPrefix() + "Unknown edge node: " + node.getNodeName() + ".");
+ break;
+ }
+ }
+ }
+ if (!graphicsParsed) {
+ throw new ConverterException(edge.getWarningPrefix() + "No Graphics information found for edge.");
+ }
+ return edge;
+ }
+
+ /**
+ * Parses graphics xml node that is part of edge xml node.
+ *
+ * @param edge
+ * edge which is parsed
+ * @param graphicsNode
+ * xml node
+ * @throws ConverterException
+ * thrown when data for the edge is invalid
+ */
+ protected void parseGraphics(Edge edge, Element graphicsNode) throws ConverterException {
+ List<Element> points = new ArrayList<Element>();
+ List<Element> anchors = new ArrayList<Element>();
+
+ GpmlLineConnectorType connectorType = GpmlLineConnectorType.STRAIGHT;
+
+ for (Pair<String, String> entry : getAttributes(graphicsNode)) {
+ switch (entry.getLeft()) {
+ case ("ConnectorType"):
+ connectorType = GpmlLineConnectorType.getByGpmlName(entry.getRight());
+ break;
+ case ("LineThickness"):
+ // line thicknes
+ edge.getLine().setWidth(entry.getRight());
+ break;
+ case ("LineStyle"):
+ // line type
+ GpmlLineType lineType = GpmlLineType.getByGpmlName(entry.getRight());
+ edge.getLine().setType(lineType.getCorrespondingGlobalLineType());
+ break;
+ case ("ZOrder"):
+ edge.setzOrder(Integer.valueOf(entry.getRight()));
+ break;
+ case ("Color"):
+ // graphics color
+ edge.setColor(hexStringToColor(entry.getRight()));
+ break;
+ default:
+ logger.warn("Unknown attribute of " + graphicsNode.getNodeName() + " node: " + entry.getLeft());
+ break;
+ }
+ }
+
+ NodeList nodes;
+ nodes = graphicsNode.getChildNodes();
+ for (int i = 0; i < nodes.getLength(); i++) {
+ Node node = nodes.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if ("Point".equalsIgnoreCase(node.getNodeName())) {
+ points.add((Element) node);
+ } else if ("Anchor".equalsIgnoreCase(node.getNodeName())) {
+ anchors.add((Element) node);
+ } else {
+ logger.warn(edge.getWarningPrefix() + "Unknown graphics edge node: " + node.getNodeName() + ".");
+ }
+ }
+ }
+
+ // lines
+
+ List<PointData> pointDataList = new ArrayList<>();
+
+ for (int j = 0; j < points.size(); j++) {
+ Node point = points.get(j);
+ PointData pointData = pointParser.parse((Element) point);
+
+ pointDataList.add(pointData);
+ if (j == 0 && pointData.hasGraphRef()) {
+ edge.setStart(pointData.getGraphRef());
+ }
+ if (j == points.size() - 1 && pointData.hasGraphRef()) {
+ edge.setEnd(pointData.getGraphRef());
+ }
+
+ edge.setType(pointData.getType());
+ }
+
+ edge.getLine().setPoints(getPoints(edge.getWarningPrefix(), pointDataList, connectorType));
+ if (edge.getLine().getPoints().size() < 2) {
+ throw new ConverterException(edge.getWarningPrefix() + "Contains too less points. At least two points are required in a line.");
+ }
+ double lineLength = 0;
+ for (Line2D line : edge.getLine().getLines()) {
+ lineLength += line.getP1().distance(line.getP2());
+ }
+ if (lineLength <= Configuration.EPSILON) {
+ throw new ConverterException(edge.getWarningPrefix() + "Line cannot have 0 length.");
+ }
+
+ // anchors
+ for (Element anchor : anchors) {
+ String anchorId = anchor.getAttribute("GraphId");
+ String position = anchor.getAttribute("Position");
+ if (anchorId != null && !anchorId.isEmpty()) {
+ edge.addAnchor(anchorId);
+ // if our edge is not connected from at first point but we have anchor
+ // there, then set this anchor there (so we could merge it later on)
+ if (edge.getStart() == null && "0.0".equals(position)) {
+ edge.setStart(anchorId);
+ }
+ // if our edge is not connected from at last point but we have anchor
+ // there, then set this anchor there (so we could merge it later on)
+ if (edge.getEnd() == null && "1.0".equals(position)) {
+ edge.setEnd(anchorId);
+ }
+ }
+ }
+ }
+
+ /**
+ * This method transforms list of {@link PointData points} from gpml xml into
+ * list of standard {@link Point2D points}.
+ *
+ * @param warningPrefix
+ * prefix that should be used for warnings
+ * @param pointDataList
+ * list of points from gpml format
+ * @param connectorType
+ * {@link GpmlLineConnectorType type} defining how points are
+ * connected in gpml format
+ * @return list of standard {@link Point2D points} obtained from input data
+ * @throws UnknownGpmlLineConnectorTypeException
+ * thrown when {@link GpmlLineConnectorType type} is unknown
+ * @throws InvalidElbowConnectorException
+ * thrown when input data define invalid line
+ * @throws UnknownTypeException
+ * throw when connector type is invalid
+ */
+ private List<Point2D> getPoints(String warningPrefix, List<PointData> pointDataList, GpmlLineConnectorType connectorType)
+ throws InvalidElbowConnectorException, UnknownTypeException {
+ List<Point2D> result = new ArrayList<>();
+ switch (connectorType) {
+ // line is a list of perpendicular segments
+ case ELBOW:
+ Direction from = pointDataList.get(0).getDirection();
+ Direction to = pointDataList.get(pointDataList.size() - 1).getDirection();
+
+ if (from == null) {
+ from = Direction.WEST;
+ }
+ if (to == null) {
+ to = Direction.EAST;
+ }
+
+ // how many segments do we have
+ int lines = computeNumberOfPerpendicularSegments(warningPrefix, pointDataList.get(0), pointDataList.get(pointDataList.size() - 1));
+ // now we know how many segments should be i the line
+
+ // if segments are defined in the input the it's easy
+ if (lines == pointDataList.size()) {
+ List<Point2D> points = new ArrayList<>();
+ for (PointData pd : pointDataList) {
+ points.add(pd.toPoint());
+ }
+ result = preparePerpendicularLines(from, points);
+
+ // if we know how many segments should be in the line, but we have
+ // only first and last point
+ // then we need to add missing points (some default behaviour).
+ } else if (pointDataList.size() == 2) {
+ List<Point2D> points = new ArrayList<>();
+ points.add(pointDataList.get(0).toPoint());
+ points.add(pointDataList.get(1).toPoint());
+ // add middle point
+ points.add(1, computeDefaultPoint(from, points.get(0)));
+ // CHECKSTYLE:OFF
+ // if something is still missing then add defult beginning line
+ if (lines > 3) {
+ points.add(2, computeDefaultPoint(to, points.get(2)));
+ }
+ // if something is still missing then add defult end line
+ if (lines > 4) {
+ double x = (points.get(1).getX() + points.get(2).getX()) / 2;
+ double y = (points.get(1).getY() + points.get(2).getY()) / 2;
+ points.add(2, new Point2D.Double(x, y));
+ }
+ // if something is still missing then there is something terrible
+ // wrong
+ if (lines > 5) {
+ throw new InvalidElbowConnectorException(warningPrefix + " Line with connector type " + connectorType + " contains too many segments: " + lines);
+ }
+ // CHECKSTYLE:ON
+
+ // and now transform the points into perpendicular segments
+ result = preparePerpendicularLines(from, points);
+
+ // if number of expectred segments is lower than number of defined
+ // segments then we probably missed something, let's assume that in
+ // gpml file the data is correct and parse it
+ } else if (pointDataList.size() > lines) {
+ List<Point2D> points = new ArrayList<>();
+ for (PointData pd : pointDataList) {
+ points.add(pd.toPoint());
+ }
+ result = preparePerpendicularLines(from, points);
+
+ // if number of expectred segments is different than number of defined
+ // segments then something is wrong
+ } else {
+ throw new InvalidElbowConnectorException(
+ warningPrefix + "Don't know how to prepare lines. " + connectorType + " contains invalid number of points: " + pointDataList.size()
+ + ". Expected: " + lines);
+ }
+
+ break;
+
+ // if line is straight then pass input points into the output
+ case STRAIGHT:
+ for (PointData pointData : pointDataList) {
+ result.add(pointData.toPoint());
+ }
+ break;
+ // if line is segmented then pass input points into the output
+ case SEGMENTED:
+ for (PointData pointData : pointDataList) {
+ result.add(pointData.toPoint());
+ }
+ break;
+ // if line is curved then inform user that we don't support it and create
+ // a default one
+ case CURVED:
+ logger.warn(warningPrefix + "Curved connections are not supported.");
+ for (PointData pointData : pointDataList) {
+ result.add(pointData.toPoint());
+ }
+ break;
+ default:
+ throw new UnknownTypeException(warningPrefix + "Connector type is not supported: " + connectorType);
+ }
+ return result;
+ }
+
+ /**
+ * Method that computes number of perpendicular lines that should connect
+ * start point with the end point.
+ *
+ * @param warningPrefix
+ * string used as a prefix for warnings/errors
+ * @param start
+ * starting point
+ * @param end
+ * end point
+ * @return number of perpendicular lines that should connect start point with
+ * the end point
+ * @throws InvalidElbowConnectorException
+ * thrown when output cannot be computed because input data is
+ * invalid
+ */
+ private int computeNumberOfPerpendicularSegments(String warningPrefix, PointData start, PointData end) throws InvalidElbowConnectorException {
+ Point2D fromPoint = start.toPoint();
+ Point2D toPoint = end.toPoint();
+
+ Direction from = start.getDirection();
+ if (from == null) {
+ from = Direction.WEST;
+ }
+ Direction to = end.getDirection();
+ if (to == null) {
+ to = Direction.EAST;
+ }
+
+ // result (2 is the minimu)
+ int lines = 2;
+
+ // if line starts and ends i nthe same axis then number of segments
+ // should be at least3
+ if (from.getAxis().equals(to.getAxis())) {
+ lines++;
+ }
+
+ // if they are not starting and ending in the same direction (for
+ // instance they both start from NORTH)
+ // then check if some addition lines are needed
+ if (!from.equals(to)) {
+ int addition = 0;
+ // check if begining requires additional lines because the end is
+ // overlapping the beginning
+ switch (from) {
+ case EAST:
+ if (fromPoint.getX() >= toPoint.getX()) {
+ addition = 2;
+ }
+ break;
+ case WEST:
+ if (fromPoint.getX() <= toPoint.getX()) {
+ addition = 2;
+ }
+ break;
+ case NORTH:
+ if (fromPoint.getY() <= toPoint.getY()) {
+ addition = 2;
+ }
+ break;
+ case SOUTH:
+ if (fromPoint.getY() >= toPoint.getY()) {
+ addition = 2;
+ }
+ break;
+ default:
+ throw new InvalidElbowConnectorException(warningPrefix + "Unknown direction: " + from);
+ }
+ // check if emdrequires additional lines because the beginning is
+ // overlapping end part
+ switch (to) {
+ case EAST:
+ if (fromPoint.getX() <= toPoint.getX()) {
+ addition = 2;
+ }
+ break;
+ case WEST:
+ if (fromPoint.getX() >= toPoint.getX()) {
+ addition = 2;
+ }
+ break;
+ case NORTH:
+ if (fromPoint.getY() >= toPoint.getY()) {
+ addition = 2;
+ }
+ break;
+ case SOUTH:
+ if (fromPoint.getY() <= toPoint.getY()) {
+ addition = 2;
+ }
+ break;
+ default:
+ throw new InvalidElbowConnectorException(warningPrefix + "Unknown direction: " + from);
+ }
+ lines += addition;
+ }
+ return lines;
+ }
+
+ /**
+ * Creates point that defines default perpendicular line from input point.
+ *
+ * @param from
+ * direction from which point is connected
+ * @param original
+ * point from where we want to have a line
+ * @return point that defines default perpendicular line from input point
+ */
+ private Point2D computeDefaultPoint(Direction from, Point2D original) {
+ switch (from) {
+ case NORTH:
+ return new Point2D.Double(original.getX(), original.getY() - DEFAULT_DISTNACE);
+ case SOUTH:
+ return new Point2D.Double(original.getX(), original.getY() + DEFAULT_DISTNACE);
+ case EAST:
+ return new Point2D.Double(original.getX() + DEFAULT_DISTNACE, original.getY());
+ case WEST:
+ return new Point2D.Double(original.getX() - DEFAULT_DISTNACE, original.getY());
+ default:
+ throw new InvalidStateException("Unknown direction: " + from);
+ }
+ }
+
+ /**
+ * Creates perpendicular lines going through all input points.
+ *
+ * @param from
+ * in which direction should go the first line
+ * @param points
+ * set of points through which perpendicular line should go
+ * @return perpendicular lines going through all input points
+ */
+ private List<Point2D> preparePerpendicularLines(Direction from, List<Point2D> points) {
+ List<Point2D> result = new ArrayList<>();
+ result.add(points.get(0));
+ Point2D lastPoint = points.get(0);
+ for (int i = 1; i < points.size(); i++) {
+ Point2D point = points.get(i);
+ switch (from.getAxis()) {
+ case NORTH_SOUTH:
+ result.add(new Point2D.Double(lastPoint.getX(), point.getY()));
+ break;
+ case EAST_WEST:
+ result.add(new Point2D.Double(point.getX(), lastPoint.getY()));
+ break;
+ default:
+ throw new InvalidStateException("Unknown direction axis: " + from.getAxis());
+ }
+ lastPoint = result.get(i);
+ from = from.nextClockwiseDirection();
+ }
+ result.add(points.get(points.size() - 1));
+ return result;
+ }
+
+ /**
+ * Creates new {@link Edge} object with unique identifier.
+ *
+ * @return new {@link Edge} object with unique identifier
+ */
+ public Edge createEmpty() {
+ return new Edge(getNewId());
+ }
+
+ /**
+ * Method that parses {@link Edge} xml attribute.
+ *
+ * @param eTmp
+ * xml node with attribute
+ * @param edge
+ * edge where data should be added
+ */
+ private void parseAttribute(Element eTmp, Edge edge) {
+ String key = eTmp.getAttribute("Key");
+ String value = eTmp.getAttribute("Value");
+ switch (key) {
+ case ("org.pathvisio.core.ds"):
+ // skip for now (no idea what des it mean)
+ break;
+ case ("org.pathvisio.core.id"):
+ // skip for now (no idea what des it mean)
+ break;
+ default:
+ logger.warn(edge.getWarningPrefix() + "Unknown attribute of node. Key: " + key + "; value: " + value);
+ break;
+ }
+ }
+
+ @Override
+ public String toXml(Edge node) throws ConverterException {
+ throw new NotImplementedException();
+ }
+
+ @Override
+ public String toXml(Collection<Edge> list) throws ConverterException {
+ throw new NotImplementedException();
+ }
+
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ElementGpmlParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ElementGpmlParser.java
index 1162229c9e..cad379fcbd 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ElementGpmlParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ElementGpmlParser.java
@@ -1,139 +1,139 @@
-package lcsb.mapviewer.wikipathway.XML;
-
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.ConverterException;
-
-import org.apache.log4j.Logger;
-import org.w3c.dom.Element;
-import org.w3c.dom.NamedNodeMap;
-import org.w3c.dom.Node;
-
-/**
- * Generic parser for GPML xml structures.
- *
- * @author Piotr Gawron
- *
- * @param <T>
- * class for which this parser aplies
- */
-public abstract class ElementGpmlParser<T> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(ElementGpmlParser.class);
-
- /**
- * Color that should be used when we have transparent color.
- */
- private static final Color TRANSPARENT_COLOR = new Color(0, 0, 0, 0);
-
- /**
- * Creates object from xml node given in parameter.
- *
- * @param node
- * xml node from which object will be created
- * @return object created from xml node
- * @throws ConverterException
- * thrown when there is severe problem with parsing xml node
- */
- public abstract T parse(Element node) throws ConverterException;
-
- /**
- * Converts object into xml string (in gpml format).
- *
- * @param object
- * object to transform
- * @return xml string representing object
- * @throws ConverterException
- * thrown when there is a problem with converting into xml
- */
- public abstract String toXml(T object) throws ConverterException;
-
- /**
- * Converts list of objects into xml string (in gpml format) representing this
- * list.
- *
- * @param list
- * list objects to transform
- * @return xml string representing objects
- * @throws ConverterException
- * thrown when there is a problem with converting into xml
- */
- public abstract String toXml(Collection<T> list) throws ConverterException;
-
- /**
- * Creates list of object from list of xml nodes.
- *
- * @param nodes
- * list of xml nodes to parse
- * @return list of object from list of xml nodes
- * @throws ConverterException
- * thrown when there is severe problem with parsing xml node
- */
- public List<T> parseCollection(Collection<Node> nodes) throws ConverterException {
- List<T> result = new ArrayList<>();
- for (Node node : nodes) {
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- T element = parse((Element) node);
- // add only not null elements (null might appear when node is partially
- // invalid and warnings are set)
- if (element != null) {
- result.add(element);
- }
- }
- }
- return result;
- }
-
- /**
- * Transforms string representing color into {@link Color}.
- *
- * @param hex
- * string representing color
- * @return {@link Color} representation of input string
- */
- protected Color hexStringToColor(String hex) {
- if (hex == null || hex.isEmpty()) {
- return null;
- }
- if ("Transparent".equalsIgnoreCase(hex)) {
- return TRANSPARENT_COLOR;
- }
- // CHECKSTYLE:OFF
- if (hex.length() != 6) {
- throw new InvalidArgumentException("Unknown color format: " + hex);
- }
- return new Color(Integer.valueOf(hex, 16));
- // CHECKSTYLE:ON
- }
-
- /**
- * Returns list of {@link Node} attributes.
- *
- * @param node
- * xml node
- * @return set of pairs containing xml node attributes
- */
- protected Set<Pair<String, String>> getAttributes(Node node) {
- Set<Pair<String, String>> result = new HashSet<>();
- NamedNodeMap map = node.getAttributes();
- for (int k = 0; k < map.getLength(); k++) {
- Node attribute = map.item(k);
- String name = attribute.getNodeName();
- String value = attribute.getNodeValue();
- result.add(new Pair<String, String>(name, value));
- }
- return result;
- }
-
-}
+package lcsb.mapviewer.wikipathway.XML;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.ConverterException;
+
+import org.apache.log4j.Logger;
+import org.w3c.dom.Element;
+import org.w3c.dom.NamedNodeMap;
+import org.w3c.dom.Node;
+
+/**
+ * Generic parser for GPML xml structures.
+ *
+ * @author Piotr Gawron
+ *
+ * @param <T>
+ * class for which this parser aplies
+ */
+public abstract class ElementGpmlParser<T> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(ElementGpmlParser.class);
+
+ /**
+ * Color that should be used when we have transparent color.
+ */
+ private static final Color TRANSPARENT_COLOR = new Color(0, 0, 0, 0);
+
+ /**
+ * Creates object from xml node given in parameter.
+ *
+ * @param node
+ * xml node from which object will be created
+ * @return object created from xml node
+ * @throws ConverterException
+ * thrown when there is severe problem with parsing xml node
+ */
+ public abstract T parse(Element node) throws ConverterException;
+
+ /**
+ * Converts object into xml string (in gpml format).
+ *
+ * @param object
+ * object to transform
+ * @return xml string representing object
+ * @throws ConverterException
+ * thrown when there is a problem with converting into xml
+ */
+ public abstract String toXml(T object) throws ConverterException;
+
+ /**
+ * Converts list of objects into xml string (in gpml format) representing this
+ * list.
+ *
+ * @param list
+ * list objects to transform
+ * @return xml string representing objects
+ * @throws ConverterException
+ * thrown when there is a problem with converting into xml
+ */
+ public abstract String toXml(Collection<T> list) throws ConverterException;
+
+ /**
+ * Creates list of object from list of xml nodes.
+ *
+ * @param nodes
+ * list of xml nodes to parse
+ * @return list of object from list of xml nodes
+ * @throws ConverterException
+ * thrown when there is severe problem with parsing xml node
+ */
+ public List<T> parseCollection(Collection<Node> nodes) throws ConverterException {
+ List<T> result = new ArrayList<>();
+ for (Node node : nodes) {
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ T element = parse((Element) node);
+ // add only not null elements (null might appear when node is partially
+ // invalid and warnings are set)
+ if (element != null) {
+ result.add(element);
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Transforms string representing color into {@link Color}.
+ *
+ * @param hex
+ * string representing color
+ * @return {@link Color} representation of input string
+ */
+ protected Color hexStringToColor(String hex) {
+ if (hex == null || hex.isEmpty()) {
+ return null;
+ }
+ if ("Transparent".equalsIgnoreCase(hex)) {
+ return TRANSPARENT_COLOR;
+ }
+ // CHECKSTYLE:OFF
+ if (hex.length() != 6) {
+ throw new InvalidArgumentException("Unknown color format: " + hex);
+ }
+ return new Color(Integer.valueOf(hex, 16));
+ // CHECKSTYLE:ON
+ }
+
+ /**
+ * Returns list of {@link Node} attributes.
+ *
+ * @param node
+ * xml node
+ * @return set of pairs containing xml node attributes
+ */
+ protected Set<Pair<String, String>> getAttributes(Node node) {
+ Set<Pair<String, String>> result = new HashSet<>();
+ NamedNodeMap map = node.getAttributes();
+ for (int k = 0; k < map.getLength(); k++) {
+ Node attribute = map.item(k);
+ String name = attribute.getNodeName();
+ String value = attribute.getNodeValue();
+ result.add(new Pair<String, String>(name, value));
+ }
+ return result;
+ }
+
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GPMLToModel.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GPMLToModel.java
index 52e273300c..90367ca264 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GPMLToModel.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GPMLToModel.java
@@ -1,51 +1,51 @@
-package lcsb.mapviewer.wikipathway.XML;
-
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-
-import lcsb.mapviewer.converter.ConverterException;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.wikipathway.model.Graph;
-
-/**
- * Class contains methods for GPMLToGraph conversion.
- *
- * @author Jan Badura
- *
- */
-public class GPMLToModel {
-
- /**
- * This function creates model from gpml input stream.
- *
- * @param stream
- * input stream that contains gpml data
- * @return {@link Model} created from gpml file
- * @throws IOException
- * thrown when there is a problem with input file
- * @throws ConverterException
- * thrown when model couldn't be created
- */
- public Model getModel(InputStream stream) throws IOException, ConverterException {
- Graph graph = new GpmlParser().createGraph(stream);
- Model model = new ModelContructor().getModel(graph);
- return model;
- }
-
- /**
- * This function creates model from gpml file.
- *
- * @param fileName
- * name of the gpml file
- * @return {@link Model} created from gpml file
- * @throws IOException
- * thrown when there is a problem with input file
- * @throws ConverterException
- * thrown when the was a problem with creating a model
- */
- public Model getModel(String fileName) throws IOException, ConverterException {
- FileInputStream fis = new FileInputStream(fileName);
- return getModel(fis);
- }
-}
+package lcsb.mapviewer.wikipathway.XML;
+
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+
+import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.wikipathway.model.Graph;
+
+/**
+ * Class contains methods for GPMLToGraph conversion.
+ *
+ * @author Jan Badura
+ *
+ */
+public class GPMLToModel {
+
+ /**
+ * This function creates model from gpml input stream.
+ *
+ * @param stream
+ * input stream that contains gpml data
+ * @return {@link Model} created from gpml file
+ * @throws IOException
+ * thrown when there is a problem with input file
+ * @throws ConverterException
+ * thrown when model couldn't be created
+ */
+ public Model getModel(InputStream stream) throws IOException, ConverterException {
+ Graph graph = new GpmlParser().createGraph(stream);
+ Model model = new ModelContructor().getModel(graph);
+ return model;
+ }
+
+ /**
+ * This function creates model from gpml file.
+ *
+ * @param fileName
+ * name of the gpml file
+ * @return {@link Model} created from gpml file
+ * @throws IOException
+ * thrown when there is a problem with input file
+ * @throws ConverterException
+ * thrown when the was a problem with creating a model
+ */
+ public Model getModel(String fileName) throws IOException, ConverterException {
+ FileInputStream fis = new FileInputStream(fileName);
+ return getModel(fis);
+ }
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GpmlParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GpmlParser.java
index 14163014d1..ba5686885f 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GpmlParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GpmlParser.java
@@ -1,657 +1,657 @@
-package lcsb.mapviewer.wikipathway.XML;
-
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
-
-import org.apache.log4j.Logger;
-import org.w3c.dom.Document;
-import org.w3c.dom.Element;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-import org.xml.sax.SAXException;
-
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.ConverterException;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.wikipathway.model.Edge;
-import lcsb.mapviewer.wikipathway.model.Graph;
-import lcsb.mapviewer.wikipathway.model.Group;
-import lcsb.mapviewer.wikipathway.model.Interaction;
-import lcsb.mapviewer.wikipathway.model.InteractionMapping;
-import lcsb.mapviewer.wikipathway.model.Label;
-import lcsb.mapviewer.wikipathway.model.MergeMapping;
-import lcsb.mapviewer.wikipathway.model.PointData;
-import lcsb.mapviewer.wikipathway.model.Shape;
-import lcsb.mapviewer.wikipathway.model.UnknownTypeException;
-
-/**
- * This class allows to parse
- * <a href="http://developers.pathvisio.org/wiki/EverythingGpml">gpml</a>.
- *
- * @author Jan Badura
- *
- */
-public class GpmlParser {
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(GpmlParser.class);
-
- /**
- * Parser used for creating {@link Shape shapes}.
- */
- private ShapeParser shapeParser = new ShapeParser();
-
- /**
- * Parser used for creating {@link lcsb.mapviewer.wikipathway.model.DataNode
- * data nodes}.
- */
- private DataNodeParser dataNodeParser = new DataNodeParser();
-
- /**
- * Parser used for creating {@link Label labels}.
- */
- private LabelParser labelParser = new LabelParser();
-
- /**
- * Parser used for creating {@link Edge edges}.
- */
- private EdgeParser edgeParser = new EdgeParser();
-
- /**
- * Parser used for creating {@link lcsb.mapviewer.wikipathway.model.State
- * states}.
- */
- private StateParser stateParser = new StateParser();
-
- /**
- * Parser used for creating {@link Edge edges} from line xml nodes.
- */
- private EdgeLineParser edgeLineParser = new EdgeLineParser();
-
- /**
- * Parser used for creating {@link PointData points} from line xml nodes.
- */
- private PointDataParser pointParser = new PointDataParser();
-
- /**
- * This function returns parent interaction for edge that has anchor at one
- * end.
- *
- * @param graph
- * model where data is stored
- * @param edge
- * edge for which interaction is looked for
- * @return {@link Interaction} that is parent reaction for given edge.
- * @throws CyclicEdgeException
- * thrown when parent interaction cannot be found because reactions
- * are cyclic
- */
- private Interaction getParentInteraction(Graph graph, Edge edge) throws CyclicEdgeException {
- // remeber what we already processed (to detect cycles)
- Set<Edge> processedEdges = new HashSet<>();
- processedEdges.add(edge);
- while (graph.getNodeByGraphId(edge.getEnd()) == null || graph.getNodeByGraphId(edge.getStart()) == null) {
- String anchor = null;
- if (graph.getEdgeByAnchor(edge.getEnd()) != null) {
- anchor = edge.getEnd();
- } else if (graph.getEdgeByAnchor(edge.getStart()) != null) {
- anchor = edge.getStart();
- } else {
- return null;
- }
-
- edge = graph.getEdgeByAnchor(anchor);
- // when we have cycle then return null
- if (processedEdges.contains(edge)) {
- throw new CyclicEdgeException(edge.getWarningPrefix() + " edge is a part of invalid, cyclic edge");
- }
- processedEdges.add(edge);
- }
- return graph.getInteractionByGraphId(edge.getGraphId());
- }
-
- /**
- * This function sets width and height in given graph.
- *
- * @param node
- * xml node where data is stored
- * @param graph
- * object where data is sotred
- */
- protected void setSize(Node node, Graph graph) {
- Element eElement = (Element) node;
- String boardWidth = eElement.getAttribute("BoardWidth");
- String boardHeight = eElement.getAttribute("BoardHeight");
- graph.setBoardWidth(Math.ceil(Double.parseDouble(boardWidth)));
- graph.setBoardHeight(Math.ceil(Double.parseDouble(boardHeight)));
- }
-
- /**
- * This function adds groups to graph and nest them.
- *
- * @param groups
- * xml nodes
- * @param graph
- * object where data is sotred
- * @throws UnknownAttributeValueException
- * thrown when there is a problem with xml attributes
- */
- protected void addGroups(List<Node> groups, Graph graph) throws UnknownAttributeValueException {
- // Adding Groups to graph
- for (Node nNode : groups) {
- if (nNode.getNodeType() == Node.ELEMENT_NODE) {
- Element eElement = (Element) nNode;
- String graphId = eElement.getAttribute("GraphId");
- String groupId = eElement.getAttribute("GroupId");
- if (graphId.equals("") || graphId == null) {
- graphId = groupId;
- }
- String style = eElement.getAttribute("Style");
- if ("".equals(style)) {
- style = null;
- }
- if (style != null && //
- !"Complex".equalsIgnoreCase(style) && //
- !"Group".equalsIgnoreCase(style)) {
- throw new UnknownAttributeValueException(
- "Unknown value of \"style\" attribute for group node: " + style + ". Only null, Complex, Group are supported.");
- }
- Group group = new Group(graphId, groupId);
- group.setStyle(style);
- graph.addGroup(group);
- }
- }
- // Handling nested groups
- Group gr1, gr2;
- for (Node nNode : groups) {
- if (nNode.getNodeType() == Node.ELEMENT_NODE) {
- Element eElement = (Element) nNode;
- String groupRef = eElement.getAttribute("GroupRef");
- String groupId = eElement.getAttribute("GroupId");
- if (groupRef != null && !groupRef.equals("")) {
- gr1 = graph.getGroupByGroupId(groupRef);
- gr2 = graph.getGroupByGroupId(groupId);
- gr1.addNode(gr2);
- }
- }
- }
- }
-
- /**
- * This function adds edges to graph. It ignores edges that have no connection
- * at one end and edges that connects to shapes or labels.
- *
- * @param nodes
- * xml nodes
- * @param graph
- * object where data is sotred
- */
- private void prepareEdges(List<Node> nodes, Graph graph) {
- for (Node nNode : nodes) {
- if (nNode.getNodeType() == Node.ELEMENT_NODE) {
- Edge edge;
- try {
- edge = edgeParser.parse((Element) nNode);
-
- if (graph.getLabelByGraphId(edge.getStart()) != null) {
- Label label = graph.getLabelByGraphId(edge.getStart());
- label.setTreatAsNode(true);
- }
- if (graph.getLabelByGraphId(edge.getEnd()) != null) {
- Label label = graph.getLabelByGraphId(edge.getEnd());
- label.setTreatAsNode(true);
- }
-
- if (graph.getShapeByGraphId(edge.getStart()) != null) {
- Shape shape = graph.getShapeByGraphId(edge.getStart());
- shape.setTreatAsNode(true);
- }
- if (graph.getShapeByGraphId(edge.getEnd()) != null) {
- Shape shape = graph.getShapeByGraphId(edge.getEnd());
- shape.setTreatAsNode(true);
- }
- if (edge.getStart() == null || edge.getEnd() == null) {
- logger.warn(edge.getWarningPrefix() + "Interaction is not connected");
-
- } else {
- graph.addEdge(edge);
- }
- } catch (ConverterException e) {
- logger.warn(e, e);
- }
- }
- }
- }
-
- /**
- * This function transforms Edges into Interactions. First: Edges with
- * NodeToNode connection are transformed into Interactions. Second: Edges with
- * AnchorToNode connection are added to right interaction. Edges with
- * AnchorToAnchor connection are ignored.
- *
- * @param graph
- * object where data is sotred
- * @throws InvalidXmlSchemaException
- * thrown when the data in input file is invalid
- */
- protected void addInteractions(Graph graph) throws InvalidXmlSchemaException {
- for (Edge edge : graph.getEdges()) {
- if (graph.getNodeByGraphId(edge.getEnd()) != null && graph.getNodeByGraphId(edge.getStart()) != null) {
- if (graph.getNodeByGraphId(edge.getEnd()) instanceof Label) {
- Label label = (Label) graph.getNodeByGraphId(edge.getEnd());
- label.setTreatAsNode(true);
- }
- if (graph.getNodeByGraphId(edge.getStart()) instanceof Label) {
- Label label = (Label) graph.getNodeByGraphId(edge.getStart());
- label.setTreatAsNode(true);
- }
- if (graph.getShapeByGraphId(edge.getEnd()) instanceof Shape) {
- Shape shape = (Shape) graph.getShapeByGraphId(edge.getEnd());
- shape.setTreatAsNode(true);
- }
- if (graph.getShapeByGraphId(edge.getStart()) instanceof Shape) {
- Shape shape = (Shape) graph.getShapeByGraphId(edge.getStart());
- shape.setTreatAsNode(true);
- }
-
- Interaction interaction = new Interaction(edge);
- graph.addInteraction(interaction);
- InteractionMapping mapping = InteractionMapping.getInteractionMapping(edge.getType(), edge.getLine().getType());
- if (mapping != null) {
- if (mapping.isInteractionWarning()) {
- logger.warn(edge.getWarningPrefix() + "Invalid interaction type.");
- }
- } else {
- throw new InvalidXmlSchemaException(
- edge.getWarningPrefix() + "Unknown interaction type: " + edge.getType() + " and line type: " + edge.getLine().getType());
- }
- }
- }
- for (Edge edge : graph.getEdges()) {
- try {
- if (graph.getEdgeByAnchor(edge.getEnd()) != null && graph.getEdgeByAnchor(edge.getStart()) != null) {
- logger.warn(edge.getWarningPrefix() + "Interaction can not connect two anchors.");
- } else if (graph.getEdgeByAnchor(edge.getEnd()) != null && graph.getNodeByGraphId(edge.getStart()) != null) {
- Interaction tmp = getParentInteraction(graph, edge);
- if (tmp != null) {
- InteractionMapping mapping = InteractionMapping.getInteractionMapping(edge.getType(), edge.getLine().getType());
- if (mapping != null) {
- if (mapping.isInputWarning()) {
- logger.warn(edge.getWarningPrefix() + "Invalid interaction type as an input to reaction.");
- }
- if (Modifier.class.isAssignableFrom(mapping.getModelInputReactionNodeType())) {
- tmp.addModifier(edge);
- } else if (Reactant.class.isAssignableFrom(mapping.getModelInputReactionNodeType())) {
- tmp.addReactant(edge);
- } else if (Product.class.isAssignableFrom(mapping.getModelInputReactionNodeType())) {
- tmp.addProduct(edge);
- } else {
- throw new InvalidStateException("Unknown internal model type: " + mapping.getModelInputReactionNodeType());
- }
- } else {
- throw new InvalidXmlSchemaException("Unknown interaction type: " + edge.getType());
- }
- } else {
- logger.warn(edge.getWarningPrefix() + "Interaction is disconnected.");
- }
- } else if (graph.getEdgeByAnchor(edge.getStart()) != null && graph.getNodeByGraphId(edge.getEnd()) != null) {
- Interaction tmp = getParentInteraction(graph, edge);
- if (tmp != null) {
- InteractionMapping mapping = InteractionMapping.getInteractionMapping(edge.getType(), edge.getLine().getType());
- if (mapping != null) {
- if (mapping.isOutputWarning()) {
- logger.warn(edge.getWarningPrefix() + "Invalid interaction type \"" + edge.getType() + "\" as an input to reaction.");
- }
- if (Modifier.class.isAssignableFrom(mapping.getModelOutputReactionNodeType())) {
- tmp.addModifier(edge);
- } else if (Reactant.class.isAssignableFrom(mapping.getModelOutputReactionNodeType())) {
- tmp.addReactant(edge);
- } else if (Product.class.isAssignableFrom(mapping.getModelOutputReactionNodeType())) {
- tmp.addProduct(edge);
- } else {
- throw new InvalidStateException("Unknown internal model type: " + mapping.getModelOutputReactionNodeType());
- }
- } else {
- throw new InvalidXmlSchemaException("Unknown interaction type: " + edge.getType());
- }
- } else {
- logger.warn(edge.getWarningPrefix() + "Interaction is disconnected.");
- }
- } else if (graph.getNodeByGraphId(edge.getEnd()) == null || graph.getNodeByGraphId(edge.getStart()) == null) {
- logger.warn(edge.getWarningPrefix() + "Interaction edge is invalid (one end is not connected).");
- }
- } catch (CyclicEdgeException e) {
- logger.warn(e, e);
- }
- }
- }
-
- /**
- * Creates gpml {@link Graph} model from gpml input stream.
- *
- * @param stream
- * input stream with gpml model
- * @return {@link Graph} model
- * @throws IOException
- * thrown when there is a problem with input file
- * @throws ConverterException
- * thrown when there is a problem with parsing input file
- */
- public Graph createGraph(InputStream stream) throws IOException, ConverterException {
- try {
- DocumentBuilder builder;
- builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
- Document document = builder.parse(stream);
-
- // Get the document's root XML node
- NodeList root = document.getElementsByTagName("Pathway");
-
- NodeList nodes = root.item(0).getChildNodes();
-
- Node dimensionNode = null;
- List<Node> dataNodes = new ArrayList<Node>();
- List<Node> interactions = new ArrayList<Node>();
- List<Node> labels = new ArrayList<Node>();
- List<Node> groups = new ArrayList<Node>();
- List<Node> shapes = new ArrayList<Node>();
- List<Node> lines = new ArrayList<Node>();
- List<Node> states = new ArrayList<Node>();
- List<Element> attributes = new ArrayList<Element>();
- Node biopax = null;
-
- Graph graph = new Graph();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("Graphics")) {
- dimensionNode = node;
- } else if (node.getNodeName().equalsIgnoreCase("DataNode")) {
- dataNodes.add(node);
- } else if (node.getNodeName().equalsIgnoreCase("Interaction")) {
- interactions.add(node);
- } else if (node.getNodeName().equalsIgnoreCase("Label")) {
- labels.add(node);
- } else if (node.getNodeName().equalsIgnoreCase("Group")) {
- groups.add(node);
- } else if (node.getNodeName().equalsIgnoreCase("Attribute")) {
- attributes.add((Element) node);
- } else if (node.getNodeName().equalsIgnoreCase("Shape")) {
- shapes.add(node);
- } else if (node.getNodeName().equalsIgnoreCase("GraphicalLine")) {
- lines.add(node);
- } else if (node.getNodeName().equalsIgnoreCase("Comment")) {
- graph.addComment(node.getTextContent());
- } else if (node.getNodeName().equalsIgnoreCase("BiopaxRef")) {
- graph.addBiopaxReferences(node.getTextContent());
- } else if (node.getNodeName().equalsIgnoreCase("State")) {
- states.add(node);
- } else if (node.getNodeName().equalsIgnoreCase("Biopax")) {
- if (biopax != null) {
- throw new ConverterException("Biopax node should appear only once");
- }
- biopax = node;
- } else if (node.getNodeName().equalsIgnoreCase("InfoBox")) {
- // infobox can be skipped
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("Legend")) {
- // legend can be skipped
- continue;
- } else {
- logger.warn("Unknown element of gpml file: " + node.getNodeName());
- }
- }
- }
- graph.addLines(parseLines(lines));
- graph.addEdges(parseEdgesFromLines(lines));
-
- if (dimensionNode != null) {
- setSize(dimensionNode, graph);
- }
- addGroups(groups, graph);
-
- graph.addDataNodes(dataNodeParser.parseCollection(dataNodes));
- graph.addLabels(labelParser.parseCollection(labels));
- graph.addShapes(shapeParser.parseCollection(shapes));
- graph.addStates(stateParser.parseCollection(states));
-
- prepareEdges(interactions, graph);
-
- mergeEdges(graph);
-
- addInteractions(graph);
- if (biopax != null) {
- graph.setBiopaxData(new BiopaxParser().parse(biopax));
- }
- Map<String, String> attributesMap = new HashMap<String, String>();
- for (Element attribute : attributes) {
- String key = attribute.getAttribute("Key");
- String value = attribute.getAttribute("Value");
- if (attributesMap.get(key) != null) {
- logger.warn("Model xml contains duplicate attributes: " + key);
- } else {
- attributesMap.put(key, value);
- }
- }
- graph.setAttributes(attributesMap);
- return graph;
- } catch (ParserConfigurationException e) {
- throw new ConverterException("Problem with input data", e);
- } catch (SAXException e) {
- throw new ConverterException("Problem with input data", e);
- } catch (InvalidXmlSchemaException e) {
- throw new ConverterException("Problem with input data", e);
- }
- }
-
- /**
- * This method merge edges that should be merged into single line.
- *
- * @param graph
- * model where edges are stored
- */
- private void mergeEdges(Graph graph) {
- List<Edge> toExtend = new ArrayList<>();
- List<Edge> toRemove = new ArrayList<>();
- List<Edge> toAdd = new ArrayList<>();
- Map<String, List<Edge>> extendable = new HashMap<>();
- for (Edge edge : graph.getEdges()) {
- if (graph.getEdgeByAnchor(edge.getStart()) == edge) {
- toExtend.add(edge);
- } else if (graph.getEdgeByAnchor(edge.getEnd()) == edge) {
- toExtend.add(edge);
- } else if (graph.getEdgeByAnchor(edge.getEnd()) != null) {
- List<Edge> list = extendable.get(edge.getEnd());
- if (list == null) {
- list = new ArrayList<>();
- extendable.put(edge.getEnd(), list);
- }
- list.add(edge);
- } else if (graph.getEdgeByAnchor(edge.getStart()) != null) {
- List<Edge> list = extendable.get(edge.getStart());
- if (list == null) {
- list = new ArrayList<>();
- extendable.put(edge.getStart(), list);
- }
- list.add(edge);
- }
-
- }
-
- for (Edge edge : toExtend) {
- String anchor = null;
- if (graph.getEdgeByAnchor(edge.getStart()) == edge) {
- anchor = edge.getStart();
- } else if (graph.getEdgeByAnchor(edge.getEnd()) == edge) {
- anchor = edge.getEnd();
- }
- List<Edge> howExtend = extendable.get(anchor);
- if (howExtend == null) {
- logger.warn(edge.getWarningPrefix() + " Should be connected with another element, but nothing found.");
- if (edge.getStart().equals(anchor)) {
- edge.setStart(null);
- } else if (edge.getEnd().equals(anchor)) {
- edge.setEnd(null);
- }
- } else if (howExtend.size() > 0) {
- try {
- Edge newEdge = mergeEdges(edge, howExtend.get(0));
- toRemove.add(edge);
- toRemove.add(howExtend.get(0));
- toAdd.add(newEdge);
- } catch (UnknownMergingMethodException exception) {
- toRemove.add(edge);
- toRemove.add(howExtend.get(0));
-
- logger.warn(exception, exception);
- }
- }
- }
- for (Edge e : toRemove) {
- graph.removeEdge(e);
- }
- for (Edge e : toAdd) {
- graph.addEdge(e);
- }
- }
-
- /**
- * Method that merge two {@link Edge edges}.
- *
- * @param edge1
- * first edge to merge
- * @param edge2
- * second edge to merge
- * @return new edge that merges two parameters
- * @throws UnknownMergingMethodException
- * thrown when edges cannot be merged
- */
- private Edge mergeEdges(Edge edge1, Edge edge2) throws UnknownMergingMethodException {
- MergeMapping mapping = null;
- if (edge1.getStart() != null && edge1.getStart().equals(edge2.getStart())) {
- mapping = MergeMapping.getMergeMappingByInteractions(edge1.getType(), true, edge2.getType(), false);
- } else if (edge1.getStart() != null && edge1.getStart().equals(edge2.getEnd())) {
- mapping = MergeMapping.getMergeMappingByInteractions(edge1.getType(), true, edge2.getType(), true);
- } else if (edge1.getEnd() != null && edge1.getEnd().equals(edge2.getStart())) {
- mapping = MergeMapping.getMergeMappingByInteractions(edge1.getType(), false, edge2.getType(), false);
- } else if (edge1.getEnd() != null && edge1.getEnd().equals(edge2.getEnd())) {
- mapping = MergeMapping.getMergeMappingByInteractions(edge1.getType(), false, edge2.getType(), true);
- }
- if (mapping == null) {
- String message = edge1.getWarningPrefix() + edge2.getWarningPrefix() + "Don't know how to merge interactions";
- throw new UnknownMergingMethodException(message);
- }
- Edge first;
- if (mapping.isReversed1()) {
- first = edge1.reverse();
- } else {
- first = new Edge(edge1);
- }
- Edge second;
- if (mapping.isReversed2()) {
- second = edge2.reverse();
- } else {
- second = new Edge(edge2);
- }
- first.extend(second);
-
- if (!first.getLine().getType().equals(second.getLine().getType())) {
- logger.warn(
- first.getWarningPrefix() + second.getWarningPrefix() + " merging edges with different line types: " + first.getLine().getType() + ", "
- + second.getLine().getType());
- }
- first.setType(mapping.getResultType());
- if (mapping.isResultReversed()) {
- return first.reverse();
- } else {
- return first;
- }
- }
-
- /**
- * Creates edges from lines when it's possible.
- *
- * @param lines
- * xml nodes with lines
- * @return list of edges that could be created from xml nodes
- */
- private Collection<Edge> parseEdgesFromLines(List<Node> lines) {
- List<Edge> result = new ArrayList<Edge>();
- for (Node lNode : lines) {
- try {
- Edge line = edgeLineParser.parse((Element) lNode);
- if (line.getStart() != null && line.getEnd() != null) {
- result.add(line);
- }
- } catch (ConverterException e) {
- logger.warn(e, e);
-
- }
- }
- return result;
- }
-
- /**
- * Creates lines from the list of gpml xml nodes.
- *
- * @param lines
- * list of xml nodes
- * @return list of {@link PolylineData lines}
- * @throws UnknownTypeException
- * thrown when the type of line defined in xml node is unknown
- */
- private Collection<PolylineData> parseLines(List<Node> lines) throws UnknownTypeException {
- List<PolylineData> result = new ArrayList<PolylineData>();
- for (Node lNode : lines) {
- int refs = 0;
- PolylineData line = new PolylineData();
- NodeList nodes = lNode.getChildNodes();
- for (int i = 0; i < nodes.getLength(); i++) {
- Node node = nodes.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("Graphics")) {
- NodeList nodes2 = node.getChildNodes();
- for (int j = 0; j < nodes2.getLength(); j++) {
- Node node2 = nodes2.item(j);
- if (node2.getNodeType() == Node.ELEMENT_NODE) {
- Element element = (Element) node2;
- if (node2.getNodeName().equalsIgnoreCase("Point")) {
- PointData point = pointParser.parse(element);
- if (point.hasGraphRef()) {
- refs++;
- }
- line.addPoint(point.toPoint());
- } else {
- logger.warn("Unknown node in line: " + node2.getNodeName());
- }
- }
- }
-
- } else {
- logger.warn("Unknown node in line: " + node.getNodeName());
- }
- }
- }
- if (refs < 2) {
- result.add(line);
- }
- }
- return result;
- }
-}
+package lcsb.mapviewer.wikipathway.XML;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.apache.log4j.Logger;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+import org.xml.sax.SAXException;
+
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.wikipathway.model.Edge;
+import lcsb.mapviewer.wikipathway.model.Graph;
+import lcsb.mapviewer.wikipathway.model.Group;
+import lcsb.mapviewer.wikipathway.model.Interaction;
+import lcsb.mapviewer.wikipathway.model.InteractionMapping;
+import lcsb.mapviewer.wikipathway.model.Label;
+import lcsb.mapviewer.wikipathway.model.MergeMapping;
+import lcsb.mapviewer.wikipathway.model.PointData;
+import lcsb.mapviewer.wikipathway.model.Shape;
+import lcsb.mapviewer.wikipathway.model.UnknownTypeException;
+
+/**
+ * This class allows to parse
+ * <a href="http://developers.pathvisio.org/wiki/EverythingGpml">gpml</a>.
+ *
+ * @author Jan Badura
+ *
+ */
+public class GpmlParser {
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(GpmlParser.class);
+
+ /**
+ * Parser used for creating {@link Shape shapes}.
+ */
+ private ShapeParser shapeParser = new ShapeParser();
+
+ /**
+ * Parser used for creating {@link lcsb.mapviewer.wikipathway.model.DataNode
+ * data nodes}.
+ */
+ private DataNodeParser dataNodeParser = new DataNodeParser();
+
+ /**
+ * Parser used for creating {@link Label labels}.
+ */
+ private LabelParser labelParser = new LabelParser();
+
+ /**
+ * Parser used for creating {@link Edge edges}.
+ */
+ private EdgeParser edgeParser = new EdgeParser();
+
+ /**
+ * Parser used for creating {@link lcsb.mapviewer.wikipathway.model.State
+ * states}.
+ */
+ private StateParser stateParser = new StateParser();
+
+ /**
+ * Parser used for creating {@link Edge edges} from line xml nodes.
+ */
+ private EdgeLineParser edgeLineParser = new EdgeLineParser();
+
+ /**
+ * Parser used for creating {@link PointData points} from line xml nodes.
+ */
+ private PointDataParser pointParser = new PointDataParser();
+
+ /**
+ * This function returns parent interaction for edge that has anchor at one
+ * end.
+ *
+ * @param graph
+ * model where data is stored
+ * @param edge
+ * edge for which interaction is looked for
+ * @return {@link Interaction} that is parent reaction for given edge.
+ * @throws CyclicEdgeException
+ * thrown when parent interaction cannot be found because reactions
+ * are cyclic
+ */
+ private Interaction getParentInteraction(Graph graph, Edge edge) throws CyclicEdgeException {
+ // remeber what we already processed (to detect cycles)
+ Set<Edge> processedEdges = new HashSet<>();
+ processedEdges.add(edge);
+ while (graph.getNodeByGraphId(edge.getEnd()) == null || graph.getNodeByGraphId(edge.getStart()) == null) {
+ String anchor = null;
+ if (graph.getEdgeByAnchor(edge.getEnd()) != null) {
+ anchor = edge.getEnd();
+ } else if (graph.getEdgeByAnchor(edge.getStart()) != null) {
+ anchor = edge.getStart();
+ } else {
+ return null;
+ }
+
+ edge = graph.getEdgeByAnchor(anchor);
+ // when we have cycle then return null
+ if (processedEdges.contains(edge)) {
+ throw new CyclicEdgeException(edge.getWarningPrefix() + " edge is a part of invalid, cyclic edge");
+ }
+ processedEdges.add(edge);
+ }
+ return graph.getInteractionByGraphId(edge.getGraphId());
+ }
+
+ /**
+ * This function sets width and height in given graph.
+ *
+ * @param node
+ * xml node where data is stored
+ * @param graph
+ * object where data is sotred
+ */
+ protected void setSize(Node node, Graph graph) {
+ Element eElement = (Element) node;
+ String boardWidth = eElement.getAttribute("BoardWidth");
+ String boardHeight = eElement.getAttribute("BoardHeight");
+ graph.setBoardWidth(Math.ceil(Double.parseDouble(boardWidth)));
+ graph.setBoardHeight(Math.ceil(Double.parseDouble(boardHeight)));
+ }
+
+ /**
+ * This function adds groups to graph and nest them.
+ *
+ * @param groups
+ * xml nodes
+ * @param graph
+ * object where data is sotred
+ * @throws UnknownAttributeValueException
+ * thrown when there is a problem with xml attributes
+ */
+ protected void addGroups(List<Node> groups, Graph graph) throws UnknownAttributeValueException {
+ // Adding Groups to graph
+ for (Node nNode : groups) {
+ if (nNode.getNodeType() == Node.ELEMENT_NODE) {
+ Element eElement = (Element) nNode;
+ String graphId = eElement.getAttribute("GraphId");
+ String groupId = eElement.getAttribute("GroupId");
+ if (graphId.equals("") || graphId == null) {
+ graphId = groupId;
+ }
+ String style = eElement.getAttribute("Style");
+ if ("".equals(style)) {
+ style = null;
+ }
+ if (style != null && //
+ !"Complex".equalsIgnoreCase(style) && //
+ !"Group".equalsIgnoreCase(style)) {
+ throw new UnknownAttributeValueException(
+ "Unknown value of \"style\" attribute for group node: " + style + ". Only null, Complex, Group are supported.");
+ }
+ Group group = new Group(graphId, groupId);
+ group.setStyle(style);
+ graph.addGroup(group);
+ }
+ }
+ // Handling nested groups
+ Group gr1, gr2;
+ for (Node nNode : groups) {
+ if (nNode.getNodeType() == Node.ELEMENT_NODE) {
+ Element eElement = (Element) nNode;
+ String groupRef = eElement.getAttribute("GroupRef");
+ String groupId = eElement.getAttribute("GroupId");
+ if (groupRef != null && !groupRef.equals("")) {
+ gr1 = graph.getGroupByGroupId(groupRef);
+ gr2 = graph.getGroupByGroupId(groupId);
+ gr1.addNode(gr2);
+ }
+ }
+ }
+ }
+
+ /**
+ * This function adds edges to graph. It ignores edges that have no connection
+ * at one end and edges that connects to shapes or labels.
+ *
+ * @param nodes
+ * xml nodes
+ * @param graph
+ * object where data is sotred
+ */
+ private void prepareEdges(List<Node> nodes, Graph graph) {
+ for (Node nNode : nodes) {
+ if (nNode.getNodeType() == Node.ELEMENT_NODE) {
+ Edge edge;
+ try {
+ edge = edgeParser.parse((Element) nNode);
+
+ if (graph.getLabelByGraphId(edge.getStart()) != null) {
+ Label label = graph.getLabelByGraphId(edge.getStart());
+ label.setTreatAsNode(true);
+ }
+ if (graph.getLabelByGraphId(edge.getEnd()) != null) {
+ Label label = graph.getLabelByGraphId(edge.getEnd());
+ label.setTreatAsNode(true);
+ }
+
+ if (graph.getShapeByGraphId(edge.getStart()) != null) {
+ Shape shape = graph.getShapeByGraphId(edge.getStart());
+ shape.setTreatAsNode(true);
+ }
+ if (graph.getShapeByGraphId(edge.getEnd()) != null) {
+ Shape shape = graph.getShapeByGraphId(edge.getEnd());
+ shape.setTreatAsNode(true);
+ }
+ if (edge.getStart() == null || edge.getEnd() == null) {
+ logger.warn(edge.getWarningPrefix() + "Interaction is not connected");
+
+ } else {
+ graph.addEdge(edge);
+ }
+ } catch (ConverterException e) {
+ logger.warn(e, e);
+ }
+ }
+ }
+ }
+
+ /**
+ * This function transforms Edges into Interactions. First: Edges with
+ * NodeToNode connection are transformed into Interactions. Second: Edges with
+ * AnchorToNode connection are added to right interaction. Edges with
+ * AnchorToAnchor connection are ignored.
+ *
+ * @param graph
+ * object where data is sotred
+ * @throws InvalidXmlSchemaException
+ * thrown when the data in input file is invalid
+ */
+ protected void addInteractions(Graph graph) throws InvalidXmlSchemaException {
+ for (Edge edge : graph.getEdges()) {
+ if (graph.getNodeByGraphId(edge.getEnd()) != null && graph.getNodeByGraphId(edge.getStart()) != null) {
+ if (graph.getNodeByGraphId(edge.getEnd()) instanceof Label) {
+ Label label = (Label) graph.getNodeByGraphId(edge.getEnd());
+ label.setTreatAsNode(true);
+ }
+ if (graph.getNodeByGraphId(edge.getStart()) instanceof Label) {
+ Label label = (Label) graph.getNodeByGraphId(edge.getStart());
+ label.setTreatAsNode(true);
+ }
+ if (graph.getShapeByGraphId(edge.getEnd()) instanceof Shape) {
+ Shape shape = (Shape) graph.getShapeByGraphId(edge.getEnd());
+ shape.setTreatAsNode(true);
+ }
+ if (graph.getShapeByGraphId(edge.getStart()) instanceof Shape) {
+ Shape shape = (Shape) graph.getShapeByGraphId(edge.getStart());
+ shape.setTreatAsNode(true);
+ }
+
+ Interaction interaction = new Interaction(edge);
+ graph.addInteraction(interaction);
+ InteractionMapping mapping = InteractionMapping.getInteractionMapping(edge.getType(), edge.getLine().getType());
+ if (mapping != null) {
+ if (mapping.isInteractionWarning()) {
+ logger.warn(edge.getWarningPrefix() + "Invalid interaction type.");
+ }
+ } else {
+ throw new InvalidXmlSchemaException(
+ edge.getWarningPrefix() + "Unknown interaction type: " + edge.getType() + " and line type: " + edge.getLine().getType());
+ }
+ }
+ }
+ for (Edge edge : graph.getEdges()) {
+ try {
+ if (graph.getEdgeByAnchor(edge.getEnd()) != null && graph.getEdgeByAnchor(edge.getStart()) != null) {
+ logger.warn(edge.getWarningPrefix() + "Interaction can not connect two anchors.");
+ } else if (graph.getEdgeByAnchor(edge.getEnd()) != null && graph.getNodeByGraphId(edge.getStart()) != null) {
+ Interaction tmp = getParentInteraction(graph, edge);
+ if (tmp != null) {
+ InteractionMapping mapping = InteractionMapping.getInteractionMapping(edge.getType(), edge.getLine().getType());
+ if (mapping != null) {
+ if (mapping.isInputWarning()) {
+ logger.warn(edge.getWarningPrefix() + "Invalid interaction type as an input to reaction.");
+ }
+ if (Modifier.class.isAssignableFrom(mapping.getModelInputReactionNodeType())) {
+ tmp.addModifier(edge);
+ } else if (Reactant.class.isAssignableFrom(mapping.getModelInputReactionNodeType())) {
+ tmp.addReactant(edge);
+ } else if (Product.class.isAssignableFrom(mapping.getModelInputReactionNodeType())) {
+ tmp.addProduct(edge);
+ } else {
+ throw new InvalidStateException("Unknown internal model type: " + mapping.getModelInputReactionNodeType());
+ }
+ } else {
+ throw new InvalidXmlSchemaException("Unknown interaction type: " + edge.getType());
+ }
+ } else {
+ logger.warn(edge.getWarningPrefix() + "Interaction is disconnected.");
+ }
+ } else if (graph.getEdgeByAnchor(edge.getStart()) != null && graph.getNodeByGraphId(edge.getEnd()) != null) {
+ Interaction tmp = getParentInteraction(graph, edge);
+ if (tmp != null) {
+ InteractionMapping mapping = InteractionMapping.getInteractionMapping(edge.getType(), edge.getLine().getType());
+ if (mapping != null) {
+ if (mapping.isOutputWarning()) {
+ logger.warn(edge.getWarningPrefix() + "Invalid interaction type \"" + edge.getType() + "\" as an input to reaction.");
+ }
+ if (Modifier.class.isAssignableFrom(mapping.getModelOutputReactionNodeType())) {
+ tmp.addModifier(edge);
+ } else if (Reactant.class.isAssignableFrom(mapping.getModelOutputReactionNodeType())) {
+ tmp.addReactant(edge);
+ } else if (Product.class.isAssignableFrom(mapping.getModelOutputReactionNodeType())) {
+ tmp.addProduct(edge);
+ } else {
+ throw new InvalidStateException("Unknown internal model type: " + mapping.getModelOutputReactionNodeType());
+ }
+ } else {
+ throw new InvalidXmlSchemaException("Unknown interaction type: " + edge.getType());
+ }
+ } else {
+ logger.warn(edge.getWarningPrefix() + "Interaction is disconnected.");
+ }
+ } else if (graph.getNodeByGraphId(edge.getEnd()) == null || graph.getNodeByGraphId(edge.getStart()) == null) {
+ logger.warn(edge.getWarningPrefix() + "Interaction edge is invalid (one end is not connected).");
+ }
+ } catch (CyclicEdgeException e) {
+ logger.warn(e, e);
+ }
+ }
+ }
+
+ /**
+ * Creates gpml {@link Graph} model from gpml input stream.
+ *
+ * @param stream
+ * input stream with gpml model
+ * @return {@link Graph} model
+ * @throws IOException
+ * thrown when there is a problem with input file
+ * @throws ConverterException
+ * thrown when there is a problem with parsing input file
+ */
+ public Graph createGraph(InputStream stream) throws IOException, ConverterException {
+ try {
+ DocumentBuilder builder;
+ builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
+ Document document = builder.parse(stream);
+
+ // Get the document's root XML node
+ NodeList root = document.getElementsByTagName("Pathway");
+
+ NodeList nodes = root.item(0).getChildNodes();
+
+ Node dimensionNode = null;
+ List<Node> dataNodes = new ArrayList<Node>();
+ List<Node> interactions = new ArrayList<Node>();
+ List<Node> labels = new ArrayList<Node>();
+ List<Node> groups = new ArrayList<Node>();
+ List<Node> shapes = new ArrayList<Node>();
+ List<Node> lines = new ArrayList<Node>();
+ List<Node> states = new ArrayList<Node>();
+ List<Element> attributes = new ArrayList<Element>();
+ Node biopax = null;
+
+ Graph graph = new Graph();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("Graphics")) {
+ dimensionNode = node;
+ } else if (node.getNodeName().equalsIgnoreCase("DataNode")) {
+ dataNodes.add(node);
+ } else if (node.getNodeName().equalsIgnoreCase("Interaction")) {
+ interactions.add(node);
+ } else if (node.getNodeName().equalsIgnoreCase("Label")) {
+ labels.add(node);
+ } else if (node.getNodeName().equalsIgnoreCase("Group")) {
+ groups.add(node);
+ } else if (node.getNodeName().equalsIgnoreCase("Attribute")) {
+ attributes.add((Element) node);
+ } else if (node.getNodeName().equalsIgnoreCase("Shape")) {
+ shapes.add(node);
+ } else if (node.getNodeName().equalsIgnoreCase("GraphicalLine")) {
+ lines.add(node);
+ } else if (node.getNodeName().equalsIgnoreCase("Comment")) {
+ graph.addComment(node.getTextContent());
+ } else if (node.getNodeName().equalsIgnoreCase("BiopaxRef")) {
+ graph.addBiopaxReferences(node.getTextContent());
+ } else if (node.getNodeName().equalsIgnoreCase("State")) {
+ states.add(node);
+ } else if (node.getNodeName().equalsIgnoreCase("Biopax")) {
+ if (biopax != null) {
+ throw new ConverterException("Biopax node should appear only once");
+ }
+ biopax = node;
+ } else if (node.getNodeName().equalsIgnoreCase("InfoBox")) {
+ // infobox can be skipped
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("Legend")) {
+ // legend can be skipped
+ continue;
+ } else {
+ logger.warn("Unknown element of gpml file: " + node.getNodeName());
+ }
+ }
+ }
+ graph.addLines(parseLines(lines));
+ graph.addEdges(parseEdgesFromLines(lines));
+
+ if (dimensionNode != null) {
+ setSize(dimensionNode, graph);
+ }
+ addGroups(groups, graph);
+
+ graph.addDataNodes(dataNodeParser.parseCollection(dataNodes));
+ graph.addLabels(labelParser.parseCollection(labels));
+ graph.addShapes(shapeParser.parseCollection(shapes));
+ graph.addStates(stateParser.parseCollection(states));
+
+ prepareEdges(interactions, graph);
+
+ mergeEdges(graph);
+
+ addInteractions(graph);
+ if (biopax != null) {
+ graph.setBiopaxData(new BiopaxParser().parse(biopax));
+ }
+ Map<String, String> attributesMap = new HashMap<String, String>();
+ for (Element attribute : attributes) {
+ String key = attribute.getAttribute("Key");
+ String value = attribute.getAttribute("Value");
+ if (attributesMap.get(key) != null) {
+ logger.warn("Model xml contains duplicate attributes: " + key);
+ } else {
+ attributesMap.put(key, value);
+ }
+ }
+ graph.setAttributes(attributesMap);
+ return graph;
+ } catch (ParserConfigurationException e) {
+ throw new ConverterException("Problem with input data", e);
+ } catch (SAXException e) {
+ throw new ConverterException("Problem with input data", e);
+ } catch (InvalidXmlSchemaException e) {
+ throw new ConverterException("Problem with input data", e);
+ }
+ }
+
+ /**
+ * This method merge edges that should be merged into single line.
+ *
+ * @param graph
+ * model where edges are stored
+ */
+ private void mergeEdges(Graph graph) {
+ List<Edge> toExtend = new ArrayList<>();
+ List<Edge> toRemove = new ArrayList<>();
+ List<Edge> toAdd = new ArrayList<>();
+ Map<String, List<Edge>> extendable = new HashMap<>();
+ for (Edge edge : graph.getEdges()) {
+ if (graph.getEdgeByAnchor(edge.getStart()) == edge) {
+ toExtend.add(edge);
+ } else if (graph.getEdgeByAnchor(edge.getEnd()) == edge) {
+ toExtend.add(edge);
+ } else if (graph.getEdgeByAnchor(edge.getEnd()) != null) {
+ List<Edge> list = extendable.get(edge.getEnd());
+ if (list == null) {
+ list = new ArrayList<>();
+ extendable.put(edge.getEnd(), list);
+ }
+ list.add(edge);
+ } else if (graph.getEdgeByAnchor(edge.getStart()) != null) {
+ List<Edge> list = extendable.get(edge.getStart());
+ if (list == null) {
+ list = new ArrayList<>();
+ extendable.put(edge.getStart(), list);
+ }
+ list.add(edge);
+ }
+
+ }
+
+ for (Edge edge : toExtend) {
+ String anchor = null;
+ if (graph.getEdgeByAnchor(edge.getStart()) == edge) {
+ anchor = edge.getStart();
+ } else if (graph.getEdgeByAnchor(edge.getEnd()) == edge) {
+ anchor = edge.getEnd();
+ }
+ List<Edge> howExtend = extendable.get(anchor);
+ if (howExtend == null) {
+ logger.warn(edge.getWarningPrefix() + " Should be connected with another element, but nothing found.");
+ if (edge.getStart().equals(anchor)) {
+ edge.setStart(null);
+ } else if (edge.getEnd().equals(anchor)) {
+ edge.setEnd(null);
+ }
+ } else if (howExtend.size() > 0) {
+ try {
+ Edge newEdge = mergeEdges(edge, howExtend.get(0));
+ toRemove.add(edge);
+ toRemove.add(howExtend.get(0));
+ toAdd.add(newEdge);
+ } catch (UnknownMergingMethodException exception) {
+ toRemove.add(edge);
+ toRemove.add(howExtend.get(0));
+
+ logger.warn(exception, exception);
+ }
+ }
+ }
+ for (Edge e : toRemove) {
+ graph.removeEdge(e);
+ }
+ for (Edge e : toAdd) {
+ graph.addEdge(e);
+ }
+ }
+
+ /**
+ * Method that merge two {@link Edge edges}.
+ *
+ * @param edge1
+ * first edge to merge
+ * @param edge2
+ * second edge to merge
+ * @return new edge that merges two parameters
+ * @throws UnknownMergingMethodException
+ * thrown when edges cannot be merged
+ */
+ private Edge mergeEdges(Edge edge1, Edge edge2) throws UnknownMergingMethodException {
+ MergeMapping mapping = null;
+ if (edge1.getStart() != null && edge1.getStart().equals(edge2.getStart())) {
+ mapping = MergeMapping.getMergeMappingByInteractions(edge1.getType(), true, edge2.getType(), false);
+ } else if (edge1.getStart() != null && edge1.getStart().equals(edge2.getEnd())) {
+ mapping = MergeMapping.getMergeMappingByInteractions(edge1.getType(), true, edge2.getType(), true);
+ } else if (edge1.getEnd() != null && edge1.getEnd().equals(edge2.getStart())) {
+ mapping = MergeMapping.getMergeMappingByInteractions(edge1.getType(), false, edge2.getType(), false);
+ } else if (edge1.getEnd() != null && edge1.getEnd().equals(edge2.getEnd())) {
+ mapping = MergeMapping.getMergeMappingByInteractions(edge1.getType(), false, edge2.getType(), true);
+ }
+ if (mapping == null) {
+ String message = edge1.getWarningPrefix() + edge2.getWarningPrefix() + "Don't know how to merge interactions";
+ throw new UnknownMergingMethodException(message);
+ }
+ Edge first;
+ if (mapping.isReversed1()) {
+ first = edge1.reverse();
+ } else {
+ first = new Edge(edge1);
+ }
+ Edge second;
+ if (mapping.isReversed2()) {
+ second = edge2.reverse();
+ } else {
+ second = new Edge(edge2);
+ }
+ first.extend(second);
+
+ if (!first.getLine().getType().equals(second.getLine().getType())) {
+ logger.warn(
+ first.getWarningPrefix() + second.getWarningPrefix() + " merging edges with different line types: " + first.getLine().getType() + ", "
+ + second.getLine().getType());
+ }
+ first.setType(mapping.getResultType());
+ if (mapping.isResultReversed()) {
+ return first.reverse();
+ } else {
+ return first;
+ }
+ }
+
+ /**
+ * Creates edges from lines when it's possible.
+ *
+ * @param lines
+ * xml nodes with lines
+ * @return list of edges that could be created from xml nodes
+ */
+ private Collection<Edge> parseEdgesFromLines(List<Node> lines) {
+ List<Edge> result = new ArrayList<Edge>();
+ for (Node lNode : lines) {
+ try {
+ Edge line = edgeLineParser.parse((Element) lNode);
+ if (line.getStart() != null && line.getEnd() != null) {
+ result.add(line);
+ }
+ } catch (ConverterException e) {
+ logger.warn(e, e);
+
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Creates lines from the list of gpml xml nodes.
+ *
+ * @param lines
+ * list of xml nodes
+ * @return list of {@link PolylineData lines}
+ * @throws UnknownTypeException
+ * thrown when the type of line defined in xml node is unknown
+ */
+ private Collection<PolylineData> parseLines(List<Node> lines) throws UnknownTypeException {
+ List<PolylineData> result = new ArrayList<PolylineData>();
+ for (Node lNode : lines) {
+ int refs = 0;
+ PolylineData line = new PolylineData();
+ NodeList nodes = lNode.getChildNodes();
+ for (int i = 0; i < nodes.getLength(); i++) {
+ Node node = nodes.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("Graphics")) {
+ NodeList nodes2 = node.getChildNodes();
+ for (int j = 0; j < nodes2.getLength(); j++) {
+ Node node2 = nodes2.item(j);
+ if (node2.getNodeType() == Node.ELEMENT_NODE) {
+ Element element = (Element) node2;
+ if (node2.getNodeName().equalsIgnoreCase("Point")) {
+ PointData point = pointParser.parse(element);
+ if (point.hasGraphRef()) {
+ refs++;
+ }
+ line.addPoint(point.toPoint());
+ } else {
+ logger.warn("Unknown node in line: " + node2.getNodeName());
+ }
+ }
+ }
+
+ } else {
+ logger.warn("Unknown node in line: " + node.getNodeName());
+ }
+ }
+ }
+ if (refs < 2) {
+ result.add(line);
+ }
+ }
+ return result;
+ }
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GraphicalPathwayElementParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GraphicalPathwayElementParser.java
index 787e11ba43..c868fdc211 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GraphicalPathwayElementParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GraphicalPathwayElementParser.java
@@ -1,77 +1,77 @@
-package lcsb.mapviewer.wikipathway.XML;
-
-import java.awt.font.TextAttribute;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.geometry.TextAlignment;
-import lcsb.mapviewer.wikipathway.model.GpmlLineType;
-import lcsb.mapviewer.wikipathway.model.GraphicalPathwayElement;
-import lcsb.mapviewer.wikipathway.model.UnknownTypeException;
-
-/**
- * Parser used for extracting common data (from gpml file) for all elements
- * extending {@link GraphicalPathwayElement} class.
- *
- * @author Piotr Gawron
- *
- * @param <T>
- */
-public abstract class GraphicalPathwayElementParser<T extends GraphicalPathwayElement> extends ElementGpmlParser<T> {
-
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(GraphicalPathwayElementParser.class);
-
- /**
- * Parse font attributes that might appear.
- *
- * @param element
- * element where data should be put
- * @param attribute
- * attribute to parse
- * @return true if element was parsed properly
- * @throws UnknownTypeException
- * thrown when some elements contains unknown values
- */
- protected boolean parseCommonGraphicAttributes(GraphicalPathwayElement element, Pair<String, String> attribute) throws UnknownTypeException {
- switch (attribute.getLeft()) {
- case ("LineThickness"):
- try {
- Double value = Double.valueOf(attribute.getRight());
- element.setLineThickness(value);
- } catch (NumberFormatException e) {
- logger.warn("Invalid LineThickness: " + attribute.getRight());
- }
- break;
- case ("LineStyle"):
- element.setLineType(GpmlLineType.getByGpmlName(attribute.getRight()).getCorrespondingGlobalLineType());
- break;
- case ("FontStyle"):
- element.addFontAttribute(TextAttribute.POSTURE, TextAttribute.POSTURE_OBLIQUE);
- break;
- case ("FontName"):
- element.setFontName(attribute.getRight());
- break;
- case ("Align"):
- switch (attribute.getRight()) {
- case ("Right"):
- element.setTextAlignment(TextAlignment.RIGHT);
- break;
- case ("Left"):
- element.setTextAlignment(TextAlignment.LEFT);
- break;
- default:
- logger.warn("Unknown value of attribute: " + attribute.getLeft() + " - " + attribute.getRight());
- break;
- }
- break;
- default:
- return false;
- }
- return true;
- }
-
-}
+package lcsb.mapviewer.wikipathway.XML;
+
+import java.awt.font.TextAttribute;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.geometry.TextAlignment;
+import lcsb.mapviewer.wikipathway.model.GpmlLineType;
+import lcsb.mapviewer.wikipathway.model.GraphicalPathwayElement;
+import lcsb.mapviewer.wikipathway.model.UnknownTypeException;
+
+/**
+ * Parser used for extracting common data (from gpml file) for all elements
+ * extending {@link GraphicalPathwayElement} class.
+ *
+ * @author Piotr Gawron
+ *
+ * @param <T>
+ */
+public abstract class GraphicalPathwayElementParser<T extends GraphicalPathwayElement> extends ElementGpmlParser<T> {
+
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(GraphicalPathwayElementParser.class);
+
+ /**
+ * Parse font attributes that might appear.
+ *
+ * @param element
+ * element where data should be put
+ * @param attribute
+ * attribute to parse
+ * @return true if element was parsed properly
+ * @throws UnknownTypeException
+ * thrown when some elements contains unknown values
+ */
+ protected boolean parseCommonGraphicAttributes(GraphicalPathwayElement element, Pair<String, String> attribute) throws UnknownTypeException {
+ switch (attribute.getLeft()) {
+ case ("LineThickness"):
+ try {
+ Double value = Double.valueOf(attribute.getRight());
+ element.setLineThickness(value);
+ } catch (NumberFormatException e) {
+ logger.warn("Invalid LineThickness: " + attribute.getRight());
+ }
+ break;
+ case ("LineStyle"):
+ element.setLineType(GpmlLineType.getByGpmlName(attribute.getRight()).getCorrespondingGlobalLineType());
+ break;
+ case ("FontStyle"):
+ element.addFontAttribute(TextAttribute.POSTURE, TextAttribute.POSTURE_OBLIQUE);
+ break;
+ case ("FontName"):
+ element.setFontName(attribute.getRight());
+ break;
+ case ("Align"):
+ switch (attribute.getRight()) {
+ case ("Right"):
+ element.setTextAlignment(TextAlignment.RIGHT);
+ break;
+ case ("Left"):
+ element.setTextAlignment(TextAlignment.LEFT);
+ break;
+ default:
+ logger.warn("Unknown value of attribute: " + attribute.getLeft() + " - " + attribute.getRight());
+ break;
+ }
+ break;
+ default:
+ return false;
+ }
+ return true;
+ }
+
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/InvalidElbowConnectorException.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/InvalidElbowConnectorException.java
index a0bd27f12a..ed81e3e0ae 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/InvalidElbowConnectorException.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/InvalidElbowConnectorException.java
@@ -1,30 +1,30 @@
-package lcsb.mapviewer.wikipathway.XML;
-
-import lcsb.mapviewer.converter.ConverterException;
-
-/**
- * Exception that shold be thrown when lines described as
- * {@link lcsb.mapviewer.wikipathway.model.GpmlLineConnectorType#ELBOW} cannot
- * be transformed into standard x,y coordinates.
- *
- * @author Piotr Gawron
- *
- */
-public class InvalidElbowConnectorException extends ConverterException {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor with message passed in the argument.
- *
- * @param string
- * message of this exception
- */
- public InvalidElbowConnectorException(String string) {
- super(string);
- }
-
-}
+package lcsb.mapviewer.wikipathway.XML;
+
+import lcsb.mapviewer.converter.ConverterException;
+
+/**
+ * Exception that shold be thrown when lines described as
+ * {@link lcsb.mapviewer.wikipathway.model.GpmlLineConnectorType#ELBOW} cannot
+ * be transformed into standard x,y coordinates.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class InvalidElbowConnectorException extends ConverterException {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor with message passed in the argument.
+ *
+ * @param string
+ * message of this exception
+ */
+ public InvalidElbowConnectorException(String string) {
+ super(string);
+ }
+
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/LabelParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/LabelParser.java
index 18cd33d369..c7f3043a93 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/LabelParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/LabelParser.java
@@ -1,178 +1,178 @@
-package lcsb.mapviewer.wikipathway.XML;
-
-import java.awt.geom.Rectangle2D;
-import java.util.Collection;
-
-import org.apache.log4j.Logger;
-import org.w3c.dom.Element;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.ConverterException;
-import lcsb.mapviewer.wikipathway.model.Label;
-import lcsb.mapviewer.wikipathway.model.UnknownTypeException;
-
-/**
- * Parser class that creates {@link Label} objects from Xml {@link Element node}
- * .
- *
- * @author Piotr Gawron
- *
- */
-public class LabelParser extends GraphicalPathwayElementParser<Label> {
-
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(LabelParser.class);
-
- @Override
- public Label parse(Element eElement) throws UnknownTypeException {
- if (!eElement.getNodeName().equals("Label")) {
- throw new InvalidArgumentException(ShapeParser.class.getSimpleName() + " can parse only Label xml nodes");
- }
- Label label = new Label(eElement.getAttribute("GraphId"));
-
- for (Pair<String, String> entry : getAttributes(eElement)) {
- switch (entry.getLeft()) {
- case ("GraphId"):
- break;
- case ("TextLabel"):
- label.setTextLabel(entry.getRight());
- break;
- case ("GroupRef"):
- label.setGroupRef(entry.getRight());
- break;
- default:
- logger.warn("Unknown attribute of " + eElement.getNodeName() + " node: " + entry.getLeft());
- break;
- }
- }
-
- NodeList tmpList = eElement.getChildNodes();
- for (int j = 0; j < tmpList.getLength(); j++) {
- Node tmpNode = tmpList.item(j);
- if (tmpNode.getNodeType() == Node.ELEMENT_NODE) {
- Element eTmp = (Element) tmpNode;
- switch (eTmp.getNodeName()) {
- case ("Comment"):
- label.addComment(eTmp.getTextContent());
- break;
- case ("BiopaxRef"):
- label.addBiopaxReference(eTmp.getTextContent());
- break;
- case ("Graphics"):
- parseGraphics(eTmp, label);
- break;
- case ("Attribute"):
- parseAttribute(eTmp, label);
- break;
- default:
- logger.warn("Unknown sub-node of " + eElement.getNodeName() + " node: " + eTmp.getNodeName());
- break;
- }
- }
- }
-
- return label;
- }
-
- /**
- * Parse graphics xml node in the shape node.
- *
- * @param eTmp
- * xml node with graphics
- * @param shape
- * shape where data should be added
- * @throws UnknownTypeException
- * thrown when some elements contain unknown typevalues
- */
- protected void parseGraphics(Element eTmp, Label shape) throws UnknownTypeException {
- Double centerX = null;
- Double centerY = null;
- Double width = null;
- Double height = null;
- for (Pair<String, String> entry : getAttributes(eTmp)) {
- if (!parseCommonGraphicAttributes(shape, entry)) {
- switch (entry.getLeft()) {
- case ("CenterX"):
- centerX = Double.valueOf(entry.getRight());
- break;
- case ("CenterY"):
- centerY = Double.valueOf(entry.getRight());
- break;
- case ("Width"):
- width = Double.valueOf(entry.getRight());
- break;
- case ("Height"):
- height = Double.valueOf(entry.getRight());
- break;
- case ("Color"):
- shape.setColor(hexStringToColor(entry.getRight()));
- break;
- case ("FillColor"):
- shape.setFillColor(hexStringToColor(entry.getRight()));
- break;
- case ("ZOrder"):
- shape.setzOrder(Integer.valueOf(entry.getRight()));
- break;
- case ("FontSize"):
- shape.setFontSize(Double.valueOf(entry.getRight()));
- break;
- case ("FontWeight"):
- shape.setFontWeight(entry.getRight());
- break;
- case ("Valign"):
- shape.setvAlign(entry.getRight());
- break;
- case ("ShapeType"):
- shape.setShape(entry.getRight());
- break;
- default:
- logger.warn("Unknown attribute of " + eTmp.getNodeName() + " node: " + entry.getLeft() + "; value: " + entry.getRight());
- break;
- }
- }
- }
- shape.setRectangle(new Rectangle2D.Double(centerX - width / 2, centerY - height / 2, width, height));
- }
-
- /**
- * Method that parses {@link Label} xml attribute.
- *
- * @param eTmp
- * xml node with attribute
- * @param shape
- * shape where data should be added
- */
- private void parseAttribute(Element eTmp, Label shape) {
- String key = eTmp.getAttribute("Key");
- String value = eTmp.getAttribute("Value");
- switch (key) {
- case ("org.pathvisio.model.GenMAPP-Xref"):
- // skip it when it's empty
- if (!value.isEmpty()) {
- logger.warn(shape.getWarningPrefix() + "Unknown attribute of node. Key: " + key + "; value: " + value);
- break;
- }
- break;
- default:
- logger.warn(shape.getWarningPrefix() + "Unknown attribute of node. Key:" + key + "; value: " + value);
- break;
- }
- }
-
- @Override
- public String toXml(Label node) throws ConverterException {
- throw new NotImplementedException();
- }
-
- @Override
- public String toXml(Collection<Label> list) throws ConverterException {
- throw new NotImplementedException();
- }
-
-}
+package lcsb.mapviewer.wikipathway.XML;
+
+import java.awt.geom.Rectangle2D;
+import java.util.Collection;
+
+import org.apache.log4j.Logger;
+import org.w3c.dom.Element;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.wikipathway.model.Label;
+import lcsb.mapviewer.wikipathway.model.UnknownTypeException;
+
+/**
+ * Parser class that creates {@link Label} objects from Xml {@link Element node}
+ * .
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class LabelParser extends GraphicalPathwayElementParser<Label> {
+
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(LabelParser.class);
+
+ @Override
+ public Label parse(Element eElement) throws UnknownTypeException {
+ if (!eElement.getNodeName().equals("Label")) {
+ throw new InvalidArgumentException(ShapeParser.class.getSimpleName() + " can parse only Label xml nodes");
+ }
+ Label label = new Label(eElement.getAttribute("GraphId"));
+
+ for (Pair<String, String> entry : getAttributes(eElement)) {
+ switch (entry.getLeft()) {
+ case ("GraphId"):
+ break;
+ case ("TextLabel"):
+ label.setTextLabel(entry.getRight());
+ break;
+ case ("GroupRef"):
+ label.setGroupRef(entry.getRight());
+ break;
+ default:
+ logger.warn("Unknown attribute of " + eElement.getNodeName() + " node: " + entry.getLeft());
+ break;
+ }
+ }
+
+ NodeList tmpList = eElement.getChildNodes();
+ for (int j = 0; j < tmpList.getLength(); j++) {
+ Node tmpNode = tmpList.item(j);
+ if (tmpNode.getNodeType() == Node.ELEMENT_NODE) {
+ Element eTmp = (Element) tmpNode;
+ switch (eTmp.getNodeName()) {
+ case ("Comment"):
+ label.addComment(eTmp.getTextContent());
+ break;
+ case ("BiopaxRef"):
+ label.addBiopaxReference(eTmp.getTextContent());
+ break;
+ case ("Graphics"):
+ parseGraphics(eTmp, label);
+ break;
+ case ("Attribute"):
+ parseAttribute(eTmp, label);
+ break;
+ default:
+ logger.warn("Unknown sub-node of " + eElement.getNodeName() + " node: " + eTmp.getNodeName());
+ break;
+ }
+ }
+ }
+
+ return label;
+ }
+
+ /**
+ * Parse graphics xml node in the shape node.
+ *
+ * @param eTmp
+ * xml node with graphics
+ * @param shape
+ * shape where data should be added
+ * @throws UnknownTypeException
+ * thrown when some elements contain unknown typevalues
+ */
+ protected void parseGraphics(Element eTmp, Label shape) throws UnknownTypeException {
+ Double centerX = null;
+ Double centerY = null;
+ Double width = null;
+ Double height = null;
+ for (Pair<String, String> entry : getAttributes(eTmp)) {
+ if (!parseCommonGraphicAttributes(shape, entry)) {
+ switch (entry.getLeft()) {
+ case ("CenterX"):
+ centerX = Double.valueOf(entry.getRight());
+ break;
+ case ("CenterY"):
+ centerY = Double.valueOf(entry.getRight());
+ break;
+ case ("Width"):
+ width = Double.valueOf(entry.getRight());
+ break;
+ case ("Height"):
+ height = Double.valueOf(entry.getRight());
+ break;
+ case ("Color"):
+ shape.setColor(hexStringToColor(entry.getRight()));
+ break;
+ case ("FillColor"):
+ shape.setFillColor(hexStringToColor(entry.getRight()));
+ break;
+ case ("ZOrder"):
+ shape.setzOrder(Integer.valueOf(entry.getRight()));
+ break;
+ case ("FontSize"):
+ shape.setFontSize(Double.valueOf(entry.getRight()));
+ break;
+ case ("FontWeight"):
+ shape.setFontWeight(entry.getRight());
+ break;
+ case ("Valign"):
+ shape.setvAlign(entry.getRight());
+ break;
+ case ("ShapeType"):
+ shape.setShape(entry.getRight());
+ break;
+ default:
+ logger.warn("Unknown attribute of " + eTmp.getNodeName() + " node: " + entry.getLeft() + "; value: " + entry.getRight());
+ break;
+ }
+ }
+ }
+ shape.setRectangle(new Rectangle2D.Double(centerX - width / 2, centerY - height / 2, width, height));
+ }
+
+ /**
+ * Method that parses {@link Label} xml attribute.
+ *
+ * @param eTmp
+ * xml node with attribute
+ * @param shape
+ * shape where data should be added
+ */
+ private void parseAttribute(Element eTmp, Label shape) {
+ String key = eTmp.getAttribute("Key");
+ String value = eTmp.getAttribute("Value");
+ switch (key) {
+ case ("org.pathvisio.model.GenMAPP-Xref"):
+ // skip it when it's empty
+ if (!value.isEmpty()) {
+ logger.warn(shape.getWarningPrefix() + "Unknown attribute of node. Key: " + key + "; value: " + value);
+ break;
+ }
+ break;
+ default:
+ logger.warn(shape.getWarningPrefix() + "Unknown attribute of node. Key:" + key + "; value: " + value);
+ break;
+ }
+ }
+
+ @Override
+ public String toXml(Label node) throws ConverterException {
+ throw new NotImplementedException();
+ }
+
+ @Override
+ public String toXml(Collection<Label> list) throws ConverterException {
+ throw new NotImplementedException();
+ }
+
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/PointDataParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/PointDataParser.java
index 044c52f28b..3538d76c4b 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/PointDataParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/PointDataParser.java
@@ -1,68 +1,68 @@
-package lcsb.mapviewer.wikipathway.XML;
-
-import java.util.Collection;
-
-import org.apache.log4j.Logger;
-import org.w3c.dom.Element;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.ConverterException;
-import lcsb.mapviewer.wikipathway.model.GpmlInteractionType;
-import lcsb.mapviewer.wikipathway.model.PointData;
-import lcsb.mapviewer.wikipathway.model.UnknownTypeException;
-
-/**
- * Parser class that creates {@link PointData} objects from Xml {@link Element
- * node}.
- *
- * @author Piotr Gawron
- *
- */
-public class PointDataParser extends ElementGpmlParser<PointData> {
-
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(PointDataParser.class);
-
- @Override
- public PointData parse(Element element) throws UnknownTypeException {
- PointData result = new PointData();
- for (Pair<String, String> entry : getAttributes(element)) {
- switch (entry.getLeft()) {
- case ("X"):
- result.setX(Double.valueOf(entry.getRight()));
- break;
- case ("Y"):
- result.setY(Double.valueOf(entry.getRight()));
- break;
- case ("GraphRef"):
- result.setGraphRef(entry.getRight());
- break;
- case ("ArrowHead"):
- result.setType(GpmlInteractionType.getTypeByGpmlString(entry.getRight()));
- break;
- case ("RelX"):
- result.setRelX(entry.getRight());
- break;
- case ("RelY"):
- result.setRelY(entry.getRight());
- break;
- default:
- logger.warn("Unknown point attribute: " + entry.getLeft());
- }
- }
- return result;
- }
-
- @Override
- public String toXml(PointData node) throws ConverterException {
- throw new NotImplementedException();
- }
-
- @Override
- public String toXml(Collection<PointData> list) throws ConverterException {
- throw new NotImplementedException();
- }
-}
+package lcsb.mapviewer.wikipathway.XML;
+
+import java.util.Collection;
+
+import org.apache.log4j.Logger;
+import org.w3c.dom.Element;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.wikipathway.model.GpmlInteractionType;
+import lcsb.mapviewer.wikipathway.model.PointData;
+import lcsb.mapviewer.wikipathway.model.UnknownTypeException;
+
+/**
+ * Parser class that creates {@link PointData} objects from Xml {@link Element
+ * node}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class PointDataParser extends ElementGpmlParser<PointData> {
+
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(PointDataParser.class);
+
+ @Override
+ public PointData parse(Element element) throws UnknownTypeException {
+ PointData result = new PointData();
+ for (Pair<String, String> entry : getAttributes(element)) {
+ switch (entry.getLeft()) {
+ case ("X"):
+ result.setX(Double.valueOf(entry.getRight()));
+ break;
+ case ("Y"):
+ result.setY(Double.valueOf(entry.getRight()));
+ break;
+ case ("GraphRef"):
+ result.setGraphRef(entry.getRight());
+ break;
+ case ("ArrowHead"):
+ result.setType(GpmlInteractionType.getTypeByGpmlString(entry.getRight()));
+ break;
+ case ("RelX"):
+ result.setRelX(entry.getRight());
+ break;
+ case ("RelY"):
+ result.setRelY(entry.getRight());
+ break;
+ default:
+ logger.warn("Unknown point attribute: " + entry.getLeft());
+ }
+ }
+ return result;
+ }
+
+ @Override
+ public String toXml(PointData node) throws ConverterException {
+ throw new NotImplementedException();
+ }
+
+ @Override
+ public String toXml(Collection<PointData> list) throws ConverterException {
+ throw new NotImplementedException();
+ }
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ReferenceParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ReferenceParser.java
index e195bd18c5..74ec378fdd 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ReferenceParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ReferenceParser.java
@@ -1,162 +1,162 @@
-package lcsb.mapviewer.wikipathway.XML;
-
-import java.util.Collection;
-
-import org.apache.log4j.Logger;
-import org.w3c.dom.Element;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import lcsb.mapviewer.common.EventStorageLoggerAppender;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.ConverterException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.wikipathway.model.ReferenceMapping;
-
-/**
- * Parser used to extract {@link MiriamData refernces} in miriam format from
- * GPML data.
- *
- * @author Piotr Gawron
- *
- */
-public class ReferenceParser extends ElementGpmlParser<MiriamData> {
-
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(ReferenceParser.class);
-
- /**
- * This function creates MiriamData from database name and id.
- *
- * @param id
- * - resource identifier
- * @param db
- * -database type
- * @return {@link MiriamData} object referenceing to the resource
- */
- protected MiriamData createMiriamData(String id, String db) {
- if (db == null || db.equals("")) {
- throw new InvalidArgumentException("Invalid db type: " + db);
- } else if (id == null || id.trim().equals("")) {
- throw new InvalidArgumentException("Invalid db resource value: " + id);
- }
- ReferenceMapping mapping = ReferenceMapping.getMappingByGpmlString(db);
- MiriamType type = null;
- if (mapping != null) {
- type = mapping.getType();
- } else {
- for (MiriamType t : MiriamType.values()) {
- if (t.getCommonName().equalsIgnoreCase(db)) {
- type = t;
- } else {
- for (String uri : t.getUris()) {
- if (uri.endsWith(db)) {
- type = t;
- }
- }
- }
- }
- }
- if (type != null) {
- return new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, type, id);
- } else {
- throw new NotImplementedException("This database type is not implemented yet: " + db + "; resource: " + id);
- }
- }
-
- @Override
- public MiriamData parse(Element node) {
- String id = null;
- String db = null;
- for (Pair<String, String> entry : getAttributes(node)) {
- switch (entry.getLeft()) {
- case ("ID"):
- id = entry.getRight();
- break;
- case ("Database"):
- db = entry.getRight();
- break;
- default:
- logger.warn("Unknown attribute of " + node.getNodeName() + " node: " + entry.getLeft());
- break;
- }
- }
-
- NodeList tmpList = node.getChildNodes();
- for (int j = 0; j < tmpList.getLength(); j++) {
- Node tmpNode = tmpList.item(j);
- if (tmpNode.getNodeType() == Node.ELEMENT_NODE) {
- Element eTmp = (Element) tmpNode;
- switch (eTmp.getNodeName()) {
- default:
- logger.warn("Unknown sub-node of " + node.getNodeName() + " node: " + eTmp.getNodeName());
- break;
- }
- }
- }
-
- if (id != null && !id.isEmpty()) {
- if (db == null || db.isEmpty()) {
- logger.warn("Reference is invalid. Database identifier exists (" + id + "), but no database type is set.");
- } else {
- MiriamData md = createMiriamData(id, db);
- return md;
- }
- }
- return null;
- }
-
- @Override
- public String toXml(MiriamData md) throws ConverterException {
- if (md == null) {
- return "<Xref ID=\"\" Database=\"\"/>\n";
- } else if (MiriamType.PUBMED.equals(md.getDataType())) {
- throw new InvalidArgumentException("Pubmed cannot be exported to XRef node.");
- } else {
- ReferenceMapping mapping = ReferenceMapping.getMappingByMiriamType(md.getDataType());
- if (mapping == null) {
- throw new InvalidArgumentException("Don't know how to export " + md.getDataType() + " annotation.");
- } else if (mapping.getGpmlString() == null) {
- logger.warn(md.getDataType().getCommonName() + " annotation is not supported by GPML");
- return "";
- } else {
- return "<Xref ID=\"" + md.getResource() + "\" Database=\"" + mapping.getGpmlString() + "\"/>\n";
- }
- }
- }
-
- @Override
- public String toXml(Collection<MiriamData> miriamData) throws ConverterException {
- StringBuilder result = new StringBuilder("");
- int counter = 0;
- for (MiriamData md : miriamData) {
- if (!md.getDataType().equals(MiriamType.PUBMED)) {
- counter++;
- if (counter == 1) {
- EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
- try {
- Logger.getRootLogger().addAppender(appender);
- result.append(toXml(md));
- if (appender.getWarnings().size() > 0) {
- counter--;
- }
- } finally {
- Logger.getRootLogger().removeAppender(appender);
- }
- } else {
- logger.warn("Annotation ommited - gpml support only one annotation per element: " + md.getDataType() + ": " + md.getResource());
- }
- }
- }
- if (counter == 0) {
- return toXml((MiriamData) null);
- }
- return result.toString();
- }
-}
+package lcsb.mapviewer.wikipathway.XML;
+
+import java.util.Collection;
+
+import org.apache.log4j.Logger;
+import org.w3c.dom.Element;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import lcsb.mapviewer.common.EventStorageLoggerAppender;
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.wikipathway.model.ReferenceMapping;
+
+/**
+ * Parser used to extract {@link MiriamData refernces} in miriam format from
+ * GPML data.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ReferenceParser extends ElementGpmlParser<MiriamData> {
+
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(ReferenceParser.class);
+
+ /**
+ * This function creates MiriamData from database name and id.
+ *
+ * @param id
+ * - resource identifier
+ * @param db
+ * -database type
+ * @return {@link MiriamData} object referenceing to the resource
+ */
+ protected MiriamData createMiriamData(String id, String db) {
+ if (db == null || db.equals("")) {
+ throw new InvalidArgumentException("Invalid db type: " + db);
+ } else if (id == null || id.trim().equals("")) {
+ throw new InvalidArgumentException("Invalid db resource value: " + id);
+ }
+ ReferenceMapping mapping = ReferenceMapping.getMappingByGpmlString(db);
+ MiriamType type = null;
+ if (mapping != null) {
+ type = mapping.getType();
+ } else {
+ for (MiriamType t : MiriamType.values()) {
+ if (t.getCommonName().equalsIgnoreCase(db)) {
+ type = t;
+ } else {
+ for (String uri : t.getUris()) {
+ if (uri.endsWith(db)) {
+ type = t;
+ }
+ }
+ }
+ }
+ }
+ if (type != null) {
+ return new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, type, id);
+ } else {
+ throw new NotImplementedException("This database type is not implemented yet: " + db + "; resource: " + id);
+ }
+ }
+
+ @Override
+ public MiriamData parse(Element node) {
+ String id = null;
+ String db = null;
+ for (Pair<String, String> entry : getAttributes(node)) {
+ switch (entry.getLeft()) {
+ case ("ID"):
+ id = entry.getRight();
+ break;
+ case ("Database"):
+ db = entry.getRight();
+ break;
+ default:
+ logger.warn("Unknown attribute of " + node.getNodeName() + " node: " + entry.getLeft());
+ break;
+ }
+ }
+
+ NodeList tmpList = node.getChildNodes();
+ for (int j = 0; j < tmpList.getLength(); j++) {
+ Node tmpNode = tmpList.item(j);
+ if (tmpNode.getNodeType() == Node.ELEMENT_NODE) {
+ Element eTmp = (Element) tmpNode;
+ switch (eTmp.getNodeName()) {
+ default:
+ logger.warn("Unknown sub-node of " + node.getNodeName() + " node: " + eTmp.getNodeName());
+ break;
+ }
+ }
+ }
+
+ if (id != null && !id.isEmpty()) {
+ if (db == null || db.isEmpty()) {
+ logger.warn("Reference is invalid. Database identifier exists (" + id + "), but no database type is set.");
+ } else {
+ MiriamData md = createMiriamData(id, db);
+ return md;
+ }
+ }
+ return null;
+ }
+
+ @Override
+ public String toXml(MiriamData md) throws ConverterException {
+ if (md == null) {
+ return "<Xref ID=\"\" Database=\"\"/>\n";
+ } else if (MiriamType.PUBMED.equals(md.getDataType())) {
+ throw new InvalidArgumentException("Pubmed cannot be exported to XRef node.");
+ } else {
+ ReferenceMapping mapping = ReferenceMapping.getMappingByMiriamType(md.getDataType());
+ if (mapping == null) {
+ throw new InvalidArgumentException("Don't know how to export " + md.getDataType() + " annotation.");
+ } else if (mapping.getGpmlString() == null) {
+ logger.warn(md.getDataType().getCommonName() + " annotation is not supported by GPML");
+ return "";
+ } else {
+ return "<Xref ID=\"" + md.getResource() + "\" Database=\"" + mapping.getGpmlString() + "\"/>\n";
+ }
+ }
+ }
+
+ @Override
+ public String toXml(Collection<MiriamData> miriamData) throws ConverterException {
+ StringBuilder result = new StringBuilder("");
+ int counter = 0;
+ for (MiriamData md : miriamData) {
+ if (!md.getDataType().equals(MiriamType.PUBMED)) {
+ counter++;
+ if (counter == 1) {
+ EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
+ try {
+ Logger.getRootLogger().addAppender(appender);
+ result.append(toXml(md));
+ if (appender.getWarnings().size() > 0) {
+ counter--;
+ }
+ } finally {
+ Logger.getRootLogger().removeAppender(appender);
+ }
+ } else {
+ logger.warn("Annotation ommited - gpml support only one annotation per element: " + md.getDataType() + ": " + md.getResource());
+ }
+ }
+ }
+ if (counter == 0) {
+ return toXml((MiriamData) null);
+ }
+ return result.toString();
+ }
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ShapeParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ShapeParser.java
index 7e72c869f7..20602560e8 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ShapeParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ShapeParser.java
@@ -1,196 +1,196 @@
-package lcsb.mapviewer.wikipathway.XML;
-
-import java.awt.font.TextAttribute;
-import java.awt.geom.Rectangle2D;
-import java.util.Collection;
-
-import org.apache.log4j.Logger;
-import org.w3c.dom.Element;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.ConverterException;
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.wikipathway.model.Shape;
-import lcsb.mapviewer.wikipathway.model.UnknownTypeException;
-
-/**
- * Parser class that creates {@link Shape} objects from Xml {@link Element node}
- * .
- *
- * @author Piotr Gawron
- *
- */
-public class ShapeParser extends GraphicalPathwayElementParser<Shape> {
-
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(ShapeParser.class);
-
- @Override
- public Shape parse(Element eElement) throws ConverterException {
- if (!eElement.getNodeName().equals("Shape")) {
- throw new InvalidArgumentException(ShapeParser.class.getSimpleName() + " can parse only Shape xml nodes");
- }
- Shape shape = new Shape(eElement.getAttribute("GraphId"));
- for (Pair<String, String> entry : getAttributes(eElement)) {
- switch (entry.getLeft()) {
- case ("GraphId"):
- break;
- case ("TextLabel"):
- shape.setTextLabel(entry.getRight());
- break;
- case ("GroupRef"):
- shape.setGroupRef(entry.getRight());
- break;
- default:
- logger.warn("Unknown attribute of " + eElement.getNodeName() + " node: " + entry.getLeft());
- break;
- }
- }
-
- NodeList tmpList = eElement.getChildNodes();
- for (int j = 0; j < tmpList.getLength(); j++) {
- Node tmpNode = tmpList.item(j);
- if (tmpNode.getNodeType() == Node.ELEMENT_NODE) {
- Element eTmp = (Element) tmpNode;
- switch (eTmp.getNodeName()) {
- case ("Graphics"):
- parseGraphics(eTmp, shape);
- break;
- case ("Attribute"):
- parseAttribute(eTmp, shape);
- break;
- case ("Comment"):
- shape.addComment(eTmp.getTextContent());
- break;
- case ("BiopaxRef"):
- shape.addBiopaxReference(eTmp.getTextContent());
- break;
- default:
- logger.warn("Unknown sub-node of " + eElement.getNodeName() + " node: " + eTmp.getNodeName());
- break;
- }
- }
- }
- return shape;
- }
-
- /**
- * Method that parses {@link Shape} xml attribute.
- *
- * @param eTmp
- * xml node with attribute
- * @param shape
- * shape where data should be added
- */
- private void parseAttribute(Element eTmp, Shape shape) {
- String key = eTmp.getAttribute("Key");
- String value = eTmp.getAttribute("Value");
- switch (key) {
- case ("org.pathvisio.CellularComponentProperty"):
- shape.setCompartment(true);
- break;
- case ("org.pathvisio.DoubleLineProperty"):
- switch (value) {
- case ("Double"):
- shape.setLineType(LineType.DOUBLE);
- break;
- default:
- logger.warn(shape.getWarningPrefix() + "Unknown line type: " + value);
- break;
- }
- break;
- default:
- logger.warn(shape.getWarningPrefix() + "Unknown attribute of node. Key:" + key + "; value: " + value);
- break;
- }
- }
-
- /**
- * Parse graphics xml node in the shape node.
- *
- * @param eTmp
- * xml node with graphics
- * @param shape
- * shape where data should be added
- * @throws UnknownTypeException
- * thrown when some types in the xml node are unknown
- */
- private void parseGraphics(Element eTmp, Shape shape) throws UnknownTypeException {
- Double centerX = null;
- Double centerY = null;
- Double width = null;
- Double height = null;
- for (Pair<String, String> entry : getAttributes(eTmp)) {
- if (!parseCommonGraphicAttributes(shape, entry)) {
- switch (entry.getLeft()) {
- case ("CenterX"):
- centerX = Double.valueOf(entry.getRight());
- break;
- case ("CenterY"):
- centerY = Double.valueOf(entry.getRight());
- break;
- case ("Width"):
- width = Double.valueOf(entry.getRight());
- break;
- case ("Height"):
- height = Double.valueOf(entry.getRight());
- break;
- case ("ShapeType"):
- shape.setShape(entry.getRight());
- break;
- case ("Color"):
- shape.setColor(hexStringToColor(entry.getRight()));
- break;
- case ("FillColor"):
- shape.setFillColor(hexStringToColor(entry.getRight()));
- break;
- case ("ZOrder"):
- shape.setzOrder(Integer.valueOf(entry.getRight()));
- break;
- case ("FontSize"):
- shape.setFontSize(Double.valueOf(entry.getRight()));
- break;
- case ("LineThickness"):
- shape.setLineThickness(Double.valueOf(entry.getRight()));
- break;
- case ("Valign"):
- shape.setvAlign(entry.getRight());
- break;
- case ("FontWeight"):
- switch (entry.getRight()) {
- case ("Bold"):
- shape.addFontAttribute(TextAttribute.WEIGHT, TextAttribute.WEIGHT_BOLD);
- break;
- default:
- logger.warn("Unknown value of attribute: " + entry.getLeft() + " - " + entry.getRight());
- break;
- }
- break;
- case ("Rotation"):
- shape.setRotation(Double.valueOf(entry.getRight()));
- break;
- default:
- logger.warn("Unknown attribute of " + eTmp.getNodeName() + " node: " + entry.getLeft());
- break;
- }
- }
- }
- shape.setRectangle(new Rectangle2D.Double(centerX - width / 2, centerY - height / 2, width, height));
- }
-
- @Override
- public String toXml(Shape node) throws ConverterException {
- throw new NotImplementedException();
- }
-
- @Override
- public String toXml(Collection<Shape> list) throws ConverterException {
- throw new NotImplementedException();
- }
-}
+package lcsb.mapviewer.wikipathway.XML;
+
+import java.awt.font.TextAttribute;
+import java.awt.geom.Rectangle2D;
+import java.util.Collection;
+
+import org.apache.log4j.Logger;
+import org.w3c.dom.Element;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.wikipathway.model.Shape;
+import lcsb.mapviewer.wikipathway.model.UnknownTypeException;
+
+/**
+ * Parser class that creates {@link Shape} objects from Xml {@link Element node}
+ * .
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ShapeParser extends GraphicalPathwayElementParser<Shape> {
+
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(ShapeParser.class);
+
+ @Override
+ public Shape parse(Element eElement) throws ConverterException {
+ if (!eElement.getNodeName().equals("Shape")) {
+ throw new InvalidArgumentException(ShapeParser.class.getSimpleName() + " can parse only Shape xml nodes");
+ }
+ Shape shape = new Shape(eElement.getAttribute("GraphId"));
+ for (Pair<String, String> entry : getAttributes(eElement)) {
+ switch (entry.getLeft()) {
+ case ("GraphId"):
+ break;
+ case ("TextLabel"):
+ shape.setTextLabel(entry.getRight());
+ break;
+ case ("GroupRef"):
+ shape.setGroupRef(entry.getRight());
+ break;
+ default:
+ logger.warn("Unknown attribute of " + eElement.getNodeName() + " node: " + entry.getLeft());
+ break;
+ }
+ }
+
+ NodeList tmpList = eElement.getChildNodes();
+ for (int j = 0; j < tmpList.getLength(); j++) {
+ Node tmpNode = tmpList.item(j);
+ if (tmpNode.getNodeType() == Node.ELEMENT_NODE) {
+ Element eTmp = (Element) tmpNode;
+ switch (eTmp.getNodeName()) {
+ case ("Graphics"):
+ parseGraphics(eTmp, shape);
+ break;
+ case ("Attribute"):
+ parseAttribute(eTmp, shape);
+ break;
+ case ("Comment"):
+ shape.addComment(eTmp.getTextContent());
+ break;
+ case ("BiopaxRef"):
+ shape.addBiopaxReference(eTmp.getTextContent());
+ break;
+ default:
+ logger.warn("Unknown sub-node of " + eElement.getNodeName() + " node: " + eTmp.getNodeName());
+ break;
+ }
+ }
+ }
+ return shape;
+ }
+
+ /**
+ * Method that parses {@link Shape} xml attribute.
+ *
+ * @param eTmp
+ * xml node with attribute
+ * @param shape
+ * shape where data should be added
+ */
+ private void parseAttribute(Element eTmp, Shape shape) {
+ String key = eTmp.getAttribute("Key");
+ String value = eTmp.getAttribute("Value");
+ switch (key) {
+ case ("org.pathvisio.CellularComponentProperty"):
+ shape.setCompartment(true);
+ break;
+ case ("org.pathvisio.DoubleLineProperty"):
+ switch (value) {
+ case ("Double"):
+ shape.setLineType(LineType.DOUBLE);
+ break;
+ default:
+ logger.warn(shape.getWarningPrefix() + "Unknown line type: " + value);
+ break;
+ }
+ break;
+ default:
+ logger.warn(shape.getWarningPrefix() + "Unknown attribute of node. Key:" + key + "; value: " + value);
+ break;
+ }
+ }
+
+ /**
+ * Parse graphics xml node in the shape node.
+ *
+ * @param eTmp
+ * xml node with graphics
+ * @param shape
+ * shape where data should be added
+ * @throws UnknownTypeException
+ * thrown when some types in the xml node are unknown
+ */
+ private void parseGraphics(Element eTmp, Shape shape) throws UnknownTypeException {
+ Double centerX = null;
+ Double centerY = null;
+ Double width = null;
+ Double height = null;
+ for (Pair<String, String> entry : getAttributes(eTmp)) {
+ if (!parseCommonGraphicAttributes(shape, entry)) {
+ switch (entry.getLeft()) {
+ case ("CenterX"):
+ centerX = Double.valueOf(entry.getRight());
+ break;
+ case ("CenterY"):
+ centerY = Double.valueOf(entry.getRight());
+ break;
+ case ("Width"):
+ width = Double.valueOf(entry.getRight());
+ break;
+ case ("Height"):
+ height = Double.valueOf(entry.getRight());
+ break;
+ case ("ShapeType"):
+ shape.setShape(entry.getRight());
+ break;
+ case ("Color"):
+ shape.setColor(hexStringToColor(entry.getRight()));
+ break;
+ case ("FillColor"):
+ shape.setFillColor(hexStringToColor(entry.getRight()));
+ break;
+ case ("ZOrder"):
+ shape.setzOrder(Integer.valueOf(entry.getRight()));
+ break;
+ case ("FontSize"):
+ shape.setFontSize(Double.valueOf(entry.getRight()));
+ break;
+ case ("LineThickness"):
+ shape.setLineThickness(Double.valueOf(entry.getRight()));
+ break;
+ case ("Valign"):
+ shape.setvAlign(entry.getRight());
+ break;
+ case ("FontWeight"):
+ switch (entry.getRight()) {
+ case ("Bold"):
+ shape.addFontAttribute(TextAttribute.WEIGHT, TextAttribute.WEIGHT_BOLD);
+ break;
+ default:
+ logger.warn("Unknown value of attribute: " + entry.getLeft() + " - " + entry.getRight());
+ break;
+ }
+ break;
+ case ("Rotation"):
+ shape.setRotation(Double.valueOf(entry.getRight()));
+ break;
+ default:
+ logger.warn("Unknown attribute of " + eTmp.getNodeName() + " node: " + entry.getLeft());
+ break;
+ }
+ }
+ }
+ shape.setRectangle(new Rectangle2D.Double(centerX - width / 2, centerY - height / 2, width, height));
+ }
+
+ @Override
+ public String toXml(Shape node) throws ConverterException {
+ throw new NotImplementedException();
+ }
+
+ @Override
+ public String toXml(Collection<Shape> list) throws ConverterException {
+ throw new NotImplementedException();
+ }
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/StateParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/StateParser.java
index 33fe1a1ecb..9117268a8a 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/StateParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/StateParser.java
@@ -1,171 +1,171 @@
-package lcsb.mapviewer.wikipathway.XML;
-
-import java.util.Collection;
-
-import org.apache.log4j.Logger;
-import org.w3c.dom.Element;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.ConverterException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.wikipathway.model.GpmlModificationType;
-import lcsb.mapviewer.wikipathway.model.GpmlStateType;
-import lcsb.mapviewer.wikipathway.model.State;
-import lcsb.mapviewer.wikipathway.model.UnknownTypeException;
-
-/**
- * Parser class that creates {@link State} objects from Xml {@link Element node}
- * .
- *
- * @author Piotr Gawron
- *
- */
-public class StateParser extends ElementGpmlParser<State> {
-
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(StateParser.class);
-
- /**
- * Parser used for extracting {@link lcsb.mapviewer.model.map.MiriamData
- * references} from GPML model.
- */
- private ReferenceParser referenceParser = new ReferenceParser();
-
- @Override
- public State parse(Element eElement) throws ConverterException {
- if (!eElement.getNodeName().equals("State")) {
- throw new InvalidArgumentException(StateParser.class.getSimpleName() + " can parse only State xml nodes");
- }
- State state = new State(eElement.getAttribute("GraphId"));
- for (Pair<String, String> entry : getAttributes(eElement)) {
- switch (entry.getLeft()) {
- case ("GraphId"):
- break;
- case ("TextLabel"):
- try {
- GpmlModificationType type = GpmlModificationType.getByGpmlName(entry.getRight());
- state.setType(type.getCorrespondingModificationState());
- } catch (UnknownTypeException e) {
- try {
- GpmlStateType type = GpmlStateType.getByGpmlName(entry.getRight());
- state.setStructuralState(type.getStringRepresenation());
- } catch (UnknownTypeException e2) {
- throw new ConverterException("Unknown state type: " + entry.getRight());
- }
- }
- break;
- case ("GraphRef"):
- state.setGraphRef(entry.getRight());
- break;
- default:
- logger.warn("Unknown attribute of " + eElement.getNodeName() + " node: " + entry.getLeft());
- break;
- }
- }
-
- NodeList tmpList = eElement.getChildNodes();
- for (int j = 0; j < tmpList.getLength(); j++) {
- Node tmpNode = tmpList.item(j);
- if (tmpNode.getNodeType() == Node.ELEMENT_NODE) {
- Element eTmp = (Element) tmpNode;
- switch (eTmp.getNodeName()) {
- case ("Comment"):
- state.addComment(eTmp.getTextContent());
- break;
- case ("Graphics"):
- parseGraphics(eTmp, state);
- break;
- case ("Attribute"):
- parseAttribute(eTmp, state);
- break;
- case ("BiopaxRef"):
- state.addBiopaxReference(eTmp.getTextContent());
- break;
- case ("Xref"):
- MiriamData md = referenceParser.parse(eTmp);
- if (md != null) {
- state.addReference(md);
- }
- break;
- default:
- logger.warn("Unknown sub-node of " + eElement.getNodeName() + " node: " + eTmp.getNodeName());
- break;
- }
- }
- }
- return state;
- }
-
- /**
- * Parse graphics xml node in the state node.
- *
- * @param eTmp
- * xml node with graphics
- * @param state
- * state where data should be added
- * @throws UnknownTypeException
- * thrown when some types in the xml node are unknown
- */
- private void parseGraphics(Element eTmp, State state) throws UnknownTypeException {
- for (Pair<String, String> entry : getAttributes(eTmp)) {
- switch (entry.getLeft()) {
- case ("RelX"):
- state.setRelX(Double.valueOf(entry.getRight()));
- break;
- case ("RelY"):
- state.setRelY(Double.valueOf(entry.getRight()));
- break;
- case ("Width"):
- state.setWidth(Double.valueOf(entry.getRight()));
- break;
- case ("Height"):
- state.setHeight(Double.valueOf(entry.getRight()));
- break;
- case ("ShapeType"):
- state.setShape(entry.getRight());
- break;
- case ("FillColor"):
- state.setFillColor(hexStringToColor(entry.getRight()));
- break;
- default:
- logger.warn("Unknown attribute of " + eTmp.getNodeName() + " node: " + entry.getLeft());
- break;
- }
- }
- }
-
- /**
- * Method that parses {@link State} xml attribute.
- *
- * @param eTmp
- * xml node with attribute
- * @param state
- * state where data should be added
- */
- private void parseAttribute(Element eTmp, State state) {
- String key = eTmp.getAttribute("Key");
- String value = eTmp.getAttribute("Value");
- switch (key) {
- default:
- logger.warn(state.getWarningPrefix() + "Unknown attribute of node. Key:" + key + "; value: " + value);
- break;
- }
- }
-
- @Override
- public String toXml(State node) throws ConverterException {
- throw new NotImplementedException();
- }
-
- @Override
- public String toXml(Collection<State> list) throws ConverterException {
- throw new NotImplementedException();
- }
-
-}
+package lcsb.mapviewer.wikipathway.XML;
+
+import java.util.Collection;
+
+import org.apache.log4j.Logger;
+import org.w3c.dom.Element;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.wikipathway.model.GpmlModificationType;
+import lcsb.mapviewer.wikipathway.model.GpmlStateType;
+import lcsb.mapviewer.wikipathway.model.State;
+import lcsb.mapviewer.wikipathway.model.UnknownTypeException;
+
+/**
+ * Parser class that creates {@link State} objects from Xml {@link Element node}
+ * .
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class StateParser extends ElementGpmlParser<State> {
+
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(StateParser.class);
+
+ /**
+ * Parser used for extracting {@link lcsb.mapviewer.model.map.MiriamData
+ * references} from GPML model.
+ */
+ private ReferenceParser referenceParser = new ReferenceParser();
+
+ @Override
+ public State parse(Element eElement) throws ConverterException {
+ if (!eElement.getNodeName().equals("State")) {
+ throw new InvalidArgumentException(StateParser.class.getSimpleName() + " can parse only State xml nodes");
+ }
+ State state = new State(eElement.getAttribute("GraphId"));
+ for (Pair<String, String> entry : getAttributes(eElement)) {
+ switch (entry.getLeft()) {
+ case ("GraphId"):
+ break;
+ case ("TextLabel"):
+ try {
+ GpmlModificationType type = GpmlModificationType.getByGpmlName(entry.getRight());
+ state.setType(type.getCorrespondingModificationState());
+ } catch (UnknownTypeException e) {
+ try {
+ GpmlStateType type = GpmlStateType.getByGpmlName(entry.getRight());
+ state.setStructuralState(type.getStringRepresenation());
+ } catch (UnknownTypeException e2) {
+ throw new ConverterException("Unknown state type: " + entry.getRight());
+ }
+ }
+ break;
+ case ("GraphRef"):
+ state.setGraphRef(entry.getRight());
+ break;
+ default:
+ logger.warn("Unknown attribute of " + eElement.getNodeName() + " node: " + entry.getLeft());
+ break;
+ }
+ }
+
+ NodeList tmpList = eElement.getChildNodes();
+ for (int j = 0; j < tmpList.getLength(); j++) {
+ Node tmpNode = tmpList.item(j);
+ if (tmpNode.getNodeType() == Node.ELEMENT_NODE) {
+ Element eTmp = (Element) tmpNode;
+ switch (eTmp.getNodeName()) {
+ case ("Comment"):
+ state.addComment(eTmp.getTextContent());
+ break;
+ case ("Graphics"):
+ parseGraphics(eTmp, state);
+ break;
+ case ("Attribute"):
+ parseAttribute(eTmp, state);
+ break;
+ case ("BiopaxRef"):
+ state.addBiopaxReference(eTmp.getTextContent());
+ break;
+ case ("Xref"):
+ MiriamData md = referenceParser.parse(eTmp);
+ if (md != null) {
+ state.addReference(md);
+ }
+ break;
+ default:
+ logger.warn("Unknown sub-node of " + eElement.getNodeName() + " node: " + eTmp.getNodeName());
+ break;
+ }
+ }
+ }
+ return state;
+ }
+
+ /**
+ * Parse graphics xml node in the state node.
+ *
+ * @param eTmp
+ * xml node with graphics
+ * @param state
+ * state where data should be added
+ * @throws UnknownTypeException
+ * thrown when some types in the xml node are unknown
+ */
+ private void parseGraphics(Element eTmp, State state) throws UnknownTypeException {
+ for (Pair<String, String> entry : getAttributes(eTmp)) {
+ switch (entry.getLeft()) {
+ case ("RelX"):
+ state.setRelX(Double.valueOf(entry.getRight()));
+ break;
+ case ("RelY"):
+ state.setRelY(Double.valueOf(entry.getRight()));
+ break;
+ case ("Width"):
+ state.setWidth(Double.valueOf(entry.getRight()));
+ break;
+ case ("Height"):
+ state.setHeight(Double.valueOf(entry.getRight()));
+ break;
+ case ("ShapeType"):
+ state.setShape(entry.getRight());
+ break;
+ case ("FillColor"):
+ state.setFillColor(hexStringToColor(entry.getRight()));
+ break;
+ default:
+ logger.warn("Unknown attribute of " + eTmp.getNodeName() + " node: " + entry.getLeft());
+ break;
+ }
+ }
+ }
+
+ /**
+ * Method that parses {@link State} xml attribute.
+ *
+ * @param eTmp
+ * xml node with attribute
+ * @param state
+ * state where data should be added
+ */
+ private void parseAttribute(Element eTmp, State state) {
+ String key = eTmp.getAttribute("Key");
+ String value = eTmp.getAttribute("Value");
+ switch (key) {
+ default:
+ logger.warn(state.getWarningPrefix() + "Unknown attribute of node. Key:" + key + "; value: " + value);
+ break;
+ }
+ }
+
+ @Override
+ public String toXml(State node) throws ConverterException {
+ throw new NotImplementedException();
+ }
+
+ @Override
+ public String toXml(Collection<State> list) throws ConverterException {
+ throw new NotImplementedException();
+ }
+
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/UnknownAttributeValueException.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/UnknownAttributeValueException.java
index 6f0717868c..f531fc0925 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/UnknownAttributeValueException.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/UnknownAttributeValueException.java
@@ -1,29 +1,29 @@
-package lcsb.mapviewer.wikipathway.XML;
-
-import lcsb.mapviewer.converter.ConverterException;
-
-/**
- * Exception that shold be thrown when the value of the attribute in xml is invalid.
- *
- * @author Piotr Gawron
- *
- */
-public class UnknownAttributeValueException extends ConverterException {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor with message passed in the argument.
- *
- * @param string
- * message of this exception
- */
- public UnknownAttributeValueException(String string) {
- super(string);
- }
-
-
-}
+package lcsb.mapviewer.wikipathway.XML;
+
+import lcsb.mapviewer.converter.ConverterException;
+
+/**
+ * Exception that shold be thrown when the value of the attribute in xml is invalid.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class UnknownAttributeValueException extends ConverterException {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor with message passed in the argument.
+ *
+ * @param string
+ * message of this exception
+ */
+ public UnknownAttributeValueException(String string) {
+ super(string);
+ }
+
+
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/UnknownChildClassException.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/UnknownChildClassException.java
index b4b3b2f768..c070d7c60a 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/UnknownChildClassException.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/UnknownChildClassException.java
@@ -1,30 +1,30 @@
-package lcsb.mapviewer.wikipathway.XML;
-
-import lcsb.mapviewer.converter.ConverterException;
-
-/**
- * Exception that shold be thrown when there are problems with finding child
- * classes in the complex structures.
- *
- * @author Piotr Gawron
- *
- */
-public class UnknownChildClassException extends ConverterException {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor with message passed in the argument.
- *
- * @param string
- * message of this exception
- */
- public UnknownChildClassException(String string) {
- super(string);
- }
-
-
-}
+package lcsb.mapviewer.wikipathway.XML;
+
+import lcsb.mapviewer.converter.ConverterException;
+
+/**
+ * Exception that shold be thrown when there are problems with finding child
+ * classes in the complex structures.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class UnknownChildClassException extends ConverterException {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor with message passed in the argument.
+ *
+ * @param string
+ * message of this exception
+ */
+ public UnknownChildClassException(String string) {
+ super(string);
+ }
+
+
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/UnknownMergingMethodException.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/UnknownMergingMethodException.java
index da6d14b2fb..6cc97d1d02 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/UnknownMergingMethodException.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/UnknownMergingMethodException.java
@@ -1,29 +1,29 @@
-package lcsb.mapviewer.wikipathway.XML;
-
-import lcsb.mapviewer.converter.ConverterException;
-
-/**
- * Exception that shold be thrown when merging of two interactions cannot be
- * performed, because we don't know what should be the result of merging.
- *
- * @author Piotr Gawron
- *
- */
-public class UnknownMergingMethodException extends ConverterException {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor with message passed in the argument.
- *
- * @param string
- * message of this exception
- */
- public UnknownMergingMethodException(String string) {
- super(string);
- }
-
-}
+package lcsb.mapviewer.wikipathway.XML;
+
+import lcsb.mapviewer.converter.ConverterException;
+
+/**
+ * Exception that shold be thrown when merging of two interactions cannot be
+ * performed, because we don't know what should be the result of merging.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class UnknownMergingMethodException extends ConverterException {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor with message passed in the argument.
+ *
+ * @param string
+ * message of this exception
+ */
+ public UnknownMergingMethodException(String string) {
+ super(string);
+ }
+
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/package-info.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/package-info.java
index b3158a06f1..1cbdfb96fc 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/package-info.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/package-info.java
@@ -1,5 +1,5 @@
-/**
- * Contains xml parser for gpml model.
- */
-package lcsb.mapviewer.wikipathway.XML;
-
+/**
+ * Contains xml parser for gpml model.
+ */
+package lcsb.mapviewer.wikipathway.XML;
+
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/DataNode.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/DataNode.java
index d5038e26f6..73f39e5788 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/DataNode.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/DataNode.java
@@ -1,214 +1,214 @@
-package lcsb.mapviewer.wikipathway.model;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.map.MiriamData;
-
-/**
- * Class used to store data from DataNode from .gpml.
- *
- * @author Jan Badura
- *
- */
-public class DataNode extends GraphicalPathwayElement {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * References.
- */
- private List<MiriamData> references = new ArrayList<>();
-
- /**
- * ???
- */
- private String type;
-
- /**
- * Type o line used to draw element.
- */
- private LineType lineType = LineType.SOLID;
-
- /**
- * ???
- */
- private String textLabel;
-
- /**
- * Where this node belongs to.
- */
- private String groupRef;
-
- /**
- * Font weight (like italic, bold) that should be used.
- */
- private String fontWeight;
-
- /**
- * Align of the description.
- */
- private String vAlign;
-
- /**
- * Default constructor.
- *
- * @param graphId
- * {@link PathwayElement#graphId}
- */
- public DataNode(String graphId) {
- super(graphId);
- }
-
- /**
- * Empty constructor that should be used only by serialization tools and
- * subclasses.
- */
- protected DataNode() {
- super();
- }
-
- @Override
- public String toString() {
- return textLabel + " " + getGraphId() + " " + groupRef + " " + type;
- }
-
- @Override
- public String getName() {
- return getTextLabel();
- }
-
- /**
- * @return the type
- * @see #type
- */
- public String getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(String type) {
- this.type = type;
- }
-
- /**
- * @return the textLabel
- * @see #textLabel
- */
- public String getTextLabel() {
- return textLabel;
- }
-
- /**
- * @param textLabel
- * the textLabel to set
- * @see #textLabel
- */
- public void setTextLabel(String textLabel) {
- this.textLabel = textLabel;
- }
-
- /**
- * @return the groupRef
- * @see #groupRef
- */
- public String getGroupRef() {
- return groupRef;
- }
-
- /**
- * @param groupRef
- * the groupRef to set
- * @see #groupRef
- */
- public void setGroupRef(String groupRef) {
- this.groupRef = groupRef;
- }
-
- /**
- * @return the references
- * @see #references
- */
- public List<MiriamData> getReferences() {
- return references;
- }
-
- /**
- * @param references
- * the references to set
- * @see #references
- */
- public void setReferences(List<MiriamData> references) {
- this.references = references;
- }
-
- /**
- * @return the vAlign
- * @see #vAlign
- */
- public String getvAlign() {
- return vAlign;
- }
-
- /**
- * @param vAlign
- * the vAlign to set
- * @see #vAlign
- */
- public void setvAlign(String vAlign) {
- this.vAlign = vAlign;
- }
-
- /**
- * Adds reference to node.
- *
- * @param md
- * objet to add
- */
- public void addReference(MiriamData md) {
- references.add(md);
- }
-
- /**
- * @return the lineType
- * @see #lineType
- */
- public LineType getLineType() {
- return lineType;
- }
-
- /**
- * @param lineType
- * the lineType to set
- * @see #lineType
- */
- public void setLineType(LineType lineType) {
- this.lineType = lineType;
- }
-
- /**
- * @return the fontWeight
- * @see #fontWeight
- */
- public String getFontWeight() {
- return fontWeight;
- }
-
- /**
- * @param fontWeight
- * the fontWeight to set
- * @see #fontWeight
- */
- public void setFontWeight(String fontWeight) {
- this.fontWeight = fontWeight;
- }
-
-}
+package lcsb.mapviewer.wikipathway.model;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.map.MiriamData;
+
+/**
+ * Class used to store data from DataNode from .gpml.
+ *
+ * @author Jan Badura
+ *
+ */
+public class DataNode extends GraphicalPathwayElement {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * References.
+ */
+ private List<MiriamData> references = new ArrayList<>();
+
+ /**
+ * ???
+ */
+ private String type;
+
+ /**
+ * Type o line used to draw element.
+ */
+ private LineType lineType = LineType.SOLID;
+
+ /**
+ * ???
+ */
+ private String textLabel;
+
+ /**
+ * Where this node belongs to.
+ */
+ private String groupRef;
+
+ /**
+ * Font weight (like italic, bold) that should be used.
+ */
+ private String fontWeight;
+
+ /**
+ * Align of the description.
+ */
+ private String vAlign;
+
+ /**
+ * Default constructor.
+ *
+ * @param graphId
+ * {@link PathwayElement#graphId}
+ */
+ public DataNode(String graphId) {
+ super(graphId);
+ }
+
+ /**
+ * Empty constructor that should be used only by serialization tools and
+ * subclasses.
+ */
+ protected DataNode() {
+ super();
+ }
+
+ @Override
+ public String toString() {
+ return textLabel + " " + getGraphId() + " " + groupRef + " " + type;
+ }
+
+ @Override
+ public String getName() {
+ return getTextLabel();
+ }
+
+ /**
+ * @return the type
+ * @see #type
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * @param type
+ * the type to set
+ * @see #type
+ */
+ public void setType(String type) {
+ this.type = type;
+ }
+
+ /**
+ * @return the textLabel
+ * @see #textLabel
+ */
+ public String getTextLabel() {
+ return textLabel;
+ }
+
+ /**
+ * @param textLabel
+ * the textLabel to set
+ * @see #textLabel
+ */
+ public void setTextLabel(String textLabel) {
+ this.textLabel = textLabel;
+ }
+
+ /**
+ * @return the groupRef
+ * @see #groupRef
+ */
+ public String getGroupRef() {
+ return groupRef;
+ }
+
+ /**
+ * @param groupRef
+ * the groupRef to set
+ * @see #groupRef
+ */
+ public void setGroupRef(String groupRef) {
+ this.groupRef = groupRef;
+ }
+
+ /**
+ * @return the references
+ * @see #references
+ */
+ public List<MiriamData> getReferences() {
+ return references;
+ }
+
+ /**
+ * @param references
+ * the references to set
+ * @see #references
+ */
+ public void setReferences(List<MiriamData> references) {
+ this.references = references;
+ }
+
+ /**
+ * @return the vAlign
+ * @see #vAlign
+ */
+ public String getvAlign() {
+ return vAlign;
+ }
+
+ /**
+ * @param vAlign
+ * the vAlign to set
+ * @see #vAlign
+ */
+ public void setvAlign(String vAlign) {
+ this.vAlign = vAlign;
+ }
+
+ /**
+ * Adds reference to node.
+ *
+ * @param md
+ * objet to add
+ */
+ public void addReference(MiriamData md) {
+ references.add(md);
+ }
+
+ /**
+ * @return the lineType
+ * @see #lineType
+ */
+ public LineType getLineType() {
+ return lineType;
+ }
+
+ /**
+ * @param lineType
+ * the lineType to set
+ * @see #lineType
+ */
+ public void setLineType(LineType lineType) {
+ this.lineType = lineType;
+ }
+
+ /**
+ * @return the fontWeight
+ * @see #fontWeight
+ */
+ public String getFontWeight() {
+ return fontWeight;
+ }
+
+ /**
+ * @param fontWeight
+ * the fontWeight to set
+ * @see #fontWeight
+ */
+ public void setFontWeight(String fontWeight) {
+ this.fontWeight = fontWeight;
+ }
+
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Direction.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Direction.java
index dc80cffbfa..6d2ec1a489 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Direction.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Direction.java
@@ -1,80 +1,80 @@
-package lcsb.mapviewer.wikipathway.model;
-
-/**
- * Class defining directions of the world. They are listed in clockwise order
- * starting from north.
- *
- * @author Piotr Gawron
- *
- */
-public enum Direction {
-
- /**
- * North.
- */
- NORTH(Axis.NORTH_SOUTH), //
-
- /**
- * East.
- */
- EAST(Axis.EAST_WEST), //
-
- /**
- * South.
- */
- SOUTH(Axis.NORTH_SOUTH), //
-
- /**
- * West.
- */
- WEST(Axis.EAST_WEST);
-
- /**
- * Defines axis in which direction lies (either {@link Axis#NORTH_SOUTH} or
- * {@link Axis#EAST_WEST}).
- */
- private Axis axis;
-
- /**
- * Default cosntructor.
- *
- * @param axis
- * {@link #axis}
- */
- Direction(Axis axis) {
- this.axis = axis;
- }
-
- /**
- * Defines axis in which {@link Direction} can lie (either
- * {@link Axis#NORTH_SOUTH} or {@link Axis#EAST_WEST}).
- */
- public enum Axis {
- /**
- * Axis going from NORTH to SOUTH (or from SOUTH to NORTH).
- */
- NORTH_SOUTH,
- /**
- * Axis going from WEST to EAST (or from EAST to WEST).
- */
-
- EAST_WEST;
- }
-
- /**
- * @return the axis
- * @see #axis
- */
- public Axis getAxis() {
- return axis;
- }
-
- /**
- * Returns next direction (by 90 degrees) in clockwise order.
- *
- * @return next direction (by 90 degrees) in clockwise order
- */
- public Direction nextClockwiseDirection() {
- return values()[(this.ordinal() + 1) % values().length];
- }
-}
+package lcsb.mapviewer.wikipathway.model;
+
+/**
+ * Class defining directions of the world. They are listed in clockwise order
+ * starting from north.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum Direction {
+
+ /**
+ * North.
+ */
+ NORTH(Axis.NORTH_SOUTH), //
+
+ /**
+ * East.
+ */
+ EAST(Axis.EAST_WEST), //
+
+ /**
+ * South.
+ */
+ SOUTH(Axis.NORTH_SOUTH), //
+
+ /**
+ * West.
+ */
+ WEST(Axis.EAST_WEST);
+
+ /**
+ * Defines axis in which direction lies (either {@link Axis#NORTH_SOUTH} or
+ * {@link Axis#EAST_WEST}).
+ */
+ private Axis axis;
+
+ /**
+ * Default cosntructor.
+ *
+ * @param axis
+ * {@link #axis}
+ */
+ Direction(Axis axis) {
+ this.axis = axis;
+ }
+
+ /**
+ * Defines axis in which {@link Direction} can lie (either
+ * {@link Axis#NORTH_SOUTH} or {@link Axis#EAST_WEST}).
+ */
+ public enum Axis {
+ /**
+ * Axis going from NORTH to SOUTH (or from SOUTH to NORTH).
+ */
+ NORTH_SOUTH,
+ /**
+ * Axis going from WEST to EAST (or from EAST to WEST).
+ */
+
+ EAST_WEST;
+ }
+
+ /**
+ * @return the axis
+ * @see #axis
+ */
+ public Axis getAxis() {
+ return axis;
+ }
+
+ /**
+ * Returns next direction (by 90 degrees) in clockwise order.
+ *
+ * @return next direction (by 90 degrees) in clockwise order
+ */
+ public Direction nextClockwiseDirection() {
+ return values()[(this.ordinal() + 1) % values().length];
+ }
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Edge.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Edge.java
index 4818da24d1..82f6247a32 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Edge.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Edge.java
@@ -1,469 +1,469 @@
-package lcsb.mapviewer.wikipathway.model;
-
-import java.awt.Color;
-import java.awt.geom.Point2D;
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.MiriamData;
-
-/**
- * Support class for Interaction between elements. It stores data parsed from
- * GPML.
- *
- * @author Jan Badura
- * @author Piotr Gawron
- *
- */
-public class Edge implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Epsilon valu used for comparison of doubles.
- */
- private static final Double EPSILON = 1e-6;
-
- /**
- * Default class logger.
- */
- private final transient Logger logger = Logger.getLogger(Edge.class);
-
- /**
- * Identifier in gpml model.
- */
- private String graphId;
-
- /**
- * In which group this edge is located.
- */
- private String groupRef;
-
- /**
- * Where this {@link Edge} starts (in which {@link Edge}/{@link Interaction}).
- */
- private String start;
-
- /**
- * Where this {@link Edge} ends (in which {@link Edge}/{@link Interaction}).
- */
- private String end;
-
- /**
- * Z-order of the line (how much to front it should be located).
- */
- private Integer zOrder;
-
- /**
- * Line representing this edge.
- */
- private PolylineData line = new PolylineData();
-
- /**
- * Gpml interaction type (arrow).
- */
- private GpmlInteractionType type = GpmlInteractionType.LINE;
-
- /**
- * References for given edge.
- */
- private List<MiriamData> references = new ArrayList<>();
-
- /**
- * List of anchors placed on the edge.
- */
- private Set<String> anchors = new HashSet<>();
-
- /**
- * Comments.
- */
- private List<String> comments = new ArrayList<>();
-
- /**
- * List of identifiers used by biopax nodes that are inside gpml. These biopax
- * nodes contain annotations.
- */
- private List<String> biopaxReferences = new ArrayList<String>();
-
- /**
- * Default constructor.
- *
- * @param graphId
- * {@link #graphId}
- */
- public Edge(String graphId) {
- this.graphId = graphId;
- }
-
- /**
- * Creates new instance that contains the same data as the parameter object.
- *
- * @param original
- * original object from which data is being copied
- */
- public Edge(Edge original) {
- this.graphId = original.getGraphId();
- this.groupRef = original.getGroupRef();
- this.start = original.getStart();
- this.end = original.getEnd();
- this.line = new PolylineData(original.getLine());
- this.type = original.getType();
- for (MiriamData md : original.getReferences()) {
- addReference(new MiriamData(md));
- }
- this.anchors.addAll(original.getAnchors());
- this.comments.addAll(original.getComments());
- this.biopaxReferences.addAll(original.getBiopaxReferences());
- this.zOrder = original.getzOrder();
- }
-
- /**
- * Empty constructor that should be used only by serialization tools and
- * subclasses.
- */
- protected Edge() {
- }
-
- /**
- * Adds reference to the object.
- *
- * @param reference
- * reference to add
- */
- public void addReference(MiriamData reference) {
- references.add(reference);
- }
-
- /**
- * Adds anchor to {@link #anchors}.
- *
- * @param anchor
- * object to add
- */
- public void addAnchor(String anchor) {
- this.anchors.add(anchor);
- }
-
- /**
- * @return the graphId
- * @see #graphId
- */
- public String getGraphId() {
- return graphId;
- }
-
- /**
- * @param graphId
- * the graphId to set
- * @see #graphId
- */
- public void setGraphId(String graphId) {
- this.graphId = graphId;
- }
-
- /**
- * @return the start
- * @see #start
- */
- public String getStart() {
- return start;
- }
-
- /**
- * @param start
- * the start to set
- * @see #start
- */
- public void setStart(String start) {
- this.start = start;
- }
-
- /**
- * @return the end
- * @see #end
- */
- public String getEnd() {
- return end;
- }
-
- /**
- * @param end
- * the end to set
- * @see #end
- */
- public void setEnd(String end) {
- this.end = end;
- }
-
- /**
- * @return the line
- * @see #line
- */
- public PolylineData getLine() {
- return line;
- }
-
- /**
- * @param line
- * the line to set
- * @see #line
- */
- public void setLine(PolylineData line) {
- this.line = line;
- }
-
- /**
- * @return the anchors
- * @see #anchors
- */
- public Set<String> getAnchors() {
- return anchors;
- }
-
- /**
- * @param anchors
- * the anchors to set
- * @see #anchors
- */
- public void setAnchors(Set<String> anchors) {
- this.anchors = anchors;
- }
-
- /**
- * @return the comments
- * @see #comments
- */
- public List<String> getComments() {
- return comments;
- }
-
- /**
- * @param comment
- * the comment to add
- * @see #comment
- */
- public void addComment(String comment) {
- this.comments.add(comment);
- }
-
- /**
- * @return the biopaxReferences
- * @see #biopaxReferences
- */
- public List<String> getBiopaxReferences() {
- return biopaxReferences;
- }
-
- /**
- * @param biopaxReferences
- * the biopaxReferences to set
- * @see #biopaxReferences
- */
- public void setBiopaxReferences(List<String> biopaxReferences) {
- this.biopaxReferences = biopaxReferences;
- }
-
- /**
- * Returns a prefix that should be used in warnings.
- *
- * @return string that identifies element in logs
- */
- public String getWarningPrefix() {
- return "[" + getType() + ", id: " + getGraphId() + "]\t";
- }
-
- /**
- * @return the type
- * @see #type
- */
- public GpmlInteractionType getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(GpmlInteractionType type) {
- if (type != null) {
- this.type = type;
- }
- }
-
- /**
- * Reverse direction of edge (order of elements).
- *
- * @return copy of the object that is reversed
- */
- public Edge reverse() {
- Edge result = new Edge(this);
- result.setLine(result.getLine().reverse());
- String tmp = result.getStart();
- result.setStart(result.getEnd());
- result.setEnd(tmp);
-
- return result;
- }
-
- /**
- * @return the references
- * @see #references
- */
- public List<MiriamData> getReferences() {
- return references;
- }
-
- /**
- * @param references
- * the references to set
- * @see #references
- */
- public void setReferences(List<MiriamData> references) {
- this.references = references;
- }
-
- /**
- * Adds set of references.
- *
- * @param references
- * references to add
- */
- public void addReferences(List<MiriamData> references) {
- for (MiriamData miriamData : references) {
- addReference(miriamData);
- }
- }
-
- /**
- * This method extend edge (the line) by adding data from the edge in
- * parameter.
- *
- * @param edge2
- * edge that should be used for extension
- */
- public void extend(Edge edge2) {
- // check if extension make sense (they should point to the same identifier)
- if (!getEnd().equals(edge2.getStart())) {
- throw new InvalidArgumentException(
- getWarningPrefix() + edge2.getWarningPrefix() + " Cannot merge - anchor points doesn't match: " + getEnd() + "," + edge2.getStart());
- }
-
- if (line.getEndPoint().distance(edge2.getLine().getBeginPoint()) > EPSILON) {
- throw new InvalidArgumentException(
- getWarningPrefix() + edge2.getWarningPrefix() + " Cannot merge - edges are far from each other: " + line.getEndPoint() + ","
- + edge2.getLine().getBeginPoint());
- }
-
- // graphId should be the same
-
- // start should be taken from the original
-
- // end should be taken from the extension
- setEnd(edge2.getEnd());
-
- // add points
- for (int i = 1; i < edge2.getLine().getPoints().size(); i++) {
- Point2D p = (Point2D) edge2.getLine().getPoints().get(i).clone();
- line.addPoint(p);
- }
-
- // skip type
-
- for (MiriamData md : edge2.getReferences()) {
- addReference(new MiriamData(md));
- }
- anchors.addAll(edge2.getAnchors());
- List<String> toAdd = new ArrayList<>();
- for (String comment : edge2.getComments()) {
- if (!comments.contains(comment)) {
- toAdd.add(comment);
- }
- }
- comments.addAll(toAdd);
-
- // color should be skipped
- if (!getColor().equals(edge2.getColor())) {
- logger.warn(getWarningPrefix() + edge2.getWarningPrefix() + " Problem with merging. Edges have different colors.");
- }
-
- // add biopax references
- biopaxReferences.addAll(edge2.getBiopaxReferences());
-
- }
-
- /**
- * @return the color
- * @see #color
- */
- public Color getColor() {
- return line.getColor();
- }
-
- /**
- * @param color
- * the color to set
- * @see #color
- */
- public void setColor(Color color) {
- if (color != null) {
- line.setColor(color);
- }
- }
-
- /**
- * @return the zOrder
- * @see #zOrder
- */
- public Integer getzOrder() {
- return zOrder;
- }
-
- /**
- * @param zOrder
- * the zOrder to set
- * @see #zOrder
- */
- public void setzOrder(Integer zOrder) {
- this.zOrder = zOrder;
- }
-
- /**
- * Adds element to {@link #biopaxReferences}.
- *
- * @param reference
- * reference to add
- */
- public void addBiopaxReference(String reference) {
- biopaxReferences.add(reference);
-
- }
-
- /**
- * @return the groupRef
- * @see #groupRef
- */
- public String getGroupRef() {
- return groupRef;
- }
-
- /**
- * @param groupRef
- * the groupRef to set
- * @see #groupRef
- */
- public void setGroupRef(String groupRef) {
- this.groupRef = groupRef;
- }
-
-}
+package lcsb.mapviewer.wikipathway.model;
+
+import java.awt.Color;
+import java.awt.geom.Point2D;
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.MiriamData;
+
+/**
+ * Support class for Interaction between elements. It stores data parsed from
+ * GPML.
+ *
+ * @author Jan Badura
+ * @author Piotr Gawron
+ *
+ */
+public class Edge implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Epsilon valu used for comparison of doubles.
+ */
+ private static final Double EPSILON = 1e-6;
+
+ /**
+ * Default class logger.
+ */
+ private final transient Logger logger = Logger.getLogger(Edge.class);
+
+ /**
+ * Identifier in gpml model.
+ */
+ private String graphId;
+
+ /**
+ * In which group this edge is located.
+ */
+ private String groupRef;
+
+ /**
+ * Where this {@link Edge} starts (in which {@link Edge}/{@link Interaction}).
+ */
+ private String start;
+
+ /**
+ * Where this {@link Edge} ends (in which {@link Edge}/{@link Interaction}).
+ */
+ private String end;
+
+ /**
+ * Z-order of the line (how much to front it should be located).
+ */
+ private Integer zOrder;
+
+ /**
+ * Line representing this edge.
+ */
+ private PolylineData line = new PolylineData();
+
+ /**
+ * Gpml interaction type (arrow).
+ */
+ private GpmlInteractionType type = GpmlInteractionType.LINE;
+
+ /**
+ * References for given edge.
+ */
+ private List<MiriamData> references = new ArrayList<>();
+
+ /**
+ * List of anchors placed on the edge.
+ */
+ private Set<String> anchors = new HashSet<>();
+
+ /**
+ * Comments.
+ */
+ private List<String> comments = new ArrayList<>();
+
+ /**
+ * List of identifiers used by biopax nodes that are inside gpml. These biopax
+ * nodes contain annotations.
+ */
+ private List<String> biopaxReferences = new ArrayList<String>();
+
+ /**
+ * Default constructor.
+ *
+ * @param graphId
+ * {@link #graphId}
+ */
+ public Edge(String graphId) {
+ this.graphId = graphId;
+ }
+
+ /**
+ * Creates new instance that contains the same data as the parameter object.
+ *
+ * @param original
+ * original object from which data is being copied
+ */
+ public Edge(Edge original) {
+ this.graphId = original.getGraphId();
+ this.groupRef = original.getGroupRef();
+ this.start = original.getStart();
+ this.end = original.getEnd();
+ this.line = new PolylineData(original.getLine());
+ this.type = original.getType();
+ for (MiriamData md : original.getReferences()) {
+ addReference(new MiriamData(md));
+ }
+ this.anchors.addAll(original.getAnchors());
+ this.comments.addAll(original.getComments());
+ this.biopaxReferences.addAll(original.getBiopaxReferences());
+ this.zOrder = original.getzOrder();
+ }
+
+ /**
+ * Empty constructor that should be used only by serialization tools and
+ * subclasses.
+ */
+ protected Edge() {
+ }
+
+ /**
+ * Adds reference to the object.
+ *
+ * @param reference
+ * reference to add
+ */
+ public void addReference(MiriamData reference) {
+ references.add(reference);
+ }
+
+ /**
+ * Adds anchor to {@link #anchors}.
+ *
+ * @param anchor
+ * object to add
+ */
+ public void addAnchor(String anchor) {
+ this.anchors.add(anchor);
+ }
+
+ /**
+ * @return the graphId
+ * @see #graphId
+ */
+ public String getGraphId() {
+ return graphId;
+ }
+
+ /**
+ * @param graphId
+ * the graphId to set
+ * @see #graphId
+ */
+ public void setGraphId(String graphId) {
+ this.graphId = graphId;
+ }
+
+ /**
+ * @return the start
+ * @see #start
+ */
+ public String getStart() {
+ return start;
+ }
+
+ /**
+ * @param start
+ * the start to set
+ * @see #start
+ */
+ public void setStart(String start) {
+ this.start = start;
+ }
+
+ /**
+ * @return the end
+ * @see #end
+ */
+ public String getEnd() {
+ return end;
+ }
+
+ /**
+ * @param end
+ * the end to set
+ * @see #end
+ */
+ public void setEnd(String end) {
+ this.end = end;
+ }
+
+ /**
+ * @return the line
+ * @see #line
+ */
+ public PolylineData getLine() {
+ return line;
+ }
+
+ /**
+ * @param line
+ * the line to set
+ * @see #line
+ */
+ public void setLine(PolylineData line) {
+ this.line = line;
+ }
+
+ /**
+ * @return the anchors
+ * @see #anchors
+ */
+ public Set<String> getAnchors() {
+ return anchors;
+ }
+
+ /**
+ * @param anchors
+ * the anchors to set
+ * @see #anchors
+ */
+ public void setAnchors(Set<String> anchors) {
+ this.anchors = anchors;
+ }
+
+ /**
+ * @return the comments
+ * @see #comments
+ */
+ public List<String> getComments() {
+ return comments;
+ }
+
+ /**
+ * @param comment
+ * the comment to add
+ * @see #comment
+ */
+ public void addComment(String comment) {
+ this.comments.add(comment);
+ }
+
+ /**
+ * @return the biopaxReferences
+ * @see #biopaxReferences
+ */
+ public List<String> getBiopaxReferences() {
+ return biopaxReferences;
+ }
+
+ /**
+ * @param biopaxReferences
+ * the biopaxReferences to set
+ * @see #biopaxReferences
+ */
+ public void setBiopaxReferences(List<String> biopaxReferences) {
+ this.biopaxReferences = biopaxReferences;
+ }
+
+ /**
+ * Returns a prefix that should be used in warnings.
+ *
+ * @return string that identifies element in logs
+ */
+ public String getWarningPrefix() {
+ return "[" + getType() + ", id: " + getGraphId() + "]\t";
+ }
+
+ /**
+ * @return the type
+ * @see #type
+ */
+ public GpmlInteractionType getType() {
+ return type;
+ }
+
+ /**
+ * @param type
+ * the type to set
+ * @see #type
+ */
+ public void setType(GpmlInteractionType type) {
+ if (type != null) {
+ this.type = type;
+ }
+ }
+
+ /**
+ * Reverse direction of edge (order of elements).
+ *
+ * @return copy of the object that is reversed
+ */
+ public Edge reverse() {
+ Edge result = new Edge(this);
+ result.setLine(result.getLine().reverse());
+ String tmp = result.getStart();
+ result.setStart(result.getEnd());
+ result.setEnd(tmp);
+
+ return result;
+ }
+
+ /**
+ * @return the references
+ * @see #references
+ */
+ public List<MiriamData> getReferences() {
+ return references;
+ }
+
+ /**
+ * @param references
+ * the references to set
+ * @see #references
+ */
+ public void setReferences(List<MiriamData> references) {
+ this.references = references;
+ }
+
+ /**
+ * Adds set of references.
+ *
+ * @param references
+ * references to add
+ */
+ public void addReferences(List<MiriamData> references) {
+ for (MiriamData miriamData : references) {
+ addReference(miriamData);
+ }
+ }
+
+ /**
+ * This method extend edge (the line) by adding data from the edge in
+ * parameter.
+ *
+ * @param edge2
+ * edge that should be used for extension
+ */
+ public void extend(Edge edge2) {
+ // check if extension make sense (they should point to the same identifier)
+ if (!getEnd().equals(edge2.getStart())) {
+ throw new InvalidArgumentException(
+ getWarningPrefix() + edge2.getWarningPrefix() + " Cannot merge - anchor points doesn't match: " + getEnd() + "," + edge2.getStart());
+ }
+
+ if (line.getEndPoint().distance(edge2.getLine().getBeginPoint()) > EPSILON) {
+ throw new InvalidArgumentException(
+ getWarningPrefix() + edge2.getWarningPrefix() + " Cannot merge - edges are far from each other: " + line.getEndPoint() + ","
+ + edge2.getLine().getBeginPoint());
+ }
+
+ // graphId should be the same
+
+ // start should be taken from the original
+
+ // end should be taken from the extension
+ setEnd(edge2.getEnd());
+
+ // add points
+ for (int i = 1; i < edge2.getLine().getPoints().size(); i++) {
+ Point2D p = (Point2D) edge2.getLine().getPoints().get(i).clone();
+ line.addPoint(p);
+ }
+
+ // skip type
+
+ for (MiriamData md : edge2.getReferences()) {
+ addReference(new MiriamData(md));
+ }
+ anchors.addAll(edge2.getAnchors());
+ List<String> toAdd = new ArrayList<>();
+ for (String comment : edge2.getComments()) {
+ if (!comments.contains(comment)) {
+ toAdd.add(comment);
+ }
+ }
+ comments.addAll(toAdd);
+
+ // color should be skipped
+ if (!getColor().equals(edge2.getColor())) {
+ logger.warn(getWarningPrefix() + edge2.getWarningPrefix() + " Problem with merging. Edges have different colors.");
+ }
+
+ // add biopax references
+ biopaxReferences.addAll(edge2.getBiopaxReferences());
+
+ }
+
+ /**
+ * @return the color
+ * @see #color
+ */
+ public Color getColor() {
+ return line.getColor();
+ }
+
+ /**
+ * @param color
+ * the color to set
+ * @see #color
+ */
+ public void setColor(Color color) {
+ if (color != null) {
+ line.setColor(color);
+ }
+ }
+
+ /**
+ * @return the zOrder
+ * @see #zOrder
+ */
+ public Integer getzOrder() {
+ return zOrder;
+ }
+
+ /**
+ * @param zOrder
+ * the zOrder to set
+ * @see #zOrder
+ */
+ public void setzOrder(Integer zOrder) {
+ this.zOrder = zOrder;
+ }
+
+ /**
+ * Adds element to {@link #biopaxReferences}.
+ *
+ * @param reference
+ * reference to add
+ */
+ public void addBiopaxReference(String reference) {
+ biopaxReferences.add(reference);
+
+ }
+
+ /**
+ * @return the groupRef
+ * @see #groupRef
+ */
+ public String getGroupRef() {
+ return groupRef;
+ }
+
+ /**
+ * @param groupRef
+ * the groupRef to set
+ * @see #groupRef
+ */
+ public void setGroupRef(String groupRef) {
+ this.groupRef = groupRef;
+ }
+
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlInteractionType.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlInteractionType.java
index bf90e6facf..27c3cbc362 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlInteractionType.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlInteractionType.java
@@ -1,135 +1,135 @@
-package lcsb.mapviewer.wikipathway.model;
-
-/**
- * Enum representing all known GPML interaction (line) types.
- *
- * @author Piotr Gawron
- *
- */
-public enum GpmlInteractionType {
-
- /**
- * Simple line.
- */
- LINE(null), //
-
- /**
- * Arrow.
- */
- ARROW("Arrow"), //
-
- /**
- * T-bar.
- */
- TBAR("TBar"), //
-
- /**
- * Necessary stimulation.
- */
- NECESSARY_STIMULATION("mim-necessary-stimulation"), //
-
- /**
- * Binding.
- */
- BINDING("mim-binding"), //
-
- /**
- * Conversion.
- */
- CONVERSION("mim-conversion"), //
-
- /**
- * Stimulation.
- */
- STIMULATION("mim-stimulation"), //
-
- /**
- * Modification.
- */
- MODIFICATION("mim-modification"), //
-
- /**
- * Catalysis.
- */
- CATALYSIS("mim-catalysis"), //
-
- /**
- * Inhibition.
- */
- INHIBITION("mim-inhibition"), //
-
- /**
- * Cleavage.
- */
- CLEAVAGE("mim-cleavage"), //
-
- /**
- * Covalent bond.
- */
- COVALENT_BOND("mim-covalent-bond"), //
-
- /**
- * Branching (to the left).
- */
- BRANCHING_LEFT("mim-branching-left"), //
-
- /**
- * Branching (to the right).
- */
- BRANCHING_RIGHT("mim-branching-right"), //
-
- /**
- * Transcription, translation.
- */
- TRANSCRIPTION_TRANSLATION("mim-transcription-translation"), //
-
- /**
- * Gap.
- */
- GAP("mim-gap");
-
- /**
- * GPML string representing this type.
- */
- private String gpmlString;
-
- /**
- * Default constructor.
- *
- * @param gpmlString
- * {@link #gpmlString}
- */
- GpmlInteractionType(String gpmlString) {
- this.gpmlString = gpmlString;
- }
-
- /**
- * @return the gpmlString
- * @see #gpmlString
- */
- public String getGpmlString() {
- return gpmlString;
- }
-
- /**
- * Returns a type identified by the gpml string.
- *
- * @param gpmlString
- * string in GPML represetning type
- * @return type identified by the gpml string
- * @throws UnknownTypeException
- * thrown when type cannot be resolved
- */
- public static GpmlInteractionType getTypeByGpmlString(String gpmlString) throws UnknownTypeException {
- for (GpmlInteractionType type : values()) {
- if (type.getGpmlString() == null) {
- if (gpmlString == null || gpmlString.isEmpty()) {
- return type;
- }
- } else if (type.getGpmlString().equals(gpmlString)) {
- return type;
- }
- }
- throw new UnknownTypeException("Unknown gpml interaction type: " + gpmlString);
- }
-}
+package lcsb.mapviewer.wikipathway.model;
+
+/**
+ * Enum representing all known GPML interaction (line) types.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum GpmlInteractionType {
+
+ /**
+ * Simple line.
+ */
+ LINE(null), //
+
+ /**
+ * Arrow.
+ */
+ ARROW("Arrow"), //
+
+ /**
+ * T-bar.
+ */
+ TBAR("TBar"), //
+
+ /**
+ * Necessary stimulation.
+ */
+ NECESSARY_STIMULATION("mim-necessary-stimulation"), //
+
+ /**
+ * Binding.
+ */
+ BINDING("mim-binding"), //
+
+ /**
+ * Conversion.
+ */
+ CONVERSION("mim-conversion"), //
+
+ /**
+ * Stimulation.
+ */
+ STIMULATION("mim-stimulation"), //
+
+ /**
+ * Modification.
+ */
+ MODIFICATION("mim-modification"), //
+
+ /**
+ * Catalysis.
+ */
+ CATALYSIS("mim-catalysis"), //
+
+ /**
+ * Inhibition.
+ */
+ INHIBITION("mim-inhibition"), //
+
+ /**
+ * Cleavage.
+ */
+ CLEAVAGE("mim-cleavage"), //
+
+ /**
+ * Covalent bond.
+ */
+ COVALENT_BOND("mim-covalent-bond"), //
+
+ /**
+ * Branching (to the left).
+ */
+ BRANCHING_LEFT("mim-branching-left"), //
+
+ /**
+ * Branching (to the right).
+ */
+ BRANCHING_RIGHT("mim-branching-right"), //
+
+ /**
+ * Transcription, translation.
+ */
+ TRANSCRIPTION_TRANSLATION("mim-transcription-translation"), //
+
+ /**
+ * Gap.
+ */
+ GAP("mim-gap");
+
+ /**
+ * GPML string representing this type.
+ */
+ private String gpmlString;
+
+ /**
+ * Default constructor.
+ *
+ * @param gpmlString
+ * {@link #gpmlString}
+ */
+ GpmlInteractionType(String gpmlString) {
+ this.gpmlString = gpmlString;
+ }
+
+ /**
+ * @return the gpmlString
+ * @see #gpmlString
+ */
+ public String getGpmlString() {
+ return gpmlString;
+ }
+
+ /**
+ * Returns a type identified by the gpml string.
+ *
+ * @param gpmlString
+ * string in GPML represetning type
+ * @return type identified by the gpml string
+ * @throws UnknownTypeException
+ * thrown when type cannot be resolved
+ */
+ public static GpmlInteractionType getTypeByGpmlString(String gpmlString) throws UnknownTypeException {
+ for (GpmlInteractionType type : values()) {
+ if (type.getGpmlString() == null) {
+ if (gpmlString == null || gpmlString.isEmpty()) {
+ return type;
+ }
+ } else if (type.getGpmlString().equals(gpmlString)) {
+ return type;
+ }
+ }
+ throw new UnknownTypeException("Unknown gpml interaction type: " + gpmlString);
+ }
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlLineConnectorType.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlLineConnectorType.java
index 9b2b93097c..4724e464ff 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlLineConnectorType.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlLineConnectorType.java
@@ -1,73 +1,73 @@
-package lcsb.mapviewer.wikipathway.model;
-
-/**
- * Defines how lines are drawn in gpml format.
- *
- * @author Piotr Gawron
- *
- */
-public enum GpmlLineConnectorType {
-
- /**
- * Line is a curve.
- */
- CURVED("Curved"), //
-
- /**
- * Line is constructed from list of perpendicular segments.
- */
- ELBOW("Elbow"), //
-
- /**
- * It's a straight line from start point to the end point.
- */
- STRAIGHT("Straight"), //
-
- /**
- * Line is constructoed from list of segement lines.
- */
- SEGMENTED("Segmented");
-
- /**
- * String used in gpml to identify this specific connection type.
- */
- private String gpmlName;
-
- /**
- * Default constructor.
- *
- * @param gpmlName
- * {@link #gpmlName}
- */
- GpmlLineConnectorType(String gpmlName) {
- this.gpmlName = gpmlName;
- }
-
- /**
- * @return the gpmlName
- * @see #gpmlName
- */
- public String getGpmlName() {
- return gpmlName;
- }
-
- /**
- * Returns {@link GpmlLineConnectorType type} identified by {@link #gpmlName
- * gpml string} identifing the type.
- *
- * @param gpmlName
- * {@link #gpmlName}
- * @return {@link GpmlLineConnectorType type} identified by {@link #gpmlName
- * gpml string} identifing the type
- * @throws UnknownTypeException
- * thrown when type cannot be found
- */
- public static GpmlLineConnectorType getByGpmlName(String gpmlName) throws UnknownTypeException {
- for (GpmlLineConnectorType type : values()) {
- if (type.getGpmlName().equals(gpmlName)) {
- return type;
- }
- }
- throw new UnknownTypeException("Unknown type name: " + gpmlName);
- }
-}
+package lcsb.mapviewer.wikipathway.model;
+
+/**
+ * Defines how lines are drawn in gpml format.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum GpmlLineConnectorType {
+
+ /**
+ * Line is a curve.
+ */
+ CURVED("Curved"), //
+
+ /**
+ * Line is constructed from list of perpendicular segments.
+ */
+ ELBOW("Elbow"), //
+
+ /**
+ * It's a straight line from start point to the end point.
+ */
+ STRAIGHT("Straight"), //
+
+ /**
+ * Line is constructoed from list of segement lines.
+ */
+ SEGMENTED("Segmented");
+
+ /**
+ * String used in gpml to identify this specific connection type.
+ */
+ private String gpmlName;
+
+ /**
+ * Default constructor.
+ *
+ * @param gpmlName
+ * {@link #gpmlName}
+ */
+ GpmlLineConnectorType(String gpmlName) {
+ this.gpmlName = gpmlName;
+ }
+
+ /**
+ * @return the gpmlName
+ * @see #gpmlName
+ */
+ public String getGpmlName() {
+ return gpmlName;
+ }
+
+ /**
+ * Returns {@link GpmlLineConnectorType type} identified by {@link #gpmlName
+ * gpml string} identifing the type.
+ *
+ * @param gpmlName
+ * {@link #gpmlName}
+ * @return {@link GpmlLineConnectorType type} identified by {@link #gpmlName
+ * gpml string} identifing the type
+ * @throws UnknownTypeException
+ * thrown when type cannot be found
+ */
+ public static GpmlLineConnectorType getByGpmlName(String gpmlName) throws UnknownTypeException {
+ for (GpmlLineConnectorType type : values()) {
+ if (type.getGpmlName().equals(gpmlName)) {
+ return type;
+ }
+ }
+ throw new UnknownTypeException("Unknown type name: " + gpmlName);
+ }
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlLineType.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlLineType.java
index ff9085e27c..6f2c441646 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlLineType.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlLineType.java
@@ -1,85 +1,85 @@
-package lcsb.mapviewer.wikipathway.model;
-
-import lcsb.mapviewer.model.graphics.LineType;
-
-/**
- * This enum represents type of line in GPML format.
- *
- * @author Piotr Gawron
- *
- */
-public enum GpmlLineType {
-
- /**
- * Sold line (global representation: {@link LineType#SOLID}).
- */
- SOLID(null, LineType.SOLID), //
-
- /**
- * Dashed line (global representation: {@link LineType#DASHED}).
- */
- DASHED("Broken", LineType.DASHED);
-
- /**
- * String in GPML format representig this type.
- */
- private String gpmlString;
-
- /**
- * Which {@link LineType} in our model should be used for this GPML line type.
- */
- private LineType correspondingGlobalLineType;
-
- /**
- * Default constructor.
- *
- * @param gpmlString
- * {@link #gpmlString}
- * @param globalLineType
- * {@link #correspondingGlobalLineType}
- */
- GpmlLineType(String gpmlString, LineType globalLineType) {
- this.gpmlString = gpmlString;
- this.correspondingGlobalLineType = globalLineType;
- }
-
- /**
- * @return the gpmlString
- * @see #gpmlString
- */
- public String getGpmlString() {
- return gpmlString;
- }
-
- /**
- * @return the correspondingGlobalLineType
- * @see #correspondingGlobalLineType
- */
- public LineType getCorrespondingGlobalLineType() {
- return correspondingGlobalLineType;
- }
-
- /**
- * Returns {@link GpmlLineType type} identified by {@link #gpmlName gpml
- * string} identifing the type.
- *
- * @param gpmlName
- * {@link #gpmlString}
- * @return {@link GpmlLineType type} identified by {@link #gpmlName gpml
- * string} identifing the type
- * @throws UnknownTypeException
- * thrown when type cannot be found
- */
- public static GpmlLineType getByGpmlName(String gpmlName) throws UnknownTypeException {
- for (GpmlLineType type : values()) {
- if (type.getGpmlString() == null) {
- if (gpmlName == null) {
- return type;
- }
- } else if (type.getGpmlString().equals(gpmlName)) {
- return type;
- }
- }
- throw new UnknownTypeException("Unknown line type: " + gpmlName);
- }
-}
+package lcsb.mapviewer.wikipathway.model;
+
+import lcsb.mapviewer.model.graphics.LineType;
+
+/**
+ * This enum represents type of line in GPML format.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum GpmlLineType {
+
+ /**
+ * Sold line (global representation: {@link LineType#SOLID}).
+ */
+ SOLID(null, LineType.SOLID), //
+
+ /**
+ * Dashed line (global representation: {@link LineType#DASHED}).
+ */
+ DASHED("Broken", LineType.DASHED);
+
+ /**
+ * String in GPML format representig this type.
+ */
+ private String gpmlString;
+
+ /**
+ * Which {@link LineType} in our model should be used for this GPML line type.
+ */
+ private LineType correspondingGlobalLineType;
+
+ /**
+ * Default constructor.
+ *
+ * @param gpmlString
+ * {@link #gpmlString}
+ * @param globalLineType
+ * {@link #correspondingGlobalLineType}
+ */
+ GpmlLineType(String gpmlString, LineType globalLineType) {
+ this.gpmlString = gpmlString;
+ this.correspondingGlobalLineType = globalLineType;
+ }
+
+ /**
+ * @return the gpmlString
+ * @see #gpmlString
+ */
+ public String getGpmlString() {
+ return gpmlString;
+ }
+
+ /**
+ * @return the correspondingGlobalLineType
+ * @see #correspondingGlobalLineType
+ */
+ public LineType getCorrespondingGlobalLineType() {
+ return correspondingGlobalLineType;
+ }
+
+ /**
+ * Returns {@link GpmlLineType type} identified by {@link #gpmlName gpml
+ * string} identifing the type.
+ *
+ * @param gpmlName
+ * {@link #gpmlString}
+ * @return {@link GpmlLineType type} identified by {@link #gpmlName gpml
+ * string} identifing the type
+ * @throws UnknownTypeException
+ * thrown when type cannot be found
+ */
+ public static GpmlLineType getByGpmlName(String gpmlName) throws UnknownTypeException {
+ for (GpmlLineType type : values()) {
+ if (type.getGpmlString() == null) {
+ if (gpmlName == null) {
+ return type;
+ }
+ } else if (type.getGpmlString().equals(gpmlName)) {
+ return type;
+ }
+ }
+ throw new UnknownTypeException("Unknown line type: " + gpmlName);
+ }
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlModificationType.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlModificationType.java
index 47b8237bf1..8f63049790 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlModificationType.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlModificationType.java
@@ -1,136 +1,136 @@
-package lcsb.mapviewer.wikipathway.model;
-
-import lcsb.mapviewer.model.map.species.field.ModificationState;
-
-/**
- * This enum represents type of line in GPML format.
- *
- * @author Piotr Gawron
- *
- */
-public enum GpmlModificationType {
-
- /**
- * Gpml type representing: {@link ModificationState#PHOSPHORYLATED}.
- */
- PHOSPHORYLATED("P", ModificationState.PHOSPHORYLATED), //
-
- /**
- * Gpml type representing: {@link ModificationState#ACETYLATED}.
- */
- ACETYLATED("Ac", ModificationState.ACETYLATED), //
-
- /**
- * Gpml type representing: {@link ModificationState#UBIQUITINATED}.
- */
- UBIQUITINATED("Ub", ModificationState.UBIQUITINATED), //
-
- /**
- * Gpml type representing: {@link ModificationState#METHYLATED}.
- */
- METHYLATED("Me", ModificationState.METHYLATED), //
-
- /**
- * Gpml type representing: {@link ModificationState#HYDROXYLATED}.
- */
- HYDROXYLATED("OH", ModificationState.HYDROXYLATED), //
-
- /**
- * Gpml type representing: {@link ModificationState#MYRISTOYLATED}.
- */
- MYRISTOYLATED("My", ModificationState.MYRISTOYLATED), //
-
- /**
- * Gpml type representing: {@link ModificationState#SULFATED}.
- */
- SULFATED("S", ModificationState.SULFATED), //
-
- /**
- * Gpml type representing: {@link ModificationState#PRENYLATED}.
- */
- PRENYLATED("Pr", ModificationState.PRENYLATED), //
-
- /**
- * Gpml type representing: {@link ModificationState#GLYCOSYLATED}.
- */
- GLYCOSYLATED("G", ModificationState.GLYCOSYLATED), //
-
- /**
- * Gpml type representing: {@link ModificationState#PALMYTOYLATED}.
- */
- PALMYTOYLATED("Pa", ModificationState.PALMYTOYLATED), //
-
- /**
- * Gpml type representing: {@link ModificationState#UNKNOWN}.
- */
- UNKOWN("", ModificationState.UNKNOWN), //
-
- /**
- * Gpml type representing: {@link ModificationState#PROTONATED}.
- */
- PROTONATED("H", ModificationState.PROTONATED);
-
- /**
- * Default constructor.
- *
- * @param gpmlString
- * {@link #gpmlString}
- * @param correspondingModificationState
- * {@link #correspondingModificationState}
- */
- GpmlModificationType(String gpmlString, ModificationState correspondingModificationState) {
- this.gpmlString = gpmlString;
- this.correspondingModificationState = correspondingModificationState;
- }
-
- /**
- * String in GPML format representig this type.
- */
- private String gpmlString;
-
- /**
- * Which {@link ModificationState} in our model should be used for this GPML
- * modification type.
- */
- private ModificationState correspondingModificationState;
-
- /**
- * @return the gpmlString
- * @see #gpmlString
- */
- public String getGpmlString() {
- return gpmlString;
- }
-
- /**
- * Returns {@link GpmlModificationType type} identified by {@link #gpmlName
- * gpml string} identifing the type.
- *
- * @param gpmlName
- * {@link #gpmlString}
- * @return {@link GpmlModificationType type} identified by {@link #gpmlName
- * gpml string} identifing the type
- * @throws UnknownTypeException
- * thrown when type cannot be found
- */
- public static GpmlModificationType getByGpmlName(String gpmlName) throws UnknownTypeException {
- for (GpmlModificationType type : values()) {
- if (type.getGpmlString() == null) {
- if (gpmlName == null) {
- return type;
- }
- } else if (type.getGpmlString().equalsIgnoreCase(gpmlName)) {
- return type;
- }
- }
- throw new UnknownTypeException("Unknown state type: " + gpmlName);
- }
-
- /**
- * @return the correspondingModificationState
- * @see #correspondingModificationState
- */
- public ModificationState getCorrespondingModificationState() {
- return correspondingModificationState;
- }
-}
+package lcsb.mapviewer.wikipathway.model;
+
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+
+/**
+ * This enum represents type of line in GPML format.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum GpmlModificationType {
+
+ /**
+ * Gpml type representing: {@link ModificationState#PHOSPHORYLATED}.
+ */
+ PHOSPHORYLATED("P", ModificationState.PHOSPHORYLATED), //
+
+ /**
+ * Gpml type representing: {@link ModificationState#ACETYLATED}.
+ */
+ ACETYLATED("Ac", ModificationState.ACETYLATED), //
+
+ /**
+ * Gpml type representing: {@link ModificationState#UBIQUITINATED}.
+ */
+ UBIQUITINATED("Ub", ModificationState.UBIQUITINATED), //
+
+ /**
+ * Gpml type representing: {@link ModificationState#METHYLATED}.
+ */
+ METHYLATED("Me", ModificationState.METHYLATED), //
+
+ /**
+ * Gpml type representing: {@link ModificationState#HYDROXYLATED}.
+ */
+ HYDROXYLATED("OH", ModificationState.HYDROXYLATED), //
+
+ /**
+ * Gpml type representing: {@link ModificationState#MYRISTOYLATED}.
+ */
+ MYRISTOYLATED("My", ModificationState.MYRISTOYLATED), //
+
+ /**
+ * Gpml type representing: {@link ModificationState#SULFATED}.
+ */
+ SULFATED("S", ModificationState.SULFATED), //
+
+ /**
+ * Gpml type representing: {@link ModificationState#PRENYLATED}.
+ */
+ PRENYLATED("Pr", ModificationState.PRENYLATED), //
+
+ /**
+ * Gpml type representing: {@link ModificationState#GLYCOSYLATED}.
+ */
+ GLYCOSYLATED("G", ModificationState.GLYCOSYLATED), //
+
+ /**
+ * Gpml type representing: {@link ModificationState#PALMYTOYLATED}.
+ */
+ PALMYTOYLATED("Pa", ModificationState.PALMYTOYLATED), //
+
+ /**
+ * Gpml type representing: {@link ModificationState#UNKNOWN}.
+ */
+ UNKOWN("", ModificationState.UNKNOWN), //
+
+ /**
+ * Gpml type representing: {@link ModificationState#PROTONATED}.
+ */
+ PROTONATED("H", ModificationState.PROTONATED);
+
+ /**
+ * Default constructor.
+ *
+ * @param gpmlString
+ * {@link #gpmlString}
+ * @param correspondingModificationState
+ * {@link #correspondingModificationState}
+ */
+ GpmlModificationType(String gpmlString, ModificationState correspondingModificationState) {
+ this.gpmlString = gpmlString;
+ this.correspondingModificationState = correspondingModificationState;
+ }
+
+ /**
+ * String in GPML format representig this type.
+ */
+ private String gpmlString;
+
+ /**
+ * Which {@link ModificationState} in our model should be used for this GPML
+ * modification type.
+ */
+ private ModificationState correspondingModificationState;
+
+ /**
+ * @return the gpmlString
+ * @see #gpmlString
+ */
+ public String getGpmlString() {
+ return gpmlString;
+ }
+
+ /**
+ * Returns {@link GpmlModificationType type} identified by {@link #gpmlName
+ * gpml string} identifing the type.
+ *
+ * @param gpmlName
+ * {@link #gpmlString}
+ * @return {@link GpmlModificationType type} identified by {@link #gpmlName
+ * gpml string} identifing the type
+ * @throws UnknownTypeException
+ * thrown when type cannot be found
+ */
+ public static GpmlModificationType getByGpmlName(String gpmlName) throws UnknownTypeException {
+ for (GpmlModificationType type : values()) {
+ if (type.getGpmlString() == null) {
+ if (gpmlName == null) {
+ return type;
+ }
+ } else if (type.getGpmlString().equalsIgnoreCase(gpmlName)) {
+ return type;
+ }
+ }
+ throw new UnknownTypeException("Unknown state type: " + gpmlName);
+ }
+
+ /**
+ * @return the correspondingModificationState
+ * @see #correspondingModificationState
+ */
+ public ModificationState getCorrespondingModificationState() {
+ return correspondingModificationState;
+ }
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlStateType.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlStateType.java
index d8ecde2aa6..87129f1689 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlStateType.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GpmlStateType.java
@@ -1,87 +1,87 @@
-package lcsb.mapviewer.wikipathway.model;
-
-/**
- * This enum represents type of line in GPML format.
- *
- * @author Piotr Gawron
- *
- */
-public enum GpmlStateType {
-
- /**
- * Gpml type representing "GTP"
- * {@link lcsb.mapviewer.model.map.species.Protein#structuralState state of
- * Protein}.
- */
- GTP("GTP", "GTP"), //
-
- /**
- * Gpml type representing "GDP"
- * {@link lcsb.mapviewer.model.map.species.Protein#structuralState state of
- * Protein}.
- */
- GDP("GDP", "GDP");
-
- /**
- * Default constructor.
- *
- * @param gpmlString
- * {@link #gpmlString}
- * @param stringRepresenation
- * {@link #stringRepresenation}
- */
- GpmlStateType(String gpmlString, String stringRepresenation) {
- this.gpmlString = gpmlString;
- this.stringRepresenation = stringRepresenation;
- }
-
- /**
- * String in GPML format representig this type.
- */
- private String gpmlString;
-
- /**
- * String that should be used in our representation.
- */
- private String stringRepresenation;
-
- /**
- * @return the gpmlString
- * @see #gpmlString
- */
- public String getGpmlString() {
- return gpmlString;
- }
-
- /**
- * Returns {@link GpmlStateType type} identified by {@link #gpmlName gpml
- * string} identifing the type.
- *
- * @param gpmlName
- * {@link #gpmlString}
- * @return {@link GpmlStateType type} identified by {@link #gpmlName gpml
- * string} identifing the type
- * @throws UnknownTypeException
- * thrown when type cannot be found
- */
- public static GpmlStateType getByGpmlName(String gpmlName) throws UnknownTypeException {
- for (GpmlStateType type : values()) {
- if (type.getGpmlString() == null) {
- if (gpmlName == null) {
- return type;
- }
- } else if (type.getGpmlString().equalsIgnoreCase(gpmlName)) {
- return type;
- }
- }
- throw new UnknownTypeException("Unknown state type: " + gpmlName);
- }
-
- /**
- * @return the stringRepresenation
- * @see #stringRepresenation
- */
- public String getStringRepresenation() {
- return stringRepresenation;
- }
-}
+package lcsb.mapviewer.wikipathway.model;
+
+/**
+ * This enum represents type of line in GPML format.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum GpmlStateType {
+
+ /**
+ * Gpml type representing "GTP"
+ * {@link lcsb.mapviewer.model.map.species.Protein#structuralState state of
+ * Protein}.
+ */
+ GTP("GTP", "GTP"), //
+
+ /**
+ * Gpml type representing "GDP"
+ * {@link lcsb.mapviewer.model.map.species.Protein#structuralState state of
+ * Protein}.
+ */
+ GDP("GDP", "GDP");
+
+ /**
+ * Default constructor.
+ *
+ * @param gpmlString
+ * {@link #gpmlString}
+ * @param stringRepresenation
+ * {@link #stringRepresenation}
+ */
+ GpmlStateType(String gpmlString, String stringRepresenation) {
+ this.gpmlString = gpmlString;
+ this.stringRepresenation = stringRepresenation;
+ }
+
+ /**
+ * String in GPML format representig this type.
+ */
+ private String gpmlString;
+
+ /**
+ * String that should be used in our representation.
+ */
+ private String stringRepresenation;
+
+ /**
+ * @return the gpmlString
+ * @see #gpmlString
+ */
+ public String getGpmlString() {
+ return gpmlString;
+ }
+
+ /**
+ * Returns {@link GpmlStateType type} identified by {@link #gpmlName gpml
+ * string} identifing the type.
+ *
+ * @param gpmlName
+ * {@link #gpmlString}
+ * @return {@link GpmlStateType type} identified by {@link #gpmlName gpml
+ * string} identifing the type
+ * @throws UnknownTypeException
+ * thrown when type cannot be found
+ */
+ public static GpmlStateType getByGpmlName(String gpmlName) throws UnknownTypeException {
+ for (GpmlStateType type : values()) {
+ if (type.getGpmlString() == null) {
+ if (gpmlName == null) {
+ return type;
+ }
+ } else if (type.getGpmlString().equalsIgnoreCase(gpmlName)) {
+ return type;
+ }
+ }
+ throw new UnknownTypeException("Unknown state type: " + gpmlName);
+ }
+
+ /**
+ * @return the stringRepresenation
+ * @see #stringRepresenation
+ */
+ public String getStringRepresenation() {
+ return stringRepresenation;
+ }
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Graph.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Graph.java
index 6a95c94342..59ac161bbc 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Graph.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Graph.java
@@ -1,583 +1,583 @@
-package lcsb.mapviewer.wikipathway.model;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.wikipathway.model.biopax.BiopaxData;
-
-import org.apache.log4j.Logger;
-
-/**
- * This class models nodes and reaction from PathVisio for easy(?) conversion to
- * Model.
- *
- * @author Jan Badura
- *
- */
-public class Graph implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default width of the graphic model.
- */
- private static final double DEFAULT_MODEL_WIDTH = 1024.0;
-
- /**
- * Default height of the graphic model.
- */
- private static final double DEFAULT_MODEL_HEIGHT = 1024.0;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(Graph.class);
-
- /**
- * Height of the model.
- */
- private double boardHeight;
-
- /**
- * Information about biopax data in the gpml file.
- */
- private BiopaxData biopaxData;
-
- /**
- * Width of the model.
- */
- private double boardWidth;
-
- /**
- * All {@link PathwayElement nodes} in the model identified by the
- * {@link PathwayElement#graphId}.
- */
- private Map<String, PathwayElement> nodes;
-
- /**
- * All {@link Group groups} in the model identified by the
- * {@link PathwayElement#graphId}.
- */
- private Map<String, Group> groupsByGraphId;
-
- /**
- * All {@link Group groups} in the model identified by the
- * {@link Group#groupId}.
- */
- private Map<String, Group> groupsByGroupId;
-
- /**
- * All {@link DataNode data nodes} in the model identified by the
- * {@link PathwayElement#graphId}.
- */
- private Map<String, DataNode> dataNodes;
-
- /**
- * All {@link Label labvels} in the model identified by the
- * {@link PathwayElement#graphId}.
- */
- private Map<String, Label> labels;
-
- /**
- * All {@link Shape shapes} in the model identified by the
- * {@link PathwayElement#graphId}.
- */
- private Map<String, Shape> shapes;
-
- /**
- * All {@link Edge edges} in the model identified by the {@link Edge#graphId}.
- */
- private Map<String, Edge> edges;
-
- /**
- * {@link Edge Edges} in the model identified by anchors .
- */
- private Map<String, Edge> anchorToEdge;
-
- /**
- * All {@link Interaction interactions} in the model identified by the
- * {@link Interaction#graphId}.
- */
- private Map<String, Interaction> interactions;
-
- /**
- * Comments on the model.
- */
- private List<String> comments = new ArrayList<>();
-
- /**
- * Pathvisio attributes of the model.
- */
- private Map<String, String> attributes = new HashMap<String, String>();
-
- /**
- * List of identifiers used by biopax nodes that are inside gpml. These biopax
- * nodes contain annotations.
- */
- private List<String> biopaxReferences = new ArrayList<String>();
-
- /**
- * List of lines in gpml model.
- */
- private List<PolylineData> lines = new ArrayList<PolylineData>();
-
- /**
- * List of states in gpml model.
- */
- private List<State> states = new ArrayList<State>();
-
- /**
- * Default constructor.
- */
- public Graph() {
- boardHeight = DEFAULT_MODEL_HEIGHT;
- boardWidth = DEFAULT_MODEL_WIDTH;
- nodes = new HashMap<String, PathwayElement>();
- groupsByGraphId = new HashMap<String, Group>();
- groupsByGroupId = new HashMap<String, Group>();
- dataNodes = new HashMap<String, DataNode>();
- labels = new HashMap<String, Label>();
- shapes = new HashMap<String, Shape>();
- edges = new HashMap<String, Edge>();
- anchorToEdge = new HashMap<String, Edge>();
- interactions = new HashMap<String, Interaction>();
- }
-
- /**
- * Adds {@link Group} to model.
- *
- * @param group
- * object to add
- */
- public void addGroup(Group group) {
- groupsByGraphId.put(group.getGraphId(), group);
- groupsByGroupId.put(group.getGroupId(), group);
- nodes.put(group.getGraphId(), group);
- }
-
- /**
- * Adds {@link DataNode} to model.
- *
- * @param node
- * object to add
- */
- public void addDataNode(DataNode node) {
- dataNodes.put(node.getGraphId(), node);
- nodes.put(node.getGraphId(), node);
- if (node.getGroupRef() != null && !node.getGroupRef().equals("")) {
- groupsByGroupId.get(node.getGroupRef()).addNode(node);
- }
- }
-
- /**
- * Adds {@link Label} to model.
- *
- * @param label
- * object to add
- */
- public void addLabel(Label label) {
- labels.put(label.getGraphId(), label);
- nodes.put(label.getGraphId(), label);
- if (label.getGroupRef() != null && !label.getGroupRef().equals("")) {
- groupsByGroupId.get(label.getGroupRef()).addNode(label);
- }
- }
-
- /**
- * Adds {@link Shape} to model.
- *
- * @param shape
- * object to add
- */
- public void addShape(Shape shape) {
- shapes.put(shape.getGraphId(), shape);
- nodes.put(shape.getGraphId(), shape);
- if (shape.getGroupRef() != null && !shape.getGroupRef().equals("")) {
- groupsByGroupId.get(shape.getGroupRef()).addNode(shape);
- }
- }
-
- /**
- * Adds {@link Edge} to model.
- *
- * @param edge
- * object to add
- */
- public void addEdge(Edge edge) {
- edges.put(edge.getGraphId(), edge);
- for (String anchor : edge.getAnchors()) {
- anchorToEdge.put(anchor, edge);
- }
- }
-
- /**
- * Adds {@link Interaction} to model.
- *
- * @param interaction
- * object to add
- */
- public void addInteraction(Interaction interaction) {
- interactions.put(interaction.getGraphId(), interaction);
- }
-
- /**
- * Returns {@link PathwayElement} identified by {@link PathwayElement#graphId}
- * .
- *
- * @param graphId
- * identifier
- * @return {@link PathwayElement} identified by {@link PathwayElement#graphId}
- */
- public PathwayElement getNodeByGraphId(String graphId) {
- return nodes.get(graphId);
- }
-
- /**
- * Returns collection of {@link Group groups} in the model.
- *
- * @return collection of {@link Group groups} in the model
- */
- public Collection<Group> getGroups() {
- return groupsByGraphId.values();
- }
-
- /**
- * Returns {@link Group} identified by {@link Group#groupId}.
- *
- * @param groupId
- * identifier
- * @return {@link Group} identified by {@link Group#groupId}
- */
- public Group getGroupByGroupId(String groupId) {
- return groupsByGroupId.get(groupId);
- }
-
- /**
- * Returns set of {@link DataNode data nodes} in model.
- *
- * @return set of {@link DataNode data nodes} in model
- */
- public Collection<DataNode> getDataNodes() {
- return dataNodes.values();
- }
-
- /**
- * Returns set of {@link Label labels} in model.
- *
- * @return set of {@link Label labels} in model.
- */
- public Collection<Label> getLabels() {
- return labels.values();
- }
-
- /**
- * Returns {@link Label} identified by {@link PathwayElement#graphId}.
- *
- * @param graphId
- * identifier
- * @return {@link Label} identified by {@link PathwayElement#graphId}.
- */
- public Label getLabelByGraphId(String graphId) {
- return labels.get(graphId);
- }
-
- /**
- * Returns set of {@link Shape shapes} in the model.
- *
- * @return set of {@link Shape shapes} in the model.
- */
- public Collection<Shape> getShapes() {
- return shapes.values();
- }
-
- /**
- * Returns {@link Shape} identified by {@link PathwayElement#graphId}.
- *
- * @param graphId
- * identifier
- * @return {@link Shape} identified by {@link PathwayElement#graphId}
- */
- public Shape getShapeByGraphId(String graphId) {
- return shapes.get(graphId);
- }
-
- /**
- * Returns set of {@link Edge edges} in the model.
- *
- * @return set of {@link Edge edges} in the model
- */
- public Collection<Edge> getEdges() {
- return edges.values();
- }
-
- /**
- * Return {@link Edge} pointed by the anchor.
- *
- * @param anchor
- * anchor string identifier
- * @return {@link Edge} pointed by the anchor
- */
- public Edge getEdgeByAnchor(String anchor) {
- return anchorToEdge.get(anchor);
- }
-
- /**
- * Returns set of {@link Interaction interactions} in the model.
- *
- * @return set of {@link Interaction interactions} in the model
- */
- public Collection<Interaction> getInteractions() {
- return interactions.values();
- }
-
- /**
- * Returns {@link Interaction} identified by {@link Interaction#graphId}.
- *
- * @param graphId
- * identifier
- * @return {@link Interaction} identified by {@link Interaction#graphId}
- */
- public Interaction getInteractionByGraphId(String graphId) {
- return interactions.get(graphId);
- }
-
- /**
- * @return the boardHeight
- * @see #boardHeight
- */
- public double getBoardHeight() {
- return boardHeight;
- }
-
- /**
- * @param boardHeight
- * the boardHeight to set
- * @see #boardHeight
- */
- public void setBoardHeight(double boardHeight) {
- this.boardHeight = boardHeight;
- }
-
- /**
- * @return the boardWidth
- * @see #boardWidth
- */
- public double getBoardWidth() {
- return boardWidth;
- }
-
- /**
- * @param boardWidth
- * the boardWidth to set
- * @see #boardWidth
- */
- public void setBoardWidth(double boardWidth) {
- this.boardWidth = boardWidth;
- }
-
- /**
- * @return the comments
- * @see #comments
- */
- public List<String> getComments() {
- return comments;
- }
-
- /**
- * @param comment
- * the comment to add
- * @see #comments
- */
- public void addComment(String comment) {
- this.comments.add(comment);
- }
-
- /**
- * @return the biopaxData
- * @see #biopaxData
- */
- public BiopaxData getBiopaxData() {
- return biopaxData;
- }
-
- /**
- * @param biopaxData
- * the biopaxData to set
- * @see #biopaxData
- */
- public void setBiopaxData(BiopaxData biopaxData) {
- this.biopaxData = biopaxData;
- }
-
- /**
- * @return the attributesMap
- * @see #attributes
- */
- public Map<String, String> getAttributes() {
- return attributes;
- }
-
- /**
- * @param attributesMap
- * the attributesMap to set
- * @see #attributes
- */
- public void setAttributes(Map<String, String> attributesMap) {
- this.attributes = attributesMap;
- }
-
- /**
- * @return the biopaxReferences
- * @see #biopaxReferences
- */
- public List<String> getBiopaxReferences() {
- return biopaxReferences;
- }
-
- /**
- * @param biopaxReference
- * the biopaxReference to add
- * @see #biopaxReferences
- */
- public void addBiopaxReferences(String biopaxReference) {
- this.biopaxReferences.add(biopaxReference);
- }
-
- /**
- * @return the lines
- * @see #lines
- */
- public List<PolylineData> getLines() {
- return lines;
- }
-
- /**
- * @param line
- * the line to add
- * @see #lines
- */
- public void addLine(PolylineData line) {
- this.lines.add(line);
- }
-
- /**
- * @param lines
- * the lines to add
- * @see #lines
- */
- public void addLines(Collection<PolylineData> lines) {
- this.lines.addAll(lines);
- }
-
- /**
- * Adds edges to the model.
- *
- * @param parseEdgesFromLines
- * set of edges to add
- */
- public void addEdges(Collection<Edge> parseEdgesFromLines) {
- for (Edge edge : parseEdgesFromLines) {
- addEdge(edge);
- }
- }
-
- /**
- * Removes edge from the model.
- *
- * @param edge
- * object to remove
- */
- public void removeEdge(Edge edge) {
- edges.remove(edge.getGraphId(), edge);
- for (String anchor : edge.getAnchors()) {
- anchorToEdge.remove(anchor, edge);
- }
- }
-
- /**
- * Adds {@link DataNode data nodes} to the graph.
- *
- * @param nodes
- * object to add
- */
- public void addDataNodes(List<DataNode> nodes) {
- for (DataNode dataNode : nodes) {
- addDataNode(dataNode);
- }
- }
-
- /**
- * Adds {@link Label labels} to the graph.
- *
- * @param nodes
- * object to add
- */
- public void addLabels(List<Label> nodes) {
- for (Label label : nodes) {
- addLabel(label);
- }
-
- }
-
- /**
- * Adds {@link Shape shapes} to the graph.
- *
- * @param nodes
- * object to add
- */
- public void addShapes(List<Shape> nodes) {
- for (Shape shape : nodes) {
- addShape(shape);
- }
- }
-
- /**
- * Adds {@link State states} to the graph.
- *
- * @param parseCollection
- * collections of objects to add
- */
- public void addStates(List<State> parseCollection) {
- for (State state : parseCollection) {
- addState(state);
- }
-
- }
-
- /**
- * Adds {@link State} to the graph.
- *
- * @param state
- * object to add
- */
- private void addState(State state) {
- this.states.add(state);
- }
-
- /**
- * @return the states
- * @see #states
- */
- public List<State> getStates() {
- return states;
- }
-
- /**
- * @param states
- * the states to set
- * @see #states
- */
- public void setStates(List<State> states) {
- this.states = states;
- }
-
-}
+package lcsb.mapviewer.wikipathway.model;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.wikipathway.model.biopax.BiopaxData;
+
+import org.apache.log4j.Logger;
+
+/**
+ * This class models nodes and reaction from PathVisio for easy(?) conversion to
+ * Model.
+ *
+ * @author Jan Badura
+ *
+ */
+public class Graph implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default width of the graphic model.
+ */
+ private static final double DEFAULT_MODEL_WIDTH = 1024.0;
+
+ /**
+ * Default height of the graphic model.
+ */
+ private static final double DEFAULT_MODEL_HEIGHT = 1024.0;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(Graph.class);
+
+ /**
+ * Height of the model.
+ */
+ private double boardHeight;
+
+ /**
+ * Information about biopax data in the gpml file.
+ */
+ private BiopaxData biopaxData;
+
+ /**
+ * Width of the model.
+ */
+ private double boardWidth;
+
+ /**
+ * All {@link PathwayElement nodes} in the model identified by the
+ * {@link PathwayElement#graphId}.
+ */
+ private Map<String, PathwayElement> nodes;
+
+ /**
+ * All {@link Group groups} in the model identified by the
+ * {@link PathwayElement#graphId}.
+ */
+ private Map<String, Group> groupsByGraphId;
+
+ /**
+ * All {@link Group groups} in the model identified by the
+ * {@link Group#groupId}.
+ */
+ private Map<String, Group> groupsByGroupId;
+
+ /**
+ * All {@link DataNode data nodes} in the model identified by the
+ * {@link PathwayElement#graphId}.
+ */
+ private Map<String, DataNode> dataNodes;
+
+ /**
+ * All {@link Label labvels} in the model identified by the
+ * {@link PathwayElement#graphId}.
+ */
+ private Map<String, Label> labels;
+
+ /**
+ * All {@link Shape shapes} in the model identified by the
+ * {@link PathwayElement#graphId}.
+ */
+ private Map<String, Shape> shapes;
+
+ /**
+ * All {@link Edge edges} in the model identified by the {@link Edge#graphId}.
+ */
+ private Map<String, Edge> edges;
+
+ /**
+ * {@link Edge Edges} in the model identified by anchors .
+ */
+ private Map<String, Edge> anchorToEdge;
+
+ /**
+ * All {@link Interaction interactions} in the model identified by the
+ * {@link Interaction#graphId}.
+ */
+ private Map<String, Interaction> interactions;
+
+ /**
+ * Comments on the model.
+ */
+ private List<String> comments = new ArrayList<>();
+
+ /**
+ * Pathvisio attributes of the model.
+ */
+ private Map<String, String> attributes = new HashMap<String, String>();
+
+ /**
+ * List of identifiers used by biopax nodes that are inside gpml. These biopax
+ * nodes contain annotations.
+ */
+ private List<String> biopaxReferences = new ArrayList<String>();
+
+ /**
+ * List of lines in gpml model.
+ */
+ private List<PolylineData> lines = new ArrayList<PolylineData>();
+
+ /**
+ * List of states in gpml model.
+ */
+ private List<State> states = new ArrayList<State>();
+
+ /**
+ * Default constructor.
+ */
+ public Graph() {
+ boardHeight = DEFAULT_MODEL_HEIGHT;
+ boardWidth = DEFAULT_MODEL_WIDTH;
+ nodes = new HashMap<String, PathwayElement>();
+ groupsByGraphId = new HashMap<String, Group>();
+ groupsByGroupId = new HashMap<String, Group>();
+ dataNodes = new HashMap<String, DataNode>();
+ labels = new HashMap<String, Label>();
+ shapes = new HashMap<String, Shape>();
+ edges = new HashMap<String, Edge>();
+ anchorToEdge = new HashMap<String, Edge>();
+ interactions = new HashMap<String, Interaction>();
+ }
+
+ /**
+ * Adds {@link Group} to model.
+ *
+ * @param group
+ * object to add
+ */
+ public void addGroup(Group group) {
+ groupsByGraphId.put(group.getGraphId(), group);
+ groupsByGroupId.put(group.getGroupId(), group);
+ nodes.put(group.getGraphId(), group);
+ }
+
+ /**
+ * Adds {@link DataNode} to model.
+ *
+ * @param node
+ * object to add
+ */
+ public void addDataNode(DataNode node) {
+ dataNodes.put(node.getGraphId(), node);
+ nodes.put(node.getGraphId(), node);
+ if (node.getGroupRef() != null && !node.getGroupRef().equals("")) {
+ groupsByGroupId.get(node.getGroupRef()).addNode(node);
+ }
+ }
+
+ /**
+ * Adds {@link Label} to model.
+ *
+ * @param label
+ * object to add
+ */
+ public void addLabel(Label label) {
+ labels.put(label.getGraphId(), label);
+ nodes.put(label.getGraphId(), label);
+ if (label.getGroupRef() != null && !label.getGroupRef().equals("")) {
+ groupsByGroupId.get(label.getGroupRef()).addNode(label);
+ }
+ }
+
+ /**
+ * Adds {@link Shape} to model.
+ *
+ * @param shape
+ * object to add
+ */
+ public void addShape(Shape shape) {
+ shapes.put(shape.getGraphId(), shape);
+ nodes.put(shape.getGraphId(), shape);
+ if (shape.getGroupRef() != null && !shape.getGroupRef().equals("")) {
+ groupsByGroupId.get(shape.getGroupRef()).addNode(shape);
+ }
+ }
+
+ /**
+ * Adds {@link Edge} to model.
+ *
+ * @param edge
+ * object to add
+ */
+ public void addEdge(Edge edge) {
+ edges.put(edge.getGraphId(), edge);
+ for (String anchor : edge.getAnchors()) {
+ anchorToEdge.put(anchor, edge);
+ }
+ }
+
+ /**
+ * Adds {@link Interaction} to model.
+ *
+ * @param interaction
+ * object to add
+ */
+ public void addInteraction(Interaction interaction) {
+ interactions.put(interaction.getGraphId(), interaction);
+ }
+
+ /**
+ * Returns {@link PathwayElement} identified by {@link PathwayElement#graphId}
+ * .
+ *
+ * @param graphId
+ * identifier
+ * @return {@link PathwayElement} identified by {@link PathwayElement#graphId}
+ */
+ public PathwayElement getNodeByGraphId(String graphId) {
+ return nodes.get(graphId);
+ }
+
+ /**
+ * Returns collection of {@link Group groups} in the model.
+ *
+ * @return collection of {@link Group groups} in the model
+ */
+ public Collection<Group> getGroups() {
+ return groupsByGraphId.values();
+ }
+
+ /**
+ * Returns {@link Group} identified by {@link Group#groupId}.
+ *
+ * @param groupId
+ * identifier
+ * @return {@link Group} identified by {@link Group#groupId}
+ */
+ public Group getGroupByGroupId(String groupId) {
+ return groupsByGroupId.get(groupId);
+ }
+
+ /**
+ * Returns set of {@link DataNode data nodes} in model.
+ *
+ * @return set of {@link DataNode data nodes} in model
+ */
+ public Collection<DataNode> getDataNodes() {
+ return dataNodes.values();
+ }
+
+ /**
+ * Returns set of {@link Label labels} in model.
+ *
+ * @return set of {@link Label labels} in model.
+ */
+ public Collection<Label> getLabels() {
+ return labels.values();
+ }
+
+ /**
+ * Returns {@link Label} identified by {@link PathwayElement#graphId}.
+ *
+ * @param graphId
+ * identifier
+ * @return {@link Label} identified by {@link PathwayElement#graphId}.
+ */
+ public Label getLabelByGraphId(String graphId) {
+ return labels.get(graphId);
+ }
+
+ /**
+ * Returns set of {@link Shape shapes} in the model.
+ *
+ * @return set of {@link Shape shapes} in the model.
+ */
+ public Collection<Shape> getShapes() {
+ return shapes.values();
+ }
+
+ /**
+ * Returns {@link Shape} identified by {@link PathwayElement#graphId}.
+ *
+ * @param graphId
+ * identifier
+ * @return {@link Shape} identified by {@link PathwayElement#graphId}
+ */
+ public Shape getShapeByGraphId(String graphId) {
+ return shapes.get(graphId);
+ }
+
+ /**
+ * Returns set of {@link Edge edges} in the model.
+ *
+ * @return set of {@link Edge edges} in the model
+ */
+ public Collection<Edge> getEdges() {
+ return edges.values();
+ }
+
+ /**
+ * Return {@link Edge} pointed by the anchor.
+ *
+ * @param anchor
+ * anchor string identifier
+ * @return {@link Edge} pointed by the anchor
+ */
+ public Edge getEdgeByAnchor(String anchor) {
+ return anchorToEdge.get(anchor);
+ }
+
+ /**
+ * Returns set of {@link Interaction interactions} in the model.
+ *
+ * @return set of {@link Interaction interactions} in the model
+ */
+ public Collection<Interaction> getInteractions() {
+ return interactions.values();
+ }
+
+ /**
+ * Returns {@link Interaction} identified by {@link Interaction#graphId}.
+ *
+ * @param graphId
+ * identifier
+ * @return {@link Interaction} identified by {@link Interaction#graphId}
+ */
+ public Interaction getInteractionByGraphId(String graphId) {
+ return interactions.get(graphId);
+ }
+
+ /**
+ * @return the boardHeight
+ * @see #boardHeight
+ */
+ public double getBoardHeight() {
+ return boardHeight;
+ }
+
+ /**
+ * @param boardHeight
+ * the boardHeight to set
+ * @see #boardHeight
+ */
+ public void setBoardHeight(double boardHeight) {
+ this.boardHeight = boardHeight;
+ }
+
+ /**
+ * @return the boardWidth
+ * @see #boardWidth
+ */
+ public double getBoardWidth() {
+ return boardWidth;
+ }
+
+ /**
+ * @param boardWidth
+ * the boardWidth to set
+ * @see #boardWidth
+ */
+ public void setBoardWidth(double boardWidth) {
+ this.boardWidth = boardWidth;
+ }
+
+ /**
+ * @return the comments
+ * @see #comments
+ */
+ public List<String> getComments() {
+ return comments;
+ }
+
+ /**
+ * @param comment
+ * the comment to add
+ * @see #comments
+ */
+ public void addComment(String comment) {
+ this.comments.add(comment);
+ }
+
+ /**
+ * @return the biopaxData
+ * @see #biopaxData
+ */
+ public BiopaxData getBiopaxData() {
+ return biopaxData;
+ }
+
+ /**
+ * @param biopaxData
+ * the biopaxData to set
+ * @see #biopaxData
+ */
+ public void setBiopaxData(BiopaxData biopaxData) {
+ this.biopaxData = biopaxData;
+ }
+
+ /**
+ * @return the attributesMap
+ * @see #attributes
+ */
+ public Map<String, String> getAttributes() {
+ return attributes;
+ }
+
+ /**
+ * @param attributesMap
+ * the attributesMap to set
+ * @see #attributes
+ */
+ public void setAttributes(Map<String, String> attributesMap) {
+ this.attributes = attributesMap;
+ }
+
+ /**
+ * @return the biopaxReferences
+ * @see #biopaxReferences
+ */
+ public List<String> getBiopaxReferences() {
+ return biopaxReferences;
+ }
+
+ /**
+ * @param biopaxReference
+ * the biopaxReference to add
+ * @see #biopaxReferences
+ */
+ public void addBiopaxReferences(String biopaxReference) {
+ this.biopaxReferences.add(biopaxReference);
+ }
+
+ /**
+ * @return the lines
+ * @see #lines
+ */
+ public List<PolylineData> getLines() {
+ return lines;
+ }
+
+ /**
+ * @param line
+ * the line to add
+ * @see #lines
+ */
+ public void addLine(PolylineData line) {
+ this.lines.add(line);
+ }
+
+ /**
+ * @param lines
+ * the lines to add
+ * @see #lines
+ */
+ public void addLines(Collection<PolylineData> lines) {
+ this.lines.addAll(lines);
+ }
+
+ /**
+ * Adds edges to the model.
+ *
+ * @param parseEdgesFromLines
+ * set of edges to add
+ */
+ public void addEdges(Collection<Edge> parseEdgesFromLines) {
+ for (Edge edge : parseEdgesFromLines) {
+ addEdge(edge);
+ }
+ }
+
+ /**
+ * Removes edge from the model.
+ *
+ * @param edge
+ * object to remove
+ */
+ public void removeEdge(Edge edge) {
+ edges.remove(edge.getGraphId(), edge);
+ for (String anchor : edge.getAnchors()) {
+ anchorToEdge.remove(anchor, edge);
+ }
+ }
+
+ /**
+ * Adds {@link DataNode data nodes} to the graph.
+ *
+ * @param nodes
+ * object to add
+ */
+ public void addDataNodes(List<DataNode> nodes) {
+ for (DataNode dataNode : nodes) {
+ addDataNode(dataNode);
+ }
+ }
+
+ /**
+ * Adds {@link Label labels} to the graph.
+ *
+ * @param nodes
+ * object to add
+ */
+ public void addLabels(List<Label> nodes) {
+ for (Label label : nodes) {
+ addLabel(label);
+ }
+
+ }
+
+ /**
+ * Adds {@link Shape shapes} to the graph.
+ *
+ * @param nodes
+ * object to add
+ */
+ public void addShapes(List<Shape> nodes) {
+ for (Shape shape : nodes) {
+ addShape(shape);
+ }
+ }
+
+ /**
+ * Adds {@link State states} to the graph.
+ *
+ * @param parseCollection
+ * collections of objects to add
+ */
+ public void addStates(List<State> parseCollection) {
+ for (State state : parseCollection) {
+ addState(state);
+ }
+
+ }
+
+ /**
+ * Adds {@link State} to the graph.
+ *
+ * @param state
+ * object to add
+ */
+ private void addState(State state) {
+ this.states.add(state);
+ }
+
+ /**
+ * @return the states
+ * @see #states
+ */
+ public List<State> getStates() {
+ return states;
+ }
+
+ /**
+ * @param states
+ * the states to set
+ * @see #states
+ */
+ public void setStates(List<State> states) {
+ this.states = states;
+ }
+
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GraphicalPathwayElement.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GraphicalPathwayElement.java
index d18394bf1a..a16f5337f1 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GraphicalPathwayElement.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/GraphicalPathwayElement.java
@@ -1,253 +1,253 @@
-package lcsb.mapviewer.wikipathway.model;
-
-import java.awt.Color;
-import java.awt.font.TextAttribute;
-import java.awt.geom.Rectangle2D;
-import java.util.HashMap;
-import java.util.Map;
-
-import lcsb.mapviewer.common.geometry.TextAlignment;
-import lcsb.mapviewer.model.graphics.LineType;
-
-/**
- * Class with common data for all Gpml elements that have a graphical
- * representation on the map.
- *
- * @author Piotr Gawron
- *
- */
-public abstract class GraphicalPathwayElement extends PathwayElement {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Color.
- */
- private Color color = Color.BLACK;
-
- /**
- * Fill color.
- */
- private Color fillColor = Color.WHITE;
-
- /**
- * Name of the font used in drawing.
- */
- private String fontName;
-
- /**
- * Font size used for description.
- */
- private Double fontSize;
-
- /**
- * Rectangle border of the element.
- */
- private Rectangle2D rectangle;
-
- /**
- * {@link TextAttribute Font attributes}.
- */
- private Map<TextAttribute, Object> fontAttributes = new HashMap<>();
-
- /**
- * {@link TextAttribute Font attributes}.
- */
- private TextAlignment textAlignment = TextAlignment.LEFT;
-
- /**
- * Thickness of the line used to draw element.
- */
- private Double lineThickness = 1.0;
-
- /**
- * Type of line used to draw the element.
- */
- private LineType lineType = LineType.SOLID;
-
- /**
- * Default constructor.
- */
- public GraphicalPathwayElement() {
- super();
- }
-
- /**
- * Default constructor.
- *
- * @param graphId
- * {@link PathwayElement#graphId}
- */
- public GraphicalPathwayElement(String graphId) {
- super(graphId);
- }
-
- /**
- * @return the fontAttributes
- * @see #fontAttributes
- */
- public Map<TextAttribute, Object> getFontAttributes() {
- return fontAttributes;
- }
-
- /**
- * @param fontAttributes
- * the fontAttributes to set
- * @see #fontAttributes
- */
- public void setFontAttributes(Map<TextAttribute, Object> fontAttributes) {
- this.fontAttributes = fontAttributes;
- }
-
- /**
- * Adds font attribute.
- *
- * @param key
- * type of the attribute
- * @param value
- * value of the attribute
- */
- public void addFontAttribute(TextAttribute key, Object value) {
- fontAttributes.put(key, value);
- }
-
- /**
- * @return the textAlignment
- * @see #textAlignment
- */
- public TextAlignment getTextAlignment() {
- return textAlignment;
- }
-
- /**
- * @param textAlignment
- * the textAlignment to set
- * @see #textAlignment
- */
- public void setTextAlignment(TextAlignment textAlignment) {
- this.textAlignment = textAlignment;
- }
-
- /**
- * @return the fontSize
- * @see #fontSize
- */
- public Double getFontSize() {
- return fontSize;
- }
-
- /**
- * @param fontSize
- * the fontSize to set
- * @see #fontSize
- */
- public void setFontSize(Double fontSize) {
- this.fontSize = fontSize;
- }
-
- /**
- * @return the color
- * @see #color
- */
- public Color getColor() {
- return color;
- }
-
- /**
- * @param color
- * the color to set
- * @see #color
- */
- public void setColor(Color color) {
- if (color != null) {
- this.color = color;
- }
- }
-
- /**
- * @return the fillColor
- * @see #fillColor
- */
- public Color getFillColor() {
- return fillColor;
- }
-
- /**
- * @param fillColor
- * the fillColor to set
- * @see #fillColor
- */
- public void setFillColor(Color fillColor) {
- if (fillColor != null) {
- this.fillColor = fillColor;
- }
- }
-
- /**
- * @return the fontName
- * @see #fontName
- */
- public String getFontName() {
- return fontName;
- }
-
- /**
- * @param fontName
- * the fontName to set
- * @see #fontName
- */
- public void setFontName(String fontName) {
- this.fontName = fontName;
- }
-
- /**
- * @return the lineThickness
- * @see #lineThickness
- */
- public Double getLineThickness() {
- return lineThickness;
- }
-
- /**
- * @param lineThickness
- * the lineThickness to set
- * @see #lineThickness
- */
- public void setLineThickness(Double lineThickness) {
- this.lineThickness = lineThickness;
- }
-
- /**
- * @return the lineType
- * @see #lineType
- */
- public LineType getLineType() {
- return lineType;
- }
-
- /**
- * @param lineType
- * the lineType to set
- * @see #lineType
- */
- public void setLineType(LineType lineType) {
- this.lineType = lineType;
- }
-
- @Override
- public Rectangle2D getRectangle() {
- return rectangle;
- }
-
- /**
- * @param rectangle the rectangle to set
- * @see #rectangle
- */
- public void setRectangle(Rectangle2D rectangle) {
- this.rectangle = rectangle;
- }
-
-}
+package lcsb.mapviewer.wikipathway.model;
+
+import java.awt.Color;
+import java.awt.font.TextAttribute;
+import java.awt.geom.Rectangle2D;
+import java.util.HashMap;
+import java.util.Map;
+
+import lcsb.mapviewer.common.geometry.TextAlignment;
+import lcsb.mapviewer.model.graphics.LineType;
+
+/**
+ * Class with common data for all Gpml elements that have a graphical
+ * representation on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public abstract class GraphicalPathwayElement extends PathwayElement {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Color.
+ */
+ private Color color = Color.BLACK;
+
+ /**
+ * Fill color.
+ */
+ private Color fillColor = Color.WHITE;
+
+ /**
+ * Name of the font used in drawing.
+ */
+ private String fontName;
+
+ /**
+ * Font size used for description.
+ */
+ private Double fontSize;
+
+ /**
+ * Rectangle border of the element.
+ */
+ private Rectangle2D rectangle;
+
+ /**
+ * {@link TextAttribute Font attributes}.
+ */
+ private Map<TextAttribute, Object> fontAttributes = new HashMap<>();
+
+ /**
+ * {@link TextAttribute Font attributes}.
+ */
+ private TextAlignment textAlignment = TextAlignment.LEFT;
+
+ /**
+ * Thickness of the line used to draw element.
+ */
+ private Double lineThickness = 1.0;
+
+ /**
+ * Type of line used to draw the element.
+ */
+ private LineType lineType = LineType.SOLID;
+
+ /**
+ * Default constructor.
+ */
+ public GraphicalPathwayElement() {
+ super();
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param graphId
+ * {@link PathwayElement#graphId}
+ */
+ public GraphicalPathwayElement(String graphId) {
+ super(graphId);
+ }
+
+ /**
+ * @return the fontAttributes
+ * @see #fontAttributes
+ */
+ public Map<TextAttribute, Object> getFontAttributes() {
+ return fontAttributes;
+ }
+
+ /**
+ * @param fontAttributes
+ * the fontAttributes to set
+ * @see #fontAttributes
+ */
+ public void setFontAttributes(Map<TextAttribute, Object> fontAttributes) {
+ this.fontAttributes = fontAttributes;
+ }
+
+ /**
+ * Adds font attribute.
+ *
+ * @param key
+ * type of the attribute
+ * @param value
+ * value of the attribute
+ */
+ public void addFontAttribute(TextAttribute key, Object value) {
+ fontAttributes.put(key, value);
+ }
+
+ /**
+ * @return the textAlignment
+ * @see #textAlignment
+ */
+ public TextAlignment getTextAlignment() {
+ return textAlignment;
+ }
+
+ /**
+ * @param textAlignment
+ * the textAlignment to set
+ * @see #textAlignment
+ */
+ public void setTextAlignment(TextAlignment textAlignment) {
+ this.textAlignment = textAlignment;
+ }
+
+ /**
+ * @return the fontSize
+ * @see #fontSize
+ */
+ public Double getFontSize() {
+ return fontSize;
+ }
+
+ /**
+ * @param fontSize
+ * the fontSize to set
+ * @see #fontSize
+ */
+ public void setFontSize(Double fontSize) {
+ this.fontSize = fontSize;
+ }
+
+ /**
+ * @return the color
+ * @see #color
+ */
+ public Color getColor() {
+ return color;
+ }
+
+ /**
+ * @param color
+ * the color to set
+ * @see #color
+ */
+ public void setColor(Color color) {
+ if (color != null) {
+ this.color = color;
+ }
+ }
+
+ /**
+ * @return the fillColor
+ * @see #fillColor
+ */
+ public Color getFillColor() {
+ return fillColor;
+ }
+
+ /**
+ * @param fillColor
+ * the fillColor to set
+ * @see #fillColor
+ */
+ public void setFillColor(Color fillColor) {
+ if (fillColor != null) {
+ this.fillColor = fillColor;
+ }
+ }
+
+ /**
+ * @return the fontName
+ * @see #fontName
+ */
+ public String getFontName() {
+ return fontName;
+ }
+
+ /**
+ * @param fontName
+ * the fontName to set
+ * @see #fontName
+ */
+ public void setFontName(String fontName) {
+ this.fontName = fontName;
+ }
+
+ /**
+ * @return the lineThickness
+ * @see #lineThickness
+ */
+ public Double getLineThickness() {
+ return lineThickness;
+ }
+
+ /**
+ * @param lineThickness
+ * the lineThickness to set
+ * @see #lineThickness
+ */
+ public void setLineThickness(Double lineThickness) {
+ this.lineThickness = lineThickness;
+ }
+
+ /**
+ * @return the lineType
+ * @see #lineType
+ */
+ public LineType getLineType() {
+ return lineType;
+ }
+
+ /**
+ * @param lineType
+ * the lineType to set
+ * @see #lineType
+ */
+ public void setLineType(LineType lineType) {
+ this.lineType = lineType;
+ }
+
+ @Override
+ public Rectangle2D getRectangle() {
+ return rectangle;
+ }
+
+ /**
+ * @param rectangle the rectangle to set
+ * @see #rectangle
+ */
+ public void setRectangle(Rectangle2D rectangle) {
+ this.rectangle = rectangle;
+ }
+
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Group.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Group.java
index 93474edfd2..954b92053a 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Group.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Group.java
@@ -1,135 +1,135 @@
-package lcsb.mapviewer.wikipathway.model;
-
-import java.awt.geom.Rectangle2D;
-import java.util.HashSet;
-import java.util.Set;
-
-/**
- * Class used to store data from Group from .gpml.
- *
- * @author Jan Badura
- *
- */
-public class Group extends PathwayElement {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Margin used when retrieving rectangle border of the group (result rectangle
- * will by wider and higher in every direction by this value).
- */
- private static final int RECTANGLE_BORDER_MARGIN = 8;
-
- /**
- * Identifier of the group.
- */
- private String groupId;
-
- /**
- * Style of the group.
- */
- private String style;
-
- /**
- * Elements in the group.
- */
- private Set<PathwayElement> nodes;
-
- /**
- * Default constructor.
- *
- * @param graphId
- * graph identifier in the model
- * @param groupId
- * {@link #groupId}
- */
- public Group(String graphId, String groupId) {
- super(graphId);
- this.groupId = groupId;
- nodes = new HashSet<PathwayElement>();
- }
-
- /**
- * Empty constructor that should be used only by serialization tools and
- * subclasses.
- */
- protected Group() {
- }
-
- @Override
- public String getName() {
- StringBuilder sb = new StringBuilder("");
- for (PathwayElement n : nodes) {
- sb.append(n.getName() + ":");
- }
- return sb.toString();
- }
-
- @Override
- public Rectangle2D getRectangle() {
-
- Rectangle2D result = null;
- boolean first = true;
-
- for (PathwayElement n : nodes) {
- if (first) {
- result = (Rectangle2D) n.getRectangle().clone();
- first = false;
- }
- Rectangle2D.union(result, n.getRectangle(), result);
- }
- if (result == null) {
- return null;
- }
- result.setRect(
- result.getX() - RECTANGLE_BORDER_MARGIN, result.getY() - RECTANGLE_BORDER_MARGIN, result.getWidth() + 2 * RECTANGLE_BORDER_MARGIN, result.getHeight()
- + 2 * RECTANGLE_BORDER_MARGIN);
- return result;
- }
-
- /**
- *
- * @return {@link #groupId}
- */
- public String getGroupId() {
- return groupId;
- }
-
- /**
- * Adds element to group.
- *
- * @param pe
- * object to add
- */
- public void addNode(PathwayElement pe) {
- nodes.add(pe);
- }
-
- /**
- *
- * @return {@link #nodes}
- */
- public Set<PathwayElement> getNodes() {
- return this.nodes;
- }
-
- /**
- * @return the style
- * @see #style
- */
- public String getStyle() {
- return style;
- }
-
- /**
- * @param style the style to set
- * @see #style
- */
- public void setStyle(String style) {
- this.style = style;
- }
-
-}
+package lcsb.mapviewer.wikipathway.model;
+
+import java.awt.geom.Rectangle2D;
+import java.util.HashSet;
+import java.util.Set;
+
+/**
+ * Class used to store data from Group from .gpml.
+ *
+ * @author Jan Badura
+ *
+ */
+public class Group extends PathwayElement {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Margin used when retrieving rectangle border of the group (result rectangle
+ * will by wider and higher in every direction by this value).
+ */
+ private static final int RECTANGLE_BORDER_MARGIN = 8;
+
+ /**
+ * Identifier of the group.
+ */
+ private String groupId;
+
+ /**
+ * Style of the group.
+ */
+ private String style;
+
+ /**
+ * Elements in the group.
+ */
+ private Set<PathwayElement> nodes;
+
+ /**
+ * Default constructor.
+ *
+ * @param graphId
+ * graph identifier in the model
+ * @param groupId
+ * {@link #groupId}
+ */
+ public Group(String graphId, String groupId) {
+ super(graphId);
+ this.groupId = groupId;
+ nodes = new HashSet<PathwayElement>();
+ }
+
+ /**
+ * Empty constructor that should be used only by serialization tools and
+ * subclasses.
+ */
+ protected Group() {
+ }
+
+ @Override
+ public String getName() {
+ StringBuilder sb = new StringBuilder("");
+ for (PathwayElement n : nodes) {
+ sb.append(n.getName() + ":");
+ }
+ return sb.toString();
+ }
+
+ @Override
+ public Rectangle2D getRectangle() {
+
+ Rectangle2D result = null;
+ boolean first = true;
+
+ for (PathwayElement n : nodes) {
+ if (first) {
+ result = (Rectangle2D) n.getRectangle().clone();
+ first = false;
+ }
+ Rectangle2D.union(result, n.getRectangle(), result);
+ }
+ if (result == null) {
+ return null;
+ }
+ result.setRect(
+ result.getX() - RECTANGLE_BORDER_MARGIN, result.getY() - RECTANGLE_BORDER_MARGIN, result.getWidth() + 2 * RECTANGLE_BORDER_MARGIN, result.getHeight()
+ + 2 * RECTANGLE_BORDER_MARGIN);
+ return result;
+ }
+
+ /**
+ *
+ * @return {@link #groupId}
+ */
+ public String getGroupId() {
+ return groupId;
+ }
+
+ /**
+ * Adds element to group.
+ *
+ * @param pe
+ * object to add
+ */
+ public void addNode(PathwayElement pe) {
+ nodes.add(pe);
+ }
+
+ /**
+ *
+ * @return {@link #nodes}
+ */
+ public Set<PathwayElement> getNodes() {
+ return this.nodes;
+ }
+
+ /**
+ * @return the style
+ * @see #style
+ */
+ public String getStyle() {
+ return style;
+ }
+
+ /**
+ * @param style the style to set
+ * @see #style
+ */
+ public void setStyle(String style) {
+ this.style = style;
+ }
+
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Interaction.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Interaction.java
index ee8577b682..69f9081aa7 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Interaction.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Interaction.java
@@ -1,390 +1,390 @@
-package lcsb.mapviewer.wikipathway.model;
-
-import java.awt.Color;
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.MiriamData;
-
-/**
- * Class used to store data from Interaction from .gpml.
- *
- * @author Jan Badura
- *
- */
-public class Interaction implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Identifier in gpml model.
- */
- private String graphId;
-
- /**
- * Where this {@link Interaction} starts (in which {@link Edge}/
- * {@link Interaction}).
- */
- private String start;
-
- /**
- * Where this {@link Interaction} ends (in which {@link Edge}/
- * {@link Interaction}).
- */
- private String end;
-
- /**
- * Line representing this edge.
- */
- private PolylineData line;
-
- /**
- * Z order of the {@link Interaction} (how far it should be located in the z
- * coordinate).
- */
- private Integer zOrder;
-
- /**
- * Gpml interaction type (arrow).
- */
- private GpmlInteractionType type = GpmlInteractionType.LINE;
-
- /**
- * List of anchors placed on the edge.
- */
- private Set<String> anchors;
-
- /**
- * Comments.
- */
- private List<String> comments = new ArrayList<>();
-
- /**
- * List of edges representing reactants in interaction.
- */
- private Set<Edge> reactants = new HashSet<Edge>();
-
- /**
- * List of edges representing products in interaction.
- */
- private Set<Edge> products = new HashSet<Edge>();
-
- /**
- * List of edges representing modifiers in interaction.
- */
- private Set<Edge> modifiers = new HashSet<Edge>();
-
- /**
- * Identifiers of biopax references.
- */
- private Set<String> biopaxReferences = new HashSet<String>();
-
- /**
- * References for given edge.
- */
- private List<MiriamData> references = new ArrayList<>();
-
- /**
- * Default constructor.
- *
- * @param edge
- * object will be created from this {@link Edge}
- */
- public Interaction(Edge edge) {
- graphId = edge.getGraphId();
- setStart(edge.getStart());
- setEnd(edge.getEnd());
- setLine(edge.getLine());
- setType(edge.getType());
- setzOrder(edge.getzOrder());
- for (MiriamData md : edge.getReferences()) {
- addReference(new MiriamData(md));
- }
- setColor(edge.getColor());
- this.comments.addAll(edge.getComments());
- biopaxReferences.addAll(edge.getBiopaxReferences());
- }
-
- /**
- * Empty constructor that should be used only by serialization tools and
- * subclasses.
- */
- protected Interaction() {
- }
-
- /**
- * Adds reference.
- *
- * @param reference
- * object to add
- */
- private void addReference(MiriamData reference) {
- references.add(reference);
- }
-
- /**
- * @return the graphId
- * @see #graphId
- */
- public String getGraphId() {
- return graphId;
- }
-
- /**
- * @param graphId
- * the graphId to set
- * @see #graphId
- */
- public void setGraphId(String graphId) {
- this.graphId = graphId;
- }
-
- /**
- * @return the start
- * @see #start
- */
- public String getStart() {
- return start;
- }
-
- /**
- * @param start
- * the start to set
- * @see #start
- */
- public void setStart(String start) {
- this.start = start;
- }
-
- /**
- * @return the end
- * @see #end
- */
- public String getEnd() {
- return end;
- }
-
- /**
- * @param end
- * the end to set
- * @see #end
- */
- public void setEnd(String end) {
- this.end = end;
- }
-
- /**
- * @return the line
- * @see #line
- */
- public PolylineData getLine() {
- return line;
- }
-
- /**
- * @param line
- * the line to set
- * @see #line
- */
- public void setLine(PolylineData line) {
- this.line = line;
- }
-
- /**
- * @return the anchors
- * @see #anchors
- */
- public Set<String> getAnchors() {
- return anchors;
- }
-
- /**
- * @param anchors
- * the anchors to set
- * @see #anchors
- */
- public void setAnchors(Set<String> anchors) {
- this.anchors = anchors;
- }
-
- /**
- * @return the comment
- * @see #comment
- */
- public List<String> getComments() {
- return comments;
- }
-
- /**
- * @param comment
- * the comment to set
- * @see #comment
- */
- public void addComment(String comment) {
- this.comments.add(comment);
- }
-
- /**
- * @return the reactants
- * @see #reactants
- */
- public Set<Edge> getReactants() {
- return reactants;
- }
-
- /**
- * @return the products
- * @see #products
- */
- public Set<Edge> getProducts() {
- return products;
- }
-
- /**
- * @return the modifiers
- * @see #modifiers
- */
- public Set<Edge> getModifiers() {
- return modifiers;
- }
-
- /**
- * Adds product.
- *
- * @param interaction
- * product to add
- */
- public void addProduct(Edge interaction) {
- this.products.add(interaction);
- interaction.setColor(getLine().getColor());
- biopaxReferences.addAll(interaction.getBiopaxReferences());
- }
-
- /**
- * Add modifier.
- *
- * @param interaction
- * modifier to add
- */
- public void addModifier(Edge interaction) {
- this.modifiers.add(interaction);
- interaction.setColor(getLine().getColor());
- biopaxReferences.addAll(interaction.getBiopaxReferences());
- }
-
- /**
- * Add modifier.
- *
- * @param interaction
- * reactant to add
- */
- public void addReactant(Edge interaction) {
- this.reactants.add(interaction);
- interaction.setColor(getLine().getColor());
- biopaxReferences.addAll(interaction.getBiopaxReferences());
- }
-
- /**
- * @return the biopaxReferences
- * @see #biopaxReferences
- */
- public Set<String> getBiopaxReferences() {
- return biopaxReferences;
- }
-
- /**
- * @param biopaxReferences
- * the biopaxReferences to set
- * @see #biopaxReferences
- */
- public void setBiopaxReferences(Set<String> biopaxReferences) {
- this.biopaxReferences = biopaxReferences;
- }
-
- /**
- * @return the type
- * @see #type
- */
- public GpmlInteractionType getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(GpmlInteractionType type) {
- this.type = type;
- }
-
- /**
- * @return the references
- * @see #references
- */
- public List<MiriamData> getReferences() {
- return references;
- }
-
- /**
- * @param references
- * the references to set
- * @see #references
- */
- public void setReferences(List<MiriamData> references) {
- this.references = references;
- }
-
- /**
- * @return the color
- * @see #color
- */
- public Color getColor() {
- return line.getColor();
- }
-
- /**
- * @param color
- * the color to set
- * @see #color
- */
- public void setColor(Color color) {
- if (color != null) {
- line.setColor(color);
- for (Edge edge : reactants) {
- edge.setColor(color);
- }
- for (Edge edge : products) {
- edge.setColor(color);
- }
- for (Edge edge : modifiers) {
- edge.setColor(color);
- }
- }
- }
-
- /**
- * @return the zOrder
- * @see #zOrder
- */
- public Integer getzOrder() {
- return zOrder;
- }
-
- /**
- * @param zOrder
- * the zOrder to set
- * @see #zOrder
- */
- public void setzOrder(Integer zOrder) {
- this.zOrder = zOrder;
- }
-
-}
+package lcsb.mapviewer.wikipathway.model;
+
+import java.awt.Color;
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.MiriamData;
+
+/**
+ * Class used to store data from Interaction from .gpml.
+ *
+ * @author Jan Badura
+ *
+ */
+public class Interaction implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Identifier in gpml model.
+ */
+ private String graphId;
+
+ /**
+ * Where this {@link Interaction} starts (in which {@link Edge}/
+ * {@link Interaction}).
+ */
+ private String start;
+
+ /**
+ * Where this {@link Interaction} ends (in which {@link Edge}/
+ * {@link Interaction}).
+ */
+ private String end;
+
+ /**
+ * Line representing this edge.
+ */
+ private PolylineData line;
+
+ /**
+ * Z order of the {@link Interaction} (how far it should be located in the z
+ * coordinate).
+ */
+ private Integer zOrder;
+
+ /**
+ * Gpml interaction type (arrow).
+ */
+ private GpmlInteractionType type = GpmlInteractionType.LINE;
+
+ /**
+ * List of anchors placed on the edge.
+ */
+ private Set<String> anchors;
+
+ /**
+ * Comments.
+ */
+ private List<String> comments = new ArrayList<>();
+
+ /**
+ * List of edges representing reactants in interaction.
+ */
+ private Set<Edge> reactants = new HashSet<Edge>();
+
+ /**
+ * List of edges representing products in interaction.
+ */
+ private Set<Edge> products = new HashSet<Edge>();
+
+ /**
+ * List of edges representing modifiers in interaction.
+ */
+ private Set<Edge> modifiers = new HashSet<Edge>();
+
+ /**
+ * Identifiers of biopax references.
+ */
+ private Set<String> biopaxReferences = new HashSet<String>();
+
+ /**
+ * References for given edge.
+ */
+ private List<MiriamData> references = new ArrayList<>();
+
+ /**
+ * Default constructor.
+ *
+ * @param edge
+ * object will be created from this {@link Edge}
+ */
+ public Interaction(Edge edge) {
+ graphId = edge.getGraphId();
+ setStart(edge.getStart());
+ setEnd(edge.getEnd());
+ setLine(edge.getLine());
+ setType(edge.getType());
+ setzOrder(edge.getzOrder());
+ for (MiriamData md : edge.getReferences()) {
+ addReference(new MiriamData(md));
+ }
+ setColor(edge.getColor());
+ this.comments.addAll(edge.getComments());
+ biopaxReferences.addAll(edge.getBiopaxReferences());
+ }
+
+ /**
+ * Empty constructor that should be used only by serialization tools and
+ * subclasses.
+ */
+ protected Interaction() {
+ }
+
+ /**
+ * Adds reference.
+ *
+ * @param reference
+ * object to add
+ */
+ private void addReference(MiriamData reference) {
+ references.add(reference);
+ }
+
+ /**
+ * @return the graphId
+ * @see #graphId
+ */
+ public String getGraphId() {
+ return graphId;
+ }
+
+ /**
+ * @param graphId
+ * the graphId to set
+ * @see #graphId
+ */
+ public void setGraphId(String graphId) {
+ this.graphId = graphId;
+ }
+
+ /**
+ * @return the start
+ * @see #start
+ */
+ public String getStart() {
+ return start;
+ }
+
+ /**
+ * @param start
+ * the start to set
+ * @see #start
+ */
+ public void setStart(String start) {
+ this.start = start;
+ }
+
+ /**
+ * @return the end
+ * @see #end
+ */
+ public String getEnd() {
+ return end;
+ }
+
+ /**
+ * @param end
+ * the end to set
+ * @see #end
+ */
+ public void setEnd(String end) {
+ this.end = end;
+ }
+
+ /**
+ * @return the line
+ * @see #line
+ */
+ public PolylineData getLine() {
+ return line;
+ }
+
+ /**
+ * @param line
+ * the line to set
+ * @see #line
+ */
+ public void setLine(PolylineData line) {
+ this.line = line;
+ }
+
+ /**
+ * @return the anchors
+ * @see #anchors
+ */
+ public Set<String> getAnchors() {
+ return anchors;
+ }
+
+ /**
+ * @param anchors
+ * the anchors to set
+ * @see #anchors
+ */
+ public void setAnchors(Set<String> anchors) {
+ this.anchors = anchors;
+ }
+
+ /**
+ * @return the comment
+ * @see #comment
+ */
+ public List<String> getComments() {
+ return comments;
+ }
+
+ /**
+ * @param comment
+ * the comment to set
+ * @see #comment
+ */
+ public void addComment(String comment) {
+ this.comments.add(comment);
+ }
+
+ /**
+ * @return the reactants
+ * @see #reactants
+ */
+ public Set<Edge> getReactants() {
+ return reactants;
+ }
+
+ /**
+ * @return the products
+ * @see #products
+ */
+ public Set<Edge> getProducts() {
+ return products;
+ }
+
+ /**
+ * @return the modifiers
+ * @see #modifiers
+ */
+ public Set<Edge> getModifiers() {
+ return modifiers;
+ }
+
+ /**
+ * Adds product.
+ *
+ * @param interaction
+ * product to add
+ */
+ public void addProduct(Edge interaction) {
+ this.products.add(interaction);
+ interaction.setColor(getLine().getColor());
+ biopaxReferences.addAll(interaction.getBiopaxReferences());
+ }
+
+ /**
+ * Add modifier.
+ *
+ * @param interaction
+ * modifier to add
+ */
+ public void addModifier(Edge interaction) {
+ this.modifiers.add(interaction);
+ interaction.setColor(getLine().getColor());
+ biopaxReferences.addAll(interaction.getBiopaxReferences());
+ }
+
+ /**
+ * Add modifier.
+ *
+ * @param interaction
+ * reactant to add
+ */
+ public void addReactant(Edge interaction) {
+ this.reactants.add(interaction);
+ interaction.setColor(getLine().getColor());
+ biopaxReferences.addAll(interaction.getBiopaxReferences());
+ }
+
+ /**
+ * @return the biopaxReferences
+ * @see #biopaxReferences
+ */
+ public Set<String> getBiopaxReferences() {
+ return biopaxReferences;
+ }
+
+ /**
+ * @param biopaxReferences
+ * the biopaxReferences to set
+ * @see #biopaxReferences
+ */
+ public void setBiopaxReferences(Set<String> biopaxReferences) {
+ this.biopaxReferences = biopaxReferences;
+ }
+
+ /**
+ * @return the type
+ * @see #type
+ */
+ public GpmlInteractionType getType() {
+ return type;
+ }
+
+ /**
+ * @param type
+ * the type to set
+ * @see #type
+ */
+ public void setType(GpmlInteractionType type) {
+ this.type = type;
+ }
+
+ /**
+ * @return the references
+ * @see #references
+ */
+ public List<MiriamData> getReferences() {
+ return references;
+ }
+
+ /**
+ * @param references
+ * the references to set
+ * @see #references
+ */
+ public void setReferences(List<MiriamData> references) {
+ this.references = references;
+ }
+
+ /**
+ * @return the color
+ * @see #color
+ */
+ public Color getColor() {
+ return line.getColor();
+ }
+
+ /**
+ * @param color
+ * the color to set
+ * @see #color
+ */
+ public void setColor(Color color) {
+ if (color != null) {
+ line.setColor(color);
+ for (Edge edge : reactants) {
+ edge.setColor(color);
+ }
+ for (Edge edge : products) {
+ edge.setColor(color);
+ }
+ for (Edge edge : modifiers) {
+ edge.setColor(color);
+ }
+ }
+ }
+
+ /**
+ * @return the zOrder
+ * @see #zOrder
+ */
+ public Integer getzOrder() {
+ return zOrder;
+ }
+
+ /**
+ * @param zOrder
+ * the zOrder to set
+ * @see #zOrder
+ */
+ public void setzOrder(Integer zOrder) {
+ this.zOrder = zOrder;
+ }
+
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/InteractionMapping.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/InteractionMapping.java
index 4ea4f01c63..23123297e1 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/InteractionMapping.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/InteractionMapping.java
@@ -1,514 +1,514 @@
-package lcsb.mapviewer.wikipathway.model;
-
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.map.modifier.Catalysis;
-import lcsb.mapviewer.model.map.modifier.Inhibition;
-import lcsb.mapviewer.model.map.modifier.Modulation;
-import lcsb.mapviewer.model.map.modifier.PhysicalStimulation;
-import lcsb.mapviewer.model.map.modifier.UnknownCatalysis;
-import lcsb.mapviewer.model.map.modifier.UnknownInhibition;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.ReactionNode;
-import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
-import lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction;
-import lcsb.mapviewer.model.map.reaction.type.PositiveInfluenceReaction;
-import lcsb.mapviewer.model.map.reaction.type.ReducedPhysicalStimulationReaction;
-import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
-import lcsb.mapviewer.model.map.reaction.type.UnknownNegativeInfluenceReaction;
-import lcsb.mapviewer.model.map.reaction.type.UnknownPositiveInfluenceReaction;
-import lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction;
-
-/**
- * This class contains mapping between gpml interactions and CellDesigner model
- * representation. Type is identified by two values:
- * {@link #gpmlInteractionType} and {@link #gpmlLineStyle}. For every type there
- * are three possible mappings:
- * <ul>
- * <li>reaction - defines to what {@link Reaction} gpml type should be
- * transformed</li>
- * <li>input - when interaction is just an input part of main reaction this
- * defines to what {@link ReactionNode} should it be transformed</li>
- * <li>output - when interaction is just an output part of main reaction this
- * defines to what {@link ReactionNode} should it be transformed</li>
- * </ul>
- *
- * @author Piotr Gawron
- *
- */
-public enum InteractionMapping {
-
- /**
- * Default line.
- */
- LINE(GpmlInteractionType.LINE, GpmlLineType.SOLID, //
- UnknownTransitionReaction.class, true, //
- Reactant.class, false, //
- Reactant.class, false, //
- true), //
-
- /**
- * Default arrow.
- */
- ARROW(GpmlInteractionType.ARROW, GpmlLineType.SOLID, //
- StateTransitionReaction.class, false, //
- Modulation.class, true, //
- Product.class, false),
-
- /**
- * Dashed line.
- */
- LINE_DASHED(GpmlInteractionType.LINE, GpmlLineType.DASHED, //
- UnknownTransitionReaction.class, true, //
- Reactant.class, true, //
- Reactant.class, true, //
- true), //
-
- /**
- * Dashed arrow.
- */
- ARROW_DASHED(GpmlInteractionType.ARROW, GpmlLineType.DASHED, //
- UnknownPositiveInfluenceReaction.class, false, //
- Modulation.class, true, //
- Product.class, true),
-
- /**
- * Line ended with T-bar.
- */
- TBAR(GpmlInteractionType.TBAR, GpmlLineType.SOLID, //
- NegativeInfluenceReaction.class, true, //
- Inhibition.class, false, //
- Product.class, true), //
-
- /**
- * Line ended with T-bar dashed.
- */
- TBAR_DASHED(GpmlInteractionType.TBAR, GpmlLineType.DASHED, //
- UnknownNegativeInfluenceReaction.class, true, //
- UnknownInhibition.class, false, //
- Product.class, true), //
-
- /**
- * Necessary stimulation.
- */
- NECESSARY_STIMULATION(GpmlInteractionType.NECESSARY_STIMULATION, GpmlLineType.SOLID, //
- ReducedPhysicalStimulationReaction.class, false, //
- PhysicalStimulation.class, false, //
- Product.class, true), //
-
- /**
- * Necessary stimulation dashed.
- */
- NECESSARY_STIMULATION_DASHED(GpmlInteractionType.NECESSARY_STIMULATION, GpmlLineType.DASHED, //
- UnknownPositiveInfluenceReaction.class, true, //
- Modulation.class, true, //
- Product.class, true), //
-
- /**
- * Binding.
- */
- BINDING(GpmlInteractionType.BINDING, GpmlLineType.SOLID, //
- HeterodimerAssociationReaction.class, false, //
- Modulation.class, true, //
- Product.class, true), //
-
- /**
- * Binding dashed.
- */
- BINDING_DASHED(GpmlInteractionType.BINDING, GpmlLineType.DASHED, //
- UnknownPositiveInfluenceReaction.class, false, //
- Modulation.class, true, //
- Product.class, true), //
-
- /**
- * Conversion.
- */
- CONVERSION(GpmlInteractionType.CONVERSION, GpmlLineType.SOLID, //
- StateTransitionReaction.class, false, //
- Modulation.class, true, //
- Product.class, false), //
-
- /**
- * Dashed conversion.
- */
- CONVERSION_DASHED(GpmlInteractionType.CONVERSION, GpmlLineType.DASHED, //
- UnknownPositiveInfluenceReaction.class, false, //
- Modulation.class, true, //
- Product.class, true),
-
- /**
- * Stimulation.
- */
- STIMULATION(GpmlInteractionType.STIMULATION, GpmlLineType.SOLID, //
- ReducedPhysicalStimulationReaction.class, true, //
- PhysicalStimulation.class, false, //
- Product.class, true), //
-
- /**
- * Stimulation dashed.
- */
- STIMULATION_DASHED(GpmlInteractionType.STIMULATION, GpmlLineType.DASHED, //
- UnknownPositiveInfluenceReaction.class, true, //
- Modulation.class, true, //
- Product.class, true), //
-
- /**
- * Modification.
- */
- MODIFICATION(GpmlInteractionType.MODIFICATION, GpmlLineType.SOLID, //
- PositiveInfluenceReaction.class, true, //
- Modulation.class, false, //
- Product.class, true), //
-
- /**
- * Modification dashed.
- */
- MODIFICATION_DASHED(GpmlInteractionType.MODIFICATION, GpmlLineType.DASHED, //
- UnknownPositiveInfluenceReaction.class, false, //
- Modulation.class, true, //
- Product.class, true), //
-
- /**
- * Catalysis.
- */
- CATALYSIS(GpmlInteractionType.CATALYSIS, GpmlLineType.SOLID, //
- PositiveInfluenceReaction.class, true, //
- Catalysis.class, false, //
- Product.class, true), //
-
- /**
- * Catalysis dashed.
- */
- CATALYSIS_DASHED(GpmlInteractionType.CATALYSIS, GpmlLineType.DASHED, //
- UnknownPositiveInfluenceReaction.class, true, //
- UnknownCatalysis.class, false, //
- Product.class, true), //
-
- /**
- * Inhibition.
- */
- INHIBITION(GpmlInteractionType.INHIBITION, GpmlLineType.SOLID, //
- NegativeInfluenceReaction.class, false, //
- Inhibition.class, false, //
- Product.class, true), //
-
- /**
- * Inhibition dashed.
- */
- INHIBITION_DASHED(GpmlInteractionType.INHIBITION, GpmlLineType.DASHED, //
- UnknownNegativeInfluenceReaction.class, true, //
- UnknownInhibition.class, true, //
- Product.class, true), //
-
- /**
- * Cleavage.
- */
- CLEAVAGE(GpmlInteractionType.CLEAVAGE, GpmlLineType.SOLID, //
- StateTransitionReaction.class, false, //
- Modulation.class, true, //
- Product.class, false), //
-
- /**
- * Cleavage dashed.
- */
- CLEAVAGE_DASHED(GpmlInteractionType.CLEAVAGE, GpmlLineType.DASHED, //
- UnknownTransitionReaction.class, true, //
- Modulation.class, true, //
- Product.class, true), //
-
- /**
- * Covalent bond.
- */
- COVALENT_BOND(GpmlInteractionType.COVALENT_BOND, GpmlLineType.SOLID, //
- UnknownTransitionReaction.class, true, //
- Reactant.class, true, //
- Product.class, true, //
- true), //
-
- /**
- * Covalent bond dashed.
- */
- COVALENT_BOND_DASHED(GpmlInteractionType.COVALENT_BOND, GpmlLineType.DASHED, //
- UnknownTransitionReaction.class, true, //
- Reactant.class, true, //
- Product.class, true, //
- true), //
-
- /**
- * Branching left.
- */
- BRANCHING_LEFT(GpmlInteractionType.BRANCHING_LEFT, GpmlLineType.SOLID, //
- UnknownTransitionReaction.class, true, //
- Reactant.class, false, //
- Reactant.class, false, //
- true), //
-
- /**
- * Branching left dashed.
- */
- BRANCHING_LEFT_DASHED(GpmlInteractionType.BRANCHING_LEFT, GpmlLineType.DASHED, //
- UnknownTransitionReaction.class, true, //
- Reactant.class, true, //
- Reactant.class, true, //
- true), //
-
- /**
- * Branching right.
- */
- BRANCHING_RIGHT(GpmlInteractionType.BRANCHING_RIGHT, GpmlLineType.SOLID, //
- UnknownTransitionReaction.class, true, //
- Reactant.class, false, //
- Reactant.class, false, //
- true), //
-
- /**
- * Branching right dashed.
- */
- BRANCHING_RIGHT_DASHED(GpmlInteractionType.BRANCHING_RIGHT, GpmlLineType.DASHED, //
- UnknownTransitionReaction.class, true, //
- Reactant.class, true, //
- Reactant.class, true, //
- true), //
-
- /**
- * Transription-translation.
- */
- TRANSCRIPTION_TRANSLATION(GpmlInteractionType.TRANSCRIPTION_TRANSLATION, GpmlLineType.SOLID, //
- PositiveInfluenceReaction.class, true, //
- Modulation.class, true, //
- Product.class, true), //
-
- /**
- * Transription-translation dashed.
- */
- TRANSCRIPTION_TRANSLATION_DASHED(GpmlInteractionType.TRANSCRIPTION_TRANSLATION, GpmlLineType.DASHED, //
- PositiveInfluenceReaction.class, true, //
- Modulation.class, true, //
- Product.class, true), //
-
- /**
- * Gap...
- */
- GAP(GpmlInteractionType.GAP, GpmlLineType.SOLID, //
- UnknownTransitionReaction.class, true, //
- Modulation.class, true, //
- Product.class, true, //
- true),
-
- /**
- * Gap dashed...
- */
- GAP_DASHED(GpmlInteractionType.GAP, GpmlLineType.DASHED, //
- UnknownTransitionReaction.class, true, //
- Modulation.class, true, //
- Product.class, true, //
- true);
-
- /**
- * Interaction type defined in gpml.
- */
- private GpmlInteractionType gpmlInteractionType;
-
- /**
- * Line type defined in gpml.
- */
- private GpmlLineType gpmlLineStyle;
-
- /**
- * Cell designer reaction to which gpml interaction should be transformed.
- */
- private Class<? extends Reaction> modelReactionType;
-
- /**
- * Cell designer reaction node to which interaction should be transformed when
- * it's an input to the reaction.
- */
- private Class<? extends ReactionNode> modelInputReactionNodeType;
-
- /**
- * Cell designer reaction node to which interaction should be transformed when
- * it's an output to the reaction.
- */
- private Class<? extends ReactionNode> modelOutputReactionNodeType;
-
- /**
- * Should CellDesigner reaction be reversible.
- */
- private boolean reversible = false;
-
- /**
- * When converting to reaction. Should the code warn.
- */
- private boolean interactionWarning = false;
-
- /**
- * When converting to input of the reaction should the code warn.
- */
- private boolean inputWarning = false;
-
- /**
- * When converting to output of the reaction should the code warn.
- */
- private boolean outputWarning = false;
-
- /**
- * Default constructor.
- *
- * @param gpmlInteractionType
- * {@link #gpmlInteractionType}
- * @param gpmlLineStyle
- * {@link #gpmlLineStyle}
- * @param modelReactionType
- * {@link #modelReactionType}
- * @param interactionWarning
- * {@link #interactionWarning}
- * @param modelInputReactionNodeType
- * {@link #modelInputReactionNodeType}
- * @param inputWarning
- * {@link #inputWarning}
- * @param modelOutputReactionNodeType
- * {@link #modelOutputReactionNodeType}
- * @param outputWarning
- * {@link #outputWarning}
- * @param reversible
- * {@link #reversible}
- */
- InteractionMapping(GpmlInteractionType gpmlInteractionType, GpmlLineType gpmlLineStyle, Class<? extends Reaction> modelReactionType,
- boolean interactionWarning, Class<? extends ReactionNode> modelInputReactionNodeType, boolean inputWarning,
- Class<? extends ReactionNode> modelOutputReactionNodeType, boolean outputWarning, boolean reversible) {
- this.gpmlInteractionType = gpmlInteractionType;
- this.modelReactionType = modelReactionType;
- this.interactionWarning = interactionWarning;
- this.modelInputReactionNodeType = modelInputReactionNodeType;
- this.inputWarning = inputWarning;
- this.modelOutputReactionNodeType = modelOutputReactionNodeType;
- this.outputWarning = outputWarning;
- this.reversible = reversible;
- this.gpmlLineStyle = gpmlLineStyle;
- }
-
- /**
- * Default constructor.
- *
- * @param gpmlInteractionType
- * {@link #gpmlInteractionType}
- * @param gpmlLineStyle
- * {@link #gpmlLineStyle}
- * @param modelReactionType
- * {@link #modelReactionType}
- * @param interactionWarning
- * {@link #interactionWarning}
- * @param modelInputReactionNodeType
- * {@link #modelInputReactionNodeType}
- * @param inputWarning
- * {@link #inputWarning}
- * @param modelOutputReactionNodeType
- * {@link #modelOutputReactionNodeType}
- * @param outputWarning
- * {@link #outputWarning}
- */
- InteractionMapping(GpmlInteractionType gpmlInteractionType, GpmlLineType gpmlLineStyle, Class<? extends Reaction> modelReactionType,
- boolean interactionWarning, Class<? extends ReactionNode> modelInputReactionNodeType, boolean inputWarning,
- Class<? extends ReactionNode> modelOutputReactionNodeType, boolean outputWarning) {
- this(
- gpmlInteractionType, gpmlLineStyle, modelReactionType, interactionWarning, modelInputReactionNodeType, inputWarning, modelOutputReactionNodeType,
- outputWarning, false);
- }
-
- /**
- * @return the gpmlInteractionType
- * @see #gpmlInteractionType
- */
- public GpmlInteractionType getGpmlInteractionType() {
- return gpmlInteractionType;
- }
-
- /**
- * @return the modelReactionType
- * @see #modelReactionType
- */
- public Class<? extends Reaction> getModelReactionType() {
- return modelReactionType;
- }
-
- /**
- * @return the modelInputReactionNodeType
- * @see #modelInputReactionNodeType
- */
- public Class<? extends ReactionNode> getModelInputReactionNodeType() {
- return modelInputReactionNodeType;
- }
-
- /**
- * @return the modelOutputReactionNodeType
- * @see #modelOutputReactionNodeType
- */
- public Class<? extends ReactionNode> getModelOutputReactionNodeType() {
- return modelOutputReactionNodeType;
- }
-
- /**
- * @return the reversible
- * @see #reversible
- */
- public boolean isReversible() {
- return reversible;
- }
-
- /**
- * @return the interactionWarning
- * @see #interactionWarning
- */
- public boolean isInteractionWarning() {
- return interactionWarning;
- }
-
- /**
- * @return the inputWarning
- * @see #inputWarning
- */
- public boolean isInputWarning() {
- return inputWarning;
- }
-
- /**
- * @return the outputWarning
- * @see #outputWarning
- */
- public boolean isOutputWarning() {
- return outputWarning;
- }
-
- /**
- * Method that is looking for the {@link InteractionMapping} that matches to
- * given gpml "arrow type" and "line type".
- *
- * @param gpmlType
- * gpml arrow type
- * @param lineType
- * gpml line type
- * @return {@link InteractionMapping} that matches to given gpml "arrow type"
- * and "line type"
- */
- public static InteractionMapping getInteractionMapping(GpmlInteractionType gpmlType, LineType lineType) {
- for (InteractionMapping mapping : InteractionMapping.values()) {
- boolean arrowMatch = mapping.getGpmlInteractionType().equals(gpmlType);
- boolean lineTypeMatch = lineType.equals(mapping.getGpmlLineStyle().getCorrespondingGlobalLineType());
-
- if (arrowMatch && lineTypeMatch) {
- return mapping;
- }
- }
- return null;
- }
-
- /**
- * @return the gpmlLineStyle
- * @see #gpmlLineStyle
- */
- public GpmlLineType getGpmlLineStyle() {
- return gpmlLineStyle;
- }
-
-}
+package lcsb.mapviewer.wikipathway.model;
+
+import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.map.modifier.Catalysis;
+import lcsb.mapviewer.model.map.modifier.Inhibition;
+import lcsb.mapviewer.model.map.modifier.Modulation;
+import lcsb.mapviewer.model.map.modifier.PhysicalStimulation;
+import lcsb.mapviewer.model.map.modifier.UnknownCatalysis;
+import lcsb.mapviewer.model.map.modifier.UnknownInhibition;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
+import lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction;
+import lcsb.mapviewer.model.map.reaction.type.PositiveInfluenceReaction;
+import lcsb.mapviewer.model.map.reaction.type.ReducedPhysicalStimulationReaction;
+import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
+import lcsb.mapviewer.model.map.reaction.type.UnknownNegativeInfluenceReaction;
+import lcsb.mapviewer.model.map.reaction.type.UnknownPositiveInfluenceReaction;
+import lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction;
+
+/**
+ * This class contains mapping between gpml interactions and CellDesigner model
+ * representation. Type is identified by two values:
+ * {@link #gpmlInteractionType} and {@link #gpmlLineStyle}. For every type there
+ * are three possible mappings:
+ * <ul>
+ * <li>reaction - defines to what {@link Reaction} gpml type should be
+ * transformed</li>
+ * <li>input - when interaction is just an input part of main reaction this
+ * defines to what {@link ReactionNode} should it be transformed</li>
+ * <li>output - when interaction is just an output part of main reaction this
+ * defines to what {@link ReactionNode} should it be transformed</li>
+ * </ul>
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum InteractionMapping {
+
+ /**
+ * Default line.
+ */
+ LINE(GpmlInteractionType.LINE, GpmlLineType.SOLID, //
+ UnknownTransitionReaction.class, true, //
+ Reactant.class, false, //
+ Reactant.class, false, //
+ true), //
+
+ /**
+ * Default arrow.
+ */
+ ARROW(GpmlInteractionType.ARROW, GpmlLineType.SOLID, //
+ StateTransitionReaction.class, false, //
+ Modulation.class, true, //
+ Product.class, false),
+
+ /**
+ * Dashed line.
+ */
+ LINE_DASHED(GpmlInteractionType.LINE, GpmlLineType.DASHED, //
+ UnknownTransitionReaction.class, true, //
+ Reactant.class, true, //
+ Reactant.class, true, //
+ true), //
+
+ /**
+ * Dashed arrow.
+ */
+ ARROW_DASHED(GpmlInteractionType.ARROW, GpmlLineType.DASHED, //
+ UnknownPositiveInfluenceReaction.class, false, //
+ Modulation.class, true, //
+ Product.class, true),
+
+ /**
+ * Line ended with T-bar.
+ */
+ TBAR(GpmlInteractionType.TBAR, GpmlLineType.SOLID, //
+ NegativeInfluenceReaction.class, true, //
+ Inhibition.class, false, //
+ Product.class, true), //
+
+ /**
+ * Line ended with T-bar dashed.
+ */
+ TBAR_DASHED(GpmlInteractionType.TBAR, GpmlLineType.DASHED, //
+ UnknownNegativeInfluenceReaction.class, true, //
+ UnknownInhibition.class, false, //
+ Product.class, true), //
+
+ /**
+ * Necessary stimulation.
+ */
+ NECESSARY_STIMULATION(GpmlInteractionType.NECESSARY_STIMULATION, GpmlLineType.SOLID, //
+ ReducedPhysicalStimulationReaction.class, false, //
+ PhysicalStimulation.class, false, //
+ Product.class, true), //
+
+ /**
+ * Necessary stimulation dashed.
+ */
+ NECESSARY_STIMULATION_DASHED(GpmlInteractionType.NECESSARY_STIMULATION, GpmlLineType.DASHED, //
+ UnknownPositiveInfluenceReaction.class, true, //
+ Modulation.class, true, //
+ Product.class, true), //
+
+ /**
+ * Binding.
+ */
+ BINDING(GpmlInteractionType.BINDING, GpmlLineType.SOLID, //
+ HeterodimerAssociationReaction.class, false, //
+ Modulation.class, true, //
+ Product.class, true), //
+
+ /**
+ * Binding dashed.
+ */
+ BINDING_DASHED(GpmlInteractionType.BINDING, GpmlLineType.DASHED, //
+ UnknownPositiveInfluenceReaction.class, false, //
+ Modulation.class, true, //
+ Product.class, true), //
+
+ /**
+ * Conversion.
+ */
+ CONVERSION(GpmlInteractionType.CONVERSION, GpmlLineType.SOLID, //
+ StateTransitionReaction.class, false, //
+ Modulation.class, true, //
+ Product.class, false), //
+
+ /**
+ * Dashed conversion.
+ */
+ CONVERSION_DASHED(GpmlInteractionType.CONVERSION, GpmlLineType.DASHED, //
+ UnknownPositiveInfluenceReaction.class, false, //
+ Modulation.class, true, //
+ Product.class, true),
+
+ /**
+ * Stimulation.
+ */
+ STIMULATION(GpmlInteractionType.STIMULATION, GpmlLineType.SOLID, //
+ ReducedPhysicalStimulationReaction.class, true, //
+ PhysicalStimulation.class, false, //
+ Product.class, true), //
+
+ /**
+ * Stimulation dashed.
+ */
+ STIMULATION_DASHED(GpmlInteractionType.STIMULATION, GpmlLineType.DASHED, //
+ UnknownPositiveInfluenceReaction.class, true, //
+ Modulation.class, true, //
+ Product.class, true), //
+
+ /**
+ * Modification.
+ */
+ MODIFICATION(GpmlInteractionType.MODIFICATION, GpmlLineType.SOLID, //
+ PositiveInfluenceReaction.class, true, //
+ Modulation.class, false, //
+ Product.class, true), //
+
+ /**
+ * Modification dashed.
+ */
+ MODIFICATION_DASHED(GpmlInteractionType.MODIFICATION, GpmlLineType.DASHED, //
+ UnknownPositiveInfluenceReaction.class, false, //
+ Modulation.class, true, //
+ Product.class, true), //
+
+ /**
+ * Catalysis.
+ */
+ CATALYSIS(GpmlInteractionType.CATALYSIS, GpmlLineType.SOLID, //
+ PositiveInfluenceReaction.class, true, //
+ Catalysis.class, false, //
+ Product.class, true), //
+
+ /**
+ * Catalysis dashed.
+ */
+ CATALYSIS_DASHED(GpmlInteractionType.CATALYSIS, GpmlLineType.DASHED, //
+ UnknownPositiveInfluenceReaction.class, true, //
+ UnknownCatalysis.class, false, //
+ Product.class, true), //
+
+ /**
+ * Inhibition.
+ */
+ INHIBITION(GpmlInteractionType.INHIBITION, GpmlLineType.SOLID, //
+ NegativeInfluenceReaction.class, false, //
+ Inhibition.class, false, //
+ Product.class, true), //
+
+ /**
+ * Inhibition dashed.
+ */
+ INHIBITION_DASHED(GpmlInteractionType.INHIBITION, GpmlLineType.DASHED, //
+ UnknownNegativeInfluenceReaction.class, true, //
+ UnknownInhibition.class, true, //
+ Product.class, true), //
+
+ /**
+ * Cleavage.
+ */
+ CLEAVAGE(GpmlInteractionType.CLEAVAGE, GpmlLineType.SOLID, //
+ StateTransitionReaction.class, false, //
+ Modulation.class, true, //
+ Product.class, false), //
+
+ /**
+ * Cleavage dashed.
+ */
+ CLEAVAGE_DASHED(GpmlInteractionType.CLEAVAGE, GpmlLineType.DASHED, //
+ UnknownTransitionReaction.class, true, //
+ Modulation.class, true, //
+ Product.class, true), //
+
+ /**
+ * Covalent bond.
+ */
+ COVALENT_BOND(GpmlInteractionType.COVALENT_BOND, GpmlLineType.SOLID, //
+ UnknownTransitionReaction.class, true, //
+ Reactant.class, true, //
+ Product.class, true, //
+ true), //
+
+ /**
+ * Covalent bond dashed.
+ */
+ COVALENT_BOND_DASHED(GpmlInteractionType.COVALENT_BOND, GpmlLineType.DASHED, //
+ UnknownTransitionReaction.class, true, //
+ Reactant.class, true, //
+ Product.class, true, //
+ true), //
+
+ /**
+ * Branching left.
+ */
+ BRANCHING_LEFT(GpmlInteractionType.BRANCHING_LEFT, GpmlLineType.SOLID, //
+ UnknownTransitionReaction.class, true, //
+ Reactant.class, false, //
+ Reactant.class, false, //
+ true), //
+
+ /**
+ * Branching left dashed.
+ */
+ BRANCHING_LEFT_DASHED(GpmlInteractionType.BRANCHING_LEFT, GpmlLineType.DASHED, //
+ UnknownTransitionReaction.class, true, //
+ Reactant.class, true, //
+ Reactant.class, true, //
+ true), //
+
+ /**
+ * Branching right.
+ */
+ BRANCHING_RIGHT(GpmlInteractionType.BRANCHING_RIGHT, GpmlLineType.SOLID, //
+ UnknownTransitionReaction.class, true, //
+ Reactant.class, false, //
+ Reactant.class, false, //
+ true), //
+
+ /**
+ * Branching right dashed.
+ */
+ BRANCHING_RIGHT_DASHED(GpmlInteractionType.BRANCHING_RIGHT, GpmlLineType.DASHED, //
+ UnknownTransitionReaction.class, true, //
+ Reactant.class, true, //
+ Reactant.class, true, //
+ true), //
+
+ /**
+ * Transription-translation.
+ */
+ TRANSCRIPTION_TRANSLATION(GpmlInteractionType.TRANSCRIPTION_TRANSLATION, GpmlLineType.SOLID, //
+ PositiveInfluenceReaction.class, true, //
+ Modulation.class, true, //
+ Product.class, true), //
+
+ /**
+ * Transription-translation dashed.
+ */
+ TRANSCRIPTION_TRANSLATION_DASHED(GpmlInteractionType.TRANSCRIPTION_TRANSLATION, GpmlLineType.DASHED, //
+ PositiveInfluenceReaction.class, true, //
+ Modulation.class, true, //
+ Product.class, true), //
+
+ /**
+ * Gap...
+ */
+ GAP(GpmlInteractionType.GAP, GpmlLineType.SOLID, //
+ UnknownTransitionReaction.class, true, //
+ Modulation.class, true, //
+ Product.class, true, //
+ true),
+
+ /**
+ * Gap dashed...
+ */
+ GAP_DASHED(GpmlInteractionType.GAP, GpmlLineType.DASHED, //
+ UnknownTransitionReaction.class, true, //
+ Modulation.class, true, //
+ Product.class, true, //
+ true);
+
+ /**
+ * Interaction type defined in gpml.
+ */
+ private GpmlInteractionType gpmlInteractionType;
+
+ /**
+ * Line type defined in gpml.
+ */
+ private GpmlLineType gpmlLineStyle;
+
+ /**
+ * Cell designer reaction to which gpml interaction should be transformed.
+ */
+ private Class<? extends Reaction> modelReactionType;
+
+ /**
+ * Cell designer reaction node to which interaction should be transformed when
+ * it's an input to the reaction.
+ */
+ private Class<? extends ReactionNode> modelInputReactionNodeType;
+
+ /**
+ * Cell designer reaction node to which interaction should be transformed when
+ * it's an output to the reaction.
+ */
+ private Class<? extends ReactionNode> modelOutputReactionNodeType;
+
+ /**
+ * Should CellDesigner reaction be reversible.
+ */
+ private boolean reversible = false;
+
+ /**
+ * When converting to reaction. Should the code warn.
+ */
+ private boolean interactionWarning = false;
+
+ /**
+ * When converting to input of the reaction should the code warn.
+ */
+ private boolean inputWarning = false;
+
+ /**
+ * When converting to output of the reaction should the code warn.
+ */
+ private boolean outputWarning = false;
+
+ /**
+ * Default constructor.
+ *
+ * @param gpmlInteractionType
+ * {@link #gpmlInteractionType}
+ * @param gpmlLineStyle
+ * {@link #gpmlLineStyle}
+ * @param modelReactionType
+ * {@link #modelReactionType}
+ * @param interactionWarning
+ * {@link #interactionWarning}
+ * @param modelInputReactionNodeType
+ * {@link #modelInputReactionNodeType}
+ * @param inputWarning
+ * {@link #inputWarning}
+ * @param modelOutputReactionNodeType
+ * {@link #modelOutputReactionNodeType}
+ * @param outputWarning
+ * {@link #outputWarning}
+ * @param reversible
+ * {@link #reversible}
+ */
+ InteractionMapping(GpmlInteractionType gpmlInteractionType, GpmlLineType gpmlLineStyle, Class<? extends Reaction> modelReactionType,
+ boolean interactionWarning, Class<? extends ReactionNode> modelInputReactionNodeType, boolean inputWarning,
+ Class<? extends ReactionNode> modelOutputReactionNodeType, boolean outputWarning, boolean reversible) {
+ this.gpmlInteractionType = gpmlInteractionType;
+ this.modelReactionType = modelReactionType;
+ this.interactionWarning = interactionWarning;
+ this.modelInputReactionNodeType = modelInputReactionNodeType;
+ this.inputWarning = inputWarning;
+ this.modelOutputReactionNodeType = modelOutputReactionNodeType;
+ this.outputWarning = outputWarning;
+ this.reversible = reversible;
+ this.gpmlLineStyle = gpmlLineStyle;
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param gpmlInteractionType
+ * {@link #gpmlInteractionType}
+ * @param gpmlLineStyle
+ * {@link #gpmlLineStyle}
+ * @param modelReactionType
+ * {@link #modelReactionType}
+ * @param interactionWarning
+ * {@link #interactionWarning}
+ * @param modelInputReactionNodeType
+ * {@link #modelInputReactionNodeType}
+ * @param inputWarning
+ * {@link #inputWarning}
+ * @param modelOutputReactionNodeType
+ * {@link #modelOutputReactionNodeType}
+ * @param outputWarning
+ * {@link #outputWarning}
+ */
+ InteractionMapping(GpmlInteractionType gpmlInteractionType, GpmlLineType gpmlLineStyle, Class<? extends Reaction> modelReactionType,
+ boolean interactionWarning, Class<? extends ReactionNode> modelInputReactionNodeType, boolean inputWarning,
+ Class<? extends ReactionNode> modelOutputReactionNodeType, boolean outputWarning) {
+ this(
+ gpmlInteractionType, gpmlLineStyle, modelReactionType, interactionWarning, modelInputReactionNodeType, inputWarning, modelOutputReactionNodeType,
+ outputWarning, false);
+ }
+
+ /**
+ * @return the gpmlInteractionType
+ * @see #gpmlInteractionType
+ */
+ public GpmlInteractionType getGpmlInteractionType() {
+ return gpmlInteractionType;
+ }
+
+ /**
+ * @return the modelReactionType
+ * @see #modelReactionType
+ */
+ public Class<? extends Reaction> getModelReactionType() {
+ return modelReactionType;
+ }
+
+ /**
+ * @return the modelInputReactionNodeType
+ * @see #modelInputReactionNodeType
+ */
+ public Class<? extends ReactionNode> getModelInputReactionNodeType() {
+ return modelInputReactionNodeType;
+ }
+
+ /**
+ * @return the modelOutputReactionNodeType
+ * @see #modelOutputReactionNodeType
+ */
+ public Class<? extends ReactionNode> getModelOutputReactionNodeType() {
+ return modelOutputReactionNodeType;
+ }
+
+ /**
+ * @return the reversible
+ * @see #reversible
+ */
+ public boolean isReversible() {
+ return reversible;
+ }
+
+ /**
+ * @return the interactionWarning
+ * @see #interactionWarning
+ */
+ public boolean isInteractionWarning() {
+ return interactionWarning;
+ }
+
+ /**
+ * @return the inputWarning
+ * @see #inputWarning
+ */
+ public boolean isInputWarning() {
+ return inputWarning;
+ }
+
+ /**
+ * @return the outputWarning
+ * @see #outputWarning
+ */
+ public boolean isOutputWarning() {
+ return outputWarning;
+ }
+
+ /**
+ * Method that is looking for the {@link InteractionMapping} that matches to
+ * given gpml "arrow type" and "line type".
+ *
+ * @param gpmlType
+ * gpml arrow type
+ * @param lineType
+ * gpml line type
+ * @return {@link InteractionMapping} that matches to given gpml "arrow type"
+ * and "line type"
+ */
+ public static InteractionMapping getInteractionMapping(GpmlInteractionType gpmlType, LineType lineType) {
+ for (InteractionMapping mapping : InteractionMapping.values()) {
+ boolean arrowMatch = mapping.getGpmlInteractionType().equals(gpmlType);
+ boolean lineTypeMatch = lineType.equals(mapping.getGpmlLineStyle().getCorrespondingGlobalLineType());
+
+ if (arrowMatch && lineTypeMatch) {
+ return mapping;
+ }
+ }
+ return null;
+ }
+
+ /**
+ * @return the gpmlLineStyle
+ * @see #gpmlLineStyle
+ */
+ public GpmlLineType getGpmlLineStyle() {
+ return gpmlLineStyle;
+ }
+
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Label.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Label.java
index 4a41f0328a..0f1ff697dc 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Label.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Label.java
@@ -1,172 +1,172 @@
-package lcsb.mapviewer.wikipathway.model;
-
-/**
- * Class used to store data from Label from .gpml.
- *
- * @author Jan Badura
- *
- */
-public class Label extends GraphicalPathwayElement {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * ???
- */
- private String textLabel;
-
- /**
- * Font weight (like italic, bold) that should be used.
- */
- private String fontWeight;
-
- /**
- * Shape associated with the label border.
- */
- private String shape;
-
- /**
- * How description should be aligned.
- */
- private String vAlign;
-
- /**
- * Where this node belongs to.
- */
- private String groupRef;
-
- /**
- * Sometimes {@link Label labels} are connected to reactions. This field
- */
- private boolean treatAsNode = false;
-
- /**
- * Default constructor.
- *
- * @param graphId
- * {@link PathwayElement#graphId}
- */
- public Label(String graphId) {
- super(graphId);
- setTextLabel(null);
- setGroupRef(null);
- }
-
- /**
- * Empty constructor that should be used only by serialization tools and
- * subclasses.
- */
- protected Label() {
- }
-
- @Override
- public String getName() {
- return getTextLabel();
- }
-
- /**
- * @return the textLabel
- * @see #textLabel
- */
- public String getTextLabel() {
- return textLabel;
- }
-
- /**
- * @param textLabel
- * the textLabel to set
- * @see #textLabel
- */
- public void setTextLabel(String textLabel) {
- this.textLabel = textLabel;
- }
-
- /**
- * @return the groupRef
- * @see #groupRef
- */
- public String getGroupRef() {
- return groupRef;
- }
-
- /**
- * @param groupRef
- * the groupRef to set
- * @see #groupRef
- */
- public void setGroupRef(String groupRef) {
- this.groupRef = groupRef;
- }
-
- /**
- * @return the treatAsNode
- * @see #treatAsNode
- */
- public boolean isTreatAsNode() {
- return treatAsNode;
- }
-
- /**
- * @param treatAsNode
- * the treatAsNode to set
- * @see #treatAsNode
- */
- public void setTreatAsNode(boolean treatAsNode) {
- this.treatAsNode = treatAsNode;
- }
-
- /**
- * @return the vAlign
- * @see #vAlign
- */
- public String getvAlign() {
- return vAlign;
- }
-
- /**
- * @param vAlign
- * the vAlign to set
- * @see #vAlign
- */
- public void setvAlign(String vAlign) {
- this.vAlign = vAlign;
- }
-
- /**
- * @return the fontWeight
- * @see #fontWeight
- */
- public String getFontWeight() {
- return fontWeight;
- }
-
- /**
- * @param fontWeight
- * the fontWeight to set
- * @see #fontWeight
- */
- public void setFontWeight(String fontWeight) {
- this.fontWeight = fontWeight;
- }
-
- /**
- * @return the shape
- * @see #shape
- */
- public String getShape() {
- return shape;
- }
-
- /**
- * @param shape
- * the shape to set
- * @see #shape
- */
- public void setShape(String shape) {
- this.shape = shape;
- }
-
-}
+package lcsb.mapviewer.wikipathway.model;
+
+/**
+ * Class used to store data from Label from .gpml.
+ *
+ * @author Jan Badura
+ *
+ */
+public class Label extends GraphicalPathwayElement {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * ???
+ */
+ private String textLabel;
+
+ /**
+ * Font weight (like italic, bold) that should be used.
+ */
+ private String fontWeight;
+
+ /**
+ * Shape associated with the label border.
+ */
+ private String shape;
+
+ /**
+ * How description should be aligned.
+ */
+ private String vAlign;
+
+ /**
+ * Where this node belongs to.
+ */
+ private String groupRef;
+
+ /**
+ * Sometimes {@link Label labels} are connected to reactions. This field
+ */
+ private boolean treatAsNode = false;
+
+ /**
+ * Default constructor.
+ *
+ * @param graphId
+ * {@link PathwayElement#graphId}
+ */
+ public Label(String graphId) {
+ super(graphId);
+ setTextLabel(null);
+ setGroupRef(null);
+ }
+
+ /**
+ * Empty constructor that should be used only by serialization tools and
+ * subclasses.
+ */
+ protected Label() {
+ }
+
+ @Override
+ public String getName() {
+ return getTextLabel();
+ }
+
+ /**
+ * @return the textLabel
+ * @see #textLabel
+ */
+ public String getTextLabel() {
+ return textLabel;
+ }
+
+ /**
+ * @param textLabel
+ * the textLabel to set
+ * @see #textLabel
+ */
+ public void setTextLabel(String textLabel) {
+ this.textLabel = textLabel;
+ }
+
+ /**
+ * @return the groupRef
+ * @see #groupRef
+ */
+ public String getGroupRef() {
+ return groupRef;
+ }
+
+ /**
+ * @param groupRef
+ * the groupRef to set
+ * @see #groupRef
+ */
+ public void setGroupRef(String groupRef) {
+ this.groupRef = groupRef;
+ }
+
+ /**
+ * @return the treatAsNode
+ * @see #treatAsNode
+ */
+ public boolean isTreatAsNode() {
+ return treatAsNode;
+ }
+
+ /**
+ * @param treatAsNode
+ * the treatAsNode to set
+ * @see #treatAsNode
+ */
+ public void setTreatAsNode(boolean treatAsNode) {
+ this.treatAsNode = treatAsNode;
+ }
+
+ /**
+ * @return the vAlign
+ * @see #vAlign
+ */
+ public String getvAlign() {
+ return vAlign;
+ }
+
+ /**
+ * @param vAlign
+ * the vAlign to set
+ * @see #vAlign
+ */
+ public void setvAlign(String vAlign) {
+ this.vAlign = vAlign;
+ }
+
+ /**
+ * @return the fontWeight
+ * @see #fontWeight
+ */
+ public String getFontWeight() {
+ return fontWeight;
+ }
+
+ /**
+ * @param fontWeight
+ * the fontWeight to set
+ * @see #fontWeight
+ */
+ public void setFontWeight(String fontWeight) {
+ this.fontWeight = fontWeight;
+ }
+
+ /**
+ * @return the shape
+ * @see #shape
+ */
+ public String getShape() {
+ return shape;
+ }
+
+ /**
+ * @param shape
+ * the shape to set
+ * @see #shape
+ */
+ public void setShape(String shape) {
+ this.shape = shape;
+ }
+
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/MergeMapping.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/MergeMapping.java
index 77ec622d88..c945b07a3a 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/MergeMapping.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/MergeMapping.java
@@ -1,199 +1,199 @@
-package lcsb.mapviewer.wikipathway.model;
-
-/**
- * This enum describes how two different {@link GpmlInteractionType types} of
- * {@link Edge edges} should be merged (what should be the output type and
- * direction of the output edge).
- *
- * @author Piotr Gawron
- *
- */
-public enum MergeMapping {
-
- /**
- * Merging {@link GpmlInteractionType#LINE} and
- * {@link GpmlInteractionType#ARROW} when both of them are in right direction.
- */
- LINE_ARROW_N_N(GpmlInteractionType.LINE, false, GpmlInteractionType.ARROW, false, GpmlInteractionType.ARROW, false), //
-
- /**
- * Merging {@link GpmlInteractionType#LINE} and
- * {@link GpmlInteractionType#ARROW} when line is reversed (user doesn't see a
- * difference) and arrow is in normal direction.
- */
- LINE_ARROW_R_N(GpmlInteractionType.LINE, true, GpmlInteractionType.ARROW, false, GpmlInteractionType.ARROW, false), //
-
- /**
- * Merging {@link GpmlInteractionType#ARROW} and
- * {@link GpmlInteractionType#LINE} when arrow is reversed and line is in
- * normal direction.
- */
- ARROW_LINE_R_N(GpmlInteractionType.ARROW, true, GpmlInteractionType.LINE, false, GpmlInteractionType.ARROW, true), //
-
- /**
- * Merging {@link GpmlInteractionType#ARROW} and
- * {@link GpmlInteractionType#LINE} when line is reversed and line is also
- * reversed (user doesn't see a difference) .
- */
- ARROW_LINE_R_R(GpmlInteractionType.ARROW, true, GpmlInteractionType.LINE, true, GpmlInteractionType.ARROW, true), //
-
- /**
- * Merging {@link GpmlInteractionType#LINE} and
- * {@link GpmlInteractionType#LINE} when both of them are in right direction.
- */
- LINE_LINE_N_N(GpmlInteractionType.LINE, false, GpmlInteractionType.LINE, false, GpmlInteractionType.LINE, false), //
-
- /**
- * Merging {@link GpmlInteractionType#LINE} and
- * {@link GpmlInteractionType#LINE} when first of them is reversed and second
- * not.
- */
- LINE_LINE_R_N(GpmlInteractionType.LINE, true, GpmlInteractionType.LINE, false, GpmlInteractionType.LINE, false), //
-
- /**
- * Merging {@link GpmlInteractionType#LINE} and
- * {@link GpmlInteractionType#LINE} when first is in right direction, but
- * second reversed.
- */
- LINE_LINE_N_R(GpmlInteractionType.LINE, false, GpmlInteractionType.LINE, true, GpmlInteractionType.LINE, false), //
-
- /**
- * Merging {@link GpmlInteractionType#LINE} and
- * {@link GpmlInteractionType#LINE} when both of them are reversed.
- */
- LINE_LINE_R_R(GpmlInteractionType.LINE, true, GpmlInteractionType.LINE, true, GpmlInteractionType.LINE, false);
-
- /**
- * Type of the first edge to merge.
- */
- private GpmlInteractionType type1;
-
- /**
- * Is the first edge reversed or not (if first edge is reversed it means that
- * the merging will be done in the beginning of first edge).
- */
- private boolean reversed1;
-
- /**
- * Type of the second edge.
- */
- private GpmlInteractionType type2;
-
- /**
- * Is the second edge reversed or not (if second edge is reversed it means
- * that the merging will be done in the end of second edge).
- */
- private boolean reversed2;
-
- /**
- * Which type should be used after merging.
- */
- private GpmlInteractionType resultType;
-
- /**
- * Should the edge after merging be reversed or not. If it's reversed it means
- * that it will go from second edge to first edge, if it's not reversed then
- * it will go from first edge to second edge.
- */
- private boolean resultReversed;
-
- /**
- * Default constructor.
- *
- * @param type1
- * {@link #type1}
- * @param reversed1
- * {@link #reversed1}
- * @param type2
- * {@link #type2}
- * @param reversed2
- * {@link #reversed2}
- * @param resultType
- * {@link #resultType}
- * @param resultReversed
- * {@link #resultReversed}
- */
- MergeMapping(GpmlInteractionType type1, boolean reversed1, GpmlInteractionType type2, boolean reversed2, GpmlInteractionType resultType,
- boolean resultReversed) {
- this.type1 = type1;
- this.reversed1 = reversed1;
- this.type2 = type2;
- this.reversed2 = reversed2;
- this.resultType = resultType;
- this.resultReversed = resultReversed;
- }
-
- /**
- * Returns {@link MergeMapping merge rule} that should be used for merging two
- * {@link Edge edges}.
- *
- * @param type1
- * {@link #type1}
- * @param reversed1
- * {@link #reversed1}
- * @param type2
- * {@link #type2}
- * @param reversed2
- * {@link #reversed2}
- * @return {@link MergeMapping merge rule} that should be used for merging two
- * {@link Edge edges} or <code>null</code> if such rule cannot be
- * found
- */
- public static MergeMapping getMergeMappingByInteractions(GpmlInteractionType type1, boolean reversed1, GpmlInteractionType type2, boolean reversed2) {
- for (MergeMapping mm : values()) {
- if (mm.getType1().equals(type1) && mm.isReversed1() == reversed1 && mm.getType2().equals(type2) && mm.isReversed2() == reversed2) {
- return mm;
- }
- }
- return null;
- }
-
- /**
- * @return the type1
- * @see #type1
- */
- public GpmlInteractionType getType1() {
- return type1;
- }
-
- /**
- * @return the reversed1
- * @see #reversed1
- */
- public boolean isReversed1() {
- return reversed1;
- }
-
- /**
- * @return the type2
- * @see #type2
- */
- public GpmlInteractionType getType2() {
- return type2;
- }
-
- /**
- * @return the reversed2
- * @see #reversed2
- */
- public boolean isReversed2() {
- return reversed2;
- }
-
- /**
- * @return the resultType
- * @see #resultType
- */
- public GpmlInteractionType getResultType() {
- return resultType;
- }
-
- /**
- * @return the resultReversed
- * @see #resultReversed
- */
- public boolean isResultReversed() {
- return resultReversed;
- }
-
-}
+package lcsb.mapviewer.wikipathway.model;
+
+/**
+ * This enum describes how two different {@link GpmlInteractionType types} of
+ * {@link Edge edges} should be merged (what should be the output type and
+ * direction of the output edge).
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum MergeMapping {
+
+ /**
+ * Merging {@link GpmlInteractionType#LINE} and
+ * {@link GpmlInteractionType#ARROW} when both of them are in right direction.
+ */
+ LINE_ARROW_N_N(GpmlInteractionType.LINE, false, GpmlInteractionType.ARROW, false, GpmlInteractionType.ARROW, false), //
+
+ /**
+ * Merging {@link GpmlInteractionType#LINE} and
+ * {@link GpmlInteractionType#ARROW} when line is reversed (user doesn't see a
+ * difference) and arrow is in normal direction.
+ */
+ LINE_ARROW_R_N(GpmlInteractionType.LINE, true, GpmlInteractionType.ARROW, false, GpmlInteractionType.ARROW, false), //
+
+ /**
+ * Merging {@link GpmlInteractionType#ARROW} and
+ * {@link GpmlInteractionType#LINE} when arrow is reversed and line is in
+ * normal direction.
+ */
+ ARROW_LINE_R_N(GpmlInteractionType.ARROW, true, GpmlInteractionType.LINE, false, GpmlInteractionType.ARROW, true), //
+
+ /**
+ * Merging {@link GpmlInteractionType#ARROW} and
+ * {@link GpmlInteractionType#LINE} when line is reversed and line is also
+ * reversed (user doesn't see a difference) .
+ */
+ ARROW_LINE_R_R(GpmlInteractionType.ARROW, true, GpmlInteractionType.LINE, true, GpmlInteractionType.ARROW, true), //
+
+ /**
+ * Merging {@link GpmlInteractionType#LINE} and
+ * {@link GpmlInteractionType#LINE} when both of them are in right direction.
+ */
+ LINE_LINE_N_N(GpmlInteractionType.LINE, false, GpmlInteractionType.LINE, false, GpmlInteractionType.LINE, false), //
+
+ /**
+ * Merging {@link GpmlInteractionType#LINE} and
+ * {@link GpmlInteractionType#LINE} when first of them is reversed and second
+ * not.
+ */
+ LINE_LINE_R_N(GpmlInteractionType.LINE, true, GpmlInteractionType.LINE, false, GpmlInteractionType.LINE, false), //
+
+ /**
+ * Merging {@link GpmlInteractionType#LINE} and
+ * {@link GpmlInteractionType#LINE} when first is in right direction, but
+ * second reversed.
+ */
+ LINE_LINE_N_R(GpmlInteractionType.LINE, false, GpmlInteractionType.LINE, true, GpmlInteractionType.LINE, false), //
+
+ /**
+ * Merging {@link GpmlInteractionType#LINE} and
+ * {@link GpmlInteractionType#LINE} when both of them are reversed.
+ */
+ LINE_LINE_R_R(GpmlInteractionType.LINE, true, GpmlInteractionType.LINE, true, GpmlInteractionType.LINE, false);
+
+ /**
+ * Type of the first edge to merge.
+ */
+ private GpmlInteractionType type1;
+
+ /**
+ * Is the first edge reversed or not (if first edge is reversed it means that
+ * the merging will be done in the beginning of first edge).
+ */
+ private boolean reversed1;
+
+ /**
+ * Type of the second edge.
+ */
+ private GpmlInteractionType type2;
+
+ /**
+ * Is the second edge reversed or not (if second edge is reversed it means
+ * that the merging will be done in the end of second edge).
+ */
+ private boolean reversed2;
+
+ /**
+ * Which type should be used after merging.
+ */
+ private GpmlInteractionType resultType;
+
+ /**
+ * Should the edge after merging be reversed or not. If it's reversed it means
+ * that it will go from second edge to first edge, if it's not reversed then
+ * it will go from first edge to second edge.
+ */
+ private boolean resultReversed;
+
+ /**
+ * Default constructor.
+ *
+ * @param type1
+ * {@link #type1}
+ * @param reversed1
+ * {@link #reversed1}
+ * @param type2
+ * {@link #type2}
+ * @param reversed2
+ * {@link #reversed2}
+ * @param resultType
+ * {@link #resultType}
+ * @param resultReversed
+ * {@link #resultReversed}
+ */
+ MergeMapping(GpmlInteractionType type1, boolean reversed1, GpmlInteractionType type2, boolean reversed2, GpmlInteractionType resultType,
+ boolean resultReversed) {
+ this.type1 = type1;
+ this.reversed1 = reversed1;
+ this.type2 = type2;
+ this.reversed2 = reversed2;
+ this.resultType = resultType;
+ this.resultReversed = resultReversed;
+ }
+
+ /**
+ * Returns {@link MergeMapping merge rule} that should be used for merging two
+ * {@link Edge edges}.
+ *
+ * @param type1
+ * {@link #type1}
+ * @param reversed1
+ * {@link #reversed1}
+ * @param type2
+ * {@link #type2}
+ * @param reversed2
+ * {@link #reversed2}
+ * @return {@link MergeMapping merge rule} that should be used for merging two
+ * {@link Edge edges} or <code>null</code> if such rule cannot be
+ * found
+ */
+ public static MergeMapping getMergeMappingByInteractions(GpmlInteractionType type1, boolean reversed1, GpmlInteractionType type2, boolean reversed2) {
+ for (MergeMapping mm : values()) {
+ if (mm.getType1().equals(type1) && mm.isReversed1() == reversed1 && mm.getType2().equals(type2) && mm.isReversed2() == reversed2) {
+ return mm;
+ }
+ }
+ return null;
+ }
+
+ /**
+ * @return the type1
+ * @see #type1
+ */
+ public GpmlInteractionType getType1() {
+ return type1;
+ }
+
+ /**
+ * @return the reversed1
+ * @see #reversed1
+ */
+ public boolean isReversed1() {
+ return reversed1;
+ }
+
+ /**
+ * @return the type2
+ * @see #type2
+ */
+ public GpmlInteractionType getType2() {
+ return type2;
+ }
+
+ /**
+ * @return the reversed2
+ * @see #reversed2
+ */
+ public boolean isReversed2() {
+ return reversed2;
+ }
+
+ /**
+ * @return the resultType
+ * @see #resultType
+ */
+ public GpmlInteractionType getResultType() {
+ return resultType;
+ }
+
+ /**
+ * @return the resultReversed
+ * @see #resultReversed
+ */
+ public boolean isResultReversed() {
+ return resultReversed;
+ }
+
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PathwayElement.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PathwayElement.java
index 1c523cec59..665c44527d 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PathwayElement.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PathwayElement.java
@@ -1,167 +1,167 @@
-package lcsb.mapviewer.wikipathway.model;
-
-import java.awt.geom.Rectangle2D;
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
-/**
- * Abstract class for pathway elements. It defines common functionalities for
- * all elements in the model. There are two known subclasses:
- * <ul>
- * <li> {@link GraphicalPathwayElement}, representing elemnts with some graphical
- * representation</li>
- * <li> {@link Group}, representing just groups of elements</li>
- * </ul>
- *
- * @author Jan Badura
- *
- */
-public abstract class PathwayElement implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Comment of the element.
- */
- private List<String> comments = new ArrayList<>();
-
- /**
- * Z order of the element.
- */
- private Integer zOrder;
-
- /**
- * Identifier of the element in model.
- */
- private String graphId;
-
- /**
- *
- * Reference to biopax node with references about this element.
- */
- private List<String> biopaxReferences = new ArrayList<>();
-
- /**
- * Default constructor.
- *
- * @param graphId
- * {@link #graphId} value
- */
- public PathwayElement(String graphId) {
- this.graphId = graphId;
- }
-
- /**
- * Empty constructor that should be used only by serialization tools and
- * subclasses.
- */
- protected PathwayElement() {
- }
-
- /**
- *
- * @return {@link #graphId}
- */
- public String getGraphId() {
- return this.graphId;
- }
-
- /**
- * Returns name of the element.
- *
- * @return name of the element
- */
- abstract String getName();
-
- /**
- * Return boundary of the element.
- *
- * @return boundary of the element
- */
- abstract Rectangle2D getRectangle();
-
- /**
- * @param graphId
- * the graphId to set
- * @see #graphId
- */
- void setGraphId(String graphId) {
- this.graphId = graphId;
- }
-
- /**
- * Returns prefix that should be used in logger for warnings about this
- * element.
- *
- * @return prefix that should be used in logger for warnings about this
- * element
- */
- public String getWarningPrefix() {
- return "[" + this.getClass().getSimpleName() + ", " + getGraphId() + "]\t";
- }
-
- /**
- * @return the biopaxReference
- * @see #biopaxReference
- */
- public List<String> getBiopaxReference() {
- return biopaxReferences;
- }
-
- /**
- * @param biopaxReferences
- * the biopaxReference to set
- * @see #biopaxReference
- */
- public void setBiopaxReference(List<String> biopaxReferences) {
- this.biopaxReferences = biopaxReferences;
- }
-
- /**
- * @return the zOrder
- * @see #zOrder
- */
- public Integer getzOrder() {
- return zOrder;
- }
-
- /**
- * @param zOrder
- * the zOrder to set
- * @see #zOrder
- */
- public void setzOrder(Integer zOrder) {
- this.zOrder = zOrder;
- }
-
- /**
- * Adds reference to {@link #biopaxReferences}.
- *
- * @param biopaxString
- * reference to add
- */
- public void addBiopaxReference(String biopaxString) {
- biopaxReferences.add(biopaxString);
- }
-
- /**
- * @return the comments
- * @see #comments
- */
- public List<String> getComments() {
- return comments;
- }
-
- /**
- * @param comment
- * the comment to set
- * @see #comment
- */
- public void addComment(String comment) {
- this.comments.add(comment);
- }
-}
+package lcsb.mapviewer.wikipathway.model;
+
+import java.awt.geom.Rectangle2D;
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * Abstract class for pathway elements. It defines common functionalities for
+ * all elements in the model. There are two known subclasses:
+ * <ul>
+ * <li> {@link GraphicalPathwayElement}, representing elemnts with some graphical
+ * representation</li>
+ * <li> {@link Group}, representing just groups of elements</li>
+ * </ul>
+ *
+ * @author Jan Badura
+ *
+ */
+public abstract class PathwayElement implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Comment of the element.
+ */
+ private List<String> comments = new ArrayList<>();
+
+ /**
+ * Z order of the element.
+ */
+ private Integer zOrder;
+
+ /**
+ * Identifier of the element in model.
+ */
+ private String graphId;
+
+ /**
+ *
+ * Reference to biopax node with references about this element.
+ */
+ private List<String> biopaxReferences = new ArrayList<>();
+
+ /**
+ * Default constructor.
+ *
+ * @param graphId
+ * {@link #graphId} value
+ */
+ public PathwayElement(String graphId) {
+ this.graphId = graphId;
+ }
+
+ /**
+ * Empty constructor that should be used only by serialization tools and
+ * subclasses.
+ */
+ protected PathwayElement() {
+ }
+
+ /**
+ *
+ * @return {@link #graphId}
+ */
+ public String getGraphId() {
+ return this.graphId;
+ }
+
+ /**
+ * Returns name of the element.
+ *
+ * @return name of the element
+ */
+ abstract String getName();
+
+ /**
+ * Return boundary of the element.
+ *
+ * @return boundary of the element
+ */
+ abstract Rectangle2D getRectangle();
+
+ /**
+ * @param graphId
+ * the graphId to set
+ * @see #graphId
+ */
+ void setGraphId(String graphId) {
+ this.graphId = graphId;
+ }
+
+ /**
+ * Returns prefix that should be used in logger for warnings about this
+ * element.
+ *
+ * @return prefix that should be used in logger for warnings about this
+ * element
+ */
+ public String getWarningPrefix() {
+ return "[" + this.getClass().getSimpleName() + ", " + getGraphId() + "]\t";
+ }
+
+ /**
+ * @return the biopaxReference
+ * @see #biopaxReference
+ */
+ public List<String> getBiopaxReference() {
+ return biopaxReferences;
+ }
+
+ /**
+ * @param biopaxReferences
+ * the biopaxReference to set
+ * @see #biopaxReference
+ */
+ public void setBiopaxReference(List<String> biopaxReferences) {
+ this.biopaxReferences = biopaxReferences;
+ }
+
+ /**
+ * @return the zOrder
+ * @see #zOrder
+ */
+ public Integer getzOrder() {
+ return zOrder;
+ }
+
+ /**
+ * @param zOrder
+ * the zOrder to set
+ * @see #zOrder
+ */
+ public void setzOrder(Integer zOrder) {
+ this.zOrder = zOrder;
+ }
+
+ /**
+ * Adds reference to {@link #biopaxReferences}.
+ *
+ * @param biopaxString
+ * reference to add
+ */
+ public void addBiopaxReference(String biopaxString) {
+ biopaxReferences.add(biopaxString);
+ }
+
+ /**
+ * @return the comments
+ * @see #comments
+ */
+ public List<String> getComments() {
+ return comments;
+ }
+
+ /**
+ * @param comment
+ * the comment to set
+ * @see #comment
+ */
+ public void addComment(String comment) {
+ this.comments.add(comment);
+ }
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PointData.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PointData.java
index ff19c422a7..824905397e 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PointData.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PointData.java
@@ -1,201 +1,201 @@
-package lcsb.mapviewer.wikipathway.model;
-
-import java.awt.geom.Point2D;
-import java.io.Serializable;
-
-import org.apache.log4j.Logger;
-
-/**
- * Class that defines infgomration about point stored in gpml structures.
- *
- * @author Piotr Gawron
- *
- */
-public class PointData implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Defdault clas logger.
- */
- private final transient Logger logger = Logger.getLogger(PointData.class);
-
- /**
- * X coordinate.
- */
- private Double x;
-
- /**
- * Y coordinate.
- */
- private Double y;
-
- /**
- * String identifing anchor point on the map.
- */
- private String graphRef;
-
- /**
- * Where the point is placed on the {@link Shape} object (it's a value between
- * -1,1).
- */
- private String relX;
-
- /**
- * Where the point is placed on the {@link Shape} object (it's a value between
- * -1,1).
- */
- private String relY;
-
- /**
- * Type of line asociated with line that ends in this point.
- */
- private GpmlInteractionType type;
-
- /**
- * @return the x
- * @see #x
- */
- public Double getX() {
- return x;
- }
-
- /**
- * @param x
- * the x to set
- * @see #x
- */
- public void setX(Double x) {
- this.x = x;
- }
-
- /**
- * @return the y
- * @see #y
- */
- public Double getY() {
- return y;
- }
-
- /**
- * @param y
- * the y to set
- * @see #y
- */
- public void setY(Double y) {
- this.y = y;
- }
-
- /**
- * @param relX
- * the relX to set
- * @see #relX
- */
- public void setRelX(String relX) {
- this.relX = relX;
- }
-
- /**
- * @param relY
- * the relY to set
- * @see #relY
- */
- public void setRelY(String relY) {
- this.relY = relY;
- }
-
- /**
- * @return the type
- * @see #type
- */
- public GpmlInteractionType getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(GpmlInteractionType type) {
- this.type = type;
- }
-
- /**
- * @return the graphRef
- * @see #graphRef
- */
- public String getGraphRef() {
- return graphRef;
- }
-
- /**
- * @param graphRef
- * the graphRef to set
- * @see #graphRef
- */
- public void setGraphRef(String graphRef) {
- this.graphRef = graphRef;
- }
-
- /**
- * Transform {@link PointData} into standard {@link Point2D point}.
- *
- * @return {@link Point2D point} represented by this structure
- */
- public Point2D toPoint() {
- return new Point2D.Double(x, y);
- }
-
- /**
- * Returns <code>true</code> if point is connected some defined point on the
- * map, <code>false</code> otherwise.
- *
- * @return <code>true</code> if point is connected some defined point on the
- * map, <code>false</code> otherwise.
- */
- public boolean hasGraphRef() {
- return graphRef != null && !graphRef.isEmpty();
- }
-
- /**
- * Returns {@link Direction direction} from which this point is placed on
- * {@link Shape} to which the point is connected.
- *
- * @return {@link Direction direction} from which this point is placed on
- * {@link Shape}
- */
- public Direction getDirection() {
- if (relX == null || relY == null) {
- return null;
- } else if (relX.equals("1.0")) {
- return Direction.EAST;
- } else if (relX.equals("-1.0")) {
- return Direction.WEST;
- } else if (relY.equals("1.0")) {
- return Direction.SOUTH;
- } else if (relY.equals("-1.0")) {
- return Direction.NORTH;
- } else {
- logger.warn("Cannot determine connection direction from values: relX=" + relX + "; relY=" + relY + ". Estimating...");
- double xVal = Double.valueOf(relX);
- double yVal = Double.valueOf(relY);
- if (Math.abs(xVal) > Math.abs(yVal)) {
- if (xVal > 0) {
- return Direction.EAST;
- } else {
- return Direction.WEST;
- }
- } else {
- if (yVal > 0) {
- return Direction.NORTH;
- } else {
- return Direction.SOUTH;
- }
- }
- }
- }
-}
+package lcsb.mapviewer.wikipathway.model;
+
+import java.awt.geom.Point2D;
+import java.io.Serializable;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Class that defines infgomration about point stored in gpml structures.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class PointData implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Defdault clas logger.
+ */
+ private final transient Logger logger = Logger.getLogger(PointData.class);
+
+ /**
+ * X coordinate.
+ */
+ private Double x;
+
+ /**
+ * Y coordinate.
+ */
+ private Double y;
+
+ /**
+ * String identifing anchor point on the map.
+ */
+ private String graphRef;
+
+ /**
+ * Where the point is placed on the {@link Shape} object (it's a value between
+ * -1,1).
+ */
+ private String relX;
+
+ /**
+ * Where the point is placed on the {@link Shape} object (it's a value between
+ * -1,1).
+ */
+ private String relY;
+
+ /**
+ * Type of line asociated with line that ends in this point.
+ */
+ private GpmlInteractionType type;
+
+ /**
+ * @return the x
+ * @see #x
+ */
+ public Double getX() {
+ return x;
+ }
+
+ /**
+ * @param x
+ * the x to set
+ * @see #x
+ */
+ public void setX(Double x) {
+ this.x = x;
+ }
+
+ /**
+ * @return the y
+ * @see #y
+ */
+ public Double getY() {
+ return y;
+ }
+
+ /**
+ * @param y
+ * the y to set
+ * @see #y
+ */
+ public void setY(Double y) {
+ this.y = y;
+ }
+
+ /**
+ * @param relX
+ * the relX to set
+ * @see #relX
+ */
+ public void setRelX(String relX) {
+ this.relX = relX;
+ }
+
+ /**
+ * @param relY
+ * the relY to set
+ * @see #relY
+ */
+ public void setRelY(String relY) {
+ this.relY = relY;
+ }
+
+ /**
+ * @return the type
+ * @see #type
+ */
+ public GpmlInteractionType getType() {
+ return type;
+ }
+
+ /**
+ * @param type
+ * the type to set
+ * @see #type
+ */
+ public void setType(GpmlInteractionType type) {
+ this.type = type;
+ }
+
+ /**
+ * @return the graphRef
+ * @see #graphRef
+ */
+ public String getGraphRef() {
+ return graphRef;
+ }
+
+ /**
+ * @param graphRef
+ * the graphRef to set
+ * @see #graphRef
+ */
+ public void setGraphRef(String graphRef) {
+ this.graphRef = graphRef;
+ }
+
+ /**
+ * Transform {@link PointData} into standard {@link Point2D point}.
+ *
+ * @return {@link Point2D point} represented by this structure
+ */
+ public Point2D toPoint() {
+ return new Point2D.Double(x, y);
+ }
+
+ /**
+ * Returns <code>true</code> if point is connected some defined point on the
+ * map, <code>false</code> otherwise.
+ *
+ * @return <code>true</code> if point is connected some defined point on the
+ * map, <code>false</code> otherwise.
+ */
+ public boolean hasGraphRef() {
+ return graphRef != null && !graphRef.isEmpty();
+ }
+
+ /**
+ * Returns {@link Direction direction} from which this point is placed on
+ * {@link Shape} to which the point is connected.
+ *
+ * @return {@link Direction direction} from which this point is placed on
+ * {@link Shape}
+ */
+ public Direction getDirection() {
+ if (relX == null || relY == null) {
+ return null;
+ } else if (relX.equals("1.0")) {
+ return Direction.EAST;
+ } else if (relX.equals("-1.0")) {
+ return Direction.WEST;
+ } else if (relY.equals("1.0")) {
+ return Direction.SOUTH;
+ } else if (relY.equals("-1.0")) {
+ return Direction.NORTH;
+ } else {
+ logger.warn("Cannot determine connection direction from values: relX=" + relX + "; relY=" + relY + ". Estimating...");
+ double xVal = Double.valueOf(relX);
+ double yVal = Double.valueOf(relY);
+ if (Math.abs(xVal) > Math.abs(yVal)) {
+ if (xVal > 0) {
+ return Direction.EAST;
+ } else {
+ return Direction.WEST;
+ }
+ } else {
+ if (yVal > 0) {
+ return Direction.NORTH;
+ } else {
+ return Direction.SOUTH;
+ }
+ }
+ }
+ }
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/ReferenceMapping.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/ReferenceMapping.java
index b2929ed2c8..236d8c972e 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/ReferenceMapping.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/ReferenceMapping.java
@@ -1,270 +1,270 @@
-package lcsb.mapviewer.wikipathway.model;
-
-import lcsb.mapviewer.model.map.MiriamType;
-
-/**
- * This enum lists mapping between strings representing annotations in gpml into
- * {@link MiriamType}.
- *
- * @author Piotr Gawron
- *
- */
-public enum ReferenceMapping {
-
- /**
- * {@link MiriamType#CAS}.
- */
- CAS("CAS", MiriamType.CAS), //
-
- /**
- * {@link MiriamType#CHEBI}.
- */
- CHEBI("Chebi", MiriamType.CHEBI), //
-
- /**
- * {@link MiriamType#CHEMBL_COMPOUND}.
- */
- CHEMBL_COMPOUND(null, MiriamType.CHEMBL_COMPOUND), //
-
- /**
- * {@link MiriamType#CHEMBL_TARGET}.
- */
- CHEMBL_TARGET(null, MiriamType.CHEMBL_TARGET), //
-
- /**
- * {@link MiriamType#CHEMSPIDER}.
- */
- CHEMSPIDER("ChemSpider", MiriamType.CHEMSPIDER), //
-
- /**
- * {@link MiriamType#EC}.
- */
- EC("Enzyme Nomenclature", MiriamType.EC), //
-
- /**
- * {@link MiriamType#ENSEMBL}.
- */
- ENSEMBL("Ensembl", MiriamType.ENSEMBL), //
-
- /**
- * {@link MiriamType#ENTREZ}.
- */
- ENTREZ("Entrez Gene", MiriamType.ENTREZ), //
-
- /**
- * Alternative name for {@link MiriamType#ENTREZ}.
- */
- GEN_BANK("GenBank", MiriamType.ENTREZ), //
-
- /**
- * {@link MiriamType#GO}.
- */
- GO("GeneOntology", MiriamType.GO), //
-
- /**
- * {@link MiriamType#HGNC}.
- */
- HGNC("HGNC Accession number", MiriamType.HGNC), //
-
- /**
- * {@link MiriamType#HGNC_SYMBOL}.
- */
- HGNC_SYMBOL("HGNC", MiriamType.HGNC_SYMBOL), //
-
- /**
- * {@link MiriamType#HMDB}.
- */
- HMDB("HMDB", MiriamType.HMDB), //
-
- /**
- * {@link MiriamType#INTERPRO}.
- */
- INTERPRO("InterPro", MiriamType.INTERPRO), //
-
- /**
- * {@link MiriamType#MESH_2012}.
- */
- MESH_2012(null, MiriamType.MESH_2012), //
-
- /**
- * {@link MiriamType#MI_RBASE_SEQUENCE}.
- */
- MI_RBASE_SEQUENCE2("miRBase", MiriamType.MI_R_BASE_SEQUENCE), //
-
- /**
- * {@link MiriamType#KEGG_COMPOUND}.
- */
- KEGG_COMPOUND("KEGG Compound", MiriamType.KEGG_COMPOUND), //
-
- /**
- * {@link MiriamType#KEGG_GENES}.
- */
- KEGG_GENES("KEGG Genes", MiriamType.KEGG_GENES), //
-
- /**
- * {@link MiriamType#KEGG_ORTHOLOGY}.
- */
- KEGG_ORTHOLOGY("Kegg ortholog", MiriamType.KEGG_ORTHOLOGY), //
-
- /**
- * {@link MiriamType#KEGG_PATHWAY}.
- */
- KEGG_PATHWAY("KEGG Pathway", MiriamType.KEGG_PATHWAY), //
-
- /**
- * {@link MiriamType#KEGG_REACTION}.
- */
- KEGG_REACTION("KEGG Reaction", MiriamType.KEGG_REACTION), //
-
- /**
- * {@link MiriamType#MGD}.
- */
- MGD("MGI", MiriamType.MGD), //
-
- /**
- * {@link MiriamType#MI_RBASE_SEQUENCE}.
- */
- MI_RBASE_SEQUENCE("miRBase Sequence", MiriamType.MI_R_BASE_SEQUENCE), //
-
- /**
- * {@link MiriamType#PANTHER}.
- */
- PANTHER(null, MiriamType.PANTHER), //
-
- /**
- * {@link MiriamType#PFAM}.
- */
- PFAM("Pfam", MiriamType.PFAM), //
-
- /**
- * {@link MiriamType#PHARM}.
- */
- PHARM("PharmGKB Pathways", MiriamType.PHARM), //
-
- /**
- * {@link MiriamType#PUBCHEM}.
- */
- PUBCHEM("PubChem-compound", MiriamType.PUBCHEM), //
-
- /**
- * {@link MiriamType#PUBCHEM_SUBSTANCE}.
- */
- PUBCHEM_SUBSTANCE("PubChem-substance", MiriamType.PUBCHEM_SUBSTANCE), //
-
- /**
- * {@link MiriamType#REACTOME}.
- */
- REACTOME("Reactome", MiriamType.REACTOME), //
-
- /**
- * {@link MiriamType#REFSEQ}.
- */
- REFSEQ("RefSeq", MiriamType.REFSEQ), //
-
- /**
- * {@link MiriamType#SGD }.
- */
- SGD("SGD", MiriamType.SGD), //
-
- /**
- * {@link MiriamType#TAIR_LOCUS}.
- */
- TAIR_LOCUS("TAIR", MiriamType.TAIR_LOCUS), //
-
- /**
- * {@link MiriamType#UNIPROT}.
- */
- UNIPROT("Uniprot-TrEMBL", MiriamType.UNIPROT), //
-
- /**
- * {@link MiriamType#UNIPROT_ISOFORM}.
- */
- UNIPROT_ISOFORM(null, MiriamType.UNIPROT_ISOFORM), //
-
- /**
- * {@link MiriamType#WIKIPATHWAYS}.
- */
- WIKIPATHWAYS("Wikipathways", MiriamType.WIKIPATHWAYS), //
-
- /**
- * {@link MiriamType#WIKIPEDIA}.
- */
- WIKIPEDIA("Wikipedia", MiriamType.WIKIPEDIA);
-
- /**
- * Gpml string representing specific database type.
- */
- private String gpmlString;
-
- /**
- * {@link MiriamType} corresponding to {@link #gpmlString}.
- */
- private MiriamType type;
-
- /**
- * Default constructor.
- *
- * @param gpmlString
- * {@link #getGpmlString()}
- * @param type
- * {@link #type}
- */
- ReferenceMapping(String gpmlString, MiriamType type) {
- this.type = type;
- this.gpmlString = gpmlString;
- }
-
- /**
- * @return the gpmlString
- * @see #gpmlString
- */
- public String getGpmlString() {
- return gpmlString;
- }
-
- /**
- * @return the type
- * @see #type
- */
- public MiriamType getType() {
- return type;
- }
-
- /**
- * Returns {@link ReferenceMapping mapping} to {@link MiriamType} that should
- * be used for gpml resource type.
- *
- * @param gpmlString
- * {@link #gpmlString}
- * @return {@link ReferenceMapping mapping} to {@link MiriamType} that should
- * be used for gpml resource type
- */
- public static ReferenceMapping getMappingByGpmlString(String gpmlString) {
- for (ReferenceMapping mm : values()) {
- if (mm.getGpmlString() != null && mm.getGpmlString().equals(gpmlString)) {
- return mm;
- }
- }
- return null;
- }
-
- /**
- * Returns {@link ReferenceMapping mapping} that should be used for
- * {@link #gpmlString gpml string} representing type of annotation.
- *
- * @param dataType
- * {@link #type}
- *
- * @return {@link ReferenceMapping mapping} that should be used for
- * {@link #gpmlString gpml string} representing type of annotation
- */
- public static ReferenceMapping getMappingByMiriamType(MiriamType dataType) {
- for (ReferenceMapping mm : values()) {
- if (mm.getType().equals(dataType)) {
- return mm;
- }
- }
- return null;
- }
-
-}
+package lcsb.mapviewer.wikipathway.model;
+
+import lcsb.mapviewer.model.map.MiriamType;
+
+/**
+ * This enum lists mapping between strings representing annotations in gpml into
+ * {@link MiriamType}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum ReferenceMapping {
+
+ /**
+ * {@link MiriamType#CAS}.
+ */
+ CAS("CAS", MiriamType.CAS), //
+
+ /**
+ * {@link MiriamType#CHEBI}.
+ */
+ CHEBI("Chebi", MiriamType.CHEBI), //
+
+ /**
+ * {@link MiriamType#CHEMBL_COMPOUND}.
+ */
+ CHEMBL_COMPOUND(null, MiriamType.CHEMBL_COMPOUND), //
+
+ /**
+ * {@link MiriamType#CHEMBL_TARGET}.
+ */
+ CHEMBL_TARGET(null, MiriamType.CHEMBL_TARGET), //
+
+ /**
+ * {@link MiriamType#CHEMSPIDER}.
+ */
+ CHEMSPIDER("ChemSpider", MiriamType.CHEMSPIDER), //
+
+ /**
+ * {@link MiriamType#EC}.
+ */
+ EC("Enzyme Nomenclature", MiriamType.EC), //
+
+ /**
+ * {@link MiriamType#ENSEMBL}.
+ */
+ ENSEMBL("Ensembl", MiriamType.ENSEMBL), //
+
+ /**
+ * {@link MiriamType#ENTREZ}.
+ */
+ ENTREZ("Entrez Gene", MiriamType.ENTREZ), //
+
+ /**
+ * Alternative name for {@link MiriamType#ENTREZ}.
+ */
+ GEN_BANK("GenBank", MiriamType.ENTREZ), //
+
+ /**
+ * {@link MiriamType#GO}.
+ */
+ GO("GeneOntology", MiriamType.GO), //
+
+ /**
+ * {@link MiriamType#HGNC}.
+ */
+ HGNC("HGNC Accession number", MiriamType.HGNC), //
+
+ /**
+ * {@link MiriamType#HGNC_SYMBOL}.
+ */
+ HGNC_SYMBOL("HGNC", MiriamType.HGNC_SYMBOL), //
+
+ /**
+ * {@link MiriamType#HMDB}.
+ */
+ HMDB("HMDB", MiriamType.HMDB), //
+
+ /**
+ * {@link MiriamType#INTERPRO}.
+ */
+ INTERPRO("InterPro", MiriamType.INTERPRO), //
+
+ /**
+ * {@link MiriamType#MESH_2012}.
+ */
+ MESH_2012(null, MiriamType.MESH_2012), //
+
+ /**
+ * {@link MiriamType#MI_RBASE_SEQUENCE}.
+ */
+ MI_RBASE_SEQUENCE2("miRBase", MiriamType.MI_R_BASE_SEQUENCE), //
+
+ /**
+ * {@link MiriamType#KEGG_COMPOUND}.
+ */
+ KEGG_COMPOUND("KEGG Compound", MiriamType.KEGG_COMPOUND), //
+
+ /**
+ * {@link MiriamType#KEGG_GENES}.
+ */
+ KEGG_GENES("KEGG Genes", MiriamType.KEGG_GENES), //
+
+ /**
+ * {@link MiriamType#KEGG_ORTHOLOGY}.
+ */
+ KEGG_ORTHOLOGY("Kegg ortholog", MiriamType.KEGG_ORTHOLOGY), //
+
+ /**
+ * {@link MiriamType#KEGG_PATHWAY}.
+ */
+ KEGG_PATHWAY("KEGG Pathway", MiriamType.KEGG_PATHWAY), //
+
+ /**
+ * {@link MiriamType#KEGG_REACTION}.
+ */
+ KEGG_REACTION("KEGG Reaction", MiriamType.KEGG_REACTION), //
+
+ /**
+ * {@link MiriamType#MGD}.
+ */
+ MGD("MGI", MiriamType.MGD), //
+
+ /**
+ * {@link MiriamType#MI_RBASE_SEQUENCE}.
+ */
+ MI_RBASE_SEQUENCE("miRBase Sequence", MiriamType.MI_R_BASE_SEQUENCE), //
+
+ /**
+ * {@link MiriamType#PANTHER}.
+ */
+ PANTHER(null, MiriamType.PANTHER), //
+
+ /**
+ * {@link MiriamType#PFAM}.
+ */
+ PFAM("Pfam", MiriamType.PFAM), //
+
+ /**
+ * {@link MiriamType#PHARM}.
+ */
+ PHARM("PharmGKB Pathways", MiriamType.PHARM), //
+
+ /**
+ * {@link MiriamType#PUBCHEM}.
+ */
+ PUBCHEM("PubChem-compound", MiriamType.PUBCHEM), //
+
+ /**
+ * {@link MiriamType#PUBCHEM_SUBSTANCE}.
+ */
+ PUBCHEM_SUBSTANCE("PubChem-substance", MiriamType.PUBCHEM_SUBSTANCE), //
+
+ /**
+ * {@link MiriamType#REACTOME}.
+ */
+ REACTOME("Reactome", MiriamType.REACTOME), //
+
+ /**
+ * {@link MiriamType#REFSEQ}.
+ */
+ REFSEQ("RefSeq", MiriamType.REFSEQ), //
+
+ /**
+ * {@link MiriamType#SGD }.
+ */
+ SGD("SGD", MiriamType.SGD), //
+
+ /**
+ * {@link MiriamType#TAIR_LOCUS}.
+ */
+ TAIR_LOCUS("TAIR", MiriamType.TAIR_LOCUS), //
+
+ /**
+ * {@link MiriamType#UNIPROT}.
+ */
+ UNIPROT("Uniprot-TrEMBL", MiriamType.UNIPROT), //
+
+ /**
+ * {@link MiriamType#UNIPROT_ISOFORM}.
+ */
+ UNIPROT_ISOFORM(null, MiriamType.UNIPROT_ISOFORM), //
+
+ /**
+ * {@link MiriamType#WIKIPATHWAYS}.
+ */
+ WIKIPATHWAYS("Wikipathways", MiriamType.WIKIPATHWAYS), //
+
+ /**
+ * {@link MiriamType#WIKIPEDIA}.
+ */
+ WIKIPEDIA("Wikipedia", MiriamType.WIKIPEDIA);
+
+ /**
+ * Gpml string representing specific database type.
+ */
+ private String gpmlString;
+
+ /**
+ * {@link MiriamType} corresponding to {@link #gpmlString}.
+ */
+ private MiriamType type;
+
+ /**
+ * Default constructor.
+ *
+ * @param gpmlString
+ * {@link #getGpmlString()}
+ * @param type
+ * {@link #type}
+ */
+ ReferenceMapping(String gpmlString, MiriamType type) {
+ this.type = type;
+ this.gpmlString = gpmlString;
+ }
+
+ /**
+ * @return the gpmlString
+ * @see #gpmlString
+ */
+ public String getGpmlString() {
+ return gpmlString;
+ }
+
+ /**
+ * @return the type
+ * @see #type
+ */
+ public MiriamType getType() {
+ return type;
+ }
+
+ /**
+ * Returns {@link ReferenceMapping mapping} to {@link MiriamType} that should
+ * be used for gpml resource type.
+ *
+ * @param gpmlString
+ * {@link #gpmlString}
+ * @return {@link ReferenceMapping mapping} to {@link MiriamType} that should
+ * be used for gpml resource type
+ */
+ public static ReferenceMapping getMappingByGpmlString(String gpmlString) {
+ for (ReferenceMapping mm : values()) {
+ if (mm.getGpmlString() != null && mm.getGpmlString().equals(gpmlString)) {
+ return mm;
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Returns {@link ReferenceMapping mapping} that should be used for
+ * {@link #gpmlString gpml string} representing type of annotation.
+ *
+ * @param dataType
+ * {@link #type}
+ *
+ * @return {@link ReferenceMapping mapping} that should be used for
+ * {@link #gpmlString gpml string} representing type of annotation
+ */
+ public static ReferenceMapping getMappingByMiriamType(MiriamType dataType) {
+ for (ReferenceMapping mm : values()) {
+ if (mm.getType().equals(dataType)) {
+ return mm;
+ }
+ }
+ return null;
+ }
+
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Shape.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Shape.java
index 5d426df051..db68dc2c69 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Shape.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Shape.java
@@ -1,224 +1,224 @@
-package lcsb.mapviewer.wikipathway.model;
-
-/**
- * Class used to store data from Shape from .gpml.
- *
- * @author Jan Badura
- *
- */
-public class Shape extends GraphicalPathwayElement {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Shape of the node. ???
- */
- private String shape;
-
- /**
- * ???
- */
- private String textLabel;
-
- /**
- * Where this node belongs to.
- */
- private String groupRef;
-
- /**
- * Is shape a compartment.
- */
- private Boolean compartment;
-
- /**
- * Thickness of the line used for drawing shape.
- */
- private Double lineThickness;
-
- /**
- * Align of the description.
- */
- private String vAlign;
-
- /**
- * Rotation of the element.
- */
- private Double rotation;
-
- /**
- * Sometimes {@link Shape labels} are connected to reactions.
- */
- private boolean treatAsNode = false;
-
- /**
- * Default constructor.
- *
- * @param graphId
- * {@link PathwayElement#graphId}
- */
- public Shape(String graphId) {
- super(graphId);
- setRectangle(null);
- setShape(null);
- setTextLabel(null);
- setGroupRef(null);
- setCompartment(false);
- }
-
- /**
- * Empty constructor that should be used only by serialization tools and
- * subclasses.
- */
- protected Shape() {
- }
-
- @Override
- public String getName() {
- return shape + ":" + textLabel;
- }
-
- /**
- * @return the shape
- * @see #shape
- */
- public String getShape() {
- return shape;
- }
-
- /**
- * @param shape
- * the shape to set
- * @see #shape
- */
- public void setShape(String shape) {
- this.shape = shape;
- }
-
- /**
- * @return the textLabel
- * @see #textLabel
- */
- public String getTextLabel() {
- return textLabel;
- }
-
- /**
- * @param textLabel
- * the textLabel to set
- * @see #textLabel
- */
- public void setTextLabel(String textLabel) {
- this.textLabel = textLabel;
- }
-
- /**
- * @param groupRef
- * the groupRef to set
- * @see #groupRef
- */
- public void setGroupRef(String groupRef) {
- this.groupRef = groupRef;
- }
-
- /**
- * @return the compartment
- * @see #compartment
- */
- public Boolean isCompartment() {
- return compartment;
- }
-
- /**
- * @param compartment
- * the compartment to set
- * @see #compartment
- */
- public void setCompartment(Boolean compartment) {
- this.compartment = compartment;
- }
-
- @Override
- public String getWarningPrefix() {
- return "[" + getShape() + " " + getGraphId() + "]\t";
- }
-
- /**
- * @return the groupRef
- * @see #groupRef
- */
- public String getGroupRef() {
- return groupRef;
- }
-
- /**
- * @return the vAlign
- * @see #vAlign
- */
- public String getvAlign() {
- return vAlign;
- }
-
- /**
- * @param vAlign
- * the vAlign to set
- * @see #vAlign
- */
- public void setvAlign(String vAlign) {
- this.vAlign = vAlign;
- }
-
- /**
- * @return the rotation
- * @see #rotation
- */
- public Double getRotation() {
- return rotation;
- }
-
- /**
- * @param rotation
- * the rotation to set
- * @see #rotation
- */
- public void setRotation(Double rotation) {
- this.rotation = rotation;
- }
-
- /**
- * @return the lineThickness
- * @see #lineThickness
- */
- public Double getLineThickness() {
- return lineThickness;
- }
-
- /**
- * @param lineThickness
- * the lineThickness to set
- * @see #lineThickness
- */
- public void setLineThickness(Double lineThickness) {
- this.lineThickness = lineThickness;
- }
-
- /**
- * @return the treatAsNode
- * @see #treatAsNode
- */
- public boolean isTreatAsNode() {
- return treatAsNode;
- }
-
- /**
- * @param treatAsNode
- * the treatAsNode to set
- * @see #treatAsNode
- */
- public void setTreatAsNode(boolean treatAsNode) {
- this.treatAsNode = treatAsNode;
- }
-
-}
+package lcsb.mapviewer.wikipathway.model;
+
+/**
+ * Class used to store data from Shape from .gpml.
+ *
+ * @author Jan Badura
+ *
+ */
+public class Shape extends GraphicalPathwayElement {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Shape of the node. ???
+ */
+ private String shape;
+
+ /**
+ * ???
+ */
+ private String textLabel;
+
+ /**
+ * Where this node belongs to.
+ */
+ private String groupRef;
+
+ /**
+ * Is shape a compartment.
+ */
+ private Boolean compartment;
+
+ /**
+ * Thickness of the line used for drawing shape.
+ */
+ private Double lineThickness;
+
+ /**
+ * Align of the description.
+ */
+ private String vAlign;
+
+ /**
+ * Rotation of the element.
+ */
+ private Double rotation;
+
+ /**
+ * Sometimes {@link Shape labels} are connected to reactions.
+ */
+ private boolean treatAsNode = false;
+
+ /**
+ * Default constructor.
+ *
+ * @param graphId
+ * {@link PathwayElement#graphId}
+ */
+ public Shape(String graphId) {
+ super(graphId);
+ setRectangle(null);
+ setShape(null);
+ setTextLabel(null);
+ setGroupRef(null);
+ setCompartment(false);
+ }
+
+ /**
+ * Empty constructor that should be used only by serialization tools and
+ * subclasses.
+ */
+ protected Shape() {
+ }
+
+ @Override
+ public String getName() {
+ return shape + ":" + textLabel;
+ }
+
+ /**
+ * @return the shape
+ * @see #shape
+ */
+ public String getShape() {
+ return shape;
+ }
+
+ /**
+ * @param shape
+ * the shape to set
+ * @see #shape
+ */
+ public void setShape(String shape) {
+ this.shape = shape;
+ }
+
+ /**
+ * @return the textLabel
+ * @see #textLabel
+ */
+ public String getTextLabel() {
+ return textLabel;
+ }
+
+ /**
+ * @param textLabel
+ * the textLabel to set
+ * @see #textLabel
+ */
+ public void setTextLabel(String textLabel) {
+ this.textLabel = textLabel;
+ }
+
+ /**
+ * @param groupRef
+ * the groupRef to set
+ * @see #groupRef
+ */
+ public void setGroupRef(String groupRef) {
+ this.groupRef = groupRef;
+ }
+
+ /**
+ * @return the compartment
+ * @see #compartment
+ */
+ public Boolean isCompartment() {
+ return compartment;
+ }
+
+ /**
+ * @param compartment
+ * the compartment to set
+ * @see #compartment
+ */
+ public void setCompartment(Boolean compartment) {
+ this.compartment = compartment;
+ }
+
+ @Override
+ public String getWarningPrefix() {
+ return "[" + getShape() + " " + getGraphId() + "]\t";
+ }
+
+ /**
+ * @return the groupRef
+ * @see #groupRef
+ */
+ public String getGroupRef() {
+ return groupRef;
+ }
+
+ /**
+ * @return the vAlign
+ * @see #vAlign
+ */
+ public String getvAlign() {
+ return vAlign;
+ }
+
+ /**
+ * @param vAlign
+ * the vAlign to set
+ * @see #vAlign
+ */
+ public void setvAlign(String vAlign) {
+ this.vAlign = vAlign;
+ }
+
+ /**
+ * @return the rotation
+ * @see #rotation
+ */
+ public Double getRotation() {
+ return rotation;
+ }
+
+ /**
+ * @param rotation
+ * the rotation to set
+ * @see #rotation
+ */
+ public void setRotation(Double rotation) {
+ this.rotation = rotation;
+ }
+
+ /**
+ * @return the lineThickness
+ * @see #lineThickness
+ */
+ public Double getLineThickness() {
+ return lineThickness;
+ }
+
+ /**
+ * @param lineThickness
+ * the lineThickness to set
+ * @see #lineThickness
+ */
+ public void setLineThickness(Double lineThickness) {
+ this.lineThickness = lineThickness;
+ }
+
+ /**
+ * @return the treatAsNode
+ * @see #treatAsNode
+ */
+ public boolean isTreatAsNode() {
+ return treatAsNode;
+ }
+
+ /**
+ * @param treatAsNode
+ * the treatAsNode to set
+ * @see #treatAsNode
+ */
+ public void setTreatAsNode(boolean treatAsNode) {
+ this.treatAsNode = treatAsNode;
+ }
+
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/State.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/State.java
index 244f58f44b..7447a82d5f 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/State.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/State.java
@@ -1,259 +1,259 @@
-package lcsb.mapviewer.wikipathway.model;
-
-import java.awt.geom.Rectangle2D;
-import java.util.ArrayList;
-import java.util.List;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.field.ModificationState;
-
-/**
- * Class used to store data about {@link DataNode} state from .gpml.
- *
- * @author Piotr Gawron
- *
- */
-public class State extends GraphicalPathwayElement {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Shape of the element.
- */
- private String shape;
-
- /**
- * References for given edge.
- */
- private List<MiriamData> references = new ArrayList<>();
-
- /**
- * Object where this state is placed.
- */
- private String graphRef;
-
- /**
- * State correspondig to {@link Protein#structuralState protein structural state}.
- */
- private String structuralState;
-
- /**
- * Type of the modification.
- */
- private ModificationState type;
-
- /**
- * X position on {@link #graphRef} element.
- */
- private Double relX;
-
- /**
- * Y position on {@link #graphRef} element.
- */
- private Double relY;
-
- /**
- * Width of the element.
- */
- private Double width;
-
- /**
- * Heightof the element.
- */
- private Double height;
-
- /**
- * Default constructor.
- *
- * @param graphId
- * {@link PathwayElement#graphId}
- */
- public State(String graphId) {
- super(graphId);
- }
-
- /**
- * Empty constructor that should be used only by serialization tools and
- * subclasses.
- */
- protected State() {
- }
-
- @Override
- String getName() {
- throw new NotImplementedException();
- }
-
- @Override
- public Rectangle2D getRectangle() {
- throw new NotImplementedException();
- }
-
- /**
- * @return the shape
- * @see #shape
- */
- public String getShape() {
- return shape;
- }
-
- /**
- * @param shape
- * the shape to set
- * @see #shape
- */
- public void setShape(String shape) {
- this.shape = shape;
- }
-
- /**
- * @return the relX
- * @see #relX
- */
- public Double getRelX() {
- return relX;
- }
-
- /**
- * @param relX
- * the relX to set
- * @see #relX
- */
- public void setRelX(Double relX) {
- this.relX = relX;
- }
-
- /**
- * @return the relY
- * @see #relY
- */
- public Double getRelY() {
- return relY;
- }
-
- /**
- * @param relY
- * the relY to set
- * @see #relY
- */
- public void setRelY(Double relY) {
- this.relY = relY;
- }
-
- /**
- * @return the width
- * @see #width
- */
- public Double getWidth() {
- return width;
- }
-
- /**
- * @param width
- * the width to set
- * @see #width
- */
- public void setWidth(Double width) {
- this.width = width;
- }
-
- /**
- * @return the height
- * @see #height
- */
- public Double getHeight() {
- return height;
- }
-
- /**
- * @param height
- * the height to set
- * @see #height
- */
- public void setHeight(Double height) {
- this.height = height;
- }
-
- /**
- * @return the graphRef
- * @see #graphRef
- */
- public String getGraphRef() {
- return graphRef;
- }
-
- /**
- * @param graphRef
- * the graphRef to set
- * @see #graphRef
- */
- public void setGraphRef(String graphRef) {
- this.graphRef = graphRef;
- }
-
- /**
- * @return the references
- * @see #references
- */
- public List<MiriamData> getReferences() {
- return references;
- }
-
- /**
- * @param references
- * the references to set
- * @see #references
- */
- public void setReferences(List<MiriamData> references) {
- this.references = references;
- }
-
- /**
- * Adds reference to object.
- *
- * @param reference
- * reference to add
- */
- public void addReference(MiriamData reference) {
- this.references.add(reference);
- }
-
- /**
- * @return the type
- * @see #type
- */
- public ModificationState getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(ModificationState type) {
- this.type = type;
- }
-
- /**
- * @return the structuralState
- * @see #structuralState
- */
- public String getStructuralState() {
- return structuralState;
- }
-
- /**
- * @param structuralState the structuralState to set
- * @see #structuralState
- */
- public void setStructuralState(String structuralState) {
- this.structuralState = structuralState;
- }
-
-}
+package lcsb.mapviewer.wikipathway.model;
+
+import java.awt.geom.Rectangle2D;
+import java.util.ArrayList;
+import java.util.List;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+
+/**
+ * Class used to store data about {@link DataNode} state from .gpml.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class State extends GraphicalPathwayElement {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Shape of the element.
+ */
+ private String shape;
+
+ /**
+ * References for given edge.
+ */
+ private List<MiriamData> references = new ArrayList<>();
+
+ /**
+ * Object where this state is placed.
+ */
+ private String graphRef;
+
+ /**
+ * State correspondig to {@link Protein#structuralState protein structural state}.
+ */
+ private String structuralState;
+
+ /**
+ * Type of the modification.
+ */
+ private ModificationState type;
+
+ /**
+ * X position on {@link #graphRef} element.
+ */
+ private Double relX;
+
+ /**
+ * Y position on {@link #graphRef} element.
+ */
+ private Double relY;
+
+ /**
+ * Width of the element.
+ */
+ private Double width;
+
+ /**
+ * Heightof the element.
+ */
+ private Double height;
+
+ /**
+ * Default constructor.
+ *
+ * @param graphId
+ * {@link PathwayElement#graphId}
+ */
+ public State(String graphId) {
+ super(graphId);
+ }
+
+ /**
+ * Empty constructor that should be used only by serialization tools and
+ * subclasses.
+ */
+ protected State() {
+ }
+
+ @Override
+ String getName() {
+ throw new NotImplementedException();
+ }
+
+ @Override
+ public Rectangle2D getRectangle() {
+ throw new NotImplementedException();
+ }
+
+ /**
+ * @return the shape
+ * @see #shape
+ */
+ public String getShape() {
+ return shape;
+ }
+
+ /**
+ * @param shape
+ * the shape to set
+ * @see #shape
+ */
+ public void setShape(String shape) {
+ this.shape = shape;
+ }
+
+ /**
+ * @return the relX
+ * @see #relX
+ */
+ public Double getRelX() {
+ return relX;
+ }
+
+ /**
+ * @param relX
+ * the relX to set
+ * @see #relX
+ */
+ public void setRelX(Double relX) {
+ this.relX = relX;
+ }
+
+ /**
+ * @return the relY
+ * @see #relY
+ */
+ public Double getRelY() {
+ return relY;
+ }
+
+ /**
+ * @param relY
+ * the relY to set
+ * @see #relY
+ */
+ public void setRelY(Double relY) {
+ this.relY = relY;
+ }
+
+ /**
+ * @return the width
+ * @see #width
+ */
+ public Double getWidth() {
+ return width;
+ }
+
+ /**
+ * @param width
+ * the width to set
+ * @see #width
+ */
+ public void setWidth(Double width) {
+ this.width = width;
+ }
+
+ /**
+ * @return the height
+ * @see #height
+ */
+ public Double getHeight() {
+ return height;
+ }
+
+ /**
+ * @param height
+ * the height to set
+ * @see #height
+ */
+ public void setHeight(Double height) {
+ this.height = height;
+ }
+
+ /**
+ * @return the graphRef
+ * @see #graphRef
+ */
+ public String getGraphRef() {
+ return graphRef;
+ }
+
+ /**
+ * @param graphRef
+ * the graphRef to set
+ * @see #graphRef
+ */
+ public void setGraphRef(String graphRef) {
+ this.graphRef = graphRef;
+ }
+
+ /**
+ * @return the references
+ * @see #references
+ */
+ public List<MiriamData> getReferences() {
+ return references;
+ }
+
+ /**
+ * @param references
+ * the references to set
+ * @see #references
+ */
+ public void setReferences(List<MiriamData> references) {
+ this.references = references;
+ }
+
+ /**
+ * Adds reference to object.
+ *
+ * @param reference
+ * reference to add
+ */
+ public void addReference(MiriamData reference) {
+ this.references.add(reference);
+ }
+
+ /**
+ * @return the type
+ * @see #type
+ */
+ public ModificationState getType() {
+ return type;
+ }
+
+ /**
+ * @param type
+ * the type to set
+ * @see #type
+ */
+ public void setType(ModificationState type) {
+ this.type = type;
+ }
+
+ /**
+ * @return the structuralState
+ * @see #structuralState
+ */
+ public String getStructuralState() {
+ return structuralState;
+ }
+
+ /**
+ * @param structuralState the structuralState to set
+ * @see #structuralState
+ */
+ public void setStructuralState(String structuralState) {
+ this.structuralState = structuralState;
+ }
+
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/UnknownTypeException.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/UnknownTypeException.java
index 3855d4e38a..f648725fbb 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/UnknownTypeException.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/UnknownTypeException.java
@@ -1,28 +1,28 @@
-package lcsb.mapviewer.wikipathway.model;
-
-import lcsb.mapviewer.converter.ConverterException;
-
-/**
- * Exception that shold be thrown when unknown type was encountered.
- *
- * @author Piotr Gawron
- *
- */
-public class UnknownTypeException extends ConverterException {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor with message passed in the argument.
- *
- * @param string
- * message of this exception
- */
- public UnknownTypeException(String string) {
- super(string);
- }
-
-}
+package lcsb.mapviewer.wikipathway.model;
+
+import lcsb.mapviewer.converter.ConverterException;
+
+/**
+ * Exception that shold be thrown when unknown type was encountered.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class UnknownTypeException extends ConverterException {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor with message passed in the argument.
+ *
+ * @param string
+ * message of this exception
+ */
+ public UnknownTypeException(String string) {
+ super(string);
+ }
+
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxData.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxData.java
index b6462971e0..64bec374b2 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxData.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxData.java
@@ -1,92 +1,92 @@
-package lcsb.mapviewer.wikipathway.model.biopax;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-
-import org.apache.log4j.Logger;
-
-/**
- * Element containg all biopax information parsed from gpml file.
- *
- * @author Piotr Gawron
- *
- */
-public class BiopaxData implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final transient Logger logger = Logger.getLogger(BiopaxData.class);
-
- /**
- * List of {@link BiopaxPublication publications}.
- */
- private Map<String, BiopaxPublication> publications = new HashMap<String, BiopaxPublication>();
-
- /**
- * List of {@link BiopaxOpenControlledVocabulary biopax vocabulary}.
- */
- private List<BiopaxOpenControlledVocabulary> openControlledVocabularies = new ArrayList<BiopaxOpenControlledVocabulary>();
-
- /**
- * @return the publications
- * @see #publications
- */
- public Collection<BiopaxPublication> getPublications() {
- return publications.values();
- }
-
- /**
- * @param publication
- * the publication to add
- * @see #publications
- */
- public void addPublication(BiopaxPublication publication) {
- String id = publication.getReferenceId();
- if (this.publications.get(publication.getReferenceId()) != null) {
- throw new InvalidArgumentException("Biopax publication with " + id + " already exists.");
- }
- this.publications.put(id, publication);
- }
-
- /**
- * Returns publication identified by reference id.
- *
- * @param ref
- * reference identifier
- * @return {@link BiopaxPublication} corresponding to the ref
- */
- public BiopaxPublication getPublicationByReference(String ref) {
- return publications.get(ref);
- }
-
- /**
- * @return the openControlledVocabularies
- * @see #openControlledVocabularies
- */
- public List<BiopaxOpenControlledVocabulary> getOpenControlledVocabularies() {
- return openControlledVocabularies;
- }
-
- /**
- * @param openControlledVocabulary
- * the openControlledVocabulary to add
- * @see #openControlledVocabularies
- */
- public void addOpenControlledVocabulary(BiopaxOpenControlledVocabulary openControlledVocabulary) {
- this.openControlledVocabularies.add(openControlledVocabulary);
- }
-
-}
+package lcsb.mapviewer.wikipathway.model.biopax;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Element containg all biopax information parsed from gpml file.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class BiopaxData implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final transient Logger logger = Logger.getLogger(BiopaxData.class);
+
+ /**
+ * List of {@link BiopaxPublication publications}.
+ */
+ private Map<String, BiopaxPublication> publications = new HashMap<String, BiopaxPublication>();
+
+ /**
+ * List of {@link BiopaxOpenControlledVocabulary biopax vocabulary}.
+ */
+ private List<BiopaxOpenControlledVocabulary> openControlledVocabularies = new ArrayList<BiopaxOpenControlledVocabulary>();
+
+ /**
+ * @return the publications
+ * @see #publications
+ */
+ public Collection<BiopaxPublication> getPublications() {
+ return publications.values();
+ }
+
+ /**
+ * @param publication
+ * the publication to add
+ * @see #publications
+ */
+ public void addPublication(BiopaxPublication publication) {
+ String id = publication.getReferenceId();
+ if (this.publications.get(publication.getReferenceId()) != null) {
+ throw new InvalidArgumentException("Biopax publication with " + id + " already exists.");
+ }
+ this.publications.put(id, publication);
+ }
+
+ /**
+ * Returns publication identified by reference id.
+ *
+ * @param ref
+ * reference identifier
+ * @return {@link BiopaxPublication} corresponding to the ref
+ */
+ public BiopaxPublication getPublicationByReference(String ref) {
+ return publications.get(ref);
+ }
+
+ /**
+ * @return the openControlledVocabularies
+ * @see #openControlledVocabularies
+ */
+ public List<BiopaxOpenControlledVocabulary> getOpenControlledVocabularies() {
+ return openControlledVocabularies;
+ }
+
+ /**
+ * @param openControlledVocabulary
+ * the openControlledVocabulary to add
+ * @see #openControlledVocabularies
+ */
+ public void addOpenControlledVocabulary(BiopaxOpenControlledVocabulary openControlledVocabulary) {
+ this.openControlledVocabularies.add(openControlledVocabulary);
+ }
+
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxOpenControlledVocabulary.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxOpenControlledVocabulary.java
index 18de470b0b..53804781d7 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxOpenControlledVocabulary.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxOpenControlledVocabulary.java
@@ -1,85 +1,85 @@
-package lcsb.mapviewer.wikipathway.model.biopax;
-
-import java.io.Serializable;
-
-/**
- * Describes biopax node with open controlled vocabulary (no idea of the
- * purpose).
- *
- * @author Piotr Gawron
- *
- */
-public class BiopaxOpenControlledVocabulary implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
-
- /**
- * ???
- */
- private String id;
-
- /**
- * ???
- */
- private String term;
-
- /**
- * ???
- */
- private String ontology;
-
- /**
- * @return the id
- * @see #id
- */
- public String getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(String id) {
- this.id = id;
- }
-
- /**
- * @return the term
- * @see #term
- */
- public String getTerm() {
- return term;
- }
-
- /**
- * @param term
- * the term to set
- * @see #term
- */
- public void setTerm(String term) {
- this.term = term;
- }
-
- /**
- * @return the ontology
- * @see #ontology
- */
- public String getOntology() {
- return ontology;
- }
-
- /**
- * @param ontology
- * the ontology to set
- * @see #ontology
- */
- public void setOntology(String ontology) {
- this.ontology = ontology;
- }
-}
+package lcsb.mapviewer.wikipathway.model.biopax;
+
+import java.io.Serializable;
+
+/**
+ * Describes biopax node with open controlled vocabulary (no idea of the
+ * purpose).
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class BiopaxOpenControlledVocabulary implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+
+ /**
+ * ???
+ */
+ private String id;
+
+ /**
+ * ???
+ */
+ private String term;
+
+ /**
+ * ???
+ */
+ private String ontology;
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(String id) {
+ this.id = id;
+ }
+
+ /**
+ * @return the term
+ * @see #term
+ */
+ public String getTerm() {
+ return term;
+ }
+
+ /**
+ * @param term
+ * the term to set
+ * @see #term
+ */
+ public void setTerm(String term) {
+ this.term = term;
+ }
+
+ /**
+ * @return the ontology
+ * @see #ontology
+ */
+ public String getOntology() {
+ return ontology;
+ }
+
+ /**
+ * @param ontology
+ * the ontology to set
+ * @see #ontology
+ */
+ public void setOntology(String ontology) {
+ this.ontology = ontology;
+ }
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxPublication.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxPublication.java
index 5af30a7497..cb561ad58e 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxPublication.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxPublication.java
@@ -1,172 +1,172 @@
-package lcsb.mapviewer.wikipathway.model.biopax;
-
-import java.io.Serializable;
-
-/**
- * Describes biopax node with publication.
- *
- * @author Piotr Gawron
- *
- */
-public class BiopaxPublication implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
-
- /**
- * Identifier of a publication in db.
- */
- private String id;
-
- /**
- * Database where publication is located.
- */
- private String db;
-
- /**
- * Title of publication.
- */
- private String title;
-
- /**
- * Source of the publication.
- */
- private String source;
-
- /**
- * Year when publication was issued.
- */
- private String year;
-
- /**
- * Authors of the publication.
- */
- private String authors;
-
- /**
- * Identifier of the object which this publication annotate.
- */
- private String referenceId;
-
- /**
- * @return the id
- * @see #id
- */
- public String getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(String id) {
- this.id = id;
- }
-
- /**
- * @return the db
- * @see #db
- */
- public String getDb() {
- return db;
- }
-
- /**
- * @param db
- * the db to set
- * @see #db
- */
- public void setDb(String db) {
- this.db = db;
- }
-
- /**
- * @return the title
- * @see #title
- */
- public String getTitle() {
- return title;
- }
-
- /**
- * @param title
- * the title to set
- * @see #title
- */
- public void setTitle(String title) {
- this.title = title;
- }
-
- /**
- * @return the source
- * @see #source
- */
- public String getSource() {
- return source;
- }
-
- /**
- * @param source
- * the source to set
- * @see #source
- */
- public void setSource(String source) {
- this.source = source;
- }
-
- /**
- * @return the year
- * @see #year
- */
- public String getYear() {
- return year;
- }
-
- /**
- * @param year
- * the year to set
- * @see #year
- */
- public void setYear(String year) {
- this.year = year;
- }
-
- /**
- * @return the authors
- * @see #authors
- */
- public String getAuthors() {
- return authors;
- }
-
- /**
- * @param authors
- * the authors to set
- * @see #authors
- */
- public void setAuthors(String authors) {
- this.authors = authors;
- }
-
- /**
- * @return the referenceId
- * @see #referenceId
- */
- public String getReferenceId() {
- return referenceId;
- }
-
- /**
- * @param referenceId
- * the referenceId to set
- * @see #referenceId
- */
- public void setReferenceId(String referenceId) {
- this.referenceId = referenceId;
- }
-}
+package lcsb.mapviewer.wikipathway.model.biopax;
+
+import java.io.Serializable;
+
+/**
+ * Describes biopax node with publication.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class BiopaxPublication implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+
+ /**
+ * Identifier of a publication in db.
+ */
+ private String id;
+
+ /**
+ * Database where publication is located.
+ */
+ private String db;
+
+ /**
+ * Title of publication.
+ */
+ private String title;
+
+ /**
+ * Source of the publication.
+ */
+ private String source;
+
+ /**
+ * Year when publication was issued.
+ */
+ private String year;
+
+ /**
+ * Authors of the publication.
+ */
+ private String authors;
+
+ /**
+ * Identifier of the object which this publication annotate.
+ */
+ private String referenceId;
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(String id) {
+ this.id = id;
+ }
+
+ /**
+ * @return the db
+ * @see #db
+ */
+ public String getDb() {
+ return db;
+ }
+
+ /**
+ * @param db
+ * the db to set
+ * @see #db
+ */
+ public void setDb(String db) {
+ this.db = db;
+ }
+
+ /**
+ * @return the title
+ * @see #title
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * @param title
+ * the title to set
+ * @see #title
+ */
+ public void setTitle(String title) {
+ this.title = title;
+ }
+
+ /**
+ * @return the source
+ * @see #source
+ */
+ public String getSource() {
+ return source;
+ }
+
+ /**
+ * @param source
+ * the source to set
+ * @see #source
+ */
+ public void setSource(String source) {
+ this.source = source;
+ }
+
+ /**
+ * @return the year
+ * @see #year
+ */
+ public String getYear() {
+ return year;
+ }
+
+ /**
+ * @param year
+ * the year to set
+ * @see #year
+ */
+ public void setYear(String year) {
+ this.year = year;
+ }
+
+ /**
+ * @return the authors
+ * @see #authors
+ */
+ public String getAuthors() {
+ return authors;
+ }
+
+ /**
+ * @param authors
+ * the authors to set
+ * @see #authors
+ */
+ public void setAuthors(String authors) {
+ this.authors = authors;
+ }
+
+ /**
+ * @return the referenceId
+ * @see #referenceId
+ */
+ public String getReferenceId() {
+ return referenceId;
+ }
+
+ /**
+ * @param referenceId
+ * the referenceId to set
+ * @see #referenceId
+ */
+ public void setReferenceId(String referenceId) {
+ this.referenceId = referenceId;
+ }
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/package-info.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/package-info.java
index dc49b1f651..fd3c232c66 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/package-info.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/package-info.java
@@ -1,7 +1,7 @@
-/**
- * This package contains elements parsed from biopax format. Main element is
- * {@link lcsb.mapviewer.wikipathway.model.biopax.BiopaxData BiopaxData}.
- *
- */
-package lcsb.mapviewer.wikipathway.model.biopax;
-
+/**
+ * This package contains elements parsed from biopax format. Main element is
+ * {@link lcsb.mapviewer.wikipathway.model.biopax.BiopaxData BiopaxData}.
+ *
+ */
+package lcsb.mapviewer.wikipathway.model.biopax;
+
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/package-info.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/package-info.java
index b4e70f81ac..bd59db6b13 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/package-info.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/package-info.java
@@ -1,15 +1,15 @@
-/**
- * Model elements obtained from gpml file. There are few basic classes in this
- * package:
- * <ul>
- * <li> {@link lcsb.mapviewer.wikipathway.model.Graph Graph} - description of the
- * whole model imported from gpml file,</li>
- * <li> {@link lcsb.mapviewer.wikipathway.model.Interaction Interaction} -
- * description of single interaction in the model,</li>
- * <li> {@link lcsb.mapviewer.wikipathway.model.PathwayElement PathwayElement} -
- * single element in the model.</li>
- * </ul>
- *
- */
-package lcsb.mapviewer.wikipathway.model;
-
+/**
+ * Model elements obtained from gpml file. There are few basic classes in this
+ * package:
+ * <ul>
+ * <li> {@link lcsb.mapviewer.wikipathway.model.Graph Graph} - description of the
+ * whole model imported from gpml file,</li>
+ * <li> {@link lcsb.mapviewer.wikipathway.model.Interaction Interaction} -
+ * description of single interaction in the model,</li>
+ * <li> {@link lcsb.mapviewer.wikipathway.model.PathwayElement PathwayElement} -
+ * single element in the model.</li>
+ * </ul>
+ *
+ */
+package lcsb.mapviewer.wikipathway.model;
+
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/package-info.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/package-info.java
index 9b38aa9ec6..24f302e3bc 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/package-info.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/package-info.java
@@ -1,10 +1,10 @@
-/**
- * Contains plugin for pathvisio that supports import and export to CellDEsigner
- * file. Main plugin class is located in
- * {@link lcsb.mapviewer.wikipathway.ImportExport ImportExport} class. According
- * to <a href="http://developers.pathvisio.org/wiki/PluginDevelopment
- * ">pathvisio guidlines</a>, plugin is implemented as an <a
- * href="http://en.wikipedia.org/wiki/OSGi#Bundles">OSGI Bundle</a>.
- */
-package lcsb.mapviewer.wikipathway;
-
+/**
+ * Contains plugin for pathvisio that supports import and export to CellDEsigner
+ * file. Main plugin class is located in
+ * {@link lcsb.mapviewer.wikipathway.ImportExport ImportExport} class. According
+ * to <a href="http://developers.pathvisio.org/wiki/PluginDevelopment
+ * ">pathvisio guidlines</a>, plugin is implemented as an <a
+ * href="http://en.wikipedia.org/wiki/OSGi#Bundles">OSGI Bundle</a>.
+ */
+package lcsb.mapviewer.wikipathway;
+
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/utils/Geo.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/utils/Geo.java
index 05dffe3fbe..3101d56c6f 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/utils/Geo.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/utils/Geo.java
@@ -1,326 +1,326 @@
-package lcsb.mapviewer.wikipathway.utils;
-
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.model.graphics.PolylineData;
-
-/**
- * This class has some geometric utils.
- *
- * @author Jan Badura
- *
- */
-public final class Geo {
-
- /**
- * Max distance betwen point and line that still allows to match intersection.
- */
- private static final int DISTANCE_PROXIMITY = 10;
-
- /**
- * Default class constructor. Prevents instatiation.
- */
- private Geo() {
-
- }
-
- /**
- * This function calculates point on line that is closest to given point.
- *
- * @param line
- * - line has to be parallel to oX or oY
- * @param point
- * point
- * @return point on line that is closest to given point
- */
- private static Point2D closestPointOnLine(Line2D line, Point2D point) {
- Point2D s = line.getP1();
- Point2D e = line.getP2();
- if (s.equals(e)) {
- return (Point2D) s.clone();
- }
-
- if (s.getX() == e.getX()) {
- if (point.getY() > Math.min(s.getY(), e.getY()) && point.getY() < Math.max(s.getY(), e.getY())) {
- return new Point2D.Double(s.getX(), point.getY());
- } else {
- if (point.distance(s) < point.distance(e)) {
- return (Point2D) s.clone();
- } else {
- return (Point2D) e.clone();
- }
- }
- } else if (s.getY() == e.getY()) {
- if (point.getX() > Math.min(s.getX(), e.getX()) && point.getX() < Math.max(s.getX(), e.getX())) {
- return new Point2D.Double(point.getX(), s.getY());
- } else {
- if (point.distance(s) < point.distance(e)) {
- return (Point2D) s.clone();
- } else {
- return (Point2D) e.clone();
- }
- }
- } else {
- throw new InvalidArgumentException("Line is invalid");
- }
- }
-
- /**
- * This function return value from <0,1>, that is the position of given point
- * on given Polyline.
- *
- * @param mainLine
- * line on which we are looking for a point
- * @param point
- * point
- * @return double position, 0 <= position <= 1
- */
- public static double distanceOnPolyline(PolylineData mainLine, Point2D point) {
- double length = 0;
- double tmp = 0;
- for (Line2D line : mainLine.getLines()) {
- length += lineLen(line);
- }
-
- for (Line2D line : mainLine.getLines()) {
- if (line.ptSegDist(point) < DISTANCE_PROXIMITY) {
- tmp += line.getP1().distance(point);
- break;
- } else {
- tmp += lineLen(line);
- }
- }
- double position = tmp / length;
- if (position < 0 || position > 1) {
- throw new InvalidStateException();
- }
- return position;
- }
-
- /**
- * Returns length of the line.
- *
- * @param line
- * line
- * @return length of the line
- */
- public static double lineLen(Line2D line) {
- return line.getP1().distance(line.getP2());
- }
-
- /**
- * Returns distance between point and rectangle border.
- *
- * @param point
- * point
- * @param rect
- * rectangle border
- * @return distance between point and rectangle border
- */
- public static double distance(Point2D point, Rectangle2D rect) {
- double res = Double.MAX_VALUE;
-
- Point2D p1 = new Point2D.Double(rect.getX(), rect.getY());
- Point2D p2 = new Point2D.Double(rect.getX(), rect.getY() + rect.getHeight());
- Point2D p3 = new Point2D.Double(rect.getX() + rect.getWidth(), rect.getY() + rect.getHeight());
- Point2D p4 = new Point2D.Double(rect.getX() + rect.getWidth(), rect.getY());
- res = Math.min(res, new Line2D.Double(p1, p2).ptSegDist(point));
- res = Math.min(res, new Line2D.Double(p2, p3).ptSegDist(point));
- res = Math.min(res, new Line2D.Double(p3, p4).ptSegDist(point));
- res = Math.min(res, new Line2D.Double(p4, p1).ptSegDist(point));
-
- return res;
- }
-
- /**
- * This function returns point on the middle of rectangle side, that is
- * closest to the given point.
- *
- * @param rect
- * rectangle on which we look for a point
- * @param point
- * point to which result should be as close as possible
- * @return point on the middle of rectangle side that is as close as possible
- * to the input point
- */
- public static Point2D pointOnRectangle(Rectangle2D rect, Point2D point) {
-
- Point2D p1 = new Point2D.Double(rect.getX(), rect.getY());
- Point2D p2 = new Point2D.Double(rect.getX(), rect.getY() + rect.getHeight());
- Point2D p3 = new Point2D.Double(rect.getX() + rect.getWidth(), rect.getY() + rect.getHeight());
- Point2D p4 = new Point2D.Double(rect.getX() + rect.getWidth(), rect.getY());
-
- Point2D p12 = new Point2D.Double((p1.getX() + p2.getX()) / 2, (p1.getY() + p2.getY()) / 2);
- Point2D p23 = new Point2D.Double((p2.getX() + p3.getX()) / 2, (p2.getY() + p3.getY()) / 2);
- Point2D p34 = new Point2D.Double((p3.getX() + p4.getX()) / 2, (p3.getY() + p4.getY()) / 2);
- Point2D p41 = new Point2D.Double((p4.getX() + p1.getX()) / 2, (p4.getY() + p1.getY()) / 2);
-
- double dis1, dis2, dis3, dis4, min;
- dis1 = point.distance(p12);
- dis2 = point.distance(p23);
- dis3 = point.distance(p34);
- dis4 = point.distance(p41);
-
- min = Math.min(dis1, dis2);
- min = Math.min(min, dis3);
- min = Math.min(min, dis4);
-
- if (min == dis1) {
- return p12;
- } else if (min == dis2) {
- return p23;
- } else if (min == dis3) {
- return p34;
- } else {
- return p41;
- }
- }
-
- /**
- * This function returns point on rectangle that is closest to given point.
- *
- * @param rect
- * rectangle on which the result poiint will be placed
- * @param point
- * point for which we look the closest reference on rectangle
- * @return the closest possible point on rectangle
- */
- public static Point2D closestPointOnRectangle(Rectangle2D rect, Point2D point) {
- Point2D p1 = new Point2D.Double(rect.getX(), rect.getY());
- Point2D p2 = new Point2D.Double(rect.getX(), rect.getY() + rect.getHeight());
- Point2D p3 = new Point2D.Double(rect.getX() + rect.getWidth(), rect.getY() + rect.getHeight());
- Point2D p4 = new Point2D.Double(rect.getX() + rect.getWidth(), rect.getY());
-
- double dis1, dis2, dis3, dis4, min;
- dis1 = new Line2D.Double(p1, p2).ptSegDist(point);
- dis2 = new Line2D.Double(p2, p3).ptSegDist(point);
- dis3 = new Line2D.Double(p3, p4).ptSegDist(point);
- dis4 = new Line2D.Double(p4, p1).ptSegDist(point);
- min = Math.min(dis1, dis2);
- min = Math.min(min, dis3);
- min = Math.min(min, dis4);
-
- if (min == dis1) {
- return closestPointOnLine(new Line2D.Double(p1, p2), point);
- } else if (min == dis2) {
- return closestPointOnLine(new Line2D.Double(p2, p3), point);
- } else if (min == dis3) {
- return closestPointOnLine(new Line2D.Double(p3, p4), point);
- } else {
- return closestPointOnLine(new Line2D.Double(p4, p1), point);
- }
- }
-
- /**
- * Returns point that is outside given rectangle, but still close to the given
- * point. If the given point is inside rec then the given point is returned.
- *
- * @param rec
- * rectangle
- * @param point
- * point
- * @return point that is outside given rectangle, but still close to the given
- * point
- */
- public static Point2D pointRightOutsideRec(Rectangle2D rec, Point2D point) {
- if (!rec.contains(point)) {
- return (Point2D) point.clone();
- } else {
- double lx = rec.getX();
- double rx = lx + rec.getWidth();
- double uy = rec.getY();
- double dy = uy + rec.getHeight();
-
- double dis1 = Math.abs(point.getX() - lx);
- double dis2 = Math.abs(point.getX() - rx);
- double dis3 = Math.abs(point.getY() - uy);
- double dis4 = Math.abs(point.getY() - dy);
-
- double min = Math.min(dis1, dis2);
- min = Math.min(min, dis3);
- min = Math.min(min, dis4);
-
- if (min == dis1) {
- return new Point2D.Double(lx - 1.0, point.getY());
- } else if (min == dis2) {
- return new Point2D.Double(rx + 1.0, point.getY());
- } else if (min == dis3) {
- return new Point2D.Double(point.getX(), uy - 1.0);
- } else {
- return new Point2D.Double(point.getX(), uy + 1.0);
- }
- }
- }
-
- /**
- * Creates a {@link PolylineData} that is identical to parameter line, but
- * doesn't contain duplicate points.
- *
- * @param line
- * line that is transformed
- * @return input line without duplicate points
- */
- public static PolylineData removeRedundantPoints(PolylineData line) {
- PolylineData res = new PolylineData(line);
-
- for (int i = 2; i < res.getPoints().size(); i++) {
- if (new Line2D.Double(res.getPoints().get(i), res.getPoints().get(i - 2)).ptSegDist(res.getPoints().get(i - 1)) < DISTANCE_PROXIMITY) {
- res.getPoints().remove(i - 1);
- i--;
- }
- }
- return res;
- }
-
- /**
- * Returns distance between point and line.
- *
- * @param point
- * point
- * @param mainLine
- * line
- * @return distance between point and line
- */
- public static double distanceFromPolyline(Point2D point, PolylineData mainLine) {
- double min = Double.MAX_VALUE;
- for (Line2D line : mainLine.getLines()) {
- min = Math.min(min, line.ptSegDist(point));
- }
- return min;
- }
-
- /**
- * Returns point on line that is as closse as possible to point.
- *
- * @param point
- * point
- * @param mainLine
- * line
- * @return point on line that is as closse as possible to point
- */
- public static Point2D closestPointOnPolyline(PolylineData mainLine, Point2D point) {
- Point2D res = null;
- double distance = distanceOnPolyline(mainLine, point);
- double lenght = 0.0;
- for (Line2D line : mainLine.getLines()) {
- lenght += lineLen(line);
- }
- lenght *= distance;
- for (Line2D line : mainLine.getLines()) {
- if (lenght - lineLen(line) > 0) {
- lenght -= lineLen(line);
- } else {
- double tmp = lenght / lineLen(line);
- double x = line.getX1() + tmp * (line.getX2() - line.getX1());
- double y = line.getY1() + tmp * (line.getY2() - line.getY1());
- res = new Point2D.Double(x, y);
- }
- }
- return res;
- }
-
-}
+package lcsb.mapviewer.wikipathway.utils;
+
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.model.graphics.PolylineData;
+
+/**
+ * This class has some geometric utils.
+ *
+ * @author Jan Badura
+ *
+ */
+public final class Geo {
+
+ /**
+ * Max distance betwen point and line that still allows to match intersection.
+ */
+ private static final int DISTANCE_PROXIMITY = 10;
+
+ /**
+ * Default class constructor. Prevents instatiation.
+ */
+ private Geo() {
+
+ }
+
+ /**
+ * This function calculates point on line that is closest to given point.
+ *
+ * @param line
+ * - line has to be parallel to oX or oY
+ * @param point
+ * point
+ * @return point on line that is closest to given point
+ */
+ private static Point2D closestPointOnLine(Line2D line, Point2D point) {
+ Point2D s = line.getP1();
+ Point2D e = line.getP2();
+ if (s.equals(e)) {
+ return (Point2D) s.clone();
+ }
+
+ if (s.getX() == e.getX()) {
+ if (point.getY() > Math.min(s.getY(), e.getY()) && point.getY() < Math.max(s.getY(), e.getY())) {
+ return new Point2D.Double(s.getX(), point.getY());
+ } else {
+ if (point.distance(s) < point.distance(e)) {
+ return (Point2D) s.clone();
+ } else {
+ return (Point2D) e.clone();
+ }
+ }
+ } else if (s.getY() == e.getY()) {
+ if (point.getX() > Math.min(s.getX(), e.getX()) && point.getX() < Math.max(s.getX(), e.getX())) {
+ return new Point2D.Double(point.getX(), s.getY());
+ } else {
+ if (point.distance(s) < point.distance(e)) {
+ return (Point2D) s.clone();
+ } else {
+ return (Point2D) e.clone();
+ }
+ }
+ } else {
+ throw new InvalidArgumentException("Line is invalid");
+ }
+ }
+
+ /**
+ * This function return value from <0,1>, that is the position of given point
+ * on given Polyline.
+ *
+ * @param mainLine
+ * line on which we are looking for a point
+ * @param point
+ * point
+ * @return double position, 0 <= position <= 1
+ */
+ public static double distanceOnPolyline(PolylineData mainLine, Point2D point) {
+ double length = 0;
+ double tmp = 0;
+ for (Line2D line : mainLine.getLines()) {
+ length += lineLen(line);
+ }
+
+ for (Line2D line : mainLine.getLines()) {
+ if (line.ptSegDist(point) < DISTANCE_PROXIMITY) {
+ tmp += line.getP1().distance(point);
+ break;
+ } else {
+ tmp += lineLen(line);
+ }
+ }
+ double position = tmp / length;
+ if (position < 0 || position > 1) {
+ throw new InvalidStateException();
+ }
+ return position;
+ }
+
+ /**
+ * Returns length of the line.
+ *
+ * @param line
+ * line
+ * @return length of the line
+ */
+ public static double lineLen(Line2D line) {
+ return line.getP1().distance(line.getP2());
+ }
+
+ /**
+ * Returns distance between point and rectangle border.
+ *
+ * @param point
+ * point
+ * @param rect
+ * rectangle border
+ * @return distance between point and rectangle border
+ */
+ public static double distance(Point2D point, Rectangle2D rect) {
+ double res = Double.MAX_VALUE;
+
+ Point2D p1 = new Point2D.Double(rect.getX(), rect.getY());
+ Point2D p2 = new Point2D.Double(rect.getX(), rect.getY() + rect.getHeight());
+ Point2D p3 = new Point2D.Double(rect.getX() + rect.getWidth(), rect.getY() + rect.getHeight());
+ Point2D p4 = new Point2D.Double(rect.getX() + rect.getWidth(), rect.getY());
+ res = Math.min(res, new Line2D.Double(p1, p2).ptSegDist(point));
+ res = Math.min(res, new Line2D.Double(p2, p3).ptSegDist(point));
+ res = Math.min(res, new Line2D.Double(p3, p4).ptSegDist(point));
+ res = Math.min(res, new Line2D.Double(p4, p1).ptSegDist(point));
+
+ return res;
+ }
+
+ /**
+ * This function returns point on the middle of rectangle side, that is
+ * closest to the given point.
+ *
+ * @param rect
+ * rectangle on which we look for a point
+ * @param point
+ * point to which result should be as close as possible
+ * @return point on the middle of rectangle side that is as close as possible
+ * to the input point
+ */
+ public static Point2D pointOnRectangle(Rectangle2D rect, Point2D point) {
+
+ Point2D p1 = new Point2D.Double(rect.getX(), rect.getY());
+ Point2D p2 = new Point2D.Double(rect.getX(), rect.getY() + rect.getHeight());
+ Point2D p3 = new Point2D.Double(rect.getX() + rect.getWidth(), rect.getY() + rect.getHeight());
+ Point2D p4 = new Point2D.Double(rect.getX() + rect.getWidth(), rect.getY());
+
+ Point2D p12 = new Point2D.Double((p1.getX() + p2.getX()) / 2, (p1.getY() + p2.getY()) / 2);
+ Point2D p23 = new Point2D.Double((p2.getX() + p3.getX()) / 2, (p2.getY() + p3.getY()) / 2);
+ Point2D p34 = new Point2D.Double((p3.getX() + p4.getX()) / 2, (p3.getY() + p4.getY()) / 2);
+ Point2D p41 = new Point2D.Double((p4.getX() + p1.getX()) / 2, (p4.getY() + p1.getY()) / 2);
+
+ double dis1, dis2, dis3, dis4, min;
+ dis1 = point.distance(p12);
+ dis2 = point.distance(p23);
+ dis3 = point.distance(p34);
+ dis4 = point.distance(p41);
+
+ min = Math.min(dis1, dis2);
+ min = Math.min(min, dis3);
+ min = Math.min(min, dis4);
+
+ if (min == dis1) {
+ return p12;
+ } else if (min == dis2) {
+ return p23;
+ } else if (min == dis3) {
+ return p34;
+ } else {
+ return p41;
+ }
+ }
+
+ /**
+ * This function returns point on rectangle that is closest to given point.
+ *
+ * @param rect
+ * rectangle on which the result poiint will be placed
+ * @param point
+ * point for which we look the closest reference on rectangle
+ * @return the closest possible point on rectangle
+ */
+ public static Point2D closestPointOnRectangle(Rectangle2D rect, Point2D point) {
+ Point2D p1 = new Point2D.Double(rect.getX(), rect.getY());
+ Point2D p2 = new Point2D.Double(rect.getX(), rect.getY() + rect.getHeight());
+ Point2D p3 = new Point2D.Double(rect.getX() + rect.getWidth(), rect.getY() + rect.getHeight());
+ Point2D p4 = new Point2D.Double(rect.getX() + rect.getWidth(), rect.getY());
+
+ double dis1, dis2, dis3, dis4, min;
+ dis1 = new Line2D.Double(p1, p2).ptSegDist(point);
+ dis2 = new Line2D.Double(p2, p3).ptSegDist(point);
+ dis3 = new Line2D.Double(p3, p4).ptSegDist(point);
+ dis4 = new Line2D.Double(p4, p1).ptSegDist(point);
+ min = Math.min(dis1, dis2);
+ min = Math.min(min, dis3);
+ min = Math.min(min, dis4);
+
+ if (min == dis1) {
+ return closestPointOnLine(new Line2D.Double(p1, p2), point);
+ } else if (min == dis2) {
+ return closestPointOnLine(new Line2D.Double(p2, p3), point);
+ } else if (min == dis3) {
+ return closestPointOnLine(new Line2D.Double(p3, p4), point);
+ } else {
+ return closestPointOnLine(new Line2D.Double(p4, p1), point);
+ }
+ }
+
+ /**
+ * Returns point that is outside given rectangle, but still close to the given
+ * point. If the given point is inside rec then the given point is returned.
+ *
+ * @param rec
+ * rectangle
+ * @param point
+ * point
+ * @return point that is outside given rectangle, but still close to the given
+ * point
+ */
+ public static Point2D pointRightOutsideRec(Rectangle2D rec, Point2D point) {
+ if (!rec.contains(point)) {
+ return (Point2D) point.clone();
+ } else {
+ double lx = rec.getX();
+ double rx = lx + rec.getWidth();
+ double uy = rec.getY();
+ double dy = uy + rec.getHeight();
+
+ double dis1 = Math.abs(point.getX() - lx);
+ double dis2 = Math.abs(point.getX() - rx);
+ double dis3 = Math.abs(point.getY() - uy);
+ double dis4 = Math.abs(point.getY() - dy);
+
+ double min = Math.min(dis1, dis2);
+ min = Math.min(min, dis3);
+ min = Math.min(min, dis4);
+
+ if (min == dis1) {
+ return new Point2D.Double(lx - 1.0, point.getY());
+ } else if (min == dis2) {
+ return new Point2D.Double(rx + 1.0, point.getY());
+ } else if (min == dis3) {
+ return new Point2D.Double(point.getX(), uy - 1.0);
+ } else {
+ return new Point2D.Double(point.getX(), uy + 1.0);
+ }
+ }
+ }
+
+ /**
+ * Creates a {@link PolylineData} that is identical to parameter line, but
+ * doesn't contain duplicate points.
+ *
+ * @param line
+ * line that is transformed
+ * @return input line without duplicate points
+ */
+ public static PolylineData removeRedundantPoints(PolylineData line) {
+ PolylineData res = new PolylineData(line);
+
+ for (int i = 2; i < res.getPoints().size(); i++) {
+ if (new Line2D.Double(res.getPoints().get(i), res.getPoints().get(i - 2)).ptSegDist(res.getPoints().get(i - 1)) < DISTANCE_PROXIMITY) {
+ res.getPoints().remove(i - 1);
+ i--;
+ }
+ }
+ return res;
+ }
+
+ /**
+ * Returns distance between point and line.
+ *
+ * @param point
+ * point
+ * @param mainLine
+ * line
+ * @return distance between point and line
+ */
+ public static double distanceFromPolyline(Point2D point, PolylineData mainLine) {
+ double min = Double.MAX_VALUE;
+ for (Line2D line : mainLine.getLines()) {
+ min = Math.min(min, line.ptSegDist(point));
+ }
+ return min;
+ }
+
+ /**
+ * Returns point on line that is as closse as possible to point.
+ *
+ * @param point
+ * point
+ * @param mainLine
+ * line
+ * @return point on line that is as closse as possible to point
+ */
+ public static Point2D closestPointOnPolyline(PolylineData mainLine, Point2D point) {
+ Point2D res = null;
+ double distance = distanceOnPolyline(mainLine, point);
+ double lenght = 0.0;
+ for (Line2D line : mainLine.getLines()) {
+ lenght += lineLen(line);
+ }
+ lenght *= distance;
+ for (Line2D line : mainLine.getLines()) {
+ if (lenght - lineLen(line) > 0) {
+ lenght -= lineLen(line);
+ } else {
+ double tmp = lenght / lineLen(line);
+ double x = line.getX1() + tmp * (line.getX2() - line.getX1());
+ double y = line.getY1() + tmp * (line.getY2() - line.getY1());
+ res = new Point2D.Double(x, y);
+ }
+ }
+ return res;
+ }
+
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/utils/package-info.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/utils/package-info.java
index ecc6a66336..491c5ebef4 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/utils/package-info.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/utils/package-info.java
@@ -1,5 +1,5 @@
-/**
- * Contains utils classes.
- */
-package lcsb.mapviewer.wikipathway.utils;
-
+/**
+ * Contains utils classes.
+ */
+package lcsb.mapviewer.wikipathway.utils;
+
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/AllWikipathwaysTests.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/AllWikipathwaysTests.java
index 4374a3c7c4..2f098eb7e2 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/AllWikipathwaysTests.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/AllWikipathwaysTests.java
@@ -1,22 +1,22 @@
-package lcsb.mapviewer.wikipathway;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-import lcsb.mapviewer.wikipathway.XML.AllXmlTests;
-import lcsb.mapviewer.wikipathway.model.AllModelTests;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AllModelTests.class, //
- AllXmlTests.class, //
- ComplexReactionToModelTest.class, //
- GPMLToModelTest.class, //
- ReactionElbowsTest.class, //
- ReactionGpmlInputToModelTest.class, //
- ReactionGpmlOutputToModelTest.class, //
- ReactionGpmlToModelTest.class, //
-})
-public class AllWikipathwaysTests {
-
-}
+package lcsb.mapviewer.wikipathway;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+import lcsb.mapviewer.wikipathway.XML.AllXmlTests;
+import lcsb.mapviewer.wikipathway.model.AllModelTests;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AllModelTests.class, //
+ AllXmlTests.class, //
+ ComplexReactionToModelTest.class, //
+ GPMLToModelTest.class, //
+ ReactionElbowsTest.class, //
+ ReactionGpmlInputToModelTest.class, //
+ ReactionGpmlOutputToModelTest.class, //
+ ReactionGpmlToModelTest.class, //
+})
+public class AllWikipathwaysTests {
+
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ComplexReactionToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ComplexReactionToModelTest.java
index 9ddcf820ee..d75e6ef106 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ComplexReactionToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ComplexReactionToModelTest.java
@@ -1,216 +1,216 @@
-package lcsb.mapviewer.wikipathway;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.Color;
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
-
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.reaction.AbstractNode;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
-
-import org.apache.log4j.Logger;
-import org.junit.Test;
-
-public class ComplexReactionToModelTest extends WikipathwaysTestFunctions{
- /**
- * Default class logger.
- */
- static Logger logger = Logger.getLogger(ComplexReactionToModelTest.class);
-
- @Test
- public void ComplexReactionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/two_segment_reaction.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(1, reaction.getReactants().size());
- assertEquals(1, reaction.getProducts().size());
-
- assertEquals(0, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void ComplexReactantReactionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/two_reactants_reaction.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(2, reaction.getReactants().size());
- assertEquals(1, reaction.getProducts().size());
-
- assertEquals(1, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void ComplexSplitReactionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/split_two_segment_reaction.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(1, reaction.getReactants().size());
- assertEquals(2, reaction.getProducts().size());
-
- assertEquals(0, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void problematicReactantTest() throws Exception {
- try {
- ModelComparator mc = new ModelComparator(1.0);
-
- String fileName = "testFiles/small/problematic_reactant.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
- assertEquals("File " + fileName + " different after transformation", 0, mc.compare(model1, model2));
-
- assertEquals(7, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void problematicReactant2Test() throws Exception {
- try {
- ModelComparator mc = new ModelComparator(1.0);
-
- String fileName = "testFiles/small/problematic_reactant_2.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
- assertEquals("File " + fileName + " different after transformation", 0, mc.compare(model1, model2));
-
- assertEquals(3, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void missingNodesInReactionTest() throws Exception {
- try {
- ModelComparator mc = new ModelComparator(1.0);
-
- String fileName = "testFiles/small/missing_nodes_in_reaction.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals("File " + fileName + " different after transformation", 0, mc.compare(model1, model2));
-
- assertEquals(5, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testColorReaction() throws Exception {
- try {
- String fileName = "testFiles/small/color_reaction.gpml";
- Model model = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model.getReactions().size());
-
- Reaction reaction = model.getReactions().iterator().next();
-
- assertFalse(Color.BLACK.equals(reaction.getReactants().get(0).getLine().getColor()));
-
- Element redAlias = model.getElementByElementId("d9620");
- Element blackAlias = model.getElementByElementId("d046f");
- assertFalse(Color.BLACK.equals(redAlias.getColor()));
- assertTrue(Color.WHITE.equals(blackAlias.getColor()));
-
- assertEquals(1, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- /**
- * @throws Exception
- */
- @Test
- public void testReactionWithTwoSegments() throws Exception {
- try {
- String fileName = "testFiles/small/color_reaction.gpml";
- Model model = new GPMLToModel().getModel(fileName);
-
- Reaction reaction = model.getReactions().iterator().next();
-
- int lineCount = 0;
- for (AbstractNode node : reaction.getNodes()) {
- lineCount += node.getLine().getLines().size();
- }
-
- assertEquals(4, lineCount);
-
- assertEquals(1, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.wikipathway;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import java.awt.Color;
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.reaction.AbstractNode;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
+
+import org.apache.log4j.Logger;
+import org.junit.Test;
+
+public class ComplexReactionToModelTest extends WikipathwaysTestFunctions{
+ /**
+ * Default class logger.
+ */
+ static Logger logger = Logger.getLogger(ComplexReactionToModelTest.class);
+
+ @Test
+ public void ComplexReactionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/two_segment_reaction.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(1, reaction.getReactants().size());
+ assertEquals(1, reaction.getProducts().size());
+
+ assertEquals(0, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void ComplexReactantReactionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/two_reactants_reaction.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(2, reaction.getReactants().size());
+ assertEquals(1, reaction.getProducts().size());
+
+ assertEquals(1, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void ComplexSplitReactionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/split_two_segment_reaction.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(1, reaction.getReactants().size());
+ assertEquals(2, reaction.getProducts().size());
+
+ assertEquals(0, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void problematicReactantTest() throws Exception {
+ try {
+ ModelComparator mc = new ModelComparator(1.0);
+
+ String fileName = "testFiles/small/problematic_reactant.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ assertEquals("File " + fileName + " different after transformation", 0, mc.compare(model1, model2));
+
+ assertEquals(7, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void problematicReactant2Test() throws Exception {
+ try {
+ ModelComparator mc = new ModelComparator(1.0);
+
+ String fileName = "testFiles/small/problematic_reactant_2.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ assertEquals("File " + fileName + " different after transformation", 0, mc.compare(model1, model2));
+
+ assertEquals(3, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void missingNodesInReactionTest() throws Exception {
+ try {
+ ModelComparator mc = new ModelComparator(1.0);
+
+ String fileName = "testFiles/small/missing_nodes_in_reaction.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals("File " + fileName + " different after transformation", 0, mc.compare(model1, model2));
+
+ assertEquals(5, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testColorReaction() throws Exception {
+ try {
+ String fileName = "testFiles/small/color_reaction.gpml";
+ Model model = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model.getReactions().size());
+
+ Reaction reaction = model.getReactions().iterator().next();
+
+ assertFalse(Color.BLACK.equals(reaction.getReactants().get(0).getLine().getColor()));
+
+ Element redAlias = model.getElementByElementId("d9620");
+ Element blackAlias = model.getElementByElementId("d046f");
+ assertFalse(Color.BLACK.equals(redAlias.getColor()));
+ assertTrue(Color.WHITE.equals(blackAlias.getColor()));
+
+ assertEquals(1, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ /**
+ * @throws Exception
+ */
+ @Test
+ public void testReactionWithTwoSegments() throws Exception {
+ try {
+ String fileName = "testFiles/small/color_reaction.gpml";
+ Model model = new GPMLToModel().getModel(fileName);
+
+ Reaction reaction = model.getReactions().iterator().next();
+
+ int lineCount = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ lineCount += node.getLine().getLines().size();
+ }
+
+ assertEquals(4, lineCount);
+
+ assertEquals(1, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionElbowsTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionElbowsTest.java
index 7fc254299a..cf795f8e45 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionElbowsTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionElbowsTest.java
@@ -1,875 +1,875 @@
-package lcsb.mapviewer.wikipathway;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.geom.Line2D;
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
-
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.reaction.AbstractNode;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
-
-import org.apache.log4j.Logger;
-import org.junit.Test;
-
-public class ReactionElbowsTest extends WikipathwaysTestFunctions{
- private final static double EPSILON = 1e-6;
-
- /**
- * Default class logger.
- */
- static Logger logger = Logger.getLogger(ReactionElbowsTest.class);
-
- private ModelComparator mc = new ModelComparator(1.0);
-
- @Test
- public void LineReactionNorthToNorth() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_n_n.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(5, lines);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionNorthToEast() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_n_e.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(6, lines);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionNorthToEast2() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_n_e_2.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(4, lines);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionNorthToSouth() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_n_s.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(7, lines);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionNorthToWest() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_n_w.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(6, lines);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionNorthToWest2() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_n_w_2.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(4, lines);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionEastToNorth() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_e_n.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(4, lines);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionEastToNorth2() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_e_n_2.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(6, lines);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionEastToEast() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_e_e.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(5, lines);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionEastToSouth() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_e_s.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(6, lines);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionEastToSouth2() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_e_s_2.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(4, lines);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionEastToWest() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_e_w.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(5, lines);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionSouthToNorth() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_s_n.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(5, lines);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionSouthToEast() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_s_e.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(6, lines);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionSouthToEast2() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_s_e_2.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(4, lines);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionSouthToSouth() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_s_s.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(5, lines);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionSouthToWest() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_s_w.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(4, lines);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionSouthToWest2() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_s_w_2.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(6, lines);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionWestToNorth() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_w_n.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(6, lines);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionWestToNorth2() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_w_n_2.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(4, lines);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionWestToEast() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_w_e.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(7, lines);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionWestToSouth() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_w_s.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(6, lines);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionWestToSouth2() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_w_s_2.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(4, lines);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineReactionWestToWest() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_w_w.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
-
- assertEquals(5, lines);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private boolean isHvLine(Line2D line) {
- return Math.abs(line.getX1() - line.getX2()) < EPSILON || Math.abs(line.getY1() - line.getY2()) < EPSILON;
- }
-}
+package lcsb.mapviewer.wikipathway;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.awt.geom.Line2D;
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.reaction.AbstractNode;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
+
+import org.apache.log4j.Logger;
+import org.junit.Test;
+
+public class ReactionElbowsTest extends WikipathwaysTestFunctions{
+ private final static double EPSILON = 1e-6;
+
+ /**
+ * Default class logger.
+ */
+ static Logger logger = Logger.getLogger(ReactionElbowsTest.class);
+
+ private ModelComparator mc = new ModelComparator(1.0);
+
+ @Test
+ public void LineReactionNorthToNorth() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_n_n.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(5, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionNorthToEast() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_n_e.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(6, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionNorthToEast2() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_n_e_2.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(4, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionNorthToSouth() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_n_s.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(7, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionNorthToWest() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_n_w.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(6, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionNorthToWest2() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_n_w_2.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(4, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionEastToNorth() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_e_n.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(4, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionEastToNorth2() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_e_n_2.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(6, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionEastToEast() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_e_e.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(5, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionEastToSouth() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_e_s.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(6, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionEastToSouth2() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_e_s_2.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(4, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionEastToWest() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_e_w.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(5, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionSouthToNorth() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_s_n.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(5, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionSouthToEast() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_s_e.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(6, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionSouthToEast2() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_s_e_2.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(4, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionSouthToSouth() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_s_s.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(5, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionSouthToWest() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_s_w.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(4, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionSouthToWest2() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_s_w_2.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(6, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionWestToNorth() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_w_n.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(6, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionWestToNorth2() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_w_n_2.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(4, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionWestToEast() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_w_e.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(7, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionWestToSouth() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_w_s.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(6, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionWestToSouth2() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_w_s_2.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(4, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineReactionWestToWest() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_w_w.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
+ lines++;
+ }
+ }
+
+ assertEquals(5, lines);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private boolean isHvLine(Line2D line) {
+ return Math.abs(line.getX1() - line.getX2()) < EPSILON || Math.abs(line.getY1() - line.getY2()) < EPSILON;
+ }
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlInputToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlInputToModelTest.java
index d0b7a19add..27d7f4d35a 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlInputToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlInputToModelTest.java
@@ -1,1417 +1,1417 @@
-package lcsb.mapviewer.wikipathway;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
-
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.modifier.Catalysis;
-import lcsb.mapviewer.model.map.modifier.Inhibition;
-import lcsb.mapviewer.model.map.modifier.Modulation;
-import lcsb.mapviewer.model.map.modifier.PhysicalStimulation;
-import lcsb.mapviewer.model.map.modifier.UnknownCatalysis;
-import lcsb.mapviewer.model.map.modifier.UnknownInhibition;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
-
-import org.apache.log4j.Logger;
-import org.junit.Test;
-
-public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
- /**
- * Default class logger.
- */
- static Logger logger = Logger.getLogger(ReactionGpmlInputToModelTest.class);
-
- private ModelComparator mc = new ModelComparator(1.0);
-
- @Test
- public void LineInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_line_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(0, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void ArrowInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_arrow_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void DashedLineInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_line_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void DashedArrowInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_arrow_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void TBarInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_tbar_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Inhibition);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(0, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void NecessaryStimulationInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_necessary_stimulation_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof PhysicalStimulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(0, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void BindingInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_binding_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void ConversionInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_conversion_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void StimulationInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_stimulation_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof PhysicalStimulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(0, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void ModificationInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_modification_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(0, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void CatalystInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_catalyst_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Catalysis);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(0, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void InhibitionInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_inhibition_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Inhibition);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(0, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void CleavageInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_cleavage_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void CovalentBondInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_covalent_bond_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void BranchingLeftInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_branching_left_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(0, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void BranchingRightInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_branching_right_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(0, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void TranscriptionTranslationInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_transcription_translation_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void GapInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_gap_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void TBarInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_tbar_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof UnknownInhibition);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void NecessaryStimulationInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_necessary_stimulation_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void BindingInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_binding_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void ConversionInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_conversion_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void StimulationInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_stimulation_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void ModificationInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_modification_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void CatalystInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_catalyst_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof UnknownCatalysis);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void InhibitionInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_inhibition_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof UnknownInhibition);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void CleavageInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_cleavage_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void CovalentBondInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_covalent_bond_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void BranchingLeftInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_branching_left_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void BranchingRightInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_branching_right_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void TranscriptionTranslationInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_transcription_translation_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void GapInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_gap_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.wikipathway;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.modifier.Catalysis;
+import lcsb.mapviewer.model.map.modifier.Inhibition;
+import lcsb.mapviewer.model.map.modifier.Modulation;
+import lcsb.mapviewer.model.map.modifier.PhysicalStimulation;
+import lcsb.mapviewer.model.map.modifier.UnknownCatalysis;
+import lcsb.mapviewer.model.map.modifier.UnknownInhibition;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
+
+import org.apache.log4j.Logger;
+import org.junit.Test;
+
+public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
+ /**
+ * Default class logger.
+ */
+ static Logger logger = Logger.getLogger(ReactionGpmlInputToModelTest.class);
+
+ private ModelComparator mc = new ModelComparator(1.0);
+
+ @Test
+ public void LineInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_line_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void ArrowInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_arrow_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void DashedLineInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_line_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void DashedArrowInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_arrow_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void TBarInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_tbar_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Inhibition);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void NecessaryStimulationInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_necessary_stimulation_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof PhysicalStimulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void BindingInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_binding_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void ConversionInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_conversion_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void StimulationInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_stimulation_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof PhysicalStimulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void ModificationInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_modification_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void CatalystInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_catalyst_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Catalysis);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void InhibitionInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_inhibition_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Inhibition);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void CleavageInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_cleavage_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void CovalentBondInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_covalent_bond_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void BranchingLeftInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_branching_left_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void BranchingRightInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_branching_right_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void TranscriptionTranslationInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_transcription_translation_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void GapInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_gap_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void TBarInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_tbar_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof UnknownInhibition);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void NecessaryStimulationInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_necessary_stimulation_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void BindingInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_binding_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void ConversionInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_conversion_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void StimulationInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_stimulation_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void ModificationInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_modification_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void CatalystInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_catalyst_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof UnknownCatalysis);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void InhibitionInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_inhibition_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof UnknownInhibition);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void CleavageInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_cleavage_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void CovalentBondInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_covalent_bond_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void BranchingLeftInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_branching_left_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void BranchingRightInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_branching_right_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void TranscriptionTranslationInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_transcription_translation_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+ @Test
+ public void GapInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_gap_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlOutputToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlOutputToModelTest.java
index c6522070e1..18048170e3 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlOutputToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlOutputToModelTest.java
@@ -1,1444 +1,1444 @@
-package lcsb.mapviewer.wikipathway;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
-
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.modifier.Catalysis;
-import lcsb.mapviewer.model.map.modifier.Inhibition;
-import lcsb.mapviewer.model.map.modifier.Modulation;
-import lcsb.mapviewer.model.map.modifier.PhysicalStimulation;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
-
-import org.apache.log4j.Logger;
-import org.junit.Test;
-
-public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
- /**
- * Default class logger.
- */
- static Logger logger = Logger.getLogger(ReactionGpmlOutputToModelTest.class);
-
- private ModelComparator mc = new ModelComparator(1.0);
-
- @Test
- public void LineInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_line_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(0, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void ArrowInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_arrow_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(0, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void DashedLineInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_line_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void DashedArrowInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_arrow_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void TBarInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_tbar_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Inhibition);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void NecessaryStimulationInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_necessary_stimulation_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof PhysicalStimulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void BindingInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_binding_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void ConversionInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_conversion_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(0, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void StimulationInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_stimulation_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof PhysicalStimulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void ModificationInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_modification_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void CatalystInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_catalyst_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Catalysis);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void InhibitionInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_inhibition_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Inhibition);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void CleavageInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_cleavage_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(0, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void CovalentBondInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_covalent_bond_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void BranchingLeftInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_branching_left_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(0, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void BranchingRightInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_branching_right_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(0, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void TranscriptionTranslationInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_transcription_translation_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void GapInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_gap_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void TBarInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_tbar_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Inhibition);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void NecessaryStimulationInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_necessary_stimulation_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof PhysicalStimulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void BindingInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_binding_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void ConversionInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_conversion_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void StimulationInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_stimulation_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof PhysicalStimulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void ModificationInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_modification_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void CatalystInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_catalyst_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Catalysis);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void InhibitionInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_inhibition_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Inhibition);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void CleavageInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_cleavage_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void CovalentBondInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_covalent_bond_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void BranchingLeftInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_branching_left_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void BranchingRightInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_branching_right_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void TranscriptionTranslationInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_transcription_translation_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void GapInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_gap_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.wikipathway;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.modifier.Catalysis;
+import lcsb.mapviewer.model.map.modifier.Inhibition;
+import lcsb.mapviewer.model.map.modifier.Modulation;
+import lcsb.mapviewer.model.map.modifier.PhysicalStimulation;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
+
+import org.apache.log4j.Logger;
+import org.junit.Test;
+
+public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
+ /**
+ * Default class logger.
+ */
+ static Logger logger = Logger.getLogger(ReactionGpmlOutputToModelTest.class);
+
+ private ModelComparator mc = new ModelComparator(1.0);
+
+ @Test
+ public void LineInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_line_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void ArrowInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_arrow_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void DashedLineInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_line_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void DashedArrowInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_arrow_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void TBarInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_tbar_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Inhibition);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void NecessaryStimulationInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_necessary_stimulation_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof PhysicalStimulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void BindingInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_binding_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void ConversionInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_conversion_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void StimulationInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_stimulation_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof PhysicalStimulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void ModificationInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_modification_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void CatalystInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_catalyst_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Catalysis);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void InhibitionInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_inhibition_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Inhibition);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void CleavageInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_cleavage_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void CovalentBondInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_covalent_bond_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void BranchingLeftInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_branching_left_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void BranchingRightInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_branching_right_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void TranscriptionTranslationInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_transcription_translation_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void GapInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_gap_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void TBarInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_tbar_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Inhibition);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void NecessaryStimulationInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_necessary_stimulation_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof PhysicalStimulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void BindingInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_binding_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void ConversionInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_conversion_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void StimulationInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_stimulation_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof PhysicalStimulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void ModificationInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_modification_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void CatalystInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_catalyst_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Catalysis);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void InhibitionInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_inhibition_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Inhibition);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void CleavageInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_cleavage_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void CovalentBondInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_covalent_bond_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void BranchingLeftInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_branching_left_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void BranchingRightInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_branching_right_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void TranscriptionTranslationInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_transcription_translation_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void GapInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_gap_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlToModelTest.java
index bacd853e52..8bc873568a 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlToModelTest.java
@@ -1,1054 +1,1054 @@
-package lcsb.mapviewer.wikipathway;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
-
-import org.apache.log4j.Logger;
-import org.junit.Test;
-
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
-import lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction;
-import lcsb.mapviewer.model.map.reaction.type.PositiveInfluenceReaction;
-import lcsb.mapviewer.model.map.reaction.type.ReducedPhysicalStimulationReaction;
-import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
-import lcsb.mapviewer.model.map.reaction.type.UnknownNegativeInfluenceReaction;
-import lcsb.mapviewer.model.map.reaction.type.UnknownPositiveInfluenceReaction;
-import lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction;
-import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
-
-public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
- /**
- * Default class logger.
- */
- static Logger logger = Logger.getLogger(ReactionGpmlToModelTest.class);
-
- private ModelComparator mc = new ModelComparator(1.0);
-
- @Test
- public void LineInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_line.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownTransitionReaction);
- assertTrue(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void ArrowInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_arrow.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(0, getWarnings().size());
- assertTrue(reaction instanceof StateTransitionReaction);
- assertFalse(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void DashedArrowInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_arrow.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(0, getWarnings().size());
- assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
- assertFalse(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void DashedLineInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_line.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownTransitionReaction);
- assertTrue(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void BindingInteractionTest() throws Exception {
- try {
- // invalid mim_binding (contains only one reactant)
- String fileName = "testFiles/reactions/interaction_mim_binding.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownTransitionReaction);
- assertFalse(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void BindingInteractionTest2() throws Exception {
- try {
- // proper mim_binding (contains two reactants)
- String fileName = "testFiles/reactions/interaction_mim_binding2.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(getWarnings().toString(), 0, getWarnings().size());
- assertTrue(reaction instanceof HeterodimerAssociationReaction);
- assertFalse(reaction.isReversible());
- assertEquals(2, reaction.getReactants().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void BranchingLeftInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_branching_left.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownTransitionReaction);
- assertTrue(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void BranchingRightInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_branching_right.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownTransitionReaction);
- assertTrue(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void CatalystInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_catalyst.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof PositiveInfluenceReaction);
- assertFalse(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void CleavageInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_cleavage.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(0, getWarnings().size());
- assertTrue(reaction instanceof StateTransitionReaction);
- assertFalse(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void ConversionInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_conversion.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(0, getWarnings().size());
- assertTrue(reaction instanceof StateTransitionReaction);
- assertFalse(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void CovalentBondInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_covalent_bond.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownTransitionReaction);
- assertTrue(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void GapInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_gap.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownTransitionReaction);
- assertTrue(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void InhibitionInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_inhibition.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(0, getWarnings().size());
- assertTrue(reaction instanceof NegativeInfluenceReaction);
- assertFalse(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void ModificationInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_modification.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof PositiveInfluenceReaction);
- assertFalse(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void NecessaryStimulationInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_necessary_stimulation.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(0, getWarnings().size());
- assertTrue(reaction instanceof ReducedPhysicalStimulationReaction);
- assertFalse(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void StimulationInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_stimulation.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof ReducedPhysicalStimulationReaction);
- assertFalse(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void TranscriptionTranslationInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_transcription_translation.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof PositiveInfluenceReaction);
- assertFalse(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void TbarTranslationInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_tbar.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof NegativeInfluenceReaction);
- assertFalse(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void LineAsInteractionTest2() throws Exception {
- try {
- // proper mim_binding (contains two reactants)
- String fileName = "testFiles/reactions/line_as_interaction.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownTransitionReaction);
- assertTrue(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void BindingInteractionDashedTest() throws Exception {
- try {
- // invalid mim_binding (contains only one reactant)
- String fileName = "testFiles/reactions/interaction_dashed_mim_binding.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(0, getWarnings().size());
- assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
- assertFalse(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void BranchingLeftInteractionDashedTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_branching_left.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownTransitionReaction);
- assertTrue(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void BranchingRightInteractionDashedTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_branching_right.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownTransitionReaction);
- assertTrue(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void CatalystInteractionDashedTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_catalyst.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
- assertFalse(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void CleavageInteractionDashedTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_cleavage.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownTransitionReaction);
- assertFalse(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void ConversionInteractionDashedTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_conversion.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(0, getWarnings().size());
- assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
- assertFalse(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void CovalentBondInteractionDashedTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_covalent_bond.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownTransitionReaction);
- assertTrue(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void GapInteractionDashedTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_gap.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownTransitionReaction);
- assertTrue(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void InhibitionInteractionDashedTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_inhibition.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownNegativeInfluenceReaction);
- assertFalse(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void ModificationInteractionDashedTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_modification.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(0, getWarnings().size());
- assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
- assertFalse(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void NecessaryStimulationInteractionDashedTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_necessary_stimulation.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
- assertFalse(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void StimulationInteractionDashedTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_stimulation.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
- assertFalse(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void TranscriptionTranslationInteractionDashedTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_transcription_translation.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof PositiveInfluenceReaction);
- assertFalse(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void TbarTranslationInteractionDashedTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_tbar.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownNegativeInfluenceReaction);
- assertFalse(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void lineLineCombinedReactionsTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/line_line_combined_reaction.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(4, model1.getReactions().size());
-
- assertEquals(4, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.wikipathway;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
+
+import org.apache.log4j.Logger;
+import org.junit.Test;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
+import lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction;
+import lcsb.mapviewer.model.map.reaction.type.PositiveInfluenceReaction;
+import lcsb.mapviewer.model.map.reaction.type.ReducedPhysicalStimulationReaction;
+import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
+import lcsb.mapviewer.model.map.reaction.type.UnknownNegativeInfluenceReaction;
+import lcsb.mapviewer.model.map.reaction.type.UnknownPositiveInfluenceReaction;
+import lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction;
+import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
+
+public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
+ /**
+ * Default class logger.
+ */
+ static Logger logger = Logger.getLogger(ReactionGpmlToModelTest.class);
+
+ private ModelComparator mc = new ModelComparator(1.0);
+
+ @Test
+ public void LineInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_line.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownTransitionReaction);
+ assertTrue(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void ArrowInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_arrow.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(0, getWarnings().size());
+ assertTrue(reaction instanceof StateTransitionReaction);
+ assertFalse(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void DashedArrowInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_arrow.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(0, getWarnings().size());
+ assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
+ assertFalse(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void DashedLineInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_line.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownTransitionReaction);
+ assertTrue(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void BindingInteractionTest() throws Exception {
+ try {
+ // invalid mim_binding (contains only one reactant)
+ String fileName = "testFiles/reactions/interaction_mim_binding.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownTransitionReaction);
+ assertFalse(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void BindingInteractionTest2() throws Exception {
+ try {
+ // proper mim_binding (contains two reactants)
+ String fileName = "testFiles/reactions/interaction_mim_binding2.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(getWarnings().toString(), 0, getWarnings().size());
+ assertTrue(reaction instanceof HeterodimerAssociationReaction);
+ assertFalse(reaction.isReversible());
+ assertEquals(2, reaction.getReactants().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void BranchingLeftInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_branching_left.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownTransitionReaction);
+ assertTrue(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void BranchingRightInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_branching_right.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownTransitionReaction);
+ assertTrue(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void CatalystInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_catalyst.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof PositiveInfluenceReaction);
+ assertFalse(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void CleavageInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_cleavage.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(0, getWarnings().size());
+ assertTrue(reaction instanceof StateTransitionReaction);
+ assertFalse(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void ConversionInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_conversion.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(0, getWarnings().size());
+ assertTrue(reaction instanceof StateTransitionReaction);
+ assertFalse(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void CovalentBondInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_covalent_bond.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownTransitionReaction);
+ assertTrue(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void GapInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_gap.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownTransitionReaction);
+ assertTrue(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void InhibitionInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_inhibition.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(0, getWarnings().size());
+ assertTrue(reaction instanceof NegativeInfluenceReaction);
+ assertFalse(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void ModificationInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_modification.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof PositiveInfluenceReaction);
+ assertFalse(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void NecessaryStimulationInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_necessary_stimulation.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(0, getWarnings().size());
+ assertTrue(reaction instanceof ReducedPhysicalStimulationReaction);
+ assertFalse(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void StimulationInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_stimulation.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof ReducedPhysicalStimulationReaction);
+ assertFalse(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void TranscriptionTranslationInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_transcription_translation.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof PositiveInfluenceReaction);
+ assertFalse(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void TbarTranslationInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_tbar.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof NegativeInfluenceReaction);
+ assertFalse(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void LineAsInteractionTest2() throws Exception {
+ try {
+ // proper mim_binding (contains two reactants)
+ String fileName = "testFiles/reactions/line_as_interaction.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownTransitionReaction);
+ assertTrue(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void BindingInteractionDashedTest() throws Exception {
+ try {
+ // invalid mim_binding (contains only one reactant)
+ String fileName = "testFiles/reactions/interaction_dashed_mim_binding.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(0, getWarnings().size());
+ assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
+ assertFalse(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void BranchingLeftInteractionDashedTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_branching_left.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownTransitionReaction);
+ assertTrue(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void BranchingRightInteractionDashedTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_branching_right.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownTransitionReaction);
+ assertTrue(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void CatalystInteractionDashedTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_catalyst.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
+ assertFalse(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void CleavageInteractionDashedTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_cleavage.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownTransitionReaction);
+ assertFalse(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void ConversionInteractionDashedTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_conversion.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(0, getWarnings().size());
+ assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
+ assertFalse(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void CovalentBondInteractionDashedTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_covalent_bond.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownTransitionReaction);
+ assertTrue(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void GapInteractionDashedTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_gap.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownTransitionReaction);
+ assertTrue(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void InhibitionInteractionDashedTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_inhibition.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownNegativeInfluenceReaction);
+ assertFalse(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void ModificationInteractionDashedTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_modification.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(0, getWarnings().size());
+ assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
+ assertFalse(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void NecessaryStimulationInteractionDashedTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_necessary_stimulation.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
+ assertFalse(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void StimulationInteractionDashedTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_stimulation.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
+ assertFalse(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void TranscriptionTranslationInteractionDashedTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_transcription_translation.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof PositiveInfluenceReaction);
+ assertFalse(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void TbarTranslationInteractionDashedTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_tbar.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownNegativeInfluenceReaction);
+ assertFalse(reaction.isReversible());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void lineLineCombinedReactionsTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/line_line_combined_reaction.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(4, model1.getReactions().size());
+
+ assertEquals(4, getWarnings().size());
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/WikipathwaysTestFunctions.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/WikipathwaysTestFunctions.java
index b61a3ed021..25874080f7 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/WikipathwaysTestFunctions.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/WikipathwaysTestFunctions.java
@@ -1,234 +1,234 @@
-package lcsb.mapviewer.wikipathway;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.Reader;
-import java.io.StringReader;
-import java.io.StringWriter;
-import java.io.UnsupportedEncodingException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.util.Arrays;
-import java.util.List;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.transform.OutputKeys;
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerException;
-import javax.xml.transform.TransformerFactory;
-import javax.xml.transform.dom.DOMSource;
-import javax.xml.transform.stream.StreamResult;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.EventStorageLoggerAppender;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-
-import org.apache.log4j.Logger;
-import org.apache.log4j.spi.LoggingEvent;
-import org.junit.After;
-import org.junit.Before;
-import org.w3c.dom.Document;
-import org.w3c.dom.Element;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-import org.xml.sax.InputSource;
-import org.xml.sax.SAXException;
-
-public abstract class WikipathwaysTestFunctions {
- private Logger logger = Logger.getLogger(WikipathwaysTestFunctions.class);
-
- protected static double EPSILON = Configuration.EPSILON;
-
- private DocumentBuilder db;
-
-
- private EventStorageLoggerAppender appender;
-
- @Before
- public final void _setUp() throws Exception {
- Logger.getRootLogger().removeAppender(appender);
- appender = new EventStorageLoggerAppender();
- Logger.getRootLogger().addAppender(appender);
- db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
- }
-
- @After
- public final void _tearDown() throws Exception {
- Logger.getRootLogger().removeAppender(appender);
- }
-
- protected List<LoggingEvent> getWarnings() {
- return appender.getWarnings();
- }
-
- protected String readFile(String file) throws IOException {
- StringBuilder stringBuilder = new StringBuilder();
- BufferedReader reader = new BufferedReader(new FileReader(file));
- try {
- String line = null;
- String ls = System.getProperty("line.separator");
-
- while ((line = reader.readLine()) != null) {
- stringBuilder.append(line);
- stringBuilder.append(ls);
- }
- } finally {
- reader.close();
- }
-
- return stringBuilder.toString();
- }
-
- protected Node getNodeFromXmlString(String text) throws InvalidXmlSchemaException {
- InputSource is = new InputSource();
- is.setCharacterStream(new StringReader(text));
- return getXmlDocumentFromInputSource(is).getChildNodes().item(0);
- }
-
- protected Document getXmlDocumentFromFile(String fileName) throws InvalidXmlSchemaException, IOException {
- File file = new File(fileName);
- InputStream inputStream = new FileInputStream(file);
- Reader reader = null;
- try {
- reader = new InputStreamReader(inputStream, "UTF-8");
- InputSource is = new InputSource(reader);
-
- Document result = getXmlDocumentFromInputSource(is);
- inputStream.close();
- return result;
- } catch (UnsupportedEncodingException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- return null;
- }
-
- protected Document getXmlDocumentFromInputSource(InputSource stream) throws InvalidXmlSchemaException {
- DocumentBuilder db;
- try {
- db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
- } catch (ParserConfigurationException e) {
- throw new InvalidXmlSchemaException("Problem with xml parser");
- }
- Document doc = null;
- try {
- doc = db.parse(stream);
- } catch (SAXException e) {
- logger.error(e);
- } catch (IOException e) {
- logger.error(e);
- }
- return doc;
- }
-
- protected String createTmpFileName() {
- try {
- File f = File.createTempFile("prefix", ".txt");
- String filename = f.getName();
- f.delete();
- return filename;
- } catch (IOException e) {
- e.printStackTrace();
- return null;
- }
- }
-
- protected String nodeToString(Node node) {
- return nodeToString(node, false);
- }
-
- protected String nodeToString(Node node, boolean includeHeadNode) {
- if (node == null)
- return null;
- StringWriter sw = new StringWriter();
- try {
- Transformer t = TransformerFactory.newInstance().newTransformer();
- t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
- t.setOutputProperty(OutputKeys.INDENT, "yes");
- t.setOutputProperty(OutputKeys.METHOD, "xml");
-
- NodeList list = node.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node element = list.item(i);
- t.transform(new DOMSource(element), new StreamResult(sw));
- }
- } catch (TransformerException te) {
- logger.debug("nodeToString Transformer Exception");
- }
- if (includeHeadNode) {
- return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
- }
- return sw.toString();
- }
-
- protected boolean equalFiles(String fileA, String fileB) throws IOException {
- int BLOCK_SIZE = 65536;
- FileInputStream inputStreamA = new FileInputStream(fileA);
- FileInputStream inputStreamB = new FileInputStream(fileB);
- // vary BLOCK_SIZE to suit yourself.
- // it should probably a factor or multiple of the size of a disk
- // sector/cluster.
- // Note that your max heap size may need to be adjused
- // if you have a very big block size or lots of these comparators.
-
- // assume inputStreamA and inputStreamB are streams from your two files.
- byte[] streamABlock = new byte[BLOCK_SIZE];
- byte[] streamBBlock = new byte[BLOCK_SIZE];
- boolean match = true;
- int bytesReadA = 0;
- int bytesReadB = 0;
- do {
- bytesReadA = inputStreamA.read(streamABlock);
- bytesReadB = inputStreamB.read(streamBBlock);
- match = ((bytesReadA == bytesReadB) && Arrays.equals(streamABlock, streamBBlock));
- } while (match && (bytesReadA > -1));
- inputStreamA.close();
- inputStreamB.close();
- return match;
- }
-
- public File createTempDirectory() throws IOException {
- final File temp;
-
- temp = File.createTempFile("temp", Long.toString(System.nanoTime()));
-
- if (!(temp.delete())) {
- throw new IOException("Could not delete temp file: " + temp.getAbsolutePath());
- }
-
- if (!(temp.mkdir())) {
- throw new IOException("Could not create temp directory: " + temp.getAbsolutePath());
- }
-
- return (temp);
- }
-
- protected String getWebpage(String accessUrl) throws IOException {
- String inputLine;
- StringBuilder tmp = new StringBuilder();
- URL url = new URL(accessUrl);
- URLConnection urlConn = url.openConnection();
- BufferedReader in = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));
-
- while ((inputLine = in.readLine()) != null) {
- tmp.append(inputLine);
- }
- in.close();
- return tmp.toString();
- }
-
- protected Element fileToNode(String filename) throws SAXException, IOException {
- InputStream is = new FileInputStream(new File(filename));
- Document doc = null;
- doc = db.parse(is);
- return doc.getDocumentElement();
- }
-
-}
+package lcsb.mapviewer.wikipathway;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.io.StringReader;
+import java.io.StringWriter;
+import java.io.UnsupportedEncodingException;
+import java.net.URL;
+import java.net.URLConnection;
+import java.util.Arrays;
+import java.util.List;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.OutputKeys;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerException;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.dom.DOMSource;
+import javax.xml.transform.stream.StreamResult;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.EventStorageLoggerAppender;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+
+import org.apache.log4j.Logger;
+import org.apache.log4j.spi.LoggingEvent;
+import org.junit.After;
+import org.junit.Before;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+
+public abstract class WikipathwaysTestFunctions {
+ private Logger logger = Logger.getLogger(WikipathwaysTestFunctions.class);
+
+ protected static double EPSILON = Configuration.EPSILON;
+
+ private DocumentBuilder db;
+
+
+ private EventStorageLoggerAppender appender;
+
+ @Before
+ public final void _setUp() throws Exception {
+ Logger.getRootLogger().removeAppender(appender);
+ appender = new EventStorageLoggerAppender();
+ Logger.getRootLogger().addAppender(appender);
+ db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
+ }
+
+ @After
+ public final void _tearDown() throws Exception {
+ Logger.getRootLogger().removeAppender(appender);
+ }
+
+ protected List<LoggingEvent> getWarnings() {
+ return appender.getWarnings();
+ }
+
+ protected String readFile(String file) throws IOException {
+ StringBuilder stringBuilder = new StringBuilder();
+ BufferedReader reader = new BufferedReader(new FileReader(file));
+ try {
+ String line = null;
+ String ls = System.getProperty("line.separator");
+
+ while ((line = reader.readLine()) != null) {
+ stringBuilder.append(line);
+ stringBuilder.append(ls);
+ }
+ } finally {
+ reader.close();
+ }
+
+ return stringBuilder.toString();
+ }
+
+ protected Node getNodeFromXmlString(String text) throws InvalidXmlSchemaException {
+ InputSource is = new InputSource();
+ is.setCharacterStream(new StringReader(text));
+ return getXmlDocumentFromInputSource(is).getChildNodes().item(0);
+ }
+
+ protected Document getXmlDocumentFromFile(String fileName) throws InvalidXmlSchemaException, IOException {
+ File file = new File(fileName);
+ InputStream inputStream = new FileInputStream(file);
+ Reader reader = null;
+ try {
+ reader = new InputStreamReader(inputStream, "UTF-8");
+ InputSource is = new InputSource(reader);
+
+ Document result = getXmlDocumentFromInputSource(is);
+ inputStream.close();
+ return result;
+ } catch (UnsupportedEncodingException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ return null;
+ }
+
+ protected Document getXmlDocumentFromInputSource(InputSource stream) throws InvalidXmlSchemaException {
+ DocumentBuilder db;
+ try {
+ db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
+ } catch (ParserConfigurationException e) {
+ throw new InvalidXmlSchemaException("Problem with xml parser");
+ }
+ Document doc = null;
+ try {
+ doc = db.parse(stream);
+ } catch (SAXException e) {
+ logger.error(e);
+ } catch (IOException e) {
+ logger.error(e);
+ }
+ return doc;
+ }
+
+ protected String createTmpFileName() {
+ try {
+ File f = File.createTempFile("prefix", ".txt");
+ String filename = f.getName();
+ f.delete();
+ return filename;
+ } catch (IOException e) {
+ e.printStackTrace();
+ return null;
+ }
+ }
+
+ protected String nodeToString(Node node) {
+ return nodeToString(node, false);
+ }
+
+ protected String nodeToString(Node node, boolean includeHeadNode) {
+ if (node == null)
+ return null;
+ StringWriter sw = new StringWriter();
+ try {
+ Transformer t = TransformerFactory.newInstance().newTransformer();
+ t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
+ t.setOutputProperty(OutputKeys.INDENT, "yes");
+ t.setOutputProperty(OutputKeys.METHOD, "xml");
+
+ NodeList list = node.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node element = list.item(i);
+ t.transform(new DOMSource(element), new StreamResult(sw));
+ }
+ } catch (TransformerException te) {
+ logger.debug("nodeToString Transformer Exception");
+ }
+ if (includeHeadNode) {
+ return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
+ }
+ return sw.toString();
+ }
+
+ protected boolean equalFiles(String fileA, String fileB) throws IOException {
+ int BLOCK_SIZE = 65536;
+ FileInputStream inputStreamA = new FileInputStream(fileA);
+ FileInputStream inputStreamB = new FileInputStream(fileB);
+ // vary BLOCK_SIZE to suit yourself.
+ // it should probably a factor or multiple of the size of a disk
+ // sector/cluster.
+ // Note that your max heap size may need to be adjused
+ // if you have a very big block size or lots of these comparators.
+
+ // assume inputStreamA and inputStreamB are streams from your two files.
+ byte[] streamABlock = new byte[BLOCK_SIZE];
+ byte[] streamBBlock = new byte[BLOCK_SIZE];
+ boolean match = true;
+ int bytesReadA = 0;
+ int bytesReadB = 0;
+ do {
+ bytesReadA = inputStreamA.read(streamABlock);
+ bytesReadB = inputStreamB.read(streamBBlock);
+ match = ((bytesReadA == bytesReadB) && Arrays.equals(streamABlock, streamBBlock));
+ } while (match && (bytesReadA > -1));
+ inputStreamA.close();
+ inputStreamB.close();
+ return match;
+ }
+
+ public File createTempDirectory() throws IOException {
+ final File temp;
+
+ temp = File.createTempFile("temp", Long.toString(System.nanoTime()));
+
+ if (!(temp.delete())) {
+ throw new IOException("Could not delete temp file: " + temp.getAbsolutePath());
+ }
+
+ if (!(temp.mkdir())) {
+ throw new IOException("Could not create temp directory: " + temp.getAbsolutePath());
+ }
+
+ return (temp);
+ }
+
+ protected String getWebpage(String accessUrl) throws IOException {
+ String inputLine;
+ StringBuilder tmp = new StringBuilder();
+ URL url = new URL(accessUrl);
+ URLConnection urlConn = url.openConnection();
+ BufferedReader in = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));
+
+ while ((inputLine = in.readLine()) != null) {
+ tmp.append(inputLine);
+ }
+ in.close();
+ return tmp.toString();
+ }
+
+ protected Element fileToNode(String filename) throws SAXException, IOException {
+ InputStream is = new FileInputStream(new File(filename));
+ Document doc = null;
+ doc = db.parse(is);
+ return doc.getDocumentElement();
+ }
+
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/AllXmlTests.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/AllXmlTests.java
index 5df9825318..0fbf211664 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/AllXmlTests.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/AllXmlTests.java
@@ -1,22 +1,22 @@
-package lcsb.mapviewer.wikipathway.XML;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ BiopaxParserTest.class,//
- DataNodeParserTest.class,//
- BugTest.class,//
- EdgeLineParserTest.class,//
- GpmlParserTest.class,//
- LabelParserTest.class,//
- ReferenceParserTest.class,//
- ModelToGPMLTest.class,//
- ModelContructorTest.class,//
- ShapeParserTest.class,//
- StateParserTest.class,//
-})
-public class AllXmlTests {
-
-}
+package lcsb.mapviewer.wikipathway.XML;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ BiopaxParserTest.class,//
+ DataNodeParserTest.class,//
+ BugTest.class,//
+ EdgeLineParserTest.class,//
+ GpmlParserTest.class,//
+ LabelParserTest.class,//
+ ReferenceParserTest.class,//
+ ModelToGPMLTest.class,//
+ ModelContructorTest.class,//
+ ShapeParserTest.class,//
+ StateParserTest.class,//
+})
+public class AllXmlTests {
+
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BiopaxParserTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BiopaxParserTest.java
index 1185363569..401f90c6b3 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BiopaxParserTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BiopaxParserTest.java
@@ -1,62 +1,62 @@
-package lcsb.mapviewer.wikipathway.XML;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.w3c.dom.Document;
-
-import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
-import lcsb.mapviewer.wikipathway.model.biopax.BiopaxData;
-import lcsb.mapviewer.wikipathway.model.biopax.BiopaxPublication;
-
-public class BiopaxParserTest extends WikipathwaysTestFunctions {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParse() throws Exception {
- try {
- BiopaxParser parser = new BiopaxParser();
- Document document = getXmlDocumentFromFile("testFiles/biopax/small.xml");
- BiopaxData data = parser.parse(document.getFirstChild());
- assertNotNull(data);
- assertEquals(2, data.getPublications().size());
- BiopaxPublication publication = data.getPublicationByReference("cf2");
- assertEquals("23456", publication.getId());
- assertEquals("PubMed", publication.getDb());
- assertEquals("[Radical resection of foci in tuberculosis of the shoulder joint].", publication.getTitle());
- assertEquals("Magy Traumatol Orthop Helyreallito Seb", publication.getSource());
- assertEquals("1977", publication.getYear());
- assertEquals("Udvarhelyi I", publication.getAuthors());
- assertEquals("cf2", publication.getReferenceId());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testIncorrectPumeds() throws Exception {
- try {
- BiopaxParser parser = new BiopaxParser();
- Document document = getXmlDocumentFromFile("testFiles/biopax/invalid_pubmed_reference.xml");
- BiopaxData data = parser.parse(document.getFirstChild());
- assertNotNull(data);
- assertTrue(getWarnings().size() > 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.wikipathway.XML;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.w3c.dom.Document;
+
+import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
+import lcsb.mapviewer.wikipathway.model.biopax.BiopaxData;
+import lcsb.mapviewer.wikipathway.model.biopax.BiopaxPublication;
+
+public class BiopaxParserTest extends WikipathwaysTestFunctions {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testParse() throws Exception {
+ try {
+ BiopaxParser parser = new BiopaxParser();
+ Document document = getXmlDocumentFromFile("testFiles/biopax/small.xml");
+ BiopaxData data = parser.parse(document.getFirstChild());
+ assertNotNull(data);
+ assertEquals(2, data.getPublications().size());
+ BiopaxPublication publication = data.getPublicationByReference("cf2");
+ assertEquals("23456", publication.getId());
+ assertEquals("PubMed", publication.getDb());
+ assertEquals("[Radical resection of foci in tuberculosis of the shoulder joint].", publication.getTitle());
+ assertEquals("Magy Traumatol Orthop Helyreallito Seb", publication.getSource());
+ assertEquals("1977", publication.getYear());
+ assertEquals("Udvarhelyi I", publication.getAuthors());
+ assertEquals("cf2", publication.getReferenceId());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testIncorrectPumeds() throws Exception {
+ try {
+ BiopaxParser parser = new BiopaxParser();
+ Document document = getXmlDocumentFromFile("testFiles/biopax/invalid_pubmed_reference.xml");
+ BiopaxData data = parser.parse(document.getFirstChild());
+ assertNotNull(data);
+ assertTrue(getWarnings().size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BugTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BugTest.java
index f955ec36c1..85cd00bac4 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BugTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BugTest.java
@@ -1,69 +1,69 @@
-package lcsb.mapviewer.wikipathway.XML;
-
-import static org.junit.Assert.assertEquals;
-
-import java.io.ByteArrayInputStream;
-import java.io.FileInputStream;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
-
-import org.apache.log4j.Logger;
-import org.junit.Test;
-
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
-
-public class BugTest extends WikipathwaysTestFunctions {
- Logger logger = Logger.getLogger(BugTest.class);
-
- @Test
- public void testBug319() throws Exception {
- try {
- String fileName = "testFiles/bugs/error_319.gpml";
- FileInputStream fis = new FileInputStream(fileName);
- new GpmlParser().createGraph(fis);
- assertEquals(1, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private ModelComparator mc = new ModelComparator(1.0);
-
- @Test
- public void testBug328() throws Exception {
- try {
- String filename = "testFiles/bugs/error_328.gpml";
- Model model1 = new GPMLToModel().getModel(filename);
-
- assertEquals(7, getWarnings().size());
-
- int complexes = 0;
- for (Element alias : model1.getElements()) {
- if (alias instanceof Complex) {
- complexes++;
- }
- }
- assertEquals("Invalid number of complexes", 1, complexes);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals("File " + filename + " different after transformation", 0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.wikipathway.XML;
+
+import static org.junit.Assert.assertEquals;
+
+import java.io.ByteArrayInputStream;
+import java.io.FileInputStream;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
+
+import org.apache.log4j.Logger;
+import org.junit.Test;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
+
+public class BugTest extends WikipathwaysTestFunctions {
+ Logger logger = Logger.getLogger(BugTest.class);
+
+ @Test
+ public void testBug319() throws Exception {
+ try {
+ String fileName = "testFiles/bugs/error_319.gpml";
+ FileInputStream fis = new FileInputStream(fileName);
+ new GpmlParser().createGraph(fis);
+ assertEquals(1, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private ModelComparator mc = new ModelComparator(1.0);
+
+ @Test
+ public void testBug328() throws Exception {
+ try {
+ String filename = "testFiles/bugs/error_328.gpml";
+ Model model1 = new GPMLToModel().getModel(filename);
+
+ assertEquals(7, getWarnings().size());
+
+ int complexes = 0;
+ for (Element alias : model1.getElements()) {
+ if (alias instanceof Complex) {
+ complexes++;
+ }
+ }
+ assertEquals("Invalid number of complexes", 1, complexes);
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ assertEquals("File " + filename + " different after transformation", 0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/DataNodeParserTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/DataNodeParserTest.java
index 6dc793949e..ff4a3f911d 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/DataNodeParserTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/DataNodeParserTest.java
@@ -1,59 +1,59 @@
-package lcsb.mapviewer.wikipathway.XML;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.w3c.dom.Element;
-
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
-import lcsb.mapviewer.wikipathway.model.DataNode;
-
-public class DataNodeParserTest extends WikipathwaysTestFunctions {
- Logger logger = Logger.getLogger(DataNodeParserTest.class);
- DataNodeParser parser = new DataNodeParser();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParseGene() throws Exception {
- try {
- Element node = fileToNode("testFiles/elements/gene.xml");
- DataNode dataNode = parser.parse(node);
-
- assertNotNull(dataNode);
- assertEquals("GeneProduct", dataNode.getTextLabel());
- assertEquals("ab30b", dataNode.getGraphId());
- assertEquals(1, dataNode.getBiopaxReference().size());
- assertEquals("aea", dataNode.getBiopaxReference().get(0));
- assertEquals(1, dataNode.getReferences().size());
- assertEquals(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"), dataNode.getReferences().get(0));
-
- assertEquals((Integer) 32768, dataNode.getzOrder());
- assertEquals((Double) 10.0, dataNode.getFontSize());
- assertEquals("Middle", dataNode.getvAlign());
- assertEquals("GeneProduct", dataNode.getType());
- assertTrue(dataNode.getComments().contains("comment 1"));
- assertTrue(dataNode.getComments().contains("Type your comment here"));
-
- assertEquals(0, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.wikipathway.XML;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.w3c.dom.Element;
+
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
+import lcsb.mapviewer.wikipathway.model.DataNode;
+
+public class DataNodeParserTest extends WikipathwaysTestFunctions {
+ Logger logger = Logger.getLogger(DataNodeParserTest.class);
+ DataNodeParser parser = new DataNodeParser();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testParseGene() throws Exception {
+ try {
+ Element node = fileToNode("testFiles/elements/gene.xml");
+ DataNode dataNode = parser.parse(node);
+
+ assertNotNull(dataNode);
+ assertEquals("GeneProduct", dataNode.getTextLabel());
+ assertEquals("ab30b", dataNode.getGraphId());
+ assertEquals(1, dataNode.getBiopaxReference().size());
+ assertEquals("aea", dataNode.getBiopaxReference().get(0));
+ assertEquals(1, dataNode.getReferences().size());
+ assertEquals(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"), dataNode.getReferences().get(0));
+
+ assertEquals((Integer) 32768, dataNode.getzOrder());
+ assertEquals((Double) 10.0, dataNode.getFontSize());
+ assertEquals("Middle", dataNode.getvAlign());
+ assertEquals("GeneProduct", dataNode.getType());
+ assertTrue(dataNode.getComments().contains("comment 1"));
+ assertTrue(dataNode.getComments().contains("Type your comment here"));
+
+ assertEquals(0, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/EdgeLineParserTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/EdgeLineParserTest.java
index 2b3c0126fc..51be34fbc8 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/EdgeLineParserTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/EdgeLineParserTest.java
@@ -1,55 +1,55 @@
-package lcsb.mapviewer.wikipathway.XML;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.geom.Point2D;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.w3c.dom.Element;
-
-import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
-import lcsb.mapviewer.wikipathway.model.Edge;
-
-public class EdgeLineParserTest extends WikipathwaysTestFunctions {
-
- EdgeLineParser parser = new EdgeLineParser();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParseLine() throws Exception {
- try {
- Element node = fileToNode("testFiles/elements/line.xml");
- Edge edge = parser.parse(node);
- assertNotNull(edge);
-
- assertEquals(1, edge.getBiopaxReferences().size());
- assertEquals("c64", edge.getBiopaxReferences().get(0));
-
- assertEquals((Integer) 12288, edge.getzOrder());
- assertEquals(1.0, edge.getLine().getWidth(), EPSILON);
- assertTrue(edge.getComments().contains("line comment"));
- assertTrue(edge.getComments().contains("Type your comment here"));
-
- assertTrue(new Point2D.Double(730, 265).distance(edge.getLine().getBeginPoint()) < EPSILON);
- assertTrue(new Point2D.Double(931.0, 442.0).distance(edge.getLine().getEndPoint()) < EPSILON);
-
- assertEquals(0, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.wikipathway.XML;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import java.awt.geom.Point2D;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.w3c.dom.Element;
+
+import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
+import lcsb.mapviewer.wikipathway.model.Edge;
+
+public class EdgeLineParserTest extends WikipathwaysTestFunctions {
+
+ EdgeLineParser parser = new EdgeLineParser();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testParseLine() throws Exception {
+ try {
+ Element node = fileToNode("testFiles/elements/line.xml");
+ Edge edge = parser.parse(node);
+ assertNotNull(edge);
+
+ assertEquals(1, edge.getBiopaxReferences().size());
+ assertEquals("c64", edge.getBiopaxReferences().get(0));
+
+ assertEquals((Integer) 12288, edge.getzOrder());
+ assertEquals(1.0, edge.getLine().getWidth(), EPSILON);
+ assertTrue(edge.getComments().contains("line comment"));
+ assertTrue(edge.getComments().contains("Type your comment here"));
+
+ assertTrue(new Point2D.Double(730, 265).distance(edge.getLine().getBeginPoint()) < EPSILON);
+ assertTrue(new Point2D.Double(931.0, 442.0).distance(edge.getLine().getEndPoint()) < EPSILON);
+
+ assertEquals(0, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ElementGpmlParserTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ElementGpmlParserTest.java
index 9a021ad85d..8e084cf53e 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ElementGpmlParserTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ElementGpmlParserTest.java
@@ -1,54 +1,54 @@
-package lcsb.mapviewer.wikipathway.XML;
-
-import static org.junit.Assert.assertNotNull;
-
-import java.awt.Color;
-import java.util.Collection;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.w3c.dom.Element;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.ConverterException;
-
-public class ElementGpmlParserTest {
-
- ElementGpmlParser<Object> parser = new ElementGpmlParser<Object>() {
- @Override
- public String toXml(Collection<Object> list) throws ConverterException {
- throw new NotImplementedException();
- }
-
- @Override
- public String toXml(Object object) throws ConverterException {
- throw new NotImplementedException();
- }
-
- @Override
- public Object parse(Element node) throws ConverterException {
- throw new NotImplementedException();
- }
- };
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParseTransparentColor() {
- try {
- Color color = parser.hexStringToColor("Transparent");
- assertNotNull(color);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.wikipathway.XML;
+
+import static org.junit.Assert.assertNotNull;
+
+import java.awt.Color;
+import java.util.Collection;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.w3c.dom.Element;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.ConverterException;
+
+public class ElementGpmlParserTest {
+
+ ElementGpmlParser<Object> parser = new ElementGpmlParser<Object>() {
+ @Override
+ public String toXml(Collection<Object> list) throws ConverterException {
+ throw new NotImplementedException();
+ }
+
+ @Override
+ public String toXml(Object object) throws ConverterException {
+ throw new NotImplementedException();
+ }
+
+ @Override
+ public Object parse(Element node) throws ConverterException {
+ throw new NotImplementedException();
+ }
+ };
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testParseTransparentColor() {
+ try {
+ Color color = parser.hexStringToColor("Transparent");
+ assertNotNull(color);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/GpmlParserTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/GpmlParserTest.java
index c9353e4940..254110e418 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/GpmlParserTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/GpmlParserTest.java
@@ -1,150 +1,150 @@
-package lcsb.mapviewer.wikipathway.XML;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.io.FileInputStream;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
-import lcsb.mapviewer.wikipathway.model.Graph;
-import lcsb.mapviewer.wikipathway.model.Interaction;
-
-public class GpmlParserTest extends WikipathwaysTestFunctions {
- Logger logger = Logger.getLogger(GpmlParserTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEdgeAttributes() throws Exception {
- try {
-
- String fileName = "testFiles/small/missing_aliases_in_compartment.gpml";
- FileInputStream fis = new FileInputStream(fileName);
- Graph graph = new GpmlParser().createGraph(fis);
- assertNotNull(graph);
- assertEquals(3, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCycliReactions() throws Exception {
- try {
-
- String fileName = "testFiles/small/cyclic_reactions.gpml";
- FileInputStream fis = new FileInputStream(fileName);
- Graph graph = new GpmlParser().createGraph(fis);
- assertNotNull(graph);
- assertEquals(3, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testBiopaxVocabulary() throws Exception {
- try {
-
- String fileName = "testFiles/small/opencontrolledvocabulary.gpml";
- FileInputStream fis = new FileInputStream(fileName);
- Graph graph = new GpmlParser().createGraph(fis);
-
- assertEquals(1, graph.getBiopaxData().getOpenControlledVocabularies().size());
- assertEquals(0, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testModelAttribute() throws Exception {
- try {
-
- String fileName = "testFiles/small/model_attribute.gpml";
- FileInputStream fis = new FileInputStream(fileName);
- Graph graph = new GpmlParser().createGraph(fis);
-
- assertEquals("428359", graph.getAttributes().get("reactome_id"));
- assertEquals(0, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testModelAnnotations() throws Exception {
- try {
-
- String fileName = "testFiles/small/model_annotations.gpml";
- FileInputStream fis = new FileInputStream(fileName);
- Graph graph = new GpmlParser().createGraph(fis);
-
- assertEquals(6, graph.getBiopaxReferences().size());
- assertEquals(0, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testModelLines() throws Exception {
- try {
-
- String fileName = "testFiles/small/model_with_line.gpml";
- FileInputStream fis = new FileInputStream(fileName);
- Graph graph = new GpmlParser().createGraph(fis);
-
- assertEquals(1, graph.getLines().size());
- PolylineData pd = graph.getLines().get(0);
- assertEquals(3, pd.getPoints().size());
- assertEquals(0, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSimpleReaction() throws Exception {
- try {
-
- String fileName = "testFiles/small/simple_reaction.gpml";
- FileInputStream fis = new FileInputStream(fileName);
- Graph graph = new GpmlParser().createGraph(fis);
-
- Interaction interaction = graph.getInteractions().iterator().next();
- PolylineData pd = interaction.getLine();
- assertTrue(pd.getPoints().get(0).distance(476.0, 351.0) < EPSILON);
- assertTrue(pd.getPoints().get(1).distance(476.0, 286.0) < EPSILON);
- assertTrue(pd.getPoints().get(2).distance(846.0, 287.0) < EPSILON);
- assertTrue(pd.getPoints().get(3).distance(846.0, 354.0) < EPSILON);
-
- assertEquals(0, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.wikipathway.XML;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import java.io.FileInputStream;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
+import lcsb.mapviewer.wikipathway.model.Graph;
+import lcsb.mapviewer.wikipathway.model.Interaction;
+
+public class GpmlParserTest extends WikipathwaysTestFunctions {
+ Logger logger = Logger.getLogger(GpmlParserTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEdgeAttributes() throws Exception {
+ try {
+
+ String fileName = "testFiles/small/missing_aliases_in_compartment.gpml";
+ FileInputStream fis = new FileInputStream(fileName);
+ Graph graph = new GpmlParser().createGraph(fis);
+ assertNotNull(graph);
+ assertEquals(3, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCycliReactions() throws Exception {
+ try {
+
+ String fileName = "testFiles/small/cyclic_reactions.gpml";
+ FileInputStream fis = new FileInputStream(fileName);
+ Graph graph = new GpmlParser().createGraph(fis);
+ assertNotNull(graph);
+ assertEquals(3, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testBiopaxVocabulary() throws Exception {
+ try {
+
+ String fileName = "testFiles/small/opencontrolledvocabulary.gpml";
+ FileInputStream fis = new FileInputStream(fileName);
+ Graph graph = new GpmlParser().createGraph(fis);
+
+ assertEquals(1, graph.getBiopaxData().getOpenControlledVocabularies().size());
+ assertEquals(0, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testModelAttribute() throws Exception {
+ try {
+
+ String fileName = "testFiles/small/model_attribute.gpml";
+ FileInputStream fis = new FileInputStream(fileName);
+ Graph graph = new GpmlParser().createGraph(fis);
+
+ assertEquals("428359", graph.getAttributes().get("reactome_id"));
+ assertEquals(0, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testModelAnnotations() throws Exception {
+ try {
+
+ String fileName = "testFiles/small/model_annotations.gpml";
+ FileInputStream fis = new FileInputStream(fileName);
+ Graph graph = new GpmlParser().createGraph(fis);
+
+ assertEquals(6, graph.getBiopaxReferences().size());
+ assertEquals(0, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testModelLines() throws Exception {
+ try {
+
+ String fileName = "testFiles/small/model_with_line.gpml";
+ FileInputStream fis = new FileInputStream(fileName);
+ Graph graph = new GpmlParser().createGraph(fis);
+
+ assertEquals(1, graph.getLines().size());
+ PolylineData pd = graph.getLines().get(0);
+ assertEquals(3, pd.getPoints().size());
+ assertEquals(0, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSimpleReaction() throws Exception {
+ try {
+
+ String fileName = "testFiles/small/simple_reaction.gpml";
+ FileInputStream fis = new FileInputStream(fileName);
+ Graph graph = new GpmlParser().createGraph(fis);
+
+ Interaction interaction = graph.getInteractions().iterator().next();
+ PolylineData pd = interaction.getLine();
+ assertTrue(pd.getPoints().get(0).distance(476.0, 351.0) < EPSILON);
+ assertTrue(pd.getPoints().get(1).distance(476.0, 286.0) < EPSILON);
+ assertTrue(pd.getPoints().get(2).distance(846.0, 287.0) < EPSILON);
+ assertTrue(pd.getPoints().get(3).distance(846.0, 354.0) < EPSILON);
+
+ assertEquals(0, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/LabelParserTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/LabelParserTest.java
index 29858d4377..711fa381ff 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/LabelParserTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/LabelParserTest.java
@@ -1,72 +1,72 @@
-package lcsb.mapviewer.wikipathway.XML;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.Color;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.w3c.dom.Element;
-
-import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
-import lcsb.mapviewer.wikipathway.model.Label;
-
-public class LabelParserTest extends WikipathwaysTestFunctions {
- LabelParser parser = new LabelParser();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParseLabel() throws Exception {
- try {
- Element node = fileToNode("testFiles/elements/label.xml");
- Label label = parser.parse(node);
- assertNotNull(label);
-
- assertEquals("Label 2", label.getTextLabel());
- assertEquals("edf06", label.getGraphId());
- assertEquals(2, label.getBiopaxReference().size());
- assertEquals("b38", label.getBiopaxReference().get(1));
-
- assertEquals((Integer) 28672, label.getzOrder());
- assertEquals((Double) 10.0, label.getFontSize());
- assertEquals("Middle", label.getvAlign());
- assertTrue(label.getComments().contains("comment 2"));
- assertEquals(Color.WHITE, label.getFillColor());
- assertEquals(Color.BLACK, label.getColor());
-
- assertEquals(0, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseGraphics() throws Exception {
- try {
- Element node = fileToNode("testFiles/elements/label_graphics.xml");
-
- Label label = new Label("test");
- parser.parseGraphics(node, label);
- assertNotNull(label);
-
- assertEquals(0, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.wikipathway.XML;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import java.awt.Color;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.w3c.dom.Element;
+
+import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
+import lcsb.mapviewer.wikipathway.model.Label;
+
+public class LabelParserTest extends WikipathwaysTestFunctions {
+ LabelParser parser = new LabelParser();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testParseLabel() throws Exception {
+ try {
+ Element node = fileToNode("testFiles/elements/label.xml");
+ Label label = parser.parse(node);
+ assertNotNull(label);
+
+ assertEquals("Label 2", label.getTextLabel());
+ assertEquals("edf06", label.getGraphId());
+ assertEquals(2, label.getBiopaxReference().size());
+ assertEquals("b38", label.getBiopaxReference().get(1));
+
+ assertEquals((Integer) 28672, label.getzOrder());
+ assertEquals((Double) 10.0, label.getFontSize());
+ assertEquals("Middle", label.getvAlign());
+ assertTrue(label.getComments().contains("comment 2"));
+ assertEquals(Color.WHITE, label.getFillColor());
+ assertEquals(Color.BLACK, label.getColor());
+
+ assertEquals(0, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseGraphics() throws Exception {
+ try {
+ Element node = fileToNode("testFiles/elements/label_graphics.xml");
+
+ Label label = new Label("test");
+ parser.parseGraphics(node, label);
+ assertNotNull(label);
+
+ assertEquals(0, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelContructorTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelContructorTest.java
index 13c333a812..a23566e038 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelContructorTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelContructorTest.java
@@ -1,45 +1,45 @@
-package lcsb.mapviewer.wikipathway.XML;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-
-import java.awt.geom.Point2D;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.model.graphics.PolylineData;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ModelContructorTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void test() {
- try {
- Point2D p1 = new Point2D.Double(1455.5988605049254, 562.0578193221613);
- Point2D p2 = new Point2D.Double(1455.5988605049254, 562.0578193221613);
- PolylineData pd = new PolylineData(p1, p2);
-
- ModelContructor mc = new ModelContructor();
- Pair<PolylineData,PolylineData> result = mc.splitPolyline(pd);
- assertNotNull(result);
- assertNotNull(result.getLeft());
- assertNotNull(result.getRight());
- assertEquals(2, result.getLeft().getPoints().size());
- assertEquals(2, result.getRight().getPoints().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.wikipathway.XML;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import java.awt.geom.Point2D;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.model.graphics.PolylineData;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ModelContructorTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void test() {
+ try {
+ Point2D p1 = new Point2D.Double(1455.5988605049254, 562.0578193221613);
+ Point2D p2 = new Point2D.Double(1455.5988605049254, 562.0578193221613);
+ PolylineData pd = new PolylineData(p1, p2);
+
+ ModelContructor mc = new ModelContructor();
+ Pair<PolylineData,PolylineData> result = mc.splitPolyline(pd);
+ assertNotNull(result);
+ assertNotNull(result.getLeft());
+ assertNotNull(result.getRight());
+ assertEquals(2, result.getLeft().getPoints().size());
+ assertEquals(2, result.getRight().getPoints().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelToGPMLTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelToGPMLTest.java
index 82c58720f5..4f58af9d75 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelToGPMLTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelToGPMLTest.java
@@ -1,94 +1,94 @@
-package lcsb.mapviewer.wikipathway.XML;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.io.ByteArrayInputStream;
-import java.nio.charset.StandardCharsets;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
-
-public class ModelToGPMLTest extends WikipathwaysTestFunctions {
- Logger logger = Logger.getLogger(ModelToGPMLTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void test() throws Exception {
- try {
- ModelToGPML parser = new ModelToGPML();
- CellDesignerXmlParser cellDesignerXmlParser = new CellDesignerXmlParser();
- Model model = cellDesignerXmlParser.createModel(new ConverterParams().filename("testFiles/other_full/GSTP1 subnetwork_220214.xml"));
- String xml = parser.getGPML(model);
- assertNotNull(xml);
- assertEquals(10, getWarnings().size());
-
- Model model2 = new GPMLToModel().getModel(new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8)));
- assertNotNull(model2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAnnotations() throws Exception {
- try {
- ModelToGPML parser = new ModelToGPML();
-
- Model model = new ModelFullIndexed(null);
- model.setWidth(1000);
- model.setHeight(1000);
-
- GenericProtein alias = new GenericProtein("sa");
- alias.setName("s2");
- alias.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
- alias.addMiriamData(new MiriamData(MiriamType.PUBMED, "123"));
- alias.addMiriamData(new MiriamData(MiriamType.PUBMED, "1234"));
- alias.setWidth(10);
- alias.setHeight(10);
- alias.setX(1);
- alias.setY(1);
-
- model.addElement(alias);
-
- String xml = parser.getGPML(model);
- assertNotNull(xml);
- assertEquals(0, getWarnings().size());
-
- Model model2 = new GPMLToModel().getModel(new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8)));
-
- Element p = model2.getElementByElementId("sa");
-
- assertEquals(alias.getMiriamData().size(), p.getMiriamData().size());
- for (MiriamData md : p.getMiriamData()) {
- assertTrue(alias.getMiriamData().contains(md));
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.wikipathway.XML;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import java.io.ByteArrayInputStream;
+import java.nio.charset.StandardCharsets;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
+
+public class ModelToGPMLTest extends WikipathwaysTestFunctions {
+ Logger logger = Logger.getLogger(ModelToGPMLTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void test() throws Exception {
+ try {
+ ModelToGPML parser = new ModelToGPML();
+ CellDesignerXmlParser cellDesignerXmlParser = new CellDesignerXmlParser();
+ Model model = cellDesignerXmlParser.createModel(new ConverterParams().filename("testFiles/other_full/GSTP1 subnetwork_220214.xml"));
+ String xml = parser.getGPML(model);
+ assertNotNull(xml);
+ assertEquals(10, getWarnings().size());
+
+ Model model2 = new GPMLToModel().getModel(new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8)));
+ assertNotNull(model2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotations() throws Exception {
+ try {
+ ModelToGPML parser = new ModelToGPML();
+
+ Model model = new ModelFullIndexed(null);
+ model.setWidth(1000);
+ model.setHeight(1000);
+
+ GenericProtein alias = new GenericProtein("sa");
+ alias.setName("s2");
+ alias.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
+ alias.addMiriamData(new MiriamData(MiriamType.PUBMED, "123"));
+ alias.addMiriamData(new MiriamData(MiriamType.PUBMED, "1234"));
+ alias.setWidth(10);
+ alias.setHeight(10);
+ alias.setX(1);
+ alias.setY(1);
+
+ model.addElement(alias);
+
+ String xml = parser.getGPML(model);
+ assertNotNull(xml);
+ assertEquals(0, getWarnings().size());
+
+ Model model2 = new GPMLToModel().getModel(new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8)));
+
+ Element p = model2.getElementByElementId("sa");
+
+ assertEquals(alias.getMiriamData().size(), p.getMiriamData().size());
+ for (MiriamData md : p.getMiriamData()) {
+ assertTrue(alias.getMiriamData().contains(md));
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ReferenceParserTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ReferenceParserTest.java
index 90b6a8c53b..a373252702 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ReferenceParserTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ReferenceParserTest.java
@@ -1,158 +1,158 @@
-package lcsb.mapviewer.wikipathway.XML;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.w3c.dom.Element;
-import org.w3c.dom.Node;
-
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
-
-public class ReferenceParserTest extends WikipathwaysTestFunctions {
- Logger logger = Logger.getLogger(ReferenceParserTest.class);
-
- ReferenceParser mc = new ReferenceParser();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testCreateHmdbMiriam() {
- MiriamData md = mc.createMiriamData("HMDB03791", "HMDB");
- assertNotNull(md);
- }
-
- @Test
- public void testCreateWormBaseMiriam() {
- MiriamData md = mc.createMiriamData("WormBase", "WormBase");
- assertNotNull(md);
- }
-
- @Test
- public void testSgdMiriam() {
- MiriamData md = mc.createMiriamData("S000028457", "SGD");
- assertNotNull(md);
- }
-
- @Test
- public void testWikidataMiriam() {
- MiriamData md = mc.createMiriamData("Q15623825", "Wikidata");
- assertNotNull(md);
- }
-
- @Test
- public void testCreateEnsemblPlantMiriam() {
- MiriamData md = mc.createMiriamData("AT3G18550", "Ensembl Plants");
- assertNotNull(md);
- }
-
- @Test
- public void testCreateCasMiriam() {
- MiriamData md = mc.createMiriamData("657-24-9", "CAS");
- assertNotNull(md);
- }
-
- @Test
- public void testCreateGenBankMiriam() {
- MiriamData md = mc.createMiriamData("123", "GenBank");
- assertNotNull(md);
- }
-
- @Test
- public void testCreatePubchemMiriam() {
- MiriamData md = mc.createMiriamData("39484", "pubchem.compound");
- assertNotNull(md);
- }
-
- @Test
- public void testCreateWikipediaMiriam() {
- MiriamData md = mc.createMiriamData("Reactive_oxygen_species", "Wikipedia");
- assertNotNull(md);
- }
-
- @Test
- public void testCreateKeggOrthologyMiriam() throws Exception {
- try {
- MiriamData md = mc.createMiriamData("K00114", "Kegg ortholog");
- assertNotNull(md);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testChemSpiderMiriam() throws Exception {
- try {
- MiriamData md = mc.createMiriamData("110354", "Chemspider");
- assertNotNull(md);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testPfamMiriam() throws Exception {
- try {
- MiriamData md = mc.createMiriamData("PF00071", "Pfam");
- assertNotNull(md);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testMiRBaseMiriam() throws Exception {
- try {
- MiriamData md = mc.createMiriamData("MI0000750", "miRBase");
- assertNotNull(md);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParse() throws Exception {
- try {
- Node node = super.getXmlDocumentFromFile("testFiles/elements/xref.xml");
- MiriamData md = mc.parse((Element) node.getFirstChild());
- assertNotNull(md);
- assertEquals(md, new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
- assertEquals(0, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXml() throws Exception {
- try {
- MiriamData md = new MiriamData(MiriamType.CHEBI, "CHEBI:123");
- String xml = mc.toXml(md);
-
- Node node = super.getNodeFromXmlString(xml);
- MiriamData md2 = mc.parse((Element) node);
- assertNotNull(md);
- assertEquals(md, md2);
- assertEquals(0, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.wikipathway.XML;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.w3c.dom.Element;
+import org.w3c.dom.Node;
+
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
+
+public class ReferenceParserTest extends WikipathwaysTestFunctions {
+ Logger logger = Logger.getLogger(ReferenceParserTest.class);
+
+ ReferenceParser mc = new ReferenceParser();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testCreateHmdbMiriam() {
+ MiriamData md = mc.createMiriamData("HMDB03791", "HMDB");
+ assertNotNull(md);
+ }
+
+ @Test
+ public void testCreateWormBaseMiriam() {
+ MiriamData md = mc.createMiriamData("WormBase", "WormBase");
+ assertNotNull(md);
+ }
+
+ @Test
+ public void testSgdMiriam() {
+ MiriamData md = mc.createMiriamData("S000028457", "SGD");
+ assertNotNull(md);
+ }
+
+ @Test
+ public void testWikidataMiriam() {
+ MiriamData md = mc.createMiriamData("Q15623825", "Wikidata");
+ assertNotNull(md);
+ }
+
+ @Test
+ public void testCreateEnsemblPlantMiriam() {
+ MiriamData md = mc.createMiriamData("AT3G18550", "Ensembl Plants");
+ assertNotNull(md);
+ }
+
+ @Test
+ public void testCreateCasMiriam() {
+ MiriamData md = mc.createMiriamData("657-24-9", "CAS");
+ assertNotNull(md);
+ }
+
+ @Test
+ public void testCreateGenBankMiriam() {
+ MiriamData md = mc.createMiriamData("123", "GenBank");
+ assertNotNull(md);
+ }
+
+ @Test
+ public void testCreatePubchemMiriam() {
+ MiriamData md = mc.createMiriamData("39484", "pubchem.compound");
+ assertNotNull(md);
+ }
+
+ @Test
+ public void testCreateWikipediaMiriam() {
+ MiriamData md = mc.createMiriamData("Reactive_oxygen_species", "Wikipedia");
+ assertNotNull(md);
+ }
+
+ @Test
+ public void testCreateKeggOrthologyMiriam() throws Exception {
+ try {
+ MiriamData md = mc.createMiriamData("K00114", "Kegg ortholog");
+ assertNotNull(md);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testChemSpiderMiriam() throws Exception {
+ try {
+ MiriamData md = mc.createMiriamData("110354", "Chemspider");
+ assertNotNull(md);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testPfamMiriam() throws Exception {
+ try {
+ MiriamData md = mc.createMiriamData("PF00071", "Pfam");
+ assertNotNull(md);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testMiRBaseMiriam() throws Exception {
+ try {
+ MiriamData md = mc.createMiriamData("MI0000750", "miRBase");
+ assertNotNull(md);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParse() throws Exception {
+ try {
+ Node node = super.getXmlDocumentFromFile("testFiles/elements/xref.xml");
+ MiriamData md = mc.parse((Element) node.getFirstChild());
+ assertNotNull(md);
+ assertEquals(md, new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
+ assertEquals(0, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXml() throws Exception {
+ try {
+ MiriamData md = new MiriamData(MiriamType.CHEBI, "CHEBI:123");
+ String xml = mc.toXml(md);
+
+ Node node = super.getNodeFromXmlString(xml);
+ MiriamData md2 = mc.parse((Element) node);
+ assertNotNull(md);
+ assertEquals(md, md2);
+ assertEquals(0, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ShapeParserTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ShapeParserTest.java
index 9240b59dac..20b89ad10a 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ShapeParserTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ShapeParserTest.java
@@ -1,215 +1,215 @@
-package lcsb.mapviewer.wikipathway.XML;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.Color;
-
-import org.junit.After;
-import org.junit.Test;
-import org.w3c.dom.Element;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
-import lcsb.mapviewer.wikipathway.model.Shape;
-
-public class ShapeParserTest extends WikipathwaysTestFunctions {
- ShapeParser parser = new ShapeParser();
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParseArc() throws Exception {
- try {
- Element node = fileToNode("testFiles/elements/arc.xml");
- Shape shape = parser.parse(node);
- assertNotNull(shape);
-
- assertEquals("arc l", shape.getTextLabel());
- assertEquals("d3af4", shape.getGraphId());
- assertEquals((Integer) 16384, shape.getzOrder());
- assertEquals((Double) 10.0, shape.getFontSize());
- assertEquals("Middle", shape.getvAlign());
- assertEquals("Arc", shape.getShape());
- assertEquals((Double) 0.0, shape.getRotation());
- assertTrue(shape.getComments().contains("arc c"));
- assertTrue(shape.getComments().contains("Type your comment here"));
-
- assertEquals(0, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseBrace() throws Exception {
- try {
- Element node = fileToNode("testFiles/elements/brace.xml");
- Shape shape = parser.parse(node);
- assertNotNull(shape);
-
- assertEquals("dfdfs fds ", shape.getTextLabel());
- assertEquals("eb55e", shape.getGraphId());
- assertEquals(1, shape.getBiopaxReference().size());
- assertEquals("d04", shape.getBiopaxReference().get(0));
-
- assertEquals((Integer) 16384, shape.getzOrder());
- assertEquals((Double) 10.0, shape.getFontSize());
- assertEquals("Middle", shape.getvAlign());
- assertEquals("Brace", shape.getShape());
- assertEquals((Double) 0.44830711094422787, shape.getRotation(), Configuration.EPSILON);
- assertTrue(shape.getComments().contains("1"));
- assertTrue(shape.getComments().contains("Type your comment here"));
-
- assertEquals(0, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseCompartment() throws Exception {
- try {
- Element node = fileToNode("testFiles/elements/compartment.xml");
- Shape shape = parser.parse(node);
- assertNotNull(shape);
-
- assertEquals("compartment title", shape.getTextLabel());
- assertEquals("c5869", shape.getGraphId());
- assertEquals(1, shape.getBiopaxReference().size());
- assertEquals("b80", shape.getBiopaxReference().get(0));
-
- assertEquals((Integer) 16384, shape.getzOrder());
- assertEquals((Double) 10.0, shape.getFontSize());
- assertEquals((Double) 3.0, shape.getLineThickness());
- assertEquals(LineType.DOUBLE, shape.getLineType());
- assertEquals("Middle", shape.getvAlign());
- assertEquals("RoundedRectangle", shape.getShape());
- assertEquals((Double) 0.0, shape.getRotation(), Configuration.EPSILON);
- assertTrue(shape.getComments().contains("compartment comment here"));
- assertTrue(shape.getComments().contains("Type your comment here"));
- assertTrue(shape.isCompartment());
- assertEquals(Color.LIGHT_GRAY, shape.getColor());
-
- assertEquals(0, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseDegraded() throws Exception {
- try {
- Element node = fileToNode("testFiles/elements/degraded.xml");
- Shape shape = parser.parse(node);
- assertNotNull(shape);
-
- assertEquals(0, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseHex() throws Exception {
- try {
- Element node = fileToNode("testFiles/elements/hex.xml");
- Shape shape = parser.parse(node);
- assertNotNull(shape);
-
- assertEquals(0, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseOval() throws Exception {
- try {
- Element node = fileToNode("testFiles/elements/oval.xml");
- Shape shape = parser.parse(node);
- assertNotNull(shape);
-
- assertEquals(0, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParsePent() throws Exception {
- try {
- Element node = fileToNode("testFiles/elements/pent.xml");
- Shape shape = parser.parse(node);
- assertNotNull(shape);
-
- assertEquals(0, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseRect() throws Exception {
- try {
- Element node = fileToNode("testFiles/elements/rect.xml");
- Shape shape = parser.parse(node);
- assertNotNull(shape);
-
- assertEquals(0, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseRoundedREct() throws Exception {
- try {
- Element node = fileToNode("testFiles/elements/rounded_rect.xml");
- Shape shape = parser.parse(node);
- assertNotNull(shape);
-
- assertEquals(0, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseTriangle() throws Exception {
- try {
- Element node = fileToNode("testFiles/elements/triangle.xml");
- Shape shape = parser.parse(node);
- assertNotNull(shape);
-
- assertEquals(0, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.wikipathway.XML;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import java.awt.Color;
+
+import org.junit.After;
+import org.junit.Test;
+import org.w3c.dom.Element;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
+import lcsb.mapviewer.wikipathway.model.Shape;
+
+public class ShapeParserTest extends WikipathwaysTestFunctions {
+ ShapeParser parser = new ShapeParser();
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testParseArc() throws Exception {
+ try {
+ Element node = fileToNode("testFiles/elements/arc.xml");
+ Shape shape = parser.parse(node);
+ assertNotNull(shape);
+
+ assertEquals("arc l", shape.getTextLabel());
+ assertEquals("d3af4", shape.getGraphId());
+ assertEquals((Integer) 16384, shape.getzOrder());
+ assertEquals((Double) 10.0, shape.getFontSize());
+ assertEquals("Middle", shape.getvAlign());
+ assertEquals("Arc", shape.getShape());
+ assertEquals((Double) 0.0, shape.getRotation());
+ assertTrue(shape.getComments().contains("arc c"));
+ assertTrue(shape.getComments().contains("Type your comment here"));
+
+ assertEquals(0, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseBrace() throws Exception {
+ try {
+ Element node = fileToNode("testFiles/elements/brace.xml");
+ Shape shape = parser.parse(node);
+ assertNotNull(shape);
+
+ assertEquals("dfdfs fds ", shape.getTextLabel());
+ assertEquals("eb55e", shape.getGraphId());
+ assertEquals(1, shape.getBiopaxReference().size());
+ assertEquals("d04", shape.getBiopaxReference().get(0));
+
+ assertEquals((Integer) 16384, shape.getzOrder());
+ assertEquals((Double) 10.0, shape.getFontSize());
+ assertEquals("Middle", shape.getvAlign());
+ assertEquals("Brace", shape.getShape());
+ assertEquals((Double) 0.44830711094422787, shape.getRotation(), Configuration.EPSILON);
+ assertTrue(shape.getComments().contains("1"));
+ assertTrue(shape.getComments().contains("Type your comment here"));
+
+ assertEquals(0, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseCompartment() throws Exception {
+ try {
+ Element node = fileToNode("testFiles/elements/compartment.xml");
+ Shape shape = parser.parse(node);
+ assertNotNull(shape);
+
+ assertEquals("compartment title", shape.getTextLabel());
+ assertEquals("c5869", shape.getGraphId());
+ assertEquals(1, shape.getBiopaxReference().size());
+ assertEquals("b80", shape.getBiopaxReference().get(0));
+
+ assertEquals((Integer) 16384, shape.getzOrder());
+ assertEquals((Double) 10.0, shape.getFontSize());
+ assertEquals((Double) 3.0, shape.getLineThickness());
+ assertEquals(LineType.DOUBLE, shape.getLineType());
+ assertEquals("Middle", shape.getvAlign());
+ assertEquals("RoundedRectangle", shape.getShape());
+ assertEquals((Double) 0.0, shape.getRotation(), Configuration.EPSILON);
+ assertTrue(shape.getComments().contains("compartment comment here"));
+ assertTrue(shape.getComments().contains("Type your comment here"));
+ assertTrue(shape.isCompartment());
+ assertEquals(Color.LIGHT_GRAY, shape.getColor());
+
+ assertEquals(0, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseDegraded() throws Exception {
+ try {
+ Element node = fileToNode("testFiles/elements/degraded.xml");
+ Shape shape = parser.parse(node);
+ assertNotNull(shape);
+
+ assertEquals(0, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseHex() throws Exception {
+ try {
+ Element node = fileToNode("testFiles/elements/hex.xml");
+ Shape shape = parser.parse(node);
+ assertNotNull(shape);
+
+ assertEquals(0, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseOval() throws Exception {
+ try {
+ Element node = fileToNode("testFiles/elements/oval.xml");
+ Shape shape = parser.parse(node);
+ assertNotNull(shape);
+
+ assertEquals(0, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParsePent() throws Exception {
+ try {
+ Element node = fileToNode("testFiles/elements/pent.xml");
+ Shape shape = parser.parse(node);
+ assertNotNull(shape);
+
+ assertEquals(0, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseRect() throws Exception {
+ try {
+ Element node = fileToNode("testFiles/elements/rect.xml");
+ Shape shape = parser.parse(node);
+ assertNotNull(shape);
+
+ assertEquals(0, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseRoundedREct() throws Exception {
+ try {
+ Element node = fileToNode("testFiles/elements/rounded_rect.xml");
+ Shape shape = parser.parse(node);
+ assertNotNull(shape);
+
+ assertEquals(0, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseTriangle() throws Exception {
+ try {
+ Element node = fileToNode("testFiles/elements/triangle.xml");
+ Shape shape = parser.parse(node);
+ assertNotNull(shape);
+
+ assertEquals(0, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/StateParserTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/StateParserTest.java
index 8cf9a8c01a..7c85b7c646 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/StateParserTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/StateParserTest.java
@@ -1,44 +1,44 @@
-package lcsb.mapviewer.wikipathway.XML;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.Test;
-import org.w3c.dom.Element;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.model.map.species.field.ModificationState;
-import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
-import lcsb.mapviewer.wikipathway.model.State;
-
-public class StateParserTest extends WikipathwaysTestFunctions {
- StateParser parser = new StateParser();
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParseState() throws Exception {
- try {
- Element node = fileToNode("testFiles/elements/state.xml");
- State state = parser.parse(node);
- assertNotNull(state);
-
- assertEquals(ModificationState.PHOSPHORYLATED, state.getType());
- assertEquals("e7637", state.getGraphId());
- assertEquals(1.0, state.getRelX(), Configuration.EPSILON);
- assertEquals(-0.9978969505783312, state.getRelY(), Configuration.EPSILON);
- assertEquals(15.0, state.getWidth(), Configuration.EPSILON);
- assertEquals(15.0, state.getHeight(), Configuration.EPSILON);
- assertEquals("Oval", state.getShape());
- assertEquals(0, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.wikipathway.XML;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.After;
+import org.junit.Test;
+import org.w3c.dom.Element;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
+import lcsb.mapviewer.wikipathway.model.State;
+
+public class StateParserTest extends WikipathwaysTestFunctions {
+ StateParser parser = new StateParser();
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testParseState() throws Exception {
+ try {
+ Element node = fileToNode("testFiles/elements/state.xml");
+ State state = parser.parse(node);
+ assertNotNull(state);
+
+ assertEquals(ModificationState.PHOSPHORYLATED, state.getType());
+ assertEquals("e7637", state.getGraphId());
+ assertEquals(1.0, state.getRelX(), Configuration.EPSILON);
+ assertEquals(-0.9978969505783312, state.getRelY(), Configuration.EPSILON);
+ assertEquals(15.0, state.getWidth(), Configuration.EPSILON);
+ assertEquals(15.0, state.getHeight(), Configuration.EPSILON);
+ assertEquals("Oval", state.getShape());
+ assertEquals(0, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/AllModelTests.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/AllModelTests.java
index a43cf5d452..9a4e932e88 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/AllModelTests.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/AllModelTests.java
@@ -1,22 +1,22 @@
-package lcsb.mapviewer.wikipathway.model;
-
-import lcsb.mapviewer.wikipathway.model.biopax.AllBiopaxTests;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AllBiopaxTests.class,//
- DataNodeTest.class,//
- EdgeTest.class,//
- GraphTest.class,//
- GroupTest.class,//
- InteractionTest.class,//
- LabelTest.class,//
- PointDataTest.class,//
- ShapeTest.class,//
- StateTest.class })
-public class AllModelTests {
-
-}
+package lcsb.mapviewer.wikipathway.model;
+
+import lcsb.mapviewer.wikipathway.model.biopax.AllBiopaxTests;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AllBiopaxTests.class,//
+ DataNodeTest.class,//
+ EdgeTest.class,//
+ GraphTest.class,//
+ GroupTest.class,//
+ InteractionTest.class,//
+ LabelTest.class,//
+ PointDataTest.class,//
+ ShapeTest.class,//
+ StateTest.class })
+public class AllModelTests {
+
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/DataNodeTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/DataNodeTest.java
index 8cb212afc2..473dc07d11 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/DataNodeTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/DataNodeTest.java
@@ -1,27 +1,27 @@
-package lcsb.mapviewer.wikipathway.model;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class DataNodeTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
- @Test
- public void testSeialization() {
- try {
- SerializationUtils.serialize(new DataNode());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.wikipathway.model;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class DataNodeTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+ @Test
+ public void testSeialization() {
+ try {
+ SerializationUtils.serialize(new DataNode());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/EdgeTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/EdgeTest.java
index 0321563f0d..4590ce4a22 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/EdgeTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/EdgeTest.java
@@ -1,27 +1,27 @@
-package lcsb.mapviewer.wikipathway.model;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class EdgeTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
- @Test
- public void testSeialization() {
- try {
- SerializationUtils.serialize(new Edge());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.wikipathway.model;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class EdgeTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+ @Test
+ public void testSeialization() {
+ try {
+ SerializationUtils.serialize(new Edge());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/GraphTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/GraphTest.java
index f8e27eb0f6..3796974d25 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/GraphTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/GraphTest.java
@@ -1,28 +1,28 @@
-package lcsb.mapviewer.wikipathway.model;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class GraphTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSeialization() {
- try {
- SerializationUtils.serialize(new Graph());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.wikipathway.model;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class GraphTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSeialization() {
+ try {
+ SerializationUtils.serialize(new Graph());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/GroupTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/GroupTest.java
index 4ad055eaea..1bfb56fe8d 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/GroupTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/GroupTest.java
@@ -1,27 +1,27 @@
-package lcsb.mapviewer.wikipathway.model;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class GroupTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
- @Test
- public void testSeialization() {
- try {
- SerializationUtils.serialize(new Group());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.wikipathway.model;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class GroupTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+ @Test
+ public void testSeialization() {
+ try {
+ SerializationUtils.serialize(new Group());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/InteractionTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/InteractionTest.java
index a768747cd6..7ad63cc099 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/InteractionTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/InteractionTest.java
@@ -1,27 +1,27 @@
-package lcsb.mapviewer.wikipathway.model;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class InteractionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
- @Test
- public void testSeialization() {
- try {
- SerializationUtils.serialize(new Interaction());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.wikipathway.model;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class InteractionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+ @Test
+ public void testSeialization() {
+ try {
+ SerializationUtils.serialize(new Interaction());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/LabelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/LabelTest.java
index c634f88a3a..9bef316064 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/LabelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/LabelTest.java
@@ -1,27 +1,27 @@
-package lcsb.mapviewer.wikipathway.model;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class LabelTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
- @Test
- public void testSeialization() {
- try {
- SerializationUtils.serialize(new Label());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.wikipathway.model;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class LabelTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+ @Test
+ public void testSeialization() {
+ try {
+ SerializationUtils.serialize(new Label());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/PointDataTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/PointDataTest.java
index 6591d93bfd..f9a69ce69f 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/PointDataTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/PointDataTest.java
@@ -1,27 +1,27 @@
-package lcsb.mapviewer.wikipathway.model;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class PointDataTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
- @Test
- public void testSeialization() {
- try {
- SerializationUtils.serialize(new PointData());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.wikipathway.model;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class PointDataTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+ @Test
+ public void testSeialization() {
+ try {
+ SerializationUtils.serialize(new PointData());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/ShapeTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/ShapeTest.java
index be34cddc14..7fef931aa3 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/ShapeTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/ShapeTest.java
@@ -1,27 +1,27 @@
-package lcsb.mapviewer.wikipathway.model;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ShapeTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
- @Test
- public void testSeialization() {
- try {
- SerializationUtils.serialize(new Shape());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.wikipathway.model;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ShapeTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+ @Test
+ public void testSeialization() {
+ try {
+ SerializationUtils.serialize(new Shape());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/StateTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/StateTest.java
index 6de71bd52c..bf38be3dc1 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/StateTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/StateTest.java
@@ -1,27 +1,27 @@
-package lcsb.mapviewer.wikipathway.model;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class StateTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
- @Test
- public void testSeialization() {
- try {
- SerializationUtils.serialize(new State());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.wikipathway.model;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class StateTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+ @Test
+ public void testSeialization() {
+ try {
+ SerializationUtils.serialize(new State());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/biopax/AllBiopaxTests.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/biopax/AllBiopaxTests.java
index 47ac53ab75..7962c204a2 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/biopax/AllBiopaxTests.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/biopax/AllBiopaxTests.java
@@ -1,11 +1,11 @@
-package lcsb.mapviewer.wikipathway.model.biopax;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ BiopaxDataTest.class, BiopaxOpenControlledVocabularyTest.class, BiopaxPublicationTest.class })
-public class AllBiopaxTests {
-
-}
+package lcsb.mapviewer.wikipathway.model.biopax;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ BiopaxDataTest.class, BiopaxOpenControlledVocabularyTest.class, BiopaxPublicationTest.class })
+public class AllBiopaxTests {
+
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxDataTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxDataTest.java
index a984bcb4ad..e3e3b7bc43 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxDataTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxDataTest.java
@@ -1,28 +1,28 @@
-package lcsb.mapviewer.wikipathway.model.biopax;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class BiopaxDataTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSeialization() {
- try {
- SerializationUtils.serialize(new BiopaxData());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.wikipathway.model.biopax;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class BiopaxDataTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSeialization() {
+ try {
+ SerializationUtils.serialize(new BiopaxData());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxOpenControlledVocabularyTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxOpenControlledVocabularyTest.java
index dbcc6545fc..c8596e88d0 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxOpenControlledVocabularyTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxOpenControlledVocabularyTest.java
@@ -1,28 +1,28 @@
-package lcsb.mapviewer.wikipathway.model.biopax;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class BiopaxOpenControlledVocabularyTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSeialization() {
- try {
- SerializationUtils.serialize(new BiopaxOpenControlledVocabulary());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.wikipathway.model.biopax;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class BiopaxOpenControlledVocabularyTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSeialization() {
+ try {
+ SerializationUtils.serialize(new BiopaxOpenControlledVocabulary());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxPublicationTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxPublicationTest.java
index d83ff0950e..044fc16215 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxPublicationTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxPublicationTest.java
@@ -1,28 +1,28 @@
-package lcsb.mapviewer.wikipathway.model.biopax;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class BiopaxPublicationTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSeialization() {
- try {
- SerializationUtils.serialize(new BiopaxPublication());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.wikipathway.model.biopax;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class BiopaxPublicationTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSeialization() {
+ try {
+ SerializationUtils.serialize(new BiopaxPublication());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/ApplicationContextLoader.java b/persist/src/main/java/lcsb/mapviewer/persist/ApplicationContextLoader.java
index 71d3fc1b01..5d898b0ee0 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/ApplicationContextLoader.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/ApplicationContextLoader.java
@@ -1,76 +1,76 @@
-package lcsb.mapviewer.persist;
-
-import org.springframework.beans.factory.config.AutowireCapableBeanFactory;
-import org.springframework.context.ConfigurableApplicationContext;
-import org.springframework.context.support.ClassPathXmlApplicationContext;
-
-/**
- * Bootstraps Spring-managed beans into an application. How to use:
- * <ul>
- * <li>Create application context XML configuration files and put them where
- * they can be loaded as class path resources. The configuration must include
- * the {@code <context:annotation-config/>} element to enable annotation-based
- * configuration, or the {@code <context:component-scan base-package="..."/>}
- * element to also detect bean definitions from annotated classes.
- * <li>Create a "main" class that will receive references to Spring-managed
- * beans. Add the {@code @Autowired} annotation to any properties you want to be
- * injected with beans from the application context.
- * <li>In your application {@code main} method, create an
- * {@link ApplicationContextLoader} instance, and call the {@link #load} method
- * with the "main" object and the configuration file locations as parameters.
- * </ul>
- */
-public final class ApplicationContextLoader {
-
- /**
- * Application context used by the application.
- */
- private static ConfigurableApplicationContext applicationContext;
-
- /**
- * Default constructor. Prevents instatiation.
- */
- private ApplicationContextLoader() {
-
- }
-
- /**
- *
- * @return {@link #applicationContext}
- */
- public static ConfigurableApplicationContext getApplicationContext() {
- return applicationContext;
- }
-
- /**
- * Loads application context. Override this method to change how the
- * application context is loaded.
- *
- * @param configLocations
- * configuration file locations
- */
- public static void loadApplicationContext(String... configLocations) {
- applicationContext = new ClassPathXmlApplicationContext(configLocations);
- applicationContext.registerShutdownHook();
- }
-
- /**
- * Injects dependencies into the object. Override this method if you need full
- * control over how dependencies are injected.
- *
- * @param main
- * object to inject dependencies into
- */
- public static void injectDependencies(Object main) {
- getApplicationContext().getBeanFactory().autowireBeanProperties(main, AutowireCapableBeanFactory.AUTOWIRE_NO, false);
- }
-
- /**
- *
- * @param applicationContext
- * {@link #applicationContext} to set
- */
- public static void setApplicationContext(ConfigurableApplicationContext applicationContext) {
- ApplicationContextLoader.applicationContext = applicationContext;
- }
+package lcsb.mapviewer.persist;
+
+import org.springframework.beans.factory.config.AutowireCapableBeanFactory;
+import org.springframework.context.ConfigurableApplicationContext;
+import org.springframework.context.support.ClassPathXmlApplicationContext;
+
+/**
+ * Bootstraps Spring-managed beans into an application. How to use:
+ * <ul>
+ * <li>Create application context XML configuration files and put them where
+ * they can be loaded as class path resources. The configuration must include
+ * the {@code <context:annotation-config/>} element to enable annotation-based
+ * configuration, or the {@code <context:component-scan base-package="..."/>}
+ * element to also detect bean definitions from annotated classes.
+ * <li>Create a "main" class that will receive references to Spring-managed
+ * beans. Add the {@code @Autowired} annotation to any properties you want to be
+ * injected with beans from the application context.
+ * <li>In your application {@code main} method, create an
+ * {@link ApplicationContextLoader} instance, and call the {@link #load} method
+ * with the "main" object and the configuration file locations as parameters.
+ * </ul>
+ */
+public final class ApplicationContextLoader {
+
+ /**
+ * Application context used by the application.
+ */
+ private static ConfigurableApplicationContext applicationContext;
+
+ /**
+ * Default constructor. Prevents instatiation.
+ */
+ private ApplicationContextLoader() {
+
+ }
+
+ /**
+ *
+ * @return {@link #applicationContext}
+ */
+ public static ConfigurableApplicationContext getApplicationContext() {
+ return applicationContext;
+ }
+
+ /**
+ * Loads application context. Override this method to change how the
+ * application context is loaded.
+ *
+ * @param configLocations
+ * configuration file locations
+ */
+ public static void loadApplicationContext(String... configLocations) {
+ applicationContext = new ClassPathXmlApplicationContext(configLocations);
+ applicationContext.registerShutdownHook();
+ }
+
+ /**
+ * Injects dependencies into the object. Override this method if you need full
+ * control over how dependencies are injected.
+ *
+ * @param main
+ * object to inject dependencies into
+ */
+ public static void injectDependencies(Object main) {
+ getApplicationContext().getBeanFactory().autowireBeanProperties(main, AutowireCapableBeanFactory.AUTOWIRE_NO, false);
+ }
+
+ /**
+ *
+ * @param applicationContext
+ * {@link #applicationContext} to set
+ */
+ public static void setApplicationContext(ConfigurableApplicationContext applicationContext) {
+ ApplicationContextLoader.applicationContext = applicationContext;
+ }
}
\ No newline at end of file
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/DbUtils.java b/persist/src/main/java/lcsb/mapviewer/persist/DbUtils.java
index e7d0a0c1a4..6729733e77 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/DbUtils.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/DbUtils.java
@@ -1,312 +1,312 @@
-package lcsb.mapviewer.persist;
-
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Observable;
-
-import javax.management.MBeanServer;
-import javax.management.ObjectName;
-
-import org.apache.log4j.Logger;
-import org.flywaydb.core.Flyway;
-import org.hibernate.SQLQuery;
-import org.hibernate.Session;
-import org.hibernate.SessionFactory;
-import org.hibernate.internal.SessionFactoryImpl;
-import org.hibernate.jmx.StatisticsService;
-import org.hibernate.service.jdbc.connections.internal.DatasourceConnectionProviderImpl;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import com.mchange.v2.c3p0.ComboPooledDataSource;
-
-import lcsb.mapviewer.common.exception.InvalidStateException;
-
-/**
- * This class contains a set of methods that allow to manage hibernate sessions
- * in multi-thread approach. There are two types of sessions used in the system:
- * <ul>
- * <li>default - created and managed by sessionFactory</li>
- * <li>custom - created and managed by this class, used only when new thread is
- * created manualy.</li>
- * </ul>
- * Class extends {@link Observable}. Whenever session is created or closed
- * observers are notified.
- *
- * @author Piotr Gawron
- *
- */
-@SuppressWarnings("deprecation")
-public class DbUtils extends Observable {
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(DbUtils.class);
-
- /**
- * Hibernate session factory.
- */
- @Autowired
- private SessionFactory sessionFactory;
-
- /**
- * Service used for connection statistics.
- */
- private StatisticsService statisticsService;
-
- /**
- * This flag indicates if the object was initialized or not.
- *
- * @see #init()
- */
- private boolean initialized = false;
-
- /**
- * Bean used for statistics.
- */
- private MBeanServer mbeanServer;
-
- /**
- * Static map containing opened custom sessions. This object is also used for
- * synchronization between threads when accessing informations about sessions.
- */
- private static Map<Long, Session> sessionForThread = new HashMap<Long, Session>();
-
- /**
- * This determines if every add/update/delete operation should be flushed (for
- * specific {@link Thread}). There are few drawbacks of this approach:
- * <ol>
- * <li>when autoflushing is set to false, then the data consistency could be
- * broken (even in the same thread/transaction)</li>,
- * <li>we have to automatically take care of the flushing, therefore there might
- * be some problems with long transactions.</li>
- * </ol>
- */
- private static Map<Long, Boolean> autoFlushForThread = new HashMap<>();
-
- /**
- * This method initialize services responsible for statistics.
- */
- private void init() {
- if (!initialized) {
- if (SpringApplicationContext.getApplicationContext().containsBean("mbeanServer")) {
- logger.info("Hibernate statistics turned on");
- mbeanServer = SpringApplicationContext.getApplicationContext().getBean(MBeanServer.class);
- statisticsService = new StatisticsService();
- statisticsService.setSessionFactory(sessionFactory);
- statisticsService.setStatisticsEnabled(true);
- ObjectName objectName;
- try {
- objectName = new ObjectName("org.hibernate:name=HibernateStatistics");
-
- mbeanServer.registerMBean(statisticsService, objectName);
- } catch (Exception e) {
- logger.error(e, e);
- }
- } else {
- logger.info("Hibernate statistics turned off");
- }
- }
- initialized = true;
-
- }
-
- /**
- * Executes sql query given in the parameter.
- *
- * @param query
- * sql query to be executed
- * @return The number of entities updated or deleted.
- */
- public int executeSqlQuery(String query) {
- return executeSqlQuery(query, new HashMap<String, Object>());
- }
-
- /**
- * Executes sql query given in the parameter.
- *
- * @param query
- * sql query to be executed
- * @param params
- * map of parameters used in the query
- * @return The number of entities updated or deleted.
- */
- public int executeSqlQuery(String query, Map<String, Object> params) {
- SQLQuery sqlQuery = getSessionFactory().getCurrentSession().createSQLQuery(query);
-
- for (Entry<String, Object> entry : params.entrySet()) {
- sqlQuery.setParameter(entry.getKey(), entry.getValue());
- }
- return sqlQuery.executeUpdate();
- }
-
- /**
- * Returns hibernate session for current thread.
- *
- * @return session for the current thread
- */
- public Session getSessionForCurrentThread() {
- Long id = Thread.currentThread().getId();
- Session session = null;
- synchronized (sessionForThread) {
- session = sessionForThread.get(id);
- }
- if (session == null) {
- session = sessionFactory.getCurrentSession();
- }
- return session;
- }
-
- /**
- * Closes custom session for current thread.
- */
- public void closeSessionForCurrentThread() {
- Long id = Thread.currentThread().getId();
- Session session = null;
- synchronized (sessionForThread) {
- session = sessionForThread.get(id);
- sessionForThread.remove(id);
- }
- if (session != null) {
- logger.debug("Closing session for thread: " + id);
- session.getTransaction().commit();
-
- session.close();
- int counter = -1;
- synchronized (sessionForThread) {
- sessionForThread.remove(id);
- counter = sessionForThread.size();
- }
- synchronized (autoFlushForThread) {
- autoFlushForThread.remove(id);
- }
- setChanged();
- notifyObservers(counter);
- logger.debug("Session closed for thread: " + id);
- }
- }
-
- /**
- * Creates custom session for current thread.
- */
- public void createSessionForCurrentThread() {
- Long id = Thread.currentThread().getId();
- Session session = null;
- synchronized (sessionForThread) {
- session = sessionForThread.get(id);
- if (!initialized) {
- init();
- }
- }
-
- // we cannot create two threads for one session
- if (session != null) {
- throw new InvalidStateException("Current thread already has an active session");
- } else {
- logger.debug("Creating session for thread: " + id);
- session = sessionFactory.openSession();
- logger.debug("Session opened: " + id);
- session.beginTransaction();
- logger.debug("Session started: " + id);
- if (statisticsService != null) {
- logger.debug("Opened sessions: " + statisticsService.getSessionOpenCount() + ". Closed sessions: "
- + statisticsService.getSessionCloseCount());
- }
- Integer counter = -1;
- synchronized (sessionForThread) {
- sessionForThread.put(id, session);
- counter = sessionForThread.size();
- }
- synchronized (autoFlushForThread) {
- autoFlushForThread.put(id, true);
- }
- setChanged();
- notifyObservers(counter);
- }
- }
-
- /**
- * Returns true if custom session was opened for this thread.
- *
- * @return <code>true</code> if custom session was created for this thread,
- * <code>false</code> otherwise
- */
- public boolean isCustomSessionForCurrentThread() {
- Long id = Thread.currentThread().getId();
- Session session = null;
- synchronized (sessionForThread) {
- session = sessionForThread.get(id);
- }
- return session != null;
-
- }
-
- /**
- * Returns number of opened custom sessions.
- *
- * @return number of sessions
- */
- public int getSessionCounter() {
- int result = -1;
- synchronized (sessionForThread) {
- result = sessionForThread.values().size();
- }
- return result;
- }
-
- /**
- * @return the sessionFactory
- * @see #sessionFactory
- */
- public SessionFactory getSessionFactory() {
- return sessionFactory;
- }
-
- /**
- * @param sessionFactory
- * the sessionFactory to set
- * @see #sessionFactory
- */
- public void setSessionFactory(SessionFactory sessionFactory) {
- this.sessionFactory = sessionFactory;
- }
-
- /**
- * Returns info if the flush is automatically done or not in current
- * {@link Thread}.
- *
- * @return <code>true</code> if flush is automatically done, <code>false</code>
- * otherwise
- * @see #autoFlushForThread
- */
- public boolean isAutoFlush() {
- Long id = Thread.currentThread().getId();
- Boolean result = true;
- synchronized (autoFlushForThread) {
- result = autoFlushForThread.get(id);
- }
- if (result == null) {
- logger.debug("autoFlush not set for thread: " + id + ". Setting true");
- synchronized (autoFlushForThread) {
- autoFlushForThread.put(id, true);
- }
- result = true;
- }
- return result;
- }
-
- /**
- * Set autoFlush for current {@link Thread}.
- *
- * @param autoFlush
- * the new autoflush value
- * @see #autoFlushForThread
- */
- public void setAutoFlush(boolean autoFlush) {
- Long id = Thread.currentThread().getId();
- synchronized (autoFlushForThread) {
- autoFlushForThread.put(id, autoFlush);
- }
- }
-}
+package lcsb.mapviewer.persist;
+
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Observable;
+
+import javax.management.MBeanServer;
+import javax.management.ObjectName;
+
+import org.apache.log4j.Logger;
+import org.flywaydb.core.Flyway;
+import org.hibernate.SQLQuery;
+import org.hibernate.Session;
+import org.hibernate.SessionFactory;
+import org.hibernate.internal.SessionFactoryImpl;
+import org.hibernate.jmx.StatisticsService;
+import org.hibernate.service.jdbc.connections.internal.DatasourceConnectionProviderImpl;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import com.mchange.v2.c3p0.ComboPooledDataSource;
+
+import lcsb.mapviewer.common.exception.InvalidStateException;
+
+/**
+ * This class contains a set of methods that allow to manage hibernate sessions
+ * in multi-thread approach. There are two types of sessions used in the system:
+ * <ul>
+ * <li>default - created and managed by sessionFactory</li>
+ * <li>custom - created and managed by this class, used only when new thread is
+ * created manualy.</li>
+ * </ul>
+ * Class extends {@link Observable}. Whenever session is created or closed
+ * observers are notified.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@SuppressWarnings("deprecation")
+public class DbUtils extends Observable {
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(DbUtils.class);
+
+ /**
+ * Hibernate session factory.
+ */
+ @Autowired
+ private SessionFactory sessionFactory;
+
+ /**
+ * Service used for connection statistics.
+ */
+ private StatisticsService statisticsService;
+
+ /**
+ * This flag indicates if the object was initialized or not.
+ *
+ * @see #init()
+ */
+ private boolean initialized = false;
+
+ /**
+ * Bean used for statistics.
+ */
+ private MBeanServer mbeanServer;
+
+ /**
+ * Static map containing opened custom sessions. This object is also used for
+ * synchronization between threads when accessing informations about sessions.
+ */
+ private static Map<Long, Session> sessionForThread = new HashMap<Long, Session>();
+
+ /**
+ * This determines if every add/update/delete operation should be flushed (for
+ * specific {@link Thread}). There are few drawbacks of this approach:
+ * <ol>
+ * <li>when autoflushing is set to false, then the data consistency could be
+ * broken (even in the same thread/transaction)</li>,
+ * <li>we have to automatically take care of the flushing, therefore there might
+ * be some problems with long transactions.</li>
+ * </ol>
+ */
+ private static Map<Long, Boolean> autoFlushForThread = new HashMap<>();
+
+ /**
+ * This method initialize services responsible for statistics.
+ */
+ private void init() {
+ if (!initialized) {
+ if (SpringApplicationContext.getApplicationContext().containsBean("mbeanServer")) {
+ logger.info("Hibernate statistics turned on");
+ mbeanServer = SpringApplicationContext.getApplicationContext().getBean(MBeanServer.class);
+ statisticsService = new StatisticsService();
+ statisticsService.setSessionFactory(sessionFactory);
+ statisticsService.setStatisticsEnabled(true);
+ ObjectName objectName;
+ try {
+ objectName = new ObjectName("org.hibernate:name=HibernateStatistics");
+
+ mbeanServer.registerMBean(statisticsService, objectName);
+ } catch (Exception e) {
+ logger.error(e, e);
+ }
+ } else {
+ logger.info("Hibernate statistics turned off");
+ }
+ }
+ initialized = true;
+
+ }
+
+ /**
+ * Executes sql query given in the parameter.
+ *
+ * @param query
+ * sql query to be executed
+ * @return The number of entities updated or deleted.
+ */
+ public int executeSqlQuery(String query) {
+ return executeSqlQuery(query, new HashMap<String, Object>());
+ }
+
+ /**
+ * Executes sql query given in the parameter.
+ *
+ * @param query
+ * sql query to be executed
+ * @param params
+ * map of parameters used in the query
+ * @return The number of entities updated or deleted.
+ */
+ public int executeSqlQuery(String query, Map<String, Object> params) {
+ SQLQuery sqlQuery = getSessionFactory().getCurrentSession().createSQLQuery(query);
+
+ for (Entry<String, Object> entry : params.entrySet()) {
+ sqlQuery.setParameter(entry.getKey(), entry.getValue());
+ }
+ return sqlQuery.executeUpdate();
+ }
+
+ /**
+ * Returns hibernate session for current thread.
+ *
+ * @return session for the current thread
+ */
+ public Session getSessionForCurrentThread() {
+ Long id = Thread.currentThread().getId();
+ Session session = null;
+ synchronized (sessionForThread) {
+ session = sessionForThread.get(id);
+ }
+ if (session == null) {
+ session = sessionFactory.getCurrentSession();
+ }
+ return session;
+ }
+
+ /**
+ * Closes custom session for current thread.
+ */
+ public void closeSessionForCurrentThread() {
+ Long id = Thread.currentThread().getId();
+ Session session = null;
+ synchronized (sessionForThread) {
+ session = sessionForThread.get(id);
+ sessionForThread.remove(id);
+ }
+ if (session != null) {
+ logger.debug("Closing session for thread: " + id);
+ session.getTransaction().commit();
+
+ session.close();
+ int counter = -1;
+ synchronized (sessionForThread) {
+ sessionForThread.remove(id);
+ counter = sessionForThread.size();
+ }
+ synchronized (autoFlushForThread) {
+ autoFlushForThread.remove(id);
+ }
+ setChanged();
+ notifyObservers(counter);
+ logger.debug("Session closed for thread: " + id);
+ }
+ }
+
+ /**
+ * Creates custom session for current thread.
+ */
+ public void createSessionForCurrentThread() {
+ Long id = Thread.currentThread().getId();
+ Session session = null;
+ synchronized (sessionForThread) {
+ session = sessionForThread.get(id);
+ if (!initialized) {
+ init();
+ }
+ }
+
+ // we cannot create two threads for one session
+ if (session != null) {
+ throw new InvalidStateException("Current thread already has an active session");
+ } else {
+ logger.debug("Creating session for thread: " + id);
+ session = sessionFactory.openSession();
+ logger.debug("Session opened: " + id);
+ session.beginTransaction();
+ logger.debug("Session started: " + id);
+ if (statisticsService != null) {
+ logger.debug("Opened sessions: " + statisticsService.getSessionOpenCount() + ". Closed sessions: "
+ + statisticsService.getSessionCloseCount());
+ }
+ Integer counter = -1;
+ synchronized (sessionForThread) {
+ sessionForThread.put(id, session);
+ counter = sessionForThread.size();
+ }
+ synchronized (autoFlushForThread) {
+ autoFlushForThread.put(id, true);
+ }
+ setChanged();
+ notifyObservers(counter);
+ }
+ }
+
+ /**
+ * Returns true if custom session was opened for this thread.
+ *
+ * @return <code>true</code> if custom session was created for this thread,
+ * <code>false</code> otherwise
+ */
+ public boolean isCustomSessionForCurrentThread() {
+ Long id = Thread.currentThread().getId();
+ Session session = null;
+ synchronized (sessionForThread) {
+ session = sessionForThread.get(id);
+ }
+ return session != null;
+
+ }
+
+ /**
+ * Returns number of opened custom sessions.
+ *
+ * @return number of sessions
+ */
+ public int getSessionCounter() {
+ int result = -1;
+ synchronized (sessionForThread) {
+ result = sessionForThread.values().size();
+ }
+ return result;
+ }
+
+ /**
+ * @return the sessionFactory
+ * @see #sessionFactory
+ */
+ public SessionFactory getSessionFactory() {
+ return sessionFactory;
+ }
+
+ /**
+ * @param sessionFactory
+ * the sessionFactory to set
+ * @see #sessionFactory
+ */
+ public void setSessionFactory(SessionFactory sessionFactory) {
+ this.sessionFactory = sessionFactory;
+ }
+
+ /**
+ * Returns info if the flush is automatically done or not in current
+ * {@link Thread}.
+ *
+ * @return <code>true</code> if flush is automatically done, <code>false</code>
+ * otherwise
+ * @see #autoFlushForThread
+ */
+ public boolean isAutoFlush() {
+ Long id = Thread.currentThread().getId();
+ Boolean result = true;
+ synchronized (autoFlushForThread) {
+ result = autoFlushForThread.get(id);
+ }
+ if (result == null) {
+ logger.debug("autoFlush not set for thread: " + id + ". Setting true");
+ synchronized (autoFlushForThread) {
+ autoFlushForThread.put(id, true);
+ }
+ result = true;
+ }
+ return result;
+ }
+
+ /**
+ * Set autoFlush for current {@link Thread}.
+ *
+ * @param autoFlush
+ * the new autoflush value
+ * @see #autoFlushForThread
+ */
+ public void setAutoFlush(boolean autoFlush) {
+ Long id = Thread.currentThread().getId();
+ synchronized (autoFlushForThread) {
+ autoFlushForThread.put(id, autoFlush);
+ }
+ }
+}
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/SpringApplicationContext.java b/persist/src/main/java/lcsb/mapviewer/persist/SpringApplicationContext.java
index 9af8f913b6..ee245cee9b 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/SpringApplicationContext.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/SpringApplicationContext.java
@@ -1,65 +1,65 @@
-package lcsb.mapviewer.persist;
-
-import org.apache.log4j.Logger;
-import org.springframework.context.ApplicationContext;
-import org.springframework.context.ApplicationContextAware;
-import org.springframework.transaction.annotation.Transactional;
-
-/**
- * Wrapper to always return a reference to the Spring Application Context from
- * within non-Spring enabled beans. Unlike Spring MVC's
- * WebApplicationContextUtils we do not need a reference to the Servlet context
- * for this. All we need is for this bean to be initialized during application
- * startup.
- */
-@Transactional(value = "txManager")
-public class SpringApplicationContext implements ApplicationContextAware {
-
- /**
- * Default logger for this class.
- */
- private static Logger logger = Logger.getLogger(SpringApplicationContext.class);
-
- /**
- * {@link ApplicationContext} used by the Spring framework.
- */
- private static ApplicationContext context;
-
- /**
- * This method is called from within the ApplicationContext once it is done
- * starting up, it will stick a reference to itself into this bean.
- *
- * @param context
- * a reference to the ApplicationContext.
- */
- @Override
- public void setApplicationContext(ApplicationContext context) {
- logger.debug("Setting application context: " + context.getDisplayName());
- SpringApplicationContext.context = context;
- }
-
- /**
- * This is about the same as context.getBean("beanName"), except it has its
- * own static handle to the Spring context, so calling this method statically
- * will give access to the beans by name in the Spring application context. As
- * in the context.getBean("beanName") call, the caller must cast to the
- * appropriate target class. If the bean does not exist, then a Runtime error
- * will be thrown.
- *
- * @param beanName
- * the name of the bean to get.
- * @return an Object reference to the named bean.
- */
- public static Object getBean(String beanName) {
- return context.getBean(beanName);
- }
-
- /**
- *
- * @return {@link #context}
- */
- public static ApplicationContext getApplicationContext() {
- return context;
- }
-
+package lcsb.mapviewer.persist;
+
+import org.apache.log4j.Logger;
+import org.springframework.context.ApplicationContext;
+import org.springframework.context.ApplicationContextAware;
+import org.springframework.transaction.annotation.Transactional;
+
+/**
+ * Wrapper to always return a reference to the Spring Application Context from
+ * within non-Spring enabled beans. Unlike Spring MVC's
+ * WebApplicationContextUtils we do not need a reference to the Servlet context
+ * for this. All we need is for this bean to be initialized during application
+ * startup.
+ */
+@Transactional(value = "txManager")
+public class SpringApplicationContext implements ApplicationContextAware {
+
+ /**
+ * Default logger for this class.
+ */
+ private static Logger logger = Logger.getLogger(SpringApplicationContext.class);
+
+ /**
+ * {@link ApplicationContext} used by the Spring framework.
+ */
+ private static ApplicationContext context;
+
+ /**
+ * This method is called from within the ApplicationContext once it is done
+ * starting up, it will stick a reference to itself into this bean.
+ *
+ * @param context
+ * a reference to the ApplicationContext.
+ */
+ @Override
+ public void setApplicationContext(ApplicationContext context) {
+ logger.debug("Setting application context: " + context.getDisplayName());
+ SpringApplicationContext.context = context;
+ }
+
+ /**
+ * This is about the same as context.getBean("beanName"), except it has its
+ * own static handle to the Spring context, so calling this method statically
+ * will give access to the beans by name in the Spring application context. As
+ * in the context.getBean("beanName") call, the caller must cast to the
+ * appropriate target class. If the bean does not exist, then a Runtime error
+ * will be thrown.
+ *
+ * @param beanName
+ * the name of the bean to get.
+ * @return an Object reference to the named bean.
+ */
+ public static Object getBean(String beanName) {
+ return context.getBean(beanName);
+ }
+
+ /**
+ *
+ * @return {@link #context}
+ */
+ public static ApplicationContext getApplicationContext() {
+ return context;
+ }
+
}
\ No newline at end of file
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/BaseDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/BaseDao.java
index ff6e427890..244554d641 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/BaseDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/BaseDao.java
@@ -1,330 +1,330 @@
-package lcsb.mapviewer.persist.dao;
-
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.hibernate.Query;
-import org.hibernate.Session;
-import org.hibernate.criterion.Projections;
-import org.hibernate.criterion.Restrictions;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.persist.DbUtils;
-
-/**
- * Abstract interface for data access object in the system. Containts the basic
- * generic functionality.
- *
- * @author Piotr Gawron
- *
- * @param <T>
- * type for which data access object is created
- */
-public abstract class BaseDao<T> {
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(BaseDao.class);
-
- /**
- * Sometimes objects have a flag that indicate that the object was removed from
- * the system (but is still there because of foreign keys etc). This column
- * determines the name of the column. If its set to null then such column
- * doesn't exist.
- */
- private String removableColumn = null;
-
- /**
- * Class of the object that DAO works on.
- */
- private Class<? extends T> clazz;
-
- /**
- * Default constructor.
- *
- * @param theClass
- * class of the object that DAO will work on
- */
- public BaseDao(Class<? extends T> theClass) {
- this.clazz = theClass;
- }
-
- /**
- * Default constructor.
- *
- * @param theClass
- * class of the object that DAO will work on
- * @param removableColumn
- * determines the column in the object table that indicates if object
- * should be considered as removed or not (see also:
- * {@link #removableColumn}.
- *
- */
- public BaseDao(Class<? extends T> theClass, String removableColumn) {
- this(theClass);
- this.removableColumn = removableColumn;
- }
-
- /**
- * Utils that help to manage the sessions in custom multithreaded
- * implementation.
- */
- @Autowired
- private DbUtils dbUtils;
-
- /**
- * Adds object to the database.
- *
- * @param object
- * object to add to database
- */
- public void add(T object) {
- getSession().save(object);
- if (dbUtils.isAutoFlush()) {
- getSession().flush();
- }
- }
-
- /**
- * Flush connection with database.
- */
- public void flush() {
- getSession().flush();
- }
-
- /**
- * Commit current transaction.
- */
- public void commit() {
- if (!dbUtils.isCustomSessionForCurrentThread()) {
- logger.warn("Manual commit with spring managed session!", new Exception());
- }
-
- getSession().getTransaction().commit();
- getSession().beginTransaction();
- }
-
- /**
- * Returns current session.
- *
- * @return session for current thread
- */
- protected Session getSession() {
- return dbUtils.getSessionForCurrentThread();
- }
-
- /**
- * Update object in the database.
- *
- * @param object
- * object to be updated
- */
- public void update(T object) {
- getSession().update(object);
- if (dbUtils.isAutoFlush()) {
- getSession().flush();
- }
- }
-
- /**
- * Removes object from the database.
- *
- * @param object
- * object to be removed from database
- */
- public void delete(T object) {
- getSession().delete(object);
- if (dbUtils.isAutoFlush()) {
- getSession().flush();
- }
- }
-
- /**
- * "Disconnects" object with the element in database. From this point on we
- * cannot update/delete it in the database.
- *
- * @param object
- * object that should be evicted
- */
- public void evict(T object) {
- getSession().evict(object);
- if (dbUtils.isAutoFlush()) {
- getSession().flush();
- }
- }
-
- /**
- * Returns number of elements in the table for this object.
- *
- * @return number of all elements in database
- */
- public long getCount() {
- if (removableColumn == null) {
- return (Long) getSession().createCriteria(this.clazz).setProjection(Projections.rowCount()).uniqueResult();
- } else {
- return (Long) getSession().createCriteria(this.clazz).add(Restrictions.eq(removableColumn, false))
- .setProjection(Projections.rowCount()).uniqueResult();
- }
- }
-
- /**
- * Returns an element that has a key parameter equal to value. If there is more
- * than one element than one of them will be returned. If there is no such
- * element then <code>null</code> is returned.
- *
- * @param key
- * which parameter will filter the data
- * @param value
- * what must be the value of parameter key
- * @return element that fulfill T.key=value criteria
- */
- @SuppressWarnings("unchecked")
- protected T getByParameter(String key, Object value) {
- List<?> list = getSession()
- .createQuery(
- " from " + this.clazz.getSimpleName() + " where " + key + " = :param_val " + removableAndStatemant())
- .setParameter("param_val", value).list();
- if (list.size() == 0) {
- return null;
- } else {
- return (T) list.get(0);
- }
- }
-
- /**
- * Returns the list of elements that have a key parameter equal to value.
- *
- * @param key
- * which parameter will filter the data
- * @param value
- * what must be the value of parameter key
- * @return list of elements that fulfill T.key=value criteria
- */
- @SuppressWarnings("unchecked")
- protected List<T> getElementsByParameter(String key, Object value) {
- List<?> list = getSession()
- .createQuery(
- " from " + this.clazz.getSimpleName() + " where " + key + " = :param_val " + removableAndStatemant())
- .setParameter("param_val", value).list();
- return (List<T>) list;
- }
-
- @SuppressWarnings("unchecked")
- protected List<T> getElementsByParameters(List<Pair<String, Object>> params) {
- String queryString = " from " + this.clazz.getSimpleName() + " where ";
- boolean firstParam = true;
- for (Pair<String, Object> param : params) {
- String key = param.getLeft();
- if (!firstParam) {
- queryString += " AND ";
- }
- if (param.getRight() == null) {
- queryString += key + " is null ";
- } else {
- queryString += key + " = :param_val_" + key + " ";
- }
-
- firstParam = false;
- }
- queryString += removableAndStatemant();
- Query query = getSession().createQuery(queryString);
- for (Pair<String, Object> param : params) {
- String key = param.getLeft();
- Object value = param.getRight();
- if (value != null) {
- query = query.setParameter("param_val_" + key, value);
- }
- }
- List<?> list = query.list();
- return (List<T>) list;
- }
-
- /**
- * Returns element with the id given as parameter.
- *
- * @param id
- * database identifier
- * @return object width identifier given as parameter
- */
- @SuppressWarnings("unchecked")
- public T getById(int id) {
- List<?> list = getSession()
- .createQuery(" from " + this.clazz.getSimpleName() + " where id=? " + removableAndStatemant())
- .setParameter(0, id).list();
- if (list.size() == 0) {
- return null;
- } else {
- return (T) list.get(0);
- }
- }
-
- /**
- * Returns list of all object in db.
- *
- * @return list of all object in db
- */
- @SuppressWarnings("unchecked")
- public List<T> getAll() {
- List<?> list = getSession().createQuery(" from " + this.clazz.getSimpleName() + " " + removableStatemant()).list();
- return (List<T>) list;
- }
-
- /**
- * Removes all elements from the database.
- */
- public void clearTable() {
- String stringQuery = "DELETE FROM " + this.clazz.getSimpleName();
- getSession().createQuery(stringQuery).executeUpdate();
- if (dbUtils.isAutoFlush()) {
- getSession().flush();
- }
- }
-
- /**
- * Refresh object with the new data taken from database.
- *
- * @param object
- * object to be refreshed
- */
- public void refresh(Object object) {
- getSession().refresh(object);
- }
-
- /**
- * @return the clazz
- */
- protected Class<? extends T> getClazz() {
- return clazz;
- }
-
- /**
- * Returns part of HQL statement responsible for {@link #removableColumn}.
- *
- * @return part of HQL statement responsible for {@link #removableColumn}.
- */
- protected String removableAndStatemant() {
- if (removableColumn == null) {
- return "";
- } else {
- return " AND " + removableColumn + " = false ";
- }
- }
-
- /**
- * Returns part of HQL statement responsible for {@link #removableColumn}
- * (without sql AND).
- *
- * @return part of HQL statement responsible for {@link #removableColumn}
- * (without sql AND).
- */
- protected String removableStatemant() {
- if (removableColumn == null) {
- return "";
- } else {
- return " WHERE " + removableColumn + " = false ";
- }
- }
-
-}
+package lcsb.mapviewer.persist.dao;
+
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.hibernate.Query;
+import org.hibernate.Session;
+import org.hibernate.criterion.Projections;
+import org.hibernate.criterion.Restrictions;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.persist.DbUtils;
+
+/**
+ * Abstract interface for data access object in the system. Containts the basic
+ * generic functionality.
+ *
+ * @author Piotr Gawron
+ *
+ * @param <T>
+ * type for which data access object is created
+ */
+public abstract class BaseDao<T> {
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(BaseDao.class);
+
+ /**
+ * Sometimes objects have a flag that indicate that the object was removed from
+ * the system (but is still there because of foreign keys etc). This column
+ * determines the name of the column. If its set to null then such column
+ * doesn't exist.
+ */
+ private String removableColumn = null;
+
+ /**
+ * Class of the object that DAO works on.
+ */
+ private Class<? extends T> clazz;
+
+ /**
+ * Default constructor.
+ *
+ * @param theClass
+ * class of the object that DAO will work on
+ */
+ public BaseDao(Class<? extends T> theClass) {
+ this.clazz = theClass;
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param theClass
+ * class of the object that DAO will work on
+ * @param removableColumn
+ * determines the column in the object table that indicates if object
+ * should be considered as removed or not (see also:
+ * {@link #removableColumn}.
+ *
+ */
+ public BaseDao(Class<? extends T> theClass, String removableColumn) {
+ this(theClass);
+ this.removableColumn = removableColumn;
+ }
+
+ /**
+ * Utils that help to manage the sessions in custom multithreaded
+ * implementation.
+ */
+ @Autowired
+ private DbUtils dbUtils;
+
+ /**
+ * Adds object to the database.
+ *
+ * @param object
+ * object to add to database
+ */
+ public void add(T object) {
+ getSession().save(object);
+ if (dbUtils.isAutoFlush()) {
+ getSession().flush();
+ }
+ }
+
+ /**
+ * Flush connection with database.
+ */
+ public void flush() {
+ getSession().flush();
+ }
+
+ /**
+ * Commit current transaction.
+ */
+ public void commit() {
+ if (!dbUtils.isCustomSessionForCurrentThread()) {
+ logger.warn("Manual commit with spring managed session!", new Exception());
+ }
+
+ getSession().getTransaction().commit();
+ getSession().beginTransaction();
+ }
+
+ /**
+ * Returns current session.
+ *
+ * @return session for current thread
+ */
+ protected Session getSession() {
+ return dbUtils.getSessionForCurrentThread();
+ }
+
+ /**
+ * Update object in the database.
+ *
+ * @param object
+ * object to be updated
+ */
+ public void update(T object) {
+ getSession().update(object);
+ if (dbUtils.isAutoFlush()) {
+ getSession().flush();
+ }
+ }
+
+ /**
+ * Removes object from the database.
+ *
+ * @param object
+ * object to be removed from database
+ */
+ public void delete(T object) {
+ getSession().delete(object);
+ if (dbUtils.isAutoFlush()) {
+ getSession().flush();
+ }
+ }
+
+ /**
+ * "Disconnects" object with the element in database. From this point on we
+ * cannot update/delete it in the database.
+ *
+ * @param object
+ * object that should be evicted
+ */
+ public void evict(T object) {
+ getSession().evict(object);
+ if (dbUtils.isAutoFlush()) {
+ getSession().flush();
+ }
+ }
+
+ /**
+ * Returns number of elements in the table for this object.
+ *
+ * @return number of all elements in database
+ */
+ public long getCount() {
+ if (removableColumn == null) {
+ return (Long) getSession().createCriteria(this.clazz).setProjection(Projections.rowCount()).uniqueResult();
+ } else {
+ return (Long) getSession().createCriteria(this.clazz).add(Restrictions.eq(removableColumn, false))
+ .setProjection(Projections.rowCount()).uniqueResult();
+ }
+ }
+
+ /**
+ * Returns an element that has a key parameter equal to value. If there is more
+ * than one element than one of them will be returned. If there is no such
+ * element then <code>null</code> is returned.
+ *
+ * @param key
+ * which parameter will filter the data
+ * @param value
+ * what must be the value of parameter key
+ * @return element that fulfill T.key=value criteria
+ */
+ @SuppressWarnings("unchecked")
+ protected T getByParameter(String key, Object value) {
+ List<?> list = getSession()
+ .createQuery(
+ " from " + this.clazz.getSimpleName() + " where " + key + " = :param_val " + removableAndStatemant())
+ .setParameter("param_val", value).list();
+ if (list.size() == 0) {
+ return null;
+ } else {
+ return (T) list.get(0);
+ }
+ }
+
+ /**
+ * Returns the list of elements that have a key parameter equal to value.
+ *
+ * @param key
+ * which parameter will filter the data
+ * @param value
+ * what must be the value of parameter key
+ * @return list of elements that fulfill T.key=value criteria
+ */
+ @SuppressWarnings("unchecked")
+ protected List<T> getElementsByParameter(String key, Object value) {
+ List<?> list = getSession()
+ .createQuery(
+ " from " + this.clazz.getSimpleName() + " where " + key + " = :param_val " + removableAndStatemant())
+ .setParameter("param_val", value).list();
+ return (List<T>) list;
+ }
+
+ @SuppressWarnings("unchecked")
+ protected List<T> getElementsByParameters(List<Pair<String, Object>> params) {
+ String queryString = " from " + this.clazz.getSimpleName() + " where ";
+ boolean firstParam = true;
+ for (Pair<String, Object> param : params) {
+ String key = param.getLeft();
+ if (!firstParam) {
+ queryString += " AND ";
+ }
+ if (param.getRight() == null) {
+ queryString += key + " is null ";
+ } else {
+ queryString += key + " = :param_val_" + key + " ";
+ }
+
+ firstParam = false;
+ }
+ queryString += removableAndStatemant();
+ Query query = getSession().createQuery(queryString);
+ for (Pair<String, Object> param : params) {
+ String key = param.getLeft();
+ Object value = param.getRight();
+ if (value != null) {
+ query = query.setParameter("param_val_" + key, value);
+ }
+ }
+ List<?> list = query.list();
+ return (List<T>) list;
+ }
+
+ /**
+ * Returns element with the id given as parameter.
+ *
+ * @param id
+ * database identifier
+ * @return object width identifier given as parameter
+ */
+ @SuppressWarnings("unchecked")
+ public T getById(int id) {
+ List<?> list = getSession()
+ .createQuery(" from " + this.clazz.getSimpleName() + " where id=? " + removableAndStatemant())
+ .setParameter(0, id).list();
+ if (list.size() == 0) {
+ return null;
+ } else {
+ return (T) list.get(0);
+ }
+ }
+
+ /**
+ * Returns list of all object in db.
+ *
+ * @return list of all object in db
+ */
+ @SuppressWarnings("unchecked")
+ public List<T> getAll() {
+ List<?> list = getSession().createQuery(" from " + this.clazz.getSimpleName() + " " + removableStatemant()).list();
+ return (List<T>) list;
+ }
+
+ /**
+ * Removes all elements from the database.
+ */
+ public void clearTable() {
+ String stringQuery = "DELETE FROM " + this.clazz.getSimpleName();
+ getSession().createQuery(stringQuery).executeUpdate();
+ if (dbUtils.isAutoFlush()) {
+ getSession().flush();
+ }
+ }
+
+ /**
+ * Refresh object with the new data taken from database.
+ *
+ * @param object
+ * object to be refreshed
+ */
+ public void refresh(Object object) {
+ getSession().refresh(object);
+ }
+
+ /**
+ * @return the clazz
+ */
+ protected Class<? extends T> getClazz() {
+ return clazz;
+ }
+
+ /**
+ * Returns part of HQL statement responsible for {@link #removableColumn}.
+ *
+ * @return part of HQL statement responsible for {@link #removableColumn}.
+ */
+ protected String removableAndStatemant() {
+ if (removableColumn == null) {
+ return "";
+ } else {
+ return " AND " + removableColumn + " = false ";
+ }
+ }
+
+ /**
+ * Returns part of HQL statement responsible for {@link #removableColumn}
+ * (without sql AND).
+ *
+ * @return part of HQL statement responsible for {@link #removableColumn}
+ * (without sql AND).
+ */
+ protected String removableStatemant() {
+ if (removableColumn == null) {
+ return "";
+ } else {
+ return " WHERE " + removableColumn + " = false ";
+ }
+ }
+
+}
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/ConfigurationDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/ConfigurationDao.java
index 3cabf75023..b90d90254f 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/ConfigurationDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/ConfigurationDao.java
@@ -1,52 +1,52 @@
-package lcsb.mapviewer.persist.dao;
-
-import lcsb.mapviewer.model.user.ConfigurationOption;
-import lcsb.mapviewer.model.user.ConfigurationElementType;
-
-/**
- * Data access object class for Configuration objects.
- *
- * @author Piotr Gawron
- *
- */
-public class ConfigurationDao extends BaseDao<ConfigurationOption> {
-
- /**
- * Default constructor.
- */
- public ConfigurationDao() {
- super(ConfigurationOption.class);
- }
-
- /**
- * Returns object with configuration value for the type given in the
- * parameter.
- *
- * @param type
- * type of the parameter that we are interested in
- * @return object with configuration value for the type given in the parameter
- */
- public ConfigurationOption getByType(ConfigurationElementType type) {
- return getByParameter("type", type);
- }
-
- /**
- * Returns value by the type.
- *
- * @param type
- * type of configuration parameter
- * @return value of the specific configuration parameter
- */
- public String getValueByType(ConfigurationElementType type) {
- ConfigurationOption val = getByParameter("type", type);
- if (val == null) {
- if (type == null) {
- return null;
- } else {
- return type.getDefaultValue();
- }
- } else {
- return val.getValue();
- }
- }
-}
+package lcsb.mapviewer.persist.dao;
+
+import lcsb.mapviewer.model.user.ConfigurationOption;
+import lcsb.mapviewer.model.user.ConfigurationElementType;
+
+/**
+ * Data access object class for Configuration objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ConfigurationDao extends BaseDao<ConfigurationOption> {
+
+ /**
+ * Default constructor.
+ */
+ public ConfigurationDao() {
+ super(ConfigurationOption.class);
+ }
+
+ /**
+ * Returns object with configuration value for the type given in the
+ * parameter.
+ *
+ * @param type
+ * type of the parameter that we are interested in
+ * @return object with configuration value for the type given in the parameter
+ */
+ public ConfigurationOption getByType(ConfigurationElementType type) {
+ return getByParameter("type", type);
+ }
+
+ /**
+ * Returns value by the type.
+ *
+ * @param type
+ * type of configuration parameter
+ * @return value of the specific configuration parameter
+ */
+ public String getValueByType(ConfigurationElementType type) {
+ ConfigurationOption val = getByParameter("type", type);
+ if (val == null) {
+ if (type == null) {
+ return null;
+ } else {
+ return type.getDefaultValue();
+ }
+ } else {
+ return val.getValue();
+ }
+ }
+}
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/ProjectDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/ProjectDao.java
index 0f698ef9c5..d03df93697 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/ProjectDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/ProjectDao.java
@@ -1,106 +1,106 @@
-package lcsb.mapviewer.persist.dao;
-
-import java.sql.Connection;
-import java.sql.PreparedStatement;
-import java.sql.ResultSet;
-import java.sql.SQLException;
-import java.util.List;
-
-import org.hibernate.dialect.Dialect;
-import org.hibernate.jdbc.ReturningWork;
-import org.hibernate.service.jdbc.dialect.internal.StandardDialectResolver;
-import org.hibernate.service.jdbc.dialect.spi.DialectResolver;
-
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.model.ModelData;
-
-/**
- * Data access object class for Project objects.
- *
- * @author Piotr Gawron
- *
- */
-public class ProjectDao extends BaseDao<Project> {
- /**
- * Default constructor.
- */
- public ProjectDao() {
- super(Project.class);
- }
-
- /**
- * Returns project with the given {@link Project#projectId project identifier} .
- *
- * @param projectId
- * {@link Project#projectId project identifier}
- * @return project for the given name
- */
- public Project getProjectByProjectId(String projectId) {
- Project project = getByParameter("projectId", projectId);
-
- return project;
- }
-
- /**
- * Returns project that contains model with a given id.
- *
- * @param id
- * id of the model
- * @return project that contains model with a given id
- */
- public Project getProjectForModelId(Integer id) {
- List<?> list = getSession()
- .createQuery("select project from " + ModelData.class.getSimpleName() + " model_t where model_t.id = :id")
- .setParameter("id", id).list();
- if (list.size() == 0) {
- return null;
- }
- return (Project) list.get(0);
- }
-
- /**
- * Returns information if the project with given name exists.
- *
- * @param projectName
- * name of the project
- * @return <code>true</code> if project with given name exists,
- * <code>false</code> otherwise
- */
- public boolean isProjectExistsByName(String projectName) {
- @SuppressWarnings("unchecked")
- List<Long> list = getSession()
- .createQuery("select count(*) from " + getClazz().getSimpleName() + " where projectId = :projectId")
- .setParameter("projectId", projectName).list();
- return list.get(0) > 0;
- }
-
- public long getNextId() {
- ReturningWork<Long> maxReturningWork = new ReturningWork<Long>() {
- @Override
- public Long execute(Connection connection) throws SQLException {
- DialectResolver dialectResolver = new StandardDialectResolver();
- Dialect dialect = dialectResolver.resolveDialect(connection.getMetaData());
- PreparedStatement preparedStatement = null;
- ResultSet resultSet = null;
- try {
- preparedStatement = connection.prepareStatement(dialect.getSequenceNextValString("project_table_iddb_seq"));
- resultSet = preparedStatement.executeQuery();
- resultSet.next();
- return resultSet.getLong(1);
- } catch (SQLException e) {
- throw e;
- } finally {
- if (preparedStatement != null) {
- preparedStatement.close();
- }
- if (resultSet != null) {
- resultSet.close();
- }
- }
-
- }
- };
- return getSession().doReturningWork(maxReturningWork);
- }
-
-}
+package lcsb.mapviewer.persist.dao;
+
+import java.sql.Connection;
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.List;
+
+import org.hibernate.dialect.Dialect;
+import org.hibernate.jdbc.ReturningWork;
+import org.hibernate.service.jdbc.dialect.internal.StandardDialectResolver;
+import org.hibernate.service.jdbc.dialect.spi.DialectResolver;
+
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.model.ModelData;
+
+/**
+ * Data access object class for Project objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ProjectDao extends BaseDao<Project> {
+ /**
+ * Default constructor.
+ */
+ public ProjectDao() {
+ super(Project.class);
+ }
+
+ /**
+ * Returns project with the given {@link Project#projectId project identifier} .
+ *
+ * @param projectId
+ * {@link Project#projectId project identifier}
+ * @return project for the given name
+ */
+ public Project getProjectByProjectId(String projectId) {
+ Project project = getByParameter("projectId", projectId);
+
+ return project;
+ }
+
+ /**
+ * Returns project that contains model with a given id.
+ *
+ * @param id
+ * id of the model
+ * @return project that contains model with a given id
+ */
+ public Project getProjectForModelId(Integer id) {
+ List<?> list = getSession()
+ .createQuery("select project from " + ModelData.class.getSimpleName() + " model_t where model_t.id = :id")
+ .setParameter("id", id).list();
+ if (list.size() == 0) {
+ return null;
+ }
+ return (Project) list.get(0);
+ }
+
+ /**
+ * Returns information if the project with given name exists.
+ *
+ * @param projectName
+ * name of the project
+ * @return <code>true</code> if project with given name exists,
+ * <code>false</code> otherwise
+ */
+ public boolean isProjectExistsByName(String projectName) {
+ @SuppressWarnings("unchecked")
+ List<Long> list = getSession()
+ .createQuery("select count(*) from " + getClazz().getSimpleName() + " where projectId = :projectId")
+ .setParameter("projectId", projectName).list();
+ return list.get(0) > 0;
+ }
+
+ public long getNextId() {
+ ReturningWork<Long> maxReturningWork = new ReturningWork<Long>() {
+ @Override
+ public Long execute(Connection connection) throws SQLException {
+ DialectResolver dialectResolver = new StandardDialectResolver();
+ Dialect dialect = dialectResolver.resolveDialect(connection.getMetaData());
+ PreparedStatement preparedStatement = null;
+ ResultSet resultSet = null;
+ try {
+ preparedStatement = connection.prepareStatement(dialect.getSequenceNextValString("project_table_iddb_seq"));
+ resultSet = preparedStatement.executeQuery();
+ resultSet.next();
+ return resultSet.getLong(1);
+ } catch (SQLException e) {
+ throw e;
+ } finally {
+ if (preparedStatement != null) {
+ preparedStatement.close();
+ }
+ if (resultSet != null) {
+ resultSet.close();
+ }
+ }
+
+ }
+ };
+ return getSession().doReturningWork(maxReturningWork);
+ }
+
+}
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/cache/BigFileEntryDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/cache/BigFileEntryDao.java
index d2ed61900f..7ddf877760 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/cache/BigFileEntryDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/cache/BigFileEntryDao.java
@@ -1,55 +1,55 @@
-package lcsb.mapviewer.persist.dao.cache;
-
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.model.cache.BigFileEntry;
-import lcsb.mapviewer.persist.dao.BaseDao;
-
-/**
- * Data access object for cached values.
- *
- * @author Piotr Gawron
- *
- */
-public class BigFileEntryDao extends BaseDao<BigFileEntry> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(BigFileEntryDao.class);
-
- /**
- * Default constructor.
- */
- public BigFileEntryDao() {
- super(BigFileEntry.class, "removed");
- }
-
- /**
- * Return {@link BigFileEntry} identified by remote url.
- *
- * @param url
- * url of the file
- * @return {@link BigFileEntry} identified by remote url
- */
- public BigFileEntry getByUrl(String url) {
- List<?> list = getElementsByParameter("url", url);
- if (list.size() == 0) {
- return null;
- }
- return (BigFileEntry) list.get(0);
- }
-
- public List<BigFileEntry> getAllByUrl(String url) {
- return getElementsByParameter("url", url);
- }
-
- @Override
- public void delete(BigFileEntry entry) {
- entry.setRemoved(true);
- update(entry);
- }
-
-}
+package lcsb.mapviewer.persist.dao.cache;
+
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.model.cache.BigFileEntry;
+import lcsb.mapviewer.persist.dao.BaseDao;
+
+/**
+ * Data access object for cached values.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class BigFileEntryDao extends BaseDao<BigFileEntry> {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(BigFileEntryDao.class);
+
+ /**
+ * Default constructor.
+ */
+ public BigFileEntryDao() {
+ super(BigFileEntry.class, "removed");
+ }
+
+ /**
+ * Return {@link BigFileEntry} identified by remote url.
+ *
+ * @param url
+ * url of the file
+ * @return {@link BigFileEntry} identified by remote url
+ */
+ public BigFileEntry getByUrl(String url) {
+ List<?> list = getElementsByParameter("url", url);
+ if (list.size() == 0) {
+ return null;
+ }
+ return (BigFileEntry) list.get(0);
+ }
+
+ public List<BigFileEntry> getAllByUrl(String url) {
+ return getElementsByParameter("url", url);
+ }
+
+ @Override
+ public void delete(BigFileEntry entry) {
+ entry.setRemoved(true);
+ update(entry);
+ }
+
+}
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/cache/CacheQueryDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/cache/CacheQueryDao.java
index fa7ced7f43..a889d72032 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/cache/CacheQueryDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/cache/CacheQueryDao.java
@@ -1,58 +1,58 @@
-package lcsb.mapviewer.persist.dao.cache;
-
-import java.util.List;
-
-import lcsb.mapviewer.model.cache.CacheQuery;
-import lcsb.mapviewer.model.cache.CacheType;
-import lcsb.mapviewer.persist.dao.BaseDao;
-
-/**
- * Data access object for cached values.
- *
- * @author Piotr Gawron
- *
- */
-public class CacheQueryDao extends BaseDao<CacheQuery> {
-
- /**
- * Default constructor.
- */
- public CacheQueryDao() {
- super(CacheQuery.class);
- }
-
- /**
- * Returns the cached value based on the type of resource and identifier in
- * remote resource.
- *
- * @param identifier
- * identifier in remote resource
- * @param type
- * type of the resource
- * @return cached value, if value wasn't cached then null is returned
- */
- public CacheQuery getByQuery(String identifier, Integer type) {
- List<?> list = getSession()
- .createQuery(" from " + this.getClazz().getSimpleName() + " where query = :query and type = :type").setParameter("query", identifier)
- .setParameter("type", type).list();
- if (list.size() == 0) {
- return null;
- }
- return (CacheQuery) list.get(0);
- }
-
- /**
- * Returns the cached value based on the type of resource and identifier in
- * remote resource.
- *
- * @param identifier
- * identifier in remote resource
- * @param type
- * type of the resource
- * @return cached value, if value wasn't cached then null is returned
- */
- public CacheQuery getByQuery(String identifier, CacheType type) {
- return getByQuery(identifier, type.getId());
- }
-
-}
+package lcsb.mapviewer.persist.dao.cache;
+
+import java.util.List;
+
+import lcsb.mapviewer.model.cache.CacheQuery;
+import lcsb.mapviewer.model.cache.CacheType;
+import lcsb.mapviewer.persist.dao.BaseDao;
+
+/**
+ * Data access object for cached values.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CacheQueryDao extends BaseDao<CacheQuery> {
+
+ /**
+ * Default constructor.
+ */
+ public CacheQueryDao() {
+ super(CacheQuery.class);
+ }
+
+ /**
+ * Returns the cached value based on the type of resource and identifier in
+ * remote resource.
+ *
+ * @param identifier
+ * identifier in remote resource
+ * @param type
+ * type of the resource
+ * @return cached value, if value wasn't cached then null is returned
+ */
+ public CacheQuery getByQuery(String identifier, Integer type) {
+ List<?> list = getSession()
+ .createQuery(" from " + this.getClazz().getSimpleName() + " where query = :query and type = :type").setParameter("query", identifier)
+ .setParameter("type", type).list();
+ if (list.size() == 0) {
+ return null;
+ }
+ return (CacheQuery) list.get(0);
+ }
+
+ /**
+ * Returns the cached value based on the type of resource and identifier in
+ * remote resource.
+ *
+ * @param identifier
+ * identifier in remote resource
+ * @param type
+ * type of the resource
+ * @return cached value, if value wasn't cached then null is returned
+ */
+ public CacheQuery getByQuery(String identifier, CacheType type) {
+ return getByQuery(identifier, type.getId());
+ }
+
+}
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/cache/CacheTypeDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/cache/CacheTypeDao.java
index f678cad053..d22ec148f0 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/cache/CacheTypeDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/cache/CacheTypeDao.java
@@ -1,45 +1,45 @@
-package lcsb.mapviewer.persist.dao.cache;
-
-import java.util.List;
-
-import lcsb.mapviewer.model.cache.CacheType;
-import lcsb.mapviewer.persist.dao.BaseDao;
-
-import org.apache.log4j.Logger;
-
-/**
- * Data access object for cached values.
- *
- * @author Piotr Gawron
- *
- */
-public class CacheTypeDao extends BaseDao<CacheType> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(CacheTypeDao.class);
-
- /**
- * Default constructor.
- */
- public CacheTypeDao() {
- super(CacheType.class);
- }
-
- /**
- * Returns the cach type for the class name identified by a canonical name.
- *
- * @param className
- * canonical name of the class
- * @return type of cache that should be used by this cachable interface
- */
- public CacheType getByClassName(String className) {
- List<?> list = getElementsByParameter("className", className);
- if (list.size() == 0) {
- return null;
- }
- return (CacheType) list.get(0);
- }
-
-}
+package lcsb.mapviewer.persist.dao.cache;
+
+import java.util.List;
+
+import lcsb.mapviewer.model.cache.CacheType;
+import lcsb.mapviewer.persist.dao.BaseDao;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Data access object for cached values.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CacheTypeDao extends BaseDao<CacheType> {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(CacheTypeDao.class);
+
+ /**
+ * Default constructor.
+ */
+ public CacheTypeDao() {
+ super(CacheType.class);
+ }
+
+ /**
+ * Returns the cach type for the class name identified by a canonical name.
+ *
+ * @param className
+ * canonical name of the class
+ * @return type of cache that should be used by this cachable interface
+ */
+ public CacheType getByClassName(String className) {
+ List<?> list = getElementsByParameter("className", className);
+ if (list.size() == 0) {
+ return null;
+ }
+ return (CacheType) list.get(0);
+ }
+
+}
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/cache/UploadedFileEntryDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/cache/UploadedFileEntryDao.java
index 1ec9fdcbb5..f5b36bf38b 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/cache/UploadedFileEntryDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/cache/UploadedFileEntryDao.java
@@ -1,34 +1,34 @@
-package lcsb.mapviewer.persist.dao.cache;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.model.cache.UploadedFileEntry;
-import lcsb.mapviewer.persist.dao.BaseDao;
-
-/**
- * Data access object for cached values.
- *
- * @author Piotr Gawron
- *
- */
-public class UploadedFileEntryDao extends BaseDao<UploadedFileEntry> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(UploadedFileEntryDao.class);
-
- /**
- * Default constructor.
- */
- public UploadedFileEntryDao() {
- super(UploadedFileEntry.class, "removed");
- }
-
- @Override
- public void delete(UploadedFileEntry entry) {
- entry.setRemoved(true);
- update(entry);
- }
-
-}
+package lcsb.mapviewer.persist.dao.cache;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
+import lcsb.mapviewer.persist.dao.BaseDao;
+
+/**
+ * Data access object for cached values.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class UploadedFileEntryDao extends BaseDao<UploadedFileEntry> {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(UploadedFileEntryDao.class);
+
+ /**
+ * Default constructor.
+ */
+ public UploadedFileEntryDao() {
+ super(UploadedFileEntry.class, "removed");
+ }
+
+ @Override
+ public void delete(UploadedFileEntry entry) {
+ entry.setRemoved(true);
+ update(entry);
+ }
+
+}
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/cache/package-info.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/cache/package-info.java
index cf296a5842..f2f2f5f53c 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/cache/package-info.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/cache/package-info.java
@@ -1,5 +1,5 @@
-/**
- * Package with data access object for cached elements.
- */
-package lcsb.mapviewer.persist.dao.cache;
-
+/**
+ * Package with data access object for cached elements.
+ */
+package lcsb.mapviewer.persist.dao.cache;
+
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/graphics/PolylineDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/graphics/PolylineDao.java
index 3c04d08812..bee80fbe88 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/graphics/PolylineDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/graphics/PolylineDao.java
@@ -1,21 +1,21 @@
-package lcsb.mapviewer.persist.dao.graphics;
-
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.persist.dao.BaseDao;
-
-/**
- * Data access object for {@link PolylineDao} class.
- *
- * @author Piotr Gawron
- *
- */
-public class PolylineDao extends BaseDao<PolylineData> {
-
- /**
- * Default constructor.
- */
- public PolylineDao() {
- super(PolylineData.class);
- }
-
-}
+package lcsb.mapviewer.persist.dao.graphics;
+
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.persist.dao.BaseDao;
+
+/**
+ * Data access object for {@link PolylineDao} class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class PolylineDao extends BaseDao<PolylineData> {
+
+ /**
+ * Default constructor.
+ */
+ public PolylineDao() {
+ super(PolylineData.class);
+ }
+
+}
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/graphics/package-info.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/graphics/package-info.java
index 4c0fedee32..ae5ee40a47 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/graphics/package-info.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/graphics/package-info.java
@@ -1,5 +1,5 @@
-/**
- * Package with data access object for graphics elements.
- */
-package lcsb.mapviewer.persist.dao.graphics;
-
+/**
+ * Package with data access object for graphics elements.
+ */
+package lcsb.mapviewer.persist.dao.graphics;
+
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/log/LogDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/log/LogDao.java
index b161fe8e13..3eb886af9b 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/log/LogDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/log/LogDao.java
@@ -1,45 +1,45 @@
-package lcsb.mapviewer.persist.dao.log;
-
-import java.util.List;
-
-import org.hibernate.Query;
-
-import lcsb.mapviewer.model.log.GenericLog;
-import lcsb.mapviewer.persist.dao.BaseDao;
-
-/**
- * Data access object class for Log objects.
- *
- * @author Piotr Gawron
- *
- */
-public class LogDao extends BaseDao<GenericLog> {
- /**
- * Default constructor.
- */
- public LogDao() {
- super(GenericLog.class);
- }
-
- /**
- * Returns last logged event.
- *
- * @return last log event
- */
- public GenericLog getLastLog() {
- String queryString = "from " + this.getClazz().getSimpleName() + " order by id desc";
- Query query = getSession().createQuery(queryString);
- List<?> list = query.list();
- if (list.size() > 0) {
- return (GenericLog) list.get(0);
- } else {
- return null;
- }
- }
-
- @Override
- protected String removableStatemant() {
- return super.removableStatemant();
- }
-
-}
+package lcsb.mapviewer.persist.dao.log;
+
+import java.util.List;
+
+import org.hibernate.Query;
+
+import lcsb.mapviewer.model.log.GenericLog;
+import lcsb.mapviewer.persist.dao.BaseDao;
+
+/**
+ * Data access object class for Log objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class LogDao extends BaseDao<GenericLog> {
+ /**
+ * Default constructor.
+ */
+ public LogDao() {
+ super(GenericLog.class);
+ }
+
+ /**
+ * Returns last logged event.
+ *
+ * @return last log event
+ */
+ public GenericLog getLastLog() {
+ String queryString = "from " + this.getClazz().getSimpleName() + " order by id desc";
+ Query query = getSession().createQuery(queryString);
+ List<?> list = query.list();
+ if (list.size() > 0) {
+ return (GenericLog) list.get(0);
+ } else {
+ return null;
+ }
+ }
+
+ @Override
+ protected String removableStatemant() {
+ return super.removableStatemant();
+ }
+
+}
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/log/package-info.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/log/package-info.java
index 30a6d19b99..f71f47992a 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/log/package-info.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/log/package-info.java
@@ -1,5 +1,5 @@
-/**
- * Package with data access object for all log elements.
- */
-package lcsb.mapviewer.persist.dao.log;
-
+/**
+ * Package with data access object for all log elements.
+ */
+package lcsb.mapviewer.persist.dao.log;
+
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/CommentDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/CommentDao.java
index 2f86837ecf..f1a1c5bb5b 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/CommentDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/CommentDao.java
@@ -1,133 +1,133 @@
-package lcsb.mapviewer.persist.dao.map;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import lcsb.mapviewer.model.map.Comment;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.persist.dao.BaseDao;
-
-import org.apache.log4j.Logger;
-
-/**
- * Data access object class for Comment objects.
- *
- * @author Piotr Gawron
- *
- */
-public class CommentDao extends BaseDao<Comment> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(CommentDao.class);
-
- /**
- * Default constructor.
- */
- public CommentDao() {
- super(Comment.class);
- }
-
- /**
- * Returns list of comments for a model given in the parameter. The comments
- * are limited by the parameters.
- *
- * @param model
- * in which model we want to find comments
- * @param pinned
- * this parameter defines what kind of comments we want to get:
- * <ul>
- * <li>null - all comments</li>
- * <li>false - comments that are not visible on the map</li>
- * <li>true - comments that are visible on the map</li>
- * </ul>
- * @param deleted
- * this parameter defines what kind of comments we want to get:
- * <ul>
- * <li>null - all comments</li>
- * <li>false - comments that are not deleted</li>
- * <li>true - comments that are deleted</li>
- * </ul>
- * @return list of comments that fulfill parameters constraints
- */
- public List<Comment> getCommentByModel(Model model, Boolean pinned, Boolean deleted) {
- return getCommentByModel(model.getId(), pinned, deleted);
- }
-
- /**
- * Returns list of comments for a model given in the parameter. The comments
- * are limited by the parameters.
- *
- * @param modelId
- * in which model we want to find comments
- * @param pinned
- * this parameter defines what kind of comments we want to get:
- * <ul>
- * <li>null - all comments</li>
- * <li>false - comments that are not visible on the map</li>
- * <li>true - comments that are visible on the map</li>
- * </ul>
- * @param deleted
- * this parameter defines what kind of comments we want to get:
- * <ul>
- * <li>null - all comments</li>
- * <li>false - comments that are not deleted</li>
- * <li>true - comments that are deleted</li>
- * </ul>
- * @return list of comments that fulfill parameters constraints
- */
- private List<Comment> getCommentByModel(int modelId, Boolean pinned, Boolean deleted) {
- List<Comment> comments = getElementsByParameter("model_iddb", modelId);
- List<Comment> result = new ArrayList<Comment>();
- if (deleted != null) {
- for (Comment comment : comments) {
- if (comment.isDeleted() == deleted) {
- result.add(comment);
- }
- }
- } else {
- result = comments;
- }
-
- if (pinned == null) {
- return result;
- }
- comments = result;
- result = new ArrayList<Comment>();
- for (Comment comment : comments) {
- if (comment.isPinned() == pinned) {
- result.add(comment);
- }
- }
- return result;
- }
-
- /**
- * Returns list of comments for a model given in the parameter. The comments
- * are limited by the parameters.
- *
- * @param model
- * in which model we want to find comments
- * @param pinned
- * this parameter defines what kind of comments we want to get:
- * <ul>
- * <li>null - all comments</li>
- * <li>false - comments that are not visible on the map</li>
- * <li>true - comments that are visible on the map</li>
- * </ul>
- * @param deleted
- * this parameter defines what kind of comments we want to get:
- * <ul>
- * <li>null - all comments</li>
- * <li>false - comments that are not deleted</li>
- * <li>true - comments that are deleted</li>
- * </ul>
- * @return list of comments that fulfill parameters constraints
- */
- public List<Comment> getCommentByModel(ModelData model, Boolean pinned, Boolean deleted) {
- return getCommentByModel(model.getId(), pinned, deleted);
- }
-
-}
+package lcsb.mapviewer.persist.dao.map;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import lcsb.mapviewer.model.map.Comment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.persist.dao.BaseDao;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Data access object class for Comment objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CommentDao extends BaseDao<Comment> {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(CommentDao.class);
+
+ /**
+ * Default constructor.
+ */
+ public CommentDao() {
+ super(Comment.class);
+ }
+
+ /**
+ * Returns list of comments for a model given in the parameter. The comments
+ * are limited by the parameters.
+ *
+ * @param model
+ * in which model we want to find comments
+ * @param pinned
+ * this parameter defines what kind of comments we want to get:
+ * <ul>
+ * <li>null - all comments</li>
+ * <li>false - comments that are not visible on the map</li>
+ * <li>true - comments that are visible on the map</li>
+ * </ul>
+ * @param deleted
+ * this parameter defines what kind of comments we want to get:
+ * <ul>
+ * <li>null - all comments</li>
+ * <li>false - comments that are not deleted</li>
+ * <li>true - comments that are deleted</li>
+ * </ul>
+ * @return list of comments that fulfill parameters constraints
+ */
+ public List<Comment> getCommentByModel(Model model, Boolean pinned, Boolean deleted) {
+ return getCommentByModel(model.getId(), pinned, deleted);
+ }
+
+ /**
+ * Returns list of comments for a model given in the parameter. The comments
+ * are limited by the parameters.
+ *
+ * @param modelId
+ * in which model we want to find comments
+ * @param pinned
+ * this parameter defines what kind of comments we want to get:
+ * <ul>
+ * <li>null - all comments</li>
+ * <li>false - comments that are not visible on the map</li>
+ * <li>true - comments that are visible on the map</li>
+ * </ul>
+ * @param deleted
+ * this parameter defines what kind of comments we want to get:
+ * <ul>
+ * <li>null - all comments</li>
+ * <li>false - comments that are not deleted</li>
+ * <li>true - comments that are deleted</li>
+ * </ul>
+ * @return list of comments that fulfill parameters constraints
+ */
+ private List<Comment> getCommentByModel(int modelId, Boolean pinned, Boolean deleted) {
+ List<Comment> comments = getElementsByParameter("model_iddb", modelId);
+ List<Comment> result = new ArrayList<Comment>();
+ if (deleted != null) {
+ for (Comment comment : comments) {
+ if (comment.isDeleted() == deleted) {
+ result.add(comment);
+ }
+ }
+ } else {
+ result = comments;
+ }
+
+ if (pinned == null) {
+ return result;
+ }
+ comments = result;
+ result = new ArrayList<Comment>();
+ for (Comment comment : comments) {
+ if (comment.isPinned() == pinned) {
+ result.add(comment);
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Returns list of comments for a model given in the parameter. The comments
+ * are limited by the parameters.
+ *
+ * @param model
+ * in which model we want to find comments
+ * @param pinned
+ * this parameter defines what kind of comments we want to get:
+ * <ul>
+ * <li>null - all comments</li>
+ * <li>false - comments that are not visible on the map</li>
+ * <li>true - comments that are visible on the map</li>
+ * </ul>
+ * @param deleted
+ * this parameter defines what kind of comments we want to get:
+ * <ul>
+ * <li>null - all comments</li>
+ * <li>false - comments that are not deleted</li>
+ * <li>true - comments that are deleted</li>
+ * </ul>
+ * @return list of comments that fulfill parameters constraints
+ */
+ public List<Comment> getCommentByModel(ModelData model, Boolean pinned, Boolean deleted) {
+ return getCommentByModel(model.getId(), pinned, deleted);
+ }
+
+}
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/LayoutDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/LayoutDao.java
index e464248cdd..7c7c4e9ad8 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/LayoutDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/LayoutDao.java
@@ -1,101 +1,101 @@
-package lcsb.mapviewer.persist.dao.map;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.hibernate.Criteria;
-import org.hibernate.criterion.Projections;
-import org.hibernate.criterion.Restrictions;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.persist.dao.BaseDao;
-
-/**
- * Data access object for {@link Layout} class.
- *
- * @author Piotr Gawron
- *
- */
-public class LayoutDao extends BaseDao<Layout> {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(LayoutDao.class);
-
- /**
- * Default constructor.
- */
- public LayoutDao() {
- super(Layout.class);
- }
-
- /**
- * Lists layouts for the model.
- *
- * @param model
- * for this model layouts will be listed
- * @return list of layouts for the model
- */
- public List<Layout> getLayoutsByModel(Model model) {
- List<Layout> layouts = getElementsByParameter("model_iddb", model.getId());
- for (Layout layout : layouts) {
- refresh(layout);
- }
- return layouts;
- }
-
- public List<Layout> getLayoutsByModel(Model model, User creator, Boolean isPublic) {
- List<Pair<String, Object>> params = new ArrayList<>();
- params.add(new Pair<String, Object>("model_iddb", model.getId()));
- if (isPublic != null) {
- params.add(new Pair<String, Object>("publicLayout", isPublic));
- }
- if (creator != null) {
- params.add(new Pair<String, Object>("creator_iddb", creator.getId()));
- }
- List<Layout> layouts = getElementsByParameters(params);
- return layouts;
- }
-
- /**
- * Return number of layouts created by the user.
- *
- * @param user
- * the user
- * @return number of layouts created by the user
- */
- public long getCountByUser(User user) {
- Criteria crit = getSession().createCriteria(this.getClazz());
- crit.setProjection(Projections.rowCount());
- crit.add(Restrictions.eq("creator", user));
- crit.createAlias("model", "m");
- crit.add(Restrictions.sizeLe("m.parentModels", 0));
- return (Long) crit.uniqueResult();
- }
-
- /**
- * Returns layout identified by name and model.
- *
- * @param model
- * model where the layouts lay on
- * @param name
- * name of the layout
- * @return layout
- */
- public Layout getLayoutByName(Model model, String name) {
- List<Layout> layouts = getElementsByParameter("model_iddb", model.getId());
- for (Layout layout : layouts) {
- refresh(layout);
- if (layout.getTitle().equals(name)) {
- return layout;
- }
- }
- return null;
- }
-}
+package lcsb.mapviewer.persist.dao.map;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.hibernate.Criteria;
+import org.hibernate.criterion.Projections;
+import org.hibernate.criterion.Restrictions;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.persist.dao.BaseDao;
+
+/**
+ * Data access object for {@link Layout} class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class LayoutDao extends BaseDao<Layout> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(LayoutDao.class);
+
+ /**
+ * Default constructor.
+ */
+ public LayoutDao() {
+ super(Layout.class);
+ }
+
+ /**
+ * Lists layouts for the model.
+ *
+ * @param model
+ * for this model layouts will be listed
+ * @return list of layouts for the model
+ */
+ public List<Layout> getLayoutsByModel(Model model) {
+ List<Layout> layouts = getElementsByParameter("model_iddb", model.getId());
+ for (Layout layout : layouts) {
+ refresh(layout);
+ }
+ return layouts;
+ }
+
+ public List<Layout> getLayoutsByModel(Model model, User creator, Boolean isPublic) {
+ List<Pair<String, Object>> params = new ArrayList<>();
+ params.add(new Pair<String, Object>("model_iddb", model.getId()));
+ if (isPublic != null) {
+ params.add(new Pair<String, Object>("publicLayout", isPublic));
+ }
+ if (creator != null) {
+ params.add(new Pair<String, Object>("creator_iddb", creator.getId()));
+ }
+ List<Layout> layouts = getElementsByParameters(params);
+ return layouts;
+ }
+
+ /**
+ * Return number of layouts created by the user.
+ *
+ * @param user
+ * the user
+ * @return number of layouts created by the user
+ */
+ public long getCountByUser(User user) {
+ Criteria crit = getSession().createCriteria(this.getClazz());
+ crit.setProjection(Projections.rowCount());
+ crit.add(Restrictions.eq("creator", user));
+ crit.createAlias("model", "m");
+ crit.add(Restrictions.sizeLe("m.parentModels", 0));
+ return (Long) crit.uniqueResult();
+ }
+
+ /**
+ * Returns layout identified by name and model.
+ *
+ * @param model
+ * model where the layouts lay on
+ * @param name
+ * name of the layout
+ * @return layout
+ */
+ public Layout getLayoutByName(Model model, String name) {
+ List<Layout> layouts = getElementsByParameter("model_iddb", model.getId());
+ for (Layout layout : layouts) {
+ refresh(layout);
+ if (layout.getTitle().equals(name)) {
+ return layout;
+ }
+ }
+ return null;
+ }
+}
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/ModelDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/ModelDao.java
index d5f0eb8301..d4dd1ef57d 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/ModelDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/ModelDao.java
@@ -1,111 +1,111 @@
-package lcsb.mapviewer.persist.dao.map;
-
-import java.util.List;
-
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.persist.dao.BaseDao;
-
-import org.apache.log4j.Logger;
-
-/**
- * Data access object for {@link Model} class.
- *
- * @author Piotr Gawron
- *
- */
-public class ModelDao extends BaseDao<ModelData> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(ModelDao.class);
-
- /**
- * Default constructor.
- */
- public ModelDao() {
- super(ModelData.class);
- }
-
- @Override
- public void delete(ModelData model) {
- if (model.getProject() != null) {
- model.getProject().removeModel(model);
- }
- model.setProject(null);
- super.delete(model);
- }
-
- @Override
- public ModelData getById(int id) {
- ModelData result = super.getById(id);
- return result;
- }
-
- /**
- * Return the latest model for the project with a given project identifier.
- *
- * @param projectId
- * identifier of the project
- * @param lazyLoad
- * if <code>false</code>, the whole model (and all substructures)
- * should be loaded at once, if <code>true</code> then some elements
- * will be loaded on demand by hibernate proxy
- * @return the latest model for the project with a given name
- */
- public ModelData getLastModelForProjectIdentifier(String projectId, boolean lazyLoad) {
- @SuppressWarnings("unchecked")
- List<ModelData> list = getSession()
- .createQuery(
- "select model_t from " + getClazz().getSimpleName()
- + " model_t join model_t.project project_t where project_t.projectId = :project_id order by model_t.id desc")
- .setParameter("project_id", projectId).setMaxResults(1).list();
- if (list.size() > 0) {
- return list.get(0);
- } else {
- return null;
- }
- }
-
- /**
- * Adds model data to the database.
- *
- * @param model
- * object containing model data to add to database
- */
- public void add(Model model) {
- add(model.getModelData());
- }
-
- /**
- * Removes model data from the database.
- *
- * @param model
- * object containing model data
- */
- public void delete(Model model) {
- delete(model.getModelData());
- }
-
- /**
- * "Disconnects" model data from database. From this point on we cannot
- * update/delete it in the database.
- *
- * @param model
- * model containing model data to disconnect
- */
- public void evict(Model model) {
- evict(model.getModelData());
- }
-
- /**
- * Removes model data int the database.
- *
- * @param model
- * object containing model data
- */
- public void update(Model model) {
- update(model.getModelData());
- }
-}
+package lcsb.mapviewer.persist.dao.map;
+
+import java.util.List;
+
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.persist.dao.BaseDao;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Data access object for {@link Model} class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ModelDao extends BaseDao<ModelData> {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(ModelDao.class);
+
+ /**
+ * Default constructor.
+ */
+ public ModelDao() {
+ super(ModelData.class);
+ }
+
+ @Override
+ public void delete(ModelData model) {
+ if (model.getProject() != null) {
+ model.getProject().removeModel(model);
+ }
+ model.setProject(null);
+ super.delete(model);
+ }
+
+ @Override
+ public ModelData getById(int id) {
+ ModelData result = super.getById(id);
+ return result;
+ }
+
+ /**
+ * Return the latest model for the project with a given project identifier.
+ *
+ * @param projectId
+ * identifier of the project
+ * @param lazyLoad
+ * if <code>false</code>, the whole model (and all substructures)
+ * should be loaded at once, if <code>true</code> then some elements
+ * will be loaded on demand by hibernate proxy
+ * @return the latest model for the project with a given name
+ */
+ public ModelData getLastModelForProjectIdentifier(String projectId, boolean lazyLoad) {
+ @SuppressWarnings("unchecked")
+ List<ModelData> list = getSession()
+ .createQuery(
+ "select model_t from " + getClazz().getSimpleName()
+ + " model_t join model_t.project project_t where project_t.projectId = :project_id order by model_t.id desc")
+ .setParameter("project_id", projectId).setMaxResults(1).list();
+ if (list.size() > 0) {
+ return list.get(0);
+ } else {
+ return null;
+ }
+ }
+
+ /**
+ * Adds model data to the database.
+ *
+ * @param model
+ * object containing model data to add to database
+ */
+ public void add(Model model) {
+ add(model.getModelData());
+ }
+
+ /**
+ * Removes model data from the database.
+ *
+ * @param model
+ * object containing model data
+ */
+ public void delete(Model model) {
+ delete(model.getModelData());
+ }
+
+ /**
+ * "Disconnects" model data from database. From this point on we cannot
+ * update/delete it in the database.
+ *
+ * @param model
+ * model containing model data to disconnect
+ */
+ public void evict(Model model) {
+ evict(model.getModelData());
+ }
+
+ /**
+ * Removes model data int the database.
+ *
+ * @param model
+ * object containing model data
+ */
+ public void update(Model model) {
+ update(model.getModelData());
+ }
+}
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/ReactionDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/ReactionDao.java
index 38d96f03b4..c6ac698a03 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/ReactionDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/ReactionDao.java
@@ -1,21 +1,21 @@
-package lcsb.mapviewer.persist.dao.map;
-
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.persist.dao.BaseDao;
-
-/**
- * Data access object for {@link Reaction} class.
- *
- * @author Piotr Gawron
- *
- */
-public class ReactionDao extends BaseDao<Reaction> {
-
- /**
- * Default constructor.
- */
- public ReactionDao() {
- super(Reaction.class);
- }
-
-}
+package lcsb.mapviewer.persist.dao.map;
+
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.persist.dao.BaseDao;
+
+/**
+ * Data access object for {@link Reaction} class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ReactionDao extends BaseDao<Reaction> {
+
+ /**
+ * Default constructor.
+ */
+ public ReactionDao() {
+ super(Reaction.class);
+ }
+
+}
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/layout/ReferenceGenomeDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/layout/ReferenceGenomeDao.java
index 89c0d8f01f..a26a5c46e9 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/layout/ReferenceGenomeDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/layout/ReferenceGenomeDao.java
@@ -1,35 +1,35 @@
-package lcsb.mapviewer.persist.dao.map.layout;
-
-import java.util.List;
-
-import lcsb.mapviewer.model.map.layout.ReferenceGenome;
-import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
-import lcsb.mapviewer.persist.dao.BaseDao;
-
-/**
- * Data access object for {@link ReferenceGenome} objects.
- *
- * @author Piotr Gawron
- *
- */
-public class ReferenceGenomeDao extends BaseDao<ReferenceGenome> {
-
- /**
- * Default constructor.
- */
- public ReferenceGenomeDao() {
- super(ReferenceGenome.class);
- }
-
- /**
- * List all reference genomes for specific reference genome type.
- *
- * @param ucsc
- * reference genome type
- * @return list of reference genomes for a given type
- */
- public List<ReferenceGenome> getByType(ReferenceGenomeType ucsc) {
- return getElementsByParameter("type", ucsc);
- }
-
-}
+package lcsb.mapviewer.persist.dao.map.layout;
+
+import java.util.List;
+
+import lcsb.mapviewer.model.map.layout.ReferenceGenome;
+import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
+import lcsb.mapviewer.persist.dao.BaseDao;
+
+/**
+ * Data access object for {@link ReferenceGenome} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ReferenceGenomeDao extends BaseDao<ReferenceGenome> {
+
+ /**
+ * Default constructor.
+ */
+ public ReferenceGenomeDao() {
+ super(ReferenceGenome.class);
+ }
+
+ /**
+ * List all reference genomes for specific reference genome type.
+ *
+ * @param ucsc
+ * reference genome type
+ * @return list of reference genomes for a given type
+ */
+ public List<ReferenceGenome> getByType(ReferenceGenomeType ucsc) {
+ return getElementsByParameter("type", ucsc);
+ }
+
+}
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/layout/ReferenceGenomeGeneMappingDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/layout/ReferenceGenomeGeneMappingDao.java
index 271e83a956..8a1ad082e4 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/layout/ReferenceGenomeGeneMappingDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/layout/ReferenceGenomeGeneMappingDao.java
@@ -1,21 +1,21 @@
-package lcsb.mapviewer.persist.dao.map.layout;
-
-import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
-import lcsb.mapviewer.persist.dao.BaseDao;
-
-/**
- * Data access object for {@link ReferenceGenomeGeneMapping} objects.
- *
- * @author Piotr Gawron
- *
- */
-public class ReferenceGenomeGeneMappingDao extends BaseDao<ReferenceGenomeGeneMapping> {
-
- /**
- * Default constructor.
- */
- public ReferenceGenomeGeneMappingDao() {
- super(ReferenceGenomeGeneMapping.class);
- }
-
-}
+package lcsb.mapviewer.persist.dao.map.layout;
+
+import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
+import lcsb.mapviewer.persist.dao.BaseDao;
+
+/**
+ * Data access object for {@link ReferenceGenomeGeneMapping} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ReferenceGenomeGeneMappingDao extends BaseDao<ReferenceGenomeGeneMapping> {
+
+ /**
+ * Default constructor.
+ */
+ public ReferenceGenomeGeneMappingDao() {
+ super(ReferenceGenomeGeneMapping.class);
+ }
+
+}
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/layout/package-info.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/layout/package-info.java
index 0c8c186cad..522503b60b 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/layout/package-info.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/layout/package-info.java
@@ -1,5 +1,5 @@
-/**
- * Data access objects for layout substructures.
- */
-package lcsb.mapviewer.persist.dao.map.layout;
-
+/**
+ * Data access objects for layout substructures.
+ */
+package lcsb.mapviewer.persist.dao.map.layout;
+
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/package-info.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/package-info.java
index 3b751ad8ae..4a4870b438 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/package-info.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/package-info.java
@@ -1,5 +1,5 @@
-/**
- * Data access objects for model and all model substructures.
- */
-package lcsb.mapviewer.persist.dao.map;
-
+/**
+ * Data access objects for model and all model substructures.
+ */
+package lcsb.mapviewer.persist.dao.map;
+
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/species/ElementDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/species/ElementDao.java
index ab1f6f21c2..9c87afdd88 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/species/ElementDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/species/ElementDao.java
@@ -1,21 +1,21 @@
-package lcsb.mapviewer.persist.dao.map.species;
-
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.persist.dao.BaseDao;
-
-/**
- * Data Access Object class for Alias class.
- *
- * @author Piotr Gawron
- *
- */
-public class ElementDao extends BaseDao<Element> {
-
- /**
- * Default constructor.
- */
- public ElementDao() {
- super(Element.class);
- }
-
-}
+package lcsb.mapviewer.persist.dao.map.species;
+
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.persist.dao.BaseDao;
+
+/**
+ * Data Access Object class for Alias class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ElementDao extends BaseDao<Element> {
+
+ /**
+ * Default constructor.
+ */
+ public ElementDao() {
+ super(Element.class);
+ }
+
+}
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/species/package-info.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/species/package-info.java
index 34416c8284..0f52154a77 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/species/package-info.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/species/package-info.java
@@ -1,5 +1,5 @@
-/**
- * Data access objects for aliases.
- */
-package lcsb.mapviewer.persist.dao.map.species;
-
+/**
+ * Data access objects for aliases.
+ */
+package lcsb.mapviewer.persist.dao.map.species;
+
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/statistics/SearchHistoryDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/statistics/SearchHistoryDao.java
index fcba272aeb..ccc0f2b828 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/statistics/SearchHistoryDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/statistics/SearchHistoryDao.java
@@ -1,28 +1,28 @@
-package lcsb.mapviewer.persist.dao.map.statistics;
-
-import lcsb.mapviewer.model.map.statistics.SearchHistory;
-import lcsb.mapviewer.persist.dao.BaseDao;
-
-import org.apache.log4j.Logger;
-
-/**
- * Data access object for {@link SearchHistory} class.
- *
- * @author Piotr Gawron
- *
- */
-public class SearchHistoryDao extends BaseDao<SearchHistory> {
- /**
- * Default constructor.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(SearchHistoryDao.class);
-
- /**
- * Default constructor.
- */
- public SearchHistoryDao() {
- super(SearchHistory.class);
- }
-
-}
+package lcsb.mapviewer.persist.dao.map.statistics;
+
+import lcsb.mapviewer.model.map.statistics.SearchHistory;
+import lcsb.mapviewer.persist.dao.BaseDao;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Data access object for {@link SearchHistory} class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class SearchHistoryDao extends BaseDao<SearchHistory> {
+ /**
+ * Default constructor.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(SearchHistoryDao.class);
+
+ /**
+ * Default constructor.
+ */
+ public SearchHistoryDao() {
+ super(SearchHistory.class);
+ }
+
+}
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/statistics/package-info.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/statistics/package-info.java
index e831b8d856..9330947661 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/map/statistics/package-info.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/map/statistics/package-info.java
@@ -1,5 +1,5 @@
-/**
- * Data access objects for statistic structures.
- */
-package lcsb.mapviewer.persist.dao.map.statistics;
-
+/**
+ * Data access objects for statistic structures.
+ */
+package lcsb.mapviewer.persist.dao.map.statistics;
+
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/package-info.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/package-info.java
index 531a6d3fef..b16509a62e 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/package-info.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/package-info.java
@@ -1,5 +1,5 @@
-/**
- * Package with data access object for all elements in the system.
- */
-package lcsb.mapviewer.persist.dao;
-
+/**
+ * Package with data access object for all elements in the system.
+ */
+package lcsb.mapviewer.persist.dao;
+
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/plugin/PluginDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/plugin/PluginDao.java
index 23152dfabb..b802607586 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/plugin/PluginDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/plugin/PluginDao.java
@@ -1,24 +1,24 @@
-package lcsb.mapviewer.persist.dao.plugin;
-
-import lcsb.mapviewer.model.plugin.Plugin;
-import lcsb.mapviewer.persist.dao.BaseDao;
-
-/**
- * Data access object class for {@link Plugin} objects.
- *
- * @author Piotr Gawron
- *
- */
-public class PluginDao extends BaseDao<Plugin> {
- /**
- * Default constructor.
- */
- public PluginDao() {
- super(Plugin.class);
- }
-
- public Plugin getByHash(String hash) {
- return getByParameter("hash", hash);
- }
-
-}
+package lcsb.mapviewer.persist.dao.plugin;
+
+import lcsb.mapviewer.model.plugin.Plugin;
+import lcsb.mapviewer.persist.dao.BaseDao;
+
+/**
+ * Data access object class for {@link Plugin} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class PluginDao extends BaseDao<Plugin> {
+ /**
+ * Default constructor.
+ */
+ public PluginDao() {
+ super(Plugin.class);
+ }
+
+ public Plugin getByHash(String hash) {
+ return getByParameter("hash", hash);
+ }
+
+}
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/plugin/PluginDataEntryDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/plugin/PluginDataEntryDao.java
index 34eaed2a25..389b3f8587 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/plugin/PluginDataEntryDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/plugin/PluginDataEntryDao.java
@@ -1,43 +1,43 @@
-package lcsb.mapviewer.persist.dao.plugin;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.model.plugin.Plugin;
-import lcsb.mapviewer.model.plugin.PluginDataEntry;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.persist.dao.BaseDao;
-
-/**
- * Data access object class for {@link PluginDataEntry} objects.
- *
- * @author Piotr Gawron
- *
- */
-public class PluginDataEntryDao extends BaseDao<PluginDataEntry> {
- /**
- * Default constructor.
- */
- public PluginDataEntryDao() {
- super(PluginDataEntry.class);
- }
-
- public PluginDataEntry getByKey(Plugin plugin, String key, User user) {
- List<Pair<String, Object>> params = new ArrayList<>();
- params.add(new Pair<String, Object>("plugin_iddb", plugin.getId()));
- params.add(new Pair<String, Object>("entry_key", key));
- if (user == null) {
- params.add(new Pair<String, Object>("user_iddb", null));
- } else {
- params.add(new Pair<String, Object>("user_iddb", user.getId()));
- }
- List<PluginDataEntry> entries = getElementsByParameters(params);
- if (entries.size() > 0) {
- return entries.get(0);
- } else {
- return null;
- }
- }
-
-}
+package lcsb.mapviewer.persist.dao.plugin;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.model.plugin.Plugin;
+import lcsb.mapviewer.model.plugin.PluginDataEntry;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.persist.dao.BaseDao;
+
+/**
+ * Data access object class for {@link PluginDataEntry} objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class PluginDataEntryDao extends BaseDao<PluginDataEntry> {
+ /**
+ * Default constructor.
+ */
+ public PluginDataEntryDao() {
+ super(PluginDataEntry.class);
+ }
+
+ public PluginDataEntry getByKey(Plugin plugin, String key, User user) {
+ List<Pair<String, Object>> params = new ArrayList<>();
+ params.add(new Pair<String, Object>("plugin_iddb", plugin.getId()));
+ params.add(new Pair<String, Object>("entry_key", key));
+ if (user == null) {
+ params.add(new Pair<String, Object>("user_iddb", null));
+ } else {
+ params.add(new Pair<String, Object>("user_iddb", user.getId()));
+ }
+ List<PluginDataEntry> entries = getElementsByParameters(params);
+ if (entries.size() > 0) {
+ return entries.get(0);
+ } else {
+ return null;
+ }
+ }
+
+}
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/user/PrivilegeDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/user/PrivilegeDao.java
index f11297ba2b..8ca46bc775 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/user/PrivilegeDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/user/PrivilegeDao.java
@@ -1,21 +1,21 @@
-package lcsb.mapviewer.persist.dao.user;
-
-import lcsb.mapviewer.model.user.ObjectPrivilege;
-import lcsb.mapviewer.persist.dao.BaseDao;
-
-/**
- * Data access object class for Privilege objects.
- *
- * @author Piotr Gawron
- *
- */
-public class PrivilegeDao extends BaseDao<ObjectPrivilege> {
-
- /**
- * Default constructor.
- */
- public PrivilegeDao() {
- super(ObjectPrivilege.class);
- }
-
-}
+package lcsb.mapviewer.persist.dao.user;
+
+import lcsb.mapviewer.model.user.ObjectPrivilege;
+import lcsb.mapviewer.persist.dao.BaseDao;
+
+/**
+ * Data access object class for Privilege objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class PrivilegeDao extends BaseDao<ObjectPrivilege> {
+
+ /**
+ * Default constructor.
+ */
+ public PrivilegeDao() {
+ super(ObjectPrivilege.class);
+ }
+
+}
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/user/UserDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/user/UserDao.java
index b40e97920c..c6580b4b2f 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/user/UserDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/user/UserDao.java
@@ -1,72 +1,72 @@
-package lcsb.mapviewer.persist.dao.user;
-
-import java.util.List;
-
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.persist.dao.BaseDao;
-
-/**
- * Data access object class for User objects.
- *
- * @author Piotr Gawron
- *
- */
-public class UserDao extends BaseDao<User> {
-
- /**
- * Default constructor.
- */
- public UserDao() {
- super(User.class, "removed");
- }
-
- /**
- * Returns user with a given login and password.
- *
- * @param login
- * user login
- * @param password
- * - user password (encrypted)
- * @return user for given login and password
- */
- public User getUserByLoginAndCryptedPassword(String login, String password) {
- List<?> list = getSession()
- .createQuery(" from User where login=:login and cryptedPassword =:passwd " + removableAndStatemant())
- .setParameter("login", login).setParameter("passwd", password).list();
- if (list.size() == 0) {
- return null;
- } else {
- User user = (User) list.get(0);
- return user;
- }
- }
-
- /**
- * Returns user with a given login.
- *
- * @param login
- * user login
- * @return user for a given login
- */
- public User getUserByLogin(String login) {
- return getByParameter("login", login);
- }
-
- /**
- * Returns user with a given email.
- *
- * @param email
- * user email
- * @return user for a given email
- */
- public User getUserByEmail(String email) {
- return getByParameter("email", email);
- }
-
- @Override
- public void delete(User object) {
- object.setRemoved(true);
- object.setLogin("[REMOVED]_" + object.getId() + "_" + object.getLogin());
- update(object);
- }
-}
+package lcsb.mapviewer.persist.dao.user;
+
+import java.util.List;
+
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.persist.dao.BaseDao;
+
+/**
+ * Data access object class for User objects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class UserDao extends BaseDao<User> {
+
+ /**
+ * Default constructor.
+ */
+ public UserDao() {
+ super(User.class, "removed");
+ }
+
+ /**
+ * Returns user with a given login and password.
+ *
+ * @param login
+ * user login
+ * @param password
+ * - user password (encrypted)
+ * @return user for given login and password
+ */
+ public User getUserByLoginAndCryptedPassword(String login, String password) {
+ List<?> list = getSession()
+ .createQuery(" from User where login=:login and cryptedPassword =:passwd " + removableAndStatemant())
+ .setParameter("login", login).setParameter("passwd", password).list();
+ if (list.size() == 0) {
+ return null;
+ } else {
+ User user = (User) list.get(0);
+ return user;
+ }
+ }
+
+ /**
+ * Returns user with a given login.
+ *
+ * @param login
+ * user login
+ * @return user for a given login
+ */
+ public User getUserByLogin(String login) {
+ return getByParameter("login", login);
+ }
+
+ /**
+ * Returns user with a given email.
+ *
+ * @param email
+ * user email
+ * @return user for a given email
+ */
+ public User getUserByEmail(String email) {
+ return getByParameter("email", email);
+ }
+
+ @Override
+ public void delete(User object) {
+ object.setRemoved(true);
+ object.setLogin("[REMOVED]_" + object.getId() + "_" + object.getLogin());
+ update(object);
+ }
+}
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/user/package-info.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/user/package-info.java
index 815b092e71..5718df5478 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/user/package-info.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/user/package-info.java
@@ -1,5 +1,5 @@
-/**
- * Package with data access object for user, privileges, etc.
- */
-package lcsb.mapviewer.persist.dao.user;
-
+/**
+ * Package with data access object for user, privileges, etc.
+ */
+package lcsb.mapviewer.persist.dao.user;
+
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/mapper/Point2DMapper.java b/persist/src/main/java/lcsb/mapviewer/persist/mapper/Point2DMapper.java
index a3865f48a2..afab6a1aab 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/mapper/Point2DMapper.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/mapper/Point2DMapper.java
@@ -1,126 +1,126 @@
-package lcsb.mapviewer.persist.mapper;
-
-import java.awt.geom.Point2D;
-import java.io.Serializable;
-import java.sql.PreparedStatement;
-import java.sql.ResultSet;
-import java.sql.SQLException;
-
-import org.hibernate.engine.spi.SessionImplementor;
-import org.hibernate.type.StringType;
-import org.hibernate.type.Type;
-import org.hibernate.usertype.CompositeUserType;
-
-/**
- * This class allows to put {@link Point2D} objects into hibernate based models.
- *
- * @author Piotr Gawron
- *
- */
-public class Point2DMapper implements CompositeUserType {
-
- @Override
- public String[] getPropertyNames() {
- return new String[] { "val" };
- }
-
- @Override
- public Type[] getPropertyTypes() {
- return new Type[] { StringType.INSTANCE };
- }
-
- @Override
- public Object getPropertyValue(Object component, int property) {
- Object returnValue = null;
- final Point2D point = (Point2D) component;
- if (0 == property) {
- returnValue = point.getX() + "," + point.getY();
- }
- return returnValue;
- }
-
- @Override
- public void setPropertyValue(Object component, int property, Object value) {
- final Point2D point = (Point2D) component;
- if (0 == property) {
- final String[] values = ((String) value).split(",");
- point.setLocation(Double.parseDouble(values[0]), Double.parseDouble(values[1]));
- }
- }
-
- @Override
- public Class<?> returnedClass() {
- return Point2D.class;
- }
-
- @Override
- public boolean equals(Object o1, Object o2) {
- boolean isEqual = false;
- if (o1 == o2) {
- isEqual = false;
- }
- if (null == o1 || null == o2) {
- isEqual = false;
- } else {
- isEqual = o1.equals(o2);
- }
- return isEqual;
- }
-
- @Override
- public int hashCode(Object x) {
- return x.hashCode();
- }
-
- @Override
- public Object nullSafeGet(ResultSet rs, String[] names, SessionImplementor session, Object owner) throws SQLException {
- Point2D point = null;
- final String val = rs.getString(names[0]);
- if (!rs.wasNull()) {
- final String[] values = val.split(",");
- point = new Point2D.Double(Double.parseDouble(values[0]), Double.parseDouble(values[1]));
- }
- return point;
- }
-
- @Override
- public void nullSafeSet(PreparedStatement st, Object value, int property, SessionImplementor session) throws SQLException {
- if (value == null) {
- st.setNull(property, StringType.INSTANCE.sqlType());
- } else {
- final Point2D point = (Point2D) value;
- st.setString(property, point.getX() + "," + point.getY());
- }
- }
-
- @Override
- public Object deepCopy(Object value) {
- if (value == null) {
- return null;
- }
- final Point2D recievedParam = (Point2D) value;
- final Point2D point = new Point2D.Double(recievedParam.getX(), recievedParam.getY());
- return point;
- }
-
- @Override
- public boolean isMutable() {
- return true;
- }
-
- @Override
- public Serializable disassemble(Object value, SessionImplementor session) {
- return (Serializable) value;
- }
-
- @Override
- public Object assemble(Serializable cached, SessionImplementor session, Object owner) {
- return cached;
- }
-
- @Override
- public Object replace(Object original, Object target, SessionImplementor session, Object owner) {
- return this.deepCopy(original);
- }
-
-}
+package lcsb.mapviewer.persist.mapper;
+
+import java.awt.geom.Point2D;
+import java.io.Serializable;
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+
+import org.hibernate.engine.spi.SessionImplementor;
+import org.hibernate.type.StringType;
+import org.hibernate.type.Type;
+import org.hibernate.usertype.CompositeUserType;
+
+/**
+ * This class allows to put {@link Point2D} objects into hibernate based models.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class Point2DMapper implements CompositeUserType {
+
+ @Override
+ public String[] getPropertyNames() {
+ return new String[] { "val" };
+ }
+
+ @Override
+ public Type[] getPropertyTypes() {
+ return new Type[] { StringType.INSTANCE };
+ }
+
+ @Override
+ public Object getPropertyValue(Object component, int property) {
+ Object returnValue = null;
+ final Point2D point = (Point2D) component;
+ if (0 == property) {
+ returnValue = point.getX() + "," + point.getY();
+ }
+ return returnValue;
+ }
+
+ @Override
+ public void setPropertyValue(Object component, int property, Object value) {
+ final Point2D point = (Point2D) component;
+ if (0 == property) {
+ final String[] values = ((String) value).split(",");
+ point.setLocation(Double.parseDouble(values[0]), Double.parseDouble(values[1]));
+ }
+ }
+
+ @Override
+ public Class<?> returnedClass() {
+ return Point2D.class;
+ }
+
+ @Override
+ public boolean equals(Object o1, Object o2) {
+ boolean isEqual = false;
+ if (o1 == o2) {
+ isEqual = false;
+ }
+ if (null == o1 || null == o2) {
+ isEqual = false;
+ } else {
+ isEqual = o1.equals(o2);
+ }
+ return isEqual;
+ }
+
+ @Override
+ public int hashCode(Object x) {
+ return x.hashCode();
+ }
+
+ @Override
+ public Object nullSafeGet(ResultSet rs, String[] names, SessionImplementor session, Object owner) throws SQLException {
+ Point2D point = null;
+ final String val = rs.getString(names[0]);
+ if (!rs.wasNull()) {
+ final String[] values = val.split(",");
+ point = new Point2D.Double(Double.parseDouble(values[0]), Double.parseDouble(values[1]));
+ }
+ return point;
+ }
+
+ @Override
+ public void nullSafeSet(PreparedStatement st, Object value, int property, SessionImplementor session) throws SQLException {
+ if (value == null) {
+ st.setNull(property, StringType.INSTANCE.sqlType());
+ } else {
+ final Point2D point = (Point2D) value;
+ st.setString(property, point.getX() + "," + point.getY());
+ }
+ }
+
+ @Override
+ public Object deepCopy(Object value) {
+ if (value == null) {
+ return null;
+ }
+ final Point2D recievedParam = (Point2D) value;
+ final Point2D point = new Point2D.Double(recievedParam.getX(), recievedParam.getY());
+ return point;
+ }
+
+ @Override
+ public boolean isMutable() {
+ return true;
+ }
+
+ @Override
+ public Serializable disassemble(Object value, SessionImplementor session) {
+ return (Serializable) value;
+ }
+
+ @Override
+ public Object assemble(Serializable cached, SessionImplementor session, Object owner) {
+ return cached;
+ }
+
+ @Override
+ public Object replace(Object original, Object target, SessionImplementor session, Object owner) {
+ return this.deepCopy(original);
+ }
+
+}
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/mapper/package-info.java b/persist/src/main/java/lcsb/mapviewer/persist/mapper/package-info.java
index 289e600e4b..1cd2295a41 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/mapper/package-info.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/mapper/package-info.java
@@ -1,5 +1,5 @@
-/**
- * Provides mappers for build-in java objects for our hibernate based model.
- */
-package lcsb.mapviewer.persist.mapper;
-
+/**
+ * Provides mappers for build-in java objects for our hibernate based model.
+ */
+package lcsb.mapviewer.persist.mapper;
+
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/package-info.java b/persist/src/main/java/lcsb/mapviewer/persist/package-info.java
index bf6e98da43..0f558d88ba 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/package-info.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/package-info.java
@@ -1,6 +1,6 @@
-/**
- * This package contains data structures and access objects for everything
- * stored in database.
- */
-package lcsb.mapviewer.persist;
-
+/**
+ * This package contains data structures and access objects for everything
+ * stored in database.
+ */
+package lcsb.mapviewer.persist;
+
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/AllDbTests.java b/persist/src/test/java/lcsb/mapviewer/persist/AllDbTests.java
index 1b6ca5379b..b93bf18b8d 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/AllDbTests.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/AllDbTests.java
@@ -1,19 +1,19 @@
-package lcsb.mapviewer.persist;
-
-import lcsb.mapviewer.persist.dao.AllDaoTests;
-import lcsb.mapviewer.persist.mapper.Point2DMapperTest;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-
-@RunWith(Suite.class)
-@Suite.SuiteClasses({ ApplicationContextLoaderTest.class, //
- AllDaoTests.class, //
- DbUtilsTest.class, //
- Point2DMapperTest.class, //
- SpringApplicationContextTest.class,//
-
-})
-public class AllDbTests {
-
-}
+package lcsb.mapviewer.persist;
+
+import lcsb.mapviewer.persist.dao.AllDaoTests;
+import lcsb.mapviewer.persist.mapper.Point2DMapperTest;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+
+@RunWith(Suite.class)
+@Suite.SuiteClasses({ ApplicationContextLoaderTest.class, //
+ AllDaoTests.class, //
+ DbUtilsTest.class, //
+ Point2DMapperTest.class, //
+ SpringApplicationContextTest.class,//
+
+})
+public class AllDbTests {
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/ApplicationContextLoaderTest.java b/persist/src/test/java/lcsb/mapviewer/persist/ApplicationContextLoaderTest.java
index ad9a0d52a1..84c1fcef64 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/ApplicationContextLoaderTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/ApplicationContextLoaderTest.java
@@ -1,81 +1,81 @@
-package lcsb.mapviewer.persist;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-
-import java.lang.reflect.Constructor;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.context.ConfigurableApplicationContext;
-import org.springframework.context.support.ClassPathXmlApplicationContext;
-import org.springframework.security.crypto.password.PasswordEncoder;
-
-public class ApplicationContextLoaderTest {
- Logger logger = Logger.getLogger(ApplicationContextLoaderTest.class);
-
- ConfigurableApplicationContext originalContext;
-
- @Before
- public void setUp() throws Exception {
- originalContext = ApplicationContextLoader.getApplicationContext();
- ApplicationContextLoader.setApplicationContext(null);
- }
-
- @After
- public void tearDown() throws Exception {
- ApplicationContextLoader.setApplicationContext(originalContext);
- }
-
- @Test
- public void testGetters() {
- ConfigurableApplicationContext context = new ClassPathXmlApplicationContext("/test-applicationContext2.xml");
- ApplicationContextLoader.setApplicationContext(context);
- assertEquals(context, ApplicationContextLoader.getApplicationContext());
- }
-
- @Test
- public void testLoadApplicationContext() {
- ApplicationContextLoader.loadApplicationContext("/test-applicationContext2.xml");
- assertNotNull(ApplicationContextLoader.getApplicationContext());
- }
-
- @Test
- public void testInject() {
- try {
- class Tmp {
- @Autowired
- private PasswordEncoder encoder;
-
- }
- ;
- Tmp obj = new Tmp();
- ApplicationContextLoader.loadApplicationContext("test-applicationContext2.xml");
- ApplicationContextLoader.injectDependencies(obj);
- assertNotNull(obj.encoder);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testPrivateConstructor() throws Exception {
-
- try {
- for (Constructor<?> constructor : ApplicationContextLoader.class.getDeclaredConstructors()) {
- logger.debug(constructor);
- constructor.setAccessible(true);
- ApplicationContextLoader obj = (ApplicationContextLoader) constructor.newInstance(new Object[] {});
- assertNotNull(obj);
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.persist;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import java.lang.reflect.Constructor;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.ConfigurableApplicationContext;
+import org.springframework.context.support.ClassPathXmlApplicationContext;
+import org.springframework.security.crypto.password.PasswordEncoder;
+
+public class ApplicationContextLoaderTest {
+ Logger logger = Logger.getLogger(ApplicationContextLoaderTest.class);
+
+ ConfigurableApplicationContext originalContext;
+
+ @Before
+ public void setUp() throws Exception {
+ originalContext = ApplicationContextLoader.getApplicationContext();
+ ApplicationContextLoader.setApplicationContext(null);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ ApplicationContextLoader.setApplicationContext(originalContext);
+ }
+
+ @Test
+ public void testGetters() {
+ ConfigurableApplicationContext context = new ClassPathXmlApplicationContext("/test-applicationContext2.xml");
+ ApplicationContextLoader.setApplicationContext(context);
+ assertEquals(context, ApplicationContextLoader.getApplicationContext());
+ }
+
+ @Test
+ public void testLoadApplicationContext() {
+ ApplicationContextLoader.loadApplicationContext("/test-applicationContext2.xml");
+ assertNotNull(ApplicationContextLoader.getApplicationContext());
+ }
+
+ @Test
+ public void testInject() {
+ try {
+ class Tmp {
+ @Autowired
+ private PasswordEncoder encoder;
+
+ }
+ ;
+ Tmp obj = new Tmp();
+ ApplicationContextLoader.loadApplicationContext("test-applicationContext2.xml");
+ ApplicationContextLoader.injectDependencies(obj);
+ assertNotNull(obj.encoder);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testPrivateConstructor() throws Exception {
+
+ try {
+ for (Constructor<?> constructor : ApplicationContextLoader.class.getDeclaredConstructors()) {
+ logger.debug(constructor);
+ constructor.setAccessible(true);
+ ApplicationContextLoader obj = (ApplicationContextLoader) constructor.newInstance(new Object[] {});
+ assertNotNull(obj);
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/DbUtilsTest.java b/persist/src/test/java/lcsb/mapviewer/persist/DbUtilsTest.java
index 3cdd131d74..894b3002b1 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/DbUtilsTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/DbUtilsTest.java
@@ -1,69 +1,69 @@
-package lcsb.mapviewer.persist;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.apache.log4j.Logger;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidStateException;
-
-public class DbUtilsTest extends PersistTestFunctions {
- Logger logger = Logger.getLogger(DbUtilsTest.class);
-
- @Test
- public void testSchema() throws Exception {
- try {
- dbUtils.executeSqlQuery("update user_table set idDb = 1 where idDb =1");
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateSession() throws Exception {
- try {
- assertFalse(dbUtils.isCustomSessionForCurrentThread());
- dbUtils.createSessionForCurrentThread();
- assertTrue(dbUtils.isCustomSessionForCurrentThread());
- assertEquals(1, dbUtils.getSessionCounter());
- dbUtils.closeSessionForCurrentThread();
- assertFalse(dbUtils.isCustomSessionForCurrentThread());
- assertEquals(0, dbUtils.getSessionCounter());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateInvalidSession() throws Exception {
- try {
- dbUtils.createSessionForCurrentThread();
- dbUtils.createSessionForCurrentThread();
- fail("Exception expected");
- } catch (InvalidStateException e) {
- dbUtils.closeSessionForCurrentThread();
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAutoFlush() {
- try {
- boolean autoflush = dbUtils.isAutoFlush();
- dbUtils.setAutoFlush(false);
- assertFalse(dbUtils.isAutoFlush());
- dbUtils.setAutoFlush(autoflush);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.persist;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.apache.log4j.Logger;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.exception.InvalidStateException;
+
+public class DbUtilsTest extends PersistTestFunctions {
+ Logger logger = Logger.getLogger(DbUtilsTest.class);
+
+ @Test
+ public void testSchema() throws Exception {
+ try {
+ dbUtils.executeSqlQuery("update user_table set idDb = 1 where idDb =1");
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCreateSession() throws Exception {
+ try {
+ assertFalse(dbUtils.isCustomSessionForCurrentThread());
+ dbUtils.createSessionForCurrentThread();
+ assertTrue(dbUtils.isCustomSessionForCurrentThread());
+ assertEquals(1, dbUtils.getSessionCounter());
+ dbUtils.closeSessionForCurrentThread();
+ assertFalse(dbUtils.isCustomSessionForCurrentThread());
+ assertEquals(0, dbUtils.getSessionCounter());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCreateInvalidSession() throws Exception {
+ try {
+ dbUtils.createSessionForCurrentThread();
+ dbUtils.createSessionForCurrentThread();
+ fail("Exception expected");
+ } catch (InvalidStateException e) {
+ dbUtils.closeSessionForCurrentThread();
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAutoFlush() {
+ try {
+ boolean autoflush = dbUtils.isAutoFlush();
+ dbUtils.setAutoFlush(false);
+ assertFalse(dbUtils.isAutoFlush());
+ dbUtils.setAutoFlush(autoflush);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/PersistTestFunctions.java b/persist/src/test/java/lcsb/mapviewer/persist/PersistTestFunctions.java
index 80cdbd417b..8f6d58b19e 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/PersistTestFunctions.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/PersistTestFunctions.java
@@ -1,296 +1,296 @@
-package lcsb.mapviewer.persist;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.Reader;
-import java.io.StringReader;
-import java.io.StringWriter;
-import java.io.UnsupportedEncodingException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.util.Arrays;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.transform.OutputKeys;
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerException;
-import javax.xml.transform.TransformerFactory;
-import javax.xml.transform.dom.DOMSource;
-import javax.xml.transform.stream.StreamResult;
-
-import org.apache.log4j.Logger;
-import org.junit.runner.RunWith;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.security.crypto.password.PasswordEncoder;
-import org.springframework.test.annotation.Rollback;
-import org.springframework.test.context.ContextConfiguration;
-import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
-import org.springframework.transaction.annotation.Transactional;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-import org.xml.sax.InputSource;
-import org.xml.sax.SAXException;
-
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.persist.dao.ProjectDao;
-import lcsb.mapviewer.persist.dao.cache.CacheQueryDao;
-import lcsb.mapviewer.persist.dao.cache.CacheTypeDao;
-import lcsb.mapviewer.persist.dao.graphics.PolylineDao;
-import lcsb.mapviewer.persist.dao.log.LogDao;
-import lcsb.mapviewer.persist.dao.map.CommentDao;
-import lcsb.mapviewer.persist.dao.map.ModelDao;
-import lcsb.mapviewer.persist.dao.map.ReactionDao;
-import lcsb.mapviewer.persist.dao.map.species.ElementDao;
-import lcsb.mapviewer.persist.dao.map.statistics.SearchHistoryDao;
-import lcsb.mapviewer.persist.dao.user.PrivilegeDao;
-import lcsb.mapviewer.persist.dao.user.UserDao;
-
-@Transactional(value = "txManager")
-@Rollback(true)
-@ContextConfiguration(locations = { "/applicationContext-persist.xml", //
- "/test-applicationContext.xml", //
- "/dataSource.xml" //
-})
-@RunWith(SpringJUnit4ClassRunner.class)
-public abstract class PersistTestFunctions {
- private Logger logger = Logger.getLogger(PersistTestFunctions.class);
-
- public double EPSILON = 1e-6;
-
- @Autowired
- protected LogDao logDao;
-
- @Autowired
- protected SearchHistoryDao searchHistoryDao;
-
- @Autowired
- private PasswordEncoder passwordEncoder;
-
- @Autowired
- protected ProjectDao projectDao;
-
- @Autowired
- protected CacheQueryDao cacheQueryDao;
-
- @Autowired
- protected PolylineDao polylineDao;
-
- @Autowired
- protected ModelDao modelDao;
-
- @Autowired
- protected UserDao userDao;
-
- @Autowired
- protected PrivilegeDao privilegeDao;
-
- @Autowired
- protected CommentDao commentDao;
-
- @Autowired
- protected DbUtils dbUtils;
-
- @Autowired
- protected ReactionDao reactionDao;
-
- @Autowired
- protected ElementDao elementDao;
-
- protected User user;
-
- @Autowired
- protected CacheTypeDao cacheTypeDao;
-
- protected String readFile(String file) throws IOException {
- StringBuilder stringBuilder = new StringBuilder();
- BufferedReader reader = new BufferedReader(new FileReader(file));
- try {
- String line = null;
- String ls = System.getProperty("line.separator");
-
- while ((line = reader.readLine()) != null) {
- stringBuilder.append(line);
- stringBuilder.append(ls);
- }
- } finally {
- reader.close();
- }
-
- return stringBuilder.toString();
- }
-
- protected Node getNodeFromXmlString(String text) throws InvalidXmlSchemaException {
- InputSource is = new InputSource();
- is.setCharacterStream(new StringReader(text));
- return getXmlDocumentFromInputSource(is).getChildNodes().item(0);
- }
-
- protected Document getXmlDocumentFromFile(String fileName) throws InvalidXmlSchemaException, IOException {
- File file = new File(fileName);
- InputStream inputStream = new FileInputStream(file);
- Reader reader = null;
- try {
- reader = new InputStreamReader(inputStream, "UTF-8");
- InputSource is = new InputSource(reader);
-
- Document result = getXmlDocumentFromInputSource(is);
- inputStream.close();
- return result;
- } catch (UnsupportedEncodingException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- return null;
- }
-
- protected Document getXmlDocumentFromInputSource(InputSource stream) throws InvalidXmlSchemaException {
- DocumentBuilder db;
- try {
- db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
- } catch (ParserConfigurationException e) {
- throw new InvalidXmlSchemaException("Problem with xml parser");
- }
- Document doc = null;
- try {
- doc = db.parse(stream);
- } catch (SAXException e) {
- logger.error(e);
- } catch (IOException e) {
- logger.error(e);
- }
- return doc;
- }
-
- /**
- * This method remove model with all connections from db (used only when the db
- * must be handled manually)
- *
- * @param id
- */
- protected void removeModelById(int id) {
- modelDao.delete(modelDao.getById(id));
- }
-
- protected void createUser() {
- user = new User();
- user.setName("John");
- user.setSurname("Doe");
- user.setEmail("john.doe@uni.lu");
- user.setLogin("john.doe");
- user.setCryptedPassword(passwordEncoder.encode("passwd"));
- userDao.add(user);
- }
-
- protected String createTmpFileName() {
- try {
- File f = File.createTempFile("prefix", ".txt");
- String filename = f.getName();
- f.delete();
- return filename;
- } catch (IOException e) {
- e.printStackTrace();
- return null;
- }
- }
-
- protected String nodeToString(Node node) {
- return nodeToString(node, false);
- }
-
- protected String nodeToString(Node node, boolean includeHeadNode) {
- if (node == null)
- return null;
- StringWriter sw = new StringWriter();
- try {
- Transformer t = TransformerFactory.newInstance().newTransformer();
- t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
- t.setOutputProperty(OutputKeys.INDENT, "yes");
- t.setOutputProperty(OutputKeys.METHOD, "xml");
-
- NodeList list = node.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node element = list.item(i);
- t.transform(new DOMSource(element), new StreamResult(sw));
- }
- } catch (TransformerException te) {
- logger.debug("nodeToString Transformer Exception");
- }
- if (includeHeadNode) {
- return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
- }
- return sw.toString();
- }
-
- protected boolean equalFiles(String fileA, String fileB) throws IOException {
- int BLOCK_SIZE = 65536;
- FileInputStream inputStreamA = new FileInputStream(fileA);
- FileInputStream inputStreamB = new FileInputStream(fileB);
- // vary BLOCK_SIZE to suit yourself.
- // it should probably a factor or multiple of the size of a disk
- // sector/cluster.
- // Note that your max heap size may need to be adjused
- // if you have a very big block size or lots of these comparators.
-
- // assume inputStreamA and inputStreamB are streams from your two files.
- byte[] streamABlock = new byte[BLOCK_SIZE];
- byte[] streamBBlock = new byte[BLOCK_SIZE];
- boolean match = true;
- int bytesReadA = 0;
- int bytesReadB = 0;
- do {
- bytesReadA = inputStreamA.read(streamABlock);
- bytesReadB = inputStreamB.read(streamBBlock);
- match = ((bytesReadA == bytesReadB) && Arrays.equals(streamABlock, streamBBlock));
- } while (match && (bytesReadA > -1));
- inputStreamA.close();
- inputStreamB.close();
- return match;
- }
-
- public PrivilegeDao getPrivilegeDao() {
- return privilegeDao;
- }
-
- public void setPrivilegeDao(PrivilegeDao privilegeDao) {
- this.privilegeDao = privilegeDao;
- }
-
- public File createTempDirectory() throws IOException {
- final File temp;
-
- temp = File.createTempFile("temp", Long.toString(System.nanoTime()));
-
- if (!(temp.delete())) {
- throw new IOException("Could not delete temp file: " + temp.getAbsolutePath());
- }
-
- if (!(temp.mkdir())) {
- throw new IOException("Could not create temp directory: " + temp.getAbsolutePath());
- }
-
- return (temp);
- }
-
- protected String getWebpage(String accessUrl) throws IOException {
- String inputLine;
- StringBuilder tmp = new StringBuilder();
- URL url = new URL(accessUrl);
- URLConnection urlConn = url.openConnection();
- BufferedReader in = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));
-
- while ((inputLine = in.readLine()) != null) {
- tmp.append(inputLine);
- }
- in.close();
- return tmp.toString();
- }
-}
+package lcsb.mapviewer.persist;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.io.StringReader;
+import java.io.StringWriter;
+import java.io.UnsupportedEncodingException;
+import java.net.URL;
+import java.net.URLConnection;
+import java.util.Arrays;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.OutputKeys;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerException;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.dom.DOMSource;
+import javax.xml.transform.stream.StreamResult;
+
+import org.apache.log4j.Logger;
+import org.junit.runner.RunWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.security.crypto.password.PasswordEncoder;
+import org.springframework.test.annotation.Rollback;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
+import org.springframework.transaction.annotation.Transactional;
+import org.w3c.dom.Document;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.persist.dao.ProjectDao;
+import lcsb.mapviewer.persist.dao.cache.CacheQueryDao;
+import lcsb.mapviewer.persist.dao.cache.CacheTypeDao;
+import lcsb.mapviewer.persist.dao.graphics.PolylineDao;
+import lcsb.mapviewer.persist.dao.log.LogDao;
+import lcsb.mapviewer.persist.dao.map.CommentDao;
+import lcsb.mapviewer.persist.dao.map.ModelDao;
+import lcsb.mapviewer.persist.dao.map.ReactionDao;
+import lcsb.mapviewer.persist.dao.map.species.ElementDao;
+import lcsb.mapviewer.persist.dao.map.statistics.SearchHistoryDao;
+import lcsb.mapviewer.persist.dao.user.PrivilegeDao;
+import lcsb.mapviewer.persist.dao.user.UserDao;
+
+@Transactional(value = "txManager")
+@Rollback(true)
+@ContextConfiguration(locations = { "/applicationContext-persist.xml", //
+ "/test-applicationContext.xml", //
+ "/dataSource.xml" //
+})
+@RunWith(SpringJUnit4ClassRunner.class)
+public abstract class PersistTestFunctions {
+ private Logger logger = Logger.getLogger(PersistTestFunctions.class);
+
+ public double EPSILON = 1e-6;
+
+ @Autowired
+ protected LogDao logDao;
+
+ @Autowired
+ protected SearchHistoryDao searchHistoryDao;
+
+ @Autowired
+ private PasswordEncoder passwordEncoder;
+
+ @Autowired
+ protected ProjectDao projectDao;
+
+ @Autowired
+ protected CacheQueryDao cacheQueryDao;
+
+ @Autowired
+ protected PolylineDao polylineDao;
+
+ @Autowired
+ protected ModelDao modelDao;
+
+ @Autowired
+ protected UserDao userDao;
+
+ @Autowired
+ protected PrivilegeDao privilegeDao;
+
+ @Autowired
+ protected CommentDao commentDao;
+
+ @Autowired
+ protected DbUtils dbUtils;
+
+ @Autowired
+ protected ReactionDao reactionDao;
+
+ @Autowired
+ protected ElementDao elementDao;
+
+ protected User user;
+
+ @Autowired
+ protected CacheTypeDao cacheTypeDao;
+
+ protected String readFile(String file) throws IOException {
+ StringBuilder stringBuilder = new StringBuilder();
+ BufferedReader reader = new BufferedReader(new FileReader(file));
+ try {
+ String line = null;
+ String ls = System.getProperty("line.separator");
+
+ while ((line = reader.readLine()) != null) {
+ stringBuilder.append(line);
+ stringBuilder.append(ls);
+ }
+ } finally {
+ reader.close();
+ }
+
+ return stringBuilder.toString();
+ }
+
+ protected Node getNodeFromXmlString(String text) throws InvalidXmlSchemaException {
+ InputSource is = new InputSource();
+ is.setCharacterStream(new StringReader(text));
+ return getXmlDocumentFromInputSource(is).getChildNodes().item(0);
+ }
+
+ protected Document getXmlDocumentFromFile(String fileName) throws InvalidXmlSchemaException, IOException {
+ File file = new File(fileName);
+ InputStream inputStream = new FileInputStream(file);
+ Reader reader = null;
+ try {
+ reader = new InputStreamReader(inputStream, "UTF-8");
+ InputSource is = new InputSource(reader);
+
+ Document result = getXmlDocumentFromInputSource(is);
+ inputStream.close();
+ return result;
+ } catch (UnsupportedEncodingException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ return null;
+ }
+
+ protected Document getXmlDocumentFromInputSource(InputSource stream) throws InvalidXmlSchemaException {
+ DocumentBuilder db;
+ try {
+ db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
+ } catch (ParserConfigurationException e) {
+ throw new InvalidXmlSchemaException("Problem with xml parser");
+ }
+ Document doc = null;
+ try {
+ doc = db.parse(stream);
+ } catch (SAXException e) {
+ logger.error(e);
+ } catch (IOException e) {
+ logger.error(e);
+ }
+ return doc;
+ }
+
+ /**
+ * This method remove model with all connections from db (used only when the db
+ * must be handled manually)
+ *
+ * @param id
+ */
+ protected void removeModelById(int id) {
+ modelDao.delete(modelDao.getById(id));
+ }
+
+ protected void createUser() {
+ user = new User();
+ user.setName("John");
+ user.setSurname("Doe");
+ user.setEmail("john.doe@uni.lu");
+ user.setLogin("john.doe");
+ user.setCryptedPassword(passwordEncoder.encode("passwd"));
+ userDao.add(user);
+ }
+
+ protected String createTmpFileName() {
+ try {
+ File f = File.createTempFile("prefix", ".txt");
+ String filename = f.getName();
+ f.delete();
+ return filename;
+ } catch (IOException e) {
+ e.printStackTrace();
+ return null;
+ }
+ }
+
+ protected String nodeToString(Node node) {
+ return nodeToString(node, false);
+ }
+
+ protected String nodeToString(Node node, boolean includeHeadNode) {
+ if (node == null)
+ return null;
+ StringWriter sw = new StringWriter();
+ try {
+ Transformer t = TransformerFactory.newInstance().newTransformer();
+ t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
+ t.setOutputProperty(OutputKeys.INDENT, "yes");
+ t.setOutputProperty(OutputKeys.METHOD, "xml");
+
+ NodeList list = node.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node element = list.item(i);
+ t.transform(new DOMSource(element), new StreamResult(sw));
+ }
+ } catch (TransformerException te) {
+ logger.debug("nodeToString Transformer Exception");
+ }
+ if (includeHeadNode) {
+ return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
+ }
+ return sw.toString();
+ }
+
+ protected boolean equalFiles(String fileA, String fileB) throws IOException {
+ int BLOCK_SIZE = 65536;
+ FileInputStream inputStreamA = new FileInputStream(fileA);
+ FileInputStream inputStreamB = new FileInputStream(fileB);
+ // vary BLOCK_SIZE to suit yourself.
+ // it should probably a factor or multiple of the size of a disk
+ // sector/cluster.
+ // Note that your max heap size may need to be adjused
+ // if you have a very big block size or lots of these comparators.
+
+ // assume inputStreamA and inputStreamB are streams from your two files.
+ byte[] streamABlock = new byte[BLOCK_SIZE];
+ byte[] streamBBlock = new byte[BLOCK_SIZE];
+ boolean match = true;
+ int bytesReadA = 0;
+ int bytesReadB = 0;
+ do {
+ bytesReadA = inputStreamA.read(streamABlock);
+ bytesReadB = inputStreamB.read(streamBBlock);
+ match = ((bytesReadA == bytesReadB) && Arrays.equals(streamABlock, streamBBlock));
+ } while (match && (bytesReadA > -1));
+ inputStreamA.close();
+ inputStreamB.close();
+ return match;
+ }
+
+ public PrivilegeDao getPrivilegeDao() {
+ return privilegeDao;
+ }
+
+ public void setPrivilegeDao(PrivilegeDao privilegeDao) {
+ this.privilegeDao = privilegeDao;
+ }
+
+ public File createTempDirectory() throws IOException {
+ final File temp;
+
+ temp = File.createTempFile("temp", Long.toString(System.nanoTime()));
+
+ if (!(temp.delete())) {
+ throw new IOException("Could not delete temp file: " + temp.getAbsolutePath());
+ }
+
+ if (!(temp.mkdir())) {
+ throw new IOException("Could not create temp directory: " + temp.getAbsolutePath());
+ }
+
+ return (temp);
+ }
+
+ protected String getWebpage(String accessUrl) throws IOException {
+ String inputLine;
+ StringBuilder tmp = new StringBuilder();
+ URL url = new URL(accessUrl);
+ URLConnection urlConn = url.openConnection();
+ BufferedReader in = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));
+
+ while ((inputLine = in.readLine()) != null) {
+ tmp.append(inputLine);
+ }
+ in.close();
+ return tmp.toString();
+ }
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/SpringApplicationContextTest.java b/persist/src/test/java/lcsb/mapviewer/persist/SpringApplicationContextTest.java
index 512df2006e..30dae41a84 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/SpringApplicationContextTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/SpringApplicationContextTest.java
@@ -1,29 +1,29 @@
-package lcsb.mapviewer.persist;
-
-import static org.junit.Assert.*;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class SpringApplicationContextTest extends PersistTestFunctions {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetter() {
- assertNotNull(SpringApplicationContext.getApplicationContext());
- }
-
- @Test
- public void testGetBean() {
- assertNotNull(SpringApplicationContext.getBean("DbUtils"));
- }
-
-}
+package lcsb.mapviewer.persist;
+
+import static org.junit.Assert.*;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class SpringApplicationContextTest extends PersistTestFunctions {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetter() {
+ assertNotNull(SpringApplicationContext.getApplicationContext());
+ }
+
+ @Test
+ public void testGetBean() {
+ assertNotNull(SpringApplicationContext.getBean("DbUtils"));
+ }
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/AllDaoTests.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/AllDaoTests.java
index 50e07ae2b1..40344ac58c 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/AllDaoTests.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/AllDaoTests.java
@@ -1,27 +1,27 @@
-package lcsb.mapviewer.persist.dao;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-
-import lcsb.mapviewer.persist.dao.cache.AllCacheDbTests;
-import lcsb.mapviewer.persist.dao.graphics.AllGraphicsDaoTests;
-import lcsb.mapviewer.persist.dao.log.AllLogTests;
-import lcsb.mapviewer.persist.dao.map.AllMapDaoTests;
-import lcsb.mapviewer.persist.dao.plugin.AllPluginTests;
-import lcsb.mapviewer.persist.dao.user.AllUserTests;
-
-@RunWith(Suite.class)
-@Suite.SuiteClasses({ AllCacheDbTests.class, //
- AllGraphicsDaoTests.class, //
- AllLogTests.class, //
- AllMapDaoTests.class, //
- AllPluginTests.class, //
- AllUserTests.class, //
- BaseDaoTest.class, //
- ConfigurationDaoTest.class, //
- ProjectDaoTest.class, //
-
-})
-public class AllDaoTests {
-
-}
+package lcsb.mapviewer.persist.dao;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+
+import lcsb.mapviewer.persist.dao.cache.AllCacheDbTests;
+import lcsb.mapviewer.persist.dao.graphics.AllGraphicsDaoTests;
+import lcsb.mapviewer.persist.dao.log.AllLogTests;
+import lcsb.mapviewer.persist.dao.map.AllMapDaoTests;
+import lcsb.mapviewer.persist.dao.plugin.AllPluginTests;
+import lcsb.mapviewer.persist.dao.user.AllUserTests;
+
+@RunWith(Suite.class)
+@Suite.SuiteClasses({ AllCacheDbTests.class, //
+ AllGraphicsDaoTests.class, //
+ AllLogTests.class, //
+ AllMapDaoTests.class, //
+ AllPluginTests.class, //
+ AllUserTests.class, //
+ BaseDaoTest.class, //
+ ConfigurationDaoTest.class, //
+ ProjectDaoTest.class, //
+
+})
+public class AllDaoTests {
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/BaseDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/BaseDaoTest.java
index 306550e4c0..7b77f30315 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/BaseDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/BaseDaoTest.java
@@ -1,45 +1,45 @@
-package lcsb.mapviewer.persist.dao;
-
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-
-import org.hibernate.Transaction;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.test.annotation.Rollback;
-
-import lcsb.mapviewer.persist.PersistTestFunctions;
-
-@Rollback(false)
-public class BaseDaoTest extends PersistTestFunctions{
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testCommit() {
- try {
-
- dbUtils.createSessionForCurrentThread();
- Transaction tr = userDao.getSession().getTransaction();
- userDao.commit();
- assertTrue(tr.equals(tr));
- Transaction tr2 = userDao.getSession().getTransaction();
-
- assertFalse(tr.equals(tr2));
-
- dbUtils.closeSessionForCurrentThread();
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.persist.dao;
+
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import org.hibernate.Transaction;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.test.annotation.Rollback;
+
+import lcsb.mapviewer.persist.PersistTestFunctions;
+
+@Rollback(false)
+public class BaseDaoTest extends PersistTestFunctions{
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testCommit() {
+ try {
+
+ dbUtils.createSessionForCurrentThread();
+ Transaction tr = userDao.getSession().getTransaction();
+ userDao.commit();
+ assertTrue(tr.equals(tr));
+ Transaction tr2 = userDao.getSession().getTransaction();
+
+ assertFalse(tr.equals(tr2));
+
+ dbUtils.closeSessionForCurrentThread();
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/ConfigurationDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/ConfigurationDaoTest.java
index 4a0573def4..096a39ad68 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/ConfigurationDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/ConfigurationDaoTest.java
@@ -1,50 +1,50 @@
-package lcsb.mapviewer.persist.dao;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.model.user.ConfigurationElementType;
-import lcsb.mapviewer.model.user.ConfigurationOption;
-import lcsb.mapviewer.persist.PersistTestFunctions;
-
-public class ConfigurationDaoTest extends PersistTestFunctions {
- @Autowired
- protected ConfigurationDao configurationDao;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetNull() {
- assertNull(configurationDao.getByType(null));
- }
-
- @Test
- public void testGetValueByType() {
- // check data for null input (failsafe test)
- assertNull(configurationDao.getValueByType(null));
-
- // check data for something that is in database
- String val = configurationDao.getValueByType(ConfigurationElementType.LOGO_TEXT);
- assertNotNull(val);
-
- // remove data from database
- ConfigurationOption obj = configurationDao.getByType(ConfigurationElementType.LOGO_TEXT);
- configurationDao.delete(obj);
-
- // and now check data for something that is not in database
- assertNotNull(configurationDao.getValueByType(ConfigurationElementType.LOGO_TEXT));
-
- }
-
-}
+package lcsb.mapviewer.persist.dao;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.model.user.ConfigurationElementType;
+import lcsb.mapviewer.model.user.ConfigurationOption;
+import lcsb.mapviewer.persist.PersistTestFunctions;
+
+public class ConfigurationDaoTest extends PersistTestFunctions {
+ @Autowired
+ protected ConfigurationDao configurationDao;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetNull() {
+ assertNull(configurationDao.getByType(null));
+ }
+
+ @Test
+ public void testGetValueByType() {
+ // check data for null input (failsafe test)
+ assertNull(configurationDao.getValueByType(null));
+
+ // check data for something that is in database
+ String val = configurationDao.getValueByType(ConfigurationElementType.LOGO_TEXT);
+ assertNotNull(val);
+
+ // remove data from database
+ ConfigurationOption obj = configurationDao.getByType(ConfigurationElementType.LOGO_TEXT);
+ configurationDao.delete(obj);
+
+ // and now check data for something that is not in database
+ assertNotNull(configurationDao.getValueByType(ConfigurationElementType.LOGO_TEXT));
+
+ }
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/ProjectDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/ProjectDaoTest.java
index 69b7cad5e9..a534023046 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/ProjectDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/ProjectDaoTest.java
@@ -1,311 +1,311 @@
-package lcsb.mapviewer.persist.dao;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.OverviewImage;
-import lcsb.mapviewer.model.map.OverviewModelLink;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.persist.PersistTestFunctions;
-
-public class ProjectDaoTest extends PersistTestFunctions {
- Logger logger = Logger.getLogger(ProjectDaoTest.class);
- int identifierCounter = 0;
- String projectId = "Some_id";
-
- @Before
- public void setUp() throws Exception {
- Project project = projectDao.getProjectByProjectId(projectId);
- if (project != null) {
- projectDao.delete(project);
- }
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetProjectByName() throws Exception {
- try {
- Project project = new Project();
- project.setProjectId(projectId);
- projectDao.add(project);
- projectDao.evict(project);
-
- Project project2 = projectDao.getProjectByProjectId(projectId);
- assertNotNull(project2);
- assertFalse(project2.equals(project));
- assertEquals(project.getId(), project2.getId());
-
- projectDao.delete(project2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetProjectForModelId() throws Exception {
- try {
- String projectId = "Some name";
- Project project = new Project();
- project.setProjectId(projectId);
- projectDao.add(project);
- Model model = new ModelFullIndexed(null);
- project.addModel(model);
- modelDao.add(model);
- modelDao.evict(model);
- projectDao.evict(project);
-
- Project project2 = projectDao.getProjectForModelId(model.getId());
- assertNotNull(project2);
- assertFalse(project2.equals(project));
- assertEquals(project.getId(), project2.getId());
-
- modelDao.delete(modelDao.getById(model.getId()));
- projectDao.delete(project2);
-
- assertNull(projectDao.getProjectForModelId(model.getId()));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProjectExists() throws Exception {
- try {
- String projectId = "Some_id";
- Project project = new Project();
- project.setProjectId(projectId);
-
- assertFalse(projectDao.isProjectExistsByName(projectId));
-
- projectDao.add(project);
- projectDao.evict(project);
-
- assertTrue(projectDao.isProjectExistsByName(projectId));
-
- Project project2 = projectDao.getProjectByProjectId(projectId);
-
- projectDao.delete(project2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCheckEqualityAfterReload() throws Exception {
- try {
-
- String projectId = "Some_id";
- Project project = new Project();
- project.setProjectId(projectId);
- projectDao.add(project);
- projectDao.flush();
-
- Model model = createModel();
- project.addModel(model);
-
- projectDao.update(project);
- projectDao.evict(project);
-
- ModelComparator comparator = new ModelComparator();
-
- Model model2 = new ModelFullIndexed(modelDao.getLastModelForProjectIdentifier(projectId, false));
-
- assertEquals(0, comparator.compare(model, model2));
-
- projectDao.delete(projectDao.getById(project.getId()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCheckEqualityAfterReload2() throws Exception {
- try {
- String project_id = "Some_id";
- Project project = new Project();
- project.setProjectId(project_id);
- Model model = createModel();
- project.addModel(model);
-
- projectDao.add(project);
- projectDao.evict(project);
-
- Project project2 = projectDao.getProjectByProjectId(project_id);
-
- ModelComparator comparator = new ModelComparator();
-
- Model fullModel1 = new ModelFullIndexed(project.getModels().iterator().next());
- Model fullModel2 = new ModelFullIndexed(project2.getModels().iterator().next());
- assertEquals(0, comparator.compare(fullModel1, fullModel2));
-
- projectDao.delete(project2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private Model createModel() {
- Model model = new ModelFullIndexed(null);
-
- model.addElement(createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "sa2"));
- model.addElement(createSpeciesAlias(267.6666666666665, 438.75, 80.0, 40.0, "sa1117"));
- model.addElement(createSpeciesAlias(261.6666666666665, 600.75, 92.0, 52.0, "sa1119"));
- model.addElement(createSpeciesAlias(203.666666666667, 687.75, 98.0, 58.0, "sa1121"));
-
- Species alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
- Species alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
- Complex alias3 = createComplexAlias(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
- alias3.addSpecies(alias);
- alias3.addSpecies(alias2);
- alias.setComplex(alias3);
- alias2.setComplex(alias3);
-
- model.addElement(alias);
- model.addElement(alias2);
- model.addElement(alias3);
-
- model.addElement(createCompartmentAlias(380.0, 416.0, 1893.0, 1866.0, "ca1"));
- model.setWidth(2000);
- model.setHeight(2000);
- return model;
- }
-
- private Compartment createCompartmentAlias(double x, double y, double width, double height, String aliasId) {
- Compartment alias = new Compartment(aliasId);
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
- }
-
- private Species createSpeciesAlias(double x, double y, double width, double height, String aliasId) {
- Species alias = new SimpleMolecule(aliasId);
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
- }
-
- private Complex createComplexAlias(double x, double y, double width, double height, String aliasId) {
- Complex alias = new Complex(aliasId);
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
- }
-
- @Test
- public void testAddGetProjectWithOverviewImage() throws Exception {
- try {
- String projectId = "Some_id";
- Project project = new Project();
- project.setProjectId(projectId);
- Model model = new ModelFullIndexed(null);
- OverviewImage oi = new OverviewImage();
- oi.setFilename("test");
- OverviewModelLink oml = new OverviewModelLink();
- oml.setPolygon("10,10 20,20 20,100");
- oml.setxCoord(1);
- oml.setyCoord(2);
- oml.setZoomLevel(3);
- oi.addLink(oml);
- project.addOverviewImage(oi);
- project.addModel(model);
-
- projectDao.add(project);
- projectDao.evict(project);
-
- Project project2 = projectDao.getProjectByProjectId(projectId);
- assertNotNull(project2);
-
- OverviewImage oi2 = project2.getOverviewImages().get(0);
- OverviewModelLink oml2 = (OverviewModelLink) oi2.getLinks().get(0);
-
- assertEquals(oi.getFilename(), oi2.getFilename());
- assertEquals(oml.getPolygon(), oml2.getPolygon());
- assertEquals(oml.getxCoord(), oml2.getxCoord());
- assertEquals(oml.getyCoord(), oml2.getyCoord());
- assertEquals(oml.getZoomLevel(), oml2.getZoomLevel());
- assertNotNull(oml2.getPolygonCoordinates());
-
- projectDao.delete(project2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- /**
- * After adding model to db with creation warnings...
- *
- * @throws Exception
- */
- @Test
- public void testCreationWarnings() throws Exception {
- try {
- Project project = new Project();
- project.addWarning("warning A");
- project.addWarning("warning B");
- assertEquals(2, project.getWarnings().size());
-
- projectDao.add(project);
-
- projectDao.evict(project);
- Project project2 = projectDao.getById(project.getId());
-
- assertEquals(2, project2.getWarnings().size());
-
- projectDao.delete(project2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAll() throws Exception {
- try {
-
- long startTime = System.currentTimeMillis();
- double max = 10;
-
- logger.debug("---");
- for (int i = 0; i < max; i++) {
- projectDao.getAll();
- }
- long estimatedTime = System.currentTimeMillis() - startTime;
- logger.debug(estimatedTime/max);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.persist.dao;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.OverviewImage;
+import lcsb.mapviewer.model.map.OverviewModelLink;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.persist.PersistTestFunctions;
+
+public class ProjectDaoTest extends PersistTestFunctions {
+ Logger logger = Logger.getLogger(ProjectDaoTest.class);
+ int identifierCounter = 0;
+ String projectId = "Some_id";
+
+ @Before
+ public void setUp() throws Exception {
+ Project project = projectDao.getProjectByProjectId(projectId);
+ if (project != null) {
+ projectDao.delete(project);
+ }
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetProjectByName() throws Exception {
+ try {
+ Project project = new Project();
+ project.setProjectId(projectId);
+ projectDao.add(project);
+ projectDao.evict(project);
+
+ Project project2 = projectDao.getProjectByProjectId(projectId);
+ assertNotNull(project2);
+ assertFalse(project2.equals(project));
+ assertEquals(project.getId(), project2.getId());
+
+ projectDao.delete(project2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetProjectForModelId() throws Exception {
+ try {
+ String projectId = "Some name";
+ Project project = new Project();
+ project.setProjectId(projectId);
+ projectDao.add(project);
+ Model model = new ModelFullIndexed(null);
+ project.addModel(model);
+ modelDao.add(model);
+ modelDao.evict(model);
+ projectDao.evict(project);
+
+ Project project2 = projectDao.getProjectForModelId(model.getId());
+ assertNotNull(project2);
+ assertFalse(project2.equals(project));
+ assertEquals(project.getId(), project2.getId());
+
+ modelDao.delete(modelDao.getById(model.getId()));
+ projectDao.delete(project2);
+
+ assertNull(projectDao.getProjectForModelId(model.getId()));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProjectExists() throws Exception {
+ try {
+ String projectId = "Some_id";
+ Project project = new Project();
+ project.setProjectId(projectId);
+
+ assertFalse(projectDao.isProjectExistsByName(projectId));
+
+ projectDao.add(project);
+ projectDao.evict(project);
+
+ assertTrue(projectDao.isProjectExistsByName(projectId));
+
+ Project project2 = projectDao.getProjectByProjectId(projectId);
+
+ projectDao.delete(project2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCheckEqualityAfterReload() throws Exception {
+ try {
+
+ String projectId = "Some_id";
+ Project project = new Project();
+ project.setProjectId(projectId);
+ projectDao.add(project);
+ projectDao.flush();
+
+ Model model = createModel();
+ project.addModel(model);
+
+ projectDao.update(project);
+ projectDao.evict(project);
+
+ ModelComparator comparator = new ModelComparator();
+
+ Model model2 = new ModelFullIndexed(modelDao.getLastModelForProjectIdentifier(projectId, false));
+
+ assertEquals(0, comparator.compare(model, model2));
+
+ projectDao.delete(projectDao.getById(project.getId()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCheckEqualityAfterReload2() throws Exception {
+ try {
+ String project_id = "Some_id";
+ Project project = new Project();
+ project.setProjectId(project_id);
+ Model model = createModel();
+ project.addModel(model);
+
+ projectDao.add(project);
+ projectDao.evict(project);
+
+ Project project2 = projectDao.getProjectByProjectId(project_id);
+
+ ModelComparator comparator = new ModelComparator();
+
+ Model fullModel1 = new ModelFullIndexed(project.getModels().iterator().next());
+ Model fullModel2 = new ModelFullIndexed(project2.getModels().iterator().next());
+ assertEquals(0, comparator.compare(fullModel1, fullModel2));
+
+ projectDao.delete(project2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Model createModel() {
+ Model model = new ModelFullIndexed(null);
+
+ model.addElement(createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "sa2"));
+ model.addElement(createSpeciesAlias(267.6666666666665, 438.75, 80.0, 40.0, "sa1117"));
+ model.addElement(createSpeciesAlias(261.6666666666665, 600.75, 92.0, 52.0, "sa1119"));
+ model.addElement(createSpeciesAlias(203.666666666667, 687.75, 98.0, 58.0, "sa1121"));
+
+ Species alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
+ Species alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
+ Complex alias3 = createComplexAlias(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
+ alias3.addSpecies(alias);
+ alias3.addSpecies(alias2);
+ alias.setComplex(alias3);
+ alias2.setComplex(alias3);
+
+ model.addElement(alias);
+ model.addElement(alias2);
+ model.addElement(alias3);
+
+ model.addElement(createCompartmentAlias(380.0, 416.0, 1893.0, 1866.0, "ca1"));
+ model.setWidth(2000);
+ model.setHeight(2000);
+ return model;
+ }
+
+ private Compartment createCompartmentAlias(double x, double y, double width, double height, String aliasId) {
+ Compartment alias = new Compartment(aliasId);
+ alias.setX(x);
+ alias.setY(y);
+ alias.setWidth(width);
+ alias.setHeight(height);
+ return alias;
+ }
+
+ private Species createSpeciesAlias(double x, double y, double width, double height, String aliasId) {
+ Species alias = new SimpleMolecule(aliasId);
+ alias.setX(x);
+ alias.setY(y);
+ alias.setWidth(width);
+ alias.setHeight(height);
+ return alias;
+ }
+
+ private Complex createComplexAlias(double x, double y, double width, double height, String aliasId) {
+ Complex alias = new Complex(aliasId);
+ alias.setX(x);
+ alias.setY(y);
+ alias.setWidth(width);
+ alias.setHeight(height);
+ return alias;
+ }
+
+ @Test
+ public void testAddGetProjectWithOverviewImage() throws Exception {
+ try {
+ String projectId = "Some_id";
+ Project project = new Project();
+ project.setProjectId(projectId);
+ Model model = new ModelFullIndexed(null);
+ OverviewImage oi = new OverviewImage();
+ oi.setFilename("test");
+ OverviewModelLink oml = new OverviewModelLink();
+ oml.setPolygon("10,10 20,20 20,100");
+ oml.setxCoord(1);
+ oml.setyCoord(2);
+ oml.setZoomLevel(3);
+ oi.addLink(oml);
+ project.addOverviewImage(oi);
+ project.addModel(model);
+
+ projectDao.add(project);
+ projectDao.evict(project);
+
+ Project project2 = projectDao.getProjectByProjectId(projectId);
+ assertNotNull(project2);
+
+ OverviewImage oi2 = project2.getOverviewImages().get(0);
+ OverviewModelLink oml2 = (OverviewModelLink) oi2.getLinks().get(0);
+
+ assertEquals(oi.getFilename(), oi2.getFilename());
+ assertEquals(oml.getPolygon(), oml2.getPolygon());
+ assertEquals(oml.getxCoord(), oml2.getxCoord());
+ assertEquals(oml.getyCoord(), oml2.getyCoord());
+ assertEquals(oml.getZoomLevel(), oml2.getZoomLevel());
+ assertNotNull(oml2.getPolygonCoordinates());
+
+ projectDao.delete(project2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ /**
+ * After adding model to db with creation warnings...
+ *
+ * @throws Exception
+ */
+ @Test
+ public void testCreationWarnings() throws Exception {
+ try {
+ Project project = new Project();
+ project.addWarning("warning A");
+ project.addWarning("warning B");
+ assertEquals(2, project.getWarnings().size());
+
+ projectDao.add(project);
+
+ projectDao.evict(project);
+ Project project2 = projectDao.getById(project.getId());
+
+ assertEquals(2, project2.getWarnings().size());
+
+ projectDao.delete(project2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAll() throws Exception {
+ try {
+
+ long startTime = System.currentTimeMillis();
+ double max = 10;
+
+ logger.debug("---");
+ for (int i = 0; i < max; i++) {
+ projectDao.getAll();
+ }
+ long estimatedTime = System.currentTimeMillis() - startTime;
+ logger.debug(estimatedTime/max);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/AllCacheDbTests.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/AllCacheDbTests.java
index e35692e70a..3c2a221595 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/AllCacheDbTests.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/AllCacheDbTests.java
@@ -1,15 +1,15 @@
-package lcsb.mapviewer.persist.dao.cache;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ BigFileEntryDaoTest.class, //
- CacheTypeDaoTest.class, //
- CacheQueryDaoTest.class, //
- UploadedFileEntryDaoTest.class,//
-})
-public class AllCacheDbTests {
-
-}
+package lcsb.mapviewer.persist.dao.cache;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ BigFileEntryDaoTest.class, //
+ CacheTypeDaoTest.class, //
+ CacheQueryDaoTest.class, //
+ UploadedFileEntryDaoTest.class,//
+})
+public class AllCacheDbTests {
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/CacheQueryDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/CacheQueryDaoTest.java
index 5b9427b925..b6f751c135 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/CacheQueryDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/CacheQueryDaoTest.java
@@ -1,42 +1,42 @@
-package lcsb.mapviewer.persist.dao.cache;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.cache.CacheQuery;
-import lcsb.mapviewer.model.cache.CacheType;
-import lcsb.mapviewer.persist.PersistTestFunctions;
-
-public class CacheQueryDaoTest extends PersistTestFunctions {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetByQuery() {
- try {
- CacheType type = cacheTypeDao.getByClassName("lcsb.mapviewer.reactome.utils.ReactomeConnector");
- CacheQuery query = new CacheQuery();
- query.setType(type);
- query.setQuery("test");
- cacheQueryDao.add(query);
- assertEquals(query, cacheQueryDao.getByQuery("test", type));
- assertNull(cacheQueryDao.getByQuery("another_test_bla", type));
-
- cacheQueryDao.delete(query);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.persist.dao.cache;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.cache.CacheQuery;
+import lcsb.mapviewer.model.cache.CacheType;
+import lcsb.mapviewer.persist.PersistTestFunctions;
+
+public class CacheQueryDaoTest extends PersistTestFunctions {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetByQuery() {
+ try {
+ CacheType type = cacheTypeDao.getByClassName("lcsb.mapviewer.reactome.utils.ReactomeConnector");
+ CacheQuery query = new CacheQuery();
+ query.setType(type);
+ query.setQuery("test");
+ cacheQueryDao.add(query);
+ assertEquals(query, cacheQueryDao.getByQuery("test", type));
+ assertNull(cacheQueryDao.getByQuery("another_test_bla", type));
+
+ cacheQueryDao.delete(query);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/CacheTypeDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/CacheTypeDaoTest.java
index 7560b89213..87761eb391 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/CacheTypeDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/CacheTypeDaoTest.java
@@ -1,124 +1,124 @@
-package lcsb.mapviewer.persist.dao.cache;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-
-import lcsb.mapviewer.model.cache.CacheType;
-import lcsb.mapviewer.persist.PersistTestFunctions;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class CacheTypeDaoTest extends PersistTestFunctions {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testReactomeCacheData() throws Exception {
- try {
- CacheType cacheType = cacheTypeDao.getByClassName("lcsb.mapviewer.reactome.utils.ReactomeConnector");
- assertNotNull(cacheType);
- assertEquals(0,cacheType.getId());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testEmpty() throws Exception {
- try {
- assertNull(cacheTypeDao.getByClassName("blablabla"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testBiocompendiumCacheData() throws Exception {
- try {
- CacheType cacheType = cacheTypeDao.getByClassName("lcsb.mapviewer.annotation.services.annotators.BiocompendiumAnnotator");
- assertNotNull(cacheType);
- assertEquals(1,cacheType.getId());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testChemblCacheData() throws Exception {
- try {
- CacheType cacheType = cacheTypeDao.getByClassName("lcsb.mapviewer.annotation.services.ChEMBLParser");
- assertNotNull(cacheType);
- assertEquals(2,cacheType.getId());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testArticleCacheData() throws Exception {
- try {
- CacheType cacheType = cacheTypeDao.getByClassName("lcsb.mapviewer.annotation.services.PubmedParser");
- assertNotNull(cacheType);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDrugBankCacheData() throws Exception {
- try {
- CacheType cacheType = cacheTypeDao.getByClassName("lcsb.mapviewer.annotation.services.DrugbankHTMLParser");
- assertNotNull(cacheType);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testMockCacheData() throws Exception {
- try {
- CacheType cacheType = cacheTypeDao.getByClassName("lcsb.mapviewer.annotation.cache.MockCacheInterface");
- assertNotNull(cacheType);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testChebiCacheData() throws Exception {
- try {
- CacheType cacheType = cacheTypeDao.getByClassName("lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator");
- assertNotNull(cacheType);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGoCacheData() throws Exception {
- try {
- CacheType cacheType = cacheTypeDao.getByClassName("lcsb.mapviewer.annotation.services.annotators.GoAnnotator");
- assertNotNull(cacheType);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.persist.dao.cache;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+
+import lcsb.mapviewer.model.cache.CacheType;
+import lcsb.mapviewer.persist.PersistTestFunctions;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class CacheTypeDaoTest extends PersistTestFunctions {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testReactomeCacheData() throws Exception {
+ try {
+ CacheType cacheType = cacheTypeDao.getByClassName("lcsb.mapviewer.reactome.utils.ReactomeConnector");
+ assertNotNull(cacheType);
+ assertEquals(0,cacheType.getId());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testEmpty() throws Exception {
+ try {
+ assertNull(cacheTypeDao.getByClassName("blablabla"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testBiocompendiumCacheData() throws Exception {
+ try {
+ CacheType cacheType = cacheTypeDao.getByClassName("lcsb.mapviewer.annotation.services.annotators.BiocompendiumAnnotator");
+ assertNotNull(cacheType);
+ assertEquals(1,cacheType.getId());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testChemblCacheData() throws Exception {
+ try {
+ CacheType cacheType = cacheTypeDao.getByClassName("lcsb.mapviewer.annotation.services.ChEMBLParser");
+ assertNotNull(cacheType);
+ assertEquals(2,cacheType.getId());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testArticleCacheData() throws Exception {
+ try {
+ CacheType cacheType = cacheTypeDao.getByClassName("lcsb.mapviewer.annotation.services.PubmedParser");
+ assertNotNull(cacheType);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDrugBankCacheData() throws Exception {
+ try {
+ CacheType cacheType = cacheTypeDao.getByClassName("lcsb.mapviewer.annotation.services.DrugbankHTMLParser");
+ assertNotNull(cacheType);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testMockCacheData() throws Exception {
+ try {
+ CacheType cacheType = cacheTypeDao.getByClassName("lcsb.mapviewer.annotation.cache.MockCacheInterface");
+ assertNotNull(cacheType);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testChebiCacheData() throws Exception {
+ try {
+ CacheType cacheType = cacheTypeDao.getByClassName("lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator");
+ assertNotNull(cacheType);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGoCacheData() throws Exception {
+ try {
+ CacheType cacheType = cacheTypeDao.getByClassName("lcsb.mapviewer.annotation.services.annotators.GoAnnotator");
+ assertNotNull(cacheType);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/UploadedFileEntryDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/UploadedFileEntryDaoTest.java
index 6fb61be8fe..59ae504017 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/UploadedFileEntryDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/UploadedFileEntryDaoTest.java
@@ -1,58 +1,58 @@
-package lcsb.mapviewer.persist.dao.cache;
-
-import static org.junit.Assert.assertEquals;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.model.cache.UploadedFileEntry;
-import lcsb.mapviewer.persist.DbUtils;
-import lcsb.mapviewer.persist.PersistTestFunctions;
-
-public class UploadedFileEntryDaoTest extends PersistTestFunctions {
-
- @Autowired
- UploadedFileEntryDao uploadedFileEntryDao;
-
- @Autowired
- DbUtils dbUtils;
-
- boolean flush;
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- flush = dbUtils.isAutoFlush();
- dbUtils.setAutoFlush(true);
- }
-
- @After
- public void tearDown() throws Exception {
- dbUtils.setAutoFlush(flush);
- }
-
- @Test
- public void testAdd() {
- try {
- UploadedFileEntry entry = new UploadedFileEntry();
- long count = uploadedFileEntryDao.getCount();
- uploadedFileEntryDao.add(entry);
- long count2 = uploadedFileEntryDao.getCount();
- uploadedFileEntryDao.delete(entry);
- long count3 = uploadedFileEntryDao.getCount();
-
- assertEquals(count + 1, count2);
- assertEquals(count2 - 1, count3);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.persist.dao.cache;
+
+import static org.junit.Assert.assertEquals;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
+import lcsb.mapviewer.persist.DbUtils;
+import lcsb.mapviewer.persist.PersistTestFunctions;
+
+public class UploadedFileEntryDaoTest extends PersistTestFunctions {
+
+ @Autowired
+ UploadedFileEntryDao uploadedFileEntryDao;
+
+ @Autowired
+ DbUtils dbUtils;
+
+ boolean flush;
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ flush = dbUtils.isAutoFlush();
+ dbUtils.setAutoFlush(true);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ dbUtils.setAutoFlush(flush);
+ }
+
+ @Test
+ public void testAdd() {
+ try {
+ UploadedFileEntry entry = new UploadedFileEntry();
+ long count = uploadedFileEntryDao.getCount();
+ uploadedFileEntryDao.add(entry);
+ long count2 = uploadedFileEntryDao.getCount();
+ uploadedFileEntryDao.delete(entry);
+ long count3 = uploadedFileEntryDao.getCount();
+
+ assertEquals(count + 1, count2);
+ assertEquals(count2 - 1, count3);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/graphics/AllGraphicsDaoTests.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/graphics/AllGraphicsDaoTests.java
index b13eb7172d..ddae26a8f6 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/graphics/AllGraphicsDaoTests.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/graphics/AllGraphicsDaoTests.java
@@ -1,11 +1,11 @@
-package lcsb.mapviewer.persist.dao.graphics;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ PolylineDataTest.class })
-public class AllGraphicsDaoTests {
-
-}
+package lcsb.mapviewer.persist.dao.graphics;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ PolylineDataTest.class })
+public class AllGraphicsDaoTests {
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/graphics/PolylineDataTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/graphics/PolylineDataTest.java
index 607e976fa1..d30fcf91f5 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/graphics/PolylineDataTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/graphics/PolylineDataTest.java
@@ -1,69 +1,69 @@
-package lcsb.mapviewer.persist.dao.graphics;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.fail;
-
-import java.awt.Color;
-import java.awt.geom.Point2D;
-
-import lcsb.mapviewer.model.graphics.ArrowType;
-import lcsb.mapviewer.model.graphics.LineType;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.persist.PersistTestFunctions;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class PolylineDataTest extends PersistTestFunctions {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void test() {
- try {
- PolylineData pd = new PolylineData();
- pd.getBeginAtd().setArrowType(ArrowType.BLANK_CROSSBAR);
- pd.getBeginAtd().setArrowLineType(LineType.DASHED);
- pd.getBeginAtd().setLen(102);
- pd.setColor(Color.CYAN);
- pd.setType(LineType.SOLID_BOLD);
- pd.setWidth(2);
- pd.getPoints().add(new Point2D.Double(1, 1));
- pd.getPoints().add(new Point2D.Double(2, 3));
- pd.getPoints().add(new Point2D.Double(10, 11));
- polylineDao.add(pd);
- assertNotNull(pd.getId());
- PolylineData pd2 = polylineDao.getById(pd.getId());
- assertNotNull(pd2);
-
- assertEquals(ArrowType.BLANK_CROSSBAR, pd2.getBeginAtd().getArrowType());
- assertEquals(LineType.DASHED, pd2.getBeginAtd().getArrowLineType());
- assertEquals(102, pd2.getBeginAtd().getLen(), EPSILON);
- assertEquals(Color.CYAN, pd2.getColor());
- assertEquals(LineType.SOLID_BOLD, pd2.getType());
- assertEquals(2, pd2.getWidth(), EPSILON);
- assertEquals(0, pd2.getPoints().get(0).distance(new Point2D.Double(1, 1)), EPSILON);
- assertEquals(0, pd2.getPoints().get(1).distance(new Point2D.Double(2, 3)), EPSILON);
- assertEquals(0, pd2.getPoints().get(2).distance(new Point2D.Double(10, 11)), EPSILON);
-
- polylineDao.delete(pd);
- pd2 = polylineDao.getById(pd.getId());
- assertNull(pd2);
-
- } catch (Exception e) {
- e.printStackTrace();
-
- fail("Unknowne exception occured");
- }
- }
-
-}
+package lcsb.mapviewer.persist.dao.graphics;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.fail;
+
+import java.awt.Color;
+import java.awt.geom.Point2D;
+
+import lcsb.mapviewer.model.graphics.ArrowType;
+import lcsb.mapviewer.model.graphics.LineType;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.persist.PersistTestFunctions;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class PolylineDataTest extends PersistTestFunctions {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void test() {
+ try {
+ PolylineData pd = new PolylineData();
+ pd.getBeginAtd().setArrowType(ArrowType.BLANK_CROSSBAR);
+ pd.getBeginAtd().setArrowLineType(LineType.DASHED);
+ pd.getBeginAtd().setLen(102);
+ pd.setColor(Color.CYAN);
+ pd.setType(LineType.SOLID_BOLD);
+ pd.setWidth(2);
+ pd.getPoints().add(new Point2D.Double(1, 1));
+ pd.getPoints().add(new Point2D.Double(2, 3));
+ pd.getPoints().add(new Point2D.Double(10, 11));
+ polylineDao.add(pd);
+ assertNotNull(pd.getId());
+ PolylineData pd2 = polylineDao.getById(pd.getId());
+ assertNotNull(pd2);
+
+ assertEquals(ArrowType.BLANK_CROSSBAR, pd2.getBeginAtd().getArrowType());
+ assertEquals(LineType.DASHED, pd2.getBeginAtd().getArrowLineType());
+ assertEquals(102, pd2.getBeginAtd().getLen(), EPSILON);
+ assertEquals(Color.CYAN, pd2.getColor());
+ assertEquals(LineType.SOLID_BOLD, pd2.getType());
+ assertEquals(2, pd2.getWidth(), EPSILON);
+ assertEquals(0, pd2.getPoints().get(0).distance(new Point2D.Double(1, 1)), EPSILON);
+ assertEquals(0, pd2.getPoints().get(1).distance(new Point2D.Double(2, 3)), EPSILON);
+ assertEquals(0, pd2.getPoints().get(2).distance(new Point2D.Double(10, 11)), EPSILON);
+
+ polylineDao.delete(pd);
+ pd2 = polylineDao.getById(pd.getId());
+ assertNull(pd2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+
+ fail("Unknowne exception occured");
+ }
+ }
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/log/AllLogTests.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/log/AllLogTests.java
index e8ee5a7b57..0e635258bc 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/log/AllLogTests.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/log/AllLogTests.java
@@ -1,12 +1,12 @@
-package lcsb.mapviewer.persist.dao.log;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ LogDaoTest.class,//
-})
-public class AllLogTests {
-
-}
+package lcsb.mapviewer.persist.dao.log;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ LogDaoTest.class,//
+})
+public class AllLogTests {
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/log/LogDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/log/LogDaoTest.java
index 3a4fd4143c..1edba2e28a 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/log/LogDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/log/LogDaoTest.java
@@ -1,47 +1,47 @@
-package lcsb.mapviewer.persist.dao.log;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.log.SystemLog;
-import lcsb.mapviewer.persist.PersistTestFunctions;
-
-public class LogDaoTest extends PersistTestFunctions {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetLastLog() {
- try {
- logDao.clearTable();
- assertNull(logDao.getLastLog());
- logDao.add(new SystemLog());
- assertNotNull(logDao.getLastLog());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRemovableStatement() {
- try {
- assertEquals("",logDao.removableStatemant());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.persist.dao.log;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.log.SystemLog;
+import lcsb.mapviewer.persist.PersistTestFunctions;
+
+public class LogDaoTest extends PersistTestFunctions {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetLastLog() {
+ try {
+ logDao.clearTable();
+ assertNull(logDao.getLastLog());
+ logDao.add(new SystemLog());
+ assertNotNull(logDao.getLastLog());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRemovableStatement() {
+ try {
+ assertEquals("",logDao.removableStatemant());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/AllMapDaoTests.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/AllMapDaoTests.java
index 8ed75a40f3..19c30d3e5b 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/AllMapDaoTests.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/AllMapDaoTests.java
@@ -1,20 +1,20 @@
-package lcsb.mapviewer.persist.dao.map;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-import lcsb.mapviewer.persist.dao.map.layout.AllLayoutTests;
-import lcsb.mapviewer.persist.dao.map.statistics.StatisticsAllTests;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AllLayoutTests.class, //
- CommentDaoTest.class, //
- FeedbackTest.class, //
- LayoutDaoTest.class, //
- ModelDaoTest.class, //
- StatisticsAllTests.class, //
-})
-public class AllMapDaoTests {
-
-}
+package lcsb.mapviewer.persist.dao.map;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+import lcsb.mapviewer.persist.dao.map.layout.AllLayoutTests;
+import lcsb.mapviewer.persist.dao.map.statistics.StatisticsAllTests;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AllLayoutTests.class, //
+ CommentDaoTest.class, //
+ FeedbackTest.class, //
+ LayoutDaoTest.class, //
+ ModelDaoTest.class, //
+ StatisticsAllTests.class, //
+})
+public class AllMapDaoTests {
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/FeedbackTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/FeedbackTest.java
index 84ce1b9118..21c42f7d9e 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/FeedbackTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/FeedbackTest.java
@@ -1,43 +1,43 @@
-package lcsb.mapviewer.persist.dao.map;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import lcsb.mapviewer.model.map.Comment;
-import lcsb.mapviewer.persist.PersistTestFunctions;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class FeedbackTest extends PersistTestFunctions {
-
- @Before
- public void setUp() throws Exception {
- createUser();
- }
-
- @After
- public void tearDown() throws Exception {
- userDao.delete(user);
- }
-
- @Test
- public void testFeedback() throws Exception {
- try {
- int counter = (int) commentDao.getCount();
- Comment feedback = new Comment();
- feedback.setUser(user);
- commentDao.add(feedback);
- int counter2 = (int) commentDao.getCount();
- assertEquals(counter + 1, counter2);
- Comment feedback2 = commentDao.getById(feedback.getId());
- assertNotNull(feedback2);
- commentDao.delete(feedback);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.persist.dao.map;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import lcsb.mapviewer.model.map.Comment;
+import lcsb.mapviewer.persist.PersistTestFunctions;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class FeedbackTest extends PersistTestFunctions {
+
+ @Before
+ public void setUp() throws Exception {
+ createUser();
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ userDao.delete(user);
+ }
+
+ @Test
+ public void testFeedback() throws Exception {
+ try {
+ int counter = (int) commentDao.getCount();
+ Comment feedback = new Comment();
+ feedback.setUser(user);
+ commentDao.add(feedback);
+ int counter2 = (int) commentDao.getCount();
+ assertEquals(counter + 1, counter2);
+ Comment feedback2 = commentDao.getById(feedback.getId());
+ assertNotNull(feedback2);
+ commentDao.delete(feedback);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java
index b2687c6e02..0d59dd755f 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java
@@ -1,498 +1,498 @@
-package lcsb.mapviewer.persist.dao.map;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.Color;
-import java.awt.geom.Point2D;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
-import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
-import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
-import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
-import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
-import lcsb.mapviewer.model.map.kinetics.SbmlUnitTypeFactor;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.type.ModulationReaction;
-import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.field.Residue;
-import lcsb.mapviewer.persist.PersistTestFunctions;
-
-public class ModelDaoTest extends PersistTestFunctions {
- ModelComparator modelComparator = new ModelComparator();
-
- Logger logger = Logger.getLogger(ModelDaoTest.class);
- private Project project;
- String projectId = "Some_id";
- int identifierCounter = 0;
-
- @Before
- public void setUp() throws Exception {
- project = projectDao.getProjectByProjectId(projectId);
- if (project != null) {
- projectDao.delete(project);
- }
- project = new Project();
- project.setProjectId(projectId);
- projectDao.add(project);
- }
-
- @After
- public void tearDown() throws Exception {
- projectDao.delete(project);
- }
-
- @Test
- public void testLoadFromDb() throws Exception {
- try {
- Model model = createModel();
- project.addModel(model);
- modelDao.add(model);
- projectDao.update(project);
- projectDao.evict(project);
-
- modelDao.evict(model);
- ModelData model2 = modelDao.getById(model.getId());
- assertNotNull(model2);
- assertFalse(model2 == model);
-
- assertEquals(model.getElements().size(), model2.getElements().size());
- assertEquals(model.getLayers().size(), model2.getLayers().size());
- assertEquals(model.getReactions().size(), model2.getReactions().size());
-
- ModelComparator comparator = new ModelComparator();
- assertEquals(0, comparator.compare(model, new ModelFullIndexed(model2)));
-
- modelDao.delete(model2);
- model2 = modelDao.getById(model.getId());
- assertNull(model2);
- project = projectDao.getById(project.getId());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testIndexesReload() throws Exception {
- try {
- Model model = createModel();
- project.addModel(model);
- modelDao.add(model);
- modelDao.evict(model);
- ModelData model2 = modelDao.getById(model.getId());
- Model fullModel = new ModelFullIndexed(model2);
- assertNotNull(model2);
-
- assertEquals(model.getElements().size(), model2.getElements().size());
- assertEquals(model.getLayers().size(), model2.getLayers().size());
- assertEquals(model.getReactions().size(), model2.getReactions().size());
-
- // check if we really performed a test
- boolean test = false;
-
- for (Element alias : model.getElements()) {
- assertNotNull(fullModel.getElementByElementId(alias.getElementId()));
- test = true;
- }
- assertTrue(test);
-
- test = false;
- for (Element alias : model.getElements()) {
- if (alias instanceof Compartment) {
- assertNotNull(fullModel.getElementByElementId(alias.getElementId()));
- test = true;
- }
- }
- assertTrue(test);
-
- model2.setHeight(32);
- modelDao.update(model2.getModel());
-
- modelDao.delete(model2);
- model2 = modelDao.getById(model.getId());
- assertNull(model2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReactionInModelAfterReload() throws Exception {
- try {
- Model model = createModel();
- Reaction reaction = model.getReactions().iterator().next();
- project.addModel(model);
- modelDao.add(model);
- projectDao.update(project);
- projectDao.evict(project);
- modelDao.evict(model);
- ModelData model2 = modelDao.getById(model.getId());
-
- Reaction reaction2 = null;
- for (Reaction r : model2.getReactions()) {
- if (r.getIdReaction().equals(reaction.getIdReaction())) {
- reaction2 = r;
- }
- }
- assertNotNull(reaction2);
- assertFalse(reaction.equals(reaction2));
-
- assertEquals(reaction.getNodes().size(), reaction2.getNodes().size());
-
- modelDao.delete(model2);
- model2 = modelDao.getById(model.getId());
- assertNull(model2);
- project = projectDao.getById(project.getId());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReactionInWithKinetics() throws Exception {
- try {
- Model model = createModel();
- Reaction reaction = model.getReactions().iterator().next();
- SbmlKinetics kinetics = new SbmlKinetics();
- kinetics.addElement(reaction.getReactants().get(0).getElement());
- kinetics.addFunction(createFunction());
- model.addFunctions(kinetics.getFunctions());
- kinetics.addParameter(createParameter());
- model.addUnit(kinetics.getParameters().iterator().next().getUnits());
- reaction.setKinetics(kinetics);
- project.addModel(model);
- modelDao.add(model);
- projectDao.update(project);
- projectDao.evict(project);
- modelDao.evict(model);
- ModelData model2 = modelDao.getById(model.getId());
-
- assertEquals(0, modelComparator.compare(model, new ModelFullIndexed(model2)));
-
- project = projectDao.getById(project.getId());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testModulationReaction() throws Exception {
- try {
- Model model = createModel();
- Reaction reaction = new ModulationReaction();
- reaction.addProduct(new Product(model.getElementByElementId("sa2")));
- reaction.addReactant(new Reactant(model.getElementByElementId("sa1117")));
- reaction.setIdReaction("re" + identifierCounter++);
- model.addReaction(reaction);
-
- project.addModel(model);
- modelDao.add(model);
- projectDao.update(project);
- projectDao.evict(project);
- modelDao.evict(model);
- ModelData model2 = modelDao.getById(model.getId());
-
- assertEquals(0, modelComparator.compare(model, new ModelFullIndexed(model2)));
-
- project = projectDao.getById(project.getId());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testModelWithParameters() throws Exception {
- try {
- Model model = createModel();
- model.addParameter(createParameter());
- model.addUnit(model.getParameters().iterator().next().getUnits());
- project.addModel(model);
- modelDao.add(model);
- projectDao.update(project);
- projectDao.evict(project);
- modelDao.evict(model);
- ModelData model2 = modelDao.getById(model.getId());
-
- assertEquals(0, modelComparator.compare(model, new ModelFullIndexed(model2)));
-
- project = projectDao.getById(project.getId());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private SbmlParameter createParameter() {
- SbmlParameter parameter = new SbmlParameter("param_id");
- parameter.setName("X");
- parameter.setValue(4.7);
- parameter.setUnits(createUnits());
- return parameter;
- }
-
- private SbmlUnit createUnits() {
- SbmlUnit unit = new SbmlUnit("unit_id");
- unit.setName("u name");
- unit.addUnitTypeFactor(new SbmlUnitTypeFactor(SbmlUnitType.AMPERE, 1, 2, 3));
- return unit;
- }
-
- private SbmlFunction createFunction() {
- SbmlFunction result = new SbmlFunction("fun_id");
- result.setDefinition("def(k1)");
- result.addArgument("k1");
- result.setName("fun name");
- return result;
- }
-
- @Test
- public void testGetLastModelForProjectName() throws Exception {
- try {
- ModelData model3 = modelDao.getLastModelForProjectIdentifier(projectId, false);
- assertNull(model3);
-
- Model model = createModel();
- project.addModel(model);
- modelDao.add(model);
-
- ModelData newModel = modelDao.getLastModelForProjectIdentifier(projectId, false);
- assertNotNull(newModel);
- assertEquals(model.getId(), newModel.getId());
-
- Model model2 = createModel();
- project.addModel(model2);
- modelDao.add(model2);
-
- newModel = modelDao.getLastModelForProjectIdentifier(projectId, false);
- assertNotNull(newModel);
- assertEquals(model2.getId(), newModel.getId());
-
- modelDao.delete(model2);
- modelDao.delete(model);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- /**
- * After adding model to db, modification residues disappear from the model...
- *
- * @throws Exception
- */
- @Test
- public void testModificationsInProteins() throws Exception {
- try {
- Model model = createModel();
- Project project = new Project();
- project.addModel(model);
- projectDao.add(project);
-
- modelDao.evict(model);
- projectDao.evict(project);
- Model model2 = new ModelFullIndexed(modelDao.getById(model.getId()));
-
- Protein originalSpecies = (Protein) model.getElementByElementId("pr1");
- Protein fromDbSpecies = (Protein) model2.getElementByElementId("pr1");
-
- assertFalse(originalSpecies.equals(fromDbSpecies));
- assertEquals(originalSpecies.getModificationResidues().size(), fromDbSpecies.getModificationResidues().size());
-
- project = projectDao.getById(project.getId());
- projectDao.delete(project);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- /**
- * After adding model to db, miriam annotations disappear...
- *
- * @throws Exception
- */
- @Test
- public void testMiriamInSpecies() throws Exception {
- try {
- Model model = createModel();
- Project project = new Project();
- project.addModel(model);
- projectDao.add(project);
-
- modelDao.evict(model);
- projectDao.evict(project);
- Model model2 = new ModelFullIndexed(modelDao.getById(model.getId()));
-
- Protein originalSpecies = (Protein) model.getElementByElementId("pr1");
- Protein fromDbSpecies = (Protein) model2.getElementByElementId("pr1");
-
- assertFalse(originalSpecies.equals(fromDbSpecies));
- assertEquals(originalSpecies.getMiriamData().size(), fromDbSpecies.getMiriamData().size());
-
- project = projectDao.getById(project.getId());
- projectDao.delete(project);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- /**
- * After adding layouts to model.
- *
- * @throws Exception
- */
- @Test
- public void testLayoutsInModel() throws Exception {
- try {
- Model model = createModel();
-
- Layout layout = new Layout();
- layout.setDirectory("tmp");
- layout.setTitle("temporary name");
- model.addLayout(layout);
- Project project = new Project();
- project.addModel(model);
- projectDao.add(project);
-
- modelDao.evict(model);
- projectDao.evict(project);
- ModelData model2 = modelDao.getById(model.getId());
-
- assertEquals(1, model2.getLayouts().size());
- assertEquals("tmp", model2.getLayouts().get(0).getDirectory());
- assertEquals("temporary name", model2.getLayouts().get(0).getTitle());
-
- project = projectDao.getById(project.getId());
- projectDao.delete(project);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private Model createModel() {
- Model model = new ModelFullIndexed(null);
-
- GenericProtein alias = createSpecies(264.8333333333335, 517.75, 86.0, 46.0, "sa2");
- model.addElement(alias);
- alias = createSpecies(267.6666666666665, 438.75, 80.0, 40.0, "sa1117");
- model.addElement(alias);
- alias = createSpecies(261.6666666666665, 600.75, 92.0, 52.0, "sa1119");
- model.addElement(alias);
- alias = createSpecies(203.666666666667, 687.75, 98.0, 58.0, "sa1121");
- model.addElement(alias);
-
- alias = createSpecies(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
- Species alias2 = createSpecies(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
- Complex alias3 = createComplex(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
- alias3.addSpecies(alias);
- alias3.addSpecies(alias2);
- alias.setComplex(alias3);
- alias2.setComplex(alias3);
-
- model.addElement(alias);
- model.addElement(alias2);
- model.addElement(alias3);
-
- Compartment cAlias = createCompartment(380.0, 416.0, 1893.0, 1866.0, "ca1");
- model.addElement(cAlias);
- model.setWidth(2000);
- model.setHeight(2000);
-
- Layer layer = new Layer();
- model.addLayer(layer);
-
- LayerRect lr = new LayerRect();
- lr.setColor(Color.YELLOW);
- layer.addLayerRect(lr);
-
- Reaction reaction = new TransportReaction();
- reaction.addProduct(new Product(alias));
- reaction.addReactant(new Reactant(alias2));
- reaction.setIdReaction("re" + identifierCounter++);
- model.addReaction(reaction);
-
- alias = createSpecies(264.8333333333335, 517.75, 86.0, 46.0, "pr1");
- model.addElement(alias);
-
- Residue mr = new Residue();
- mr.setName("mr");
- mr.setPosition(new Point2D.Double(10, 20));
- alias.addModificationResidue(mr);
-
- alias.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, "c"));
- return model;
- }
-
- private Compartment createCompartment(double x, double y, double width, double height, String aliasId) {
- Compartment alias = new Compartment(aliasId);
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
- }
-
- private GenericProtein createSpecies(double x, double y, double width, double height, String aliasId) {
- GenericProtein alias = new GenericProtein(aliasId);
- alias.setName("SNCA");
- alias.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
- alias.addMiriamData(new MiriamData(MiriamType.HGNC, "11138"));
- alias.setElementId(aliasId);
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
- }
-
- private Complex createComplex(double x, double y, double width, double height, String aliasId) {
- Complex alias = new Complex(aliasId);
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
- }
-
-}
+package lcsb.mapviewer.persist.dao.map;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+
+import java.awt.Color;
+import java.awt.geom.Point2D;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
+import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
+import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnitTypeFactor;
+import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.type.ModulationReaction;
+import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.Residue;
+import lcsb.mapviewer.persist.PersistTestFunctions;
+
+public class ModelDaoTest extends PersistTestFunctions {
+ ModelComparator modelComparator = new ModelComparator();
+
+ Logger logger = Logger.getLogger(ModelDaoTest.class);
+ private Project project;
+ String projectId = "Some_id";
+ int identifierCounter = 0;
+
+ @Before
+ public void setUp() throws Exception {
+ project = projectDao.getProjectByProjectId(projectId);
+ if (project != null) {
+ projectDao.delete(project);
+ }
+ project = new Project();
+ project.setProjectId(projectId);
+ projectDao.add(project);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ projectDao.delete(project);
+ }
+
+ @Test
+ public void testLoadFromDb() throws Exception {
+ try {
+ Model model = createModel();
+ project.addModel(model);
+ modelDao.add(model);
+ projectDao.update(project);
+ projectDao.evict(project);
+
+ modelDao.evict(model);
+ ModelData model2 = modelDao.getById(model.getId());
+ assertNotNull(model2);
+ assertFalse(model2 == model);
+
+ assertEquals(model.getElements().size(), model2.getElements().size());
+ assertEquals(model.getLayers().size(), model2.getLayers().size());
+ assertEquals(model.getReactions().size(), model2.getReactions().size());
+
+ ModelComparator comparator = new ModelComparator();
+ assertEquals(0, comparator.compare(model, new ModelFullIndexed(model2)));
+
+ modelDao.delete(model2);
+ model2 = modelDao.getById(model.getId());
+ assertNull(model2);
+ project = projectDao.getById(project.getId());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testIndexesReload() throws Exception {
+ try {
+ Model model = createModel();
+ project.addModel(model);
+ modelDao.add(model);
+ modelDao.evict(model);
+ ModelData model2 = modelDao.getById(model.getId());
+ Model fullModel = new ModelFullIndexed(model2);
+ assertNotNull(model2);
+
+ assertEquals(model.getElements().size(), model2.getElements().size());
+ assertEquals(model.getLayers().size(), model2.getLayers().size());
+ assertEquals(model.getReactions().size(), model2.getReactions().size());
+
+ // check if we really performed a test
+ boolean test = false;
+
+ for (Element alias : model.getElements()) {
+ assertNotNull(fullModel.getElementByElementId(alias.getElementId()));
+ test = true;
+ }
+ assertTrue(test);
+
+ test = false;
+ for (Element alias : model.getElements()) {
+ if (alias instanceof Compartment) {
+ assertNotNull(fullModel.getElementByElementId(alias.getElementId()));
+ test = true;
+ }
+ }
+ assertTrue(test);
+
+ model2.setHeight(32);
+ modelDao.update(model2.getModel());
+
+ modelDao.delete(model2);
+ model2 = modelDao.getById(model.getId());
+ assertNull(model2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionInModelAfterReload() throws Exception {
+ try {
+ Model model = createModel();
+ Reaction reaction = model.getReactions().iterator().next();
+ project.addModel(model);
+ modelDao.add(model);
+ projectDao.update(project);
+ projectDao.evict(project);
+ modelDao.evict(model);
+ ModelData model2 = modelDao.getById(model.getId());
+
+ Reaction reaction2 = null;
+ for (Reaction r : model2.getReactions()) {
+ if (r.getIdReaction().equals(reaction.getIdReaction())) {
+ reaction2 = r;
+ }
+ }
+ assertNotNull(reaction2);
+ assertFalse(reaction.equals(reaction2));
+
+ assertEquals(reaction.getNodes().size(), reaction2.getNodes().size());
+
+ modelDao.delete(model2);
+ model2 = modelDao.getById(model.getId());
+ assertNull(model2);
+ project = projectDao.getById(project.getId());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionInWithKinetics() throws Exception {
+ try {
+ Model model = createModel();
+ Reaction reaction = model.getReactions().iterator().next();
+ SbmlKinetics kinetics = new SbmlKinetics();
+ kinetics.addElement(reaction.getReactants().get(0).getElement());
+ kinetics.addFunction(createFunction());
+ model.addFunctions(kinetics.getFunctions());
+ kinetics.addParameter(createParameter());
+ model.addUnit(kinetics.getParameters().iterator().next().getUnits());
+ reaction.setKinetics(kinetics);
+ project.addModel(model);
+ modelDao.add(model);
+ projectDao.update(project);
+ projectDao.evict(project);
+ modelDao.evict(model);
+ ModelData model2 = modelDao.getById(model.getId());
+
+ assertEquals(0, modelComparator.compare(model, new ModelFullIndexed(model2)));
+
+ project = projectDao.getById(project.getId());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testModulationReaction() throws Exception {
+ try {
+ Model model = createModel();
+ Reaction reaction = new ModulationReaction();
+ reaction.addProduct(new Product(model.getElementByElementId("sa2")));
+ reaction.addReactant(new Reactant(model.getElementByElementId("sa1117")));
+ reaction.setIdReaction("re" + identifierCounter++);
+ model.addReaction(reaction);
+
+ project.addModel(model);
+ modelDao.add(model);
+ projectDao.update(project);
+ projectDao.evict(project);
+ modelDao.evict(model);
+ ModelData model2 = modelDao.getById(model.getId());
+
+ assertEquals(0, modelComparator.compare(model, new ModelFullIndexed(model2)));
+
+ project = projectDao.getById(project.getId());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testModelWithParameters() throws Exception {
+ try {
+ Model model = createModel();
+ model.addParameter(createParameter());
+ model.addUnit(model.getParameters().iterator().next().getUnits());
+ project.addModel(model);
+ modelDao.add(model);
+ projectDao.update(project);
+ projectDao.evict(project);
+ modelDao.evict(model);
+ ModelData model2 = modelDao.getById(model.getId());
+
+ assertEquals(0, modelComparator.compare(model, new ModelFullIndexed(model2)));
+
+ project = projectDao.getById(project.getId());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private SbmlParameter createParameter() {
+ SbmlParameter parameter = new SbmlParameter("param_id");
+ parameter.setName("X");
+ parameter.setValue(4.7);
+ parameter.setUnits(createUnits());
+ return parameter;
+ }
+
+ private SbmlUnit createUnits() {
+ SbmlUnit unit = new SbmlUnit("unit_id");
+ unit.setName("u name");
+ unit.addUnitTypeFactor(new SbmlUnitTypeFactor(SbmlUnitType.AMPERE, 1, 2, 3));
+ return unit;
+ }
+
+ private SbmlFunction createFunction() {
+ SbmlFunction result = new SbmlFunction("fun_id");
+ result.setDefinition("def(k1)");
+ result.addArgument("k1");
+ result.setName("fun name");
+ return result;
+ }
+
+ @Test
+ public void testGetLastModelForProjectName() throws Exception {
+ try {
+ ModelData model3 = modelDao.getLastModelForProjectIdentifier(projectId, false);
+ assertNull(model3);
+
+ Model model = createModel();
+ project.addModel(model);
+ modelDao.add(model);
+
+ ModelData newModel = modelDao.getLastModelForProjectIdentifier(projectId, false);
+ assertNotNull(newModel);
+ assertEquals(model.getId(), newModel.getId());
+
+ Model model2 = createModel();
+ project.addModel(model2);
+ modelDao.add(model2);
+
+ newModel = modelDao.getLastModelForProjectIdentifier(projectId, false);
+ assertNotNull(newModel);
+ assertEquals(model2.getId(), newModel.getId());
+
+ modelDao.delete(model2);
+ modelDao.delete(model);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ /**
+ * After adding model to db, modification residues disappear from the model...
+ *
+ * @throws Exception
+ */
+ @Test
+ public void testModificationsInProteins() throws Exception {
+ try {
+ Model model = createModel();
+ Project project = new Project();
+ project.addModel(model);
+ projectDao.add(project);
+
+ modelDao.evict(model);
+ projectDao.evict(project);
+ Model model2 = new ModelFullIndexed(modelDao.getById(model.getId()));
+
+ Protein originalSpecies = (Protein) model.getElementByElementId("pr1");
+ Protein fromDbSpecies = (Protein) model2.getElementByElementId("pr1");
+
+ assertFalse(originalSpecies.equals(fromDbSpecies));
+ assertEquals(originalSpecies.getModificationResidues().size(), fromDbSpecies.getModificationResidues().size());
+
+ project = projectDao.getById(project.getId());
+ projectDao.delete(project);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ /**
+ * After adding model to db, miriam annotations disappear...
+ *
+ * @throws Exception
+ */
+ @Test
+ public void testMiriamInSpecies() throws Exception {
+ try {
+ Model model = createModel();
+ Project project = new Project();
+ project.addModel(model);
+ projectDao.add(project);
+
+ modelDao.evict(model);
+ projectDao.evict(project);
+ Model model2 = new ModelFullIndexed(modelDao.getById(model.getId()));
+
+ Protein originalSpecies = (Protein) model.getElementByElementId("pr1");
+ Protein fromDbSpecies = (Protein) model2.getElementByElementId("pr1");
+
+ assertFalse(originalSpecies.equals(fromDbSpecies));
+ assertEquals(originalSpecies.getMiriamData().size(), fromDbSpecies.getMiriamData().size());
+
+ project = projectDao.getById(project.getId());
+ projectDao.delete(project);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ /**
+ * After adding layouts to model.
+ *
+ * @throws Exception
+ */
+ @Test
+ public void testLayoutsInModel() throws Exception {
+ try {
+ Model model = createModel();
+
+ Layout layout = new Layout();
+ layout.setDirectory("tmp");
+ layout.setTitle("temporary name");
+ model.addLayout(layout);
+ Project project = new Project();
+ project.addModel(model);
+ projectDao.add(project);
+
+ modelDao.evict(model);
+ projectDao.evict(project);
+ ModelData model2 = modelDao.getById(model.getId());
+
+ assertEquals(1, model2.getLayouts().size());
+ assertEquals("tmp", model2.getLayouts().get(0).getDirectory());
+ assertEquals("temporary name", model2.getLayouts().get(0).getTitle());
+
+ project = projectDao.getById(project.getId());
+ projectDao.delete(project);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Model createModel() {
+ Model model = new ModelFullIndexed(null);
+
+ GenericProtein alias = createSpecies(264.8333333333335, 517.75, 86.0, 46.0, "sa2");
+ model.addElement(alias);
+ alias = createSpecies(267.6666666666665, 438.75, 80.0, 40.0, "sa1117");
+ model.addElement(alias);
+ alias = createSpecies(261.6666666666665, 600.75, 92.0, 52.0, "sa1119");
+ model.addElement(alias);
+ alias = createSpecies(203.666666666667, 687.75, 98.0, 58.0, "sa1121");
+ model.addElement(alias);
+
+ alias = createSpecies(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
+ Species alias2 = createSpecies(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
+ Complex alias3 = createComplex(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
+ alias3.addSpecies(alias);
+ alias3.addSpecies(alias2);
+ alias.setComplex(alias3);
+ alias2.setComplex(alias3);
+
+ model.addElement(alias);
+ model.addElement(alias2);
+ model.addElement(alias3);
+
+ Compartment cAlias = createCompartment(380.0, 416.0, 1893.0, 1866.0, "ca1");
+ model.addElement(cAlias);
+ model.setWidth(2000);
+ model.setHeight(2000);
+
+ Layer layer = new Layer();
+ model.addLayer(layer);
+
+ LayerRect lr = new LayerRect();
+ lr.setColor(Color.YELLOW);
+ layer.addLayerRect(lr);
+
+ Reaction reaction = new TransportReaction();
+ reaction.addProduct(new Product(alias));
+ reaction.addReactant(new Reactant(alias2));
+ reaction.setIdReaction("re" + identifierCounter++);
+ model.addReaction(reaction);
+
+ alias = createSpecies(264.8333333333335, 517.75, 86.0, 46.0, "pr1");
+ model.addElement(alias);
+
+ Residue mr = new Residue();
+ mr.setName("mr");
+ mr.setPosition(new Point2D.Double(10, 20));
+ alias.addModificationResidue(mr);
+
+ alias.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, "c"));
+ return model;
+ }
+
+ private Compartment createCompartment(double x, double y, double width, double height, String aliasId) {
+ Compartment alias = new Compartment(aliasId);
+ alias.setX(x);
+ alias.setY(y);
+ alias.setWidth(width);
+ alias.setHeight(height);
+ return alias;
+ }
+
+ private GenericProtein createSpecies(double x, double y, double width, double height, String aliasId) {
+ GenericProtein alias = new GenericProtein(aliasId);
+ alias.setName("SNCA");
+ alias.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
+ alias.addMiriamData(new MiriamData(MiriamType.HGNC, "11138"));
+ alias.setElementId(aliasId);
+ alias.setX(x);
+ alias.setY(y);
+ alias.setWidth(width);
+ alias.setHeight(height);
+ return alias;
+ }
+
+ private Complex createComplex(double x, double y, double width, double height, String aliasId) {
+ Complex alias = new Complex(aliasId);
+ alias.setX(x);
+ alias.setY(y);
+ alias.setWidth(width);
+ alias.setHeight(height);
+ return alias;
+ }
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/AllLayoutTests.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/AllLayoutTests.java
index c16b2f161c..944cbb34d9 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/AllLayoutTests.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/AllLayoutTests.java
@@ -1,16 +1,16 @@
-package lcsb.mapviewer.persist.dao.map.layout;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-import lcsb.mapviewer.persist.dao.map.layout.alias.AllAliasTests;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AllAliasTests.class, //
- ReferenceGenomeDaoTest.class, //
- ReferenceGenomeGeneMappingDaoTest.class,//
-})
-public class AllLayoutTests {
-
-}
+package lcsb.mapviewer.persist.dao.map.layout;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+import lcsb.mapviewer.persist.dao.map.layout.alias.AllAliasTests;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AllAliasTests.class, //
+ ReferenceGenomeDaoTest.class, //
+ ReferenceGenomeGeneMappingDaoTest.class,//
+})
+public class AllLayoutTests {
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/ReferenceGenomeDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/ReferenceGenomeDaoTest.java
index 3e0f11f2c9..8dae9dbe89 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/ReferenceGenomeDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/ReferenceGenomeDaoTest.java
@@ -1,71 +1,71 @@
-package lcsb.mapviewer.persist.dao.map.layout;
-
-import static org.junit.Assert.assertEquals;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.ReferenceGenome;
-import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
-import lcsb.mapviewer.persist.PersistTestFunctions;
-
-public class ReferenceGenomeDaoTest extends PersistTestFunctions {
-
- @Autowired
- ReferenceGenomeDao referenceGenomeDao;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void test() {
- try {
- ReferenceGenome genome = new ReferenceGenome();
- genome.setOrganism(new MiriamData(MiriamType.TAXONOMY, "9606"));
- genome.setType(ReferenceGenomeType.UCSC);
- genome.setVersion("x");
- long count = referenceGenomeDao.getCount();
- referenceGenomeDao.add(genome);
- long count2 = referenceGenomeDao.getCount();
- referenceGenomeDao.delete(genome);
- long count3 = referenceGenomeDao.getCount();
-
- assertEquals(count + 1, count2);
- assertEquals(count, count3);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetByType() {
- try {
- ReferenceGenome genome = new ReferenceGenome();
- genome.setOrganism(new MiriamData(MiriamType.TAXONOMY, "111111"));
- genome.setType(ReferenceGenomeType.UCSC);
- genome.setVersion("unknown");
- long count = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC).size();
- referenceGenomeDao.add(genome);
- long count2 = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC).size();;
- referenceGenomeDao.delete(genome);
- long count3 = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC).size();;
-
- assertEquals(count + 1, count2);
- assertEquals(count, count3);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.persist.dao.map.layout;
+
+import static org.junit.Assert.assertEquals;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.layout.ReferenceGenome;
+import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
+import lcsb.mapviewer.persist.PersistTestFunctions;
+
+public class ReferenceGenomeDaoTest extends PersistTestFunctions {
+
+ @Autowired
+ ReferenceGenomeDao referenceGenomeDao;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void test() {
+ try {
+ ReferenceGenome genome = new ReferenceGenome();
+ genome.setOrganism(new MiriamData(MiriamType.TAXONOMY, "9606"));
+ genome.setType(ReferenceGenomeType.UCSC);
+ genome.setVersion("x");
+ long count = referenceGenomeDao.getCount();
+ referenceGenomeDao.add(genome);
+ long count2 = referenceGenomeDao.getCount();
+ referenceGenomeDao.delete(genome);
+ long count3 = referenceGenomeDao.getCount();
+
+ assertEquals(count + 1, count2);
+ assertEquals(count, count3);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetByType() {
+ try {
+ ReferenceGenome genome = new ReferenceGenome();
+ genome.setOrganism(new MiriamData(MiriamType.TAXONOMY, "111111"));
+ genome.setType(ReferenceGenomeType.UCSC);
+ genome.setVersion("unknown");
+ long count = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC).size();
+ referenceGenomeDao.add(genome);
+ long count2 = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC).size();;
+ referenceGenomeDao.delete(genome);
+ long count3 = referenceGenomeDao.getByType(ReferenceGenomeType.UCSC).size();;
+
+ assertEquals(count + 1, count2);
+ assertEquals(count, count3);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/ReferenceGenomeGeneMappingDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/ReferenceGenomeGeneMappingDaoTest.java
index 70db7b6e51..89cbff108f 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/ReferenceGenomeGeneMappingDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/ReferenceGenomeGeneMappingDaoTest.java
@@ -1,62 +1,62 @@
-package lcsb.mapviewer.persist.dao.map.layout;
-
-import static org.junit.Assert.assertEquals;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.ReferenceGenome;
-import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
-import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
-import lcsb.mapviewer.persist.PersistTestFunctions;
-
-public class ReferenceGenomeGeneMappingDaoTest extends PersistTestFunctions {
-
- @Autowired
- ReferenceGenomeGeneMappingDao referenceGenomeGeneMappingDao;
-
- @Autowired
- ReferenceGenomeDao referenceGenomeDao;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void test() {
- try {
- ReferenceGenome genome = new ReferenceGenome();
- genome.setOrganism(new MiriamData(MiriamType.TAXONOMY, "9606"));
- genome.setType(ReferenceGenomeType.UCSC);
- genome.setVersion("x");
- referenceGenomeDao.add(genome);
-
- ReferenceGenomeGeneMapping mapping = new ReferenceGenomeGeneMapping();
- mapping.setName("Xxx");
- mapping.setReferenceGenome(genome);
- mapping.setSourceUrl("http://xxx.xx/");
- long count = referenceGenomeGeneMappingDao.getCount();
- referenceGenomeGeneMappingDao.add(mapping);
- long count2 = referenceGenomeGeneMappingDao.getCount();
- referenceGenomeGeneMappingDao.delete(mapping);
- long count3 = referenceGenomeGeneMappingDao.getCount();
-
- referenceGenomeDao.delete(genome);
-
- assertEquals(count + 1, count2);
- assertEquals(count, count3);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.persist.dao.map.layout;
+
+import static org.junit.Assert.assertEquals;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.layout.ReferenceGenome;
+import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
+import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
+import lcsb.mapviewer.persist.PersistTestFunctions;
+
+public class ReferenceGenomeGeneMappingDaoTest extends PersistTestFunctions {
+
+ @Autowired
+ ReferenceGenomeGeneMappingDao referenceGenomeGeneMappingDao;
+
+ @Autowired
+ ReferenceGenomeDao referenceGenomeDao;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void test() {
+ try {
+ ReferenceGenome genome = new ReferenceGenome();
+ genome.setOrganism(new MiriamData(MiriamType.TAXONOMY, "9606"));
+ genome.setType(ReferenceGenomeType.UCSC);
+ genome.setVersion("x");
+ referenceGenomeDao.add(genome);
+
+ ReferenceGenomeGeneMapping mapping = new ReferenceGenomeGeneMapping();
+ mapping.setName("Xxx");
+ mapping.setReferenceGenome(genome);
+ mapping.setSourceUrl("http://xxx.xx/");
+ long count = referenceGenomeGeneMappingDao.getCount();
+ referenceGenomeGeneMappingDao.add(mapping);
+ long count2 = referenceGenomeGeneMappingDao.getCount();
+ referenceGenomeGeneMappingDao.delete(mapping);
+ long count3 = referenceGenomeGeneMappingDao.getCount();
+
+ referenceGenomeDao.delete(genome);
+
+ assertEquals(count + 1, count2);
+ assertEquals(count, count3);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AllAliasTests.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AllAliasTests.java
index 2461742e20..a2c62e35b1 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AllAliasTests.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AllAliasTests.java
@@ -1,15 +1,15 @@
-package lcsb.mapviewer.persist.dao.map.layout.alias;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AliasDaoTest.class, //
- AliasDaoTest2.class, //
- AntisenseRnaTest.class, //
- RnaTest.class, //
-})
-public class AllAliasTests {
-
-}
+package lcsb.mapviewer.persist.dao.map.layout.alias;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AliasDaoTest.class, //
+ AliasDaoTest2.class, //
+ AntisenseRnaTest.class, //
+ RnaTest.class, //
+})
+public class AllAliasTests {
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/statistics/SearchHistoryDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/statistics/SearchHistoryDaoTest.java
index b86ee77f23..2acc3d8a3f 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/statistics/SearchHistoryDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/statistics/SearchHistoryDaoTest.java
@@ -1,40 +1,40 @@
-package lcsb.mapviewer.persist.dao.map.statistics;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.fail;
-import lcsb.mapviewer.model.map.statistics.SearchHistory;
-import lcsb.mapviewer.model.map.statistics.SearchType;
-import lcsb.mapviewer.persist.PersistTestFunctions;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class SearchHistoryDaoTest extends PersistTestFunctions{
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void test() {
- try {
- SearchHistory searchHistory = new SearchHistory();
- long count = searchHistoryDao.getCount();
- searchHistory.setIpAddress("0.0.0.0");
- searchHistory.setQuery("query ...");
- searchHistory.setType(SearchType.GENERAL);
- searchHistoryDao.add(searchHistory);
- long count1 = searchHistoryDao.getCount();
- assertEquals(count+1,count1);
- } catch (Exception e) {
- e.printStackTrace();
- fail("Exception occurred");
- }
- }
-
-}
+package lcsb.mapviewer.persist.dao.map.statistics;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.fail;
+import lcsb.mapviewer.model.map.statistics.SearchHistory;
+import lcsb.mapviewer.model.map.statistics.SearchType;
+import lcsb.mapviewer.persist.PersistTestFunctions;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class SearchHistoryDaoTest extends PersistTestFunctions{
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void test() {
+ try {
+ SearchHistory searchHistory = new SearchHistory();
+ long count = searchHistoryDao.getCount();
+ searchHistory.setIpAddress("0.0.0.0");
+ searchHistory.setQuery("query ...");
+ searchHistory.setType(SearchType.GENERAL);
+ searchHistoryDao.add(searchHistory);
+ long count1 = searchHistoryDao.getCount();
+ assertEquals(count+1,count1);
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Exception occurred");
+ }
+ }
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/statistics/StatisticsAllTests.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/statistics/StatisticsAllTests.java
index 3e424f9c1d..37f2534d88 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/statistics/StatisticsAllTests.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/statistics/StatisticsAllTests.java
@@ -1,11 +1,11 @@
-package lcsb.mapviewer.persist.dao.map.statistics;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ SearchHistoryDaoTest.class })
-public class StatisticsAllTests {
-
-}
+package lcsb.mapviewer.persist.dao.map.statistics;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ SearchHistoryDaoTest.class })
+public class StatisticsAllTests {
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/user/AllUserTests.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/user/AllUserTests.java
index 7775b245e9..dd2ee9fc3c 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/user/AllUserTests.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/user/AllUserTests.java
@@ -1,12 +1,12 @@
-package lcsb.mapviewer.persist.dao.user;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ UserDaoTest.class, //
-})
-public class AllUserTests {
-
-}
+package lcsb.mapviewer.persist.dao.user;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ UserDaoTest.class, //
+})
+public class AllUserTests {
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/user/UserDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/user/UserDaoTest.java
index aad6f041c4..72be9f15ec 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/user/UserDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/user/UserDaoTest.java
@@ -1,245 +1,245 @@
-package lcsb.mapviewer.persist.dao.user;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.security.crypto.password.PasswordEncoder;
-
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.user.BasicPrivilege;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.model.user.UserAnnotationSchema;
-import lcsb.mapviewer.model.user.UserClassAnnotators;
-import lcsb.mapviewer.model.user.UserClassValidAnnotations;
-import lcsb.mapviewer.model.user.UserGuiPreference;
-import lcsb.mapviewer.persist.PersistTestFunctions;
-
-public class UserDaoTest extends PersistTestFunctions {
-
- @Autowired
- protected PasswordEncoder passwordEncoder;
-
- protected Logger logger = Logger.getLogger(UserDaoTest.class.getName());
- String testLogin = "test_login123";
- String testEmail = "a@a.pl";
- String testPasswd = "pwd";
- String testLogin2 = "test_login_tmp";
- String testName = "John";
- String testSurname = "Doe";
-
- @Before
- public void setUp() throws Exception {
- Map<String, Object> params = new HashMap<String, Object>();
- params.put("login_param", testLogin);
- params.put("login_param2", testLogin2);
- dbUtils.executeSqlQuery("delete from user_table where login = :login_param or login = :login_param2", params);
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testAddUpdateDelete() {
- try {
- User user = userDao.getUserByLogin(testLogin);
- assertNull(user);
-
- long counter = userDao.getCount();
-
- user = new User();
- user.setLogin(testLogin);
- user.addPrivilege(new BasicPrivilege(0, PrivilegeType.ADD_MAP, user));
- userDao.add(user);
-
- long counter2 = userDao.getCount();
- assertEquals(counter + 1, counter2);
-
- user.setLogin(testLogin2);
- userDao.update(user);
-
- User user2 = userDao.getUserByLogin(testLogin2);
- assertNotNull(user2);
-
- userDao.delete(user);
-
- user2 = userDao.getUserByLogin(testLogin2);
- assertNull(user2);
- counter2 = userDao.getCount();
- assertEquals(counter, counter2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddDeleteAdd() {
- try {
- User user = userDao.getUserByLogin(testLogin);
- assertNull(user);
-
- long counter = userDao.getCount();
-
- user = new User();
- user.setLogin(testLogin);
- userDao.add(user);
-
- long counter2 = userDao.getCount();
- assertEquals(counter + 1, counter2);
-
- userDao.delete(user);
-
- User user2 = userDao.getUserByLogin(testLogin);
- assertNull(user2);
-
- user2 = new User();
- user2.setLogin(testLogin);
- userDao.add(user2);
-
- assertNotNull(userDao.getUserByLogin(testLogin));
-
- userDao.delete(user2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetUserByLogin() throws Exception {
- try {
- User user = new User();
- user.setCryptedPassword(passwordEncoder.encode(testPasswd));
- user.setLogin(testLogin);
- userDao.add(user);
- User user2 = userDao.getUserByLogin(testLogin);
- assertNotNull(user2);
- assertEquals(user2.getId(), user.getId());
- assertEquals(user2.getLogin(), user.getLogin());
- assertEquals(user2.getCryptedPassword(), user.getCryptedPassword());
- user2 = userDao.getUserByLogin(testLogin2);
- assertNull(user2);
- userDao.delete(user);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetUserByEmail() throws Exception {
- try {
- User user = new User();
- user.setCryptedPassword(passwordEncoder.encode(testPasswd));
- user.setLogin(testLogin);
- user.setEmail(testEmail);
- userDao.add(user);
- User user2 = userDao.getUserByEmail(testEmail);
- assertNotNull(user2);
- assertEquals(user2.getId(), user.getId());
- assertEquals(user2.getLogin(), user.getLogin());
- assertEquals(user2.getCryptedPassword(), user.getCryptedPassword());
- user2 = userDao.getUserByEmail(testEmail + "sadas");
- assertNull(user2);
- userDao.delete(user);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAll() throws Exception {
- try {
- assertTrue(userDao.getAll().size() > 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUserWithAnnotatorSchema() throws Exception {
- try {
- User user = new User();
- UserAnnotationSchema uas = new UserAnnotationSchema();
- uas.setValidateMiriamTypes(true);
- UserClassAnnotators ca = new UserClassAnnotators();
- ca.setClassName(Species.class);
- ca.addAnnotator(String.class);
- ca.addAnnotator(Integer.class);
- uas.addClassAnnotator(ca);
- uas.addClassAnnotator(new UserClassAnnotators(String.class, new ArrayList<String>()));
- UserClassValidAnnotations cva = new UserClassValidAnnotations();
- cva.setClassName(Reaction.class);
- cva.addValidMiriamType(MiriamType.HGNC);
- cva.addValidMiriamType(MiriamType.HGNC_SYMBOL);
- uas.addClassValidAnnotations(cva);
- uas.addClassValidAnnotations(new UserClassValidAnnotations(String.class, new ArrayList<MiriamType>()));
- uas.addClassValidAnnotations(new UserClassValidAnnotations(Integer.class, new ArrayList<MiriamType>()));
- user.setAnnotationSchema(uas);
- userDao.add(user);
- userDao.evict(user);
- User user2 = userDao.getById(user.getId());
- assertNotNull(user2);
- UserAnnotationSchema uas2 = user2.getAnnotationSchema();
- assertNotNull(uas2);
- assertEquals(2, uas2.getClassAnnotators().size());
- assertEquals(3, uas2.getClassValidAnnotators().size());
- assertEquals(Species.class.getCanonicalName(), uas.getClassAnnotators().get(0).getClassName());
- assertEquals(String.class.getCanonicalName(), uas.getClassAnnotators().get(0).getAnnotators().get(0));
- assertEquals(Integer.class.getCanonicalName(), uas.getClassAnnotators().get(0).getAnnotators().get(1));
- assertEquals(Reaction.class.getCanonicalName(), uas.getClassValidAnnotators().get(0).getClassName());
- assertEquals(MiriamType.HGNC, uas.getClassValidAnnotators().get(0).getValidMiriamTypes().get(0));
- assertEquals(MiriamType.HGNC_SYMBOL, uas.getClassValidAnnotators().get(0).getValidMiriamTypes().get(1));
-
- userDao.delete(user2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUserWithAnnotatorSchemaGuiPreferences() throws Exception {
- try {
- User user = new User();
- UserAnnotationSchema uas = new UserAnnotationSchema();
- user.setAnnotationSchema(uas);
- UserGuiPreference option = new UserGuiPreference();
- option.setKey("key");
- option.setValue("val");
- uas.addGuiPreference(option);
- userDao.add(user);
- userDao.evict(user);
- User user2 = userDao.getById(user.getId());
- assertNotNull(user2);
- UserAnnotationSchema uas2 = user2.getAnnotationSchema();
- assertNotNull(uas2);
- assertEquals(1, uas2.getGuiPreferences().size());
-
- userDao.delete(user2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.persist.dao.user;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.security.crypto.password.PasswordEncoder;
+
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.user.BasicPrivilege;
+import lcsb.mapviewer.model.user.PrivilegeType;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.model.user.UserAnnotationSchema;
+import lcsb.mapviewer.model.user.UserClassAnnotators;
+import lcsb.mapviewer.model.user.UserClassValidAnnotations;
+import lcsb.mapviewer.model.user.UserGuiPreference;
+import lcsb.mapviewer.persist.PersistTestFunctions;
+
+public class UserDaoTest extends PersistTestFunctions {
+
+ @Autowired
+ protected PasswordEncoder passwordEncoder;
+
+ protected Logger logger = Logger.getLogger(UserDaoTest.class.getName());
+ String testLogin = "test_login123";
+ String testEmail = "a@a.pl";
+ String testPasswd = "pwd";
+ String testLogin2 = "test_login_tmp";
+ String testName = "John";
+ String testSurname = "Doe";
+
+ @Before
+ public void setUp() throws Exception {
+ Map<String, Object> params = new HashMap<String, Object>();
+ params.put("login_param", testLogin);
+ params.put("login_param2", testLogin2);
+ dbUtils.executeSqlQuery("delete from user_table where login = :login_param or login = :login_param2", params);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testAddUpdateDelete() {
+ try {
+ User user = userDao.getUserByLogin(testLogin);
+ assertNull(user);
+
+ long counter = userDao.getCount();
+
+ user = new User();
+ user.setLogin(testLogin);
+ user.addPrivilege(new BasicPrivilege(0, PrivilegeType.ADD_MAP, user));
+ userDao.add(user);
+
+ long counter2 = userDao.getCount();
+ assertEquals(counter + 1, counter2);
+
+ user.setLogin(testLogin2);
+ userDao.update(user);
+
+ User user2 = userDao.getUserByLogin(testLogin2);
+ assertNotNull(user2);
+
+ userDao.delete(user);
+
+ user2 = userDao.getUserByLogin(testLogin2);
+ assertNull(user2);
+ counter2 = userDao.getCount();
+ assertEquals(counter, counter2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddDeleteAdd() {
+ try {
+ User user = userDao.getUserByLogin(testLogin);
+ assertNull(user);
+
+ long counter = userDao.getCount();
+
+ user = new User();
+ user.setLogin(testLogin);
+ userDao.add(user);
+
+ long counter2 = userDao.getCount();
+ assertEquals(counter + 1, counter2);
+
+ userDao.delete(user);
+
+ User user2 = userDao.getUserByLogin(testLogin);
+ assertNull(user2);
+
+ user2 = new User();
+ user2.setLogin(testLogin);
+ userDao.add(user2);
+
+ assertNotNull(userDao.getUserByLogin(testLogin));
+
+ userDao.delete(user2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetUserByLogin() throws Exception {
+ try {
+ User user = new User();
+ user.setCryptedPassword(passwordEncoder.encode(testPasswd));
+ user.setLogin(testLogin);
+ userDao.add(user);
+ User user2 = userDao.getUserByLogin(testLogin);
+ assertNotNull(user2);
+ assertEquals(user2.getId(), user.getId());
+ assertEquals(user2.getLogin(), user.getLogin());
+ assertEquals(user2.getCryptedPassword(), user.getCryptedPassword());
+ user2 = userDao.getUserByLogin(testLogin2);
+ assertNull(user2);
+ userDao.delete(user);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetUserByEmail() throws Exception {
+ try {
+ User user = new User();
+ user.setCryptedPassword(passwordEncoder.encode(testPasswd));
+ user.setLogin(testLogin);
+ user.setEmail(testEmail);
+ userDao.add(user);
+ User user2 = userDao.getUserByEmail(testEmail);
+ assertNotNull(user2);
+ assertEquals(user2.getId(), user.getId());
+ assertEquals(user2.getLogin(), user.getLogin());
+ assertEquals(user2.getCryptedPassword(), user.getCryptedPassword());
+ user2 = userDao.getUserByEmail(testEmail + "sadas");
+ assertNull(user2);
+ userDao.delete(user);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAll() throws Exception {
+ try {
+ assertTrue(userDao.getAll().size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUserWithAnnotatorSchema() throws Exception {
+ try {
+ User user = new User();
+ UserAnnotationSchema uas = new UserAnnotationSchema();
+ uas.setValidateMiriamTypes(true);
+ UserClassAnnotators ca = new UserClassAnnotators();
+ ca.setClassName(Species.class);
+ ca.addAnnotator(String.class);
+ ca.addAnnotator(Integer.class);
+ uas.addClassAnnotator(ca);
+ uas.addClassAnnotator(new UserClassAnnotators(String.class, new ArrayList<String>()));
+ UserClassValidAnnotations cva = new UserClassValidAnnotations();
+ cva.setClassName(Reaction.class);
+ cva.addValidMiriamType(MiriamType.HGNC);
+ cva.addValidMiriamType(MiriamType.HGNC_SYMBOL);
+ uas.addClassValidAnnotations(cva);
+ uas.addClassValidAnnotations(new UserClassValidAnnotations(String.class, new ArrayList<MiriamType>()));
+ uas.addClassValidAnnotations(new UserClassValidAnnotations(Integer.class, new ArrayList<MiriamType>()));
+ user.setAnnotationSchema(uas);
+ userDao.add(user);
+ userDao.evict(user);
+ User user2 = userDao.getById(user.getId());
+ assertNotNull(user2);
+ UserAnnotationSchema uas2 = user2.getAnnotationSchema();
+ assertNotNull(uas2);
+ assertEquals(2, uas2.getClassAnnotators().size());
+ assertEquals(3, uas2.getClassValidAnnotators().size());
+ assertEquals(Species.class.getCanonicalName(), uas.getClassAnnotators().get(0).getClassName());
+ assertEquals(String.class.getCanonicalName(), uas.getClassAnnotators().get(0).getAnnotators().get(0));
+ assertEquals(Integer.class.getCanonicalName(), uas.getClassAnnotators().get(0).getAnnotators().get(1));
+ assertEquals(Reaction.class.getCanonicalName(), uas.getClassValidAnnotators().get(0).getClassName());
+ assertEquals(MiriamType.HGNC, uas.getClassValidAnnotators().get(0).getValidMiriamTypes().get(0));
+ assertEquals(MiriamType.HGNC_SYMBOL, uas.getClassValidAnnotators().get(0).getValidMiriamTypes().get(1));
+
+ userDao.delete(user2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUserWithAnnotatorSchemaGuiPreferences() throws Exception {
+ try {
+ User user = new User();
+ UserAnnotationSchema uas = new UserAnnotationSchema();
+ user.setAnnotationSchema(uas);
+ UserGuiPreference option = new UserGuiPreference();
+ option.setKey("key");
+ option.setValue("val");
+ uas.addGuiPreference(option);
+ userDao.add(user);
+ userDao.evict(user);
+ User user2 = userDao.getById(user.getId());
+ assertNotNull(user2);
+ UserAnnotationSchema uas2 = user2.getAnnotationSchema();
+ assertNotNull(uas2);
+ assertEquals(1, uas2.getGuiPreferences().size());
+
+ userDao.delete(user2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/mapper/Point2DMapperTest.java b/persist/src/test/java/lcsb/mapviewer/persist/mapper/Point2DMapperTest.java
index 9508f2a87b..e7283b7171 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/mapper/Point2DMapperTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/mapper/Point2DMapperTest.java
@@ -1,60 +1,60 @@
-package lcsb.mapviewer.persist.mapper;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.geom.Point2D;
-import java.io.Serializable;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class Point2DMapperTest {
-
- Point2DMapper mapper = new Point2DMapper();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSetPropertyValue() {
- Point2D component = new Point2D.Double(0, 3);
- Point2D component2 = new Point2D.Double(0, 0);
- Object val = mapper.getPropertyValue(component, 0);
- mapper.setPropertyValue(component2, 0, val);
- assertTrue(component.equals(component2));
- }
-
- @Test
- public void testReturnedClass() {
- assertNotNull(mapper.returnedClass());
- }
-
- @Test
- public void testHashCode() {
- Point2D component = new Point2D.Double(0, 3);
- Point2D component2 = new Point2D.Double(0, 0);
- assertTrue(mapper.hashCode(component) != mapper.hashCode(component2));
- }
-
- @Test
- public void testDisassemble() {
- Point2D object = new Point2D.Double(0, 3);
- Serializable obj = mapper.disassemble(object, null);
- Point2D object2 = (Point2D) mapper.assemble(obj, null, null);
-
- assertTrue(object.equals(object2));
- }
-
- @Test
- public void testReplace() {
- assertNotNull(mapper.replace(new Point2D.Double(0, 3), new Point2D.Double(0, 9), null, null));
- }
-
-}
+package lcsb.mapviewer.persist.mapper;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import java.awt.geom.Point2D;
+import java.io.Serializable;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class Point2DMapperTest {
+
+ Point2DMapper mapper = new Point2DMapper();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSetPropertyValue() {
+ Point2D component = new Point2D.Double(0, 3);
+ Point2D component2 = new Point2D.Double(0, 0);
+ Object val = mapper.getPropertyValue(component, 0);
+ mapper.setPropertyValue(component2, 0, val);
+ assertTrue(component.equals(component2));
+ }
+
+ @Test
+ public void testReturnedClass() {
+ assertNotNull(mapper.returnedClass());
+ }
+
+ @Test
+ public void testHashCode() {
+ Point2D component = new Point2D.Double(0, 3);
+ Point2D component2 = new Point2D.Double(0, 0);
+ assertTrue(mapper.hashCode(component) != mapper.hashCode(component2));
+ }
+
+ @Test
+ public void testDisassemble() {
+ Point2D object = new Point2D.Double(0, 3);
+ Serializable obj = mapper.disassemble(object, null);
+ Point2D object2 = (Point2D) mapper.assemble(obj, null, null);
+
+ assertTrue(object.equals(object2));
+ }
+
+ @Test
+ public void testReplace() {
+ assertNotNull(mapper.replace(new Point2D.Double(0, 3), new Point2D.Double(0, 9), null, null));
+ }
+
+}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/BaseController.java b/rest-api/src/main/java/lcsb/mapviewer/api/BaseController.java
index 8ebc1d5730..d93c477c3d 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/BaseController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/BaseController.java
@@ -1,93 +1,93 @@
-package lcsb.mapviewer.api;
-
-import java.io.IOException;
-import java.io.UnsupportedEncodingException;
-import java.net.URLDecoder;
-import java.util.TreeMap;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-import org.springframework.http.HttpHeaders;
-import org.springframework.http.HttpStatus;
-import org.springframework.http.ResponseEntity;
-import org.springframework.web.bind.ServletRequestBindingException;
-import org.springframework.web.bind.annotation.ExceptionHandler;
-import org.springframework.web.context.request.WebRequest;
-
-import com.fasterxml.jackson.core.JsonParseException;
-import com.fasterxml.jackson.databind.JsonMappingException;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.databind.node.ObjectNode;
-import com.google.gson.Gson;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-
-public abstract class BaseController {
- private Logger logger = Logger.getLogger(BaseController.class);
-
- private ObjectMapper mapper = new ObjectMapper();
-
- @ExceptionHandler({ Exception.class })
- public ResponseEntity<Object> handleException(Exception e, WebRequest request) {
- if (e instanceof lcsb.mapviewer.services.SecurityException) {
- return createErrorResponse("Access denied.", e.getMessage(), new HttpHeaders(), HttpStatus.FORBIDDEN);
- } else if (e instanceof ObjectNotFoundException) {
- return createErrorResponse("Object not found.", e.getMessage(), new HttpHeaders(), HttpStatus.NOT_FOUND);
- } else if (e instanceof ObjectExistsException) {
- return createErrorResponse("Object already exists.", e.getMessage(), new HttpHeaders(), HttpStatus.CONFLICT);
- } else if (e instanceof QueryException) {
- logger.error(e, e);
- return createErrorResponse("Query server error.", e.getMessage(), new HttpHeaders(), HttpStatus.BAD_REQUEST);
- } else if (e instanceof ServletRequestBindingException && e.getMessage().indexOf(Configuration.AUTH_TOKEN) >= 0) {
- return createErrorResponse("Access denied.", e.getMessage(), new HttpHeaders(), HttpStatus.FORBIDDEN);
- } else {
- logger.error(e, e);
- return createErrorResponse("Internal server error.", e.getMessage(), new HttpHeaders(),
- HttpStatus.INTERNAL_SERVER_ERROR);
- }
- }
-
- private ResponseEntity<Object> createErrorResponse(String errorMessage, String error, HttpHeaders httpHeaders,
- HttpStatus status) {
-
- return new ResponseEntity<Object>(
- "{\"error\" : \"" + errorMessage + "\",\"reason\":" + new Gson().toJson(error) + "}", httpHeaders, status);
- }
-
- public Map<String, Object> parseBody(String body) throws IOException, JsonParseException, JsonMappingException {
- if (body == null || body.isEmpty()) {
- return new TreeMap<>();
- }
- ObjectNode result = mapper.readValue(body, ObjectNode.class);
- return mapper.convertValue(result, Map.class);
- }
-
- protected Map<String, Object> getData(Map<String, Object> node, String objectName) {
- return (Map<String, Object>) node.get(objectName);
- }
-
- protected Map<String, String> parsePostBody(String body) {
- Map<String, String> result = new TreeMap<>();
- String[] parameters = body.split("&");
- for (String string : parameters) {
- int position = string.indexOf("=");
- if (position < 0) {
- position = string.length();
- }
- String key = string.substring(0, position);
- String value = null;
- if (position < string.length()) {
- value = string.substring(position + 1, string.length());
- try {
- value = URLDecoder.decode(value, "UTF-8");
- } catch (UnsupportedEncodingException e) {
- throw new InvalidStateException("Cannot decode input", e);
- }
- }
- result.put(key, value);
- }
- return result;
- }
-
-}
+package lcsb.mapviewer.api;
+
+import java.io.IOException;
+import java.io.UnsupportedEncodingException;
+import java.net.URLDecoder;
+import java.util.TreeMap;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+import org.springframework.http.HttpHeaders;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.ServletRequestBindingException;
+import org.springframework.web.bind.annotation.ExceptionHandler;
+import org.springframework.web.context.request.WebRequest;
+
+import com.fasterxml.jackson.core.JsonParseException;
+import com.fasterxml.jackson.databind.JsonMappingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+import com.google.gson.Gson;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+
+public abstract class BaseController {
+ private Logger logger = Logger.getLogger(BaseController.class);
+
+ private ObjectMapper mapper = new ObjectMapper();
+
+ @ExceptionHandler({ Exception.class })
+ public ResponseEntity<Object> handleException(Exception e, WebRequest request) {
+ if (e instanceof lcsb.mapviewer.services.SecurityException) {
+ return createErrorResponse("Access denied.", e.getMessage(), new HttpHeaders(), HttpStatus.FORBIDDEN);
+ } else if (e instanceof ObjectNotFoundException) {
+ return createErrorResponse("Object not found.", e.getMessage(), new HttpHeaders(), HttpStatus.NOT_FOUND);
+ } else if (e instanceof ObjectExistsException) {
+ return createErrorResponse("Object already exists.", e.getMessage(), new HttpHeaders(), HttpStatus.CONFLICT);
+ } else if (e instanceof QueryException) {
+ logger.error(e, e);
+ return createErrorResponse("Query server error.", e.getMessage(), new HttpHeaders(), HttpStatus.BAD_REQUEST);
+ } else if (e instanceof ServletRequestBindingException && e.getMessage().indexOf(Configuration.AUTH_TOKEN) >= 0) {
+ return createErrorResponse("Access denied.", e.getMessage(), new HttpHeaders(), HttpStatus.FORBIDDEN);
+ } else {
+ logger.error(e, e);
+ return createErrorResponse("Internal server error.", e.getMessage(), new HttpHeaders(),
+ HttpStatus.INTERNAL_SERVER_ERROR);
+ }
+ }
+
+ private ResponseEntity<Object> createErrorResponse(String errorMessage, String error, HttpHeaders httpHeaders,
+ HttpStatus status) {
+
+ return new ResponseEntity<Object>(
+ "{\"error\" : \"" + errorMessage + "\",\"reason\":" + new Gson().toJson(error) + "}", httpHeaders, status);
+ }
+
+ public Map<String, Object> parseBody(String body) throws IOException, JsonParseException, JsonMappingException {
+ if (body == null || body.isEmpty()) {
+ return new TreeMap<>();
+ }
+ ObjectNode result = mapper.readValue(body, ObjectNode.class);
+ return mapper.convertValue(result, Map.class);
+ }
+
+ protected Map<String, Object> getData(Map<String, Object> node, String objectName) {
+ return (Map<String, Object>) node.get(objectName);
+ }
+
+ protected Map<String, String> parsePostBody(String body) {
+ Map<String, String> result = new TreeMap<>();
+ String[] parameters = body.split("&");
+ for (String string : parameters) {
+ int position = string.indexOf("=");
+ if (position < 0) {
+ position = string.length();
+ }
+ String key = string.substring(0, position);
+ String value = null;
+ if (position < string.length()) {
+ value = string.substring(position + 1, string.length());
+ try {
+ value = URLDecoder.decode(value, "UTF-8");
+ } catch (UnsupportedEncodingException e) {
+ throw new InvalidStateException("Cannot decode input", e);
+ }
+ }
+ result.put(key, value);
+ }
+ return result;
+ }
+
+}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
index 6b2b55b27b..7cf58274ce 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
@@ -1,390 +1,390 @@
-package lcsb.mapviewer.api;
-
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Comparator;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerConfigurationException;
-import javax.xml.transform.TransformerException;
-import javax.xml.transform.TransformerFactory;
-import javax.xml.transform.TransformerFactoryConfigurationError;
-import javax.xml.transform.stream.StreamResult;
-import javax.xml.transform.stream.StreamSource;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.core.io.ClassPathResource;
-import org.springframework.core.io.Resource;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.annotation.data.Article;
-import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.annotation.services.MiriamConnector;
-import lcsb.mapviewer.annotation.services.PubmedParser;
-import lcsb.mapviewer.annotation.services.PubmedSearchException;
-import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
-import lcsb.mapviewer.common.comparator.StringComparator;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.IConverter;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter;
-import lcsb.mapviewer.converter.model.sbml.SbmlParser;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.interfaces.IConfigurationService;
-import lcsb.mapviewer.services.interfaces.IModelService;
-import lcsb.mapviewer.services.interfaces.IProjectService;
-import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.search.ElementMatcher;
-
-@Transactional(value = "txManager")
-public abstract class BaseRestImpl {
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(BaseRestImpl.class);
-
- @Autowired
- private IModelService modelService;
-
- @Autowired
- private IProjectService projectService;
-
- @Autowired
- private IUserService userService;
-
- @Autowired
- private IConfigurationService configurationService;
-
- @Autowired
- private MiriamConnector miriamConnector;
-
- @Autowired
- private PubmedParser pubmedParser;
-
- private ElementMatcher elementMatcher = new ElementMatcher();
-
- private Transformer mathMlTransformer;
-
- protected Map<String, Object> okStatus() {
- Map<String, Object> result = new TreeMap<>();
- return result;
- }
-
- protected Map<String, Object> createMinifiedSearchResult(BioEntity object) {
- Map<String, Object> result = new TreeMap<>();
- if (object instanceof Element) {
- result.put("type", ElementIdentifierType.ALIAS);
- Element element = (Element) object;
- result.put("id", element.getId());
- result.put("modelId", element.getModel().getId());
- } else if (object instanceof Reaction) {
- result.put("type", ElementIdentifierType.REACTION);
- Reaction element = (Reaction) object;
- result.put("id", element.getId());
- result.put("modelId", element.getModel().getId());
-
- } else {
- throw new InvalidStateException("Unknown type of result: " + object.getClass());
- }
- return result;
- };
-
- protected Map<String, Object> createAnnotation(MiriamData annotation) {
- if (annotation != null && annotation.getDataType() != null) {
- Map<String, Object> result = new TreeMap<>();
- if (annotation.getDataType().getUris().size() > 0) {
- try {
- result.put("link", miriamConnector.getUrlString(annotation));
- } catch (Exception e) {
- logger.error("Problem with miriam: " + annotation, e);
- }
- }
- if (MiriamType.PUBMED.equals(annotation.getDataType())) {
- try {
- Article article = pubmedParser.getPubmedArticleById(Integer.valueOf(annotation.getResource()));
- result.put("article", article);
- } catch (PubmedSearchException e) {
- logger.error("Problem with accessing info about pubmed", e);
- }
- }
- result.put("type", annotation.getDataType().name());
- result.put("resource", annotation.getResource());
- result.put("id", annotation.getId());
-
- if (annotation.getAnnotator() != null) {
- try {
- result.put("annotatorClassName", annotation.getAnnotator().getName());
- result.put("descriptionByType", ((ElementAnnotator) annotation.getAnnotator().getConstructor().newInstance())
- .getDescription(annotation.getDataType()));
- result.put("descriptionByTypeRelation",
- ((ElementAnnotator) annotation.getAnnotator().getConstructor().newInstance())
- .getDescription(annotation.getDataType(), annotation.getRelationType()));
-
- } catch (Exception e) {
- logger.error("Problem with retrieving description from annotator", e);
- result.put("annotatorClassName", "");
- result.put("descriptionByType", "");
- result.put("descriptionByTypeRelation", "");
- }
- } else {
- result.put("annotatorClassName", "");
- result.put("descriptionByType", "");
- result.put("descriptionByTypeRelation", "");
- }
-
- return result;
- } else {
- throw new InvalidArgumentException("invalid miriam data: " + annotation);
- }
- };
-
- protected Map<String, Object> createAnnotation(Article article) {
- Map<String, Object> result = new TreeMap<>();
- if (article != null) {
- MiriamType type = MiriamType.PUBMED;
- result.put("link", miriamConnector.getUrlString(new MiriamData(MiriamType.PUBMED, article.getId())));
- result.put("article", article);
- result.put("type", type);
- result.put("resource", article.getId());
- }
- return result;
- }
-
- protected List<Map<String, Object>> createAnnotations(Collection<?> references) {
- List<Map<String, Object>> result = new ArrayList<>();
- for (Object miriamData : references) {
- if (miriamData instanceof MiriamData) {
- result.add(createAnnotation((MiriamData) miriamData));
- } else if (miriamData instanceof Article) {
- result.add(createAnnotation((Article) miriamData));
- } else {
- throw new InvalidArgumentException();
- }
- }
- return result;
- }
-
- protected List<Model> getModels(String projectId, String modelId, String token)
- throws SecurityException, ObjectNotFoundException {
- Model model = modelService.getLastModelByProjectId(projectId, token);
- if (model == null) {
- throw new ObjectNotFoundException("Project with given id doesn't exist");
- }
- List<Model> models = new ArrayList<>();
-
- if (!modelId.equals("*")) {
- for (String str : modelId.split(",")) {
- models.add(model.getSubmodelById(Integer.valueOf(str)));
- }
- } else {
- models.addAll(model.getSubmodels());
- models.add(model);
- }
- models.sort(Model.ID_COMPARATOR);
- return models;
- }
-
- /**
- * @return the modelService
- * @see #modelService
- */
- public IModelService getModelService() {
- return modelService;
- }
-
- /**
- * @param modelService
- * the modelService to set
- * @see #modelService
- */
- public void setModelService(IModelService modelService) {
- this.modelService = modelService;
- }
-
- /**
- * @return the userService
- * @see #userService
- */
- public IUserService getUserService() {
- return userService;
- }
-
- /**
- * @param userService
- * the userService to set
- * @see #userService
- */
- public void setUserService(IUserService userService) {
- this.userService = userService;
- }
-
- protected List<Map<String, Object>> prepareTargets(Collection<Target> targets, List<Model> models) {
- List<Map<String, Object>> result = new ArrayList<>();
- for (Target target : targets) {
- result.add(prepareTarget(target, models));
- }
- result.sort(new Comparator<Map<String, Object>>() {
-
- @Override
- public int compare(Map<String, Object> o1, Map<String, Object> o2) {
- List<?> targetedObjects1 = (List<?>) o1.get("targetElements");
- List<?> targetedObjects2 = (List<?>) o2.get("targetElements");
- Integer size1 = 0;
- Integer size2 = 0;
- if (targetedObjects1 != null) {
- size1 = targetedObjects1.size();
- }
- if (targetedObjects2 != null) {
- size2 = targetedObjects2.size();
- }
- if (size1 == size2) {
- String name1 = (String) o1.get("name");
- String name2 = (String) o2.get("name");
- return new StringComparator().compare(name1, name2);
- }
- return -size1.compareTo(size2);
- }
- });
- return result;
- }
-
- protected Map<String, Object> prepareTarget(Target target, List<Model> models) {
- Map<String, Object> result = new TreeMap<>();
- result.put("name", target.getName());
- result.put("references", createAnnotations(target.getReferences()));
- result.put("targetParticipants", createAnnotations(target.getGenes()));
-
- List<Map<String, Object>> targetedObjects = new ArrayList<>();
- List<BioEntity> bioEntities = new ArrayList<>();
- for (Model model : models) {
- bioEntities.addAll(model.getBioEntities());
- }
- bioEntities.sort(BioEntity.ID_COMPARATOR);
- for (BioEntity bioEntity : bioEntities) {
- if (elementMatcher.elementMatch(target, bioEntity)) {
- Map<String, Object> elementMapping = new TreeMap<>();
- elementMapping.put("id", bioEntity.getId());
- elementMapping.put("type", getType(bioEntity));
- elementMapping.put("modelId", bioEntity.getModel().getId());
- targetedObjects.add(elementMapping);
- }
- }
-
- result.put("targetElements", targetedObjects);
-
- return result;
- }
-
- private String getType(BioEntity object) {
- if (object instanceof Reaction) {
- return ElementIdentifierType.REACTION.getJsName();
- } else if (object instanceof Element) {
- return ElementIdentifierType.ALIAS.getJsName();
- } else {
- throw new InvalidArgumentException("Unknown type of element " + object.getClass());
- }
- }
-
- /**
- * @return the projectService
- * @see #projectService
- */
- public IProjectService getProjectService() {
- return projectService;
- }
-
- /**
- * @param projectService
- * the projectService to set
- * @see #projectService
- */
- public void setProjectService(IProjectService projectService) {
- this.projectService = projectService;
- }
-
- protected IConverter getModelParser(String handlerClass) throws QueryException {
- for (IConverter converter : getModelConverters()) {
- if (converter.getClass().getCanonicalName().equals(handlerClass)) {
- return converter;
- }
- }
- throw new QueryException("Unknown handlerClass: " + handlerClass);
- }
-
- protected List<IConverter> getModelConverters() {
- List<IConverter> result = new ArrayList<>();
- result.add(new CellDesignerXmlParser());
- result.add(new SbgnmlXmlConverter());
- result.add(new SbmlParser());
- return result;
- }
-
- protected String getFirstValue(List<Object> list) {
- if (list == null) {
- return null;
- }
- if (list.size() > 0) {
- return (String) list.get(0);
- }
- return null;
- }
-
- protected String mathMLToPresentationML(String xmlContent)
- throws IOException, InvalidXmlSchemaException, TransformerException {
- Transformer transformer = getMathMLTransformer();
-
- ByteArrayOutputStream baos = new ByteArrayOutputStream();
- transformer.transform(new StreamSource(new ByteArrayInputStream(xmlContent.getBytes())), new StreamResult(baos));
- String result = baos.toString("UTF-8");
- if (result.startsWith("<?xml")) {
- result = result.substring(result.indexOf(">") + 1);
- }
- return result;
- }
-
- private Transformer getMathMLTransformer()
- throws TransformerFactoryConfigurationError, IOException, TransformerConfigurationException {
- if (this.mathMlTransformer == null) {
- TransformerFactory factory = TransformerFactory.newInstance();
-
- Resource resource = new ClassPathResource("mathmlc2p.xsl");
- InputStream styleInputStream = resource.getInputStream();
-
- StreamSource stylesource = new StreamSource(styleInputStream);
- this.mathMlTransformer = factory.newTransformer(stylesource);
- }
- return this.mathMlTransformer;
- }
-
- protected void verifyToken(String token) throws SecurityException {
- if (getUserService().getUserByToken(token) == null) {
- throw new SecurityException("Invalid token");
- }
- }
-
- public IConfigurationService getConfigurationService() {
- return configurationService;
- }
-
- public void setConfigurationService(IConfigurationService configurationService) {
- this.configurationService = configurationService;
- }
-
-}
+package lcsb.mapviewer.api;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Comparator;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerConfigurationException;
+import javax.xml.transform.TransformerException;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.TransformerFactoryConfigurationError;
+import javax.xml.transform.stream.StreamResult;
+import javax.xml.transform.stream.StreamSource;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.core.io.ClassPathResource;
+import org.springframework.core.io.Resource;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.annotation.data.Article;
+import lcsb.mapviewer.annotation.data.Target;
+import lcsb.mapviewer.annotation.services.MiriamConnector;
+import lcsb.mapviewer.annotation.services.PubmedParser;
+import lcsb.mapviewer.annotation.services.PubmedSearchException;
+import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
+import lcsb.mapviewer.common.comparator.StringComparator;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter;
+import lcsb.mapviewer.converter.model.sbml.SbmlParser;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.interfaces.IConfigurationService;
+import lcsb.mapviewer.services.interfaces.IModelService;
+import lcsb.mapviewer.services.interfaces.IProjectService;
+import lcsb.mapviewer.services.interfaces.IUserService;
+import lcsb.mapviewer.services.search.ElementMatcher;
+
+@Transactional(value = "txManager")
+public abstract class BaseRestImpl {
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(BaseRestImpl.class);
+
+ @Autowired
+ private IModelService modelService;
+
+ @Autowired
+ private IProjectService projectService;
+
+ @Autowired
+ private IUserService userService;
+
+ @Autowired
+ private IConfigurationService configurationService;
+
+ @Autowired
+ private MiriamConnector miriamConnector;
+
+ @Autowired
+ private PubmedParser pubmedParser;
+
+ private ElementMatcher elementMatcher = new ElementMatcher();
+
+ private Transformer mathMlTransformer;
+
+ protected Map<String, Object> okStatus() {
+ Map<String, Object> result = new TreeMap<>();
+ return result;
+ }
+
+ protected Map<String, Object> createMinifiedSearchResult(BioEntity object) {
+ Map<String, Object> result = new TreeMap<>();
+ if (object instanceof Element) {
+ result.put("type", ElementIdentifierType.ALIAS);
+ Element element = (Element) object;
+ result.put("id", element.getId());
+ result.put("modelId", element.getModel().getId());
+ } else if (object instanceof Reaction) {
+ result.put("type", ElementIdentifierType.REACTION);
+ Reaction element = (Reaction) object;
+ result.put("id", element.getId());
+ result.put("modelId", element.getModel().getId());
+
+ } else {
+ throw new InvalidStateException("Unknown type of result: " + object.getClass());
+ }
+ return result;
+ };
+
+ protected Map<String, Object> createAnnotation(MiriamData annotation) {
+ if (annotation != null && annotation.getDataType() != null) {
+ Map<String, Object> result = new TreeMap<>();
+ if (annotation.getDataType().getUris().size() > 0) {
+ try {
+ result.put("link", miriamConnector.getUrlString(annotation));
+ } catch (Exception e) {
+ logger.error("Problem with miriam: " + annotation, e);
+ }
+ }
+ if (MiriamType.PUBMED.equals(annotation.getDataType())) {
+ try {
+ Article article = pubmedParser.getPubmedArticleById(Integer.valueOf(annotation.getResource()));
+ result.put("article", article);
+ } catch (PubmedSearchException e) {
+ logger.error("Problem with accessing info about pubmed", e);
+ }
+ }
+ result.put("type", annotation.getDataType().name());
+ result.put("resource", annotation.getResource());
+ result.put("id", annotation.getId());
+
+ if (annotation.getAnnotator() != null) {
+ try {
+ result.put("annotatorClassName", annotation.getAnnotator().getName());
+ result.put("descriptionByType", ((ElementAnnotator) annotation.getAnnotator().getConstructor().newInstance())
+ .getDescription(annotation.getDataType()));
+ result.put("descriptionByTypeRelation",
+ ((ElementAnnotator) annotation.getAnnotator().getConstructor().newInstance())
+ .getDescription(annotation.getDataType(), annotation.getRelationType()));
+
+ } catch (Exception e) {
+ logger.error("Problem with retrieving description from annotator", e);
+ result.put("annotatorClassName", "");
+ result.put("descriptionByType", "");
+ result.put("descriptionByTypeRelation", "");
+ }
+ } else {
+ result.put("annotatorClassName", "");
+ result.put("descriptionByType", "");
+ result.put("descriptionByTypeRelation", "");
+ }
+
+ return result;
+ } else {
+ throw new InvalidArgumentException("invalid miriam data: " + annotation);
+ }
+ };
+
+ protected Map<String, Object> createAnnotation(Article article) {
+ Map<String, Object> result = new TreeMap<>();
+ if (article != null) {
+ MiriamType type = MiriamType.PUBMED;
+ result.put("link", miriamConnector.getUrlString(new MiriamData(MiriamType.PUBMED, article.getId())));
+ result.put("article", article);
+ result.put("type", type);
+ result.put("resource", article.getId());
+ }
+ return result;
+ }
+
+ protected List<Map<String, Object>> createAnnotations(Collection<?> references) {
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (Object miriamData : references) {
+ if (miriamData instanceof MiriamData) {
+ result.add(createAnnotation((MiriamData) miriamData));
+ } else if (miriamData instanceof Article) {
+ result.add(createAnnotation((Article) miriamData));
+ } else {
+ throw new InvalidArgumentException();
+ }
+ }
+ return result;
+ }
+
+ protected List<Model> getModels(String projectId, String modelId, String token)
+ throws SecurityException, ObjectNotFoundException {
+ Model model = modelService.getLastModelByProjectId(projectId, token);
+ if (model == null) {
+ throw new ObjectNotFoundException("Project with given id doesn't exist");
+ }
+ List<Model> models = new ArrayList<>();
+
+ if (!modelId.equals("*")) {
+ for (String str : modelId.split(",")) {
+ models.add(model.getSubmodelById(Integer.valueOf(str)));
+ }
+ } else {
+ models.addAll(model.getSubmodels());
+ models.add(model);
+ }
+ models.sort(Model.ID_COMPARATOR);
+ return models;
+ }
+
+ /**
+ * @return the modelService
+ * @see #modelService
+ */
+ public IModelService getModelService() {
+ return modelService;
+ }
+
+ /**
+ * @param modelService
+ * the modelService to set
+ * @see #modelService
+ */
+ public void setModelService(IModelService modelService) {
+ this.modelService = modelService;
+ }
+
+ /**
+ * @return the userService
+ * @see #userService
+ */
+ public IUserService getUserService() {
+ return userService;
+ }
+
+ /**
+ * @param userService
+ * the userService to set
+ * @see #userService
+ */
+ public void setUserService(IUserService userService) {
+ this.userService = userService;
+ }
+
+ protected List<Map<String, Object>> prepareTargets(Collection<Target> targets, List<Model> models) {
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (Target target : targets) {
+ result.add(prepareTarget(target, models));
+ }
+ result.sort(new Comparator<Map<String, Object>>() {
+
+ @Override
+ public int compare(Map<String, Object> o1, Map<String, Object> o2) {
+ List<?> targetedObjects1 = (List<?>) o1.get("targetElements");
+ List<?> targetedObjects2 = (List<?>) o2.get("targetElements");
+ Integer size1 = 0;
+ Integer size2 = 0;
+ if (targetedObjects1 != null) {
+ size1 = targetedObjects1.size();
+ }
+ if (targetedObjects2 != null) {
+ size2 = targetedObjects2.size();
+ }
+ if (size1 == size2) {
+ String name1 = (String) o1.get("name");
+ String name2 = (String) o2.get("name");
+ return new StringComparator().compare(name1, name2);
+ }
+ return -size1.compareTo(size2);
+ }
+ });
+ return result;
+ }
+
+ protected Map<String, Object> prepareTarget(Target target, List<Model> models) {
+ Map<String, Object> result = new TreeMap<>();
+ result.put("name", target.getName());
+ result.put("references", createAnnotations(target.getReferences()));
+ result.put("targetParticipants", createAnnotations(target.getGenes()));
+
+ List<Map<String, Object>> targetedObjects = new ArrayList<>();
+ List<BioEntity> bioEntities = new ArrayList<>();
+ for (Model model : models) {
+ bioEntities.addAll(model.getBioEntities());
+ }
+ bioEntities.sort(BioEntity.ID_COMPARATOR);
+ for (BioEntity bioEntity : bioEntities) {
+ if (elementMatcher.elementMatch(target, bioEntity)) {
+ Map<String, Object> elementMapping = new TreeMap<>();
+ elementMapping.put("id", bioEntity.getId());
+ elementMapping.put("type", getType(bioEntity));
+ elementMapping.put("modelId", bioEntity.getModel().getId());
+ targetedObjects.add(elementMapping);
+ }
+ }
+
+ result.put("targetElements", targetedObjects);
+
+ return result;
+ }
+
+ private String getType(BioEntity object) {
+ if (object instanceof Reaction) {
+ return ElementIdentifierType.REACTION.getJsName();
+ } else if (object instanceof Element) {
+ return ElementIdentifierType.ALIAS.getJsName();
+ } else {
+ throw new InvalidArgumentException("Unknown type of element " + object.getClass());
+ }
+ }
+
+ /**
+ * @return the projectService
+ * @see #projectService
+ */
+ public IProjectService getProjectService() {
+ return projectService;
+ }
+
+ /**
+ * @param projectService
+ * the projectService to set
+ * @see #projectService
+ */
+ public void setProjectService(IProjectService projectService) {
+ this.projectService = projectService;
+ }
+
+ protected IConverter getModelParser(String handlerClass) throws QueryException {
+ for (IConverter converter : getModelConverters()) {
+ if (converter.getClass().getCanonicalName().equals(handlerClass)) {
+ return converter;
+ }
+ }
+ throw new QueryException("Unknown handlerClass: " + handlerClass);
+ }
+
+ protected List<IConverter> getModelConverters() {
+ List<IConverter> result = new ArrayList<>();
+ result.add(new CellDesignerXmlParser());
+ result.add(new SbgnmlXmlConverter());
+ result.add(new SbmlParser());
+ return result;
+ }
+
+ protected String getFirstValue(List<Object> list) {
+ if (list == null) {
+ return null;
+ }
+ if (list.size() > 0) {
+ return (String) list.get(0);
+ }
+ return null;
+ }
+
+ protected String mathMLToPresentationML(String xmlContent)
+ throws IOException, InvalidXmlSchemaException, TransformerException {
+ Transformer transformer = getMathMLTransformer();
+
+ ByteArrayOutputStream baos = new ByteArrayOutputStream();
+ transformer.transform(new StreamSource(new ByteArrayInputStream(xmlContent.getBytes())), new StreamResult(baos));
+ String result = baos.toString("UTF-8");
+ if (result.startsWith("<?xml")) {
+ result = result.substring(result.indexOf(">") + 1);
+ }
+ return result;
+ }
+
+ private Transformer getMathMLTransformer()
+ throws TransformerFactoryConfigurationError, IOException, TransformerConfigurationException {
+ if (this.mathMlTransformer == null) {
+ TransformerFactory factory = TransformerFactory.newInstance();
+
+ Resource resource = new ClassPathResource("mathmlc2p.xsl");
+ InputStream styleInputStream = resource.getInputStream();
+
+ StreamSource stylesource = new StreamSource(styleInputStream);
+ this.mathMlTransformer = factory.newTransformer(stylesource);
+ }
+ return this.mathMlTransformer;
+ }
+
+ protected void verifyToken(String token) throws SecurityException {
+ if (getUserService().getUserByToken(token) == null) {
+ throw new SecurityException("Invalid token");
+ }
+ }
+
+ public IConfigurationService getConfigurationService() {
+ return configurationService;
+ }
+
+ public void setConfigurationService(IConfigurationService configurationService) {
+ this.configurationService = configurationService;
+ }
+
+}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/ObjectExistsException.java b/rest-api/src/main/java/lcsb/mapviewer/api/ObjectExistsException.java
index 8528592e84..f840f0a273 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/ObjectExistsException.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/ObjectExistsException.java
@@ -1,38 +1,38 @@
-package lcsb.mapviewer.api;
-
-/**
- * Thrown when object cannot be found via API.
- *
- * @author Piotr Gawron
- *
- */
-public class ObjectExistsException extends QueryException {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- *
- * @param message
- * error message
- */
- public ObjectExistsException(String message) {
- super(message);
- }
-
- /**
- * Constructor with error message and parent exception.
- *
- * @param message
- * error message
- * @param reason
- * parent exception that caused this one
- */
- public ObjectExistsException(String message, Exception reason) {
- super(message, reason);
- }
-
-}
+package lcsb.mapviewer.api;
+
+/**
+ * Thrown when object cannot be found via API.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ObjectExistsException extends QueryException {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * error message
+ */
+ public ObjectExistsException(String message) {
+ super(message);
+ }
+
+ /**
+ * Constructor with error message and parent exception.
+ *
+ * @param message
+ * error message
+ * @param reason
+ * parent exception that caused this one
+ */
+ public ObjectExistsException(String message, Exception reason) {
+ super(message, reason);
+ }
+
+}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/ObjectNotFoundException.java b/rest-api/src/main/java/lcsb/mapviewer/api/ObjectNotFoundException.java
index c5ccd931ed..5754c1c7d3 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/ObjectNotFoundException.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/ObjectNotFoundException.java
@@ -1,38 +1,38 @@
-package lcsb.mapviewer.api;
-
-/**
- * Thrown when object cannot be found via API.
- *
- * @author Piotr Gawron
- *
- */
-public class ObjectNotFoundException extends QueryException {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- *
- * @param message
- * error message
- */
- public ObjectNotFoundException(String message) {
- super(message);
- }
-
- /**
- * Constructor with error message and parent exception.
- *
- * @param message
- * error message
- * @param reason
- * parent exception that caused this one
- */
- public ObjectNotFoundException(String message, Exception reason) {
- super(message, reason);
- }
-
-}
+package lcsb.mapviewer.api;
+
+/**
+ * Thrown when object cannot be found via API.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ObjectNotFoundException extends QueryException {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * error message
+ */
+ public ObjectNotFoundException(String message) {
+ super(message);
+ }
+
+ /**
+ * Constructor with error message and parent exception.
+ *
+ * @param message
+ * error message
+ * @param reason
+ * parent exception that caused this one
+ */
+ public ObjectNotFoundException(String message, Exception reason) {
+ super(message, reason);
+ }
+
+}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/QueryException.java b/rest-api/src/main/java/lcsb/mapviewer/api/QueryException.java
index 5569e874e1..f3e367c483 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/QueryException.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/QueryException.java
@@ -1,38 +1,38 @@
-package lcsb.mapviewer.api;
-
-/**
- * Generic exception thrown when there is a problem with API query.
- *
- * @author Piotr Gawron
- *
- */
-public class QueryException extends Exception {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default constructor.
- *
- * @param message
- * error message
- */
- public QueryException(String message) {
- super(message);
- }
-
- /**
- * Constructor with error message and parent exception.
- *
- * @param message
- * error message
- * @param reason
- * parent exception that caused this one
- */
- public QueryException(String message, Exception reason) {
- super(message, reason);
- }
-
-}
+package lcsb.mapviewer.api;
+
+/**
+ * Generic exception thrown when there is a problem with API query.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class QueryException extends Exception {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * error message
+ */
+ public QueryException(String message) {
+ super(message);
+ }
+
+ /**
+ * Constructor with error message and parent exception.
+ *
+ * @param message
+ * error message
+ * @param reason
+ * parent exception that caused this one
+ */
+ public QueryException(String message, Exception reason) {
+ super(message, reason);
+ }
+
+}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationController.java b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationController.java
index a9458b0148..faf0b5f30b 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationController.java
@@ -1,119 +1,119 @@
-package lcsb.mapviewer.api.configuration;
-
-import java.io.IOException;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-
-import javax.servlet.ServletContext;
-
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.MediaType;
-import org.springframework.web.bind.annotation.CookieValue;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestBody;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RestController;
-
-import com.fasterxml.jackson.core.JsonParseException;
-import com.fasterxml.jackson.databind.JsonMappingException;
-
-import lcsb.mapviewer.api.BaseController;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.interfaces.IConfigurationService;
-
-@RestController
-public class ConfigurationController extends BaseController {
- @Autowired
- private ConfigurationRestImpl configurationController;
-
- @Autowired
- private IConfigurationService configurationService;
-
- /**
- * Context used to determine deployment path.
- */
- @Autowired
- private ServletContext context;
-
- @RequestMapping(value = "/configuration/", method = { RequestMethod.GET }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getConfiguration(@CookieValue(value = Configuration.AUTH_TOKEN) String token)
- throws SecurityException {
- Map<String, Object> result = new TreeMap<>();
- result.put("options", configurationController.getAllValues(token));
- result.put("imageFormats", configurationController.getImageFormats(token));
- result.put("modelFormats", configurationController.getModelFormats(token));
- result.put("overlayTypes", configurationController.getOverlayTypes(token));
- result.put("elementTypes", configurationController.getElementTypes(token));
- result.put("reactionTypes", configurationController.getReactionTypes(token));
- result.put("miriamTypes", configurationController.getMiriamTypes(token));
- result.put("mapTypes", configurationController.getMapTypes(token));
- result.put("mapCanvasTypes", configurationController.getMapCanvasTypes(token));
- result.put("unitTypes", configurationController.getUnitTypes(token));
- result.put("modificationStateTypes", configurationController.getModificationStateTypes(token));
- result.put("privilegeTypes", configurationController.getPrivilegeTypes(token));
- result.put("version", configurationService.getSystemSvnVersion(context.getRealPath("/")));
- result.put("buildDate", configurationService.getSystemBuild(context.getRealPath("/")));
- result.put("gitHash", configurationService.getSystemGitVersion(context.getRealPath("/")));
- result.put("annotators", configurationController.getAnnotators(token));
- result.put("plugins", configurationController.getPlugins(token, context.getRealPath("/")));
- return result;
- }
-
- @RequestMapping(value = "/configuration/options/", method = { RequestMethod.GET }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getOptions(@CookieValue(value = Configuration.AUTH_TOKEN) String token)
- throws SecurityException {
- return configurationController.getAllValues(token);
- }
-
- @RequestMapping(value = "/configuration/options/{option}", method = { RequestMethod.PATCH }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getOption( //
- @RequestBody String body, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "option") String option //
- ) throws SecurityException, JsonParseException, JsonMappingException, IOException {
- Map<String, Object> node = parseBody(body);
- Map<String, Object> data = getData(node, "option");
- return configurationController.updateOption(token, option, data);
- }
-
- /**
- * @return the configurationController
- * @see #configurationController
- */
- public ConfigurationRestImpl getConfigurationController() {
- return configurationController;
- }
-
- /**
- * @param configurationController
- * the configurationController to set
- * @see #configurationController
- */
- public void setConfigurationController(ConfigurationRestImpl configurationController) {
- this.configurationController = configurationController;
- }
-
- /**
- * @return the configurationService
- * @see #configurationService
- */
- public IConfigurationService getConfigurationService() {
- return configurationService;
- }
-
- /**
- * @param configurationService
- * the configurationService to set
- * @see #configurationService
- */
- public void setConfigurationService(IConfigurationService configurationService) {
- this.configurationService = configurationService;
- }
-
+package lcsb.mapviewer.api.configuration;
+
+import java.io.IOException;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+
+import javax.servlet.ServletContext;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.web.bind.annotation.CookieValue;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestBody;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RestController;
+
+import com.fasterxml.jackson.core.JsonParseException;
+import com.fasterxml.jackson.databind.JsonMappingException;
+
+import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.interfaces.IConfigurationService;
+
+@RestController
+public class ConfigurationController extends BaseController {
+ @Autowired
+ private ConfigurationRestImpl configurationController;
+
+ @Autowired
+ private IConfigurationService configurationService;
+
+ /**
+ * Context used to determine deployment path.
+ */
+ @Autowired
+ private ServletContext context;
+
+ @RequestMapping(value = "/configuration/", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> getConfiguration(@CookieValue(value = Configuration.AUTH_TOKEN) String token)
+ throws SecurityException {
+ Map<String, Object> result = new TreeMap<>();
+ result.put("options", configurationController.getAllValues(token));
+ result.put("imageFormats", configurationController.getImageFormats(token));
+ result.put("modelFormats", configurationController.getModelFormats(token));
+ result.put("overlayTypes", configurationController.getOverlayTypes(token));
+ result.put("elementTypes", configurationController.getElementTypes(token));
+ result.put("reactionTypes", configurationController.getReactionTypes(token));
+ result.put("miriamTypes", configurationController.getMiriamTypes(token));
+ result.put("mapTypes", configurationController.getMapTypes(token));
+ result.put("mapCanvasTypes", configurationController.getMapCanvasTypes(token));
+ result.put("unitTypes", configurationController.getUnitTypes(token));
+ result.put("modificationStateTypes", configurationController.getModificationStateTypes(token));
+ result.put("privilegeTypes", configurationController.getPrivilegeTypes(token));
+ result.put("version", configurationService.getSystemSvnVersion(context.getRealPath("/")));
+ result.put("buildDate", configurationService.getSystemBuild(context.getRealPath("/")));
+ result.put("gitHash", configurationService.getSystemGitVersion(context.getRealPath("/")));
+ result.put("annotators", configurationController.getAnnotators(token));
+ result.put("plugins", configurationController.getPlugins(token, context.getRealPath("/")));
+ return result;
+ }
+
+ @RequestMapping(value = "/configuration/options/", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getOptions(@CookieValue(value = Configuration.AUTH_TOKEN) String token)
+ throws SecurityException {
+ return configurationController.getAllValues(token);
+ }
+
+ @RequestMapping(value = "/configuration/options/{option}", method = { RequestMethod.PATCH }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> getOption( //
+ @RequestBody String body, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "option") String option //
+ ) throws SecurityException, JsonParseException, JsonMappingException, IOException {
+ Map<String, Object> node = parseBody(body);
+ Map<String, Object> data = getData(node, "option");
+ return configurationController.updateOption(token, option, data);
+ }
+
+ /**
+ * @return the configurationController
+ * @see #configurationController
+ */
+ public ConfigurationRestImpl getConfigurationController() {
+ return configurationController;
+ }
+
+ /**
+ * @param configurationController
+ * the configurationController to set
+ * @see #configurationController
+ */
+ public void setConfigurationController(ConfigurationRestImpl configurationController) {
+ this.configurationController = configurationController;
+ }
+
+ /**
+ * @return the configurationService
+ * @see #configurationService
+ */
+ public IConfigurationService getConfigurationService() {
+ return configurationService;
+ }
+
+ /**
+ * @param configurationService
+ * the configurationService to set
+ * @see #configurationService
+ */
+ public void setConfigurationService(IConfigurationService configurationService) {
+ this.configurationService = configurationService;
+ }
+
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
index 544664a32b..f39bc6d4b6 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
@@ -1,318 +1,318 @@
-package lcsb.mapviewer.api.configuration;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashSet;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-import java.util.Queue;
-import java.util.Set;
-import java.util.TreeMap;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.annotation.services.ModelAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
-import lcsb.mapviewer.api.BaseRestImpl;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.converter.IConverter;
-import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
-import lcsb.mapviewer.converter.graphics.ImageGenerators;
-import lcsb.mapviewer.model.graphics.MapCanvasType;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
-import lcsb.mapviewer.model.map.model.SubmodelType;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.field.ModificationState;
-import lcsb.mapviewer.model.user.ConfigurationElementType;
-import lcsb.mapviewer.model.user.ConfigurationOption;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.modelutils.map.ClassTreeNode;
-import lcsb.mapviewer.modelutils.map.ElementUtils;
-import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.interfaces.IConfigurationService;
-import lcsb.mapviewer.services.utils.data.ColorSchemaType;
-
-@Transactional(value = "txManager")
-public class ConfigurationRestImpl extends BaseRestImpl {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(ConfigurationRestImpl.class);
-
- @Autowired
- private IConfigurationService configurationService;
-
- @Autowired
- private ModelAnnotator modelAnnotator;
-
- public List<Map<String, Object>> getAllValues(String token) throws SecurityException {
- List<Map<String, Object>> result = new ArrayList<>();
- for (ConfigurationOption option : configurationService
- .getAllValues(getUserService().userHasPrivilege(token, PrivilegeType.CONFIGURATION_MANAGE))) {
- result.add(optionToMap(option));
- }
- return result;
- }
-
- private Map<String, Object> optionToMap(ConfigurationOption option) {
- Map<String, Object> result = new TreeMap<>();
- result.put("idObject", option.getId());
- result.put("type", option.getType());
- result.put("valueType", option.getType().getEditType());
- result.put("commonName", option.getType().getCommonName());
- result.put("value", option.getValue());
- if (option.getType().getGroup() != null) {
- result.put("group", option.getType().getGroup().getCommonName());
- }
- return result;
- }
-
- /**
- * @return the configurationService
- * @see #configurationService
- */
- public IConfigurationService getConfigurationService() {
- return configurationService;
- }
-
- /**
- * @param configurationService
- * the configurationService to set
- * @see #configurationService
- */
- public void setConfigurationService(IConfigurationService configurationService) {
- this.configurationService = configurationService;
- }
-
- public List<Map<String, Object>> getImageFormats(String token) throws SecurityException {
- verifyToken(token);
-
- List<Map<String, Object>> result = new ArrayList<>();
- ImageGenerators imageGenerators = new ImageGenerators();
- List<Pair<String, Class<? extends AbstractImageGenerator>>> imageGeneratorList = imageGenerators
- .getAvailableImageGenerators();
-
- for (Pair<String, Class<? extends AbstractImageGenerator>> element : imageGeneratorList) {
- Map<String, Object> row = new TreeMap<>();
- row.put("name", element.getLeft());
- row.put("handler", element.getRight().getCanonicalName());
- row.put("extension", imageGenerators.getExtension(element.getRight()));
- result.add(row);
- }
- return result;
- }
-
- public List<Map<String, Object>> getModelFormats(String token) throws SecurityException {
- verifyToken(token);
- List<IConverter> converters = getModelConverters();
-
- List<Map<String, Object>> result = new ArrayList<>();
-
- for (IConverter converter : converters) {
- Map<String, Object> row = new TreeMap<>();
- row.put("name", converter.getCommonName());
- row.put("handler", converter.getClass().getCanonicalName());
- row.put("extension", converter.getFileExtension());
- result.add(row);
- }
- return result;
- }
-
- public List<Map<String, Object>> getOverlayTypes(String token) throws SecurityException {
- verifyToken(token);
- List<Map<String, Object>> result = new ArrayList<>();
- for (ColorSchemaType type : ColorSchemaType.values()) {
- Map<String, Object> map = new TreeMap<>();
- map.put("name", type.name());
- result.add(map);
- }
- return result;
- }
-
- public Set<Map<String, String>> getElementTypes(String token) throws SecurityException {
- verifyToken(token);
-
- return getClassStringTypesList(Element.class);
- }
-
- private Set<Map<String, String>> getClassStringTypesList(Class<?> elementClass) {
- Set<Map<String, String>> result = new HashSet<>();
- ElementUtils elementUtils = new ElementUtils();
- ClassTreeNode top = elementUtils.getAnnotatedElementClassTree();
- Queue<ClassTreeNode> queue = new LinkedList<>();
- queue.add(top);
- while (!queue.isEmpty()) {
- ClassTreeNode clazz = queue.poll();
- for (ClassTreeNode child : clazz.getChildren()) {
- queue.add(child);
- }
- if (elementClass.isAssignableFrom(clazz.getClazz())) {
- Map<String, String> row = new TreeMap<>();
- row.put("className", clazz.getClazz().getName());
- row.put("name", clazz.getCommonName());
- if (clazz.getParent() == null) {
- row.put("parentClass", null);
- } else {
- row.put("parentClass", clazz.getParent().getClazz().getName());
- }
- result.add(row);
- }
- }
- return result;
- }
-
- public Set<Map<String, String>> getReactionTypes(String token) throws SecurityException {
- verifyToken(token);
-
- return getClassStringTypesList(Reaction.class);
- }
-
- public Map<String, Object> getMiriamTypes(String id) {
- Map<String, Object> result = new TreeMap<>();
- for (MiriamType type : MiriamType.values()) {
- result.put(type.name(), createMiriamTypeResponse(type));
- }
- return result;
- }
-
- private Map<String, Object> createMiriamTypeResponse(MiriamType type) {
- Map<String, Object> result = new TreeMap<>();
- result.put("commonName", type.getCommonName());
- result.put("homepage", type.getDbHomepage());
- result.put("registryIdentifier", type.getRegistryIdentifier());
- result.put("uris", type.getUris());
-
- return result;
- }
-
- public Object getModificationStateTypes(String token) {
- Map<String, Object> result = new TreeMap<>();
- for (ModificationState type : ModificationState.values()) {
- result.put(type.name(), createModificationStateResponse(type));
- }
- return result;
- }
-
- private Map<String, Object> createModificationStateResponse(ModificationState type) {
- Map<String, Object> result = new TreeMap<>();
- result.put("commonName", type.getFullName());
- result.put("abbreviation", type.getAbbreviation());
- return result;
- }
-
- public Map<String, Object> getPrivilegeTypes(String id) {
- Map<String, Object> result = new TreeMap<>();
- for (PrivilegeType type : PrivilegeType.values()) {
- result.put(type.name(), createPrivilegeTypeResponse(type));
- }
- return result;
- }
-
- private Map<String, Object> createPrivilegeTypeResponse(PrivilegeType type) {
- Map<String, Object> result = new TreeMap<>();
- result.put("commonName", type.getCommonName());
- if (type.getPrivilegeObjectType() != null) {
- result.put("objectType", type.getPrivilegeObjectType().getSimpleName());
- } else {
- result.put("objectType", null);
- }
- if (type.isNumeric()) {
- result.put("valueType", "int");
- } else {
- result.put("valueType", "boolean");
- }
- return result;
- }
-
- public List<Map<String, Object>> getAnnotators(String token) {
- List<Map<String, Object>> result = new ArrayList<>();
- for (ElementAnnotator annotator : modelAnnotator.getAvailableAnnotators()) {
- result.add(prepareAnnotator(annotator));
- }
- return result;
- }
-
- private Map<String, Object> prepareAnnotator(ElementAnnotator annotator) {
- Map<String, Object> result = new TreeMap<>();
- result.put("className", annotator.getClass().getName());
- result.put("name", annotator.getCommonName());
- result.put("description", annotator.getDescription());
- result.put("url", annotator.getUrl());
- result.put("elementClassNames", annotator.getValidClasses());
- result.put("parametersDefinitions", annotator.getParametersDefinitions());
- return result;
- }
-
- public List<Map<String, Object>> getMapTypes(String token) {
- List<Map<String, Object>> result = new ArrayList<>();
- for (SubmodelType type : SubmodelType.values()) {
- Map<String, Object> row = new TreeMap<>();
- row.put("id", type.name());
- row.put("name", type.getCommonName());
- result.add(row);
- }
- return result;
- }
-
- public List<Map<String, Object>> getMapCanvasTypes(String token) {
- List<Map<String, Object>> result = new ArrayList<>();
- for (MapCanvasType type : MapCanvasType.values()) {
- Map<String, Object> row = new TreeMap<>();
- row.put("id", type.name());
- row.put("name", type.getCommonName());
- result.add(row);
- }
- return result;
- }
-
- public Map<String, Object> updateOption(String token, String option, Map<String, Object> data)
- throws SecurityException {
- if (!getUserService().userHasPrivilege(token, PrivilegeType.CONFIGURATION_MANAGE)) {
- throw new SecurityException("Acces denied");
- }
- ConfigurationElementType type = ConfigurationElementType.valueOf(option);
- String value = (String) data.get("value");
- configurationService.setConfigurationValue(type, value);
- return optionToMap(configurationService.getValue(type));
- }
-
- public List<Map<String, Object>> getPlugins(String token, String rootPath) {
- String path = rootPath + "/resources/js/plugins/";
- File folder = new File(path);
- List<Map<String, Object>> result = new ArrayList<>();
- if (folder.exists()) {
- File[] listOfFiles = folder.listFiles();
- Arrays.sort(listOfFiles);
-
- for (int i = 0; i < listOfFiles.length; i++) {
- if (listOfFiles[i].isFile()) {
- Map<String, Object> row = new TreeMap<>();
- row.put("url", "resources/js/plugins/" + listOfFiles[i].getName());
- row.put("load-on-start", false);
- result.add(row);
- }
- }
-
- }
- return result;
- }
-
- public List<Map<String, Object>> getUnitTypes(String token) {
- List<Map<String, Object>> result = new ArrayList<>();
- for (SbmlUnitType type : SbmlUnitType.values()) {
- Map<String, Object> row = new TreeMap<>();
- row.put("id", type.name());
- row.put("name", type.getCommonName());
- result.add(row);
- }
- return result;
- }
-
-}
+package lcsb.mapviewer.api.configuration;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+import java.util.Queue;
+import java.util.Set;
+import java.util.TreeMap;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.annotation.services.ModelAnnotator;
+import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
+import lcsb.mapviewer.api.BaseRestImpl;
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
+import lcsb.mapviewer.converter.graphics.ImageGenerators;
+import lcsb.mapviewer.model.graphics.MapCanvasType;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
+import lcsb.mapviewer.model.map.model.SubmodelType;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+import lcsb.mapviewer.model.user.ConfigurationElementType;
+import lcsb.mapviewer.model.user.ConfigurationOption;
+import lcsb.mapviewer.model.user.PrivilegeType;
+import lcsb.mapviewer.modelutils.map.ClassTreeNode;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
+import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.interfaces.IConfigurationService;
+import lcsb.mapviewer.services.utils.data.ColorSchemaType;
+
+@Transactional(value = "txManager")
+public class ConfigurationRestImpl extends BaseRestImpl {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(ConfigurationRestImpl.class);
+
+ @Autowired
+ private IConfigurationService configurationService;
+
+ @Autowired
+ private ModelAnnotator modelAnnotator;
+
+ public List<Map<String, Object>> getAllValues(String token) throws SecurityException {
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (ConfigurationOption option : configurationService
+ .getAllValues(getUserService().userHasPrivilege(token, PrivilegeType.CONFIGURATION_MANAGE))) {
+ result.add(optionToMap(option));
+ }
+ return result;
+ }
+
+ private Map<String, Object> optionToMap(ConfigurationOption option) {
+ Map<String, Object> result = new TreeMap<>();
+ result.put("idObject", option.getId());
+ result.put("type", option.getType());
+ result.put("valueType", option.getType().getEditType());
+ result.put("commonName", option.getType().getCommonName());
+ result.put("value", option.getValue());
+ if (option.getType().getGroup() != null) {
+ result.put("group", option.getType().getGroup().getCommonName());
+ }
+ return result;
+ }
+
+ /**
+ * @return the configurationService
+ * @see #configurationService
+ */
+ public IConfigurationService getConfigurationService() {
+ return configurationService;
+ }
+
+ /**
+ * @param configurationService
+ * the configurationService to set
+ * @see #configurationService
+ */
+ public void setConfigurationService(IConfigurationService configurationService) {
+ this.configurationService = configurationService;
+ }
+
+ public List<Map<String, Object>> getImageFormats(String token) throws SecurityException {
+ verifyToken(token);
+
+ List<Map<String, Object>> result = new ArrayList<>();
+ ImageGenerators imageGenerators = new ImageGenerators();
+ List<Pair<String, Class<? extends AbstractImageGenerator>>> imageGeneratorList = imageGenerators
+ .getAvailableImageGenerators();
+
+ for (Pair<String, Class<? extends AbstractImageGenerator>> element : imageGeneratorList) {
+ Map<String, Object> row = new TreeMap<>();
+ row.put("name", element.getLeft());
+ row.put("handler", element.getRight().getCanonicalName());
+ row.put("extension", imageGenerators.getExtension(element.getRight()));
+ result.add(row);
+ }
+ return result;
+ }
+
+ public List<Map<String, Object>> getModelFormats(String token) throws SecurityException {
+ verifyToken(token);
+ List<IConverter> converters = getModelConverters();
+
+ List<Map<String, Object>> result = new ArrayList<>();
+
+ for (IConverter converter : converters) {
+ Map<String, Object> row = new TreeMap<>();
+ row.put("name", converter.getCommonName());
+ row.put("handler", converter.getClass().getCanonicalName());
+ row.put("extension", converter.getFileExtension());
+ result.add(row);
+ }
+ return result;
+ }
+
+ public List<Map<String, Object>> getOverlayTypes(String token) throws SecurityException {
+ verifyToken(token);
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (ColorSchemaType type : ColorSchemaType.values()) {
+ Map<String, Object> map = new TreeMap<>();
+ map.put("name", type.name());
+ result.add(map);
+ }
+ return result;
+ }
+
+ public Set<Map<String, String>> getElementTypes(String token) throws SecurityException {
+ verifyToken(token);
+
+ return getClassStringTypesList(Element.class);
+ }
+
+ private Set<Map<String, String>> getClassStringTypesList(Class<?> elementClass) {
+ Set<Map<String, String>> result = new HashSet<>();
+ ElementUtils elementUtils = new ElementUtils();
+ ClassTreeNode top = elementUtils.getAnnotatedElementClassTree();
+ Queue<ClassTreeNode> queue = new LinkedList<>();
+ queue.add(top);
+ while (!queue.isEmpty()) {
+ ClassTreeNode clazz = queue.poll();
+ for (ClassTreeNode child : clazz.getChildren()) {
+ queue.add(child);
+ }
+ if (elementClass.isAssignableFrom(clazz.getClazz())) {
+ Map<String, String> row = new TreeMap<>();
+ row.put("className", clazz.getClazz().getName());
+ row.put("name", clazz.getCommonName());
+ if (clazz.getParent() == null) {
+ row.put("parentClass", null);
+ } else {
+ row.put("parentClass", clazz.getParent().getClazz().getName());
+ }
+ result.add(row);
+ }
+ }
+ return result;
+ }
+
+ public Set<Map<String, String>> getReactionTypes(String token) throws SecurityException {
+ verifyToken(token);
+
+ return getClassStringTypesList(Reaction.class);
+ }
+
+ public Map<String, Object> getMiriamTypes(String id) {
+ Map<String, Object> result = new TreeMap<>();
+ for (MiriamType type : MiriamType.values()) {
+ result.put(type.name(), createMiriamTypeResponse(type));
+ }
+ return result;
+ }
+
+ private Map<String, Object> createMiriamTypeResponse(MiriamType type) {
+ Map<String, Object> result = new TreeMap<>();
+ result.put("commonName", type.getCommonName());
+ result.put("homepage", type.getDbHomepage());
+ result.put("registryIdentifier", type.getRegistryIdentifier());
+ result.put("uris", type.getUris());
+
+ return result;
+ }
+
+ public Object getModificationStateTypes(String token) {
+ Map<String, Object> result = new TreeMap<>();
+ for (ModificationState type : ModificationState.values()) {
+ result.put(type.name(), createModificationStateResponse(type));
+ }
+ return result;
+ }
+
+ private Map<String, Object> createModificationStateResponse(ModificationState type) {
+ Map<String, Object> result = new TreeMap<>();
+ result.put("commonName", type.getFullName());
+ result.put("abbreviation", type.getAbbreviation());
+ return result;
+ }
+
+ public Map<String, Object> getPrivilegeTypes(String id) {
+ Map<String, Object> result = new TreeMap<>();
+ for (PrivilegeType type : PrivilegeType.values()) {
+ result.put(type.name(), createPrivilegeTypeResponse(type));
+ }
+ return result;
+ }
+
+ private Map<String, Object> createPrivilegeTypeResponse(PrivilegeType type) {
+ Map<String, Object> result = new TreeMap<>();
+ result.put("commonName", type.getCommonName());
+ if (type.getPrivilegeObjectType() != null) {
+ result.put("objectType", type.getPrivilegeObjectType().getSimpleName());
+ } else {
+ result.put("objectType", null);
+ }
+ if (type.isNumeric()) {
+ result.put("valueType", "int");
+ } else {
+ result.put("valueType", "boolean");
+ }
+ return result;
+ }
+
+ public List<Map<String, Object>> getAnnotators(String token) {
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (ElementAnnotator annotator : modelAnnotator.getAvailableAnnotators()) {
+ result.add(prepareAnnotator(annotator));
+ }
+ return result;
+ }
+
+ private Map<String, Object> prepareAnnotator(ElementAnnotator annotator) {
+ Map<String, Object> result = new TreeMap<>();
+ result.put("className", annotator.getClass().getName());
+ result.put("name", annotator.getCommonName());
+ result.put("description", annotator.getDescription());
+ result.put("url", annotator.getUrl());
+ result.put("elementClassNames", annotator.getValidClasses());
+ result.put("parametersDefinitions", annotator.getParametersDefinitions());
+ return result;
+ }
+
+ public List<Map<String, Object>> getMapTypes(String token) {
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (SubmodelType type : SubmodelType.values()) {
+ Map<String, Object> row = new TreeMap<>();
+ row.put("id", type.name());
+ row.put("name", type.getCommonName());
+ result.add(row);
+ }
+ return result;
+ }
+
+ public List<Map<String, Object>> getMapCanvasTypes(String token) {
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (MapCanvasType type : MapCanvasType.values()) {
+ Map<String, Object> row = new TreeMap<>();
+ row.put("id", type.name());
+ row.put("name", type.getCommonName());
+ result.add(row);
+ }
+ return result;
+ }
+
+ public Map<String, Object> updateOption(String token, String option, Map<String, Object> data)
+ throws SecurityException {
+ if (!getUserService().userHasPrivilege(token, PrivilegeType.CONFIGURATION_MANAGE)) {
+ throw new SecurityException("Acces denied");
+ }
+ ConfigurationElementType type = ConfigurationElementType.valueOf(option);
+ String value = (String) data.get("value");
+ configurationService.setConfigurationValue(type, value);
+ return optionToMap(configurationService.getValue(type));
+ }
+
+ public List<Map<String, Object>> getPlugins(String token, String rootPath) {
+ String path = rootPath + "/resources/js/plugins/";
+ File folder = new File(path);
+ List<Map<String, Object>> result = new ArrayList<>();
+ if (folder.exists()) {
+ File[] listOfFiles = folder.listFiles();
+ Arrays.sort(listOfFiles);
+
+ for (int i = 0; i < listOfFiles.length; i++) {
+ if (listOfFiles[i].isFile()) {
+ Map<String, Object> row = new TreeMap<>();
+ row.put("url", "resources/js/plugins/" + listOfFiles[i].getName());
+ row.put("load-on-start", false);
+ result.add(row);
+ }
+ }
+
+ }
+ return result;
+ }
+
+ public List<Map<String, Object>> getUnitTypes(String token) {
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (SbmlUnitType type : SbmlUnitType.values()) {
+ Map<String, Object> row = new TreeMap<>();
+ row.put("id", type.name());
+ row.put("name", type.getCommonName());
+ result.add(row);
+ }
+ return result;
+ }
+
+}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/files/FileController.java b/rest-api/src/main/java/lcsb/mapviewer/api/files/FileController.java
index ed2a03cd09..820c35bbce 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/files/FileController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/files/FileController.java
@@ -1,59 +1,59 @@
-package lcsb.mapviewer.api.files;
-
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.MediaType;
-import org.springframework.web.bind.annotation.CookieValue;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestBody;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RequestParam;
-import org.springframework.web.bind.annotation.RestController;
-
-import lcsb.mapviewer.api.BaseController;
-import lcsb.mapviewer.api.ObjectNotFoundException;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.services.SecurityException;
-
-@RestController
-public class FileController extends BaseController {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(FileController.class);
-
- @Autowired
- private FileRestImpl fileRest;
-
- @RequestMapping(value = "/files/", method = { RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> createFile(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @RequestParam(value = "filename") String filename, //
- @RequestParam(value = "length") String length //
- ) throws SecurityException {
- return fileRest.createFile(token, filename, length);
- }
-
- @RequestMapping(value = "/files/{id}", method = { RequestMethod.GET }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getFile(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "id") String id //
- ) throws SecurityException, ObjectNotFoundException {
- return fileRest.getFile(token, id);
- }
-
- @RequestMapping(value = "/files/{id}:uploadContent", method = { RequestMethod.POST }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> uploadContent(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "id") String id, //
- @RequestBody byte[] data) throws SecurityException, ObjectNotFoundException {
- return fileRest.uploadContent(token, id, data);
- }
-
+package lcsb.mapviewer.api.files;
+
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.web.bind.annotation.CookieValue;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestBody;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.RestController;
+
+import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.api.ObjectNotFoundException;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.services.SecurityException;
+
+@RestController
+public class FileController extends BaseController {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(FileController.class);
+
+ @Autowired
+ private FileRestImpl fileRest;
+
+ @RequestMapping(value = "/files/", method = { RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> createFile(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @RequestParam(value = "filename") String filename, //
+ @RequestParam(value = "length") String length //
+ ) throws SecurityException {
+ return fileRest.createFile(token, filename, length);
+ }
+
+ @RequestMapping(value = "/files/{id}", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> getFile(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "id") String id //
+ ) throws SecurityException, ObjectNotFoundException {
+ return fileRest.getFile(token, id);
+ }
+
+ @RequestMapping(value = "/files/{id}:uploadContent", method = { RequestMethod.POST }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> uploadContent(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "id") String id, //
+ @RequestBody byte[] data) throws SecurityException, ObjectNotFoundException {
+ return fileRest.uploadContent(token, id, data);
+ }
+
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/files/FileRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/files/FileRestImpl.java
index d2ab017ef8..c273bdf938 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/files/FileRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/files/FileRestImpl.java
@@ -1,107 +1,107 @@
-package lcsb.mapviewer.api.files;
-
-import java.util.TreeMap;
-import java.util.Map;
-
-import org.apache.commons.lang3.ArrayUtils;
-import org.hibernate.QueryException;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.api.BaseRestImpl;
-import lcsb.mapviewer.api.ObjectNotFoundException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.model.cache.UploadedFileEntry;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.persist.dao.cache.UploadedFileEntryDao;
-import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.interfaces.ILayoutService;
-
-@Transactional(value = "txManager")
-public class FileRestImpl extends BaseRestImpl {
-
- @Autowired
- private ILayoutService overlayService;
-
- @Autowired
- private UploadedFileEntryDao uploadedFileEntryDao;
-
- public Map<String, Object> createFile(String token, String filename, String length) throws SecurityException {
- User user = getUserService().getUserByToken(token);
- if (!getUserService().userHasPrivilege(user, PrivilegeType.ADD_MAP)
- && overlayService.getAvailableCustomLayoutsNumber(user) == 0) {
- throw new SecurityException("Access denied");
- }
- UploadedFileEntry entry = new UploadedFileEntry();
- entry.setOriginalFileName(filename);
- entry.setFileContent(new byte[] {});
- entry.setLength(Long.valueOf(length));
- entry.setOwner(user);
- uploadedFileEntryDao.add(entry);
- try {
- return getFile(token, entry.getId() + "");
- } catch (ObjectNotFoundException e) {
- throw new InvalidStateException(e);
- }
- }
-
- public Map<String, Object> getFile(String token, String id) throws SecurityException, ObjectNotFoundException {
- User user = getUserService().getUserByToken(token);
- int fileId = Integer.valueOf(id);
- UploadedFileEntry fileEntry = uploadedFileEntryDao.getById(fileId);
- if (fileEntry == null) {
- throw new ObjectNotFoundException("Object not found");
- }
- if (fileEntry.getOwner() == null) {
- throw new SecurityException("Access denied");
- }
- if (!fileEntry.getOwner().getLogin().equals(user.getLogin())) {
- throw new SecurityException("Access denied");
- }
- return serializeEntry(fileEntry);
- }
-
- private Map<String, Object> serializeEntry(UploadedFileEntry fileEntry) {
- Map<String, Object> result = new TreeMap<>();
- result.put("id", fileEntry.getId());
- result.put("filename", fileEntry.getOriginalFileName());
- result.put("length", fileEntry.getLength());
- result.put("owner", fileEntry.getOwner().getLogin());
- result.put("uploadedDataLength", fileEntry.getFileContent().length);
- return result;
- }
-
- public Map<String, Object> uploadContent(String token, String id, byte[] data) throws SecurityException, ObjectNotFoundException {
- User user = getUserService().getUserByToken(token);
- int fileId = Integer.valueOf(id);
- UploadedFileEntry fileEntry = uploadedFileEntryDao.getById(fileId);
- if (fileEntry == null) {
- throw new ObjectNotFoundException("Object not found");
- }
- if (fileEntry.getOwner() == null) {
- throw new SecurityException("Access denied");
- }
- if (!fileEntry.getOwner().getLogin().equals(user.getLogin())) {
- throw new SecurityException("Access denied");
- }
- long missingByteLength = fileEntry.getLength() - fileEntry.getFileContent().length;
- if (data.length > missingByteLength) {
- throw new QueryException(
- "Too many bytes sent. There are " + missingByteLength + " missing bytes, but " + data.length + " sent.");
- }
- byte[] newConent = ArrayUtils.addAll(fileEntry.getFileContent(), data);
- fileEntry.setFileContent(newConent);
- uploadedFileEntryDao.update(fileEntry);
- return serializeEntry(fileEntry);
- }
-
- public UploadedFileEntryDao getUploadedFileEntryDao() {
- return uploadedFileEntryDao;
- }
-
- public void setUploadedFileEntryDao(UploadedFileEntryDao uploadedFileEntryDao) {
- this.uploadedFileEntryDao = uploadedFileEntryDao;
- }
-
-}
+package lcsb.mapviewer.api.files;
+
+import java.util.TreeMap;
+import java.util.Map;
+
+import org.apache.commons.lang3.ArrayUtils;
+import org.hibernate.QueryException;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.api.BaseRestImpl;
+import lcsb.mapviewer.api.ObjectNotFoundException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
+import lcsb.mapviewer.model.user.PrivilegeType;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.persist.dao.cache.UploadedFileEntryDao;
+import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.interfaces.ILayoutService;
+
+@Transactional(value = "txManager")
+public class FileRestImpl extends BaseRestImpl {
+
+ @Autowired
+ private ILayoutService overlayService;
+
+ @Autowired
+ private UploadedFileEntryDao uploadedFileEntryDao;
+
+ public Map<String, Object> createFile(String token, String filename, String length) throws SecurityException {
+ User user = getUserService().getUserByToken(token);
+ if (!getUserService().userHasPrivilege(user, PrivilegeType.ADD_MAP)
+ && overlayService.getAvailableCustomLayoutsNumber(user) == 0) {
+ throw new SecurityException("Access denied");
+ }
+ UploadedFileEntry entry = new UploadedFileEntry();
+ entry.setOriginalFileName(filename);
+ entry.setFileContent(new byte[] {});
+ entry.setLength(Long.valueOf(length));
+ entry.setOwner(user);
+ uploadedFileEntryDao.add(entry);
+ try {
+ return getFile(token, entry.getId() + "");
+ } catch (ObjectNotFoundException e) {
+ throw new InvalidStateException(e);
+ }
+ }
+
+ public Map<String, Object> getFile(String token, String id) throws SecurityException, ObjectNotFoundException {
+ User user = getUserService().getUserByToken(token);
+ int fileId = Integer.valueOf(id);
+ UploadedFileEntry fileEntry = uploadedFileEntryDao.getById(fileId);
+ if (fileEntry == null) {
+ throw new ObjectNotFoundException("Object not found");
+ }
+ if (fileEntry.getOwner() == null) {
+ throw new SecurityException("Access denied");
+ }
+ if (!fileEntry.getOwner().getLogin().equals(user.getLogin())) {
+ throw new SecurityException("Access denied");
+ }
+ return serializeEntry(fileEntry);
+ }
+
+ private Map<String, Object> serializeEntry(UploadedFileEntry fileEntry) {
+ Map<String, Object> result = new TreeMap<>();
+ result.put("id", fileEntry.getId());
+ result.put("filename", fileEntry.getOriginalFileName());
+ result.put("length", fileEntry.getLength());
+ result.put("owner", fileEntry.getOwner().getLogin());
+ result.put("uploadedDataLength", fileEntry.getFileContent().length);
+ return result;
+ }
+
+ public Map<String, Object> uploadContent(String token, String id, byte[] data) throws SecurityException, ObjectNotFoundException {
+ User user = getUserService().getUserByToken(token);
+ int fileId = Integer.valueOf(id);
+ UploadedFileEntry fileEntry = uploadedFileEntryDao.getById(fileId);
+ if (fileEntry == null) {
+ throw new ObjectNotFoundException("Object not found");
+ }
+ if (fileEntry.getOwner() == null) {
+ throw new SecurityException("Access denied");
+ }
+ if (!fileEntry.getOwner().getLogin().equals(user.getLogin())) {
+ throw new SecurityException("Access denied");
+ }
+ long missingByteLength = fileEntry.getLength() - fileEntry.getFileContent().length;
+ if (data.length > missingByteLength) {
+ throw new QueryException(
+ "Too many bytes sent. There are " + missingByteLength + " missing bytes, but " + data.length + " sent.");
+ }
+ byte[] newConent = ArrayUtils.addAll(fileEntry.getFileContent(), data);
+ fileEntry.setFileContent(newConent);
+ uploadedFileEntryDao.update(fileEntry);
+ return serializeEntry(fileEntry);
+ }
+
+ public UploadedFileEntryDao getUploadedFileEntryDao() {
+ return uploadedFileEntryDao;
+ }
+
+ public void setUploadedFileEntryDao(UploadedFileEntryDao uploadedFileEntryDao) {
+ this.uploadedFileEntryDao = uploadedFileEntryDao;
+ }
+
+}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeController.java b/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeController.java
index cbcb47bcad..5a8dab518f 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeController.java
@@ -1,124 +1,124 @@
-package lcsb.mapviewer.api.genomics;
-
-import java.io.IOException;
-import java.util.List;
-import java.util.Map;
-
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.MediaType;
-import org.springframework.util.MultiValueMap;
-import org.springframework.web.bind.annotation.CookieValue;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestBody;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RestController;
-
-import javassist.tools.rmi.ObjectNotFoundException;
-import lcsb.mapviewer.annotation.services.genome.ReferenceGenomeConnectorException;
-import lcsb.mapviewer.api.BaseController;
-import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.services.SecurityException;
-
-@RestController
-public class ReferenceGenomeController extends BaseController {
-
- @Autowired
- private ReferenceGenomeRestImpl referenceGenomeController;
-
- @RequestMapping(value = "/genomics/taxonomies/{organismId}/genomeTypes/{type}/versions/{version}/", method = {
- RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getGenomesByQuery(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "organismId") String organism, //
- @PathVariable(value = "type") String type, //
- @PathVariable(value = "version") String version//
- ) throws SecurityException, QueryException, ObjectNotFoundException {
- return referenceGenomeController.getReferenceGenome(token, organism, type, version);
- }
-
- @RequestMapping(value = "/genomics/taxonomies/{organismId}/genomeTypes/{type}/versions/{version}:getAvailableRemoteUrls", method = {
- RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getRemoteUrls(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "organismId") String organism, //
- @PathVariable(value = "type") String type, //
- @PathVariable(value = "version") String version//
- ) throws SecurityException, QueryException, ObjectNotFoundException {
- return referenceGenomeController.getRemoteUrls(token, organism, type, version);
- }
-
- @RequestMapping(value = "/genomics/taxonomies/", method = { RequestMethod.GET }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getGenomeTaxonomies(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
- ) throws SecurityException, QueryException, ObjectNotFoundException {
- return referenceGenomeController.getReferenceGenomeTaxonomies(token);
- }
-
- @RequestMapping(value = "/genomics/", method = { RequestMethod.POST }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> addGenome(//
- @RequestBody MultiValueMap<String, Object> formData, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
- ) throws SecurityException, QueryException, IOException, ReferenceGenomeConnectorException {
- return referenceGenomeController.addReferenceGenome(formData, token);
- }
-
- @RequestMapping(value = "/genomics/taxonomies/{organismId}/genomeTypes/", method = { RequestMethod.GET }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getGenomeTaxonomyTypes(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "organismId") String organism //
- ) throws SecurityException, QueryException, ObjectNotFoundException {
- return referenceGenomeController.getReferenceGenomeTypes(token, organism);
- }
-
- @RequestMapping(value = "/genomics/taxonomies/{organismId}/genomeTypes/{type}/versions/", method = {
- RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getGenomeVersion(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "organismId") String organism, //
- @PathVariable(value = "type") String type //
- ) throws SecurityException, QueryException, ObjectNotFoundException {
- return referenceGenomeController.getReferenceGenomeVersions(token, organism, type);
- }
-
- @RequestMapping(value = "/genomics/", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getDownloaded(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
- ) throws SecurityException, QueryException, ObjectNotFoundException {
- return referenceGenomeController.getReferenceGenomes(token);
- }
-
- @RequestMapping(value = "/genomics/{genomeId}/", method = { RequestMethod.DELETE }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> removeGenome(//
- @PathVariable(value = "genomeId") String genomeId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
- ) throws SecurityException, IOException {
- return referenceGenomeController.removeGenome(genomeId, token);
- }
-
- @RequestMapping(value = "/genomics/{genomeId}/geneMapping/{mappingId}/", method = { RequestMethod.DELETE }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> removeGeneMapping(//
- @PathVariable(value = "genomeId") String genomeId, //
- @PathVariable(value = "mappingId") String mappingId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
- ) throws SecurityException, IOException, lcsb.mapviewer.api.ObjectNotFoundException {
- return referenceGenomeController.removeGeneMapping(genomeId,mappingId, token);
- }
-
- @RequestMapping(value = "/genomics/{genomeId}/geneMapping/", method = { RequestMethod.POST }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> addGeneMapping(//
- @PathVariable(value = "genomeId") String genomeId, //
- @RequestBody MultiValueMap<String, Object> formData, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
- ) throws SecurityException, QueryException, IOException, ReferenceGenomeConnectorException {
- return referenceGenomeController.addGeneMapping(formData, genomeId, token);
- }
-
+package lcsb.mapviewer.api.genomics;
+
+import java.io.IOException;
+import java.util.List;
+import java.util.Map;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.util.MultiValueMap;
+import org.springframework.web.bind.annotation.CookieValue;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestBody;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RestController;
+
+import javassist.tools.rmi.ObjectNotFoundException;
+import lcsb.mapviewer.annotation.services.genome.ReferenceGenomeConnectorException;
+import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.services.SecurityException;
+
+@RestController
+public class ReferenceGenomeController extends BaseController {
+
+ @Autowired
+ private ReferenceGenomeRestImpl referenceGenomeController;
+
+ @RequestMapping(value = "/genomics/taxonomies/{organismId}/genomeTypes/{type}/versions/{version}/", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> getGenomesByQuery(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "organismId") String organism, //
+ @PathVariable(value = "type") String type, //
+ @PathVariable(value = "version") String version//
+ ) throws SecurityException, QueryException, ObjectNotFoundException {
+ return referenceGenomeController.getReferenceGenome(token, organism, type, version);
+ }
+
+ @RequestMapping(value = "/genomics/taxonomies/{organismId}/genomeTypes/{type}/versions/{version}:getAvailableRemoteUrls", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getRemoteUrls(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "organismId") String organism, //
+ @PathVariable(value = "type") String type, //
+ @PathVariable(value = "version") String version//
+ ) throws SecurityException, QueryException, ObjectNotFoundException {
+ return referenceGenomeController.getRemoteUrls(token, organism, type, version);
+ }
+
+ @RequestMapping(value = "/genomics/taxonomies/", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getGenomeTaxonomies(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, QueryException, ObjectNotFoundException {
+ return referenceGenomeController.getReferenceGenomeTaxonomies(token);
+ }
+
+ @RequestMapping(value = "/genomics/", method = { RequestMethod.POST }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> addGenome(//
+ @RequestBody MultiValueMap<String, Object> formData, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, QueryException, IOException, ReferenceGenomeConnectorException {
+ return referenceGenomeController.addReferenceGenome(formData, token);
+ }
+
+ @RequestMapping(value = "/genomics/taxonomies/{organismId}/genomeTypes/", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getGenomeTaxonomyTypes(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "organismId") String organism //
+ ) throws SecurityException, QueryException, ObjectNotFoundException {
+ return referenceGenomeController.getReferenceGenomeTypes(token, organism);
+ }
+
+ @RequestMapping(value = "/genomics/taxonomies/{organismId}/genomeTypes/{type}/versions/", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getGenomeVersion(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "organismId") String organism, //
+ @PathVariable(value = "type") String type //
+ ) throws SecurityException, QueryException, ObjectNotFoundException {
+ return referenceGenomeController.getReferenceGenomeVersions(token, organism, type);
+ }
+
+ @RequestMapping(value = "/genomics/", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getDownloaded(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, QueryException, ObjectNotFoundException {
+ return referenceGenomeController.getReferenceGenomes(token);
+ }
+
+ @RequestMapping(value = "/genomics/{genomeId}/", method = { RequestMethod.DELETE }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> removeGenome(//
+ @PathVariable(value = "genomeId") String genomeId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, IOException {
+ return referenceGenomeController.removeGenome(genomeId, token);
+ }
+
+ @RequestMapping(value = "/genomics/{genomeId}/geneMapping/{mappingId}/", method = { RequestMethod.DELETE }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> removeGeneMapping(//
+ @PathVariable(value = "genomeId") String genomeId, //
+ @PathVariable(value = "mappingId") String mappingId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, IOException, lcsb.mapviewer.api.ObjectNotFoundException {
+ return referenceGenomeController.removeGeneMapping(genomeId,mappingId, token);
+ }
+
+ @RequestMapping(value = "/genomics/{genomeId}/geneMapping/", method = { RequestMethod.POST }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> addGeneMapping(//
+ @PathVariable(value = "genomeId") String genomeId, //
+ @RequestBody MultiValueMap<String, Object> formData, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, QueryException, IOException, ReferenceGenomeConnectorException {
+ return referenceGenomeController.addGeneMapping(formData, genomeId, token);
+ }
+
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeRestImpl.java
index b47cf24709..8ad4e7b71b 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeRestImpl.java
@@ -1,285 +1,285 @@
-package lcsb.mapviewer.api.genomics;
-
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.net.URISyntaxException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeMap;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.annotation.Transactional;
-import org.springframework.util.MultiValueMap;
-
-import lcsb.mapviewer.annotation.cache.BigFileCache;
-import lcsb.mapviewer.annotation.services.genome.ReferenceGenomeConnectorException;
-import lcsb.mapviewer.api.BaseRestImpl;
-import lcsb.mapviewer.api.ObjectNotFoundException;
-import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.ReferenceGenome;
-import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
-import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.interfaces.IReferenceGenomeService;
-
-@Transactional(value = "txManager")
-public class ReferenceGenomeRestImpl extends BaseRestImpl {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(ReferenceGenomeRestImpl.class);
-
- /**
- * Service that manages reference genomes.
- */
- @Autowired
- private IReferenceGenomeService referenceGenomeService;
-
- @Autowired
- private BigFileCache bigFileCache;
-
- public Map<String, Object> getReferenceGenome(String token, String organismId, String type, String version)
- throws SecurityException, QueryException, ObjectNotFoundException {
- MiriamData organism = null;
- if (organismId != null && !organismId.isEmpty()) {
- organism = new MiriamData(MiriamType.TAXONOMY, organismId);
- } else {
- throw new QueryException("Unknown taxonomy organism: " + organismId);
- }
- try {
- ReferenceGenomeType genomeType = ReferenceGenomeType.valueOf(type);
- version = version.replaceAll("\\*", "");
- ReferenceGenome genome = referenceGenomeService.getReferenceGenomeViewByParams(organism, genomeType, version,
- token);
- if (genome == null) {
- throw new ObjectNotFoundException("Cannot find requested reference genome");
- }
- return genomeToMap(genome);
- } catch (IllegalArgumentException e) {
- throw new QueryException("Cannot find type: " + type);
- }
- }
-
- public List<Map<String, Object>> getRemoteUrls(String token, String organismId, String type, String version)
- throws SecurityException, QueryException, ObjectNotFoundException {
- MiriamData organism = null;
- if (organismId != null && !organismId.isEmpty()) {
- organism = new MiriamData(MiriamType.TAXONOMY, organismId);
- } else {
- throw new QueryException("Unknown taxonomy organism: " + organismId);
- }
- try {
- ReferenceGenomeType genomeType = ReferenceGenomeType.valueOf(type);
- String url = referenceGenomeService.getUrlForGenomeVersion(genomeType, organism, version);
-
- List<Map<String, Object>> result = new ArrayList<>();
- if (url != null) {
- Map<String, Object> row = new TreeMap<>();
- row.put("url", url);
- result.add(row);
- }
- return result;
- } catch (IllegalArgumentException e) {
- throw new QueryException("Cannot find type: " + type);
- }
- }
-
- private Map<String, Object> genomeToMap(ReferenceGenome genome) {
- Map<String, Object> result = new TreeMap<>();
- result.put("organism", super.createAnnotation(genome.getOrganism()));
- result.put("version", genome.getVersion());
- result.put("type", genome.getType());
- result.put("downloadProgress", genome.getDownloadProgress());
- result.put("sourceUrl", genome.getSourceUrl());
- result.put("localUrl", getLocalUrl(genome.getSourceUrl()));
- result.put("idObject", genome.getId());
- result.put("geneMapping", geneMappingToMaps(genome.getGeneMapping()));
-
- return result;
- }
-
- private String getLocalUrl(String sourceUrl) {
- String url = null;
- try {
- url = "../" + bigFileCache.getLocalPathForFile(sourceUrl);
- } catch (FileNotFoundException e) {
- logger.warn("Cannot find local file", e);
- }
- return url;
- }
-
- private List<Map<String, Object>> geneMappingToMaps(List<ReferenceGenomeGeneMapping> geneMapping) {
- List<Map<String, Object>> result = new ArrayList<>();
- for (ReferenceGenomeGeneMapping referenceGenomeGeneMapping : geneMapping) {
- result.add(geneMappingToMap(referenceGenomeGeneMapping));
- }
-
- return result;
- }
-
- private Map<String, Object> geneMappingToMap(ReferenceGenomeGeneMapping mapping) {
- Map<String, Object> result = new TreeMap<>();
- result.put("downloadProgress", mapping.getDownloadProgress());
- result.put("localUrl", getLocalUrl(mapping.getSourceUrl()));
- result.put("sourceUrl", mapping.getSourceUrl());
- result.put("name", mapping.getName());
- result.put("idObject", mapping.getId());
- return result;
- }
-
- public List<Map<String, Object>> getReferenceGenomeTaxonomies(String token) throws QueryException {
- try {
- Set<MiriamData> organisms = new HashSet<>();
- for (ReferenceGenomeType type : ReferenceGenomeType.values()) {
- organisms.addAll(referenceGenomeService.getOrganismsByReferenceGenomeType(type));
- }
- List<Map<String, Object>> result = new ArrayList<>();
- for (MiriamData miriamData : organisms) {
- result.add(createAnnotation(miriamData));
- }
- return result;
- } catch (ReferenceGenomeConnectorException e) {
- throw new QueryException("Problem with obtaining organism list", e);
- }
- }
-
- public List<Map<String, Object>> getReferenceGenomeTypes(String token, String organismId) throws QueryException {
- try {
- Set<MiriamData> organisms = new HashSet<>();
- for (ReferenceGenomeType type : ReferenceGenomeType.values()) {
- organisms.addAll(referenceGenomeService.getOrganismsByReferenceGenomeType(type));
- }
- List<Map<String, Object>> result = new ArrayList<>();
- for (MiriamData miriamData : organisms) {
- if (miriamData.getResource().equals(organismId)) {
- Map<String, Object> entry = new HashMap<>();
- entry.put("type", ReferenceGenomeType.UCSC.toString());
- result.add(entry);
- }
- }
- return result;
- } catch (ReferenceGenomeConnectorException e) {
- throw new QueryException("Problem with obtaining organism list", e);
- }
- }
-
- public List<Map<String, Object>> getReferenceGenomeVersions(String token, String organismId, String type)
- throws QueryException {
- ReferenceGenomeType genomeType = ReferenceGenomeType.valueOf(type);
- MiriamData organism = null;
- if (organismId != null && !organismId.isEmpty()) {
- organism = new MiriamData(MiriamType.TAXONOMY, organismId);
- } else {
- throw new QueryException("Unknown taxonomy organism: " + organismId);
- }
- List<String> versions;
- try {
- versions = referenceGenomeService.getAvailableGenomeVersions(genomeType, organism);
- } catch (ReferenceGenomeConnectorException e) {
- throw new QueryException("Problem with obtaining version list", e);
- }
-
- List<Map<String, Object>> result = new ArrayList<>();
- for (String string : versions) {
- Map<String, Object> entry = new HashMap<>();
- entry.put("version", string);
- result.add(entry);
- }
- return result;
- }
-
- public List<Map<String, Object>> getReferenceGenomes(String token)
- throws SecurityException, QueryException, ObjectNotFoundException {
- List<Map<String, Object>> result = new ArrayList<>();
- for (ReferenceGenome genome : referenceGenomeService.getDownloadedGenomes()) {
- result.add(genomeToMap(genome));
- }
- return result;
- }
-
- public Map<String, Object> removeGenome(String genomeId, String token) throws SecurityException, IOException {
- if (!getUserService().userHasPrivilege(token, PrivilegeType.MANAGE_GENOMES)) {
- throw new SecurityException("Access denied");
- }
- ReferenceGenome genome = referenceGenomeService.getReferenceGenomeById(Integer.parseInt(genomeId), token);
- referenceGenomeService.removeGenome(genome);
- return okStatus();
- }
-
- public Map<String, Object> addReferenceGenome(MultiValueMap<String, Object> formData, String token)
- throws SecurityException, QueryException, IOException, ReferenceGenomeConnectorException {
- if (!getUserService().userHasPrivilege(token, PrivilegeType.MANAGE_GENOMES)) {
- throw new SecurityException("Access denied");
- }
-
- String organismId = getFirstValue(formData.get("organismId"));
- String type = getFirstValue(formData.get("type"));
- String version = getFirstValue(formData.get("version"));
- String url = getFirstValue(formData.get("sourceUrl"));
- MiriamData organism = null;
- if (organismId != null && !organismId.isEmpty()) {
- organism = new MiriamData(MiriamType.TAXONOMY, organismId);
- } else {
- throw new QueryException("Unknown taxonomy organism: " + organismId);
- }
- ReferenceGenomeType genomeType = ReferenceGenomeType.valueOf(type);
- try {
- referenceGenomeService.addReferenceGenome(genomeType, organism, version, url);
- return okStatus();
- } catch (URISyntaxException e) {
- throw new QueryException("Problem wih given uri", e);
- }
- }
-
- public Map<String, Object> addGeneMapping(MultiValueMap<String, Object> formData, String genomeId, String token)
- throws SecurityException, QueryException, IOException, ReferenceGenomeConnectorException {
- if (!getUserService().userHasPrivilege(token, PrivilegeType.MANAGE_GENOMES)) {
- throw new SecurityException("Access denied");
- }
-
- int id = Integer.parseInt(genomeId);
- try {
- ReferenceGenome genome = referenceGenomeService.getReferenceGenomeById(id, token);
- String name = getFirstValue(formData.get("name"));
- String url = getFirstValue(formData.get("url"));
- referenceGenomeService.addReferenceGenomeGeneMapping(genome, name, url);
- return okStatus();
- } catch (URISyntaxException e) {
- throw new QueryException("Problem wih given uri", e);
- }
- }
-
- public Map<String, Object> removeGeneMapping(String genomeId, String mappingId, String token)
- throws SecurityException, IOException, ObjectNotFoundException {
- if (!getUserService().userHasPrivilege(token, PrivilegeType.MANAGE_GENOMES)) {
- throw new SecurityException("Access denied");
- }
- ReferenceGenome genome = referenceGenomeService.getReferenceGenomeById(Integer.parseInt(genomeId), token);
- if (genome == null) {
- throw new ObjectNotFoundException("Genome doesn't exist");
- }
- int id = Integer.parseInt(mappingId);
- ReferenceGenomeGeneMapping geneMapping = null;
- for (ReferenceGenomeGeneMapping mapping : genome.getGeneMapping()) {
- if (mapping.getId() == id) {
- geneMapping = mapping;
- }
- }
- if (geneMapping == null) {
- throw new ObjectNotFoundException("Gene mapping doesn't exist");
- }
- referenceGenomeService.removeReferenceGenomeGeneMapping(geneMapping);
- return okStatus();
- }
-
-}
+package lcsb.mapviewer.api.genomics;
+
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.net.URISyntaxException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeMap;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+import org.springframework.util.MultiValueMap;
+
+import lcsb.mapviewer.annotation.cache.BigFileCache;
+import lcsb.mapviewer.annotation.services.genome.ReferenceGenomeConnectorException;
+import lcsb.mapviewer.api.BaseRestImpl;
+import lcsb.mapviewer.api.ObjectNotFoundException;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.layout.ReferenceGenome;
+import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
+import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
+import lcsb.mapviewer.model.user.PrivilegeType;
+import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.interfaces.IReferenceGenomeService;
+
+@Transactional(value = "txManager")
+public class ReferenceGenomeRestImpl extends BaseRestImpl {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(ReferenceGenomeRestImpl.class);
+
+ /**
+ * Service that manages reference genomes.
+ */
+ @Autowired
+ private IReferenceGenomeService referenceGenomeService;
+
+ @Autowired
+ private BigFileCache bigFileCache;
+
+ public Map<String, Object> getReferenceGenome(String token, String organismId, String type, String version)
+ throws SecurityException, QueryException, ObjectNotFoundException {
+ MiriamData organism = null;
+ if (organismId != null && !organismId.isEmpty()) {
+ organism = new MiriamData(MiriamType.TAXONOMY, organismId);
+ } else {
+ throw new QueryException("Unknown taxonomy organism: " + organismId);
+ }
+ try {
+ ReferenceGenomeType genomeType = ReferenceGenomeType.valueOf(type);
+ version = version.replaceAll("\\*", "");
+ ReferenceGenome genome = referenceGenomeService.getReferenceGenomeViewByParams(organism, genomeType, version,
+ token);
+ if (genome == null) {
+ throw new ObjectNotFoundException("Cannot find requested reference genome");
+ }
+ return genomeToMap(genome);
+ } catch (IllegalArgumentException e) {
+ throw new QueryException("Cannot find type: " + type);
+ }
+ }
+
+ public List<Map<String, Object>> getRemoteUrls(String token, String organismId, String type, String version)
+ throws SecurityException, QueryException, ObjectNotFoundException {
+ MiriamData organism = null;
+ if (organismId != null && !organismId.isEmpty()) {
+ organism = new MiriamData(MiriamType.TAXONOMY, organismId);
+ } else {
+ throw new QueryException("Unknown taxonomy organism: " + organismId);
+ }
+ try {
+ ReferenceGenomeType genomeType = ReferenceGenomeType.valueOf(type);
+ String url = referenceGenomeService.getUrlForGenomeVersion(genomeType, organism, version);
+
+ List<Map<String, Object>> result = new ArrayList<>();
+ if (url != null) {
+ Map<String, Object> row = new TreeMap<>();
+ row.put("url", url);
+ result.add(row);
+ }
+ return result;
+ } catch (IllegalArgumentException e) {
+ throw new QueryException("Cannot find type: " + type);
+ }
+ }
+
+ private Map<String, Object> genomeToMap(ReferenceGenome genome) {
+ Map<String, Object> result = new TreeMap<>();
+ result.put("organism", super.createAnnotation(genome.getOrganism()));
+ result.put("version", genome.getVersion());
+ result.put("type", genome.getType());
+ result.put("downloadProgress", genome.getDownloadProgress());
+ result.put("sourceUrl", genome.getSourceUrl());
+ result.put("localUrl", getLocalUrl(genome.getSourceUrl()));
+ result.put("idObject", genome.getId());
+ result.put("geneMapping", geneMappingToMaps(genome.getGeneMapping()));
+
+ return result;
+ }
+
+ private String getLocalUrl(String sourceUrl) {
+ String url = null;
+ try {
+ url = "../" + bigFileCache.getLocalPathForFile(sourceUrl);
+ } catch (FileNotFoundException e) {
+ logger.warn("Cannot find local file", e);
+ }
+ return url;
+ }
+
+ private List<Map<String, Object>> geneMappingToMaps(List<ReferenceGenomeGeneMapping> geneMapping) {
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (ReferenceGenomeGeneMapping referenceGenomeGeneMapping : geneMapping) {
+ result.add(geneMappingToMap(referenceGenomeGeneMapping));
+ }
+
+ return result;
+ }
+
+ private Map<String, Object> geneMappingToMap(ReferenceGenomeGeneMapping mapping) {
+ Map<String, Object> result = new TreeMap<>();
+ result.put("downloadProgress", mapping.getDownloadProgress());
+ result.put("localUrl", getLocalUrl(mapping.getSourceUrl()));
+ result.put("sourceUrl", mapping.getSourceUrl());
+ result.put("name", mapping.getName());
+ result.put("idObject", mapping.getId());
+ return result;
+ }
+
+ public List<Map<String, Object>> getReferenceGenomeTaxonomies(String token) throws QueryException {
+ try {
+ Set<MiriamData> organisms = new HashSet<>();
+ for (ReferenceGenomeType type : ReferenceGenomeType.values()) {
+ organisms.addAll(referenceGenomeService.getOrganismsByReferenceGenomeType(type));
+ }
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (MiriamData miriamData : organisms) {
+ result.add(createAnnotation(miriamData));
+ }
+ return result;
+ } catch (ReferenceGenomeConnectorException e) {
+ throw new QueryException("Problem with obtaining organism list", e);
+ }
+ }
+
+ public List<Map<String, Object>> getReferenceGenomeTypes(String token, String organismId) throws QueryException {
+ try {
+ Set<MiriamData> organisms = new HashSet<>();
+ for (ReferenceGenomeType type : ReferenceGenomeType.values()) {
+ organisms.addAll(referenceGenomeService.getOrganismsByReferenceGenomeType(type));
+ }
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (MiriamData miriamData : organisms) {
+ if (miriamData.getResource().equals(organismId)) {
+ Map<String, Object> entry = new HashMap<>();
+ entry.put("type", ReferenceGenomeType.UCSC.toString());
+ result.add(entry);
+ }
+ }
+ return result;
+ } catch (ReferenceGenomeConnectorException e) {
+ throw new QueryException("Problem with obtaining organism list", e);
+ }
+ }
+
+ public List<Map<String, Object>> getReferenceGenomeVersions(String token, String organismId, String type)
+ throws QueryException {
+ ReferenceGenomeType genomeType = ReferenceGenomeType.valueOf(type);
+ MiriamData organism = null;
+ if (organismId != null && !organismId.isEmpty()) {
+ organism = new MiriamData(MiriamType.TAXONOMY, organismId);
+ } else {
+ throw new QueryException("Unknown taxonomy organism: " + organismId);
+ }
+ List<String> versions;
+ try {
+ versions = referenceGenomeService.getAvailableGenomeVersions(genomeType, organism);
+ } catch (ReferenceGenomeConnectorException e) {
+ throw new QueryException("Problem with obtaining version list", e);
+ }
+
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (String string : versions) {
+ Map<String, Object> entry = new HashMap<>();
+ entry.put("version", string);
+ result.add(entry);
+ }
+ return result;
+ }
+
+ public List<Map<String, Object>> getReferenceGenomes(String token)
+ throws SecurityException, QueryException, ObjectNotFoundException {
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (ReferenceGenome genome : referenceGenomeService.getDownloadedGenomes()) {
+ result.add(genomeToMap(genome));
+ }
+ return result;
+ }
+
+ public Map<String, Object> removeGenome(String genomeId, String token) throws SecurityException, IOException {
+ if (!getUserService().userHasPrivilege(token, PrivilegeType.MANAGE_GENOMES)) {
+ throw new SecurityException("Access denied");
+ }
+ ReferenceGenome genome = referenceGenomeService.getReferenceGenomeById(Integer.parseInt(genomeId), token);
+ referenceGenomeService.removeGenome(genome);
+ return okStatus();
+ }
+
+ public Map<String, Object> addReferenceGenome(MultiValueMap<String, Object> formData, String token)
+ throws SecurityException, QueryException, IOException, ReferenceGenomeConnectorException {
+ if (!getUserService().userHasPrivilege(token, PrivilegeType.MANAGE_GENOMES)) {
+ throw new SecurityException("Access denied");
+ }
+
+ String organismId = getFirstValue(formData.get("organismId"));
+ String type = getFirstValue(formData.get("type"));
+ String version = getFirstValue(formData.get("version"));
+ String url = getFirstValue(formData.get("sourceUrl"));
+ MiriamData organism = null;
+ if (organismId != null && !organismId.isEmpty()) {
+ organism = new MiriamData(MiriamType.TAXONOMY, organismId);
+ } else {
+ throw new QueryException("Unknown taxonomy organism: " + organismId);
+ }
+ ReferenceGenomeType genomeType = ReferenceGenomeType.valueOf(type);
+ try {
+ referenceGenomeService.addReferenceGenome(genomeType, organism, version, url);
+ return okStatus();
+ } catch (URISyntaxException e) {
+ throw new QueryException("Problem wih given uri", e);
+ }
+ }
+
+ public Map<String, Object> addGeneMapping(MultiValueMap<String, Object> formData, String genomeId, String token)
+ throws SecurityException, QueryException, IOException, ReferenceGenomeConnectorException {
+ if (!getUserService().userHasPrivilege(token, PrivilegeType.MANAGE_GENOMES)) {
+ throw new SecurityException("Access denied");
+ }
+
+ int id = Integer.parseInt(genomeId);
+ try {
+ ReferenceGenome genome = referenceGenomeService.getReferenceGenomeById(id, token);
+ String name = getFirstValue(formData.get("name"));
+ String url = getFirstValue(formData.get("url"));
+ referenceGenomeService.addReferenceGenomeGeneMapping(genome, name, url);
+ return okStatus();
+ } catch (URISyntaxException e) {
+ throw new QueryException("Problem wih given uri", e);
+ }
+ }
+
+ public Map<String, Object> removeGeneMapping(String genomeId, String mappingId, String token)
+ throws SecurityException, IOException, ObjectNotFoundException {
+ if (!getUserService().userHasPrivilege(token, PrivilegeType.MANAGE_GENOMES)) {
+ throw new SecurityException("Access denied");
+ }
+ ReferenceGenome genome = referenceGenomeService.getReferenceGenomeById(Integer.parseInt(genomeId), token);
+ if (genome == null) {
+ throw new ObjectNotFoundException("Genome doesn't exist");
+ }
+ int id = Integer.parseInt(mappingId);
+ ReferenceGenomeGeneMapping geneMapping = null;
+ for (ReferenceGenomeGeneMapping mapping : genome.getGeneMapping()) {
+ if (mapping.getId() == id) {
+ geneMapping = mapping;
+ }
+ }
+ if (geneMapping == null) {
+ throw new ObjectNotFoundException("Gene mapping doesn't exist");
+ }
+ referenceGenomeService.removeReferenceGenomeGeneMapping(geneMapping);
+ return okStatus();
+ }
+
+}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/mesh/MeshController.java b/rest-api/src/main/java/lcsb/mapviewer/api/mesh/MeshController.java
index 378fc0ac29..a5937dbfbd 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/mesh/MeshController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/mesh/MeshController.java
@@ -1,45 +1,45 @@
-package lcsb.mapviewer.api.mesh;
-
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.MediaType;
-import org.springframework.web.bind.annotation.CookieValue;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RestController;
-
-import lcsb.mapviewer.api.BaseController;
-import lcsb.mapviewer.common.Configuration;
-
-@RestController
-public class MeshController extends BaseController {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(MeshController.class);
-
- @Autowired
- private MeshRestImpl userRest;
-
- @RequestMapping(value = "/mesh/{id:.+}", method = { RequestMethod.GET }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getMesh(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "id") String id //
- ) throws Exception {
- return userRest.getMesh(token, id);
- }
-
- public MeshRestImpl getUserRest() {
- return userRest;
- }
-
- public void setUserRest(MeshRestImpl userRest) {
- this.userRest = userRest;
- }
-
+package lcsb.mapviewer.api.mesh;
+
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.web.bind.annotation.CookieValue;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RestController;
+
+import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.common.Configuration;
+
+@RestController
+public class MeshController extends BaseController {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(MeshController.class);
+
+ @Autowired
+ private MeshRestImpl userRest;
+
+ @RequestMapping(value = "/mesh/{id:.+}", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> getMesh(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "id") String id //
+ ) throws Exception {
+ return userRest.getMesh(token, id);
+ }
+
+ public MeshRestImpl getUserRest() {
+ return userRest;
+ }
+
+ public void setUserRest(MeshRestImpl userRest) {
+ this.userRest = userRest;
+ }
+
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/mesh/MeshRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/mesh/MeshRestImpl.java
index e3f8eb6da2..5092915294 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/mesh/MeshRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/mesh/MeshRestImpl.java
@@ -1,43 +1,43 @@
-package lcsb.mapviewer.api.mesh;
-
-import java.util.TreeMap;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.annotation.data.MeSH;
-import lcsb.mapviewer.annotation.services.MeSHParser;
-import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
-import lcsb.mapviewer.api.BaseRestImpl;
-import lcsb.mapviewer.api.ObjectNotFoundException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-
-@Transactional(value = "txManager")
-public class MeshRestImpl extends BaseRestImpl {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(MeshRestImpl.class);
-
- @Autowired
- private MeSHParser meSHParser;
-
- public Map<String, Object> getMesh(String token, String id) throws AnnotatorException, ObjectNotFoundException {
-
- MeSH mesh = meSHParser.getMeSH(new MiriamData(MiriamType.MESH_2012, id));
- if (mesh == null) {
- throw new ObjectNotFoundException("Object not found: " + id);
- }
- Map<String, Object> result = new TreeMap<>();
- result.put("name", mesh.getName());
- result.put("id", mesh.getMeSHId());
- result.put("description", mesh.getDescription());
- result.put("synonyms", mesh.getSynonyms());
- return result;
- }
-}
+package lcsb.mapviewer.api.mesh;
+
+import java.util.TreeMap;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.annotation.data.MeSH;
+import lcsb.mapviewer.annotation.services.MeSHParser;
+import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
+import lcsb.mapviewer.api.BaseRestImpl;
+import lcsb.mapviewer.api.ObjectNotFoundException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+
+@Transactional(value = "txManager")
+public class MeshRestImpl extends BaseRestImpl {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(MeshRestImpl.class);
+
+ @Autowired
+ private MeSHParser meSHParser;
+
+ public Map<String, Object> getMesh(String token, String id) throws AnnotatorException, ObjectNotFoundException {
+
+ MeSH mesh = meSHParser.getMeSH(new MiriamData(MiriamType.MESH_2012, id));
+ if (mesh == null) {
+ throw new ObjectNotFoundException("Object not found: " + id);
+ }
+ Map<String, Object> result = new TreeMap<>();
+ result.put("name", mesh.getName());
+ result.put("id", mesh.getMeSHId());
+ result.put("description", mesh.getDescription());
+ result.put("synonyms", mesh.getSynonyms());
+ return result;
+ }
+}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/package-info.java b/rest-api/src/main/java/lcsb/mapviewer/api/package-info.java
index acca7bd59d..473f769cbb 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/package-info.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/package-info.java
@@ -1,4 +1,4 @@
-/**
- * Package provides implementation of RESTfull API.
- */
-package lcsb.mapviewer.api;
+/**
+ * Package provides implementation of RESTfull API.
+ */
+package lcsb.mapviewer.api;
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/plugins/PluginController.java b/rest-api/src/main/java/lcsb/mapviewer/api/plugins/PluginController.java
index bb69ed94e3..c4fe120617 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/plugins/PluginController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/plugins/PluginController.java
@@ -1,101 +1,101 @@
-package lcsb.mapviewer.api.plugins;
-
-import java.util.List;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.MediaType;
-import org.springframework.web.bind.annotation.CookieValue;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RequestParam;
-import org.springframework.web.bind.annotation.RestController;
-
-import lcsb.mapviewer.api.BaseController;
-import lcsb.mapviewer.api.ObjectNotFoundException;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.services.SecurityException;
-
-@RestController
-public class PluginController extends BaseController {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(PluginController.class);
-
- @Autowired
- private PluginRestImpl pluginRest;
-
- @RequestMapping(value = "/plugins/", method = { RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> createPlugin(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @RequestParam(value = "hash") String hash, //
- @RequestParam(value = "name") String name, //
- @RequestParam(value = "version") String version, //
- @RequestParam(value = "url", defaultValue = "") String url //
- ) throws SecurityException {
- return pluginRest.createPlugin(token, hash, name, version, url);
- }
-
- @RequestMapping(value = "/plugins/", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getPlugins(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
- ) throws SecurityException {
- return pluginRest.getPlugins(token);
- }
-
- @RequestMapping(value = "/plugins/{hash}", method = { RequestMethod.GET }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getFile(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "hash") String hash //
- ) throws SecurityException, ObjectNotFoundException {
- return pluginRest.getPlugin(token, hash);
- }
-
- @RequestMapping(value = "/plugins/{hash}/data/users/{login}/{key}", method = { RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> createPluginDataEntry(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "hash") String hash, //
- @PathVariable(value = "login") String login, //
- @PathVariable(value = "key") String key, //
- @RequestParam(value = "value", defaultValue = "") String value //
- ) throws SecurityException, ObjectNotFoundException {
- return pluginRest.createPluginDataEntry(token, hash, login, key, value);
- }
-
- @RequestMapping(value = "/plugins/{hash}/data/users/{login}/{key}", method = { RequestMethod.GET }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getPluginDataEntry(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "hash") String hash, //
- @PathVariable(value = "login") String login, //
- @PathVariable(value = "key") String key //
- ) throws SecurityException, ObjectNotFoundException {
- return pluginRest.getPluginDataEntry(token, hash, login, key);
- }
-
- @RequestMapping(value = "/plugins/{hash}/data/global/{key}", method = { RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> createPluginDataEntry(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "hash") String hash, //
- @PathVariable(value = "key") String key, //
- @RequestParam(value = "value", defaultValue = "") String value //
- ) throws SecurityException, ObjectNotFoundException {
- return pluginRest.createPluginDataEntry(token, hash, null, key, value);
- }
-
- @RequestMapping(value = "/plugins/{hash}/data/global/{key}", method = { RequestMethod.GET }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getPluginDataEntry(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "hash") String hash, //
- @PathVariable(value = "key") String key //
- ) throws SecurityException, ObjectNotFoundException {
- return pluginRest.getPluginDataEntry(token, hash, null, key);
- }
-
+package lcsb.mapviewer.api.plugins;
+
+import java.util.List;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.web.bind.annotation.CookieValue;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.RestController;
+
+import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.api.ObjectNotFoundException;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.services.SecurityException;
+
+@RestController
+public class PluginController extends BaseController {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(PluginController.class);
+
+ @Autowired
+ private PluginRestImpl pluginRest;
+
+ @RequestMapping(value = "/plugins/", method = { RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> createPlugin(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @RequestParam(value = "hash") String hash, //
+ @RequestParam(value = "name") String name, //
+ @RequestParam(value = "version") String version, //
+ @RequestParam(value = "url", defaultValue = "") String url //
+ ) throws SecurityException {
+ return pluginRest.createPlugin(token, hash, name, version, url);
+ }
+
+ @RequestMapping(value = "/plugins/", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getPlugins(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException {
+ return pluginRest.getPlugins(token);
+ }
+
+ @RequestMapping(value = "/plugins/{hash}", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> getFile(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "hash") String hash //
+ ) throws SecurityException, ObjectNotFoundException {
+ return pluginRest.getPlugin(token, hash);
+ }
+
+ @RequestMapping(value = "/plugins/{hash}/data/users/{login}/{key}", method = { RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> createPluginDataEntry(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "hash") String hash, //
+ @PathVariable(value = "login") String login, //
+ @PathVariable(value = "key") String key, //
+ @RequestParam(value = "value", defaultValue = "") String value //
+ ) throws SecurityException, ObjectNotFoundException {
+ return pluginRest.createPluginDataEntry(token, hash, login, key, value);
+ }
+
+ @RequestMapping(value = "/plugins/{hash}/data/users/{login}/{key}", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> getPluginDataEntry(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "hash") String hash, //
+ @PathVariable(value = "login") String login, //
+ @PathVariable(value = "key") String key //
+ ) throws SecurityException, ObjectNotFoundException {
+ return pluginRest.getPluginDataEntry(token, hash, login, key);
+ }
+
+ @RequestMapping(value = "/plugins/{hash}/data/global/{key}", method = { RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> createPluginDataEntry(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "hash") String hash, //
+ @PathVariable(value = "key") String key, //
+ @RequestParam(value = "value", defaultValue = "") String value //
+ ) throws SecurityException, ObjectNotFoundException {
+ return pluginRest.createPluginDataEntry(token, hash, null, key, value);
+ }
+
+ @RequestMapping(value = "/plugins/{hash}/data/global/{key}", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> getPluginDataEntry(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "hash") String hash, //
+ @PathVariable(value = "key") String key //
+ ) throws SecurityException, ObjectNotFoundException {
+ return pluginRest.getPluginDataEntry(token, hash, null, key);
+ }
+
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/plugins/PluginRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/plugins/PluginRestImpl.java
index c07ce9b016..a39dc9ae87 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/plugins/PluginRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/plugins/PluginRestImpl.java
@@ -1,139 +1,139 @@
-package lcsb.mapviewer.api.plugins;
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.api.BaseRestImpl;
-import lcsb.mapviewer.api.ObjectNotFoundException;
-import lcsb.mapviewer.model.plugin.Plugin;
-import lcsb.mapviewer.model.plugin.PluginDataEntry;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.persist.dao.plugin.PluginDao;
-import lcsb.mapviewer.persist.dao.plugin.PluginDataEntryDao;
-import lcsb.mapviewer.services.SecurityException;
-
-@Transactional(value = "txManager")
-public class PluginRestImpl extends BaseRestImpl {
-
- @Autowired
- private PluginDao pluginDao;
-
- @Autowired
- private PluginDataEntryDao pluginDataEntryDao;
-
- public Map<String, Object> createPlugin(String token, String hash, String name, String version, String url) {
- Plugin plugin = pluginDao.getByHash(hash);
- if (plugin != null) {
- plugin.getUrls().add(url);
- pluginDao.update(plugin);
- } else {
- plugin = new Plugin();
- plugin.setHash(hash);
- plugin.setName(name);
- plugin.setVersion(version);
- if (!url.isEmpty()) {
- plugin.getUrls().add(url);
- }
- pluginDao.add(plugin);
- }
- return pluginToMap(plugin);
- }
-
- private Map<String, Object> pluginToMap(Plugin plugin) {
- Map<String, Object> result = new TreeMap<>();
- result.put("hash", plugin.getHash());
- result.put("name", plugin.getName());
- result.put("version", plugin.getVersion());
- List<String> urls = new ArrayList<>();
- urls.addAll(plugin.getUrls());
- Collections.sort(urls);
- result.put("urls", urls);
- return result;
- }
-
- public Map<String, Object> getPlugin(String token, String hash) throws ObjectNotFoundException {
- Plugin plugin = pluginDao.getByHash(hash);
- if (plugin == null) {
- throw new ObjectNotFoundException("Plugin doesn't exist");
- }
- return pluginToMap(plugin);
- }
-
- public Map<String, Object> createPluginDataEntry(String token, String hash, String login, String key, String value)
- throws SecurityException, ObjectNotFoundException {
- User user = null;
- if (login != null) {
- user = getUserService().getUserByToken(token);
- if (!user.getLogin().equals(login)) {
- throw new SecurityException();
- }
- }
- Plugin plugin = pluginDao.getByHash(hash);
- if (plugin == null) {
- throw new ObjectNotFoundException("Plugin doesn't exist");
- }
- PluginDataEntry entry = pluginDataEntryDao.getByKey(plugin, key, user);
- if (entry == null) {
- entry = new PluginDataEntry();
- entry.setKey(key);
- entry.setPlugin(plugin);
- entry.setUser(user);
- entry.setValue(value);
- pluginDataEntryDao.add(entry);
- } else {
- entry.setValue(value);
- pluginDataEntryDao.update(entry);
- }
-
- return pluginEntryToMap(entry);
- }
-
- private Map<String, Object> pluginEntryToMap(PluginDataEntry entry) {
- Map<String, Object> result = new TreeMap<>();
- result.put("key", entry.getKey());
- result.put("value", entry.getValue());
- if (entry.getUser() != null) {
- result.put("user", entry.getUser().getLogin());
- }
- return result;
- }
-
- public Map<String, Object> getPluginDataEntry(String token, String hash, String login, String key)
- throws SecurityException, ObjectNotFoundException {
- User user = null;
- if (login != null) {
- user = getUserService().getUserByToken(token);
- if (!user.getLogin().equals(login)) {
- throw new SecurityException();
- }
- }
- Plugin plugin = pluginDao.getByHash(hash);
- if (plugin == null) {
- throw new ObjectNotFoundException("Plugin doesn't exist");
- }
- PluginDataEntry entry = pluginDataEntryDao.getByKey(plugin, key, user);
- if (entry == null) {
- throw new ObjectNotFoundException("Entry doesn't exist");
- }
-
- return pluginEntryToMap(entry);
- }
-
- public List<Map<String, Object>> getPlugins(String token) {
- List<Plugin> plugins = pluginDao.getAll();
- plugins.sort(Plugin.ID_COMPARATOR);
-
- List<Map<String, Object>> result = new ArrayList<>();
- for (Plugin plugin : plugins) {
- result.add(pluginToMap(plugin));
- }
- return result;
- }
-
-}
+package lcsb.mapviewer.api.plugins;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.api.BaseRestImpl;
+import lcsb.mapviewer.api.ObjectNotFoundException;
+import lcsb.mapviewer.model.plugin.Plugin;
+import lcsb.mapviewer.model.plugin.PluginDataEntry;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.persist.dao.plugin.PluginDao;
+import lcsb.mapviewer.persist.dao.plugin.PluginDataEntryDao;
+import lcsb.mapviewer.services.SecurityException;
+
+@Transactional(value = "txManager")
+public class PluginRestImpl extends BaseRestImpl {
+
+ @Autowired
+ private PluginDao pluginDao;
+
+ @Autowired
+ private PluginDataEntryDao pluginDataEntryDao;
+
+ public Map<String, Object> createPlugin(String token, String hash, String name, String version, String url) {
+ Plugin plugin = pluginDao.getByHash(hash);
+ if (plugin != null) {
+ plugin.getUrls().add(url);
+ pluginDao.update(plugin);
+ } else {
+ plugin = new Plugin();
+ plugin.setHash(hash);
+ plugin.setName(name);
+ plugin.setVersion(version);
+ if (!url.isEmpty()) {
+ plugin.getUrls().add(url);
+ }
+ pluginDao.add(plugin);
+ }
+ return pluginToMap(plugin);
+ }
+
+ private Map<String, Object> pluginToMap(Plugin plugin) {
+ Map<String, Object> result = new TreeMap<>();
+ result.put("hash", plugin.getHash());
+ result.put("name", plugin.getName());
+ result.put("version", plugin.getVersion());
+ List<String> urls = new ArrayList<>();
+ urls.addAll(plugin.getUrls());
+ Collections.sort(urls);
+ result.put("urls", urls);
+ return result;
+ }
+
+ public Map<String, Object> getPlugin(String token, String hash) throws ObjectNotFoundException {
+ Plugin plugin = pluginDao.getByHash(hash);
+ if (plugin == null) {
+ throw new ObjectNotFoundException("Plugin doesn't exist");
+ }
+ return pluginToMap(plugin);
+ }
+
+ public Map<String, Object> createPluginDataEntry(String token, String hash, String login, String key, String value)
+ throws SecurityException, ObjectNotFoundException {
+ User user = null;
+ if (login != null) {
+ user = getUserService().getUserByToken(token);
+ if (!user.getLogin().equals(login)) {
+ throw new SecurityException();
+ }
+ }
+ Plugin plugin = pluginDao.getByHash(hash);
+ if (plugin == null) {
+ throw new ObjectNotFoundException("Plugin doesn't exist");
+ }
+ PluginDataEntry entry = pluginDataEntryDao.getByKey(plugin, key, user);
+ if (entry == null) {
+ entry = new PluginDataEntry();
+ entry.setKey(key);
+ entry.setPlugin(plugin);
+ entry.setUser(user);
+ entry.setValue(value);
+ pluginDataEntryDao.add(entry);
+ } else {
+ entry.setValue(value);
+ pluginDataEntryDao.update(entry);
+ }
+
+ return pluginEntryToMap(entry);
+ }
+
+ private Map<String, Object> pluginEntryToMap(PluginDataEntry entry) {
+ Map<String, Object> result = new TreeMap<>();
+ result.put("key", entry.getKey());
+ result.put("value", entry.getValue());
+ if (entry.getUser() != null) {
+ result.put("user", entry.getUser().getLogin());
+ }
+ return result;
+ }
+
+ public Map<String, Object> getPluginDataEntry(String token, String hash, String login, String key)
+ throws SecurityException, ObjectNotFoundException {
+ User user = null;
+ if (login != null) {
+ user = getUserService().getUserByToken(token);
+ if (!user.getLogin().equals(login)) {
+ throw new SecurityException();
+ }
+ }
+ Plugin plugin = pluginDao.getByHash(hash);
+ if (plugin == null) {
+ throw new ObjectNotFoundException("Plugin doesn't exist");
+ }
+ PluginDataEntry entry = pluginDataEntryDao.getByKey(plugin, key, user);
+ if (entry == null) {
+ throw new ObjectNotFoundException("Entry doesn't exist");
+ }
+
+ return pluginEntryToMap(entry);
+ }
+
+ public List<Map<String, Object>> getPlugins(String token) {
+ List<Plugin> plugins = pluginDao.getAll();
+ plugins.sort(Plugin.ID_COMPARATOR);
+
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (Plugin plugin : plugins) {
+ result.add(pluginToMap(plugin));
+ }
+ return result;
+ }
+
+}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java
index 1b49fc86c4..c2171f9fb9 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java
@@ -1,209 +1,209 @@
-package lcsb.mapviewer.api.projects;
-
-import java.io.IOException;
-import java.util.List;
-import java.util.Map;
-
-import javax.servlet.ServletContext;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.MediaType;
-import org.springframework.http.ResponseEntity;
-import org.springframework.util.MultiValueMap;
-import org.springframework.web.bind.annotation.CookieValue;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestBody;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RequestParam;
-import org.springframework.web.bind.annotation.RestController;
-
-import lcsb.mapviewer.api.BaseController;
-import lcsb.mapviewer.api.ObjectNotFoundException;
-import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.converter.ConverterException;
-import lcsb.mapviewer.converter.graphics.DrawingException;
-import lcsb.mapviewer.model.cache.FileEntry;
-import lcsb.mapviewer.model.map.InconsistentModelException;
-import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
-import lcsb.mapviewer.services.SecurityException;
-
-@RestController
-public class ProjectController extends BaseController {
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(ProjectController.class);
-
- @Autowired
- private ServletContext context;
-
- @Autowired
- private ProjectRestImpl projectController;
-
- @RequestMapping(value = "/projects/{projectId:.+}", method = { RequestMethod.GET }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getProject(//
- @PathVariable(value = "projectId") String projectId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
- ) throws SecurityException, ObjectNotFoundException {
- return projectController.getProject(projectId, token);
- }
-
- @RequestMapping(value = "/projects/{projectId:.+}", method = { RequestMethod.PATCH }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> updateProject(//
- @RequestBody String body, //
- @PathVariable(value = "projectId") String projectId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
- ) throws SecurityException, IOException, QueryException {
- Map<String, Object> node = parseBody(body);
- Map<String, Object> data = getData(node, "project");
- return projectController.updateProject(token, projectId, data);
-
- }
-
- @RequestMapping(value = "/projects/{projectId:.+}", method = { RequestMethod.POST }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> addProject(//
- @RequestBody MultiValueMap<String, Object> formData, //
- @PathVariable(value = "projectId") String projectId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
- ) throws SecurityException, IOException, QueryException {
- return projectController.addProject(token, projectId, formData, context.getRealPath("/"));
-
- }
-
- @RequestMapping(value = "/projects/{projectId:.+}", method = { RequestMethod.DELETE }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> removeProject(//
- @PathVariable(value = "projectId") String projectId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
- ) throws SecurityException, IOException, QueryException {
- return projectController.removeProject(token, projectId, context.getRealPath("/"));
-
- }
-
- @RequestMapping(value = "/projects/", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getProjects(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
- ) throws SecurityException, ObjectNotFoundException {
- return projectController.getProjects(token);
- }
-
- @RequestMapping(value = "/projects/{projectId}/statistics", method = { RequestMethod.GET }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public Object getStatistics(//
- @PathVariable(value = "projectId") String projectId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
- ) throws SecurityException, ObjectNotFoundException {
- return projectController.getStatistics(projectId, token);
- }
-
- @RequestMapping(value = "/projects/{projectId}:downloadSource", method = { RequestMethod.GET }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public ResponseEntity<byte[]> getProjectSource(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId //
- ) throws SecurityException, QueryException {
-
- FileEntry file = projectController.getSource(token, projectId);
- MediaType type = MediaType.TEXT_PLAIN;
- if (file.getOriginalFileName().endsWith("xml")) {
- type = MediaType.APPLICATION_XML;
- } else if (file.getOriginalFileName().endsWith("zip")) {
- type = MediaType.APPLICATION_OCTET_STREAM;
- }
- return ResponseEntity.ok().contentLength(file.getFileContent().length).contentType(type)
- .header("Content-Disposition", "attachment; filename=" + file.getOriginalFileName())
- .body(file.getFileContent());
- }
-
- @RequestMapping(value = "/projects/{projectId}/models/{modelId}:downloadImage", method = {
- RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public ResponseEntity<byte[]> getModelAsImage(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @RequestParam(value = "handlerClass") String handlerClass, //
- @RequestParam(value = "backgroundOverlayId", defaultValue = "") String backgroundOverlayId, //
- @RequestParam(value = "overlayIds", defaultValue = "") String overlayIds, //
- @RequestParam(value = "zoomLevel", defaultValue = "") String zoomLevel, //
- @RequestParam(value = "polygonString", defaultValue = "") String polygonString//
- ) throws SecurityException, QueryException, IOException, InvalidColorSchemaException, CommandExecutionException,
- DrawingException {
-
- FileEntry file = projectController.getModelAsImage(token, projectId, modelId, handlerClass, backgroundOverlayId,
- overlayIds, zoomLevel, polygonString);
- MediaType type = MediaType.APPLICATION_OCTET_STREAM;
- return ResponseEntity.ok().contentLength(file.getFileContent().length).contentType(type)
- .header("Content-Disposition", "attachment; filename=" + file.getOriginalFileName())
- .body(file.getFileContent());
- }
-
- @RequestMapping(value = "/projects/{projectId}/models/{modelId}:downloadModel", method = {
- RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public ResponseEntity<byte[]> getModelAsModelFile(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @RequestParam(value = "handlerClass") String handlerClass, //
- @RequestParam(value = "backgroundOverlayId", defaultValue = "") String backgroundOverlayId, //
- @RequestParam(value = "overlayIds", defaultValue = "") String overlayIds, //
- @RequestParam(value = "zoomLevel", defaultValue = "") String zoomLevel, //
- @RequestParam(value = "polygonString", defaultValue = "") String polygonString//
- ) throws SecurityException, QueryException, IOException, InvalidColorSchemaException, CommandExecutionException,
- ConverterException, InconsistentModelException {
-
- FileEntry file = projectController.getModelAsModelFile(token, projectId, modelId, handlerClass, backgroundOverlayId,
- overlayIds, zoomLevel, polygonString);
- MediaType type = MediaType.APPLICATION_OCTET_STREAM;
- return ResponseEntity.ok().contentLength(file.getFileContent().length).contentType(type)
- .header("Content-Disposition", "attachment; filename=" + file.getOriginalFileName())
- .body(file.getFileContent());
- }
-
- @RequestMapping(value = "/projects/{projectId}/logs/", method = { RequestMethod.GET }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getLogs(//
- @PathVariable(value = "projectId") String projectId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @RequestParam(value = "level", defaultValue = "warning") String level, //
- @RequestParam(value = "start", defaultValue = "0") String start, //
- @RequestParam(value = "length", defaultValue = "10") Integer length, //
- @RequestParam(value = "sortColumn", defaultValue = "id") String sortColumn, //
- @RequestParam(value = "sortOrder", defaultValue = "asc") String sortOrder, //
- @RequestParam(value = "search", defaultValue = "") String search//
- ) throws QueryException, SecurityException {
- return projectController.getLogs(projectId, level, token, start, length, sortColumn, sortOrder, search);
- }
-
- /**
- * @return the context
- * @see #context
- */
- public ServletContext getContext() {
- return context;
- }
-
- /**
- * @param context
- * the context to set
- * @see #context
- */
- public void setContext(ServletContext context) {
- this.context = context;
- }
-
- @RequestMapping(value = "/projects/{projectId}/submapConnections", method = { RequestMethod.GET }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getSubmapConnections(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId //
- ) throws SecurityException, QueryException {
-
- return projectController.getSubmapConnections(token, projectId);
- }
-
+package lcsb.mapviewer.api.projects;
+
+import java.io.IOException;
+import java.util.List;
+import java.util.Map;
+
+import javax.servlet.ServletContext;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.http.ResponseEntity;
+import org.springframework.util.MultiValueMap;
+import org.springframework.web.bind.annotation.CookieValue;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestBody;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.RestController;
+
+import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.api.ObjectNotFoundException;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.commands.CommandExecutionException;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.converter.graphics.DrawingException;
+import lcsb.mapviewer.model.cache.FileEntry;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
+import lcsb.mapviewer.services.SecurityException;
+
+@RestController
+public class ProjectController extends BaseController {
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(ProjectController.class);
+
+ @Autowired
+ private ServletContext context;
+
+ @Autowired
+ private ProjectRestImpl projectController;
+
+ @RequestMapping(value = "/projects/{projectId:.+}", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> getProject(//
+ @PathVariable(value = "projectId") String projectId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, ObjectNotFoundException {
+ return projectController.getProject(projectId, token);
+ }
+
+ @RequestMapping(value = "/projects/{projectId:.+}", method = { RequestMethod.PATCH }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> updateProject(//
+ @RequestBody String body, //
+ @PathVariable(value = "projectId") String projectId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, IOException, QueryException {
+ Map<String, Object> node = parseBody(body);
+ Map<String, Object> data = getData(node, "project");
+ return projectController.updateProject(token, projectId, data);
+
+ }
+
+ @RequestMapping(value = "/projects/{projectId:.+}", method = { RequestMethod.POST }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> addProject(//
+ @RequestBody MultiValueMap<String, Object> formData, //
+ @PathVariable(value = "projectId") String projectId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, IOException, QueryException {
+ return projectController.addProject(token, projectId, formData, context.getRealPath("/"));
+
+ }
+
+ @RequestMapping(value = "/projects/{projectId:.+}", method = { RequestMethod.DELETE }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> removeProject(//
+ @PathVariable(value = "projectId") String projectId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, IOException, QueryException {
+ return projectController.removeProject(token, projectId, context.getRealPath("/"));
+
+ }
+
+ @RequestMapping(value = "/projects/", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getProjects(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, ObjectNotFoundException {
+ return projectController.getProjects(token);
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/statistics", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Object getStatistics(//
+ @PathVariable(value = "projectId") String projectId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, ObjectNotFoundException {
+ return projectController.getStatistics(projectId, token);
+ }
+
+ @RequestMapping(value = "/projects/{projectId}:downloadSource", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public ResponseEntity<byte[]> getProjectSource(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "projectId") String projectId //
+ ) throws SecurityException, QueryException {
+
+ FileEntry file = projectController.getSource(token, projectId);
+ MediaType type = MediaType.TEXT_PLAIN;
+ if (file.getOriginalFileName().endsWith("xml")) {
+ type = MediaType.APPLICATION_XML;
+ } else if (file.getOriginalFileName().endsWith("zip")) {
+ type = MediaType.APPLICATION_OCTET_STREAM;
+ }
+ return ResponseEntity.ok().contentLength(file.getFileContent().length).contentType(type)
+ .header("Content-Disposition", "attachment; filename=" + file.getOriginalFileName())
+ .body(file.getFileContent());
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/models/{modelId}:downloadImage", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public ResponseEntity<byte[]> getModelAsImage(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "modelId") String modelId, //
+ @RequestParam(value = "handlerClass") String handlerClass, //
+ @RequestParam(value = "backgroundOverlayId", defaultValue = "") String backgroundOverlayId, //
+ @RequestParam(value = "overlayIds", defaultValue = "") String overlayIds, //
+ @RequestParam(value = "zoomLevel", defaultValue = "") String zoomLevel, //
+ @RequestParam(value = "polygonString", defaultValue = "") String polygonString//
+ ) throws SecurityException, QueryException, IOException, InvalidColorSchemaException, CommandExecutionException,
+ DrawingException {
+
+ FileEntry file = projectController.getModelAsImage(token, projectId, modelId, handlerClass, backgroundOverlayId,
+ overlayIds, zoomLevel, polygonString);
+ MediaType type = MediaType.APPLICATION_OCTET_STREAM;
+ return ResponseEntity.ok().contentLength(file.getFileContent().length).contentType(type)
+ .header("Content-Disposition", "attachment; filename=" + file.getOriginalFileName())
+ .body(file.getFileContent());
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/models/{modelId}:downloadModel", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public ResponseEntity<byte[]> getModelAsModelFile(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "modelId") String modelId, //
+ @RequestParam(value = "handlerClass") String handlerClass, //
+ @RequestParam(value = "backgroundOverlayId", defaultValue = "") String backgroundOverlayId, //
+ @RequestParam(value = "overlayIds", defaultValue = "") String overlayIds, //
+ @RequestParam(value = "zoomLevel", defaultValue = "") String zoomLevel, //
+ @RequestParam(value = "polygonString", defaultValue = "") String polygonString//
+ ) throws SecurityException, QueryException, IOException, InvalidColorSchemaException, CommandExecutionException,
+ ConverterException, InconsistentModelException {
+
+ FileEntry file = projectController.getModelAsModelFile(token, projectId, modelId, handlerClass, backgroundOverlayId,
+ overlayIds, zoomLevel, polygonString);
+ MediaType type = MediaType.APPLICATION_OCTET_STREAM;
+ return ResponseEntity.ok().contentLength(file.getFileContent().length).contentType(type)
+ .header("Content-Disposition", "attachment; filename=" + file.getOriginalFileName())
+ .body(file.getFileContent());
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/logs/", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> getLogs(//
+ @PathVariable(value = "projectId") String projectId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @RequestParam(value = "level", defaultValue = "warning") String level, //
+ @RequestParam(value = "start", defaultValue = "0") String start, //
+ @RequestParam(value = "length", defaultValue = "10") Integer length, //
+ @RequestParam(value = "sortColumn", defaultValue = "id") String sortColumn, //
+ @RequestParam(value = "sortOrder", defaultValue = "asc") String sortOrder, //
+ @RequestParam(value = "search", defaultValue = "") String search//
+ ) throws QueryException, SecurityException {
+ return projectController.getLogs(projectId, level, token, start, length, sortColumn, sortOrder, search);
+ }
+
+ /**
+ * @return the context
+ * @see #context
+ */
+ public ServletContext getContext() {
+ return context;
+ }
+
+ /**
+ * @param context
+ * the context to set
+ * @see #context
+ */
+ public void setContext(ServletContext context) {
+ this.context = context;
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/submapConnections", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getSubmapConnections(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "projectId") String projectId //
+ ) throws SecurityException, QueryException {
+
+ return projectController.getSubmapConnections(token, projectId);
+ }
+
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
index ec2559f0b9..317f1afede 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
@@ -1,938 +1,938 @@
-package lcsb.mapviewer.api.projects;
-
-import java.awt.Color;
-import java.awt.geom.Path2D;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-import java.io.ByteArrayInputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.Serializable;
-import java.security.MessageDigest;
-import java.security.NoSuchAlgorithmException;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Comparator;
-import java.util.HashSet;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeMap;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.annotation.Transactional;
-import org.springframework.util.MultiValueMap;
-
-import lcsb.mapviewer.api.BaseRestImpl;
-import lcsb.mapviewer.api.ObjectExistsException;
-import lcsb.mapviewer.api.ObjectNotFoundException;
-import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.api.projects.models.publications.PublicationsRestImpl;
-import lcsb.mapviewer.commands.ClearColorModelCommand;
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.commands.ColorModelCommand;
-import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.commands.CopyCommand;
-import lcsb.mapviewer.commands.SetFixedHierarchyLevelCommand;
-import lcsb.mapviewer.commands.SubModelCommand;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.ConverterException;
-import lcsb.mapviewer.converter.IConverter;
-import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
-import lcsb.mapviewer.converter.graphics.DrawingException;
-import lcsb.mapviewer.converter.graphics.ImageGenerators;
-import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
-import lcsb.mapviewer.converter.zip.LayoutZipEntryFile;
-import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
-import lcsb.mapviewer.converter.zip.ZipEntryFile;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.cache.FileEntry;
-import lcsb.mapviewer.model.cache.UploadedFileEntry;
-import lcsb.mapviewer.model.graphics.MapCanvasType;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.InconsistentModelException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.OverviewImage;
-import lcsb.mapviewer.model.map.OverviewImageLink;
-import lcsb.mapviewer.model.map.OverviewLink;
-import lcsb.mapviewer.model.map.OverviewModelLink;
-import lcsb.mapviewer.model.map.OverviewSearchLink;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.SubmodelType;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.user.ConfigurationElementType;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.persist.dao.ProjectDao;
-import lcsb.mapviewer.persist.dao.cache.UploadedFileEntryDao;
-import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.interfaces.ILayoutService;
-import lcsb.mapviewer.services.interfaces.IProjectService;
-import lcsb.mapviewer.services.utils.ColorSchemaReader;
-import lcsb.mapviewer.services.utils.CreateProjectParams;
-import lcsb.mapviewer.services.utils.data.BuildInLayout;
-
-@Transactional(value = "txManager")
-public class ProjectRestImpl extends BaseRestImpl {
-
- /**
- * Constant defining size of the array returned by
- * {@link PathIterator#currentSegment(double[])} method. More information can be
- * found <a href=
- * "http://docs.oracle.com/javase/7/docs/api/java/awt/geom/PathIterator.html#currentSegment(double[])"
- * >here</a>
- */
- private static final int PATH_ITERATOR_SEGMENT_SIZE = 6;
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(ProjectRestImpl.class);
-
- @Autowired
- private PublicationsRestImpl publicationsRestImpl;
-
- @Autowired
- private ILayoutService layoutService;
-
- @Autowired
- private IProjectService projectService;
-
- @Autowired
- private ProjectDao projectDao;
-
- @Autowired
- private UploadedFileEntryDao uploadedFileEntryDao;
-
- public Map<String, Object> getProject(String projectId, String token)
- throws SecurityException, ObjectNotFoundException {
- Project project = getProjectService().getProjectByProjectId(projectId, token);
- if (project == null) {
- throw new ObjectNotFoundException("Project with given id doesn't exist");
- }
- return createData(project);
- }
-
- private Map<String, Object> createData(Project project) {
- Map<String, Object> result = new LinkedHashMap<>();
-
- result.put("version", project.getVersion());
- if (project.getDisease() != null) {
- result.put("disease", createAnnotation(project.getDisease()));
- } else {
- result.put("disease", null);
- }
- if (project.getOrganism() != null) {
- result.put("organism", createAnnotation(project.getOrganism()));
- } else {
- result.put("organism", null);
- }
- result.put("idObject", project.getId());
- if (project.getStatus() != null) {
- result.put("status", project.getStatus().toString());
- }
- result.put("directory", project.getDirectory());
- result.put("progress", project.getProgress());
- result.put("notifyEmail", project.getNotifyEmail());
- result.put("warnings", project.getWarnings().size() > 0);
- result.put("errors", project.getErrors() != null && !project.getErrors().isEmpty());
- result.put("name", project.getName());
- result.put("projectId", project.getProjectId());
- result.put("mapCanvasType", project.getMapCanvasType());
-
- List<Map<String, Object>> images = new ArrayList<>();
- for (OverviewImage image : project.getOverviewImages()) {
- images.add(imageToMap(image));
- }
- result.put("overviewImageViews", images);
-
- Set<OverviewImage> set = new HashSet<>();
- set.addAll(project.getOverviewImages());
- for (OverviewImage image : project.getOverviewImages()) {
- for (OverviewLink ol : image.getLinks()) {
- if (ol instanceof OverviewImageLink) {
- set.remove(((OverviewImageLink) ol).getLinkedOverviewImage());
- }
- }
- }
- if (set.size() > 0) {
- result.put("topOverviewImage", imageToMap(set.iterator().next()));
- } else if (project.getOverviewImages().size() > 0) {
- logger.warn(
- "Cannot determine top level image. Taking first one. " + project.getOverviewImages().get(0).getFilename());
- result.put("topOverviewImage", imageToMap(project.getOverviewImages().get(0)));
- } else {
- result.put("topOverviewImage", null);
- }
-
- return result;
- }
-
- private Map<String, Object> imageToMap(OverviewImage image) {
- Map<String, Object> result = new LinkedHashMap<>();
- result.put("idObject", image.getId());
- result.put("filename", image.getProject().getDirectory() + "/" + image.getFilename());
- result.put("width", image.getWidth());
- result.put("height", image.getHeight());
- List<Map<String, Object>> links = new ArrayList<>();
- for (OverviewLink link : image.getLinks()) {
- links.add(overviewLinkToMap(link));
- }
- result.put("links", links);
- return result;
- }
-
- private Map<String, Object> overviewLinkToMap(OverviewLink link) {
- Map<String, Object> result = new LinkedHashMap<>();
- result.put("idObject", link.getId());
- result.put("polygon", polygonToMap(link.getPolygon()));
- if (link instanceof OverviewModelLink) {
- OverviewModelLink modelLink = (OverviewModelLink) link;
- result.put("zoomLevel", modelLink.getZoomLevel());
- result.put("modelPoint", new Point2D.Double(modelLink.getxCoord(), modelLink.getyCoord()));
- result.put("modelLinkId", modelLink.getLinkedModel().getId());
-
- } else if (link instanceof OverviewImageLink) {
- result.put("imageLinkId", ((OverviewImageLink) link).getLinkedOverviewImage().getId());
- } else if (link instanceof OverviewSearchLink) {
- result.put("query", ((OverviewSearchLink) link).getQuery());
- } else {
- throw new NotImplementedException("Not implemented behaviour for class: " + link.getClass());
- }
- result.put("type", link.getClass().getSimpleName());
- return result;
- }
-
- private List<Map<String, Double>> polygonToMap(String polygon) {
- List<Map<String, Double>> result = new ArrayList<>();
- for (String string : polygon.split(" ")) {
- String tmp[] = string.split(",");
- Map<String, Double> point = new TreeMap<>();
- point.put("x", Double.parseDouble(tmp[0]));
- point.put("y", Double.parseDouble(tmp[1]));
- result.add(point);
- }
- return result;
- }
-
- public FileEntry getSource(String token, String projectId) throws SecurityException, QueryException {
- Project project = getProjectService().getProjectByProjectId(projectId, token);
- if (project == null) {
- throw new ObjectNotFoundException("Project with given id doesn't exist");
- }
- if (project.getInputData() != null) {
- // fetch the data from db
- project.getInputData().getFileContent();
- }
- return project.getInputData();
- }
-
- public FileEntry getModelAsImage(String token, String projectId, String modelId, String handlerClass,
- String backgroundOverlayId, String overlayIds, String zoomLevel, String polygonString) throws SecurityException,
- QueryException, IOException, InvalidColorSchemaException, CommandExecutionException, DrawingException {
- User user = getUserService().getUserByToken(token);
-
- Model topModel = getModelService().getLastModelByProjectId(projectId, token);
- if (topModel == null) {
- throw new ObjectNotFoundException("Project with given id doesn't exist");
- }
-
- Model originalModel = topModel.getSubmodelById(modelId);
-
- if (originalModel == null) {
- throw new ObjectNotFoundException("Model with given id doesn't exist");
- }
-
- Layout overlay = null;
- if (!backgroundOverlayId.equals("")) {
- overlay = topModel.getLayoutByIdentifier(Integer.valueOf(backgroundOverlayId));
-
- if (overlay == null) {
- throw new ObjectNotFoundException("Unknown overlay in model. Layout.id=" + backgroundOverlayId);
- }
- } else {
- if (topModel.getLayouts().size() > 0) {
- overlay = topModel.getLayouts().get(0);
- }
- }
-
- Model colorModel = new CopyCommand(originalModel).execute();
- if (overlay != null) {
- if (overlay.getInputData() != null) {
- ColorSchemaReader reader = new ColorSchemaReader();
- Collection<ColorSchema> schemas = reader.readColorSchema(overlay.getInputData().getFileContent());
-
- new ColorModelCommand(colorModel, schemas, getUserService().getColorExtractorForUser(user)).execute();
- } else if (overlay.getTitle().equals(BuildInLayout.CLEAN.getTitle())) {
- // this might not return true if we change CLEAN.title in future...
-
- // if it's clean then remove coloring
- new ClearColorModelCommand(colorModel).execute();
- } else if (overlay.isHierarchicalView()) {
- new SetFixedHierarchyLevelCommand(colorModel, overlay.getHierarchyViewLevel()).execute();
- }
- }
-
- Integer level = Configuration.MIN_ZOOM_LEVEL;
- if (!zoomLevel.equals("")) {
- level = Integer.valueOf(zoomLevel);
- }
-
- Path2D polygon = stringToPolygon(polygonString, colorModel);
-
- Double minX = originalModel.getWidth();
- Double minY = originalModel.getHeight();
- Double maxX = 0.0;
- Double maxY = 0.0;
-
- PathIterator pathIter = polygon.getPathIterator(null);
- while (!pathIter.isDone()) {
- final double[] segment = new double[PATH_ITERATOR_SEGMENT_SIZE];
- if (pathIter.currentSegment(segment) != PathIterator.SEG_CLOSE) {
- minX = Math.min(minX, segment[0]);
- maxX = Math.max(maxX, segment[0]);
- minY = Math.min(minY, segment[1]);
- maxY = Math.max(maxY, segment[1]);
- }
- pathIter.next();
- }
-
- maxX = Math.min(originalModel.getWidth(), maxX);
- maxY = Math.min(originalModel.getHeight(), maxY);
- minX = Math.max(0.0, minX);
- minY = Math.max(0.0, minY);
-
- Double scale = Math.max(originalModel.getHeight(), originalModel.getWidth()) / (originalModel.getTileSize());
-
- for (int i = level; i > Configuration.MIN_ZOOM_LEVEL; i--) {
- scale /= 2;
- }
-
- ColorExtractor colorExtractor = getUserService().getColorExtractorForUser(user);
-
- Params params = new Params().//
- x(minX).//
- y(minY).//
- height((maxY - minY) / scale).//
- width((maxX - minX) / scale).//
- level(level - Configuration.MIN_ZOOM_LEVEL).//
- nested(false).// automatically set nested view as invalid
- scale(scale).//
- colorExtractor(colorExtractor).//
- sbgn(topModel.getProject().isSbgnFormat()).//
- model(colorModel);
- if (overlay != null) {
- params.nested(overlay.isHierarchicalView());
- }
- List<Integer> visibleLayoutIds = deserializeIdList(overlayIds);
- for (Integer integer : visibleLayoutIds) {
- Map<Object, ColorSchema> map = layoutService.getElementsForLayout(colorModel, integer, token);
- params.addVisibleLayout(map);
- }
-
- ImageGenerators imageGenerator = new ImageGenerators();
- String extension = imageGenerator.getExtension(handlerClass);
- File file = File.createTempFile("map", "." + extension);
-
- imageGenerator.generate(handlerClass, params, file.getAbsolutePath());
-
- UploadedFileEntry entry = new UploadedFileEntry();
- entry.setOriginalFileName("map." + extension);
- entry.setFileContent(IOUtils.toByteArray(new FileInputStream(file)));
- entry.setLength(entry.getFileContent().length);
- file.delete();
- return entry;
-
- }
-
- private Path2D stringToPolygon(String polygonString, Model colorModel) {
- String[] stringPointArray = polygonString.split(";");
-
- List<Point2D> points = new ArrayList<>();
- for (String string : stringPointArray) {
- if (!string.trim().equals("")) {
- double x = Double.valueOf(string.split(",")[0]);
- double y = Double.valueOf(string.split(",")[1]);
- points.add(new Point2D.Double(x, y));
- }
- }
-
- if (points.size() <= 2) {
- points.clear();
- points.add(new Point2D.Double(0, 0));
- points.add(new Point2D.Double(colorModel.getWidth(), 0));
- points.add(new Point2D.Double(colorModel.getWidth(), colorModel.getHeight()));
- points.add(new Point2D.Double(0, colorModel.getHeight()));
- }
-
- Path2D polygon = new Path2D.Double();
- polygon.moveTo(points.get(0).getX(), points.get(0).getY());
- for (int i = 1; i < points.size(); i++) {
- Point2D point = points.get(i);
- polygon.lineTo(point.getX(), point.getY());
- }
- polygon.closePath();
- return polygon;
- }
-
- private List<Integer> deserializeIdList(String overlayIds) {
- List<Integer> result = new ArrayList<>();
- String[] tmp = overlayIds.split(",");
- for (String string : tmp) {
- if (!string.equals("")) {
- result.add(Integer.valueOf(string));
- }
- }
- return result;
- }
-
- public FileEntry getModelAsModelFile(String token, String projectId, String modelId, String handlerClass,
- String backgroundOverlayId, String overlayIds, String zoomLevel, String polygonString)
- throws SecurityException, QueryException, IOException, InvalidColorSchemaException, CommandExecutionException,
- ConverterException, InconsistentModelException {
- User user = getUserService().getUserByToken(token);
- Model topModel = getModelService().getLastModelByProjectId(projectId, token);
- if (topModel == null) {
- throw new ObjectNotFoundException("Project with given id doesn't exist");
- }
-
- Model originalModel = topModel.getSubmodelById(modelId);
-
- if (originalModel == null) {
- throw new ObjectNotFoundException("Model with given id doesn't exist");
- }
-
- Path2D polygon = stringToPolygon(polygonString, originalModel);
-
- // create model bounded by the polygon
- SubModelCommand subModelCommand = new SubModelCommand(originalModel, polygon);
- Model part = subModelCommand.execute();
-
- // Get list of overlay ids
- String[] overlayIdsList;
- if (overlayIds == null || overlayIds.trim().isEmpty()) {
- overlayIdsList = new String[0];
- } else {
- overlayIdsList = overlayIds.split(",");
- }
- // Remove all colors
- if (overlayIdsList.length > 0) {
-
- for (Element element : part.getElements()) {
- element.setColor(Color.WHITE);
- }
- }
- // Color with overlays
- for (String overlayId : overlayIdsList) {
- Layout overlay = layoutService.getLayoutById(Integer.parseInt(overlayId.trim()), token);
-
- ColorSchemaReader reader = new ColorSchemaReader();
- Collection<ColorSchema> schemas = reader.readColorSchema(overlay.getInputData().getFileContent());
-
- new ColorModelCommand(part, schemas, getUserService().getColorExtractorForUser(user)).execute();
- }
-
- IConverter parser = getModelParser(handlerClass);
- InputStream is = parser.exportModelToInputStream(part);
-
- String fileExtension = parser.getFileExtension();
-
- UploadedFileEntry entry = new UploadedFileEntry();
- entry.setOriginalFileName("model." + fileExtension);
- entry.setFileContent(IOUtils.toByteArray(is));
- entry.setLength(entry.getFileContent().length);
- return entry;
-
- }
-
- public Map<String, Object> getStatistics(String projectId, String token)
- throws SecurityException, ObjectNotFoundException {
- Map<String, Object> result = new TreeMap<>();
-
- Map<MiriamType, Integer> elementAnnotations = new TreeMap<>();
- for (MiriamType mt : MiriamType.values()) {
- elementAnnotations.put(mt, 0);
- }
- List<Model> models = super.getModels(projectId, "*", token);
-
- for (Model model2 : models) {
- for (Element alias : model2.getElements()) {
- for (MiriamData md : alias.getMiriamData()) {
- Integer amount = elementAnnotations.get(md.getDataType());
- amount += 1;
- elementAnnotations.put(md.getDataType(), amount);
- }
- }
- }
- result.put("elementAnnotations", elementAnnotations);
-
- Map<MiriamType, Integer> reactionAnnotations = new TreeMap<>();
- for (MiriamType mt : MiriamType.values()) {
- reactionAnnotations.put(mt, 0);
- }
- for (Model model2 : models) {
- for (Reaction reaction : model2.getReactions()) {
- for (MiriamData md : reaction.getMiriamData()) {
- Integer amount = reactionAnnotations.get(md.getDataType());
- amount += 1;
- reactionAnnotations.put(md.getDataType(), amount);
- }
- }
- }
-
- result.put("reactionAnnotations", reactionAnnotations);
-
- result.put("publications", publicationsRestImpl.getPublications(models).size());
-
- return result;
- }
-
- public List<Map<String, Object>> getProjects(String token) throws SecurityException {
- List<Project> projects = getProjectService().getAllProjects(token);
- List<Map<String, Object>> result = new ArrayList<>();
- for (Project project : projects) {
- result.add(createData(project));
- }
- return result;
- }
-
- public Map<String, Object> updateProject(String token, String projectId, Map<String, Object> data)
- throws SecurityException, QueryException {
- Project project = getProjectService().getProjectByProjectId(projectId, token);
- if (project == null) {
- throw new ObjectNotFoundException("Project with given id doesn't exist");
- }
- boolean canModify = getUserService().userHasPrivilege(token, PrivilegeType.PROJECT_MANAGEMENT);
- if (!canModify) {
- throw new SecurityException("You cannot update projects");
- }
- Set<String> fields = data.keySet();
- for (String fieldName : fields) {
- Object value = data.get(fieldName);
- String stringValue = null;
- if (value instanceof String) {
- stringValue = (String) value;
- }
- if (fieldName.equalsIgnoreCase("version")) {
- project.setVersion((String) value);
- } else if (fieldName.equalsIgnoreCase("id")) {
- try {
- int id = Integer.parseInt(stringValue);
- if (id != project.getId()) {
- throw new QueryException("Invalid id: " + stringValue);
- }
- } catch (NumberFormatException e) {
- throw new QueryException("Invalid id: " + stringValue);
- }
- } else if (fieldName.equalsIgnoreCase("projectId")) {
- if (!project.getProjectId().equalsIgnoreCase(stringValue)) {
- throw new QueryException("You cannot modify projectId");
- }
- } else if (fieldName.equalsIgnoreCase("name")) {
- project.setName((String) value);
- } else if (fieldName.equalsIgnoreCase("notifyEmail")) {
- project.setNotifyEmail(stringValue);
- } else if (fieldName.equalsIgnoreCase("organism")) {
- MiriamData organism = updateMiriamData(project.getOrganism(), value);
- project.setOrganism(organism);
- } else if (fieldName.equalsIgnoreCase("disease")) {
- MiriamData disease = updateMiriamData(project.getDisease(), value);
- project.setDisease(disease);
- } else if (fieldName.equalsIgnoreCase("mapCanvasType")) {
- MapCanvasType mapCanvasType;
- try {
- mapCanvasType = MapCanvasType.valueOf(stringValue);
- } catch (Exception e) {
- throw new QueryException("Invalid mapCanvasType value");
- }
- project.setMapCanvasType(mapCanvasType);
- } else {
- throw new QueryException("Unknown field: " + fieldName);
- }
- }
- getProjectService().updateProject(project, token);
- return getProject(projectId, token);
- }
-
- private MiriamData updateMiriamData(MiriamData organism, Object res) {
- if (res == null) {
- return null;
- }
- if (organism == null) {
- organism = new MiriamData();
- }
-
- if (res instanceof Map) {
- @SuppressWarnings("unchecked")
- Map<String, Object> map = (Map<String, Object>) res;
- organism.setDataType(MiriamType.valueOf((String) map.get("type")));
- organism.setResource((String) map.get("resource"));
- return organism;
- } else {
- throw new InvalidArgumentException("invalid miriamdData: " + res);
- }
- }
-
- public Map<String, Object> addProject(String token, String projectId, MultiValueMap<String, Object> data, String path)
- throws SecurityException, QueryException, IOException {
- User user = getUserService().getUserByToken(token);
- Project project = getProjectService().getProjectByProjectId(projectId, token);
- if (project != null) {
- logger.debug(project.getProjectId());
- throw new ObjectExistsException("Project with given id already exists");
- }
- CreateProjectParams params = new CreateProjectParams();
- String directory = computePathForProject(projectId, path);
- String fileId = getFirstValue(data.get("file-id"));
- if (fileId == null) {
- throw new QueryException("file-id is obligatory");
- }
- UploadedFileEntry file = uploadedFileEntryDao.getById(Integer.valueOf(fileId));
- if (file == null) {
- throw new QueryException("Invalid file id: " + fileId);
- }
- if (file.getOwner() == null || !file.getOwner().getLogin().equals(user.getLogin())) {
- throw new SecurityException("Access denied to source file");
- }
- String parserClass = getFirstValue(data.get("parser"));
- if (parserClass == null) {
- throw new QueryException("parser is obligatory");
- }
- IConverter parser = getModelParser(parserClass);
-
- List<ZipEntryFile> zipEntries = extractZipEntries(data);
- params.complex(zipEntries.size() > 0);
- for (ZipEntryFile entry : zipEntries) {
- params.addZipEntry(entry);
- }
-
- params.addUser(user.getLogin(), null);
- params.async(true);
- params.parser(parser);
- params.authenticationToken(token);
- params.autoResize(getFirstValue(data.get("auto-resize")));
- params.cacheModel(getFirstValue(data.get("cache")));
- params.description(getFirstValue(data.get("description")));
- params.images(true);
- params.notifyEmail(getFirstValue(data.get("notify-email")));
- params.projectDir(directory);
- params.projectDisease(getFirstValue(data.get("disease")));
- params.projectFile(new ByteArrayInputStream(file.getFileContent()));
- params.projectId(projectId);
- params.projectName(getFirstValue(data.get("name")));
- params.projectOrganism(getFirstValue(data.get("organism")));
- params.sbgnFormat(getFirstValue(data.get("sbgn")));
- params.semanticZoom(getFirstValue(data.get("semantic-zoom")));
- params.semanticZoomContainsMultipleLayouts(getFirstValue(data.get("semantic-zoom-contains-multiple-layouts")));
- params.version(getFirstValue(data.get("version")));
- params.annotations(getFirstValue(data.get("annotate")));
- MapCanvasType mapCanvasType;
- try {
- mapCanvasType = MapCanvasType.valueOf(getFirstValue(data.get("mapCanvasType")));
- } catch (Exception e) {
- throw new QueryException("Invalid mapCanvasType value");
- }
- params.mapCanvasType(mapCanvasType);
-
- if (params.isUpdateAnnotations()) {
- params.annotatorsMap(projectService.createClassAnnotatorTree(user));
- }
- params.analyzeAnnotations(getFirstValue(data.get("verify-annotations")));
- if (params.isAnalyzeAnnotations()) {
- params.requiredAnnotations(projectService.createClassAnnotatorTree(user));
- params.validAnnotations(projectService.createClassAnnotatorTree(user));
- }
- params.setAnnotatorParams(projectService.getAnnotatorsParams(user));
-
- getProjectService().createProject(params);
- return getProject(projectId, token);
- }
-
- protected String computePathForProject(String projectId, String path) {
- long id = projectDao.getNextId();
- return path + "/../map_images/" + md5(projectId + "-" + id) + "/";
- }
-
- protected List<ZipEntryFile> extractZipEntries(MultiValueMap<String, Object> data) {
- int fileIndex = 0;
- List<ZipEntryFile> result = new ArrayList<>();
- while (data.get("zip-entries[" + fileIndex + "][_filename]") != null) {
- ZipEntryFile entry = null;
- String entryType = (String) data.get("zip-entries[" + fileIndex + "][_type]").get(0);
- String filename = (String) data.get("zip-entries[" + fileIndex + "][_filename]").get(0);
- if ("MAP".equalsIgnoreCase(entryType)) {
- String submodelTypeKey = "zip-entries[" + fileIndex + "][_data][type][id]";
- String rootKey = "zip-entries[" + fileIndex + "][_data][root]";
- String mappingKey = "zip-entries[" + fileIndex + "][_data][mapping]";
- SubmodelType mapType = SubmodelType.valueOf((String) data.get(submodelTypeKey).get(0));
- String name = (String) data.get("zip-entries[" + fileIndex + "][_data][name]").get(0);
- Boolean root = getBoolValue(data.get(rootKey), false);
- Boolean mapping = getBoolValue(data.get(mappingKey), false);
-
- entry = new ModelZipEntryFile(filename, name, root, mapping, mapType);
- } else if ("OVERLAY".equalsIgnoreCase(entryType)) {
- String name = (String) data.get("zip-entries[" + fileIndex + "][_data][name]").get(0);
- String description = (String) data.get("zip-entries[" + fileIndex + "][_data][description]").get(0);
- entry = new LayoutZipEntryFile(filename, name, description);
- } else if ("IMAGE".equalsIgnoreCase(entryType)) {
- entry = new ImageZipEntryFile(filename);
- } else {
- throw new Error("Unknown entry type: " + entryType);
- }
- fileIndex++;
- result.add(entry);
-
- }
- return result;
- }
-
- private Boolean getBoolValue(List<Object> list, boolean defaultValue) {
- if (list == null) {
- return defaultValue;
- }
- Object obj = list.get(0);
- if (obj instanceof Boolean) {
- return (Boolean) list.get(0);
- } else {
- return "true".equalsIgnoreCase((String) obj);
- }
- }
-
- /**
- * Method that computes md5 hash for a given {@link String}.
- *
- * @param data
- * input string
- * @return md5 hash for input string
- */
- private String md5(String data) {
- try {
- MessageDigest md = MessageDigest.getInstance("MD5");
- byte[] mdbytes = md.digest(data.getBytes());
- StringBuffer sb = new StringBuffer();
- for (int i = 0; i < mdbytes.length; i++) {
- // CHECKSTYLE:OFF
- // this magic formula transforms integer into hex value
- sb.append(Integer.toString((mdbytes[i] & 0xff) + 0x100, 16).substring(1));
- // CHECKSTYLE:ON
- }
- return sb.toString();
- } catch (NoSuchAlgorithmException e) {
- logger.fatal("Problem with instance of MD5 encoder", e);
- }
-
- return null;
- }
-
- public Map<String, Object> removeProject(String token, String projectId, String path)
- throws SecurityException, QueryException {
- Project project = getProjectService().getProjectByProjectId(projectId, token);
- if (getConfigurationService().getConfigurationValue(ConfigurationElementType.DEFAULT_MAP).equals(project.getProjectId())) {
- throw new QueryException("You cannot remove default map");
- }
- getProjectService().removeProject(project, path, true, token);
- return getProject(projectId, token);
- }
-
- public UploadedFileEntryDao getUploadedFileEntryDao() {
- return uploadedFileEntryDao;
- }
-
- public void setUploadedFileEntryDao(UploadedFileEntryDao uploadedFileEntryDao) {
- this.uploadedFileEntryDao = uploadedFileEntryDao;
- }
-
- private enum LogSortColumn {
- ID("id"), //
- CONTENT("content"); //
-
- private String commonName;
-
- LogSortColumn(String commonName) {
- this.commonName = commonName;
- }
- }
-
- private class LogEntry implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- public LogEntry(int id, String content, String level) {
- this.id = id;
- this.content = content;
- this.level = level;
- }
-
- public Integer id;
- public String content;
- public String level;
- }
-
- public Map<String, Object> getLogs(String projectId, String level, String token, String startString, Integer length,
- String sortColumn, String sortOrder, String search) throws SecurityException, QueryException {
- Project project = getProjectService().getProjectByProjectId(projectId, token);
- if (project == null) {
- throw new ObjectNotFoundException("Project with given id doesn't exist");
- }
-
- LogSortColumn sortColumnEnum = getSortOrderColumn(sortColumn);
- Comparator<LogEntry> comparator = getComparatorForColumn(sortColumnEnum, sortOrder);
-
- Integer start = Math.max(0, Integer.valueOf(startString));
- List<LogEntry> resultList = new ArrayList<>();
-
- List<LogEntry> logEntries = getEntries(project, level);
-
- List<LogEntry> filteredList = new ArrayList<>();
-
- search = search.toLowerCase();
- for (LogEntry entry : logEntries) {
- if (isSearchResult(entry, search)) {
- filteredList.add(entry);
- }
- }
- if (comparator != null) {
- filteredList.sort(comparator);
- }
-
- int index = 0;
- for (LogEntry entry : filteredList) {
- if (index >= start && index < start + length) {
- resultList.add(entry);
- }
- index++;
- }
-
- Map<String, Object> result = new TreeMap<>();
- result.put("data", resultList);
- result.put("totalSize", logEntries.size());
- result.put("filteredSize", filteredList.size());
- result.put("start", start);
- result.put("length", resultList.size());
- return result;
-
- }
-
- private boolean isSearchResult(LogEntry entry, String search) {
- if (search == null || search.isEmpty()) {
- return true;
- }
- if (entry.content.toLowerCase().contains(search) || entry.id.toString().contains(search)) {
- return true;
- }
-
- return false;
-
- }
-
- private List<LogEntry> getEntries(Project project, String level) {
- List<LogEntry> result = new ArrayList<>();
- int id = 0;
- for (String s : project.getWarnings()) {
- if (!s.isEmpty()) {
- if (level.equalsIgnoreCase("warning") || level.equals("")) {
- result.add(new LogEntry(id, s, "WARNING"));
- }
- id++;
- }
- }
- String errors = project.getErrors();
- if (errors == null) {
- errors = "";
- }
- for (String s : errors.split("\n")) {
- if (!s.isEmpty()) {
- if (level.equalsIgnoreCase("error") || level.equals("")) {
- result.add(new LogEntry(id, s, "ERROR"));
- }
- id++;
- }
- }
- return result;
- }
-
- private Comparator<LogEntry> getComparatorForColumn(LogSortColumn sortColumnEnum, String sortOrder)
- throws QueryException {
- final int orderFactor;
- if (sortOrder.toLowerCase().equals("desc")) {
- orderFactor = -1;
- } else {
- orderFactor = 1;
- }
- if (sortColumnEnum == null) {
- return null;
- } else if (sortColumnEnum.equals(LogSortColumn.ID)) {
- return new Comparator<LogEntry>() {
- @Override
- public int compare(LogEntry o1, LogEntry o2) {
- return o1.id.compareTo(o2.id) * orderFactor;
-
- }
- };
- } else if (sortColumnEnum.equals(LogSortColumn.CONTENT)) {
- return new Comparator<LogEntry>() {
- @Override
- public int compare(LogEntry o1, LogEntry o2) {
- return o1.content.compareTo(o2.content) * orderFactor;
-
- }
- };
-
- } else {
- throw new QueryException("Sort order not implemented for: " + sortColumnEnum);
- }
- }
-
- private LogSortColumn getSortOrderColumn(String sortColumn) throws QueryException {
- if (!sortColumn.isEmpty()) {
- for (LogSortColumn type : LogSortColumn.values()) {
- if (type.commonName.toLowerCase().equals(sortColumn.toLowerCase())) {
- return type;
- }
- }
- throw new QueryException("Unknown sortColumn: " + sortColumn);
- }
- return null;
- }
-
- public List<Map<String, Object>> getSubmapConnections(String token, String projectId)
- throws ObjectNotFoundException, SecurityException {
- List<Map<String, Object>> result = new ArrayList<>();
- List<Model> models = getModels(projectId, "*", token);
- List<Element> elements = new ArrayList<>();
- for (Model model : models) {
- elements.addAll(model.getElements());
- }
- elements.sort(BioEntity.ID_COMPARATOR);
- for (Element element : elements) {
- if (element.getSubmodel() != null) {
- result.add(submodelConnectionToMap(element));
- }
- }
- return result;
- }
-
- private Map<String, Object> submodelConnectionToMap(Element element) {
- Map<String, Object> result = new TreeMap<>();
- result.put("from", super.createMinifiedSearchResult(element));
- Map<String, Object> to = new TreeMap<>();
- to.put("modelId", element.getSubmodel().getSubmodel().getId());
- result.put("to", to);
- return result;
- }
-
-}
+package lcsb.mapviewer.api.projects;
+
+import java.awt.Color;
+import java.awt.geom.Path2D;
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.Serializable;
+import java.security.MessageDigest;
+import java.security.NoSuchAlgorithmException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Comparator;
+import java.util.HashSet;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeMap;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+import org.springframework.util.MultiValueMap;
+
+import lcsb.mapviewer.api.BaseRestImpl;
+import lcsb.mapviewer.api.ObjectExistsException;
+import lcsb.mapviewer.api.ObjectNotFoundException;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.api.projects.models.publications.PublicationsRestImpl;
+import lcsb.mapviewer.commands.ClearColorModelCommand;
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.commands.ColorModelCommand;
+import lcsb.mapviewer.commands.CommandExecutionException;
+import lcsb.mapviewer.commands.CopyCommand;
+import lcsb.mapviewer.commands.SetFixedHierarchyLevelCommand;
+import lcsb.mapviewer.commands.SubModelCommand;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
+import lcsb.mapviewer.converter.graphics.DrawingException;
+import lcsb.mapviewer.converter.graphics.ImageGenerators;
+import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
+import lcsb.mapviewer.converter.zip.LayoutZipEntryFile;
+import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
+import lcsb.mapviewer.converter.zip.ZipEntryFile;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.cache.FileEntry;
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
+import lcsb.mapviewer.model.graphics.MapCanvasType;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.OverviewImage;
+import lcsb.mapviewer.model.map.OverviewImageLink;
+import lcsb.mapviewer.model.map.OverviewLink;
+import lcsb.mapviewer.model.map.OverviewModelLink;
+import lcsb.mapviewer.model.map.OverviewSearchLink;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
+import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.SubmodelType;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.user.ConfigurationElementType;
+import lcsb.mapviewer.model.user.PrivilegeType;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.persist.dao.ProjectDao;
+import lcsb.mapviewer.persist.dao.cache.UploadedFileEntryDao;
+import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.interfaces.ILayoutService;
+import lcsb.mapviewer.services.interfaces.IProjectService;
+import lcsb.mapviewer.services.utils.ColorSchemaReader;
+import lcsb.mapviewer.services.utils.CreateProjectParams;
+import lcsb.mapviewer.services.utils.data.BuildInLayout;
+
+@Transactional(value = "txManager")
+public class ProjectRestImpl extends BaseRestImpl {
+
+ /**
+ * Constant defining size of the array returned by
+ * {@link PathIterator#currentSegment(double[])} method. More information can be
+ * found <a href=
+ * "http://docs.oracle.com/javase/7/docs/api/java/awt/geom/PathIterator.html#currentSegment(double[])"
+ * >here</a>
+ */
+ private static final int PATH_ITERATOR_SEGMENT_SIZE = 6;
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(ProjectRestImpl.class);
+
+ @Autowired
+ private PublicationsRestImpl publicationsRestImpl;
+
+ @Autowired
+ private ILayoutService layoutService;
+
+ @Autowired
+ private IProjectService projectService;
+
+ @Autowired
+ private ProjectDao projectDao;
+
+ @Autowired
+ private UploadedFileEntryDao uploadedFileEntryDao;
+
+ public Map<String, Object> getProject(String projectId, String token)
+ throws SecurityException, ObjectNotFoundException {
+ Project project = getProjectService().getProjectByProjectId(projectId, token);
+ if (project == null) {
+ throw new ObjectNotFoundException("Project with given id doesn't exist");
+ }
+ return createData(project);
+ }
+
+ private Map<String, Object> createData(Project project) {
+ Map<String, Object> result = new LinkedHashMap<>();
+
+ result.put("version", project.getVersion());
+ if (project.getDisease() != null) {
+ result.put("disease", createAnnotation(project.getDisease()));
+ } else {
+ result.put("disease", null);
+ }
+ if (project.getOrganism() != null) {
+ result.put("organism", createAnnotation(project.getOrganism()));
+ } else {
+ result.put("organism", null);
+ }
+ result.put("idObject", project.getId());
+ if (project.getStatus() != null) {
+ result.put("status", project.getStatus().toString());
+ }
+ result.put("directory", project.getDirectory());
+ result.put("progress", project.getProgress());
+ result.put("notifyEmail", project.getNotifyEmail());
+ result.put("warnings", project.getWarnings().size() > 0);
+ result.put("errors", project.getErrors() != null && !project.getErrors().isEmpty());
+ result.put("name", project.getName());
+ result.put("projectId", project.getProjectId());
+ result.put("mapCanvasType", project.getMapCanvasType());
+
+ List<Map<String, Object>> images = new ArrayList<>();
+ for (OverviewImage image : project.getOverviewImages()) {
+ images.add(imageToMap(image));
+ }
+ result.put("overviewImageViews", images);
+
+ Set<OverviewImage> set = new HashSet<>();
+ set.addAll(project.getOverviewImages());
+ for (OverviewImage image : project.getOverviewImages()) {
+ for (OverviewLink ol : image.getLinks()) {
+ if (ol instanceof OverviewImageLink) {
+ set.remove(((OverviewImageLink) ol).getLinkedOverviewImage());
+ }
+ }
+ }
+ if (set.size() > 0) {
+ result.put("topOverviewImage", imageToMap(set.iterator().next()));
+ } else if (project.getOverviewImages().size() > 0) {
+ logger.warn(
+ "Cannot determine top level image. Taking first one. " + project.getOverviewImages().get(0).getFilename());
+ result.put("topOverviewImage", imageToMap(project.getOverviewImages().get(0)));
+ } else {
+ result.put("topOverviewImage", null);
+ }
+
+ return result;
+ }
+
+ private Map<String, Object> imageToMap(OverviewImage image) {
+ Map<String, Object> result = new LinkedHashMap<>();
+ result.put("idObject", image.getId());
+ result.put("filename", image.getProject().getDirectory() + "/" + image.getFilename());
+ result.put("width", image.getWidth());
+ result.put("height", image.getHeight());
+ List<Map<String, Object>> links = new ArrayList<>();
+ for (OverviewLink link : image.getLinks()) {
+ links.add(overviewLinkToMap(link));
+ }
+ result.put("links", links);
+ return result;
+ }
+
+ private Map<String, Object> overviewLinkToMap(OverviewLink link) {
+ Map<String, Object> result = new LinkedHashMap<>();
+ result.put("idObject", link.getId());
+ result.put("polygon", polygonToMap(link.getPolygon()));
+ if (link instanceof OverviewModelLink) {
+ OverviewModelLink modelLink = (OverviewModelLink) link;
+ result.put("zoomLevel", modelLink.getZoomLevel());
+ result.put("modelPoint", new Point2D.Double(modelLink.getxCoord(), modelLink.getyCoord()));
+ result.put("modelLinkId", modelLink.getLinkedModel().getId());
+
+ } else if (link instanceof OverviewImageLink) {
+ result.put("imageLinkId", ((OverviewImageLink) link).getLinkedOverviewImage().getId());
+ } else if (link instanceof OverviewSearchLink) {
+ result.put("query", ((OverviewSearchLink) link).getQuery());
+ } else {
+ throw new NotImplementedException("Not implemented behaviour for class: " + link.getClass());
+ }
+ result.put("type", link.getClass().getSimpleName());
+ return result;
+ }
+
+ private List<Map<String, Double>> polygonToMap(String polygon) {
+ List<Map<String, Double>> result = new ArrayList<>();
+ for (String string : polygon.split(" ")) {
+ String tmp[] = string.split(",");
+ Map<String, Double> point = new TreeMap<>();
+ point.put("x", Double.parseDouble(tmp[0]));
+ point.put("y", Double.parseDouble(tmp[1]));
+ result.add(point);
+ }
+ return result;
+ }
+
+ public FileEntry getSource(String token, String projectId) throws SecurityException, QueryException {
+ Project project = getProjectService().getProjectByProjectId(projectId, token);
+ if (project == null) {
+ throw new ObjectNotFoundException("Project with given id doesn't exist");
+ }
+ if (project.getInputData() != null) {
+ // fetch the data from db
+ project.getInputData().getFileContent();
+ }
+ return project.getInputData();
+ }
+
+ public FileEntry getModelAsImage(String token, String projectId, String modelId, String handlerClass,
+ String backgroundOverlayId, String overlayIds, String zoomLevel, String polygonString) throws SecurityException,
+ QueryException, IOException, InvalidColorSchemaException, CommandExecutionException, DrawingException {
+ User user = getUserService().getUserByToken(token);
+
+ Model topModel = getModelService().getLastModelByProjectId(projectId, token);
+ if (topModel == null) {
+ throw new ObjectNotFoundException("Project with given id doesn't exist");
+ }
+
+ Model originalModel = topModel.getSubmodelById(modelId);
+
+ if (originalModel == null) {
+ throw new ObjectNotFoundException("Model with given id doesn't exist");
+ }
+
+ Layout overlay = null;
+ if (!backgroundOverlayId.equals("")) {
+ overlay = topModel.getLayoutByIdentifier(Integer.valueOf(backgroundOverlayId));
+
+ if (overlay == null) {
+ throw new ObjectNotFoundException("Unknown overlay in model. Layout.id=" + backgroundOverlayId);
+ }
+ } else {
+ if (topModel.getLayouts().size() > 0) {
+ overlay = topModel.getLayouts().get(0);
+ }
+ }
+
+ Model colorModel = new CopyCommand(originalModel).execute();
+ if (overlay != null) {
+ if (overlay.getInputData() != null) {
+ ColorSchemaReader reader = new ColorSchemaReader();
+ Collection<ColorSchema> schemas = reader.readColorSchema(overlay.getInputData().getFileContent());
+
+ new ColorModelCommand(colorModel, schemas, getUserService().getColorExtractorForUser(user)).execute();
+ } else if (overlay.getTitle().equals(BuildInLayout.CLEAN.getTitle())) {
+ // this might not return true if we change CLEAN.title in future...
+
+ // if it's clean then remove coloring
+ new ClearColorModelCommand(colorModel).execute();
+ } else if (overlay.isHierarchicalView()) {
+ new SetFixedHierarchyLevelCommand(colorModel, overlay.getHierarchyViewLevel()).execute();
+ }
+ }
+
+ Integer level = Configuration.MIN_ZOOM_LEVEL;
+ if (!zoomLevel.equals("")) {
+ level = Integer.valueOf(zoomLevel);
+ }
+
+ Path2D polygon = stringToPolygon(polygonString, colorModel);
+
+ Double minX = originalModel.getWidth();
+ Double minY = originalModel.getHeight();
+ Double maxX = 0.0;
+ Double maxY = 0.0;
+
+ PathIterator pathIter = polygon.getPathIterator(null);
+ while (!pathIter.isDone()) {
+ final double[] segment = new double[PATH_ITERATOR_SEGMENT_SIZE];
+ if (pathIter.currentSegment(segment) != PathIterator.SEG_CLOSE) {
+ minX = Math.min(minX, segment[0]);
+ maxX = Math.max(maxX, segment[0]);
+ minY = Math.min(minY, segment[1]);
+ maxY = Math.max(maxY, segment[1]);
+ }
+ pathIter.next();
+ }
+
+ maxX = Math.min(originalModel.getWidth(), maxX);
+ maxY = Math.min(originalModel.getHeight(), maxY);
+ minX = Math.max(0.0, minX);
+ minY = Math.max(0.0, minY);
+
+ Double scale = Math.max(originalModel.getHeight(), originalModel.getWidth()) / (originalModel.getTileSize());
+
+ for (int i = level; i > Configuration.MIN_ZOOM_LEVEL; i--) {
+ scale /= 2;
+ }
+
+ ColorExtractor colorExtractor = getUserService().getColorExtractorForUser(user);
+
+ Params params = new Params().//
+ x(minX).//
+ y(minY).//
+ height((maxY - minY) / scale).//
+ width((maxX - minX) / scale).//
+ level(level - Configuration.MIN_ZOOM_LEVEL).//
+ nested(false).// automatically set nested view as invalid
+ scale(scale).//
+ colorExtractor(colorExtractor).//
+ sbgn(topModel.getProject().isSbgnFormat()).//
+ model(colorModel);
+ if (overlay != null) {
+ params.nested(overlay.isHierarchicalView());
+ }
+ List<Integer> visibleLayoutIds = deserializeIdList(overlayIds);
+ for (Integer integer : visibleLayoutIds) {
+ Map<Object, ColorSchema> map = layoutService.getElementsForLayout(colorModel, integer, token);
+ params.addVisibleLayout(map);
+ }
+
+ ImageGenerators imageGenerator = new ImageGenerators();
+ String extension = imageGenerator.getExtension(handlerClass);
+ File file = File.createTempFile("map", "." + extension);
+
+ imageGenerator.generate(handlerClass, params, file.getAbsolutePath());
+
+ UploadedFileEntry entry = new UploadedFileEntry();
+ entry.setOriginalFileName("map." + extension);
+ entry.setFileContent(IOUtils.toByteArray(new FileInputStream(file)));
+ entry.setLength(entry.getFileContent().length);
+ file.delete();
+ return entry;
+
+ }
+
+ private Path2D stringToPolygon(String polygonString, Model colorModel) {
+ String[] stringPointArray = polygonString.split(";");
+
+ List<Point2D> points = new ArrayList<>();
+ for (String string : stringPointArray) {
+ if (!string.trim().equals("")) {
+ double x = Double.valueOf(string.split(",")[0]);
+ double y = Double.valueOf(string.split(",")[1]);
+ points.add(new Point2D.Double(x, y));
+ }
+ }
+
+ if (points.size() <= 2) {
+ points.clear();
+ points.add(new Point2D.Double(0, 0));
+ points.add(new Point2D.Double(colorModel.getWidth(), 0));
+ points.add(new Point2D.Double(colorModel.getWidth(), colorModel.getHeight()));
+ points.add(new Point2D.Double(0, colorModel.getHeight()));
+ }
+
+ Path2D polygon = new Path2D.Double();
+ polygon.moveTo(points.get(0).getX(), points.get(0).getY());
+ for (int i = 1; i < points.size(); i++) {
+ Point2D point = points.get(i);
+ polygon.lineTo(point.getX(), point.getY());
+ }
+ polygon.closePath();
+ return polygon;
+ }
+
+ private List<Integer> deserializeIdList(String overlayIds) {
+ List<Integer> result = new ArrayList<>();
+ String[] tmp = overlayIds.split(",");
+ for (String string : tmp) {
+ if (!string.equals("")) {
+ result.add(Integer.valueOf(string));
+ }
+ }
+ return result;
+ }
+
+ public FileEntry getModelAsModelFile(String token, String projectId, String modelId, String handlerClass,
+ String backgroundOverlayId, String overlayIds, String zoomLevel, String polygonString)
+ throws SecurityException, QueryException, IOException, InvalidColorSchemaException, CommandExecutionException,
+ ConverterException, InconsistentModelException {
+ User user = getUserService().getUserByToken(token);
+ Model topModel = getModelService().getLastModelByProjectId(projectId, token);
+ if (topModel == null) {
+ throw new ObjectNotFoundException("Project with given id doesn't exist");
+ }
+
+ Model originalModel = topModel.getSubmodelById(modelId);
+
+ if (originalModel == null) {
+ throw new ObjectNotFoundException("Model with given id doesn't exist");
+ }
+
+ Path2D polygon = stringToPolygon(polygonString, originalModel);
+
+ // create model bounded by the polygon
+ SubModelCommand subModelCommand = new SubModelCommand(originalModel, polygon);
+ Model part = subModelCommand.execute();
+
+ // Get list of overlay ids
+ String[] overlayIdsList;
+ if (overlayIds == null || overlayIds.trim().isEmpty()) {
+ overlayIdsList = new String[0];
+ } else {
+ overlayIdsList = overlayIds.split(",");
+ }
+ // Remove all colors
+ if (overlayIdsList.length > 0) {
+
+ for (Element element : part.getElements()) {
+ element.setColor(Color.WHITE);
+ }
+ }
+ // Color with overlays
+ for (String overlayId : overlayIdsList) {
+ Layout overlay = layoutService.getLayoutById(Integer.parseInt(overlayId.trim()), token);
+
+ ColorSchemaReader reader = new ColorSchemaReader();
+ Collection<ColorSchema> schemas = reader.readColorSchema(overlay.getInputData().getFileContent());
+
+ new ColorModelCommand(part, schemas, getUserService().getColorExtractorForUser(user)).execute();
+ }
+
+ IConverter parser = getModelParser(handlerClass);
+ InputStream is = parser.exportModelToInputStream(part);
+
+ String fileExtension = parser.getFileExtension();
+
+ UploadedFileEntry entry = new UploadedFileEntry();
+ entry.setOriginalFileName("model." + fileExtension);
+ entry.setFileContent(IOUtils.toByteArray(is));
+ entry.setLength(entry.getFileContent().length);
+ return entry;
+
+ }
+
+ public Map<String, Object> getStatistics(String projectId, String token)
+ throws SecurityException, ObjectNotFoundException {
+ Map<String, Object> result = new TreeMap<>();
+
+ Map<MiriamType, Integer> elementAnnotations = new TreeMap<>();
+ for (MiriamType mt : MiriamType.values()) {
+ elementAnnotations.put(mt, 0);
+ }
+ List<Model> models = super.getModels(projectId, "*", token);
+
+ for (Model model2 : models) {
+ for (Element alias : model2.getElements()) {
+ for (MiriamData md : alias.getMiriamData()) {
+ Integer amount = elementAnnotations.get(md.getDataType());
+ amount += 1;
+ elementAnnotations.put(md.getDataType(), amount);
+ }
+ }
+ }
+ result.put("elementAnnotations", elementAnnotations);
+
+ Map<MiriamType, Integer> reactionAnnotations = new TreeMap<>();
+ for (MiriamType mt : MiriamType.values()) {
+ reactionAnnotations.put(mt, 0);
+ }
+ for (Model model2 : models) {
+ for (Reaction reaction : model2.getReactions()) {
+ for (MiriamData md : reaction.getMiriamData()) {
+ Integer amount = reactionAnnotations.get(md.getDataType());
+ amount += 1;
+ reactionAnnotations.put(md.getDataType(), amount);
+ }
+ }
+ }
+
+ result.put("reactionAnnotations", reactionAnnotations);
+
+ result.put("publications", publicationsRestImpl.getPublications(models).size());
+
+ return result;
+ }
+
+ public List<Map<String, Object>> getProjects(String token) throws SecurityException {
+ List<Project> projects = getProjectService().getAllProjects(token);
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (Project project : projects) {
+ result.add(createData(project));
+ }
+ return result;
+ }
+
+ public Map<String, Object> updateProject(String token, String projectId, Map<String, Object> data)
+ throws SecurityException, QueryException {
+ Project project = getProjectService().getProjectByProjectId(projectId, token);
+ if (project == null) {
+ throw new ObjectNotFoundException("Project with given id doesn't exist");
+ }
+ boolean canModify = getUserService().userHasPrivilege(token, PrivilegeType.PROJECT_MANAGEMENT);
+ if (!canModify) {
+ throw new SecurityException("You cannot update projects");
+ }
+ Set<String> fields = data.keySet();
+ for (String fieldName : fields) {
+ Object value = data.get(fieldName);
+ String stringValue = null;
+ if (value instanceof String) {
+ stringValue = (String) value;
+ }
+ if (fieldName.equalsIgnoreCase("version")) {
+ project.setVersion((String) value);
+ } else if (fieldName.equalsIgnoreCase("id")) {
+ try {
+ int id = Integer.parseInt(stringValue);
+ if (id != project.getId()) {
+ throw new QueryException("Invalid id: " + stringValue);
+ }
+ } catch (NumberFormatException e) {
+ throw new QueryException("Invalid id: " + stringValue);
+ }
+ } else if (fieldName.equalsIgnoreCase("projectId")) {
+ if (!project.getProjectId().equalsIgnoreCase(stringValue)) {
+ throw new QueryException("You cannot modify projectId");
+ }
+ } else if (fieldName.equalsIgnoreCase("name")) {
+ project.setName((String) value);
+ } else if (fieldName.equalsIgnoreCase("notifyEmail")) {
+ project.setNotifyEmail(stringValue);
+ } else if (fieldName.equalsIgnoreCase("organism")) {
+ MiriamData organism = updateMiriamData(project.getOrganism(), value);
+ project.setOrganism(organism);
+ } else if (fieldName.equalsIgnoreCase("disease")) {
+ MiriamData disease = updateMiriamData(project.getDisease(), value);
+ project.setDisease(disease);
+ } else if (fieldName.equalsIgnoreCase("mapCanvasType")) {
+ MapCanvasType mapCanvasType;
+ try {
+ mapCanvasType = MapCanvasType.valueOf(stringValue);
+ } catch (Exception e) {
+ throw new QueryException("Invalid mapCanvasType value");
+ }
+ project.setMapCanvasType(mapCanvasType);
+ } else {
+ throw new QueryException("Unknown field: " + fieldName);
+ }
+ }
+ getProjectService().updateProject(project, token);
+ return getProject(projectId, token);
+ }
+
+ private MiriamData updateMiriamData(MiriamData organism, Object res) {
+ if (res == null) {
+ return null;
+ }
+ if (organism == null) {
+ organism = new MiriamData();
+ }
+
+ if (res instanceof Map) {
+ @SuppressWarnings("unchecked")
+ Map<String, Object> map = (Map<String, Object>) res;
+ organism.setDataType(MiriamType.valueOf((String) map.get("type")));
+ organism.setResource((String) map.get("resource"));
+ return organism;
+ } else {
+ throw new InvalidArgumentException("invalid miriamdData: " + res);
+ }
+ }
+
+ public Map<String, Object> addProject(String token, String projectId, MultiValueMap<String, Object> data, String path)
+ throws SecurityException, QueryException, IOException {
+ User user = getUserService().getUserByToken(token);
+ Project project = getProjectService().getProjectByProjectId(projectId, token);
+ if (project != null) {
+ logger.debug(project.getProjectId());
+ throw new ObjectExistsException("Project with given id already exists");
+ }
+ CreateProjectParams params = new CreateProjectParams();
+ String directory = computePathForProject(projectId, path);
+ String fileId = getFirstValue(data.get("file-id"));
+ if (fileId == null) {
+ throw new QueryException("file-id is obligatory");
+ }
+ UploadedFileEntry file = uploadedFileEntryDao.getById(Integer.valueOf(fileId));
+ if (file == null) {
+ throw new QueryException("Invalid file id: " + fileId);
+ }
+ if (file.getOwner() == null || !file.getOwner().getLogin().equals(user.getLogin())) {
+ throw new SecurityException("Access denied to source file");
+ }
+ String parserClass = getFirstValue(data.get("parser"));
+ if (parserClass == null) {
+ throw new QueryException("parser is obligatory");
+ }
+ IConverter parser = getModelParser(parserClass);
+
+ List<ZipEntryFile> zipEntries = extractZipEntries(data);
+ params.complex(zipEntries.size() > 0);
+ for (ZipEntryFile entry : zipEntries) {
+ params.addZipEntry(entry);
+ }
+
+ params.addUser(user.getLogin(), null);
+ params.async(true);
+ params.parser(parser);
+ params.authenticationToken(token);
+ params.autoResize(getFirstValue(data.get("auto-resize")));
+ params.cacheModel(getFirstValue(data.get("cache")));
+ params.description(getFirstValue(data.get("description")));
+ params.images(true);
+ params.notifyEmail(getFirstValue(data.get("notify-email")));
+ params.projectDir(directory);
+ params.projectDisease(getFirstValue(data.get("disease")));
+ params.projectFile(new ByteArrayInputStream(file.getFileContent()));
+ params.projectId(projectId);
+ params.projectName(getFirstValue(data.get("name")));
+ params.projectOrganism(getFirstValue(data.get("organism")));
+ params.sbgnFormat(getFirstValue(data.get("sbgn")));
+ params.semanticZoom(getFirstValue(data.get("semantic-zoom")));
+ params.semanticZoomContainsMultipleLayouts(getFirstValue(data.get("semantic-zoom-contains-multiple-layouts")));
+ params.version(getFirstValue(data.get("version")));
+ params.annotations(getFirstValue(data.get("annotate")));
+ MapCanvasType mapCanvasType;
+ try {
+ mapCanvasType = MapCanvasType.valueOf(getFirstValue(data.get("mapCanvasType")));
+ } catch (Exception e) {
+ throw new QueryException("Invalid mapCanvasType value");
+ }
+ params.mapCanvasType(mapCanvasType);
+
+ if (params.isUpdateAnnotations()) {
+ params.annotatorsMap(projectService.createClassAnnotatorTree(user));
+ }
+ params.analyzeAnnotations(getFirstValue(data.get("verify-annotations")));
+ if (params.isAnalyzeAnnotations()) {
+ params.requiredAnnotations(projectService.createClassAnnotatorTree(user));
+ params.validAnnotations(projectService.createClassAnnotatorTree(user));
+ }
+ params.setAnnotatorParams(projectService.getAnnotatorsParams(user));
+
+ getProjectService().createProject(params);
+ return getProject(projectId, token);
+ }
+
+ protected String computePathForProject(String projectId, String path) {
+ long id = projectDao.getNextId();
+ return path + "/../map_images/" + md5(projectId + "-" + id) + "/";
+ }
+
+ protected List<ZipEntryFile> extractZipEntries(MultiValueMap<String, Object> data) {
+ int fileIndex = 0;
+ List<ZipEntryFile> result = new ArrayList<>();
+ while (data.get("zip-entries[" + fileIndex + "][_filename]") != null) {
+ ZipEntryFile entry = null;
+ String entryType = (String) data.get("zip-entries[" + fileIndex + "][_type]").get(0);
+ String filename = (String) data.get("zip-entries[" + fileIndex + "][_filename]").get(0);
+ if ("MAP".equalsIgnoreCase(entryType)) {
+ String submodelTypeKey = "zip-entries[" + fileIndex + "][_data][type][id]";
+ String rootKey = "zip-entries[" + fileIndex + "][_data][root]";
+ String mappingKey = "zip-entries[" + fileIndex + "][_data][mapping]";
+ SubmodelType mapType = SubmodelType.valueOf((String) data.get(submodelTypeKey).get(0));
+ String name = (String) data.get("zip-entries[" + fileIndex + "][_data][name]").get(0);
+ Boolean root = getBoolValue(data.get(rootKey), false);
+ Boolean mapping = getBoolValue(data.get(mappingKey), false);
+
+ entry = new ModelZipEntryFile(filename, name, root, mapping, mapType);
+ } else if ("OVERLAY".equalsIgnoreCase(entryType)) {
+ String name = (String) data.get("zip-entries[" + fileIndex + "][_data][name]").get(0);
+ String description = (String) data.get("zip-entries[" + fileIndex + "][_data][description]").get(0);
+ entry = new LayoutZipEntryFile(filename, name, description);
+ } else if ("IMAGE".equalsIgnoreCase(entryType)) {
+ entry = new ImageZipEntryFile(filename);
+ } else {
+ throw new Error("Unknown entry type: " + entryType);
+ }
+ fileIndex++;
+ result.add(entry);
+
+ }
+ return result;
+ }
+
+ private Boolean getBoolValue(List<Object> list, boolean defaultValue) {
+ if (list == null) {
+ return defaultValue;
+ }
+ Object obj = list.get(0);
+ if (obj instanceof Boolean) {
+ return (Boolean) list.get(0);
+ } else {
+ return "true".equalsIgnoreCase((String) obj);
+ }
+ }
+
+ /**
+ * Method that computes md5 hash for a given {@link String}.
+ *
+ * @param data
+ * input string
+ * @return md5 hash for input string
+ */
+ private String md5(String data) {
+ try {
+ MessageDigest md = MessageDigest.getInstance("MD5");
+ byte[] mdbytes = md.digest(data.getBytes());
+ StringBuffer sb = new StringBuffer();
+ for (int i = 0; i < mdbytes.length; i++) {
+ // CHECKSTYLE:OFF
+ // this magic formula transforms integer into hex value
+ sb.append(Integer.toString((mdbytes[i] & 0xff) + 0x100, 16).substring(1));
+ // CHECKSTYLE:ON
+ }
+ return sb.toString();
+ } catch (NoSuchAlgorithmException e) {
+ logger.fatal("Problem with instance of MD5 encoder", e);
+ }
+
+ return null;
+ }
+
+ public Map<String, Object> removeProject(String token, String projectId, String path)
+ throws SecurityException, QueryException {
+ Project project = getProjectService().getProjectByProjectId(projectId, token);
+ if (getConfigurationService().getConfigurationValue(ConfigurationElementType.DEFAULT_MAP).equals(project.getProjectId())) {
+ throw new QueryException("You cannot remove default map");
+ }
+ getProjectService().removeProject(project, path, true, token);
+ return getProject(projectId, token);
+ }
+
+ public UploadedFileEntryDao getUploadedFileEntryDao() {
+ return uploadedFileEntryDao;
+ }
+
+ public void setUploadedFileEntryDao(UploadedFileEntryDao uploadedFileEntryDao) {
+ this.uploadedFileEntryDao = uploadedFileEntryDao;
+ }
+
+ private enum LogSortColumn {
+ ID("id"), //
+ CONTENT("content"); //
+
+ private String commonName;
+
+ LogSortColumn(String commonName) {
+ this.commonName = commonName;
+ }
+ }
+
+ private class LogEntry implements Serializable {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ public LogEntry(int id, String content, String level) {
+ this.id = id;
+ this.content = content;
+ this.level = level;
+ }
+
+ public Integer id;
+ public String content;
+ public String level;
+ }
+
+ public Map<String, Object> getLogs(String projectId, String level, String token, String startString, Integer length,
+ String sortColumn, String sortOrder, String search) throws SecurityException, QueryException {
+ Project project = getProjectService().getProjectByProjectId(projectId, token);
+ if (project == null) {
+ throw new ObjectNotFoundException("Project with given id doesn't exist");
+ }
+
+ LogSortColumn sortColumnEnum = getSortOrderColumn(sortColumn);
+ Comparator<LogEntry> comparator = getComparatorForColumn(sortColumnEnum, sortOrder);
+
+ Integer start = Math.max(0, Integer.valueOf(startString));
+ List<LogEntry> resultList = new ArrayList<>();
+
+ List<LogEntry> logEntries = getEntries(project, level);
+
+ List<LogEntry> filteredList = new ArrayList<>();
+
+ search = search.toLowerCase();
+ for (LogEntry entry : logEntries) {
+ if (isSearchResult(entry, search)) {
+ filteredList.add(entry);
+ }
+ }
+ if (comparator != null) {
+ filteredList.sort(comparator);
+ }
+
+ int index = 0;
+ for (LogEntry entry : filteredList) {
+ if (index >= start && index < start + length) {
+ resultList.add(entry);
+ }
+ index++;
+ }
+
+ Map<String, Object> result = new TreeMap<>();
+ result.put("data", resultList);
+ result.put("totalSize", logEntries.size());
+ result.put("filteredSize", filteredList.size());
+ result.put("start", start);
+ result.put("length", resultList.size());
+ return result;
+
+ }
+
+ private boolean isSearchResult(LogEntry entry, String search) {
+ if (search == null || search.isEmpty()) {
+ return true;
+ }
+ if (entry.content.toLowerCase().contains(search) || entry.id.toString().contains(search)) {
+ return true;
+ }
+
+ return false;
+
+ }
+
+ private List<LogEntry> getEntries(Project project, String level) {
+ List<LogEntry> result = new ArrayList<>();
+ int id = 0;
+ for (String s : project.getWarnings()) {
+ if (!s.isEmpty()) {
+ if (level.equalsIgnoreCase("warning") || level.equals("")) {
+ result.add(new LogEntry(id, s, "WARNING"));
+ }
+ id++;
+ }
+ }
+ String errors = project.getErrors();
+ if (errors == null) {
+ errors = "";
+ }
+ for (String s : errors.split("\n")) {
+ if (!s.isEmpty()) {
+ if (level.equalsIgnoreCase("error") || level.equals("")) {
+ result.add(new LogEntry(id, s, "ERROR"));
+ }
+ id++;
+ }
+ }
+ return result;
+ }
+
+ private Comparator<LogEntry> getComparatorForColumn(LogSortColumn sortColumnEnum, String sortOrder)
+ throws QueryException {
+ final int orderFactor;
+ if (sortOrder.toLowerCase().equals("desc")) {
+ orderFactor = -1;
+ } else {
+ orderFactor = 1;
+ }
+ if (sortColumnEnum == null) {
+ return null;
+ } else if (sortColumnEnum.equals(LogSortColumn.ID)) {
+ return new Comparator<LogEntry>() {
+ @Override
+ public int compare(LogEntry o1, LogEntry o2) {
+ return o1.id.compareTo(o2.id) * orderFactor;
+
+ }
+ };
+ } else if (sortColumnEnum.equals(LogSortColumn.CONTENT)) {
+ return new Comparator<LogEntry>() {
+ @Override
+ public int compare(LogEntry o1, LogEntry o2) {
+ return o1.content.compareTo(o2.content) * orderFactor;
+
+ }
+ };
+
+ } else {
+ throw new QueryException("Sort order not implemented for: " + sortColumnEnum);
+ }
+ }
+
+ private LogSortColumn getSortOrderColumn(String sortColumn) throws QueryException {
+ if (!sortColumn.isEmpty()) {
+ for (LogSortColumn type : LogSortColumn.values()) {
+ if (type.commonName.toLowerCase().equals(sortColumn.toLowerCase())) {
+ return type;
+ }
+ }
+ throw new QueryException("Unknown sortColumn: " + sortColumn);
+ }
+ return null;
+ }
+
+ public List<Map<String, Object>> getSubmapConnections(String token, String projectId)
+ throws ObjectNotFoundException, SecurityException {
+ List<Map<String, Object>> result = new ArrayList<>();
+ List<Model> models = getModels(projectId, "*", token);
+ List<Element> elements = new ArrayList<>();
+ for (Model model : models) {
+ elements.addAll(model.getElements());
+ }
+ elements.sort(BioEntity.ID_COMPARATOR);
+ for (Element element : elements) {
+ if (element.getSubmodel() != null) {
+ result.add(submodelConnectionToMap(element));
+ }
+ }
+ return result;
+ }
+
+ private Map<String, Object> submodelConnectionToMap(Element element) {
+ Map<String, Object> result = new TreeMap<>();
+ result.put("from", super.createMinifiedSearchResult(element));
+ Map<String, Object> to = new TreeMap<>();
+ to.put("modelId", element.getSubmodel().getSubmodel().getId());
+ result.put("to", to);
+ return result;
+ }
+
+}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalController.java
index fd5533ecfa..4b72c31db3 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalController.java
@@ -1,56 +1,56 @@
-package lcsb.mapviewer.api.projects.chemicals;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.MediaType;
-import org.springframework.web.bind.annotation.CookieValue;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RequestParam;
-import org.springframework.web.bind.annotation.RestController;
-
-import lcsb.mapviewer.annotation.services.ChemicalSearchException;
-import lcsb.mapviewer.api.BaseController;
-import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.services.SecurityException;
-
-@RestController
-public class ChemicalController extends BaseController {
-
- @Autowired
- private ChemicalRestImpl chemicalController;
-
- @RequestMapping(value = "/projects/{projectId}/chemicals:search", method = { RequestMethod.GET }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getChemicalsByQuery(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @RequestParam(value = "columns", defaultValue = "") String columns, //
- @RequestParam(value = "query", defaultValue = "") String query, //
- @RequestParam(value = "target", defaultValue = "") String target //
- ) throws SecurityException, QueryException {
- if (!query.equals("")) {
- return chemicalController.getChemicalsByQuery(token, projectId, columns, query);
- } else if (target.indexOf(":") >= 0) {
- String targetType = target.split(":", -1)[0];
- String targetId = target.split(":", -1)[1];
- return chemicalController.getChemicalsByTarget(token, projectId, targetType, targetId, columns);
- } else {
- return new ArrayList<>();
- }
- }
-
- @RequestMapping(value = "/projects/{projectId}/chemicals/suggestedQueryList", method = {
- RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<String> getSuggestedQueryList(//
- @PathVariable(value = "projectId") String projectId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token//
- ) throws SecurityException, ChemicalSearchException {
- return chemicalController.getSuggestedQueryList(projectId, token);
- }
+package lcsb.mapviewer.api.projects.chemicals;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.web.bind.annotation.CookieValue;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.RestController;
+
+import lcsb.mapviewer.annotation.services.ChemicalSearchException;
+import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.services.SecurityException;
+
+@RestController
+public class ChemicalController extends BaseController {
+
+ @Autowired
+ private ChemicalRestImpl chemicalController;
+
+ @RequestMapping(value = "/projects/{projectId}/chemicals:search", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getChemicalsByQuery(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "projectId") String projectId, //
+ @RequestParam(value = "columns", defaultValue = "") String columns, //
+ @RequestParam(value = "query", defaultValue = "") String query, //
+ @RequestParam(value = "target", defaultValue = "") String target //
+ ) throws SecurityException, QueryException {
+ if (!query.equals("")) {
+ return chemicalController.getChemicalsByQuery(token, projectId, columns, query);
+ } else if (target.indexOf(":") >= 0) {
+ String targetType = target.split(":", -1)[0];
+ String targetId = target.split(":", -1)[1];
+ return chemicalController.getChemicalsByTarget(token, projectId, targetType, targetId, columns);
+ } else {
+ return new ArrayList<>();
+ }
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/chemicals/suggestedQueryList", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<String> getSuggestedQueryList(//
+ @PathVariable(value = "projectId") String projectId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token//
+ ) throws SecurityException, ChemicalSearchException {
+ return chemicalController.getSuggestedQueryList(projectId, token);
+ }
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java
index babedeb740..3156285b77 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java
@@ -1,220 +1,220 @@
-package lcsb.mapviewer.api.projects.chemicals;
-
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeMap;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.annotation.data.Chemical;
-import lcsb.mapviewer.annotation.data.MeSH;
-import lcsb.mapviewer.annotation.services.ChemicalParser;
-import lcsb.mapviewer.annotation.services.ChemicalSearchException;
-import lcsb.mapviewer.annotation.services.MeSHParser;
-import lcsb.mapviewer.annotation.services.TaxonomyBackend;
-import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
-import lcsb.mapviewer.api.BaseRestImpl;
-import lcsb.mapviewer.api.ElementIdentifierType;
-import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.search.DbSearchCriteria;
-import lcsb.mapviewer.services.search.chemical.IChemicalService;
-
-@Transactional(value = "txManager")
-public class ChemicalRestImpl extends BaseRestImpl {
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(ChemicalRestImpl.class);
-
- @Autowired
- private IChemicalService chemicalService;
-
- @Autowired
- private ChemicalParser chemicalParser;
-
- @Autowired
- private MeSHParser meSHParser;
-
- public List<Map<String, Object>> getChemicalsByQuery(String token, String projectId, String columns, String query)
- throws SecurityException, QueryException {
- Model model = getModelService().getLastModelByProjectId(projectId, token);
- if (model == null) {
- throw new QueryException("Project with given id doesn't exist");
- }
- Project project = model.getProject();
- if (project.getDisease() == null) {
- throw new QueryException("Project doesn't have disease associated to it");
- }
-
- Set<String> columnSet = createChemicalColumnSet(columns);
-
- List<Map<String, Object>> result = new ArrayList<>();
-
- MiriamData organism = project.getOrganism();
- if (organism == null) {
- organism = TaxonomyBackend.HUMAN_TAXONOMY;
- }
- Chemical chemical = chemicalService.getByName(query,
- new DbSearchCriteria().project(project).organisms(organism).colorSet(0).disease(project.getDisease()));
- if (chemical != null) {
- List<Model> models = getModels(projectId, "*", token);
- result.add(prepareChemical(chemical, columnSet, models));
- }
-
- return result;
- }
-
- protected Map<String, Object> prepareChemical(Chemical chemical, Set<String> columnsSet, List<Model> models) {
- Map<String, Object> result = new TreeMap<>();
-
- String description = "Mesh term not available";
- List<String> synonyms = new ArrayList<>();
-
- try {
- MeSH mesh = meSHParser.getMeSH(chemical.getChemicalId());
- if (mesh != null) {
- description = mesh.getDescription();
- synonyms = mesh.getSynonyms();
- } else {
- logger.warn("Mesh used by chemical is invalid: " + chemical.getChemicalId());
- }
- } catch (AnnotatorException e) {
- logger.error("Problem with accessing mesh database", e);
- }
-
- for (String string : columnsSet) {
- String column = string.toLowerCase();
- Object value = null;
- if (column.equals("id") || column.equals("idobject")) {
- value = chemical.getChemicalId();
- } else if (column.equals("name")) {
- value = chemical.getChemicalName();
- } else if (column.equals("references")) {
- List<Map<String, Object>> references = new ArrayList<>();
- references.add(createAnnotation(chemical.getChemicalId()));
- if (chemical.getCasID() != null) {
- references.add(createAnnotation(chemical.getCasID()));
- }
- value = references;
- } else if (column.equals("directevidencereferences")) {
- value = createAnnotations(chemical.getDirectEvidencePublication());
- } else if (column.equals("description")) {
- value = description;
- } else if (column.equals("directevidence")) {
- if (chemical.getDirectEvidence() != null) {
- value = chemical.getDirectEvidence().getValue();
- }
- } else if (column.equals("synonyms")) {
- value = synonyms;
- } else if (column.equals("targets")) {
- value = prepareTargets(chemical.getInferenceNetwork(), models);
- } else {
- value = "Unknown column";
- }
- result.put(string, value);
- }
- return result;
- }
-
- protected Set<String> createChemicalColumnSet(String columns) {
- Set<String> columnsSet = new HashSet<>();
- if (columns.equals("")) {
- columnsSet.add("name");
- columnsSet.add("references");
- columnsSet.add("description");
- columnsSet.add("synonyms");
- columnsSet.add("id");
- columnsSet.add("directEvidenceReferences");
- columnsSet.add("directEvidence");
- columnsSet.add("targets");
- } else {
- for (String str : columns.split(",")) {
- columnsSet.add(str);
- }
- }
- return columnsSet;
- }
-
- /**
- * @return the chemicalService
- * @see #chemicalService
- */
- public IChemicalService getChemicalService() {
- return chemicalService;
- }
-
- /**
- * @param chemicalService
- * the chemicalService to set
- * @see #chemicalService
- */
- public void setChemicalService(IChemicalService chemicalService) {
- this.chemicalService = chemicalService;
- }
-
- public List<Map<String, Object>> getChemicalsByTarget(String token, String projectId, String targetType,
- String targetId, String columns) throws SecurityException, QueryException {
- Model model = getModelService().getLastModelByProjectId(projectId, token);
- if (model == null) {
- throw new QueryException("Project with given id doesn't exist");
- }
- Project project = model.getProject();
-
- if (project.getDisease() == null) {
- throw new QueryException("Project doesn't have disease associated to it");
- }
-
- List<Model> models = getModels(projectId, "*", token);
- Element element = null;
-
- Integer dbId = Integer.valueOf(targetId);
- List<Element> targets = new ArrayList<>();
- if (targetType.equals(ElementIdentifierType.ALIAS.getJsName())) {
- for (Model m : models) {
- if (element == null) {
- element = m.getElementByDbId(dbId);
- }
- }
- if (element == null) {
- throw new QueryException("Invalid element identifier for given project");
- }
- targets.add(element);
- } else {
- throw new QueryException("Targeting for the type not implemented");
- }
- MiriamData organism = project.getOrganism();
- if (organism == null) {
- organism = TaxonomyBackend.HUMAN_TAXONOMY;
- }
-
- Set<String> columnSet = createChemicalColumnSet(columns);
-
- List<Chemical> chemicals = chemicalService.getForTargets(targets,
- new DbSearchCriteria().project(project).organisms(organism).disease(project.getDisease()));
-
- List<Map<String, Object>> result = new ArrayList<>();
-
- for (Chemical chemical : chemicals) {
- result.add(prepareChemical(chemical, columnSet, models));
- }
-
- return result;
- }
-
- public List<String> getSuggestedQueryList(String projectId, String token)
- throws SecurityException, ChemicalSearchException {
- Project project = getProjectService().getProjectByProjectId(projectId, token);
- return chemicalParser.getSuggestedQueryList(project, project.getDisease());
- }
-}
+package lcsb.mapviewer.api.projects.chemicals;
+
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeMap;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.annotation.data.Chemical;
+import lcsb.mapviewer.annotation.data.MeSH;
+import lcsb.mapviewer.annotation.services.ChemicalParser;
+import lcsb.mapviewer.annotation.services.ChemicalSearchException;
+import lcsb.mapviewer.annotation.services.MeSHParser;
+import lcsb.mapviewer.annotation.services.TaxonomyBackend;
+import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
+import lcsb.mapviewer.api.BaseRestImpl;
+import lcsb.mapviewer.api.ElementIdentifierType;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.search.DbSearchCriteria;
+import lcsb.mapviewer.services.search.chemical.IChemicalService;
+
+@Transactional(value = "txManager")
+public class ChemicalRestImpl extends BaseRestImpl {
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(ChemicalRestImpl.class);
+
+ @Autowired
+ private IChemicalService chemicalService;
+
+ @Autowired
+ private ChemicalParser chemicalParser;
+
+ @Autowired
+ private MeSHParser meSHParser;
+
+ public List<Map<String, Object>> getChemicalsByQuery(String token, String projectId, String columns, String query)
+ throws SecurityException, QueryException {
+ Model model = getModelService().getLastModelByProjectId(projectId, token);
+ if (model == null) {
+ throw new QueryException("Project with given id doesn't exist");
+ }
+ Project project = model.getProject();
+ if (project.getDisease() == null) {
+ throw new QueryException("Project doesn't have disease associated to it");
+ }
+
+ Set<String> columnSet = createChemicalColumnSet(columns);
+
+ List<Map<String, Object>> result = new ArrayList<>();
+
+ MiriamData organism = project.getOrganism();
+ if (organism == null) {
+ organism = TaxonomyBackend.HUMAN_TAXONOMY;
+ }
+ Chemical chemical = chemicalService.getByName(query,
+ new DbSearchCriteria().project(project).organisms(organism).colorSet(0).disease(project.getDisease()));
+ if (chemical != null) {
+ List<Model> models = getModels(projectId, "*", token);
+ result.add(prepareChemical(chemical, columnSet, models));
+ }
+
+ return result;
+ }
+
+ protected Map<String, Object> prepareChemical(Chemical chemical, Set<String> columnsSet, List<Model> models) {
+ Map<String, Object> result = new TreeMap<>();
+
+ String description = "Mesh term not available";
+ List<String> synonyms = new ArrayList<>();
+
+ try {
+ MeSH mesh = meSHParser.getMeSH(chemical.getChemicalId());
+ if (mesh != null) {
+ description = mesh.getDescription();
+ synonyms = mesh.getSynonyms();
+ } else {
+ logger.warn("Mesh used by chemical is invalid: " + chemical.getChemicalId());
+ }
+ } catch (AnnotatorException e) {
+ logger.error("Problem with accessing mesh database", e);
+ }
+
+ for (String string : columnsSet) {
+ String column = string.toLowerCase();
+ Object value = null;
+ if (column.equals("id") || column.equals("idobject")) {
+ value = chemical.getChemicalId();
+ } else if (column.equals("name")) {
+ value = chemical.getChemicalName();
+ } else if (column.equals("references")) {
+ List<Map<String, Object>> references = new ArrayList<>();
+ references.add(createAnnotation(chemical.getChemicalId()));
+ if (chemical.getCasID() != null) {
+ references.add(createAnnotation(chemical.getCasID()));
+ }
+ value = references;
+ } else if (column.equals("directevidencereferences")) {
+ value = createAnnotations(chemical.getDirectEvidencePublication());
+ } else if (column.equals("description")) {
+ value = description;
+ } else if (column.equals("directevidence")) {
+ if (chemical.getDirectEvidence() != null) {
+ value = chemical.getDirectEvidence().getValue();
+ }
+ } else if (column.equals("synonyms")) {
+ value = synonyms;
+ } else if (column.equals("targets")) {
+ value = prepareTargets(chemical.getInferenceNetwork(), models);
+ } else {
+ value = "Unknown column";
+ }
+ result.put(string, value);
+ }
+ return result;
+ }
+
+ protected Set<String> createChemicalColumnSet(String columns) {
+ Set<String> columnsSet = new HashSet<>();
+ if (columns.equals("")) {
+ columnsSet.add("name");
+ columnsSet.add("references");
+ columnsSet.add("description");
+ columnsSet.add("synonyms");
+ columnsSet.add("id");
+ columnsSet.add("directEvidenceReferences");
+ columnsSet.add("directEvidence");
+ columnsSet.add("targets");
+ } else {
+ for (String str : columns.split(",")) {
+ columnsSet.add(str);
+ }
+ }
+ return columnsSet;
+ }
+
+ /**
+ * @return the chemicalService
+ * @see #chemicalService
+ */
+ public IChemicalService getChemicalService() {
+ return chemicalService;
+ }
+
+ /**
+ * @param chemicalService
+ * the chemicalService to set
+ * @see #chemicalService
+ */
+ public void setChemicalService(IChemicalService chemicalService) {
+ this.chemicalService = chemicalService;
+ }
+
+ public List<Map<String, Object>> getChemicalsByTarget(String token, String projectId, String targetType,
+ String targetId, String columns) throws SecurityException, QueryException {
+ Model model = getModelService().getLastModelByProjectId(projectId, token);
+ if (model == null) {
+ throw new QueryException("Project with given id doesn't exist");
+ }
+ Project project = model.getProject();
+
+ if (project.getDisease() == null) {
+ throw new QueryException("Project doesn't have disease associated to it");
+ }
+
+ List<Model> models = getModels(projectId, "*", token);
+ Element element = null;
+
+ Integer dbId = Integer.valueOf(targetId);
+ List<Element> targets = new ArrayList<>();
+ if (targetType.equals(ElementIdentifierType.ALIAS.getJsName())) {
+ for (Model m : models) {
+ if (element == null) {
+ element = m.getElementByDbId(dbId);
+ }
+ }
+ if (element == null) {
+ throw new QueryException("Invalid element identifier for given project");
+ }
+ targets.add(element);
+ } else {
+ throw new QueryException("Targeting for the type not implemented");
+ }
+ MiriamData organism = project.getOrganism();
+ if (organism == null) {
+ organism = TaxonomyBackend.HUMAN_TAXONOMY;
+ }
+
+ Set<String> columnSet = createChemicalColumnSet(columns);
+
+ List<Chemical> chemicals = chemicalService.getForTargets(targets,
+ new DbSearchCriteria().project(project).organisms(organism).disease(project.getDisease()));
+
+ List<Map<String, Object>> result = new ArrayList<>();
+
+ for (Chemical chemical : chemicals) {
+ result.add(prepareChemical(chemical, columnSet, models));
+ }
+
+ return result;
+ }
+
+ public List<String> getSuggestedQueryList(String projectId, String token)
+ throws SecurityException, ChemicalSearchException {
+ Project project = getProjectService().getProjectByProjectId(projectId, token);
+ return chemicalParser.getSuggestedQueryList(project, project.getDisease());
+ }
+}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/comments/CommentController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/comments/CommentController.java
index f2c2cd8bdc..512d760e82 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/comments/CommentController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/comments/CommentController.java
@@ -1,183 +1,183 @@
-package lcsb.mapviewer.api.projects.comments;
-
-import java.awt.geom.Point2D;
-import java.io.IOException;
-import java.util.List;
-import java.util.Map;
-
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.MediaType;
-import org.springframework.web.bind.annotation.CookieValue;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestBody;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RequestParam;
-import org.springframework.web.bind.annotation.RestController;
-
-import com.fasterxml.jackson.core.JsonParseException;
-import com.fasterxml.jackson.databind.JsonMappingException;
-
-import lcsb.mapviewer.api.BaseController;
-import lcsb.mapviewer.api.ElementIdentifierType;
-import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.services.SecurityException;
-
-@RestController
-public class CommentController extends BaseController {
-
- @Autowired
- private CommentRestImpl commentController;
-
- @RequestMapping(value = "/projects/{projectId}/comments/models/{modelId}/", method = {
- RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getComments(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @RequestParam(value = "columns", defaultValue = "") String columns, //
- @RequestParam(value = "removed", defaultValue = "") String removed //
- ) throws SecurityException, QueryException {
- return commentController.getCommentList(token, projectId, columns, "", "", removed);
- }
-
- @RequestMapping(value = "/projects/{projectId}/comments/{commentId}/", method = { RequestMethod.DELETE }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> removeComment(//
- @RequestBody(required = false) String body, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "commentId") String commentId //
- ) throws SecurityException, QueryException, JsonParseException, JsonMappingException, IOException {
- Map<String, Object> node = parseBody(body);
- String reason = (String) node.get("reason");
- return commentController.removeComment(token, projectId, commentId, reason);
- }
-
- @RequestMapping(value = "/projects/{projectId}/comments/models/{modelId}/bioEntities/reactions/{reactionId}", method = {
- RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getCommentsByReaction(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @RequestParam(value = "columns", defaultValue = "") String columns, //
- @PathVariable(value = "reactionId") String reactionId, //
- @RequestParam(value = "removed", defaultValue = "") String removed //
- ) throws SecurityException, QueryException {
- return commentController.getCommentList(token, projectId, columns, reactionId,
- ElementIdentifierType.REACTION.getJsName(), removed);
- }
-
- @RequestMapping(value = "/projects/{projectId}/comments/models/{modelId}/bioEntities/elements/{elementId}", method = {
- RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getCommentsByElement(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @RequestParam(value = "columns", defaultValue = "") String columns, //
- @PathVariable(value = "elementId") String elementId, //
- @RequestParam(value = "removed", defaultValue = "") String removed //
- ) throws SecurityException, QueryException {
- return commentController.getCommentList(token, projectId, columns, elementId,
- ElementIdentifierType.ALIAS.getJsName(), removed);
- }
-
- @RequestMapping(value = "/projects/{projectId}/comments/models/{modelId}/points/{coordinates:.+}", method = {
- RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getCommentsByPoint(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @RequestParam(value = "columns", defaultValue = "") String columns, //
- @PathVariable(value = "coordinates") String coordinates, //
- @RequestParam(value = "removed", defaultValue = "") String removed //
- ) throws SecurityException, QueryException {
- return commentController.getCommentList(token, projectId, columns, coordinates,
- ElementIdentifierType.POINT.getJsName(), removed);
- }
-
- @RequestMapping(value = "/projects/{projectId}/comments/models/{modelId}/bioEntities/elements/{elementId}", method = {
- RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> addCommentForElement(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "elementId") String elementId, //
- @RequestParam(value = "name") String name, //
- @RequestParam(value = "email") String email, //
- @RequestParam(value = "content") String content, //
- @RequestParam(value = "pinned", defaultValue = "true") String pinned, //
- @RequestParam(value = "coordinates") String coordinates, //
- @PathVariable(value = "modelId") String modelId //
- ) throws SecurityException, QueryException {
- Point2D pointCoordinates = parseCoordinates(coordinates);
- return commentController.addComment(token, projectId, ElementIdentifierType.ALIAS.getJsName(), elementId, name,
- email, content, pinned.toLowerCase().equals("true"), pointCoordinates, modelId);
- }
-
- @RequestMapping(value = "/projects/{projectId}/comments/models/{modelId}/bioEntities/reactions/{reactionId}", method = {
- RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> addCommentForReaction(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "reactionId") String reactionId, //
- @RequestParam(value = "name") String name, //
- @RequestParam(value = "email") String email, //
- @RequestParam(value = "content") String content, //
- @RequestParam(value = "pinned", defaultValue = "true") String pinned, //
- @RequestParam(value = "coordinates") String coordinates, //
- @PathVariable(value = "modelId") String modelId //
- ) throws SecurityException, QueryException {
- Point2D pointCoordinates = parseCoordinates(coordinates);
- return commentController.addComment(token, projectId, ElementIdentifierType.REACTION.getJsName(), reactionId, name,
- email, content, pinned.toLowerCase().equals("true"), pointCoordinates, modelId);
- }
-
- @RequestMapping(value = "/projects/{projectId}/comments/models/{modelId}/points/{coordinates}", method = {
- RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> addCommentForPoint(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @RequestParam(value = "name") String name, //
- @RequestParam(value = "email") String email, //
- @RequestParam(value = "content") String content, //
- @RequestParam(value = "pinned", defaultValue = "true") String pinned, //
- @PathVariable(value = "coordinates") String coordinates, //
- @PathVariable(value = "modelId") String modelId //
- ) throws SecurityException, QueryException {
- Point2D pointCoordinates = parseCoordinates(coordinates);
- return commentController.addComment(token, projectId, ElementIdentifierType.POINT.getJsName(), coordinates, name,
- email, content, pinned.toLowerCase().equals("true"), pointCoordinates, modelId);
- }
-
- private Point2D parseCoordinates(String coordinates) throws QueryException {
- String[] tmp = coordinates.split(",");
- if (tmp.length != 2) {
- throw new QueryException("Coordinates must be in the format: 'xxx.xx,yyy.yy'");
- }
- Double x = null;
- Double y = null;
- try {
- x = Double.valueOf(tmp[0]);
- y = Double.valueOf(tmp[1]);
- } catch (NumberFormatException e) {
- throw new QueryException("Coordinates must be in the format: 'xxx.xx,yyy.yy'", e);
- }
- Point2D pointCoordinates = new Point2D.Double(x, y);
- return pointCoordinates;
- }
-
- /**
- * @return the overlayController
- * @see #commentController
- */
- public CommentRestImpl getOverlayController() {
- return commentController;
- }
-
- /**
- * @param overlayController
- * the overlayController to set
- * @see #commentController
- */
- public void setOverlayController(CommentRestImpl overlayController) {
- this.commentController = overlayController;
- }
-
+package lcsb.mapviewer.api.projects.comments;
+
+import java.awt.geom.Point2D;
+import java.io.IOException;
+import java.util.List;
+import java.util.Map;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.web.bind.annotation.CookieValue;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestBody;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.RestController;
+
+import com.fasterxml.jackson.core.JsonParseException;
+import com.fasterxml.jackson.databind.JsonMappingException;
+
+import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.api.ElementIdentifierType;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.services.SecurityException;
+
+@RestController
+public class CommentController extends BaseController {
+
+ @Autowired
+ private CommentRestImpl commentController;
+
+ @RequestMapping(value = "/projects/{projectId}/comments/models/{modelId}/", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getComments(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "projectId") String projectId, //
+ @RequestParam(value = "columns", defaultValue = "") String columns, //
+ @RequestParam(value = "removed", defaultValue = "") String removed //
+ ) throws SecurityException, QueryException {
+ return commentController.getCommentList(token, projectId, columns, "", "", removed);
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/comments/{commentId}/", method = { RequestMethod.DELETE }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> removeComment(//
+ @RequestBody(required = false) String body, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "commentId") String commentId //
+ ) throws SecurityException, QueryException, JsonParseException, JsonMappingException, IOException {
+ Map<String, Object> node = parseBody(body);
+ String reason = (String) node.get("reason");
+ return commentController.removeComment(token, projectId, commentId, reason);
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/comments/models/{modelId}/bioEntities/reactions/{reactionId}", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getCommentsByReaction(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "projectId") String projectId, //
+ @RequestParam(value = "columns", defaultValue = "") String columns, //
+ @PathVariable(value = "reactionId") String reactionId, //
+ @RequestParam(value = "removed", defaultValue = "") String removed //
+ ) throws SecurityException, QueryException {
+ return commentController.getCommentList(token, projectId, columns, reactionId,
+ ElementIdentifierType.REACTION.getJsName(), removed);
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/comments/models/{modelId}/bioEntities/elements/{elementId}", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getCommentsByElement(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "projectId") String projectId, //
+ @RequestParam(value = "columns", defaultValue = "") String columns, //
+ @PathVariable(value = "elementId") String elementId, //
+ @RequestParam(value = "removed", defaultValue = "") String removed //
+ ) throws SecurityException, QueryException {
+ return commentController.getCommentList(token, projectId, columns, elementId,
+ ElementIdentifierType.ALIAS.getJsName(), removed);
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/comments/models/{modelId}/points/{coordinates:.+}", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getCommentsByPoint(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "projectId") String projectId, //
+ @RequestParam(value = "columns", defaultValue = "") String columns, //
+ @PathVariable(value = "coordinates") String coordinates, //
+ @RequestParam(value = "removed", defaultValue = "") String removed //
+ ) throws SecurityException, QueryException {
+ return commentController.getCommentList(token, projectId, columns, coordinates,
+ ElementIdentifierType.POINT.getJsName(), removed);
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/comments/models/{modelId}/bioEntities/elements/{elementId}", method = {
+ RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> addCommentForElement(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "elementId") String elementId, //
+ @RequestParam(value = "name") String name, //
+ @RequestParam(value = "email") String email, //
+ @RequestParam(value = "content") String content, //
+ @RequestParam(value = "pinned", defaultValue = "true") String pinned, //
+ @RequestParam(value = "coordinates") String coordinates, //
+ @PathVariable(value = "modelId") String modelId //
+ ) throws SecurityException, QueryException {
+ Point2D pointCoordinates = parseCoordinates(coordinates);
+ return commentController.addComment(token, projectId, ElementIdentifierType.ALIAS.getJsName(), elementId, name,
+ email, content, pinned.toLowerCase().equals("true"), pointCoordinates, modelId);
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/comments/models/{modelId}/bioEntities/reactions/{reactionId}", method = {
+ RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> addCommentForReaction(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "reactionId") String reactionId, //
+ @RequestParam(value = "name") String name, //
+ @RequestParam(value = "email") String email, //
+ @RequestParam(value = "content") String content, //
+ @RequestParam(value = "pinned", defaultValue = "true") String pinned, //
+ @RequestParam(value = "coordinates") String coordinates, //
+ @PathVariable(value = "modelId") String modelId //
+ ) throws SecurityException, QueryException {
+ Point2D pointCoordinates = parseCoordinates(coordinates);
+ return commentController.addComment(token, projectId, ElementIdentifierType.REACTION.getJsName(), reactionId, name,
+ email, content, pinned.toLowerCase().equals("true"), pointCoordinates, modelId);
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/comments/models/{modelId}/points/{coordinates}", method = {
+ RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> addCommentForPoint(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "projectId") String projectId, //
+ @RequestParam(value = "name") String name, //
+ @RequestParam(value = "email") String email, //
+ @RequestParam(value = "content") String content, //
+ @RequestParam(value = "pinned", defaultValue = "true") String pinned, //
+ @PathVariable(value = "coordinates") String coordinates, //
+ @PathVariable(value = "modelId") String modelId //
+ ) throws SecurityException, QueryException {
+ Point2D pointCoordinates = parseCoordinates(coordinates);
+ return commentController.addComment(token, projectId, ElementIdentifierType.POINT.getJsName(), coordinates, name,
+ email, content, pinned.toLowerCase().equals("true"), pointCoordinates, modelId);
+ }
+
+ private Point2D parseCoordinates(String coordinates) throws QueryException {
+ String[] tmp = coordinates.split(",");
+ if (tmp.length != 2) {
+ throw new QueryException("Coordinates must be in the format: 'xxx.xx,yyy.yy'");
+ }
+ Double x = null;
+ Double y = null;
+ try {
+ x = Double.valueOf(tmp[0]);
+ y = Double.valueOf(tmp[1]);
+ } catch (NumberFormatException e) {
+ throw new QueryException("Coordinates must be in the format: 'xxx.xx,yyy.yy'", e);
+ }
+ Point2D pointCoordinates = new Point2D.Double(x, y);
+ return pointCoordinates;
+ }
+
+ /**
+ * @return the overlayController
+ * @see #commentController
+ */
+ public CommentRestImpl getOverlayController() {
+ return commentController;
+ }
+
+ /**
+ * @param overlayController
+ * the overlayController to set
+ * @see #commentController
+ */
+ public void setOverlayController(CommentRestImpl overlayController) {
+ this.commentController = overlayController;
+ }
+
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/comments/CommentRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/comments/CommentRestImpl.java
index 933e3d6d4d..6bff363d7d 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/comments/CommentRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/comments/CommentRestImpl.java
@@ -1,344 +1,344 @@
-package lcsb.mapviewer.api.projects.comments;
-
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeMap;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.api.BaseRestImpl;
-import lcsb.mapviewer.api.ElementIdentifierType;
-import lcsb.mapviewer.api.ObjectNotFoundException;
-import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.Comment;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.persist.dao.map.ReactionDao;
-import lcsb.mapviewer.persist.dao.map.species.ElementDao;
-import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.interfaces.ICommentService;
-import lcsb.mapviewer.services.overlay.IconManager;
-
-@Transactional(value = "txManager")
-public class CommentRestImpl extends BaseRestImpl {
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(CommentRestImpl.class);
-
- @Autowired
- private ICommentService commentService;
-
- @Autowired
- private ReactionDao reactionDao;
-
- @Autowired
- private ElementDao elementDao;
-
- public List<Map<String, Object>> getCommentList(String token, String projectId, String columns, String elementId,
- String elementType, String removed) throws SecurityException, QueryException {
- Project project = getProjectService().getProjectByProjectId(projectId, token);
- if (project == null) {
- throw new ObjectNotFoundException("Project with given id doesn't exist");
- }
- boolean isAdmin = getUserService().userHasPrivilege(token, PrivilegeType.EDIT_COMMENTS_PROJECT, project);
- Set<String> columnsSet = createCommentColumnSet(columns, isAdmin);
-
- List<Map<String, Object>> result = new ArrayList<>();
-
- List<Comment> comments = commentService.getCommentsByProject(project, token);
- for (Comment comment : comments) {
- boolean reject = false;
- if (!"".equals(elementType)) {
- if (elementType.equals(ElementIdentifierType.POINT.getJsName())) {
- reject = comment.getTableName() != null;
- } else if (elementType.equals(ElementIdentifierType.REACTION.getJsName())) {
- reject = comment.getTableName() == null || !comment.getTableName().getName().contains("Reaction");
- } else if (elementType.equals(ElementIdentifierType.ALIAS.getJsName())) {
- reject = comment.getTableName() == null || comment.getTableName().getName().contains("Reaction");
- } else {
- throw new QueryException("Unknown element type: " + elementType);
- }
- }
- if (!"".equals(elementId)) {
- Object id = getId(comment).toString();
- reject |= (!elementId.equals(id));
- }
- if (!"".equals(removed)) {
- boolean expectedRemoved = removed.equalsIgnoreCase("true");
- reject |= (comment.isDeleted() != expectedRemoved);
- }
- if (!isAdmin) {
- reject |= (!comment.isPinned());
- }
- if (!reject) {
- result.add(preparedComment(comment, columnsSet, isAdmin));
- }
- }
-
- return result;
- }
-
- /**
- * @return the commentService
- * @see #commentService
- */
- public ICommentService getCommentService() {
- return commentService;
- }
-
- /**
- * @param commentService
- * the commentService to set
- * @see #commentService
- */
- public void setCommentService(ICommentService commentService) {
- this.commentService = commentService;
- }
-
- private Map<String, Object> preparedComment(Comment comment, Set<String> columnsSet, boolean admin) {
- Map<String, Object> result = new TreeMap<>();
- for (String string : columnsSet) {
- String column = string.toLowerCase();
- Object value = null;
- if (column.equals("id") || column.equals("idobject")) {
- value = comment.getId();
- } else if (column.equals("elementid")) {
- value = getId(comment);
- } else if (column.equals("modelid")) {
- value = comment.getSubmodelData().getId();
- } else if (column.equals("title")) {
- value = getTitle(comment);
- } else if (column.equals("pinned")) {
- value = comment.isPinned();
- } else if (column.equals("content")) {
- value = comment.getContent();
- } else if (column.equals("removed")) {
- value = comment.isDeleted();
- } else if (column.equals("coord")) {
- value = getCoordinates(comment);
- } else if (column.equals("removereason")) {
- value = comment.getRemoveReason();
- } else if (column.equals("type")) {
- value = getType(comment);
- } else if (column.equals("icon")) {
- value = IconManager.getInstance().getCommentIcon();
- } else if (admin) {
- if (column.equals("author")) {
- value = comment.getName();
- } else if (column.equals("email")) {
- value = comment.getEmail();
- } else {
- value = "Unknown column";
- }
- } else {
- value = "Unknown column";
- }
- result.put(string, value);
- }
- return result;
- }
-
- private Object getId(Comment comment) {
- if (comment.getTableName() == null) {
- return String.format("%.2f", comment.getCoordinates().getX()) + ","
- + String.format("%.2f", comment.getCoordinates().getY());
- } else {
- return comment.getTableId();
- }
- }
-
- private Object getType(Comment comment) {
- if (comment.getTableName() != null) {
- if (comment.getTableName().getName().contains("Reaction")) {
- return ElementIdentifierType.REACTION;
- } else {
- return ElementIdentifierType.ALIAS;
- }
- } else {
- return ElementIdentifierType.POINT;
- }
- }
-
- private String getTitle(Comment comment) {
- String title = "";
- if (comment.getCoordinates() != null) {
- title = "Comment (coord: " + String.format("%.2f", comment.getCoordinates().getX()) + ", "
- + String.format("%.2f", comment.getCoordinates().getY()) + ")";
- }
- if (comment.getTableName() != null) {
- if (comment.getTableName().getName().contains("Reaction")) {
- Reaction reaction = reactionDao.getById(comment.getTableId());
- if (reaction != null) {
- title = "Reaction " + reaction.getIdReaction();
- } else {
- logger.warn("Invalid reaction dbID: " + comment.getTableId());
- }
-
- } else {
- Element alias = elementDao.getById(comment.getTableId());
- if (alias != null) {
- title = alias.getName();
- } else {
- logger.warn("Invalid alias dbID: " + comment.getTableId());
- }
- }
- }
- return title;
- }
-
- private Point2D getCoordinates(Comment comment) {
- Point2D coordinates = comment.getCoordinates();
- if (comment.getCoordinates() != null) {
- coordinates = comment.getCoordinates();
- }
- if (comment.getTableName() != null) {
- if (comment.getTableName().getName().contains("Reaction")) {
- Reaction reaction = reactionDao.getById(comment.getTableId());
- if (reaction != null) {
- coordinates = reaction.getCenterPoint();
- } else {
- logger.warn("Invalid reaction dbID: " + comment.getTableId());
- }
-
- } else {
- Element alias = elementDao.getById(comment.getTableId());
- if (alias != null) {
- coordinates = alias.getCenter();
- } else {
- logger.warn("Invalid alias dbID: " + comment.getTableId());
- }
- }
- }
- return coordinates;
- }
-
- private Set<String> createCommentColumnSet(String columns, boolean admin) {
- Set<String> columnsSet = new HashSet<>();
- if (columns.equals("")) {
- columnsSet.add("title");
- columnsSet.add("icon");
- columnsSet.add("type");
- columnsSet.add("content");
- columnsSet.add("removed");
- columnsSet.add("coord");
- columnsSet.add("modelId");
- columnsSet.add("elementId");
- columnsSet.add("id");
- columnsSet.add("pinned");
- if (admin) {
- columnsSet.add("author");
- columnsSet.add("email");
- columnsSet.add("removeReason");
- }
- } else {
- for (String str : columns.split(",")) {
- columnsSet.add(str);
- }
- }
- return columnsSet;
- }
-
- /**
- * @return the reactionDao
- * @see #reactionDao
- */
- public ReactionDao getReactionDao() {
- return reactionDao;
- }
-
- /**
- * @param reactionDao
- * the reactionDao to set
- * @see #reactionDao
- */
- public void setReactionDao(ReactionDao reactionDao) {
- this.reactionDao = reactionDao;
- }
-
- /**
- * @return the elementDao
- * @see #elementDao
- */
- public ElementDao getElementDao() {
- return elementDao;
- }
-
- /**
- * @param elementDao
- * the elementDao to set
- * @see #elementDao
- */
- public void setElementDao(ElementDao elementDao) {
- this.elementDao = elementDao;
- }
-
- public Map<String, Object> addComment(String token, String projectId, String elementType, String elementId,
- String name, String email, String content, boolean pinned, Point2D pointCoordinates, String submodelId)
- throws QueryException, SecurityException {
- Model model = getModelService().getLastModelByProjectId(projectId, token);
- if (model == null) {
- throw new ObjectNotFoundException("Project with given id doesn't exist");
- }
-
- Integer modelId = null;
- try {
- modelId = Integer.valueOf(submodelId);
- } catch (NumberFormatException e) {
- throw new QueryException("Invalid model identifier for given project", e);
- }
- Model submodel = model.getSubmodelById(modelId);
- if (submodel == null) {
- throw new QueryException("Invalid model identifier for given project");
- }
- Object commentedObject;
- if (elementType.equals(ElementIdentifierType.ALIAS.getJsName())) {
- commentedObject = submodel.getElementByDbId(Integer.valueOf(elementId));
- if (commentedObject == null) {
- throw new QueryException("Invalid commented element identifier for given project");
- }
- } else if (elementType.equals(ElementIdentifierType.REACTION.getJsName())) {
- commentedObject = submodel.getReactionByDbId(Integer.valueOf(elementId));
- if (commentedObject == null) {
- throw new QueryException("Invalid commented element identifier for given project");
- }
- } else if (elementType.equals(ElementIdentifierType.POINT.getJsName())) {
- commentedObject = null;
- } else {
- throw new QueryException("Unknown type of commented object: " + elementType);
- }
-
- Comment comment = commentService.addComment(name, email, content, model, pointCoordinates, commentedObject, pinned,
- submodel);
-
- Project project = model.getProject();
- boolean isAdmin = getUserService().userHasPrivilege(token, PrivilegeType.EDIT_COMMENTS_PROJECT, project);
- return preparedComment(comment, createCommentColumnSet("", isAdmin), isAdmin);
- }
-
- public Map<String, Object> removeComment(String token, String projectId, String commentId, String reason)
- throws SecurityException, QueryException {
- Project project = getProjectService().getProjectByProjectId(projectId, token);
- if (project == null) {
- throw new ObjectNotFoundException("Project with given id doesn't exist");
- }
- Comment comment = commentService.getCommentById(commentId);
- if (comment == null || comment.getModelData().getProject().getId() != project.getId()) {
- throw new ObjectNotFoundException("Comment with given id doesn't exist");
- }
-
- commentService.deleteComment(comment, token, reason);
- return okStatus();
- }
-
-}
+package lcsb.mapviewer.api.projects.comments;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeMap;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.api.BaseRestImpl;
+import lcsb.mapviewer.api.ElementIdentifierType;
+import lcsb.mapviewer.api.ObjectNotFoundException;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.Comment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.user.PrivilegeType;
+import lcsb.mapviewer.persist.dao.map.ReactionDao;
+import lcsb.mapviewer.persist.dao.map.species.ElementDao;
+import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.interfaces.ICommentService;
+import lcsb.mapviewer.services.overlay.IconManager;
+
+@Transactional(value = "txManager")
+public class CommentRestImpl extends BaseRestImpl {
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(CommentRestImpl.class);
+
+ @Autowired
+ private ICommentService commentService;
+
+ @Autowired
+ private ReactionDao reactionDao;
+
+ @Autowired
+ private ElementDao elementDao;
+
+ public List<Map<String, Object>> getCommentList(String token, String projectId, String columns, String elementId,
+ String elementType, String removed) throws SecurityException, QueryException {
+ Project project = getProjectService().getProjectByProjectId(projectId, token);
+ if (project == null) {
+ throw new ObjectNotFoundException("Project with given id doesn't exist");
+ }
+ boolean isAdmin = getUserService().userHasPrivilege(token, PrivilegeType.EDIT_COMMENTS_PROJECT, project);
+ Set<String> columnsSet = createCommentColumnSet(columns, isAdmin);
+
+ List<Map<String, Object>> result = new ArrayList<>();
+
+ List<Comment> comments = commentService.getCommentsByProject(project, token);
+ for (Comment comment : comments) {
+ boolean reject = false;
+ if (!"".equals(elementType)) {
+ if (elementType.equals(ElementIdentifierType.POINT.getJsName())) {
+ reject = comment.getTableName() != null;
+ } else if (elementType.equals(ElementIdentifierType.REACTION.getJsName())) {
+ reject = comment.getTableName() == null || !comment.getTableName().getName().contains("Reaction");
+ } else if (elementType.equals(ElementIdentifierType.ALIAS.getJsName())) {
+ reject = comment.getTableName() == null || comment.getTableName().getName().contains("Reaction");
+ } else {
+ throw new QueryException("Unknown element type: " + elementType);
+ }
+ }
+ if (!"".equals(elementId)) {
+ Object id = getId(comment).toString();
+ reject |= (!elementId.equals(id));
+ }
+ if (!"".equals(removed)) {
+ boolean expectedRemoved = removed.equalsIgnoreCase("true");
+ reject |= (comment.isDeleted() != expectedRemoved);
+ }
+ if (!isAdmin) {
+ reject |= (!comment.isPinned());
+ }
+ if (!reject) {
+ result.add(preparedComment(comment, columnsSet, isAdmin));
+ }
+ }
+
+ return result;
+ }
+
+ /**
+ * @return the commentService
+ * @see #commentService
+ */
+ public ICommentService getCommentService() {
+ return commentService;
+ }
+
+ /**
+ * @param commentService
+ * the commentService to set
+ * @see #commentService
+ */
+ public void setCommentService(ICommentService commentService) {
+ this.commentService = commentService;
+ }
+
+ private Map<String, Object> preparedComment(Comment comment, Set<String> columnsSet, boolean admin) {
+ Map<String, Object> result = new TreeMap<>();
+ for (String string : columnsSet) {
+ String column = string.toLowerCase();
+ Object value = null;
+ if (column.equals("id") || column.equals("idobject")) {
+ value = comment.getId();
+ } else if (column.equals("elementid")) {
+ value = getId(comment);
+ } else if (column.equals("modelid")) {
+ value = comment.getSubmodelData().getId();
+ } else if (column.equals("title")) {
+ value = getTitle(comment);
+ } else if (column.equals("pinned")) {
+ value = comment.isPinned();
+ } else if (column.equals("content")) {
+ value = comment.getContent();
+ } else if (column.equals("removed")) {
+ value = comment.isDeleted();
+ } else if (column.equals("coord")) {
+ value = getCoordinates(comment);
+ } else if (column.equals("removereason")) {
+ value = comment.getRemoveReason();
+ } else if (column.equals("type")) {
+ value = getType(comment);
+ } else if (column.equals("icon")) {
+ value = IconManager.getInstance().getCommentIcon();
+ } else if (admin) {
+ if (column.equals("author")) {
+ value = comment.getName();
+ } else if (column.equals("email")) {
+ value = comment.getEmail();
+ } else {
+ value = "Unknown column";
+ }
+ } else {
+ value = "Unknown column";
+ }
+ result.put(string, value);
+ }
+ return result;
+ }
+
+ private Object getId(Comment comment) {
+ if (comment.getTableName() == null) {
+ return String.format("%.2f", comment.getCoordinates().getX()) + ","
+ + String.format("%.2f", comment.getCoordinates().getY());
+ } else {
+ return comment.getTableId();
+ }
+ }
+
+ private Object getType(Comment comment) {
+ if (comment.getTableName() != null) {
+ if (comment.getTableName().getName().contains("Reaction")) {
+ return ElementIdentifierType.REACTION;
+ } else {
+ return ElementIdentifierType.ALIAS;
+ }
+ } else {
+ return ElementIdentifierType.POINT;
+ }
+ }
+
+ private String getTitle(Comment comment) {
+ String title = "";
+ if (comment.getCoordinates() != null) {
+ title = "Comment (coord: " + String.format("%.2f", comment.getCoordinates().getX()) + ", "
+ + String.format("%.2f", comment.getCoordinates().getY()) + ")";
+ }
+ if (comment.getTableName() != null) {
+ if (comment.getTableName().getName().contains("Reaction")) {
+ Reaction reaction = reactionDao.getById(comment.getTableId());
+ if (reaction != null) {
+ title = "Reaction " + reaction.getIdReaction();
+ } else {
+ logger.warn("Invalid reaction dbID: " + comment.getTableId());
+ }
+
+ } else {
+ Element alias = elementDao.getById(comment.getTableId());
+ if (alias != null) {
+ title = alias.getName();
+ } else {
+ logger.warn("Invalid alias dbID: " + comment.getTableId());
+ }
+ }
+ }
+ return title;
+ }
+
+ private Point2D getCoordinates(Comment comment) {
+ Point2D coordinates = comment.getCoordinates();
+ if (comment.getCoordinates() != null) {
+ coordinates = comment.getCoordinates();
+ }
+ if (comment.getTableName() != null) {
+ if (comment.getTableName().getName().contains("Reaction")) {
+ Reaction reaction = reactionDao.getById(comment.getTableId());
+ if (reaction != null) {
+ coordinates = reaction.getCenterPoint();
+ } else {
+ logger.warn("Invalid reaction dbID: " + comment.getTableId());
+ }
+
+ } else {
+ Element alias = elementDao.getById(comment.getTableId());
+ if (alias != null) {
+ coordinates = alias.getCenter();
+ } else {
+ logger.warn("Invalid alias dbID: " + comment.getTableId());
+ }
+ }
+ }
+ return coordinates;
+ }
+
+ private Set<String> createCommentColumnSet(String columns, boolean admin) {
+ Set<String> columnsSet = new HashSet<>();
+ if (columns.equals("")) {
+ columnsSet.add("title");
+ columnsSet.add("icon");
+ columnsSet.add("type");
+ columnsSet.add("content");
+ columnsSet.add("removed");
+ columnsSet.add("coord");
+ columnsSet.add("modelId");
+ columnsSet.add("elementId");
+ columnsSet.add("id");
+ columnsSet.add("pinned");
+ if (admin) {
+ columnsSet.add("author");
+ columnsSet.add("email");
+ columnsSet.add("removeReason");
+ }
+ } else {
+ for (String str : columns.split(",")) {
+ columnsSet.add(str);
+ }
+ }
+ return columnsSet;
+ }
+
+ /**
+ * @return the reactionDao
+ * @see #reactionDao
+ */
+ public ReactionDao getReactionDao() {
+ return reactionDao;
+ }
+
+ /**
+ * @param reactionDao
+ * the reactionDao to set
+ * @see #reactionDao
+ */
+ public void setReactionDao(ReactionDao reactionDao) {
+ this.reactionDao = reactionDao;
+ }
+
+ /**
+ * @return the elementDao
+ * @see #elementDao
+ */
+ public ElementDao getElementDao() {
+ return elementDao;
+ }
+
+ /**
+ * @param elementDao
+ * the elementDao to set
+ * @see #elementDao
+ */
+ public void setElementDao(ElementDao elementDao) {
+ this.elementDao = elementDao;
+ }
+
+ public Map<String, Object> addComment(String token, String projectId, String elementType, String elementId,
+ String name, String email, String content, boolean pinned, Point2D pointCoordinates, String submodelId)
+ throws QueryException, SecurityException {
+ Model model = getModelService().getLastModelByProjectId(projectId, token);
+ if (model == null) {
+ throw new ObjectNotFoundException("Project with given id doesn't exist");
+ }
+
+ Integer modelId = null;
+ try {
+ modelId = Integer.valueOf(submodelId);
+ } catch (NumberFormatException e) {
+ throw new QueryException("Invalid model identifier for given project", e);
+ }
+ Model submodel = model.getSubmodelById(modelId);
+ if (submodel == null) {
+ throw new QueryException("Invalid model identifier for given project");
+ }
+ Object commentedObject;
+ if (elementType.equals(ElementIdentifierType.ALIAS.getJsName())) {
+ commentedObject = submodel.getElementByDbId(Integer.valueOf(elementId));
+ if (commentedObject == null) {
+ throw new QueryException("Invalid commented element identifier for given project");
+ }
+ } else if (elementType.equals(ElementIdentifierType.REACTION.getJsName())) {
+ commentedObject = submodel.getReactionByDbId(Integer.valueOf(elementId));
+ if (commentedObject == null) {
+ throw new QueryException("Invalid commented element identifier for given project");
+ }
+ } else if (elementType.equals(ElementIdentifierType.POINT.getJsName())) {
+ commentedObject = null;
+ } else {
+ throw new QueryException("Unknown type of commented object: " + elementType);
+ }
+
+ Comment comment = commentService.addComment(name, email, content, model, pointCoordinates, commentedObject, pinned,
+ submodel);
+
+ Project project = model.getProject();
+ boolean isAdmin = getUserService().userHasPrivilege(token, PrivilegeType.EDIT_COMMENTS_PROJECT, project);
+ return preparedComment(comment, createCommentColumnSet("", isAdmin), isAdmin);
+ }
+
+ public Map<String, Object> removeComment(String token, String projectId, String commentId, String reason)
+ throws SecurityException, QueryException {
+ Project project = getProjectService().getProjectByProjectId(projectId, token);
+ if (project == null) {
+ throw new ObjectNotFoundException("Project with given id doesn't exist");
+ }
+ Comment comment = commentService.getCommentById(commentId);
+ if (comment == null || comment.getModelData().getProject().getId() != project.getId()) {
+ throw new ObjectNotFoundException("Comment with given id doesn't exist");
+ }
+
+ commentService.deleteComment(comment, token, reason);
+ return okStatus();
+ }
+
+}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugController.java
index 43c1cd3a7b..c4a084cddd 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugController.java
@@ -1,57 +1,57 @@
-package lcsb.mapviewer.api.projects.drugs;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.MediaType;
-import org.springframework.web.bind.annotation.CookieValue;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RequestParam;
-import org.springframework.web.bind.annotation.RestController;
-
-import lcsb.mapviewer.annotation.services.DrugSearchException;
-import lcsb.mapviewer.api.BaseController;
-import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.services.SecurityException;
-
-@RestController
-public class DrugController extends BaseController {
-
- @Autowired
- private DrugRestImpl drugController;
-
- @RequestMapping(value = "/projects/{projectId}/drugs:search", method = { RequestMethod.GET }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getDrugsByQuery(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @RequestParam(value = "columns", defaultValue = "") String columns, //
- @RequestParam(value = "query", defaultValue = "") String query, //
- @RequestParam(value = "target", defaultValue = "") String target //
- ) throws SecurityException, QueryException {
- if (!query.equals("")) {
- return drugController.getDrugsByQuery(token, projectId, columns, query);
- } else if (target.indexOf(":") >= 0) {
- String targetType = target.split(":", -1)[0];
- String targetId = target.split(":", -1)[1];
- return drugController.getDrugsByTarget(token, projectId, targetType, targetId, columns);
- } else {
- return new ArrayList<>();
- }
- }
-
- @RequestMapping(value = "/projects/{projectId}/drugs/suggestedQueryList", method = { RequestMethod.GET }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public List<String> getSuggestedQueryList(//
- @PathVariable(value = "projectId") String projectId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token//
- ) throws SecurityException, DrugSearchException {
- return drugController.getSuggestedQueryList(projectId, token);
- }
-
+package lcsb.mapviewer.api.projects.drugs;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.web.bind.annotation.CookieValue;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.RestController;
+
+import lcsb.mapviewer.annotation.services.DrugSearchException;
+import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.services.SecurityException;
+
+@RestController
+public class DrugController extends BaseController {
+
+ @Autowired
+ private DrugRestImpl drugController;
+
+ @RequestMapping(value = "/projects/{projectId}/drugs:search", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getDrugsByQuery(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "projectId") String projectId, //
+ @RequestParam(value = "columns", defaultValue = "") String columns, //
+ @RequestParam(value = "query", defaultValue = "") String query, //
+ @RequestParam(value = "target", defaultValue = "") String target //
+ ) throws SecurityException, QueryException {
+ if (!query.equals("")) {
+ return drugController.getDrugsByQuery(token, projectId, columns, query);
+ } else if (target.indexOf(":") >= 0) {
+ String targetType = target.split(":", -1)[0];
+ String targetId = target.split(":", -1)[1];
+ return drugController.getDrugsByTarget(token, projectId, targetType, targetId, columns);
+ } else {
+ return new ArrayList<>();
+ }
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/drugs/suggestedQueryList", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public List<String> getSuggestedQueryList(//
+ @PathVariable(value = "projectId") String projectId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token//
+ ) throws SecurityException, DrugSearchException {
+ return drugController.getSuggestedQueryList(projectId, token);
+ }
+
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
index 785e3def80..4881c9da07 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
@@ -1,207 +1,207 @@
-package lcsb.mapviewer.api.projects.drugs;
-
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeMap;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.annotation.data.Drug;
-import lcsb.mapviewer.annotation.services.DrugSearchException;
-import lcsb.mapviewer.annotation.services.TaxonomyBackend;
-import lcsb.mapviewer.api.BaseRestImpl;
-import lcsb.mapviewer.api.ElementIdentifierType;
-import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.interfaces.IModelService;
-import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.search.DbSearchCriteria;
-import lcsb.mapviewer.services.search.drug.IDrugService;
-
-@Transactional(value = "txManager")
-public class DrugRestImpl extends BaseRestImpl {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(DrugRestImpl.class);
-
- @Autowired
- private IDrugService drugService;
-
- @Autowired
- private IUserService userService;
-
- public List<Map<String, Object>> getDrugsByQuery(String token, String projectId, String columns, String query)
- throws SecurityException, QueryException {
- Model model = getModelService().getLastModelByProjectId(projectId, token);
- if (model == null) {
- throw new QueryException("Project with given id doesn't exist");
- }
- Project project = model.getProject();
-
- Set<String> columnSet = createDrugColumnSet(columns);
-
- List<Map<String, Object>> result = new ArrayList<>();
-
- MiriamData organism = project.getOrganism();
- if (organism == null) {
- organism = TaxonomyBackend.HUMAN_TAXONOMY;
- }
- Drug drug = drugService.getByName(query, new DbSearchCriteria().project(project).organisms(organism).colorSet(0));
- if (drug != null) {
- List<Model> models = getModels(projectId, "*", token);
- result.add(prepareDrug(drug, columnSet, models));
- }
-
- return result;
- }
-
- /**
- * @return the userService
- * @see #userService
- */
- public IUserService getUserService() {
- return userService;
- }
-
- /**
- * @param userService
- * the userService to set
- * @see #userService
- */
- public void setUserService(IUserService userService) {
- this.userService = userService;
- }
-
- private Map<String, Object> prepareDrug(Drug drug, Set<String> columnsSet, List<Model> models) {
- Map<String, Object> result = new TreeMap<>();
- for (String string : columnsSet) {
- String column = string.toLowerCase();
- Object value = null;
- if (column.equals("id") || column.equals("idobject")) {
- value = drug.getName();
- } else if (column.equals("name")) {
- value = drug.getName();
- } else if (column.equals("references")) {
- value = createAnnotations(drug.getSources());
- } else if (column.equals("description")) {
- value = drug.getDescription();
- } else if (column.equals("bloodbrainbarrier")) {
- value = drug.getBloodBrainBarrier();
- } else if (column.equals("brandnames")) {
- value = drug.getBrandNames();
- } else if (column.equals("synonyms")) {
- value = drug.getSynonyms();
- } else if (column.equals("targets")) {
- value = prepareTargets(drug.getTargets(), models);
- } else {
- value = "Unknown column";
- }
- result.put(string, value);
- }
- return result;
- }
-
- private Set<String> createDrugColumnSet(String columns) {
- Set<String> columnsSet = new HashSet<>();
- if (columns.equals("")) {
- columnsSet.add("name");
- columnsSet.add("references");
- columnsSet.add("description");
- columnsSet.add("bloodBrainBarrier");
- columnsSet.add("brandNames");
- columnsSet.add("synonyms");
- columnsSet.add("id");
- columnsSet.add("targets");
- } else {
- for (String str : columns.split(",")) {
- columnsSet.add(str);
- }
- }
- return columnsSet;
- }
-
- /**
- * @return the drugService
- * @see #drugService
- */
- public IDrugService getDrugService() {
- return drugService;
- }
-
- /**
- * @param drugService
- * the drugService to set
- * @see #drugService
- */
- public void setDrugService(IDrugService drugService) {
- this.drugService = drugService;
- }
-
- public List<Map<String, Object>> getDrugsByTarget(String token, String projectId, String targetType, String targetId,
- String columns) throws SecurityException, QueryException {
- Model model = getModelService().getLastModelByProjectId(projectId, token);
- if (model == null) {
- throw new QueryException("Project with given id doesn't exist");
- }
- Project project = model.getProject();
-
- List<Model> models = getModels(projectId, "*", token);
-
- Integer dbId = Integer.valueOf(targetId);
- List<Element> targets = getTargets(targetType, models, dbId);
- MiriamData organism = project.getOrganism();
- if (organism == null) {
- organism = TaxonomyBackend.HUMAN_TAXONOMY;
- }
-
- Set<String> columnSet = createDrugColumnSet(columns);
-
- List<Drug> drugs = drugService.getForTargets(targets, new DbSearchCriteria().project(project).organisms(organism));
-
- List<Map<String, Object>> result = new ArrayList<>();
-
- for (Drug drug : drugs) {
- result.add(prepareDrug(drug, columnSet, models));
- }
-
- return result;
- }
-
- private List<Element> getTargets(String targetType, List<Model> models, Integer dbId) throws QueryException {
- List<Element> targets = new ArrayList<>();
- if (targetType.equals(ElementIdentifierType.ALIAS.getJsName())) {
- Element element = null;
- for (Model m : models) {
- if (element == null) {
- element = m.getElementByDbId(dbId);
- }
- }
- if (element == null) {
- throw new QueryException("Invalid element identifier for given project");
- }
- targets.add(element);
- } else {
- throw new QueryException("Targeting for the type not implemented");
- }
- return targets;
- }
-
- public List<String> getSuggestedQueryList(String projectId, String token)
- throws SecurityException, DrugSearchException {
- Project project = getProjectService().getProjectByProjectId(projectId, token);
- return drugService.getSuggestedQueryList(project, project.getOrganism());
- }
-
-}
+package lcsb.mapviewer.api.projects.drugs;
+
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeMap;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.annotation.data.Drug;
+import lcsb.mapviewer.annotation.services.DrugSearchException;
+import lcsb.mapviewer.annotation.services.TaxonomyBackend;
+import lcsb.mapviewer.api.BaseRestImpl;
+import lcsb.mapviewer.api.ElementIdentifierType;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.interfaces.IModelService;
+import lcsb.mapviewer.services.interfaces.IUserService;
+import lcsb.mapviewer.services.search.DbSearchCriteria;
+import lcsb.mapviewer.services.search.drug.IDrugService;
+
+@Transactional(value = "txManager")
+public class DrugRestImpl extends BaseRestImpl {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(DrugRestImpl.class);
+
+ @Autowired
+ private IDrugService drugService;
+
+ @Autowired
+ private IUserService userService;
+
+ public List<Map<String, Object>> getDrugsByQuery(String token, String projectId, String columns, String query)
+ throws SecurityException, QueryException {
+ Model model = getModelService().getLastModelByProjectId(projectId, token);
+ if (model == null) {
+ throw new QueryException("Project with given id doesn't exist");
+ }
+ Project project = model.getProject();
+
+ Set<String> columnSet = createDrugColumnSet(columns);
+
+ List<Map<String, Object>> result = new ArrayList<>();
+
+ MiriamData organism = project.getOrganism();
+ if (organism == null) {
+ organism = TaxonomyBackend.HUMAN_TAXONOMY;
+ }
+ Drug drug = drugService.getByName(query, new DbSearchCriteria().project(project).organisms(organism).colorSet(0));
+ if (drug != null) {
+ List<Model> models = getModels(projectId, "*", token);
+ result.add(prepareDrug(drug, columnSet, models));
+ }
+
+ return result;
+ }
+
+ /**
+ * @return the userService
+ * @see #userService
+ */
+ public IUserService getUserService() {
+ return userService;
+ }
+
+ /**
+ * @param userService
+ * the userService to set
+ * @see #userService
+ */
+ public void setUserService(IUserService userService) {
+ this.userService = userService;
+ }
+
+ private Map<String, Object> prepareDrug(Drug drug, Set<String> columnsSet, List<Model> models) {
+ Map<String, Object> result = new TreeMap<>();
+ for (String string : columnsSet) {
+ String column = string.toLowerCase();
+ Object value = null;
+ if (column.equals("id") || column.equals("idobject")) {
+ value = drug.getName();
+ } else if (column.equals("name")) {
+ value = drug.getName();
+ } else if (column.equals("references")) {
+ value = createAnnotations(drug.getSources());
+ } else if (column.equals("description")) {
+ value = drug.getDescription();
+ } else if (column.equals("bloodbrainbarrier")) {
+ value = drug.getBloodBrainBarrier();
+ } else if (column.equals("brandnames")) {
+ value = drug.getBrandNames();
+ } else if (column.equals("synonyms")) {
+ value = drug.getSynonyms();
+ } else if (column.equals("targets")) {
+ value = prepareTargets(drug.getTargets(), models);
+ } else {
+ value = "Unknown column";
+ }
+ result.put(string, value);
+ }
+ return result;
+ }
+
+ private Set<String> createDrugColumnSet(String columns) {
+ Set<String> columnsSet = new HashSet<>();
+ if (columns.equals("")) {
+ columnsSet.add("name");
+ columnsSet.add("references");
+ columnsSet.add("description");
+ columnsSet.add("bloodBrainBarrier");
+ columnsSet.add("brandNames");
+ columnsSet.add("synonyms");
+ columnsSet.add("id");
+ columnsSet.add("targets");
+ } else {
+ for (String str : columns.split(",")) {
+ columnsSet.add(str);
+ }
+ }
+ return columnsSet;
+ }
+
+ /**
+ * @return the drugService
+ * @see #drugService
+ */
+ public IDrugService getDrugService() {
+ return drugService;
+ }
+
+ /**
+ * @param drugService
+ * the drugService to set
+ * @see #drugService
+ */
+ public void setDrugService(IDrugService drugService) {
+ this.drugService = drugService;
+ }
+
+ public List<Map<String, Object>> getDrugsByTarget(String token, String projectId, String targetType, String targetId,
+ String columns) throws SecurityException, QueryException {
+ Model model = getModelService().getLastModelByProjectId(projectId, token);
+ if (model == null) {
+ throw new QueryException("Project with given id doesn't exist");
+ }
+ Project project = model.getProject();
+
+ List<Model> models = getModels(projectId, "*", token);
+
+ Integer dbId = Integer.valueOf(targetId);
+ List<Element> targets = getTargets(targetType, models, dbId);
+ MiriamData organism = project.getOrganism();
+ if (organism == null) {
+ organism = TaxonomyBackend.HUMAN_TAXONOMY;
+ }
+
+ Set<String> columnSet = createDrugColumnSet(columns);
+
+ List<Drug> drugs = drugService.getForTargets(targets, new DbSearchCriteria().project(project).organisms(organism));
+
+ List<Map<String, Object>> result = new ArrayList<>();
+
+ for (Drug drug : drugs) {
+ result.add(prepareDrug(drug, columnSet, models));
+ }
+
+ return result;
+ }
+
+ private List<Element> getTargets(String targetType, List<Model> models, Integer dbId) throws QueryException {
+ List<Element> targets = new ArrayList<>();
+ if (targetType.equals(ElementIdentifierType.ALIAS.getJsName())) {
+ Element element = null;
+ for (Model m : models) {
+ if (element == null) {
+ element = m.getElementByDbId(dbId);
+ }
+ }
+ if (element == null) {
+ throw new QueryException("Invalid element identifier for given project");
+ }
+ targets.add(element);
+ } else {
+ throw new QueryException("Targeting for the type not implemented");
+ }
+ return targets;
+ }
+
+ public List<String> getSuggestedQueryList(String projectId, String token)
+ throws SecurityException, DrugSearchException {
+ Project project = getProjectService().getProjectByProjectId(projectId, token);
+ return drugService.getSuggestedQueryList(project, project.getOrganism());
+ }
+
+}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaController.java
index 953cb26f25..51fdd905a2 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaController.java
@@ -1,57 +1,57 @@
-package lcsb.mapviewer.api.projects.mirnas;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.MediaType;
-import org.springframework.web.bind.annotation.CookieValue;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RequestParam;
-import org.springframework.web.bind.annotation.RestController;
-
-import lcsb.mapviewer.annotation.services.MiRNASearchException;
-import lcsb.mapviewer.api.BaseController;
-import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.services.SecurityException;
-
-@RestController
-public class MiRnaController extends BaseController {
-
- @Autowired
- private MiRnaRestImpl miRnaController;
-
- @RequestMapping(value = "/projects/{projectId}/miRnas:search", method = { RequestMethod.GET }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getMiRnasByQuery(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @RequestParam(value = "columns", defaultValue = "") String columns, //
- @RequestParam(value = "query", defaultValue = "") String query, //
- @RequestParam(value = "target", defaultValue = "") String target //
- ) throws SecurityException, QueryException {
- if (!query.equals("")) {
- return miRnaController.getMiRnasByQuery(token, projectId, columns, query);
- } else if (target.indexOf(":") >= 0) {
- String targetType = target.split(":", -1)[0];
- String targetId = target.split(":", -1)[1];
- return miRnaController.getMiRnasByTarget(token, projectId, targetType, targetId, columns);
- } else {
- return new ArrayList<>();
- }
- }
-
- @RequestMapping(value = "/projects/{projectId}/miRnas/suggestedQueryList", method = {
- RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<String> getSuggestedQueryList(//
- @PathVariable(value = "projectId") String projectId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token//
- ) throws SecurityException, MiRNASearchException {
- return miRnaController.getSuggestedQueryList(projectId, token);
- }
-
+package lcsb.mapviewer.api.projects.mirnas;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.web.bind.annotation.CookieValue;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.RestController;
+
+import lcsb.mapviewer.annotation.services.MiRNASearchException;
+import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.services.SecurityException;
+
+@RestController
+public class MiRnaController extends BaseController {
+
+ @Autowired
+ private MiRnaRestImpl miRnaController;
+
+ @RequestMapping(value = "/projects/{projectId}/miRnas:search", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getMiRnasByQuery(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "projectId") String projectId, //
+ @RequestParam(value = "columns", defaultValue = "") String columns, //
+ @RequestParam(value = "query", defaultValue = "") String query, //
+ @RequestParam(value = "target", defaultValue = "") String target //
+ ) throws SecurityException, QueryException {
+ if (!query.equals("")) {
+ return miRnaController.getMiRnasByQuery(token, projectId, columns, query);
+ } else if (target.indexOf(":") >= 0) {
+ String targetType = target.split(":", -1)[0];
+ String targetId = target.split(":", -1)[1];
+ return miRnaController.getMiRnasByTarget(token, projectId, targetType, targetId, columns);
+ } else {
+ return new ArrayList<>();
+ }
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/miRnas/suggestedQueryList", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<String> getSuggestedQueryList(//
+ @PathVariable(value = "projectId") String projectId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token//
+ ) throws SecurityException, MiRNASearchException {
+ return miRnaController.getSuggestedQueryList(projectId, token);
+ }
+
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImpl.java
index 7d68790e85..0ecf29fdd4 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImpl.java
@@ -1,171 +1,171 @@
-package lcsb.mapviewer.api.projects.mirnas;
-
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeMap;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.annotation.data.MiRNA;
-import lcsb.mapviewer.annotation.services.MiRNAParser;
-import lcsb.mapviewer.annotation.services.MiRNASearchException;
-import lcsb.mapviewer.annotation.services.TaxonomyBackend;
-import lcsb.mapviewer.api.BaseRestImpl;
-import lcsb.mapviewer.api.ElementIdentifierType;
-import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.search.DbSearchCriteria;
-import lcsb.mapviewer.services.search.mirna.IMiRNAService;
-
-@Transactional(value = "txManager")
-public class MiRnaRestImpl extends BaseRestImpl {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(MiRnaRestImpl.class);
-
- @Autowired
- private IMiRNAService miRnaService;
-
- @Autowired
- private MiRNAParser miRNAParser;
-
- public List<Map<String, Object>> getMiRnasByQuery(String token, String projectId, String columns, String query)
- throws SecurityException, QueryException {
- Model model = getModelService().getLastModelByProjectId(projectId, token);
- if (model == null) {
- throw new QueryException("Project with given id doesn't exist");
- }
- Project project = model.getProject();
-
- Set<String> columnSet = createMiRnaColumnSet(columns);
-
- List<Map<String, Object>> result = new ArrayList<>();
-
- MiriamData organism = project.getOrganism();
- if (organism == null) {
- organism = TaxonomyBackend.HUMAN_TAXONOMY;
- }
- MiRNA miRna = miRnaService.getByName(query,
- new DbSearchCriteria().project(project).organisms(organism).colorSet(0));
- if (miRna != null) {
- List<Model> models = getModels(projectId, "*", token);
- result.add(prepareMiRna(miRna, columnSet, models));
- }
-
- return result;
- }
-
- private Map<String, Object> prepareMiRna(MiRNA miRna, Set<String> columnsSet, List<Model> models) {
- Map<String, Object> result = new TreeMap<>();
- for (String string : columnsSet) {
- String column = string.toLowerCase();
- Object value = null;
- if (column.equals("id") || column.equals("idobject")) {
- value = miRna.getName();
- } else if (column.equals("name")) {
- value = miRna.getName();
- } else if (column.equals("targets")) {
- value = prepareTargets(miRna.getTargets(), models);
- } else {
- value = "Unknown column";
- }
- result.put(string, value);
- }
- return result;
- }
-
- private Set<String> createMiRnaColumnSet(String columns) {
- Set<String> columnsSet = new HashSet<>();
- if (columns.equals("")) {
- columnsSet.add("name");
- columnsSet.add("id");
- columnsSet.add("targets");
- } else {
- for (String str : columns.split(",")) {
- columnsSet.add(str);
- }
- }
- return columnsSet;
- }
-
- /**
- * @return the miRnaService
- * @see #miRnaService
- */
- public IMiRNAService getMiRnaService() {
- return miRnaService;
- }
-
- /**
- * @param miRnaService
- * the miRnaService to set
- * @see #miRnaService
- */
- public void setMiRnaService(IMiRNAService miRnaService) {
- this.miRnaService = miRnaService;
- }
-
- public List<Map<String, Object>> getMiRnasByTarget(String token, String projectId, String targetType, String targetId,
- String columns) throws SecurityException, QueryException {
- Model model = getModelService().getLastModelByProjectId(projectId, token);
- if (model == null) {
- throw new QueryException("Project with given id doesn't exist");
- }
- Project project = model.getProject();
-
- List<Model> models = getModels(projectId, "*", token);
-
- Integer dbId = Integer.valueOf(targetId);
- List<Element> targets = new ArrayList<>();
- if (targetType.equals(ElementIdentifierType.ALIAS.getJsName())) {
- Element element = null;
- for (Model m : models) {
- if (element == null) {
- element = m.getElementByDbId(dbId);
- }
- }
- if (element == null) {
- throw new QueryException("Invalid element identifier for given project");
- }
- targets.add(element);
- } else {
- throw new QueryException("Targeting for the type not implemented");
- }
- MiriamData organism = project.getOrganism();
- if (organism == null) {
- organism = TaxonomyBackend.HUMAN_TAXONOMY;
- }
-
- Set<String> columnSet = createMiRnaColumnSet(columns);
-
- List<MiRNA> miRnas = miRnaService.getForTargets(targets,
- new DbSearchCriteria().project(project).organisms(organism));
-
- List<Map<String, Object>> result = new ArrayList<>();
-
- for (MiRNA miRna : miRnas) {
- result.add(prepareMiRna(miRna, columnSet, models));
- }
-
- return result;
- }
-
- public List<String> getSuggestedQueryList(String projectId, String token)
- throws SecurityException, MiRNASearchException {
- Project project = getProjectService().getProjectByProjectId(projectId, token);
- return miRNAParser.getSuggestedQueryList(project);
- }
-
-}
+package lcsb.mapviewer.api.projects.mirnas;
+
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeMap;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.annotation.data.MiRNA;
+import lcsb.mapviewer.annotation.services.MiRNAParser;
+import lcsb.mapviewer.annotation.services.MiRNASearchException;
+import lcsb.mapviewer.annotation.services.TaxonomyBackend;
+import lcsb.mapviewer.api.BaseRestImpl;
+import lcsb.mapviewer.api.ElementIdentifierType;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.search.DbSearchCriteria;
+import lcsb.mapviewer.services.search.mirna.IMiRNAService;
+
+@Transactional(value = "txManager")
+public class MiRnaRestImpl extends BaseRestImpl {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(MiRnaRestImpl.class);
+
+ @Autowired
+ private IMiRNAService miRnaService;
+
+ @Autowired
+ private MiRNAParser miRNAParser;
+
+ public List<Map<String, Object>> getMiRnasByQuery(String token, String projectId, String columns, String query)
+ throws SecurityException, QueryException {
+ Model model = getModelService().getLastModelByProjectId(projectId, token);
+ if (model == null) {
+ throw new QueryException("Project with given id doesn't exist");
+ }
+ Project project = model.getProject();
+
+ Set<String> columnSet = createMiRnaColumnSet(columns);
+
+ List<Map<String, Object>> result = new ArrayList<>();
+
+ MiriamData organism = project.getOrganism();
+ if (organism == null) {
+ organism = TaxonomyBackend.HUMAN_TAXONOMY;
+ }
+ MiRNA miRna = miRnaService.getByName(query,
+ new DbSearchCriteria().project(project).organisms(organism).colorSet(0));
+ if (miRna != null) {
+ List<Model> models = getModels(projectId, "*", token);
+ result.add(prepareMiRna(miRna, columnSet, models));
+ }
+
+ return result;
+ }
+
+ private Map<String, Object> prepareMiRna(MiRNA miRna, Set<String> columnsSet, List<Model> models) {
+ Map<String, Object> result = new TreeMap<>();
+ for (String string : columnsSet) {
+ String column = string.toLowerCase();
+ Object value = null;
+ if (column.equals("id") || column.equals("idobject")) {
+ value = miRna.getName();
+ } else if (column.equals("name")) {
+ value = miRna.getName();
+ } else if (column.equals("targets")) {
+ value = prepareTargets(miRna.getTargets(), models);
+ } else {
+ value = "Unknown column";
+ }
+ result.put(string, value);
+ }
+ return result;
+ }
+
+ private Set<String> createMiRnaColumnSet(String columns) {
+ Set<String> columnsSet = new HashSet<>();
+ if (columns.equals("")) {
+ columnsSet.add("name");
+ columnsSet.add("id");
+ columnsSet.add("targets");
+ } else {
+ for (String str : columns.split(",")) {
+ columnsSet.add(str);
+ }
+ }
+ return columnsSet;
+ }
+
+ /**
+ * @return the miRnaService
+ * @see #miRnaService
+ */
+ public IMiRNAService getMiRnaService() {
+ return miRnaService;
+ }
+
+ /**
+ * @param miRnaService
+ * the miRnaService to set
+ * @see #miRnaService
+ */
+ public void setMiRnaService(IMiRNAService miRnaService) {
+ this.miRnaService = miRnaService;
+ }
+
+ public List<Map<String, Object>> getMiRnasByTarget(String token, String projectId, String targetType, String targetId,
+ String columns) throws SecurityException, QueryException {
+ Model model = getModelService().getLastModelByProjectId(projectId, token);
+ if (model == null) {
+ throw new QueryException("Project with given id doesn't exist");
+ }
+ Project project = model.getProject();
+
+ List<Model> models = getModels(projectId, "*", token);
+
+ Integer dbId = Integer.valueOf(targetId);
+ List<Element> targets = new ArrayList<>();
+ if (targetType.equals(ElementIdentifierType.ALIAS.getJsName())) {
+ Element element = null;
+ for (Model m : models) {
+ if (element == null) {
+ element = m.getElementByDbId(dbId);
+ }
+ }
+ if (element == null) {
+ throw new QueryException("Invalid element identifier for given project");
+ }
+ targets.add(element);
+ } else {
+ throw new QueryException("Targeting for the type not implemented");
+ }
+ MiriamData organism = project.getOrganism();
+ if (organism == null) {
+ organism = TaxonomyBackend.HUMAN_TAXONOMY;
+ }
+
+ Set<String> columnSet = createMiRnaColumnSet(columns);
+
+ List<MiRNA> miRnas = miRnaService.getForTargets(targets,
+ new DbSearchCriteria().project(project).organisms(organism));
+
+ List<Map<String, Object>> result = new ArrayList<>();
+
+ for (MiRNA miRna : miRnas) {
+ result.add(prepareMiRna(miRna, columnSet, models));
+ }
+
+ return result;
+ }
+
+ public List<String> getSuggestedQueryList(String projectId, String token)
+ throws SecurityException, MiRNASearchException {
+ Project project = getProjectService().getProjectByProjectId(projectId, token);
+ return miRNAParser.getSuggestedQueryList(project);
+ }
+
+}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesController.java
index 693bbdc2a0..891e8871b4 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesController.java
@@ -1,81 +1,81 @@
-package lcsb.mapviewer.api.projects.models.bioEntities;
-
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.MediaType;
-import org.springframework.web.bind.annotation.CookieValue;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RequestParam;
-import org.springframework.web.bind.annotation.RestController;
-
-import lcsb.mapviewer.api.BaseController;
-import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.services.SecurityException;
-
-@RestController
-public class BioEntitiesController extends BaseController {
- @Autowired
- private BioEntitiesRestImpl bioEntitiesRestImpl;
-
- @RequestMapping(value = "/projects/{projectId}/models/{modelId}/bioEntities:search", method = {
- RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getClosestElementsByCoordinates(//
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @RequestParam(value = "coordinates", defaultValue = "") String coordinates, //
- @RequestParam(value = "query", defaultValue = "") String query, //
- @RequestParam(value = "count", defaultValue = "") String count, //
- @RequestParam(value = "type", defaultValue = "") String type, //
- @RequestParam(value = "perfectMatch", defaultValue = "false") String perfectMatch//
- ) throws QueryException, SecurityException {
- if (!coordinates.trim().isEmpty()) {
- if (modelId.equals("*")) {
- throw new QueryException("modelId must be defined when searching by coordinates");
- }
- if (count.trim().isEmpty()) {
- count = "5";
- }
- String[] tmp = coordinates.split(",");
- if (tmp.length != 2) {
- throw new QueryException("Coordinates must be in the format: 'xxx.xx,yyy.yy'");
- }
- Double x = null;
- Double y = null;
- try {
- x = Double.valueOf(tmp[0]);
- y = Double.valueOf(tmp[1]);
- } catch (NumberFormatException e) {
- throw new QueryException("Coordinates must be in the format: 'xxx.xx,yyy.yy'", e);
- }
- Point2D pointCoordinates = new Point2D.Double(x, y);
- return bioEntitiesRestImpl.getClosestElementsByCoordinates(projectId, modelId, token, pointCoordinates,
- Integer.valueOf(count), perfectMatch, type);
- } else if (!query.trim().isEmpty()) {
- if (count.trim().isEmpty()) {
- count = "100";
- }
- return bioEntitiesRestImpl.getElementsByQuery(projectId, token, modelId, query, Integer.valueOf(count),
- perfectMatch);
- } else {
- return new ArrayList<>();
- }
- }
-
- @RequestMapping(value = "/projects/{projectId}/models/{modelId}/bioEntities/suggestedQueryList", method = {
- RequestMethod.GET, RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public String[] getSuggestedQueryList(//
- @PathVariable(value = "projectId") String projectId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token//
- ) throws SecurityException {
- return bioEntitiesRestImpl.getSuggestedQueryList(projectId, token);
- }
-
+package lcsb.mapviewer.api.projects.models.bioEntities;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.web.bind.annotation.CookieValue;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.RestController;
+
+import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.services.SecurityException;
+
+@RestController
+public class BioEntitiesController extends BaseController {
+ @Autowired
+ private BioEntitiesRestImpl bioEntitiesRestImpl;
+
+ @RequestMapping(value = "/projects/{projectId}/models/{modelId}/bioEntities:search", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getClosestElementsByCoordinates(//
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "modelId") String modelId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @RequestParam(value = "coordinates", defaultValue = "") String coordinates, //
+ @RequestParam(value = "query", defaultValue = "") String query, //
+ @RequestParam(value = "count", defaultValue = "") String count, //
+ @RequestParam(value = "type", defaultValue = "") String type, //
+ @RequestParam(value = "perfectMatch", defaultValue = "false") String perfectMatch//
+ ) throws QueryException, SecurityException {
+ if (!coordinates.trim().isEmpty()) {
+ if (modelId.equals("*")) {
+ throw new QueryException("modelId must be defined when searching by coordinates");
+ }
+ if (count.trim().isEmpty()) {
+ count = "5";
+ }
+ String[] tmp = coordinates.split(",");
+ if (tmp.length != 2) {
+ throw new QueryException("Coordinates must be in the format: 'xxx.xx,yyy.yy'");
+ }
+ Double x = null;
+ Double y = null;
+ try {
+ x = Double.valueOf(tmp[0]);
+ y = Double.valueOf(tmp[1]);
+ } catch (NumberFormatException e) {
+ throw new QueryException("Coordinates must be in the format: 'xxx.xx,yyy.yy'", e);
+ }
+ Point2D pointCoordinates = new Point2D.Double(x, y);
+ return bioEntitiesRestImpl.getClosestElementsByCoordinates(projectId, modelId, token, pointCoordinates,
+ Integer.valueOf(count), perfectMatch, type);
+ } else if (!query.trim().isEmpty()) {
+ if (count.trim().isEmpty()) {
+ count = "100";
+ }
+ return bioEntitiesRestImpl.getElementsByQuery(projectId, token, modelId, query, Integer.valueOf(count),
+ perfectMatch);
+ } else {
+ return new ArrayList<>();
+ }
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/models/{modelId}/bioEntities/suggestedQueryList", method = {
+ RequestMethod.GET, RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public String[] getSuggestedQueryList(//
+ @PathVariable(value = "projectId") String projectId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token//
+ ) throws SecurityException {
+ return bioEntitiesRestImpl.getSuggestedQueryList(projectId, token);
+ }
+
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesRestImpl.java
index 25b6104750..2ef9290744 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesRestImpl.java
@@ -1,97 +1,97 @@
-package lcsb.mapviewer.api.projects.models.bioEntities;
-
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.api.BaseRestImpl;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.UserAccessException;
-import lcsb.mapviewer.services.interfaces.IModelService;
-import lcsb.mapviewer.services.interfaces.ISearchService;
-import lcsb.mapviewer.services.interfaces.IUserService;
-
-@Transactional(value = "txManager")
-public class BioEntitiesRestImpl extends BaseRestImpl {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(BioEntitiesRestImpl.class);
-
- @Autowired
- private ISearchService searchService;
-
- public List<Map<String, Object>> getClosestElementsByCoordinates(String projectId, String modelId, String token,
- Point2D coordinates, Integer count, String perfectMatch, String type) throws UserAccessException, SecurityException {
- List<Map<String, Object>> resultMap = new ArrayList<>();
-
- Model model = getModelService().getLastModelByProjectId(projectId, token);
-
- Model submodel = model.getSubmodelById(modelId);
-
- Set<String> types = new HashSet<>();
- if (!type.isEmpty()) {
- for (String str : type.split(",")) {
- types.add(str.toLowerCase());
- }
- }
-
- List<BioEntity> elements = searchService.getClosestElements(submodel, coordinates, count,
- perfectMatch.equalsIgnoreCase("true"), types);
- for (BioEntity object : elements) {
- Map<String, Object> result = createMinifiedSearchResult(object);
- resultMap.add(result);
- }
- return resultMap;
- }
-
- /**
- * @return the searchService
- * @see #searchService
- */
- public ISearchService getSearchService() {
- return searchService;
- }
-
- /**
- * @param searchService
- * the searchService to set
- * @see #searchService
- */
- public void setSearchService(ISearchService searchService) {
- this.searchService = searchService;
- }
-
- public List<Map<String, Object>> getElementsByQuery(String projectId, String token, String modelId, String query,
- Integer maxElements, String perfectMatch) throws SecurityException {
- List<Map<String, Object>> resultMap = new ArrayList<>();
-
- Model model = getModelService().getLastModelByProjectId(projectId, token);
-
- Integer limit = Integer.valueOf(maxElements);
- boolean match = perfectMatch.equals("true");
- List<BioEntity> elements = searchService.searchByQuery(model, query, limit, match);
- for (BioEntity object : elements) {
- Map<String, Object> result = createMinifiedSearchResult(object);
- resultMap.add(result);
- }
- return resultMap;
- }
-
- public String[] getSuggestedQueryList(String projectId, String token) throws SecurityException {
- Model model = getModelService().getLastModelByProjectId(projectId, token);
- return searchService.getSuggestedQueryList(model);
- }
-
-}
+package lcsb.mapviewer.api.projects.models.bioEntities;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.api.BaseRestImpl;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.UserAccessException;
+import lcsb.mapviewer.services.interfaces.IModelService;
+import lcsb.mapviewer.services.interfaces.ISearchService;
+import lcsb.mapviewer.services.interfaces.IUserService;
+
+@Transactional(value = "txManager")
+public class BioEntitiesRestImpl extends BaseRestImpl {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(BioEntitiesRestImpl.class);
+
+ @Autowired
+ private ISearchService searchService;
+
+ public List<Map<String, Object>> getClosestElementsByCoordinates(String projectId, String modelId, String token,
+ Point2D coordinates, Integer count, String perfectMatch, String type) throws UserAccessException, SecurityException {
+ List<Map<String, Object>> resultMap = new ArrayList<>();
+
+ Model model = getModelService().getLastModelByProjectId(projectId, token);
+
+ Model submodel = model.getSubmodelById(modelId);
+
+ Set<String> types = new HashSet<>();
+ if (!type.isEmpty()) {
+ for (String str : type.split(",")) {
+ types.add(str.toLowerCase());
+ }
+ }
+
+ List<BioEntity> elements = searchService.getClosestElements(submodel, coordinates, count,
+ perfectMatch.equalsIgnoreCase("true"), types);
+ for (BioEntity object : elements) {
+ Map<String, Object> result = createMinifiedSearchResult(object);
+ resultMap.add(result);
+ }
+ return resultMap;
+ }
+
+ /**
+ * @return the searchService
+ * @see #searchService
+ */
+ public ISearchService getSearchService() {
+ return searchService;
+ }
+
+ /**
+ * @param searchService
+ * the searchService to set
+ * @see #searchService
+ */
+ public void setSearchService(ISearchService searchService) {
+ this.searchService = searchService;
+ }
+
+ public List<Map<String, Object>> getElementsByQuery(String projectId, String token, String modelId, String query,
+ Integer maxElements, String perfectMatch) throws SecurityException {
+ List<Map<String, Object>> resultMap = new ArrayList<>();
+
+ Model model = getModelService().getLastModelByProjectId(projectId, token);
+
+ Integer limit = Integer.valueOf(maxElements);
+ boolean match = perfectMatch.equals("true");
+ List<BioEntity> elements = searchService.searchByQuery(model, query, limit, match);
+ for (BioEntity object : elements) {
+ Map<String, Object> result = createMinifiedSearchResult(object);
+ resultMap.add(result);
+ }
+ return resultMap;
+ }
+
+ public String[] getSuggestedQueryList(String projectId, String token) throws SecurityException {
+ Model model = getModelService().getLastModelByProjectId(projectId, token);
+ return searchService.getSuggestedQueryList(model);
+ }
+
+}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsController.java
index 8a45c60fa2..d5e58fdbb4 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsController.java
@@ -1,40 +1,40 @@
-package lcsb.mapviewer.api.projects.models.bioEntities.elements;
-
-import java.util.List;
-import java.util.Map;
-
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.MediaType;
-import org.springframework.web.bind.annotation.CookieValue;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RequestParam;
-import org.springframework.web.bind.annotation.RestController;
-
-import lcsb.mapviewer.api.BaseController;
-import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.services.SecurityException;
-
-@RestController
-public class ElementsController extends BaseController {
- @Autowired
- private ElementsRestImpl projectController;
-
- @RequestMapping(value = "/projects/{projectId}/models/{modelId}/bioEntities/elements/", method = { RequestMethod.GET, RequestMethod.POST },
- produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getElements(//
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @RequestParam(value = "id", defaultValue = "") String id, //
- @RequestParam(value = "type", defaultValue = "") String type, //
- @RequestParam(value = "columns", defaultValue = "") String columns, //
- @RequestParam(value = "includedCompartmentIds", defaultValue = "") String includedCompartmentIds, //
- @RequestParam(value = "excludedCompartmentIds", defaultValue = "") String excludedCompartmentIds, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token//
- ) throws SecurityException, QueryException {
- return projectController.getElements(projectId, id, columns, modelId, token, type, includedCompartmentIds, excludedCompartmentIds);
- }
-
+package lcsb.mapviewer.api.projects.models.bioEntities.elements;
+
+import java.util.List;
+import java.util.Map;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.web.bind.annotation.CookieValue;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.RestController;
+
+import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.services.SecurityException;
+
+@RestController
+public class ElementsController extends BaseController {
+ @Autowired
+ private ElementsRestImpl projectController;
+
+ @RequestMapping(value = "/projects/{projectId}/models/{modelId}/bioEntities/elements/", method = { RequestMethod.GET, RequestMethod.POST },
+ produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getElements(//
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "modelId") String modelId, //
+ @RequestParam(value = "id", defaultValue = "") String id, //
+ @RequestParam(value = "type", defaultValue = "") String type, //
+ @RequestParam(value = "columns", defaultValue = "") String columns, //
+ @RequestParam(value = "includedCompartmentIds", defaultValue = "") String includedCompartmentIds, //
+ @RequestParam(value = "excludedCompartmentIds", defaultValue = "") String excludedCompartmentIds, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token//
+ ) throws SecurityException, QueryException {
+ return projectController.getElements(projectId, id, columns, modelId, token, type, includedCompartmentIds, excludedCompartmentIds);
+ }
+
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
index d2f3739d54..533a8bfd2e 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
@@ -1,346 +1,346 @@
-package lcsb.mapviewer.api.projects.models.bioEntities.elements;
-
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeMap;
-
-import org.apache.log4j.Logger;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.api.BaseRestImpl;
-import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.ModificationType;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.field.AbstractSiteModification;
-import lcsb.mapviewer.model.map.species.field.BindingRegion;
-import lcsb.mapviewer.model.map.species.field.CodingRegion;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.model.map.species.field.ModificationSite;
-import lcsb.mapviewer.model.map.species.field.ProteinBindingDomain;
-import lcsb.mapviewer.model.map.species.field.RegulatoryRegion;
-import lcsb.mapviewer.model.map.species.field.Residue;
-import lcsb.mapviewer.model.map.species.field.Structure;
-import lcsb.mapviewer.model.map.species.field.TranscriptionSite;
-import lcsb.mapviewer.model.map.species.field.UniprotRecord;
-import lcsb.mapviewer.services.SecurityException;
-
-@Transactional(value = "txManager")
-public class ElementsRestImpl extends BaseRestImpl {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(ElementsRestImpl.class);
-
- public List<Map<String, Object>> getElements(String projectId, String id, String columns, String modelId,
- String token, String type, String includedCompartmentIds, String excludedCompartmentIds)
- throws QueryException, SecurityException {
- Set<Integer> ids = new HashSet<>();
- if (!id.equals("")) {
- for (String str : id.split(",")) {
- ids.add(Integer.valueOf(str));
- }
- }
- Set<String> types = new HashSet<>();
- if (!type.isEmpty()) {
- for (String str : type.split(",")) {
- types.add(str.toLowerCase());
- }
- }
- List<Model> models = getModels(projectId, modelId, token);
-
- Set<Compartment> includedCompartments = getCompartments(includedCompartmentIds, models);
- Set<Compartment> excludedCompartments = getCompartments(excludedCompartmentIds, models);
- Set<String> columnsSet = createElementColumnSet(columns);
-
- List<Element> elements = new ArrayList<>();
-
- for (Model model2 : models) {
- for (Element element : model2.getElements()) {
- if (ids.size() == 0 || ids.contains(element.getId())) {
- if (types.size() == 0 || types.contains(element.getStringType().toLowerCase())) {
- if (matchIncludedExcludedCompartments(element, includedCompartments, excludedCompartments)) {
- elements.add(element);
- }
- }
- }
- }
- }
- elements.sort(BioEntity.ID_COMPARATOR);
- List<Map<String, Object>> result = new ArrayList<>();
- for (Element element : elements) {
- result.add(preparedElement(element, columnsSet));
-
- }
- return result;
- }
-
- private boolean matchIncludedExcludedCompartments(Element element, Set<Compartment> includedCompartments,
- Set<Compartment> excludedCompartments) {
- boolean matchIncluded = true;
- boolean matchExcluded = false;
-
- if (includedCompartments.size() > 0) {
- matchIncluded = matchCompartments(element, includedCompartments);
- }
- if (excludedCompartments.size() > 0) {
- matchExcluded = matchCompartments(element, excludedCompartments);
- }
-
- return matchIncluded && !matchExcluded;
- }
-
- private boolean matchCompartments(Element element, Set<Compartment> compartmentList) {
- boolean isInside = false;
- if (element != null) {
- for (Compartment compartment : compartmentList) {
- if (compartment.contains(element) && element.getModel().getId().equals(compartment.getModel().getId())) {
- isInside = true;
- }
- }
- }
- return isInside;
- }
-
- private Set<Compartment> getCompartments(String includedCompartmentIds, List<Model> models) {
- Set<Compartment> includedCompartments = new HashSet<>();
- int count = 0;
- if (!includedCompartmentIds.isEmpty()) {
- for (String compartmentId : includedCompartmentIds.split(",")) {
- Integer integerId = Integer.valueOf(compartmentId);
- for (Model model : models) {
- Compartment compartment = model.getElementByDbId(integerId);
- if (compartment != null) {
- includedCompartments.add(compartment);
- }
- }
- count++;
- }
- if (count > 0 && includedCompartments.size() == 0) {
- includedCompartments.add(new Compartment("empty_comp_to_reject_all_elements"));
- }
- }
- return includedCompartments;
- }
-
- private Map<String, Object> preparedElement(Element element, Set<String> columnsSet) {
- Map<String, Object> result = new TreeMap<>();
- for (String string : columnsSet) {
- String column = string.toLowerCase();
- Object value = null;
- if (column.equals("id") || column.equals("idobject")) {
- value = element.getId();
- } else if (column.equals("modelid")) {
- value = element.getModelData().getId();
- } else if (column.equals("elementid")) {
- value = element.getElementId();
- } else if (column.equals("name")) {
- value = element.getName();
- } else if (column.equals("type")) {
- value = element.getStringType();
- } else if (column.equals("symbol")) {
- value = element.getSymbol();
- } else if (column.equals("fullname")) {
- value = element.getFullName();
- } else if (column.equals("abbreviation")) {
- value = element.getAbbreviation();
- } else if (column.equals("compartmentid")) {
- if (element.getCompartment() != null) {
- value = element.getCompartment().getId();
- }
- } else if (column.equals("complexid")) {
- if (element instanceof Species) {
- if (((Species) element).getComplex() != null) {
- value = ((Species) element).getComplex().getId();
- }
- }
- } else if (column.equals("initialconcentration")) {
- if (element instanceof Species) {
- value = ((Species) element).getInitialConcentration();
- }
- } else if (column.equals("initialamount")) {
- if (element instanceof Species) {
- value = ((Species) element).getInitialAmount();
- }
- } else if (column.equals("boundarycondition")) {
- if (element instanceof Species) {
- value = ((Species) element).isBoundaryCondition();
- }
- } else if (column.equals("constant")) {
- if (element instanceof Species) {
- value = ((Species) element).isConstant();
- }
- } else if (column.equals("references")) {
- value = createAnnotations(element.getMiriamData());
- } else if (column.equals("synonyms")) {
- value = element.getSynonyms();
- } else if (column.equals("formula")) {
- value = element.getFormula();
- } else if (column.equals("notes")) {
- value = element.getNotes();
- } else if (column.equals("other")) {
- value = getOthersForElement(element);
- } else if (column.equals("formersymbols")) {
- value = element.getFormerSymbols();
- } else if (column.equals("hierarchyvisibilitylevel")) {
- value = element.getVisibilityLevel();
- } else if (column.equals("transparencylevel")) {
- value = element.getTransparencyLevel();
- } else if (column.equals("linkedsubmodel")) {
- if (element.getSubmodel() != null) {
- value = element.getSubmodel().getSubmodel().getId();
- }
- } else if (column.equals("bounds")) {
- value = createBounds(element.getX(), element.getY(), element.getWidth(), element.getHeight());
- } else {
- value = "Unknown column";
- }
- result.put(string, value);
- }
- return result;
- }
-
- protected Map<String, Object> getOthersForElement(Element element) {
- Map<String, Object> result = new TreeMap<>();
- List<Map<String, Object>> modifications = new ArrayList<>();
- String structuralState = null;
- Map<String, Object> structures = new TreeMap<>();
- if (element instanceof Protein) {
- Protein protein = ((Protein) element);
- modifications = getModifications(protein.getModificationResidues());
- structuralState = protein.getStructuralState();
- } else if (element instanceof Rna) {
- Rna rna = ((Rna) element);
- modifications = getModifications(rna.getRegions());
- structuralState = rna.getState();
- } else if (element instanceof AntisenseRna) {
- AntisenseRna antisenseRna = ((AntisenseRna) element);
- modifications = getModifications(antisenseRna.getRegions());
- structuralState = antisenseRna.getState();
- } else if (element instanceof Gene) {
- Gene gene = ((Gene) element);
- modifications = getModifications(gene.getModificationResidues());
- structuralState = gene.getState();
- }
- if (element instanceof Species) {
- structures = getStructures(((Species) element).getUniprots());
- }
- result.put("modifications", modifications);
- result.put("structuralState", structuralState);
- result.put("structures", structures);
-
- return result;
- }
-
- private List<Map<String, Object>> getModifications(List<? extends ModificationResidue> elements) {
- List<Map<String, Object>> result = new ArrayList<>();
- for (ModificationResidue region : elements) {
- Map<String, Object> row = new TreeMap<>();
- row.put("name", region.getName());
- row.put("modificationId", region.getIdModificationResidue());
- if (region instanceof AbstractSiteModification) {
- AbstractSiteModification siteModification = ((AbstractSiteModification) region);
- if (siteModification.getState() != null) {
- row.put("state", siteModification.getState().name());
- }
- }
- String type = null;
- if (region instanceof Residue) {
- type = ModificationType.RESIDUE.name();
- } else if (region instanceof BindingRegion) {
- type = ModificationType.BINDING_REGION.name();
- } else if (region instanceof CodingRegion) {
- type = ModificationType.CODING_REGION.name();
- } else if (region instanceof ProteinBindingDomain) {
- type = ModificationType.PROTEIN_BINDING_DOMAIN.name();
- } else if (region instanceof RegulatoryRegion) {
- type = ModificationType.REGULATORY_REGION.name();
- } else if (region instanceof TranscriptionSite) {
- if (((TranscriptionSite) region).getDirection().equals("LEFT")) {
- type = ModificationType.TRANSCRIPTION_SITE_LEFT.name();
- } else {
- type = ModificationType.TRANSCRIPTION_SITE_RIGHT.name();
- }
- } else if (region instanceof ModificationSite) {
- type = ModificationType.MODIFICATION_SITE.name();
- } else {
- throw new InvalidArgumentException("Unknown class: " + region.getClass());
- }
- row.put("type", type);
- result.add(row);
- }
- return result;
- }
-
- private Map<String, Object> getStructures(Set<UniprotRecord> uniprots) {
- Map<String, Object> result = new TreeMap<>();
- for (UniprotRecord uniprotRec : uniprots) {
- Set<Object> structs = new HashSet<>();
- for (Structure struct : uniprotRec.getStructures()) {
- structs.add(struct.toMap());
- }
- result.put(uniprotRec.getUniprotId(), structs);
- }
- return result;
- }
-
- private Map<String, Object> createBounds(Double x, Double y, Double width, Double height) {
- Map<String, Object> result = new TreeMap<>();
- result.put("x", x);
- result.put("y", y);
- result.put("width", width);
- result.put("height", height);
- return result;
- }
-
- private Set<String> createElementColumnSet(String columns) {
- Set<String> columnsSet = new HashSet<>();
- if (columns.equals("")) {
- columnsSet.add("id");
- columnsSet.add("elementId");
- columnsSet.add("modelId");
- columnsSet.add("name");
- columnsSet.add("type");
- columnsSet.add("notes");
- columnsSet.add("type");
- columnsSet.add("symbol");
- columnsSet.add("complexId");
- columnsSet.add("compartmentId");
- columnsSet.add("fullName");
- columnsSet.add("abbreviation");
- columnsSet.add("formula");
- columnsSet.add("name");
- columnsSet.add("synonyms");
- columnsSet.add("formerSymbols");
- columnsSet.add("references");
- columnsSet.add("bounds");
- columnsSet.add("hierarchyVisibilityLevel");
- columnsSet.add("transparencyLevel");
- columnsSet.add("linkedSubmodel");
- columnsSet.add("other");
- columnsSet.add("initialConcentration");
- columnsSet.add("boundaryCondition");
- columnsSet.add("constant");
- columnsSet.add("initialAmount");
- } else {
- for (String str : columns.split(",")) {
- columnsSet.add(str);
- }
- }
- return columnsSet;
- }
-
-}
+package lcsb.mapviewer.api.projects.models.bioEntities.elements;
+
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeMap;
+
+import org.apache.log4j.Logger;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.api.BaseRestImpl;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.ModificationType;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.AbstractSiteModification;
+import lcsb.mapviewer.model.map.species.field.BindingRegion;
+import lcsb.mapviewer.model.map.species.field.CodingRegion;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
+import lcsb.mapviewer.model.map.species.field.ProteinBindingDomain;
+import lcsb.mapviewer.model.map.species.field.RegulatoryRegion;
+import lcsb.mapviewer.model.map.species.field.Residue;
+import lcsb.mapviewer.model.map.species.field.Structure;
+import lcsb.mapviewer.model.map.species.field.TranscriptionSite;
+import lcsb.mapviewer.model.map.species.field.UniprotRecord;
+import lcsb.mapviewer.services.SecurityException;
+
+@Transactional(value = "txManager")
+public class ElementsRestImpl extends BaseRestImpl {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(ElementsRestImpl.class);
+
+ public List<Map<String, Object>> getElements(String projectId, String id, String columns, String modelId,
+ String token, String type, String includedCompartmentIds, String excludedCompartmentIds)
+ throws QueryException, SecurityException {
+ Set<Integer> ids = new HashSet<>();
+ if (!id.equals("")) {
+ for (String str : id.split(",")) {
+ ids.add(Integer.valueOf(str));
+ }
+ }
+ Set<String> types = new HashSet<>();
+ if (!type.isEmpty()) {
+ for (String str : type.split(",")) {
+ types.add(str.toLowerCase());
+ }
+ }
+ List<Model> models = getModels(projectId, modelId, token);
+
+ Set<Compartment> includedCompartments = getCompartments(includedCompartmentIds, models);
+ Set<Compartment> excludedCompartments = getCompartments(excludedCompartmentIds, models);
+ Set<String> columnsSet = createElementColumnSet(columns);
+
+ List<Element> elements = new ArrayList<>();
+
+ for (Model model2 : models) {
+ for (Element element : model2.getElements()) {
+ if (ids.size() == 0 || ids.contains(element.getId())) {
+ if (types.size() == 0 || types.contains(element.getStringType().toLowerCase())) {
+ if (matchIncludedExcludedCompartments(element, includedCompartments, excludedCompartments)) {
+ elements.add(element);
+ }
+ }
+ }
+ }
+ }
+ elements.sort(BioEntity.ID_COMPARATOR);
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (Element element : elements) {
+ result.add(preparedElement(element, columnsSet));
+
+ }
+ return result;
+ }
+
+ private boolean matchIncludedExcludedCompartments(Element element, Set<Compartment> includedCompartments,
+ Set<Compartment> excludedCompartments) {
+ boolean matchIncluded = true;
+ boolean matchExcluded = false;
+
+ if (includedCompartments.size() > 0) {
+ matchIncluded = matchCompartments(element, includedCompartments);
+ }
+ if (excludedCompartments.size() > 0) {
+ matchExcluded = matchCompartments(element, excludedCompartments);
+ }
+
+ return matchIncluded && !matchExcluded;
+ }
+
+ private boolean matchCompartments(Element element, Set<Compartment> compartmentList) {
+ boolean isInside = false;
+ if (element != null) {
+ for (Compartment compartment : compartmentList) {
+ if (compartment.contains(element) && element.getModel().getId().equals(compartment.getModel().getId())) {
+ isInside = true;
+ }
+ }
+ }
+ return isInside;
+ }
+
+ private Set<Compartment> getCompartments(String includedCompartmentIds, List<Model> models) {
+ Set<Compartment> includedCompartments = new HashSet<>();
+ int count = 0;
+ if (!includedCompartmentIds.isEmpty()) {
+ for (String compartmentId : includedCompartmentIds.split(",")) {
+ Integer integerId = Integer.valueOf(compartmentId);
+ for (Model model : models) {
+ Compartment compartment = model.getElementByDbId(integerId);
+ if (compartment != null) {
+ includedCompartments.add(compartment);
+ }
+ }
+ count++;
+ }
+ if (count > 0 && includedCompartments.size() == 0) {
+ includedCompartments.add(new Compartment("empty_comp_to_reject_all_elements"));
+ }
+ }
+ return includedCompartments;
+ }
+
+ private Map<String, Object> preparedElement(Element element, Set<String> columnsSet) {
+ Map<String, Object> result = new TreeMap<>();
+ for (String string : columnsSet) {
+ String column = string.toLowerCase();
+ Object value = null;
+ if (column.equals("id") || column.equals("idobject")) {
+ value = element.getId();
+ } else if (column.equals("modelid")) {
+ value = element.getModelData().getId();
+ } else if (column.equals("elementid")) {
+ value = element.getElementId();
+ } else if (column.equals("name")) {
+ value = element.getName();
+ } else if (column.equals("type")) {
+ value = element.getStringType();
+ } else if (column.equals("symbol")) {
+ value = element.getSymbol();
+ } else if (column.equals("fullname")) {
+ value = element.getFullName();
+ } else if (column.equals("abbreviation")) {
+ value = element.getAbbreviation();
+ } else if (column.equals("compartmentid")) {
+ if (element.getCompartment() != null) {
+ value = element.getCompartment().getId();
+ }
+ } else if (column.equals("complexid")) {
+ if (element instanceof Species) {
+ if (((Species) element).getComplex() != null) {
+ value = ((Species) element).getComplex().getId();
+ }
+ }
+ } else if (column.equals("initialconcentration")) {
+ if (element instanceof Species) {
+ value = ((Species) element).getInitialConcentration();
+ }
+ } else if (column.equals("initialamount")) {
+ if (element instanceof Species) {
+ value = ((Species) element).getInitialAmount();
+ }
+ } else if (column.equals("boundarycondition")) {
+ if (element instanceof Species) {
+ value = ((Species) element).isBoundaryCondition();
+ }
+ } else if (column.equals("constant")) {
+ if (element instanceof Species) {
+ value = ((Species) element).isConstant();
+ }
+ } else if (column.equals("references")) {
+ value = createAnnotations(element.getMiriamData());
+ } else if (column.equals("synonyms")) {
+ value = element.getSynonyms();
+ } else if (column.equals("formula")) {
+ value = element.getFormula();
+ } else if (column.equals("notes")) {
+ value = element.getNotes();
+ } else if (column.equals("other")) {
+ value = getOthersForElement(element);
+ } else if (column.equals("formersymbols")) {
+ value = element.getFormerSymbols();
+ } else if (column.equals("hierarchyvisibilitylevel")) {
+ value = element.getVisibilityLevel();
+ } else if (column.equals("transparencylevel")) {
+ value = element.getTransparencyLevel();
+ } else if (column.equals("linkedsubmodel")) {
+ if (element.getSubmodel() != null) {
+ value = element.getSubmodel().getSubmodel().getId();
+ }
+ } else if (column.equals("bounds")) {
+ value = createBounds(element.getX(), element.getY(), element.getWidth(), element.getHeight());
+ } else {
+ value = "Unknown column";
+ }
+ result.put(string, value);
+ }
+ return result;
+ }
+
+ protected Map<String, Object> getOthersForElement(Element element) {
+ Map<String, Object> result = new TreeMap<>();
+ List<Map<String, Object>> modifications = new ArrayList<>();
+ String structuralState = null;
+ Map<String, Object> structures = new TreeMap<>();
+ if (element instanceof Protein) {
+ Protein protein = ((Protein) element);
+ modifications = getModifications(protein.getModificationResidues());
+ structuralState = protein.getStructuralState();
+ } else if (element instanceof Rna) {
+ Rna rna = ((Rna) element);
+ modifications = getModifications(rna.getRegions());
+ structuralState = rna.getState();
+ } else if (element instanceof AntisenseRna) {
+ AntisenseRna antisenseRna = ((AntisenseRna) element);
+ modifications = getModifications(antisenseRna.getRegions());
+ structuralState = antisenseRna.getState();
+ } else if (element instanceof Gene) {
+ Gene gene = ((Gene) element);
+ modifications = getModifications(gene.getModificationResidues());
+ structuralState = gene.getState();
+ }
+ if (element instanceof Species) {
+ structures = getStructures(((Species) element).getUniprots());
+ }
+ result.put("modifications", modifications);
+ result.put("structuralState", structuralState);
+ result.put("structures", structures);
+
+ return result;
+ }
+
+ private List<Map<String, Object>> getModifications(List<? extends ModificationResidue> elements) {
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (ModificationResidue region : elements) {
+ Map<String, Object> row = new TreeMap<>();
+ row.put("name", region.getName());
+ row.put("modificationId", region.getIdModificationResidue());
+ if (region instanceof AbstractSiteModification) {
+ AbstractSiteModification siteModification = ((AbstractSiteModification) region);
+ if (siteModification.getState() != null) {
+ row.put("state", siteModification.getState().name());
+ }
+ }
+ String type = null;
+ if (region instanceof Residue) {
+ type = ModificationType.RESIDUE.name();
+ } else if (region instanceof BindingRegion) {
+ type = ModificationType.BINDING_REGION.name();
+ } else if (region instanceof CodingRegion) {
+ type = ModificationType.CODING_REGION.name();
+ } else if (region instanceof ProteinBindingDomain) {
+ type = ModificationType.PROTEIN_BINDING_DOMAIN.name();
+ } else if (region instanceof RegulatoryRegion) {
+ type = ModificationType.REGULATORY_REGION.name();
+ } else if (region instanceof TranscriptionSite) {
+ if (((TranscriptionSite) region).getDirection().equals("LEFT")) {
+ type = ModificationType.TRANSCRIPTION_SITE_LEFT.name();
+ } else {
+ type = ModificationType.TRANSCRIPTION_SITE_RIGHT.name();
+ }
+ } else if (region instanceof ModificationSite) {
+ type = ModificationType.MODIFICATION_SITE.name();
+ } else {
+ throw new InvalidArgumentException("Unknown class: " + region.getClass());
+ }
+ row.put("type", type);
+ result.add(row);
+ }
+ return result;
+ }
+
+ private Map<String, Object> getStructures(Set<UniprotRecord> uniprots) {
+ Map<String, Object> result = new TreeMap<>();
+ for (UniprotRecord uniprotRec : uniprots) {
+ Set<Object> structs = new HashSet<>();
+ for (Structure struct : uniprotRec.getStructures()) {
+ structs.add(struct.toMap());
+ }
+ result.put(uniprotRec.getUniprotId(), structs);
+ }
+ return result;
+ }
+
+ private Map<String, Object> createBounds(Double x, Double y, Double width, Double height) {
+ Map<String, Object> result = new TreeMap<>();
+ result.put("x", x);
+ result.put("y", y);
+ result.put("width", width);
+ result.put("height", height);
+ return result;
+ }
+
+ private Set<String> createElementColumnSet(String columns) {
+ Set<String> columnsSet = new HashSet<>();
+ if (columns.equals("")) {
+ columnsSet.add("id");
+ columnsSet.add("elementId");
+ columnsSet.add("modelId");
+ columnsSet.add("name");
+ columnsSet.add("type");
+ columnsSet.add("notes");
+ columnsSet.add("type");
+ columnsSet.add("symbol");
+ columnsSet.add("complexId");
+ columnsSet.add("compartmentId");
+ columnsSet.add("fullName");
+ columnsSet.add("abbreviation");
+ columnsSet.add("formula");
+ columnsSet.add("name");
+ columnsSet.add("synonyms");
+ columnsSet.add("formerSymbols");
+ columnsSet.add("references");
+ columnsSet.add("bounds");
+ columnsSet.add("hierarchyVisibilityLevel");
+ columnsSet.add("transparencyLevel");
+ columnsSet.add("linkedSubmodel");
+ columnsSet.add("other");
+ columnsSet.add("initialConcentration");
+ columnsSet.add("boundaryCondition");
+ columnsSet.add("constant");
+ columnsSet.add("initialAmount");
+ } else {
+ for (String str : columns.split(",")) {
+ columnsSet.add(str);
+ }
+ }
+ return columnsSet;
+ }
+
+}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsController.java
index b53c678caf..06c2d1390e 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsController.java
@@ -1,38 +1,38 @@
-package lcsb.mapviewer.api.projects.models.bioEntities.reactions;
-
-import java.util.List;
-import java.util.Map;
-
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.MediaType;
-import org.springframework.web.bind.annotation.CookieValue;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RequestParam;
-import org.springframework.web.bind.annotation.RestController;
-
-import lcsb.mapviewer.api.BaseController;
-import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.services.SecurityException;
-
-@RestController
-public class ReactionsController extends BaseController {
- @Autowired
- private ReactionsRestImpl reactionController;
-
- @RequestMapping(value = "/projects/{projectId}/models/{modelId}/bioEntities/reactions/", method = { RequestMethod.GET, RequestMethod.POST },
- produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getReactions(//
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @RequestParam(value = "id", defaultValue = "") String id, //
- @RequestParam(value = "columns", defaultValue = "") String columns, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @RequestParam(value = "participantId", defaultValue = "") String participantId//
- ) throws SecurityException,QueryException {
- return reactionController.getReactions(projectId, id, columns, modelId, token, participantId);
- }
-
+package lcsb.mapviewer.api.projects.models.bioEntities.reactions;
+
+import java.util.List;
+import java.util.Map;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.web.bind.annotation.CookieValue;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.RestController;
+
+import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.services.SecurityException;
+
+@RestController
+public class ReactionsController extends BaseController {
+ @Autowired
+ private ReactionsRestImpl reactionController;
+
+ @RequestMapping(value = "/projects/{projectId}/models/{modelId}/bioEntities/reactions/", method = { RequestMethod.GET, RequestMethod.POST },
+ produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getReactions(//
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "modelId") String modelId, //
+ @RequestParam(value = "id", defaultValue = "") String id, //
+ @RequestParam(value = "columns", defaultValue = "") String columns, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @RequestParam(value = "participantId", defaultValue = "") String participantId//
+ ) throws SecurityException,QueryException {
+ return reactionController.getReactions(projectId, id, columns, modelId, token, participantId);
+ }
+
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java
index 07e712a2f3..86bf92fb37 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java
@@ -1,315 +1,315 @@
-package lcsb.mapviewer.api.projects.models.bioEntities.reactions;
-
-import java.awt.geom.Line2D;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeMap;
-
-import javax.xml.transform.TransformerException;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.api.BaseRestImpl;
-import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
-import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
-import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.AbstractNode;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.reaction.NodeOperator;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.ReactionNode;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.UserAccessException;
-import lcsb.mapviewer.services.interfaces.IModelService;
-import lcsb.mapviewer.services.interfaces.IUserService;
-
-@Transactional(value = "txManager")
-public class ReactionsRestImpl extends BaseRestImpl {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(ReactionsRestImpl.class);
-
- @Autowired
- private IUserService userService;
-
- @Autowired
- private IModelService modelService;
-
- /**
- * @return the userService
- * @see #userService
- */
- public IUserService getUserService() {
- return userService;
- }
-
- /**
- * @param userService
- * the userService to set
- * @see #userService
- */
- public void setUserService(IUserService userService) {
- this.userService = userService;
- }
-
- public List<Map<String, Object>> getReactions(String projectId, String id, String columns, String modelId,
- String token, String participantElementId) throws UserAccessException, SecurityException, QueryException {
- Set<Integer> ids = new HashSet<>();
- if (!id.equals("")) {
- for (String str : id.split(",")) {
- ids.add(Integer.valueOf(str));
- }
- }
- List<Model> models = getModels(projectId, modelId, token);
-
- Set<Element> elementSet = new HashSet<>();
- if (!participantElementId.equals("")) {
- for (String str : participantElementId.split(",")) {
- for (Model model : models) {
- elementSet.add(model.getElementByDbId(Integer.valueOf(str)));
- }
- }
- }
- Set<String> columnsSet = createReactionColumnSet(columns);
-
- List<Reaction> elements = new ArrayList<>();
-
- for (Model model2 : models) {
- for (Reaction reaction : model2.getReactions()) {
- if (ids.size() == 0 || ids.contains(reaction.getId())) {
- if (elementSet.size() == 0 || reactionContainsElement(reaction, elementSet)) {
- elements.add(reaction);
- }
- }
- }
- }
- elements.sort(BioEntity.ID_COMPARATOR);
- List<Map<String, Object>> result = new ArrayList<>();
- for (Reaction element : elements) {
- result.add(preparedReaction(element, columnsSet));
-
- }
- return result;
- }
-
- private boolean reactionContainsElement(Reaction reaction, Set<Element> elementSet) {
- for (Element element : elementSet) {
- if (reaction.containsElement(element)) {
- return true;
- }
- }
- return false;
- }
-
- private Map<String, Object> preparedReaction(Reaction reaction, Set<String> columnsSet) {
- Map<String, Object> result = new TreeMap<>();
- for (String string : columnsSet) {
- String column = string.toLowerCase();
- Object value = null;
- if (column.equals("id") || column.equals("idobject")) {
- value = reaction.getId();
- } else if (column.equals("modelid")) {
- value = reaction.getModelData().getId();
- } else if (column.equals("reactionid")) {
- value = reaction.getIdReaction();
- } else if (column.equals("name")) {
- value = reaction.getName();
- } else if (column.equals("centerpoint")) {
- value = reaction.getCenterPoint();
- } else if (column.equals("products")) {
- List<Map<String, Object>> ids = new ArrayList<>();
- for (Product product : reaction.getProducts()) {
- ids.add(createReactionNode(product));
- }
- value = ids;
- } else if (column.equals("reactants")) {
- List<Map<String, Object>> ids = new ArrayList<>();
- for (Reactant reactant : reaction.getReactants()) {
- ids.add(createReactionNode(reactant));
- }
- value = ids;
- } else if (column.equals("modifiers")) {
- List<Map<String, Object>> ids = new ArrayList<>();
- for (Modifier modifier : reaction.getModifiers()) {
- ids.add(createReactionNode(modifier));
- }
- value = ids;
- } else if (column.equals("type")) {
- value = reaction.getStringType();
- } else if (column.equals("hierarchyvisibilitylevel")) {
- value = reaction.getVisibilityLevel();
- } else if (column.equals("lines")) {
- value = getLines(reaction);
- } else if (column.equals("notes")) {
- value = reaction.getNotes();
- } else if (column.equals("kineticlaw")) {
- value = kineticsToMap(reaction.getKinetics());
- } else if (column.equals("references")) {
- value = createAnnotations(reaction.getMiriamData());
- } else {
- value = "Unknown column";
- }
- result.put(string, value);
- }
- return result;
- }
-
- private List<Map<String, Object>> getLines(Reaction reaction) {
- List<Map<String, Object>> result = new ArrayList<>();
- for (Reactant reactant : reaction.getReactants()) {
- result.addAll(getLines(reactant));
- }
- for (Product product : reaction.getProducts()) {
- result.addAll(getLines(product));
- }
- for (Modifier modifier : reaction.getModifiers()) {
- result.addAll(getLines(modifier));
- }
- for (NodeOperator operator : reaction.getOperators()) {
- result.addAll(getLines(operator));
- }
- return result;
- }
-
- protected List<Map<String, Object>> getLines(AbstractNode reactant) {
- // order in this method is to keep the order from previous version, it can be
- // changed in the future, but I wanted to make that it's giving the same results
- // when refactoring
- List<Map<String, Object>> result = new ArrayList<>();
- List<Line2D> startLines = new ArrayList<>();
- List<Line2D> middleLines = new ArrayList<>();
- List<Line2D> endLines = new ArrayList<>();
-
- List<Line2D> lines = reactant.getLine().getLines();
-
- if (reactant instanceof Reactant) {
- startLines.add(lines.get(0));
- for (int i = 1; i < lines.size(); i++) {
- middleLines.add(lines.get(i));
- }
- } else if (reactant instanceof Product) {
- endLines.add(lines.get(lines.size() - 1));
- for (int i = 0; i < lines.size()-1; i++) {
- middleLines.add(lines.get(i));
- }
- } else if (reactant instanceof Modifier) {
- middleLines.add(lines.get(lines.size() - 1));
- for (int i = 0; i < lines.size()-1; i++) {
- middleLines.add(lines.get(i));
- }
- } else {
- middleLines.addAll(lines);
- }
-
- for (Line2D line2d : startLines) {
- result.add(lineToMap(line2d, "START"));
- }
- for (Line2D line2d : endLines) {
- result.add(lineToMap(line2d, "END"));
- }
- for (Line2D line2d : middleLines) {
- result.add(lineToMap(line2d, "MIDDLE"));
- }
-
- return result;
- }
-
- private Map<String, Object> lineToMap(Line2D line2d, String type) {
- Map<String, Object> result = new LinkedHashMap<>();
- result.put("start", line2d.getP1());
- result.put("end", line2d.getP2());
- result.put("type", type);
- return result;
- }
-
- private Map<String, Object> createReactionNode(ReactionNode node) {
- Map<String, Object> result = new TreeMap<>();
- result.put("aliasId", node.getElement().getId());
- result.put("stoichiometry", node.getStoichiometry());
- return result;
- }
-
- private Map<String, Object> kineticsToMap(SbmlKinetics kinetics) {
- if (kinetics == null) {
- return null;
- }
- Map<String, Object> result = new TreeMap<>();
- result.put("definition", kinetics.getDefinition());
- try {
- result.put("mathMlPresentation", super.mathMLToPresentationML(kinetics.getDefinition()));
- } catch (IOException | InvalidXmlSchemaException | TransformerException e) {
- logger.error("Problems with transforming kinetics", e);
- }
-
- List<Integer> functionIds = new ArrayList<>();
- for (SbmlFunction function : kinetics.getFunctions()) {
- functionIds.add(function.getId());
- }
- result.put("functionIds", functionIds);
- List<Integer> parameterIds = new ArrayList<>();
- for (SbmlParameter parameter : kinetics.getParameters()) {
- parameterIds.add(parameter.getId());
- }
- result.put("parameterIds", parameterIds);
- return result;
- }
-
- private Set<String> createReactionColumnSet(String columns) {
- Set<String> columnsSet = new HashSet<>();
- if (columns.equals("")) {
- columnsSet.add("id");
- columnsSet.add("reactionId");
- columnsSet.add("modelId");
- columnsSet.add("type");
- columnsSet.add("lines");
- columnsSet.add("kineticLaw");
- columnsSet.add("centerPoint");
- columnsSet.add("products");
- columnsSet.add("reactants");
- columnsSet.add("modifiers");
- columnsSet.add("hierarchyVisibilityLevel");
- columnsSet.add("references");
- columnsSet.add("notes");
- } else {
- for (String str : columns.split(",")) {
- columnsSet.add(str);
- }
- }
- return columnsSet;
- }
-
- /**
- * @return the modelService
- * @see #modelService
- */
- public IModelService getModelService() {
- return modelService;
- }
-
- /**
- * @param modelService
- * the modelService to set
- * @see #modelService
- */
- public void setModelService(IModelService modelService) {
- this.modelService = modelService;
- }
-
-}
+package lcsb.mapviewer.api.projects.models.bioEntities.reactions;
+
+import java.awt.geom.Line2D;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeMap;
+
+import javax.xml.transform.TransformerException;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.api.BaseRestImpl;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
+import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
+import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.AbstractNode;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.reaction.NodeOperator;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.UserAccessException;
+import lcsb.mapviewer.services.interfaces.IModelService;
+import lcsb.mapviewer.services.interfaces.IUserService;
+
+@Transactional(value = "txManager")
+public class ReactionsRestImpl extends BaseRestImpl {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(ReactionsRestImpl.class);
+
+ @Autowired
+ private IUserService userService;
+
+ @Autowired
+ private IModelService modelService;
+
+ /**
+ * @return the userService
+ * @see #userService
+ */
+ public IUserService getUserService() {
+ return userService;
+ }
+
+ /**
+ * @param userService
+ * the userService to set
+ * @see #userService
+ */
+ public void setUserService(IUserService userService) {
+ this.userService = userService;
+ }
+
+ public List<Map<String, Object>> getReactions(String projectId, String id, String columns, String modelId,
+ String token, String participantElementId) throws UserAccessException, SecurityException, QueryException {
+ Set<Integer> ids = new HashSet<>();
+ if (!id.equals("")) {
+ for (String str : id.split(",")) {
+ ids.add(Integer.valueOf(str));
+ }
+ }
+ List<Model> models = getModels(projectId, modelId, token);
+
+ Set<Element> elementSet = new HashSet<>();
+ if (!participantElementId.equals("")) {
+ for (String str : participantElementId.split(",")) {
+ for (Model model : models) {
+ elementSet.add(model.getElementByDbId(Integer.valueOf(str)));
+ }
+ }
+ }
+ Set<String> columnsSet = createReactionColumnSet(columns);
+
+ List<Reaction> elements = new ArrayList<>();
+
+ for (Model model2 : models) {
+ for (Reaction reaction : model2.getReactions()) {
+ if (ids.size() == 0 || ids.contains(reaction.getId())) {
+ if (elementSet.size() == 0 || reactionContainsElement(reaction, elementSet)) {
+ elements.add(reaction);
+ }
+ }
+ }
+ }
+ elements.sort(BioEntity.ID_COMPARATOR);
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (Reaction element : elements) {
+ result.add(preparedReaction(element, columnsSet));
+
+ }
+ return result;
+ }
+
+ private boolean reactionContainsElement(Reaction reaction, Set<Element> elementSet) {
+ for (Element element : elementSet) {
+ if (reaction.containsElement(element)) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ private Map<String, Object> preparedReaction(Reaction reaction, Set<String> columnsSet) {
+ Map<String, Object> result = new TreeMap<>();
+ for (String string : columnsSet) {
+ String column = string.toLowerCase();
+ Object value = null;
+ if (column.equals("id") || column.equals("idobject")) {
+ value = reaction.getId();
+ } else if (column.equals("modelid")) {
+ value = reaction.getModelData().getId();
+ } else if (column.equals("reactionid")) {
+ value = reaction.getIdReaction();
+ } else if (column.equals("name")) {
+ value = reaction.getName();
+ } else if (column.equals("centerpoint")) {
+ value = reaction.getCenterPoint();
+ } else if (column.equals("products")) {
+ List<Map<String, Object>> ids = new ArrayList<>();
+ for (Product product : reaction.getProducts()) {
+ ids.add(createReactionNode(product));
+ }
+ value = ids;
+ } else if (column.equals("reactants")) {
+ List<Map<String, Object>> ids = new ArrayList<>();
+ for (Reactant reactant : reaction.getReactants()) {
+ ids.add(createReactionNode(reactant));
+ }
+ value = ids;
+ } else if (column.equals("modifiers")) {
+ List<Map<String, Object>> ids = new ArrayList<>();
+ for (Modifier modifier : reaction.getModifiers()) {
+ ids.add(createReactionNode(modifier));
+ }
+ value = ids;
+ } else if (column.equals("type")) {
+ value = reaction.getStringType();
+ } else if (column.equals("hierarchyvisibilitylevel")) {
+ value = reaction.getVisibilityLevel();
+ } else if (column.equals("lines")) {
+ value = getLines(reaction);
+ } else if (column.equals("notes")) {
+ value = reaction.getNotes();
+ } else if (column.equals("kineticlaw")) {
+ value = kineticsToMap(reaction.getKinetics());
+ } else if (column.equals("references")) {
+ value = createAnnotations(reaction.getMiriamData());
+ } else {
+ value = "Unknown column";
+ }
+ result.put(string, value);
+ }
+ return result;
+ }
+
+ private List<Map<String, Object>> getLines(Reaction reaction) {
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (Reactant reactant : reaction.getReactants()) {
+ result.addAll(getLines(reactant));
+ }
+ for (Product product : reaction.getProducts()) {
+ result.addAll(getLines(product));
+ }
+ for (Modifier modifier : reaction.getModifiers()) {
+ result.addAll(getLines(modifier));
+ }
+ for (NodeOperator operator : reaction.getOperators()) {
+ result.addAll(getLines(operator));
+ }
+ return result;
+ }
+
+ protected List<Map<String, Object>> getLines(AbstractNode reactant) {
+ // order in this method is to keep the order from previous version, it can be
+ // changed in the future, but I wanted to make that it's giving the same results
+ // when refactoring
+ List<Map<String, Object>> result = new ArrayList<>();
+ List<Line2D> startLines = new ArrayList<>();
+ List<Line2D> middleLines = new ArrayList<>();
+ List<Line2D> endLines = new ArrayList<>();
+
+ List<Line2D> lines = reactant.getLine().getLines();
+
+ if (reactant instanceof Reactant) {
+ startLines.add(lines.get(0));
+ for (int i = 1; i < lines.size(); i++) {
+ middleLines.add(lines.get(i));
+ }
+ } else if (reactant instanceof Product) {
+ endLines.add(lines.get(lines.size() - 1));
+ for (int i = 0; i < lines.size()-1; i++) {
+ middleLines.add(lines.get(i));
+ }
+ } else if (reactant instanceof Modifier) {
+ middleLines.add(lines.get(lines.size() - 1));
+ for (int i = 0; i < lines.size()-1; i++) {
+ middleLines.add(lines.get(i));
+ }
+ } else {
+ middleLines.addAll(lines);
+ }
+
+ for (Line2D line2d : startLines) {
+ result.add(lineToMap(line2d, "START"));
+ }
+ for (Line2D line2d : endLines) {
+ result.add(lineToMap(line2d, "END"));
+ }
+ for (Line2D line2d : middleLines) {
+ result.add(lineToMap(line2d, "MIDDLE"));
+ }
+
+ return result;
+ }
+
+ private Map<String, Object> lineToMap(Line2D line2d, String type) {
+ Map<String, Object> result = new LinkedHashMap<>();
+ result.put("start", line2d.getP1());
+ result.put("end", line2d.getP2());
+ result.put("type", type);
+ return result;
+ }
+
+ private Map<String, Object> createReactionNode(ReactionNode node) {
+ Map<String, Object> result = new TreeMap<>();
+ result.put("aliasId", node.getElement().getId());
+ result.put("stoichiometry", node.getStoichiometry());
+ return result;
+ }
+
+ private Map<String, Object> kineticsToMap(SbmlKinetics kinetics) {
+ if (kinetics == null) {
+ return null;
+ }
+ Map<String, Object> result = new TreeMap<>();
+ result.put("definition", kinetics.getDefinition());
+ try {
+ result.put("mathMlPresentation", super.mathMLToPresentationML(kinetics.getDefinition()));
+ } catch (IOException | InvalidXmlSchemaException | TransformerException e) {
+ logger.error("Problems with transforming kinetics", e);
+ }
+
+ List<Integer> functionIds = new ArrayList<>();
+ for (SbmlFunction function : kinetics.getFunctions()) {
+ functionIds.add(function.getId());
+ }
+ result.put("functionIds", functionIds);
+ List<Integer> parameterIds = new ArrayList<>();
+ for (SbmlParameter parameter : kinetics.getParameters()) {
+ parameterIds.add(parameter.getId());
+ }
+ result.put("parameterIds", parameterIds);
+ return result;
+ }
+
+ private Set<String> createReactionColumnSet(String columns) {
+ Set<String> columnsSet = new HashSet<>();
+ if (columns.equals("")) {
+ columnsSet.add("id");
+ columnsSet.add("reactionId");
+ columnsSet.add("modelId");
+ columnsSet.add("type");
+ columnsSet.add("lines");
+ columnsSet.add("kineticLaw");
+ columnsSet.add("centerPoint");
+ columnsSet.add("products");
+ columnsSet.add("reactants");
+ columnsSet.add("modifiers");
+ columnsSet.add("hierarchyVisibilityLevel");
+ columnsSet.add("references");
+ columnsSet.add("notes");
+ } else {
+ for (String str : columns.split(",")) {
+ columnsSet.add(str);
+ }
+ }
+ return columnsSet;
+ }
+
+ /**
+ * @return the modelService
+ * @see #modelService
+ */
+ public IModelService getModelService() {
+ return modelService;
+ }
+
+ /**
+ * @param modelService
+ * the modelService to set
+ * @see #modelService
+ */
+ public void setModelService(IModelService modelService) {
+ this.modelService = modelService;
+ }
+
+}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/functions/FunctionsController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/functions/FunctionsController.java
index 5dc88ab8c5..163b6bf66c 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/functions/FunctionsController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/functions/FunctionsController.java
@@ -1,45 +1,45 @@
-package lcsb.mapviewer.api.projects.models.functions;
-
-import java.util.List;
-import java.util.Map;
-
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.MediaType;
-import org.springframework.web.bind.annotation.CookieValue;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RestController;
-
-import lcsb.mapviewer.api.BaseController;
-import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.services.SecurityException;
-
-@RestController
-public class FunctionsController extends BaseController {
- @Autowired
- private FunctionsRestImpl functionController;
-
- @RequestMapping(value = "/projects/{projectId}/models/{modelId}/functions/{functionId}", method = {
- RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getFunction(//
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @PathVariable(value = "functionId") String functionId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
- ) throws QueryException, SecurityException {
- return functionController.getFunction(projectId, modelId, token, functionId);
- }
-
- @RequestMapping(value = "/projects/{projectId}/models/{modelId}/functions/", method = {
- RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getFunctions(//
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
- ) throws QueryException, SecurityException {
- return functionController.getFunctions(projectId, modelId, token);
- }
-
+package lcsb.mapviewer.api.projects.models.functions;
+
+import java.util.List;
+import java.util.Map;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.web.bind.annotation.CookieValue;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RestController;
+
+import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.services.SecurityException;
+
+@RestController
+public class FunctionsController extends BaseController {
+ @Autowired
+ private FunctionsRestImpl functionController;
+
+ @RequestMapping(value = "/projects/{projectId}/models/{modelId}/functions/{functionId}", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> getFunction(//
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "modelId") String modelId, //
+ @PathVariable(value = "functionId") String functionId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws QueryException, SecurityException {
+ return functionController.getFunction(projectId, modelId, token, functionId);
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/models/{modelId}/functions/", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getFunctions(//
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "modelId") String modelId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws QueryException, SecurityException {
+ return functionController.getFunctions(projectId, modelId, token);
+ }
+
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/functions/FunctionsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/functions/FunctionsRestImpl.java
index f864bb3428..2cc1d8e75b 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/functions/FunctionsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/functions/FunctionsRestImpl.java
@@ -1,106 +1,106 @@
-package lcsb.mapviewer.api.projects.models.functions;
-
-import java.io.ByteArrayInputStream;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerException;
-import javax.xml.transform.TransformerFactory;
-import javax.xml.transform.dom.DOMSource;
-import javax.xml.transform.stream.StreamResult;
-import javax.xml.xpath.XPathExpressionException;
-
-import org.apache.axis.utils.ByteArrayOutputStream;
-import org.apache.log4j.Logger;
-import org.springframework.transaction.annotation.Transactional;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-import org.xml.sax.InputSource;
-import org.xml.sax.SAXException;
-
-import lcsb.mapviewer.api.BaseRestImpl;
-import lcsb.mapviewer.api.ObjectNotFoundException;
-import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.services.SecurityException;
-
-@Transactional(value = "txManager")
-public class FunctionsRestImpl extends BaseRestImpl {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(FunctionsRestImpl.class);
-
- public Map<String, Object> getFunction(String projectId, String modelId, String token, String functionId)
- throws SecurityException, QueryException {
- List<Model> models = getModels(projectId, modelId, token);
- int id = Integer.valueOf(functionId);
- for (Model model : models) {
- for (SbmlFunction function : model.getFunctions()) {
- if (function.getId() == id) {
- return functionToMap(function);
- }
- }
- }
- throw new ObjectNotFoundException("Function with given id doesn't exist");
- }
-
- private Map<String, Object> functionToMap(SbmlFunction function) {
- Map<String, Object> result = new TreeMap<>();
- result.put("id", function.getId());
- result.put("functionId", function.getFunctionId());
- result.put("name", function.getName());
- result.put("definition", function.getDefinition());
- try {
- String definition = extractLambda(function.getDefinition());
- result.put("mathMlPresentation", super.mathMLToPresentationML(definition));
- } catch (Exception e) {
- logger.error("Problems with transforming kinetics", e);
- }
- result.put("arguments", function.getArguments());
- return result;
- }
-
- protected String extractLambda(String definition)
- throws SAXException, IOException, ParserConfigurationException, XPathExpressionException, TransformerException {
- String result = definition.replaceAll("<lambda>", "").replaceAll("</lambda>", "");
-
- DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
- Document document = dbf.newDocumentBuilder().parse(new InputSource(new ByteArrayInputStream(result.getBytes())));
-
- NodeList nodes = document.getElementsByTagName("bvar");
- for (int i = nodes.getLength() - 1; i >= 0; i--) {
- Node e = nodes.item(i);
- e.getParentNode().removeChild(e);
- }
-
- TransformerFactory tf = TransformerFactory.newInstance();
- Transformer t = tf.newTransformer();
- ByteArrayOutputStream baos = new ByteArrayOutputStream();
- t.transform(new DOMSource(document), new StreamResult(baos));
-
- return baos.toString();
- }
-
- public List<Map<String, Object>> getFunctions(String projectId, String modelId, String token)
- throws SecurityException, QueryException {
- List<Map<String, Object>> result = new ArrayList<>();
- List<Model> models = getModels(projectId, modelId, token);
- for (Model model : models) {
- for (SbmlFunction function : model.getFunctions()) {
- result.add(functionToMap(function));
- }
- }
- return result;
- }
-}
+package lcsb.mapviewer.api.projects.models.functions;
+
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerException;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.dom.DOMSource;
+import javax.xml.transform.stream.StreamResult;
+import javax.xml.xpath.XPathExpressionException;
+
+import org.apache.axis.utils.ByteArrayOutputStream;
+import org.apache.log4j.Logger;
+import org.springframework.transaction.annotation.Transactional;
+import org.w3c.dom.Document;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+
+import lcsb.mapviewer.api.BaseRestImpl;
+import lcsb.mapviewer.api.ObjectNotFoundException;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.services.SecurityException;
+
+@Transactional(value = "txManager")
+public class FunctionsRestImpl extends BaseRestImpl {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(FunctionsRestImpl.class);
+
+ public Map<String, Object> getFunction(String projectId, String modelId, String token, String functionId)
+ throws SecurityException, QueryException {
+ List<Model> models = getModels(projectId, modelId, token);
+ int id = Integer.valueOf(functionId);
+ for (Model model : models) {
+ for (SbmlFunction function : model.getFunctions()) {
+ if (function.getId() == id) {
+ return functionToMap(function);
+ }
+ }
+ }
+ throw new ObjectNotFoundException("Function with given id doesn't exist");
+ }
+
+ private Map<String, Object> functionToMap(SbmlFunction function) {
+ Map<String, Object> result = new TreeMap<>();
+ result.put("id", function.getId());
+ result.put("functionId", function.getFunctionId());
+ result.put("name", function.getName());
+ result.put("definition", function.getDefinition());
+ try {
+ String definition = extractLambda(function.getDefinition());
+ result.put("mathMlPresentation", super.mathMLToPresentationML(definition));
+ } catch (Exception e) {
+ logger.error("Problems with transforming kinetics", e);
+ }
+ result.put("arguments", function.getArguments());
+ return result;
+ }
+
+ protected String extractLambda(String definition)
+ throws SAXException, IOException, ParserConfigurationException, XPathExpressionException, TransformerException {
+ String result = definition.replaceAll("<lambda>", "").replaceAll("</lambda>", "");
+
+ DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
+ Document document = dbf.newDocumentBuilder().parse(new InputSource(new ByteArrayInputStream(result.getBytes())));
+
+ NodeList nodes = document.getElementsByTagName("bvar");
+ for (int i = nodes.getLength() - 1; i >= 0; i--) {
+ Node e = nodes.item(i);
+ e.getParentNode().removeChild(e);
+ }
+
+ TransformerFactory tf = TransformerFactory.newInstance();
+ Transformer t = tf.newTransformer();
+ ByteArrayOutputStream baos = new ByteArrayOutputStream();
+ t.transform(new DOMSource(document), new StreamResult(baos));
+
+ return baos.toString();
+ }
+
+ public List<Map<String, Object>> getFunctions(String projectId, String modelId, String token)
+ throws SecurityException, QueryException {
+ List<Map<String, Object>> result = new ArrayList<>();
+ List<Model> models = getModels(projectId, modelId, token);
+ for (Model model : models) {
+ for (SbmlFunction function : model.getFunctions()) {
+ result.add(functionToMap(function));
+ }
+ }
+ return result;
+ }
+}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/parameters/ParametersController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/parameters/ParametersController.java
index 4316a71f8b..f4caca35ec 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/parameters/ParametersController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/parameters/ParametersController.java
@@ -1,45 +1,45 @@
-package lcsb.mapviewer.api.projects.models.parameters;
-
-import java.util.List;
-import java.util.Map;
-
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.MediaType;
-import org.springframework.web.bind.annotation.CookieValue;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RestController;
-
-import lcsb.mapviewer.api.BaseController;
-import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.services.SecurityException;
-
-@RestController
-public class ParametersController extends BaseController {
- @Autowired
- private ParametersRestImpl parameterController;
-
- @RequestMapping(value = "/projects/{projectId}/models/{modelId}/parameters/{parameterId}", method = {
- RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getParameter(//
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @PathVariable(value = "parameterId") String parameterId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
- ) throws QueryException, SecurityException {
- return parameterController.getParameter(projectId, modelId, token, parameterId);
- }
-
- @RequestMapping(value = "/projects/{projectId}/models/{modelId}/parameters/", method = {
- RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getParameters(//
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
- ) throws QueryException, SecurityException {
- return parameterController.getParameters(projectId, modelId, token);
- }
-
+package lcsb.mapviewer.api.projects.models.parameters;
+
+import java.util.List;
+import java.util.Map;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.web.bind.annotation.CookieValue;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RestController;
+
+import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.services.SecurityException;
+
+@RestController
+public class ParametersController extends BaseController {
+ @Autowired
+ private ParametersRestImpl parameterController;
+
+ @RequestMapping(value = "/projects/{projectId}/models/{modelId}/parameters/{parameterId}", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> getParameter(//
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "modelId") String modelId, //
+ @PathVariable(value = "parameterId") String parameterId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws QueryException, SecurityException {
+ return parameterController.getParameter(projectId, modelId, token, parameterId);
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/models/{modelId}/parameters/", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getParameters(//
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "modelId") String modelId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws QueryException, SecurityException {
+ return parameterController.getParameters(projectId, modelId, token);
+ }
+
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/parameters/ParametersRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/parameters/ParametersRestImpl.java
index 5cf7ba05c9..4968d139ff 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/parameters/ParametersRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/parameters/ParametersRestImpl.java
@@ -1,95 +1,95 @@
-package lcsb.mapviewer.api.projects.models.parameters;
-
-import java.util.ArrayList;
-import java.util.TreeMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.api.BaseRestImpl;
-import lcsb.mapviewer.api.ObjectNotFoundException;
-import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.services.SecurityException;
-
-@Transactional(value = "txManager")
-public class ParametersRestImpl extends BaseRestImpl {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(ParametersRestImpl.class);
-
- public Map<String, Object> getParameter(String projectId, String modelId, String token, String parameterId)
- throws SecurityException, QueryException {
- Set<SbmlParameter> globalParameters = getGlobalParametersFromProject(projectId, modelId, token);
- Set<SbmlParameter> parameters = getParametersFromProject(projectId, modelId, token);
- int id = Integer.valueOf(parameterId);
- for (SbmlParameter parameter : parameters) {
- if (parameter.getId() == id) {
- return parameterToMap(parameter, globalParameters.contains(parameter));
- }
- }
- throw new ObjectNotFoundException("Parameter with given id doesn't exist");
- }
-
- private Set<SbmlParameter> getParametersFromProject(String projectId, String modelId, String token)
- throws SecurityException, ObjectNotFoundException {
- List<Model> models = getModels(projectId, modelId, token);
- Set<SbmlParameter> parameters = new HashSet<>();
-
- for (Model model : models) {
- parameters.addAll(model.getParameters());
- for (Reaction reaction : model.getReactions()) {
- if (reaction.getKinetics() != null) {
- parameters.addAll(reaction.getKinetics().getParameters());
- }
- }
- }
- return parameters;
- }
-
- private Set<SbmlParameter> getGlobalParametersFromProject(String projectId, String modelId, String token)
- throws SecurityException, ObjectNotFoundException {
- List<Model> models = getModels(projectId, modelId, token);
- Set<SbmlParameter> parameters = new HashSet<>();
-
- for (Model model : models) {
- parameters.addAll(model.getParameters());
- }
- return parameters;
- }
-
- private Map<String, Object> parameterToMap(SbmlParameter parameter, boolean global) {
- Map<String, Object> result = new TreeMap<>();
- result.put("id", parameter.getId());
- result.put("parameterId", parameter.getParameterId());
- result.put("name", parameter.getName());
- result.put("value", parameter.getValue());
- result.put("global", global);
- if (parameter.getUnits() != null) {
- result.put("unitsId", parameter.getUnits().getId());
- } else {
- result.put("unitsId", null);
- }
- return result;
- }
-
- public List<Map<String, Object>> getParameters(String projectId, String modelId, String token)
- throws SecurityException, QueryException {
- List<Map<String, Object>> result = new ArrayList<>();
- Set<SbmlParameter> globalParameters = getGlobalParametersFromProject(projectId, modelId, token);
- Set<SbmlParameter> parameters = getParametersFromProject(projectId, modelId, token);
- for (SbmlParameter parameter : parameters) {
- result.add(parameterToMap(parameter, globalParameters.contains(parameter)));
- }
- return result;
- }
-}
+package lcsb.mapviewer.api.projects.models.parameters;
+
+import java.util.ArrayList;
+import java.util.TreeMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.api.BaseRestImpl;
+import lcsb.mapviewer.api.ObjectNotFoundException;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.services.SecurityException;
+
+@Transactional(value = "txManager")
+public class ParametersRestImpl extends BaseRestImpl {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(ParametersRestImpl.class);
+
+ public Map<String, Object> getParameter(String projectId, String modelId, String token, String parameterId)
+ throws SecurityException, QueryException {
+ Set<SbmlParameter> globalParameters = getGlobalParametersFromProject(projectId, modelId, token);
+ Set<SbmlParameter> parameters = getParametersFromProject(projectId, modelId, token);
+ int id = Integer.valueOf(parameterId);
+ for (SbmlParameter parameter : parameters) {
+ if (parameter.getId() == id) {
+ return parameterToMap(parameter, globalParameters.contains(parameter));
+ }
+ }
+ throw new ObjectNotFoundException("Parameter with given id doesn't exist");
+ }
+
+ private Set<SbmlParameter> getParametersFromProject(String projectId, String modelId, String token)
+ throws SecurityException, ObjectNotFoundException {
+ List<Model> models = getModels(projectId, modelId, token);
+ Set<SbmlParameter> parameters = new HashSet<>();
+
+ for (Model model : models) {
+ parameters.addAll(model.getParameters());
+ for (Reaction reaction : model.getReactions()) {
+ if (reaction.getKinetics() != null) {
+ parameters.addAll(reaction.getKinetics().getParameters());
+ }
+ }
+ }
+ return parameters;
+ }
+
+ private Set<SbmlParameter> getGlobalParametersFromProject(String projectId, String modelId, String token)
+ throws SecurityException, ObjectNotFoundException {
+ List<Model> models = getModels(projectId, modelId, token);
+ Set<SbmlParameter> parameters = new HashSet<>();
+
+ for (Model model : models) {
+ parameters.addAll(model.getParameters());
+ }
+ return parameters;
+ }
+
+ private Map<String, Object> parameterToMap(SbmlParameter parameter, boolean global) {
+ Map<String, Object> result = new TreeMap<>();
+ result.put("id", parameter.getId());
+ result.put("parameterId", parameter.getParameterId());
+ result.put("name", parameter.getName());
+ result.put("value", parameter.getValue());
+ result.put("global", global);
+ if (parameter.getUnits() != null) {
+ result.put("unitsId", parameter.getUnits().getId());
+ } else {
+ result.put("unitsId", null);
+ }
+ return result;
+ }
+
+ public List<Map<String, Object>> getParameters(String projectId, String modelId, String token)
+ throws SecurityException, QueryException {
+ List<Map<String, Object>> result = new ArrayList<>();
+ Set<SbmlParameter> globalParameters = getGlobalParametersFromProject(projectId, modelId, token);
+ Set<SbmlParameter> parameters = getParametersFromProject(projectId, modelId, token);
+ for (SbmlParameter parameter : parameters) {
+ result.add(parameterToMap(parameter, globalParameters.contains(parameter)));
+ }
+ return result;
+ }
+}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsController.java
index 4fb9008935..311c327b3a 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsController.java
@@ -1,39 +1,39 @@
-package lcsb.mapviewer.api.projects.models.publications;
-
-import java.util.Map;
-
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.MediaType;
-import org.springframework.web.bind.annotation.CookieValue;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RequestParam;
-import org.springframework.web.bind.annotation.RestController;
-
-import lcsb.mapviewer.api.BaseController;
-import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.services.SecurityException;
-
-@RestController
-public class PublicationsController extends BaseController {
- @Autowired
- private PublicationsRestImpl projectController;
-
- @RequestMapping(value = "/projects/{projectId}/models/{modelId}/publications/", method = { RequestMethod.GET },
- produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getPublications(//
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @RequestParam(value = "start", defaultValue = "0") String start, //
- @RequestParam(value = "length", defaultValue = "10") Integer length, //
- @RequestParam(value = "sortColumn", defaultValue = "pubmedId") String sortColumn, //
- @RequestParam(value = "sortOrder", defaultValue = "asc") String sortOrder, //
- @RequestParam(value = "search", defaultValue = "") String search//
- ) throws QueryException, SecurityException {
- return projectController.getPublications(projectId, modelId, token, start, length, sortColumn, sortOrder, search);
- }
-
+package lcsb.mapviewer.api.projects.models.publications;
+
+import java.util.Map;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.web.bind.annotation.CookieValue;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.RestController;
+
+import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.services.SecurityException;
+
+@RestController
+public class PublicationsController extends BaseController {
+ @Autowired
+ private PublicationsRestImpl projectController;
+
+ @RequestMapping(value = "/projects/{projectId}/models/{modelId}/publications/", method = { RequestMethod.GET },
+ produces = { MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> getPublications(//
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "modelId") String modelId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @RequestParam(value = "start", defaultValue = "0") String start, //
+ @RequestParam(value = "length", defaultValue = "10") Integer length, //
+ @RequestParam(value = "sortColumn", defaultValue = "pubmedId") String sortColumn, //
+ @RequestParam(value = "sortOrder", defaultValue = "asc") String sortOrder, //
+ @RequestParam(value = "search", defaultValue = "") String search//
+ ) throws QueryException, SecurityException {
+ return projectController.getPublications(projectId, modelId, token, start, length, sortColumn, sortOrder, search);
+ }
+
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
index 6565b23e84..b45034dfaf 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
@@ -1,296 +1,296 @@
-package lcsb.mapviewer.api.projects.models.publications;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Comparator;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-import java.util.SortedMap;
-import java.util.TreeMap;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.annotation.data.Article;
-import lcsb.mapviewer.annotation.services.PubmedParser;
-import lcsb.mapviewer.annotation.services.PubmedSearchException;
-import lcsb.mapviewer.api.BaseRestImpl;
-import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.interfaces.ISearchService;
-
-@Transactional(value = "txManager")
-public class PublicationsRestImpl extends BaseRestImpl {
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(PublicationsRestImpl.class);
-
- @Autowired
- private ISearchService searchService;
-
- @Autowired
- private PubmedParser pubmedParser;
-
- public SortedMap<MiriamData, List<BioEntity>> getPublications(Collection<Model> models) {
- SortedMap<MiriamData, List<BioEntity>> publications = new TreeMap<>();
-
- List<BioEntity> bioEntities = new ArrayList<>();
- for (Model modelData : models) {
- bioEntities.addAll(modelData.getBioEntities());
- }
- bioEntities.sort(BioEntity.ID_COMPARATOR);
- for (BioEntity bioEntity : bioEntities) {
- for (MiriamData md : bioEntity.getMiriamData()) {
- if (md.getDataType().equals(MiriamType.PUBMED)) {
- List<BioEntity> list = publications.get(md);
- if (list == null) {
- list = new ArrayList<>();
- publications.put(md, list);
- }
- list.add(bioEntity);
- }
- }
-
- }
- return publications;
- }
-
- /**
- * @return the searchService
- * @see #searchService
- */
- public ISearchService getSearchService() {
- return searchService;
- }
-
- /**
- * @param searchService
- * the searchService to set
- * @see #searchService
- */
- public void setSearchService(ISearchService searchService) {
- this.searchService = searchService;
- }
-
- private enum SortColumn {
- PUBMED_ID("pubmedId"), //
- YEAR("year"), //
- JOURNAL("journal"), //
- TITLE("title"), //
- AUTHORS("authors");
-
- private String commonName;
-
- SortColumn(String commonName) {
- this.commonName = commonName;
- }
- }
-
- public Map<String, Object> getPublications(String projectId, String modelId, String token, String startString,
- Integer length, String sortColumn, String sortOrder, String search) throws SecurityException, QueryException {
- List<Model> models = getModels(projectId, modelId, token);
-
- SortColumn sortColumnEnum = getSortOrderColumn(sortColumn);
- Comparator<Map.Entry<MiriamData, List<BioEntity>>> comparator = getComparatorForColumn(sortColumnEnum, sortOrder);
-
- Integer start = Math.max(0, Integer.valueOf(startString));
- List<Map<String, Object>> resultList = new ArrayList<>();
-
- SortedMap<MiriamData, List<BioEntity>> publications = getPublications(models);
- Set<String> columns = new HashSet<>();
- columns.add("id");
- columns.add("type");
- columns.add("modelid");
-
- List<Map.Entry<MiriamData, List<BioEntity>>> filteredList = new ArrayList<>();
-
- for (Map.Entry<MiriamData, List<BioEntity>> entry : publications.entrySet()) {
- if (isSearchResult(entry.getKey(), search)) {
- filteredList.add(entry);
- }
- }
- if (comparator != null) {
- filteredList.sort(comparator);
- }
-
- int index = 0;
- for (Map.Entry<MiriamData, List<BioEntity>> entry : filteredList) {
- if (index >= start && index < start + length) {
- List<Object> elements = new ArrayList<>();
- for (BioEntity object : entry.getValue()) {
- elements.add(createMinifiedSearchResult(object));
- }
-
- Map<String, Object> row = new TreeMap<>();
- row.put("elements", elements);
- row.put("publication", createAnnotation(entry.getKey()));
- resultList.add(row);
- }
- index++;
- }
-
- Map<String, Object> result = new TreeMap<>();
- result.put("data", resultList);
- result.put("totalSize", publications.size());
- result.put("filteredSize", filteredList.size());
- result.put("start", start);
- result.put("length", resultList.size());
- return result;
- }
-
- private Comparator<Entry<MiriamData, List<BioEntity>>> getComparatorForColumn(SortColumn sortColumnEnum,
- String sortOrder) {
- final int orderFactor;
- if (sortOrder.toLowerCase().equals("desc")) {
- orderFactor = -1;
- } else {
- orderFactor = 1;
- }
- if (sortColumnEnum == null) {
- return null;
- } else if (sortColumnEnum.equals(SortColumn.PUBMED_ID)) {
- return new Comparator<Map.Entry<MiriamData, List<BioEntity>>>() {
- @Override
- public int compare(Entry<MiriamData, List<BioEntity>> o1, Entry<MiriamData, List<BioEntity>> o2) {
- Integer id1 = Integer.valueOf(o1.getKey().getResource());
- Integer id2 = Integer.valueOf(o2.getKey().getResource());
- return id1.compareTo(id2) * orderFactor;
-
- }
- };
- } else if (sortColumnEnum.equals(SortColumn.YEAR)) {
- return new Comparator<Map.Entry<MiriamData, List<BioEntity>>>() {
- @Override
- public int compare(Entry<MiriamData, List<BioEntity>> o1, Entry<MiriamData, List<BioEntity>> o2) {
- try {
- Article article1 = getArticle(o1.getKey().getResource());
- Article article2 = getArticle(o2.getKey().getResource());
- return article1.getYear().compareTo(article2.getYear()) * orderFactor;
- } catch (Exception e) {
- logger.error("Problem with accessing article data ", e);
- return 0;
- }
- }
- };
- } else if (sortColumnEnum.equals(SortColumn.JOURNAL)) {
- return new Comparator<Map.Entry<MiriamData, List<BioEntity>>>() {
- @Override
- public int compare(Entry<MiriamData, List<BioEntity>> o1, Entry<MiriamData, List<BioEntity>> o2) {
- try {
- Article article1 = getArticle(o1.getKey().getResource());
- Article article2 = getArticle(o2.getKey().getResource());
- return article1.getJournal().compareTo(article2.getJournal()) * orderFactor;
- } catch (Exception e) {
- logger.error("Problem with accessing article data ", e);
- return 0;
- }
- }
- };
- } else if (sortColumnEnum.equals(SortColumn.TITLE)) {
- return new Comparator<Map.Entry<MiriamData, List<BioEntity>>>() {
- @Override
- public int compare(Entry<MiriamData, List<BioEntity>> o1, Entry<MiriamData, List<BioEntity>> o2) {
- try {
- Article article1 = getArticle(o1.getKey().getResource());
- Article article2 = getArticle(o2.getKey().getResource());
- return article1.getTitle().compareTo(article2.getTitle()) * orderFactor;
- } catch (Exception e) {
- logger.error("Problem with accessing article data ", e);
- return 0;
- }
-
- }
- };
- } else if (sortColumnEnum.equals(SortColumn.AUTHORS)) {
- return new Comparator<Map.Entry<MiriamData, List<BioEntity>>>() {
- @Override
- public int compare(Entry<MiriamData, List<BioEntity>> o1, Entry<MiriamData, List<BioEntity>> o2) {
- try {
- Article article1 = getArticle(o1.getKey().getResource());
- Article article2 = getArticle(o2.getKey().getResource());
- return article1.getStringAuthors().compareTo(article2.getStringAuthors()) * orderFactor;
- } catch (Exception e) {
- logger.error("Problem with accessing article data ", e);
- return 0;
- }
- }
- };
- } else {
- throw new InvalidArgumentException("Unknown column type: " + sortColumnEnum);
- }
- }
-
- private SortColumn getSortOrderColumn(String sortColumn) throws QueryException {
- if (!sortColumn.isEmpty()) {
- for (SortColumn type : SortColumn.values()) {
- if (type.commonName.toLowerCase().equals(sortColumn.toLowerCase())) {
- return type;
- }
- }
- throw new QueryException("Unknown sortColumn: " + sortColumn);
- }
- return null;
- }
-
- private boolean isSearchResult(MiriamData key, String search) {
- String lowerCaseSearch = search.toLowerCase();
- if (search == null || search.isEmpty()) {
- return true;
- }
- Article article = null;
- if (MiriamType.PUBMED.equals(key.getDataType())) {
- try {
- article = pubmedParser.getPubmedArticleById(Integer.valueOf(key.getResource()));
- } catch (PubmedSearchException e) {
- logger.error("Problem with accessing info about pubmed", e);
- }
- }
- if (article != null) {
- if (article.getId().toLowerCase().contains(lowerCaseSearch)) {
- return true;
- } else if (article.getJournal().toLowerCase().contains(lowerCaseSearch)) {
- return true;
- } else if (article.getStringAuthors().toLowerCase().contains(lowerCaseSearch)) {
- return true;
- } else if (article.getTitle().toLowerCase().contains(lowerCaseSearch)) {
- return true;
- } else if (article.getYear().toString().toLowerCase().contains(lowerCaseSearch)) {
- return true;
- }
- }
- return false;
- }
-
- /**
- * @return the pubmedParser
- * @see #pubmedParser
- */
- public PubmedParser getPubmedParser() {
- return pubmedParser;
- }
-
- /**
- * @param pubmedParser
- * the pubmedParser to set
- * @see #pubmedParser
- */
- public void setPubmedParser(PubmedParser pubmedParser) {
- this.pubmedParser = pubmedParser;
- }
-
- private Article getArticle(String resource) throws NumberFormatException, PubmedSearchException {
- return pubmedParser.getPubmedArticleById(Integer.valueOf(resource));
- }
-
-}
+package lcsb.mapviewer.api.projects.models.publications;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Comparator;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.SortedMap;
+import java.util.TreeMap;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.annotation.data.Article;
+import lcsb.mapviewer.annotation.services.PubmedParser;
+import lcsb.mapviewer.annotation.services.PubmedSearchException;
+import lcsb.mapviewer.api.BaseRestImpl;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.interfaces.ISearchService;
+
+@Transactional(value = "txManager")
+public class PublicationsRestImpl extends BaseRestImpl {
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(PublicationsRestImpl.class);
+
+ @Autowired
+ private ISearchService searchService;
+
+ @Autowired
+ private PubmedParser pubmedParser;
+
+ public SortedMap<MiriamData, List<BioEntity>> getPublications(Collection<Model> models) {
+ SortedMap<MiriamData, List<BioEntity>> publications = new TreeMap<>();
+
+ List<BioEntity> bioEntities = new ArrayList<>();
+ for (Model modelData : models) {
+ bioEntities.addAll(modelData.getBioEntities());
+ }
+ bioEntities.sort(BioEntity.ID_COMPARATOR);
+ for (BioEntity bioEntity : bioEntities) {
+ for (MiriamData md : bioEntity.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.PUBMED)) {
+ List<BioEntity> list = publications.get(md);
+ if (list == null) {
+ list = new ArrayList<>();
+ publications.put(md, list);
+ }
+ list.add(bioEntity);
+ }
+ }
+
+ }
+ return publications;
+ }
+
+ /**
+ * @return the searchService
+ * @see #searchService
+ */
+ public ISearchService getSearchService() {
+ return searchService;
+ }
+
+ /**
+ * @param searchService
+ * the searchService to set
+ * @see #searchService
+ */
+ public void setSearchService(ISearchService searchService) {
+ this.searchService = searchService;
+ }
+
+ private enum SortColumn {
+ PUBMED_ID("pubmedId"), //
+ YEAR("year"), //
+ JOURNAL("journal"), //
+ TITLE("title"), //
+ AUTHORS("authors");
+
+ private String commonName;
+
+ SortColumn(String commonName) {
+ this.commonName = commonName;
+ }
+ }
+
+ public Map<String, Object> getPublications(String projectId, String modelId, String token, String startString,
+ Integer length, String sortColumn, String sortOrder, String search) throws SecurityException, QueryException {
+ List<Model> models = getModels(projectId, modelId, token);
+
+ SortColumn sortColumnEnum = getSortOrderColumn(sortColumn);
+ Comparator<Map.Entry<MiriamData, List<BioEntity>>> comparator = getComparatorForColumn(sortColumnEnum, sortOrder);
+
+ Integer start = Math.max(0, Integer.valueOf(startString));
+ List<Map<String, Object>> resultList = new ArrayList<>();
+
+ SortedMap<MiriamData, List<BioEntity>> publications = getPublications(models);
+ Set<String> columns = new HashSet<>();
+ columns.add("id");
+ columns.add("type");
+ columns.add("modelid");
+
+ List<Map.Entry<MiriamData, List<BioEntity>>> filteredList = new ArrayList<>();
+
+ for (Map.Entry<MiriamData, List<BioEntity>> entry : publications.entrySet()) {
+ if (isSearchResult(entry.getKey(), search)) {
+ filteredList.add(entry);
+ }
+ }
+ if (comparator != null) {
+ filteredList.sort(comparator);
+ }
+
+ int index = 0;
+ for (Map.Entry<MiriamData, List<BioEntity>> entry : filteredList) {
+ if (index >= start && index < start + length) {
+ List<Object> elements = new ArrayList<>();
+ for (BioEntity object : entry.getValue()) {
+ elements.add(createMinifiedSearchResult(object));
+ }
+
+ Map<String, Object> row = new TreeMap<>();
+ row.put("elements", elements);
+ row.put("publication", createAnnotation(entry.getKey()));
+ resultList.add(row);
+ }
+ index++;
+ }
+
+ Map<String, Object> result = new TreeMap<>();
+ result.put("data", resultList);
+ result.put("totalSize", publications.size());
+ result.put("filteredSize", filteredList.size());
+ result.put("start", start);
+ result.put("length", resultList.size());
+ return result;
+ }
+
+ private Comparator<Entry<MiriamData, List<BioEntity>>> getComparatorForColumn(SortColumn sortColumnEnum,
+ String sortOrder) {
+ final int orderFactor;
+ if (sortOrder.toLowerCase().equals("desc")) {
+ orderFactor = -1;
+ } else {
+ orderFactor = 1;
+ }
+ if (sortColumnEnum == null) {
+ return null;
+ } else if (sortColumnEnum.equals(SortColumn.PUBMED_ID)) {
+ return new Comparator<Map.Entry<MiriamData, List<BioEntity>>>() {
+ @Override
+ public int compare(Entry<MiriamData, List<BioEntity>> o1, Entry<MiriamData, List<BioEntity>> o2) {
+ Integer id1 = Integer.valueOf(o1.getKey().getResource());
+ Integer id2 = Integer.valueOf(o2.getKey().getResource());
+ return id1.compareTo(id2) * orderFactor;
+
+ }
+ };
+ } else if (sortColumnEnum.equals(SortColumn.YEAR)) {
+ return new Comparator<Map.Entry<MiriamData, List<BioEntity>>>() {
+ @Override
+ public int compare(Entry<MiriamData, List<BioEntity>> o1, Entry<MiriamData, List<BioEntity>> o2) {
+ try {
+ Article article1 = getArticle(o1.getKey().getResource());
+ Article article2 = getArticle(o2.getKey().getResource());
+ return article1.getYear().compareTo(article2.getYear()) * orderFactor;
+ } catch (Exception e) {
+ logger.error("Problem with accessing article data ", e);
+ return 0;
+ }
+ }
+ };
+ } else if (sortColumnEnum.equals(SortColumn.JOURNAL)) {
+ return new Comparator<Map.Entry<MiriamData, List<BioEntity>>>() {
+ @Override
+ public int compare(Entry<MiriamData, List<BioEntity>> o1, Entry<MiriamData, List<BioEntity>> o2) {
+ try {
+ Article article1 = getArticle(o1.getKey().getResource());
+ Article article2 = getArticle(o2.getKey().getResource());
+ return article1.getJournal().compareTo(article2.getJournal()) * orderFactor;
+ } catch (Exception e) {
+ logger.error("Problem with accessing article data ", e);
+ return 0;
+ }
+ }
+ };
+ } else if (sortColumnEnum.equals(SortColumn.TITLE)) {
+ return new Comparator<Map.Entry<MiriamData, List<BioEntity>>>() {
+ @Override
+ public int compare(Entry<MiriamData, List<BioEntity>> o1, Entry<MiriamData, List<BioEntity>> o2) {
+ try {
+ Article article1 = getArticle(o1.getKey().getResource());
+ Article article2 = getArticle(o2.getKey().getResource());
+ return article1.getTitle().compareTo(article2.getTitle()) * orderFactor;
+ } catch (Exception e) {
+ logger.error("Problem with accessing article data ", e);
+ return 0;
+ }
+
+ }
+ };
+ } else if (sortColumnEnum.equals(SortColumn.AUTHORS)) {
+ return new Comparator<Map.Entry<MiriamData, List<BioEntity>>>() {
+ @Override
+ public int compare(Entry<MiriamData, List<BioEntity>> o1, Entry<MiriamData, List<BioEntity>> o2) {
+ try {
+ Article article1 = getArticle(o1.getKey().getResource());
+ Article article2 = getArticle(o2.getKey().getResource());
+ return article1.getStringAuthors().compareTo(article2.getStringAuthors()) * orderFactor;
+ } catch (Exception e) {
+ logger.error("Problem with accessing article data ", e);
+ return 0;
+ }
+ }
+ };
+ } else {
+ throw new InvalidArgumentException("Unknown column type: " + sortColumnEnum);
+ }
+ }
+
+ private SortColumn getSortOrderColumn(String sortColumn) throws QueryException {
+ if (!sortColumn.isEmpty()) {
+ for (SortColumn type : SortColumn.values()) {
+ if (type.commonName.toLowerCase().equals(sortColumn.toLowerCase())) {
+ return type;
+ }
+ }
+ throw new QueryException("Unknown sortColumn: " + sortColumn);
+ }
+ return null;
+ }
+
+ private boolean isSearchResult(MiriamData key, String search) {
+ String lowerCaseSearch = search.toLowerCase();
+ if (search == null || search.isEmpty()) {
+ return true;
+ }
+ Article article = null;
+ if (MiriamType.PUBMED.equals(key.getDataType())) {
+ try {
+ article = pubmedParser.getPubmedArticleById(Integer.valueOf(key.getResource()));
+ } catch (PubmedSearchException e) {
+ logger.error("Problem with accessing info about pubmed", e);
+ }
+ }
+ if (article != null) {
+ if (article.getId().toLowerCase().contains(lowerCaseSearch)) {
+ return true;
+ } else if (article.getJournal().toLowerCase().contains(lowerCaseSearch)) {
+ return true;
+ } else if (article.getStringAuthors().toLowerCase().contains(lowerCaseSearch)) {
+ return true;
+ } else if (article.getTitle().toLowerCase().contains(lowerCaseSearch)) {
+ return true;
+ } else if (article.getYear().toString().toLowerCase().contains(lowerCaseSearch)) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ * @return the pubmedParser
+ * @see #pubmedParser
+ */
+ public PubmedParser getPubmedParser() {
+ return pubmedParser;
+ }
+
+ /**
+ * @param pubmedParser
+ * the pubmedParser to set
+ * @see #pubmedParser
+ */
+ public void setPubmedParser(PubmedParser pubmedParser) {
+ this.pubmedParser = pubmedParser;
+ }
+
+ private Article getArticle(String resource) throws NumberFormatException, PubmedSearchException {
+ return pubmedParser.getPubmedArticleById(Integer.valueOf(resource));
+ }
+
+}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/units/UnitsController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/units/UnitsController.java
index c55f3b092c..7f7b035060 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/units/UnitsController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/units/UnitsController.java
@@ -1,45 +1,45 @@
-package lcsb.mapviewer.api.projects.models.units;
-
-import java.util.List;
-import java.util.Map;
-
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.MediaType;
-import org.springframework.web.bind.annotation.CookieValue;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RestController;
-
-import lcsb.mapviewer.api.BaseController;
-import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.services.SecurityException;
-
-@RestController
-public class UnitsController extends BaseController {
- @Autowired
- private UnitsRestImpl unitController;
-
- @RequestMapping(value = "/projects/{projectId}/models/{modelId}/units/{unitId}", method = {
- RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getUnit(//
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @PathVariable(value = "unitId") String unitId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
- ) throws QueryException, SecurityException {
- return unitController.getUnit(projectId, modelId, token, unitId);
- }
-
- @RequestMapping(value = "/projects/{projectId}/models/{modelId}/units/", method = {
- RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getUnits(//
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
- ) throws QueryException, SecurityException {
- return unitController.getUnits(projectId, modelId, token);
- }
-
+package lcsb.mapviewer.api.projects.models.units;
+
+import java.util.List;
+import java.util.Map;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.web.bind.annotation.CookieValue;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RestController;
+
+import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.services.SecurityException;
+
+@RestController
+public class UnitsController extends BaseController {
+ @Autowired
+ private UnitsRestImpl unitController;
+
+ @RequestMapping(value = "/projects/{projectId}/models/{modelId}/units/{unitId}", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> getUnit(//
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "modelId") String modelId, //
+ @PathVariable(value = "unitId") String unitId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws QueryException, SecurityException {
+ return unitController.getUnit(projectId, modelId, token, unitId);
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/models/{modelId}/units/", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getUnits(//
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "modelId") String modelId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws QueryException, SecurityException {
+ return unitController.getUnits(projectId, modelId, token);
+ }
+
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/units/UnitsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/units/UnitsRestImpl.java
index 9ceda914f5..84eff0426b 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/units/UnitsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/units/UnitsRestImpl.java
@@ -1,75 +1,75 @@
-package lcsb.mapviewer.api.projects.models.units;
-
-import java.util.ArrayList;
-import java.util.TreeMap;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.api.BaseRestImpl;
-import lcsb.mapviewer.api.ObjectNotFoundException;
-import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
-import lcsb.mapviewer.model.map.kinetics.SbmlUnitTypeFactor;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.services.SecurityException;
-
-@Transactional(value = "txManager")
-public class UnitsRestImpl extends BaseRestImpl {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(UnitsRestImpl.class);
-
- public Map<String, Object> getUnit(String projectId, String modelId, String token, String unitId)
- throws SecurityException, QueryException {
- List<Model> models = getModels(projectId, modelId, token);
- int id = Integer.valueOf(unitId);
- for (Model model : models) {
- for (SbmlUnit unit : model.getUnits()) {
- if (unit.getId() == id) {
- return unitToMap(unit);
- }
- }
- }
- throw new ObjectNotFoundException("Unit with given id doesn't exist");
- }
-
- private Map<String, Object> unitToMap(SbmlUnit unit) {
- Map<String, Object> result = new TreeMap<>();
- result.put("id", unit.getId());
- result.put("unitId", unit.getUnitId());
- result.put("name", unit.getName());
- List<Map<String, Object>> factors = new ArrayList<>();
- for (SbmlUnitTypeFactor factor : unit.getUnitTypeFactors()) {
- factors.add(factorToMap(factor));
- }
- result.put("unitTypeFactors", factors);
- return result;
- }
-
- private Map<String, Object> factorToMap(SbmlUnitTypeFactor factor) {
- Map<String, Object> result = new TreeMap<>();
- result.put("id", factor.getId());
- result.put("exponent", factor.getExponent());
- result.put("multiplier", factor.getMultiplier());
- result.put("scale", factor.getScale());
- result.put("unitType", factor.getUnitType());
- return result;
- }
-
- public List<Map<String, Object>> getUnits(String projectId, String modelId, String token) throws SecurityException, ObjectNotFoundException {
- List<Map<String, Object>> result = new ArrayList<>();
- List<Model> models = getModels(projectId, modelId, token);
- for (Model model : models) {
- for (SbmlUnit unit : model.getUnits()) {
- result.add(unitToMap(unit));
- }
- }
- return result;
- }
-}
+package lcsb.mapviewer.api.projects.models.units;
+
+import java.util.ArrayList;
+import java.util.TreeMap;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.api.BaseRestImpl;
+import lcsb.mapviewer.api.ObjectNotFoundException;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnitTypeFactor;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.services.SecurityException;
+
+@Transactional(value = "txManager")
+public class UnitsRestImpl extends BaseRestImpl {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(UnitsRestImpl.class);
+
+ public Map<String, Object> getUnit(String projectId, String modelId, String token, String unitId)
+ throws SecurityException, QueryException {
+ List<Model> models = getModels(projectId, modelId, token);
+ int id = Integer.valueOf(unitId);
+ for (Model model : models) {
+ for (SbmlUnit unit : model.getUnits()) {
+ if (unit.getId() == id) {
+ return unitToMap(unit);
+ }
+ }
+ }
+ throw new ObjectNotFoundException("Unit with given id doesn't exist");
+ }
+
+ private Map<String, Object> unitToMap(SbmlUnit unit) {
+ Map<String, Object> result = new TreeMap<>();
+ result.put("id", unit.getId());
+ result.put("unitId", unit.getUnitId());
+ result.put("name", unit.getName());
+ List<Map<String, Object>> factors = new ArrayList<>();
+ for (SbmlUnitTypeFactor factor : unit.getUnitTypeFactors()) {
+ factors.add(factorToMap(factor));
+ }
+ result.put("unitTypeFactors", factors);
+ return result;
+ }
+
+ private Map<String, Object> factorToMap(SbmlUnitTypeFactor factor) {
+ Map<String, Object> result = new TreeMap<>();
+ result.put("id", factor.getId());
+ result.put("exponent", factor.getExponent());
+ result.put("multiplier", factor.getMultiplier());
+ result.put("scale", factor.getScale());
+ result.put("unitType", factor.getUnitType());
+ return result;
+ }
+
+ public List<Map<String, Object>> getUnits(String projectId, String modelId, String token) throws SecurityException, ObjectNotFoundException {
+ List<Map<String, Object>> result = new ArrayList<>();
+ List<Model> models = getModels(projectId, modelId, token);
+ for (Model model : models) {
+ for (SbmlUnit unit : model.getUnits()) {
+ result.add(unitToMap(unit));
+ }
+ }
+ return result;
+ }
+}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayController.java
index fb2f9e247b..26865a0295 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayController.java
@@ -1,177 +1,177 @@
-package lcsb.mapviewer.api.projects.overlays;
-
-import java.io.IOException;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.MediaType;
-import org.springframework.http.ResponseEntity;
-import org.springframework.web.bind.annotation.CookieValue;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestBody;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RequestParam;
-import org.springframework.web.bind.annotation.RestController;
-
-import com.fasterxml.jackson.core.JsonParseException;
-import com.fasterxml.jackson.databind.JsonMappingException;
-
-import lcsb.mapviewer.api.BaseController;
-import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.model.cache.FileEntry;
-import lcsb.mapviewer.services.SecurityException;
-
-@RestController
-public class OverlayController extends BaseController {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(OverlayController.class);
-
- @Autowired
- private OverlayRestImpl overlayRestImp;
-
- @RequestMapping(value = "/projects/{projectId}/overlays/", method = { RequestMethod.GET }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getOverlayList(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @RequestParam(value = "creator", defaultValue = "") String creator, //
- @RequestParam(value = "publicOverlay", defaultValue = "") String publicOverlay //
- ) throws SecurityException, QueryException {
- return overlayRestImp.getOverlayList(token, projectId, creator, publicOverlay);
- }
-
- @RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}/", method = { RequestMethod.GET }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getOverlayById(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "overlayId") String overlayId//
- ) throws SecurityException, QueryException {
- return overlayRestImp.getOverlayById(token, projectId, overlayId);
- }
-
- @RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}/models/{modelId}/bioEntities/", method = {
- RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getOverlayElements(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "overlayId") String overlayId,
- @RequestParam(value = "columns", defaultValue = "") String columns) throws SecurityException, QueryException {
- return overlayRestImp.getOverlayElements(token, projectId, Integer.valueOf(overlayId), columns);
- }
-
- @RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}/models/{modelId}/bioEntities/reactions/{reactionId}/", method = {
- RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getFullReaction(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @PathVariable(value = "overlayId") String overlayId, //
- @PathVariable(value = "reactionId") String reactionId, //
- @RequestParam(value = "columns", defaultValue = "") String columns //
- ) throws SecurityException, QueryException {
- return overlayRestImp.getOverlayElement(token, projectId, Integer.valueOf(modelId), Integer.valueOf(overlayId),
- Integer.valueOf(reactionId), "REACTION", columns);
- }
-
- @RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}/models/{modelId}/bioEntities/elements/{elementId}/", method = {
- RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getFullSpecies(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @PathVariable(value = "overlayId") String overlayId, //
- @PathVariable(value = "elementId") String reactionId, //
- @RequestParam(value = "columns", defaultValue = "") String columns //
- ) throws SecurityException, QueryException {
- return overlayRestImp.getOverlayElement(token, projectId, Integer.valueOf(modelId), Integer.valueOf(overlayId),
- Integer.valueOf(reactionId), "ALIAS", columns);
- }
-
- @RequestMapping(value = "/projects/{projectId}/overlays/", method = { RequestMethod.POST }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> addOverlay(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @RequestParam(value = "name") String name, //
- @RequestParam(value = "description") String description, //
- @RequestParam(value = "content", defaultValue = "") String content, //
- @RequestParam(value = "fileId", defaultValue = "") String fileId, //
- @RequestParam(value = "filename") String filename, //
- @RequestParam(value = "googleLicenseConsent") String googleLicenseConsent, //
- @RequestParam(value = "type", defaultValue = "") String type //
- ) throws SecurityException, QueryException, IOException {
- return overlayRestImp.addOverlay(token, projectId, name, description, content, fileId, filename, type, googleLicenseConsent);
- }
-
- @RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}", method = { RequestMethod.DELETE }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> removeOverlay(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "overlayId") String overlayId //
- ) throws SecurityException, QueryException, IOException {
- return overlayRestImp.removeOverlay(token, projectId, overlayId);
- }
-
- @RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}", method = { RequestMethod.PATCH }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> updateOverlay(//
- @RequestBody String body, //
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "overlayId") String overlayId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
- ) throws SecurityException, QueryException, IOException {
- Map<String, Object> node = parseBody(body);
- Map<String, Object> data = getData(node, "overlay");
- return overlayRestImp.updateOverlay(token, projectId, overlayId, data);
- }
-
- @RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}:downloadSource", method = {
- RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public ResponseEntity<byte[]> getOverlaySource(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "overlayId") String overlayId //
- ) throws SecurityException, QueryException, JsonParseException, JsonMappingException, IOException {
-
- FileEntry file = overlayRestImp.getOverlaySource(token, projectId, overlayId);
- MediaType type = MediaType.TEXT_PLAIN;
- String filename = file.getOriginalFileName();
- if (filename != null) {
- if (file.getOriginalFileName().endsWith("xml")) {
- type = MediaType.APPLICATION_XML;
- }
- } else {
- filename = overlayId + ".txt";
- }
- return ResponseEntity.ok().contentLength(file.getFileContent().length).contentType(type)
- .header("Content-Disposition", "attachment; filename=" + filename).body(file.getFileContent());
- }
-
- /**
- * @return the overlayRestImp
- * @see #overlayRestImp
- */
- public OverlayRestImpl getOverlayRestImp() {
- return overlayRestImp;
- }
-
- /**
- * @param overlayRestImp
- * the overlayRestImp to set
- * @see #overlayRestImp
- */
- public void setOverlayRestImp(OverlayRestImpl overlayRestImp) {
- this.overlayRestImp = overlayRestImp;
- }
-
+package lcsb.mapviewer.api.projects.overlays;
+
+import java.io.IOException;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.annotation.CookieValue;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestBody;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.RestController;
+
+import com.fasterxml.jackson.core.JsonParseException;
+import com.fasterxml.jackson.databind.JsonMappingException;
+
+import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.model.cache.FileEntry;
+import lcsb.mapviewer.services.SecurityException;
+
+@RestController
+public class OverlayController extends BaseController {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(OverlayController.class);
+
+ @Autowired
+ private OverlayRestImpl overlayRestImp;
+
+ @RequestMapping(value = "/projects/{projectId}/overlays/", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getOverlayList(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "projectId") String projectId, //
+ @RequestParam(value = "creator", defaultValue = "") String creator, //
+ @RequestParam(value = "publicOverlay", defaultValue = "") String publicOverlay //
+ ) throws SecurityException, QueryException {
+ return overlayRestImp.getOverlayList(token, projectId, creator, publicOverlay);
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}/", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> getOverlayById(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "overlayId") String overlayId//
+ ) throws SecurityException, QueryException {
+ return overlayRestImp.getOverlayById(token, projectId, overlayId);
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}/models/{modelId}/bioEntities/", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getOverlayElements(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "overlayId") String overlayId,
+ @RequestParam(value = "columns", defaultValue = "") String columns) throws SecurityException, QueryException {
+ return overlayRestImp.getOverlayElements(token, projectId, Integer.valueOf(overlayId), columns);
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}/models/{modelId}/bioEntities/reactions/{reactionId}/", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> getFullReaction(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "modelId") String modelId, //
+ @PathVariable(value = "overlayId") String overlayId, //
+ @PathVariable(value = "reactionId") String reactionId, //
+ @RequestParam(value = "columns", defaultValue = "") String columns //
+ ) throws SecurityException, QueryException {
+ return overlayRestImp.getOverlayElement(token, projectId, Integer.valueOf(modelId), Integer.valueOf(overlayId),
+ Integer.valueOf(reactionId), "REACTION", columns);
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}/models/{modelId}/bioEntities/elements/{elementId}/", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> getFullSpecies(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "modelId") String modelId, //
+ @PathVariable(value = "overlayId") String overlayId, //
+ @PathVariable(value = "elementId") String reactionId, //
+ @RequestParam(value = "columns", defaultValue = "") String columns //
+ ) throws SecurityException, QueryException {
+ return overlayRestImp.getOverlayElement(token, projectId, Integer.valueOf(modelId), Integer.valueOf(overlayId),
+ Integer.valueOf(reactionId), "ALIAS", columns);
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/overlays/", method = { RequestMethod.POST }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> addOverlay(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "projectId") String projectId, //
+ @RequestParam(value = "name") String name, //
+ @RequestParam(value = "description") String description, //
+ @RequestParam(value = "content", defaultValue = "") String content, //
+ @RequestParam(value = "fileId", defaultValue = "") String fileId, //
+ @RequestParam(value = "filename") String filename, //
+ @RequestParam(value = "googleLicenseConsent") String googleLicenseConsent, //
+ @RequestParam(value = "type", defaultValue = "") String type //
+ ) throws SecurityException, QueryException, IOException {
+ return overlayRestImp.addOverlay(token, projectId, name, description, content, fileId, filename, type, googleLicenseConsent);
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}", method = { RequestMethod.DELETE }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> removeOverlay(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "overlayId") String overlayId //
+ ) throws SecurityException, QueryException, IOException {
+ return overlayRestImp.removeOverlay(token, projectId, overlayId);
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}", method = { RequestMethod.PATCH }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> updateOverlay(//
+ @RequestBody String body, //
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "overlayId") String overlayId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, QueryException, IOException {
+ Map<String, Object> node = parseBody(body);
+ Map<String, Object> data = getData(node, "overlay");
+ return overlayRestImp.updateOverlay(token, projectId, overlayId, data);
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}:downloadSource", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public ResponseEntity<byte[]> getOverlaySource(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "overlayId") String overlayId //
+ ) throws SecurityException, QueryException, JsonParseException, JsonMappingException, IOException {
+
+ FileEntry file = overlayRestImp.getOverlaySource(token, projectId, overlayId);
+ MediaType type = MediaType.TEXT_PLAIN;
+ String filename = file.getOriginalFileName();
+ if (filename != null) {
+ if (file.getOriginalFileName().endsWith("xml")) {
+ type = MediaType.APPLICATION_XML;
+ }
+ } else {
+ filename = overlayId + ".txt";
+ }
+ return ResponseEntity.ok().contentLength(file.getFileContent().length).contentType(type)
+ .header("Content-Disposition", "attachment; filename=" + filename).body(file.getFileContent());
+ }
+
+ /**
+ * @return the overlayRestImp
+ * @see #overlayRestImp
+ */
+ public OverlayRestImpl getOverlayRestImp() {
+ return overlayRestImp;
+ }
+
+ /**
+ * @param overlayRestImp
+ * the overlayRestImp to set
+ * @see #overlayRestImp
+ */
+ public void setOverlayRestImp(OverlayRestImpl overlayRestImp) {
+ this.overlayRestImp = overlayRestImp;
+ }
+
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
index f85cafd562..79ef412677 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
@@ -1,224 +1,224 @@
-package lcsb.mapviewer.api.users;
-
-import java.io.IOException;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-
-import javax.servlet.http.Cookie;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.MediaType;
-import org.springframework.security.authentication.AuthenticationProvider;
-import org.springframework.security.authentication.UsernamePasswordAuthenticationToken;
-import org.springframework.security.core.Authentication;
-import org.springframework.security.core.AuthenticationException;
-import org.springframework.security.core.context.SecurityContextHolder;
-import org.springframework.security.web.authentication.WebAuthenticationDetails;
-import org.springframework.security.web.authentication.logout.SecurityContextLogoutHandler;
-import org.springframework.util.MultiValueMap;
-import org.springframework.web.bind.annotation.CookieValue;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestBody;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RequestParam;
-import org.springframework.web.bind.annotation.RestController;
-
-import com.fasterxml.jackson.core.JsonParseException;
-import com.fasterxml.jackson.databind.JsonMappingException;
-
-import lcsb.mapviewer.api.BaseController;
-import lcsb.mapviewer.api.ObjectNotFoundException;
-import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.interfaces.IUserService;
-
-@RestController
-public class UserController extends BaseController {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(UserController.class);
-
- @Autowired
- private IUserService userService;
-
- @Autowired
- private UserRestImpl userRest;
-
- @Autowired
- private AuthenticationProvider authenticationProvider;
-
- @RequestMapping(value = "/doLogin", method = { RequestMethod.GET, RequestMethod.POST }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> login(//
- @RequestParam(value = "login", defaultValue = Configuration.ANONYMOUS_LOGIN) String login, //
- @RequestParam(value = "password", defaultValue = "") String password, //
- HttpServletResponse response, //
- HttpServletRequest request//
- ) throws SecurityException, IOException {
- try {
- UsernamePasswordAuthenticationToken springToken = new UsernamePasswordAuthenticationToken(login, password);
- springToken.setDetails(new WebAuthenticationDetails(request));
- Authentication authentication = this.authenticationProvider.authenticate(springToken);
- SecurityContextHolder.getContext().setAuthentication(authentication);
-
- userService.login(login, password, request.getSession().getId());
-
- Map<String, Object> result = new TreeMap<>();
-
- result.put("info", "Login successful. TOKEN returned as a cookie");
- return result;
- } catch (AuthenticationException e) {
- throw new SecurityException("Invalid credentials");
- }
- }
-
- @RequestMapping(value = "/users/{login:.+}", method = { RequestMethod.GET }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getUser(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "login") String login, //
- @RequestParam(value = "columns", defaultValue = "") String columns//
- ) throws SecurityException, ObjectNotFoundException {
- return userRest.getUser(token, login, columns);
- }
-
- @RequestMapping(value = "/users/{login}:updatePrivileges", method = { RequestMethod.PATCH }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> updatePrivileges(//
- @RequestBody String body, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "login") String login //
- ) throws SecurityException, JsonParseException, JsonMappingException, IOException, QueryException {
- Map<String, Object> node = parseBody(body);
- Map<String, Object> data = getData(node, "privileges");
- return userRest.updatePrivileges(token, login, data);
- }
-
- @RequestMapping(value = "/users/{login}:updatePreferences", method = { RequestMethod.PATCH }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> updatePreferences(//
- @RequestBody String body, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "login") String login //
- ) throws SecurityException, JsonParseException, JsonMappingException, IOException, QueryException {
- Map<String, Object> node = parseBody(body);
- Map<String, Object> data = getData(node, "preferences");
- return userRest.updatePreferences(token, login, data);
- }
-
- @RequestMapping(value = "/users/", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getUsers(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @RequestParam(value = "columns", defaultValue = "") String columns//
- ) throws SecurityException, ObjectNotFoundException {
- return userRest.getUsers(token, columns);
- }
-
- @RequestMapping(value = "/doLogout", method = { RequestMethod.GET, RequestMethod.POST }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> logout(@CookieValue(value = Configuration.AUTH_TOKEN) String token,
- HttpServletRequest request, HttpServletResponse response //
- ) throws SecurityException, IOException {
- // spring logout
- Authentication auth = SecurityContextHolder.getContext().getAuthentication();
- if (auth != null) {
- new SecurityContextLogoutHandler().logout(request, response, auth);
- }
-
- Map<String, Object> result = new TreeMap<>();
- result.put("status", "OK");
-
- final Boolean useSecureCookie = false;
- final String cookiePath = "/";
-
- Cookie cookie = new Cookie("MINERVA_AUTH_TOKEN", token);
-
- cookie.setSecure(useSecureCookie);
- cookie.setMaxAge(0);
- cookie.setPath(cookiePath);
-
- response.addCookie(cookie);
- result.put("status", "OK");
- return result;
- }
-
- @RequestMapping(value = "/users/{login:.+}", method = { RequestMethod.PATCH }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> updateUser(//
- @RequestBody String body, //
- @PathVariable(value = "login") String login, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
- ) throws SecurityException, QueryException, IOException {
- Map<String, Object> node = parseBody(body);
- Map<String, Object> data = getData(node, "user");
- return userRest.updateUser(token, login, data);
- }
-
- @RequestMapping(value = "/users/{login:.+}", method = { RequestMethod.POST }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> addOverlay(//
- @RequestBody MultiValueMap<String, Object> formData, //
- @PathVariable(value = "login") String login, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
- ) throws SecurityException, IOException, QueryException {
- return userRest.addProject(token, login, formData);
-
- }
-
- @RequestMapping(value = "/users/{login:.+}", method = { RequestMethod.DELETE }, produces = {
- MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> removeUser(//
- @PathVariable(value = "login") String login, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- HttpServletRequest request, HttpServletResponse response //
- ) throws SecurityException, IOException, QueryException {
- String currentUserLogin = getUserService().getUserByToken(token).getLogin();
- Map<String, Object> result = userRest.removeUser(token, login);
- if (login.equals(currentUserLogin)) {
- return logout(token, request, response);
- }
- return result;
- }
-
- /**
- * @return the userService
- * @see #userService
- */
- public IUserService getUserService() {
- return userService;
- }
-
- /**
- * @param userService
- * the userService to set
- * @see #userService
- */
- public void setUserService(IUserService userService) {
- this.userService = userService;
- }
-
- /**
- * @return the userRest
- * @see #userRest
- */
- public UserRestImpl getUserRest() {
- return userRest;
- }
-
- /**
- * @param userRest
- * the userRest to set
- * @see #userRest
- */
- public void setUserRest(UserRestImpl userRest) {
- this.userRest = userRest;
- }
+package lcsb.mapviewer.api.users;
+
+import java.io.IOException;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+
+import javax.servlet.http.Cookie;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.security.authentication.AuthenticationProvider;
+import org.springframework.security.authentication.UsernamePasswordAuthenticationToken;
+import org.springframework.security.core.Authentication;
+import org.springframework.security.core.AuthenticationException;
+import org.springframework.security.core.context.SecurityContextHolder;
+import org.springframework.security.web.authentication.WebAuthenticationDetails;
+import org.springframework.security.web.authentication.logout.SecurityContextLogoutHandler;
+import org.springframework.util.MultiValueMap;
+import org.springframework.web.bind.annotation.CookieValue;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestBody;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.RestController;
+
+import com.fasterxml.jackson.core.JsonParseException;
+import com.fasterxml.jackson.databind.JsonMappingException;
+
+import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.api.ObjectNotFoundException;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.interfaces.IUserService;
+
+@RestController
+public class UserController extends BaseController {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(UserController.class);
+
+ @Autowired
+ private IUserService userService;
+
+ @Autowired
+ private UserRestImpl userRest;
+
+ @Autowired
+ private AuthenticationProvider authenticationProvider;
+
+ @RequestMapping(value = "/doLogin", method = { RequestMethod.GET, RequestMethod.POST }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> login(//
+ @RequestParam(value = "login", defaultValue = Configuration.ANONYMOUS_LOGIN) String login, //
+ @RequestParam(value = "password", defaultValue = "") String password, //
+ HttpServletResponse response, //
+ HttpServletRequest request//
+ ) throws SecurityException, IOException {
+ try {
+ UsernamePasswordAuthenticationToken springToken = new UsernamePasswordAuthenticationToken(login, password);
+ springToken.setDetails(new WebAuthenticationDetails(request));
+ Authentication authentication = this.authenticationProvider.authenticate(springToken);
+ SecurityContextHolder.getContext().setAuthentication(authentication);
+
+ userService.login(login, password, request.getSession().getId());
+
+ Map<String, Object> result = new TreeMap<>();
+
+ result.put("info", "Login successful. TOKEN returned as a cookie");
+ return result;
+ } catch (AuthenticationException e) {
+ throw new SecurityException("Invalid credentials");
+ }
+ }
+
+ @RequestMapping(value = "/users/{login:.+}", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> getUser(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "login") String login, //
+ @RequestParam(value = "columns", defaultValue = "") String columns//
+ ) throws SecurityException, ObjectNotFoundException {
+ return userRest.getUser(token, login, columns);
+ }
+
+ @RequestMapping(value = "/users/{login}:updatePrivileges", method = { RequestMethod.PATCH }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> updatePrivileges(//
+ @RequestBody String body, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "login") String login //
+ ) throws SecurityException, JsonParseException, JsonMappingException, IOException, QueryException {
+ Map<String, Object> node = parseBody(body);
+ Map<String, Object> data = getData(node, "privileges");
+ return userRest.updatePrivileges(token, login, data);
+ }
+
+ @RequestMapping(value = "/users/{login}:updatePreferences", method = { RequestMethod.PATCH }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> updatePreferences(//
+ @RequestBody String body, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "login") String login //
+ ) throws SecurityException, JsonParseException, JsonMappingException, IOException, QueryException {
+ Map<String, Object> node = parseBody(body);
+ Map<String, Object> data = getData(node, "preferences");
+ return userRest.updatePreferences(token, login, data);
+ }
+
+ @RequestMapping(value = "/users/", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getUsers(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @RequestParam(value = "columns", defaultValue = "") String columns//
+ ) throws SecurityException, ObjectNotFoundException {
+ return userRest.getUsers(token, columns);
+ }
+
+ @RequestMapping(value = "/doLogout", method = { RequestMethod.GET, RequestMethod.POST }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> logout(@CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ HttpServletRequest request, HttpServletResponse response //
+ ) throws SecurityException, IOException {
+ // spring logout
+ Authentication auth = SecurityContextHolder.getContext().getAuthentication();
+ if (auth != null) {
+ new SecurityContextLogoutHandler().logout(request, response, auth);
+ }
+
+ Map<String, Object> result = new TreeMap<>();
+ result.put("status", "OK");
+
+ final Boolean useSecureCookie = false;
+ final String cookiePath = "/";
+
+ Cookie cookie = new Cookie("MINERVA_AUTH_TOKEN", token);
+
+ cookie.setSecure(useSecureCookie);
+ cookie.setMaxAge(0);
+ cookie.setPath(cookiePath);
+
+ response.addCookie(cookie);
+ result.put("status", "OK");
+ return result;
+ }
+
+ @RequestMapping(value = "/users/{login:.+}", method = { RequestMethod.PATCH }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> updateUser(//
+ @RequestBody String body, //
+ @PathVariable(value = "login") String login, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, QueryException, IOException {
+ Map<String, Object> node = parseBody(body);
+ Map<String, Object> data = getData(node, "user");
+ return userRest.updateUser(token, login, data);
+ }
+
+ @RequestMapping(value = "/users/{login:.+}", method = { RequestMethod.POST }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> addOverlay(//
+ @RequestBody MultiValueMap<String, Object> formData, //
+ @PathVariable(value = "login") String login, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, IOException, QueryException {
+ return userRest.addProject(token, login, formData);
+
+ }
+
+ @RequestMapping(value = "/users/{login:.+}", method = { RequestMethod.DELETE }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> removeUser(//
+ @PathVariable(value = "login") String login, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ HttpServletRequest request, HttpServletResponse response //
+ ) throws SecurityException, IOException, QueryException {
+ String currentUserLogin = getUserService().getUserByToken(token).getLogin();
+ Map<String, Object> result = userRest.removeUser(token, login);
+ if (login.equals(currentUserLogin)) {
+ return logout(token, request, response);
+ }
+ return result;
+ }
+
+ /**
+ * @return the userService
+ * @see #userService
+ */
+ public IUserService getUserService() {
+ return userService;
+ }
+
+ /**
+ * @param userService
+ * the userService to set
+ * @see #userService
+ */
+ public void setUserService(IUserService userService) {
+ this.userService = userService;
+ }
+
+ /**
+ * @return the userRest
+ * @see #userRest
+ */
+ public UserRestImpl getUserRest() {
+ return userRest;
+ }
+
+ /**
+ * @param userRest
+ * the userRest to set
+ * @see #userRest
+ */
+ public void setUserRest(UserRestImpl userRest) {
+ this.userRest = userRest;
+ }
}
\ No newline at end of file
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/AllRestTests.java b/rest-api/src/test/java/lcsb/mapviewer/api/AllRestTests.java
index 0adc758211..e9cb89ddf8 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/AllRestTests.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/AllRestTests.java
@@ -1,24 +1,24 @@
-package lcsb.mapviewer.api;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-import lcsb.mapviewer.api.configuration.AllConfigurationTests;
-import lcsb.mapviewer.api.files.AllFileTests;
-import lcsb.mapviewer.api.genomics.AllGenomicsTests;
-import lcsb.mapviewer.api.mesh.AllMeshTests;
-import lcsb.mapviewer.api.projects.AllProjectTests;
-import lcsb.mapviewer.api.users.AllUserTests;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AllConfigurationTests.class, //
- AllFileTests.class, //
- AllGenomicsTests.class, //
- AllMeshTests.class, //
- AllProjectTests.class, //
- AllUserTests.class,//
-})
-public class AllRestTests {
-
-}
+package lcsb.mapviewer.api;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+import lcsb.mapviewer.api.configuration.AllConfigurationTests;
+import lcsb.mapviewer.api.files.AllFileTests;
+import lcsb.mapviewer.api.genomics.AllGenomicsTests;
+import lcsb.mapviewer.api.mesh.AllMeshTests;
+import lcsb.mapviewer.api.projects.AllProjectTests;
+import lcsb.mapviewer.api.users.AllUserTests;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AllConfigurationTests.class, //
+ AllFileTests.class, //
+ AllGenomicsTests.class, //
+ AllMeshTests.class, //
+ AllProjectTests.class, //
+ AllUserTests.class,//
+})
+public class AllRestTests {
+
+}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java b/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java
index 48dd19fd01..bf772d9828 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java
@@ -1,319 +1,319 @@
-package lcsb.mapviewer.api;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.Reader;
-import java.io.StringReader;
-import java.io.StringWriter;
-import java.io.UnsupportedEncodingException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.Map;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.transform.OutputKeys;
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerException;
-import javax.xml.transform.TransformerFactory;
-import javax.xml.transform.dom.DOMSource;
-import javax.xml.transform.stream.StreamResult;
-
-import org.apache.commons.io.FileUtils;
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.runner.RunWith;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.security.crypto.password.PasswordEncoder;
-import org.springframework.test.annotation.Rollback;
-import org.springframework.test.context.ContextConfiguration;
-import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
-import org.springframework.transaction.annotation.Transactional;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-import org.xml.sax.InputSource;
-import org.xml.sax.SAXException;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.ComplexZipConverter;
-import lcsb.mapviewer.converter.ComplexZipConverterParams;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.InvalidInputDataExecption;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
-import lcsb.mapviewer.converter.zip.ZipEntryFile;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
-import lcsb.mapviewer.model.map.model.SubmodelType;
-import lcsb.mapviewer.persist.DbUtils;
-import lcsb.mapviewer.services.interfaces.IUserService;
-
-@Transactional(value = "txManager")
-@Rollback(true)
-@ContextConfiguration(locations = { "/applicationContext-persist.xml", //
- "/applicationContext-annotation.xml", //
- "/applicationContext-service.xml", //
- "/applicationContext-rest.xml", //
- "/test-applicationContext.xml", //
- "/dataSource.xml", //
-})
-@RunWith(SpringJUnit4ClassRunner.class)
-public abstract class RestTestFunctions {
- private Logger logger = Logger.getLogger(RestTestFunctions.class);
-
- public double EPSILON = 1e-6;
-
- @Autowired
- protected PasswordEncoder passwordEncoder;
-
- @Autowired
- protected IUserService userService;
-
- @Autowired
- protected DbUtils dbUtils;
-
- protected String token;
-
- protected String adminToken;
-
- @Before
- public void generalSetUp() {
- dbUtils.setAutoFlush(false);
-
- token = userService.login(Configuration.ANONYMOUS_LOGIN, "");
-
- // assume that we have admin account with all the privileges
- adminToken = userService.login("admin", "admin");
-
- }
-
- @After
- public void generatTearDown() throws IOException {
- File f = new File("map_images");
- if (f.exists()) {
- logger.info("Removing output test directory: " + f.getAbsolutePath());
- FileUtils.deleteDirectory(f);
- }
-
- }
-
- protected String readFile(String file) throws IOException {
- StringBuilder stringBuilder = new StringBuilder();
- BufferedReader reader = new BufferedReader(new FileReader(file));
- try {
- String line = null;
- String ls = System.getProperty("line.separator");
-
- while ((line = reader.readLine()) != null) {
- stringBuilder.append(line);
- stringBuilder.append(ls);
- }
- } finally {
- reader.close();
- }
-
- return stringBuilder.toString();
- }
-
- protected Node getNodeFromXmlString(String text) throws InvalidXmlSchemaException {
- InputSource is = new InputSource();
- is.setCharacterStream(new StringReader(text));
- return getXmlDocumentFromInputSource(is).getChildNodes().item(0);
- }
-
- protected Document getXmlDocumentFromFile(String fileName) throws InvalidXmlSchemaException, IOException {
- File file = new File(fileName);
- InputStream inputStream = new FileInputStream(file);
- Reader reader = null;
- try {
- reader = new InputStreamReader(inputStream, "UTF-8");
- InputSource is = new InputSource(reader);
-
- Document result = getXmlDocumentFromInputSource(is);
- inputStream.close();
- return result;
- } catch (UnsupportedEncodingException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- return null;
- }
-
- protected Document getXmlDocumentFromInputSource(InputSource stream) throws InvalidXmlSchemaException {
- DocumentBuilder db;
- try {
- db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
- } catch (ParserConfigurationException e) {
- throw new InvalidXmlSchemaException("Problem with xml parser");
- }
- Document doc = null;
- try {
- doc = db.parse(stream);
- } catch (SAXException e) {
- logger.error(e);
- } catch (IOException e) {
- logger.error(e);
- }
- return doc;
- }
-
- private static Map<String, Model> models = new HashMap<>();
-
- protected Model getModelForFile(String fileName, boolean fromCache) throws Exception {
- Model result = null;
- if (!fromCache) {
- logger.debug("File without cache: " + fileName);
- result = getModelForFile(fileName);
- } else {
- result = RestTestFunctions.models.get(fileName);
- if (result == null) {
- logger.debug("File to cache: " + fileName);
-
- result = getModelForFile(fileName);
- RestTestFunctions.models.put(fileName, result);
- }
- }
- return result;
- }
-
- private Model getModelForFile(String fileName) throws InvalidInputDataExecption, IOException {
- if (fileName.endsWith("zip")) {
- ComplexZipConverter parser = new ComplexZipConverter(CellDesignerXmlParser.class);
- ComplexZipConverterParams complexParams;
- complexParams = new ComplexZipConverterParams().zipFile(fileName);
- ZipEntryFile entry1 = new ModelZipEntryFile("main.xml", "main", true, false, SubmodelType.UNKNOWN);
- ZipEntryFile entry2 = new ModelZipEntryFile("submaps/s1.xml", "s1", false, false, SubmodelType.UNKNOWN);
- ZipEntryFile entry3 = new ModelZipEntryFile("submaps/s2.xml", "s2", false, false, SubmodelType.UNKNOWN);
- ZipEntryFile entry4 = new ModelZipEntryFile("submaps/s3.xml", "s3", false, false, SubmodelType.UNKNOWN);
- ZipEntryFile entry5 = new ModelZipEntryFile("submaps/mapping.xml", "mapping", false, true, SubmodelType.UNKNOWN);
- complexParams.entry(entry1);
- complexParams.entry(entry2);
- complexParams.entry(entry3);
- complexParams.entry(entry4);
- complexParams.entry(entry5);
-
- Model model = parser.createModel(complexParams);
- model.setTileSize(256);
- for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
- connection.getSubmodel().setTileSize(256);
- }
- model.setProject(new Project());
- return model;
-
- } else {
- Model model = new CellDesignerXmlParser().createModel(new ConverterParams().filename(fileName));
- model.setTileSize(256);
- model.setProject(new Project());
- return model;
- }
- }
-
- protected String createTmpFileName() {
- try {
- File f = File.createTempFile("prefix", ".txt");
- String filename = f.getName();
- f.delete();
- return filename;
- } catch (IOException e) {
- e.printStackTrace();
- return null;
- }
- }
-
- protected String nodeToString(Node node) {
- return nodeToString(node, false);
- }
-
- protected String nodeToString(Node node, boolean includeHeadNode) {
- if (node == null)
- return null;
- StringWriter sw = new StringWriter();
- try {
- Transformer t = TransformerFactory.newInstance().newTransformer();
- t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
- t.setOutputProperty(OutputKeys.INDENT, "yes");
- t.setOutputProperty(OutputKeys.METHOD, "xml");
-
- NodeList list = node.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node element = list.item(i);
- t.transform(new DOMSource(element), new StreamResult(sw));
- }
- } catch (TransformerException te) {
- logger.debug("nodeToString Transformer Exception");
- }
- if (includeHeadNode) {
- return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
- }
- return sw.toString();
- }
-
- protected boolean equalFiles(String fileA, String fileB) throws IOException {
- int BLOCK_SIZE = 65536;
- FileInputStream inputStreamA = new FileInputStream(fileA);
- FileInputStream inputStreamB = new FileInputStream(fileB);
- // vary BLOCK_SIZE to suit yourself.
- // it should probably a factor or multiple of the size of a disk
- // sector/cluster.
- // Note that your max heap size may need to be adjused
- // if you have a very big block size or lots of these comparators.
-
- // assume inputStreamA and inputStreamB are streams from your two files.
- byte[] streamABlock = new byte[BLOCK_SIZE];
- byte[] streamBBlock = new byte[BLOCK_SIZE];
- boolean match = true;
- int bytesReadA = 0;
- int bytesReadB = 0;
- do {
- bytesReadA = inputStreamA.read(streamABlock);
- bytesReadB = inputStreamB.read(streamBBlock);
- match = ((bytesReadA == bytesReadB) && Arrays.equals(streamABlock, streamBBlock));
- } while (match && (bytesReadA > -1));
- inputStreamA.close();
- inputStreamB.close();
- return match;
- }
-
- public File createTempDirectory() throws IOException {
- final File temp;
-
- temp = File.createTempFile("temp", Long.toString(System.nanoTime()));
-
- if (!(temp.delete())) {
- throw new IOException("Could not delete temp file: " + temp.getAbsolutePath());
- }
-
- if (!(temp.mkdir())) {
- throw new IOException("Could not create temp directory: " + temp.getAbsolutePath());
- }
-
- return (temp);
- }
-
- protected String getWebpage(String accessUrl) throws IOException {
- String inputLine;
- StringBuilder tmp = new StringBuilder();
- URL url = new URL(accessUrl);
- URLConnection urlConn = url.openConnection();
- BufferedReader in = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));
-
- while ((inputLine = in.readLine()) != null) {
- tmp.append(inputLine);
- }
- in.close();
- return tmp.toString();
- }
-
-}
+package lcsb.mapviewer.api;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.io.StringReader;
+import java.io.StringWriter;
+import java.io.UnsupportedEncodingException;
+import java.net.URL;
+import java.net.URLConnection;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Map;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.OutputKeys;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerException;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.dom.DOMSource;
+import javax.xml.transform.stream.StreamResult;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.runner.RunWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.security.crypto.password.PasswordEncoder;
+import org.springframework.test.annotation.Rollback;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
+import org.springframework.transaction.annotation.Transactional;
+import org.w3c.dom.Document;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.ComplexZipConverter;
+import lcsb.mapviewer.converter.ComplexZipConverterParams;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
+import lcsb.mapviewer.converter.zip.ZipEntryFile;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
+import lcsb.mapviewer.model.map.model.SubmodelType;
+import lcsb.mapviewer.persist.DbUtils;
+import lcsb.mapviewer.services.interfaces.IUserService;
+
+@Transactional(value = "txManager")
+@Rollback(true)
+@ContextConfiguration(locations = { "/applicationContext-persist.xml", //
+ "/applicationContext-annotation.xml", //
+ "/applicationContext-service.xml", //
+ "/applicationContext-rest.xml", //
+ "/test-applicationContext.xml", //
+ "/dataSource.xml", //
+})
+@RunWith(SpringJUnit4ClassRunner.class)
+public abstract class RestTestFunctions {
+ private Logger logger = Logger.getLogger(RestTestFunctions.class);
+
+ public double EPSILON = 1e-6;
+
+ @Autowired
+ protected PasswordEncoder passwordEncoder;
+
+ @Autowired
+ protected IUserService userService;
+
+ @Autowired
+ protected DbUtils dbUtils;
+
+ protected String token;
+
+ protected String adminToken;
+
+ @Before
+ public void generalSetUp() {
+ dbUtils.setAutoFlush(false);
+
+ token = userService.login(Configuration.ANONYMOUS_LOGIN, "");
+
+ // assume that we have admin account with all the privileges
+ adminToken = userService.login("admin", "admin");
+
+ }
+
+ @After
+ public void generatTearDown() throws IOException {
+ File f = new File("map_images");
+ if (f.exists()) {
+ logger.info("Removing output test directory: " + f.getAbsolutePath());
+ FileUtils.deleteDirectory(f);
+ }
+
+ }
+
+ protected String readFile(String file) throws IOException {
+ StringBuilder stringBuilder = new StringBuilder();
+ BufferedReader reader = new BufferedReader(new FileReader(file));
+ try {
+ String line = null;
+ String ls = System.getProperty("line.separator");
+
+ while ((line = reader.readLine()) != null) {
+ stringBuilder.append(line);
+ stringBuilder.append(ls);
+ }
+ } finally {
+ reader.close();
+ }
+
+ return stringBuilder.toString();
+ }
+
+ protected Node getNodeFromXmlString(String text) throws InvalidXmlSchemaException {
+ InputSource is = new InputSource();
+ is.setCharacterStream(new StringReader(text));
+ return getXmlDocumentFromInputSource(is).getChildNodes().item(0);
+ }
+
+ protected Document getXmlDocumentFromFile(String fileName) throws InvalidXmlSchemaException, IOException {
+ File file = new File(fileName);
+ InputStream inputStream = new FileInputStream(file);
+ Reader reader = null;
+ try {
+ reader = new InputStreamReader(inputStream, "UTF-8");
+ InputSource is = new InputSource(reader);
+
+ Document result = getXmlDocumentFromInputSource(is);
+ inputStream.close();
+ return result;
+ } catch (UnsupportedEncodingException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ return null;
+ }
+
+ protected Document getXmlDocumentFromInputSource(InputSource stream) throws InvalidXmlSchemaException {
+ DocumentBuilder db;
+ try {
+ db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
+ } catch (ParserConfigurationException e) {
+ throw new InvalidXmlSchemaException("Problem with xml parser");
+ }
+ Document doc = null;
+ try {
+ doc = db.parse(stream);
+ } catch (SAXException e) {
+ logger.error(e);
+ } catch (IOException e) {
+ logger.error(e);
+ }
+ return doc;
+ }
+
+ private static Map<String, Model> models = new HashMap<>();
+
+ protected Model getModelForFile(String fileName, boolean fromCache) throws Exception {
+ Model result = null;
+ if (!fromCache) {
+ logger.debug("File without cache: " + fileName);
+ result = getModelForFile(fileName);
+ } else {
+ result = RestTestFunctions.models.get(fileName);
+ if (result == null) {
+ logger.debug("File to cache: " + fileName);
+
+ result = getModelForFile(fileName);
+ RestTestFunctions.models.put(fileName, result);
+ }
+ }
+ return result;
+ }
+
+ private Model getModelForFile(String fileName) throws InvalidInputDataExecption, IOException {
+ if (fileName.endsWith("zip")) {
+ ComplexZipConverter parser = new ComplexZipConverter(CellDesignerXmlParser.class);
+ ComplexZipConverterParams complexParams;
+ complexParams = new ComplexZipConverterParams().zipFile(fileName);
+ ZipEntryFile entry1 = new ModelZipEntryFile("main.xml", "main", true, false, SubmodelType.UNKNOWN);
+ ZipEntryFile entry2 = new ModelZipEntryFile("submaps/s1.xml", "s1", false, false, SubmodelType.UNKNOWN);
+ ZipEntryFile entry3 = new ModelZipEntryFile("submaps/s2.xml", "s2", false, false, SubmodelType.UNKNOWN);
+ ZipEntryFile entry4 = new ModelZipEntryFile("submaps/s3.xml", "s3", false, false, SubmodelType.UNKNOWN);
+ ZipEntryFile entry5 = new ModelZipEntryFile("submaps/mapping.xml", "mapping", false, true, SubmodelType.UNKNOWN);
+ complexParams.entry(entry1);
+ complexParams.entry(entry2);
+ complexParams.entry(entry3);
+ complexParams.entry(entry4);
+ complexParams.entry(entry5);
+
+ Model model = parser.createModel(complexParams);
+ model.setTileSize(256);
+ for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
+ connection.getSubmodel().setTileSize(256);
+ }
+ model.setProject(new Project());
+ return model;
+
+ } else {
+ Model model = new CellDesignerXmlParser().createModel(new ConverterParams().filename(fileName));
+ model.setTileSize(256);
+ model.setProject(new Project());
+ return model;
+ }
+ }
+
+ protected String createTmpFileName() {
+ try {
+ File f = File.createTempFile("prefix", ".txt");
+ String filename = f.getName();
+ f.delete();
+ return filename;
+ } catch (IOException e) {
+ e.printStackTrace();
+ return null;
+ }
+ }
+
+ protected String nodeToString(Node node) {
+ return nodeToString(node, false);
+ }
+
+ protected String nodeToString(Node node, boolean includeHeadNode) {
+ if (node == null)
+ return null;
+ StringWriter sw = new StringWriter();
+ try {
+ Transformer t = TransformerFactory.newInstance().newTransformer();
+ t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
+ t.setOutputProperty(OutputKeys.INDENT, "yes");
+ t.setOutputProperty(OutputKeys.METHOD, "xml");
+
+ NodeList list = node.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node element = list.item(i);
+ t.transform(new DOMSource(element), new StreamResult(sw));
+ }
+ } catch (TransformerException te) {
+ logger.debug("nodeToString Transformer Exception");
+ }
+ if (includeHeadNode) {
+ return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
+ }
+ return sw.toString();
+ }
+
+ protected boolean equalFiles(String fileA, String fileB) throws IOException {
+ int BLOCK_SIZE = 65536;
+ FileInputStream inputStreamA = new FileInputStream(fileA);
+ FileInputStream inputStreamB = new FileInputStream(fileB);
+ // vary BLOCK_SIZE to suit yourself.
+ // it should probably a factor or multiple of the size of a disk
+ // sector/cluster.
+ // Note that your max heap size may need to be adjused
+ // if you have a very big block size or lots of these comparators.
+
+ // assume inputStreamA and inputStreamB are streams from your two files.
+ byte[] streamABlock = new byte[BLOCK_SIZE];
+ byte[] streamBBlock = new byte[BLOCK_SIZE];
+ boolean match = true;
+ int bytesReadA = 0;
+ int bytesReadB = 0;
+ do {
+ bytesReadA = inputStreamA.read(streamABlock);
+ bytesReadB = inputStreamB.read(streamBBlock);
+ match = ((bytesReadA == bytesReadB) && Arrays.equals(streamABlock, streamBBlock));
+ } while (match && (bytesReadA > -1));
+ inputStreamA.close();
+ inputStreamB.close();
+ return match;
+ }
+
+ public File createTempDirectory() throws IOException {
+ final File temp;
+
+ temp = File.createTempFile("temp", Long.toString(System.nanoTime()));
+
+ if (!(temp.delete())) {
+ throw new IOException("Could not delete temp file: " + temp.getAbsolutePath());
+ }
+
+ if (!(temp.mkdir())) {
+ throw new IOException("Could not create temp directory: " + temp.getAbsolutePath());
+ }
+
+ return (temp);
+ }
+
+ protected String getWebpage(String accessUrl) throws IOException {
+ String inputLine;
+ StringBuilder tmp = new StringBuilder();
+ URL url = new URL(accessUrl);
+ URLConnection urlConn = url.openConnection();
+ BufferedReader in = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));
+
+ while ((inputLine = in.readLine()) != null) {
+ tmp.append(inputLine);
+ }
+ in.close();
+ return tmp.toString();
+ }
+
+}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/AllProjectTests.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/AllProjectTests.java
index 8285a5ea73..7219f18b9b 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/AllProjectTests.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/AllProjectTests.java
@@ -1,22 +1,22 @@
-package lcsb.mapviewer.api.projects;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-import lcsb.mapviewer.api.projects.chemicals.AllChemicalTests;
-import lcsb.mapviewer.api.projects.comments.AllCommentTests;
-import lcsb.mapviewer.api.projects.drugs.AllDrugTests;
-import lcsb.mapviewer.api.projects.mirnas.AllMiRnaTests;
-import lcsb.mapviewer.api.projects.models.AllModelsTests;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AllChemicalTests.class, //
- AllCommentTests.class, //
- AllDrugTests.class, //
- AllMiRnaTests.class, //
- AllModelsTests.class, //
- ProjectRestImplTest.class })
-public class AllProjectTests {
-
-}
+package lcsb.mapviewer.api.projects;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+import lcsb.mapviewer.api.projects.chemicals.AllChemicalTests;
+import lcsb.mapviewer.api.projects.comments.AllCommentTests;
+import lcsb.mapviewer.api.projects.drugs.AllDrugTests;
+import lcsb.mapviewer.api.projects.mirnas.AllMiRnaTests;
+import lcsb.mapviewer.api.projects.models.AllModelsTests;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AllChemicalTests.class, //
+ AllCommentTests.class, //
+ AllDrugTests.class, //
+ AllMiRnaTests.class, //
+ AllModelsTests.class, //
+ ProjectRestImplTest.class })
+public class AllProjectTests {
+
+}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java
index 6d2a2b0aab..79afcc01ea 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java
@@ -1,343 +1,343 @@
-package lcsb.mapviewer.api.projects;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-import static org.mockito.Matchers.any;
-import static org.mockito.Matchers.anyString;
-import static org.mockito.Mockito.times;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.util.LinkedMultiValueMap;
-import org.springframework.util.MultiValueMap;
-
-import com.google.gson.Gson;
-
-import lcsb.mapviewer.api.ObjectNotFoundException;
-import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.api.RestTestFunctions;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.graphics.PdfImageGenerator;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
-import lcsb.mapviewer.converter.zip.LayoutZipEntryFile;
-import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
-import lcsb.mapviewer.converter.zip.ZipEntryFile;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.cache.FileEntry;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.persist.dao.ProjectDao;
-import lcsb.mapviewer.services.interfaces.IModelService;
-import lcsb.mapviewer.services.interfaces.IProjectService;
-
-public class ProjectRestImplTest extends RestTestFunctions {
- Logger logger = Logger.getLogger(ProjectRestImplTest.class);
-
- @Autowired
- ProjectRestImpl _projectRestImpl;
-
- @Autowired
- IModelService modelService;
- @Autowired
- IProjectService projectService;
-
- @Autowired
- ProjectDao projectDao;
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetModelAsImageForInvalidConverter() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- projectRest.getModelAsImage(token, "sample", "0", "", "", "", "", "");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetModelAsImage() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- FileEntry result = projectRest.getModelAsImage(token, "sample", "0", PdfImageGenerator.class.getCanonicalName(),
- "", "", "", "");
- assertNotNull(result);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetModelDataDependencies() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- Map<String, Object> result = projectRest.getProject("sample", token);
- Gson gson = new Gson();
- assertNotNull(gson.toJson(result));
- Mockito.verify(projectRest.getModelService(), times(0)).getLastModelByProjectId(anyString(), any());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test(expected = ObjectNotFoundException.class)
- public void testGetInvalidMetaData() throws Exception {
- ProjectRestImpl projectRest = createMockProjectRest(null);
- projectRest.getProject("unknown_model_id", token);
- }
-
- @Test
- public void testGetModelAsImage2() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- projectRest.getModelAsImage(token, "sample", "0", PdfImageGenerator.class.getCanonicalName(), "", "", "", "");
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetModelAsFileModel() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- projectRest.getModelAsModelFile(token, "sample", "0", "", "", "", "", "");
- fail("Exception expected");
- } catch (QueryException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetModelAsFileModel2() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- projectRest.getModelAsModelFile(token, "sample", "0", CellDesignerXmlParser.class.getCanonicalName(), "", "", "",
- "0,0;90,0;90,90;90,0");
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetModelAsFileModel3() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- projectRest.getModelAsModelFile(token, "sample", "0", "", "", "", "", "0,0;90,0;90,90;90,0");
- fail("Exception expected");
- } catch (QueryException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetProject() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- Map<String, Object> result = projectRest.getProject("sample", token);
- Gson gson = new Gson();
- assertNotNull(gson.toJson(result));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdateProject() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- Map<String, String> disease = new HashMap<>();
- disease.put("type", MiriamType.MESH_2012.name());
- disease.put("resource", "D010300");
- Map<String, Object> data = new HashMap<>();
- data.put("version", "1");
- data.put("name", "test");
- data.put("organism", null);
- data.put("disease", disease);
- data.put("projectId", "sample");
- data.put("id", "0");
- projectRest.updateProject(adminToken, "sample", data);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testComputePathForProject() throws Exception {
- try {
- String project_id = "Some_id";
- String directory1 = _projectRestImpl.computePathForProject(project_id, ".");
- Project project = new Project();
- project.setProjectId(project_id);
- projectDao.add(project);
- projectDao.delete(project);
- String directory2 = _projectRestImpl.computePathForProject(project_id, ".");
-
- assertFalse(directory1.equals(directory2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetProjects() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- List<Map<String, Object>> result = projectRest.getProjects(token);
- Gson gson = new Gson();
- assertNotNull(gson.toJson(result));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetStatistics() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- Map<String, Object> result = projectRest.getStatistics("sample", token);
- Gson gson = new Gson();
- assertNotNull(gson.toJson(result));
-
- Map<?, ?> elementAnnotations = (Map<?, ?>) result.get("elementAnnotations");
- assertEquals(elementAnnotations.get(MiriamType.CAS), 0);
- assertTrue((Integer) elementAnnotations.get(MiriamType.ENTREZ) > 0);
-
- Map<?, ?> reactionAnnotations = (Map<?, ?>) result.get("reactionAnnotations");
- assertEquals(reactionAnnotations.get(MiriamType.ENTREZ), 0);
- assertEquals(reactionAnnotations.get(MiriamType.PUBMED), 1);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetMetaDataForComplexWithImages() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/complex_model_with_submaps.zip");
- Map<String, Object> result = projectRest.getProject("sample", token);
- Gson gson = new Gson();
- assertNotNull(gson.toJson(result));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testExtractZipEntries() throws Exception {
- try {
- MultiValueMap<String, Object> data = new LinkedMultiValueMap<>();
- data.put("zip-entries[0][_type]", createLinkedList("MAP"));
- data.put("zip-entries[0][_filename]", createLinkedList("main.xml"));
- data.put("zip-entries[0][_data][root]", createLinkedList("true"));
- data.put("zip-entries[0][_data][name]", createLinkedList("main"));
- data.put("zip-entries[0][_data][type][id]", createLinkedList("UNKNOWN"));
- data.put("zip-entries[0][_data][type][name]", createLinkedList("Unknown"));
- data.put("zip-entries[1][_type]", createLinkedList("OVERLAY"));
- data.put("zip-entries[1][_filename]", createLinkedList("layouts/goodschema.txt"));
- data.put("zip-entries[1][_data][name]", createLinkedList("example name"));
- data.put("zip-entries[1][_data][description]", createLinkedList("layout description"));
- data.put("zip-entries[2][_type]", createLinkedList("IMAGE"));
- data.put("zip-entries[2][_filename]", createLinkedList("images/test.png"));
- List<ZipEntryFile> result = _projectRestImpl.extractZipEntries(data);
- assertNotNull(result);
- assertEquals(3, result.size());
- assertTrue(result.get(0) instanceof ModelZipEntryFile);
- assertTrue(result.get(1) instanceof LayoutZipEntryFile);
- assertTrue(result.get(2) instanceof ImageZipEntryFile);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private LinkedList<Object> createLinkedList(Object string) {
- LinkedList<Object> result = new LinkedList<>();
- result.add(string);
- return result;
- }
-
- private ProjectRestImpl createMockProjectRest(String string) throws Exception {
- Model model = null;
- Project project = null;
- if (string != null) {
- project = new Project();
- model = super.getModelForFile(string, true);
- project.addModel(model);
- project.setProjectId(model.getName());
- project.addWarning("some warning");
- }
- IModelService mockModelService = Mockito.mock(IModelService.class);
- Mockito.when(mockModelService.getLastModelByProjectId(anyString(), any())).thenReturn(model);
- _projectRestImpl.setModelService(mockModelService);
-
- IProjectService projectServiceMock = Mockito.mock(IProjectService.class);
- Mockito.when(projectServiceMock.getProjectByProjectId(anyString(), any())).thenReturn(project);
- List<Project> projects = new ArrayList<>();
- projects.add(project);
- Mockito.when(projectServiceMock.getAllProjects(any())).thenReturn(projects);
- _projectRestImpl.setProjectService(projectServiceMock);
-
- return _projectRestImpl;
- }
-
- @Test
- public void testGetLogs() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- Map<String, Object> result = projectRest.getLogs("sample", "", token, "0", 10, "id", "asc", "");
- assertNotNull(result);
- Gson gson = new Gson();
- assertNotNull(gson.toJson(result));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.api.projects;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import static org.mockito.Matchers.any;
+import static org.mockito.Matchers.anyString;
+import static org.mockito.Mockito.times;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.util.LinkedMultiValueMap;
+import org.springframework.util.MultiValueMap;
+
+import com.google.gson.Gson;
+
+import lcsb.mapviewer.api.ObjectNotFoundException;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.api.RestTestFunctions;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.graphics.PdfImageGenerator;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
+import lcsb.mapviewer.converter.zip.LayoutZipEntryFile;
+import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
+import lcsb.mapviewer.converter.zip.ZipEntryFile;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.cache.FileEntry;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.persist.dao.ProjectDao;
+import lcsb.mapviewer.services.interfaces.IModelService;
+import lcsb.mapviewer.services.interfaces.IProjectService;
+
+public class ProjectRestImplTest extends RestTestFunctions {
+ Logger logger = Logger.getLogger(ProjectRestImplTest.class);
+
+ @Autowired
+ ProjectRestImpl _projectRestImpl;
+
+ @Autowired
+ IModelService modelService;
+ @Autowired
+ IProjectService projectService;
+
+ @Autowired
+ ProjectDao projectDao;
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetModelAsImageForInvalidConverter() throws Exception {
+ try {
+ ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ projectRest.getModelAsImage(token, "sample", "0", "", "", "", "", "");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetModelAsImage() throws Exception {
+ try {
+ ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ FileEntry result = projectRest.getModelAsImage(token, "sample", "0", PdfImageGenerator.class.getCanonicalName(),
+ "", "", "", "");
+ assertNotNull(result);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetModelDataDependencies() throws Exception {
+ try {
+ ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ Map<String, Object> result = projectRest.getProject("sample", token);
+ Gson gson = new Gson();
+ assertNotNull(gson.toJson(result));
+ Mockito.verify(projectRest.getModelService(), times(0)).getLastModelByProjectId(anyString(), any());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test(expected = ObjectNotFoundException.class)
+ public void testGetInvalidMetaData() throws Exception {
+ ProjectRestImpl projectRest = createMockProjectRest(null);
+ projectRest.getProject("unknown_model_id", token);
+ }
+
+ @Test
+ public void testGetModelAsImage2() throws Exception {
+ try {
+ ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ projectRest.getModelAsImage(token, "sample", "0", PdfImageGenerator.class.getCanonicalName(), "", "", "", "");
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetModelAsFileModel() throws Exception {
+ try {
+ ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ projectRest.getModelAsModelFile(token, "sample", "0", "", "", "", "", "");
+ fail("Exception expected");
+ } catch (QueryException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetModelAsFileModel2() throws Exception {
+ try {
+ ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ projectRest.getModelAsModelFile(token, "sample", "0", CellDesignerXmlParser.class.getCanonicalName(), "", "", "",
+ "0,0;90,0;90,90;90,0");
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetModelAsFileModel3() throws Exception {
+ try {
+ ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ projectRest.getModelAsModelFile(token, "sample", "0", "", "", "", "", "0,0;90,0;90,90;90,0");
+ fail("Exception expected");
+ } catch (QueryException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetProject() throws Exception {
+ try {
+ ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ Map<String, Object> result = projectRest.getProject("sample", token);
+ Gson gson = new Gson();
+ assertNotNull(gson.toJson(result));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdateProject() throws Exception {
+ try {
+ ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ Map<String, String> disease = new HashMap<>();
+ disease.put("type", MiriamType.MESH_2012.name());
+ disease.put("resource", "D010300");
+ Map<String, Object> data = new HashMap<>();
+ data.put("version", "1");
+ data.put("name", "test");
+ data.put("organism", null);
+ data.put("disease", disease);
+ data.put("projectId", "sample");
+ data.put("id", "0");
+ projectRest.updateProject(adminToken, "sample", data);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testComputePathForProject() throws Exception {
+ try {
+ String project_id = "Some_id";
+ String directory1 = _projectRestImpl.computePathForProject(project_id, ".");
+ Project project = new Project();
+ project.setProjectId(project_id);
+ projectDao.add(project);
+ projectDao.delete(project);
+ String directory2 = _projectRestImpl.computePathForProject(project_id, ".");
+
+ assertFalse(directory1.equals(directory2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetProjects() throws Exception {
+ try {
+ ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ List<Map<String, Object>> result = projectRest.getProjects(token);
+ Gson gson = new Gson();
+ assertNotNull(gson.toJson(result));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetStatistics() throws Exception {
+ try {
+ ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ Map<String, Object> result = projectRest.getStatistics("sample", token);
+ Gson gson = new Gson();
+ assertNotNull(gson.toJson(result));
+
+ Map<?, ?> elementAnnotations = (Map<?, ?>) result.get("elementAnnotations");
+ assertEquals(elementAnnotations.get(MiriamType.CAS), 0);
+ assertTrue((Integer) elementAnnotations.get(MiriamType.ENTREZ) > 0);
+
+ Map<?, ?> reactionAnnotations = (Map<?, ?>) result.get("reactionAnnotations");
+ assertEquals(reactionAnnotations.get(MiriamType.ENTREZ), 0);
+ assertEquals(reactionAnnotations.get(MiriamType.PUBMED), 1);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetMetaDataForComplexWithImages() throws Exception {
+ try {
+ ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/complex_model_with_submaps.zip");
+ Map<String, Object> result = projectRest.getProject("sample", token);
+ Gson gson = new Gson();
+ assertNotNull(gson.toJson(result));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testExtractZipEntries() throws Exception {
+ try {
+ MultiValueMap<String, Object> data = new LinkedMultiValueMap<>();
+ data.put("zip-entries[0][_type]", createLinkedList("MAP"));
+ data.put("zip-entries[0][_filename]", createLinkedList("main.xml"));
+ data.put("zip-entries[0][_data][root]", createLinkedList("true"));
+ data.put("zip-entries[0][_data][name]", createLinkedList("main"));
+ data.put("zip-entries[0][_data][type][id]", createLinkedList("UNKNOWN"));
+ data.put("zip-entries[0][_data][type][name]", createLinkedList("Unknown"));
+ data.put("zip-entries[1][_type]", createLinkedList("OVERLAY"));
+ data.put("zip-entries[1][_filename]", createLinkedList("layouts/goodschema.txt"));
+ data.put("zip-entries[1][_data][name]", createLinkedList("example name"));
+ data.put("zip-entries[1][_data][description]", createLinkedList("layout description"));
+ data.put("zip-entries[2][_type]", createLinkedList("IMAGE"));
+ data.put("zip-entries[2][_filename]", createLinkedList("images/test.png"));
+ List<ZipEntryFile> result = _projectRestImpl.extractZipEntries(data);
+ assertNotNull(result);
+ assertEquals(3, result.size());
+ assertTrue(result.get(0) instanceof ModelZipEntryFile);
+ assertTrue(result.get(1) instanceof LayoutZipEntryFile);
+ assertTrue(result.get(2) instanceof ImageZipEntryFile);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private LinkedList<Object> createLinkedList(Object string) {
+ LinkedList<Object> result = new LinkedList<>();
+ result.add(string);
+ return result;
+ }
+
+ private ProjectRestImpl createMockProjectRest(String string) throws Exception {
+ Model model = null;
+ Project project = null;
+ if (string != null) {
+ project = new Project();
+ model = super.getModelForFile(string, true);
+ project.addModel(model);
+ project.setProjectId(model.getName());
+ project.addWarning("some warning");
+ }
+ IModelService mockModelService = Mockito.mock(IModelService.class);
+ Mockito.when(mockModelService.getLastModelByProjectId(anyString(), any())).thenReturn(model);
+ _projectRestImpl.setModelService(mockModelService);
+
+ IProjectService projectServiceMock = Mockito.mock(IProjectService.class);
+ Mockito.when(projectServiceMock.getProjectByProjectId(anyString(), any())).thenReturn(project);
+ List<Project> projects = new ArrayList<>();
+ projects.add(project);
+ Mockito.when(projectServiceMock.getAllProjects(any())).thenReturn(projects);
+ _projectRestImpl.setProjectService(projectServiceMock);
+
+ return _projectRestImpl;
+ }
+
+ @Test
+ public void testGetLogs() throws Exception {
+ try {
+ ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ Map<String, Object> result = projectRest.getLogs("sample", "", token, "0", 10, "id", "asc", "");
+ assertNotNull(result);
+ Gson gson = new Gson();
+ assertNotNull(gson.toJson(result));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/comments/AllCommentTests.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/comments/AllCommentTests.java
index de0f5a2fdc..bca706c499 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/comments/AllCommentTests.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/comments/AllCommentTests.java
@@ -1,11 +1,11 @@
-package lcsb.mapviewer.api.projects.comments;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ CommentRestImplTest.class })
-public class AllCommentTests {
-
-}
+package lcsb.mapviewer.api.projects.comments;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ CommentRestImplTest.class })
+public class AllCommentTests {
+
+}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/comments/CommentRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/comments/CommentRestImplTest.java
index 75b9c48eb4..3f929a04e7 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/comments/CommentRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/comments/CommentRestImplTest.java
@@ -1,93 +1,93 @@
-package lcsb.mapviewer.api.projects.comments;
-
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-import static org.mockito.Matchers.any;
-import static org.mockito.Matchers.anyString;
-import static org.mockito.Matchers.eq;
-import static org.mockito.Mockito.times;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.api.RestTestFunctions;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.services.interfaces.IModelService;
-import lcsb.mapviewer.services.interfaces.IProjectService;
-
-public class CommentRestImplTest extends RestTestFunctions {
-
- @Autowired
- public CommentRestImpl _commentRestImpl;
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetForNonExisting() throws Exception {
- try {
- _commentRestImpl.getCommentList(token, "unk", "", "", "", "");
- fail("Exception expected");
- } catch (QueryException e2) {
- assertTrue(e2.getMessage().contains("Project with given id doesn't exist"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetCommentsDependencies() throws Exception {
- try {
- CommentRestImpl commentRestImpl = createMockProjectRest("testFiles/model/sample.xml");
- commentRestImpl.getCommentList(adminToken, "sample", "", "", "", "");
- Mockito.verify(commentRestImpl.getModelService(), times(0)).getLastModelByProjectId(anyString(), any());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private CommentRestImpl createMockProjectRest(String string) throws Exception {
- Model model = null;
- Project project = null;
- String modelName = "";
- if (string != null) {
- project = new Project();
- model = super.getModelForFile(string, true);
- project.addModel(model);
- modelName = model.getName();
- }
- IModelService mockModelService = Mockito.mock(IModelService.class);
- Mockito.when(mockModelService.getLastModelByProjectId(eq(modelName), any())).thenReturn(model);
- _commentRestImpl.setModelService(mockModelService);
-
- IProjectService projectServiceMock = Mockito.mock(IProjectService.class);
- Mockito.when(projectServiceMock.getProjectByProjectId(eq(modelName), any())).thenReturn(project);
- List<Project> projects = new ArrayList<>();
- projects.add(project);
- Mockito.when(projectServiceMock.getAllProjects(any())).thenReturn(projects);
- _commentRestImpl.setProjectService(projectServiceMock);
-
- return _commentRestImpl;
- }
-
-}
+package lcsb.mapviewer.api.projects.comments;
+
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import static org.mockito.Matchers.any;
+import static org.mockito.Matchers.anyString;
+import static org.mockito.Matchers.eq;
+import static org.mockito.Mockito.times;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.api.RestTestFunctions;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.services.interfaces.IModelService;
+import lcsb.mapviewer.services.interfaces.IProjectService;
+
+public class CommentRestImplTest extends RestTestFunctions {
+
+ @Autowired
+ public CommentRestImpl _commentRestImpl;
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetForNonExisting() throws Exception {
+ try {
+ _commentRestImpl.getCommentList(token, "unk", "", "", "", "");
+ fail("Exception expected");
+ } catch (QueryException e2) {
+ assertTrue(e2.getMessage().contains("Project with given id doesn't exist"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetCommentsDependencies() throws Exception {
+ try {
+ CommentRestImpl commentRestImpl = createMockProjectRest("testFiles/model/sample.xml");
+ commentRestImpl.getCommentList(adminToken, "sample", "", "", "", "");
+ Mockito.verify(commentRestImpl.getModelService(), times(0)).getLastModelByProjectId(anyString(), any());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private CommentRestImpl createMockProjectRest(String string) throws Exception {
+ Model model = null;
+ Project project = null;
+ String modelName = "";
+ if (string != null) {
+ project = new Project();
+ model = super.getModelForFile(string, true);
+ project.addModel(model);
+ modelName = model.getName();
+ }
+ IModelService mockModelService = Mockito.mock(IModelService.class);
+ Mockito.when(mockModelService.getLastModelByProjectId(eq(modelName), any())).thenReturn(model);
+ _commentRestImpl.setModelService(mockModelService);
+
+ IProjectService projectServiceMock = Mockito.mock(IProjectService.class);
+ Mockito.when(projectServiceMock.getProjectByProjectId(eq(modelName), any())).thenReturn(project);
+ List<Project> projects = new ArrayList<>();
+ projects.add(project);
+ Mockito.when(projectServiceMock.getAllProjects(any())).thenReturn(projects);
+ _commentRestImpl.setProjectService(projectServiceMock);
+
+ return _commentRestImpl;
+ }
+
+}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/users/AllUserTests.java b/rest-api/src/test/java/lcsb/mapviewer/api/users/AllUserTests.java
index 992680c301..a2f4121784 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/users/AllUserTests.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/users/AllUserTests.java
@@ -1,11 +1,11 @@
-package lcsb.mapviewer.api.users;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ UserRestImplTest.class })
-public class AllUserTests {
-
-}
+package lcsb.mapviewer.api.users;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ UserRestImplTest.class })
+public class AllUserTests {
+
+}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/users/UserRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/users/UserRestImplTest.java
index 102ad90636..1ba413ed2a 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/users/UserRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/users/UserRestImplTest.java
@@ -1,144 +1,144 @@
-package lcsb.mapviewer.api.users;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.io.IOException;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import com.fasterxml.jackson.core.JsonParseException;
-import com.fasterxml.jackson.databind.JsonMappingException;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.databind.node.ObjectNode;
-import com.google.gson.Gson;
-
-import lcsb.mapviewer.api.RestTestFunctions;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.model.user.UserGuiPreference;
-
-public class UserRestImplTest extends RestTestFunctions {
- Logger logger = Logger.getLogger(UserRestImplTest.class);
-
- @Autowired
- UserRestImpl userRestImpl;
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetUser() throws Exception {
- try {
- Object response = userRestImpl.getUser(token, Configuration.ANONYMOUS_LOGIN, "");
- assertNotNull(response);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdatePrivileges() throws Exception {
- try {
- Map<String, Object> data = new HashMap<>();
- data.put(PrivilegeType.ADD_MAP.name(), 1);
- userRestImpl.updatePrivileges(adminToken, Configuration.ANONYMOUS_LOGIN, data);
- assertTrue(userService.userHasPrivilege(userService.getUserByLogin(Configuration.ANONYMOUS_LOGIN),
- PrivilegeType.ADD_MAP));
-
- data.put(PrivilegeType.ADD_MAP.name(), 0);
- userRestImpl.updatePrivileges(adminToken, Configuration.ANONYMOUS_LOGIN, data);
- assertFalse(userService.userHasPrivilege(userService.getUserByLogin(Configuration.ANONYMOUS_LOGIN),
- PrivilegeType.ADD_MAP));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdatePreferences() throws Exception {
- try {
- Map<String, Object> data = deserialize(
- userRestImpl.getUser(adminToken, Configuration.ANONYMOUS_LOGIN, "preferences"));
- userRestImpl.updatePreferences(adminToken, Configuration.ANONYMOUS_LOGIN,
- (Map<String, Object>) data.get("preferences"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private Map<String, Object> deserialize(Map<String, Object> data)
- throws JsonParseException, JsonMappingException, IOException {
- String body = new Gson().toJson(data);
- ObjectMapper mapper = new ObjectMapper();
- ObjectNode result = mapper.readValue(body, ObjectNode.class);
- return mapper.convertValue(result, Map.class);
- }
-
- @Test
- public void testGetUsers() throws Exception {
- try {
- Object response = userRestImpl.getUsers(adminToken, "");
- assertNotNull(response);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testPrepareGuiPreferencesSimple() throws Exception {
- try {
- Map<String, Object> response = userRestImpl.prepareGuiPreferences(new HashSet<>());
- assertNotNull(response);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testPrepareGuiPreferencesWithOption() throws Exception {
- try {
- Set<UserGuiPreference> guiPreferences = new HashSet<>();
- UserGuiPreference option = new UserGuiPreference();
- option.setKey("TestKey");
- option.setValue("TestValue");
- guiPreferences.add(option);
-
- Map<String, Object> response = userRestImpl.prepareGuiPreferences(guiPreferences);
- assertNotNull(response);
- assertEquals("TestValue", response.get(option.getKey()));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.api.users;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import com.fasterxml.jackson.core.JsonParseException;
+import com.fasterxml.jackson.databind.JsonMappingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+import com.google.gson.Gson;
+
+import lcsb.mapviewer.api.RestTestFunctions;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.model.user.PrivilegeType;
+import lcsb.mapviewer.model.user.UserGuiPreference;
+
+public class UserRestImplTest extends RestTestFunctions {
+ Logger logger = Logger.getLogger(UserRestImplTest.class);
+
+ @Autowired
+ UserRestImpl userRestImpl;
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetUser() throws Exception {
+ try {
+ Object response = userRestImpl.getUser(token, Configuration.ANONYMOUS_LOGIN, "");
+ assertNotNull(response);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdatePrivileges() throws Exception {
+ try {
+ Map<String, Object> data = new HashMap<>();
+ data.put(PrivilegeType.ADD_MAP.name(), 1);
+ userRestImpl.updatePrivileges(adminToken, Configuration.ANONYMOUS_LOGIN, data);
+ assertTrue(userService.userHasPrivilege(userService.getUserByLogin(Configuration.ANONYMOUS_LOGIN),
+ PrivilegeType.ADD_MAP));
+
+ data.put(PrivilegeType.ADD_MAP.name(), 0);
+ userRestImpl.updatePrivileges(adminToken, Configuration.ANONYMOUS_LOGIN, data);
+ assertFalse(userService.userHasPrivilege(userService.getUserByLogin(Configuration.ANONYMOUS_LOGIN),
+ PrivilegeType.ADD_MAP));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdatePreferences() throws Exception {
+ try {
+ Map<String, Object> data = deserialize(
+ userRestImpl.getUser(adminToken, Configuration.ANONYMOUS_LOGIN, "preferences"));
+ userRestImpl.updatePreferences(adminToken, Configuration.ANONYMOUS_LOGIN,
+ (Map<String, Object>) data.get("preferences"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Map<String, Object> deserialize(Map<String, Object> data)
+ throws JsonParseException, JsonMappingException, IOException {
+ String body = new Gson().toJson(data);
+ ObjectMapper mapper = new ObjectMapper();
+ ObjectNode result = mapper.readValue(body, ObjectNode.class);
+ return mapper.convertValue(result, Map.class);
+ }
+
+ @Test
+ public void testGetUsers() throws Exception {
+ try {
+ Object response = userRestImpl.getUsers(adminToken, "");
+ assertNotNull(response);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testPrepareGuiPreferencesSimple() throws Exception {
+ try {
+ Map<String, Object> response = userRestImpl.prepareGuiPreferences(new HashSet<>());
+ assertNotNull(response);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testPrepareGuiPreferencesWithOption() throws Exception {
+ try {
+ Set<UserGuiPreference> guiPreferences = new HashSet<>();
+ UserGuiPreference option = new UserGuiPreference();
+ option.setKey("TestKey");
+ option.setValue("TestValue");
+ guiPreferences.add(option);
+
+ Map<String, Object> response = userRestImpl.prepareGuiPreferences(guiPreferences);
+ assertNotNull(response);
+ assertEquals("TestValue", response.get(option.getKey()));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/AuthenticationTokenExpireException.java b/service/src/main/java/lcsb/mapviewer/services/AuthenticationTokenExpireException.java
index bd7338ce3d..4a184fd3e2 100644
--- a/service/src/main/java/lcsb/mapviewer/services/AuthenticationTokenExpireException.java
+++ b/service/src/main/java/lcsb/mapviewer/services/AuthenticationTokenExpireException.java
@@ -1,14 +1,14 @@
-package lcsb.mapviewer.services;
-
-public class AuthenticationTokenExpireException extends SecurityException {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- public AuthenticationTokenExpireException(String message) {
- super(message);
- }
-
-}
+package lcsb.mapviewer.services;
+
+public class AuthenticationTokenExpireException extends SecurityException {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ public AuthenticationTokenExpireException(String message) {
+ super(message);
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/InvalidTokenException.java b/service/src/main/java/lcsb/mapviewer/services/InvalidTokenException.java
index 0b26b89210..a82e8327f9 100644
--- a/service/src/main/java/lcsb/mapviewer/services/InvalidTokenException.java
+++ b/service/src/main/java/lcsb/mapviewer/services/InvalidTokenException.java
@@ -1,14 +1,14 @@
-package lcsb.mapviewer.services;
-
-public class InvalidTokenException extends SecurityException {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- public InvalidTokenException(String message) {
- super(message);
- }
-
-}
+package lcsb.mapviewer.services;
+
+public class InvalidTokenException extends SecurityException {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ public InvalidTokenException(String message) {
+ super(message);
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/SecurityException.java b/service/src/main/java/lcsb/mapviewer/services/SecurityException.java
index de076a2bbc..bd7b172040 100644
--- a/service/src/main/java/lcsb/mapviewer/services/SecurityException.java
+++ b/service/src/main/java/lcsb/mapviewer/services/SecurityException.java
@@ -1,18 +1,18 @@
-package lcsb.mapviewer.services;
-
-public class SecurityException extends Exception {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- public SecurityException(String message) {
- super(message);
- }
-
- public SecurityException() {
- super();
- }
-
-}
+package lcsb.mapviewer.services;
+
+public class SecurityException extends Exception {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ public SecurityException(String message) {
+ super(message);
+ }
+
+ public SecurityException() {
+ super();
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/UserAccessException.java b/service/src/main/java/lcsb/mapviewer/services/UserAccessException.java
index 730b6e8197..53c705b7ba 100644
--- a/service/src/main/java/lcsb/mapviewer/services/UserAccessException.java
+++ b/service/src/main/java/lcsb/mapviewer/services/UserAccessException.java
@@ -1,14 +1,14 @@
-package lcsb.mapviewer.services;
-
-public class UserAccessException extends SecurityException {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- public UserAccessException(String message) {
- super(message);
- }
-
-}
+package lcsb.mapviewer.services;
+
+public class UserAccessException extends SecurityException {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ public UserAccessException(String message) {
+ super(message);
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/CommentService.java b/service/src/main/java/lcsb/mapviewer/services/impl/CommentService.java
index cb1d33bfb3..71c9cd2a07 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/CommentService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/CommentService.java
@@ -1,332 +1,332 @@
-package lcsb.mapviewer.services.impl;
-
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import javax.mail.MessagingException;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.common.ObjectUtils;
-import lcsb.mapviewer.common.exception.InvalidClassException;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.Comment;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.persist.dao.map.CommentDao;
-import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.UserAccessException;
-import lcsb.mapviewer.services.interfaces.ICommentService;
-import lcsb.mapviewer.services.interfaces.IConfigurationService;
-import lcsb.mapviewer.services.interfaces.IModelService;
-import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.utils.EmailSender;
-
-/**
- * This class is responsible for all services connected with comments
- * functionality.
- *
- * @author Piotr Gawron
- *
- */
-
-@Transactional(value = "txManager")
-public class CommentService implements ICommentService {
-
- /**
- * Max distance between two points on map for which two comments should be
- * considered as referring to the same point.
- */
- private static final double COMMENT_POINT_DISTANCE_EPSILON = 0.02;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(CommentService.class);
-
- /**
- * Data access object fir comments.
- */
- @Autowired
- private CommentDao commentDao;
-
- /**
- * Service for operations on Model object.
- */
- @Autowired
- private IModelService modelService;
-
- /**
- * Service for operations on User object.
- */
- @Autowired
- private IUserService userService;
-
- /**
- * Service for operations on Configuration object.
- */
- @Autowired
- private IConfigurationService configurationService;
-
- @Override
- public Comment addComment(String name, String email, String content, Model model, Point2D coordinates, Object object,
- boolean pinned, Model submodel) {
- Comment comment = new Comment();
- comment.setName(name);
- comment.setEmail(email);
- comment.setContent(content);
- comment.setModel(model);
- comment.setCoordinates(coordinates);
- if (object != null) {
- comment.setTableName(object.getClass());
- comment.setTableId(ObjectUtils.getIdOfObject(object));
- if (object instanceof Element) {
- comment.setSubmodel(((Element) object).getModel());
- } else if (object instanceof Reaction) {
- comment.setSubmodel(((Reaction) object).getModel());
- } else {
- throw new InvalidClassException("Cannot comment on object of class: " + object.getClass());
- }
- } else {
- comment.setSubmodel(submodel);
- }
- comment.setUser(null);
- comment.setPinned(pinned);
- commentDao.add(comment);
-
- try {
- EmailSender emailSender = new EmailSender(configurationService);
- emailSender.sendEmail("New comment appeard in the " + model.getProject().getProjectId(), content,
- model.getProject().getNotifyEmail());
- } catch (MessagingException e) {
- logger.error("Problem with sending email.", e);
- }
-
- return comment;
- }
-
- /**
- * This method returns all comments for model agregated by commented elements.
- *
- * @param model
- * object to which we are looking for comments
- * @param pinned
- * this parameter defines what kind of comments we want to see:
- * <ul>
- * <li>null - all comments</li>
- * <li>false - comments that are not visible on the map</li>
- * <li>true - comments that are visible on the map</li>
- * </ul>
- * @return list of comments grouped by commented elements
- */
- protected List<List<Comment>> getAgregatedComments(Model model, Boolean pinned) {
- List<Comment> comments = commentDao.getCommentByModel((Model) model, pinned, false);
- List<List<Comment>> result = new ArrayList<List<Comment>>();
-
- Map<String, List<Comment>> objects = new HashMap<String, List<Comment>>();
- for (Comment comment : comments) {
- if (comment.getTableName() == null) {
- List<Comment> list = new ArrayList<Comment>();
- list.add(comment);
- result.add(list);
- } else {
- String id = comment.getTableId() + "," + comment.getTableName();
-
- List<Comment> list = objects.get(id);
- if (list == null) {
- list = new ArrayList<Comment>();
- objects.put(id, list);
- result.add(list);
- }
- list.add(comment);
- }
- }
- return result;
- }
-
- @Override
- public void deleteComment(User loggedUser, String commentId, String reason) {
- int id = -1;
- try {
- id = Integer.parseInt(commentId);
-
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- }
- Comment comment = commentDao.getById(id);
- if (comment == null) {
- logger.error("Invalid comment id: " + commentId);
- } else {
- comment.setDeleted(true);
- comment.setRemoveReason(reason);
- commentDao.update(comment);
- }
- }
-
- @Override
- public long getCommentCount() {
- return commentDao.getCount();
- }
-
- @Override
- public void removeCommentsForModel(Model model) {
- List<Comment> comments = commentDao.getCommentByModel(model, null, null);
- for (Comment comment : comments) {
- commentDao.delete(comment);
- }
- }
-
- /**
- * @return the commentDao
- * @see #commentDao
- */
- public CommentDao getCommentDao() {
- return commentDao;
- }
-
- /**
- * @param commentDao
- * the commentDao to set
- * @see #commentDao
- */
- public void setCommentDao(CommentDao commentDao) {
- this.commentDao = commentDao;
- }
-
- /**
- * @return the modelService
- * @see #modelService
- */
- public IModelService getModelService() {
- return modelService;
- }
-
- /**
- * @param modelService
- * the modelService to set
- * @see #modelService
- */
- public void setModelService(IModelService modelService) {
- this.modelService = modelService;
- }
-
- /**
- * @return the userService
- * @see #userService
- */
- public IUserService getUserService() {
- return userService;
- }
-
- /**
- * @param userService
- * the userService to set
- * @see #userService
- */
- public void setUserService(IUserService userService) {
- this.userService = userService;
- }
-
- /**
- * @return the configurationService
- * @see #configurationService
- */
- public IConfigurationService getConfigurationService() {
- return configurationService;
- }
-
- /**
- * @param configurationService
- * the configurationService to set
- * @see #configurationService
- */
- public void setConfigurationService(IConfigurationService configurationService) {
- this.configurationService = configurationService;
- }
-
- @Override
- public void removeCommentsForModel(ModelData model) {
- List<Comment> comments = commentDao.getCommentByModel(model, null, null);
- for (Comment comment : comments) {
- commentDao.delete(comment);
- }
- }
-
- /**
- * Checks if identifier of the points refer to the same point.
- *
- * @param uniqueId
- * identifier assigned by the java code
- * @param objectId
- * identifier assigned by the javascript code (browser)
- * @return <code>true</code> if both identifiers refer to the same point,
- * <code>false</code> otherwise
- */
- protected boolean equalPoints(String uniqueId, String objectId) {
- String tmp = uniqueId.substring(uniqueId.indexOf("[") + 1, uniqueId.indexOf("]"));
- String[] ids = tmp.split(",");
- Double x1 = Double.valueOf(ids[0].trim());
- Double y1 = Double.valueOf(ids[1].trim());
-
- tmp = objectId.substring(objectId.indexOf("(") + 1, objectId.indexOf(")"));
- ids = tmp.split(",");
- Double x2 = Double.valueOf(ids[0].trim());
- Double y2 = Double.valueOf(ids[1].trim());
-
- if (Math.abs(x1 - x2) > COMMENT_POINT_DISTANCE_EPSILON || Math.abs(y1 - y2) > COMMENT_POINT_DISTANCE_EPSILON) {
- return false;
- }
- return true;
- }
-
- @Override
- public List<Comment> getCommentsByProject(Project project, String token) throws SecurityException {
- boolean editComments = userService.userHasPrivilege(token, PrivilegeType.EDIT_COMMENTS_PROJECT, project);
- boolean viewProject = userService.userHasPrivilege(token, PrivilegeType.VIEW_PROJECT, project);
- boolean manageProjects = userService.userHasPrivilege(token, PrivilegeType.PROJECT_MANAGEMENT);
- if (!editComments && !viewProject && !manageProjects) {
- throw new UserAccessException("You have no privileges to see comments for given project");
- }
- List<Comment> comments = new ArrayList<>();
- for (ModelData model : project.getModels()) {
- List<Comment> modelComments = commentDao.getCommentByModel(model, null, null);
- comments.addAll(modelComments);
- }
-
- return comments;
- }
-
- @Override
- public void deleteComment(Comment comment, String token, String reason) throws SecurityException {
- Project project = comment.getModelData().getProject();
- boolean editComments = userService.userHasPrivilege(token, PrivilegeType.EDIT_COMMENTS_PROJECT, project);
- User user = userService.getUserByToken(token);
- if (editComments || user.equals(comment.getUser())) {
- comment.setDeleted(true);
- comment.setRemoveReason(reason);
- commentDao.update(comment);
- } else {
- throw new UserAccessException("You have no privileges to remove the comment");
- }
- }
-
- @Override
- public Comment getCommentById(String commentId) {
- int id = -1;
- try {
- id = Integer.parseInt(commentId);
- } catch (NumberFormatException e) {
- }
- return commentDao.getById(id);
- }
-
-}
+package lcsb.mapviewer.services.impl;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.mail.MessagingException;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.common.ObjectUtils;
+import lcsb.mapviewer.common.exception.InvalidClassException;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.Comment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.user.PrivilegeType;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.persist.dao.map.CommentDao;
+import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.UserAccessException;
+import lcsb.mapviewer.services.interfaces.ICommentService;
+import lcsb.mapviewer.services.interfaces.IConfigurationService;
+import lcsb.mapviewer.services.interfaces.IModelService;
+import lcsb.mapviewer.services.interfaces.IUserService;
+import lcsb.mapviewer.services.utils.EmailSender;
+
+/**
+ * This class is responsible for all services connected with comments
+ * functionality.
+ *
+ * @author Piotr Gawron
+ *
+ */
+
+@Transactional(value = "txManager")
+public class CommentService implements ICommentService {
+
+ /**
+ * Max distance between two points on map for which two comments should be
+ * considered as referring to the same point.
+ */
+ private static final double COMMENT_POINT_DISTANCE_EPSILON = 0.02;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(CommentService.class);
+
+ /**
+ * Data access object fir comments.
+ */
+ @Autowired
+ private CommentDao commentDao;
+
+ /**
+ * Service for operations on Model object.
+ */
+ @Autowired
+ private IModelService modelService;
+
+ /**
+ * Service for operations on User object.
+ */
+ @Autowired
+ private IUserService userService;
+
+ /**
+ * Service for operations on Configuration object.
+ */
+ @Autowired
+ private IConfigurationService configurationService;
+
+ @Override
+ public Comment addComment(String name, String email, String content, Model model, Point2D coordinates, Object object,
+ boolean pinned, Model submodel) {
+ Comment comment = new Comment();
+ comment.setName(name);
+ comment.setEmail(email);
+ comment.setContent(content);
+ comment.setModel(model);
+ comment.setCoordinates(coordinates);
+ if (object != null) {
+ comment.setTableName(object.getClass());
+ comment.setTableId(ObjectUtils.getIdOfObject(object));
+ if (object instanceof Element) {
+ comment.setSubmodel(((Element) object).getModel());
+ } else if (object instanceof Reaction) {
+ comment.setSubmodel(((Reaction) object).getModel());
+ } else {
+ throw new InvalidClassException("Cannot comment on object of class: " + object.getClass());
+ }
+ } else {
+ comment.setSubmodel(submodel);
+ }
+ comment.setUser(null);
+ comment.setPinned(pinned);
+ commentDao.add(comment);
+
+ try {
+ EmailSender emailSender = new EmailSender(configurationService);
+ emailSender.sendEmail("New comment appeard in the " + model.getProject().getProjectId(), content,
+ model.getProject().getNotifyEmail());
+ } catch (MessagingException e) {
+ logger.error("Problem with sending email.", e);
+ }
+
+ return comment;
+ }
+
+ /**
+ * This method returns all comments for model agregated by commented elements.
+ *
+ * @param model
+ * object to which we are looking for comments
+ * @param pinned
+ * this parameter defines what kind of comments we want to see:
+ * <ul>
+ * <li>null - all comments</li>
+ * <li>false - comments that are not visible on the map</li>
+ * <li>true - comments that are visible on the map</li>
+ * </ul>
+ * @return list of comments grouped by commented elements
+ */
+ protected List<List<Comment>> getAgregatedComments(Model model, Boolean pinned) {
+ List<Comment> comments = commentDao.getCommentByModel((Model) model, pinned, false);
+ List<List<Comment>> result = new ArrayList<List<Comment>>();
+
+ Map<String, List<Comment>> objects = new HashMap<String, List<Comment>>();
+ for (Comment comment : comments) {
+ if (comment.getTableName() == null) {
+ List<Comment> list = new ArrayList<Comment>();
+ list.add(comment);
+ result.add(list);
+ } else {
+ String id = comment.getTableId() + "," + comment.getTableName();
+
+ List<Comment> list = objects.get(id);
+ if (list == null) {
+ list = new ArrayList<Comment>();
+ objects.put(id, list);
+ result.add(list);
+ }
+ list.add(comment);
+ }
+ }
+ return result;
+ }
+
+ @Override
+ public void deleteComment(User loggedUser, String commentId, String reason) {
+ int id = -1;
+ try {
+ id = Integer.parseInt(commentId);
+
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ }
+ Comment comment = commentDao.getById(id);
+ if (comment == null) {
+ logger.error("Invalid comment id: " + commentId);
+ } else {
+ comment.setDeleted(true);
+ comment.setRemoveReason(reason);
+ commentDao.update(comment);
+ }
+ }
+
+ @Override
+ public long getCommentCount() {
+ return commentDao.getCount();
+ }
+
+ @Override
+ public void removeCommentsForModel(Model model) {
+ List<Comment> comments = commentDao.getCommentByModel(model, null, null);
+ for (Comment comment : comments) {
+ commentDao.delete(comment);
+ }
+ }
+
+ /**
+ * @return the commentDao
+ * @see #commentDao
+ */
+ public CommentDao getCommentDao() {
+ return commentDao;
+ }
+
+ /**
+ * @param commentDao
+ * the commentDao to set
+ * @see #commentDao
+ */
+ public void setCommentDao(CommentDao commentDao) {
+ this.commentDao = commentDao;
+ }
+
+ /**
+ * @return the modelService
+ * @see #modelService
+ */
+ public IModelService getModelService() {
+ return modelService;
+ }
+
+ /**
+ * @param modelService
+ * the modelService to set
+ * @see #modelService
+ */
+ public void setModelService(IModelService modelService) {
+ this.modelService = modelService;
+ }
+
+ /**
+ * @return the userService
+ * @see #userService
+ */
+ public IUserService getUserService() {
+ return userService;
+ }
+
+ /**
+ * @param userService
+ * the userService to set
+ * @see #userService
+ */
+ public void setUserService(IUserService userService) {
+ this.userService = userService;
+ }
+
+ /**
+ * @return the configurationService
+ * @see #configurationService
+ */
+ public IConfigurationService getConfigurationService() {
+ return configurationService;
+ }
+
+ /**
+ * @param configurationService
+ * the configurationService to set
+ * @see #configurationService
+ */
+ public void setConfigurationService(IConfigurationService configurationService) {
+ this.configurationService = configurationService;
+ }
+
+ @Override
+ public void removeCommentsForModel(ModelData model) {
+ List<Comment> comments = commentDao.getCommentByModel(model, null, null);
+ for (Comment comment : comments) {
+ commentDao.delete(comment);
+ }
+ }
+
+ /**
+ * Checks if identifier of the points refer to the same point.
+ *
+ * @param uniqueId
+ * identifier assigned by the java code
+ * @param objectId
+ * identifier assigned by the javascript code (browser)
+ * @return <code>true</code> if both identifiers refer to the same point,
+ * <code>false</code> otherwise
+ */
+ protected boolean equalPoints(String uniqueId, String objectId) {
+ String tmp = uniqueId.substring(uniqueId.indexOf("[") + 1, uniqueId.indexOf("]"));
+ String[] ids = tmp.split(",");
+ Double x1 = Double.valueOf(ids[0].trim());
+ Double y1 = Double.valueOf(ids[1].trim());
+
+ tmp = objectId.substring(objectId.indexOf("(") + 1, objectId.indexOf(")"));
+ ids = tmp.split(",");
+ Double x2 = Double.valueOf(ids[0].trim());
+ Double y2 = Double.valueOf(ids[1].trim());
+
+ if (Math.abs(x1 - x2) > COMMENT_POINT_DISTANCE_EPSILON || Math.abs(y1 - y2) > COMMENT_POINT_DISTANCE_EPSILON) {
+ return false;
+ }
+ return true;
+ }
+
+ @Override
+ public List<Comment> getCommentsByProject(Project project, String token) throws SecurityException {
+ boolean editComments = userService.userHasPrivilege(token, PrivilegeType.EDIT_COMMENTS_PROJECT, project);
+ boolean viewProject = userService.userHasPrivilege(token, PrivilegeType.VIEW_PROJECT, project);
+ boolean manageProjects = userService.userHasPrivilege(token, PrivilegeType.PROJECT_MANAGEMENT);
+ if (!editComments && !viewProject && !manageProjects) {
+ throw new UserAccessException("You have no privileges to see comments for given project");
+ }
+ List<Comment> comments = new ArrayList<>();
+ for (ModelData model : project.getModels()) {
+ List<Comment> modelComments = commentDao.getCommentByModel(model, null, null);
+ comments.addAll(modelComments);
+ }
+
+ return comments;
+ }
+
+ @Override
+ public void deleteComment(Comment comment, String token, String reason) throws SecurityException {
+ Project project = comment.getModelData().getProject();
+ boolean editComments = userService.userHasPrivilege(token, PrivilegeType.EDIT_COMMENTS_PROJECT, project);
+ User user = userService.getUserByToken(token);
+ if (editComments || user.equals(comment.getUser())) {
+ comment.setDeleted(true);
+ comment.setRemoveReason(reason);
+ commentDao.update(comment);
+ } else {
+ throw new UserAccessException("You have no privileges to remove the comment");
+ }
+ }
+
+ @Override
+ public Comment getCommentById(String commentId) {
+ int id = -1;
+ try {
+ id = Integer.parseInt(commentId);
+ } catch (NumberFormatException e) {
+ }
+ return commentDao.getById(id);
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ConfigurationService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ConfigurationService.java
index 5cc62565ad..491868922a 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ConfigurationService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ConfigurationService.java
@@ -1,174 +1,174 @@
-package lcsb.mapviewer.services.impl;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.commons.lang3.EnumUtils;
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.FrameworkVersion;
-import lcsb.mapviewer.model.user.ConfigurationElementType;
-import lcsb.mapviewer.model.user.ConfigurationOption;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.persist.dao.ConfigurationDao;
-import lcsb.mapviewer.services.interfaces.IConfigurationService;
-
-/**
- * Service implementation used for accessing and modifying configuration
- * parameters.
- *
- * @author Piotr Gawron
- *
- */
-@Transactional(value = "txManager")
-public class ConfigurationService implements IConfigurationService {
-
- /**
- * Number of bytes in a megabyte.
- */
- private static final int MEGABYTE_SIZE = 1024 * 1024;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(ConfigurationService.class);
-
- /**
- * Data access object for configuration parameters.
- */
- @Autowired
- private ConfigurationDao configurationDao;
-
- @Override
- public String getConfigurationValue(ConfigurationElementType type) {
- ConfigurationOption result = configurationDao.getByType(type);
- if (result == null) {
- result = new ConfigurationOption();
- result.setType(type);
- result.setValue(type.getDefaultValue());
- configurationDao.add(result);
- }
- return result.getValue();
- }
-
- @Override
- public void setConfigurationValue(ConfigurationElementType type, String value) {
- ConfigurationOption configuration = configurationDao.getByType(type);
- if (configuration == null) {
- configuration = new ConfigurationOption();
- configuration.setType(type);
- }
- configuration.setValue(value);
- configurationDao.add(configuration);
-
- if (type.equals(ConfigurationElementType.X_FRAME_DOMAIN)) {
- Configuration.getxFrameDomain().clear();
- for (String domain : getConfigurationValue(ConfigurationElementType.X_FRAME_DOMAIN).split(";")) {
- Configuration.getxFrameDomain().add(domain);
- }
- }
- }
-
- @Override
- public void deleteConfigurationValue(ConfigurationElementType type) {
- configurationDao.delete(configurationDao.getByType(type));
- }
-
- @Override
- public List<ConfigurationOption> getAllValues(boolean includeServerSide) {
- List<ConfigurationOption> result = new ArrayList<>();
-
- for (ConfigurationElementType type : ConfigurationElementType.values()) {
- if (!type.isServerSide() || (type.isServerSide() && includeServerSide)) {
- ConfigurationOption configuration = configurationDao.getByType(type);
- if (configuration == null) {
- getConfigurationValue(type);
- configuration = configurationDao.getByType(type);
- }
- result.add(configuration);
- }
- }
- return result;
- }
-
- @Override
- public ConfigurationOption getValue(ConfigurationElementType type) {
- ConfigurationOption configuration = configurationDao.getByType(type);
- if (configuration == null) {
- getConfigurationValue(type);
- configuration = configurationDao.getByType(type);
- }
- return configuration;
- }
-
- @Override
- public void updateConfiguration(List<ConfigurationOption> values) {
- for (ConfigurationOption configurationElement : values) {
- setConfigurationValue(configurationElement.getType(), configurationElement.getValue());
- }
- }
-
- /**
- * @return the configurationDao
- */
- public ConfigurationDao getConfigurationDao() {
- return configurationDao;
- }
-
- /**
- * @param configurationDao
- * the configurationDao to set
- */
- public void setConfigurationDao(ConfigurationDao configurationDao) {
- this.configurationDao = configurationDao;
- }
-
- @Override
- public String getSystemSvnVersion(String baseDir) {
- return lcsb.mapviewer.common.Configuration.getSystemVersion(baseDir);
- }
-
- @Override
- public String getSystemGitVersion(String baseDir) {
- return lcsb.mapviewer.common.Configuration.getSystemBuildVersion(baseDir);
- }
-
- @Override
- public String getSystemBuild(String baseDir) {
- return lcsb.mapviewer.common.Configuration.getSystemBuild(baseDir);
- }
-
- @Override
- public FrameworkVersion getSystemVersion(String baseDir) {
- return lcsb.mapviewer.common.Configuration.getFrameworkVersion(baseDir);
- }
-
- @Override
- public Long getMemoryUsage() {
- Runtime runtime = Runtime.getRuntime();
-
- return (runtime.totalMemory() - runtime.freeMemory()) / MEGABYTE_SIZE;
- }
-
- @Override
- public Long getMaxMemory() {
- Runtime runtime = Runtime.getRuntime();
-
- return runtime.maxMemory() / MEGABYTE_SIZE;
- }
-
- @Override
- public ConfigurationOption getValue(PrivilegeType type) {
- String name = "DEFAULT_" + type.name();
- if (EnumUtils.isValidEnum(ConfigurationElementType.class, name)) {
- return getValue(ConfigurationElementType.valueOf(name));
- } else {
- return null;
- }
- }
-
-}
+package lcsb.mapviewer.services.impl;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang3.EnumUtils;
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.FrameworkVersion;
+import lcsb.mapviewer.model.user.ConfigurationElementType;
+import lcsb.mapviewer.model.user.ConfigurationOption;
+import lcsb.mapviewer.model.user.PrivilegeType;
+import lcsb.mapviewer.persist.dao.ConfigurationDao;
+import lcsb.mapviewer.services.interfaces.IConfigurationService;
+
+/**
+ * Service implementation used for accessing and modifying configuration
+ * parameters.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Transactional(value = "txManager")
+public class ConfigurationService implements IConfigurationService {
+
+ /**
+ * Number of bytes in a megabyte.
+ */
+ private static final int MEGABYTE_SIZE = 1024 * 1024;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(ConfigurationService.class);
+
+ /**
+ * Data access object for configuration parameters.
+ */
+ @Autowired
+ private ConfigurationDao configurationDao;
+
+ @Override
+ public String getConfigurationValue(ConfigurationElementType type) {
+ ConfigurationOption result = configurationDao.getByType(type);
+ if (result == null) {
+ result = new ConfigurationOption();
+ result.setType(type);
+ result.setValue(type.getDefaultValue());
+ configurationDao.add(result);
+ }
+ return result.getValue();
+ }
+
+ @Override
+ public void setConfigurationValue(ConfigurationElementType type, String value) {
+ ConfigurationOption configuration = configurationDao.getByType(type);
+ if (configuration == null) {
+ configuration = new ConfigurationOption();
+ configuration.setType(type);
+ }
+ configuration.setValue(value);
+ configurationDao.add(configuration);
+
+ if (type.equals(ConfigurationElementType.X_FRAME_DOMAIN)) {
+ Configuration.getxFrameDomain().clear();
+ for (String domain : getConfigurationValue(ConfigurationElementType.X_FRAME_DOMAIN).split(";")) {
+ Configuration.getxFrameDomain().add(domain);
+ }
+ }
+ }
+
+ @Override
+ public void deleteConfigurationValue(ConfigurationElementType type) {
+ configurationDao.delete(configurationDao.getByType(type));
+ }
+
+ @Override
+ public List<ConfigurationOption> getAllValues(boolean includeServerSide) {
+ List<ConfigurationOption> result = new ArrayList<>();
+
+ for (ConfigurationElementType type : ConfigurationElementType.values()) {
+ if (!type.isServerSide() || (type.isServerSide() && includeServerSide)) {
+ ConfigurationOption configuration = configurationDao.getByType(type);
+ if (configuration == null) {
+ getConfigurationValue(type);
+ configuration = configurationDao.getByType(type);
+ }
+ result.add(configuration);
+ }
+ }
+ return result;
+ }
+
+ @Override
+ public ConfigurationOption getValue(ConfigurationElementType type) {
+ ConfigurationOption configuration = configurationDao.getByType(type);
+ if (configuration == null) {
+ getConfigurationValue(type);
+ configuration = configurationDao.getByType(type);
+ }
+ return configuration;
+ }
+
+ @Override
+ public void updateConfiguration(List<ConfigurationOption> values) {
+ for (ConfigurationOption configurationElement : values) {
+ setConfigurationValue(configurationElement.getType(), configurationElement.getValue());
+ }
+ }
+
+ /**
+ * @return the configurationDao
+ */
+ public ConfigurationDao getConfigurationDao() {
+ return configurationDao;
+ }
+
+ /**
+ * @param configurationDao
+ * the configurationDao to set
+ */
+ public void setConfigurationDao(ConfigurationDao configurationDao) {
+ this.configurationDao = configurationDao;
+ }
+
+ @Override
+ public String getSystemSvnVersion(String baseDir) {
+ return lcsb.mapviewer.common.Configuration.getSystemVersion(baseDir);
+ }
+
+ @Override
+ public String getSystemGitVersion(String baseDir) {
+ return lcsb.mapviewer.common.Configuration.getSystemBuildVersion(baseDir);
+ }
+
+ @Override
+ public String getSystemBuild(String baseDir) {
+ return lcsb.mapviewer.common.Configuration.getSystemBuild(baseDir);
+ }
+
+ @Override
+ public FrameworkVersion getSystemVersion(String baseDir) {
+ return lcsb.mapviewer.common.Configuration.getFrameworkVersion(baseDir);
+ }
+
+ @Override
+ public Long getMemoryUsage() {
+ Runtime runtime = Runtime.getRuntime();
+
+ return (runtime.totalMemory() - runtime.freeMemory()) / MEGABYTE_SIZE;
+ }
+
+ @Override
+ public Long getMaxMemory() {
+ Runtime runtime = Runtime.getRuntime();
+
+ return runtime.maxMemory() / MEGABYTE_SIZE;
+ }
+
+ @Override
+ public ConfigurationOption getValue(PrivilegeType type) {
+ String name = "DEFAULT_" + type.name();
+ if (EnumUtils.isValidEnum(ConfigurationElementType.class, name)) {
+ return getValue(ConfigurationElementType.valueOf(name));
+ } else {
+ return null;
+ }
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ExternalServicesService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ExternalServicesService.java
index 468c59b69a..e444f8fd8e 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ExternalServicesService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ExternalServicesService.java
@@ -1,169 +1,169 @@
-package lcsb.mapviewer.services.impl;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import lcsb.mapviewer.annotation.services.ChEMBLParser;
-import lcsb.mapviewer.annotation.services.DrugbankHTMLParser;
-import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
-import lcsb.mapviewer.annotation.services.IExternalService;
-import lcsb.mapviewer.annotation.services.MiriamConnector;
-import lcsb.mapviewer.annotation.services.PubmedParser;
-import lcsb.mapviewer.annotation.services.ChemicalParser;
-import lcsb.mapviewer.annotation.services.annotators.BiocompendiumAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.EnsemblAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.EntrezAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.GoAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator;
-import lcsb.mapviewer.persist.DbUtils;
-import lcsb.mapviewer.services.interfaces.IExternalServicesService;
-
-import org.springframework.beans.factory.annotation.Autowired;
-
-/**
- * Implementation of the service that retrieves information about services that
- * access external resources (like chebi, chembl, etc.).
- *
- * @author Piotr Gawron
- *
- */
-public class ExternalServicesService implements IExternalServicesService {
-
- /**
- * List of services that should be checked for status.
- */
- private List<IExternalService> services = new ArrayList<IExternalService>();
-
- /**
- * Service accessing <a href="http://www.drugbank.ca/">drugbank</a>.
- */
- @Autowired
- private DrugbankHTMLParser drugbankHTMLParser;
-
-
- /**
- * Service accessing <a href="http://ctdbase.org/">ctd</a>.
- */
- @Autowired
- private ChemicalParser ctdParser;
-
- /**
- * Service accessing <a
- * href="https://www.ebi.ac.uk/chembl/compound/inspect/">chembl</a>.
- */
- @Autowired
- private ChEMBLParser chEMBLParser;
-
- /**
- * Service accessing <a
- * href="http://www.ebi.ac.uk/chebi/webServices.do">chebi</a>.
- */
- @Autowired
- private ChebiAnnotator chebiBackend;
-
- /**
- * Service accessing <a
- * href="http://europepmc.org/RestfulWebService">pubmed</a>.
- */
- @Autowired
- private PubmedParser pubmedParser;
-
- /**
- * Service accessing <a href= "http://www.ebi.ac.uk/miriam/main/" >miriam
- * registry</a>.
- */
- @Autowired
- private MiriamConnector miriamConnector;
-
- /**
- * Service accessing <a href= "http://biocompendium.embl.de/" >internal
- * annotating service</a>.
- */
- @Autowired
- private BiocompendiumAnnotator annotationRestService;
-
- /**
- * Service accessing <a href= "http://www.uniprot.org/" >uniprot</a>.
- */
- @Autowired
- private UniprotAnnotator uniprotAnnotator;
-
- /**
- * Service accessing Ensembl database.
- */
- @Autowired
- private EnsemblAnnotator ensemblAnnotator;
-
- /**
- * Service accessing Entrez database.
- */
- @Autowired
- private EntrezAnnotator entrezAnnotator;
-
- /**
- * Service accessing <a href= "http://www.ebi.ac.uk/QuickGO/" >Gene
- * Ontology</a>.
- */
- @Autowired
- private GoAnnotator goBackend;
-
- /**
- * Service accessing HGNC restfull API .
- */
- @Autowired
- private HgncAnnotator hgncBackend;
-
- /**
- * Utils that help to manage the sessions in custom multithreaded
- * implementation.
- */
- @Autowired
- private DbUtils dbUtils;
-
- @Override
- public List<ExternalServiceStatus> getExternalServiceStatuses() {
- List<ExternalServiceStatus> result = new ArrayList<ExternalServiceStatus>();
- for (IExternalService service : services) {
- boolean sessionOpened = false;
- if (!dbUtils.isCustomSessionForCurrentThread()) {
- sessionOpened = true;
- dbUtils.createSessionForCurrentThread();
- }
- result.add(service.getServiceStatus());
- if (sessionOpened) {
- dbUtils.closeSessionForCurrentThread();
- }
- }
- return result;
- }
-
- @Override
- public void registerService(IExternalService service) {
- services.add(service);
-
- }
-
- @Override
- public void registerDefaultServices() {
- registerService(drugbankHTMLParser);
- registerService(chEMBLParser);
- registerService(chebiBackend);
- registerService(pubmedParser);
- registerService(miriamConnector);
- registerService(annotationRestService);
- registerService(ensemblAnnotator);
- registerService(entrezAnnotator);
- registerService(goBackend);
- registerService(ctdParser);
- registerService(hgncBackend);
- registerService(uniprotAnnotator);
- }
-
- @Override
- public void clearServices() {
- services.clear();
-
- }
-}
+package lcsb.mapviewer.services.impl;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import lcsb.mapviewer.annotation.services.ChEMBLParser;
+import lcsb.mapviewer.annotation.services.DrugbankHTMLParser;
+import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
+import lcsb.mapviewer.annotation.services.IExternalService;
+import lcsb.mapviewer.annotation.services.MiriamConnector;
+import lcsb.mapviewer.annotation.services.PubmedParser;
+import lcsb.mapviewer.annotation.services.ChemicalParser;
+import lcsb.mapviewer.annotation.services.annotators.BiocompendiumAnnotator;
+import lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator;
+import lcsb.mapviewer.annotation.services.annotators.EnsemblAnnotator;
+import lcsb.mapviewer.annotation.services.annotators.EntrezAnnotator;
+import lcsb.mapviewer.annotation.services.annotators.GoAnnotator;
+import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
+import lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator;
+import lcsb.mapviewer.persist.DbUtils;
+import lcsb.mapviewer.services.interfaces.IExternalServicesService;
+
+import org.springframework.beans.factory.annotation.Autowired;
+
+/**
+ * Implementation of the service that retrieves information about services that
+ * access external resources (like chebi, chembl, etc.).
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ExternalServicesService implements IExternalServicesService {
+
+ /**
+ * List of services that should be checked for status.
+ */
+ private List<IExternalService> services = new ArrayList<IExternalService>();
+
+ /**
+ * Service accessing <a href="http://www.drugbank.ca/">drugbank</a>.
+ */
+ @Autowired
+ private DrugbankHTMLParser drugbankHTMLParser;
+
+
+ /**
+ * Service accessing <a href="http://ctdbase.org/">ctd</a>.
+ */
+ @Autowired
+ private ChemicalParser ctdParser;
+
+ /**
+ * Service accessing <a
+ * href="https://www.ebi.ac.uk/chembl/compound/inspect/">chembl</a>.
+ */
+ @Autowired
+ private ChEMBLParser chEMBLParser;
+
+ /**
+ * Service accessing <a
+ * href="http://www.ebi.ac.uk/chebi/webServices.do">chebi</a>.
+ */
+ @Autowired
+ private ChebiAnnotator chebiBackend;
+
+ /**
+ * Service accessing <a
+ * href="http://europepmc.org/RestfulWebService">pubmed</a>.
+ */
+ @Autowired
+ private PubmedParser pubmedParser;
+
+ /**
+ * Service accessing <a href= "http://www.ebi.ac.uk/miriam/main/" >miriam
+ * registry</a>.
+ */
+ @Autowired
+ private MiriamConnector miriamConnector;
+
+ /**
+ * Service accessing <a href= "http://biocompendium.embl.de/" >internal
+ * annotating service</a>.
+ */
+ @Autowired
+ private BiocompendiumAnnotator annotationRestService;
+
+ /**
+ * Service accessing <a href= "http://www.uniprot.org/" >uniprot</a>.
+ */
+ @Autowired
+ private UniprotAnnotator uniprotAnnotator;
+
+ /**
+ * Service accessing Ensembl database.
+ */
+ @Autowired
+ private EnsemblAnnotator ensemblAnnotator;
+
+ /**
+ * Service accessing Entrez database.
+ */
+ @Autowired
+ private EntrezAnnotator entrezAnnotator;
+
+ /**
+ * Service accessing <a href= "http://www.ebi.ac.uk/QuickGO/" >Gene
+ * Ontology</a>.
+ */
+ @Autowired
+ private GoAnnotator goBackend;
+
+ /**
+ * Service accessing HGNC restfull API .
+ */
+ @Autowired
+ private HgncAnnotator hgncBackend;
+
+ /**
+ * Utils that help to manage the sessions in custom multithreaded
+ * implementation.
+ */
+ @Autowired
+ private DbUtils dbUtils;
+
+ @Override
+ public List<ExternalServiceStatus> getExternalServiceStatuses() {
+ List<ExternalServiceStatus> result = new ArrayList<ExternalServiceStatus>();
+ for (IExternalService service : services) {
+ boolean sessionOpened = false;
+ if (!dbUtils.isCustomSessionForCurrentThread()) {
+ sessionOpened = true;
+ dbUtils.createSessionForCurrentThread();
+ }
+ result.add(service.getServiceStatus());
+ if (sessionOpened) {
+ dbUtils.closeSessionForCurrentThread();
+ }
+ }
+ return result;
+ }
+
+ @Override
+ public void registerService(IExternalService service) {
+ services.add(service);
+
+ }
+
+ @Override
+ public void registerDefaultServices() {
+ registerService(drugbankHTMLParser);
+ registerService(chEMBLParser);
+ registerService(chebiBackend);
+ registerService(pubmedParser);
+ registerService(miriamConnector);
+ registerService(annotationRestService);
+ registerService(ensemblAnnotator);
+ registerService(entrezAnnotator);
+ registerService(goBackend);
+ registerService(ctdParser);
+ registerService(hgncBackend);
+ registerService(uniprotAnnotator);
+ }
+
+ @Override
+ public void clearServices() {
+ services.clear();
+
+ }
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/LogService.java b/service/src/main/java/lcsb/mapviewer/services/impl/LogService.java
index 972c148b69..dbe11f6a66 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/LogService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/LogService.java
@@ -1,118 +1,118 @@
-package lcsb.mapviewer.services.impl;
-
-import java.util.Calendar;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.ObjectUtils;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.log.GenericLog;
-import lcsb.mapviewer.model.log.ObjectLog;
-import lcsb.mapviewer.model.log.SystemLog;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.persist.dao.log.LogDao;
-import lcsb.mapviewer.persist.dao.user.UserDao;
-import lcsb.mapviewer.services.interfaces.ILogService;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.annotation.Transactional;
-
-/**
- * Class responsible for logging.
- *
- * @author Piotr Gawron
- *
- */
-@Transactional(value = "txManager")
-public class LogService implements ILogService {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(LogService.class);
-
- /**
- * Data access object for log entries.
- */
- @Autowired
- private LogDao logDao;
-
- /**
- * Default used used for loggin events.
- */
- private User loggedUser;
-
- /**
- * Service used to access logs.
- *
- * @see ILogService
- */
- @Autowired
- private UserDao userDao;
-
- /**
- * @return the logDao
- * @see #logDao
- */
- public LogDao getLogDao() {
- return logDao;
- }
-
- /**
- * @param logDao
- * the logDao to set
- * @see #logDao
- */
- public void setLogDao(LogDao logDao) {
- this.logDao = logDao;
- }
-
- @Override
- public void setLoggedUser(User user) {
- this.loggedUser = user;
- }
-
- @Override
- public GenericLog log(LogParams params) {
- if (params.getType() == null) {
- throw new InvalidArgumentException("Type cannot be null");
- }
-
- GenericLog log;
- if (params.getObject() != null) {
- Object object = params.getObject();
- // get identifier of an object
- Integer id = null;
- try {
- id = ObjectUtils.getIdOfObject(object);
- } catch (Exception e) {
- throw new InvalidArgumentException("Invalid object: " + object.getClass());
- }
- if (id == null) {
- throw new InvalidArgumentException("Object must contain not null id");
- }
-
- log = new ObjectLog();
- ((ObjectLog) log).setTable(object.getClass());
- ((ObjectLog) log).setObjectId(id);
-
- } else {
- log = new SystemLog();
- }
- log.setTime(Calendar.getInstance());
- log.setType(params.getType());
- log.setDescription(params.description());
-
- if (params.getUser() != null) {
- log.setUser(params.getUser());
- } else if (loggedUser != null) {
- log.setUser(loggedUser);
- } else {
- log.setUser(userDao.getUserByLogin(Configuration.ANONYMOUS_LOGIN));
- }
- logDao.add(log);
- return log;
- }
-
-}
+package lcsb.mapviewer.services.impl;
+
+import java.util.Calendar;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.ObjectUtils;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.log.GenericLog;
+import lcsb.mapviewer.model.log.ObjectLog;
+import lcsb.mapviewer.model.log.SystemLog;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.persist.dao.log.LogDao;
+import lcsb.mapviewer.persist.dao.user.UserDao;
+import lcsb.mapviewer.services.interfaces.ILogService;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+/**
+ * Class responsible for logging.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Transactional(value = "txManager")
+public class LogService implements ILogService {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(LogService.class);
+
+ /**
+ * Data access object for log entries.
+ */
+ @Autowired
+ private LogDao logDao;
+
+ /**
+ * Default used used for loggin events.
+ */
+ private User loggedUser;
+
+ /**
+ * Service used to access logs.
+ *
+ * @see ILogService
+ */
+ @Autowired
+ private UserDao userDao;
+
+ /**
+ * @return the logDao
+ * @see #logDao
+ */
+ public LogDao getLogDao() {
+ return logDao;
+ }
+
+ /**
+ * @param logDao
+ * the logDao to set
+ * @see #logDao
+ */
+ public void setLogDao(LogDao logDao) {
+ this.logDao = logDao;
+ }
+
+ @Override
+ public void setLoggedUser(User user) {
+ this.loggedUser = user;
+ }
+
+ @Override
+ public GenericLog log(LogParams params) {
+ if (params.getType() == null) {
+ throw new InvalidArgumentException("Type cannot be null");
+ }
+
+ GenericLog log;
+ if (params.getObject() != null) {
+ Object object = params.getObject();
+ // get identifier of an object
+ Integer id = null;
+ try {
+ id = ObjectUtils.getIdOfObject(object);
+ } catch (Exception e) {
+ throw new InvalidArgumentException("Invalid object: " + object.getClass());
+ }
+ if (id == null) {
+ throw new InvalidArgumentException("Object must contain not null id");
+ }
+
+ log = new ObjectLog();
+ ((ObjectLog) log).setTable(object.getClass());
+ ((ObjectLog) log).setObjectId(id);
+
+ } else {
+ log = new SystemLog();
+ }
+ log.setTime(Calendar.getInstance());
+ log.setType(params.getType());
+ log.setDescription(params.description());
+
+ if (params.getUser() != null) {
+ log.setUser(params.getUser());
+ } else if (loggedUser != null) {
+ log.setUser(loggedUser);
+ } else {
+ log.setUser(userDao.getUserByLogin(Configuration.ANONYMOUS_LOGIN));
+ }
+ logDao.add(log);
+ return log;
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/Md5PasswordEncoder.java b/service/src/main/java/lcsb/mapviewer/services/impl/Md5PasswordEncoder.java
index 67cb5e202a..c0a0cf41ae 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/Md5PasswordEncoder.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/Md5PasswordEncoder.java
@@ -1,58 +1,58 @@
-package lcsb.mapviewer.services.impl;
-
-import java.nio.ByteBuffer;
-import java.nio.CharBuffer;
-import java.nio.charset.Charset;
-import java.security.MessageDigest;
-import java.security.NoSuchAlgorithmException;
-
-import org.springframework.security.crypto.password.PasswordEncoder;
-
-/**
- * Custom password encoder using MD5 hash. Used for compatibility reasons.
- *
- * @author Piotr Gawron
- *
- */
-
-public class Md5PasswordEncoder implements PasswordEncoder {
-
- @Override
- public String encode(CharSequence password) {
-
- try {
- MessageDigest md = MessageDigest.getInstance("MD5");
- byte[] thedigest = md.digest(encodeUtf8(password));
- StringBuffer sb = new StringBuffer();
- for (int i = 0; i < thedigest.length; ++i) {
- // CHECKSTYLE:OFF
- // this line transforms single byte into hex representation
- sb.append(Integer.toHexString((thedigest[i] & 0xFF) | 0x100).substring(1, 3));
- // CHECKSTYLE:ON
- }
- return sb.toString();
- } catch (NoSuchAlgorithmException e) {
- e.printStackTrace();
- }
- return null;
- }
-
- @Override
- public boolean matches(CharSequence arg0, String arg1) {
- return encode(arg0).equals(arg1);
- }
-
- /**
- * Transforms {@link CharSequence} into byte array.
- *
- * @param string
- * input {@link CharSequence}
- * @return byte array representation of the input {@link CharSequence}
- */
- private static byte[] encodeUtf8(CharSequence string) {
- ByteBuffer bb = Charset.forName("UTF-8").encode(CharBuffer.wrap(string));
- byte[] result = new byte[bb.remaining()];
- bb.get(result);
- return result;
- }
-}
+package lcsb.mapviewer.services.impl;
+
+import java.nio.ByteBuffer;
+import java.nio.CharBuffer;
+import java.nio.charset.Charset;
+import java.security.MessageDigest;
+import java.security.NoSuchAlgorithmException;
+
+import org.springframework.security.crypto.password.PasswordEncoder;
+
+/**
+ * Custom password encoder using MD5 hash. Used for compatibility reasons.
+ *
+ * @author Piotr Gawron
+ *
+ */
+
+public class Md5PasswordEncoder implements PasswordEncoder {
+
+ @Override
+ public String encode(CharSequence password) {
+
+ try {
+ MessageDigest md = MessageDigest.getInstance("MD5");
+ byte[] thedigest = md.digest(encodeUtf8(password));
+ StringBuffer sb = new StringBuffer();
+ for (int i = 0; i < thedigest.length; ++i) {
+ // CHECKSTYLE:OFF
+ // this line transforms single byte into hex representation
+ sb.append(Integer.toHexString((thedigest[i] & 0xFF) | 0x100).substring(1, 3));
+ // CHECKSTYLE:ON
+ }
+ return sb.toString();
+ } catch (NoSuchAlgorithmException e) {
+ e.printStackTrace();
+ }
+ return null;
+ }
+
+ @Override
+ public boolean matches(CharSequence arg0, String arg1) {
+ return encode(arg0).equals(arg1);
+ }
+
+ /**
+ * Transforms {@link CharSequence} into byte array.
+ *
+ * @param string
+ * input {@link CharSequence}
+ * @return byte array representation of the input {@link CharSequence}
+ */
+ private static byte[] encodeUtf8(CharSequence string) {
+ ByteBuffer bb = Charset.forName("UTF-8").encode(CharBuffer.wrap(string));
+ byte[] result = new byte[bb.remaining()];
+ bb.get(result);
+ return result;
+ }
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/MiriamService.java b/service/src/main/java/lcsb/mapviewer/services/impl/MiriamService.java
index cdd55a3469..a9193f4fde 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/MiriamService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/MiriamService.java
@@ -1,54 +1,54 @@
-package lcsb.mapviewer.services.impl;
-
-import lcsb.mapviewer.annotation.services.MiriamConnector;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.services.interfaces.IMiriamService;
-
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.annotation.Transactional;
-
-/**
- * Implementation of service responsible for accessing miriam registry.
- *
- * @author Piotr Gawron
- *
- */
-@Transactional(value = "txManager")
-public class MiriamService implements IMiriamService {
-
- /**
- * Object accessing <a href= "http://www.ebi.ac.uk/miriam/main/" >miriam
- * registry</a>.
- */
- @Autowired
- private MiriamConnector miriamConnector;
-
- @Override
- public String getUrlForMiriamData(MiriamData md) {
- return miriamConnector.getUrlString(md);
- }
-
- /**
- * @return the miriamConnector
- * @see #miriamConnector
- */
- public MiriamConnector getMiriamConnector() {
- return miriamConnector;
- }
-
- /**
- * @param miriamConnector
- * the miriamConnector to set
- * @see #miriamConnector
- */
- public void setMiriamConnector(MiriamConnector miriamConnector) {
- this.miriamConnector = miriamConnector;
- }
-
- @Override
- public MiriamType getTypeForUri(String uri) {
- return MiriamType.getTypeByUri(uri);
- }
-
-}
+package lcsb.mapviewer.services.impl;
+
+import lcsb.mapviewer.annotation.services.MiriamConnector;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.services.interfaces.IMiriamService;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+/**
+ * Implementation of service responsible for accessing miriam registry.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Transactional(value = "txManager")
+public class MiriamService implements IMiriamService {
+
+ /**
+ * Object accessing <a href= "http://www.ebi.ac.uk/miriam/main/" >miriam
+ * registry</a>.
+ */
+ @Autowired
+ private MiriamConnector miriamConnector;
+
+ @Override
+ public String getUrlForMiriamData(MiriamData md) {
+ return miriamConnector.getUrlString(md);
+ }
+
+ /**
+ * @return the miriamConnector
+ * @see #miriamConnector
+ */
+ public MiriamConnector getMiriamConnector() {
+ return miriamConnector;
+ }
+
+ /**
+ * @param miriamConnector
+ * the miriamConnector to set
+ * @see #miriamConnector
+ */
+ public void setMiriamConnector(MiriamConnector miriamConnector) {
+ this.miriamConnector = miriamConnector;
+ }
+
+ @Override
+ public MiriamType getTypeForUri(String uri) {
+ return MiriamType.getTypeByUri(uri);
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
index 5afc54a15a..fd3fdeb116 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -1,1412 +1,1412 @@
-package lcsb.mapviewer.services.impl;
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-import java.util.Queue;
-import java.util.Set;
-import java.util.concurrent.CountDownLatch;
-
-import javax.mail.MessagingException;
-
-import org.apache.commons.io.FileUtils;
-import org.apache.commons.io.FilenameUtils;
-import org.apache.commons.io.IOUtils;
-import org.apache.log4j.Logger;
-import org.hibernate.HibernateException;
-import org.primefaces.model.DefaultTreeNode;
-import org.primefaces.model.TreeNode;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.security.crypto.password.PasswordEncoder;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.annotation.services.MeSHParser;
-import lcsb.mapviewer.annotation.services.ModelAnnotator;
-import lcsb.mapviewer.annotation.services.ProblematicAnnotation;
-import lcsb.mapviewer.annotation.services.TaxonomyBackend;
-import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
-import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
-import lcsb.mapviewer.commands.ClearColorModelCommand;
-import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.commands.CopyCommand;
-import lcsb.mapviewer.commands.CreateHierarchyCommand;
-import lcsb.mapviewer.commands.SetFixedHierarchyLevelCommand;
-import lcsb.mapviewer.common.EventStorageLoggerAppender;
-import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.ComplexZipConverter;
-import lcsb.mapviewer.converter.ComplexZipConverterParams;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.IConverter;
-import lcsb.mapviewer.converter.InvalidInputDataExecption;
-import lcsb.mapviewer.converter.ProjectFactory;
-import lcsb.mapviewer.converter.graphics.DrawingException;
-import lcsb.mapviewer.converter.graphics.MapGenerator;
-import lcsb.mapviewer.converter.graphics.MapGenerator.MapGeneratorParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter;
-import lcsb.mapviewer.converter.zip.ZipEntryFile;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.ProjectStatus;
-import lcsb.mapviewer.model.cache.UploadedFileEntry;
-import lcsb.mapviewer.model.log.LogType;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.LayoutStatus;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
-import lcsb.mapviewer.model.user.ObjectPrivilege;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.model.user.UserAnnotationSchema;
-import lcsb.mapviewer.model.user.UserAnnotatorsParam;
-import lcsb.mapviewer.model.user.UserClassAnnotators;
-import lcsb.mapviewer.model.user.UserClassRequiredAnnotations;
-import lcsb.mapviewer.model.user.UserClassValidAnnotations;
-import lcsb.mapviewer.modelutils.map.ClassTreeNode;
-import lcsb.mapviewer.modelutils.map.ElementUtils;
-import lcsb.mapviewer.persist.DbUtils;
-import lcsb.mapviewer.persist.dao.ProjectDao;
-import lcsb.mapviewer.persist.dao.map.CommentDao;
-import lcsb.mapviewer.persist.dao.map.ModelDao;
-import lcsb.mapviewer.persist.dao.user.UserDao;
-import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.UserAccessException;
-import lcsb.mapviewer.services.interfaces.ICommentService;
-import lcsb.mapviewer.services.interfaces.IConfigurationService;
-import lcsb.mapviewer.services.interfaces.ILogService;
-import lcsb.mapviewer.services.interfaces.ILogService.LogParams;
-import lcsb.mapviewer.services.interfaces.IModelService;
-import lcsb.mapviewer.services.interfaces.IProjectService;
-import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.overlay.AnnotatedObjectTreeRow;
-import lcsb.mapviewer.services.search.chemical.IChemicalService;
-import lcsb.mapviewer.services.search.drug.IDrugService;
-import lcsb.mapviewer.services.search.mirna.IMiRNAService;
-import lcsb.mapviewer.services.utils.CreateProjectParams;
-import lcsb.mapviewer.services.utils.EmailSender;
-import lcsb.mapviewer.services.utils.data.BuildInLayout;
-
-/**
- * Implementation of the project service. It allows to manage and access project
- * data.
- *
- * @author Piotr Gawron
- *
- */
-@Transactional(value = "txManager")
-public class ProjectService implements IProjectService {
-
- /**
- * Size of the artificial buffer that will be released when
- * {@link OutOfMemoryError} is thrown to gain some free memory and report
- * problem.
- */
- private static final int OUT_OF_MEMORY_BACKUP_BUFFER_SIZE = 10000;
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(ProjectService.class);
-
- /**
- * Data access object for projects.
- */
- @Autowired
- private ProjectDao projectDao;
-
- /**
- * Data access object for models.
- */
- @Autowired
- private ModelDao modelDao;
-
- /**
- * Data access object for users.
- */
- @Autowired
- private UserDao userDao;
-
- /**
- * Service that allows to access and manage models.
- */
- @Autowired
- private IModelService modelService;
-
- /**
- * Service that allows to access and manage comments.
- */
- @Autowired
- private ICommentService commentService;
-
- /**
- * Service used to access logs.
- *
- * @see ILogService
- */
- @Autowired
- private ILogService logService;
-
- /**
- * Service that manages and gives access to configuration parameters.
- */
- @Autowired
- private IConfigurationService configurationService;
-
- /**
- * Services that manages and gives access to user information.
- */
- @Autowired
- private IUserService userService;
-
- /**
- * Services that access data about chemicals.
- */
- @Autowired
- private IChemicalService chemicalService;
-
- /**
- * Services that access data about drugs.
- */
- @Autowired
- private IDrugService drugService;
-
- /**
- * Services that access data about mirna.
- */
- @Autowired
- private IMiRNAService mirnaService;
-
- /**
- * Data access object for comments.
- */
- @Autowired
- private CommentDao commentDao;
-
- /**
- * Service that provides password encoding.
- */
- @Autowired
- private PasswordEncoder passwordEncoder;
-
- /**
- * Module that allows to annotate maps.
- */
- @Autowired
- private ModelAnnotator modelAnnotator;
-
- /**
- * Utils that help to manage the sessions in custom multithreaded
- * implementation.
- */
- @Autowired
- private DbUtils dbUtils;
-
- /**
- * Access point and parser for the online ctd database.
- */
- @Autowired
- private MeSHParser meshParser;
-
- /**
- * Access point and parser for the online ctd database.
- */
- @Autowired
- private TaxonomyBackend taxonomyBackend;
-
- /**
- * Class that helps to generate images for google maps API.
- */
- private MapGenerator generator = new MapGenerator();
-
- @Override
- public Project getProjectByProjectId(String name, String token) throws SecurityException {
- Project result = projectDao.getProjectByProjectId(name);
- if (result == null) {
- return result;
- }
- if (userService.userHasPrivilege(token, PrivilegeType.VIEW_PROJECT, result)) {
- return result;
- } else if (userService.userHasPrivilege(token, PrivilegeType.ADD_MAP)) {
- return result;
- }
- throw new UserAccessException("User cannot access project");
- }
-
- @Override
- public boolean projectExists(String projectName) {
- if (projectName == null || projectName.equals("")) {
- return false;
- }
- return projectDao.isProjectExistsByName(projectName);
- }
-
- @Override
- public List<Project> getAllProjects(String token) throws SecurityException {
- List<Project> projects = projectDao.getAll();
- if (userService.userHasPrivilege(token, PrivilegeType.ADD_MAP)) {
- return projects;
- }
- List<Project> result = new ArrayList<>();
- for (Project project : projects) {
- if (userService.userHasPrivilege(token, PrivilegeType.VIEW_PROJECT, project)) {
- result.add(project);
- }
- }
- return result;
- }
-
- /**
- * Removes all types of privileges from every user to the project given in the
- * parameter.
- *
- * @param project
- * from which project we remove privileges
- */
- private void removePrivilegesForProject(Project project) {
- for (PrivilegeType type : PrivilegeType.values()) {
- if (type.getPrivilegeObjectType() == Project.class) {
- userService.dropPrivilegesForObjectType(type, project.getId());
- }
- }
- }
-
- @Override
- public void removeProject(final Project p, final String dir, final boolean async, String token)
- throws SecurityException {
- if (!userService.userHasPrivilege(userService.getUserByToken(token), PrivilegeType.PROJECT_MANAGEMENT)) {
- throw new UserAccessException("User cannot remove project");
- }
-
- final String homeDir;
- if (dir != null) {
- if (p.getDirectory() != null) {
- homeDir = dir + "/../map_images/" + p.getDirectory() + "/";
- } else {
- homeDir = dir + "/../map_images/";
- }
- } else {
- if (p.getDirectory() != null) {
- homeDir = p.getDirectory() + "/";
- } else {
- homeDir = null;
- }
- }
- removePrivilegesForProject(p);
- updateProjectStatus(p, ProjectStatus.REMOVING, 0, new CreateProjectParams());
- Thread computations = new Thread(new Runnable() {
-
- @Override
- public void run() {
- if (async) {
- // because we are running this in separate thread we need to open a
- // new session for db connection
- dbUtils.createSessionForCurrentThread();
- }
-
- Project project = projectDao.getById(p.getId());
-
- try {
- String email = null;
- MapGenerator mapGenerator = new MapGenerator();
- for (ModelData originalModel : project.getModels()) {
- List<ModelData> models = new ArrayList<ModelData>();
- models.add(originalModel);
- for (ModelSubmodelConnection connection : originalModel.getSubmodels()) {
- models.add(connection.getSubmodel());
- }
- modelService.removeModelFromCache(originalModel);
- for (ModelData model : models) {
- logger.debug("Remove model: " + model.getId());
- commentService.removeCommentsForModel(model);
-
- for (Layout layout : model.getLayouts()) {
- try {
- mapGenerator.removeLayout(layout, homeDir);
- } catch (IOException e) {
- logger.error("Problem with removing directory: " + layout.getDirectory(), e);
- }
- }
- }
- email = project.getNotifyEmail();
- }
- if (homeDir != null) {
- File homeDirFile = new File(homeDir);
- if (homeDirFile.exists()) {
- logger.debug("Removing project directory: " + homeDirFile.getAbsolutePath());
- try {
- FileUtils.deleteDirectory(homeDirFile);
- } catch (IOException e) {
- logger.error("Problem with removing diriectory", e);
- }
- }
- }
- projectDao.delete(project);
- if (async) {
- projectDao.commit();
- }
-
- LogParams params = new LogParams().type(LogType.MAP_REMOVED).object(project);
- logService.log(params);
-
- if (email != null) {
- try {
- sendSuccesfullRemoveEmail(project.getProjectId(), email);
- } catch (MessagingException e) {
- logger.error("Problem with sending remove email.", e);
- }
- }
- modelService.removeModelFromCacheByProjectId(p.getProjectId());
-
- } catch (HibernateException e) {
- logger.error("Problem with database", e);
- handleHibernateExceptionRemovingReporting(project, e, token);
- } finally {
- if (async) {
- // close the transaction for this thread
- dbUtils.closeSessionForCurrentThread();
- }
- }
-
- }
- });
-
- if (async) {
- computations.start();
- } else {
- computations.run();
- }
-
- }
-
- /**
- * When we encountered hibernate exception we need to handle error reporting
- * differently (hibernate session is broken). This method handles such case when
- * hibernate exception occurred when removing project.
- *
- * @param originalProject
- * project that was being removed
- * @param exception
- * hibernate exception that caused problems
- */
- protected void handleHibernateExceptionRemovingReporting(Project originalProject, HibernateException exception,
- String token) {
- // we need to open separate thread because current one thrown db exception
- // and transaction is corrupted and will be rolledback
- Thread reportInSeparateThread = new Thread(new Runnable() {
-
- @Override
- public void run() {
- dbUtils.createSessionForCurrentThread();
- try {
- // we need to get the project from db, because session where
- // originalProject was retrieved is broken
- Project project = getProjectByProjectId(originalProject.getProjectId(), token);
- String errorMessage = "Severe problem with removing object. Underlaying eror:\n" + exception.getMessage()
- + "\nMore information can be found in log file.";
- project.setErrors(errorMessage + "\n" + project.getErrors());
- project.setStatus(ProjectStatus.FAIL);
- projectDao.update(project);
- } catch (SecurityException e) {
- logger.error(e, e);
- } finally {
- dbUtils.closeSessionForCurrentThread();
- }
- }
-
- });
- reportInSeparateThread.start();
- }
-
- @Override
- public void addProject(Project project) {
- projectDao.add(project);
-
- }
-
- /**
- * This methods add privileges for the users listed in params to the project.
- *
- * @param project
- * to which project we add privileges
- * @param params
- * which users should be included to have privileges to the project
- */
- private void addUsers(Project project, CreateProjectParams params) {
- if (project == null) {
- logger.warn("Users won't be added. Project not defined");
- return;
- }
- List<String[]> users = params.getUsers();
- String[][] newUsers = new String[users.size() + 1][2];
- for (int i = 0; i < users.size(); i++) {
- for (int j = 0; j < 2; j++) {
- newUsers[i][j] = users.get(i)[j];
- }
- }
- Set<User> processedUser = new HashSet<>();
- for (int i = 0; i < newUsers.length; i++) {
- String login = newUsers[i][0];
- User user = userService.getUserByLogin(login);
- if (user != null) {
- processedUser.add(user);
- logger.debug("Root privileges for " + login + " for project " + project.getProjectId());
- ObjectPrivilege privilege = new ObjectPrivilege(project, 1, PrivilegeType.VIEW_PROJECT, user);
- userService.setUserPrivilege(user, privilege);
- privilege = new ObjectPrivilege(project, 1, PrivilegeType.LAYOUT_MANAGEMENT, user);
- userService.setUserPrivilege(user, privilege);
- privilege = new ObjectPrivilege(project, 1, PrivilegeType.EDIT_COMMENTS_PROJECT, user);
- userService.setUserPrivilege(user, privilege);
- }
- }
- for (User user : userDao.getAll()) {
- if (!processedUser.contains(user)) {
- processedUser.add(user);
- userService.createDefaultProjectPrivilegesForUser(project, user);
- }
- }
-
- }
-
- /**
- * This method creates set of images for the model layouts.
- *
- * @param originalModel
- * model for which we create layout images
- * @param params
- * configuration parameters including set of layouts to generate
- * @throws IOException
- * thrown when there are problems with generating files
- * @throws DrawingException
- * thrown when there was a problem with drawing a map
- * @throws CommandExecutionException
- * thrown when one of the files describing layouts is invalid
- */
- protected void createImages(final Model originalModel, final CreateProjectParams params)
- throws IOException, DrawingException, CommandExecutionException {
- if (!params.isImages()) {
- return;
- }
- updateProjectStatus(originalModel.getProject(), ProjectStatus.GENERATING_IMAGES, 0, params);
-
- List<Model> models = new ArrayList<>();
- models.add(originalModel);
- int size = originalModel.getLayouts().size();
- for (ModelSubmodelConnection connection : originalModel.getSubmodelConnections()) {
- models.add(connection.getSubmodel().getModel());
- size += connection.getSubmodel().getModel().getLayouts().size();
- }
- int counter = 0;
- for (final Model model : models) {
- for (int i = 0; i < model.getLayouts().size(); i++) {
- Layout layout = model.getLayouts().get(i);
- if (layout.getInputData() == null) {
- final double imgCounter = counter;
- final double finalSize = size;
- IProgressUpdater updater = new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- updateProjectStatus(originalModel.getProject(), ProjectStatus.GENERATING_IMAGES,
- IProgressUpdater.MAX_PROGRESS * imgCounter / finalSize + progress / finalSize, params);
- }
- };
- generateImagesForBuiltInOverlay(params, model, layout, updater);
- }
- counter++;
- }
- }
- }
-
- private void generateImagesForBuiltInOverlay(final CreateProjectParams params, final Model model, Layout layout,
- IProgressUpdater updater) throws CommandExecutionException, IOException, DrawingException {
- String directory = layout.getDirectory();
- Model output = model;
- if (layout.isHierarchicalView()) {
- output = new CopyCommand(model).execute();
- new SetFixedHierarchyLevelCommand(output, layout.getHierarchyViewLevel()).execute();
- }
- if (layout.getTitle().equals(BuildInLayout.CLEAN.getTitle())) {
- output = new CopyCommand(model).execute();
- new ClearColorModelCommand(output).execute();
- }
- MapGeneratorParams imgParams = generator.new MapGeneratorParams().directory(directory).sbgn(params.isSbgnFormat())
- .nested(layout.isHierarchicalView()).updater(updater);
- imgParams.model(output);
- generator.generateMapImages(imgParams);
- }
-
- /**
- * Creates project. Loads model from the input and run PostLoadModification.
- *
- * @param params
- * params used to create model
- * @param dbProject
- * project where the model should be placed
- * @throws InvalidInputDataExecption
- * thrown when there is a problem with input file
- */
- protected void createModel(final CreateProjectParams params, Project dbProject) throws InvalidInputDataExecption {
- ModelData modelData = modelDao.getLastModelForProjectIdentifier(params.getProjectId(), false);
- if (modelData != null) {
- throw new InvalidArgumentException("Model with the given name already exists");
- }
-
- final Project project = dbProject;
- updateProjectStatus(project, ProjectStatus.PARSING_DATA, 0.0, params);
-
- if (params.isComplex()) {
- try {
- Class<? extends IConverter> clazz = CellDesignerXmlParser.class;
- if (params.getParser() != null) {
- clazz = params.getParser().getClass();
- }
- ComplexZipConverter parser = new ComplexZipConverter(clazz);
- ComplexZipConverterParams complexParams;
- complexParams = new ComplexZipConverterParams().zipFile(params.getProjectFile());
- complexParams.visualizationDir(params.getProjectDir());
- for (ZipEntryFile entry : params.getZipEntries()) {
- complexParams.entry(entry);
- }
- ProjectFactory projectFactory = new ProjectFactory(parser);
- projectFactory.create(complexParams, dbProject);
- } catch (IOException e) {
- throw new InvalidInputDataExecption(e);
- }
- } else {
- IConverter parser;
- if (params.getParser() != null) {
- parser = params.getParser();
- } else if (params.getProjectFile().endsWith("sbgn")) {
- parser = new SbgnmlXmlConverter();
- } else {
- parser = new CellDesignerXmlParser();
- }
- try {
- Model model = parser.createModel(new ConverterParams().filename(params.getProjectFile())
- .sizeAutoAdjust(params.isAutoResize()).sbgnFormat(params.isSbgnFormat()));
- model.setName(params.getProjectName());
- project.addModel(model);
- } catch (FileNotFoundException ex) {
- throw new InvalidInputDataExecption(ex);
- }
- }
- Model topModel = project.getModels().iterator().next().getModel();
- topModel.setZoomLevels(generator.computeZoomLevels(topModel));
- topModel.setTileSize(MapGenerator.TILE_SIZE);
- dbProject.setNotifyEmail(params.getNotifyEmail());
-
- updateProjectStatus(project, ProjectStatus.UPLOADING_TO_DB, 0.0, params);
- dbUtils.setAutoFlush(false);
- projectDao.update(project);
- dbUtils.setAutoFlush(true);
- projectDao.flush();
-
- List<BuildInLayout> buildInLayouts = new ArrayList<>();
- BuildInLayout nested = null;
- if (params.isSemanticZoom()) {
- nested = BuildInLayout.SEMANTIC;
- } else {
- nested = BuildInLayout.NESTED;
- }
- if (params.isNetworkLayoutAsDefault()) {
- buildInLayouts.add(BuildInLayout.NORMAL);
- buildInLayouts.add(nested);
- } else {
- buildInLayouts.add(nested);
- buildInLayouts.add(BuildInLayout.NORMAL);
- }
- buildInLayouts.add(BuildInLayout.CLEAN);
-
- // reverse the order of build in layouts, so we can insert them at the
- // beginning of list of layouts (the order will be the same)
- Collections.reverse(buildInLayouts);
-
- for (BuildInLayout buildInLayout : buildInLayouts) {
- Layout topLayout = new Layout(buildInLayout.getTitle(),
- params.getProjectDir() + "/" + buildInLayout.getDirectorySuffix() + topModel.getId() + "/", true);
- topLayout.setStatus(LayoutStatus.NA);
- topLayout.setProgress(0.0);
- topLayout.setHierarchicalView(buildInLayout.isNested());
- topModel.addLayout(0, topLayout);
- int submodelId = 1;
- List<Layout> semanticLevelOverlays = new ArrayList<>();
- if (buildInLayout.equals(BuildInLayout.SEMANTIC) && params.isSemanticZoomContainsMultipleLayouts()) {
- for (int i = 0; i <= topModel.getZoomLevels(); i++) {
- String directory = params.getProjectDir() + "/" + buildInLayout.getDirectorySuffix() + "-" + i + "-"
- + topModel.getId() + "/";
- Layout semanticOverlay = new Layout(buildInLayout.getTitle() + "-" + i, directory, true);
- semanticOverlay.setStatus(LayoutStatus.NA);
- semanticOverlay.setProgress(0.0);
- semanticOverlay.setHierarchicalView(buildInLayout.isNested());
- semanticOverlay.setHierarchyViewLevel(i);
- semanticLevelOverlays.add(semanticOverlay);
- topModel.addLayout(1, semanticOverlay);
- }
- }
- for (ModelSubmodelConnection connection : topModel.getSubmodelConnections()) {
- Layout layout = new Layout(buildInLayout.getTitle(),
- params.getProjectDir() + "/" + buildInLayout.getDirectorySuffix() + submodelId + "/", true);
- layout.setStatus(LayoutStatus.NA);
- layout.setProgress(0.0);
- layout.setHierarchicalView(buildInLayout.isNested());
- layout.setParentLayout(topLayout);
- connection.getSubmodel().addLayout(0, layout);
-
- connection.getSubmodel().setZoomLevels(generator.computeZoomLevels(connection.getSubmodel().getModel()));
- connection.getSubmodel().setTileSize(MapGenerator.TILE_SIZE);
- if (buildInLayout.equals(BuildInLayout.SEMANTIC) && params.isSemanticZoomContainsMultipleLayouts()) {
- for (int i = 0; i <= topModel.getZoomLevels(); i++) {
- String directory = params.getProjectDir() + "/" + buildInLayout.getDirectorySuffix() + "-" + i + "-"
- + submodelId + "/";
- Layout semanticOverlay = new Layout(buildInLayout.getTitle() + "-" + i, directory, true);
- semanticOverlay.setStatus(LayoutStatus.NA);
- semanticOverlay.setProgress(0.0);
- semanticOverlay.setHierarchicalView(buildInLayout.isNested());
- semanticOverlay.setParentLayout(semanticLevelOverlays.get(i));
- semanticOverlay.setHierarchyViewLevel(i);
- connection.getSubmodel().addLayout(1, semanticOverlay);
- }
- }
- submodelId++;
- }
- }
-
- if (params.isUpdateAnnotations()) {
- Map<Class<?>, List<ElementAnnotator>> annotators = null;
- if (params.getAnnotatorsMap() != null) {
- annotators = new HashMap<Class<?>, List<ElementAnnotator>>();
- for (Class<?> clazz : params.getAnnotatorsMap().keySet()) {
- annotators.put(clazz, modelAnnotator.getAnnotatorsFromCommonNames(params.getAnnotatorsMap().get(clazz)));
- }
- }
- logger.debug("Updating annotations");
- modelAnnotator.performAnnotations(topModel, new IProgressUpdater() {
-
- @Override
- public void setProgress(final double progress) {
- updateProjectStatus(project, ProjectStatus.ANNOTATING, progress, params);
- }
- }, annotators, params.getAnnotatorsParamsAsMap());
- logger.debug("Annotations updated");
- }
- logger.debug("Model created");
-
- }
-
- /**
- * Updates status of the generating project.
- *
- * @param project
- * project that is generated
- * @param status
- * what is the current status
- * @param progress
- * what is the progress
- * @param params
- * parameters used for project creation
- */
- private void updateProjectStatus(Project project, ProjectStatus status, double progress, CreateProjectParams params) {
- if (project != null) {
- if (!status.equals(project.getStatus())
- || (Math.abs(progress - project.getProgress()) > IProgressUpdater.PROGRESS_BAR_UPDATE_RESOLUTION)) {
- project.setStatus(status);
- project.setProgress(progress);
- projectDao.update(project);
- if (params.isAsync()) {
- projectDao.commit();
- }
- }
- } else {
- logger.debug("status: " + status + ", " + progress);
- }
- }
-
- @Override
- public void createProject(final CreateProjectParams params) throws SecurityException {
- if (!userService.userHasPrivilege(params.getAuthenticationToken(), PrivilegeType.ADD_MAP)) {
- throw new SecurityException("Adding projects not allowed.");
- }
-
- // this count down is used to wait for asynchronous thread to initialize
- // data in the db (probably it would be better to move the initialization to
- // main thread)
- final CountDownLatch waitForInitialData = new CountDownLatch(1);
-
- Thread computations = new Thread(new Runnable() {
-
- @Override
- public void run() {
- if (params.isAsync()) {
- // because we are running this in separate thread we need to open a
- // new session for db connection
- dbUtils.createSessionForCurrentThread();
- }
-
- Project project = new Project();
- project.setProjectId(params.getProjectId());
- project.setName(params.getProjectName());
- if (params.getProjectDir() == null) {
- logger.warn("Project directory not set");
- project.setDirectory(null);
- } else {
- project.setDirectory(new File(params.getProjectDir()).getName());
- }
- project.setSbgnFormat(params.isSbgnFormat());
-
- MiriamData disease = null;
- if (params.getDisease() != null && !params.getDisease().isEmpty()) {
- disease = new MiriamData(MiriamType.MESH_2012, params.getDisease());
- }
- MiriamData organism = null;
- if (params.getOrganism() != null && !params.getOrganism().isEmpty()) {
- organism = new MiriamData(MiriamType.TAXONOMY, params.getOrganism());
- }
- project.setMapCanvasType(params.getMapCanvasType());
- project.setVersion(params.getVersion());
- projectDao.add(project);
- if (params.isAsync()) {
- projectDao.commit();
- }
- waitForInitialData.countDown();
- double[] outOfMemoryBuffer;
- EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
- try {
- Logger.getRootLogger().addAppender(appender);
- logger.debug("Running: " + params.getProjectId() + "; " + params.getProjectFile());
- outOfMemoryBuffer = new double[OUT_OF_MEMORY_BACKUP_BUFFER_SIZE];
- for (int i = 0; i < OUT_OF_MEMORY_BACKUP_BUFFER_SIZE; i++) {
- outOfMemoryBuffer[i] = Math.random() * OUT_OF_MEMORY_BACKUP_BUFFER_SIZE;
- }
-
- File inputFile = new File(params.getProjectFile());
- if (inputFile.exists()) {
- UploadedFileEntry file = new UploadedFileEntry();
- file.setFileContent(IOUtils.toByteArray(new FileInputStream(inputFile)));
- file.setOriginalFileName(FilenameUtils.getName(params.getProjectFile()));
- file.setLength(file.getFileContent().length);
- User owner = null;
- for (String[] userRow : params.getUsers()) {
- User user = userService.getUserByLogin(userRow[0]);
- if (user != null) {
- owner = user;
- }
- }
- file.setOwner(owner);
- project.setInputData(file);
- }
-
- createModel(params, project);
- Model originalModel = project.getModels().iterator().next().getModel();
- if (!params.isSemanticZoom()) {
- new CreateHierarchyCommand(originalModel, generator.computeZoomLevels(originalModel),
- generator.computeZoomFactor(originalModel)).execute();
- for (Model model : originalModel.getSubmodels()) {
- new CreateHierarchyCommand(model, generator.computeZoomLevels(model), generator.computeZoomFactor(model))
- .execute();
- }
- }
-
- addUsers(project, params);
- createImages(originalModel, params);
-
- for (Layout layout : originalModel.getLayouts()) {
- String[] tmp = layout.getDirectory().split("[\\\\/]");
- layout.setDirectory(tmp[tmp.length - 1]);
- }
- for (ModelSubmodelConnection connection : originalModel.getSubmodelConnections()) {
- for (Layout layout : connection.getSubmodel().getLayouts()) {
- String[] tmp = layout.getDirectory().split("[\\\\/]");
- layout.setDirectory(tmp[tmp.length - 1]);
- }
- }
-
- try {
- if (meshParser.isValidMeshId(disease)) {
- project.setDisease(disease);
- } else {
- logger.warn("No valid disease is provided for project:" + project.getName());
- }
- } catch (AnnotatorException e1) {
- logger.warn("Problem with accessing mesh db. More info in logs.");
- }
-
- if (taxonomyBackend.getNameForTaxonomy(organism) != null) {
- project.setOrganism(organism);
- } else {
- logger.warn(project.getProjectId() + "\tNo valid organism is provided for project. " + organism);
- }
-
- modelDao.update(originalModel);
-
- if (params.isAnalyzeAnnotations()) {
- analyzeAnnotations(originalModel, params);
- }
- Logger.getRootLogger().removeAppender(appender);
- project.addLoggingInfo(appender);
-
- if (params.isCacheModel()) {
- cacheData(originalModel, params);
- }
-
- updateProjectStatus(project, ProjectStatus.DONE, IProgressUpdater.MAX_PROGRESS, params);
- if (project.getNotifyEmail() != null && !project.getNotifyEmail().equals("")) {
- try {
- sendSuccesfullEmail(originalModel);
- } catch (MessagingException e) {
- logger.error(e, e);
- }
- }
-
- LogParams params = new LogParams().description("Created successfully").type(LogType.MAP_CREATED)
- .object(originalModel);
- logService.log(params);
-
- } catch (HibernateException e) {
- outOfMemoryBuffer = null;
- logger.error("Problem with database", e);
- handleHibernateExceptionReporting(params, e);
- } catch (Exception e) {
- outOfMemoryBuffer = null;
- handleCreateProjectException(params, e);
- } catch (OutOfMemoryError oome) {
- // release some memory
- outOfMemoryBuffer = null;
- logger.error("Out of memory", oome);
- if (project != null) {
- project.setErrors("Out of memory: " + oome.getMessage());
- }
- updateProjectStatus(project, ProjectStatus.FAIL, IProgressUpdater.MAX_PROGRESS, params);
- } finally {
- if (params.isAsync()) {
- // close the transaction for this thread
- dbUtils.closeSessionForCurrentThread();
- }
- Logger.getRootLogger().removeAppender(appender);
- }
- }
- });
- if (params.isAsync()) {
- computations.start();
- } else {
- computations.run();
- }
-
- try {
- waitForInitialData.await();
- } catch (InterruptedException e1) {
- logger.error(e1, e1);
- }
-
- }
-
- /**
- * Cache pubmed data for the model.
- *
- * @param originalModel
- * model for which we want to cache data.
- * @param params
- * parameters used for model generation
- */
- private void cacheData(final Model originalModel, final CreateProjectParams params) {
- modelService.cacheAllPubmedIds(originalModel, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- updateProjectStatus(originalModel.getProject(), ProjectStatus.CACHING, progress, params);
- }
- });
- modelService.cacheAllMiriamLinks(originalModel, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- updateProjectStatus(originalModel.getProject(), ProjectStatus.CACHING_MIRIAM, progress, params);
- }
- });
-
- chemicalService.cacheDataForModel(originalModel, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- updateProjectStatus(originalModel.getProject(), ProjectStatus.CACHING_CHEMICAL, progress, params);
- }
- });
-
- drugService.cacheDataForModel(originalModel, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- updateProjectStatus(originalModel.getProject(), ProjectStatus.CACHING_DRUG, progress, params);
- }
- });
-
- mirnaService.cacheDataForModel(originalModel, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- updateProjectStatus(originalModel.getProject(), ProjectStatus.CACHING_MI_RNA, progress, params);
- }
- });
-
- }
-
- /**
- * @return the modelDao
- * @see #modelDao
- */
- public ModelDao getModelDao() {
- return modelDao;
- }
-
- /**
- * @param modelDao
- * the modelDao to set
- * @see #modelDao
- */
- public void setModelDao(ModelDao modelDao) {
- this.modelDao = modelDao;
- }
-
- /**
- * @return the commentService
- * @see #commentService
- */
- public ICommentService getCommentService() {
- return commentService;
- }
-
- /**
- * @param commentService
- * the commentService to set
- * @see #commentService
- */
- public void setCommentService(ICommentService commentService) {
- this.commentService = commentService;
- }
-
- /**
- * @return the passwordEncoder
- * @see #passwordEncoder
- */
- public PasswordEncoder getPasswordEncoder() {
- return passwordEncoder;
- }
-
- /**
- * @param passwordEncoder
- * the passwordEncoder to set
- * @see #passwordEncoder
- */
- public void setPasswordEncoder(PasswordEncoder passwordEncoder) {
- this.passwordEncoder = passwordEncoder;
- }
-
- /**
- * @return the commentDao
- * @see #commentDao
- */
- public CommentDao getCommentDao() {
- return commentDao;
- }
-
- /**
- * @param commentDao
- * the commentDao to set
- * @see #commentDao
- */
- public void setCommentDao(CommentDao commentDao) {
- this.commentDao = commentDao;
- }
-
- /**
- * @return the modelAnnotator
- * @see #modelAnnotator
- */
- public ModelAnnotator getModelAnnotator() {
- return modelAnnotator;
- }
-
- /**
- * @param modelAnnotator
- * the modelAnnotator to set
- * @see #modelAnnotator
- */
- public void setModelAnnotator(ModelAnnotator modelAnnotator) {
- this.modelAnnotator = modelAnnotator;
- }
-
- /**
- * @return the dbUtils
- * @see #dbUtils
- */
- public DbUtils getDbUtils() {
- return dbUtils;
- }
-
- /**
- * @param dbUtils
- * the dbUtils to set
- * @see #dbUtils
- */
- public void setDbUtils(DbUtils dbUtils) {
- this.dbUtils = dbUtils;
- }
-
- /**
- * @return the projectDao
- * @see #projectDao
- */
- public ProjectDao getProjectDao() {
- return projectDao;
- }
-
- /**
- * @param projectDao
- * the projectDao to set
- * @see #projectDao
- */
- public void setProjectDao(ProjectDao projectDao) {
- this.projectDao = projectDao;
- }
-
- /**
- * Analyzes annotation of the model and put information about invalid
- * annotations into the {@link Model#creationWarnings} field.
- *
- * @param originalModel
- * model to analyze
- * @param params
- * parameters used for model generation
- */
- protected void analyzeAnnotations(final Model originalModel, final CreateProjectParams params) {
- logger.debug("Analyze annotations");
- Collection<? extends ProblematicAnnotation> improperAnnotations = modelAnnotator
- .findImproperAnnotations(originalModel, new IProgressUpdater() {
-
- @Override
- public void setProgress(double progress) {
- updateProjectStatus(originalModel.getProject(), ProjectStatus.VALIDATING_MIRIAM, progress, params);
- }
- }, params.getValidAnnotations());
- List<String> res = new ArrayList<>();
- for (ProblematicAnnotation improperAnnotation : improperAnnotations) {
- res.add(improperAnnotation.toString());
- }
- Collections.sort(res);
-
- Collection<? extends ProblematicAnnotation> missingAnnotations = modelAnnotator
- .findMissingAnnotations(originalModel, params.getRequiredAnnotations());
- for (ProblematicAnnotation improperAnnotation : missingAnnotations) {
- res.add(improperAnnotation.toString());
- }
- for (String message : res) {
- logger.warn(message);
- }
- logger.debug("Analyze finished");
- }
-
- /**
- * Sends notification email that map was removed.
- *
- * @param projectId
- * identifier of the project
- * @param email
- * otification email
- * @throws MessagingException
- * thrown when there is a problem with sending email
- */
- protected void sendSuccesfullRemoveEmail(String projectId, String email) throws MessagingException {
- EmailSender emailSender = new EmailSender(configurationService);
- StringBuilder content = new StringBuilder("Map " + projectId + " was successfully removed.<br/>");
- emailSender.sendEmail("MapViewer notification", content.toString(), email);
- }
-
- @Override
- public TreeNode createClassAnnotatorTree(User user) {
-
- UserAnnotationSchema annotationSchema = prepareUserAnnotationSchema(user);
-
- ElementUtils elementUtils = new ElementUtils();
-
- ClassTreeNode top = elementUtils.getAnnotatedElementClassTree();
-
- Class<?> clazz = top.getClazz();
- top.setData(annotationSchema.requiresAtLeastOneAnnotation(clazz));
- TreeNode root = new DefaultTreeNode(new AnnotatedObjectTreeRow(top, modelAnnotator.getAvailableAnnotators(clazz),
- modelAnnotator.getAnnotatorsFromCommonNames(annotationSchema.getAnnotatorsForClass(clazz)),
- annotationSchema.getValidAnnotations(clazz), annotationSchema.getRequiredAnnotations(clazz)), null);
-
- root.setExpanded(true);
-
- Queue<Pair<ClassTreeNode, TreeNode>> nodes = new LinkedList<Pair<ClassTreeNode, TreeNode>>();
- nodes.add(new Pair<ClassTreeNode, TreeNode>(top, root));
- // create children
-
- Queue<TreeNode> expandParents = new LinkedList<TreeNode>();
-
- while (!nodes.isEmpty()) {
- Pair<ClassTreeNode, TreeNode> element = nodes.poll();
-
- for (ClassTreeNode node : element.getLeft().getChildren()) {
-
- clazz = node.getClazz();
- node.setData(annotationSchema.requiresAtLeastOneAnnotation(clazz));
- AnnotatedObjectTreeRow data = new AnnotatedObjectTreeRow(node, modelAnnotator.getAvailableAnnotators(clazz),
- modelAnnotator.getAnnotatorsFromCommonNames(annotationSchema.getAnnotatorsForClass(clazz)),
- annotationSchema.getValidAnnotations(clazz), annotationSchema.getRequiredAnnotations(clazz));
- TreeNode treeNode = new DefaultTreeNode(data, element.getRight());
- nodes.add(new Pair<ClassTreeNode, TreeNode>(node, treeNode));
- if (data.getUsedAnnotators().size() > 0 || data.getValidAnnotators().size() > 0) {
- expandParents.add(treeNode);
- }
- }
- }
- while (!expandParents.isEmpty()) {
- TreeNode node = expandParents.poll();
- if (node.getParent() != null && !node.getParent().isExpanded()) {
- node.getParent().setExpanded(true);
- expandParents.add(node.getParent());
- }
- }
-
- return root;
-
- }
-
- /**
- * Retrieves (or creates) annotation schema for a given user.
- *
- * @param user
- * for this users {@link UserAnnotationSchema} will be prepared
- * @return {@link UserAnnotationSchema} for {@link User}
- */
- public UserAnnotationSchema prepareUserAnnotationSchema(User user) {
- UserAnnotationSchema annotationSchema = null;
- if (user != null) {
- annotationSchema = userDao.getById(user.getId()).getAnnotationSchema();
- }
- if (annotationSchema == null) {
- annotationSchema = new UserAnnotationSchema();
-
- ElementUtils elementUtils = new ElementUtils();
-
- ClassTreeNode top = elementUtils.getAnnotatedElementClassTree();
-
- Map<Class<? extends BioEntity>, Set<MiriamType>> validMiriam = modelAnnotator.getDefaultValidClasses();
- Map<Class<? extends BioEntity>, Set<MiriamType>> requiredMiriam = modelAnnotator.getDefaultRequiredClasses();
-
- Queue<ClassTreeNode> nodes = new LinkedList<ClassTreeNode>();
- nodes.add(top);
-
- while (!nodes.isEmpty()) {
- ClassTreeNode element = nodes.poll();
- annotationSchema.addClassAnnotator(new UserClassAnnotators(element.getClazz(),
- modelAnnotator.getAvailableDefaultAnnotatorNames(element.getClazz())));
- annotationSchema.addClassValidAnnotations(
- new UserClassValidAnnotations(element.getClazz(), validMiriam.get(element.getClazz())));
- annotationSchema.addClassRequiredAnnotations(
- new UserClassRequiredAnnotations(element.getClazz(), requiredMiriam.get(element.getClazz())));
- for (ClassTreeNode node : element.getChildren()) {
- nodes.add(node);
- }
- }
- if (user != null) {
- User dbUser = userDao.getById(user.getId());
- dbUser.setAnnotationSchema(annotationSchema);
- userDao.update(dbUser);
- }
- }
- return annotationSchema;
- }
-
- @Override
- public void updateClassAnnotatorTreeForUser(User user, TreeNode annotatorsTree, boolean sbgnFormat,
- boolean networkLayoutAsDefault) {
- User dbUser = userDao.getById(user.getId());
- if (dbUser.getAnnotationSchema() == null) {
- dbUser.setAnnotationSchema(new UserAnnotationSchema());
- }
- UserAnnotationSchema annotationSchema = dbUser.getAnnotationSchema();
-
- Queue<TreeNode> queue = new LinkedList<TreeNode>();
- queue.add(annotatorsTree);
- while (!queue.isEmpty()) {
- TreeNode node = queue.poll();
- for (TreeNode child : node.getChildren()) {
- queue.add(child);
- }
- AnnotatedObjectTreeRow data = (AnnotatedObjectTreeRow) node.getData();
- annotationSchema.addClassAnnotator(new UserClassAnnotators(data.getClazz(), data.getUsedAnnotators()));
- annotationSchema.addClassRequiredAnnotations(
- new UserClassRequiredAnnotations(data.getClazz(), data.getRequiredAnnotations()));
- annotationSchema
- .addClassValidAnnotations(new UserClassValidAnnotations(data.getClazz(), data.getValidAnnotations()));
- }
- annotationSchema.setSbgnFormat(sbgnFormat);
- annotationSchema.setNetworkLayoutAsDefault(networkLayoutAsDefault);
- userService.updateUser(dbUser);
- user.setAnnotationSchema(annotationSchema);
- }
-
- @Override
- public List<UserAnnotatorsParam> getAnnotatorsParams(User user) {
- User dbUser = userDao.getById(user.getId());
- UserAnnotationSchema annotationSchema = dbUser.getAnnotationSchema();
- if (annotationSchema == null) {
- annotationSchema = new UserAnnotationSchema();
- dbUser.setAnnotationSchema(annotationSchema);
- }
-
- /*
- * Hibernate lazy loads collections so each element needs to be accessed to be
- * loaded now or otherwise the data might not be available when accessed because
- * the session might not be available at that time.
- */
- List<UserAnnotatorsParam> aps = new ArrayList<>();
- for (UserAnnotatorsParam ap : annotationSchema.getAnnotatorsParams()) {
- aps.add(ap);
- }
- return aps;
- }
-
- /**
- * Sends email about unsuccessful project creation.
- *
- * @param projectName
- * name of the project
- * @param email
- * email where we want to send information
- * @param e
- * exception that caused problem
- */
- private void sendUnsuccesfullEmail(String projectName, String email, Exception e) {
- EmailSender emailSender = new EmailSender(configurationService);
- StringBuilder content = new StringBuilder("");
- content.append("There was a problem with generating " + projectName + " map.<br/>");
- content.append(e.getClass().getName() + ": " + e.getMessage());
- try {
- emailSender.sendEmail("MapViewer notification", content.toString(), email);
- } catch (MessagingException e1) {
- logger.error(e1);
- }
- }
-
- /**
- * Sends email about successful project creation.
- *
- * @param originalModel
- * model that was created
- * @throws MessagingException
- * exception thrown when there is a problem with sending email
- */
- protected void sendSuccesfullEmail(Model originalModel) throws MessagingException {
- EmailSender emailSender = new EmailSender(configurationService);
- StringBuilder content = new StringBuilder("Your map was generated successfully.<br/>");
- emailSender.sendEmail("MapViewer notification", content.toString(), originalModel.getProject().getNotifyEmail());
- }
-
- @Override
- public void updateProject(Project project, String token) throws SecurityException {
- projectDao.update(project);
- if (token != null) {
- Model model = modelService.getLastModelByProjectId(project.getProjectId(), token);
- if (model != null) {
- model.setProject(project);
- }
- }
- }
-
- /**
- * This method handles situation when sever db error appeared during uploading
- * of the project into database.
- *
- * @param params
- * parameters used to create project
- * @param e
- * exception that occurred during uploading of the project
- */
- private void handleHibernateExceptionReporting(CreateProjectParams params, HibernateException e) {
- // we need to open separate thread because current one thrown db exception
- // and transaction is corrupted and will be rolledback
- Thread reportInSeparateThread = new Thread(new Runnable() {
-
- @Override
- public void run() {
- dbUtils.createSessionForCurrentThread();
-
- try {
- Project project = getProjectByProjectId(params.getProjectId(), params.getAuthenticationToken());
- String errorMessage = "Problem with uploading to database. "
- + "You might violated some unhandled constraints or you run out of memory. Underlaying eror:\n"
- + e.getMessage() + "\nMore information can be found in log file.";
- project.setErrors(errorMessage);
- project.setStatus(ProjectStatus.FAIL);
- projectDao.update(project);
- } catch (Exception e) {
- logger.error(e, e);
- } finally {
- dbUtils.closeSessionForCurrentThread();
- }
- }
-
- });
- reportInSeparateThread.start();
-
- }
-
- /**
- * Method that handles exception reporting during creation of a project.
- *
- * @param params
- * set of parameters used to create project
- * @param e
- * exception that caused problems
- */
- private void handleCreateProjectException(final CreateProjectParams params, Exception e) {
- Project p = projectDao.getProjectByProjectId(params.getProjectId());
- logger.error(e.getMessage(), e);
- if (p != null) {
- p.setErrors("Problem with uploading map: " + e.getMessage() + ". More details can be found in log file.");
- }
- updateProjectStatus(p, ProjectStatus.FAIL, IProgressUpdater.MAX_PROGRESS, params);
-
- String email = params.getNotifyEmail();
- String projectName = params.getProjectId();
-
- LogParams logParams = new LogParams().description("Failed: " + e.getMessage()).type(LogType.MAP_CREATED).object(p);
- logService.log(logParams);
- if (email != null) {
- sendUnsuccesfullEmail(projectName, email, e);
- }
- }
-
- /**
- * @return the taxonomyBackend
- * @see #taxonomyBackend
- */
- public TaxonomyBackend getTaxonomyBackend() {
- return taxonomyBackend;
- }
-
- /**
- * @param taxonomyBackend
- * the taxonomyBackend to set
- * @see #taxonomyBackend
- */
- public void setTaxonomyBackend(TaxonomyBackend taxonomyBackend) {
- this.taxonomyBackend = taxonomyBackend;
- }
-
- @Override
- public List<Project> getAllProjects() {
- return projectDao.getAll();
- }
-
-}
+package lcsb.mapviewer.services.impl;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+import java.util.Queue;
+import java.util.Set;
+import java.util.concurrent.CountDownLatch;
+
+import javax.mail.MessagingException;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.FilenameUtils;
+import org.apache.commons.io.IOUtils;
+import org.apache.log4j.Logger;
+import org.hibernate.HibernateException;
+import org.primefaces.model.DefaultTreeNode;
+import org.primefaces.model.TreeNode;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.security.crypto.password.PasswordEncoder;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.annotation.services.MeSHParser;
+import lcsb.mapviewer.annotation.services.ModelAnnotator;
+import lcsb.mapviewer.annotation.services.ProblematicAnnotation;
+import lcsb.mapviewer.annotation.services.TaxonomyBackend;
+import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
+import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
+import lcsb.mapviewer.commands.ClearColorModelCommand;
+import lcsb.mapviewer.commands.CommandExecutionException;
+import lcsb.mapviewer.commands.CopyCommand;
+import lcsb.mapviewer.commands.CreateHierarchyCommand;
+import lcsb.mapviewer.commands.SetFixedHierarchyLevelCommand;
+import lcsb.mapviewer.common.EventStorageLoggerAppender;
+import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.ComplexZipConverter;
+import lcsb.mapviewer.converter.ComplexZipConverterParams;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.ProjectFactory;
+import lcsb.mapviewer.converter.graphics.DrawingException;
+import lcsb.mapviewer.converter.graphics.MapGenerator;
+import lcsb.mapviewer.converter.graphics.MapGenerator.MapGeneratorParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter;
+import lcsb.mapviewer.converter.zip.ZipEntryFile;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.ProjectStatus;
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
+import lcsb.mapviewer.model.log.LogType;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.layout.LayoutStatus;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
+import lcsb.mapviewer.model.user.ObjectPrivilege;
+import lcsb.mapviewer.model.user.PrivilegeType;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.model.user.UserAnnotationSchema;
+import lcsb.mapviewer.model.user.UserAnnotatorsParam;
+import lcsb.mapviewer.model.user.UserClassAnnotators;
+import lcsb.mapviewer.model.user.UserClassRequiredAnnotations;
+import lcsb.mapviewer.model.user.UserClassValidAnnotations;
+import lcsb.mapviewer.modelutils.map.ClassTreeNode;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
+import lcsb.mapviewer.persist.DbUtils;
+import lcsb.mapviewer.persist.dao.ProjectDao;
+import lcsb.mapviewer.persist.dao.map.CommentDao;
+import lcsb.mapviewer.persist.dao.map.ModelDao;
+import lcsb.mapviewer.persist.dao.user.UserDao;
+import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.UserAccessException;
+import lcsb.mapviewer.services.interfaces.ICommentService;
+import lcsb.mapviewer.services.interfaces.IConfigurationService;
+import lcsb.mapviewer.services.interfaces.ILogService;
+import lcsb.mapviewer.services.interfaces.ILogService.LogParams;
+import lcsb.mapviewer.services.interfaces.IModelService;
+import lcsb.mapviewer.services.interfaces.IProjectService;
+import lcsb.mapviewer.services.interfaces.IUserService;
+import lcsb.mapviewer.services.overlay.AnnotatedObjectTreeRow;
+import lcsb.mapviewer.services.search.chemical.IChemicalService;
+import lcsb.mapviewer.services.search.drug.IDrugService;
+import lcsb.mapviewer.services.search.mirna.IMiRNAService;
+import lcsb.mapviewer.services.utils.CreateProjectParams;
+import lcsb.mapviewer.services.utils.EmailSender;
+import lcsb.mapviewer.services.utils.data.BuildInLayout;
+
+/**
+ * Implementation of the project service. It allows to manage and access project
+ * data.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Transactional(value = "txManager")
+public class ProjectService implements IProjectService {
+
+ /**
+ * Size of the artificial buffer that will be released when
+ * {@link OutOfMemoryError} is thrown to gain some free memory and report
+ * problem.
+ */
+ private static final int OUT_OF_MEMORY_BACKUP_BUFFER_SIZE = 10000;
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(ProjectService.class);
+
+ /**
+ * Data access object for projects.
+ */
+ @Autowired
+ private ProjectDao projectDao;
+
+ /**
+ * Data access object for models.
+ */
+ @Autowired
+ private ModelDao modelDao;
+
+ /**
+ * Data access object for users.
+ */
+ @Autowired
+ private UserDao userDao;
+
+ /**
+ * Service that allows to access and manage models.
+ */
+ @Autowired
+ private IModelService modelService;
+
+ /**
+ * Service that allows to access and manage comments.
+ */
+ @Autowired
+ private ICommentService commentService;
+
+ /**
+ * Service used to access logs.
+ *
+ * @see ILogService
+ */
+ @Autowired
+ private ILogService logService;
+
+ /**
+ * Service that manages and gives access to configuration parameters.
+ */
+ @Autowired
+ private IConfigurationService configurationService;
+
+ /**
+ * Services that manages and gives access to user information.
+ */
+ @Autowired
+ private IUserService userService;
+
+ /**
+ * Services that access data about chemicals.
+ */
+ @Autowired
+ private IChemicalService chemicalService;
+
+ /**
+ * Services that access data about drugs.
+ */
+ @Autowired
+ private IDrugService drugService;
+
+ /**
+ * Services that access data about mirna.
+ */
+ @Autowired
+ private IMiRNAService mirnaService;
+
+ /**
+ * Data access object for comments.
+ */
+ @Autowired
+ private CommentDao commentDao;
+
+ /**
+ * Service that provides password encoding.
+ */
+ @Autowired
+ private PasswordEncoder passwordEncoder;
+
+ /**
+ * Module that allows to annotate maps.
+ */
+ @Autowired
+ private ModelAnnotator modelAnnotator;
+
+ /**
+ * Utils that help to manage the sessions in custom multithreaded
+ * implementation.
+ */
+ @Autowired
+ private DbUtils dbUtils;
+
+ /**
+ * Access point and parser for the online ctd database.
+ */
+ @Autowired
+ private MeSHParser meshParser;
+
+ /**
+ * Access point and parser for the online ctd database.
+ */
+ @Autowired
+ private TaxonomyBackend taxonomyBackend;
+
+ /**
+ * Class that helps to generate images for google maps API.
+ */
+ private MapGenerator generator = new MapGenerator();
+
+ @Override
+ public Project getProjectByProjectId(String name, String token) throws SecurityException {
+ Project result = projectDao.getProjectByProjectId(name);
+ if (result == null) {
+ return result;
+ }
+ if (userService.userHasPrivilege(token, PrivilegeType.VIEW_PROJECT, result)) {
+ return result;
+ } else if (userService.userHasPrivilege(token, PrivilegeType.ADD_MAP)) {
+ return result;
+ }
+ throw new UserAccessException("User cannot access project");
+ }
+
+ @Override
+ public boolean projectExists(String projectName) {
+ if (projectName == null || projectName.equals("")) {
+ return false;
+ }
+ return projectDao.isProjectExistsByName(projectName);
+ }
+
+ @Override
+ public List<Project> getAllProjects(String token) throws SecurityException {
+ List<Project> projects = projectDao.getAll();
+ if (userService.userHasPrivilege(token, PrivilegeType.ADD_MAP)) {
+ return projects;
+ }
+ List<Project> result = new ArrayList<>();
+ for (Project project : projects) {
+ if (userService.userHasPrivilege(token, PrivilegeType.VIEW_PROJECT, project)) {
+ result.add(project);
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Removes all types of privileges from every user to the project given in the
+ * parameter.
+ *
+ * @param project
+ * from which project we remove privileges
+ */
+ private void removePrivilegesForProject(Project project) {
+ for (PrivilegeType type : PrivilegeType.values()) {
+ if (type.getPrivilegeObjectType() == Project.class) {
+ userService.dropPrivilegesForObjectType(type, project.getId());
+ }
+ }
+ }
+
+ @Override
+ public void removeProject(final Project p, final String dir, final boolean async, String token)
+ throws SecurityException {
+ if (!userService.userHasPrivilege(userService.getUserByToken(token), PrivilegeType.PROJECT_MANAGEMENT)) {
+ throw new UserAccessException("User cannot remove project");
+ }
+
+ final String homeDir;
+ if (dir != null) {
+ if (p.getDirectory() != null) {
+ homeDir = dir + "/../map_images/" + p.getDirectory() + "/";
+ } else {
+ homeDir = dir + "/../map_images/";
+ }
+ } else {
+ if (p.getDirectory() != null) {
+ homeDir = p.getDirectory() + "/";
+ } else {
+ homeDir = null;
+ }
+ }
+ removePrivilegesForProject(p);
+ updateProjectStatus(p, ProjectStatus.REMOVING, 0, new CreateProjectParams());
+ Thread computations = new Thread(new Runnable() {
+
+ @Override
+ public void run() {
+ if (async) {
+ // because we are running this in separate thread we need to open a
+ // new session for db connection
+ dbUtils.createSessionForCurrentThread();
+ }
+
+ Project project = projectDao.getById(p.getId());
+
+ try {
+ String email = null;
+ MapGenerator mapGenerator = new MapGenerator();
+ for (ModelData originalModel : project.getModels()) {
+ List<ModelData> models = new ArrayList<ModelData>();
+ models.add(originalModel);
+ for (ModelSubmodelConnection connection : originalModel.getSubmodels()) {
+ models.add(connection.getSubmodel());
+ }
+ modelService.removeModelFromCache(originalModel);
+ for (ModelData model : models) {
+ logger.debug("Remove model: " + model.getId());
+ commentService.removeCommentsForModel(model);
+
+ for (Layout layout : model.getLayouts()) {
+ try {
+ mapGenerator.removeLayout(layout, homeDir);
+ } catch (IOException e) {
+ logger.error("Problem with removing directory: " + layout.getDirectory(), e);
+ }
+ }
+ }
+ email = project.getNotifyEmail();
+ }
+ if (homeDir != null) {
+ File homeDirFile = new File(homeDir);
+ if (homeDirFile.exists()) {
+ logger.debug("Removing project directory: " + homeDirFile.getAbsolutePath());
+ try {
+ FileUtils.deleteDirectory(homeDirFile);
+ } catch (IOException e) {
+ logger.error("Problem with removing diriectory", e);
+ }
+ }
+ }
+ projectDao.delete(project);
+ if (async) {
+ projectDao.commit();
+ }
+
+ LogParams params = new LogParams().type(LogType.MAP_REMOVED).object(project);
+ logService.log(params);
+
+ if (email != null) {
+ try {
+ sendSuccesfullRemoveEmail(project.getProjectId(), email);
+ } catch (MessagingException e) {
+ logger.error("Problem with sending remove email.", e);
+ }
+ }
+ modelService.removeModelFromCacheByProjectId(p.getProjectId());
+
+ } catch (HibernateException e) {
+ logger.error("Problem with database", e);
+ handleHibernateExceptionRemovingReporting(project, e, token);
+ } finally {
+ if (async) {
+ // close the transaction for this thread
+ dbUtils.closeSessionForCurrentThread();
+ }
+ }
+
+ }
+ });
+
+ if (async) {
+ computations.start();
+ } else {
+ computations.run();
+ }
+
+ }
+
+ /**
+ * When we encountered hibernate exception we need to handle error reporting
+ * differently (hibernate session is broken). This method handles such case when
+ * hibernate exception occurred when removing project.
+ *
+ * @param originalProject
+ * project that was being removed
+ * @param exception
+ * hibernate exception that caused problems
+ */
+ protected void handleHibernateExceptionRemovingReporting(Project originalProject, HibernateException exception,
+ String token) {
+ // we need to open separate thread because current one thrown db exception
+ // and transaction is corrupted and will be rolledback
+ Thread reportInSeparateThread = new Thread(new Runnable() {
+
+ @Override
+ public void run() {
+ dbUtils.createSessionForCurrentThread();
+ try {
+ // we need to get the project from db, because session where
+ // originalProject was retrieved is broken
+ Project project = getProjectByProjectId(originalProject.getProjectId(), token);
+ String errorMessage = "Severe problem with removing object. Underlaying eror:\n" + exception.getMessage()
+ + "\nMore information can be found in log file.";
+ project.setErrors(errorMessage + "\n" + project.getErrors());
+ project.setStatus(ProjectStatus.FAIL);
+ projectDao.update(project);
+ } catch (SecurityException e) {
+ logger.error(e, e);
+ } finally {
+ dbUtils.closeSessionForCurrentThread();
+ }
+ }
+
+ });
+ reportInSeparateThread.start();
+ }
+
+ @Override
+ public void addProject(Project project) {
+ projectDao.add(project);
+
+ }
+
+ /**
+ * This methods add privileges for the users listed in params to the project.
+ *
+ * @param project
+ * to which project we add privileges
+ * @param params
+ * which users should be included to have privileges to the project
+ */
+ private void addUsers(Project project, CreateProjectParams params) {
+ if (project == null) {
+ logger.warn("Users won't be added. Project not defined");
+ return;
+ }
+ List<String[]> users = params.getUsers();
+ String[][] newUsers = new String[users.size() + 1][2];
+ for (int i = 0; i < users.size(); i++) {
+ for (int j = 0; j < 2; j++) {
+ newUsers[i][j] = users.get(i)[j];
+ }
+ }
+ Set<User> processedUser = new HashSet<>();
+ for (int i = 0; i < newUsers.length; i++) {
+ String login = newUsers[i][0];
+ User user = userService.getUserByLogin(login);
+ if (user != null) {
+ processedUser.add(user);
+ logger.debug("Root privileges for " + login + " for project " + project.getProjectId());
+ ObjectPrivilege privilege = new ObjectPrivilege(project, 1, PrivilegeType.VIEW_PROJECT, user);
+ userService.setUserPrivilege(user, privilege);
+ privilege = new ObjectPrivilege(project, 1, PrivilegeType.LAYOUT_MANAGEMENT, user);
+ userService.setUserPrivilege(user, privilege);
+ privilege = new ObjectPrivilege(project, 1, PrivilegeType.EDIT_COMMENTS_PROJECT, user);
+ userService.setUserPrivilege(user, privilege);
+ }
+ }
+ for (User user : userDao.getAll()) {
+ if (!processedUser.contains(user)) {
+ processedUser.add(user);
+ userService.createDefaultProjectPrivilegesForUser(project, user);
+ }
+ }
+
+ }
+
+ /**
+ * This method creates set of images for the model layouts.
+ *
+ * @param originalModel
+ * model for which we create layout images
+ * @param params
+ * configuration parameters including set of layouts to generate
+ * @throws IOException
+ * thrown when there are problems with generating files
+ * @throws DrawingException
+ * thrown when there was a problem with drawing a map
+ * @throws CommandExecutionException
+ * thrown when one of the files describing layouts is invalid
+ */
+ protected void createImages(final Model originalModel, final CreateProjectParams params)
+ throws IOException, DrawingException, CommandExecutionException {
+ if (!params.isImages()) {
+ return;
+ }
+ updateProjectStatus(originalModel.getProject(), ProjectStatus.GENERATING_IMAGES, 0, params);
+
+ List<Model> models = new ArrayList<>();
+ models.add(originalModel);
+ int size = originalModel.getLayouts().size();
+ for (ModelSubmodelConnection connection : originalModel.getSubmodelConnections()) {
+ models.add(connection.getSubmodel().getModel());
+ size += connection.getSubmodel().getModel().getLayouts().size();
+ }
+ int counter = 0;
+ for (final Model model : models) {
+ for (int i = 0; i < model.getLayouts().size(); i++) {
+ Layout layout = model.getLayouts().get(i);
+ if (layout.getInputData() == null) {
+ final double imgCounter = counter;
+ final double finalSize = size;
+ IProgressUpdater updater = new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ updateProjectStatus(originalModel.getProject(), ProjectStatus.GENERATING_IMAGES,
+ IProgressUpdater.MAX_PROGRESS * imgCounter / finalSize + progress / finalSize, params);
+ }
+ };
+ generateImagesForBuiltInOverlay(params, model, layout, updater);
+ }
+ counter++;
+ }
+ }
+ }
+
+ private void generateImagesForBuiltInOverlay(final CreateProjectParams params, final Model model, Layout layout,
+ IProgressUpdater updater) throws CommandExecutionException, IOException, DrawingException {
+ String directory = layout.getDirectory();
+ Model output = model;
+ if (layout.isHierarchicalView()) {
+ output = new CopyCommand(model).execute();
+ new SetFixedHierarchyLevelCommand(output, layout.getHierarchyViewLevel()).execute();
+ }
+ if (layout.getTitle().equals(BuildInLayout.CLEAN.getTitle())) {
+ output = new CopyCommand(model).execute();
+ new ClearColorModelCommand(output).execute();
+ }
+ MapGeneratorParams imgParams = generator.new MapGeneratorParams().directory(directory).sbgn(params.isSbgnFormat())
+ .nested(layout.isHierarchicalView()).updater(updater);
+ imgParams.model(output);
+ generator.generateMapImages(imgParams);
+ }
+
+ /**
+ * Creates project. Loads model from the input and run PostLoadModification.
+ *
+ * @param params
+ * params used to create model
+ * @param dbProject
+ * project where the model should be placed
+ * @throws InvalidInputDataExecption
+ * thrown when there is a problem with input file
+ */
+ protected void createModel(final CreateProjectParams params, Project dbProject) throws InvalidInputDataExecption {
+ ModelData modelData = modelDao.getLastModelForProjectIdentifier(params.getProjectId(), false);
+ if (modelData != null) {
+ throw new InvalidArgumentException("Model with the given name already exists");
+ }
+
+ final Project project = dbProject;
+ updateProjectStatus(project, ProjectStatus.PARSING_DATA, 0.0, params);
+
+ if (params.isComplex()) {
+ try {
+ Class<? extends IConverter> clazz = CellDesignerXmlParser.class;
+ if (params.getParser() != null) {
+ clazz = params.getParser().getClass();
+ }
+ ComplexZipConverter parser = new ComplexZipConverter(clazz);
+ ComplexZipConverterParams complexParams;
+ complexParams = new ComplexZipConverterParams().zipFile(params.getProjectFile());
+ complexParams.visualizationDir(params.getProjectDir());
+ for (ZipEntryFile entry : params.getZipEntries()) {
+ complexParams.entry(entry);
+ }
+ ProjectFactory projectFactory = new ProjectFactory(parser);
+ projectFactory.create(complexParams, dbProject);
+ } catch (IOException e) {
+ throw new InvalidInputDataExecption(e);
+ }
+ } else {
+ IConverter parser;
+ if (params.getParser() != null) {
+ parser = params.getParser();
+ } else if (params.getProjectFile().endsWith("sbgn")) {
+ parser = new SbgnmlXmlConverter();
+ } else {
+ parser = new CellDesignerXmlParser();
+ }
+ try {
+ Model model = parser.createModel(new ConverterParams().filename(params.getProjectFile())
+ .sizeAutoAdjust(params.isAutoResize()).sbgnFormat(params.isSbgnFormat()));
+ model.setName(params.getProjectName());
+ project.addModel(model);
+ } catch (FileNotFoundException ex) {
+ throw new InvalidInputDataExecption(ex);
+ }
+ }
+ Model topModel = project.getModels().iterator().next().getModel();
+ topModel.setZoomLevels(generator.computeZoomLevels(topModel));
+ topModel.setTileSize(MapGenerator.TILE_SIZE);
+ dbProject.setNotifyEmail(params.getNotifyEmail());
+
+ updateProjectStatus(project, ProjectStatus.UPLOADING_TO_DB, 0.0, params);
+ dbUtils.setAutoFlush(false);
+ projectDao.update(project);
+ dbUtils.setAutoFlush(true);
+ projectDao.flush();
+
+ List<BuildInLayout> buildInLayouts = new ArrayList<>();
+ BuildInLayout nested = null;
+ if (params.isSemanticZoom()) {
+ nested = BuildInLayout.SEMANTIC;
+ } else {
+ nested = BuildInLayout.NESTED;
+ }
+ if (params.isNetworkLayoutAsDefault()) {
+ buildInLayouts.add(BuildInLayout.NORMAL);
+ buildInLayouts.add(nested);
+ } else {
+ buildInLayouts.add(nested);
+ buildInLayouts.add(BuildInLayout.NORMAL);
+ }
+ buildInLayouts.add(BuildInLayout.CLEAN);
+
+ // reverse the order of build in layouts, so we can insert them at the
+ // beginning of list of layouts (the order will be the same)
+ Collections.reverse(buildInLayouts);
+
+ for (BuildInLayout buildInLayout : buildInLayouts) {
+ Layout topLayout = new Layout(buildInLayout.getTitle(),
+ params.getProjectDir() + "/" + buildInLayout.getDirectorySuffix() + topModel.getId() + "/", true);
+ topLayout.setStatus(LayoutStatus.NA);
+ topLayout.setProgress(0.0);
+ topLayout.setHierarchicalView(buildInLayout.isNested());
+ topModel.addLayout(0, topLayout);
+ int submodelId = 1;
+ List<Layout> semanticLevelOverlays = new ArrayList<>();
+ if (buildInLayout.equals(BuildInLayout.SEMANTIC) && params.isSemanticZoomContainsMultipleLayouts()) {
+ for (int i = 0; i <= topModel.getZoomLevels(); i++) {
+ String directory = params.getProjectDir() + "/" + buildInLayout.getDirectorySuffix() + "-" + i + "-"
+ + topModel.getId() + "/";
+ Layout semanticOverlay = new Layout(buildInLayout.getTitle() + "-" + i, directory, true);
+ semanticOverlay.setStatus(LayoutStatus.NA);
+ semanticOverlay.setProgress(0.0);
+ semanticOverlay.setHierarchicalView(buildInLayout.isNested());
+ semanticOverlay.setHierarchyViewLevel(i);
+ semanticLevelOverlays.add(semanticOverlay);
+ topModel.addLayout(1, semanticOverlay);
+ }
+ }
+ for (ModelSubmodelConnection connection : topModel.getSubmodelConnections()) {
+ Layout layout = new Layout(buildInLayout.getTitle(),
+ params.getProjectDir() + "/" + buildInLayout.getDirectorySuffix() + submodelId + "/", true);
+ layout.setStatus(LayoutStatus.NA);
+ layout.setProgress(0.0);
+ layout.setHierarchicalView(buildInLayout.isNested());
+ layout.setParentLayout(topLayout);
+ connection.getSubmodel().addLayout(0, layout);
+
+ connection.getSubmodel().setZoomLevels(generator.computeZoomLevels(connection.getSubmodel().getModel()));
+ connection.getSubmodel().setTileSize(MapGenerator.TILE_SIZE);
+ if (buildInLayout.equals(BuildInLayout.SEMANTIC) && params.isSemanticZoomContainsMultipleLayouts()) {
+ for (int i = 0; i <= topModel.getZoomLevels(); i++) {
+ String directory = params.getProjectDir() + "/" + buildInLayout.getDirectorySuffix() + "-" + i + "-"
+ + submodelId + "/";
+ Layout semanticOverlay = new Layout(buildInLayout.getTitle() + "-" + i, directory, true);
+ semanticOverlay.setStatus(LayoutStatus.NA);
+ semanticOverlay.setProgress(0.0);
+ semanticOverlay.setHierarchicalView(buildInLayout.isNested());
+ semanticOverlay.setParentLayout(semanticLevelOverlays.get(i));
+ semanticOverlay.setHierarchyViewLevel(i);
+ connection.getSubmodel().addLayout(1, semanticOverlay);
+ }
+ }
+ submodelId++;
+ }
+ }
+
+ if (params.isUpdateAnnotations()) {
+ Map<Class<?>, List<ElementAnnotator>> annotators = null;
+ if (params.getAnnotatorsMap() != null) {
+ annotators = new HashMap<Class<?>, List<ElementAnnotator>>();
+ for (Class<?> clazz : params.getAnnotatorsMap().keySet()) {
+ annotators.put(clazz, modelAnnotator.getAnnotatorsFromCommonNames(params.getAnnotatorsMap().get(clazz)));
+ }
+ }
+ logger.debug("Updating annotations");
+ modelAnnotator.performAnnotations(topModel, new IProgressUpdater() {
+
+ @Override
+ public void setProgress(final double progress) {
+ updateProjectStatus(project, ProjectStatus.ANNOTATING, progress, params);
+ }
+ }, annotators, params.getAnnotatorsParamsAsMap());
+ logger.debug("Annotations updated");
+ }
+ logger.debug("Model created");
+
+ }
+
+ /**
+ * Updates status of the generating project.
+ *
+ * @param project
+ * project that is generated
+ * @param status
+ * what is the current status
+ * @param progress
+ * what is the progress
+ * @param params
+ * parameters used for project creation
+ */
+ private void updateProjectStatus(Project project, ProjectStatus status, double progress, CreateProjectParams params) {
+ if (project != null) {
+ if (!status.equals(project.getStatus())
+ || (Math.abs(progress - project.getProgress()) > IProgressUpdater.PROGRESS_BAR_UPDATE_RESOLUTION)) {
+ project.setStatus(status);
+ project.setProgress(progress);
+ projectDao.update(project);
+ if (params.isAsync()) {
+ projectDao.commit();
+ }
+ }
+ } else {
+ logger.debug("status: " + status + ", " + progress);
+ }
+ }
+
+ @Override
+ public void createProject(final CreateProjectParams params) throws SecurityException {
+ if (!userService.userHasPrivilege(params.getAuthenticationToken(), PrivilegeType.ADD_MAP)) {
+ throw new SecurityException("Adding projects not allowed.");
+ }
+
+ // this count down is used to wait for asynchronous thread to initialize
+ // data in the db (probably it would be better to move the initialization to
+ // main thread)
+ final CountDownLatch waitForInitialData = new CountDownLatch(1);
+
+ Thread computations = new Thread(new Runnable() {
+
+ @Override
+ public void run() {
+ if (params.isAsync()) {
+ // because we are running this in separate thread we need to open a
+ // new session for db connection
+ dbUtils.createSessionForCurrentThread();
+ }
+
+ Project project = new Project();
+ project.setProjectId(params.getProjectId());
+ project.setName(params.getProjectName());
+ if (params.getProjectDir() == null) {
+ logger.warn("Project directory not set");
+ project.setDirectory(null);
+ } else {
+ project.setDirectory(new File(params.getProjectDir()).getName());
+ }
+ project.setSbgnFormat(params.isSbgnFormat());
+
+ MiriamData disease = null;
+ if (params.getDisease() != null && !params.getDisease().isEmpty()) {
+ disease = new MiriamData(MiriamType.MESH_2012, params.getDisease());
+ }
+ MiriamData organism = null;
+ if (params.getOrganism() != null && !params.getOrganism().isEmpty()) {
+ organism = new MiriamData(MiriamType.TAXONOMY, params.getOrganism());
+ }
+ project.setMapCanvasType(params.getMapCanvasType());
+ project.setVersion(params.getVersion());
+ projectDao.add(project);
+ if (params.isAsync()) {
+ projectDao.commit();
+ }
+ waitForInitialData.countDown();
+ double[] outOfMemoryBuffer;
+ EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
+ try {
+ Logger.getRootLogger().addAppender(appender);
+ logger.debug("Running: " + params.getProjectId() + "; " + params.getProjectFile());
+ outOfMemoryBuffer = new double[OUT_OF_MEMORY_BACKUP_BUFFER_SIZE];
+ for (int i = 0; i < OUT_OF_MEMORY_BACKUP_BUFFER_SIZE; i++) {
+ outOfMemoryBuffer[i] = Math.random() * OUT_OF_MEMORY_BACKUP_BUFFER_SIZE;
+ }
+
+ File inputFile = new File(params.getProjectFile());
+ if (inputFile.exists()) {
+ UploadedFileEntry file = new UploadedFileEntry();
+ file.setFileContent(IOUtils.toByteArray(new FileInputStream(inputFile)));
+ file.setOriginalFileName(FilenameUtils.getName(params.getProjectFile()));
+ file.setLength(file.getFileContent().length);
+ User owner = null;
+ for (String[] userRow : params.getUsers()) {
+ User user = userService.getUserByLogin(userRow[0]);
+ if (user != null) {
+ owner = user;
+ }
+ }
+ file.setOwner(owner);
+ project.setInputData(file);
+ }
+
+ createModel(params, project);
+ Model originalModel = project.getModels().iterator().next().getModel();
+ if (!params.isSemanticZoom()) {
+ new CreateHierarchyCommand(originalModel, generator.computeZoomLevels(originalModel),
+ generator.computeZoomFactor(originalModel)).execute();
+ for (Model model : originalModel.getSubmodels()) {
+ new CreateHierarchyCommand(model, generator.computeZoomLevels(model), generator.computeZoomFactor(model))
+ .execute();
+ }
+ }
+
+ addUsers(project, params);
+ createImages(originalModel, params);
+
+ for (Layout layout : originalModel.getLayouts()) {
+ String[] tmp = layout.getDirectory().split("[\\\\/]");
+ layout.setDirectory(tmp[tmp.length - 1]);
+ }
+ for (ModelSubmodelConnection connection : originalModel.getSubmodelConnections()) {
+ for (Layout layout : connection.getSubmodel().getLayouts()) {
+ String[] tmp = layout.getDirectory().split("[\\\\/]");
+ layout.setDirectory(tmp[tmp.length - 1]);
+ }
+ }
+
+ try {
+ if (meshParser.isValidMeshId(disease)) {
+ project.setDisease(disease);
+ } else {
+ logger.warn("No valid disease is provided for project:" + project.getName());
+ }
+ } catch (AnnotatorException e1) {
+ logger.warn("Problem with accessing mesh db. More info in logs.");
+ }
+
+ if (taxonomyBackend.getNameForTaxonomy(organism) != null) {
+ project.setOrganism(organism);
+ } else {
+ logger.warn(project.getProjectId() + "\tNo valid organism is provided for project. " + organism);
+ }
+
+ modelDao.update(originalModel);
+
+ if (params.isAnalyzeAnnotations()) {
+ analyzeAnnotations(originalModel, params);
+ }
+ Logger.getRootLogger().removeAppender(appender);
+ project.addLoggingInfo(appender);
+
+ if (params.isCacheModel()) {
+ cacheData(originalModel, params);
+ }
+
+ updateProjectStatus(project, ProjectStatus.DONE, IProgressUpdater.MAX_PROGRESS, params);
+ if (project.getNotifyEmail() != null && !project.getNotifyEmail().equals("")) {
+ try {
+ sendSuccesfullEmail(originalModel);
+ } catch (MessagingException e) {
+ logger.error(e, e);
+ }
+ }
+
+ LogParams params = new LogParams().description("Created successfully").type(LogType.MAP_CREATED)
+ .object(originalModel);
+ logService.log(params);
+
+ } catch (HibernateException e) {
+ outOfMemoryBuffer = null;
+ logger.error("Problem with database", e);
+ handleHibernateExceptionReporting(params, e);
+ } catch (Exception e) {
+ outOfMemoryBuffer = null;
+ handleCreateProjectException(params, e);
+ } catch (OutOfMemoryError oome) {
+ // release some memory
+ outOfMemoryBuffer = null;
+ logger.error("Out of memory", oome);
+ if (project != null) {
+ project.setErrors("Out of memory: " + oome.getMessage());
+ }
+ updateProjectStatus(project, ProjectStatus.FAIL, IProgressUpdater.MAX_PROGRESS, params);
+ } finally {
+ if (params.isAsync()) {
+ // close the transaction for this thread
+ dbUtils.closeSessionForCurrentThread();
+ }
+ Logger.getRootLogger().removeAppender(appender);
+ }
+ }
+ });
+ if (params.isAsync()) {
+ computations.start();
+ } else {
+ computations.run();
+ }
+
+ try {
+ waitForInitialData.await();
+ } catch (InterruptedException e1) {
+ logger.error(e1, e1);
+ }
+
+ }
+
+ /**
+ * Cache pubmed data for the model.
+ *
+ * @param originalModel
+ * model for which we want to cache data.
+ * @param params
+ * parameters used for model generation
+ */
+ private void cacheData(final Model originalModel, final CreateProjectParams params) {
+ modelService.cacheAllPubmedIds(originalModel, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ updateProjectStatus(originalModel.getProject(), ProjectStatus.CACHING, progress, params);
+ }
+ });
+ modelService.cacheAllMiriamLinks(originalModel, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ updateProjectStatus(originalModel.getProject(), ProjectStatus.CACHING_MIRIAM, progress, params);
+ }
+ });
+
+ chemicalService.cacheDataForModel(originalModel, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ updateProjectStatus(originalModel.getProject(), ProjectStatus.CACHING_CHEMICAL, progress, params);
+ }
+ });
+
+ drugService.cacheDataForModel(originalModel, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ updateProjectStatus(originalModel.getProject(), ProjectStatus.CACHING_DRUG, progress, params);
+ }
+ });
+
+ mirnaService.cacheDataForModel(originalModel, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ updateProjectStatus(originalModel.getProject(), ProjectStatus.CACHING_MI_RNA, progress, params);
+ }
+ });
+
+ }
+
+ /**
+ * @return the modelDao
+ * @see #modelDao
+ */
+ public ModelDao getModelDao() {
+ return modelDao;
+ }
+
+ /**
+ * @param modelDao
+ * the modelDao to set
+ * @see #modelDao
+ */
+ public void setModelDao(ModelDao modelDao) {
+ this.modelDao = modelDao;
+ }
+
+ /**
+ * @return the commentService
+ * @see #commentService
+ */
+ public ICommentService getCommentService() {
+ return commentService;
+ }
+
+ /**
+ * @param commentService
+ * the commentService to set
+ * @see #commentService
+ */
+ public void setCommentService(ICommentService commentService) {
+ this.commentService = commentService;
+ }
+
+ /**
+ * @return the passwordEncoder
+ * @see #passwordEncoder
+ */
+ public PasswordEncoder getPasswordEncoder() {
+ return passwordEncoder;
+ }
+
+ /**
+ * @param passwordEncoder
+ * the passwordEncoder to set
+ * @see #passwordEncoder
+ */
+ public void setPasswordEncoder(PasswordEncoder passwordEncoder) {
+ this.passwordEncoder = passwordEncoder;
+ }
+
+ /**
+ * @return the commentDao
+ * @see #commentDao
+ */
+ public CommentDao getCommentDao() {
+ return commentDao;
+ }
+
+ /**
+ * @param commentDao
+ * the commentDao to set
+ * @see #commentDao
+ */
+ public void setCommentDao(CommentDao commentDao) {
+ this.commentDao = commentDao;
+ }
+
+ /**
+ * @return the modelAnnotator
+ * @see #modelAnnotator
+ */
+ public ModelAnnotator getModelAnnotator() {
+ return modelAnnotator;
+ }
+
+ /**
+ * @param modelAnnotator
+ * the modelAnnotator to set
+ * @see #modelAnnotator
+ */
+ public void setModelAnnotator(ModelAnnotator modelAnnotator) {
+ this.modelAnnotator = modelAnnotator;
+ }
+
+ /**
+ * @return the dbUtils
+ * @see #dbUtils
+ */
+ public DbUtils getDbUtils() {
+ return dbUtils;
+ }
+
+ /**
+ * @param dbUtils
+ * the dbUtils to set
+ * @see #dbUtils
+ */
+ public void setDbUtils(DbUtils dbUtils) {
+ this.dbUtils = dbUtils;
+ }
+
+ /**
+ * @return the projectDao
+ * @see #projectDao
+ */
+ public ProjectDao getProjectDao() {
+ return projectDao;
+ }
+
+ /**
+ * @param projectDao
+ * the projectDao to set
+ * @see #projectDao
+ */
+ public void setProjectDao(ProjectDao projectDao) {
+ this.projectDao = projectDao;
+ }
+
+ /**
+ * Analyzes annotation of the model and put information about invalid
+ * annotations into the {@link Model#creationWarnings} field.
+ *
+ * @param originalModel
+ * model to analyze
+ * @param params
+ * parameters used for model generation
+ */
+ protected void analyzeAnnotations(final Model originalModel, final CreateProjectParams params) {
+ logger.debug("Analyze annotations");
+ Collection<? extends ProblematicAnnotation> improperAnnotations = modelAnnotator
+ .findImproperAnnotations(originalModel, new IProgressUpdater() {
+
+ @Override
+ public void setProgress(double progress) {
+ updateProjectStatus(originalModel.getProject(), ProjectStatus.VALIDATING_MIRIAM, progress, params);
+ }
+ }, params.getValidAnnotations());
+ List<String> res = new ArrayList<>();
+ for (ProblematicAnnotation improperAnnotation : improperAnnotations) {
+ res.add(improperAnnotation.toString());
+ }
+ Collections.sort(res);
+
+ Collection<? extends ProblematicAnnotation> missingAnnotations = modelAnnotator
+ .findMissingAnnotations(originalModel, params.getRequiredAnnotations());
+ for (ProblematicAnnotation improperAnnotation : missingAnnotations) {
+ res.add(improperAnnotation.toString());
+ }
+ for (String message : res) {
+ logger.warn(message);
+ }
+ logger.debug("Analyze finished");
+ }
+
+ /**
+ * Sends notification email that map was removed.
+ *
+ * @param projectId
+ * identifier of the project
+ * @param email
+ * otification email
+ * @throws MessagingException
+ * thrown when there is a problem with sending email
+ */
+ protected void sendSuccesfullRemoveEmail(String projectId, String email) throws MessagingException {
+ EmailSender emailSender = new EmailSender(configurationService);
+ StringBuilder content = new StringBuilder("Map " + projectId + " was successfully removed.<br/>");
+ emailSender.sendEmail("MapViewer notification", content.toString(), email);
+ }
+
+ @Override
+ public TreeNode createClassAnnotatorTree(User user) {
+
+ UserAnnotationSchema annotationSchema = prepareUserAnnotationSchema(user);
+
+ ElementUtils elementUtils = new ElementUtils();
+
+ ClassTreeNode top = elementUtils.getAnnotatedElementClassTree();
+
+ Class<?> clazz = top.getClazz();
+ top.setData(annotationSchema.requiresAtLeastOneAnnotation(clazz));
+ TreeNode root = new DefaultTreeNode(new AnnotatedObjectTreeRow(top, modelAnnotator.getAvailableAnnotators(clazz),
+ modelAnnotator.getAnnotatorsFromCommonNames(annotationSchema.getAnnotatorsForClass(clazz)),
+ annotationSchema.getValidAnnotations(clazz), annotationSchema.getRequiredAnnotations(clazz)), null);
+
+ root.setExpanded(true);
+
+ Queue<Pair<ClassTreeNode, TreeNode>> nodes = new LinkedList<Pair<ClassTreeNode, TreeNode>>();
+ nodes.add(new Pair<ClassTreeNode, TreeNode>(top, root));
+ // create children
+
+ Queue<TreeNode> expandParents = new LinkedList<TreeNode>();
+
+ while (!nodes.isEmpty()) {
+ Pair<ClassTreeNode, TreeNode> element = nodes.poll();
+
+ for (ClassTreeNode node : element.getLeft().getChildren()) {
+
+ clazz = node.getClazz();
+ node.setData(annotationSchema.requiresAtLeastOneAnnotation(clazz));
+ AnnotatedObjectTreeRow data = new AnnotatedObjectTreeRow(node, modelAnnotator.getAvailableAnnotators(clazz),
+ modelAnnotator.getAnnotatorsFromCommonNames(annotationSchema.getAnnotatorsForClass(clazz)),
+ annotationSchema.getValidAnnotations(clazz), annotationSchema.getRequiredAnnotations(clazz));
+ TreeNode treeNode = new DefaultTreeNode(data, element.getRight());
+ nodes.add(new Pair<ClassTreeNode, TreeNode>(node, treeNode));
+ if (data.getUsedAnnotators().size() > 0 || data.getValidAnnotators().size() > 0) {
+ expandParents.add(treeNode);
+ }
+ }
+ }
+ while (!expandParents.isEmpty()) {
+ TreeNode node = expandParents.poll();
+ if (node.getParent() != null && !node.getParent().isExpanded()) {
+ node.getParent().setExpanded(true);
+ expandParents.add(node.getParent());
+ }
+ }
+
+ return root;
+
+ }
+
+ /**
+ * Retrieves (or creates) annotation schema for a given user.
+ *
+ * @param user
+ * for this users {@link UserAnnotationSchema} will be prepared
+ * @return {@link UserAnnotationSchema} for {@link User}
+ */
+ public UserAnnotationSchema prepareUserAnnotationSchema(User user) {
+ UserAnnotationSchema annotationSchema = null;
+ if (user != null) {
+ annotationSchema = userDao.getById(user.getId()).getAnnotationSchema();
+ }
+ if (annotationSchema == null) {
+ annotationSchema = new UserAnnotationSchema();
+
+ ElementUtils elementUtils = new ElementUtils();
+
+ ClassTreeNode top = elementUtils.getAnnotatedElementClassTree();
+
+ Map<Class<? extends BioEntity>, Set<MiriamType>> validMiriam = modelAnnotator.getDefaultValidClasses();
+ Map<Class<? extends BioEntity>, Set<MiriamType>> requiredMiriam = modelAnnotator.getDefaultRequiredClasses();
+
+ Queue<ClassTreeNode> nodes = new LinkedList<ClassTreeNode>();
+ nodes.add(top);
+
+ while (!nodes.isEmpty()) {
+ ClassTreeNode element = nodes.poll();
+ annotationSchema.addClassAnnotator(new UserClassAnnotators(element.getClazz(),
+ modelAnnotator.getAvailableDefaultAnnotatorNames(element.getClazz())));
+ annotationSchema.addClassValidAnnotations(
+ new UserClassValidAnnotations(element.getClazz(), validMiriam.get(element.getClazz())));
+ annotationSchema.addClassRequiredAnnotations(
+ new UserClassRequiredAnnotations(element.getClazz(), requiredMiriam.get(element.getClazz())));
+ for (ClassTreeNode node : element.getChildren()) {
+ nodes.add(node);
+ }
+ }
+ if (user != null) {
+ User dbUser = userDao.getById(user.getId());
+ dbUser.setAnnotationSchema(annotationSchema);
+ userDao.update(dbUser);
+ }
+ }
+ return annotationSchema;
+ }
+
+ @Override
+ public void updateClassAnnotatorTreeForUser(User user, TreeNode annotatorsTree, boolean sbgnFormat,
+ boolean networkLayoutAsDefault) {
+ User dbUser = userDao.getById(user.getId());
+ if (dbUser.getAnnotationSchema() == null) {
+ dbUser.setAnnotationSchema(new UserAnnotationSchema());
+ }
+ UserAnnotationSchema annotationSchema = dbUser.getAnnotationSchema();
+
+ Queue<TreeNode> queue = new LinkedList<TreeNode>();
+ queue.add(annotatorsTree);
+ while (!queue.isEmpty()) {
+ TreeNode node = queue.poll();
+ for (TreeNode child : node.getChildren()) {
+ queue.add(child);
+ }
+ AnnotatedObjectTreeRow data = (AnnotatedObjectTreeRow) node.getData();
+ annotationSchema.addClassAnnotator(new UserClassAnnotators(data.getClazz(), data.getUsedAnnotators()));
+ annotationSchema.addClassRequiredAnnotations(
+ new UserClassRequiredAnnotations(data.getClazz(), data.getRequiredAnnotations()));
+ annotationSchema
+ .addClassValidAnnotations(new UserClassValidAnnotations(data.getClazz(), data.getValidAnnotations()));
+ }
+ annotationSchema.setSbgnFormat(sbgnFormat);
+ annotationSchema.setNetworkLayoutAsDefault(networkLayoutAsDefault);
+ userService.updateUser(dbUser);
+ user.setAnnotationSchema(annotationSchema);
+ }
+
+ @Override
+ public List<UserAnnotatorsParam> getAnnotatorsParams(User user) {
+ User dbUser = userDao.getById(user.getId());
+ UserAnnotationSchema annotationSchema = dbUser.getAnnotationSchema();
+ if (annotationSchema == null) {
+ annotationSchema = new UserAnnotationSchema();
+ dbUser.setAnnotationSchema(annotationSchema);
+ }
+
+ /*
+ * Hibernate lazy loads collections so each element needs to be accessed to be
+ * loaded now or otherwise the data might not be available when accessed because
+ * the session might not be available at that time.
+ */
+ List<UserAnnotatorsParam> aps = new ArrayList<>();
+ for (UserAnnotatorsParam ap : annotationSchema.getAnnotatorsParams()) {
+ aps.add(ap);
+ }
+ return aps;
+ }
+
+ /**
+ * Sends email about unsuccessful project creation.
+ *
+ * @param projectName
+ * name of the project
+ * @param email
+ * email where we want to send information
+ * @param e
+ * exception that caused problem
+ */
+ private void sendUnsuccesfullEmail(String projectName, String email, Exception e) {
+ EmailSender emailSender = new EmailSender(configurationService);
+ StringBuilder content = new StringBuilder("");
+ content.append("There was a problem with generating " + projectName + " map.<br/>");
+ content.append(e.getClass().getName() + ": " + e.getMessage());
+ try {
+ emailSender.sendEmail("MapViewer notification", content.toString(), email);
+ } catch (MessagingException e1) {
+ logger.error(e1);
+ }
+ }
+
+ /**
+ * Sends email about successful project creation.
+ *
+ * @param originalModel
+ * model that was created
+ * @throws MessagingException
+ * exception thrown when there is a problem with sending email
+ */
+ protected void sendSuccesfullEmail(Model originalModel) throws MessagingException {
+ EmailSender emailSender = new EmailSender(configurationService);
+ StringBuilder content = new StringBuilder("Your map was generated successfully.<br/>");
+ emailSender.sendEmail("MapViewer notification", content.toString(), originalModel.getProject().getNotifyEmail());
+ }
+
+ @Override
+ public void updateProject(Project project, String token) throws SecurityException {
+ projectDao.update(project);
+ if (token != null) {
+ Model model = modelService.getLastModelByProjectId(project.getProjectId(), token);
+ if (model != null) {
+ model.setProject(project);
+ }
+ }
+ }
+
+ /**
+ * This method handles situation when sever db error appeared during uploading
+ * of the project into database.
+ *
+ * @param params
+ * parameters used to create project
+ * @param e
+ * exception that occurred during uploading of the project
+ */
+ private void handleHibernateExceptionReporting(CreateProjectParams params, HibernateException e) {
+ // we need to open separate thread because current one thrown db exception
+ // and transaction is corrupted and will be rolledback
+ Thread reportInSeparateThread = new Thread(new Runnable() {
+
+ @Override
+ public void run() {
+ dbUtils.createSessionForCurrentThread();
+
+ try {
+ Project project = getProjectByProjectId(params.getProjectId(), params.getAuthenticationToken());
+ String errorMessage = "Problem with uploading to database. "
+ + "You might violated some unhandled constraints or you run out of memory. Underlaying eror:\n"
+ + e.getMessage() + "\nMore information can be found in log file.";
+ project.setErrors(errorMessage);
+ project.setStatus(ProjectStatus.FAIL);
+ projectDao.update(project);
+ } catch (Exception e) {
+ logger.error(e, e);
+ } finally {
+ dbUtils.closeSessionForCurrentThread();
+ }
+ }
+
+ });
+ reportInSeparateThread.start();
+
+ }
+
+ /**
+ * Method that handles exception reporting during creation of a project.
+ *
+ * @param params
+ * set of parameters used to create project
+ * @param e
+ * exception that caused problems
+ */
+ private void handleCreateProjectException(final CreateProjectParams params, Exception e) {
+ Project p = projectDao.getProjectByProjectId(params.getProjectId());
+ logger.error(e.getMessage(), e);
+ if (p != null) {
+ p.setErrors("Problem with uploading map: " + e.getMessage() + ". More details can be found in log file.");
+ }
+ updateProjectStatus(p, ProjectStatus.FAIL, IProgressUpdater.MAX_PROGRESS, params);
+
+ String email = params.getNotifyEmail();
+ String projectName = params.getProjectId();
+
+ LogParams logParams = new LogParams().description("Failed: " + e.getMessage()).type(LogType.MAP_CREATED).object(p);
+ logService.log(logParams);
+ if (email != null) {
+ sendUnsuccesfullEmail(projectName, email, e);
+ }
+ }
+
+ /**
+ * @return the taxonomyBackend
+ * @see #taxonomyBackend
+ */
+ public TaxonomyBackend getTaxonomyBackend() {
+ return taxonomyBackend;
+ }
+
+ /**
+ * @param taxonomyBackend
+ * the taxonomyBackend to set
+ * @see #taxonomyBackend
+ */
+ public void setTaxonomyBackend(TaxonomyBackend taxonomyBackend) {
+ this.taxonomyBackend = taxonomyBackend;
+ }
+
+ @Override
+ public List<Project> getAllProjects() {
+ return projectDao.getAll();
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ReferenceGenomeService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ReferenceGenomeService.java
index b7c1d54c7c..bccf0714c9 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ReferenceGenomeService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ReferenceGenomeService.java
@@ -1,151 +1,151 @@
-package lcsb.mapviewer.services.impl;
-
-import java.io.IOException;
-import java.net.URISyntaxException;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.annotation.services.genome.FileNotAvailableException;
-import lcsb.mapviewer.annotation.services.genome.ReferenceGenomeConnector;
-import lcsb.mapviewer.annotation.services.genome.ReferenceGenomeConnectorException;
-import lcsb.mapviewer.annotation.services.genome.UcscReferenceGenomeConnector;
-import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.layout.ReferenceGenome;
-import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
-import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
-import lcsb.mapviewer.persist.dao.map.layout.ReferenceGenomeDao;
-import lcsb.mapviewer.services.interfaces.IReferenceGenomeService;
-import lcsb.mapviewer.services.utils.ReferenceGenomeExistsException;
-
-/**
- * Service managing reference genomes.
- *
- * @author Piotr Gawron
- *
- */
-@Transactional(value = "txManager")
-public class ReferenceGenomeService implements IReferenceGenomeService {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(ReferenceGenomeService.class);
-
- /**
- * Class responsible for connection to {@link ReferenceGenomeType#UCSC}
- * database.
- */
- @Autowired
- private UcscReferenceGenomeConnector ucscReferenceGenomeConnector;
-
- /**
- * Data access object for {@link ReferenceGenome} objects.
- */
- @Autowired
- private ReferenceGenomeDao referenceGenomeDao;
-
- @Override
- public void addReferenceGenome(ReferenceGenomeType type, MiriamData organism, String version, String customUrl)
- throws IOException, URISyntaxException, ReferenceGenomeConnectorException {
- for (ReferenceGenome genome : getDownloadedGenomes()) {
- if (genome.getType().equals(type) && genome.getOrganism().equals(organism)
- && genome.getVersion().equals(version)) {
- throw new ReferenceGenomeExistsException("Selected reference genome already downloaded");
- }
- }
- getReferenceGenomeConnector(type).downloadGenomeVersion(organism, version, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, true, customUrl);
- }
-
- /**
- * Return {@link ReferenceGenomeConnector} implementation for given reference
- * genome type.
- *
- * @param type
- * type of reference genome
- * @return {@link ReferenceGenomeConnector} implementation for given reference
- * genome type
- */
- private ReferenceGenomeConnector getReferenceGenomeConnector(ReferenceGenomeType type) {
- if (type == ReferenceGenomeType.UCSC) {
- return ucscReferenceGenomeConnector;
- } else {
- throw new InvalidArgumentException("Unknown reference genome type: " + type);
- }
- }
-
- @Override
- public List<MiriamData> getOrganismsByReferenceGenomeType(ReferenceGenomeType type)
- throws ReferenceGenomeConnectorException {
- return getReferenceGenomeConnector(type).getAvailableOrganisms();
- }
-
- @Override
- public List<String> getAvailableGenomeVersions(ReferenceGenomeType type, MiriamData organism)
- throws ReferenceGenomeConnectorException {
- return getReferenceGenomeConnector(type).getAvailableGenomeVersion(organism);
- }
-
- @Override
- public String getUrlForGenomeVersion(ReferenceGenomeType type, MiriamData organism, String version) {
- try {
- return getReferenceGenomeConnector(type).getGenomeVersionFile(organism, version);
- } catch (FileNotAvailableException e) {
- return null;
- }
- }
-
- @Override
- public List<ReferenceGenome> getDownloadedGenomes() {
- return referenceGenomeDao.getAll();
- }
-
- @Override
- public void removeGenome(ReferenceGenome genome) throws IOException {
- getReferenceGenomeConnector(genome.getType()).removeGenomeVersion(genome.getOrganism(), genome.getVersion());
- }
-
- @Override
- public void addReferenceGenomeGeneMapping(ReferenceGenome referenceGenome, String name, String url)
- throws IOException, URISyntaxException, ReferenceGenomeConnectorException {
- getReferenceGenomeConnector(referenceGenome.getType()).downloadGeneMappingGenomeVersion(referenceGenome, name,
- new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, true, url);
-
- }
-
- @Override
- public void removeReferenceGenomeGeneMapping(ReferenceGenomeGeneMapping genome) throws IOException {
- getReferenceGenomeConnector(genome.getReferenceGenome().getType()).removeGeneMapping(genome);
- }
-
- @Override
- public ReferenceGenome getReferenceGenomeViewByParams(MiriamData miriamData, ReferenceGenomeType genomeType,
- String version, String authenticationToken) {
- List<ReferenceGenome> list = referenceGenomeDao.getByType(genomeType);
- for (ReferenceGenome referenceGenome : list) {
- if (referenceGenome.getOrganism().equals(miriamData) && referenceGenome.getVersion().equals(version)) {
- return referenceGenome;
- }
- }
- return null;
- }
-
- @Override
- public ReferenceGenome getReferenceGenomeById(int id, String authenticationToken) {
- return referenceGenomeDao.getById(id);
- }
-
-}
+package lcsb.mapviewer.services.impl;
+
+import java.io.IOException;
+import java.net.URISyntaxException;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.annotation.services.genome.FileNotAvailableException;
+import lcsb.mapviewer.annotation.services.genome.ReferenceGenomeConnector;
+import lcsb.mapviewer.annotation.services.genome.ReferenceGenomeConnectorException;
+import lcsb.mapviewer.annotation.services.genome.UcscReferenceGenomeConnector;
+import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.layout.ReferenceGenome;
+import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
+import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
+import lcsb.mapviewer.persist.dao.map.layout.ReferenceGenomeDao;
+import lcsb.mapviewer.services.interfaces.IReferenceGenomeService;
+import lcsb.mapviewer.services.utils.ReferenceGenomeExistsException;
+
+/**
+ * Service managing reference genomes.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Transactional(value = "txManager")
+public class ReferenceGenomeService implements IReferenceGenomeService {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(ReferenceGenomeService.class);
+
+ /**
+ * Class responsible for connection to {@link ReferenceGenomeType#UCSC}
+ * database.
+ */
+ @Autowired
+ private UcscReferenceGenomeConnector ucscReferenceGenomeConnector;
+
+ /**
+ * Data access object for {@link ReferenceGenome} objects.
+ */
+ @Autowired
+ private ReferenceGenomeDao referenceGenomeDao;
+
+ @Override
+ public void addReferenceGenome(ReferenceGenomeType type, MiriamData organism, String version, String customUrl)
+ throws IOException, URISyntaxException, ReferenceGenomeConnectorException {
+ for (ReferenceGenome genome : getDownloadedGenomes()) {
+ if (genome.getType().equals(type) && genome.getOrganism().equals(organism)
+ && genome.getVersion().equals(version)) {
+ throw new ReferenceGenomeExistsException("Selected reference genome already downloaded");
+ }
+ }
+ getReferenceGenomeConnector(type).downloadGenomeVersion(organism, version, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, true, customUrl);
+ }
+
+ /**
+ * Return {@link ReferenceGenomeConnector} implementation for given reference
+ * genome type.
+ *
+ * @param type
+ * type of reference genome
+ * @return {@link ReferenceGenomeConnector} implementation for given reference
+ * genome type
+ */
+ private ReferenceGenomeConnector getReferenceGenomeConnector(ReferenceGenomeType type) {
+ if (type == ReferenceGenomeType.UCSC) {
+ return ucscReferenceGenomeConnector;
+ } else {
+ throw new InvalidArgumentException("Unknown reference genome type: " + type);
+ }
+ }
+
+ @Override
+ public List<MiriamData> getOrganismsByReferenceGenomeType(ReferenceGenomeType type)
+ throws ReferenceGenomeConnectorException {
+ return getReferenceGenomeConnector(type).getAvailableOrganisms();
+ }
+
+ @Override
+ public List<String> getAvailableGenomeVersions(ReferenceGenomeType type, MiriamData organism)
+ throws ReferenceGenomeConnectorException {
+ return getReferenceGenomeConnector(type).getAvailableGenomeVersion(organism);
+ }
+
+ @Override
+ public String getUrlForGenomeVersion(ReferenceGenomeType type, MiriamData organism, String version) {
+ try {
+ return getReferenceGenomeConnector(type).getGenomeVersionFile(organism, version);
+ } catch (FileNotAvailableException e) {
+ return null;
+ }
+ }
+
+ @Override
+ public List<ReferenceGenome> getDownloadedGenomes() {
+ return referenceGenomeDao.getAll();
+ }
+
+ @Override
+ public void removeGenome(ReferenceGenome genome) throws IOException {
+ getReferenceGenomeConnector(genome.getType()).removeGenomeVersion(genome.getOrganism(), genome.getVersion());
+ }
+
+ @Override
+ public void addReferenceGenomeGeneMapping(ReferenceGenome referenceGenome, String name, String url)
+ throws IOException, URISyntaxException, ReferenceGenomeConnectorException {
+ getReferenceGenomeConnector(referenceGenome.getType()).downloadGeneMappingGenomeVersion(referenceGenome, name,
+ new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, true, url);
+
+ }
+
+ @Override
+ public void removeReferenceGenomeGeneMapping(ReferenceGenomeGeneMapping genome) throws IOException {
+ getReferenceGenomeConnector(genome.getReferenceGenome().getType()).removeGeneMapping(genome);
+ }
+
+ @Override
+ public ReferenceGenome getReferenceGenomeViewByParams(MiriamData miriamData, ReferenceGenomeType genomeType,
+ String version, String authenticationToken) {
+ List<ReferenceGenome> list = referenceGenomeDao.getByType(genomeType);
+ for (ReferenceGenome referenceGenome : list) {
+ if (referenceGenome.getOrganism().equals(miriamData) && referenceGenome.getVersion().equals(version)) {
+ return referenceGenome;
+ }
+ }
+ return null;
+ }
+
+ @Override
+ public ReferenceGenome getReferenceGenomeById(int id, String authenticationToken) {
+ return referenceGenomeDao.getById(id);
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/SearchHistoryService.java b/service/src/main/java/lcsb/mapviewer/services/impl/SearchHistoryService.java
index 7af75743e1..abce9c4ccb 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/SearchHistoryService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/SearchHistoryService.java
@@ -1,51 +1,51 @@
-package lcsb.mapviewer.services.impl;
-
-import lcsb.mapviewer.model.map.statistics.SearchHistory;
-import lcsb.mapviewer.model.map.statistics.SearchType;
-import lcsb.mapviewer.persist.dao.map.statistics.SearchHistoryDao;
-import lcsb.mapviewer.services.interfaces.ISearchHistoryService;
-
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.annotation.Transactional;
-
-/**
- * Implementation of the service that manages search history.
- *
- * @author Piotr Gawron
- *
- */
-@Transactional(value = "txManager")
-public class SearchHistoryService implements ISearchHistoryService {
-
- /**
- * Data access object for search history entries.
- */
- @Autowired
- private SearchHistoryDao searchHistoryDao;
-
- @Override
- public void addQuery(String query, SearchType type, String ipAddress, String map) {
- SearchHistory searchHistory = new SearchHistory();
- searchHistory.setIpAddress(ipAddress);
- searchHistory.setQuery(query);
- searchHistory.setType(type);
- searchHistory.setMap(map);
- searchHistoryDao.add(searchHistory);
- }
-
- /**
- * @return the searchHistoryDao
- */
- public SearchHistoryDao getSearchHistoryDao() {
- return searchHistoryDao;
- }
-
- /**
- * @param searchHistoryDao
- * the searchHistoryDao to set
- */
- public void setSearchHistoryDao(SearchHistoryDao searchHistoryDao) {
- this.searchHistoryDao = searchHistoryDao;
- }
-
-}
+package lcsb.mapviewer.services.impl;
+
+import lcsb.mapviewer.model.map.statistics.SearchHistory;
+import lcsb.mapviewer.model.map.statistics.SearchType;
+import lcsb.mapviewer.persist.dao.map.statistics.SearchHistoryDao;
+import lcsb.mapviewer.services.interfaces.ISearchHistoryService;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+/**
+ * Implementation of the service that manages search history.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Transactional(value = "txManager")
+public class SearchHistoryService implements ISearchHistoryService {
+
+ /**
+ * Data access object for search history entries.
+ */
+ @Autowired
+ private SearchHistoryDao searchHistoryDao;
+
+ @Override
+ public void addQuery(String query, SearchType type, String ipAddress, String map) {
+ SearchHistory searchHistory = new SearchHistory();
+ searchHistory.setIpAddress(ipAddress);
+ searchHistory.setQuery(query);
+ searchHistory.setType(type);
+ searchHistory.setMap(map);
+ searchHistoryDao.add(searchHistory);
+ }
+
+ /**
+ * @return the searchHistoryDao
+ */
+ public SearchHistoryDao getSearchHistoryDao() {
+ return searchHistoryDao;
+ }
+
+ /**
+ * @param searchHistoryDao
+ * the searchHistoryDao to set
+ */
+ public void setSearchHistoryDao(SearchHistoryDao searchHistoryDao) {
+ this.searchHistoryDao = searchHistoryDao;
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java b/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
index 523faab4c6..dd7607fd2c 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
@@ -1,841 +1,841 @@
-package lcsb.mapviewer.services.impl;
-
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.commands.SemanticZoomLevelMatcher;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidClassException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.SearchIndex;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.ReactionNode;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Degraded;
-import lcsb.mapviewer.model.map.species.Drug;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.Ion;
-import lcsb.mapviewer.model.map.species.Phenotype;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.Unknown;
-import lcsb.mapviewer.model.map.statistics.SearchType;
-import lcsb.mapviewer.persist.dao.map.ModelDao;
-import lcsb.mapviewer.services.interfaces.ISearchHistoryService;
-import lcsb.mapviewer.services.interfaces.ISearchService;
-import lcsb.mapviewer.services.utils.SearchIndexer;
-
-/**
- * This is implementation of the service that returns information about species,
- * paths etc in the model.
- *
- *
- * @author Piotr Gawron
- *
- */
-@Transactional(value = "txManager")
-public class SearchService implements ISearchService {
-
- private SemanticZoomLevelMatcher zoomLevelMatcher = new SemanticZoomLevelMatcher();
-
- /**
- * Prefix used in search by name interface to limit results only to species.
- */
- public static final String SPECIES_SEARCH_PREFIX = "species";
-
- /**
- * Prefix used in search by name interface to limit results only to reactions.
- */
- public static final String REACTION_SEARCH_PREFIX = "reaction";
-
- /**
- * Prefix used in search by name interface to limit results only to
- * {@link Element}.
- */
- private static final String ELEMENT_SEARCH_PREFIX = "element";
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(SearchService.class.getName());
-
- /**
- * Data access object for models.
- */
- @Autowired
- private ModelDao modelDao;
-
- /**
- * Service used for managing search history.
- */
- @Autowired
- private ISearchHistoryService searchHistoryService;
-
- /**
- * Object used for indexing elements on the map.
- */
- private SearchIndexer searchIndexer = new SearchIndexer();
-
- /**
- * This object maps class of elements on the map into short string prefixes used
- * in the search query. For instance elements of the {@link Complex} class could
- * be searched with the prefix "complex" (example query: "complex:alpha
- * subcomplex").
- */
- private Map<Class<? extends Element>, String> speciesSearchPrefix = new HashMap<>();
-
- /**
- * This object maps short string prefixes into class of elements on the map that
- * will be searched. For instance prefix "complex" might refer to
- * {@link Complex} class and and example query would look like: "complex:alpha
- * subcomplex".
- */
- private Map<String, Class<? extends Element>> speciesSearchReversePrefix = new HashMap<>();
-
- /**
- * Default constructor that set list of prefixes used in the search queries.
- */
- public SearchService() {
- addSearchPrefix("complex", Complex.class);
- addSearchPrefix("degrded", Degraded.class);
- addSearchPrefix("drug", Drug.class);
- addSearchPrefix("gene", Gene.class);
- addSearchPrefix("ion", Ion.class);
- addSearchPrefix("phenotype", Phenotype.class);
- addSearchPrefix("protein", Protein.class);
- addSearchPrefix("rna", Rna.class);
- addSearchPrefix("molecule", SimpleMolecule.class);
- addSearchPrefix("unknown", Unknown.class);
- }
-
- /**
- * Adds search prefix for an element class.
- *
- * @param prefix
- * string prefix used in search queries
- * @param clazz
- * class for which this prefix stands
- */
- private void addSearchPrefix(String prefix, Class<? extends Element> clazz) {
- speciesSearchPrefix.put(clazz, prefix);
- speciesSearchReversePrefix.put(prefix, clazz);
- }
-
- /**
- * Private class that defines internal search result element. Contains reference
- * to original result and match score of the result.
- *
- * @author Piotr Gawron
- *
- */
- private class SearchResult implements Comparable<SearchResult> {
- /**
- * Reference to the original object.
- */
- private BioEntity obj;
-
- /**
- * Score of the result.
- */
- private double score;
-
- @Override
- public int compareTo(SearchResult o) {
- if (score == o.getScore()) {
- return obj.getId() - o.getObj().getId();
- } else if (score < o.getScore()) {
- return 1;
- } else {
- return -1;
- }
- }
-
- /**
- * @return the obj
- */
- public BioEntity getObj() {
- return obj;
- }
-
- /**
- * @param obj
- * the obj to set
- */
- public void setObj(BioEntity obj) {
- this.obj = obj;
- }
-
- /**
- * @return the score
- */
- public double getScore() {
- return score;
- }
-
- /**
- * @param score
- * the score to set
- */
- public void setScore(double score) {
- this.score = score;
- }
- };
-
- /**
- * Return the list of elements that match the query (sorted by match score)
- * limited to the element of class defined by type.
- *
- * @param model
- * model where the search is performed
- * @param query
- * query string
- * @param limit
- * maximum number of elements that can be returned by the search engine
- * @param perfectMatch
- * should only perfect match be allowed
- * @param type
- * class type of the elements that limits the results
- * @return list of object found for the query string sorted by the score value
- */
- protected List<BioEntity> searchByIndexedQuery(Model model, String query, int limit, Boolean perfectMatch,
- Class<? extends Element> type) {
- List<BioEntity> result = new ArrayList<>();
- if (query.startsWith(REACTION_SEARCH_PREFIX)) {
- return getReactionById(model, query.replaceFirst(REACTION_SEARCH_PREFIX, "").toLowerCase());
- } else if (query.startsWith(SPECIES_SEARCH_PREFIX)) {
- Element element = model.getElementByElementId(query.replaceFirst(SPECIES_SEARCH_PREFIX, ""));
- if (element !=null) {
- result.add(element);
- }
- } else if (query.startsWith(ELEMENT_SEARCH_PREFIX)) {
- return getElementById(model, query.replaceFirst(ELEMENT_SEARCH_PREFIX, "").toLowerCase());
- } else {
- Set<Element> aliases = model.getElements();
-
- List<SearchResult> sortedResults = new ArrayList<>();
- for (Element alias : aliases) {
- if (type.isAssignableFrom(alias.getClass())) {
- List<SearchIndex> indexes = alias.getSearchIndexes();
- if (indexes.size() == 0) {
- indexes = searchIndexer.createIndexForAlias(alias);
- alias.setSearchIndexes(indexes);
- }
- for (SearchIndex searchIndex : indexes) {
- double score = searchIndexer.match(query, searchIndex);
- if (perfectMatch != null && perfectMatch) {
- if (query.equals(searchIndex.getValue())) {
- SearchResult sResult = new SearchResult();
- sResult.setObj(alias);
- sResult.setScore(1);
- sortedResults.add(sResult);
- break;
- }
- } else if (score > 0 || (query.equals("") && type != Element.class)) {
- SearchResult sResult = new SearchResult();
- sResult.setObj(alias);
- sResult.setScore(score);
- if (score == 0) {
- sResult.setScore(alias.getId());
- }
- sortedResults.add(sResult);
- break;
- }
- }
- }
- if (result.size() >= limit) {
- break;
-
- }
- }
- Collections.sort(sortedResults);
- for (SearchResult searchResult : sortedResults) {
- if (searchResult.getObj() instanceof Reaction) {
- result.add(searchResult.getObj());
- } else if (searchResult.getObj() instanceof Element) {
- result.add(searchResult.getObj());
- } else {
- throw new InvalidStateException("Unknown class type: " + searchResult.getObj().getClass());
- }
- if (result.size() >= limit) {
- break;
- }
- }
- }
- return result;
- }
-
- /**
- * Returns list with the reaction with a given id. If reaction with such id
- * doesn't exist then empty list is returned.
- *
- * @param model
- * where the search is performed
- * @param reactionId
- * id of the reaction
- * @return list that contains reaction with given id (or empty list if such
- * reaction doesn't exist)
- */
- private List<BioEntity> getReactionById(Model model, String reactionId) {
- Set<Reaction> reactions = model.getReactions();
- for (Reaction reaction : reactions) {
- if (searchIndexer.getQueryStringForIndex(reaction.getIdReaction().toLowerCase(), new ArrayList<>())
- .equals(reactionId)) {
- return reactionToResultList(reaction);
- }
- if (Integer.toString(reaction.getId()).equals(reactionId)) {
- return reactionToResultList(reaction);
- }
- }
- return new ArrayList<>();
- }
-
- /**
- * Returns list with the element with a given id. If element with such id
- * doesn't exist then empty list is returned.
- *
- * @param topModel
- * where the search is performed
- * @param elementId
- * id of the element
- * @return list that contains element with given id (or empty list if such
- * element doesn't exist)
- */
- private List<BioEntity> getElementById(Model topModel, String elementId) {
- List<BioEntity> result = new ArrayList<>();
-
- Set<Model> models = new HashSet<>();
- models.add(topModel);
- models.addAll(topModel.getSubmodels());
- for (Model model : models) {
- for (Element element : model.getElements()) {
- if (searchIndexer.getQueryStringForIndex(element.getElementId().toLowerCase(), new ArrayList<>())
- .equals(elementId)) {
- result.add(element);
- } else if (Integer.toString(element.getId()).equals(elementId)) {
- result.add(element);
- }
- }
- }
- return result;
- }
-
- /**
- * Transform {@link Reaction} into set of result entries.
- *
- * @param reaction
- * reaction to be transformed
- * @return set of result entries for all element of the {@link Reaction}
- */
- private List<BioEntity> reactionToResultList(Reaction reaction) {
- List<BioEntity> result = new ArrayList<>();
- result.add(reaction);
- for (ReactionNode node : reaction.getReactionNodes()) {
- result.add(node.getElement());
- }
- return result;
- }
-
- @Override
- public List<BioEntity> searchByCoordinates(CoordinatesSearchParams params) {
- boolean nested = params.isNested();
-
- List<Object> results = new ArrayList<Object>();
-
- Set<Element> aliases = params.getModel().getElements();
- Point2D point = new Point2D.Double(params.getX(), params.getY());
- for (Element alias : aliases) {
- if (alias instanceof Species) {
- if (alias.contains(point)) {
- if (isVisible(alias, params)) {
- results.add(alias);
- }
- }
- }
- }
- List<BioEntity> result = new ArrayList<>();
- double dist = params.getDistance();
- if (results.size() == 0) {
- Reaction r = null;
- Set<Reaction> reactions = params.getModel().getReactions();
- for (Reaction reaction : reactions) {
- double newDist = reaction.getDistanceFromPoint(point);
- if (newDist < dist) {
- if (isVisible(reaction, params)) {
- r = reaction;
- dist = reaction.getDistanceFromPoint(point);
- }
- }
- }
- if (r != null) {
- result.addAll(reactionToResultList(r));
- return result;
- } else if (nested) {
- for (Element alias : aliases) {
- if (alias instanceof Compartment) {
- if (alias.contains(point)) {
- if (isVisible(alias, params)) {
- results.add(alias);
- }
- }
- }
- }
- }
- }
-
- if (results.size() > 1) {
- Element alias = (Element) results.get(0);
- for (Object obj : results) {
- if (((Element) (obj)).getSize() < alias.getSize()) {
- alias = (Element) obj;
- }
- }
- results.clear();
- results.add(alias);
- }
- if (results.size() == 0) {
- return result;
- } else {
- Object obj = results.get(0);
- if (obj instanceof Element) {
- result.add((BioEntity) obj);
- return result;
- } else if (obj instanceof Reaction) {
- result.addAll(reactionToResultList((Reaction) obj));
- return result;
- } else {
- throw new InvalidStateException("Unknown class type: " + obj.getClass());
- }
- }
- }
-
- /**
- * Check if reaction is visible for the user. Reaction is visible when at least
- * one node of the reaction is visible.
- *
- * @param reaction
- * which reaction is tested
- * @param params
- * params that determines the client search environment (zoom level,
- * type of the layout)
- * @return <code>true</code> if reaction is visible for the user,
- * <code>false</code> otherwise
- */
- private boolean isVisible(Reaction reaction, CoordinatesSearchParams params) {
- if (params.getLevel() == null || params.getLayoutIdentfier() == null) {
- return true;
- }
- if (!params.isNested()) {
- return true;
- }
- for (ReactionNode node : reaction.getReactionNodes()) {
- if (isVisible(node.getElement(), params)) {
- return true;
- }
- }
- return false;
- }
-
- /**
- * Checks if alias is visible for the user. Alias is invisible when the search
- * is performed on the hierarchical layout and the alias is hidden by the
- * complex or compartment.
- *
- * @param alias
- * alias to be checked for visibility
- * @param params
- * that determines the client search environment (zoom level, type of
- * the layout)
- * @return <code>true</code> if alias is visible for the user,
- * <code>false</code> otherwise
- */
- private boolean isVisible(Element alias, CoordinatesSearchParams params) {
- if (params.getLevel() == null || params.getLayoutIdentfier() == null) {
- return true;
- }
- return (!params.isNested()) || zoomLevelMatcher.isVisible(params.getLevel(), alias.getVisibilityLevel());
- }
-
- @Override
- public List<BioEntity> searchByQuery(Model model, String query, int limit, Boolean perfectMatch,
- String ipAddress) {
- query = query.toLowerCase();
- if (query == null) {
- throw new InvalidArgumentException("Invalid query: null");
- }
-
- MiriamData mt = getMiriamTypeForQuery(query);
- List<BioEntity> result = new ArrayList<>();
- if (mt != null) {
- result.addAll(searchByMiriam(model, mt, limit));
- } else {
- String indexQuery = searchIndexer.getQueryStringForIndex(query, speciesSearchReversePrefix.keySet());
- Class<? extends Element> type = searchIndexer.getTypeForQuery(query, speciesSearchReversePrefix);
-
- List<BioEntity> partResult = searchByIndexedQuery(model, indexQuery, limit, perfectMatch, type);
-
- for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
- partResult.addAll(searchByIndexedQuery(connection.getSubmodel().getModel(), indexQuery,
- limit - partResult.size(), perfectMatch, type));
- if (partResult.size() >= limit) {
- break;
- }
- }
-
- result.addAll(partResult);
- }
- if (model.getProject() != null && ipAddress != null) {
- searchHistoryService.addQuery(query, SearchType.GENERAL, ipAddress, model.getProject().getProjectId());
- }
- return result;
- }
-
- /**
- * Returns elements that are annotated with the given miriam data.
- *
- * @param topModel
- * model where elements are looked for
- * @param md
- * miriam annotation to identify interesting elements
- * @param limit
- * max number of elements to find
- * @return elements that are annotated with the given miriam data
- */
- private List<BioEntity> searchByMiriam(Model topModel, MiriamData md, int limit) {
- List<BioEntity> result = new ArrayList<>();
- Set<Model> models = new HashSet<>();
- models.add(topModel);
- models.addAll(topModel.getSubmodels());
- List<BioEntity> elements = new ArrayList<>();
- for (Model model : models) {
- elements.addAll(model.getElementsByAnnotation(md));
- }
- elements.sort(BioEntity.ID_COMPARATOR);
- for (BioEntity obj : elements) {
- if (result.size() >= limit) {
- break;
- }
- if (obj instanceof Element) {
- result.add((Element) obj);
- } else if (obj instanceof Reaction) {
- result.addAll(reactionToResultList((Reaction) obj));
- } else {
- throw new InvalidClassException("Unknown class: " + obj.getClass());
- }
- }
- return result;
- }
-
- /**
- * Tries to transform query into {@link MiriamData}.
- *
- * @param string
- * query to transform
- * @return {@link MiriamData} that described query or null if query cannot be
- * converted
- */
- protected MiriamData getMiriamTypeForQuery(String string) {
- for (MiriamType mt : MiriamType.values()) {
- if (string.startsWith(mt.toString().toLowerCase() + ":")) {
- return new MiriamData(mt, string.substring(mt.toString().length() + 1));
- }
- }
- return null;
- }
-
- @Override
- public List<BioEntity> getClosestElements(Model model, Point2D point, int numberOfElements, boolean perfectHit,
- Collection<String> types) {
- List<BioEntity> result = new ArrayList<>();
-
- // probably this could be improved algorithmitically, right now all objects
- // are sorted by distance, and numberOfElements closest are chosen as a list
- // of results
- List<DistanceToObject> tmpList = new ArrayList<>();
- for (Reaction reaction : model.getReactions()) {
- if (types.size() == 0 || types.contains(reaction.getStringType().toLowerCase())) {
- tmpList.add(new DistanceToObject(reaction, point));
- }
- }
- for (Element element : model.getElements()) {
- if ((element instanceof Species && types.size() == 0) || types.contains(element.getStringType().toLowerCase())) {
- tmpList.add(new DistanceToObject(element, point));
- }
- }
- Collections.sort(tmpList);
- int size = Math.min(tmpList.size(), numberOfElements);
- for (int i = 0; i < size; i++) {
- if (!perfectHit) {
- result.add(tmpList.get(i).getReference());
- } else if (tmpList.get(i).getDistance() < Configuration.EPSILON) {
- result.add(tmpList.get(i).getReference());
- }
- }
- return result;
- }
-
- /**
- * This class represents distance between object and some point. It's designed
- * to help sort objects by their distance to some point. It It contains two
- * fields: object reference and distance.
- *
- * @author Piotr Gawron
- *
- */
- private class DistanceToObject implements Comparable<DistanceToObject> {
- /**
- * Reference to the object.
- */
- private BioEntity reference;
-
- /**
- * Distance between the object and some point.
- */
- private double distance;
-
- /**
- * Size of the object.
- */
- private double size;
-
- /**
- * Constructor for reaction objects.
- *
- * @param reaction
- * reaction reference to store
- * @param point
- * point from which the distance will be computed
- */
- DistanceToObject(Reaction reaction, Point2D point) {
- reference = reaction;
- distance = reaction.getDistanceFromPoint(point);
- size = 0;
- }
-
- /**
- * Constructor for alias objects.
- *
- * @param alias
- * alias reference to store
- * @param point
- * point from which the distance will be computed
- */
- DistanceToObject(Element alias, Point2D point) {
- reference = alias;
- distance = alias.getDistanceFromPoint(point);
- size = alias.getSize();
-
- }
-
- @Override
- public int compareTo(DistanceToObject arg0) {
- if (arg0.getDistance() < getDistance()) {
- return 1;
- } else if (arg0.getDistance() > getDistance()) {
- return -1;
- } else {
- if (arg0.getSize() < getSize()) {
- return 1;
- } else if (arg0.getSize() > getSize()) {
- return -1;
- } else {
- return 0;
- }
- }
- }
-
- /**
- * @return the reference
- * @see #reference
- */
- public BioEntity getReference() {
- return reference;
- }
-
- /**
- * @return the distance
- * @see #distance
- */
- public double getDistance() {
- return distance;
- }
-
- /**
- * @return the size
- * @see #size
- */
- public double getSize() {
- return size;
- }
- }
-
- /**
- * Object containing autocomplete lists for models. For every model the map
- * between String and List is stored. The key in this map is incomplete typed
- * word, and value list contains suggestions that should appear for this word.
- */
- private Map<Model, Map<String, List<String>>> autoCompleteLists = new HashMap<Model, Map<String, List<String>>>();
-
- @Override
- public List<String> getAutocompleteList(Model model, String query) {
- Map<String, List<String>> autoCompleteMap = autoCompleteLists.get(model);
- if (autoCompleteMap == null) {
- autoCompleteMap = createAutocompleteMap(model);
- autoCompleteLists.put(model, autoCompleteMap);
- }
- List<String> result = autoCompleteMap.get(query.toLowerCase().trim());
- if (result == null) {
- result = new ArrayList<String>();
- }
- return result;
- }
-
- /**
- * Creates autocomplete map for a model. The key in this map is incomplete typed
- * word, and value list contains suggestions that should appear for this word.
- *
- * @param model
- * model for which the autocomplete map is created
- * @return autocomplete map for a model. The key in this map is incomplete typed
- * word, and value list contains suggestions that should appear for this
- * word.
- */
- private Map<String, List<String>> createAutocompleteMap(Model model) {
- Map<String, List<String>> result = new HashMap<String, List<String>>();
-
- String[] sortedPossibilites = getSuggestedQueryList(model);
- for (int i = 0; i < sortedPossibilites.length; i++) {
- String mainString = sortedPossibilites[i];
- for (int j = 0; j < mainString.length(); j++) {
- String substring = mainString.substring(0, j + 1);
- if (result.get(substring) != null) {
- continue;
- }
-
- List<String> list = new ArrayList<String>();
- for (int k = 0; k < Configuration.getAutocompleteSize(); k++) {
- if (k + i >= sortedPossibilites.length) {
- break;
- } else if (sortedPossibilites[k + i].startsWith(substring)) {
- list.add(sortedPossibilites[k + i]);
- }
- }
-
- // by default, the selection in autocomplete is set on the first
- // element, so if the first element is not equals to the query then add
- // the element
- if (!list.get(0).equalsIgnoreCase(substring)) {
- list.add(0, substring);
- }
-
- result.put(substring, list);
- }
- }
- return result;
- }
-
- @Override
- public String[] getSuggestedQueryList(Model model) {
- Set<String> possibilities = new HashSet<String>();
- for (Element alias : model.getElements()) {
- if (alias instanceof Species) {
- possibilities.addAll(getSearchPossibilitiesForAlias(alias));
- }
- }
- for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
- for (Element alias : connection.getSubmodel().getModel().getElements()) {
- if (alias instanceof Species) {
- possibilities.addAll(getSearchPossibilitiesForAlias(alias));
- }
- }
- }
- String[] sortedPossibilites = new String[possibilities.size()];
- int index = 0;
- for (String string : possibilities) {
- sortedPossibilites[index++] = string;
- }
- Arrays.sort(sortedPossibilites);
- return sortedPossibilites;
- }
-
- /**
- * Returns the list of all human readable search possibilities for alias.
- *
- * @param element
- * object for which we look for a list of searchable strings
- * @return the list of all human readable search possibilities for alias
- */
- private List<String> getSearchPossibilitiesForAlias(Element element) {
- List<String> result = new ArrayList<String>();
- result.add(element.getName().trim().toLowerCase().replace(",", ""));
- for (String string : element.getSynonyms()) {
- result.add(string.trim().toLowerCase().replace(",", ""));
- }
- for (String string : element.getFormerSymbols()) {
- result.add(string.trim().toLowerCase().replace(",", ""));
- }
- String name = element.getFullName();
- if (name != null) {
- result.add(name.trim().toLowerCase().replace(",", ""));
- }
- return result;
- }
-
- /**
- * @return the modelDao
- */
- public ModelDao getModelDao() {
- return modelDao;
- }
-
- /**
- * @param modelDao
- * the modelDao to set
- */
- public void setModelDao(ModelDao modelDao) {
- this.modelDao = modelDao;
- }
-
- /**
- * @return the searchHistoryService
- */
- public ISearchHistoryService getSearchHistoryService() {
- return searchHistoryService;
- }
-
- /**
- * @param searchHistoryService
- * the searchHistoryService to set
- */
- public void setSearchHistoryService(ISearchHistoryService searchHistoryService) {
- this.searchHistoryService = searchHistoryService;
- }
-
- @Override
- public List<BioEntity> searchByQuery(Model model, String query, int limit, Boolean perfectMatch) {
- return searchByQuery(model, query, limit, perfectMatch, null);
- }
-
+package lcsb.mapviewer.services.impl;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.commands.SemanticZoomLevelMatcher;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidClassException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.SearchIndex;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Degraded;
+import lcsb.mapviewer.model.map.species.Drug;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.Unknown;
+import lcsb.mapviewer.model.map.statistics.SearchType;
+import lcsb.mapviewer.persist.dao.map.ModelDao;
+import lcsb.mapviewer.services.interfaces.ISearchHistoryService;
+import lcsb.mapviewer.services.interfaces.ISearchService;
+import lcsb.mapviewer.services.utils.SearchIndexer;
+
+/**
+ * This is implementation of the service that returns information about species,
+ * paths etc in the model.
+ *
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Transactional(value = "txManager")
+public class SearchService implements ISearchService {
+
+ private SemanticZoomLevelMatcher zoomLevelMatcher = new SemanticZoomLevelMatcher();
+
+ /**
+ * Prefix used in search by name interface to limit results only to species.
+ */
+ public static final String SPECIES_SEARCH_PREFIX = "species";
+
+ /**
+ * Prefix used in search by name interface to limit results only to reactions.
+ */
+ public static final String REACTION_SEARCH_PREFIX = "reaction";
+
+ /**
+ * Prefix used in search by name interface to limit results only to
+ * {@link Element}.
+ */
+ private static final String ELEMENT_SEARCH_PREFIX = "element";
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(SearchService.class.getName());
+
+ /**
+ * Data access object for models.
+ */
+ @Autowired
+ private ModelDao modelDao;
+
+ /**
+ * Service used for managing search history.
+ */
+ @Autowired
+ private ISearchHistoryService searchHistoryService;
+
+ /**
+ * Object used for indexing elements on the map.
+ */
+ private SearchIndexer searchIndexer = new SearchIndexer();
+
+ /**
+ * This object maps class of elements on the map into short string prefixes used
+ * in the search query. For instance elements of the {@link Complex} class could
+ * be searched with the prefix "complex" (example query: "complex:alpha
+ * subcomplex").
+ */
+ private Map<Class<? extends Element>, String> speciesSearchPrefix = new HashMap<>();
+
+ /**
+ * This object maps short string prefixes into class of elements on the map that
+ * will be searched. For instance prefix "complex" might refer to
+ * {@link Complex} class and and example query would look like: "complex:alpha
+ * subcomplex".
+ */
+ private Map<String, Class<? extends Element>> speciesSearchReversePrefix = new HashMap<>();
+
+ /**
+ * Default constructor that set list of prefixes used in the search queries.
+ */
+ public SearchService() {
+ addSearchPrefix("complex", Complex.class);
+ addSearchPrefix("degrded", Degraded.class);
+ addSearchPrefix("drug", Drug.class);
+ addSearchPrefix("gene", Gene.class);
+ addSearchPrefix("ion", Ion.class);
+ addSearchPrefix("phenotype", Phenotype.class);
+ addSearchPrefix("protein", Protein.class);
+ addSearchPrefix("rna", Rna.class);
+ addSearchPrefix("molecule", SimpleMolecule.class);
+ addSearchPrefix("unknown", Unknown.class);
+ }
+
+ /**
+ * Adds search prefix for an element class.
+ *
+ * @param prefix
+ * string prefix used in search queries
+ * @param clazz
+ * class for which this prefix stands
+ */
+ private void addSearchPrefix(String prefix, Class<? extends Element> clazz) {
+ speciesSearchPrefix.put(clazz, prefix);
+ speciesSearchReversePrefix.put(prefix, clazz);
+ }
+
+ /**
+ * Private class that defines internal search result element. Contains reference
+ * to original result and match score of the result.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ private class SearchResult implements Comparable<SearchResult> {
+ /**
+ * Reference to the original object.
+ */
+ private BioEntity obj;
+
+ /**
+ * Score of the result.
+ */
+ private double score;
+
+ @Override
+ public int compareTo(SearchResult o) {
+ if (score == o.getScore()) {
+ return obj.getId() - o.getObj().getId();
+ } else if (score < o.getScore()) {
+ return 1;
+ } else {
+ return -1;
+ }
+ }
+
+ /**
+ * @return the obj
+ */
+ public BioEntity getObj() {
+ return obj;
+ }
+
+ /**
+ * @param obj
+ * the obj to set
+ */
+ public void setObj(BioEntity obj) {
+ this.obj = obj;
+ }
+
+ /**
+ * @return the score
+ */
+ public double getScore() {
+ return score;
+ }
+
+ /**
+ * @param score
+ * the score to set
+ */
+ public void setScore(double score) {
+ this.score = score;
+ }
+ };
+
+ /**
+ * Return the list of elements that match the query (sorted by match score)
+ * limited to the element of class defined by type.
+ *
+ * @param model
+ * model where the search is performed
+ * @param query
+ * query string
+ * @param limit
+ * maximum number of elements that can be returned by the search engine
+ * @param perfectMatch
+ * should only perfect match be allowed
+ * @param type
+ * class type of the elements that limits the results
+ * @return list of object found for the query string sorted by the score value
+ */
+ protected List<BioEntity> searchByIndexedQuery(Model model, String query, int limit, Boolean perfectMatch,
+ Class<? extends Element> type) {
+ List<BioEntity> result = new ArrayList<>();
+ if (query.startsWith(REACTION_SEARCH_PREFIX)) {
+ return getReactionById(model, query.replaceFirst(REACTION_SEARCH_PREFIX, "").toLowerCase());
+ } else if (query.startsWith(SPECIES_SEARCH_PREFIX)) {
+ Element element = model.getElementByElementId(query.replaceFirst(SPECIES_SEARCH_PREFIX, ""));
+ if (element !=null) {
+ result.add(element);
+ }
+ } else if (query.startsWith(ELEMENT_SEARCH_PREFIX)) {
+ return getElementById(model, query.replaceFirst(ELEMENT_SEARCH_PREFIX, "").toLowerCase());
+ } else {
+ Set<Element> aliases = model.getElements();
+
+ List<SearchResult> sortedResults = new ArrayList<>();
+ for (Element alias : aliases) {
+ if (type.isAssignableFrom(alias.getClass())) {
+ List<SearchIndex> indexes = alias.getSearchIndexes();
+ if (indexes.size() == 0) {
+ indexes = searchIndexer.createIndexForAlias(alias);
+ alias.setSearchIndexes(indexes);
+ }
+ for (SearchIndex searchIndex : indexes) {
+ double score = searchIndexer.match(query, searchIndex);
+ if (perfectMatch != null && perfectMatch) {
+ if (query.equals(searchIndex.getValue())) {
+ SearchResult sResult = new SearchResult();
+ sResult.setObj(alias);
+ sResult.setScore(1);
+ sortedResults.add(sResult);
+ break;
+ }
+ } else if (score > 0 || (query.equals("") && type != Element.class)) {
+ SearchResult sResult = new SearchResult();
+ sResult.setObj(alias);
+ sResult.setScore(score);
+ if (score == 0) {
+ sResult.setScore(alias.getId());
+ }
+ sortedResults.add(sResult);
+ break;
+ }
+ }
+ }
+ if (result.size() >= limit) {
+ break;
+
+ }
+ }
+ Collections.sort(sortedResults);
+ for (SearchResult searchResult : sortedResults) {
+ if (searchResult.getObj() instanceof Reaction) {
+ result.add(searchResult.getObj());
+ } else if (searchResult.getObj() instanceof Element) {
+ result.add(searchResult.getObj());
+ } else {
+ throw new InvalidStateException("Unknown class type: " + searchResult.getObj().getClass());
+ }
+ if (result.size() >= limit) {
+ break;
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Returns list with the reaction with a given id. If reaction with such id
+ * doesn't exist then empty list is returned.
+ *
+ * @param model
+ * where the search is performed
+ * @param reactionId
+ * id of the reaction
+ * @return list that contains reaction with given id (or empty list if such
+ * reaction doesn't exist)
+ */
+ private List<BioEntity> getReactionById(Model model, String reactionId) {
+ Set<Reaction> reactions = model.getReactions();
+ for (Reaction reaction : reactions) {
+ if (searchIndexer.getQueryStringForIndex(reaction.getIdReaction().toLowerCase(), new ArrayList<>())
+ .equals(reactionId)) {
+ return reactionToResultList(reaction);
+ }
+ if (Integer.toString(reaction.getId()).equals(reactionId)) {
+ return reactionToResultList(reaction);
+ }
+ }
+ return new ArrayList<>();
+ }
+
+ /**
+ * Returns list with the element with a given id. If element with such id
+ * doesn't exist then empty list is returned.
+ *
+ * @param topModel
+ * where the search is performed
+ * @param elementId
+ * id of the element
+ * @return list that contains element with given id (or empty list if such
+ * element doesn't exist)
+ */
+ private List<BioEntity> getElementById(Model topModel, String elementId) {
+ List<BioEntity> result = new ArrayList<>();
+
+ Set<Model> models = new HashSet<>();
+ models.add(topModel);
+ models.addAll(topModel.getSubmodels());
+ for (Model model : models) {
+ for (Element element : model.getElements()) {
+ if (searchIndexer.getQueryStringForIndex(element.getElementId().toLowerCase(), new ArrayList<>())
+ .equals(elementId)) {
+ result.add(element);
+ } else if (Integer.toString(element.getId()).equals(elementId)) {
+ result.add(element);
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Transform {@link Reaction} into set of result entries.
+ *
+ * @param reaction
+ * reaction to be transformed
+ * @return set of result entries for all element of the {@link Reaction}
+ */
+ private List<BioEntity> reactionToResultList(Reaction reaction) {
+ List<BioEntity> result = new ArrayList<>();
+ result.add(reaction);
+ for (ReactionNode node : reaction.getReactionNodes()) {
+ result.add(node.getElement());
+ }
+ return result;
+ }
+
+ @Override
+ public List<BioEntity> searchByCoordinates(CoordinatesSearchParams params) {
+ boolean nested = params.isNested();
+
+ List<Object> results = new ArrayList<Object>();
+
+ Set<Element> aliases = params.getModel().getElements();
+ Point2D point = new Point2D.Double(params.getX(), params.getY());
+ for (Element alias : aliases) {
+ if (alias instanceof Species) {
+ if (alias.contains(point)) {
+ if (isVisible(alias, params)) {
+ results.add(alias);
+ }
+ }
+ }
+ }
+ List<BioEntity> result = new ArrayList<>();
+ double dist = params.getDistance();
+ if (results.size() == 0) {
+ Reaction r = null;
+ Set<Reaction> reactions = params.getModel().getReactions();
+ for (Reaction reaction : reactions) {
+ double newDist = reaction.getDistanceFromPoint(point);
+ if (newDist < dist) {
+ if (isVisible(reaction, params)) {
+ r = reaction;
+ dist = reaction.getDistanceFromPoint(point);
+ }
+ }
+ }
+ if (r != null) {
+ result.addAll(reactionToResultList(r));
+ return result;
+ } else if (nested) {
+ for (Element alias : aliases) {
+ if (alias instanceof Compartment) {
+ if (alias.contains(point)) {
+ if (isVisible(alias, params)) {
+ results.add(alias);
+ }
+ }
+ }
+ }
+ }
+ }
+
+ if (results.size() > 1) {
+ Element alias = (Element) results.get(0);
+ for (Object obj : results) {
+ if (((Element) (obj)).getSize() < alias.getSize()) {
+ alias = (Element) obj;
+ }
+ }
+ results.clear();
+ results.add(alias);
+ }
+ if (results.size() == 0) {
+ return result;
+ } else {
+ Object obj = results.get(0);
+ if (obj instanceof Element) {
+ result.add((BioEntity) obj);
+ return result;
+ } else if (obj instanceof Reaction) {
+ result.addAll(reactionToResultList((Reaction) obj));
+ return result;
+ } else {
+ throw new InvalidStateException("Unknown class type: " + obj.getClass());
+ }
+ }
+ }
+
+ /**
+ * Check if reaction is visible for the user. Reaction is visible when at least
+ * one node of the reaction is visible.
+ *
+ * @param reaction
+ * which reaction is tested
+ * @param params
+ * params that determines the client search environment (zoom level,
+ * type of the layout)
+ * @return <code>true</code> if reaction is visible for the user,
+ * <code>false</code> otherwise
+ */
+ private boolean isVisible(Reaction reaction, CoordinatesSearchParams params) {
+ if (params.getLevel() == null || params.getLayoutIdentfier() == null) {
+ return true;
+ }
+ if (!params.isNested()) {
+ return true;
+ }
+ for (ReactionNode node : reaction.getReactionNodes()) {
+ if (isVisible(node.getElement(), params)) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Checks if alias is visible for the user. Alias is invisible when the search
+ * is performed on the hierarchical layout and the alias is hidden by the
+ * complex or compartment.
+ *
+ * @param alias
+ * alias to be checked for visibility
+ * @param params
+ * that determines the client search environment (zoom level, type of
+ * the layout)
+ * @return <code>true</code> if alias is visible for the user,
+ * <code>false</code> otherwise
+ */
+ private boolean isVisible(Element alias, CoordinatesSearchParams params) {
+ if (params.getLevel() == null || params.getLayoutIdentfier() == null) {
+ return true;
+ }
+ return (!params.isNested()) || zoomLevelMatcher.isVisible(params.getLevel(), alias.getVisibilityLevel());
+ }
+
+ @Override
+ public List<BioEntity> searchByQuery(Model model, String query, int limit, Boolean perfectMatch,
+ String ipAddress) {
+ query = query.toLowerCase();
+ if (query == null) {
+ throw new InvalidArgumentException("Invalid query: null");
+ }
+
+ MiriamData mt = getMiriamTypeForQuery(query);
+ List<BioEntity> result = new ArrayList<>();
+ if (mt != null) {
+ result.addAll(searchByMiriam(model, mt, limit));
+ } else {
+ String indexQuery = searchIndexer.getQueryStringForIndex(query, speciesSearchReversePrefix.keySet());
+ Class<? extends Element> type = searchIndexer.getTypeForQuery(query, speciesSearchReversePrefix);
+
+ List<BioEntity> partResult = searchByIndexedQuery(model, indexQuery, limit, perfectMatch, type);
+
+ for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
+ partResult.addAll(searchByIndexedQuery(connection.getSubmodel().getModel(), indexQuery,
+ limit - partResult.size(), perfectMatch, type));
+ if (partResult.size() >= limit) {
+ break;
+ }
+ }
+
+ result.addAll(partResult);
+ }
+ if (model.getProject() != null && ipAddress != null) {
+ searchHistoryService.addQuery(query, SearchType.GENERAL, ipAddress, model.getProject().getProjectId());
+ }
+ return result;
+ }
+
+ /**
+ * Returns elements that are annotated with the given miriam data.
+ *
+ * @param topModel
+ * model where elements are looked for
+ * @param md
+ * miriam annotation to identify interesting elements
+ * @param limit
+ * max number of elements to find
+ * @return elements that are annotated with the given miriam data
+ */
+ private List<BioEntity> searchByMiriam(Model topModel, MiriamData md, int limit) {
+ List<BioEntity> result = new ArrayList<>();
+ Set<Model> models = new HashSet<>();
+ models.add(topModel);
+ models.addAll(topModel.getSubmodels());
+ List<BioEntity> elements = new ArrayList<>();
+ for (Model model : models) {
+ elements.addAll(model.getElementsByAnnotation(md));
+ }
+ elements.sort(BioEntity.ID_COMPARATOR);
+ for (BioEntity obj : elements) {
+ if (result.size() >= limit) {
+ break;
+ }
+ if (obj instanceof Element) {
+ result.add((Element) obj);
+ } else if (obj instanceof Reaction) {
+ result.addAll(reactionToResultList((Reaction) obj));
+ } else {
+ throw new InvalidClassException("Unknown class: " + obj.getClass());
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Tries to transform query into {@link MiriamData}.
+ *
+ * @param string
+ * query to transform
+ * @return {@link MiriamData} that described query or null if query cannot be
+ * converted
+ */
+ protected MiriamData getMiriamTypeForQuery(String string) {
+ for (MiriamType mt : MiriamType.values()) {
+ if (string.startsWith(mt.toString().toLowerCase() + ":")) {
+ return new MiriamData(mt, string.substring(mt.toString().length() + 1));
+ }
+ }
+ return null;
+ }
+
+ @Override
+ public List<BioEntity> getClosestElements(Model model, Point2D point, int numberOfElements, boolean perfectHit,
+ Collection<String> types) {
+ List<BioEntity> result = new ArrayList<>();
+
+ // probably this could be improved algorithmitically, right now all objects
+ // are sorted by distance, and numberOfElements closest are chosen as a list
+ // of results
+ List<DistanceToObject> tmpList = new ArrayList<>();
+ for (Reaction reaction : model.getReactions()) {
+ if (types.size() == 0 || types.contains(reaction.getStringType().toLowerCase())) {
+ tmpList.add(new DistanceToObject(reaction, point));
+ }
+ }
+ for (Element element : model.getElements()) {
+ if ((element instanceof Species && types.size() == 0) || types.contains(element.getStringType().toLowerCase())) {
+ tmpList.add(new DistanceToObject(element, point));
+ }
+ }
+ Collections.sort(tmpList);
+ int size = Math.min(tmpList.size(), numberOfElements);
+ for (int i = 0; i < size; i++) {
+ if (!perfectHit) {
+ result.add(tmpList.get(i).getReference());
+ } else if (tmpList.get(i).getDistance() < Configuration.EPSILON) {
+ result.add(tmpList.get(i).getReference());
+ }
+ }
+ return result;
+ }
+
+ /**
+ * This class represents distance between object and some point. It's designed
+ * to help sort objects by their distance to some point. It It contains two
+ * fields: object reference and distance.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ private class DistanceToObject implements Comparable<DistanceToObject> {
+ /**
+ * Reference to the object.
+ */
+ private BioEntity reference;
+
+ /**
+ * Distance between the object and some point.
+ */
+ private double distance;
+
+ /**
+ * Size of the object.
+ */
+ private double size;
+
+ /**
+ * Constructor for reaction objects.
+ *
+ * @param reaction
+ * reaction reference to store
+ * @param point
+ * point from which the distance will be computed
+ */
+ DistanceToObject(Reaction reaction, Point2D point) {
+ reference = reaction;
+ distance = reaction.getDistanceFromPoint(point);
+ size = 0;
+ }
+
+ /**
+ * Constructor for alias objects.
+ *
+ * @param alias
+ * alias reference to store
+ * @param point
+ * point from which the distance will be computed
+ */
+ DistanceToObject(Element alias, Point2D point) {
+ reference = alias;
+ distance = alias.getDistanceFromPoint(point);
+ size = alias.getSize();
+
+ }
+
+ @Override
+ public int compareTo(DistanceToObject arg0) {
+ if (arg0.getDistance() < getDistance()) {
+ return 1;
+ } else if (arg0.getDistance() > getDistance()) {
+ return -1;
+ } else {
+ if (arg0.getSize() < getSize()) {
+ return 1;
+ } else if (arg0.getSize() > getSize()) {
+ return -1;
+ } else {
+ return 0;
+ }
+ }
+ }
+
+ /**
+ * @return the reference
+ * @see #reference
+ */
+ public BioEntity getReference() {
+ return reference;
+ }
+
+ /**
+ * @return the distance
+ * @see #distance
+ */
+ public double getDistance() {
+ return distance;
+ }
+
+ /**
+ * @return the size
+ * @see #size
+ */
+ public double getSize() {
+ return size;
+ }
+ }
+
+ /**
+ * Object containing autocomplete lists for models. For every model the map
+ * between String and List is stored. The key in this map is incomplete typed
+ * word, and value list contains suggestions that should appear for this word.
+ */
+ private Map<Model, Map<String, List<String>>> autoCompleteLists = new HashMap<Model, Map<String, List<String>>>();
+
+ @Override
+ public List<String> getAutocompleteList(Model model, String query) {
+ Map<String, List<String>> autoCompleteMap = autoCompleteLists.get(model);
+ if (autoCompleteMap == null) {
+ autoCompleteMap = createAutocompleteMap(model);
+ autoCompleteLists.put(model, autoCompleteMap);
+ }
+ List<String> result = autoCompleteMap.get(query.toLowerCase().trim());
+ if (result == null) {
+ result = new ArrayList<String>();
+ }
+ return result;
+ }
+
+ /**
+ * Creates autocomplete map for a model. The key in this map is incomplete typed
+ * word, and value list contains suggestions that should appear for this word.
+ *
+ * @param model
+ * model for which the autocomplete map is created
+ * @return autocomplete map for a model. The key in this map is incomplete typed
+ * word, and value list contains suggestions that should appear for this
+ * word.
+ */
+ private Map<String, List<String>> createAutocompleteMap(Model model) {
+ Map<String, List<String>> result = new HashMap<String, List<String>>();
+
+ String[] sortedPossibilites = getSuggestedQueryList(model);
+ for (int i = 0; i < sortedPossibilites.length; i++) {
+ String mainString = sortedPossibilites[i];
+ for (int j = 0; j < mainString.length(); j++) {
+ String substring = mainString.substring(0, j + 1);
+ if (result.get(substring) != null) {
+ continue;
+ }
+
+ List<String> list = new ArrayList<String>();
+ for (int k = 0; k < Configuration.getAutocompleteSize(); k++) {
+ if (k + i >= sortedPossibilites.length) {
+ break;
+ } else if (sortedPossibilites[k + i].startsWith(substring)) {
+ list.add(sortedPossibilites[k + i]);
+ }
+ }
+
+ // by default, the selection in autocomplete is set on the first
+ // element, so if the first element is not equals to the query then add
+ // the element
+ if (!list.get(0).equalsIgnoreCase(substring)) {
+ list.add(0, substring);
+ }
+
+ result.put(substring, list);
+ }
+ }
+ return result;
+ }
+
+ @Override
+ public String[] getSuggestedQueryList(Model model) {
+ Set<String> possibilities = new HashSet<String>();
+ for (Element alias : model.getElements()) {
+ if (alias instanceof Species) {
+ possibilities.addAll(getSearchPossibilitiesForAlias(alias));
+ }
+ }
+ for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
+ for (Element alias : connection.getSubmodel().getModel().getElements()) {
+ if (alias instanceof Species) {
+ possibilities.addAll(getSearchPossibilitiesForAlias(alias));
+ }
+ }
+ }
+ String[] sortedPossibilites = new String[possibilities.size()];
+ int index = 0;
+ for (String string : possibilities) {
+ sortedPossibilites[index++] = string;
+ }
+ Arrays.sort(sortedPossibilites);
+ return sortedPossibilites;
+ }
+
+ /**
+ * Returns the list of all human readable search possibilities for alias.
+ *
+ * @param element
+ * object for which we look for a list of searchable strings
+ * @return the list of all human readable search possibilities for alias
+ */
+ private List<String> getSearchPossibilitiesForAlias(Element element) {
+ List<String> result = new ArrayList<String>();
+ result.add(element.getName().trim().toLowerCase().replace(",", ""));
+ for (String string : element.getSynonyms()) {
+ result.add(string.trim().toLowerCase().replace(",", ""));
+ }
+ for (String string : element.getFormerSymbols()) {
+ result.add(string.trim().toLowerCase().replace(",", ""));
+ }
+ String name = element.getFullName();
+ if (name != null) {
+ result.add(name.trim().toLowerCase().replace(",", ""));
+ }
+ return result;
+ }
+
+ /**
+ * @return the modelDao
+ */
+ public ModelDao getModelDao() {
+ return modelDao;
+ }
+
+ /**
+ * @param modelDao
+ * the modelDao to set
+ */
+ public void setModelDao(ModelDao modelDao) {
+ this.modelDao = modelDao;
+ }
+
+ /**
+ * @return the searchHistoryService
+ */
+ public ISearchHistoryService getSearchHistoryService() {
+ return searchHistoryService;
+ }
+
+ /**
+ * @param searchHistoryService
+ * the searchHistoryService to set
+ */
+ public void setSearchHistoryService(ISearchHistoryService searchHistoryService) {
+ this.searchHistoryService = searchHistoryService;
+ }
+
+ @Override
+ public List<BioEntity> searchByQuery(Model model, String query, int limit, Boolean perfectMatch) {
+ return searchByQuery(model, query, limit, perfectMatch, null);
+ }
+
}
\ No newline at end of file
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/package-info.java b/service/src/main/java/lcsb/mapviewer/services/impl/package-info.java
index 310f9a816c..8579684cb4 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/package-info.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/package-info.java
@@ -1,6 +1,6 @@
-/**
- * This package contains implementation of the services provided by the service
- * layer.
- */
-package lcsb.mapviewer.services.impl;
-
+/**
+ * This package contains implementation of the services provided by the service
+ * layer.
+ */
+package lcsb.mapviewer.services.impl;
+
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/ICommentService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/ICommentService.java
index 554da7657e..e684f7089a 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/ICommentService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/ICommentService.java
@@ -1,89 +1,89 @@
-package lcsb.mapviewer.services.interfaces;
-
-import java.awt.geom.Point2D;
-import java.util.List;
-
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.Comment;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.UserAccessException;
-
-/**
- * Service responsible for comments functionality.
- *
- * @author Piotr Gawron
- *
- */
-public interface ICommentService {
- /**
- * Adds comment to the map.
- *
- * @param pinned
- * parameter that defines if comment should be visible on the map.
- * @param object
- * determines which object is commented - it could be null; in this
- * case it means that a comment is general one.
- * @param name
- * name of person that comments
- * @param email
- * email of the person that comments
- * @param content
- * content of the comment
- * @param model
- * which map we comment on
- * @param submodel
- * on which submodel we comment on
- * @param coordinates
- * where exactly the comment should be placed on
- *
- * @return comment object created based on the data provided as parameters
- */
- Comment addComment(String name, String email, String content, Model model, Point2D coordinates, Object object,
- boolean pinned, Model submodel);
-
- /**
- * This method remove comment. Comment is not removed from the system, only
- * 'deleted' flag is set.
- *
- * @param loggedUser
- * user that wants to remove the comment
- * @param commentId
- * identifier of the comment that user wants to remove
- * @param reason
- * why user wants to remove the comment
- */
- void deleteComment(User loggedUser, String commentId, String reason);
-
- void deleteComment(Comment comment, String token, String reason) throws UserAccessException, SecurityException;
-
- List<Comment> getCommentsByProject(Project project, String token) throws UserAccessException, SecurityException;
-
- /**
- * Returns number of comments in the system.
- *
- * @return number of comments in the system
- */
- long getCommentCount();
-
- /**
- * Removes comments from the model.
- *
- * @param model
- * from which model we want to remove comments
- */
- void removeCommentsForModel(Model model);
-
- /**
- * Removes comments from the model.
- *
- * @param model
- * from which model we want to remove comments
- */
- void removeCommentsForModel(ModelData model);
-
- Comment getCommentById(String commentId);
-
-}
+package lcsb.mapviewer.services.interfaces;
+
+import java.awt.geom.Point2D;
+import java.util.List;
+
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.Comment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.UserAccessException;
+
+/**
+ * Service responsible for comments functionality.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface ICommentService {
+ /**
+ * Adds comment to the map.
+ *
+ * @param pinned
+ * parameter that defines if comment should be visible on the map.
+ * @param object
+ * determines which object is commented - it could be null; in this
+ * case it means that a comment is general one.
+ * @param name
+ * name of person that comments
+ * @param email
+ * email of the person that comments
+ * @param content
+ * content of the comment
+ * @param model
+ * which map we comment on
+ * @param submodel
+ * on which submodel we comment on
+ * @param coordinates
+ * where exactly the comment should be placed on
+ *
+ * @return comment object created based on the data provided as parameters
+ */
+ Comment addComment(String name, String email, String content, Model model, Point2D coordinates, Object object,
+ boolean pinned, Model submodel);
+
+ /**
+ * This method remove comment. Comment is not removed from the system, only
+ * 'deleted' flag is set.
+ *
+ * @param loggedUser
+ * user that wants to remove the comment
+ * @param commentId
+ * identifier of the comment that user wants to remove
+ * @param reason
+ * why user wants to remove the comment
+ */
+ void deleteComment(User loggedUser, String commentId, String reason);
+
+ void deleteComment(Comment comment, String token, String reason) throws UserAccessException, SecurityException;
+
+ List<Comment> getCommentsByProject(Project project, String token) throws UserAccessException, SecurityException;
+
+ /**
+ * Returns number of comments in the system.
+ *
+ * @return number of comments in the system
+ */
+ long getCommentCount();
+
+ /**
+ * Removes comments from the model.
+ *
+ * @param model
+ * from which model we want to remove comments
+ */
+ void removeCommentsForModel(Model model);
+
+ /**
+ * Removes comments from the model.
+ *
+ * @param model
+ * from which model we want to remove comments
+ */
+ void removeCommentsForModel(ModelData model);
+
+ Comment getCommentById(String commentId);
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IConfigurationService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IConfigurationService.java
index 99cb6ccf5d..f4351a47af 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IConfigurationService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IConfigurationService.java
@@ -1,118 +1,118 @@
-package lcsb.mapviewer.services.interfaces;
-
-import java.util.List;
-
-import lcsb.mapviewer.common.FrameworkVersion;
-import lcsb.mapviewer.model.user.ConfigurationElementType;
-import lcsb.mapviewer.model.user.ConfigurationOption;
-import lcsb.mapviewer.model.user.PrivilegeType;
-
-/**
- * Service used for accessing and modifying configuration parameters.
- *
- * @author Piotr Gawron
- *
- */
-public interface IConfigurationService {
-
- /**
- * Returns value of the configuration parameter.
- *
- * @param type
- * configuration parameter
- * @return value of the configuration parameter given in type
- */
- String getConfigurationValue(ConfigurationElementType type);
-
- /**
- * Sets configuration parameter.
- *
- * @param type
- * which configuration parameter
- * @param value
- * what value
- */
- void setConfigurationValue(ConfigurationElementType type, String value);
-
- /**
- * Removes configuration parameter.
- *
- * @param type
- * which configuration parameter
- */
- void deleteConfigurationValue(ConfigurationElementType type);
-
- /**
- * Returns information about all configuration parameters with current values.
- *
- * @return list of all configuration parameters with current values
- */
- List<ConfigurationOption> getAllValues(boolean includeServerSide);
-
- /**
- * Updates configuration parameters.
- *
- * @param values
- * new values of the parameters
- */
- void updateConfiguration(List<ConfigurationOption> values);
-
- /**
- * Returns {@link lcsb.mapviewer.common.Configuration#systemVersion git version}
- * from which the system was built.
- *
- * @param baseDir
- * directory where the system is placed
- * @return git version
- */
- String getSystemSvnVersion(String baseDir);
-
- /**
- * Returns estimated current memory usage (in MB).
- *
- * @return estimated current memory usage (in MB)
- */
- Long getMemoryUsage();
-
- /**
- * Returns max memory available to JVM (in MB).
- *
- * @return max memory available to JVM (in MB)
- */
- Long getMaxMemory();
-
- /**
- * Returns currently build framework version.
- *
- * @param baseDir
- * directory where the system is placed
- * @return currently build {@link FrameworkVersion framework version}
- * @throws InvalidSvnVersionException
- * thrown when the git version of the build system is invalid
- */
- FrameworkVersion getSystemVersion(String baseDir);
-
- /**
- * Returns system {@link lcsb.mapviewer.common.Configuration#systemBuild build
- * date}.
- *
- * @param baseDir
- * directory where the system is placed
- * @return system build date
- */
- String getSystemBuild(String baseDir);
-
- /**
- * Returns {@link lcsb.mapviewer.common.Configuration#systemBuildVersion git
- * hash} of build process.
- *
- * @param baseDir
- * directory where the system is placed
- * @return git hash
- */
- String getSystemGitVersion(String baseDir);
-
- ConfigurationOption getValue(ConfigurationElementType type);
-
- ConfigurationOption getValue(PrivilegeType type);
-}
+package lcsb.mapviewer.services.interfaces;
+
+import java.util.List;
+
+import lcsb.mapviewer.common.FrameworkVersion;
+import lcsb.mapviewer.model.user.ConfigurationElementType;
+import lcsb.mapviewer.model.user.ConfigurationOption;
+import lcsb.mapviewer.model.user.PrivilegeType;
+
+/**
+ * Service used for accessing and modifying configuration parameters.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface IConfigurationService {
+
+ /**
+ * Returns value of the configuration parameter.
+ *
+ * @param type
+ * configuration parameter
+ * @return value of the configuration parameter given in type
+ */
+ String getConfigurationValue(ConfigurationElementType type);
+
+ /**
+ * Sets configuration parameter.
+ *
+ * @param type
+ * which configuration parameter
+ * @param value
+ * what value
+ */
+ void setConfigurationValue(ConfigurationElementType type, String value);
+
+ /**
+ * Removes configuration parameter.
+ *
+ * @param type
+ * which configuration parameter
+ */
+ void deleteConfigurationValue(ConfigurationElementType type);
+
+ /**
+ * Returns information about all configuration parameters with current values.
+ *
+ * @return list of all configuration parameters with current values
+ */
+ List<ConfigurationOption> getAllValues(boolean includeServerSide);
+
+ /**
+ * Updates configuration parameters.
+ *
+ * @param values
+ * new values of the parameters
+ */
+ void updateConfiguration(List<ConfigurationOption> values);
+
+ /**
+ * Returns {@link lcsb.mapviewer.common.Configuration#systemVersion git version}
+ * from which the system was built.
+ *
+ * @param baseDir
+ * directory where the system is placed
+ * @return git version
+ */
+ String getSystemSvnVersion(String baseDir);
+
+ /**
+ * Returns estimated current memory usage (in MB).
+ *
+ * @return estimated current memory usage (in MB)
+ */
+ Long getMemoryUsage();
+
+ /**
+ * Returns max memory available to JVM (in MB).
+ *
+ * @return max memory available to JVM (in MB)
+ */
+ Long getMaxMemory();
+
+ /**
+ * Returns currently build framework version.
+ *
+ * @param baseDir
+ * directory where the system is placed
+ * @return currently build {@link FrameworkVersion framework version}
+ * @throws InvalidSvnVersionException
+ * thrown when the git version of the build system is invalid
+ */
+ FrameworkVersion getSystemVersion(String baseDir);
+
+ /**
+ * Returns system {@link lcsb.mapviewer.common.Configuration#systemBuild build
+ * date}.
+ *
+ * @param baseDir
+ * directory where the system is placed
+ * @return system build date
+ */
+ String getSystemBuild(String baseDir);
+
+ /**
+ * Returns {@link lcsb.mapviewer.common.Configuration#systemBuildVersion git
+ * hash} of build process.
+ *
+ * @param baseDir
+ * directory where the system is placed
+ * @return git hash
+ */
+ String getSystemGitVersion(String baseDir);
+
+ ConfigurationOption getValue(ConfigurationElementType type);
+
+ ConfigurationOption getValue(PrivilegeType type);
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IExternalServicesService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IExternalServicesService.java
index 4710ae4a6b..241fdc2422 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IExternalServicesService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IExternalServicesService.java
@@ -1,42 +1,42 @@
-package lcsb.mapviewer.services.interfaces;
-
-import java.util.List;
-
-import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
-import lcsb.mapviewer.annotation.services.IExternalService;
-
-/**
- * Service that retrieves information about services that access external
- * resources (like chebi, chembl, etc.).
- *
- * @author Piotr Gawron
- *
- */
-public interface IExternalServicesService {
-
- /**
- * Returns status information about all services.
- *
- * @return status information about all services
- */
- List<ExternalServiceStatus> getExternalServiceStatuses();
-
- /**
- * Registers service that access external resource.
- *
- * @param service
- * service that access external resource
- */
- void registerService(IExternalService service);
-
- /**
- * Registers default list of services.
- */
- void registerDefaultServices();
-
- /**
- * Clears list of known services.
- */
- void clearServices();
-
-}
+package lcsb.mapviewer.services.interfaces;
+
+import java.util.List;
+
+import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
+import lcsb.mapviewer.annotation.services.IExternalService;
+
+/**
+ * Service that retrieves information about services that access external
+ * resources (like chebi, chembl, etc.).
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface IExternalServicesService {
+
+ /**
+ * Returns status information about all services.
+ *
+ * @return status information about all services
+ */
+ List<ExternalServiceStatus> getExternalServiceStatuses();
+
+ /**
+ * Registers service that access external resource.
+ *
+ * @param service
+ * service that access external resource
+ */
+ void registerService(IExternalService service);
+
+ /**
+ * Registers default list of services.
+ */
+ void registerDefaultServices();
+
+ /**
+ * Clears list of known services.
+ */
+ void clearServices();
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java
index 7ae9622f42..1ce62ebd1f 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java
@@ -1,495 +1,495 @@
-package lcsb.mapviewer.services.interfaces;
-
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.List;
-import java.util.Map;
-
-import lcsb.mapviewer.commands.CommandExecutionException;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.utils.EmailSender;
-import lcsb.mapviewer.services.utils.data.ColorSchemaType;
-
-/**
- * Service that manages layouts of the map.
- *
- * @author Piotr Gawron
- *
- */
-public interface ILayoutService {
-
- /**
- * Parameters used for creation of the layout.
- *
- * @author Piotr Gawron
- *
- */
- class CreateLayoutParams {
-
- /**
- * Size of the buffer used to copy stream data.
- */
- private static final int BUFFER_SIZE = 1024;
-
- /**
- * Name of the layout.
- *
- */
- private String name;
-
- /**
- * Description of the layout.
- *
- */
- private String description;
-
- /**
- * Where the graphic files should be saved.
- *
- */
- private String directory;
-
- /**
- *
- * {@link Model} for which the layout is created.
- */
- private Model model;
-
- /**
- * Who creates the layout.
- *
- */
- private User user;
-
- /**
- *
- * Input stream with coloring information data in the stream should correspond
- * to a file that can be parsed by
- * {@link lcsb.mapviewer.services.utils.ColorSchemaXlsxReader ColorSchemaReader}
- * . This is a copy of original input stream, so we can read this input stream
- * multiple times.
- */
- private ByteArrayOutputStream colorInputStreamCopy;
-
- /**
- * Name of the file used as input (if available).
- */
- private String layoutFileName;
-
- /**
- * Determines if creation of the output files should be done asynchronously who
- * creates the layout.
- *
- */
- private boolean async = false;
-
- private boolean googleLicenseConsent = false;
-
- /**
- * Type of the uploaded file.
- */
- private ColorSchemaType colorSchemaType;
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- * @return {@link CreateLayoutParams} object
- */
- public CreateLayoutParams name(String name) {
- this.name = name;
- return this;
- }
-
- /**
- * @return the directory
- * @see #directory
- */
- public String getDirectory() {
- return directory;
- }
-
- /**
- * @param directory
- * the directory to set
- * @see #directory
- * @return {@link CreateLayoutParams} object
- */
- public CreateLayoutParams directory(String directory) {
- this.directory = directory;
- return this;
- }
-
- /**
- * @return the model
- * @see #model
- */
- public Model getModel() {
- return model;
- }
-
- /**
- * @param model
- * the model to set
- * @see #model
- * @return {@link CreateLayoutParams} object
- */
- public CreateLayoutParams model(Model model) {
- this.model = model;
- return this;
- }
-
- /**
- * @return the user
- * @see #user
- */
- public User getUser() {
- return user;
- }
-
- /**
- * @param user
- * the user to set
- * @see #user
- * @return {@link CreateLayoutParams} object
- */
- public CreateLayoutParams user(User user) {
- this.user = user;
- return this;
- }
-
- /**
- * @return the colorInputStream
- * @see #colorInputStream
- */
- public InputStream getColorInputStream() {
- return new ByteArrayInputStream(colorInputStreamCopy.toByteArray());
- }
-
- /**
- * @param colorInputStream
- * the colorInputStream to set
- * @see #colorInputStream
- * @return {@link CreateLayoutParams} object
- * @throws IOException
- * thrown when there is a problem with accessing input stream
- */
- public CreateLayoutParams colorInputStream(InputStream colorInputStream) throws IOException {
- if (colorInputStream == null) {
- this.colorInputStreamCopy = null;
- } else {
- this.colorInputStreamCopy = new ByteArrayOutputStream();
-
- byte[] buffer = new byte[BUFFER_SIZE];
- int len;
- while ((len = colorInputStream.read(buffer)) > -1) {
- this.colorInputStreamCopy.write(buffer, 0, len);
- }
- this.colorInputStreamCopy.flush();
- }
- return this;
- }
-
- /**
- * @return the async
- * @see #async
- */
- public boolean isAsync() {
- return async;
- }
-
- /**
- * @param async
- * the async to set
- * @see #async
- * @return {@link CreateLayoutParams} object
- */
- public CreateLayoutParams async(boolean async) {
- this.async = async;
- return this;
- }
-
- /**
- * @return the googleLicenseConsent
- * @see #googleLicenseConsent
- */
- public boolean isGoogleLicenseConsent() {
- return googleLicenseConsent;
- }
-
- /**
- * @param googleLicenseConsent
- * the googleLicenseConsent to set
- * @see #googleLicenseConsent
- * @return {@link CreateLayoutParams} object
- */
- public CreateLayoutParams googleLicenseConsent(boolean googleLicenseConsent) {
- this.googleLicenseConsent = googleLicenseConsent;
- return this;
- }
-
- /**
- * @return the description
- * @see #description
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * @param description
- * the description to set
- * @see #description
- * @return {@link CreateLayoutParams} object
- */
- public CreateLayoutParams description(String description) {
- this.description = description;
- return this;
- }
-
- /**
- *
- * @return {@link #colorSchemaType}
- */
- public ColorSchemaType getColorSchemaType() {
- return colorSchemaType;
- }
-
- /**
- * @param colorSchemaType
- * the colorSchemaType to set
- * @see #colorSchemaType
- * @return {@link CreateLayoutParams} object
- */
- public CreateLayoutParams colorSchemaType(ColorSchemaType colorSchemaType) {
- this.colorSchemaType = colorSchemaType;
- return this;
- }
-
- /**
- * @return the layoutFileName
- * @see #layoutFileName
- */
- public String getLayoutFileName() {
- return layoutFileName;
- }
-
- /**
- * @param layoutFileName
- * the layoutFileName to set
- * @return {@link CreateLayoutParams} object
- * @see #layoutFileName
- */
- public CreateLayoutParams layoutFileName(String layoutFileName) {
- this.layoutFileName = layoutFileName;
- return this;
- }
- }
-
- /**
- * Returns true if user can add layout to the model.
- *
- * @param model
- * to which model user wants to add layout
- * @param user
- * who wants to add layout
- * @return <code>true</code> if user can add layout, <code>false</code>
- * otherwise
- */
- boolean userCanAddLayout(Model model, User user);
-
- /**
- * Returns true if user can remove layout from the model.
- *
- * @param layout
- * which layout user want to remove
- * @param user
- * who wants to remove layout
- * @return <code>true</code> if user can remove layout, <code>false</code>
- * otherwise
- */
- boolean userCanRemoveLayout(Layout layout, User user);
-
- /**
- * Removes layout from the system.
- *
- * @param layout
- * layout to remove
- * @param homeDir
- * directory where the system is deployed
- * @throws IOException
- * thrown when there are problems with removing layout files
- */
- void removeLayout(Layout layout, String homeDir) throws IOException;
-
- /**
- * Updates data about the layout.
- *
- * @param layout
- * layout to update
- */
- void updateLayout(Layout layout);
-
- /**
- * Adds view privilege to the layout for the user.
- *
- * @param layout
- * layout for privilege
- * @param user
- * who should own the privilege
- */
- void addViewPrivilegeToLayout(Layout layout, User user);
-
- /**
- * Removes view privilege to the layout from the user.
- *
- * @param layout
- * layout for privilege remove
- * @param user
- * who shouldn't have the privilege
- */
- void dropViewPrivilegeFromLayout(Layout layout, User user);
-
- /**
- * Create layout based on the data in the parameter.
- *
- * @param params
- * list of {@link CreateLayoutParams params} necessary to create layout
- * @return object that refers to created layout
- * @throws IOException
- * thrown when there are problems with files
- * @throws InvalidColorSchemaException
- * if the coloring source is invalid
- * @throws CommandExecutionException
- */
- Layout createLayout(CreateLayoutParams params) throws IOException, InvalidColorSchemaException;
-
- /**
- * Create layout based on the data in the parameter. Layout will contain set of
- * images that can be further visualized in goolge maps api.
- *
- * @param params
- * list of {@link CreateLayoutParams params} necessary to create layout
- * @return object that refers to created layout
- * @throws IOException
- * thrown when there are problems with files
- * @throws CommandExecutionException
- * if the coloring source is invalid
- * @throws InvalidColorSchemaException
- * if the coloring source is invalid
- */
- Layout createLayoutWithImages(CreateLayoutParams params)
- throws IOException, CommandExecutionException, InvalidColorSchemaException;
-
- /**
- * Returns number of still available custom layouts for the user.
- *
- * @param user
- * user for which the number of available custom layouts will be
- * returned
- * @return number of available custom layouts
- */
- long getAvailableCustomLayoutsNumber(User user);
-
- /**
- * Returns a list of pairs {@link Element} - {@link ColorSchema} that are visualized in
- * a {@link lcsb.mapviewer.model.map.layout.Layout}.
- *
- * @param model
- * model where data is located
- * @param layoutId
- * identifier of the layout
- * @return a list of pairs {@link Element} - {@link ColorSchema} that are visualized in
- * a {@link lcsb.mapviewer.model.map.layout.Layout}
- * @throws SecurityException
- */
- List<Pair<Element, ColorSchema>> getAliasesForLayout(Model model, int layoutId, String token)
- throws SecurityException;
-
- /**
- * Returns a list of pairs {@link Reaction} - {@link ColorSchema}} that are
- * visualized in a {@link lcsb.mapviewer.model.map.layout.Layout}.
- *
- * @param model
- * model where data is located
- * @param layoutId
- * identifier of the layout
- * @return a list of pairs {@link Reaction} - {@link ColorSchema} that are
- * visualized in a {@link lcsb.mapviewer.model.map.layout.Layout}
- * @throws SecurityException
- */
- List<Pair<Reaction, ColorSchema>> getReactionsForLayout(Model model, int layoutId, String token)
- throws SecurityException;
-
- /**
- * Returns mapping between {@link lcsb.mapviewer.model.map.species.Element
- * Alias}/ {@link lcsb.mapviewer.model.map.reaction.Reaction Reaction} and
- * {@link ColorSchema} used for coloring object in the layout given in the
- * parameter.
- *
- * @param model
- * model where data is located
- * @param layoutId
- * identifier of the layout
- * @return a list of pairs {@link Element} - {@link ColorSchema} that are
- * visualized in a {@link lcsb.mapviewer.model.map.layout.Layout}
- * @throws SecurityException
- */
- Map<Object, ColorSchema> getElementsForLayout(Model model, Integer layoutId, String token) throws SecurityException;
-
- Pair<Element, ColorSchema> getFullAliasForLayout(Model model, Integer id, int layoutId, String token)
- throws SecurityException;
-
- Pair<Reaction, ColorSchema> getFullReactionForLayout(Model model, Integer id, int layoutId, String token)
- throws SecurityException;
-
- /**
- * Returns {@link EmailSender} used by the service.
- *
- * @return {@link EmailSender} used by the service
- */
- EmailSender getEmailSender();
-
- /**
- * Sets {@link EmailSender} used by the service.
- *
- * @param emailSender
- * {@link EmailSender} used by the service
- */
- void setEmailSender(EmailSender emailSender);
-
- /**
- * Returns list of custom layouts.
- *
- * @param model
- * model where the layouts lay on
- * @param user
- * user who asks for the layouts
- * @return list of custom layouts
- */
- List<Layout> getCustomLayouts(Model model, String token, Boolean publicOverlay, User creator)
- throws SecurityException;
-
- Layout getLayoutById(int overlayId, String token) throws SecurityException;
-
- boolean userCanRemoveLayout(Layout layout, String authenticationToken) throws SecurityException;
-
-}
+package lcsb.mapviewer.services.interfaces;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.List;
+import java.util.Map;
+
+import lcsb.mapviewer.commands.CommandExecutionException;
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
+import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.utils.EmailSender;
+import lcsb.mapviewer.services.utils.data.ColorSchemaType;
+
+/**
+ * Service that manages layouts of the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface ILayoutService {
+
+ /**
+ * Parameters used for creation of the layout.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ class CreateLayoutParams {
+
+ /**
+ * Size of the buffer used to copy stream data.
+ */
+ private static final int BUFFER_SIZE = 1024;
+
+ /**
+ * Name of the layout.
+ *
+ */
+ private String name;
+
+ /**
+ * Description of the layout.
+ *
+ */
+ private String description;
+
+ /**
+ * Where the graphic files should be saved.
+ *
+ */
+ private String directory;
+
+ /**
+ *
+ * {@link Model} for which the layout is created.
+ */
+ private Model model;
+
+ /**
+ * Who creates the layout.
+ *
+ */
+ private User user;
+
+ /**
+ *
+ * Input stream with coloring information data in the stream should correspond
+ * to a file that can be parsed by
+ * {@link lcsb.mapviewer.services.utils.ColorSchemaXlsxReader ColorSchemaReader}
+ * . This is a copy of original input stream, so we can read this input stream
+ * multiple times.
+ */
+ private ByteArrayOutputStream colorInputStreamCopy;
+
+ /**
+ * Name of the file used as input (if available).
+ */
+ private String layoutFileName;
+
+ /**
+ * Determines if creation of the output files should be done asynchronously who
+ * creates the layout.
+ *
+ */
+ private boolean async = false;
+
+ private boolean googleLicenseConsent = false;
+
+ /**
+ * Type of the uploaded file.
+ */
+ private ColorSchemaType colorSchemaType;
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ * @return {@link CreateLayoutParams} object
+ */
+ public CreateLayoutParams name(String name) {
+ this.name = name;
+ return this;
+ }
+
+ /**
+ * @return the directory
+ * @see #directory
+ */
+ public String getDirectory() {
+ return directory;
+ }
+
+ /**
+ * @param directory
+ * the directory to set
+ * @see #directory
+ * @return {@link CreateLayoutParams} object
+ */
+ public CreateLayoutParams directory(String directory) {
+ this.directory = directory;
+ return this;
+ }
+
+ /**
+ * @return the model
+ * @see #model
+ */
+ public Model getModel() {
+ return model;
+ }
+
+ /**
+ * @param model
+ * the model to set
+ * @see #model
+ * @return {@link CreateLayoutParams} object
+ */
+ public CreateLayoutParams model(Model model) {
+ this.model = model;
+ return this;
+ }
+
+ /**
+ * @return the user
+ * @see #user
+ */
+ public User getUser() {
+ return user;
+ }
+
+ /**
+ * @param user
+ * the user to set
+ * @see #user
+ * @return {@link CreateLayoutParams} object
+ */
+ public CreateLayoutParams user(User user) {
+ this.user = user;
+ return this;
+ }
+
+ /**
+ * @return the colorInputStream
+ * @see #colorInputStream
+ */
+ public InputStream getColorInputStream() {
+ return new ByteArrayInputStream(colorInputStreamCopy.toByteArray());
+ }
+
+ /**
+ * @param colorInputStream
+ * the colorInputStream to set
+ * @see #colorInputStream
+ * @return {@link CreateLayoutParams} object
+ * @throws IOException
+ * thrown when there is a problem with accessing input stream
+ */
+ public CreateLayoutParams colorInputStream(InputStream colorInputStream) throws IOException {
+ if (colorInputStream == null) {
+ this.colorInputStreamCopy = null;
+ } else {
+ this.colorInputStreamCopy = new ByteArrayOutputStream();
+
+ byte[] buffer = new byte[BUFFER_SIZE];
+ int len;
+ while ((len = colorInputStream.read(buffer)) > -1) {
+ this.colorInputStreamCopy.write(buffer, 0, len);
+ }
+ this.colorInputStreamCopy.flush();
+ }
+ return this;
+ }
+
+ /**
+ * @return the async
+ * @see #async
+ */
+ public boolean isAsync() {
+ return async;
+ }
+
+ /**
+ * @param async
+ * the async to set
+ * @see #async
+ * @return {@link CreateLayoutParams} object
+ */
+ public CreateLayoutParams async(boolean async) {
+ this.async = async;
+ return this;
+ }
+
+ /**
+ * @return the googleLicenseConsent
+ * @see #googleLicenseConsent
+ */
+ public boolean isGoogleLicenseConsent() {
+ return googleLicenseConsent;
+ }
+
+ /**
+ * @param googleLicenseConsent
+ * the googleLicenseConsent to set
+ * @see #googleLicenseConsent
+ * @return {@link CreateLayoutParams} object
+ */
+ public CreateLayoutParams googleLicenseConsent(boolean googleLicenseConsent) {
+ this.googleLicenseConsent = googleLicenseConsent;
+ return this;
+ }
+
+ /**
+ * @return the description
+ * @see #description
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * @param description
+ * the description to set
+ * @see #description
+ * @return {@link CreateLayoutParams} object
+ */
+ public CreateLayoutParams description(String description) {
+ this.description = description;
+ return this;
+ }
+
+ /**
+ *
+ * @return {@link #colorSchemaType}
+ */
+ public ColorSchemaType getColorSchemaType() {
+ return colorSchemaType;
+ }
+
+ /**
+ * @param colorSchemaType
+ * the colorSchemaType to set
+ * @see #colorSchemaType
+ * @return {@link CreateLayoutParams} object
+ */
+ public CreateLayoutParams colorSchemaType(ColorSchemaType colorSchemaType) {
+ this.colorSchemaType = colorSchemaType;
+ return this;
+ }
+
+ /**
+ * @return the layoutFileName
+ * @see #layoutFileName
+ */
+ public String getLayoutFileName() {
+ return layoutFileName;
+ }
+
+ /**
+ * @param layoutFileName
+ * the layoutFileName to set
+ * @return {@link CreateLayoutParams} object
+ * @see #layoutFileName
+ */
+ public CreateLayoutParams layoutFileName(String layoutFileName) {
+ this.layoutFileName = layoutFileName;
+ return this;
+ }
+ }
+
+ /**
+ * Returns true if user can add layout to the model.
+ *
+ * @param model
+ * to which model user wants to add layout
+ * @param user
+ * who wants to add layout
+ * @return <code>true</code> if user can add layout, <code>false</code>
+ * otherwise
+ */
+ boolean userCanAddLayout(Model model, User user);
+
+ /**
+ * Returns true if user can remove layout from the model.
+ *
+ * @param layout
+ * which layout user want to remove
+ * @param user
+ * who wants to remove layout
+ * @return <code>true</code> if user can remove layout, <code>false</code>
+ * otherwise
+ */
+ boolean userCanRemoveLayout(Layout layout, User user);
+
+ /**
+ * Removes layout from the system.
+ *
+ * @param layout
+ * layout to remove
+ * @param homeDir
+ * directory where the system is deployed
+ * @throws IOException
+ * thrown when there are problems with removing layout files
+ */
+ void removeLayout(Layout layout, String homeDir) throws IOException;
+
+ /**
+ * Updates data about the layout.
+ *
+ * @param layout
+ * layout to update
+ */
+ void updateLayout(Layout layout);
+
+ /**
+ * Adds view privilege to the layout for the user.
+ *
+ * @param layout
+ * layout for privilege
+ * @param user
+ * who should own the privilege
+ */
+ void addViewPrivilegeToLayout(Layout layout, User user);
+
+ /**
+ * Removes view privilege to the layout from the user.
+ *
+ * @param layout
+ * layout for privilege remove
+ * @param user
+ * who shouldn't have the privilege
+ */
+ void dropViewPrivilegeFromLayout(Layout layout, User user);
+
+ /**
+ * Create layout based on the data in the parameter.
+ *
+ * @param params
+ * list of {@link CreateLayoutParams params} necessary to create layout
+ * @return object that refers to created layout
+ * @throws IOException
+ * thrown when there are problems with files
+ * @throws InvalidColorSchemaException
+ * if the coloring source is invalid
+ * @throws CommandExecutionException
+ */
+ Layout createLayout(CreateLayoutParams params) throws IOException, InvalidColorSchemaException;
+
+ /**
+ * Create layout based on the data in the parameter. Layout will contain set of
+ * images that can be further visualized in goolge maps api.
+ *
+ * @param params
+ * list of {@link CreateLayoutParams params} necessary to create layout
+ * @return object that refers to created layout
+ * @throws IOException
+ * thrown when there are problems with files
+ * @throws CommandExecutionException
+ * if the coloring source is invalid
+ * @throws InvalidColorSchemaException
+ * if the coloring source is invalid
+ */
+ Layout createLayoutWithImages(CreateLayoutParams params)
+ throws IOException, CommandExecutionException, InvalidColorSchemaException;
+
+ /**
+ * Returns number of still available custom layouts for the user.
+ *
+ * @param user
+ * user for which the number of available custom layouts will be
+ * returned
+ * @return number of available custom layouts
+ */
+ long getAvailableCustomLayoutsNumber(User user);
+
+ /**
+ * Returns a list of pairs {@link Element} - {@link ColorSchema} that are visualized in
+ * a {@link lcsb.mapviewer.model.map.layout.Layout}.
+ *
+ * @param model
+ * model where data is located
+ * @param layoutId
+ * identifier of the layout
+ * @return a list of pairs {@link Element} - {@link ColorSchema} that are visualized in
+ * a {@link lcsb.mapviewer.model.map.layout.Layout}
+ * @throws SecurityException
+ */
+ List<Pair<Element, ColorSchema>> getAliasesForLayout(Model model, int layoutId, String token)
+ throws SecurityException;
+
+ /**
+ * Returns a list of pairs {@link Reaction} - {@link ColorSchema}} that are
+ * visualized in a {@link lcsb.mapviewer.model.map.layout.Layout}.
+ *
+ * @param model
+ * model where data is located
+ * @param layoutId
+ * identifier of the layout
+ * @return a list of pairs {@link Reaction} - {@link ColorSchema} that are
+ * visualized in a {@link lcsb.mapviewer.model.map.layout.Layout}
+ * @throws SecurityException
+ */
+ List<Pair<Reaction, ColorSchema>> getReactionsForLayout(Model model, int layoutId, String token)
+ throws SecurityException;
+
+ /**
+ * Returns mapping between {@link lcsb.mapviewer.model.map.species.Element
+ * Alias}/ {@link lcsb.mapviewer.model.map.reaction.Reaction Reaction} and
+ * {@link ColorSchema} used for coloring object in the layout given in the
+ * parameter.
+ *
+ * @param model
+ * model where data is located
+ * @param layoutId
+ * identifier of the layout
+ * @return a list of pairs {@link Element} - {@link ColorSchema} that are
+ * visualized in a {@link lcsb.mapviewer.model.map.layout.Layout}
+ * @throws SecurityException
+ */
+ Map<Object, ColorSchema> getElementsForLayout(Model model, Integer layoutId, String token) throws SecurityException;
+
+ Pair<Element, ColorSchema> getFullAliasForLayout(Model model, Integer id, int layoutId, String token)
+ throws SecurityException;
+
+ Pair<Reaction, ColorSchema> getFullReactionForLayout(Model model, Integer id, int layoutId, String token)
+ throws SecurityException;
+
+ /**
+ * Returns {@link EmailSender} used by the service.
+ *
+ * @return {@link EmailSender} used by the service
+ */
+ EmailSender getEmailSender();
+
+ /**
+ * Sets {@link EmailSender} used by the service.
+ *
+ * @param emailSender
+ * {@link EmailSender} used by the service
+ */
+ void setEmailSender(EmailSender emailSender);
+
+ /**
+ * Returns list of custom layouts.
+ *
+ * @param model
+ * model where the layouts lay on
+ * @param user
+ * user who asks for the layouts
+ * @return list of custom layouts
+ */
+ List<Layout> getCustomLayouts(Model model, String token, Boolean publicOverlay, User creator)
+ throws SecurityException;
+
+ Layout getLayoutById(int overlayId, String token) throws SecurityException;
+
+ boolean userCanRemoveLayout(Layout layout, String authenticationToken) throws SecurityException;
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/ILdapService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/ILdapService.java
index 8a56e5c37b..9312868b8c 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/ILdapService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/ILdapService.java
@@ -1,61 +1,61 @@
-package lcsb.mapviewer.services.interfaces;
-
-import java.util.List;
-
-import com.unboundid.ldap.sdk.LDAPException;
-
-import lcsb.mapviewer.model.user.ConfigurationElementTypeGroup;
-import lcsb.mapviewer.services.UserDTO;
-
-/**
- * Connection service to LDAP server.
- *
- * @author Piotr Gawron
- *
- */
-public interface ILdapService {
-
- /**
- * Checks if login and password match
- *
- * @param login
- * user login
- * @param password
- * password
- * @return true if user login/password match
- * @throws LDAPException
- * thrown when there is problem with LDAP connection
- */
- boolean login(String login, String password) throws LDAPException;
-
- /**
- * Returns list of user names available in the LDAP server.
- *
- * @return list of user names
- * @throws LDAPException
- * thrown when there is problem with LDAP connection
- */
- List<String> getUsernames() throws LDAPException;
-
- /**
- * Returns user data information from LDAP for given login.
- *
- * @param login
- * user for which we obtain data
- * @return user data information from LDAP for given login or null if such user
- * doesn't exist
- * @throws LDAPException
- * thrown when there is problem with LDAP connection
- */
- UserDTO getUserByLogin(String login) throws LDAPException;
-
- /**
- * Checks if LDAP configuration
- * ({@link ConfigurationElementTypeGroup#LDAP_CONFIGURATION}) is valid.
- *
- * @return true if LDAP configuration
- * ({@link ConfigurationElementTypeGroup#LDAP_CONFIGURATION}) is valid
- */
- boolean isValidConfiguration();
-
-}
+package lcsb.mapviewer.services.interfaces;
+
+import java.util.List;
+
+import com.unboundid.ldap.sdk.LDAPException;
+
+import lcsb.mapviewer.model.user.ConfigurationElementTypeGroup;
+import lcsb.mapviewer.services.UserDTO;
+
+/**
+ * Connection service to LDAP server.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface ILdapService {
+
+ /**
+ * Checks if login and password match
+ *
+ * @param login
+ * user login
+ * @param password
+ * password
+ * @return true if user login/password match
+ * @throws LDAPException
+ * thrown when there is problem with LDAP connection
+ */
+ boolean login(String login, String password) throws LDAPException;
+
+ /**
+ * Returns list of user names available in the LDAP server.
+ *
+ * @return list of user names
+ * @throws LDAPException
+ * thrown when there is problem with LDAP connection
+ */
+ List<String> getUsernames() throws LDAPException;
+
+ /**
+ * Returns user data information from LDAP for given login.
+ *
+ * @param login
+ * user for which we obtain data
+ * @return user data information from LDAP for given login or null if such user
+ * doesn't exist
+ * @throws LDAPException
+ * thrown when there is problem with LDAP connection
+ */
+ UserDTO getUserByLogin(String login) throws LDAPException;
+
+ /**
+ * Checks if LDAP configuration
+ * ({@link ConfigurationElementTypeGroup#LDAP_CONFIGURATION}) is valid.
+ *
+ * @return true if LDAP configuration
+ * ({@link ConfigurationElementTypeGroup#LDAP_CONFIGURATION}) is valid
+ */
+ boolean isValidConfiguration();
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/ILogService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/ILogService.java
index 981853902d..dec650d971 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/ILogService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/ILogService.java
@@ -1,135 +1,135 @@
-package lcsb.mapviewer.services.interfaces;
-
-import lcsb.mapviewer.model.log.GenericLog;
-import lcsb.mapviewer.model.log.LogType;
-import lcsb.mapviewer.model.user.User;
-
-/**
- * Service that allows to log some system messages.
- *
- * @author Piotr Gawron
- *
- */
-public interface ILogService {
- /**
- * Structure describing log event parameters.
- *
- * @author Piotr Gawron
- *
- */
- class LogParams {
- /**
- * Type of the log event. Field is obligatory.
- */
- private LogType type;
- /**
- * Description of the log event.
- */
- private String description;
- /**
- * Object to which this entry refers to.
- */
- private Object object;
- /**
- * Logged user that caused this entry. If set to null then value from
- * {@link ILogService#setLoggedUser(User)} will be used.
- */
- private User user;
-
- /**
- * @return the type
- * @see #type
- */
- public LogType getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- * @return {@link LogParams object} with all params
- */
- public LogParams type(LogType type) {
- this.type = type;
- return this;
- }
-
- /**
- * @return the description
- * @see #description
- */
- public String description() {
- return description;
- }
-
- /**
- * @param description
- * the description to set
- * @see #description
- * @return {@link LogParams object} with all params
- */
- public LogParams description(String description) {
- this.description = description;
- return this;
- }
-
- /**
- * @return the object
- * @see #object
- */
- public Object getObject() {
- return object;
- }
-
- /**
- * @param object
- * the object to set
- * @see #object
- * @return {@link LogParams object} with all params
- */
- public LogParams object(Object object) {
- this.object = object;
- return this;
- }
-
- /**
- * @return the user
- * @see #user
- */
- public User getUser() {
- return user;
- }
-
- /**
- * @param user
- * the user to set
- * @see #user
- * @return {@link LogParams object} with all params
- */
- public LogParams user(User user) {
- this.user = user;
- return this;
- }
- }
-
- /**
- * Method adds a log entry. The parameters define additional information about
- * log.
- *
- * @param params
- * {@link LogParams params} of the log
- * @return returns created log entry
- */
- GenericLog log(LogParams params);
-
- /**
- * Sets user that should be used as default user to be put as the author of
- * new entries.
- *
- * @param loggedUser
- * user that should be used as a deafult one for loggin events. This
- * value is always overriden by {@link LogParams#user} (if set).
- */
- void setLoggedUser(User loggedUser);
-}
+package lcsb.mapviewer.services.interfaces;
+
+import lcsb.mapviewer.model.log.GenericLog;
+import lcsb.mapviewer.model.log.LogType;
+import lcsb.mapviewer.model.user.User;
+
+/**
+ * Service that allows to log some system messages.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface ILogService {
+ /**
+ * Structure describing log event parameters.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ class LogParams {
+ /**
+ * Type of the log event. Field is obligatory.
+ */
+ private LogType type;
+ /**
+ * Description of the log event.
+ */
+ private String description;
+ /**
+ * Object to which this entry refers to.
+ */
+ private Object object;
+ /**
+ * Logged user that caused this entry. If set to null then value from
+ * {@link ILogService#setLoggedUser(User)} will be used.
+ */
+ private User user;
+
+ /**
+ * @return the type
+ * @see #type
+ */
+ public LogType getType() {
+ return type;
+ }
+
+ /**
+ * @param type
+ * the type to set
+ * @see #type
+ * @return {@link LogParams object} with all params
+ */
+ public LogParams type(LogType type) {
+ this.type = type;
+ return this;
+ }
+
+ /**
+ * @return the description
+ * @see #description
+ */
+ public String description() {
+ return description;
+ }
+
+ /**
+ * @param description
+ * the description to set
+ * @see #description
+ * @return {@link LogParams object} with all params
+ */
+ public LogParams description(String description) {
+ this.description = description;
+ return this;
+ }
+
+ /**
+ * @return the object
+ * @see #object
+ */
+ public Object getObject() {
+ return object;
+ }
+
+ /**
+ * @param object
+ * the object to set
+ * @see #object
+ * @return {@link LogParams object} with all params
+ */
+ public LogParams object(Object object) {
+ this.object = object;
+ return this;
+ }
+
+ /**
+ * @return the user
+ * @see #user
+ */
+ public User getUser() {
+ return user;
+ }
+
+ /**
+ * @param user
+ * the user to set
+ * @see #user
+ * @return {@link LogParams object} with all params
+ */
+ public LogParams user(User user) {
+ this.user = user;
+ return this;
+ }
+ }
+
+ /**
+ * Method adds a log entry. The parameters define additional information about
+ * log.
+ *
+ * @param params
+ * {@link LogParams params} of the log
+ * @return returns created log entry
+ */
+ GenericLog log(LogParams params);
+
+ /**
+ * Sets user that should be used as default user to be put as the author of
+ * new entries.
+ *
+ * @param loggedUser
+ * user that should be used as a deafult one for loggin events. This
+ * value is always overriden by {@link LogParams#user} (if set).
+ */
+ void setLoggedUser(User loggedUser);
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IMiriamService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IMiriamService.java
index 8afe870925..b0fca3a3e3 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IMiriamService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IMiriamService.java
@@ -1,32 +1,32 @@
-package lcsb.mapviewer.services.interfaces;
-
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-
-/**
- * Service responsible for accessing miriam registry.
- *
- * @author Piotr Gawron
- *
- */
-public interface IMiriamService {
-
- /**
- * Returns url for data represented by {@link MiriamData}.
- *
- * @param md
- * object to which link will be returned
- * @return url to miriam data
- */
- String getUrlForMiriamData(MiriamData md);
-
- /**
- * Returns {@link MiriamType} associated with parameter uri address.
- *
- * @param uri
- * uri to check
- * @return {@link MiriamType} for given uri
- */
- MiriamType getTypeForUri(String uri);
-
-}
+package lcsb.mapviewer.services.interfaces;
+
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+
+/**
+ * Service responsible for accessing miriam registry.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface IMiriamService {
+
+ /**
+ * Returns url for data represented by {@link MiriamData}.
+ *
+ * @param md
+ * object to which link will be returned
+ * @return url to miriam data
+ */
+ String getUrlForMiriamData(MiriamData md);
+
+ /**
+ * Returns {@link MiriamType} associated with parameter uri address.
+ *
+ * @param uri
+ * uri to check
+ * @return {@link MiriamType} for given uri
+ */
+ MiriamType getTypeForUri(String uri);
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java
index a5e8532d9b..7916e1a38e 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java
@@ -1,136 +1,136 @@
-package lcsb.mapviewer.services.interfaces;
-
-import java.util.List;
-
-import org.primefaces.model.TreeNode;
-
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.model.user.UserAnnotationSchema;
-import lcsb.mapviewer.model.user.UserAnnotatorsParam;
-import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.UserAccessException;
-import lcsb.mapviewer.services.utils.CreateProjectParams;
-
-/**
- * Service that manages projects.
- *
- * @author Piotr Gawron
- *
- */
-public interface IProjectService {
-
- /**
- * Returns a project with a give {@link Project#projectId project identifier}.
- *
- * @param projectId
- * {@link Project#projectId project identifier}
- * @return project with an identifier given as parameter. Null if such project
- * doesn't exist.
- * @throws SecurityException
- */
- Project getProjectByProjectId(String projectId, String token) throws UserAccessException, SecurityException;
-
- /**
- * Checks if project with a given {@link Project#projectId identifier} exists.
- *
- * @param projectId
- * {@link Project#projectId project identifier}
- * @return <code>true</code> if the project with the given name exists,
- * <code>false</code> otherwise
- */
- boolean projectExists(String projectId);
-
- /**
- * Returns list of all projects.
- *
- * @return list of all projects.
- * @throws SecurityException
- */
- List<Project> getAllProjects(String token) throws SecurityException;
-
- /**
- * Removes project from the system.
- *
- * @param homeDir
- * directory where the system is deployed
- * @param project
- * object to remove
- * @param async
- * should the operation be done asynchronously
- * @throws SecurityException
- */
- void removeProject(Project project, String homeDir, boolean async, String token) throws SecurityException;
-
- /**
- * Adds project to the system.
- *
- * @param project
- * object to add
- */
- void addProject(Project project);
-
- /**
- * Creates project using give parameters. See {@link CreateProjectParams}.
- *
- * @param params
- * information about project to create
- * @throws SecurityException
- */
- void createProject(CreateProjectParams params) throws SecurityException;
-
- /**
- * Creates {@link TreeNode} that contains information about all classes that can
- * be annotated and associate set of
- * {@link lcsb.mapviewer.annotation.services.annotators.ElementAnnotator
- * ElementAnnotator} valid for these classes.
- *
- * @param user
- * for which information should be retrieved
- * @return {@link TreeNode} that contains information about all classes that can
- * be annotated
- */
- TreeNode createClassAnnotatorTree(User user);
-
- /**
- * Update default set of annotators, lists of required/valid annotations for a
- * given user and default params used when creating project.
- *
- * @param user
- * user for which we update information
- * @param sbgnFormat
- * new
- * {@link lcsb.mapviewer.model.user.UserAnnotationSchema#sbgnFormat}
- * value
- * @param networkLayoutAsDefault
- * new
- * {@link lcsb.mapviewer.model.user.UserAnnotationSchema#networkLayoutAsDefault}
- * value
- * @param annotatorsTree
- * {@link TreeNode} that contains information about all classes that
- * can be annotated
- */
- void updateClassAnnotatorTreeForUser(User user, TreeNode annotatorsTree, boolean sbgnFormat,
- boolean networkLayoutAsDefault);
-
- /**
- * Method that updates information about raw {@link Project} object.
- *
- * @param project
- * project to update
- * @throws SecurityException
- */
- void updateProject(Project project, String token) throws SecurityException;
-
- UserAnnotationSchema prepareUserAnnotationSchema(User user);
-
- /**
- * Retrieves list of annotators {@link UserAnnotatorsParam parameters}
- *
- * @return list of annotators parameters
- */
- List<UserAnnotatorsParam> getAnnotatorsParams(User user);
-
- List<Project> getAllProjects();
-
-}
+package lcsb.mapviewer.services.interfaces;
+
+import java.util.List;
+
+import org.primefaces.model.TreeNode;
+
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.model.user.UserAnnotationSchema;
+import lcsb.mapviewer.model.user.UserAnnotatorsParam;
+import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.UserAccessException;
+import lcsb.mapviewer.services.utils.CreateProjectParams;
+
+/**
+ * Service that manages projects.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface IProjectService {
+
+ /**
+ * Returns a project with a give {@link Project#projectId project identifier}.
+ *
+ * @param projectId
+ * {@link Project#projectId project identifier}
+ * @return project with an identifier given as parameter. Null if such project
+ * doesn't exist.
+ * @throws SecurityException
+ */
+ Project getProjectByProjectId(String projectId, String token) throws UserAccessException, SecurityException;
+
+ /**
+ * Checks if project with a given {@link Project#projectId identifier} exists.
+ *
+ * @param projectId
+ * {@link Project#projectId project identifier}
+ * @return <code>true</code> if the project with the given name exists,
+ * <code>false</code> otherwise
+ */
+ boolean projectExists(String projectId);
+
+ /**
+ * Returns list of all projects.
+ *
+ * @return list of all projects.
+ * @throws SecurityException
+ */
+ List<Project> getAllProjects(String token) throws SecurityException;
+
+ /**
+ * Removes project from the system.
+ *
+ * @param homeDir
+ * directory where the system is deployed
+ * @param project
+ * object to remove
+ * @param async
+ * should the operation be done asynchronously
+ * @throws SecurityException
+ */
+ void removeProject(Project project, String homeDir, boolean async, String token) throws SecurityException;
+
+ /**
+ * Adds project to the system.
+ *
+ * @param project
+ * object to add
+ */
+ void addProject(Project project);
+
+ /**
+ * Creates project using give parameters. See {@link CreateProjectParams}.
+ *
+ * @param params
+ * information about project to create
+ * @throws SecurityException
+ */
+ void createProject(CreateProjectParams params) throws SecurityException;
+
+ /**
+ * Creates {@link TreeNode} that contains information about all classes that can
+ * be annotated and associate set of
+ * {@link lcsb.mapviewer.annotation.services.annotators.ElementAnnotator
+ * ElementAnnotator} valid for these classes.
+ *
+ * @param user
+ * for which information should be retrieved
+ * @return {@link TreeNode} that contains information about all classes that can
+ * be annotated
+ */
+ TreeNode createClassAnnotatorTree(User user);
+
+ /**
+ * Update default set of annotators, lists of required/valid annotations for a
+ * given user and default params used when creating project.
+ *
+ * @param user
+ * user for which we update information
+ * @param sbgnFormat
+ * new
+ * {@link lcsb.mapviewer.model.user.UserAnnotationSchema#sbgnFormat}
+ * value
+ * @param networkLayoutAsDefault
+ * new
+ * {@link lcsb.mapviewer.model.user.UserAnnotationSchema#networkLayoutAsDefault}
+ * value
+ * @param annotatorsTree
+ * {@link TreeNode} that contains information about all classes that
+ * can be annotated
+ */
+ void updateClassAnnotatorTreeForUser(User user, TreeNode annotatorsTree, boolean sbgnFormat,
+ boolean networkLayoutAsDefault);
+
+ /**
+ * Method that updates information about raw {@link Project} object.
+ *
+ * @param project
+ * project to update
+ * @throws SecurityException
+ */
+ void updateProject(Project project, String token) throws SecurityException;
+
+ UserAnnotationSchema prepareUserAnnotationSchema(User user);
+
+ /**
+ * Retrieves list of annotators {@link UserAnnotatorsParam parameters}
+ *
+ * @return list of annotators parameters
+ */
+ List<UserAnnotatorsParam> getAnnotatorsParams(User user);
+
+ List<Project> getAllProjects();
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IReferenceGenomeService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IReferenceGenomeService.java
index 71af2fae75..de95af36b2 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IReferenceGenomeService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IReferenceGenomeService.java
@@ -1,147 +1,147 @@
-package lcsb.mapviewer.services.interfaces;
-
-import java.io.IOException;
-import java.net.URISyntaxException;
-import java.util.List;
-
-import lcsb.mapviewer.annotation.services.genome.ReferenceGenomeConnectorException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.layout.ReferenceGenome;
-import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
-import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
-
-/**
- * Service used to maintain reference genome data.
- *
- * @author Piotr Gawron
- *
- */
-public interface IReferenceGenomeService {
-
- /**
- * Adds reference genome to the system.
- *
- * @param type
- * {@link ReferenceGenomeType type} of reference genome
- * @param organism
- * organism for which reference genome is added
- * @param version
- * version of the reference genome
- * @param customUrl
- * url from which reference genome should be downloaded
- * @throws IOException
- * thrown when there is a problem with downloading file
- * @throws URISyntaxException
- * thrown when url is invalid
- * @throws ReferenceGenomeConnectorException
- * thrown when reference genome already exists or there is problem
- * with adding genome
- */
- void addReferenceGenome(ReferenceGenomeType type, MiriamData organism, String version, String customUrl)
- throws IOException, URISyntaxException, ReferenceGenomeConnectorException;
-
- /**
- * Returns list of organisms available for {@link ReferenceGenomeType reference
- * genome type}.
- *
- * @param type
- * type of reference genome
- * @return list of available organisms
- * @throws ReferenceGenomeConnectorException
- * thrown when there is a problem with accessing information about
- * reference genomes
- */
- List<MiriamData> getOrganismsByReferenceGenomeType(ReferenceGenomeType type) throws ReferenceGenomeConnectorException;
-
- /**
- * Returns list of genome versions available for organism of specific
- * {@link ReferenceGenomeType reference genome type}.
- *
- * @param type
- * type of reference genome
- * @param organism
- * organism for which we check genome versions
- * @return list of available organisms
- * @throws ReferenceGenomeConnectorException
- * thrown when there is a problem with accessing information about
- * reference genomes
- */
- List<String> getAvailableGenomeVersions(ReferenceGenomeType type, MiriamData organism)
- throws ReferenceGenomeConnectorException;
-
- /**
- * Returns url to the file that describes genome.
- *
- * @param type
- * type of reference genome
- * @param organism
- * organism of reference genome
- * @param version
- * version of reference genome
- * @return url to the file that describes genome
- */
- String getUrlForGenomeVersion(ReferenceGenomeType type, MiriamData organism, String version);
-
- /**
- * Returns list of all downloaded reference genomes.
- *
- * @return list of all downloaded reference genomes
- */
- List<ReferenceGenome> getDownloadedGenomes();
-
- /**
- * Removes reference genome from the system.
- *
- * @param genome
- * genome to be removed
- * @throws IOException
- * thrown when there is a problem with removing genome
- */
- void removeGenome(ReferenceGenome genome) throws IOException;
-
- /**
- * Adds gene mapping to reference genome.
- *
- * @param referenceGenome
- * reference genome where we add mapping
- * @param name
- * name of the mapping
- * @param url
- * url to the file that describes mapping
- * @throws IOException
- * thrown when there is a problem with downloading file
- * @throws URISyntaxException
- * thrown when url is invalid
- * @throws ReferenceGenomeConnectorException
- * thrown when there is a problem with manipulating information about
- * reference genome
- */
- void addReferenceGenomeGeneMapping(ReferenceGenome referenceGenome, String name, String url)
- throws IOException, URISyntaxException, ReferenceGenomeConnectorException;
-
- /**
- * Removes gene mapping for reference genome.
- *
- * @param mapping
- * mapping to be removed
- * @throws IOException
- * thrown when there is a problem with removing file
- */
- void removeReferenceGenomeGeneMapping(ReferenceGenomeGeneMapping mapping) throws IOException;
-
- /**
- * Returns {@link ReferenceGenome} for specific reference genome.
- *
- * @param organism
- * organism of reference genome
- * @param genomeType
- * reference genome type
- * @param version
- * version of the reference genome
- * @return {@link ReferenceGenome} for specific reference genome
- */
- ReferenceGenome getReferenceGenomeViewByParams(MiriamData organism, ReferenceGenomeType genomeType, String version,
- String authenticationToken);
-
- ReferenceGenome getReferenceGenomeById(int id, String authenticationToken);
-}
+package lcsb.mapviewer.services.interfaces;
+
+import java.io.IOException;
+import java.net.URISyntaxException;
+import java.util.List;
+
+import lcsb.mapviewer.annotation.services.genome.ReferenceGenomeConnectorException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.layout.ReferenceGenome;
+import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
+import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
+
+/**
+ * Service used to maintain reference genome data.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface IReferenceGenomeService {
+
+ /**
+ * Adds reference genome to the system.
+ *
+ * @param type
+ * {@link ReferenceGenomeType type} of reference genome
+ * @param organism
+ * organism for which reference genome is added
+ * @param version
+ * version of the reference genome
+ * @param customUrl
+ * url from which reference genome should be downloaded
+ * @throws IOException
+ * thrown when there is a problem with downloading file
+ * @throws URISyntaxException
+ * thrown when url is invalid
+ * @throws ReferenceGenomeConnectorException
+ * thrown when reference genome already exists or there is problem
+ * with adding genome
+ */
+ void addReferenceGenome(ReferenceGenomeType type, MiriamData organism, String version, String customUrl)
+ throws IOException, URISyntaxException, ReferenceGenomeConnectorException;
+
+ /**
+ * Returns list of organisms available for {@link ReferenceGenomeType reference
+ * genome type}.
+ *
+ * @param type
+ * type of reference genome
+ * @return list of available organisms
+ * @throws ReferenceGenomeConnectorException
+ * thrown when there is a problem with accessing information about
+ * reference genomes
+ */
+ List<MiriamData> getOrganismsByReferenceGenomeType(ReferenceGenomeType type) throws ReferenceGenomeConnectorException;
+
+ /**
+ * Returns list of genome versions available for organism of specific
+ * {@link ReferenceGenomeType reference genome type}.
+ *
+ * @param type
+ * type of reference genome
+ * @param organism
+ * organism for which we check genome versions
+ * @return list of available organisms
+ * @throws ReferenceGenomeConnectorException
+ * thrown when there is a problem with accessing information about
+ * reference genomes
+ */
+ List<String> getAvailableGenomeVersions(ReferenceGenomeType type, MiriamData organism)
+ throws ReferenceGenomeConnectorException;
+
+ /**
+ * Returns url to the file that describes genome.
+ *
+ * @param type
+ * type of reference genome
+ * @param organism
+ * organism of reference genome
+ * @param version
+ * version of reference genome
+ * @return url to the file that describes genome
+ */
+ String getUrlForGenomeVersion(ReferenceGenomeType type, MiriamData organism, String version);
+
+ /**
+ * Returns list of all downloaded reference genomes.
+ *
+ * @return list of all downloaded reference genomes
+ */
+ List<ReferenceGenome> getDownloadedGenomes();
+
+ /**
+ * Removes reference genome from the system.
+ *
+ * @param genome
+ * genome to be removed
+ * @throws IOException
+ * thrown when there is a problem with removing genome
+ */
+ void removeGenome(ReferenceGenome genome) throws IOException;
+
+ /**
+ * Adds gene mapping to reference genome.
+ *
+ * @param referenceGenome
+ * reference genome where we add mapping
+ * @param name
+ * name of the mapping
+ * @param url
+ * url to the file that describes mapping
+ * @throws IOException
+ * thrown when there is a problem with downloading file
+ * @throws URISyntaxException
+ * thrown when url is invalid
+ * @throws ReferenceGenomeConnectorException
+ * thrown when there is a problem with manipulating information about
+ * reference genome
+ */
+ void addReferenceGenomeGeneMapping(ReferenceGenome referenceGenome, String name, String url)
+ throws IOException, URISyntaxException, ReferenceGenomeConnectorException;
+
+ /**
+ * Removes gene mapping for reference genome.
+ *
+ * @param mapping
+ * mapping to be removed
+ * @throws IOException
+ * thrown when there is a problem with removing file
+ */
+ void removeReferenceGenomeGeneMapping(ReferenceGenomeGeneMapping mapping) throws IOException;
+
+ /**
+ * Returns {@link ReferenceGenome} for specific reference genome.
+ *
+ * @param organism
+ * organism of reference genome
+ * @param genomeType
+ * reference genome type
+ * @param version
+ * version of the reference genome
+ * @return {@link ReferenceGenome} for specific reference genome
+ */
+ ReferenceGenome getReferenceGenomeViewByParams(MiriamData organism, ReferenceGenomeType genomeType, String version,
+ String authenticationToken);
+
+ ReferenceGenome getReferenceGenomeById(int id, String authenticationToken);
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchHistoryService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchHistoryService.java
index 63884a9ac6..2770c7a866 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchHistoryService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchHistoryService.java
@@ -1,25 +1,25 @@
-package lcsb.mapviewer.services.interfaces;
-
-import lcsb.mapviewer.model.map.statistics.SearchType;
-
-/**
- * Service that manages search history.
- *
- * @author Piotr Gawron
- *
- */
-public interface ISearchHistoryService {
- /**
- * Adds search query entry into database.
- *
- * @param query
- * what has been searched for
- * @param type
- * type of the search
- * @param ipAddress
- * ip address that was searching
- * @param projectId
- * identifier of the project where search was performed
- */
- void addQuery(String query, SearchType type, String ipAddress, String projectId);
-}
+package lcsb.mapviewer.services.interfaces;
+
+import lcsb.mapviewer.model.map.statistics.SearchType;
+
+/**
+ * Service that manages search history.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface ISearchHistoryService {
+ /**
+ * Adds search query entry into database.
+ *
+ * @param query
+ * what has been searched for
+ * @param type
+ * type of the search
+ * @param ipAddress
+ * ip address that was searching
+ * @param projectId
+ * identifier of the project where search was performed
+ */
+ void addQuery(String query, SearchType type, String ipAddress, String projectId);
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchService.java
index 3f5ba52722..6606fa6001 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchService.java
@@ -1,314 +1,314 @@
-package lcsb.mapviewer.services.interfaces;
-
-import java.awt.geom.Point2D;
-import java.util.Collection;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
-import lcsb.mapviewer.model.map.model.SubmodelConnection;
-
-/**
- * Service that gives access to search functionalities.
- *
- * @author Piotr Gawron
- *
- */
-public interface ISearchService {
- /**
- * Parameters of search objects on the map using coordinates. It's possible to
- * add also information about nested model and level at which searching is
- * performed in the hierarchical view. More information about hierarchical
- * view can be found in the definition of
- * {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator
- * AbstractImageGenerator}.
- *
- * @author Piotr Gawron
- *
- */
- class CoordinatesSearchParams {
-
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(CoordinatesSearchParams.class);
-
- /**
- * Model where we perform search.
- */
- private Model model = null;
-
- /**
- * X coordinate of the search event.
- */
- private double x = 0;
-
- /**
- * Y coordinate of the search event.
- */
- private double y = 0;
-
- /**
- * Maximum distance between object that could be found and point that is
- * valid.
- */
- private double distance = 0;
-
- /**
- * Index of the layout in model for which we perform search. It allows to
- * determine if the layout is hierarchical or not.
- */
- private Integer layoutIdentifier = null;
-
- /**
- * Level at which the search is performed. It's used during determining if
- * the object is visible in hierarchical view.
- */
- private Integer level = null;
-
- /**
- * @return the model
- * @see #model
- */
- public Model getModel() {
- return model;
- }
-
- /**
- * @param model
- * the model to set
- * @return object with all parameters
- * @see #model
- */
- public CoordinatesSearchParams model(Model model) {
- this.model = model;
- return this;
- }
-
- /**
- * @param point
- * the coordinates to set
- * @return object with all parameters
- * @see #model
- */
- public CoordinatesSearchParams point(Point2D point) {
- this.x = point.getX();
- this.y = point.getY();
- return this;
- }
-
- /**
- * @return the x
- * @see #x
- */
- public double getX() {
- return x;
- }
-
- /**
- * @param x
- * the x to set
- * @return object with all parameters
- * @see #x
- */
- public CoordinatesSearchParams x(double x) {
- this.x = x;
- return this;
- }
-
- /**
- * @return the y
- * @see #y
- */
- public double getY() {
- return y;
- }
-
- /**
- * @param y
- * the y to set
- * @return object with all parameters
- * @see #y
- */
- public CoordinatesSearchParams y(double y) {
- this.y = y;
- return this;
- }
-
- /**
- * @return the distance
- * @see #distance
- */
- public double getDistance() {
- return distance;
- }
-
- /**
- * @param distance
- * the distance to set
- * @return object with all parameters
- * @see #distance
- */
- public CoordinatesSearchParams distance(double distance) {
- this.distance = distance;
- return this;
- }
-
- /**
- * @return layout database identifier
- * @see #layoutIdentifier
- */
- public Integer getLayoutIdentfier() {
- return layoutIdentifier;
- }
-
- /**
- * @param layoutIdentifier
- * layout database identifier to set
- * @return object with all parameters
- * @see #layoutIdentifier
- */
- public CoordinatesSearchParams layoutIdentifier(Integer layoutIdentifier) {
- nested = null;
- this.layoutIdentifier = layoutIdentifier;
- return this;
- }
-
- /**
- * @param level
- * the level to set
- * @return object with all parameters
- * @see #level
- */
- public CoordinatesSearchParams level(Integer level) {
- this.level = level;
- nested = null;
- return this;
- }
-
- /**
- * @return the level
- * @see #level
- */
- public Integer getLevel() {
- return level;
- }
-
- /**
- * This value determines if the search is performed on the nested
- * (hierarchical) view or not. If nested is <code>null</code>, then it means
- * that the nested state is unknown and should be recomputed.
- */
- private Boolean nested = null;
-
- /**
- * Checks if the search param point to search in nested (hierarchical) view.
- *
- * @return <code>true</code> if search param point to search in nested
- * (hierarchical) view, <code>false</code> otherwise
- */
- public boolean isNested() {
- if (nested == null) {
- computeNested();
- }
- return nested;
- }
-
- /**
- * This method finds out if the search is performed on the nested
- * (hierarchical) view or not and saves it in the local state.
- */
- private void computeNested() {
- nested = false;
- if (getLayoutIdentfier() != null) {
- Layout layout = getModel().getLayoutByIdentifier(getLayoutIdentfier());
- if (layout != null) {
- nested = layout.isHierarchicalView();
- } else {
- for (SubmodelConnection sc : getModel().getParentModels()) {
- if (sc instanceof ModelSubmodelConnection) {
-
- layout = ((ModelSubmodelConnection) sc).getParentModel().getModel().getLayoutByIdentifier(getLayoutIdentfier());
- if (layout != null) {
- break;
- }
- }
- }
- if (layout != null) {
- nested = layout.isHierarchicalView();
- } else {
- logger.warn("Unkown layout with id: " + getLayoutIdentfier());
- }
- }
- } else {
- logger.warn("Layout identifier is null");
- }
-
- }
-
- }
-
- /**
- * Search the element on the map using coordinates. It is also possible to
- * provide information about layout (if it's nested or not) and hierarchical
- * level.
- *
- * @param params
- * set of search params. More information can be found here:
- * {@link CoordinatesSearchParams}
- * @return object that match best the search criteria. If such object doesn't
- * exist then <code>null</code> is returned.
- */
- List<BioEntity> searchByCoordinates(CoordinatesSearchParams params);
-
- /**
- * Search for elements on the map by query. Returns many possibilities from
- * best matching to less matching possibility.
- *
- * @param model
- * model on which we perform search
- * @param query
- * the query
- * @param limit
- * maximum number of results
- * @param perfectMatch
- * should the match be perfect
- * @param ipAddress
- * ip address of a client who is searching (used for logging purpose)
- * @return list of objects that matches the query sorted by the match quality
- */
- List<BioEntity> searchByQuery(Model model, String query, int limit, Boolean perfectMatch, String ipAddress);
-
- List<BioEntity> searchByQuery(Model model, String query, int limit, Boolean perfectMatch);
-
- /**
- * Returns the closest elements to the coordinates on the model.
- *
- * @param model
- * model on which the search is performed
- * @param point
- * coordinates where search is performed
- * @param numberOfElements
- * how many closest elements should be returned
- * @return list of the closest elements
- */
- List<BioEntity> getClosestElements(Model model, Point2D point, int numberOfElements, boolean perfectHit, Collection<String> types);
-
- /**
- * Returns list of autocomplete strings for the partial query.
- *
- * @param model
- * on which model the search is performed
- * @param query
- * partial query used for autocomplete
- * @return list of strings that could be used for autocomplete the query
- */
- List<String> getAutocompleteList(Model model, String query);
-
- String[] getSuggestedQueryList(Model model);
-
-}
+package lcsb.mapviewer.services.interfaces;
+
+import java.awt.geom.Point2D;
+import java.util.Collection;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
+import lcsb.mapviewer.model.map.model.SubmodelConnection;
+
+/**
+ * Service that gives access to search functionalities.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface ISearchService {
+ /**
+ * Parameters of search objects on the map using coordinates. It's possible to
+ * add also information about nested model and level at which searching is
+ * performed in the hierarchical view. More information about hierarchical
+ * view can be found in the definition of
+ * {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator
+ * AbstractImageGenerator}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ class CoordinatesSearchParams {
+
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(CoordinatesSearchParams.class);
+
+ /**
+ * Model where we perform search.
+ */
+ private Model model = null;
+
+ /**
+ * X coordinate of the search event.
+ */
+ private double x = 0;
+
+ /**
+ * Y coordinate of the search event.
+ */
+ private double y = 0;
+
+ /**
+ * Maximum distance between object that could be found and point that is
+ * valid.
+ */
+ private double distance = 0;
+
+ /**
+ * Index of the layout in model for which we perform search. It allows to
+ * determine if the layout is hierarchical or not.
+ */
+ private Integer layoutIdentifier = null;
+
+ /**
+ * Level at which the search is performed. It's used during determining if
+ * the object is visible in hierarchical view.
+ */
+ private Integer level = null;
+
+ /**
+ * @return the model
+ * @see #model
+ */
+ public Model getModel() {
+ return model;
+ }
+
+ /**
+ * @param model
+ * the model to set
+ * @return object with all parameters
+ * @see #model
+ */
+ public CoordinatesSearchParams model(Model model) {
+ this.model = model;
+ return this;
+ }
+
+ /**
+ * @param point
+ * the coordinates to set
+ * @return object with all parameters
+ * @see #model
+ */
+ public CoordinatesSearchParams point(Point2D point) {
+ this.x = point.getX();
+ this.y = point.getY();
+ return this;
+ }
+
+ /**
+ * @return the x
+ * @see #x
+ */
+ public double getX() {
+ return x;
+ }
+
+ /**
+ * @param x
+ * the x to set
+ * @return object with all parameters
+ * @see #x
+ */
+ public CoordinatesSearchParams x(double x) {
+ this.x = x;
+ return this;
+ }
+
+ /**
+ * @return the y
+ * @see #y
+ */
+ public double getY() {
+ return y;
+ }
+
+ /**
+ * @param y
+ * the y to set
+ * @return object with all parameters
+ * @see #y
+ */
+ public CoordinatesSearchParams y(double y) {
+ this.y = y;
+ return this;
+ }
+
+ /**
+ * @return the distance
+ * @see #distance
+ */
+ public double getDistance() {
+ return distance;
+ }
+
+ /**
+ * @param distance
+ * the distance to set
+ * @return object with all parameters
+ * @see #distance
+ */
+ public CoordinatesSearchParams distance(double distance) {
+ this.distance = distance;
+ return this;
+ }
+
+ /**
+ * @return layout database identifier
+ * @see #layoutIdentifier
+ */
+ public Integer getLayoutIdentfier() {
+ return layoutIdentifier;
+ }
+
+ /**
+ * @param layoutIdentifier
+ * layout database identifier to set
+ * @return object with all parameters
+ * @see #layoutIdentifier
+ */
+ public CoordinatesSearchParams layoutIdentifier(Integer layoutIdentifier) {
+ nested = null;
+ this.layoutIdentifier = layoutIdentifier;
+ return this;
+ }
+
+ /**
+ * @param level
+ * the level to set
+ * @return object with all parameters
+ * @see #level
+ */
+ public CoordinatesSearchParams level(Integer level) {
+ this.level = level;
+ nested = null;
+ return this;
+ }
+
+ /**
+ * @return the level
+ * @see #level
+ */
+ public Integer getLevel() {
+ return level;
+ }
+
+ /**
+ * This value determines if the search is performed on the nested
+ * (hierarchical) view or not. If nested is <code>null</code>, then it means
+ * that the nested state is unknown and should be recomputed.
+ */
+ private Boolean nested = null;
+
+ /**
+ * Checks if the search param point to search in nested (hierarchical) view.
+ *
+ * @return <code>true</code> if search param point to search in nested
+ * (hierarchical) view, <code>false</code> otherwise
+ */
+ public boolean isNested() {
+ if (nested == null) {
+ computeNested();
+ }
+ return nested;
+ }
+
+ /**
+ * This method finds out if the search is performed on the nested
+ * (hierarchical) view or not and saves it in the local state.
+ */
+ private void computeNested() {
+ nested = false;
+ if (getLayoutIdentfier() != null) {
+ Layout layout = getModel().getLayoutByIdentifier(getLayoutIdentfier());
+ if (layout != null) {
+ nested = layout.isHierarchicalView();
+ } else {
+ for (SubmodelConnection sc : getModel().getParentModels()) {
+ if (sc instanceof ModelSubmodelConnection) {
+
+ layout = ((ModelSubmodelConnection) sc).getParentModel().getModel().getLayoutByIdentifier(getLayoutIdentfier());
+ if (layout != null) {
+ break;
+ }
+ }
+ }
+ if (layout != null) {
+ nested = layout.isHierarchicalView();
+ } else {
+ logger.warn("Unkown layout with id: " + getLayoutIdentfier());
+ }
+ }
+ } else {
+ logger.warn("Layout identifier is null");
+ }
+
+ }
+
+ }
+
+ /**
+ * Search the element on the map using coordinates. It is also possible to
+ * provide information about layout (if it's nested or not) and hierarchical
+ * level.
+ *
+ * @param params
+ * set of search params. More information can be found here:
+ * {@link CoordinatesSearchParams}
+ * @return object that match best the search criteria. If such object doesn't
+ * exist then <code>null</code> is returned.
+ */
+ List<BioEntity> searchByCoordinates(CoordinatesSearchParams params);
+
+ /**
+ * Search for elements on the map by query. Returns many possibilities from
+ * best matching to less matching possibility.
+ *
+ * @param model
+ * model on which we perform search
+ * @param query
+ * the query
+ * @param limit
+ * maximum number of results
+ * @param perfectMatch
+ * should the match be perfect
+ * @param ipAddress
+ * ip address of a client who is searching (used for logging purpose)
+ * @return list of objects that matches the query sorted by the match quality
+ */
+ List<BioEntity> searchByQuery(Model model, String query, int limit, Boolean perfectMatch, String ipAddress);
+
+ List<BioEntity> searchByQuery(Model model, String query, int limit, Boolean perfectMatch);
+
+ /**
+ * Returns the closest elements to the coordinates on the model.
+ *
+ * @param model
+ * model on which the search is performed
+ * @param point
+ * coordinates where search is performed
+ * @param numberOfElements
+ * how many closest elements should be returned
+ * @return list of the closest elements
+ */
+ List<BioEntity> getClosestElements(Model model, Point2D point, int numberOfElements, boolean perfectHit, Collection<String> types);
+
+ /**
+ * Returns list of autocomplete strings for the partial query.
+ *
+ * @param model
+ * on which model the search is performed
+ * @param query
+ * partial query used for autocomplete
+ * @return list of strings that could be used for autocomplete the query
+ */
+ List<String> getAutocompleteList(Model model, String query);
+
+ String[] getSuggestedQueryList(Model model);
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/package-info.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/package-info.java
index 0bd67627af..adb9ff9cd6 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/package-info.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/package-info.java
@@ -1,6 +1,6 @@
-/**
- * This package contains interfaces to all services provided by the service
- * layer.
- */
-package lcsb.mapviewer.services.interfaces;
-
+/**
+ * This package contains interfaces to all services provided by the service
+ * layer.
+ */
+package lcsb.mapviewer.services.interfaces;
+
diff --git a/service/src/main/java/lcsb/mapviewer/services/overlay/AnnotatedObjectTreeRow.java b/service/src/main/java/lcsb/mapviewer/services/overlay/AnnotatedObjectTreeRow.java
index 12d1463750..ba95a41bb0 100644
--- a/service/src/main/java/lcsb/mapviewer/services/overlay/AnnotatedObjectTreeRow.java
+++ b/service/src/main/java/lcsb/mapviewer/services/overlay/AnnotatedObjectTreeRow.java
@@ -1,296 +1,296 @@
-package lcsb.mapviewer.services.overlay;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-
-import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.modelutils.map.ClassTreeNode;
-
-import org.apache.log4j.Logger;
-
-/**
- * This object is used for representing row of class type for annotators on the
- * client side.
- *
- * @author Piotr Gawron
- *
- */
-public class AnnotatedObjectTreeRow implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final transient Logger logger = Logger.getLogger(AnnotatedObjectTreeRow.class);
-
- /**
- * Name of the class.
- */
- private String name;
- /**
- * Class.
- */
- private Class<?> clazz;
-
- /**
- * List of annotators that could be used for annotating {@link #clazz}.
- */
- private List<String> validAnnotators = new ArrayList<String>();
-
- /**
- * List of annotators that will be used for annotating {@link #clazz}.
- */
- private List<String> usedAnnotators = new ArrayList<String>();
-
- /**
- * Should the type be checked to contain at least one of the
- * {@link #requiredAnnotations required miriam}.
- */
- private Boolean require = null;
-
- /**
- * List of valid {@link MiriamType} for the class. <br/>
- * SizeOf({@link #validAnnotations} + {@link #missingValidAnnotations}) ==
- * sizeOf( {@link MiriamType#values()}).
- */
- private List<MiriamType> validAnnotations = new ArrayList<MiriamType>();
-
- /**
- * List of {@link MiriamType} that may be moved to {@link #validAnnotations}.
- *
- * <br/>
- * SizeOf({@link #validAnnotations} + {@link #missingValidAnnotations}) ==
- * sizeOf( {@link MiriamType#values()}).
- */
- private List<MiriamType> missingValidAnnotations = new ArrayList<MiriamType>();
-
- /**
- * List of required {@link MiriamType} for the class. <br/>
- * SizeOf({@link #requiredAnnotations} + {@link #missingRequiredAnnotations})
- * == sizeOf( {@link MiriamType#values()}).
- */
- private List<MiriamType> requiredAnnotations = new ArrayList<MiriamType>();
-
- /**
- * List of {@link MiriamType} that may be moved to
- * {@link #requiredAnnotations}.
- *
- * <br/>
- * SizeOf({@link #requiredAnnotations} + {@link #missingRequiredAnnotations})
- * == sizeOf( {@link MiriamType#values()}).
- */
- private List<MiriamType> missingRequiredAnnotations = new ArrayList<MiriamType>();
-
- /**
- * Default constructor.
- *
- * @param node
- * information about {@link #clazz}
- */
- public AnnotatedObjectTreeRow(ClassTreeNode node) {
- this(node, new ArrayList<ElementAnnotator>(), new ArrayList<ElementAnnotator>(), new HashSet<MiriamType>(), new HashSet<MiriamType>());
- }
-
- /**
- * Default constructor.
- *
- * @param node
- * information about {@link #clazz}
- * @param validAnnonators
- * set of annotators that are available for {@link #clazz}
- * @param usedAnnonators
- * set of annotators that should be used by default
- * @param validMiriam
- * set of {@link MiriamType} that are valid by default
- * @param requiredMiriam
- * set of {@link MiriamType} that are required by default
- */
- public AnnotatedObjectTreeRow(ClassTreeNode node, Collection<ElementAnnotator> validAnnonators, Collection<ElementAnnotator> usedAnnonators,
- Collection<MiriamType> validMiriam, Collection<MiriamType> requiredMiriam) {
- this.name = node.getCommonName();
- this.clazz = node.getClazz();
- for (ElementAnnotator elementAnnotator : validAnnonators) {
- if (usedAnnonators.contains(elementAnnotator)) {
- this.usedAnnotators.add(elementAnnotator.getCommonName());
- } else {
- this.validAnnotators.add(elementAnnotator.getCommonName());
- }
- }
- for (MiriamType mt : MiriamType.values()) {
- if (validMiriam != null && validMiriam.contains(mt)) {
- validAnnotations.add(mt);
- } else {
- missingValidAnnotations.add(mt);
- }
-
- if (requiredMiriam != null && requiredMiriam.contains(mt)) {
- requiredAnnotations.add(mt);
- } else {
- missingRequiredAnnotations.add(mt);
- }
- }
- this.require = (Boolean) node.getData();
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return the clazz
- * @see #clazz
- */
- public Class<?> getClazz() {
- return clazz;
- }
-
- /**
- * @param clazz
- * the clazz to set
- * @see #clazz
- */
- public void setClazz(Class<?> clazz) {
- this.clazz = clazz;
- }
-
- /**
- * @return the validAnnotators
- * @see #validAnnotators
- */
- public List<String> getValidAnnotators() {
- return validAnnotators;
- }
-
- /**
- * @param validAnnotators
- * the validAnnotators to set
- * @see #validAnnotators
- */
- public void setValidAnnotators(List<String> validAnnotators) {
- this.validAnnotators = validAnnotators;
- }
-
- /**
- * @return the usedAnnotators
- * @see #usedAnnotators
- */
- public List<String> getUsedAnnotators() {
- return usedAnnotators;
- }
-
- /**
- * @param usedAnnotators
- * the usedAnnotators to set
- * @see #usedAnnotators
- */
- public void setUsedAnnotators(List<String> usedAnnotators) {
- this.usedAnnotators = usedAnnotators;
- }
-
- /**
- * @return the validAnnotations
- * @see #validAnnotations
- */
- public List<MiriamType> getValidAnnotations() {
- return validAnnotations;
- }
-
- /**
- * @param validAnnotations
- * the validAnnotations to set
- * @see #validAnnotations
- */
- public void setValidAnnotations(List<MiriamType> validAnnotations) {
- this.validAnnotations = validAnnotations;
- }
-
- /**
- * @return the require
- * @see #require
- */
- public Boolean getRequire() {
- return require;
- }
-
- /**
- * @param require
- * the require to set
- * @see #require
- */
- public void setRequire(Boolean require) {
- this.require = require;
- }
-
- /**
- * @return the missingRequiredAnnotations
- * @see #missingRequiredAnnotations
- */
- public List<MiriamType> getMissingRequiredAnnotations() {
- return missingRequiredAnnotations;
- }
-
- /**
- * @param missingRequiredAnnotations
- * the missingRequiredAnnotations to set
- * @see #missingRequiredAnnotations
- */
- public void setMissingRequiredAnnotations(List<MiriamType> missingRequiredAnnotations) {
- this.missingRequiredAnnotations = missingRequiredAnnotations;
- }
-
- /**
- * @return the requiredAnnotations
- * @see #requiredAnnotations
- */
- public List<MiriamType> getRequiredAnnotations() {
- return requiredAnnotations;
- }
-
- /**
- * @param requiredAnnotations
- * the requiredAnnotations to set
- * @see #requiredAnnotations
- */
- public void setRequiredAnnotations(List<MiriamType> requiredAnnotations) {
- this.requiredAnnotations = requiredAnnotations;
- }
-
- /**
- * @return the missingValidAnnotations
- * @see #missingValidAnnotations
- */
- public List<MiriamType> getMissingValidAnnotations() {
- return missingValidAnnotations;
- }
-
- /**
- * @param missingValidAnnotations
- * the missingValidAnnotations to set
- * @see #missingValidAnnotations
- */
- public void setMissingValidAnnotations(List<MiriamType> missingValidAnnotations) {
- this.missingValidAnnotations = missingValidAnnotations;
- }
-}
+package lcsb.mapviewer.services.overlay;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.List;
+
+import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.modelutils.map.ClassTreeNode;
+
+import org.apache.log4j.Logger;
+
+/**
+ * This object is used for representing row of class type for annotators on the
+ * client side.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class AnnotatedObjectTreeRow implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final transient Logger logger = Logger.getLogger(AnnotatedObjectTreeRow.class);
+
+ /**
+ * Name of the class.
+ */
+ private String name;
+ /**
+ * Class.
+ */
+ private Class<?> clazz;
+
+ /**
+ * List of annotators that could be used for annotating {@link #clazz}.
+ */
+ private List<String> validAnnotators = new ArrayList<String>();
+
+ /**
+ * List of annotators that will be used for annotating {@link #clazz}.
+ */
+ private List<String> usedAnnotators = new ArrayList<String>();
+
+ /**
+ * Should the type be checked to contain at least one of the
+ * {@link #requiredAnnotations required miriam}.
+ */
+ private Boolean require = null;
+
+ /**
+ * List of valid {@link MiriamType} for the class. <br/>
+ * SizeOf({@link #validAnnotations} + {@link #missingValidAnnotations}) ==
+ * sizeOf( {@link MiriamType#values()}).
+ */
+ private List<MiriamType> validAnnotations = new ArrayList<MiriamType>();
+
+ /**
+ * List of {@link MiriamType} that may be moved to {@link #validAnnotations}.
+ *
+ * <br/>
+ * SizeOf({@link #validAnnotations} + {@link #missingValidAnnotations}) ==
+ * sizeOf( {@link MiriamType#values()}).
+ */
+ private List<MiriamType> missingValidAnnotations = new ArrayList<MiriamType>();
+
+ /**
+ * List of required {@link MiriamType} for the class. <br/>
+ * SizeOf({@link #requiredAnnotations} + {@link #missingRequiredAnnotations})
+ * == sizeOf( {@link MiriamType#values()}).
+ */
+ private List<MiriamType> requiredAnnotations = new ArrayList<MiriamType>();
+
+ /**
+ * List of {@link MiriamType} that may be moved to
+ * {@link #requiredAnnotations}.
+ *
+ * <br/>
+ * SizeOf({@link #requiredAnnotations} + {@link #missingRequiredAnnotations})
+ * == sizeOf( {@link MiriamType#values()}).
+ */
+ private List<MiriamType> missingRequiredAnnotations = new ArrayList<MiriamType>();
+
+ /**
+ * Default constructor.
+ *
+ * @param node
+ * information about {@link #clazz}
+ */
+ public AnnotatedObjectTreeRow(ClassTreeNode node) {
+ this(node, new ArrayList<ElementAnnotator>(), new ArrayList<ElementAnnotator>(), new HashSet<MiriamType>(), new HashSet<MiriamType>());
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param node
+ * information about {@link #clazz}
+ * @param validAnnonators
+ * set of annotators that are available for {@link #clazz}
+ * @param usedAnnonators
+ * set of annotators that should be used by default
+ * @param validMiriam
+ * set of {@link MiriamType} that are valid by default
+ * @param requiredMiriam
+ * set of {@link MiriamType} that are required by default
+ */
+ public AnnotatedObjectTreeRow(ClassTreeNode node, Collection<ElementAnnotator> validAnnonators, Collection<ElementAnnotator> usedAnnonators,
+ Collection<MiriamType> validMiriam, Collection<MiriamType> requiredMiriam) {
+ this.name = node.getCommonName();
+ this.clazz = node.getClazz();
+ for (ElementAnnotator elementAnnotator : validAnnonators) {
+ if (usedAnnonators.contains(elementAnnotator)) {
+ this.usedAnnotators.add(elementAnnotator.getCommonName());
+ } else {
+ this.validAnnotators.add(elementAnnotator.getCommonName());
+ }
+ }
+ for (MiriamType mt : MiriamType.values()) {
+ if (validMiriam != null && validMiriam.contains(mt)) {
+ validAnnotations.add(mt);
+ } else {
+ missingValidAnnotations.add(mt);
+ }
+
+ if (requiredMiriam != null && requiredMiriam.contains(mt)) {
+ requiredAnnotations.add(mt);
+ } else {
+ missingRequiredAnnotations.add(mt);
+ }
+ }
+ this.require = (Boolean) node.getData();
+ }
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * @return the clazz
+ * @see #clazz
+ */
+ public Class<?> getClazz() {
+ return clazz;
+ }
+
+ /**
+ * @param clazz
+ * the clazz to set
+ * @see #clazz
+ */
+ public void setClazz(Class<?> clazz) {
+ this.clazz = clazz;
+ }
+
+ /**
+ * @return the validAnnotators
+ * @see #validAnnotators
+ */
+ public List<String> getValidAnnotators() {
+ return validAnnotators;
+ }
+
+ /**
+ * @param validAnnotators
+ * the validAnnotators to set
+ * @see #validAnnotators
+ */
+ public void setValidAnnotators(List<String> validAnnotators) {
+ this.validAnnotators = validAnnotators;
+ }
+
+ /**
+ * @return the usedAnnotators
+ * @see #usedAnnotators
+ */
+ public List<String> getUsedAnnotators() {
+ return usedAnnotators;
+ }
+
+ /**
+ * @param usedAnnotators
+ * the usedAnnotators to set
+ * @see #usedAnnotators
+ */
+ public void setUsedAnnotators(List<String> usedAnnotators) {
+ this.usedAnnotators = usedAnnotators;
+ }
+
+ /**
+ * @return the validAnnotations
+ * @see #validAnnotations
+ */
+ public List<MiriamType> getValidAnnotations() {
+ return validAnnotations;
+ }
+
+ /**
+ * @param validAnnotations
+ * the validAnnotations to set
+ * @see #validAnnotations
+ */
+ public void setValidAnnotations(List<MiriamType> validAnnotations) {
+ this.validAnnotations = validAnnotations;
+ }
+
+ /**
+ * @return the require
+ * @see #require
+ */
+ public Boolean getRequire() {
+ return require;
+ }
+
+ /**
+ * @param require
+ * the require to set
+ * @see #require
+ */
+ public void setRequire(Boolean require) {
+ this.require = require;
+ }
+
+ /**
+ * @return the missingRequiredAnnotations
+ * @see #missingRequiredAnnotations
+ */
+ public List<MiriamType> getMissingRequiredAnnotations() {
+ return missingRequiredAnnotations;
+ }
+
+ /**
+ * @param missingRequiredAnnotations
+ * the missingRequiredAnnotations to set
+ * @see #missingRequiredAnnotations
+ */
+ public void setMissingRequiredAnnotations(List<MiriamType> missingRequiredAnnotations) {
+ this.missingRequiredAnnotations = missingRequiredAnnotations;
+ }
+
+ /**
+ * @return the requiredAnnotations
+ * @see #requiredAnnotations
+ */
+ public List<MiriamType> getRequiredAnnotations() {
+ return requiredAnnotations;
+ }
+
+ /**
+ * @param requiredAnnotations
+ * the requiredAnnotations to set
+ * @see #requiredAnnotations
+ */
+ public void setRequiredAnnotations(List<MiriamType> requiredAnnotations) {
+ this.requiredAnnotations = requiredAnnotations;
+ }
+
+ /**
+ * @return the missingValidAnnotations
+ * @see #missingValidAnnotations
+ */
+ public List<MiriamType> getMissingValidAnnotations() {
+ return missingValidAnnotations;
+ }
+
+ /**
+ * @param missingValidAnnotations
+ * the missingValidAnnotations to set
+ * @see #missingValidAnnotations
+ */
+ public void setMissingValidAnnotations(List<MiriamType> missingValidAnnotations) {
+ this.missingValidAnnotations = missingValidAnnotations;
+ }
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/overlay/ChebiTreeRow.java b/service/src/main/java/lcsb/mapviewer/services/overlay/ChebiTreeRow.java
index 966d949d28..0a023e2e13 100644
--- a/service/src/main/java/lcsb/mapviewer/services/overlay/ChebiTreeRow.java
+++ b/service/src/main/java/lcsb/mapviewer/services/overlay/ChebiTreeRow.java
@@ -1,125 +1,125 @@
-package lcsb.mapviewer.services.overlay;
-
-import java.io.Serializable;
-
-/**
- * This object is used for representing row of object in chebi ontology in the
- * client side Primefaces p:treeTable object.
- *
- * @author Piotr Gawron
- *
- */
-public class ChebiTreeRow implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Name of the chebi entity.
- */
- private String name;
-
- /**
- * Identifier of chebi entity.
- */
- private String id;
-
- /**
- * Link to the chebi entity in chebi webpage.
- */
- private String link;
-
- /**
- * Relation associated with this entity.
- */
- private String relationType;
-
- /**
- * Default constructor.
- *
- * @param name
- * Name of the chebi entity
- * @param id
- * Identifier of chebi entity
- * @param link
- * Link to the chebi entity in chebi webpage
- * @param relationType
- * Relation associated with this entity
- */
- public ChebiTreeRow(String name, String id, String link, String relationType) {
- this.name = name;
- this.id = id;
- this.link = link;
- this.relationType = relationType;
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return the id
- * @see #id
- */
- public String getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(String id) {
- this.id = id;
- }
-
- /**
- * @return the link
- * @see #link
- */
- public String getLink() {
- return link;
- }
-
- /**
- * @param link
- * the link to set
- * @see #link
- */
- public void setLink(String link) {
- this.link = link;
- }
-
- /**
- * @return the relationType
- * @see #relationType
- */
- public String getRelationType() {
- return relationType;
- }
-
- /**
- * @param relationType
- * the relationType to set
- * @see #relationType
- */
- public void setRelationType(String relationType) {
- this.relationType = relationType;
- }
-
-}
+package lcsb.mapviewer.services.overlay;
+
+import java.io.Serializable;
+
+/**
+ * This object is used for representing row of object in chebi ontology in the
+ * client side Primefaces p:treeTable object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ChebiTreeRow implements Serializable {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Name of the chebi entity.
+ */
+ private String name;
+
+ /**
+ * Identifier of chebi entity.
+ */
+ private String id;
+
+ /**
+ * Link to the chebi entity in chebi webpage.
+ */
+ private String link;
+
+ /**
+ * Relation associated with this entity.
+ */
+ private String relationType;
+
+ /**
+ * Default constructor.
+ *
+ * @param name
+ * Name of the chebi entity
+ * @param id
+ * Identifier of chebi entity
+ * @param link
+ * Link to the chebi entity in chebi webpage
+ * @param relationType
+ * Relation associated with this entity
+ */
+ public ChebiTreeRow(String name, String id, String link, String relationType) {
+ this.name = name;
+ this.id = id;
+ this.link = link;
+ this.relationType = relationType;
+ }
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(String id) {
+ this.id = id;
+ }
+
+ /**
+ * @return the link
+ * @see #link
+ */
+ public String getLink() {
+ return link;
+ }
+
+ /**
+ * @param link
+ * the link to set
+ * @see #link
+ */
+ public void setLink(String link) {
+ this.link = link;
+ }
+
+ /**
+ * @return the relationType
+ * @see #relationType
+ */
+ public String getRelationType() {
+ return relationType;
+ }
+
+ /**
+ * @param relationType
+ * the relationType to set
+ * @see #relationType
+ */
+ public void setRelationType(String relationType) {
+ this.relationType = relationType;
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/overlay/IconManager.java b/service/src/main/java/lcsb/mapviewer/services/overlay/IconManager.java
index 2d460d1dc0..7cf52eb49e 100644
--- a/service/src/main/java/lcsb/mapviewer/services/overlay/IconManager.java
+++ b/service/src/main/java/lcsb/mapviewer/services/overlay/IconManager.java
@@ -1,144 +1,144 @@
-package lcsb.mapviewer.services.overlay;
-
-import org.apache.commons.lang3.mutable.MutableInt;
-
-import lcsb.mapviewer.common.Configuration;
-
-/**
- * This class return links to icons used by the client. It might be good idea to
- * move part of the functionality to client side as server shouldn't decide
- * about representation layer.
- *
- * @author Piotr Gawron
- *
- */
-public final class IconManager {
- /**
- * Max index of the image.
- */
- private static final int MAX_INDEX = 99;
-
- /**
- * Colors available for bubble icons.
- */
- private String[] colors = { "red", "blue", "green", "purple", "yellow", "pink", "paleblue", "brown", "orange" };
-
- /**
- * Singelton.
- */
- private static IconManager manager;
-
- /**
- * Default singleton constructor.
- */
- private IconManager() {
-
- }
-
- /**
- * Returns only available instance of this class.
- *
- * @return singletone instance
- */
- public static IconManager getInstance() {
- if (manager == null) {
- manager = new IconManager();
- }
- return manager;
- }
-
- /**
- * Returns path to the search icon with the given index.
- *
- * @param index
- * identifier of the icon
- * @param type
- * type of the icon to be generated
- * @param colorSet
- * number of the color set that should be used in the generasted icon
- * (number is influenced by {@link IconType#startingColorSet}
- *
- * @return path to the icon
- */
- public String getIconForIndex(MutableInt index, IconType type, int colorSet) {
- return getIconForIndex(index.toInteger(), type, colorSet);
- }
-
- /**
- * Returns path to the search icon with the given index.
- *
- * @param index
- * identifier of the icon
- * @param type
- * type of the icon to be generated
- * @param colorSet
- * number of the color set that should be used in the generasted icon
- * (number is influenced by {@link IconType#startingColorSet}
- *
- * @return path to the icon
- */
- public String getIconForIndex(int index, IconType type, int colorSet) {
- String color = normalizeColor(colorSet + type.getStartingColorSet());
- index = normalizeIndex(index);
- String result = "marker/" + type.getIconFileSystemName() + "/" + type.getIconFileSystemName() + "_" + color + "_" + index + ".png";
- return result;
- }
-
- /**
- * Returns index of the icon that is not out of the range.
- *
- * @param index
- * original index
- * @return index of the icon that is not out of the range
- */
- public int normalizeIndex(int index) {
- return (index % MAX_INDEX) + 1;
- }
-
- /**
- * Returns color set of the icon that is not out of the range.
- *
- * @param set
- * original index of the color set
- * @return index of the color set that is not out of the range
- */
- private String normalizeColor(int set) {
- return colors[Math.abs(set % colors.length)];
- }
-
- /**
- * Returns path to empty icon.
- *
- * @return path to empty icon
- */
- public String getEmpyIcon() {
- return "marker/empty.png";
- }
-
- /**
- * Returns path to delete icon.
- *
- * @return path to delete icon
- */
- public String getDeleteIcon() {
- return "icons/delete.png";
- }
-
- /**
- * Returns path to icon that indicate similarity search.
- *
- * @return path to icon that indicate similarity search
- */
- public String getSimilarIcon() {
- return "icons/gunsight.png";
- }
-
- /**
- * Returns path to comment icon.
- *
- * @return path to comment icon
- */
- public String getCommentIcon() {
- return "icons/comment.png?v="+Configuration.getSystemBuildVersion(null);
- }
-}
+package lcsb.mapviewer.services.overlay;
+
+import org.apache.commons.lang3.mutable.MutableInt;
+
+import lcsb.mapviewer.common.Configuration;
+
+/**
+ * This class return links to icons used by the client. It might be good idea to
+ * move part of the functionality to client side as server shouldn't decide
+ * about representation layer.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public final class IconManager {
+ /**
+ * Max index of the image.
+ */
+ private static final int MAX_INDEX = 99;
+
+ /**
+ * Colors available for bubble icons.
+ */
+ private String[] colors = { "red", "blue", "green", "purple", "yellow", "pink", "paleblue", "brown", "orange" };
+
+ /**
+ * Singelton.
+ */
+ private static IconManager manager;
+
+ /**
+ * Default singleton constructor.
+ */
+ private IconManager() {
+
+ }
+
+ /**
+ * Returns only available instance of this class.
+ *
+ * @return singletone instance
+ */
+ public static IconManager getInstance() {
+ if (manager == null) {
+ manager = new IconManager();
+ }
+ return manager;
+ }
+
+ /**
+ * Returns path to the search icon with the given index.
+ *
+ * @param index
+ * identifier of the icon
+ * @param type
+ * type of the icon to be generated
+ * @param colorSet
+ * number of the color set that should be used in the generasted icon
+ * (number is influenced by {@link IconType#startingColorSet}
+ *
+ * @return path to the icon
+ */
+ public String getIconForIndex(MutableInt index, IconType type, int colorSet) {
+ return getIconForIndex(index.toInteger(), type, colorSet);
+ }
+
+ /**
+ * Returns path to the search icon with the given index.
+ *
+ * @param index
+ * identifier of the icon
+ * @param type
+ * type of the icon to be generated
+ * @param colorSet
+ * number of the color set that should be used in the generasted icon
+ * (number is influenced by {@link IconType#startingColorSet}
+ *
+ * @return path to the icon
+ */
+ public String getIconForIndex(int index, IconType type, int colorSet) {
+ String color = normalizeColor(colorSet + type.getStartingColorSet());
+ index = normalizeIndex(index);
+ String result = "marker/" + type.getIconFileSystemName() + "/" + type.getIconFileSystemName() + "_" + color + "_" + index + ".png";
+ return result;
+ }
+
+ /**
+ * Returns index of the icon that is not out of the range.
+ *
+ * @param index
+ * original index
+ * @return index of the icon that is not out of the range
+ */
+ public int normalizeIndex(int index) {
+ return (index % MAX_INDEX) + 1;
+ }
+
+ /**
+ * Returns color set of the icon that is not out of the range.
+ *
+ * @param set
+ * original index of the color set
+ * @return index of the color set that is not out of the range
+ */
+ private String normalizeColor(int set) {
+ return colors[Math.abs(set % colors.length)];
+ }
+
+ /**
+ * Returns path to empty icon.
+ *
+ * @return path to empty icon
+ */
+ public String getEmpyIcon() {
+ return "marker/empty.png";
+ }
+
+ /**
+ * Returns path to delete icon.
+ *
+ * @return path to delete icon
+ */
+ public String getDeleteIcon() {
+ return "icons/delete.png";
+ }
+
+ /**
+ * Returns path to icon that indicate similarity search.
+ *
+ * @return path to icon that indicate similarity search
+ */
+ public String getSimilarIcon() {
+ return "icons/gunsight.png";
+ }
+
+ /**
+ * Returns path to comment icon.
+ *
+ * @return path to comment icon
+ */
+ public String getCommentIcon() {
+ return "icons/comment.png?v="+Configuration.getSystemBuildVersion(null);
+ }
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/overlay/IconType.java b/service/src/main/java/lcsb/mapviewer/services/overlay/IconType.java
index 1a96c37bf9..ef96af73c4 100644
--- a/service/src/main/java/lcsb/mapviewer/services/overlay/IconType.java
+++ b/service/src/main/java/lcsb/mapviewer/services/overlay/IconType.java
@@ -1,68 +1,68 @@
-package lcsb.mapviewer.services.overlay;
-
-/**
- * Type of the icon that is returned to the client.
- *
- * @author Piotr Gawron
- *
- */
-public enum IconType {
-
- /**
- * Search result.
- */
- SEARCH("marker", 0),
-
- /**
- * Result of the drug search.
- */
- DRUG("drug", 5),
- /**
- * Result of the drug search.
- */
- CHEMICAL("ball", 1),
- /**
- * Result of the drug search.
- */
- MI_RNA("target", 2);
-
- /**
- * Name of the icons in filesystem.
- */
- private String iconFileSystemName;
-
- /**
- * Color set starting index from which generasted icons should start for given
- * type.
- */
- private int startingColorSet;
-
- /**
- * Default constructor.
- *
- * @param name
- * {@link #iconFileSystemName}
- * @param startColorSet
- * {@link #startingColorSet}
- */
- IconType(String name, int startColorSet) {
- this.iconFileSystemName = name;
- this.startingColorSet = startColorSet;
- }
-
- /**
- * @return the iconFileSystemName
- * @see #iconFileSystemName
- */
- public String getIconFileSystemName() {
- return iconFileSystemName;
- }
-
- /**
- * @return the startingColorSet
- * @see #startingColorSet
- */
- public int getStartingColorSet() {
- return startingColorSet;
- }
-}
+package lcsb.mapviewer.services.overlay;
+
+/**
+ * Type of the icon that is returned to the client.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum IconType {
+
+ /**
+ * Search result.
+ */
+ SEARCH("marker", 0),
+
+ /**
+ * Result of the drug search.
+ */
+ DRUG("drug", 5),
+ /**
+ * Result of the drug search.
+ */
+ CHEMICAL("ball", 1),
+ /**
+ * Result of the drug search.
+ */
+ MI_RNA("target", 2);
+
+ /**
+ * Name of the icons in filesystem.
+ */
+ private String iconFileSystemName;
+
+ /**
+ * Color set starting index from which generasted icons should start for given
+ * type.
+ */
+ private int startingColorSet;
+
+ /**
+ * Default constructor.
+ *
+ * @param name
+ * {@link #iconFileSystemName}
+ * @param startColorSet
+ * {@link #startingColorSet}
+ */
+ IconType(String name, int startColorSet) {
+ this.iconFileSystemName = name;
+ this.startingColorSet = startColorSet;
+ }
+
+ /**
+ * @return the iconFileSystemName
+ * @see #iconFileSystemName
+ */
+ public String getIconFileSystemName() {
+ return iconFileSystemName;
+ }
+
+ /**
+ * @return the startingColorSet
+ * @see #startingColorSet
+ */
+ public int getStartingColorSet() {
+ return startingColorSet;
+ }
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/overlay/package-info.java b/service/src/main/java/lcsb/mapviewer/services/overlay/package-info.java
index 9f6a493220..e11e591303 100644
--- a/service/src/main/java/lcsb/mapviewer/services/overlay/package-info.java
+++ b/service/src/main/java/lcsb/mapviewer/services/overlay/package-info.java
@@ -1,7 +1,7 @@
-/**
- * This package contains data structure used by PrimeFaces framework or Google
- * Maps API.
- *
- */
-package lcsb.mapviewer.services.overlay;
-
+/**
+ * This package contains data structure used by PrimeFaces framework or Google
+ * Maps API.
+ *
+ */
+package lcsb.mapviewer.services.overlay;
+
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/DbSearchCriteria.java b/service/src/main/java/lcsb/mapviewer/services/search/DbSearchCriteria.java
index 7caabc9aab..1b5c960eea 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/DbSearchCriteria.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/DbSearchCriteria.java
@@ -1,168 +1,168 @@
-package lcsb.mapviewer.services.search;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.model.Model;
-
-/**
- * Class with search criteria used by {@link IDbSearchService}. Contains
- * information about {@link lcsb.mapviewer.model.map.MiriamType#TAXONOMY
- * organisms}, {@link Model} where the search is performed, etc.
- *
- * @author Piotr Gawron
- *
- */
-public class DbSearchCriteria {
-
- /**
- * Ip address of the client that requested this search.
- */
- private String ipAddress;
-
- /**
- * Id of disease to which results should be contextualized.
- *
- */
- private MiriamData disease;
-
- /**
- * Project where client is looking for the results.
- */
- private Project project;
-
- /**
- * List of organisms used for filtering results. If the list is null or empty
- * then filtering shouldn't be applied. Organisms must be represented as
- * {@link lcsb.mapviewer.model.map.MiriamType#TAXONOMY} MiriamData objects.
- *
- */
- private List<MiriamData> organisms = new ArrayList<>();
-
- /**
- * Which set of icons should be used for representing results.
- *
- */
- private int colorSet = 0;
-
- /**
- * @return the ipAddress
- * @see #ipAddress
- */
- public String getIpAddress() {
- return ipAddress;
- }
-
- /**
- * @param ipAddress
- * the ipAddress to set
- * @see #ipAddress
- * @return this object after changes
- */
- public DbSearchCriteria ipAddress(String ipAddress) {
- this.ipAddress = ipAddress;
- return this;
- }
-
- /**
- * @return the project
- * @see #model
- */
- public Project getProject() {
- return project;
- }
-
- /**
- * @param project
- * the project to set
- * @see #project
- * @return this object after changes
- */
- public DbSearchCriteria project(Project project) {
- this.project = project;
- return this;
- }
-
- /**
- * @return the organisms
- * @see #organisms
- */
- public List<MiriamData> getOrganisms() {
- return organisms;
- }
-
- /**
- * @param organisms
- * the organisms to add
- * @see #organisms
- * @return this object after changes
- */
- public DbSearchCriteria organisms(List<MiriamData> organisms) {
- this.organisms.addAll(organisms);
- return this;
- }
-
- /**
- * @return the colorSet
- * @see #colorSet
- */
- public int getColorSet() {
- return colorSet;
- }
-
- /**
- * @param colorSet
- * the colorSet to set
- * @see #colorSet
- * @return this object after changes
- */
- public DbSearchCriteria colorSet(int colorSet) {
- this.colorSet = colorSet;
- return this;
- }
-
- /**
- * @param organism
- * the organism to add
- * @see #organisms
- * @return this object after changes
- */
- public DbSearchCriteria organisms(MiriamData organism) {
- this.organisms.add(organism);
- return this;
- }
-
- /**
- * @param organisms
- * the organisms to add
- * @see #organisms
- * @return this object after changes
- */
- public DbSearchCriteria organisms(MiriamData[] organisms) {
- for (MiriamData miriamData : organisms) {
- this.organisms.add(miriamData);
- }
- return this;
- }
-
- /**
- * @return the disease
- * @see #disease
- */
- public MiriamData getDisease() {
- return disease;
- }
-
- /**
- * @param disease
- * the disease to set
- * @see #disease
- * @return this object after changes
- */
- public DbSearchCriteria disease(MiriamData disease) {
- this.disease = disease;
- return this;
- }
-}
+package lcsb.mapviewer.services.search;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.model.Model;
+
+/**
+ * Class with search criteria used by {@link IDbSearchService}. Contains
+ * information about {@link lcsb.mapviewer.model.map.MiriamType#TAXONOMY
+ * organisms}, {@link Model} where the search is performed, etc.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class DbSearchCriteria {
+
+ /**
+ * Ip address of the client that requested this search.
+ */
+ private String ipAddress;
+
+ /**
+ * Id of disease to which results should be contextualized.
+ *
+ */
+ private MiriamData disease;
+
+ /**
+ * Project where client is looking for the results.
+ */
+ private Project project;
+
+ /**
+ * List of organisms used for filtering results. If the list is null or empty
+ * then filtering shouldn't be applied. Organisms must be represented as
+ * {@link lcsb.mapviewer.model.map.MiriamType#TAXONOMY} MiriamData objects.
+ *
+ */
+ private List<MiriamData> organisms = new ArrayList<>();
+
+ /**
+ * Which set of icons should be used for representing results.
+ *
+ */
+ private int colorSet = 0;
+
+ /**
+ * @return the ipAddress
+ * @see #ipAddress
+ */
+ public String getIpAddress() {
+ return ipAddress;
+ }
+
+ /**
+ * @param ipAddress
+ * the ipAddress to set
+ * @see #ipAddress
+ * @return this object after changes
+ */
+ public DbSearchCriteria ipAddress(String ipAddress) {
+ this.ipAddress = ipAddress;
+ return this;
+ }
+
+ /**
+ * @return the project
+ * @see #model
+ */
+ public Project getProject() {
+ return project;
+ }
+
+ /**
+ * @param project
+ * the project to set
+ * @see #project
+ * @return this object after changes
+ */
+ public DbSearchCriteria project(Project project) {
+ this.project = project;
+ return this;
+ }
+
+ /**
+ * @return the organisms
+ * @see #organisms
+ */
+ public List<MiriamData> getOrganisms() {
+ return organisms;
+ }
+
+ /**
+ * @param organisms
+ * the organisms to add
+ * @see #organisms
+ * @return this object after changes
+ */
+ public DbSearchCriteria organisms(List<MiriamData> organisms) {
+ this.organisms.addAll(organisms);
+ return this;
+ }
+
+ /**
+ * @return the colorSet
+ * @see #colorSet
+ */
+ public int getColorSet() {
+ return colorSet;
+ }
+
+ /**
+ * @param colorSet
+ * the colorSet to set
+ * @see #colorSet
+ * @return this object after changes
+ */
+ public DbSearchCriteria colorSet(int colorSet) {
+ this.colorSet = colorSet;
+ return this;
+ }
+
+ /**
+ * @param organism
+ * the organism to add
+ * @see #organisms
+ * @return this object after changes
+ */
+ public DbSearchCriteria organisms(MiriamData organism) {
+ this.organisms.add(organism);
+ return this;
+ }
+
+ /**
+ * @param organisms
+ * the organisms to add
+ * @see #organisms
+ * @return this object after changes
+ */
+ public DbSearchCriteria organisms(MiriamData[] organisms) {
+ for (MiriamData miriamData : organisms) {
+ this.organisms.add(miriamData);
+ }
+ return this;
+ }
+
+ /**
+ * @return the disease
+ * @see #disease
+ */
+ public MiriamData getDisease() {
+ return disease;
+ }
+
+ /**
+ * @param disease
+ * the disease to set
+ * @see #disease
+ * @return this object after changes
+ */
+ public DbSearchCriteria disease(MiriamData disease) {
+ this.disease = disease;
+ return this;
+ }
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/ElementMatcher.java b/service/src/main/java/lcsb/mapviewer/services/search/ElementMatcher.java
index 24f495eed9..25e33b912e 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/ElementMatcher.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/ElementMatcher.java
@@ -1,113 +1,113 @@
-package lcsb.mapviewer.services.search;
-
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class ElementMatcher {
-
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(ElementMatcher.class);
-
- public boolean elementMatch(Target target, BioEntity element) {
- MiriamData targetAnnotation = target.getSource();
- switch (target.getType()) {
- case COMPLEX_PROTEIN:
- if (MiriamType.CHEMBL_TARGET.equals(targetAnnotation.getDataType())) {
- if (element.getMiriamData().contains(targetAnnotation)) {
- return true;
- }
- }
- Collection<String> ids = new HashSet<String>();
- for (MiriamData row : target.getGenes()) {
- ids.add(row.getResource());
- }
-
- if (element instanceof Complex) {
- Complex complex = (Complex) element;
- Set<Species> speciesSet = complex.getAllSimpleChildren();
- if (speciesSet.size() != ids.size()) {
- return false;
- }
-
- for (Element id : speciesSet) {
- if (!ids.contains(id.getName())) {
- return false;
- }
- }
- return true;
- }
- return false;
- case SINGLE_PROTEIN:
- if (target.getSource() != null) {
- targetAnnotation = target.getSource();
- } else if (target.getGenes().size() > 0) {
- targetAnnotation = target.getGenes().get(0);
- } else {
- logger.warn("Invalid target found: " + target);
- }
- if (targetAnnotation != null && element.getMiriamData().contains(targetAnnotation)) {
- return true;
- }
- if (element instanceof Protein || element instanceof Rna || element instanceof Gene) {
- if (target.getGenes().size() > 0) {
- String hgncId = target.getGenes().get(0).getResource();
- if (element.getName().equalsIgnoreCase(hgncId)) {
- return true;
- }
- }
- }
- return false;
- case PROTEIN_FAMILY:
- if (element instanceof Protein || element instanceof Rna || element instanceof Gene) {
- String hgncId = target.getGenes().get(0).getResource();
- if (element.getName().equalsIgnoreCase(hgncId)) {
- return true;
- } else if (element.getMiriamData().contains(new MiriamData(MiriamType.HGNC_SYMBOL, hgncId))) {
- return true;
- }
- for (MiriamData protein : target.getGenes()) {
- hgncId = protein.getResource();
- if (element.getName().equalsIgnoreCase(hgncId)) {
- return true;
- } else if (element.getMiriamData().contains(new MiriamData(MiriamType.HGNC_SYMBOL, hgncId))) {
- return true;
- }
- }
- }
- return false;
- case OTHER:
- // in other case just compare names
- String targetName = null;
- if (target.getGenes().size() > 0) {
- targetName = target.getGenes().get(0).getResource();
- }
- if (targetName == null) {
- targetName = target.getName();
- }
- if (targetName == null) {
- return false;
- }
- return element.getName().equalsIgnoreCase(targetName);
- default:
- throw new InvalidArgumentException("Unknown drug target type: " + target.getType());
- }
- }
-
-}
+package lcsb.mapviewer.services.search;
+
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.annotation.data.Target;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class ElementMatcher {
+
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(ElementMatcher.class);
+
+ public boolean elementMatch(Target target, BioEntity element) {
+ MiriamData targetAnnotation = target.getSource();
+ switch (target.getType()) {
+ case COMPLEX_PROTEIN:
+ if (MiriamType.CHEMBL_TARGET.equals(targetAnnotation.getDataType())) {
+ if (element.getMiriamData().contains(targetAnnotation)) {
+ return true;
+ }
+ }
+ Collection<String> ids = new HashSet<String>();
+ for (MiriamData row : target.getGenes()) {
+ ids.add(row.getResource());
+ }
+
+ if (element instanceof Complex) {
+ Complex complex = (Complex) element;
+ Set<Species> speciesSet = complex.getAllSimpleChildren();
+ if (speciesSet.size() != ids.size()) {
+ return false;
+ }
+
+ for (Element id : speciesSet) {
+ if (!ids.contains(id.getName())) {
+ return false;
+ }
+ }
+ return true;
+ }
+ return false;
+ case SINGLE_PROTEIN:
+ if (target.getSource() != null) {
+ targetAnnotation = target.getSource();
+ } else if (target.getGenes().size() > 0) {
+ targetAnnotation = target.getGenes().get(0);
+ } else {
+ logger.warn("Invalid target found: " + target);
+ }
+ if (targetAnnotation != null && element.getMiriamData().contains(targetAnnotation)) {
+ return true;
+ }
+ if (element instanceof Protein || element instanceof Rna || element instanceof Gene) {
+ if (target.getGenes().size() > 0) {
+ String hgncId = target.getGenes().get(0).getResource();
+ if (element.getName().equalsIgnoreCase(hgncId)) {
+ return true;
+ }
+ }
+ }
+ return false;
+ case PROTEIN_FAMILY:
+ if (element instanceof Protein || element instanceof Rna || element instanceof Gene) {
+ String hgncId = target.getGenes().get(0).getResource();
+ if (element.getName().equalsIgnoreCase(hgncId)) {
+ return true;
+ } else if (element.getMiriamData().contains(new MiriamData(MiriamType.HGNC_SYMBOL, hgncId))) {
+ return true;
+ }
+ for (MiriamData protein : target.getGenes()) {
+ hgncId = protein.getResource();
+ if (element.getName().equalsIgnoreCase(hgncId)) {
+ return true;
+ } else if (element.getMiriamData().contains(new MiriamData(MiriamType.HGNC_SYMBOL, hgncId))) {
+ return true;
+ }
+ }
+ }
+ return false;
+ case OTHER:
+ // in other case just compare names
+ String targetName = null;
+ if (target.getGenes().size() > 0) {
+ targetName = target.getGenes().get(0).getResource();
+ }
+ if (targetName == null) {
+ targetName = target.getName();
+ }
+ if (targetName == null) {
+ return false;
+ }
+ return element.getName().equalsIgnoreCase(targetName);
+ default:
+ throw new InvalidArgumentException("Unknown drug target type: " + target.getType());
+ }
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/IDbSearchService.java b/service/src/main/java/lcsb/mapviewer/services/search/IDbSearchService.java
index c78786d85c..ff5f7e3562 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/IDbSearchService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/IDbSearchService.java
@@ -1,56 +1,56 @@
-package lcsb.mapviewer.services.search;
-
-import java.util.Collection;
-import java.util.List;
-
-import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * Service that allows to retrieve information of type T from external
- * resources/databases.
- *
- * @author Piotr Gawron
- *
- * @param <T>
- * type of returned results
- */
-public interface IDbSearchService<T> {
-
- /**
- * Returns the drugs found by drug name.
- *
- * @param name
- * name of the drug
- * @param searchCriteria
- * set of {@link DbSearchCriteria} used for searching (like:
- * {@link lcsb.mapviewer.model.map.model.Model Model})
- * @return list of drugs for drug names
- */
- T getByName(String name, DbSearchCriteria searchCriteria);
-
- /**
- * Returns the list of drugs that target at least one of the element in the
- * parameter.
- *
- * @param targetElements
- * list of elements that should be targeted by drug
- * @param searchCriteria
- * set of {@link DbSearchCriteria} used for searching (like:
- * {@link lcsb.mapviewer.model.map.model.Model Model})
- * @return list of drugs that targets something from the elements collection
- */
- List<T> getForTargets(Collection<Element> targetElements, DbSearchCriteria searchCriteria);
-
- /**
- * This method will cache all queries that make sense for the model.
- *
- * @param originalModel
- * model to be considered for database queries
- * @param progressUpdater
- * callback function updating information about cache progress
- */
- void cacheDataForModel(Model originalModel, IProgressUpdater progressUpdater);
-
-}
+package lcsb.mapviewer.services.search;
+
+import java.util.Collection;
+import java.util.List;
+
+import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * Service that allows to retrieve information of type T from external
+ * resources/databases.
+ *
+ * @author Piotr Gawron
+ *
+ * @param <T>
+ * type of returned results
+ */
+public interface IDbSearchService<T> {
+
+ /**
+ * Returns the drugs found by drug name.
+ *
+ * @param name
+ * name of the drug
+ * @param searchCriteria
+ * set of {@link DbSearchCriteria} used for searching (like:
+ * {@link lcsb.mapviewer.model.map.model.Model Model})
+ * @return list of drugs for drug names
+ */
+ T getByName(String name, DbSearchCriteria searchCriteria);
+
+ /**
+ * Returns the list of drugs that target at least one of the element in the
+ * parameter.
+ *
+ * @param targetElements
+ * list of elements that should be targeted by drug
+ * @param searchCriteria
+ * set of {@link DbSearchCriteria} used for searching (like:
+ * {@link lcsb.mapviewer.model.map.model.Model Model})
+ * @return list of drugs that targets something from the elements collection
+ */
+ List<T> getForTargets(Collection<Element> targetElements, DbSearchCriteria searchCriteria);
+
+ /**
+ * This method will cache all queries that make sense for the model.
+ *
+ * @param originalModel
+ * model to be considered for database queries
+ * @param progressUpdater
+ * callback function updating information about cache progress
+ */
+ void cacheDataForModel(Model originalModel, IProgressUpdater progressUpdater);
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/chemical/ChemicalService.java b/service/src/main/java/lcsb/mapviewer/services/search/chemical/ChemicalService.java
index 711494ee85..bdece1a402 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/chemical/ChemicalService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/chemical/ChemicalService.java
@@ -1,294 +1,294 @@
-package lcsb.mapviewer.services.search.chemical;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.annotation.data.Chemical;
-import lcsb.mapviewer.annotation.services.ChemicalParser;
-import lcsb.mapviewer.annotation.services.ChemicalSearchException;
-import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
-import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
-import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.services.search.DbSearchCriteria;
-import lcsb.mapviewer.services.search.DbSearchService;
-
-/**
- * Implementation of the service that allows access information about chemicals.
- *
- * @author Ayan Rota
- *
- */
-@Transactional(value = "txManager")
-public class ChemicalService extends DbSearchService implements IChemicalService {
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(ChemicalService.class);
-
- /**
- * List of chemicals pairs of id and name.
- */
- private Map<MiriamData, Map<MiriamData, String>> diseases = new HashMap<>();
-
- /**
- * Access point and parser for the online ctd database.
- */
- @Autowired
- private ChemicalParser chemicalParser;
-
- /**
- * Object used to perform operations on {@link MiriamType#HGNC} annotations.
- */
- @Autowired
- private HgncAnnotator hgncAnnotator;
-
- /**
- * Default constructor.
- */
- public ChemicalService() {
- super();
- }
-
- /**
- * Returns list of {@link Chemical chemicals} for a given disease and list of
- * names.
- *
- * @param diseaseID
- * {@link MiriamData} identifying disease; it should be a
- * {@link MiriamType#MESH_2012} identifier
- * @param names
- * list of drug names that we are looking for
- * @return list of {@link Chemical chemicals} that were found
- */
- protected List<Chemical> getChemicalByName(MiriamData diseaseID, List<String> names) {
- if (diseaseID == null || names == null) {
- throw new InvalidArgumentException("diseaseID cannot be null");
- }
- names.removeAll(Collections.singleton(null));
-
- // Create a map with the each search string and chemical id.
- // Remove empty string and special characters.
- Map<String, MiriamData> searchNamesMap = new LinkedHashMap<String, MiriamData>();
- for (int i = 0; i < names.size(); i++) {
- String name = names.get(i).trim().toLowerCase().replaceAll("[^\\w]", "");
- if (!name.isEmpty()) {
- searchNamesMap.put(name, null);
- }
- }
- try {
-
- // Search id, name Map for matching records
- List<MiriamData> ids = new ArrayList<MiriamData>();
- Iterator<Entry<MiriamData, String>> idNameEnteries = getChemicalsByDisease(diseaseID).entrySet().iterator();
- int namesFound = 0;
- while (idNameEnteries.hasNext() && namesFound < searchNamesMap.size()) {
- Map.Entry<MiriamData, String> pair = idNameEnteries.next();
- String chemicalName = pair.getValue();
- if (chemicalName != null) {
- chemicalName = chemicalName.toLowerCase().replaceAll("[^\\w]", "");
- for (Map.Entry<String, MiriamData> nameEntry : searchNamesMap.entrySet()) {
- if (nameEntry.getKey().equals(chemicalName)) {
- nameEntry.setValue(pair.getKey());
- namesFound++;
-
- }
- }
-
- }
- }
-
- // Get what all values include null where no matching record is found,
- // remove null and look in the database.
- ids.addAll(searchNamesMap.values());
- ids.removeAll(Collections.singleton(null));
- List<Chemical> sortedResult = new ArrayList<Chemical>();
- if (!ids.isEmpty()) {
- List<Chemical> result = chemicalParser.getChemicals(diseaseID, ids);
-
- // If the result is not empty and we found chemicals, try to sort as
- // by the initial list provided.
- Map<MiriamData, Chemical> resultAsMap = new HashMap<MiriamData, Chemical>();
- if (result != null && !result.isEmpty()) {
- for (Chemical chemo : result) {
- resultAsMap.put(chemo.getChemicalId(), chemo);
- }
-
- for (Map.Entry<String, MiriamData> nameEntry : searchNamesMap.entrySet()) {
- if (nameEntry.getValue() != null) {
- sortedResult.add(resultAsMap.get(nameEntry.getValue()));
- }
- }
- }
- }
-
- return sortedResult;
- } catch (ChemicalSearchException e) {
- logger.error("Problem with accessing database", e);
- return new ArrayList<Chemical>();
- }
- }
-
- @Override
- public Chemical getByName(String name, DbSearchCriteria searchCriteria) {
- if (searchCriteria.getDisease() == null) {
- throw new InvalidArgumentException("diseaseID cannot be null");
- }
- if (name == null || name.isEmpty()) {
- return null;
- }
- MiriamData id = null;
- List<Chemical> result = new ArrayList<Chemical>();
- name = name.toLowerCase().replaceAll("[^\\w]", "");
- try {
- Iterator<Entry<MiriamData, String>> mapValues = getChemicalsByDisease(searchCriteria.getDisease()).entrySet()
- .iterator();
- int shortestName = Integer.MAX_VALUE;
- while (mapValues.hasNext()) {
- Map.Entry<MiriamData, String> pair = mapValues.next();
- String chemicalName = pair.getValue();
- if (chemicalName != null) {
- chemicalName = chemicalName.toLowerCase().replaceAll("[^\\w]", "");
- if (chemicalName.contains(name) && name.length() < shortestName) {
- id = pair.getKey();
- shortestName = chemicalName.length();
- }
- }
- }
- if (id != null) {
- List<MiriamData> chemicalId = new ArrayList<>();
- chemicalId.add(id);
- result = chemicalParser.getChemicals(searchCriteria.getDisease(), chemicalId);
- } else {
- result = chemicalParser.getChemicalsBySynonym(searchCriteria.getDisease(), name);
- }
- } catch (ChemicalSearchException e) {
- logger.error("Problem with accesing database", e);
- }
- if (result.size() == 0) {
- return null;
- } else {
- return result.get(0);
- }
-
- }
-
- @Override
- public List<Chemical> getForTargets(Collection<Element> targets, DbSearchCriteria searchCriteria) {
- List<Chemical> chemicalList = new ArrayList<>();
- Set<MiriamData> targetsMiriam = new HashSet<MiriamData>();
- for (Element alias : targets) {
- if (alias instanceof Protein || alias instanceof Gene || alias instanceof Rna) {
- boolean hgncFound = false;
- for (MiriamData md : alias.getMiriamData()) {
- if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
- targetsMiriam.add(md);
- hgncFound = true;
- } else if (MiriamType.ENTREZ.equals(md.getDataType())) {
- // ad also entrez in case of mouse, rat, etc
- targetsMiriam.add(md);
- }
-
- }
- if (!hgncFound) {
- MiriamData md = new MiriamData(MiriamType.HGNC_SYMBOL, alias.getName());
- try {
- if (hgncAnnotator.isValidHgncMiriam(md)) {
- targetsMiriam.add(md);
- }
- } catch (AnnotatorException e) {
- logger.error("Problem with accessing HGNC database", e);
- }
- }
- }
- }
- try {
- chemicalList = chemicalParser.getChemicalListByTarget(targetsMiriam, searchCriteria.getDisease());
- } catch (ChemicalSearchException e) {
- logger.error("Problem with accessing chemical database", e);
- }
-
- Collections.sort(chemicalList, new Chemical.NameComparator());
- return chemicalList;
- }
-
- /**
- * @param disease
- * {@link MiriamType#MESH_2012 mesh term} describing disease
- *
- * @return chemicals related to the disease
- * @see #diseases
- * @throws ChemicalSearchException
- * thrown when there is problem with accessing ctd database
- */
- private Map<MiriamData, String> getChemicalsByDisease(MiriamData disease) throws ChemicalSearchException {
- if (diseases.get(disease) == null) {
- diseases.put(disease, chemicalParser.getChemicalsForDisease(disease));
- }
- return diseases.get(disease);
- }
-
- @Override
- public void cacheDataForModel(Model originalModel, IProgressUpdater iProgressUpdater) {
- double progress = 0.0;
- iProgressUpdater.setProgress(progress * IProgressUpdater.MAX_PROGRESS);
- MiriamData disease = originalModel.getProject().getDisease();
- if (disease != null) {
- logger.debug("Caching chemical queries...");
- Set<MiriamData> targetMiriams = new HashSet<>();
- List<Model> models = new ArrayList<>();
- models.add(originalModel);
- models.addAll(originalModel.getSubmodels());
- for (Model model : models) {
- for (BioEntity element : model.getBioEntities()) {
- for (MiriamData md : element.getMiriamData()) {
- if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
- targetMiriams.add(md);
- } else if (MiriamType.ENTREZ.equals(md.getDataType())) {
- targetMiriams.add(md);
- }
- }
- }
- }
- double counter = 0.0;
- for (MiriamData md : targetMiriams) {
- try {
- List<Chemical> chemicalList = chemicalParser.getChemicalListByTarget(md, disease);
- for (Chemical chemical : chemicalList) {
- cacheMiriamData(chemical);
- }
- } catch (ChemicalSearchException | AnnotatorException e) {
- logger.error("Problem with accessing info about chemical for target: " + md, e);
- }
- counter += 1;
- progress = counter / (double) targetMiriams.size();
- iProgressUpdater.setProgress(progress * IProgressUpdater.MAX_PROGRESS);
- }
- } else {
- logger.debug("Caching chemical queries not possible...");
- }
- }
-
-}
+package lcsb.mapviewer.services.search.chemical;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.annotation.data.Chemical;
+import lcsb.mapviewer.annotation.services.ChemicalParser;
+import lcsb.mapviewer.annotation.services.ChemicalSearchException;
+import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
+import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
+import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.services.search.DbSearchCriteria;
+import lcsb.mapviewer.services.search.DbSearchService;
+
+/**
+ * Implementation of the service that allows access information about chemicals.
+ *
+ * @author Ayan Rota
+ *
+ */
+@Transactional(value = "txManager")
+public class ChemicalService extends DbSearchService implements IChemicalService {
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(ChemicalService.class);
+
+ /**
+ * List of chemicals pairs of id and name.
+ */
+ private Map<MiriamData, Map<MiriamData, String>> diseases = new HashMap<>();
+
+ /**
+ * Access point and parser for the online ctd database.
+ */
+ @Autowired
+ private ChemicalParser chemicalParser;
+
+ /**
+ * Object used to perform operations on {@link MiriamType#HGNC} annotations.
+ */
+ @Autowired
+ private HgncAnnotator hgncAnnotator;
+
+ /**
+ * Default constructor.
+ */
+ public ChemicalService() {
+ super();
+ }
+
+ /**
+ * Returns list of {@link Chemical chemicals} for a given disease and list of
+ * names.
+ *
+ * @param diseaseID
+ * {@link MiriamData} identifying disease; it should be a
+ * {@link MiriamType#MESH_2012} identifier
+ * @param names
+ * list of drug names that we are looking for
+ * @return list of {@link Chemical chemicals} that were found
+ */
+ protected List<Chemical> getChemicalByName(MiriamData diseaseID, List<String> names) {
+ if (diseaseID == null || names == null) {
+ throw new InvalidArgumentException("diseaseID cannot be null");
+ }
+ names.removeAll(Collections.singleton(null));
+
+ // Create a map with the each search string and chemical id.
+ // Remove empty string and special characters.
+ Map<String, MiriamData> searchNamesMap = new LinkedHashMap<String, MiriamData>();
+ for (int i = 0; i < names.size(); i++) {
+ String name = names.get(i).trim().toLowerCase().replaceAll("[^\\w]", "");
+ if (!name.isEmpty()) {
+ searchNamesMap.put(name, null);
+ }
+ }
+ try {
+
+ // Search id, name Map for matching records
+ List<MiriamData> ids = new ArrayList<MiriamData>();
+ Iterator<Entry<MiriamData, String>> idNameEnteries = getChemicalsByDisease(diseaseID).entrySet().iterator();
+ int namesFound = 0;
+ while (idNameEnteries.hasNext() && namesFound < searchNamesMap.size()) {
+ Map.Entry<MiriamData, String> pair = idNameEnteries.next();
+ String chemicalName = pair.getValue();
+ if (chemicalName != null) {
+ chemicalName = chemicalName.toLowerCase().replaceAll("[^\\w]", "");
+ for (Map.Entry<String, MiriamData> nameEntry : searchNamesMap.entrySet()) {
+ if (nameEntry.getKey().equals(chemicalName)) {
+ nameEntry.setValue(pair.getKey());
+ namesFound++;
+
+ }
+ }
+
+ }
+ }
+
+ // Get what all values include null where no matching record is found,
+ // remove null and look in the database.
+ ids.addAll(searchNamesMap.values());
+ ids.removeAll(Collections.singleton(null));
+ List<Chemical> sortedResult = new ArrayList<Chemical>();
+ if (!ids.isEmpty()) {
+ List<Chemical> result = chemicalParser.getChemicals(diseaseID, ids);
+
+ // If the result is not empty and we found chemicals, try to sort as
+ // by the initial list provided.
+ Map<MiriamData, Chemical> resultAsMap = new HashMap<MiriamData, Chemical>();
+ if (result != null && !result.isEmpty()) {
+ for (Chemical chemo : result) {
+ resultAsMap.put(chemo.getChemicalId(), chemo);
+ }
+
+ for (Map.Entry<String, MiriamData> nameEntry : searchNamesMap.entrySet()) {
+ if (nameEntry.getValue() != null) {
+ sortedResult.add(resultAsMap.get(nameEntry.getValue()));
+ }
+ }
+ }
+ }
+
+ return sortedResult;
+ } catch (ChemicalSearchException e) {
+ logger.error("Problem with accessing database", e);
+ return new ArrayList<Chemical>();
+ }
+ }
+
+ @Override
+ public Chemical getByName(String name, DbSearchCriteria searchCriteria) {
+ if (searchCriteria.getDisease() == null) {
+ throw new InvalidArgumentException("diseaseID cannot be null");
+ }
+ if (name == null || name.isEmpty()) {
+ return null;
+ }
+ MiriamData id = null;
+ List<Chemical> result = new ArrayList<Chemical>();
+ name = name.toLowerCase().replaceAll("[^\\w]", "");
+ try {
+ Iterator<Entry<MiriamData, String>> mapValues = getChemicalsByDisease(searchCriteria.getDisease()).entrySet()
+ .iterator();
+ int shortestName = Integer.MAX_VALUE;
+ while (mapValues.hasNext()) {
+ Map.Entry<MiriamData, String> pair = mapValues.next();
+ String chemicalName = pair.getValue();
+ if (chemicalName != null) {
+ chemicalName = chemicalName.toLowerCase().replaceAll("[^\\w]", "");
+ if (chemicalName.contains(name) && name.length() < shortestName) {
+ id = pair.getKey();
+ shortestName = chemicalName.length();
+ }
+ }
+ }
+ if (id != null) {
+ List<MiriamData> chemicalId = new ArrayList<>();
+ chemicalId.add(id);
+ result = chemicalParser.getChemicals(searchCriteria.getDisease(), chemicalId);
+ } else {
+ result = chemicalParser.getChemicalsBySynonym(searchCriteria.getDisease(), name);
+ }
+ } catch (ChemicalSearchException e) {
+ logger.error("Problem with accesing database", e);
+ }
+ if (result.size() == 0) {
+ return null;
+ } else {
+ return result.get(0);
+ }
+
+ }
+
+ @Override
+ public List<Chemical> getForTargets(Collection<Element> targets, DbSearchCriteria searchCriteria) {
+ List<Chemical> chemicalList = new ArrayList<>();
+ Set<MiriamData> targetsMiriam = new HashSet<MiriamData>();
+ for (Element alias : targets) {
+ if (alias instanceof Protein || alias instanceof Gene || alias instanceof Rna) {
+ boolean hgncFound = false;
+ for (MiriamData md : alias.getMiriamData()) {
+ if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
+ targetsMiriam.add(md);
+ hgncFound = true;
+ } else if (MiriamType.ENTREZ.equals(md.getDataType())) {
+ // ad also entrez in case of mouse, rat, etc
+ targetsMiriam.add(md);
+ }
+
+ }
+ if (!hgncFound) {
+ MiriamData md = new MiriamData(MiriamType.HGNC_SYMBOL, alias.getName());
+ try {
+ if (hgncAnnotator.isValidHgncMiriam(md)) {
+ targetsMiriam.add(md);
+ }
+ } catch (AnnotatorException e) {
+ logger.error("Problem with accessing HGNC database", e);
+ }
+ }
+ }
+ }
+ try {
+ chemicalList = chemicalParser.getChemicalListByTarget(targetsMiriam, searchCriteria.getDisease());
+ } catch (ChemicalSearchException e) {
+ logger.error("Problem with accessing chemical database", e);
+ }
+
+ Collections.sort(chemicalList, new Chemical.NameComparator());
+ return chemicalList;
+ }
+
+ /**
+ * @param disease
+ * {@link MiriamType#MESH_2012 mesh term} describing disease
+ *
+ * @return chemicals related to the disease
+ * @see #diseases
+ * @throws ChemicalSearchException
+ * thrown when there is problem with accessing ctd database
+ */
+ private Map<MiriamData, String> getChemicalsByDisease(MiriamData disease) throws ChemicalSearchException {
+ if (diseases.get(disease) == null) {
+ diseases.put(disease, chemicalParser.getChemicalsForDisease(disease));
+ }
+ return diseases.get(disease);
+ }
+
+ @Override
+ public void cacheDataForModel(Model originalModel, IProgressUpdater iProgressUpdater) {
+ double progress = 0.0;
+ iProgressUpdater.setProgress(progress * IProgressUpdater.MAX_PROGRESS);
+ MiriamData disease = originalModel.getProject().getDisease();
+ if (disease != null) {
+ logger.debug("Caching chemical queries...");
+ Set<MiriamData> targetMiriams = new HashSet<>();
+ List<Model> models = new ArrayList<>();
+ models.add(originalModel);
+ models.addAll(originalModel.getSubmodels());
+ for (Model model : models) {
+ for (BioEntity element : model.getBioEntities()) {
+ for (MiriamData md : element.getMiriamData()) {
+ if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
+ targetMiriams.add(md);
+ } else if (MiriamType.ENTREZ.equals(md.getDataType())) {
+ targetMiriams.add(md);
+ }
+ }
+ }
+ }
+ double counter = 0.0;
+ for (MiriamData md : targetMiriams) {
+ try {
+ List<Chemical> chemicalList = chemicalParser.getChemicalListByTarget(md, disease);
+ for (Chemical chemical : chemicalList) {
+ cacheMiriamData(chemical);
+ }
+ } catch (ChemicalSearchException | AnnotatorException e) {
+ logger.error("Problem with accessing info about chemical for target: " + md, e);
+ }
+ counter += 1;
+ progress = counter / (double) targetMiriams.size();
+ iProgressUpdater.setProgress(progress * IProgressUpdater.MAX_PROGRESS);
+ }
+ } else {
+ logger.debug("Caching chemical queries not possible...");
+ }
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/chemical/IChemicalService.java b/service/src/main/java/lcsb/mapviewer/services/search/chemical/IChemicalService.java
index b98a74fd96..f3ede82dbc 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/chemical/IChemicalService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/chemical/IChemicalService.java
@@ -1,14 +1,14 @@
-package lcsb.mapviewer.services.search.chemical;
-
-import lcsb.mapviewer.annotation.data.Chemical;
-import lcsb.mapviewer.services.search.IDbSearchService;
-
-/**
- * Service for accessing information about chemical.
- *
- * @author Ayan Rota
- *
- */
-public interface IChemicalService extends IDbSearchService<Chemical> {
-
-}
+package lcsb.mapviewer.services.search.chemical;
+
+import lcsb.mapviewer.annotation.data.Chemical;
+import lcsb.mapviewer.services.search.IDbSearchService;
+
+/**
+ * Service for accessing information about chemical.
+ *
+ * @author Ayan Rota
+ *
+ */
+public interface IChemicalService extends IDbSearchService<Chemical> {
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/chemical/package-info.java b/service/src/main/java/lcsb/mapviewer/services/search/chemical/package-info.java
index 4734da5e9d..def4ed3c60 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/chemical/package-info.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/chemical/package-info.java
@@ -1,8 +1,8 @@
-/**
- * This package contains structures used for passing chemical related data about
- * elements to the client.
- * <p/>
- * Be carefull when refactoring classes in this package. Data are accessed not
- * directly (not via managable code) by client side.
- */
-package lcsb.mapviewer.services.search.chemical;
+/**
+ * This package contains structures used for passing chemical related data about
+ * elements to the client.
+ * <p/>
+ * Be carefull when refactoring classes in this package. Data are accessed not
+ * directly (not via managable code) by client side.
+ */
+package lcsb.mapviewer.services.search.chemical;
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/drug/DrugService.java b/service/src/main/java/lcsb/mapviewer/services/search/drug/DrugService.java
index ed07cf3b62..d33932a457 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/drug/DrugService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/drug/DrugService.java
@@ -1,375 +1,375 @@
-package lcsb.mapviewer.services.search.drug;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.annotation.data.Drug;
-import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.annotation.services.ChEMBLParser;
-import lcsb.mapviewer.annotation.services.DrugSearchException;
-import lcsb.mapviewer.annotation.services.DrugbankHTMLParser;
-import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
-import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
-import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.statistics.SearchType;
-import lcsb.mapviewer.services.interfaces.ISearchHistoryService;
-import lcsb.mapviewer.services.search.DbSearchCriteria;
-import lcsb.mapviewer.services.search.DbSearchService;
-
-/**
- * Implementation of the service that allows access information about drugs.
- *
- * @author Piotr Gawron
- *
- */
-@Transactional(value = "txManager")
-public class DrugService extends DbSearchService implements IDrugService {
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(DrugService.class);
-
- /**
- * Access point and parser for the online drugbank database.
- */
- @Autowired
- private DrugbankHTMLParser drugBankParser;
-
- /**
- * Access point and parser for the online ChEMBL database.
- */
- @Autowired
- private ChEMBLParser chEMBLParser;
-
- /**
- * Object used to get information about {@link MiriamType#HGNC} annotations and
- * transformations.
- */
- @Autowired
- private HgncAnnotator hgncAnnotator;
-
- /**
- * Service that manages search history.
- */
- @Autowired
- private ISearchHistoryService searchHistoryService;
-
- /**
- * Removes targets for unknown organisms from the drug.
- *
- * @param drug
- * drug from which we want to remove targets
- * @param organisms
- * organisms that should be kept
- */
- private void removeUnknownOrganisms(Drug drug, List<MiriamData> organisms) {
- if (organisms.size() > 0) {
- List<Target> toRemove = new ArrayList<Target>();
- for (Target target : drug.getTargets()) {
- boolean remove = true;
- for (MiriamData organism : organisms) {
- if (target.getOrganism() == null) {
- remove = false;
- } else if (target.getOrganism().equals(organism)) {
- remove = false;
- }
- }
- if (remove) {
- logger.debug(
- "Target " + drug.getName() + " removed from list because results are limited to organisms: " + organisms);
- toRemove.add(target);
- }
- }
- drug.getTargets().removeAll(toRemove);
- }
- }
-
- /**
- * Merges two drugs (typically from different databases) into one
- * representation.
- *
- * @param drug
- * first drug to merge
- * @param drug2
- * second drug to merge
- * @return merged drug
- */
- private Drug mergeDrugs(Drug drug, Drug drug2) {
- if (drug == null) {
- return drug2;
- }
- if (drug2 == null) {
- return drug;
- }
-
- Drug result = new Drug(drug);
- result.getSources().addAll(drug2.getSources());
- if (result.getName() == null || result.getName().trim().equals("")) {
- result.setName(drug2.getName());
- }
- if (result.getDescription() == null || result.getDescription().trim().equals("")) {
- result.setDescription(drug2.getDescription());
- }
- for (String synonym : drug2.getSynonyms()) {
- if (!result.getSynonyms().contains(synonym)) {
- result.addSynonym(synonym);
- }
- }
- for (String brandName : drug2.getBrandNames()) {
- if (!result.getBrandNames().contains(brandName)) {
- result.addBrandName(brandName);
- }
- }
-
- if (result.getBloodBrainBarrier().equals("YES")) {
- if (drug2.getBloodBrainBarrier().equals("NO")) {
- logger.warn("Problem with merging drugs. Blood Brain Barrier contains opposite values: "
- + result.getBloodBrainBarrier() + ", " + drug2.getBloodBrainBarrier());
- result.setBloodBrainBarrier("N/A");
- }
- } else if (result.getBloodBrainBarrier().equals("NO")) {
- if (drug2.getBloodBrainBarrier().equals("YES")) {
- logger.warn("Problem with merging drugs. Blood Brain Barrier contains opposite values: "
- + result.getBloodBrainBarrier() + ", " + drug2.getBloodBrainBarrier());
- result.setBloodBrainBarrier("N/A");
- }
- } else if (result.getBloodBrainBarrier().equals("N/A")) {
- result.setBloodBrainBarrier(drug.getBloodBrainBarrier());
- } else {
- logger.warn("Unknown status of drug BBB:" + result.getBloodBrainBarrier());
- }
-
- if (result.getApproved() == null) {
- result.setApproved(drug2.getApproved());
- } else if (drug2.getApproved() != null) {
- if (!drug2.getApproved().equals(result.getApproved())) {
- logger.warn("Problem with merging drugs. Approved contains opposite values: " + result.getApproved() + ", "
- + drug2.getApproved());
- result.setApproved(null);
- }
- }
-
- result.getTargets().addAll(drug2.getTargets());
- return result;
- }
-
- @Override
- public Drug getByName(String name, DbSearchCriteria searchCriteria) {
- if (name.trim().equals("")) {
- return null;
- }
- Drug drug = null;
- try {
- drug = drugBankParser.findDrug(name);
- if (drug != null) {
- removeUnknownOrganisms(drug, searchCriteria.getOrganisms());
- }
- } catch (DrugSearchException e) {
- logger.error("Problem with accessing drugBank parser", e);
- }
- try {
- Set<String> foundDrugs = new HashSet<String>();
- Set<String> searchNames = new HashSet<String>();
- // two step searching in Chembl:
- // * search for name
- searchNames.add(name);
- if (drug != null && drug.getName() != null) {
- // * search for name of a drug in drugbanke
- searchNames.add(drug.getName());
- // * search for all synonyms found in drugbank
- // searchNames.addAll(drug.getSynonyms());
- }
- for (String string : searchNames) {
- Drug drug2 = chEMBLParser.findDrug(string);
- if (drug2 != null) {
- removeUnknownOrganisms(drug2, searchCriteria.getOrganisms());
- // don't add drugs that were already found
- if (!foundDrugs.contains(drug2.getSources().get(0).getResource())) {
- drug = mergeDrugs(drug, drug2);
- foundDrugs.add(drug2.getSources().get(0).getResource());
- }
- }
- }
- } catch (DrugSearchException e) {
- logger.error("Problem with accessing ChEMBL parser", e);
- }
- if (searchCriteria.getIpAddress() != null && searchCriteria.getProject() != null) {
- searchHistoryService.addQuery(name, SearchType.GENERAL, searchCriteria.getIpAddress(),
- searchCriteria.getProject().getProjectId());
- }
-
- return drug;
- }
-
- @Override
- public List<Drug> getForTargets(Collection<Element> targets, DbSearchCriteria searchCriteria) {
- List<Drug> drugList = new ArrayList<>();
- Set<MiriamData> targetsMiriam = new HashSet<>();
- for (Element target : targets) {
- if (target instanceof Protein || target instanceof Gene || target instanceof Rna) {
- boolean hgncFound = false;
- for (MiriamData md : target.getMiriamData()) {
- if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
- targetsMiriam.add(md);
- hgncFound = true;
- }
- }
- if (!hgncFound) {
- MiriamData md = new MiriamData(MiriamType.HGNC_SYMBOL, target.getName());
- try {
- if (hgncAnnotator.isValidHgncMiriam(md)) {
- targetsMiriam.add(md);
- }
- } catch (AnnotatorException e) {
- logger.error("Problem with accessing HGNC database", e);
- }
- }
- }
- }
- try {
- List<Drug> drugs = drugBankParser.getDrugListByTargets(targetsMiriam, searchCriteria.getOrganisms());
- drugList.addAll(drugs);
- } catch (DrugSearchException e) {
- logger.error("Problem with accessing drugBank parser", e);
- }
-
- try {
- List<Drug> drugs = chEMBLParser.getDrugListByTargets(targetsMiriam, searchCriteria.getOrganisms());
- drugList.addAll(drugs);
- } catch (DrugSearchException e) {
- logger.error("Problem with accessing chembl parser", e);
- }
-
- for (Drug drug : drugList) {
- removeUnknownOrganisms(drug, searchCriteria.getOrganisms());
- }
-
- Collections.sort(drugList, new Drug.NameComparator());
- return drugList;
- }
-
- /**
- * @return the drugBankParser
- */
- public DrugbankHTMLParser getDrugBankParser() {
- return drugBankParser;
- }
-
- /**
- * @param drugBankParser
- * the drugBankParser to set
- */
- public void setDrugBankParser(DrugbankHTMLParser drugBankParser) {
- this.drugBankParser = drugBankParser;
- }
-
- /**
- * @return the chEMBLParser
- */
- public ChEMBLParser getChEMBLParser() {
- return chEMBLParser;
- }
-
- /**
- * @param chEMBLParser
- * the chEMBLParser to set
- */
- public void setChEMBLParser(ChEMBLParser chEMBLParser) {
- this.chEMBLParser = chEMBLParser;
- }
-
- /**
- * @return the searchHistoryService
- */
- public ISearchHistoryService getSearchHistoryService() {
- return searchHistoryService;
- }
-
- /**
- * @param searchHistoryService
- * the searchHistoryService to set
- */
- public void setSearchHistoryService(ISearchHistoryService searchHistoryService) {
- this.searchHistoryService = searchHistoryService;
- }
-
- @Override
- public void cacheDataForModel(Model originalModel, IProgressUpdater iProgressUpdater) {
- logger.debug("Caching drug queries...");
- double progress = 0.0;
- iProgressUpdater.setProgress(progress * IProgressUpdater.MAX_PROGRESS);
- MiriamData disease = originalModel.getProject().getDisease();
- if (disease != null) {
- Set<MiriamData> targetMiriams = new HashSet<>();
- List<Model> models = new ArrayList<>();
- models.add(originalModel);
- models.addAll(originalModel.getSubmodels());
- for (Model model : models) {
- for (BioEntity element : model.getBioEntities()) {
- for (MiriamData md : element.getMiriamData()) {
- if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
- targetMiriams.add(md);
- }
- }
- }
- }
- double counter = 0.0;
- List<MiriamData> organisms = new ArrayList<>();
- for (MiriamData md : targetMiriams) {
- try {
- List<Drug> chemicalList = drugBankParser.getDrugListByTarget(md, organisms);
- for (Drug chemical : chemicalList) {
- cacheMiriamData(chemical);
- }
- } catch (DrugSearchException | AnnotatorException e) {
- logger.error("Problem with accessing info about drugbank for target: " + md, e);
- }
- try {
- List<Drug> chemicalList = chEMBLParser.getDrugListByTarget(md, organisms);
- for (Drug chemical : chemicalList) {
- cacheMiriamData(chemical);
- }
- } catch (DrugSearchException | AnnotatorException e) {
- logger.error("Problem with accessing info about chembl for target: " + md, e);
- }
- counter += 1;
- progress = counter / (double) targetMiriams.size();
- iProgressUpdater.setProgress(progress * IProgressUpdater.MAX_PROGRESS);
- }
- }
- }
-
- @Override
- public List<String> getSuggestedQueryList(Project project, MiriamData organism) throws DrugSearchException {
- Set<String> resultSet = new HashSet<>();
- for (String string : drugBankParser.getSuggestedQueryList(project, organism)) {
- resultSet.add(string.toLowerCase());
- }
- for (String string : chEMBLParser.getSuggestedQueryList(project, organism)) {
- resultSet.add(string.toLowerCase());
- }
-
- List<String> result = new ArrayList<>();
- result.addAll(resultSet);
- Collections.sort(result);
- return result;
- }
-}
+package lcsb.mapviewer.services.search.drug;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.annotation.data.Drug;
+import lcsb.mapviewer.annotation.data.Target;
+import lcsb.mapviewer.annotation.services.ChEMBLParser;
+import lcsb.mapviewer.annotation.services.DrugSearchException;
+import lcsb.mapviewer.annotation.services.DrugbankHTMLParser;
+import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
+import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
+import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.statistics.SearchType;
+import lcsb.mapviewer.services.interfaces.ISearchHistoryService;
+import lcsb.mapviewer.services.search.DbSearchCriteria;
+import lcsb.mapviewer.services.search.DbSearchService;
+
+/**
+ * Implementation of the service that allows access information about drugs.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Transactional(value = "txManager")
+public class DrugService extends DbSearchService implements IDrugService {
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(DrugService.class);
+
+ /**
+ * Access point and parser for the online drugbank database.
+ */
+ @Autowired
+ private DrugbankHTMLParser drugBankParser;
+
+ /**
+ * Access point and parser for the online ChEMBL database.
+ */
+ @Autowired
+ private ChEMBLParser chEMBLParser;
+
+ /**
+ * Object used to get information about {@link MiriamType#HGNC} annotations and
+ * transformations.
+ */
+ @Autowired
+ private HgncAnnotator hgncAnnotator;
+
+ /**
+ * Service that manages search history.
+ */
+ @Autowired
+ private ISearchHistoryService searchHistoryService;
+
+ /**
+ * Removes targets for unknown organisms from the drug.
+ *
+ * @param drug
+ * drug from which we want to remove targets
+ * @param organisms
+ * organisms that should be kept
+ */
+ private void removeUnknownOrganisms(Drug drug, List<MiriamData> organisms) {
+ if (organisms.size() > 0) {
+ List<Target> toRemove = new ArrayList<Target>();
+ for (Target target : drug.getTargets()) {
+ boolean remove = true;
+ for (MiriamData organism : organisms) {
+ if (target.getOrganism() == null) {
+ remove = false;
+ } else if (target.getOrganism().equals(organism)) {
+ remove = false;
+ }
+ }
+ if (remove) {
+ logger.debug(
+ "Target " + drug.getName() + " removed from list because results are limited to organisms: " + organisms);
+ toRemove.add(target);
+ }
+ }
+ drug.getTargets().removeAll(toRemove);
+ }
+ }
+
+ /**
+ * Merges two drugs (typically from different databases) into one
+ * representation.
+ *
+ * @param drug
+ * first drug to merge
+ * @param drug2
+ * second drug to merge
+ * @return merged drug
+ */
+ private Drug mergeDrugs(Drug drug, Drug drug2) {
+ if (drug == null) {
+ return drug2;
+ }
+ if (drug2 == null) {
+ return drug;
+ }
+
+ Drug result = new Drug(drug);
+ result.getSources().addAll(drug2.getSources());
+ if (result.getName() == null || result.getName().trim().equals("")) {
+ result.setName(drug2.getName());
+ }
+ if (result.getDescription() == null || result.getDescription().trim().equals("")) {
+ result.setDescription(drug2.getDescription());
+ }
+ for (String synonym : drug2.getSynonyms()) {
+ if (!result.getSynonyms().contains(synonym)) {
+ result.addSynonym(synonym);
+ }
+ }
+ for (String brandName : drug2.getBrandNames()) {
+ if (!result.getBrandNames().contains(brandName)) {
+ result.addBrandName(brandName);
+ }
+ }
+
+ if (result.getBloodBrainBarrier().equals("YES")) {
+ if (drug2.getBloodBrainBarrier().equals("NO")) {
+ logger.warn("Problem with merging drugs. Blood Brain Barrier contains opposite values: "
+ + result.getBloodBrainBarrier() + ", " + drug2.getBloodBrainBarrier());
+ result.setBloodBrainBarrier("N/A");
+ }
+ } else if (result.getBloodBrainBarrier().equals("NO")) {
+ if (drug2.getBloodBrainBarrier().equals("YES")) {
+ logger.warn("Problem with merging drugs. Blood Brain Barrier contains opposite values: "
+ + result.getBloodBrainBarrier() + ", " + drug2.getBloodBrainBarrier());
+ result.setBloodBrainBarrier("N/A");
+ }
+ } else if (result.getBloodBrainBarrier().equals("N/A")) {
+ result.setBloodBrainBarrier(drug.getBloodBrainBarrier());
+ } else {
+ logger.warn("Unknown status of drug BBB:" + result.getBloodBrainBarrier());
+ }
+
+ if (result.getApproved() == null) {
+ result.setApproved(drug2.getApproved());
+ } else if (drug2.getApproved() != null) {
+ if (!drug2.getApproved().equals(result.getApproved())) {
+ logger.warn("Problem with merging drugs. Approved contains opposite values: " + result.getApproved() + ", "
+ + drug2.getApproved());
+ result.setApproved(null);
+ }
+ }
+
+ result.getTargets().addAll(drug2.getTargets());
+ return result;
+ }
+
+ @Override
+ public Drug getByName(String name, DbSearchCriteria searchCriteria) {
+ if (name.trim().equals("")) {
+ return null;
+ }
+ Drug drug = null;
+ try {
+ drug = drugBankParser.findDrug(name);
+ if (drug != null) {
+ removeUnknownOrganisms(drug, searchCriteria.getOrganisms());
+ }
+ } catch (DrugSearchException e) {
+ logger.error("Problem with accessing drugBank parser", e);
+ }
+ try {
+ Set<String> foundDrugs = new HashSet<String>();
+ Set<String> searchNames = new HashSet<String>();
+ // two step searching in Chembl:
+ // * search for name
+ searchNames.add(name);
+ if (drug != null && drug.getName() != null) {
+ // * search for name of a drug in drugbanke
+ searchNames.add(drug.getName());
+ // * search for all synonyms found in drugbank
+ // searchNames.addAll(drug.getSynonyms());
+ }
+ for (String string : searchNames) {
+ Drug drug2 = chEMBLParser.findDrug(string);
+ if (drug2 != null) {
+ removeUnknownOrganisms(drug2, searchCriteria.getOrganisms());
+ // don't add drugs that were already found
+ if (!foundDrugs.contains(drug2.getSources().get(0).getResource())) {
+ drug = mergeDrugs(drug, drug2);
+ foundDrugs.add(drug2.getSources().get(0).getResource());
+ }
+ }
+ }
+ } catch (DrugSearchException e) {
+ logger.error("Problem with accessing ChEMBL parser", e);
+ }
+ if (searchCriteria.getIpAddress() != null && searchCriteria.getProject() != null) {
+ searchHistoryService.addQuery(name, SearchType.GENERAL, searchCriteria.getIpAddress(),
+ searchCriteria.getProject().getProjectId());
+ }
+
+ return drug;
+ }
+
+ @Override
+ public List<Drug> getForTargets(Collection<Element> targets, DbSearchCriteria searchCriteria) {
+ List<Drug> drugList = new ArrayList<>();
+ Set<MiriamData> targetsMiriam = new HashSet<>();
+ for (Element target : targets) {
+ if (target instanceof Protein || target instanceof Gene || target instanceof Rna) {
+ boolean hgncFound = false;
+ for (MiriamData md : target.getMiriamData()) {
+ if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
+ targetsMiriam.add(md);
+ hgncFound = true;
+ }
+ }
+ if (!hgncFound) {
+ MiriamData md = new MiriamData(MiriamType.HGNC_SYMBOL, target.getName());
+ try {
+ if (hgncAnnotator.isValidHgncMiriam(md)) {
+ targetsMiriam.add(md);
+ }
+ } catch (AnnotatorException e) {
+ logger.error("Problem with accessing HGNC database", e);
+ }
+ }
+ }
+ }
+ try {
+ List<Drug> drugs = drugBankParser.getDrugListByTargets(targetsMiriam, searchCriteria.getOrganisms());
+ drugList.addAll(drugs);
+ } catch (DrugSearchException e) {
+ logger.error("Problem with accessing drugBank parser", e);
+ }
+
+ try {
+ List<Drug> drugs = chEMBLParser.getDrugListByTargets(targetsMiriam, searchCriteria.getOrganisms());
+ drugList.addAll(drugs);
+ } catch (DrugSearchException e) {
+ logger.error("Problem with accessing chembl parser", e);
+ }
+
+ for (Drug drug : drugList) {
+ removeUnknownOrganisms(drug, searchCriteria.getOrganisms());
+ }
+
+ Collections.sort(drugList, new Drug.NameComparator());
+ return drugList;
+ }
+
+ /**
+ * @return the drugBankParser
+ */
+ public DrugbankHTMLParser getDrugBankParser() {
+ return drugBankParser;
+ }
+
+ /**
+ * @param drugBankParser
+ * the drugBankParser to set
+ */
+ public void setDrugBankParser(DrugbankHTMLParser drugBankParser) {
+ this.drugBankParser = drugBankParser;
+ }
+
+ /**
+ * @return the chEMBLParser
+ */
+ public ChEMBLParser getChEMBLParser() {
+ return chEMBLParser;
+ }
+
+ /**
+ * @param chEMBLParser
+ * the chEMBLParser to set
+ */
+ public void setChEMBLParser(ChEMBLParser chEMBLParser) {
+ this.chEMBLParser = chEMBLParser;
+ }
+
+ /**
+ * @return the searchHistoryService
+ */
+ public ISearchHistoryService getSearchHistoryService() {
+ return searchHistoryService;
+ }
+
+ /**
+ * @param searchHistoryService
+ * the searchHistoryService to set
+ */
+ public void setSearchHistoryService(ISearchHistoryService searchHistoryService) {
+ this.searchHistoryService = searchHistoryService;
+ }
+
+ @Override
+ public void cacheDataForModel(Model originalModel, IProgressUpdater iProgressUpdater) {
+ logger.debug("Caching drug queries...");
+ double progress = 0.0;
+ iProgressUpdater.setProgress(progress * IProgressUpdater.MAX_PROGRESS);
+ MiriamData disease = originalModel.getProject().getDisease();
+ if (disease != null) {
+ Set<MiriamData> targetMiriams = new HashSet<>();
+ List<Model> models = new ArrayList<>();
+ models.add(originalModel);
+ models.addAll(originalModel.getSubmodels());
+ for (Model model : models) {
+ for (BioEntity element : model.getBioEntities()) {
+ for (MiriamData md : element.getMiriamData()) {
+ if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
+ targetMiriams.add(md);
+ }
+ }
+ }
+ }
+ double counter = 0.0;
+ List<MiriamData> organisms = new ArrayList<>();
+ for (MiriamData md : targetMiriams) {
+ try {
+ List<Drug> chemicalList = drugBankParser.getDrugListByTarget(md, organisms);
+ for (Drug chemical : chemicalList) {
+ cacheMiriamData(chemical);
+ }
+ } catch (DrugSearchException | AnnotatorException e) {
+ logger.error("Problem with accessing info about drugbank for target: " + md, e);
+ }
+ try {
+ List<Drug> chemicalList = chEMBLParser.getDrugListByTarget(md, organisms);
+ for (Drug chemical : chemicalList) {
+ cacheMiriamData(chemical);
+ }
+ } catch (DrugSearchException | AnnotatorException e) {
+ logger.error("Problem with accessing info about chembl for target: " + md, e);
+ }
+ counter += 1;
+ progress = counter / (double) targetMiriams.size();
+ iProgressUpdater.setProgress(progress * IProgressUpdater.MAX_PROGRESS);
+ }
+ }
+ }
+
+ @Override
+ public List<String> getSuggestedQueryList(Project project, MiriamData organism) throws DrugSearchException {
+ Set<String> resultSet = new HashSet<>();
+ for (String string : drugBankParser.getSuggestedQueryList(project, organism)) {
+ resultSet.add(string.toLowerCase());
+ }
+ for (String string : chEMBLParser.getSuggestedQueryList(project, organism)) {
+ resultSet.add(string.toLowerCase());
+ }
+
+ List<String> result = new ArrayList<>();
+ result.addAll(resultSet);
+ Collections.sort(result);
+ return result;
+ }
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/drug/IDrugService.java b/service/src/main/java/lcsb/mapviewer/services/search/drug/IDrugService.java
index 9cf0bf0c21..e7d343e94c 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/drug/IDrugService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/drug/IDrugService.java
@@ -1,21 +1,21 @@
-package lcsb.mapviewer.services.search.drug;
-
-import java.util.List;
-
-import lcsb.mapviewer.annotation.data.Drug;
-import lcsb.mapviewer.annotation.services.DrugSearchException;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.services.search.IDbSearchService;
-
-/**
- * Service for accessing information about drugs.
- *
- * @author Piotr Gawron
- *
- */
-public interface IDrugService extends IDbSearchService<Drug> {
-
- List<String> getSuggestedQueryList(Project project, MiriamData disease) throws DrugSearchException;
-
-}
+package lcsb.mapviewer.services.search.drug;
+
+import java.util.List;
+
+import lcsb.mapviewer.annotation.data.Drug;
+import lcsb.mapviewer.annotation.services.DrugSearchException;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.services.search.IDbSearchService;
+
+/**
+ * Service for accessing information about drugs.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface IDrugService extends IDbSearchService<Drug> {
+
+ List<String> getSuggestedQueryList(Project project, MiriamData disease) throws DrugSearchException;
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/drug/package-info.java b/service/src/main/java/lcsb/mapviewer/services/search/drug/package-info.java
index 1f2a7b8f34..a605f8aa4b 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/drug/package-info.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/drug/package-info.java
@@ -1,8 +1,8 @@
-/**
- * This package contains structures used for passing drug related data about
- * elements to the client.
- * <p/>
- * Be carefull when refactoring classes in this package. Data are accessed not
- * directly (not via managable code) by client side.
- */
-package lcsb.mapviewer.services.search.drug;
+/**
+ * This package contains structures used for passing drug related data about
+ * elements to the client.
+ * <p/>
+ * Be carefull when refactoring classes in this package. Data are accessed not
+ * directly (not via managable code) by client side.
+ */
+package lcsb.mapviewer.services.search.drug;
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/mirna/IMiRNAService.java b/service/src/main/java/lcsb/mapviewer/services/search/mirna/IMiRNAService.java
index bfe7184ae2..9fa5ce2619 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/mirna/IMiRNAService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/mirna/IMiRNAService.java
@@ -1,14 +1,14 @@
-package lcsb.mapviewer.services.search.mirna;
-
-import lcsb.mapviewer.annotation.data.MiRNA;
-import lcsb.mapviewer.services.search.IDbSearchService;
-
-/**
- * Service for accessing information about miRNA.
- *
- * @author Ayan Rota
- *
- */
-public interface IMiRNAService extends IDbSearchService<MiRNA> {
-
-}
+package lcsb.mapviewer.services.search.mirna;
+
+import lcsb.mapviewer.annotation.data.MiRNA;
+import lcsb.mapviewer.services.search.IDbSearchService;
+
+/**
+ * Service for accessing information about miRNA.
+ *
+ * @author Ayan Rota
+ *
+ */
+public interface IMiRNAService extends IDbSearchService<MiRNA> {
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/mirna/MiRNAService.java b/service/src/main/java/lcsb/mapviewer/services/search/mirna/MiRNAService.java
index a6bd2243ed..1655449625 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/mirna/MiRNAService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/mirna/MiRNAService.java
@@ -1,205 +1,205 @@
-package lcsb.mapviewer.services.search.mirna;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import javax.annotation.PostConstruct;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.annotation.data.MiRNA;
-import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.annotation.services.MiRNAParser;
-import lcsb.mapviewer.annotation.services.MiRNASearchException;
-import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
-import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
-import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.services.search.DbSearchCriteria;
-import lcsb.mapviewer.services.search.DbSearchService;
-
-/**
- * Implementation of the service that allows access information about miRNAs.
- *
- * @author Ayan Rota
- *
- */
-@Transactional(value = "txManager")
-public class MiRNAService extends DbSearchService implements IMiRNAService {
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(MiRNAService.class);
-
- /**
- * Access point and parser for the online ctd database.
- */
- @Autowired
- private MiRNAParser miRNAParser;
-
- /**
- * Object used to get information about {@link MiriamType#HGNC} annotations and
- * transformations.
- */
- @Autowired
- private HgncAnnotator hgncAnnotator;
-
- /**
- * Default constructor.
- */
- public MiRNAService() {
- super();
- }
-
- @Override
- public MiRNA getByName(String name, DbSearchCriteria searchCriteria) {
- if ("".equals(name)) {
- return null;
- }
- try {
- List<String> names = new ArrayList<>();
- names.add(name);
- List<MiRNA> miRNAs = miRNAParser.getMiRnasByNames(names);
- if (miRNAs.size() > 0) {
- return miRNAs.get(0);
- }
- return null;
- // return miRNAViewFactory.create(miRNAs.get(0),
- // searchCriteria.getModel(), searchCriteria.getColorSet());
- } catch (MiRNASearchException e) {
- logger.error("Problem with accessing mirna database", e);
- return null;
- }
- }
-
- @Override
- public List<MiRNA> getForTargets(Collection<Element> targets, DbSearchCriteria searchCriteria) {
- List<MiRNA> mirnaList = new ArrayList<MiRNA>();
- Set<MiriamData> targetsMiriam = new HashSet<MiriamData>();
- for (Element element : targets) {
- if (element instanceof Protein || element instanceof Gene || element instanceof Rna) {
- boolean hgncFound = false;
- for (MiriamData md : element.getMiriamData()) {
- if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
- targetsMiriam.add(md);
- hgncFound = true;
- } else if (MiriamType.ENTREZ.equals(md.getDataType())) {
- // ad also entrez in case of mouse, rat, etc
- targetsMiriam.add(md);
- }
-
- }
- if (!hgncFound) {
- MiriamData md = new MiriamData(MiriamType.HGNC_SYMBOL, element.getName());
- try {
- if (hgncAnnotator.isValidHgncMiriam(md)) {
- targetsMiriam.add(md);
- }
- } catch (AnnotatorException e) {
- logger.error("Problem with accessing HGNC database", e);
- }
- }
- }
- }
- try {
- mirnaList = miRNAParser.getMiRnaListByTargets(targetsMiriam);
- } catch (MiRNASearchException e) {
- logger.error("Problem with accessing mirna database", e);
- }
-
- for (MiRNA drug : mirnaList) {
- removeUnknownOrganisms(drug, searchCriteria.getOrganisms());
- }
-
- Collections.sort(mirnaList, new MiRNA.NameComparator());
- return mirnaList;
- }
-
- /**
- * Removes targets for unknown organisms from the mirna.
- *
- * @param drug
- * drug from which we want to remove targets
- * @param organisms
- * organisms that should be kept
- */
- private void removeUnknownOrganisms(MiRNA drug, List<MiriamData> organisms) {
- if (organisms.size() > 0) {
- List<Target> toRemove = new ArrayList<Target>();
- for (Target target : drug.getTargets()) {
- boolean remove = true;
- for (MiriamData organism : organisms) {
- if (target.getOrganism() == null) {
- remove = false;
- } else if (target.getOrganism().equals(organism)) {
- remove = false;
- }
- }
- if (remove) {
- logger.debug("Target " + target.getName() + " removed from list because results are limited to organisms: "
- + organisms);
- toRemove.add(target);
- }
- }
- drug.getTargets().removeAll(toRemove);
- }
- }
-
- @Override
- public void cacheDataForModel(Model originalModel, IProgressUpdater iProgressUpdater) {
- logger.debug("Caching mirna queries...");
- double progress = 0.0;
- iProgressUpdater.setProgress(progress * IProgressUpdater.MAX_PROGRESS);
- Set<MiriamData> targetMiriams = new HashSet<>();
- List<Model> models = new ArrayList<>();
- models.add(originalModel);
- models.addAll(originalModel.getSubmodels());
- for (Model model : models) {
- for (BioEntity element : model.getBioEntities()) {
- for (MiriamData md : element.getMiriamData()) {
- if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
- targetMiriams.add(md);
- } else if (MiriamType.ENTREZ.equals(md.getDataType())) {
- targetMiriams.add(md);
- }
- }
- }
- }
- double counter = 0.0;
- int step = Math.max(targetMiriams.size() / 100, 1);
- List<MiriamData> currentList = new ArrayList<>();
- for (MiriamData md : targetMiriams) {
- counter += 1;
- currentList.add(md);
- if (currentList.size() >= step) {
- logger.debug("check mirna target: " + currentList);
- try {
- List<MiRNA> chemicalList = miRNAParser.getMiRnaListByTargets(currentList);
- for (MiRNA chemical : chemicalList) {
- cacheMiriamData(chemical);
- }
- } catch (MiRNASearchException | AnnotatorException e) {
- logger.error("Problem with accessing info about mirna for target: " + md, e);
- }
- progress = counter / (double) targetMiriams.size();
- iProgressUpdater.setProgress(progress * IProgressUpdater.MAX_PROGRESS);
- currentList.clear();
- }
- }
- }
-
-}
+package lcsb.mapviewer.services.search.mirna;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import javax.annotation.PostConstruct;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.annotation.data.MiRNA;
+import lcsb.mapviewer.annotation.data.Target;
+import lcsb.mapviewer.annotation.services.MiRNAParser;
+import lcsb.mapviewer.annotation.services.MiRNASearchException;
+import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
+import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
+import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.services.search.DbSearchCriteria;
+import lcsb.mapviewer.services.search.DbSearchService;
+
+/**
+ * Implementation of the service that allows access information about miRNAs.
+ *
+ * @author Ayan Rota
+ *
+ */
+@Transactional(value = "txManager")
+public class MiRNAService extends DbSearchService implements IMiRNAService {
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(MiRNAService.class);
+
+ /**
+ * Access point and parser for the online ctd database.
+ */
+ @Autowired
+ private MiRNAParser miRNAParser;
+
+ /**
+ * Object used to get information about {@link MiriamType#HGNC} annotations and
+ * transformations.
+ */
+ @Autowired
+ private HgncAnnotator hgncAnnotator;
+
+ /**
+ * Default constructor.
+ */
+ public MiRNAService() {
+ super();
+ }
+
+ @Override
+ public MiRNA getByName(String name, DbSearchCriteria searchCriteria) {
+ if ("".equals(name)) {
+ return null;
+ }
+ try {
+ List<String> names = new ArrayList<>();
+ names.add(name);
+ List<MiRNA> miRNAs = miRNAParser.getMiRnasByNames(names);
+ if (miRNAs.size() > 0) {
+ return miRNAs.get(0);
+ }
+ return null;
+ // return miRNAViewFactory.create(miRNAs.get(0),
+ // searchCriteria.getModel(), searchCriteria.getColorSet());
+ } catch (MiRNASearchException e) {
+ logger.error("Problem with accessing mirna database", e);
+ return null;
+ }
+ }
+
+ @Override
+ public List<MiRNA> getForTargets(Collection<Element> targets, DbSearchCriteria searchCriteria) {
+ List<MiRNA> mirnaList = new ArrayList<MiRNA>();
+ Set<MiriamData> targetsMiriam = new HashSet<MiriamData>();
+ for (Element element : targets) {
+ if (element instanceof Protein || element instanceof Gene || element instanceof Rna) {
+ boolean hgncFound = false;
+ for (MiriamData md : element.getMiriamData()) {
+ if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
+ targetsMiriam.add(md);
+ hgncFound = true;
+ } else if (MiriamType.ENTREZ.equals(md.getDataType())) {
+ // ad also entrez in case of mouse, rat, etc
+ targetsMiriam.add(md);
+ }
+
+ }
+ if (!hgncFound) {
+ MiriamData md = new MiriamData(MiriamType.HGNC_SYMBOL, element.getName());
+ try {
+ if (hgncAnnotator.isValidHgncMiriam(md)) {
+ targetsMiriam.add(md);
+ }
+ } catch (AnnotatorException e) {
+ logger.error("Problem with accessing HGNC database", e);
+ }
+ }
+ }
+ }
+ try {
+ mirnaList = miRNAParser.getMiRnaListByTargets(targetsMiriam);
+ } catch (MiRNASearchException e) {
+ logger.error("Problem with accessing mirna database", e);
+ }
+
+ for (MiRNA drug : mirnaList) {
+ removeUnknownOrganisms(drug, searchCriteria.getOrganisms());
+ }
+
+ Collections.sort(mirnaList, new MiRNA.NameComparator());
+ return mirnaList;
+ }
+
+ /**
+ * Removes targets for unknown organisms from the mirna.
+ *
+ * @param drug
+ * drug from which we want to remove targets
+ * @param organisms
+ * organisms that should be kept
+ */
+ private void removeUnknownOrganisms(MiRNA drug, List<MiriamData> organisms) {
+ if (organisms.size() > 0) {
+ List<Target> toRemove = new ArrayList<Target>();
+ for (Target target : drug.getTargets()) {
+ boolean remove = true;
+ for (MiriamData organism : organisms) {
+ if (target.getOrganism() == null) {
+ remove = false;
+ } else if (target.getOrganism().equals(organism)) {
+ remove = false;
+ }
+ }
+ if (remove) {
+ logger.debug("Target " + target.getName() + " removed from list because results are limited to organisms: "
+ + organisms);
+ toRemove.add(target);
+ }
+ }
+ drug.getTargets().removeAll(toRemove);
+ }
+ }
+
+ @Override
+ public void cacheDataForModel(Model originalModel, IProgressUpdater iProgressUpdater) {
+ logger.debug("Caching mirna queries...");
+ double progress = 0.0;
+ iProgressUpdater.setProgress(progress * IProgressUpdater.MAX_PROGRESS);
+ Set<MiriamData> targetMiriams = new HashSet<>();
+ List<Model> models = new ArrayList<>();
+ models.add(originalModel);
+ models.addAll(originalModel.getSubmodels());
+ for (Model model : models) {
+ for (BioEntity element : model.getBioEntities()) {
+ for (MiriamData md : element.getMiriamData()) {
+ if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
+ targetMiriams.add(md);
+ } else if (MiriamType.ENTREZ.equals(md.getDataType())) {
+ targetMiriams.add(md);
+ }
+ }
+ }
+ }
+ double counter = 0.0;
+ int step = Math.max(targetMiriams.size() / 100, 1);
+ List<MiriamData> currentList = new ArrayList<>();
+ for (MiriamData md : targetMiriams) {
+ counter += 1;
+ currentList.add(md);
+ if (currentList.size() >= step) {
+ logger.debug("check mirna target: " + currentList);
+ try {
+ List<MiRNA> chemicalList = miRNAParser.getMiRnaListByTargets(currentList);
+ for (MiRNA chemical : chemicalList) {
+ cacheMiriamData(chemical);
+ }
+ } catch (MiRNASearchException | AnnotatorException e) {
+ logger.error("Problem with accessing info about mirna for target: " + md, e);
+ }
+ progress = counter / (double) targetMiriams.size();
+ iProgressUpdater.setProgress(progress * IProgressUpdater.MAX_PROGRESS);
+ currentList.clear();
+ }
+ }
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/mirna/package-info.java b/service/src/main/java/lcsb/mapviewer/services/search/mirna/package-info.java
index d87f2a0285..cbb58aa8ac 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/mirna/package-info.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/mirna/package-info.java
@@ -1,8 +1,8 @@
-/**
- * This package contains structures used for passing mi rna related data about
- * elements to the client.
- * <p/>
- * Be carefull when refactoring classes in this package. Data are accessed not
- * directly (not via managable code) by client side.
- */
-package lcsb.mapviewer.services.search.mirna;
+/**
+ * This package contains structures used for passing mi rna related data about
+ * elements to the client.
+ * <p/>
+ * Be carefull when refactoring classes in this package. Data are accessed not
+ * directly (not via managable code) by client side.
+ */
+package lcsb.mapviewer.services.search.mirna;
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/package-info.java b/service/src/main/java/lcsb/mapviewer/services/search/package-info.java
index 04fbe31395..d5beae4668 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/package-info.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/package-info.java
@@ -1,8 +1,8 @@
-/**
- * This package contains structures used for passing search results (based on
- * external database search) related data about elements to the client.
- * <p/>
- * Be carefull when refactoring classes in this package. Data are accessed not
- * directly (not via managable code) by client side.
- */
-package lcsb.mapviewer.services.search;
+/**
+ * This package contains structures used for passing search results (based on
+ * external database search) related data about elements to the client.
+ * <p/>
+ * Be carefull when refactoring classes in this package. Data are accessed not
+ * directly (not via managable code) by client side.
+ */
+package lcsb.mapviewer.services.search;
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java
index c3df713257..4948d346f2 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java
@@ -1,347 +1,347 @@
-package lcsb.mapviewer.services.utils;
-
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.apache.commons.io.FilenameUtils;
-import org.apache.log4j.Logger;
-import org.apache.poi.hssf.usermodel.HSSFWorkbook;
-import org.apache.poi.ss.usermodel.Cell;
-import org.apache.poi.ss.usermodel.CellStyle;
-import org.apache.poi.ss.usermodel.DataFormat;
-import org.apache.poi.ss.usermodel.Row;
-import org.apache.poi.ss.usermodel.Sheet;
-import org.apache.poi.ss.usermodel.Workbook;
-import org.apache.poi.xssf.usermodel.XSSFWorkbook;
-
-import lcsb.mapviewer.annotation.services.MiriamConnector;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.geometry.ColorParser;
-import lcsb.mapviewer.converter.model.celldesigner.species.SpeciesMapping;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.layout.GenericColorSchema;
-import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
-import lcsb.mapviewer.services.utils.data.ColorSchemaColumn;
-
-/**
- * Class that reads information about set of {@link ColorSchema color schemas}
- * from the input file.
- *
- * @author Piotr Gawron
- *
- */
-public class ColorSchemaXlsxReader {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(ColorSchemaXlsxReader.class);
-
- /**
- * @param fileName
- * file name
- * @param sheetName
- * sheet name.
- * @return list of ColorSchema.
- * @throws IOException
- * exception related to opening the input stream.
- * @throws InvalidColorSchemaException
- * invalid color schema exception.
- */
- public Collection<ColorSchema> readColorSchema(String fileName, String sheetName)
- throws IOException, InvalidColorSchemaException {
- ColorParser colorParser = new ColorParser();
- List<ColorSchema> result = new ArrayList<>();
- FileInputStream file = null;
- Workbook workbook = null;
-
- try {
- file = new FileInputStream(fileName);
- // Using XSSF for xlsx format, for xls use HSSF
- // <-Interface, accepts both HSSF and XSSF.
- if (FilenameUtils.getExtension(fileName).equalsIgnoreCase("xls")) {
- workbook = new HSSFWorkbook(file);
- } else if (FilenameUtils.getExtension(fileName).equalsIgnoreCase("xlsx")) {
- workbook = new XSSFWorkbook(file);
- } else {
- throw new IllegalArgumentException("Received file does not have a standard excel extension.");
- }
- Sheet sheet = null;
- if (sheetName == null) {
- sheet = workbook.getSheetAt(0);
- } else {
- sheet = workbook.getSheet(sheetName);
- }
- DataFormat fmt = workbook.createDataFormat();
- CellStyle textStyle = workbook.createCellStyle();
- textStyle.setDataFormat(fmt.getFormat("@"));
-
- Iterator<Row> rowIterator = sheet.iterator();
- Integer valueColumn = null;
- Integer colorColumn = null;
- Integer nameColumn = null;
- Integer modelNameColumn = null;
- Integer identifierColumn = null;
- Integer elementIdentifierColumn = null;
- Integer compartmentColumn = null;
- Integer typeColumn = null;
- Integer lineWidthColumn = null;
- Integer reverseReactionColumn = null;
- List<Pair<MiriamType, Integer>> foundCustomIdentifiers = new ArrayList<Pair<MiriamType, Integer>>();
- int lineIndex = 0;
- Map<ColorSchemaColumn, Integer> foundSchemaColumns = new HashMap<ColorSchemaColumn, Integer>();
- while (rowIterator.hasNext()) {
- Row row = rowIterator.next();
- Cell cell = row.getCell(0, Row.RETURN_BLANK_AS_NULL);
- if (cell == null) {
- continue;
- } else {
- cell.setCellType(Cell.CELL_TYPE_STRING);
- if (cell.getStringCellValue().startsWith("#")) {
- continue;
- }
- }
- lineIndex++;
- if (lineIndex == 1) {
-
- Map<String, MiriamType> acceptableIdentifiers = new HashMap<String, MiriamType>();
- for (MiriamType type : MiriamType.values()) {
- acceptableIdentifiers.put(type.getCommonName().toLowerCase(), type);
- }
-
- Iterator<Cell> cellIterator = row.cellIterator();
- int columnIndex = 0;
- while (cellIterator.hasNext()) {
- columnIndex++;
- sheet.setDefaultColumnStyle(columnIndex, textStyle);
- cell = cellIterator.next();
- cell.setCellType(Cell.CELL_TYPE_STRING);
- String value = cell.getStringCellValue();
- boolean found = false;
- for (ColorSchemaColumn schemaColumn : ColorSchemaColumn.values()) {
- if (value.trim().equalsIgnoreCase(schemaColumn.getTitle())) {
- foundSchemaColumns.put(schemaColumn, columnIndex - 1);
- found = true;
- break;
- }
- }
- if (!found) {
- if (acceptableIdentifiers.keySet().contains(value.toLowerCase())) {
- foundCustomIdentifiers.add(
- new Pair<MiriamType, Integer>(acceptableIdentifiers.get(value.toLowerCase()), columnIndex - 1));
- } else {
- String columnNames = "";
- for (ColorSchemaColumn schemaColumn : ColorSchemaColumn.values()) {
- columnNames += schemaColumn.getTitle() + ", ";
- }
- for (String string : acceptableIdentifiers.keySet()) {
- columnNames += ", " + string;
- }
- throw new InvalidColorSchemaException(
- "Unknown column type: " + value + ". Acceptable column name: " + columnNames);
- }
- }
- }
- valueColumn = foundSchemaColumns.get(ColorSchemaColumn.VALUE);
- colorColumn = foundSchemaColumns.get(ColorSchemaColumn.COLOR);
- nameColumn = foundSchemaColumns.get(ColorSchemaColumn.NAME);
- modelNameColumn = foundSchemaColumns.get(ColorSchemaColumn.MODEL_NAME);
- identifierColumn = foundSchemaColumns.get(ColorSchemaColumn.IDENTIFIER);
- elementIdentifierColumn = foundSchemaColumns.get(ColorSchemaColumn.ELEMENT_IDENTIFIER);
- if (elementIdentifierColumn == null) {
- elementIdentifierColumn = foundSchemaColumns.get(ColorSchemaColumn.REACTION_IDENTIFIER);
- }
- compartmentColumn = foundSchemaColumns.get(ColorSchemaColumn.COMPARTMENT);
- typeColumn = foundSchemaColumns.get(ColorSchemaColumn.TYPE);
- lineWidthColumn = foundSchemaColumns.get(ColorSchemaColumn.LINE_WIDTH);
- reverseReactionColumn = foundSchemaColumns.get(ColorSchemaColumn.REVERSE_REACTION);
-
- if (valueColumn != null && colorColumn != null) {
- throw new InvalidColorSchemaException("Schema can contain only one of these two columns: ");
- }
-
- if (nameColumn == null && identifierColumn == null && foundCustomIdentifiers.size() == 0
- && elementIdentifierColumn == null) {
- throw new InvalidColorSchemaException(
- "One of these columns is obligatory: " + ColorSchemaColumn.NAME.getTitle() + ","
- + ColorSchemaColumn.IDENTIFIER.getTitle() + "," + ColorSchemaColumn.ELEMENT_IDENTIFIER.getTitle());
- }
-
- if (valueColumn == null && colorColumn == null) {
- throw new InvalidColorSchemaException("Schema must contain one of these two columns: value, name");
- }
-
- } else {
- ColorSchema schema = new GenericColorSchema();
- if (nameColumn != null) {
- schema.setName(row.getCell(nameColumn).getStringCellValue());
- }
- if (modelNameColumn != null) {
- schema.setModelName(row.getCell(modelNameColumn).getStringCellValue());
- }
- if (valueColumn != null) {
- try {
- cell = row.getCell(valueColumn);
- cell.setCellType(Cell.CELL_TYPE_STRING);
- schema.setValue(Double.parseDouble(cell.getStringCellValue().replace(",", ".")));
- } catch (Exception e) {
- throw new InvalidColorSchemaException(
- "[Line " + lineIndex + "] Problem with parsing value for value column. Cell value" + cell);
- }
- if (schema.getValue() > 1 + Configuration.EPSILON || schema.getValue() < -1 - Configuration.EPSILON) {
- throw new InvalidColorSchemaException("[Line " + lineIndex + "] Value " + schema.getValue()
- + " out of range. Only values between -1 and 1 are allowed.");
- }
- }
- if (compartmentColumn != null) {
- String value = row.getCell(compartmentColumn).getStringCellValue();
- if (value != null) {
- String[] compartments = value.split(",");
- schema.addCompartments(compartments);
- }
- }
- if (typeColumn != null) {
- String value = row.getCell(typeColumn).getStringCellValue();
- if (value != null) {
- String[] types = value.split(",");
- for (String string : types) {
- SpeciesMapping mapping = SpeciesMapping.getMappingByString(string);
- if (mapping != null) {
- schema.addType(mapping.getModelClazz());
- } else {
- throw new InvalidColorSchemaException("Unknown class type: " + string + ".");
- }
- }
- }
- }
- if (colorColumn != null) {
- schema.setColor(colorParser.parse(row.getCell(colorColumn).getStringCellValue()));
- }
- if (elementIdentifierColumn != null) {
- schema.setElementId(row.getCell(elementIdentifierColumn).getStringCellValue());
- }
- if (lineWidthColumn != null) {
- cell = row.getCell(lineWidthColumn);
- cell.setCellType(Cell.CELL_TYPE_STRING);
- String value = cell.getStringCellValue();
- if (value != null && !value.trim().isEmpty()) {
- try {
- schema.setLineWidth(Double.parseDouble(value.replace(",", ".")));
- } catch (NumberFormatException e) {
- throw new InvalidColorSchemaException(
- "[Line " + lineIndex + "] Problem with parsing value: \"" + value + "\"");
- }
- }
- }
- if (reverseReactionColumn != null) {
- cell = row.getCell(reverseReactionColumn);
- if (cell != null) {
- cell.setCellType(Cell.CELL_TYPE_STRING);
- schema.setReverseReaction("true".equalsIgnoreCase(cell.getStringCellValue()));
- }
- }
- if (identifierColumn != null) {
- cell = row.getCell(identifierColumn);
- if (cell != null && !cell.getStringCellValue().trim().isEmpty()) {
- MiriamConnector miriamConnector = new MiriamConnector();
- String value = cell.getStringCellValue().trim();
- if (miriamConnector.isValidIdentifier(value)) {
- schema.addMiriamData(MiriamType.getMiriamDataFromIdentifier(value));
- } else {
- throw new InvalidColorSchemaException("[Line " + lineIndex + "]" + " Invalid identifier: " + value);
- }
- }
- }
- for (Pair<MiriamType, Integer> pair : foundCustomIdentifiers) {
- cell = row.getCell(pair.getRight());
- if (cell != null) {
- schema.addMiriamData(new MiriamData(pair.getLeft(), cell.getStringCellValue()));
- }
- }
-
- if ((schema.getValue() != null && schema.getColor() != null)
- || (schema.getValue() == null && schema.getColor() == null)) {
- throw new InvalidColorSchemaException("Value or Color is needed not both");
- }
-
- if (schema.getName() == null && schema.getMiriamData().size() == 0 && foundCustomIdentifiers.size() == 0
- && schema.getElementId() == null) {
- throw new InvalidColorSchemaException(
- "One of these columns values is obligatory: name, identifier, reactionIdentifier");
- }
- result.add(schema);
- }
- }
- } finally {
- try {
- if (file != null) {
- file.close();
- }
- if (workbook != null) {
- workbook.close();
- }
- } catch (Exception e) {
-
- }
- }
- return result;
-
- }
-
- /**
- * Returns list of columns that should be printed for given coloring schemas.
- *
- * @param schemas
- * list of schemas
- * @return list of columns that should be printed (were set in the coloring
- * schemas)
- */
- public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
- Set<ColorSchemaColumn> result = new HashSet<ColorSchemaColumn>();
- for (ColorSchema schema : schemas) {
- if (schema.getColor() != null) {
- result.add(ColorSchemaColumn.COLOR);
- }
- if (schema.getCompartments().size() > 0) {
- result.add(ColorSchemaColumn.COMPARTMENT);
- }
- if (schema.getMiriamData().size() > 0) {
- result.add(ColorSchemaColumn.IDENTIFIER);
- }
- if (schema.getLineWidth() != null) {
- result.add(ColorSchemaColumn.LINE_WIDTH);
- }
- if (schema.getName() != null) {
- result.add(ColorSchemaColumn.NAME);
- }
- if (schema.getModelName() != null) {
- result.add(ColorSchemaColumn.MODEL_NAME);
- }
- if (schema.getElementId() != null) {
- result.add(ColorSchemaColumn.ELEMENT_IDENTIFIER);
- }
- if (schema.getReverseReaction() != null) {
- result.add(ColorSchemaColumn.REVERSE_REACTION);
- }
- if (schema.getTypes().size() > 0) {
- result.add(ColorSchemaColumn.TYPE);
- }
- if (schema.getValue() != null) {
- result.add(ColorSchemaColumn.VALUE);
- }
- }
- return result;
- }
-
-}
+package lcsb.mapviewer.services.utils;
+
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.commons.io.FilenameUtils;
+import org.apache.log4j.Logger;
+import org.apache.poi.hssf.usermodel.HSSFWorkbook;
+import org.apache.poi.ss.usermodel.Cell;
+import org.apache.poi.ss.usermodel.CellStyle;
+import org.apache.poi.ss.usermodel.DataFormat;
+import org.apache.poi.ss.usermodel.Row;
+import org.apache.poi.ss.usermodel.Sheet;
+import org.apache.poi.ss.usermodel.Workbook;
+import org.apache.poi.xssf.usermodel.XSSFWorkbook;
+
+import lcsb.mapviewer.annotation.services.MiriamConnector;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.geometry.ColorParser;
+import lcsb.mapviewer.converter.model.celldesigner.species.SpeciesMapping;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.layout.GenericColorSchema;
+import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
+import lcsb.mapviewer.services.utils.data.ColorSchemaColumn;
+
+/**
+ * Class that reads information about set of {@link ColorSchema color schemas}
+ * from the input file.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ColorSchemaXlsxReader {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(ColorSchemaXlsxReader.class);
+
+ /**
+ * @param fileName
+ * file name
+ * @param sheetName
+ * sheet name.
+ * @return list of ColorSchema.
+ * @throws IOException
+ * exception related to opening the input stream.
+ * @throws InvalidColorSchemaException
+ * invalid color schema exception.
+ */
+ public Collection<ColorSchema> readColorSchema(String fileName, String sheetName)
+ throws IOException, InvalidColorSchemaException {
+ ColorParser colorParser = new ColorParser();
+ List<ColorSchema> result = new ArrayList<>();
+ FileInputStream file = null;
+ Workbook workbook = null;
+
+ try {
+ file = new FileInputStream(fileName);
+ // Using XSSF for xlsx format, for xls use HSSF
+ // <-Interface, accepts both HSSF and XSSF.
+ if (FilenameUtils.getExtension(fileName).equalsIgnoreCase("xls")) {
+ workbook = new HSSFWorkbook(file);
+ } else if (FilenameUtils.getExtension(fileName).equalsIgnoreCase("xlsx")) {
+ workbook = new XSSFWorkbook(file);
+ } else {
+ throw new IllegalArgumentException("Received file does not have a standard excel extension.");
+ }
+ Sheet sheet = null;
+ if (sheetName == null) {
+ sheet = workbook.getSheetAt(0);
+ } else {
+ sheet = workbook.getSheet(sheetName);
+ }
+ DataFormat fmt = workbook.createDataFormat();
+ CellStyle textStyle = workbook.createCellStyle();
+ textStyle.setDataFormat(fmt.getFormat("@"));
+
+ Iterator<Row> rowIterator = sheet.iterator();
+ Integer valueColumn = null;
+ Integer colorColumn = null;
+ Integer nameColumn = null;
+ Integer modelNameColumn = null;
+ Integer identifierColumn = null;
+ Integer elementIdentifierColumn = null;
+ Integer compartmentColumn = null;
+ Integer typeColumn = null;
+ Integer lineWidthColumn = null;
+ Integer reverseReactionColumn = null;
+ List<Pair<MiriamType, Integer>> foundCustomIdentifiers = new ArrayList<Pair<MiriamType, Integer>>();
+ int lineIndex = 0;
+ Map<ColorSchemaColumn, Integer> foundSchemaColumns = new HashMap<ColorSchemaColumn, Integer>();
+ while (rowIterator.hasNext()) {
+ Row row = rowIterator.next();
+ Cell cell = row.getCell(0, Row.RETURN_BLANK_AS_NULL);
+ if (cell == null) {
+ continue;
+ } else {
+ cell.setCellType(Cell.CELL_TYPE_STRING);
+ if (cell.getStringCellValue().startsWith("#")) {
+ continue;
+ }
+ }
+ lineIndex++;
+ if (lineIndex == 1) {
+
+ Map<String, MiriamType> acceptableIdentifiers = new HashMap<String, MiriamType>();
+ for (MiriamType type : MiriamType.values()) {
+ acceptableIdentifiers.put(type.getCommonName().toLowerCase(), type);
+ }
+
+ Iterator<Cell> cellIterator = row.cellIterator();
+ int columnIndex = 0;
+ while (cellIterator.hasNext()) {
+ columnIndex++;
+ sheet.setDefaultColumnStyle(columnIndex, textStyle);
+ cell = cellIterator.next();
+ cell.setCellType(Cell.CELL_TYPE_STRING);
+ String value = cell.getStringCellValue();
+ boolean found = false;
+ for (ColorSchemaColumn schemaColumn : ColorSchemaColumn.values()) {
+ if (value.trim().equalsIgnoreCase(schemaColumn.getTitle())) {
+ foundSchemaColumns.put(schemaColumn, columnIndex - 1);
+ found = true;
+ break;
+ }
+ }
+ if (!found) {
+ if (acceptableIdentifiers.keySet().contains(value.toLowerCase())) {
+ foundCustomIdentifiers.add(
+ new Pair<MiriamType, Integer>(acceptableIdentifiers.get(value.toLowerCase()), columnIndex - 1));
+ } else {
+ String columnNames = "";
+ for (ColorSchemaColumn schemaColumn : ColorSchemaColumn.values()) {
+ columnNames += schemaColumn.getTitle() + ", ";
+ }
+ for (String string : acceptableIdentifiers.keySet()) {
+ columnNames += ", " + string;
+ }
+ throw new InvalidColorSchemaException(
+ "Unknown column type: " + value + ". Acceptable column name: " + columnNames);
+ }
+ }
+ }
+ valueColumn = foundSchemaColumns.get(ColorSchemaColumn.VALUE);
+ colorColumn = foundSchemaColumns.get(ColorSchemaColumn.COLOR);
+ nameColumn = foundSchemaColumns.get(ColorSchemaColumn.NAME);
+ modelNameColumn = foundSchemaColumns.get(ColorSchemaColumn.MODEL_NAME);
+ identifierColumn = foundSchemaColumns.get(ColorSchemaColumn.IDENTIFIER);
+ elementIdentifierColumn = foundSchemaColumns.get(ColorSchemaColumn.ELEMENT_IDENTIFIER);
+ if (elementIdentifierColumn == null) {
+ elementIdentifierColumn = foundSchemaColumns.get(ColorSchemaColumn.REACTION_IDENTIFIER);
+ }
+ compartmentColumn = foundSchemaColumns.get(ColorSchemaColumn.COMPARTMENT);
+ typeColumn = foundSchemaColumns.get(ColorSchemaColumn.TYPE);
+ lineWidthColumn = foundSchemaColumns.get(ColorSchemaColumn.LINE_WIDTH);
+ reverseReactionColumn = foundSchemaColumns.get(ColorSchemaColumn.REVERSE_REACTION);
+
+ if (valueColumn != null && colorColumn != null) {
+ throw new InvalidColorSchemaException("Schema can contain only one of these two columns: ");
+ }
+
+ if (nameColumn == null && identifierColumn == null && foundCustomIdentifiers.size() == 0
+ && elementIdentifierColumn == null) {
+ throw new InvalidColorSchemaException(
+ "One of these columns is obligatory: " + ColorSchemaColumn.NAME.getTitle() + ","
+ + ColorSchemaColumn.IDENTIFIER.getTitle() + "," + ColorSchemaColumn.ELEMENT_IDENTIFIER.getTitle());
+ }
+
+ if (valueColumn == null && colorColumn == null) {
+ throw new InvalidColorSchemaException("Schema must contain one of these two columns: value, name");
+ }
+
+ } else {
+ ColorSchema schema = new GenericColorSchema();
+ if (nameColumn != null) {
+ schema.setName(row.getCell(nameColumn).getStringCellValue());
+ }
+ if (modelNameColumn != null) {
+ schema.setModelName(row.getCell(modelNameColumn).getStringCellValue());
+ }
+ if (valueColumn != null) {
+ try {
+ cell = row.getCell(valueColumn);
+ cell.setCellType(Cell.CELL_TYPE_STRING);
+ schema.setValue(Double.parseDouble(cell.getStringCellValue().replace(",", ".")));
+ } catch (Exception e) {
+ throw new InvalidColorSchemaException(
+ "[Line " + lineIndex + "] Problem with parsing value for value column. Cell value" + cell);
+ }
+ if (schema.getValue() > 1 + Configuration.EPSILON || schema.getValue() < -1 - Configuration.EPSILON) {
+ throw new InvalidColorSchemaException("[Line " + lineIndex + "] Value " + schema.getValue()
+ + " out of range. Only values between -1 and 1 are allowed.");
+ }
+ }
+ if (compartmentColumn != null) {
+ String value = row.getCell(compartmentColumn).getStringCellValue();
+ if (value != null) {
+ String[] compartments = value.split(",");
+ schema.addCompartments(compartments);
+ }
+ }
+ if (typeColumn != null) {
+ String value = row.getCell(typeColumn).getStringCellValue();
+ if (value != null) {
+ String[] types = value.split(",");
+ for (String string : types) {
+ SpeciesMapping mapping = SpeciesMapping.getMappingByString(string);
+ if (mapping != null) {
+ schema.addType(mapping.getModelClazz());
+ } else {
+ throw new InvalidColorSchemaException("Unknown class type: " + string + ".");
+ }
+ }
+ }
+ }
+ if (colorColumn != null) {
+ schema.setColor(colorParser.parse(row.getCell(colorColumn).getStringCellValue()));
+ }
+ if (elementIdentifierColumn != null) {
+ schema.setElementId(row.getCell(elementIdentifierColumn).getStringCellValue());
+ }
+ if (lineWidthColumn != null) {
+ cell = row.getCell(lineWidthColumn);
+ cell.setCellType(Cell.CELL_TYPE_STRING);
+ String value = cell.getStringCellValue();
+ if (value != null && !value.trim().isEmpty()) {
+ try {
+ schema.setLineWidth(Double.parseDouble(value.replace(",", ".")));
+ } catch (NumberFormatException e) {
+ throw new InvalidColorSchemaException(
+ "[Line " + lineIndex + "] Problem with parsing value: \"" + value + "\"");
+ }
+ }
+ }
+ if (reverseReactionColumn != null) {
+ cell = row.getCell(reverseReactionColumn);
+ if (cell != null) {
+ cell.setCellType(Cell.CELL_TYPE_STRING);
+ schema.setReverseReaction("true".equalsIgnoreCase(cell.getStringCellValue()));
+ }
+ }
+ if (identifierColumn != null) {
+ cell = row.getCell(identifierColumn);
+ if (cell != null && !cell.getStringCellValue().trim().isEmpty()) {
+ MiriamConnector miriamConnector = new MiriamConnector();
+ String value = cell.getStringCellValue().trim();
+ if (miriamConnector.isValidIdentifier(value)) {
+ schema.addMiriamData(MiriamType.getMiriamDataFromIdentifier(value));
+ } else {
+ throw new InvalidColorSchemaException("[Line " + lineIndex + "]" + " Invalid identifier: " + value);
+ }
+ }
+ }
+ for (Pair<MiriamType, Integer> pair : foundCustomIdentifiers) {
+ cell = row.getCell(pair.getRight());
+ if (cell != null) {
+ schema.addMiriamData(new MiriamData(pair.getLeft(), cell.getStringCellValue()));
+ }
+ }
+
+ if ((schema.getValue() != null && schema.getColor() != null)
+ || (schema.getValue() == null && schema.getColor() == null)) {
+ throw new InvalidColorSchemaException("Value or Color is needed not both");
+ }
+
+ if (schema.getName() == null && schema.getMiriamData().size() == 0 && foundCustomIdentifiers.size() == 0
+ && schema.getElementId() == null) {
+ throw new InvalidColorSchemaException(
+ "One of these columns values is obligatory: name, identifier, reactionIdentifier");
+ }
+ result.add(schema);
+ }
+ }
+ } finally {
+ try {
+ if (file != null) {
+ file.close();
+ }
+ if (workbook != null) {
+ workbook.close();
+ }
+ } catch (Exception e) {
+
+ }
+ }
+ return result;
+
+ }
+
+ /**
+ * Returns list of columns that should be printed for given coloring schemas.
+ *
+ * @param schemas
+ * list of schemas
+ * @return list of columns that should be printed (were set in the coloring
+ * schemas)
+ */
+ public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
+ Set<ColorSchemaColumn> result = new HashSet<ColorSchemaColumn>();
+ for (ColorSchema schema : schemas) {
+ if (schema.getColor() != null) {
+ result.add(ColorSchemaColumn.COLOR);
+ }
+ if (schema.getCompartments().size() > 0) {
+ result.add(ColorSchemaColumn.COMPARTMENT);
+ }
+ if (schema.getMiriamData().size() > 0) {
+ result.add(ColorSchemaColumn.IDENTIFIER);
+ }
+ if (schema.getLineWidth() != null) {
+ result.add(ColorSchemaColumn.LINE_WIDTH);
+ }
+ if (schema.getName() != null) {
+ result.add(ColorSchemaColumn.NAME);
+ }
+ if (schema.getModelName() != null) {
+ result.add(ColorSchemaColumn.MODEL_NAME);
+ }
+ if (schema.getElementId() != null) {
+ result.add(ColorSchemaColumn.ELEMENT_IDENTIFIER);
+ }
+ if (schema.getReverseReaction() != null) {
+ result.add(ColorSchemaColumn.REVERSE_REACTION);
+ }
+ if (schema.getTypes().size() > 0) {
+ result.add(ColorSchemaColumn.TYPE);
+ }
+ if (schema.getValue() != null) {
+ result.add(ColorSchemaColumn.VALUE);
+ }
+ }
+ return result;
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/CreateProjectParams.java b/service/src/main/java/lcsb/mapviewer/services/utils/CreateProjectParams.java
index 80e1f978fa..a7b7d87c1e 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/CreateProjectParams.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/CreateProjectParams.java
@@ -1,832 +1,832 @@
-package lcsb.mapviewer.services.utils;
-
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-import java.util.Queue;
-import java.util.Set;
-
-import org.apache.commons.io.IOUtils;
-import org.primefaces.model.TreeNode;
-
-import lcsb.mapviewer.converter.IConverter;
-import lcsb.mapviewer.converter.zip.ZipEntryFile;
-import lcsb.mapviewer.model.graphics.MapCanvasType;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.user.UserAnnotatorsParam;
-import lcsb.mapviewer.services.overlay.AnnotatedObjectTreeRow;
-
-/**
- * Set of parameters used during creation of new project.
- *
- * @author Piotr Gawron
- *
- */
-public class CreateProjectParams {
-
- /**
- * User defined project identifier.
- */
- private String projectId;
-
- /**
- * Name of the project.
- */
- private String projectName;
-
- /**
- * Disease associated to the project.
- */
- private String disease;
-
- /**
- * Organism associated to the project.
- */
- private String organism;
-
- /**
- * Path to a file used as a model.
- */
- private String projectFile;
-
- private IConverter parser;
-
- /**
- * Is the project a complex multi-file project.
- */
- private boolean complex;
- private boolean semanticZoom;
- private boolean semanticZoomContainsMultipleLayouts = false;
-
- /**
- * List of zip entries in the complex model definition.
- */
- private List<ZipEntryFile> zipEntries = new ArrayList<>();
-
- /**
- * Should the elements be annotated by the external resources.
- */
- private boolean updateAnnotations = false;
-
- /**
- * Do we want to generate images for all available layers.
- */
- private boolean images = false;
-
- /**
- * Should the map be autoresized after processing (to trim unnecessary margins).
- */
- private boolean autoResize = true;
-
- /**
- * Should the data from external resources but linked to model be cached.
- */
- private boolean cacheModel = true;
-
- /**
- * Should the process of creation of the project be asynchronous (in separate
- * thread).
- */
- private boolean async = false;
-
- /**
- * Should the map be displayed in SBGN format.
- */
- private boolean sbgnFormat = false;
-
- /**
- * Is the {@link lcsb.mapviewer.services.utils.data.BuildInLayout#NORMAL}
- * default {@link lcsb.mapviewer.model.map.layout.Layout Layout} when generating
- * new project.
- */
- private boolean networkLayoutAsDefault = false;
-
- /**
- * Do we want to analyze annotations after processing of the map. If yes then in
- * the email with summary of the generation process information about improper
- * annotations will be sent.
- */
- private boolean analyzeAnnotations = false;
-
- /**
- * Email address that should be notified after everything is done.
- */
- private String notifyEmail = null;
-
- /**
- * Description of the project.
- */
- private String description = "";
-
- /**
- * Version of the map.
- */
- private String version = "0";
-
- /**
- * Users that should have access to the map.
- */
- private List<String[]> users = new ArrayList<String[]>();
-
- /**
- * Directory with the static images that will be stored on server. This
- * directory is relative and it's a simple unique name within folder with
- * images.
- */
- private String projectDir;
-
- private String authenticationToken;
-
- /**
- * Map that contains information what kind of annotators should be used for
- * specific class.
- */
- private Map<Class<?>, List<String>> annotatorsMap = null;
-
- /**
- * Map that contains information which {@link MiriamType miriam types} are valid
- * for which class.
- */
- private Map<Class<? extends BioEntity>, Set<MiriamType>> validAnnotations = null;
-
- /**
- * Map that contains information which {@link MiriamType miriam types} are
- * obligatory for which class.
- */
- private Map<Class<? extends BioEntity>, Set<MiriamType>> requiredAnnotations = null;
-
- /**
- * List with annotators parameters.
- */
- private List<UserAnnotatorsParam> annotatorsParams = new ArrayList<>();
-
- private MapCanvasType mapCanvasType = MapCanvasType.OPEN_LAYERS;
-
- /**
- * @param projectId
- * the projectId to set
- * @return object with all parameters
- * @see #projectId
- */
- public CreateProjectParams projectId(String projectId) {
- this.projectId = projectId;
- return this;
- }
-
- public CreateProjectParams parser(IConverter parser) {
- this.parser = parser;
- return this;
- }
-
- /**
- * @param notifyEmail
- * the notifyEmail to set
- * @return object with all parameters
- * @see #notifyEmail
- */
- public CreateProjectParams notifyEmail(String notifyEmail) {
- this.notifyEmail = notifyEmail;
- return this;
- }
-
- /**
- * @param projectFile
- * the projectFile to set
- * @return object with all parameters
- * @see #projectFile
- */
- public CreateProjectParams projectFile(String projectFile) {
- this.projectFile = projectFile;
- return this;
- }
-
- /**
- * @param autoResize
- * the autoResize to set
- * @return object with all parameters
- * @see #autoResize
- */
- public CreateProjectParams autoResize(boolean autoResize) {
- this.autoResize = autoResize;
- return this;
- }
-
- public CreateProjectParams autoResize(String value) {
- return this.autoResize("true".equalsIgnoreCase(value));
- }
-
- /**
- * Sets input stream from which projects should be generated.
- *
- * @param is
- * inputstream with the data of the project to be generated
- * @return object with all parameters
- * @throws IOException
- * thrown if there are some problem with the stream
- */
- public CreateProjectParams projectFile(InputStream is) throws IOException {
- File temp = File.createTempFile("model", ".xml");
- IOUtils.copy(is, new FileOutputStream(temp));
- this.projectFile = temp.getAbsolutePath();
- return this;
- }
-
- /**
- * Sets file from which projects should be generated.
- *
- * @param file
- * file with the data of the project to be generated
- * @return object with all parameters
- */
- public CreateProjectParams projectFile(File file) {
- this.projectFile = file.getAbsolutePath();
- return this;
- }
-
- /**
- * @param async
- * the async to set
- * @return object with all parameters
- * @see #async
- */
- public CreateProjectParams async(boolean async) {
- this.async = async;
- return this;
- }
-
- /**
- * @param analyzeAnnotations
- * the analyzeAnnotations to set
- * @return object with all parameters
- * @see #analyzeAnnotations
- */
- public CreateProjectParams analyzeAnnotations(boolean analyzeAnnotations) {
- this.analyzeAnnotations = analyzeAnnotations;
- return this;
- }
-
- /**
- * @param updateAnnotations
- * the updateAnnotations to set
- * @return object with all parameters
- * @see #updateAnnotations
- */
- public CreateProjectParams annotations(boolean updateAnnotations) {
- this.updateAnnotations = updateAnnotations;
- return this;
- }
-
- /**
- * @param images
- * the images to set
- * @return object with all parameters
- * @see #images
- */
- public CreateProjectParams images(boolean images) {
- this.images = images;
- return this;
- }
-
- /**
- * @param description
- * the description to set
- * @return object with all parameters
- * @see #description
- */
- public CreateProjectParams description(String description) {
- this.description = description;
- return this;
- }
-
- /**
- * @param version
- * the version to set
- * @return object with all parameters
- * @see #version
- */
- public CreateProjectParams version(String version) {
- this.version = version;
- return this;
- }
-
- /**
- * Adds a user to the list of users that should have access to the project from
- * the beginning.
- *
- * @param login
- * login of the user
- * @param password
- * password (in case user doesn't exist yet)
- * @return object with all parameters
- * @return
- */
- public CreateProjectParams addUser(String login, String password) {
- this.users.add(new String[] { login, password });
- return this;
- }
-
- /**
- * @return the users
- * @see #users
- */
- public List<String[]> getUsers() {
- return users;
- }
-
- /**
- * @return the version
- * @see #version
- */
- public String getVersion() {
- return version;
- }
-
- /**
- * @return the description
- * @see #description
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * @return the notifyEmail
- * @see #notifyEmail
- */
- public String getNotifyEmail() {
- return notifyEmail;
- }
-
- /**
- * @return the analyzeAnnotations
- * @see #analyzeAnnotations
- */
- public boolean isAnalyzeAnnotations() {
- return analyzeAnnotations;
- }
-
- /**
- * @return the async
- * @see #async
- */
- public boolean isAsync() {
- return async;
- }
-
- /**
- * @return the autoResize
- * @see #autoResize
- */
- public boolean isAutoResize() {
- return autoResize;
- }
-
- /**
- * @return the images
- * @see #images
- */
- public boolean isImages() {
- return images;
- }
-
- /**
- * @return the updateAnnotations
- * @see #updateAnnotations
- */
- public boolean isUpdateAnnotations() {
- return updateAnnotations;
- }
-
- /**
- * @return the projectFile
- * @see #projectFile
- */
- public String getProjectFile() {
- return projectFile;
- }
-
- /**
- * @return the projectId
- * @see #projectId
- */
- public String getProjectId() {
- return projectId;
- }
-
- /**
- * @return the cacheModel
- * @see #cacheModel
- */
- public boolean isCacheModel() {
- return cacheModel;
- }
-
- /**
- * @param cacheModel
- * the cacheModel to set
- * @see #cacheModel
- * @return object with all parameters
- */
- public CreateProjectParams cacheModel(boolean cacheModel) {
- this.cacheModel = cacheModel;
- return this;
- }
-
- public CreateProjectParams cacheModel(String value) {
- return this.cacheModel("true".equalsIgnoreCase(value));
- }
-
- /**
- * @return the submodels
- * @see #zipEntries
- */
- public List<ZipEntryFile> getZipEntries() {
- return zipEntries;
- }
-
- /**
- * @param entry
- * the submodel to add
- * @see #zipEntries
- * @return object with all parameters
- */
- public CreateProjectParams addZipEntry(ZipEntryFile entry) {
- if (entry != null) {
- this.zipEntries.add(entry);
- }
- return this;
- }
-
- /**
- * @return the complex
- * @see #complex
- */
- public boolean isComplex() {
- return complex;
- }
-
- /**
- * @return the sbgnFormat
- * @see #sbgnFormat
- */
- public boolean isSbgnFormat() {
- return sbgnFormat;
- }
-
- /**
- * @param sbgnFormat
- * the sbgnFormat to set
- * @see #sbgnFormat
- */
- public CreateProjectParams sbgnFormat(boolean sbgnFormat) {
- this.sbgnFormat = sbgnFormat;
- return this;
- }
-
- public CreateProjectParams sbgnFormat(String value) {
- return this.sbgnFormat("true".equalsIgnoreCase(value));
- }
-
- /**
- * @param complex
- * the complex to set
- * @see #complex
- * @return object with all parameters
- */
- public CreateProjectParams complex(boolean complex) {
- this.complex = complex;
- return this;
- }
-
- /**
- * Creates {@link #annotatorsMap}.
- *
- * @param annotatorsTree
- * tree containing information about annotators for given classes
- */
- public void annotatorsMap(TreeNode annotatorsTree) {
- Map<Class<?>, List<String>> map = new HashMap<Class<?>, List<String>>();
- Queue<TreeNode> queue = new LinkedList<TreeNode>();
- queue.add(annotatorsTree);
- while (!queue.isEmpty()) {
- TreeNode node = queue.poll();
-
- Set<String> set = new HashSet<String>();
-
- TreeNode parent = node;
- while (parent != null) {
- set.addAll(((AnnotatedObjectTreeRow) parent.getData()).getUsedAnnotators());
- parent = parent.getParent();
- }
- List<String> list = new ArrayList<String>();
- list.addAll(set);
- map.put(((AnnotatedObjectTreeRow) node.getData()).getClazz(), list);
-
- for (TreeNode node2 : node.getChildren()) {
- queue.add(node2);
- }
- }
- annotatorsMap = map;
- }
-
- /**
- * @return the annotatorsMap
- * @see #annotatorsMap
- */
- public Map<Class<?>, List<String>> getAnnotatorsMap() {
- return annotatorsMap;
- }
-
- /**
- * @param annotatorsMap
- * the annotatorsMap to set
- * @see #annotatorsMap
- */
- public void setAnnotatorsMap(Map<Class<?>, List<String>> annotatorsMap) {
- this.annotatorsMap = annotatorsMap;
- }
-
- /**
- * @return the annotators params
- */
- public List<UserAnnotatorsParam> getAnnotatorsParams() {
- return annotatorsParams;
- }
-
- public Map<Class<?>, List<UserAnnotatorsParam>> getAnnotatorsParamsAsMap() {
-
- Map<Class<?>, List<UserAnnotatorsParam>> paramsMap = new HashMap<>();
-
- for (UserAnnotatorsParam param : getAnnotatorsParams()) {
- Class<?> annotatorClassName = param.getAnnotatorClassName();
- if (!paramsMap.containsKey(annotatorClassName)) {
- paramsMap.put(annotatorClassName, new ArrayList<>());
- }
- paramsMap.get(annotatorClassName).add(param);
- }
-
- return paramsMap;
- }
-
- /**
- * @param annotatorsParams
- * the annotatorsParams to set
- */
- public void setAnnotatorParams(List<UserAnnotatorsParam> annotatorsParams) {
- this.annotatorsParams = annotatorsParams;
- }
-
- /**
- * Creates {@link #validAnnotations}.
- *
- * @param annotatorsTree
- * tree containing information about valid {@link MiriamType miriam
- * types}
- */
- @SuppressWarnings("unchecked")
- public void validAnnotations(TreeNode annotatorsTree) {
- Map<Class<? extends BioEntity>, Set<MiriamType>> map = new HashMap<Class<? extends BioEntity>, Set<MiriamType>>();
- Queue<TreeNode> queue = new LinkedList<TreeNode>();
- queue.add(annotatorsTree);
- while (!queue.isEmpty()) {
- TreeNode node = queue.poll();
- Set<MiriamType> set = new HashSet<MiriamType>();
-
- TreeNode parent = node;
- while (parent != null) {
- set.addAll(((AnnotatedObjectTreeRow) parent.getData()).getValidAnnotations());
- parent = parent.getParent();
- }
- map.put((Class<? extends BioEntity>) ((AnnotatedObjectTreeRow) node.getData()).getClazz(), set);
-
- for (TreeNode node2 : node.getChildren()) {
- queue.add(node2);
- }
- }
- validAnnotations = map;
- }
-
- /**
- * Creates {@link #requiredAnnotations}.
- *
- * @param annotatorsTree
- * tree containing information about required {@link MiriamType miriam
- * types}
- */
- @SuppressWarnings("unchecked")
- public void requiredAnnotations(TreeNode annotatorsTree) {
- Map<Class<? extends BioEntity>, Set<MiriamType>> map = new HashMap<Class<? extends BioEntity>, Set<MiriamType>>();
- Queue<TreeNode> queue = new LinkedList<TreeNode>();
- queue.add(annotatorsTree);
- while (!queue.isEmpty()) {
- TreeNode node = queue.poll();
- boolean valid = ((AnnotatedObjectTreeRow) node.getData()).getRequire();
- Set<MiriamType> set = new HashSet<MiriamType>();
-
- TreeNode parent = node;
- while (parent != null) {
- set.addAll(((AnnotatedObjectTreeRow) parent.getData()).getRequiredAnnotations());
- if (((AnnotatedObjectTreeRow) parent.getData()).getRequire()) {
- valid = true;
- }
- parent = parent.getParent();
- }
- if (!valid) {
- set = null;
- }
- map.put((Class<? extends BioEntity>) ((AnnotatedObjectTreeRow) node.getData()).getClazz(), set);
-
- for (TreeNode node2 : node.getChildren()) {
- queue.add(node2);
- }
- }
- requiredAnnotations = map;
- }
-
- /**
- * Returns {@link #validAnnotations}.
- *
- * @return {@link #validAnnotations}.
- */
- public Map<Class<? extends BioEntity>, Set<MiriamType>> getValidAnnotations() {
- return validAnnotations;
- }
-
- /**
- * Returns {@link #requiredAnnotations}.
- *
- * @return {@link #requiredAnnotations}.
- */
- public Map<Class<? extends BioEntity>, Set<MiriamType>> getRequiredAnnotations() {
- return requiredAnnotations;
- }
-
- /**
- * Sets {@link #projectDir}.
- *
- * @param directory
- * new {@link #projectDir} value
- * @return instance of this class with new value set
- */
- public CreateProjectParams projectDir(String directory) {
- this.projectDir = directory;
- return this;
- }
-
- /**
- * @return the projectDir
- * @see #projectDir
- */
- public String getProjectDir() {
- return projectDir;
- }
-
- /**
- *
- * @param projectName
- * new {@link #projectName}
- * @return instance of this class with new value set
- */
- public CreateProjectParams projectName(String projectName) {
- this.projectName = projectName;
- return this;
- }
-
- /**
- * @return the projectName
- * @see #projectName
- */
- public String getProjectName() {
- return projectName;
- }
-
- /**
- * @param value
- * the networkLayoutAsDefault to set
- * @see #networkLayoutAsDefault
- * @return instance of this class with new value set
- */
- public CreateProjectParams networkLayoutAsDefault(boolean value) {
- this.networkLayoutAsDefault = value;
- return this;
-
- }
-
- /**
- * @return the networkLayoutAsDefault
- * @see #networkLayoutAsDefault
- */
- public boolean isNetworkLayoutAsDefault() {
- return networkLayoutAsDefault;
- }
-
- /**
- * @return disease MESH code.
- */
- public String getDisease() {
- return disease;
- }
-
- /**
- * @param disease
- * the code of the disease.
- * @return updated params object.
- */
- public CreateProjectParams projectDisease(String disease) {
- this.disease = disease;
- return this;
- }
-
- /**
- * @return the organism
- * @see #organism
- */
- public String getOrganism() {
- return organism;
- }
-
- /**
- * @param organism
- * the organism to set
- * @return updated params object.
- */
- public CreateProjectParams projectOrganism(String organism) {
- this.organism = organism;
- return this;
- }
-
- /**
- * @return the authenticationToken
- * @see #authenticationToken
- */
- public String getAuthenticationToken() {
- return authenticationToken;
- }
-
- /**
- * @param authenticationToken
- * the authenticationToken to set
- * @see #authenticationToken
- */
- public CreateProjectParams authenticationToken(String authenticationToken) {
- this.authenticationToken = authenticationToken;
-
- return this;
- }
-
- public CreateProjectParams semanticZoom(boolean semanticZoom) {
- this.semanticZoom = semanticZoom;
- return this;
- }
-
- public CreateProjectParams semanticZoom(String value) {
- return this.semanticZoom("true".equals(value));
- }
-
- public boolean isSemanticZoom() {
- return this.semanticZoom;
- }
-
- public CreateProjectParams semanticZoomContainsMultipleLayouts(boolean semanticZoomContainsMultipleLayouts) {
- this.semanticZoomContainsMultipleLayouts = semanticZoomContainsMultipleLayouts;
- return this;
- }
-
- public CreateProjectParams semanticZoomContainsMultipleLayouts(String value) {
- return this.semanticZoomContainsMultipleLayouts("true".equals(value));
- }
-
- public boolean isSemanticZoomContainsMultipleLayouts() {
- return this.semanticZoomContainsMultipleLayouts;
- }
-
- public IConverter getParser() {
- return this.parser;
- }
-
- public CreateProjectParams annotations(String value) {
- return this.annotations("true".equalsIgnoreCase(value));
- }
-
- public CreateProjectParams analyzeAnnotations(String value) {
- return this.analyzeAnnotations("true".equalsIgnoreCase(value));
- }
-
- public MapCanvasType getMapCanvasType() {
- return mapCanvasType;
- }
-
- public CreateProjectParams mapCanvasType(MapCanvasType mapCanvasType) {
- this.mapCanvasType = mapCanvasType;
- return this;
- }
-
-}
+package lcsb.mapviewer.services.utils;
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+import java.util.Queue;
+import java.util.Set;
+
+import org.apache.commons.io.IOUtils;
+import org.primefaces.model.TreeNode;
+
+import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.zip.ZipEntryFile;
+import lcsb.mapviewer.model.graphics.MapCanvasType;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.user.UserAnnotatorsParam;
+import lcsb.mapviewer.services.overlay.AnnotatedObjectTreeRow;
+
+/**
+ * Set of parameters used during creation of new project.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CreateProjectParams {
+
+ /**
+ * User defined project identifier.
+ */
+ private String projectId;
+
+ /**
+ * Name of the project.
+ */
+ private String projectName;
+
+ /**
+ * Disease associated to the project.
+ */
+ private String disease;
+
+ /**
+ * Organism associated to the project.
+ */
+ private String organism;
+
+ /**
+ * Path to a file used as a model.
+ */
+ private String projectFile;
+
+ private IConverter parser;
+
+ /**
+ * Is the project a complex multi-file project.
+ */
+ private boolean complex;
+ private boolean semanticZoom;
+ private boolean semanticZoomContainsMultipleLayouts = false;
+
+ /**
+ * List of zip entries in the complex model definition.
+ */
+ private List<ZipEntryFile> zipEntries = new ArrayList<>();
+
+ /**
+ * Should the elements be annotated by the external resources.
+ */
+ private boolean updateAnnotations = false;
+
+ /**
+ * Do we want to generate images for all available layers.
+ */
+ private boolean images = false;
+
+ /**
+ * Should the map be autoresized after processing (to trim unnecessary margins).
+ */
+ private boolean autoResize = true;
+
+ /**
+ * Should the data from external resources but linked to model be cached.
+ */
+ private boolean cacheModel = true;
+
+ /**
+ * Should the process of creation of the project be asynchronous (in separate
+ * thread).
+ */
+ private boolean async = false;
+
+ /**
+ * Should the map be displayed in SBGN format.
+ */
+ private boolean sbgnFormat = false;
+
+ /**
+ * Is the {@link lcsb.mapviewer.services.utils.data.BuildInLayout#NORMAL}
+ * default {@link lcsb.mapviewer.model.map.layout.Layout Layout} when generating
+ * new project.
+ */
+ private boolean networkLayoutAsDefault = false;
+
+ /**
+ * Do we want to analyze annotations after processing of the map. If yes then in
+ * the email with summary of the generation process information about improper
+ * annotations will be sent.
+ */
+ private boolean analyzeAnnotations = false;
+
+ /**
+ * Email address that should be notified after everything is done.
+ */
+ private String notifyEmail = null;
+
+ /**
+ * Description of the project.
+ */
+ private String description = "";
+
+ /**
+ * Version of the map.
+ */
+ private String version = "0";
+
+ /**
+ * Users that should have access to the map.
+ */
+ private List<String[]> users = new ArrayList<String[]>();
+
+ /**
+ * Directory with the static images that will be stored on server. This
+ * directory is relative and it's a simple unique name within folder with
+ * images.
+ */
+ private String projectDir;
+
+ private String authenticationToken;
+
+ /**
+ * Map that contains information what kind of annotators should be used for
+ * specific class.
+ */
+ private Map<Class<?>, List<String>> annotatorsMap = null;
+
+ /**
+ * Map that contains information which {@link MiriamType miriam types} are valid
+ * for which class.
+ */
+ private Map<Class<? extends BioEntity>, Set<MiriamType>> validAnnotations = null;
+
+ /**
+ * Map that contains information which {@link MiriamType miriam types} are
+ * obligatory for which class.
+ */
+ private Map<Class<? extends BioEntity>, Set<MiriamType>> requiredAnnotations = null;
+
+ /**
+ * List with annotators parameters.
+ */
+ private List<UserAnnotatorsParam> annotatorsParams = new ArrayList<>();
+
+ private MapCanvasType mapCanvasType = MapCanvasType.OPEN_LAYERS;
+
+ /**
+ * @param projectId
+ * the projectId to set
+ * @return object with all parameters
+ * @see #projectId
+ */
+ public CreateProjectParams projectId(String projectId) {
+ this.projectId = projectId;
+ return this;
+ }
+
+ public CreateProjectParams parser(IConverter parser) {
+ this.parser = parser;
+ return this;
+ }
+
+ /**
+ * @param notifyEmail
+ * the notifyEmail to set
+ * @return object with all parameters
+ * @see #notifyEmail
+ */
+ public CreateProjectParams notifyEmail(String notifyEmail) {
+ this.notifyEmail = notifyEmail;
+ return this;
+ }
+
+ /**
+ * @param projectFile
+ * the projectFile to set
+ * @return object with all parameters
+ * @see #projectFile
+ */
+ public CreateProjectParams projectFile(String projectFile) {
+ this.projectFile = projectFile;
+ return this;
+ }
+
+ /**
+ * @param autoResize
+ * the autoResize to set
+ * @return object with all parameters
+ * @see #autoResize
+ */
+ public CreateProjectParams autoResize(boolean autoResize) {
+ this.autoResize = autoResize;
+ return this;
+ }
+
+ public CreateProjectParams autoResize(String value) {
+ return this.autoResize("true".equalsIgnoreCase(value));
+ }
+
+ /**
+ * Sets input stream from which projects should be generated.
+ *
+ * @param is
+ * inputstream with the data of the project to be generated
+ * @return object with all parameters
+ * @throws IOException
+ * thrown if there are some problem with the stream
+ */
+ public CreateProjectParams projectFile(InputStream is) throws IOException {
+ File temp = File.createTempFile("model", ".xml");
+ IOUtils.copy(is, new FileOutputStream(temp));
+ this.projectFile = temp.getAbsolutePath();
+ return this;
+ }
+
+ /**
+ * Sets file from which projects should be generated.
+ *
+ * @param file
+ * file with the data of the project to be generated
+ * @return object with all parameters
+ */
+ public CreateProjectParams projectFile(File file) {
+ this.projectFile = file.getAbsolutePath();
+ return this;
+ }
+
+ /**
+ * @param async
+ * the async to set
+ * @return object with all parameters
+ * @see #async
+ */
+ public CreateProjectParams async(boolean async) {
+ this.async = async;
+ return this;
+ }
+
+ /**
+ * @param analyzeAnnotations
+ * the analyzeAnnotations to set
+ * @return object with all parameters
+ * @see #analyzeAnnotations
+ */
+ public CreateProjectParams analyzeAnnotations(boolean analyzeAnnotations) {
+ this.analyzeAnnotations = analyzeAnnotations;
+ return this;
+ }
+
+ /**
+ * @param updateAnnotations
+ * the updateAnnotations to set
+ * @return object with all parameters
+ * @see #updateAnnotations
+ */
+ public CreateProjectParams annotations(boolean updateAnnotations) {
+ this.updateAnnotations = updateAnnotations;
+ return this;
+ }
+
+ /**
+ * @param images
+ * the images to set
+ * @return object with all parameters
+ * @see #images
+ */
+ public CreateProjectParams images(boolean images) {
+ this.images = images;
+ return this;
+ }
+
+ /**
+ * @param description
+ * the description to set
+ * @return object with all parameters
+ * @see #description
+ */
+ public CreateProjectParams description(String description) {
+ this.description = description;
+ return this;
+ }
+
+ /**
+ * @param version
+ * the version to set
+ * @return object with all parameters
+ * @see #version
+ */
+ public CreateProjectParams version(String version) {
+ this.version = version;
+ return this;
+ }
+
+ /**
+ * Adds a user to the list of users that should have access to the project from
+ * the beginning.
+ *
+ * @param login
+ * login of the user
+ * @param password
+ * password (in case user doesn't exist yet)
+ * @return object with all parameters
+ * @return
+ */
+ public CreateProjectParams addUser(String login, String password) {
+ this.users.add(new String[] { login, password });
+ return this;
+ }
+
+ /**
+ * @return the users
+ * @see #users
+ */
+ public List<String[]> getUsers() {
+ return users;
+ }
+
+ /**
+ * @return the version
+ * @see #version
+ */
+ public String getVersion() {
+ return version;
+ }
+
+ /**
+ * @return the description
+ * @see #description
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * @return the notifyEmail
+ * @see #notifyEmail
+ */
+ public String getNotifyEmail() {
+ return notifyEmail;
+ }
+
+ /**
+ * @return the analyzeAnnotations
+ * @see #analyzeAnnotations
+ */
+ public boolean isAnalyzeAnnotations() {
+ return analyzeAnnotations;
+ }
+
+ /**
+ * @return the async
+ * @see #async
+ */
+ public boolean isAsync() {
+ return async;
+ }
+
+ /**
+ * @return the autoResize
+ * @see #autoResize
+ */
+ public boolean isAutoResize() {
+ return autoResize;
+ }
+
+ /**
+ * @return the images
+ * @see #images
+ */
+ public boolean isImages() {
+ return images;
+ }
+
+ /**
+ * @return the updateAnnotations
+ * @see #updateAnnotations
+ */
+ public boolean isUpdateAnnotations() {
+ return updateAnnotations;
+ }
+
+ /**
+ * @return the projectFile
+ * @see #projectFile
+ */
+ public String getProjectFile() {
+ return projectFile;
+ }
+
+ /**
+ * @return the projectId
+ * @see #projectId
+ */
+ public String getProjectId() {
+ return projectId;
+ }
+
+ /**
+ * @return the cacheModel
+ * @see #cacheModel
+ */
+ public boolean isCacheModel() {
+ return cacheModel;
+ }
+
+ /**
+ * @param cacheModel
+ * the cacheModel to set
+ * @see #cacheModel
+ * @return object with all parameters
+ */
+ public CreateProjectParams cacheModel(boolean cacheModel) {
+ this.cacheModel = cacheModel;
+ return this;
+ }
+
+ public CreateProjectParams cacheModel(String value) {
+ return this.cacheModel("true".equalsIgnoreCase(value));
+ }
+
+ /**
+ * @return the submodels
+ * @see #zipEntries
+ */
+ public List<ZipEntryFile> getZipEntries() {
+ return zipEntries;
+ }
+
+ /**
+ * @param entry
+ * the submodel to add
+ * @see #zipEntries
+ * @return object with all parameters
+ */
+ public CreateProjectParams addZipEntry(ZipEntryFile entry) {
+ if (entry != null) {
+ this.zipEntries.add(entry);
+ }
+ return this;
+ }
+
+ /**
+ * @return the complex
+ * @see #complex
+ */
+ public boolean isComplex() {
+ return complex;
+ }
+
+ /**
+ * @return the sbgnFormat
+ * @see #sbgnFormat
+ */
+ public boolean isSbgnFormat() {
+ return sbgnFormat;
+ }
+
+ /**
+ * @param sbgnFormat
+ * the sbgnFormat to set
+ * @see #sbgnFormat
+ */
+ public CreateProjectParams sbgnFormat(boolean sbgnFormat) {
+ this.sbgnFormat = sbgnFormat;
+ return this;
+ }
+
+ public CreateProjectParams sbgnFormat(String value) {
+ return this.sbgnFormat("true".equalsIgnoreCase(value));
+ }
+
+ /**
+ * @param complex
+ * the complex to set
+ * @see #complex
+ * @return object with all parameters
+ */
+ public CreateProjectParams complex(boolean complex) {
+ this.complex = complex;
+ return this;
+ }
+
+ /**
+ * Creates {@link #annotatorsMap}.
+ *
+ * @param annotatorsTree
+ * tree containing information about annotators for given classes
+ */
+ public void annotatorsMap(TreeNode annotatorsTree) {
+ Map<Class<?>, List<String>> map = new HashMap<Class<?>, List<String>>();
+ Queue<TreeNode> queue = new LinkedList<TreeNode>();
+ queue.add(annotatorsTree);
+ while (!queue.isEmpty()) {
+ TreeNode node = queue.poll();
+
+ Set<String> set = new HashSet<String>();
+
+ TreeNode parent = node;
+ while (parent != null) {
+ set.addAll(((AnnotatedObjectTreeRow) parent.getData()).getUsedAnnotators());
+ parent = parent.getParent();
+ }
+ List<String> list = new ArrayList<String>();
+ list.addAll(set);
+ map.put(((AnnotatedObjectTreeRow) node.getData()).getClazz(), list);
+
+ for (TreeNode node2 : node.getChildren()) {
+ queue.add(node2);
+ }
+ }
+ annotatorsMap = map;
+ }
+
+ /**
+ * @return the annotatorsMap
+ * @see #annotatorsMap
+ */
+ public Map<Class<?>, List<String>> getAnnotatorsMap() {
+ return annotatorsMap;
+ }
+
+ /**
+ * @param annotatorsMap
+ * the annotatorsMap to set
+ * @see #annotatorsMap
+ */
+ public void setAnnotatorsMap(Map<Class<?>, List<String>> annotatorsMap) {
+ this.annotatorsMap = annotatorsMap;
+ }
+
+ /**
+ * @return the annotators params
+ */
+ public List<UserAnnotatorsParam> getAnnotatorsParams() {
+ return annotatorsParams;
+ }
+
+ public Map<Class<?>, List<UserAnnotatorsParam>> getAnnotatorsParamsAsMap() {
+
+ Map<Class<?>, List<UserAnnotatorsParam>> paramsMap = new HashMap<>();
+
+ for (UserAnnotatorsParam param : getAnnotatorsParams()) {
+ Class<?> annotatorClassName = param.getAnnotatorClassName();
+ if (!paramsMap.containsKey(annotatorClassName)) {
+ paramsMap.put(annotatorClassName, new ArrayList<>());
+ }
+ paramsMap.get(annotatorClassName).add(param);
+ }
+
+ return paramsMap;
+ }
+
+ /**
+ * @param annotatorsParams
+ * the annotatorsParams to set
+ */
+ public void setAnnotatorParams(List<UserAnnotatorsParam> annotatorsParams) {
+ this.annotatorsParams = annotatorsParams;
+ }
+
+ /**
+ * Creates {@link #validAnnotations}.
+ *
+ * @param annotatorsTree
+ * tree containing information about valid {@link MiriamType miriam
+ * types}
+ */
+ @SuppressWarnings("unchecked")
+ public void validAnnotations(TreeNode annotatorsTree) {
+ Map<Class<? extends BioEntity>, Set<MiriamType>> map = new HashMap<Class<? extends BioEntity>, Set<MiriamType>>();
+ Queue<TreeNode> queue = new LinkedList<TreeNode>();
+ queue.add(annotatorsTree);
+ while (!queue.isEmpty()) {
+ TreeNode node = queue.poll();
+ Set<MiriamType> set = new HashSet<MiriamType>();
+
+ TreeNode parent = node;
+ while (parent != null) {
+ set.addAll(((AnnotatedObjectTreeRow) parent.getData()).getValidAnnotations());
+ parent = parent.getParent();
+ }
+ map.put((Class<? extends BioEntity>) ((AnnotatedObjectTreeRow) node.getData()).getClazz(), set);
+
+ for (TreeNode node2 : node.getChildren()) {
+ queue.add(node2);
+ }
+ }
+ validAnnotations = map;
+ }
+
+ /**
+ * Creates {@link #requiredAnnotations}.
+ *
+ * @param annotatorsTree
+ * tree containing information about required {@link MiriamType miriam
+ * types}
+ */
+ @SuppressWarnings("unchecked")
+ public void requiredAnnotations(TreeNode annotatorsTree) {
+ Map<Class<? extends BioEntity>, Set<MiriamType>> map = new HashMap<Class<? extends BioEntity>, Set<MiriamType>>();
+ Queue<TreeNode> queue = new LinkedList<TreeNode>();
+ queue.add(annotatorsTree);
+ while (!queue.isEmpty()) {
+ TreeNode node = queue.poll();
+ boolean valid = ((AnnotatedObjectTreeRow) node.getData()).getRequire();
+ Set<MiriamType> set = new HashSet<MiriamType>();
+
+ TreeNode parent = node;
+ while (parent != null) {
+ set.addAll(((AnnotatedObjectTreeRow) parent.getData()).getRequiredAnnotations());
+ if (((AnnotatedObjectTreeRow) parent.getData()).getRequire()) {
+ valid = true;
+ }
+ parent = parent.getParent();
+ }
+ if (!valid) {
+ set = null;
+ }
+ map.put((Class<? extends BioEntity>) ((AnnotatedObjectTreeRow) node.getData()).getClazz(), set);
+
+ for (TreeNode node2 : node.getChildren()) {
+ queue.add(node2);
+ }
+ }
+ requiredAnnotations = map;
+ }
+
+ /**
+ * Returns {@link #validAnnotations}.
+ *
+ * @return {@link #validAnnotations}.
+ */
+ public Map<Class<? extends BioEntity>, Set<MiriamType>> getValidAnnotations() {
+ return validAnnotations;
+ }
+
+ /**
+ * Returns {@link #requiredAnnotations}.
+ *
+ * @return {@link #requiredAnnotations}.
+ */
+ public Map<Class<? extends BioEntity>, Set<MiriamType>> getRequiredAnnotations() {
+ return requiredAnnotations;
+ }
+
+ /**
+ * Sets {@link #projectDir}.
+ *
+ * @param directory
+ * new {@link #projectDir} value
+ * @return instance of this class with new value set
+ */
+ public CreateProjectParams projectDir(String directory) {
+ this.projectDir = directory;
+ return this;
+ }
+
+ /**
+ * @return the projectDir
+ * @see #projectDir
+ */
+ public String getProjectDir() {
+ return projectDir;
+ }
+
+ /**
+ *
+ * @param projectName
+ * new {@link #projectName}
+ * @return instance of this class with new value set
+ */
+ public CreateProjectParams projectName(String projectName) {
+ this.projectName = projectName;
+ return this;
+ }
+
+ /**
+ * @return the projectName
+ * @see #projectName
+ */
+ public String getProjectName() {
+ return projectName;
+ }
+
+ /**
+ * @param value
+ * the networkLayoutAsDefault to set
+ * @see #networkLayoutAsDefault
+ * @return instance of this class with new value set
+ */
+ public CreateProjectParams networkLayoutAsDefault(boolean value) {
+ this.networkLayoutAsDefault = value;
+ return this;
+
+ }
+
+ /**
+ * @return the networkLayoutAsDefault
+ * @see #networkLayoutAsDefault
+ */
+ public boolean isNetworkLayoutAsDefault() {
+ return networkLayoutAsDefault;
+ }
+
+ /**
+ * @return disease MESH code.
+ */
+ public String getDisease() {
+ return disease;
+ }
+
+ /**
+ * @param disease
+ * the code of the disease.
+ * @return updated params object.
+ */
+ public CreateProjectParams projectDisease(String disease) {
+ this.disease = disease;
+ return this;
+ }
+
+ /**
+ * @return the organism
+ * @see #organism
+ */
+ public String getOrganism() {
+ return organism;
+ }
+
+ /**
+ * @param organism
+ * the organism to set
+ * @return updated params object.
+ */
+ public CreateProjectParams projectOrganism(String organism) {
+ this.organism = organism;
+ return this;
+ }
+
+ /**
+ * @return the authenticationToken
+ * @see #authenticationToken
+ */
+ public String getAuthenticationToken() {
+ return authenticationToken;
+ }
+
+ /**
+ * @param authenticationToken
+ * the authenticationToken to set
+ * @see #authenticationToken
+ */
+ public CreateProjectParams authenticationToken(String authenticationToken) {
+ this.authenticationToken = authenticationToken;
+
+ return this;
+ }
+
+ public CreateProjectParams semanticZoom(boolean semanticZoom) {
+ this.semanticZoom = semanticZoom;
+ return this;
+ }
+
+ public CreateProjectParams semanticZoom(String value) {
+ return this.semanticZoom("true".equals(value));
+ }
+
+ public boolean isSemanticZoom() {
+ return this.semanticZoom;
+ }
+
+ public CreateProjectParams semanticZoomContainsMultipleLayouts(boolean semanticZoomContainsMultipleLayouts) {
+ this.semanticZoomContainsMultipleLayouts = semanticZoomContainsMultipleLayouts;
+ return this;
+ }
+
+ public CreateProjectParams semanticZoomContainsMultipleLayouts(String value) {
+ return this.semanticZoomContainsMultipleLayouts("true".equals(value));
+ }
+
+ public boolean isSemanticZoomContainsMultipleLayouts() {
+ return this.semanticZoomContainsMultipleLayouts;
+ }
+
+ public IConverter getParser() {
+ return this.parser;
+ }
+
+ public CreateProjectParams annotations(String value) {
+ return this.annotations("true".equalsIgnoreCase(value));
+ }
+
+ public CreateProjectParams analyzeAnnotations(String value) {
+ return this.analyzeAnnotations("true".equalsIgnoreCase(value));
+ }
+
+ public MapCanvasType getMapCanvasType() {
+ return mapCanvasType;
+ }
+
+ public CreateProjectParams mapCanvasType(MapCanvasType mapCanvasType) {
+ this.mapCanvasType = mapCanvasType;
+ return this;
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/EmailSender.java b/service/src/main/java/lcsb/mapviewer/services/utils/EmailSender.java
index 4aa84c18f5..cbcb2a57e6 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/EmailSender.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/EmailSender.java
@@ -1,313 +1,313 @@
-package lcsb.mapviewer.services.utils;
-
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.List;
-import java.util.Properties;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipOutputStream;
-
-import javax.activation.DataHandler;
-import javax.activation.DataSource;
-import javax.activation.FileDataSource;
-import javax.mail.Folder;
-import javax.mail.Message;
-import javax.mail.MessagingException;
-import javax.mail.Multipart;
-import javax.mail.Session;
-import javax.mail.Store;
-import javax.mail.internet.InternetAddress;
-import javax.mail.internet.MimeBodyPart;
-import javax.mail.internet.MimeMessage;
-import javax.mail.internet.MimeMultipart;
-
-import org.apache.log4j.Logger;
-
-import com.sun.mail.smtp.SMTPTransport;
-
-import lcsb.mapviewer.model.user.ConfigurationElementType;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.services.interfaces.IConfigurationService;
-
-/**
- * Class that allows to send emails. It requires access to email account from
- * which emails will be sent.
- *
- * @author Piotr Gawron
- *
- */
-public class EmailSender {
-
- /**
- * Max size of the content that is allowed as plain text. For emails with longer
- * content the content will be compressed and added as an attachment file.
- */
- private static final int MAX_EMAIL_CONTENT_SIZE = 32 * 1024;
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(EmailSender.class);
-
- /**
- * String (usually email address) that should appear in sender field of the
- * email.
- */
- private String sender;
- /**
- * Login used for accessing mail account.
- */
- private String login;
- /**
- * Password used for accessing mail account.
- */
- private String password;
- /**
- * Server used for SMTP.
- */
- private String smtpHost;
- /**
- * Port on the server used by IMAP.
- */
- private String imapHost;
- /**
- * Port on the server used by SMTP.
- */
- private String smtpPort;
-
- /**
- * Default constructor that initializes data.
- *
- * @param address
- * {@link #sender}
- * @param login
- * {@link #login}
- * @param password
- * {@link #password}
- * @param smtpServerAddress
- * {@link #smtpHost}
- * @param imapServerAddress
- * {@link #imapHost}
- * @param smtpServerPort
- * {@link #smtpPort}
- */
- public EmailSender(String address, String login, String password, String smtpServerAddress, String imapServerAddress,
- String smtpServerPort) {
- this.sender = address;
- this.login = login;
- this.password = password;
- this.smtpHost = smtpServerAddress;
- this.imapHost = imapServerAddress;
- this.smtpPort = smtpServerPort;
-
- }
-
- /**
- * Creates email sender class from data taken from
- * {@link IConfigurationService}.
- *
- * @param configurationService
- * configuration service that contains information required to access
- * email account
- */
- public EmailSender(IConfigurationService configurationService) {
- this(configurationService.getConfigurationValue(ConfigurationElementType.EMAIL_ADDRESS), //
- configurationService.getConfigurationValue(ConfigurationElementType.EMAIL_LOGIN), //
- configurationService.getConfigurationValue(ConfigurationElementType.EMAIL_PASSWORD), //
- configurationService.getConfigurationValue(ConfigurationElementType.EMAIL_SMTP_SERVER), //
- configurationService.getConfigurationValue(ConfigurationElementType.EMAIL_IMAP_SERVER), //
- configurationService.getConfigurationValue(ConfigurationElementType.EMAIL_SMTP_PORT));
- }
-
- /**
- * Sends email.
- *
- * @param subject
- * subject of the email
- * @param message
- * content of the message
- * @param receiver
- * user that should receive email
- * @throws MessagingException
- * thrown when there is a problem with sending email
- */
- public void sendEmail(String subject, String message, User receiver) throws MessagingException {
- if (receiver.getEmail() == null || receiver.getEmail().equals("")) {
- logger.warn(
- "Cannot send email to user: " + receiver.getName() + " " + receiver.getSurname() + ". Email set to null");
- return;
- }
- List<String> recipients = new ArrayList<String>();
- recipients.add(receiver.getEmail());
- sendEmail(recipients, new ArrayList<String>(), subject, message);
-
- }
-
- /**
- * Sends email.
- *
- * @param recipients
- * list of email recipients
- * @param ccRecipients
- * list of cc email recipients
- * @param subject
- * subject of the email
- * @param message
- * message content
- * @throws MessagingException
- * thrown when there is a problem with sending email
- */
- public void sendEmail(List<String> recipients, List<String> ccRecipients, String subject, String message)
- throws MessagingException {
- if (smtpHost.equals(ConfigurationElementType.EMAIL_SMTP_SERVER.getDefaultValue())) {
- logger.warn("Cannot send email. No smpt server defined");
- return;
- }
- // set data of the mail account
-
- Properties props = System.getProperties();
- props.setProperty("mail.smtp.host", smtpHost);
- props.setProperty("mail.smtp.port", smtpPort);
-// props.setProperty("mail.smtp.user", login);
-// props.setProperty("mail.smtp.password", password);
-// props.setProperty("mail.smtp.auth", "true");
-
- props.put("mail.smtps.quitwait", "false");
-
- Session session = Session.getInstance(props, null);
-
- final MimeMessage msg = new MimeMessage(session);
-
- // set from address
-
- msg.setFrom(new InternetAddress(sender));
-
- // add recipients
- InternetAddress[] rec = new InternetAddress[recipients.size()];
- for (int i = 0; i < recipients.size(); i++) {
- rec[i] = new InternetAddress(recipients.get(i));
- }
-
- msg.setRecipients(Message.RecipientType.TO, rec);
-
- // add cc recipients
- InternetAddress[] cc = new InternetAddress[ccRecipients.size()];
- for (int i = 0; i < ccRecipients.size(); i++) {
- rec[i] = new InternetAddress(ccRecipients.get(i));
- }
-
- msg.setRecipients(Message.RecipientType.CC, cc);
-
- // set subject
- msg.setSubject(subject);
-
- // set time stamp
- msg.setSentDate(new Date());
-
- File attachment = createAttachmentZipForBigMessage(message);
-
- if (attachment != null) {
- MimeBodyPart textBodyPart = new MimeBodyPart();
- textBodyPart.setText("Content zipped, because it's size exceeded max size: " + MAX_EMAIL_CONTENT_SIZE, "UTF-8");
-
- MimeBodyPart attachmentBodyPart = new MimeBodyPart();
- attachmentBodyPart = new MimeBodyPart();
- DataSource source = new FileDataSource(attachment);
- attachmentBodyPart.setDataHandler(new DataHandler(source));
- attachmentBodyPart.setFileName("content.zip");
-
- Multipart multipart = new MimeMultipart();
- multipart.addBodyPart(textBodyPart);
- multipart.addBodyPart(attachmentBodyPart);
-
- msg.setContent(multipart);
- } else {
- // and content
- msg.setContent(message, "text/html; charset=utf-8");
- }
-
- // connect and send
- SMTPTransport t = (SMTPTransport) session.getTransport("smtp");
-
- t.connect(smtpHost, login, password);
- t.sendMessage(msg, msg.getAllRecipients());
- t.close();
- }
-
- private File createAttachmentZipForBigMessage(String message) {
- File attachment = null;
- if (message.length() > MAX_EMAIL_CONTENT_SIZE) {
- try {
- attachment = File.createTempFile("attachment", ".zip");
-
- ZipOutputStream out = new ZipOutputStream(new FileOutputStream(attachment));
- ZipEntry e = new ZipEntry("content.txt");
- out.putNextEntry(e);
-
- byte[] data = message.getBytes();
- out.write(data, 0, data.length);
- out.closeEntry();
-
- out.close();
- } catch (IOException e1) {
- logger.error("Problem with creating attachment. Fall back into putting everything into content");
- attachment = null;
- }
- }
- return attachment;
- }
-
- /**
- * Returns number of emails in email account.
- *
- * @return number of emails in email account.
- * @throws MessagingException
- * thrown when there is a problem with accessing email account
- */
- public int getInboxCount() throws MessagingException {
- /* Set the mail properties */
- Properties props = System.getProperties();
- props.setProperty(imapHost, "imaps");
-
- /* Create the session and get the store for read the mail. */
- Session session = Session.getDefaultInstance(props, null);
- Store store = session.getStore("imaps");
- store.connect(imapHost, login, password);
-
- /* Mention the folder name which you want to read. */
- Folder inbox = store.getFolder("Inbox");
- int result = inbox.getUnreadMessageCount();
-
- store.close();
-
- return result;
-
- }
-
- /**
- * Sends email.
- *
- * @param subject
- * subject of the email
- * @param message
- * content of the message
- * @param emailAddress
- * email address that should receive email
- * @throws MessagingException
- * thrown whene there is a problem with sending email
- */
- public void sendEmail(String subject, String message, String emailAddress) throws MessagingException {
- if (emailAddress == null || emailAddress.equals("")) {
- logger.warn("Cannot send email to user: " + emailAddress + ". Email set to null");
- return;
- }
- List<String> recipients = new ArrayList<String>();
- recipients.add(emailAddress);
- sendEmail(recipients, new ArrayList<String>(), subject, message);
-
- }
-
-}
+package lcsb.mapviewer.services.utils;
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
+import java.util.Properties;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipOutputStream;
+
+import javax.activation.DataHandler;
+import javax.activation.DataSource;
+import javax.activation.FileDataSource;
+import javax.mail.Folder;
+import javax.mail.Message;
+import javax.mail.MessagingException;
+import javax.mail.Multipart;
+import javax.mail.Session;
+import javax.mail.Store;
+import javax.mail.internet.InternetAddress;
+import javax.mail.internet.MimeBodyPart;
+import javax.mail.internet.MimeMessage;
+import javax.mail.internet.MimeMultipart;
+
+import org.apache.log4j.Logger;
+
+import com.sun.mail.smtp.SMTPTransport;
+
+import lcsb.mapviewer.model.user.ConfigurationElementType;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.services.interfaces.IConfigurationService;
+
+/**
+ * Class that allows to send emails. It requires access to email account from
+ * which emails will be sent.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class EmailSender {
+
+ /**
+ * Max size of the content that is allowed as plain text. For emails with longer
+ * content the content will be compressed and added as an attachment file.
+ */
+ private static final int MAX_EMAIL_CONTENT_SIZE = 32 * 1024;
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(EmailSender.class);
+
+ /**
+ * String (usually email address) that should appear in sender field of the
+ * email.
+ */
+ private String sender;
+ /**
+ * Login used for accessing mail account.
+ */
+ private String login;
+ /**
+ * Password used for accessing mail account.
+ */
+ private String password;
+ /**
+ * Server used for SMTP.
+ */
+ private String smtpHost;
+ /**
+ * Port on the server used by IMAP.
+ */
+ private String imapHost;
+ /**
+ * Port on the server used by SMTP.
+ */
+ private String smtpPort;
+
+ /**
+ * Default constructor that initializes data.
+ *
+ * @param address
+ * {@link #sender}
+ * @param login
+ * {@link #login}
+ * @param password
+ * {@link #password}
+ * @param smtpServerAddress
+ * {@link #smtpHost}
+ * @param imapServerAddress
+ * {@link #imapHost}
+ * @param smtpServerPort
+ * {@link #smtpPort}
+ */
+ public EmailSender(String address, String login, String password, String smtpServerAddress, String imapServerAddress,
+ String smtpServerPort) {
+ this.sender = address;
+ this.login = login;
+ this.password = password;
+ this.smtpHost = smtpServerAddress;
+ this.imapHost = imapServerAddress;
+ this.smtpPort = smtpServerPort;
+
+ }
+
+ /**
+ * Creates email sender class from data taken from
+ * {@link IConfigurationService}.
+ *
+ * @param configurationService
+ * configuration service that contains information required to access
+ * email account
+ */
+ public EmailSender(IConfigurationService configurationService) {
+ this(configurationService.getConfigurationValue(ConfigurationElementType.EMAIL_ADDRESS), //
+ configurationService.getConfigurationValue(ConfigurationElementType.EMAIL_LOGIN), //
+ configurationService.getConfigurationValue(ConfigurationElementType.EMAIL_PASSWORD), //
+ configurationService.getConfigurationValue(ConfigurationElementType.EMAIL_SMTP_SERVER), //
+ configurationService.getConfigurationValue(ConfigurationElementType.EMAIL_IMAP_SERVER), //
+ configurationService.getConfigurationValue(ConfigurationElementType.EMAIL_SMTP_PORT));
+ }
+
+ /**
+ * Sends email.
+ *
+ * @param subject
+ * subject of the email
+ * @param message
+ * content of the message
+ * @param receiver
+ * user that should receive email
+ * @throws MessagingException
+ * thrown when there is a problem with sending email
+ */
+ public void sendEmail(String subject, String message, User receiver) throws MessagingException {
+ if (receiver.getEmail() == null || receiver.getEmail().equals("")) {
+ logger.warn(
+ "Cannot send email to user: " + receiver.getName() + " " + receiver.getSurname() + ". Email set to null");
+ return;
+ }
+ List<String> recipients = new ArrayList<String>();
+ recipients.add(receiver.getEmail());
+ sendEmail(recipients, new ArrayList<String>(), subject, message);
+
+ }
+
+ /**
+ * Sends email.
+ *
+ * @param recipients
+ * list of email recipients
+ * @param ccRecipients
+ * list of cc email recipients
+ * @param subject
+ * subject of the email
+ * @param message
+ * message content
+ * @throws MessagingException
+ * thrown when there is a problem with sending email
+ */
+ public void sendEmail(List<String> recipients, List<String> ccRecipients, String subject, String message)
+ throws MessagingException {
+ if (smtpHost.equals(ConfigurationElementType.EMAIL_SMTP_SERVER.getDefaultValue())) {
+ logger.warn("Cannot send email. No smpt server defined");
+ return;
+ }
+ // set data of the mail account
+
+ Properties props = System.getProperties();
+ props.setProperty("mail.smtp.host", smtpHost);
+ props.setProperty("mail.smtp.port", smtpPort);
+// props.setProperty("mail.smtp.user", login);
+// props.setProperty("mail.smtp.password", password);
+// props.setProperty("mail.smtp.auth", "true");
+
+ props.put("mail.smtps.quitwait", "false");
+
+ Session session = Session.getInstance(props, null);
+
+ final MimeMessage msg = new MimeMessage(session);
+
+ // set from address
+
+ msg.setFrom(new InternetAddress(sender));
+
+ // add recipients
+ InternetAddress[] rec = new InternetAddress[recipients.size()];
+ for (int i = 0; i < recipients.size(); i++) {
+ rec[i] = new InternetAddress(recipients.get(i));
+ }
+
+ msg.setRecipients(Message.RecipientType.TO, rec);
+
+ // add cc recipients
+ InternetAddress[] cc = new InternetAddress[ccRecipients.size()];
+ for (int i = 0; i < ccRecipients.size(); i++) {
+ rec[i] = new InternetAddress(ccRecipients.get(i));
+ }
+
+ msg.setRecipients(Message.RecipientType.CC, cc);
+
+ // set subject
+ msg.setSubject(subject);
+
+ // set time stamp
+ msg.setSentDate(new Date());
+
+ File attachment = createAttachmentZipForBigMessage(message);
+
+ if (attachment != null) {
+ MimeBodyPart textBodyPart = new MimeBodyPart();
+ textBodyPart.setText("Content zipped, because it's size exceeded max size: " + MAX_EMAIL_CONTENT_SIZE, "UTF-8");
+
+ MimeBodyPart attachmentBodyPart = new MimeBodyPart();
+ attachmentBodyPart = new MimeBodyPart();
+ DataSource source = new FileDataSource(attachment);
+ attachmentBodyPart.setDataHandler(new DataHandler(source));
+ attachmentBodyPart.setFileName("content.zip");
+
+ Multipart multipart = new MimeMultipart();
+ multipart.addBodyPart(textBodyPart);
+ multipart.addBodyPart(attachmentBodyPart);
+
+ msg.setContent(multipart);
+ } else {
+ // and content
+ msg.setContent(message, "text/html; charset=utf-8");
+ }
+
+ // connect and send
+ SMTPTransport t = (SMTPTransport) session.getTransport("smtp");
+
+ t.connect(smtpHost, login, password);
+ t.sendMessage(msg, msg.getAllRecipients());
+ t.close();
+ }
+
+ private File createAttachmentZipForBigMessage(String message) {
+ File attachment = null;
+ if (message.length() > MAX_EMAIL_CONTENT_SIZE) {
+ try {
+ attachment = File.createTempFile("attachment", ".zip");
+
+ ZipOutputStream out = new ZipOutputStream(new FileOutputStream(attachment));
+ ZipEntry e = new ZipEntry("content.txt");
+ out.putNextEntry(e);
+
+ byte[] data = message.getBytes();
+ out.write(data, 0, data.length);
+ out.closeEntry();
+
+ out.close();
+ } catch (IOException e1) {
+ logger.error("Problem with creating attachment. Fall back into putting everything into content");
+ attachment = null;
+ }
+ }
+ return attachment;
+ }
+
+ /**
+ * Returns number of emails in email account.
+ *
+ * @return number of emails in email account.
+ * @throws MessagingException
+ * thrown when there is a problem with accessing email account
+ */
+ public int getInboxCount() throws MessagingException {
+ /* Set the mail properties */
+ Properties props = System.getProperties();
+ props.setProperty(imapHost, "imaps");
+
+ /* Create the session and get the store for read the mail. */
+ Session session = Session.getDefaultInstance(props, null);
+ Store store = session.getStore("imaps");
+ store.connect(imapHost, login, password);
+
+ /* Mention the folder name which you want to read. */
+ Folder inbox = store.getFolder("Inbox");
+ int result = inbox.getUnreadMessageCount();
+
+ store.close();
+
+ return result;
+
+ }
+
+ /**
+ * Sends email.
+ *
+ * @param subject
+ * subject of the email
+ * @param message
+ * content of the message
+ * @param emailAddress
+ * email address that should receive email
+ * @throws MessagingException
+ * thrown whene there is a problem with sending email
+ */
+ public void sendEmail(String subject, String message, String emailAddress) throws MessagingException {
+ if (emailAddress == null || emailAddress.equals("")) {
+ logger.warn("Cannot send email to user: " + emailAddress + ". Email set to null");
+ return;
+ }
+ List<String> recipients = new ArrayList<String>();
+ recipients.add(emailAddress);
+ sendEmail(recipients, new ArrayList<String>(), subject, message);
+
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/InvalidPrivilegeException.java b/service/src/main/java/lcsb/mapviewer/services/utils/InvalidPrivilegeException.java
index a371a61c87..6a8506ada0 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/InvalidPrivilegeException.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/InvalidPrivilegeException.java
@@ -1,24 +1,24 @@
-package lcsb.mapviewer.services.utils;
-
-/**
- * Exception used when there are problems with privileges.
- *
- * @author Piotr Gawron
- *
- */
-public class InvalidPrivilegeException extends RuntimeException {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Public constructor with message that should be reported.
- *
- * @param string
- * message
- */
- public InvalidPrivilegeException(String string) {
- super(string);
- }
-}
+package lcsb.mapviewer.services.utils;
+
+/**
+ * Exception used when there are problems with privileges.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class InvalidPrivilegeException extends RuntimeException {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Public constructor with message that should be reported.
+ *
+ * @param string
+ * message
+ */
+ public InvalidPrivilegeException(String string) {
+ super(string);
+ }
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/ReferenceGenomeExistsException.java b/service/src/main/java/lcsb/mapviewer/services/utils/ReferenceGenomeExistsException.java
index 6a7e5df2ae..fe163d7dea 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/ReferenceGenomeExistsException.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/ReferenceGenomeExistsException.java
@@ -1,26 +1,26 @@
-package lcsb.mapviewer.services.utils;
-
-import lcsb.mapviewer.annotation.services.genome.ReferenceGenomeConnectorException;
-
-/**
- * Exception used when there are problems with privileges.
- *
- * @author Piotr Gawron
- *
- */
-public class ReferenceGenomeExistsException extends ReferenceGenomeConnectorException {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Public constructor with message that should be reported.
- *
- * @param string
- * message
- */
- public ReferenceGenomeExistsException(String string) {
- super(string);
- }
-}
+package lcsb.mapviewer.services.utils;
+
+import lcsb.mapviewer.annotation.services.genome.ReferenceGenomeConnectorException;
+
+/**
+ * Exception used when there are problems with privileges.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ReferenceGenomeExistsException extends ReferenceGenomeConnectorException {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Public constructor with message that should be reported.
+ *
+ * @param string
+ * message
+ */
+ public ReferenceGenomeExistsException(String string) {
+ super(string);
+ }
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/SearchIndexer.java b/service/src/main/java/lcsb/mapviewer/services/utils/SearchIndexer.java
index 92ad037b37..9089a3fd4b 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/SearchIndexer.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/SearchIndexer.java
@@ -1,178 +1,178 @@
-package lcsb.mapviewer.services.utils;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.model.map.SearchIndex;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * This class is responsible for seqrch queries. It allows to create an index
- * for an alias and a query this index in a way.
- *
- * @author Piotr Gawron
- *
- */
-public class SearchIndexer {
-
- /**
- * Base score of the index generated for alias id. It will be used as a shift
- * for {@link SearchIndex#weight} value.
- */
- private static final int SEARCH_SCORE_LEVEL_FOR_ALIAS_ID = 60;
-
- /**
- * Base score of the index generated for {@link Element#formerSymbols}. It will
- * be used as a shift for {@link SearchIndex#weight} value.
- */
- private static final int SEARCH_SCORE_LEVEL_FOR_SPECIES_FORMER_SYMBOL = 75;
-
- /**
- * Base score of the index generated for full name. It will be used as a shift
- * for {@link SearchIndex#weight} value.
- */
- private static final int SEARCH_SCORE_LEVEL_FOR_SPECIES_FULL_NAME = 80;
-
- /**
- * Base score of the index generated for synonims. It will be used as a shift
- * for {@link SearchIndex#weight} value.
- */
- private static final int SEARCH_SCORE_LEVEL_FOR_SPECIES_SYNONIM = 90;
-
- /**
- * Base score of the index generated for name. It will be used as a shift for
- * {@link SearchIndex#weight} value.
- */
- private static final int SEARCH_SCORE_LEVEL_FOR_SPECIES_NAME = 100;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(SearchIndexer.class);
-
- /**
- * This method create list of indexes for an alias. Right now every index is
- * one of the following indexed strings (from most important to less
- * important): <br/>
- * <ul>
- * <li>species name,</li>
- * <li>synonyms (only for proteins annotated by vencata server),</li>
- * <li>common names (only for proteins annotated by vencata server),</li>
- * <li>former symbols,</li>
- * <li>speciesID,</li>
- * <li>aliasID,</li>
- * </ul>
- *
- * @param species
- * object to be indexed
- * @return list of indexes for an alias
- */
- public List<SearchIndex> createIndexForAlias(Element species) {
- List<SearchIndex> result = new ArrayList<>();
- String id1 = species.getElementId();
- result.add(new SearchIndex(getIndexStringForString(id1), SEARCH_SCORE_LEVEL_FOR_ALIAS_ID));
- String id3 = species.getName();
-
- result.add(new SearchIndex(getIndexStringForString(id3), SEARCH_SCORE_LEVEL_FOR_SPECIES_NAME));
-
- for (String string : species.getSynonyms()) {
- result.add(new SearchIndex(getIndexStringForString(string), SEARCH_SCORE_LEVEL_FOR_SPECIES_SYNONIM));
- }
- for (String string : species.getFormerSymbols()) {
- result.add(new SearchIndex(getIndexStringForString(string), SEARCH_SCORE_LEVEL_FOR_SPECIES_FORMER_SYMBOL));
- }
- String name = species.getFullName();
- if (name != null && !name.equals("")) {
- result.add(new SearchIndex(getIndexStringForString(name), SEARCH_SCORE_LEVEL_FOR_SPECIES_FULL_NAME));
- }
- return result;
- }
-
- /**
- * This method transform a string into indexed string version. Right now the
- * indexed version is a lowercase string which contains only alphanumerical
- * characters.
- *
- * @param str
- * string for conversion
- * @return indexed version of the input string
- */
- private String getIndexStringForString(String str) {
- return str.toLowerCase().replaceAll("[^a-z0-9]", "");
- }
-
- /**
- * This method transform a string into indexed query. AvailablePrefixes
- * contains a collection of all possible prefixes for query string that should
- * be ommitted.
- *
- * @param originalQuery
- * query to be transformed
- * @param availablePrefixes
- * collection of valid prefixes in the query
- *
- * @return indexed string of the qoriginal query
- */
- public String getQueryStringForIndex(String originalQuery, Collection<String> availablePrefixes) {
- String result = originalQuery;
- for (String string : availablePrefixes) {
- if (result.startsWith(string + ":")) {
- result = result.replaceFirst(string + ":", "");
- break;
- }
- }
-
- return getIndexStringForString(result);
- }
-
- /**
- * This method check if query match search index and return probability of the
- * hit between <0,1> (0 - means query is not similar to index, 1 means perfect
- * match) increased by the index weight if probability is higher than 0.
- *
- * @param query
- * query to be checked (it should be already prepared in the same way
- * as index is)
- * @param index
- * search index value to be checked
- * @return probabily value (range <0,1>) of match between query and index
- * increased by the index weight
- */
- public double match(String query, SearchIndex index) {
- double partialValue = 0;
- if (index.getValue().contains(query)) {
- partialValue = ((double) query.length()) / ((double) index.getValue().length());
- }
- if (partialValue > 0) {
- return index.getWeight() + partialValue;
- } else {
- return 0;
- }
- }
-
- /**
- * Return type of elements that can be returned for the query.
- *
- * @param string
- * query string.
- * @param speciesSearchReversePrefix
- * map containing information about possible prefixes used in the
- * query
- * @return class of the element that might exist in the result
- */
- public Class<? extends Element> getTypeForQuery(String string, Map<String, Class<? extends Element>> speciesSearchReversePrefix) {
- String result = string;
- for (Entry<String, Class<? extends Element>> entry : speciesSearchReversePrefix.entrySet()) {
- if (result.startsWith(entry.getKey() + ":")) {
- return entry.getValue();
- }
- }
- return Element.class;
- }
-}
+package lcsb.mapviewer.services.utils;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.model.map.SearchIndex;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * This class is responsible for seqrch queries. It allows to create an index
+ * for an alias and a query this index in a way.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class SearchIndexer {
+
+ /**
+ * Base score of the index generated for alias id. It will be used as a shift
+ * for {@link SearchIndex#weight} value.
+ */
+ private static final int SEARCH_SCORE_LEVEL_FOR_ALIAS_ID = 60;
+
+ /**
+ * Base score of the index generated for {@link Element#formerSymbols}. It will
+ * be used as a shift for {@link SearchIndex#weight} value.
+ */
+ private static final int SEARCH_SCORE_LEVEL_FOR_SPECIES_FORMER_SYMBOL = 75;
+
+ /**
+ * Base score of the index generated for full name. It will be used as a shift
+ * for {@link SearchIndex#weight} value.
+ */
+ private static final int SEARCH_SCORE_LEVEL_FOR_SPECIES_FULL_NAME = 80;
+
+ /**
+ * Base score of the index generated for synonims. It will be used as a shift
+ * for {@link SearchIndex#weight} value.
+ */
+ private static final int SEARCH_SCORE_LEVEL_FOR_SPECIES_SYNONIM = 90;
+
+ /**
+ * Base score of the index generated for name. It will be used as a shift for
+ * {@link SearchIndex#weight} value.
+ */
+ private static final int SEARCH_SCORE_LEVEL_FOR_SPECIES_NAME = 100;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(SearchIndexer.class);
+
+ /**
+ * This method create list of indexes for an alias. Right now every index is
+ * one of the following indexed strings (from most important to less
+ * important): <br/>
+ * <ul>
+ * <li>species name,</li>
+ * <li>synonyms (only for proteins annotated by vencata server),</li>
+ * <li>common names (only for proteins annotated by vencata server),</li>
+ * <li>former symbols,</li>
+ * <li>speciesID,</li>
+ * <li>aliasID,</li>
+ * </ul>
+ *
+ * @param species
+ * object to be indexed
+ * @return list of indexes for an alias
+ */
+ public List<SearchIndex> createIndexForAlias(Element species) {
+ List<SearchIndex> result = new ArrayList<>();
+ String id1 = species.getElementId();
+ result.add(new SearchIndex(getIndexStringForString(id1), SEARCH_SCORE_LEVEL_FOR_ALIAS_ID));
+ String id3 = species.getName();
+
+ result.add(new SearchIndex(getIndexStringForString(id3), SEARCH_SCORE_LEVEL_FOR_SPECIES_NAME));
+
+ for (String string : species.getSynonyms()) {
+ result.add(new SearchIndex(getIndexStringForString(string), SEARCH_SCORE_LEVEL_FOR_SPECIES_SYNONIM));
+ }
+ for (String string : species.getFormerSymbols()) {
+ result.add(new SearchIndex(getIndexStringForString(string), SEARCH_SCORE_LEVEL_FOR_SPECIES_FORMER_SYMBOL));
+ }
+ String name = species.getFullName();
+ if (name != null && !name.equals("")) {
+ result.add(new SearchIndex(getIndexStringForString(name), SEARCH_SCORE_LEVEL_FOR_SPECIES_FULL_NAME));
+ }
+ return result;
+ }
+
+ /**
+ * This method transform a string into indexed string version. Right now the
+ * indexed version is a lowercase string which contains only alphanumerical
+ * characters.
+ *
+ * @param str
+ * string for conversion
+ * @return indexed version of the input string
+ */
+ private String getIndexStringForString(String str) {
+ return str.toLowerCase().replaceAll("[^a-z0-9]", "");
+ }
+
+ /**
+ * This method transform a string into indexed query. AvailablePrefixes
+ * contains a collection of all possible prefixes for query string that should
+ * be ommitted.
+ *
+ * @param originalQuery
+ * query to be transformed
+ * @param availablePrefixes
+ * collection of valid prefixes in the query
+ *
+ * @return indexed string of the qoriginal query
+ */
+ public String getQueryStringForIndex(String originalQuery, Collection<String> availablePrefixes) {
+ String result = originalQuery;
+ for (String string : availablePrefixes) {
+ if (result.startsWith(string + ":")) {
+ result = result.replaceFirst(string + ":", "");
+ break;
+ }
+ }
+
+ return getIndexStringForString(result);
+ }
+
+ /**
+ * This method check if query match search index and return probability of the
+ * hit between <0,1> (0 - means query is not similar to index, 1 means perfect
+ * match) increased by the index weight if probability is higher than 0.
+ *
+ * @param query
+ * query to be checked (it should be already prepared in the same way
+ * as index is)
+ * @param index
+ * search index value to be checked
+ * @return probabily value (range <0,1>) of match between query and index
+ * increased by the index weight
+ */
+ public double match(String query, SearchIndex index) {
+ double partialValue = 0;
+ if (index.getValue().contains(query)) {
+ partialValue = ((double) query.length()) / ((double) index.getValue().length());
+ }
+ if (partialValue > 0) {
+ return index.getWeight() + partialValue;
+ } else {
+ return 0;
+ }
+ }
+
+ /**
+ * Return type of elements that can be returned for the query.
+ *
+ * @param string
+ * query string.
+ * @param speciesSearchReversePrefix
+ * map containing information about possible prefixes used in the
+ * query
+ * @return class of the element that might exist in the result
+ */
+ public Class<? extends Element> getTypeForQuery(String string, Map<String, Class<? extends Element>> speciesSearchReversePrefix) {
+ String result = string;
+ for (Entry<String, Class<? extends Element>> entry : speciesSearchReversePrefix.entrySet()) {
+ if (result.startsWith(entry.getKey() + ":")) {
+ return entry.getValue();
+ }
+ }
+ return Element.class;
+ }
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/data/BuildInLayout.java b/service/src/main/java/lcsb/mapviewer/services/utils/data/BuildInLayout.java
index c0edc377be..3a54c156fb 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/data/BuildInLayout.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/data/BuildInLayout.java
@@ -1,112 +1,112 @@
-package lcsb.mapviewer.services.utils.data;
-
-/**
- * This enum defines set of build-in layouts. Some of them are PD related.
- * Layout is a way of visualizing map.
- *
- * @author Piotr Gawron
- *
- */
-public enum BuildInLayout { //
- /**
- * Normal strainghtforward visualization.
- */
- NORMAL("Network", "_normal", null, false), //
- // /**
- // * Set of data containing Substantia Nigra data for Parkinson Disease (false
- // * discovery ratio 0.01).
- // */
- // FDR_001("PD Substantia Nigra FDR=0.01", "_001", "/enricoData/ge001.txt",
- // false), //
- // /**
- // * Set of data containing Substantia Nigra data for Parkinson Disease (false
- // * discovery ratio 0.05).
- // */
- // FDR_005("PD Substantia Nigra FDR=0.05", "_005", "/enricoData/ge005.txt",
- // false), //
- // /**
- // * Set of data containing aging data for Parkinson Disease .
- // */
- // AGING("Aging", "_ageing", "/enricoData/ageing.txt", false), //
- /**
- * Standard visualization with hierarchical view.
- */
- NESTED("Pathways and compartments", "_nested", null, true), //
- SEMANTIC("Semantic zoom", "_semantic", null, true),
- /**
- * Clean visualization (with colors reset to black and white).
- */
- CLEAN("Empty", "_empty", null, false); //
-
- /**
- * Title of the layout.
- */
- private String title;
-
- /**
- * Suffix used for the directory name during image generation.
- */
- private String directorySuffix;
-
- /**
- * File with the color values for the layout.
- */
- private String coloringFile;
-
- /**
- * Should visualization be hierarchical or simple.
- */
- private boolean nested;
-
- /**
- * Default constructor with all information needed by layout.
- *
- * @param title
- * Title of the layout
- * @param directorySuffix
- * Suffix used for the directory name during image generation
- * @param coloringFileName
- * File with the color values for the layout
- * @param nested
- * Should visualization be hierarchical or simple
- */
- BuildInLayout(String title, String directorySuffix, String coloringFileName, boolean nested) {
- this.title = title;
- this.directorySuffix = directorySuffix;
- this.coloringFile = coloringFileName;
- this.nested = nested;
- }
-
- /**
- * @return the title
- * @see #title
- */
- public String getTitle() {
- return title;
- }
-
- /**
- * @return the directorySuffix
- * @see #directorySuffix
- */
- public String getDirectorySuffix() {
- return directorySuffix;
- }
-
- /**
- * @return the coloringFile
- * @see #coloringFile
- */
- public String getColoringFile() {
- return coloringFile;
- }
-
- /**
- * @return the nested
- * @see #nested
- */
- public boolean isNested() {
- return nested;
- }
-
-}
+package lcsb.mapviewer.services.utils.data;
+
+/**
+ * This enum defines set of build-in layouts. Some of them are PD related.
+ * Layout is a way of visualizing map.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum BuildInLayout { //
+ /**
+ * Normal strainghtforward visualization.
+ */
+ NORMAL("Network", "_normal", null, false), //
+ // /**
+ // * Set of data containing Substantia Nigra data for Parkinson Disease (false
+ // * discovery ratio 0.01).
+ // */
+ // FDR_001("PD Substantia Nigra FDR=0.01", "_001", "/enricoData/ge001.txt",
+ // false), //
+ // /**
+ // * Set of data containing Substantia Nigra data for Parkinson Disease (false
+ // * discovery ratio 0.05).
+ // */
+ // FDR_005("PD Substantia Nigra FDR=0.05", "_005", "/enricoData/ge005.txt",
+ // false), //
+ // /**
+ // * Set of data containing aging data for Parkinson Disease .
+ // */
+ // AGING("Aging", "_ageing", "/enricoData/ageing.txt", false), //
+ /**
+ * Standard visualization with hierarchical view.
+ */
+ NESTED("Pathways and compartments", "_nested", null, true), //
+ SEMANTIC("Semantic zoom", "_semantic", null, true),
+ /**
+ * Clean visualization (with colors reset to black and white).
+ */
+ CLEAN("Empty", "_empty", null, false); //
+
+ /**
+ * Title of the layout.
+ */
+ private String title;
+
+ /**
+ * Suffix used for the directory name during image generation.
+ */
+ private String directorySuffix;
+
+ /**
+ * File with the color values for the layout.
+ */
+ private String coloringFile;
+
+ /**
+ * Should visualization be hierarchical or simple.
+ */
+ private boolean nested;
+
+ /**
+ * Default constructor with all information needed by layout.
+ *
+ * @param title
+ * Title of the layout
+ * @param directorySuffix
+ * Suffix used for the directory name during image generation
+ * @param coloringFileName
+ * File with the color values for the layout
+ * @param nested
+ * Should visualization be hierarchical or simple
+ */
+ BuildInLayout(String title, String directorySuffix, String coloringFileName, boolean nested) {
+ this.title = title;
+ this.directorySuffix = directorySuffix;
+ this.coloringFile = coloringFileName;
+ this.nested = nested;
+ }
+
+ /**
+ * @return the title
+ * @see #title
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * @return the directorySuffix
+ * @see #directorySuffix
+ */
+ public String getDirectorySuffix() {
+ return directorySuffix;
+ }
+
+ /**
+ * @return the coloringFile
+ * @see #coloringFile
+ */
+ public String getColoringFile() {
+ return coloringFile;
+ }
+
+ /**
+ * @return the nested
+ * @see #nested
+ */
+ public boolean isNested() {
+ return nested;
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java b/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java
index 0423331172..fc641afe49 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java
@@ -1,161 +1,161 @@
-package lcsb.mapviewer.services.utils.data;
-
-import java.util.HashSet;
-import java.util.Set;
-
-import lcsb.mapviewer.model.map.layout.ReferenceGenome;
-import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
-
-/**
- * This enum defines which columns are available for defining
- * {@link lcsb.mapviewer.model.map.layout.ColorSchema}.
- *
- * @author Piotr Gawron
- *
- */
-public enum ColorSchemaColumn {
-
- /**
- * Name of the element.
- */
- NAME("name", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * Name of the element.
- */
- MODEL_NAME("model_name", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * Value that will be transformed into new color.
- *
- * @see ColorSchemaColumn#COLOR
- */
- VALUE("value", new ColorSchemaType[] { ColorSchemaType.GENERIC }), //
-
- /**
- * In which compartment the element should be located.
- */
- COMPARTMENT("compartment", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * Class type of the element.
- */
- TYPE("type", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * New element/reaction color.
- */
- COLOR("color", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * Identifier of the element.
- */
- IDENTIFIER("identifier", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * Element identifier.
- */
- ELEMENT_IDENTIFIER("elementIdentifier", new ColorSchemaType[] { ColorSchemaType.GENERIC }), //
-
- /**
- * Element identifier.
- */
- @Deprecated
- REACTION_IDENTIFIER("reactionIdentifier", new ColorSchemaType[] { ColorSchemaType.GENERIC }), //
-
- /**
- * New line width of the reaction.
- */
- LINE_WIDTH("lineWidth", new ColorSchemaType[] { ColorSchemaType.GENERIC }), //
-
- /**
- * Position where gene variants starts.
- */
- POSITION("position", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * Original DNA of the variant.
- */
- ORIGINAL_DNA("original_dna", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * Alternative DNA of the variant.
- */
- ALTERNATIVE_DNA("alternative_dna", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * Short description of the entry.
- */
- DESCRIPTION("description", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT, ColorSchemaType.GENERIC }), //
-
- /**
- * Variant references.
- */
- REFERENCES("references", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * What's the {@link ReferenceGenomeType}.
- */
- REFERENCE_GENOME_TYPE("reference_genome_type", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * {@link ReferenceGenome#version Version} of the reference genome.
- */
- REFERENCE_GENOME_VERSION("reference_genome_version", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * Contig where variant was observed.
- */
- CONTIG("contig", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
-
- ALLEL_FREQUENCY("allel_frequency", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
-
- VARIANT_IDENTIFIER("variant_identifier", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * Should the direction of reaction be reversed.
- */
- REVERSE_REACTION("reverseReaction", new ColorSchemaType[] { ColorSchemaType.GENERIC }); //
-
- /**
- * Default constructor that creates enum entry.
- *
- * @param title
- * {@link #title}
- * @param types
- * list of {@link ColumnType types} where this column is allowed
- */
- ColorSchemaColumn(String title, ColorSchemaType[] types) {
- this.title = title;
- for (ColorSchemaType colorSchemaType : types) {
- this.types.add(colorSchemaType);
- }
- }
-
- /**
- * Human readable title used in input file.
- */
- private String title;
-
- /**
- * Set of types where column is allowed.
- */
- private Set<ColorSchemaType> types = new HashSet<>();
-
- /**
- *
- * @return {@link #title}
- */
- public String getTitle() {
- return title;
- }
-
- /**
- * @return the types
- * @see #types
- */
- public Set<ColorSchemaType> getTypes() {
- return types;
- }
-
-}
+package lcsb.mapviewer.services.utils.data;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import lcsb.mapviewer.model.map.layout.ReferenceGenome;
+import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
+
+/**
+ * This enum defines which columns are available for defining
+ * {@link lcsb.mapviewer.model.map.layout.ColorSchema}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum ColorSchemaColumn {
+
+ /**
+ * Name of the element.
+ */
+ NAME("name", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * Name of the element.
+ */
+ MODEL_NAME("model_name", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * Value that will be transformed into new color.
+ *
+ * @see ColorSchemaColumn#COLOR
+ */
+ VALUE("value", new ColorSchemaType[] { ColorSchemaType.GENERIC }), //
+
+ /**
+ * In which compartment the element should be located.
+ */
+ COMPARTMENT("compartment", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * Class type of the element.
+ */
+ TYPE("type", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * New element/reaction color.
+ */
+ COLOR("color", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * Identifier of the element.
+ */
+ IDENTIFIER("identifier", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * Element identifier.
+ */
+ ELEMENT_IDENTIFIER("elementIdentifier", new ColorSchemaType[] { ColorSchemaType.GENERIC }), //
+
+ /**
+ * Element identifier.
+ */
+ @Deprecated
+ REACTION_IDENTIFIER("reactionIdentifier", new ColorSchemaType[] { ColorSchemaType.GENERIC }), //
+
+ /**
+ * New line width of the reaction.
+ */
+ LINE_WIDTH("lineWidth", new ColorSchemaType[] { ColorSchemaType.GENERIC }), //
+
+ /**
+ * Position where gene variants starts.
+ */
+ POSITION("position", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * Original DNA of the variant.
+ */
+ ORIGINAL_DNA("original_dna", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * Alternative DNA of the variant.
+ */
+ ALTERNATIVE_DNA("alternative_dna", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * Short description of the entry.
+ */
+ DESCRIPTION("description", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT, ColorSchemaType.GENERIC }), //
+
+ /**
+ * Variant references.
+ */
+ REFERENCES("references", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * What's the {@link ReferenceGenomeType}.
+ */
+ REFERENCE_GENOME_TYPE("reference_genome_type", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * {@link ReferenceGenome#version Version} of the reference genome.
+ */
+ REFERENCE_GENOME_VERSION("reference_genome_version", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * Contig where variant was observed.
+ */
+ CONTIG("contig", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+
+ ALLEL_FREQUENCY("allel_frequency", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+
+ VARIANT_IDENTIFIER("variant_identifier", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * Should the direction of reaction be reversed.
+ */
+ REVERSE_REACTION("reverseReaction", new ColorSchemaType[] { ColorSchemaType.GENERIC }); //
+
+ /**
+ * Default constructor that creates enum entry.
+ *
+ * @param title
+ * {@link #title}
+ * @param types
+ * list of {@link ColumnType types} where this column is allowed
+ */
+ ColorSchemaColumn(String title, ColorSchemaType[] types) {
+ this.title = title;
+ for (ColorSchemaType colorSchemaType : types) {
+ this.types.add(colorSchemaType);
+ }
+ }
+
+ /**
+ * Human readable title used in input file.
+ */
+ private String title;
+
+ /**
+ * Set of types where column is allowed.
+ */
+ private Set<ColorSchemaType> types = new HashSet<>();
+
+ /**
+ *
+ * @return {@link #title}
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * @return the types
+ * @see #types
+ */
+ public Set<ColorSchemaType> getTypes() {
+ return types;
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaType.java b/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaType.java
index 7ab4f41a6f..108a4ce7b1 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaType.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaType.java
@@ -1,21 +1,21 @@
-package lcsb.mapviewer.services.utils.data;
-
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-
-/**
- * Type of the {@link ColorSchema}.
- *
- * @author Piotr Gawron
- *
- */
-public enum ColorSchemaType {
- /**
- * Generic color schema (used for expression levels, etc).
- */
- GENERIC,
-
- /**
- * Customized color schema used for highlightig genetic variants.
- */
- GENETIC_VARIANT
-}
+package lcsb.mapviewer.services.utils.data;
+
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+
+/**
+ * Type of the {@link ColorSchema}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum ColorSchemaType {
+ /**
+ * Generic color schema (used for expression levels, etc).
+ */
+ GENERIC,
+
+ /**
+ * Customized color schema used for highlightig genetic variants.
+ */
+ GENETIC_VARIANT
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/data/ExportColumn.java b/service/src/main/java/lcsb/mapviewer/services/utils/data/ExportColumn.java
index 93855824f8..721e9eee4d 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/data/ExportColumn.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/data/ExportColumn.java
@@ -1,114 +1,114 @@
-package lcsb.mapviewer.services.utils.data;
-
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * This enum defines which columns are available in export function.
- *
- * @author Piotr Gawron
- *
- */
-public enum ExportColumn {
-
- /**
- * Name of the species.
- */
- NAME("Name", Species.class), //
-
- /**
- * Name of compartment.
- */
- COMPARTMENT_NAME("Compartment", Species.class), //
-
- /**
- * Name of compartment.
- */
- POSITION_TO_COMPARTMENT("Position to compartment", Species.class), //
-
- /**
- * Name of pathway.
- */
- COMPONENT_NAME("Pathway", Species.class), //
-
- /**
- * Type of the species.
- */
- TYPE("Type", Species.class), //
-
- /**
- * Identifier.
- */
- ID("Id", Object.class), //
-
- /**
- * Complex in which element is localized.
- */
- COMPLEX("Parent complex", Species.class), //
-
- /**
- * Complex in which element is localized.
- */
- SUBMODEL("Submodel", Species.class), //
-
- /**
- * Reaction identifier.
- */
- REACTION_ID("Reaction id", Reaction.class), //
-
- /**
- * Reaction type.
- */
- REACTION_TYPE("Reaction type", Reaction.class), //
-
- /**
- * Information if reaction is reversible.
- */
- REACTION_REVERSIBLE("Reversible", Reaction.class), //
-
- /**
- * Every reaction is split into two elements interactions.
- */
- REACTION_TWO_ELEMENT("Split reaction to two element interaction", Reaction.class);
-
- /**
- * Default constructor that creates enum entry.
- *
- * @param title
- * {@link #title}
- * @param clazz
- * {@link #clazz}
- */
- ExportColumn(String title, Class<?> clazz) {
- this.title = title;
- this.clazz = clazz;
- }
-
- /**
- * Human readable title.
- */
- private String title;
-
- /**
- * Class for which this column should be accessible.
- */
- private Class<?> clazz;
-
- /**
- *
- * @return {@link #title}
- */
- public String getTitle() {
- return title;
- }
-
- /**
- *
- *
- * @return {@link #clazz}
- */
- public Class<?> getClazz() {
- return clazz;
- }
-
-}
+package lcsb.mapviewer.services.utils.data;
+
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This enum defines which columns are available in export function.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum ExportColumn {
+
+ /**
+ * Name of the species.
+ */
+ NAME("Name", Species.class), //
+
+ /**
+ * Name of compartment.
+ */
+ COMPARTMENT_NAME("Compartment", Species.class), //
+
+ /**
+ * Name of compartment.
+ */
+ POSITION_TO_COMPARTMENT("Position to compartment", Species.class), //
+
+ /**
+ * Name of pathway.
+ */
+ COMPONENT_NAME("Pathway", Species.class), //
+
+ /**
+ * Type of the species.
+ */
+ TYPE("Type", Species.class), //
+
+ /**
+ * Identifier.
+ */
+ ID("Id", Object.class), //
+
+ /**
+ * Complex in which element is localized.
+ */
+ COMPLEX("Parent complex", Species.class), //
+
+ /**
+ * Complex in which element is localized.
+ */
+ SUBMODEL("Submodel", Species.class), //
+
+ /**
+ * Reaction identifier.
+ */
+ REACTION_ID("Reaction id", Reaction.class), //
+
+ /**
+ * Reaction type.
+ */
+ REACTION_TYPE("Reaction type", Reaction.class), //
+
+ /**
+ * Information if reaction is reversible.
+ */
+ REACTION_REVERSIBLE("Reversible", Reaction.class), //
+
+ /**
+ * Every reaction is split into two elements interactions.
+ */
+ REACTION_TWO_ELEMENT("Split reaction to two element interaction", Reaction.class);
+
+ /**
+ * Default constructor that creates enum entry.
+ *
+ * @param title
+ * {@link #title}
+ * @param clazz
+ * {@link #clazz}
+ */
+ ExportColumn(String title, Class<?> clazz) {
+ this.title = title;
+ this.clazz = clazz;
+ }
+
+ /**
+ * Human readable title.
+ */
+ private String title;
+
+ /**
+ * Class for which this column should be accessible.
+ */
+ private Class<?> clazz;
+
+ /**
+ *
+ * @return {@link #title}
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ *
+ *
+ * @return {@link #clazz}
+ */
+ public Class<?> getClazz() {
+ return clazz;
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/data/ExportFileType.java b/service/src/main/java/lcsb/mapviewer/services/utils/data/ExportFileType.java
index 19e0fd5ca6..1578fe18a2 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/data/ExportFileType.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/data/ExportFileType.java
@@ -1,46 +1,46 @@
-package lcsb.mapviewer.services.utils.data;
-
-/**
- * Defines types of files that can be used in export function.
- *
- * @author Piotr Gawron
- *
- */
-public enum ExportFileType {
-
- /**
- * Tab separated file.
- */
- TAB_SEPARATED("Tab separated"),
-
- /**
- * Simnple interaction format used by <a
- * href="http://wiki.cytoscape.org/Cytoscape_User_Manual/Network_Formats"
- * >Cytoscape</a>.
- */
-
- SIF("SIF");
-
- /**
- * Default constructor.
- *
- * @param title
- * {@link #title}
- */
- ExportFileType(final String title) {
- this.title = title;
- }
-
- /**
- * Human readable name of the format.
- */
- private String title;
-
- /**
- *
- * @return {@link #title}
- */
- public String getTitle() {
- return title;
- }
-}
+package lcsb.mapviewer.services.utils.data;
+
+/**
+ * Defines types of files that can be used in export function.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public enum ExportFileType {
+
+ /**
+ * Tab separated file.
+ */
+ TAB_SEPARATED("Tab separated"),
+
+ /**
+ * Simnple interaction format used by <a
+ * href="http://wiki.cytoscape.org/Cytoscape_User_Manual/Network_Formats"
+ * >Cytoscape</a>.
+ */
+
+ SIF("SIF");
+
+ /**
+ * Default constructor.
+ *
+ * @param title
+ * {@link #title}
+ */
+ ExportFileType(final String title) {
+ this.title = title;
+ }
+
+ /**
+ * Human readable name of the format.
+ */
+ private String title;
+
+ /**
+ *
+ * @return {@link #title}
+ */
+ public String getTitle() {
+ return title;
+ }
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/data/package-info.java b/service/src/main/java/lcsb/mapviewer/services/utils/data/package-info.java
index d8cdc5721b..7f4ef6a31e 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/data/package-info.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/data/package-info.java
@@ -1,6 +1,6 @@
-/**
- * This package contains data structures used in
- * {@link lcsb.mapviewer.services.utils} package.
- */
-package lcsb.mapviewer.services.utils.data;
-
+/**
+ * This package contains data structures used in
+ * {@link lcsb.mapviewer.services.utils} package.
+ */
+package lcsb.mapviewer.services.utils.data;
+
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/package-info.java b/service/src/main/java/lcsb/mapviewer/services/utils/package-info.java
index b39665b0a5..7f289e56f9 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/package-info.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/package-info.java
@@ -1,5 +1,5 @@
-/**
- * This package contains some util classes used in service package.
- */
-package lcsb.mapviewer.services.utils;
-
+/**
+ * This package contains some util classes used in service package.
+ */
+package lcsb.mapviewer.services.utils;
+
diff --git a/service/src/test/java/lcsb/mapviewer/services/AllServicesTests.java b/service/src/test/java/lcsb/mapviewer/services/AllServicesTests.java
index 2936ac1fb2..fa417aad64 100644
--- a/service/src/test/java/lcsb/mapviewer/services/AllServicesTests.java
+++ b/service/src/test/java/lcsb/mapviewer/services/AllServicesTests.java
@@ -1,20 +1,20 @@
-package lcsb.mapviewer.services;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-import lcsb.mapviewer.services.impl.AllImplServiceTests;
-import lcsb.mapviewer.services.overlay.AllOverlayTests;
-import lcsb.mapviewer.services.search.AllSearchTests;
-import lcsb.mapviewer.services.utils.AllUtilsTests;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AllImplServiceTests.class, //
- AllOverlayTests.class, //
- AllSearchTests.class, //
- AllUtilsTests.class, //
-})
-public class AllServicesTests {
-
+package lcsb.mapviewer.services;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+import lcsb.mapviewer.services.impl.AllImplServiceTests;
+import lcsb.mapviewer.services.overlay.AllOverlayTests;
+import lcsb.mapviewer.services.search.AllSearchTests;
+import lcsb.mapviewer.services.utils.AllUtilsTests;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AllImplServiceTests.class, //
+ AllOverlayTests.class, //
+ AllSearchTests.class, //
+ AllUtilsTests.class, //
+})
+public class AllServicesTests {
+
};
\ No newline at end of file
diff --git a/service/src/test/java/lcsb/mapviewer/services/ServiceTestFunctions.java b/service/src/test/java/lcsb/mapviewer/services/ServiceTestFunctions.java
index d64f4d476f..28f4529955 100644
--- a/service/src/test/java/lcsb/mapviewer/services/ServiceTestFunctions.java
+++ b/service/src/test/java/lcsb/mapviewer/services/ServiceTestFunctions.java
@@ -1,427 +1,427 @@
-package lcsb.mapviewer.services;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.Reader;
-import java.io.StringReader;
-import java.io.StringWriter;
-import java.io.UnsupportedEncodingException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.transform.OutputKeys;
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerException;
-import javax.xml.transform.TransformerFactory;
-import javax.xml.transform.dom.DOMSource;
-import javax.xml.transform.stream.StreamResult;
-
-import org.apache.log4j.Logger;
-import org.apache.log4j.spi.LoggingEvent;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.runner.RunWith;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.security.crypto.password.PasswordEncoder;
-import org.springframework.test.annotation.Rollback;
-import org.springframework.test.context.ContextConfiguration;
-import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
-import org.springframework.transaction.annotation.Transactional;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-import org.xml.sax.InputSource;
-import org.xml.sax.SAXException;
-
-import lcsb.mapviewer.annotation.services.ChEMBLParser;
-import lcsb.mapviewer.annotation.services.DrugbankHTMLParser;
-import lcsb.mapviewer.annotation.services.ModelAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.BiocompendiumAnnotator;
-import lcsb.mapviewer.common.EventStorageLoggerAppender;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.persist.DbUtils;
-import lcsb.mapviewer.persist.dao.ConfigurationDao;
-import lcsb.mapviewer.persist.dao.ProjectDao;
-import lcsb.mapviewer.persist.dao.cache.CacheQueryDao;
-import lcsb.mapviewer.persist.dao.graphics.PolylineDao;
-import lcsb.mapviewer.persist.dao.log.LogDao;
-import lcsb.mapviewer.persist.dao.map.CommentDao;
-import lcsb.mapviewer.persist.dao.map.ModelDao;
-import lcsb.mapviewer.persist.dao.map.ReactionDao;
-import lcsb.mapviewer.persist.dao.map.species.ElementDao;
-import lcsb.mapviewer.persist.dao.map.statistics.SearchHistoryDao;
-import lcsb.mapviewer.persist.dao.user.PrivilegeDao;
-import lcsb.mapviewer.persist.dao.user.UserDao;
-import lcsb.mapviewer.services.interfaces.ICommentService;
-import lcsb.mapviewer.services.interfaces.IConfigurationService;
-import lcsb.mapviewer.services.interfaces.IExternalServicesService;
-import lcsb.mapviewer.services.interfaces.ILayoutService;
-import lcsb.mapviewer.services.interfaces.ILogService;
-import lcsb.mapviewer.services.interfaces.IModelService;
-import lcsb.mapviewer.services.interfaces.IProjectService;
-import lcsb.mapviewer.services.interfaces.ISearchService;
-import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.search.chemical.IChemicalService;
-import lcsb.mapviewer.services.search.drug.IDrugService;
-
-@Transactional(value = "txManager")
-@Rollback(false)
-@ContextConfiguration(locations = { "/applicationContext-annotation.xml", //
- "/applicationContext-persist.xml", //
- "/applicationContext-service.xml", //
- "/test-applicationContext.xml", //
- "/dataSource.xml", //
-})
-@RunWith(SpringJUnit4ClassRunner.class)
-public abstract class ServiceTestFunctions {
- private Logger logger = Logger.getLogger(ServiceTestFunctions.class);
-
- @Autowired
- protected ChEMBLParser chemblParser;
-
- @Autowired
- protected DrugbankHTMLParser drugBankHTMLParser;
-
- @Autowired
- protected ModelAnnotator modelAnnotator;
-
- @Autowired
- protected BiocompendiumAnnotator restService;
-
- public double EPSILON = 1e-6;
-
- @Autowired
- protected IConfigurationService configurationService;
-
- @Autowired
- protected IModelService modelService;
-
- @Autowired
- protected IExternalServicesService externalServicesService;
-
- @Autowired
- protected ILayoutService layoutService;
-
- @Autowired
- protected ILogService logService;
-
- @Autowired
- protected LogDao logDao;
-
- @Autowired
- protected SearchHistoryDao searchHistoryDao;
-
- @Autowired
- protected PasswordEncoder passwordEncoder;
-
- @Autowired
- protected IUserService userService;
-
- @Autowired
- protected ConfigurationDao configurationDao;
-
- @Autowired
- protected ISearchService searchService;
-
- @Autowired
- protected IDrugService drugService;
-
- @Autowired
- protected IChemicalService chemicalService;
-
- @Autowired
- protected IProjectService projectService;
-
- @Autowired
- protected ProjectDao projectDao;
-
- @Autowired
- protected CacheQueryDao cacheQueryDao;
-
- @Autowired
- protected PolylineDao polylineDao;
-
- @Autowired
- protected ModelDao modelDao;
-
- @Autowired
- protected ICommentService commentService;
-
- @Autowired
- protected UserDao userDao;
-
- @Autowired
- protected PrivilegeDao privilegeDao;
-
- @Autowired
- protected CommentDao commentDao;
-
- @Autowired
- protected DbUtils dbUtils;
-
- @Autowired
- protected ReactionDao reactionDao;
-
- @Autowired
- protected ElementDao aliasDao;
-
- protected User user;
- protected User user2 = null;
-
- private EventStorageLoggerAppender appender;
-
- @Before
- public final void _setUp() throws Exception {
- Logger.getRootLogger().removeAppender(appender);
- appender = new EventStorageLoggerAppender();
- Logger.getRootLogger().addAppender(appender);
- dbUtils.setAutoFlush(false);
- }
-
- @After
- public final void _tearDown() throws Exception {
- Logger.getRootLogger().removeAppender(appender);
- }
-
- protected List<LoggingEvent> getWarnings() {
- return appender.getWarnings();
- }
-
- protected String readFile(String file) throws IOException {
- StringBuilder stringBuilder = new StringBuilder();
- BufferedReader reader = new BufferedReader(new FileReader(file));
- try {
- String line = null;
- String ls = System.getProperty("line.separator");
-
- while ((line = reader.readLine()) != null) {
- stringBuilder.append(line);
- stringBuilder.append(ls);
- }
- } finally {
- reader.close();
- }
-
- return stringBuilder.toString();
- }
-
- protected Node getNodeFromXmlString(String text) throws InvalidXmlSchemaException {
- InputSource is = new InputSource();
- is.setCharacterStream(new StringReader(text));
- return getXmlDocumentFromInputSource(is).getChildNodes().item(0);
- }
-
- protected Document getXmlDocumentFromFile(String fileName) throws InvalidXmlSchemaException, IOException {
- File file = new File(fileName);
- InputStream inputStream = new FileInputStream(file);
- Reader reader = null;
- try {
- reader = new InputStreamReader(inputStream, "UTF-8");
- InputSource is = new InputSource(reader);
-
- Document result = getXmlDocumentFromInputSource(is);
- inputStream.close();
- return result;
- } catch (UnsupportedEncodingException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- return null;
- }
-
- protected Document getXmlDocumentFromInputSource(InputSource stream) throws InvalidXmlSchemaException {
- DocumentBuilder db;
- try {
- db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
- } catch (ParserConfigurationException e) {
- throw new InvalidXmlSchemaException("Problem with xml parser");
- }
- Document doc = null;
- try {
- doc = db.parse(stream);
- } catch (SAXException e) {
- logger.error(e);
- } catch (IOException e) {
- logger.error(e);
- }
- return doc;
- }
-
- /**
- * This method remove model with all connections from db (used only when the db
- * must be handled manually)
- *
- * @param id
- */
- protected void removeModelById(int id) {
- modelDao.delete(modelDao.getById(id));
- }
-
- protected void createUser() {
- user = userDao.getUserByLogin("john.doe");
- if (user != null) {
- logger.debug("remove user");
- userDao.delete(user);
- userDao.flush();
- }
- user = new User();
- user.setName("John");
- user.setSurname("Doe");
- user.setEmail("john.doe@uni.lu");
- user.setLogin("john.doe");
- user.setCryptedPassword(passwordEncoder.encode("passwd"));
- userDao.add(user);
- }
-
- protected void createUser2() {
- user2 = userDao.getUserByLogin("john.doe.bis");
- if (user2 != null) {
- userDao.delete(user2);
- }
- user2 = new User();
- user2.setName("John");
- user2.setSurname("Doe BIS");
- user2.setEmail("john.doe@uni.lux");
- user2.setLogin("john.doe.bis");
- user2.setCryptedPassword(passwordEncoder.encode("passwd"));
- userDao.add(user2);
- }
-
- private static Map<String, Model> models = new HashMap<String, Model>();
-
- protected Model getModelForFile(String fileName, boolean fromCache) throws Exception {
- if (!fromCache) {
- logger.debug("File without cache: " + fileName);
- return new CellDesignerXmlParser().createModel(new ConverterParams().filename(fileName));
- }
- Model result = ServiceTestFunctions.models.get(fileName);
- if (result == null) {
- logger.debug("File to cache: " + fileName);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- result = parser.createModel(new ConverterParams().filename(fileName).sizeAutoAdjust(false));
- ServiceTestFunctions.models.put(fileName, result);
- }
- return result;
- }
-
- protected String createTmpFileName() {
- try {
- File f = File.createTempFile("prefix", ".txt");
- String filename = f.getName();
- f.delete();
- return filename;
- } catch (IOException e) {
- e.printStackTrace();
- return null;
- }
- }
-
- protected String nodeToString(Node node) {
- return nodeToString(node, false);
- }
-
- protected String nodeToString(Node node, boolean includeHeadNode) {
- if (node == null)
- return null;
- StringWriter sw = new StringWriter();
- try {
- Transformer t = TransformerFactory.newInstance().newTransformer();
- t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
- t.setOutputProperty(OutputKeys.INDENT, "yes");
- t.setOutputProperty(OutputKeys.METHOD, "xml");
-
- NodeList list = node.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node element = list.item(i);
- t.transform(new DOMSource(element), new StreamResult(sw));
- }
- } catch (TransformerException te) {
- logger.debug("nodeToString Transformer Exception");
- }
- if (includeHeadNode) {
- return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
- }
- return sw.toString();
- }
-
- protected boolean equalFiles(String fileA, String fileB) throws IOException {
- int BLOCK_SIZE = 65536;
- FileInputStream inputStreamA = new FileInputStream(fileA);
- FileInputStream inputStreamB = new FileInputStream(fileB);
- // vary BLOCK_SIZE to suit yourself.
- // it should probably a factor or multiple of the size of a disk
- // sector/cluster.
- // Note that your max heap size may need to be adjused
- // if you have a very big block size or lots of these comparators.
-
- // assume inputStreamA and inputStreamB are streams from your two files.
- byte[] streamABlock = new byte[BLOCK_SIZE];
- byte[] streamBBlock = new byte[BLOCK_SIZE];
- boolean match = true;
- int bytesReadA = 0;
- int bytesReadB = 0;
- do {
- bytesReadA = inputStreamA.read(streamABlock);
- bytesReadB = inputStreamB.read(streamBBlock);
- match = ((bytesReadA == bytesReadB) && Arrays.equals(streamABlock, streamBBlock));
- } while (match && (bytesReadA > -1));
- inputStreamA.close();
- inputStreamB.close();
- return match;
- }
-
- public PrivilegeDao getPrivilegeDao() {
- return privilegeDao;
- }
-
- public void setPrivilegeDao(PrivilegeDao privilegeDao) {
- this.privilegeDao = privilegeDao;
- }
-
- public File createTempDirectory() throws IOException {
- final File temp;
-
- temp = File.createTempFile("temp", Long.toString(System.nanoTime()));
-
- if (!(temp.delete())) {
- throw new IOException("Could not delete temp file: " + temp.getAbsolutePath());
- }
-
- if (!(temp.mkdir())) {
- throw new IOException("Could not create temp directory: " + temp.getAbsolutePath());
- }
-
- return (temp);
- }
-
- protected String getWebpage(String accessUrl) throws IOException {
- String inputLine;
- StringBuilder tmp = new StringBuilder();
- URL url = new URL(accessUrl);
- URLConnection urlConn = url.openConnection();
- BufferedReader in = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));
-
- while ((inputLine = in.readLine()) != null) {
- tmp.append(inputLine);
- }
- in.close();
- return tmp.toString();
- }
-}
+package lcsb.mapviewer.services;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.io.StringReader;
+import java.io.StringWriter;
+import java.io.UnsupportedEncodingException;
+import java.net.URL;
+import java.net.URLConnection;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.OutputKeys;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerException;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.dom.DOMSource;
+import javax.xml.transform.stream.StreamResult;
+
+import org.apache.log4j.Logger;
+import org.apache.log4j.spi.LoggingEvent;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.runner.RunWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.security.crypto.password.PasswordEncoder;
+import org.springframework.test.annotation.Rollback;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
+import org.springframework.transaction.annotation.Transactional;
+import org.w3c.dom.Document;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+
+import lcsb.mapviewer.annotation.services.ChEMBLParser;
+import lcsb.mapviewer.annotation.services.DrugbankHTMLParser;
+import lcsb.mapviewer.annotation.services.ModelAnnotator;
+import lcsb.mapviewer.annotation.services.annotators.BiocompendiumAnnotator;
+import lcsb.mapviewer.common.EventStorageLoggerAppender;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.persist.DbUtils;
+import lcsb.mapviewer.persist.dao.ConfigurationDao;
+import lcsb.mapviewer.persist.dao.ProjectDao;
+import lcsb.mapviewer.persist.dao.cache.CacheQueryDao;
+import lcsb.mapviewer.persist.dao.graphics.PolylineDao;
+import lcsb.mapviewer.persist.dao.log.LogDao;
+import lcsb.mapviewer.persist.dao.map.CommentDao;
+import lcsb.mapviewer.persist.dao.map.ModelDao;
+import lcsb.mapviewer.persist.dao.map.ReactionDao;
+import lcsb.mapviewer.persist.dao.map.species.ElementDao;
+import lcsb.mapviewer.persist.dao.map.statistics.SearchHistoryDao;
+import lcsb.mapviewer.persist.dao.user.PrivilegeDao;
+import lcsb.mapviewer.persist.dao.user.UserDao;
+import lcsb.mapviewer.services.interfaces.ICommentService;
+import lcsb.mapviewer.services.interfaces.IConfigurationService;
+import lcsb.mapviewer.services.interfaces.IExternalServicesService;
+import lcsb.mapviewer.services.interfaces.ILayoutService;
+import lcsb.mapviewer.services.interfaces.ILogService;
+import lcsb.mapviewer.services.interfaces.IModelService;
+import lcsb.mapviewer.services.interfaces.IProjectService;
+import lcsb.mapviewer.services.interfaces.ISearchService;
+import lcsb.mapviewer.services.interfaces.IUserService;
+import lcsb.mapviewer.services.search.chemical.IChemicalService;
+import lcsb.mapviewer.services.search.drug.IDrugService;
+
+@Transactional(value = "txManager")
+@Rollback(false)
+@ContextConfiguration(locations = { "/applicationContext-annotation.xml", //
+ "/applicationContext-persist.xml", //
+ "/applicationContext-service.xml", //
+ "/test-applicationContext.xml", //
+ "/dataSource.xml", //
+})
+@RunWith(SpringJUnit4ClassRunner.class)
+public abstract class ServiceTestFunctions {
+ private Logger logger = Logger.getLogger(ServiceTestFunctions.class);
+
+ @Autowired
+ protected ChEMBLParser chemblParser;
+
+ @Autowired
+ protected DrugbankHTMLParser drugBankHTMLParser;
+
+ @Autowired
+ protected ModelAnnotator modelAnnotator;
+
+ @Autowired
+ protected BiocompendiumAnnotator restService;
+
+ public double EPSILON = 1e-6;
+
+ @Autowired
+ protected IConfigurationService configurationService;
+
+ @Autowired
+ protected IModelService modelService;
+
+ @Autowired
+ protected IExternalServicesService externalServicesService;
+
+ @Autowired
+ protected ILayoutService layoutService;
+
+ @Autowired
+ protected ILogService logService;
+
+ @Autowired
+ protected LogDao logDao;
+
+ @Autowired
+ protected SearchHistoryDao searchHistoryDao;
+
+ @Autowired
+ protected PasswordEncoder passwordEncoder;
+
+ @Autowired
+ protected IUserService userService;
+
+ @Autowired
+ protected ConfigurationDao configurationDao;
+
+ @Autowired
+ protected ISearchService searchService;
+
+ @Autowired
+ protected IDrugService drugService;
+
+ @Autowired
+ protected IChemicalService chemicalService;
+
+ @Autowired
+ protected IProjectService projectService;
+
+ @Autowired
+ protected ProjectDao projectDao;
+
+ @Autowired
+ protected CacheQueryDao cacheQueryDao;
+
+ @Autowired
+ protected PolylineDao polylineDao;
+
+ @Autowired
+ protected ModelDao modelDao;
+
+ @Autowired
+ protected ICommentService commentService;
+
+ @Autowired
+ protected UserDao userDao;
+
+ @Autowired
+ protected PrivilegeDao privilegeDao;
+
+ @Autowired
+ protected CommentDao commentDao;
+
+ @Autowired
+ protected DbUtils dbUtils;
+
+ @Autowired
+ protected ReactionDao reactionDao;
+
+ @Autowired
+ protected ElementDao aliasDao;
+
+ protected User user;
+ protected User user2 = null;
+
+ private EventStorageLoggerAppender appender;
+
+ @Before
+ public final void _setUp() throws Exception {
+ Logger.getRootLogger().removeAppender(appender);
+ appender = new EventStorageLoggerAppender();
+ Logger.getRootLogger().addAppender(appender);
+ dbUtils.setAutoFlush(false);
+ }
+
+ @After
+ public final void _tearDown() throws Exception {
+ Logger.getRootLogger().removeAppender(appender);
+ }
+
+ protected List<LoggingEvent> getWarnings() {
+ return appender.getWarnings();
+ }
+
+ protected String readFile(String file) throws IOException {
+ StringBuilder stringBuilder = new StringBuilder();
+ BufferedReader reader = new BufferedReader(new FileReader(file));
+ try {
+ String line = null;
+ String ls = System.getProperty("line.separator");
+
+ while ((line = reader.readLine()) != null) {
+ stringBuilder.append(line);
+ stringBuilder.append(ls);
+ }
+ } finally {
+ reader.close();
+ }
+
+ return stringBuilder.toString();
+ }
+
+ protected Node getNodeFromXmlString(String text) throws InvalidXmlSchemaException {
+ InputSource is = new InputSource();
+ is.setCharacterStream(new StringReader(text));
+ return getXmlDocumentFromInputSource(is).getChildNodes().item(0);
+ }
+
+ protected Document getXmlDocumentFromFile(String fileName) throws InvalidXmlSchemaException, IOException {
+ File file = new File(fileName);
+ InputStream inputStream = new FileInputStream(file);
+ Reader reader = null;
+ try {
+ reader = new InputStreamReader(inputStream, "UTF-8");
+ InputSource is = new InputSource(reader);
+
+ Document result = getXmlDocumentFromInputSource(is);
+ inputStream.close();
+ return result;
+ } catch (UnsupportedEncodingException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ return null;
+ }
+
+ protected Document getXmlDocumentFromInputSource(InputSource stream) throws InvalidXmlSchemaException {
+ DocumentBuilder db;
+ try {
+ db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
+ } catch (ParserConfigurationException e) {
+ throw new InvalidXmlSchemaException("Problem with xml parser");
+ }
+ Document doc = null;
+ try {
+ doc = db.parse(stream);
+ } catch (SAXException e) {
+ logger.error(e);
+ } catch (IOException e) {
+ logger.error(e);
+ }
+ return doc;
+ }
+
+ /**
+ * This method remove model with all connections from db (used only when the db
+ * must be handled manually)
+ *
+ * @param id
+ */
+ protected void removeModelById(int id) {
+ modelDao.delete(modelDao.getById(id));
+ }
+
+ protected void createUser() {
+ user = userDao.getUserByLogin("john.doe");
+ if (user != null) {
+ logger.debug("remove user");
+ userDao.delete(user);
+ userDao.flush();
+ }
+ user = new User();
+ user.setName("John");
+ user.setSurname("Doe");
+ user.setEmail("john.doe@uni.lu");
+ user.setLogin("john.doe");
+ user.setCryptedPassword(passwordEncoder.encode("passwd"));
+ userDao.add(user);
+ }
+
+ protected void createUser2() {
+ user2 = userDao.getUserByLogin("john.doe.bis");
+ if (user2 != null) {
+ userDao.delete(user2);
+ }
+ user2 = new User();
+ user2.setName("John");
+ user2.setSurname("Doe BIS");
+ user2.setEmail("john.doe@uni.lux");
+ user2.setLogin("john.doe.bis");
+ user2.setCryptedPassword(passwordEncoder.encode("passwd"));
+ userDao.add(user2);
+ }
+
+ private static Map<String, Model> models = new HashMap<String, Model>();
+
+ protected Model getModelForFile(String fileName, boolean fromCache) throws Exception {
+ if (!fromCache) {
+ logger.debug("File without cache: " + fileName);
+ return new CellDesignerXmlParser().createModel(new ConverterParams().filename(fileName));
+ }
+ Model result = ServiceTestFunctions.models.get(fileName);
+ if (result == null) {
+ logger.debug("File to cache: " + fileName);
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ result = parser.createModel(new ConverterParams().filename(fileName).sizeAutoAdjust(false));
+ ServiceTestFunctions.models.put(fileName, result);
+ }
+ return result;
+ }
+
+ protected String createTmpFileName() {
+ try {
+ File f = File.createTempFile("prefix", ".txt");
+ String filename = f.getName();
+ f.delete();
+ return filename;
+ } catch (IOException e) {
+ e.printStackTrace();
+ return null;
+ }
+ }
+
+ protected String nodeToString(Node node) {
+ return nodeToString(node, false);
+ }
+
+ protected String nodeToString(Node node, boolean includeHeadNode) {
+ if (node == null)
+ return null;
+ StringWriter sw = new StringWriter();
+ try {
+ Transformer t = TransformerFactory.newInstance().newTransformer();
+ t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
+ t.setOutputProperty(OutputKeys.INDENT, "yes");
+ t.setOutputProperty(OutputKeys.METHOD, "xml");
+
+ NodeList list = node.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node element = list.item(i);
+ t.transform(new DOMSource(element), new StreamResult(sw));
+ }
+ } catch (TransformerException te) {
+ logger.debug("nodeToString Transformer Exception");
+ }
+ if (includeHeadNode) {
+ return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
+ }
+ return sw.toString();
+ }
+
+ protected boolean equalFiles(String fileA, String fileB) throws IOException {
+ int BLOCK_SIZE = 65536;
+ FileInputStream inputStreamA = new FileInputStream(fileA);
+ FileInputStream inputStreamB = new FileInputStream(fileB);
+ // vary BLOCK_SIZE to suit yourself.
+ // it should probably a factor or multiple of the size of a disk
+ // sector/cluster.
+ // Note that your max heap size may need to be adjused
+ // if you have a very big block size or lots of these comparators.
+
+ // assume inputStreamA and inputStreamB are streams from your two files.
+ byte[] streamABlock = new byte[BLOCK_SIZE];
+ byte[] streamBBlock = new byte[BLOCK_SIZE];
+ boolean match = true;
+ int bytesReadA = 0;
+ int bytesReadB = 0;
+ do {
+ bytesReadA = inputStreamA.read(streamABlock);
+ bytesReadB = inputStreamB.read(streamBBlock);
+ match = ((bytesReadA == bytesReadB) && Arrays.equals(streamABlock, streamBBlock));
+ } while (match && (bytesReadA > -1));
+ inputStreamA.close();
+ inputStreamB.close();
+ return match;
+ }
+
+ public PrivilegeDao getPrivilegeDao() {
+ return privilegeDao;
+ }
+
+ public void setPrivilegeDao(PrivilegeDao privilegeDao) {
+ this.privilegeDao = privilegeDao;
+ }
+
+ public File createTempDirectory() throws IOException {
+ final File temp;
+
+ temp = File.createTempFile("temp", Long.toString(System.nanoTime()));
+
+ if (!(temp.delete())) {
+ throw new IOException("Could not delete temp file: " + temp.getAbsolutePath());
+ }
+
+ if (!(temp.mkdir())) {
+ throw new IOException("Could not create temp directory: " + temp.getAbsolutePath());
+ }
+
+ return (temp);
+ }
+
+ protected String getWebpage(String accessUrl) throws IOException {
+ String inputLine;
+ StringBuilder tmp = new StringBuilder();
+ URL url = new URL(accessUrl);
+ URLConnection urlConn = url.openConnection();
+ BufferedReader in = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));
+
+ while ((inputLine = in.readLine()) != null) {
+ tmp.append(inputLine);
+ }
+ in.close();
+ return tmp.toString();
+ }
+}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/AllImplServiceTests.java b/service/src/test/java/lcsb/mapviewer/services/impl/AllImplServiceTests.java
index 3a5bb0badd..383ad23d91 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/AllImplServiceTests.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/AllImplServiceTests.java
@@ -1,20 +1,20 @@
-package lcsb.mapviewer.services.impl;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ CommentServiceTest.class, //
- ConfigurationServiceTest.class, //
- ExternalServicesServiceTest.class, //
- LayoutServiceTest.class, //
- LdapServiceTest.class, //
- Md5PasswordEncoderTest.class, //
- ProjectServiceTest.class, //
- SearchServiceTest.class, //
- UserServiceTest.class,//
-})
-public class AllImplServiceTests {
-
-}
+package lcsb.mapviewer.services.impl;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ CommentServiceTest.class, //
+ ConfigurationServiceTest.class, //
+ ExternalServicesServiceTest.class, //
+ LayoutServiceTest.class, //
+ LdapServiceTest.class, //
+ Md5PasswordEncoderTest.class, //
+ ProjectServiceTest.class, //
+ SearchServiceTest.class, //
+ UserServiceTest.class,//
+})
+public class AllImplServiceTests {
+
+}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/CommentServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/CommentServiceTest.java
index 673ade770f..5525c6d0eb 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/CommentServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/CommentServiceTest.java
@@ -1,190 +1,190 @@
-package lcsb.mapviewer.services.impl;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.geom.Point2D;
-import java.util.List;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.test.annotation.Rollback;
-
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.Comment;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.services.ServiceTestFunctions;
-
-@Rollback(true)
-public class CommentServiceTest extends ServiceTestFunctions {
- static Logger logger = Logger.getLogger(CommentServiceTest.class);
- Model model;
- Project project;
- Element alias;
- Element alias2;
- private String projectId = "Some_id";
-
- @Before
- public void setUp() throws Exception {
- try {
- dbUtils.setAutoFlush(true);
- project = projectDao.getProjectByProjectId(projectId);
- if (project != null) {
- projectDao.delete(project);
- }
- project = new Project();
- project.setProjectId(projectId);
- model = getModelForFile("testFiles/centeredAnchorInModifier.xml", false);
- model.setTileSize(128);
- Set<Element> aliases = model.getElements();
- alias = null;
- alias2 = null;
- for (Element nAlias : aliases) {
- alias2 = alias;
- alias = nAlias;
- }
- project.addModel(model);
- projectDao.add(project);
-
- projectDao.evict(project);
- modelDao.evict(model);
-
- project = projectDao.getById(project.getId());
- model = new ModelFullIndexed(modelDao.getLastModelForProjectIdentifier(project.getProjectId(), false));
- } catch (Exception e) {
- e.printStackTrace();
- }
- }
-
- @After
- public void tearDown() throws Exception {
- try {
- projectDao.delete(project);
- } catch (Exception e) {
- e.printStackTrace();
- }
- }
-
- @Test
- public void testGetAgregatedComments() throws Exception {
- try {
- commentService.addComment("John Doe", "a@a.pl", "Conteneta 1", model, new Point2D.Double(0, 1), alias, false,
- model);
- commentService.addComment("John Doe", "a@a.pl", "Contenetb 2", model, new Point2D.Double(0, 2), alias, false,
- model);
- commentService.addComment("John Doe", "a@a.pl", "Contenetc 3", model, new Point2D.Double(0, 3), alias2, false,
- model);
- commentService.addComment("John Doe", "a@a.pl", "Contenetc 4", model, new Point2D.Double(0, 4), null, false,
- model);
- commentService.addComment("John Doe", "a@a.pl", "Contenetc 5", model, new Point2D.Double(0, 5), null, false,
- model);
- CommentService service = new CommentService();
- service.setCommentDao(commentDao);
- List<List<Comment>> comments = service.getAgregatedComments(model, null);
- assertEquals(4, comments.size());
- int size = 0;
- for (List<Comment> list : comments) {
- size += list.size();
- }
- assertEquals(5, size);
-
- List<Comment> allComments = commentDao.getCommentByModel(model, null, null);
- assertEquals(5, allComments.size());
- for (Comment comment : allComments) {
- commentDao.delete(comment);
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddComment() throws Exception {
- try {
-
- long counter = commentService.getCommentCount();
- Comment feedback = commentService.addComment("a", "b", "c", model, new Point2D.Double(0, 0), null, false, model);
- long counter2 = commentService.getCommentCount();
- assertEquals(counter + 1, counter2);
- commentDao.delete(feedback);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddCommentForReaction() throws Exception {
- try {
-
- long counter = commentService.getCommentCount();
- Comment feedback = commentService.addComment("a", "b", "c", model, new Point2D.Double(0, 0),
- model.getReactions().iterator().next(), false, model);
- long counter2 = commentService.getCommentCount();
- assertEquals(counter + 1, counter2);
- commentDao.delete(feedback);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddCommentForAlias() throws Exception {
- try {
- Element alias = model.getElementByElementId("sa1");
- long counter = commentService.getCommentCount();
- Comment feedback = commentService.addComment("a", "b", "c", model, new Point2D.Double(0, 0), alias, false, model);
- long counter2 = commentService.getCommentCount();
- assertEquals(counter + 1, counter2);
- commentDao.delete(feedback);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testComparePointCommentId() throws Exception {
- try {
- CommentService cs = new CommentService();
- assertTrue(cs.equalPoints("Point2D.Double[117.685546875, 204.6923828125001]", "(117.69, 204.69)"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testComparePointCommentId2() throws Exception {
- try {
- CommentService cs = new CommentService();
- assertFalse(cs.equalPoints("Point2D.Double[118.685546875, 204.6923828125001]", "(117.69, 204.69)"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testComparePointCommentId3() throws Exception {
- try {
- CommentService cs = new CommentService();
- assertFalse(cs.equalPoints("Point2D.Double[117.685546875, 205.6923828125001]", "(117.69, 204.69)"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.services.impl;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import java.awt.geom.Point2D;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.test.annotation.Rollback;
+
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.Comment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.services.ServiceTestFunctions;
+
+@Rollback(true)
+public class CommentServiceTest extends ServiceTestFunctions {
+ static Logger logger = Logger.getLogger(CommentServiceTest.class);
+ Model model;
+ Project project;
+ Element alias;
+ Element alias2;
+ private String projectId = "Some_id";
+
+ @Before
+ public void setUp() throws Exception {
+ try {
+ dbUtils.setAutoFlush(true);
+ project = projectDao.getProjectByProjectId(projectId);
+ if (project != null) {
+ projectDao.delete(project);
+ }
+ project = new Project();
+ project.setProjectId(projectId);
+ model = getModelForFile("testFiles/centeredAnchorInModifier.xml", false);
+ model.setTileSize(128);
+ Set<Element> aliases = model.getElements();
+ alias = null;
+ alias2 = null;
+ for (Element nAlias : aliases) {
+ alias2 = alias;
+ alias = nAlias;
+ }
+ project.addModel(model);
+ projectDao.add(project);
+
+ projectDao.evict(project);
+ modelDao.evict(model);
+
+ project = projectDao.getById(project.getId());
+ model = new ModelFullIndexed(modelDao.getLastModelForProjectIdentifier(project.getProjectId(), false));
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ try {
+ projectDao.delete(project);
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+
+ @Test
+ public void testGetAgregatedComments() throws Exception {
+ try {
+ commentService.addComment("John Doe", "a@a.pl", "Conteneta 1", model, new Point2D.Double(0, 1), alias, false,
+ model);
+ commentService.addComment("John Doe", "a@a.pl", "Contenetb 2", model, new Point2D.Double(0, 2), alias, false,
+ model);
+ commentService.addComment("John Doe", "a@a.pl", "Contenetc 3", model, new Point2D.Double(0, 3), alias2, false,
+ model);
+ commentService.addComment("John Doe", "a@a.pl", "Contenetc 4", model, new Point2D.Double(0, 4), null, false,
+ model);
+ commentService.addComment("John Doe", "a@a.pl", "Contenetc 5", model, new Point2D.Double(0, 5), null, false,
+ model);
+ CommentService service = new CommentService();
+ service.setCommentDao(commentDao);
+ List<List<Comment>> comments = service.getAgregatedComments(model, null);
+ assertEquals(4, comments.size());
+ int size = 0;
+ for (List<Comment> list : comments) {
+ size += list.size();
+ }
+ assertEquals(5, size);
+
+ List<Comment> allComments = commentDao.getCommentByModel(model, null, null);
+ assertEquals(5, allComments.size());
+ for (Comment comment : allComments) {
+ commentDao.delete(comment);
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddComment() throws Exception {
+ try {
+
+ long counter = commentService.getCommentCount();
+ Comment feedback = commentService.addComment("a", "b", "c", model, new Point2D.Double(0, 0), null, false, model);
+ long counter2 = commentService.getCommentCount();
+ assertEquals(counter + 1, counter2);
+ commentDao.delete(feedback);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddCommentForReaction() throws Exception {
+ try {
+
+ long counter = commentService.getCommentCount();
+ Comment feedback = commentService.addComment("a", "b", "c", model, new Point2D.Double(0, 0),
+ model.getReactions().iterator().next(), false, model);
+ long counter2 = commentService.getCommentCount();
+ assertEquals(counter + 1, counter2);
+ commentDao.delete(feedback);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddCommentForAlias() throws Exception {
+ try {
+ Element alias = model.getElementByElementId("sa1");
+ long counter = commentService.getCommentCount();
+ Comment feedback = commentService.addComment("a", "b", "c", model, new Point2D.Double(0, 0), alias, false, model);
+ long counter2 = commentService.getCommentCount();
+ assertEquals(counter + 1, counter2);
+ commentDao.delete(feedback);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testComparePointCommentId() throws Exception {
+ try {
+ CommentService cs = new CommentService();
+ assertTrue(cs.equalPoints("Point2D.Double[117.685546875, 204.6923828125001]", "(117.69, 204.69)"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testComparePointCommentId2() throws Exception {
+ try {
+ CommentService cs = new CommentService();
+ assertFalse(cs.equalPoints("Point2D.Double[118.685546875, 204.6923828125001]", "(117.69, 204.69)"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testComparePointCommentId3() throws Exception {
+ try {
+ CommentService cs = new CommentService();
+ assertFalse(cs.equalPoints("Point2D.Double[117.685546875, 205.6923828125001]", "(117.69, 204.69)"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/ConfigurationServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/ConfigurationServiceTest.java
index fb692fb1d3..d23a2bebc3 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ConfigurationServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ConfigurationServiceTest.java
@@ -1,140 +1,140 @@
-package lcsb.mapviewer.services.impl;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.test.annotation.Rollback;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.FrameworkVersion;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.user.ConfigurationElementType;
-import lcsb.mapviewer.model.user.ConfigurationOption;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.services.ServiceTestFunctions;
-
-@Rollback(true)
-public class ConfigurationServiceTest extends ServiceTestFunctions {
- Logger logger = Logger.getLogger(ConfigurationServiceTest.class);
-
- @Before
- public void setUp() throws Exception {
- // clear information about git version
- Configuration.getSystemBuildVersion(null, true);
- }
-
- @After
- public void tearDown() throws Exception {
- // clear information about git version
- Configuration.getSystemBuildVersion(null, true);
- }
-
- @Test
- public void testGetUpdate() throws Exception {
- try {
- String address = configurationService.getConfigurationValue(ConfigurationElementType.EMAIL_ADDRESS);
- configurationService.deleteConfigurationValue(ConfigurationElementType.EMAIL_ADDRESS);
- String newAddress = configurationService.getConfigurationValue(ConfigurationElementType.EMAIL_ADDRESS);
- assertEquals(ConfigurationElementType.EMAIL_ADDRESS.getDefaultValue(), newAddress);
- configurationService.setConfigurationValue(ConfigurationElementType.EMAIL_ADDRESS, "hello@world");
- newAddress = configurationService.getConfigurationValue(ConfigurationElementType.EMAIL_ADDRESS);
- assertEquals("hello@world", newAddress);
-
- configurationService.setConfigurationValue(ConfigurationElementType.EMAIL_ADDRESS, address);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testList() throws Exception {
- try {
- List<ConfigurationOption> list = configurationService.getAllValues(true);
- assertEquals(ConfigurationElementType.values().length, list.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testLimitedList() throws Exception {
- try {
- List<ConfigurationOption> list = configurationService.getAllValues(false);
- assertTrue(ConfigurationElementType.values().length > list.size());
- assertTrue(list.size() > 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetSystemVersion() throws Exception {
- try {
- FrameworkVersion view = configurationService.getSystemVersion("testFiles/gitVersionTest/testNormal/");
- assertNotNull(view);
- assertEquals("100", view.getGitVersion());
- assertEquals("202", view.getVersion());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetSystemVersion2() throws Exception {
- try {
- FrameworkVersion view = configurationService.getSystemVersion("testFiles/gitVersionTest/testModified/");
- assertNotNull(view);
- assertEquals("100:105", view.getGitVersion());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetSystemVersion3() throws Exception {
- try {
- FrameworkVersion view = configurationService.getSystemVersion("testFiles/gitVersionTest/testCorrectSvn/");
- assertNotNull(view);
- assertEquals("117", view.getGitVersion());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetConfiguratioElemntForPrivilege() throws Exception {
- try {
- for (PrivilegeType type : PrivilegeType.values()) {
- ConfigurationOption value = configurationService.getValue(type);
- if (Project.class.equals(type.getPrivilegeObjectType())) {
- assertNotNull("No default value for privilege " + type.getCommonName(), value);
- assertNotNull(value.getValue());
- } else {
- assertNull(value);
- }
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.services.impl;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.test.annotation.Rollback;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.FrameworkVersion;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.user.ConfigurationElementType;
+import lcsb.mapviewer.model.user.ConfigurationOption;
+import lcsb.mapviewer.model.user.PrivilegeType;
+import lcsb.mapviewer.services.ServiceTestFunctions;
+
+@Rollback(true)
+public class ConfigurationServiceTest extends ServiceTestFunctions {
+ Logger logger = Logger.getLogger(ConfigurationServiceTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ // clear information about git version
+ Configuration.getSystemBuildVersion(null, true);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ // clear information about git version
+ Configuration.getSystemBuildVersion(null, true);
+ }
+
+ @Test
+ public void testGetUpdate() throws Exception {
+ try {
+ String address = configurationService.getConfigurationValue(ConfigurationElementType.EMAIL_ADDRESS);
+ configurationService.deleteConfigurationValue(ConfigurationElementType.EMAIL_ADDRESS);
+ String newAddress = configurationService.getConfigurationValue(ConfigurationElementType.EMAIL_ADDRESS);
+ assertEquals(ConfigurationElementType.EMAIL_ADDRESS.getDefaultValue(), newAddress);
+ configurationService.setConfigurationValue(ConfigurationElementType.EMAIL_ADDRESS, "hello@world");
+ newAddress = configurationService.getConfigurationValue(ConfigurationElementType.EMAIL_ADDRESS);
+ assertEquals("hello@world", newAddress);
+
+ configurationService.setConfigurationValue(ConfigurationElementType.EMAIL_ADDRESS, address);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testList() throws Exception {
+ try {
+ List<ConfigurationOption> list = configurationService.getAllValues(true);
+ assertEquals(ConfigurationElementType.values().length, list.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testLimitedList() throws Exception {
+ try {
+ List<ConfigurationOption> list = configurationService.getAllValues(false);
+ assertTrue(ConfigurationElementType.values().length > list.size());
+ assertTrue(list.size() > 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetSystemVersion() throws Exception {
+ try {
+ FrameworkVersion view = configurationService.getSystemVersion("testFiles/gitVersionTest/testNormal/");
+ assertNotNull(view);
+ assertEquals("100", view.getGitVersion());
+ assertEquals("202", view.getVersion());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetSystemVersion2() throws Exception {
+ try {
+ FrameworkVersion view = configurationService.getSystemVersion("testFiles/gitVersionTest/testModified/");
+ assertNotNull(view);
+ assertEquals("100:105", view.getGitVersion());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetSystemVersion3() throws Exception {
+ try {
+ FrameworkVersion view = configurationService.getSystemVersion("testFiles/gitVersionTest/testCorrectSvn/");
+ assertNotNull(view);
+ assertEquals("117", view.getGitVersion());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetConfiguratioElemntForPrivilege() throws Exception {
+ try {
+ for (PrivilegeType type : PrivilegeType.values()) {
+ ConfigurationOption value = configurationService.getValue(type);
+ if (Project.class.equals(type.getPrivilegeObjectType())) {
+ assertNotNull("No default value for privilege " + type.getCommonName(), value);
+ assertNotNull(value.getValue());
+ } else {
+ assertNull(value);
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/ExternalServicesServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/ExternalServicesServiceTest.java
index 66041bf94d..8b1db0dd70 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ExternalServicesServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ExternalServicesServiceTest.java
@@ -1,67 +1,67 @@
-package lcsb.mapviewer.services.impl;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.util.List;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Ignore;
-import org.junit.Test;
-
-import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
-import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
-import lcsb.mapviewer.services.ServiceTestFunctions;
-
-public class ExternalServicesServiceTest extends ServiceTestFunctions {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test(timeout = 60000)
- @Ignore("Bug 451")
- public void testDefaultServices() throws Exception {
- try {
- externalServicesService.clearServices();
- externalServicesService.registerDefaultServices();
- List<ExternalServiceStatus> statuses = externalServicesService.getExternalServiceStatuses();
- assertNotNull(statuses);
- assertTrue(statuses.size() > 0);
-
- for (ExternalServiceStatus externalServiceStatus : statuses) {
- assertEquals(externalServiceStatus.getName() + " is down", ExternalServiceStatusType.OK, externalServiceStatus.getStatus());
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRegister() throws Exception {
- try {
- externalServicesService.clearServices();
- externalServicesService.registerService(new OkServiceMock());
- externalServicesService.registerService(new FailServiceMock());
-
- List<ExternalServiceStatus> statuses = externalServicesService.getExternalServiceStatuses();
- assertNotNull(statuses);
- assertEquals(2, statuses.size());
-
- assertEquals(ExternalServiceStatusType.OK, statuses.get(0).getStatus());
- assertEquals(ExternalServiceStatusType.DOWN, statuses.get(1).getStatus());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.services.impl;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import java.util.List;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Ignore;
+import org.junit.Test;
+
+import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
+import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
+import lcsb.mapviewer.services.ServiceTestFunctions;
+
+public class ExternalServicesServiceTest extends ServiceTestFunctions {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test(timeout = 60000)
+ @Ignore("Bug 451")
+ public void testDefaultServices() throws Exception {
+ try {
+ externalServicesService.clearServices();
+ externalServicesService.registerDefaultServices();
+ List<ExternalServiceStatus> statuses = externalServicesService.getExternalServiceStatuses();
+ assertNotNull(statuses);
+ assertTrue(statuses.size() > 0);
+
+ for (ExternalServiceStatus externalServiceStatus : statuses) {
+ assertEquals(externalServiceStatus.getName() + " is down", ExternalServiceStatusType.OK, externalServiceStatus.getStatus());
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRegister() throws Exception {
+ try {
+ externalServicesService.clearServices();
+ externalServicesService.registerService(new OkServiceMock());
+ externalServicesService.registerService(new FailServiceMock());
+
+ List<ExternalServiceStatus> statuses = externalServicesService.getExternalServiceStatuses();
+ assertNotNull(statuses);
+ assertEquals(2, statuses.size());
+
+ assertEquals(ExternalServiceStatusType.OK, statuses.get(0).getStatus());
+ assertEquals(ExternalServiceStatusType.DOWN, statuses.get(1).getStatus());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/FailServiceMock.java b/service/src/test/java/lcsb/mapviewer/services/impl/FailServiceMock.java
index b147987259..c7a4866c06 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/FailServiceMock.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/FailServiceMock.java
@@ -1,16 +1,16 @@
-package lcsb.mapviewer.services.impl;
-
-import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
-import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
-import lcsb.mapviewer.annotation.services.IExternalService;
-
-public class FailServiceMock implements IExternalService {
-
- @Override
- public ExternalServiceStatus getServiceStatus() {
- ExternalServiceStatus status = new ExternalServiceStatus("Test service", "unknown");
- status.setStatus(ExternalServiceStatusType.DOWN);
- return status;
- }
-
-}
+package lcsb.mapviewer.services.impl;
+
+import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
+import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
+import lcsb.mapviewer.annotation.services.IExternalService;
+
+public class FailServiceMock implements IExternalService {
+
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ ExternalServiceStatus status = new ExternalServiceStatus("Test service", "unknown");
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ return status;
+ }
+
+}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
index 850c869589..1f80000e20 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest2.java
@@ -1,249 +1,249 @@
-package lcsb.mapviewer.services.impl;
-
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-
-import java.awt.Color;
-import java.io.FileInputStream;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.commands.ColorModelCommand;
-import lcsb.mapviewer.common.TextFileUtils;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.layout.GeneVariation;
-import lcsb.mapviewer.model.map.layout.GeneVariationColorSchema;
-import lcsb.mapviewer.model.map.layout.GenericColorSchema;
-import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.services.interfaces.ILayoutService.CreateLayoutParams;
-import lcsb.mapviewer.services.utils.ColorSchemaReader;
-import lcsb.mapviewer.services.utils.data.ColorSchemaColumn;
-import lcsb.mapviewer.services.utils.data.ColorSchemaType;
-
-public class LayoutServiceTest2 {
- Logger logger = Logger.getLogger(LayoutServiceTest2.class);
- ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testValidPreprareTableResultForGeneric() throws Exception {
- try {
- class CSR extends ColorSchemaReader {
- public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
- List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
- for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
- if (csc.getTypes().contains(ColorSchemaType.GENERIC)) {
- result.add(csc);
- }
- }
- return result;
- }
- }
- ;
- List<ColorSchema> schemas = new ArrayList<ColorSchema>();
- ColorSchema cs = new GenericColorSchema();
- cs.setColor(Color.CYAN);
- cs.addCompartment("BLA");
- cs.addMiriamData(new MiriamData(MiriamType.CAS, "CAS_ID"));
- cs.setLineWidth(3.3);
- cs.setMatches(2);
- cs.setName("UUU");
- cs.setElementId("RE ID");
- cs.setReverseReaction(true);
- cs.addType(GenericProtein.class);
- cs.setValue(1111.1111);
- schemas.add(cs);
-
- LayoutService ls = new LayoutService();
- String result = ls.prepareTableResult(schemas, new CSR());
- assertNotNull(result);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testValidPreprareTableResultForGeneVariation() throws Exception {
- try {
- class CSR extends ColorSchemaReader {
- public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
- List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
- for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
- if (csc.getTypes().contains(ColorSchemaType.GENETIC_VARIANT)) {
- result.add(csc);
- }
- }
- return result;
- }
- }
- ;
- List<ColorSchema> schemas = new ArrayList<ColorSchema>();
- GeneVariationColorSchema cs = new GeneVariationColorSchema();
- cs.setColor(Color.CYAN);
- cs.addCompartment("BLA");
- cs.addMiriamData(new MiriamData(MiriamType.CAS, "CAS_ID"));
- cs.setLineWidth(3.3);
- cs.setMatches(2);
- cs.setName("UUU");
- cs.setElementId("RE ID");
- cs.setReverseReaction(true);
- cs.addType(GenericProtein.class);
- cs.setValue(1111.1111);
- GeneVariation gv = new GeneVariation();
- gv.setModifiedDna("C");
- gv.setContig("chr1");
- gv.setOriginalDna("T");
- gv.setPosition(12);
- gv.setReferenceGenomeType(ReferenceGenomeType.UCSC);
- gv.setReferenceGenomeVersion("hg19");
- cs.addGeneVariation(gv);
- GeneVariation gv2 = new GeneVariation();
- gv2.setModifiedDna("CC");
- gv2.setContig("chr2");
- gv2.setOriginalDna("TT");
- gv2.setPosition(124);
- gv2.setReferenceGenomeType(ReferenceGenomeType.UCSC);
- gv2.setReferenceGenomeVersion("hg18");
- gv2.addReference(new MiriamData(MiriamType.CHEBI, "XXX"));
- cs.addGeneVariation(gv2);
- schemas.add(cs);
-
- LayoutService ls = new LayoutService();
- String result = ls.prepareTableResult(schemas, new CSR());
- assertNotNull(result);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testEmptyPreprareTableResultForGeneric() throws Exception {
- try {
- class CSR extends ColorSchemaReader {
- public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
- List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
- for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
- if (csc.getTypes().contains(ColorSchemaType.GENERIC)) {
- result.add(csc);
- }
- }
- return result;
- }
- }
- ;
- List<ColorSchema> schemas = new ArrayList<ColorSchema>();
- ColorSchema cs = new GenericColorSchema();
- schemas.add(cs);
-
- LayoutService ls = new LayoutService();
- String result = ls.prepareTableResult(schemas, new CSR());
- assertNotNull(result);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testEmptyPreprareTableResultForGeneVariant() throws Exception {
- try {
- class CSR extends ColorSchemaReader {
- public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
- List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
- for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
- if (csc.getTypes().contains(ColorSchemaType.GENETIC_VARIANT)) {
- result.add(csc);
- }
- }
- return result;
- }
- }
- ;
- List<ColorSchema> schemas = new ArrayList<ColorSchema>();
- ColorSchema cs = new GeneVariationColorSchema();
- schemas.add(cs);
-
- LayoutService ls = new LayoutService();
- String result = ls.prepareTableResult(schemas, new CSR());
- assertNotNull(result);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetLayoutAliasesForInvalidAlias() throws Exception {
- try {
-
- Model model = new CellDesignerXmlParser()
- .createModel(new ConverterParams().filename("testFiles/coloring/problematicModel2.xml"));
-
- FileInputStream fis = new FileInputStream("testFiles/coloring/problematicSchema2.txt");
- CreateLayoutParams params = new CreateLayoutParams().name("Test").//
- directory("testDir").//
- model(model).//
- colorInputStream(fis).//
- async(false);
- ColorSchemaReader reader = new ColorSchemaReader();
- final Collection<ColorSchema> schemas = reader.readColorSchema(params.getColorInputStream(),
- TextFileUtils.getHeaderParametersFromFile(params.getColorInputStream()));
-
- ColorModelCommand command = new ColorModelCommand(model, schemas, colorExtractor);
- command.execute();
-
- command.getModifiedElements();
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSchemaWithCompartments() throws Exception {
- try {
- FileInputStream fis = new FileInputStream("testFiles/coloring/schemaWithCompartment.txt");
- ColorSchemaReader reader = new ColorSchemaReader();
- final Collection<ColorSchema> schemas = reader.readColorSchema(fis, new HashMap<>());
- for (ColorSchema colorSchema : schemas) {
- for (String string : colorSchema.getCompartments()) {
- assertNotNull(string);
- assertFalse(string.isEmpty());
- }
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.services.impl;
+
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+
+import java.awt.Color;
+import java.io.FileInputStream;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.commands.ColorModelCommand;
+import lcsb.mapviewer.common.TextFileUtils;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.layout.GeneVariation;
+import lcsb.mapviewer.model.map.layout.GeneVariationColorSchema;
+import lcsb.mapviewer.model.map.layout.GenericColorSchema;
+import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.services.interfaces.ILayoutService.CreateLayoutParams;
+import lcsb.mapviewer.services.utils.ColorSchemaReader;
+import lcsb.mapviewer.services.utils.data.ColorSchemaColumn;
+import lcsb.mapviewer.services.utils.data.ColorSchemaType;
+
+public class LayoutServiceTest2 {
+ Logger logger = Logger.getLogger(LayoutServiceTest2.class);
+ ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testValidPreprareTableResultForGeneric() throws Exception {
+ try {
+ class CSR extends ColorSchemaReader {
+ public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
+ List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
+ for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
+ if (csc.getTypes().contains(ColorSchemaType.GENERIC)) {
+ result.add(csc);
+ }
+ }
+ return result;
+ }
+ }
+ ;
+ List<ColorSchema> schemas = new ArrayList<ColorSchema>();
+ ColorSchema cs = new GenericColorSchema();
+ cs.setColor(Color.CYAN);
+ cs.addCompartment("BLA");
+ cs.addMiriamData(new MiriamData(MiriamType.CAS, "CAS_ID"));
+ cs.setLineWidth(3.3);
+ cs.setMatches(2);
+ cs.setName("UUU");
+ cs.setElementId("RE ID");
+ cs.setReverseReaction(true);
+ cs.addType(GenericProtein.class);
+ cs.setValue(1111.1111);
+ schemas.add(cs);
+
+ LayoutService ls = new LayoutService();
+ String result = ls.prepareTableResult(schemas, new CSR());
+ assertNotNull(result);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testValidPreprareTableResultForGeneVariation() throws Exception {
+ try {
+ class CSR extends ColorSchemaReader {
+ public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
+ List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
+ for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
+ if (csc.getTypes().contains(ColorSchemaType.GENETIC_VARIANT)) {
+ result.add(csc);
+ }
+ }
+ return result;
+ }
+ }
+ ;
+ List<ColorSchema> schemas = new ArrayList<ColorSchema>();
+ GeneVariationColorSchema cs = new GeneVariationColorSchema();
+ cs.setColor(Color.CYAN);
+ cs.addCompartment("BLA");
+ cs.addMiriamData(new MiriamData(MiriamType.CAS, "CAS_ID"));
+ cs.setLineWidth(3.3);
+ cs.setMatches(2);
+ cs.setName("UUU");
+ cs.setElementId("RE ID");
+ cs.setReverseReaction(true);
+ cs.addType(GenericProtein.class);
+ cs.setValue(1111.1111);
+ GeneVariation gv = new GeneVariation();
+ gv.setModifiedDna("C");
+ gv.setContig("chr1");
+ gv.setOriginalDna("T");
+ gv.setPosition(12);
+ gv.setReferenceGenomeType(ReferenceGenomeType.UCSC);
+ gv.setReferenceGenomeVersion("hg19");
+ cs.addGeneVariation(gv);
+ GeneVariation gv2 = new GeneVariation();
+ gv2.setModifiedDna("CC");
+ gv2.setContig("chr2");
+ gv2.setOriginalDna("TT");
+ gv2.setPosition(124);
+ gv2.setReferenceGenomeType(ReferenceGenomeType.UCSC);
+ gv2.setReferenceGenomeVersion("hg18");
+ gv2.addReference(new MiriamData(MiriamType.CHEBI, "XXX"));
+ cs.addGeneVariation(gv2);
+ schemas.add(cs);
+
+ LayoutService ls = new LayoutService();
+ String result = ls.prepareTableResult(schemas, new CSR());
+ assertNotNull(result);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testEmptyPreprareTableResultForGeneric() throws Exception {
+ try {
+ class CSR extends ColorSchemaReader {
+ public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
+ List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
+ for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
+ if (csc.getTypes().contains(ColorSchemaType.GENERIC)) {
+ result.add(csc);
+ }
+ }
+ return result;
+ }
+ }
+ ;
+ List<ColorSchema> schemas = new ArrayList<ColorSchema>();
+ ColorSchema cs = new GenericColorSchema();
+ schemas.add(cs);
+
+ LayoutService ls = new LayoutService();
+ String result = ls.prepareTableResult(schemas, new CSR());
+ assertNotNull(result);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testEmptyPreprareTableResultForGeneVariant() throws Exception {
+ try {
+ class CSR extends ColorSchemaReader {
+ public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
+ List<ColorSchemaColumn> result = new ArrayList<ColorSchemaColumn>();
+ for (ColorSchemaColumn csc : ColorSchemaColumn.values()) {
+ if (csc.getTypes().contains(ColorSchemaType.GENETIC_VARIANT)) {
+ result.add(csc);
+ }
+ }
+ return result;
+ }
+ }
+ ;
+ List<ColorSchema> schemas = new ArrayList<ColorSchema>();
+ ColorSchema cs = new GeneVariationColorSchema();
+ schemas.add(cs);
+
+ LayoutService ls = new LayoutService();
+ String result = ls.prepareTableResult(schemas, new CSR());
+ assertNotNull(result);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetLayoutAliasesForInvalidAlias() throws Exception {
+ try {
+
+ Model model = new CellDesignerXmlParser()
+ .createModel(new ConverterParams().filename("testFiles/coloring/problematicModel2.xml"));
+
+ FileInputStream fis = new FileInputStream("testFiles/coloring/problematicSchema2.txt");
+ CreateLayoutParams params = new CreateLayoutParams().name("Test").//
+ directory("testDir").//
+ model(model).//
+ colorInputStream(fis).//
+ async(false);
+ ColorSchemaReader reader = new ColorSchemaReader();
+ final Collection<ColorSchema> schemas = reader.readColorSchema(params.getColorInputStream(),
+ TextFileUtils.getHeaderParametersFromFile(params.getColorInputStream()));
+
+ ColorModelCommand command = new ColorModelCommand(model, schemas, colorExtractor);
+ command.execute();
+
+ command.getModifiedElements();
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSchemaWithCompartments() throws Exception {
+ try {
+ FileInputStream fis = new FileInputStream("testFiles/coloring/schemaWithCompartment.txt");
+ ColorSchemaReader reader = new ColorSchemaReader();
+ final Collection<ColorSchema> schemas = reader.readColorSchema(fis, new HashMap<>());
+ for (ColorSchema colorSchema : schemas) {
+ for (String string : colorSchema.getCompartments()) {
+ assertNotNull(string);
+ assertFalse(string.isEmpty());
+ }
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/LdapServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/LdapServiceTest.java
index 6e9446bb0c..b62549d9d8 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/LdapServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/LdapServiceTest.java
@@ -1,136 +1,136 @@
-package lcsb.mapviewer.services.impl;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-import org.mockito.invocation.InvocationOnMock;
-import org.mockito.stubbing.Answer;
-import org.springframework.test.annotation.Rollback;
-
-import com.unboundid.ldap.listener.InMemoryDirectoryServer;
-import com.unboundid.ldap.listener.InMemoryDirectoryServerConfig;
-import com.unboundid.ldap.sdk.LDAPConnection;
-
-import lcsb.mapviewer.model.user.ConfigurationElementType;
-import lcsb.mapviewer.services.ServiceTestFunctions;
-import lcsb.mapviewer.services.UserDTO;
-
-@Rollback(true)
-public class LdapServiceTest extends ServiceTestFunctions {
- static Logger logger = Logger.getLogger(LdapServiceTest.class);
-
- LdapService ldapService;
-
- @Before
- public void setUp() throws Exception {
- try {
- configurationService.setConfigurationValue(ConfigurationElementType.LDAP_BASE_DN, "dc=uni,dc=lu");
- configurationService.setConfigurationValue(ConfigurationElementType.LDAP_OBJECT_CLASS, "person");
- configurationService.setConfigurationValue(ConfigurationElementType.LDAP_FILTER, "memberof=cn=gitlab,cn=groups,cn=accounts,dc=uni,dc=lu");
-
- ldapService = Mockito.spy(LdapService.class);
- ldapService.setConfigurationService(configurationService);
- Mockito.when(ldapService.getConnection()).thenAnswer(new Answer<LDAPConnection>() {
-
- @Override
- public LDAPConnection answer(InvocationOnMock invocation) throws Throwable {
- // Create the configuration to use for the server.
- InMemoryDirectoryServerConfig config = new InMemoryDirectoryServerConfig("dc=uni,dc=lu");
- config.addAdditionalBindCredentials("uid=piotr.gawron,cn=users,cn=accounts,dc=uni,dc=lu", "test_passwd");
- config.setSchema(null);
-
- // Create the directory server instance, populate it with data from the
- // "test-data.ldif" file, and start listening for client connections.
- InMemoryDirectoryServer ds = new InMemoryDirectoryServer(config);
- ds.importFromLDIF(true, "testFiles/ldap/testdata.ldif");
- ds.startListening();
- return ds.getConnection();
- }
- });
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testIsValidConfiguration() throws Exception {
- try {
- assertTrue(ldapService.isValidConfiguration());
- configurationService.setConfigurationValue(ConfigurationElementType.LDAP_BASE_DN, "");
- assertFalse(ldapService.isValidConfiguration());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testLogin() throws Exception {
- try {
- assertTrue(ldapService.login("piotr.gawron", "test_passwd"));
- assertFalse(ldapService.login("piotr.gawron", "invalid_password"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetUsernames() throws Exception {
- try {
- List<String> list = ldapService.getUsernames();
- assertEquals(2, list.size());
- assertTrue(list.contains("piotr.gawron"));
- assertFalse(list.contains("john.doe"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetUsernamesWithFiltering() throws Exception {
- try {
- configurationService.setConfigurationValue(ConfigurationElementType.LDAP_FILTER,
- "(memberof=cn=owncloud,cn=groups,cn=accounts,dc=uni,dc=lu)");
-
- List<String> list = ldapService.getUsernames();
- assertEquals(1, list.size());
- assertTrue(list.contains("piotr.gawron"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetUserByLogin() throws Exception {
- try {
- UserDTO user = ldapService.getUserByLogin("piotr.gawron");
- assertEquals("Piotr", user.getFirstName());
- assertEquals("Gawron", user.getLastName());
- assertEquals("piotr.gawron", user.getLogin());
- assertEquals("piotr.gawron@uni.lu", user.getEmail());
- assertNotNull(user.getBindDn());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.services.impl;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+import org.mockito.invocation.InvocationOnMock;
+import org.mockito.stubbing.Answer;
+import org.springframework.test.annotation.Rollback;
+
+import com.unboundid.ldap.listener.InMemoryDirectoryServer;
+import com.unboundid.ldap.listener.InMemoryDirectoryServerConfig;
+import com.unboundid.ldap.sdk.LDAPConnection;
+
+import lcsb.mapviewer.model.user.ConfigurationElementType;
+import lcsb.mapviewer.services.ServiceTestFunctions;
+import lcsb.mapviewer.services.UserDTO;
+
+@Rollback(true)
+public class LdapServiceTest extends ServiceTestFunctions {
+ static Logger logger = Logger.getLogger(LdapServiceTest.class);
+
+ LdapService ldapService;
+
+ @Before
+ public void setUp() throws Exception {
+ try {
+ configurationService.setConfigurationValue(ConfigurationElementType.LDAP_BASE_DN, "dc=uni,dc=lu");
+ configurationService.setConfigurationValue(ConfigurationElementType.LDAP_OBJECT_CLASS, "person");
+ configurationService.setConfigurationValue(ConfigurationElementType.LDAP_FILTER, "memberof=cn=gitlab,cn=groups,cn=accounts,dc=uni,dc=lu");
+
+ ldapService = Mockito.spy(LdapService.class);
+ ldapService.setConfigurationService(configurationService);
+ Mockito.when(ldapService.getConnection()).thenAnswer(new Answer<LDAPConnection>() {
+
+ @Override
+ public LDAPConnection answer(InvocationOnMock invocation) throws Throwable {
+ // Create the configuration to use for the server.
+ InMemoryDirectoryServerConfig config = new InMemoryDirectoryServerConfig("dc=uni,dc=lu");
+ config.addAdditionalBindCredentials("uid=piotr.gawron,cn=users,cn=accounts,dc=uni,dc=lu", "test_passwd");
+ config.setSchema(null);
+
+ // Create the directory server instance, populate it with data from the
+ // "test-data.ldif" file, and start listening for client connections.
+ InMemoryDirectoryServer ds = new InMemoryDirectoryServer(config);
+ ds.importFromLDIF(true, "testFiles/ldap/testdata.ldif");
+ ds.startListening();
+ return ds.getConnection();
+ }
+ });
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testIsValidConfiguration() throws Exception {
+ try {
+ assertTrue(ldapService.isValidConfiguration());
+ configurationService.setConfigurationValue(ConfigurationElementType.LDAP_BASE_DN, "");
+ assertFalse(ldapService.isValidConfiguration());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testLogin() throws Exception {
+ try {
+ assertTrue(ldapService.login("piotr.gawron", "test_passwd"));
+ assertFalse(ldapService.login("piotr.gawron", "invalid_password"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetUsernames() throws Exception {
+ try {
+ List<String> list = ldapService.getUsernames();
+ assertEquals(2, list.size());
+ assertTrue(list.contains("piotr.gawron"));
+ assertFalse(list.contains("john.doe"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetUsernamesWithFiltering() throws Exception {
+ try {
+ configurationService.setConfigurationValue(ConfigurationElementType.LDAP_FILTER,
+ "(memberof=cn=owncloud,cn=groups,cn=accounts,dc=uni,dc=lu)");
+
+ List<String> list = ldapService.getUsernames();
+ assertEquals(1, list.size());
+ assertTrue(list.contains("piotr.gawron"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetUserByLogin() throws Exception {
+ try {
+ UserDTO user = ldapService.getUserByLogin("piotr.gawron");
+ assertEquals("Piotr", user.getFirstName());
+ assertEquals("Gawron", user.getLastName());
+ assertEquals("piotr.gawron", user.getLogin());
+ assertEquals("piotr.gawron@uni.lu", user.getEmail());
+ assertNotNull(user.getBindDn());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/Md5PasswordEncoderTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/Md5PasswordEncoderTest.java
index 3cc5810830..e91d17c186 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/Md5PasswordEncoderTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/Md5PasswordEncoderTest.java
@@ -1,47 +1,47 @@
-package lcsb.mapviewer.services.impl;
-
-import static org.junit.Assert.*;
-import lcsb.mapviewer.services.ServiceTestFunctions;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.security.crypto.password.PasswordEncoder;
-
-public class Md5PasswordEncoderTest extends ServiceTestFunctions {
- @Autowired
- PasswordEncoder passwordEncoder;
-
- String passwd = "test";
- String hash = "098f6bcd4621d373cade4e832627b4f6";
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEncode() {
- try {
- assertEquals(hash, passwordEncoder.encode(passwd));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testMatch() {
- try {
- assertTrue(passwordEncoder.matches(passwd, hash));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.services.impl;
+
+import static org.junit.Assert.*;
+import lcsb.mapviewer.services.ServiceTestFunctions;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.security.crypto.password.PasswordEncoder;
+
+public class Md5PasswordEncoderTest extends ServiceTestFunctions {
+ @Autowired
+ PasswordEncoder passwordEncoder;
+
+ String passwd = "test";
+ String hash = "098f6bcd4621d373cade4e832627b4f6";
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEncode() {
+ try {
+ assertEquals(hash, passwordEncoder.encode(passwd));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testMatch() {
+ try {
+ assertTrue(passwordEncoder.matches(passwd, hash));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/OkServiceMock.java b/service/src/test/java/lcsb/mapviewer/services/impl/OkServiceMock.java
index d184b82fb3..e26c4c69e1 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/OkServiceMock.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/OkServiceMock.java
@@ -1,16 +1,16 @@
-package lcsb.mapviewer.services.impl;
-
-import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
-import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
-import lcsb.mapviewer.annotation.services.IExternalService;
-
-public class OkServiceMock implements IExternalService {
-
- @Override
- public ExternalServiceStatus getServiceStatus() {
- ExternalServiceStatus status = new ExternalServiceStatus("Test service", "unknown");
- status.setStatus(ExternalServiceStatusType.OK);
- return status;
- }
-
-}
+package lcsb.mapviewer.services.impl;
+
+import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
+import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
+import lcsb.mapviewer.annotation.services.IExternalService;
+
+public class OkServiceMock implements IExternalService {
+
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ ExternalServiceStatus status = new ExternalServiceStatus("Test service", "unknown");
+ status.setStatus(ExternalServiceStatusType.OK);
+ return status;
+ }
+
+}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
index 336e30a486..45bd7fb327 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
@@ -1,613 +1,613 @@
-package lcsb.mapviewer.services.impl;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
-import lcsb.mapviewer.model.map.model.SubmodelType;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Degraded;
-import lcsb.mapviewer.model.map.species.Drug;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Ion;
-import lcsb.mapviewer.model.map.species.Phenotype;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.species.SimpleMolecule;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.Unknown;
-import lcsb.mapviewer.services.ServiceTestFunctions;
-import lcsb.mapviewer.services.interfaces.ISearchService.CoordinatesSearchParams;
-import lcsb.mapviewer.services.utils.SearchIndexer;
-
-public class SearchServiceTest extends ServiceTestFunctions {
- static Logger logger = Logger.getLogger(SearchServiceTest.class);
-
- SearchIndexer indexer = new SearchIndexer();
-
- Map<Class<?>, String> speciesSearchPrefix = new HashMap<Class<?>, String>();
- Map<String, Class<?>> speciesSearchReversePrefix = new HashMap<String, Class<?>>();
-
- @Before
- public void setUp() throws Exception {
- addSearchPrefix("complex", Complex.class);
- addSearchPrefix("degrded", Degraded.class);
- addSearchPrefix("drug", Drug.class);
- addSearchPrefix("gene", Gene.class);
- addSearchPrefix("ion", Ion.class);
- addSearchPrefix("phenotype", Phenotype.class);
- addSearchPrefix("protein", Protein.class);
- addSearchPrefix("rna", Rna.class);
- addSearchPrefix("molecule", SimpleMolecule.class);
- addSearchPrefix("unknown", Unknown.class);
- }
-
- private void addSearchPrefix(String prefix, Class<?> clazz) {
- speciesSearchPrefix.put(clazz, prefix);
- speciesSearchReversePrefix.put(prefix, clazz);
- }
-
- protected Model createFullModel() throws Exception {
- Model model = getModelForFile("testFiles/searchModel.xml", false);
- model.setProject(new Project("unknown project"));
- return model;
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSearchByName() throws Exception {
- try {
- Model model = createFullModel();
- long count = searchHistoryDao.getCount();
- List<BioEntity> result = searchService.searchByQuery(model, "reaction:re21", 50, null, "127.0.0.1");
-
- assertNotNull(result);
- assertEquals(4, result.size());
- Reaction reaction = (Reaction) result.get(0);
- assertTrue(reaction.getIdReaction().contains("re21"));
-
- long count2 = searchHistoryDao.getCount();
-
- assertEquals(count + 1, count2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSearchByName2() throws Exception {
- try {
- Model model = createFullModel();
- List<BioEntity> result = searchService.searchByQuery(model, "BAD:BCL-2", 50, null, "127.0.0.1");
-
- assertNotNull(result);
- assertTrue(result.size() > 0);
- Species alias = (Species) result.get(0);
- assertEquals("BAD:BCL-2", alias.getName());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSearchById() throws Exception {
- try {
- Model model = createFullModel();
- MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_HAS_VERSION, MiriamType.CAS, "123");
- model.getElements().iterator().next().addMiriamData(md);
- List<BioEntity> global = searchService.searchByQuery(model, "CAS:123", 50, null, "127.0.0.1");
- assertNotNull(global);
- assertEquals(1, global.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSearchByElementId() throws Exception {
- try {
- Model model = createFullModel();
- Element element = model.getElements().iterator().next();
- element.setId(907);
- List<BioEntity> global = searchService.searchByQuery(model, "element:907", 50, null, "127.0.0.1");
- assertNotNull(global);
- assertEquals(1, global.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSearchByUnknwonElementId() throws Exception {
- try {
- Model model = createFullModel();
- Element element =model.getElements().iterator().next();
- element.setId(907);
- List<BioEntity> global = searchService.searchByQuery(model, "species:90111117", 50, null, "127.0.0.1");
- assertEquals(0, global.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSearchByName4() throws Exception {
- try {
- Model model = createFullModel();
- List<BioEntity> result = searchService.searchByQuery(model, "BC", 50, true, "127.0.0.1");
-
- assertNotNull(result);
- assertEquals(0, result.size());
-
- result = searchService.searchByQuery(model, "BC", 50, false, "127.0.0.1");
- assertNotNull(result);
- assertTrue(result.size() > 0);
-
- result = searchService.searchByQuery(model, "BAD:BCL-2", 50, true, "127.0.0.1");
- assertNotNull(result);
- assertEquals(1, result.size());
- Species alias = (Species) result.get(0);
- assertEquals("BAD:BCL-2", alias.getName());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testQueryName() throws Exception {
- try {
- Model model = createFullModel();
- List<BioEntity> result = searchService.searchByQuery(model,
- indexer.getQueryStringForIndex("reaction:re21", new HashSet<>()), 50, null, "127.0.0.1");
-
- assertNotNull(result);
- assertEquals(4, result.size());
- Reaction reaction = (Reaction) result.get(0);
- assertEquals("re21", reaction.getIdReaction());
- assertTrue(result.get(1) instanceof Species);
- assertTrue(result.get(2) instanceof Species);
- assertTrue(result.get(3) instanceof Species);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testQueryReactionId() throws Exception {
- try {
- Model model = createFullModel();
- model.getReactions().iterator().next().setIdReaction("R_x1");
- List<BioEntity> result = searchService.searchByQuery(model,
- indexer.getQueryStringForIndex("reaction:r_x1", new HashSet<>()), 50, null, "127.0.0.1");
-
- assertNotNull(result);
- assertTrue(result.size() > 0);
- Reaction reaction = (Reaction) result.get(0);
- assertTrue(reaction.getIdReaction().contains("R_x1"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testQueryReactionId2() throws Exception {
- try {
- Model model = createFullModel();
- Reaction reaction = model.getReactions().iterator().next();
- reaction.setId(154);
- reaction.setIdReaction("test-name");
- List<BioEntity> result = searchService.searchByQuery(model,
- indexer.getQueryStringForIndex("reaction:154", new HashSet<>()), 50, null, "127.0.0.1");
-
- assertNotNull(result);
- assertTrue(result.size() > 0);
- Reaction resultReaction = (Reaction) result.get(0);
- assertTrue(resultReaction.getIdReaction().contains("test-name"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testQueryName2() throws Exception {
- try {
- Model model = createFullModel();
- model.getModelData().setId(-13);
- List<BioEntity> result = searchService.searchByQuery(model,
- indexer.getQueryStringForIndex("BCL-2", speciesSearchReversePrefix.keySet()), 50, null, "127.0.0.1");
- assertNotNull(result);
- assertTrue(result.size() > 0);
- Species alias = (Species) result.get(0);
- assertTrue("Invalid alias: " + alias.getName(), alias.getName().toUpperCase().contains("BCL"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testQueryName3() throws Exception {
- try {
- Model model = createFullModel();
- List<BioEntity> result = searchService.searchByQuery(model, "fdhgjkhdsfsdhfgfhsd", 50, null, "127.0.0.1");
-
- assertNotNull(result);
- assertEquals(0, result.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testQueryName4() throws Exception {
- try {
- Model model = createFullModel();
- List<BioEntity> result = searchService.searchByQuery(model,
- indexer.getQueryStringForIndex("protein:BCL-2", speciesSearchReversePrefix.keySet()), 50, null, "127.0.0.1");
- assertNotNull(result);
- assertTrue(result.size() > 0);
- Species alias = (Species) result.get(0);
- assertTrue("Invalid alias: " + alias.getName(), alias.getName().toUpperCase().contains("BCL"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSearchClosest() throws Exception {
- try {
- Model model = getModelForFile("testFiles/graph_path_example3.xml", true);
- List<BioEntity> elements = searchService.getClosestElements(model, new Point2D.Double(0, 0), 5, false,
- new ArrayList<>());
- assertNotNull(elements);
- assertEquals(5, elements.size());
- assertTrue(elements.get(0) instanceof Species);
- Species sAlias = (Species) elements.get(0);
- assertEquals("s1", sAlias.getName());
- assertTrue(elements.get(1) instanceof Reaction);
- Reaction reaction = (Reaction) elements.get(1);
- assertEquals("re1", reaction.getIdReaction());
- assertTrue(elements.get(2) instanceof Species);
- sAlias = (Species) elements.get(2);
- assertEquals("s3", sAlias.getName());
- assertTrue(elements.get(3) instanceof Reaction);
- reaction = (Reaction) elements.get(3);
- assertEquals("re2", reaction.getIdReaction());
- assertTrue(elements.get(4) instanceof Species);
- sAlias = (Species) elements.get(4);
- assertEquals("s2", sAlias.getName());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSearchClosest2() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
- GenericProtein protein1 = new GenericProtein("s1");
- protein1.setWidth(20);
- protein1.setHeight(20);
- protein1.setX(5);
- protein1.setY(5);
- model.addElement(protein1);
- GenericProtein protein2 = new GenericProtein("s2");
- protein2.setWidth(10);
- protein2.setHeight(10);
- protein2.setX(5);
- protein2.setY(5);
- model.addElement(protein2);
- GenericProtein protein3 = new GenericProtein("s3");
- protein3.setWidth(30);
- protein3.setHeight(30);
- protein3.setX(0);
- protein3.setY(0);
- model.addElement(protein3);
-
- List<BioEntity> elements = searchService.getClosestElements(model, new Point2D.Double(10, 10), 5, false,
- new ArrayList<>());
- assertNotNull(elements);
- assertEquals(3, elements.size());
- BioEntity sAlias = elements.get(0);
- assertEquals("s2", sAlias.getName());
- BioEntity reaction = elements.get(1);
- assertEquals("s1", reaction.getName());
- sAlias = elements.get(2);
- assertEquals("s3", sAlias.getName());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSearchClosestWithEmptyModel() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
- List<BioEntity> elements = searchService.getClosestElements(model, new Point2D.Double(0, 0), 5, false,
- new ArrayList<>());
- assertNotNull(elements);
- assertEquals(0, elements.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAutocompleList() {
- try {
- Model model = new ModelFullIndexed(null);
- Species proteinAlias = new GenericProtein("a");
- proteinAlias.setName("PROT identifier");
- proteinAlias.getSynonyms().add("PROT synonym");
- proteinAlias.getSynonyms().add("another synonym");
- proteinAlias.setFullName("Protein common name");
- model.addElement(proteinAlias);
-
- SimpleMolecule alias = new SimpleMolecule("a2");
- alias.setName("Molecule2");
- model.addElement(alias);
-
- int oldVal = Configuration.getAutocompleteSize();
- Configuration.setAutocompleteSize(5);
-
- List<String> list = searchService.getAutocompleteList(model, "P");
- assertNotNull(list);
- assertEquals(4, list.size());
- assertTrue(list.contains("PROT identifier".toLowerCase()));
- assertTrue(list.contains("PROT synonym".toLowerCase()));
- assertTrue(list.contains("Protein common name".toLowerCase()));
-
- list = searchService.getAutocompleteList(model, "PROTEIN");
- assertNotNull(list);
- assertEquals(2, list.size());
- assertTrue(list.contains("Protein common name".toLowerCase()));
-
- list = searchService.getAutocompleteList(model, "m");
- assertNotNull(list);
- assertEquals(2, list.size());
- assertTrue(list.contains("Molecule2".toLowerCase()));
-
- list = searchService.getAutocompleteList(model, "blablabla");
- assertNotNull(list);
- assertEquals(0, list.size());
-
- Configuration.setAutocompleteSize(oldVal);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetAutocompleList2() {
- try {
- Model model = new ModelFullIndexed(null);
- GenericProtein proteinAlias = new GenericProtein("a1");
- proteinAlias.setName("PROT identifier");
- proteinAlias.setNotes("Synonyms: PROT synonym, another synonym\nName: Protein common name");
- model.addElement(proteinAlias);
-
- SimpleMolecule alias = new SimpleMolecule("a2");
- alias.setName("Molecule2");
- model.addElement(alias);
-
- List<String> list = searchService.getAutocompleteList(model, "PROT identifier");
- assertNotNull(list);
- assertEquals(1, list.size());
- assertTrue(list.get(0).equalsIgnoreCase("PROT identifier"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testSearchGenericProtein() throws Exception {
- try {
- Model model = getModelForFile("testFiles/generic.xml", true);
-
- List<String> list = searchService.getAutocompleteList(model, "generic");
- assertNotNull(list);
- assertEquals(2, list.size());
- assertTrue(list.contains("generic"));
- assertTrue(list.contains("generic protein"));
-
- List<BioEntity> result = searchService.searchByQuery(model, "generic protein", 10, false, null);
- assertNotNull(result);
-
- assertTrue(result.size() > 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testSearchByCoordCompartment() throws Exception {
- try {
- Model model = getModelForFile("testFiles/graph_path_example3.xml", true);
-
- // we search in non-nested model
- List<BioEntity> res = searchService.searchByCoordinates(new CoordinatesSearchParams().model(model).x(50).y(50));
- assertNotNull(res);
- assertEquals(0, res.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testSearchByCoordCompartment2() throws Exception {
- try {
- Model model = getModelForFile("testFiles/graph_path_example3.xml", true);
-
- Layout layout = new Layout();
- layout.setHierarchicalView(true);
- model.addLayout(layout);
- // we search in nested model
- List<BioEntity> res = searchService
- .searchByCoordinates(new CoordinatesSearchParams().model(model).x(50).y(50).layoutIdentifier(0));
- assertNotNull(res);
-
- assertTrue(res.get(0) instanceof Compartment);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testSearchByCoordReaction() throws Exception {
- try {
- Model model = getModelForFile("testFiles/graph_path_example3.xml", true);
-
- // find compartment
- List<BioEntity> res = searchService.searchByCoordinates(new CoordinatesSearchParams().model(model));
- // reaction is too far
- assertEquals(0, res.size());
-
- res = searchService.searchByCoordinates(new CoordinatesSearchParams().model(model).distance(1000));
- assertEquals(3, res.size());
-
- assertTrue(res.get(0) instanceof Reaction);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testSearchByCoordAlias() throws Exception {
- try {
- Model model = getModelForFile("testFiles/graph_path_example3.xml", true);
-
- List<BioEntity> res = searchService.searchByCoordinates(new CoordinatesSearchParams().model(model).x(60).y(60));
- assertNotNull(res);
- assertTrue(res.size() > 0);
-
- assertTrue(res.get(0) instanceof Species);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetMiriamTypeForQuery() throws Exception {
- try {
- MiriamData md = new SearchService().getMiriamTypeForQuery("hgnc:SNCA");
- assertNotNull(md);
- assertEquals(MiriamType.HGNC, md.getDataType());
- assertEquals("SNCA", md.getResource());
-
- md = new SearchService().getMiriamTypeForQuery("reactome:REACT_15128");
- assertNotNull(md);
- assertEquals(MiriamType.REACTOME, md.getDataType());
- assertEquals("REACT_15128", md.getResource());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testSearchByMiriamInSubmap() throws Exception {
- try {
- String query = "HGNC_SYMBOL:SNCA";
- Model model = new ModelFullIndexed(null);
- Model submodel = new ModelFullIndexed(null);
- GenericProtein protein = new GenericProtein("s1");
- protein.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
- submodel.addElement(protein);
- model.addSubmodelConnection(new ModelSubmodelConnection(submodel, SubmodelType.UNKNOWN));
-
- List<BioEntity> result = searchService.searchByQuery(model, query, 50, null, "127.0.0.1");
-
- assertEquals(1, result.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetMiriamTypeForQuery2() throws Exception {
- try {
- MiriamData md = new SearchService().getMiriamTypeForQuery("UNKNOWN_HGNC:SNCA");
- assertNull(md);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
-}
+package lcsb.mapviewer.services.impl;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
+import lcsb.mapviewer.model.map.model.SubmodelType;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Degraded;
+import lcsb.mapviewer.model.map.species.Drug;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.Unknown;
+import lcsb.mapviewer.services.ServiceTestFunctions;
+import lcsb.mapviewer.services.interfaces.ISearchService.CoordinatesSearchParams;
+import lcsb.mapviewer.services.utils.SearchIndexer;
+
+public class SearchServiceTest extends ServiceTestFunctions {
+ static Logger logger = Logger.getLogger(SearchServiceTest.class);
+
+ SearchIndexer indexer = new SearchIndexer();
+
+ Map<Class<?>, String> speciesSearchPrefix = new HashMap<Class<?>, String>();
+ Map<String, Class<?>> speciesSearchReversePrefix = new HashMap<String, Class<?>>();
+
+ @Before
+ public void setUp() throws Exception {
+ addSearchPrefix("complex", Complex.class);
+ addSearchPrefix("degrded", Degraded.class);
+ addSearchPrefix("drug", Drug.class);
+ addSearchPrefix("gene", Gene.class);
+ addSearchPrefix("ion", Ion.class);
+ addSearchPrefix("phenotype", Phenotype.class);
+ addSearchPrefix("protein", Protein.class);
+ addSearchPrefix("rna", Rna.class);
+ addSearchPrefix("molecule", SimpleMolecule.class);
+ addSearchPrefix("unknown", Unknown.class);
+ }
+
+ private void addSearchPrefix(String prefix, Class<?> clazz) {
+ speciesSearchPrefix.put(clazz, prefix);
+ speciesSearchReversePrefix.put(prefix, clazz);
+ }
+
+ protected Model createFullModel() throws Exception {
+ Model model = getModelForFile("testFiles/searchModel.xml", false);
+ model.setProject(new Project("unknown project"));
+ return model;
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSearchByName() throws Exception {
+ try {
+ Model model = createFullModel();
+ long count = searchHistoryDao.getCount();
+ List<BioEntity> result = searchService.searchByQuery(model, "reaction:re21", 50, null, "127.0.0.1");
+
+ assertNotNull(result);
+ assertEquals(4, result.size());
+ Reaction reaction = (Reaction) result.get(0);
+ assertTrue(reaction.getIdReaction().contains("re21"));
+
+ long count2 = searchHistoryDao.getCount();
+
+ assertEquals(count + 1, count2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSearchByName2() throws Exception {
+ try {
+ Model model = createFullModel();
+ List<BioEntity> result = searchService.searchByQuery(model, "BAD:BCL-2", 50, null, "127.0.0.1");
+
+ assertNotNull(result);
+ assertTrue(result.size() > 0);
+ Species alias = (Species) result.get(0);
+ assertEquals("BAD:BCL-2", alias.getName());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSearchById() throws Exception {
+ try {
+ Model model = createFullModel();
+ MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_HAS_VERSION, MiriamType.CAS, "123");
+ model.getElements().iterator().next().addMiriamData(md);
+ List<BioEntity> global = searchService.searchByQuery(model, "CAS:123", 50, null, "127.0.0.1");
+ assertNotNull(global);
+ assertEquals(1, global.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSearchByElementId() throws Exception {
+ try {
+ Model model = createFullModel();
+ Element element = model.getElements().iterator().next();
+ element.setId(907);
+ List<BioEntity> global = searchService.searchByQuery(model, "element:907", 50, null, "127.0.0.1");
+ assertNotNull(global);
+ assertEquals(1, global.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSearchByUnknwonElementId() throws Exception {
+ try {
+ Model model = createFullModel();
+ Element element =model.getElements().iterator().next();
+ element.setId(907);
+ List<BioEntity> global = searchService.searchByQuery(model, "species:90111117", 50, null, "127.0.0.1");
+ assertEquals(0, global.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSearchByName4() throws Exception {
+ try {
+ Model model = createFullModel();
+ List<BioEntity> result = searchService.searchByQuery(model, "BC", 50, true, "127.0.0.1");
+
+ assertNotNull(result);
+ assertEquals(0, result.size());
+
+ result = searchService.searchByQuery(model, "BC", 50, false, "127.0.0.1");
+ assertNotNull(result);
+ assertTrue(result.size() > 0);
+
+ result = searchService.searchByQuery(model, "BAD:BCL-2", 50, true, "127.0.0.1");
+ assertNotNull(result);
+ assertEquals(1, result.size());
+ Species alias = (Species) result.get(0);
+ assertEquals("BAD:BCL-2", alias.getName());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testQueryName() throws Exception {
+ try {
+ Model model = createFullModel();
+ List<BioEntity> result = searchService.searchByQuery(model,
+ indexer.getQueryStringForIndex("reaction:re21", new HashSet<>()), 50, null, "127.0.0.1");
+
+ assertNotNull(result);
+ assertEquals(4, result.size());
+ Reaction reaction = (Reaction) result.get(0);
+ assertEquals("re21", reaction.getIdReaction());
+ assertTrue(result.get(1) instanceof Species);
+ assertTrue(result.get(2) instanceof Species);
+ assertTrue(result.get(3) instanceof Species);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testQueryReactionId() throws Exception {
+ try {
+ Model model = createFullModel();
+ model.getReactions().iterator().next().setIdReaction("R_x1");
+ List<BioEntity> result = searchService.searchByQuery(model,
+ indexer.getQueryStringForIndex("reaction:r_x1", new HashSet<>()), 50, null, "127.0.0.1");
+
+ assertNotNull(result);
+ assertTrue(result.size() > 0);
+ Reaction reaction = (Reaction) result.get(0);
+ assertTrue(reaction.getIdReaction().contains("R_x1"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testQueryReactionId2() throws Exception {
+ try {
+ Model model = createFullModel();
+ Reaction reaction = model.getReactions().iterator().next();
+ reaction.setId(154);
+ reaction.setIdReaction("test-name");
+ List<BioEntity> result = searchService.searchByQuery(model,
+ indexer.getQueryStringForIndex("reaction:154", new HashSet<>()), 50, null, "127.0.0.1");
+
+ assertNotNull(result);
+ assertTrue(result.size() > 0);
+ Reaction resultReaction = (Reaction) result.get(0);
+ assertTrue(resultReaction.getIdReaction().contains("test-name"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testQueryName2() throws Exception {
+ try {
+ Model model = createFullModel();
+ model.getModelData().setId(-13);
+ List<BioEntity> result = searchService.searchByQuery(model,
+ indexer.getQueryStringForIndex("BCL-2", speciesSearchReversePrefix.keySet()), 50, null, "127.0.0.1");
+ assertNotNull(result);
+ assertTrue(result.size() > 0);
+ Species alias = (Species) result.get(0);
+ assertTrue("Invalid alias: " + alias.getName(), alias.getName().toUpperCase().contains("BCL"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testQueryName3() throws Exception {
+ try {
+ Model model = createFullModel();
+ List<BioEntity> result = searchService.searchByQuery(model, "fdhgjkhdsfsdhfgfhsd", 50, null, "127.0.0.1");
+
+ assertNotNull(result);
+ assertEquals(0, result.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testQueryName4() throws Exception {
+ try {
+ Model model = createFullModel();
+ List<BioEntity> result = searchService.searchByQuery(model,
+ indexer.getQueryStringForIndex("protein:BCL-2", speciesSearchReversePrefix.keySet()), 50, null, "127.0.0.1");
+ assertNotNull(result);
+ assertTrue(result.size() > 0);
+ Species alias = (Species) result.get(0);
+ assertTrue("Invalid alias: " + alias.getName(), alias.getName().toUpperCase().contains("BCL"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSearchClosest() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/graph_path_example3.xml", true);
+ List<BioEntity> elements = searchService.getClosestElements(model, new Point2D.Double(0, 0), 5, false,
+ new ArrayList<>());
+ assertNotNull(elements);
+ assertEquals(5, elements.size());
+ assertTrue(elements.get(0) instanceof Species);
+ Species sAlias = (Species) elements.get(0);
+ assertEquals("s1", sAlias.getName());
+ assertTrue(elements.get(1) instanceof Reaction);
+ Reaction reaction = (Reaction) elements.get(1);
+ assertEquals("re1", reaction.getIdReaction());
+ assertTrue(elements.get(2) instanceof Species);
+ sAlias = (Species) elements.get(2);
+ assertEquals("s3", sAlias.getName());
+ assertTrue(elements.get(3) instanceof Reaction);
+ reaction = (Reaction) elements.get(3);
+ assertEquals("re2", reaction.getIdReaction());
+ assertTrue(elements.get(4) instanceof Species);
+ sAlias = (Species) elements.get(4);
+ assertEquals("s2", sAlias.getName());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSearchClosest2() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+ GenericProtein protein1 = new GenericProtein("s1");
+ protein1.setWidth(20);
+ protein1.setHeight(20);
+ protein1.setX(5);
+ protein1.setY(5);
+ model.addElement(protein1);
+ GenericProtein protein2 = new GenericProtein("s2");
+ protein2.setWidth(10);
+ protein2.setHeight(10);
+ protein2.setX(5);
+ protein2.setY(5);
+ model.addElement(protein2);
+ GenericProtein protein3 = new GenericProtein("s3");
+ protein3.setWidth(30);
+ protein3.setHeight(30);
+ protein3.setX(0);
+ protein3.setY(0);
+ model.addElement(protein3);
+
+ List<BioEntity> elements = searchService.getClosestElements(model, new Point2D.Double(10, 10), 5, false,
+ new ArrayList<>());
+ assertNotNull(elements);
+ assertEquals(3, elements.size());
+ BioEntity sAlias = elements.get(0);
+ assertEquals("s2", sAlias.getName());
+ BioEntity reaction = elements.get(1);
+ assertEquals("s1", reaction.getName());
+ sAlias = elements.get(2);
+ assertEquals("s3", sAlias.getName());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSearchClosestWithEmptyModel() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+ List<BioEntity> elements = searchService.getClosestElements(model, new Point2D.Double(0, 0), 5, false,
+ new ArrayList<>());
+ assertNotNull(elements);
+ assertEquals(0, elements.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAutocompleList() {
+ try {
+ Model model = new ModelFullIndexed(null);
+ Species proteinAlias = new GenericProtein("a");
+ proteinAlias.setName("PROT identifier");
+ proteinAlias.getSynonyms().add("PROT synonym");
+ proteinAlias.getSynonyms().add("another synonym");
+ proteinAlias.setFullName("Protein common name");
+ model.addElement(proteinAlias);
+
+ SimpleMolecule alias = new SimpleMolecule("a2");
+ alias.setName("Molecule2");
+ model.addElement(alias);
+
+ int oldVal = Configuration.getAutocompleteSize();
+ Configuration.setAutocompleteSize(5);
+
+ List<String> list = searchService.getAutocompleteList(model, "P");
+ assertNotNull(list);
+ assertEquals(4, list.size());
+ assertTrue(list.contains("PROT identifier".toLowerCase()));
+ assertTrue(list.contains("PROT synonym".toLowerCase()));
+ assertTrue(list.contains("Protein common name".toLowerCase()));
+
+ list = searchService.getAutocompleteList(model, "PROTEIN");
+ assertNotNull(list);
+ assertEquals(2, list.size());
+ assertTrue(list.contains("Protein common name".toLowerCase()));
+
+ list = searchService.getAutocompleteList(model, "m");
+ assertNotNull(list);
+ assertEquals(2, list.size());
+ assertTrue(list.contains("Molecule2".toLowerCase()));
+
+ list = searchService.getAutocompleteList(model, "blablabla");
+ assertNotNull(list);
+ assertEquals(0, list.size());
+
+ Configuration.setAutocompleteSize(oldVal);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetAutocompleList2() {
+ try {
+ Model model = new ModelFullIndexed(null);
+ GenericProtein proteinAlias = new GenericProtein("a1");
+ proteinAlias.setName("PROT identifier");
+ proteinAlias.setNotes("Synonyms: PROT synonym, another synonym\nName: Protein common name");
+ model.addElement(proteinAlias);
+
+ SimpleMolecule alias = new SimpleMolecule("a2");
+ alias.setName("Molecule2");
+ model.addElement(alias);
+
+ List<String> list = searchService.getAutocompleteList(model, "PROT identifier");
+ assertNotNull(list);
+ assertEquals(1, list.size());
+ assertTrue(list.get(0).equalsIgnoreCase("PROT identifier"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testSearchGenericProtein() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/generic.xml", true);
+
+ List<String> list = searchService.getAutocompleteList(model, "generic");
+ assertNotNull(list);
+ assertEquals(2, list.size());
+ assertTrue(list.contains("generic"));
+ assertTrue(list.contains("generic protein"));
+
+ List<BioEntity> result = searchService.searchByQuery(model, "generic protein", 10, false, null);
+ assertNotNull(result);
+
+ assertTrue(result.size() > 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testSearchByCoordCompartment() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/graph_path_example3.xml", true);
+
+ // we search in non-nested model
+ List<BioEntity> res = searchService.searchByCoordinates(new CoordinatesSearchParams().model(model).x(50).y(50));
+ assertNotNull(res);
+ assertEquals(0, res.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testSearchByCoordCompartment2() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/graph_path_example3.xml", true);
+
+ Layout layout = new Layout();
+ layout.setHierarchicalView(true);
+ model.addLayout(layout);
+ // we search in nested model
+ List<BioEntity> res = searchService
+ .searchByCoordinates(new CoordinatesSearchParams().model(model).x(50).y(50).layoutIdentifier(0));
+ assertNotNull(res);
+
+ assertTrue(res.get(0) instanceof Compartment);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testSearchByCoordReaction() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/graph_path_example3.xml", true);
+
+ // find compartment
+ List<BioEntity> res = searchService.searchByCoordinates(new CoordinatesSearchParams().model(model));
+ // reaction is too far
+ assertEquals(0, res.size());
+
+ res = searchService.searchByCoordinates(new CoordinatesSearchParams().model(model).distance(1000));
+ assertEquals(3, res.size());
+
+ assertTrue(res.get(0) instanceof Reaction);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testSearchByCoordAlias() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/graph_path_example3.xml", true);
+
+ List<BioEntity> res = searchService.searchByCoordinates(new CoordinatesSearchParams().model(model).x(60).y(60));
+ assertNotNull(res);
+ assertTrue(res.size() > 0);
+
+ assertTrue(res.get(0) instanceof Species);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetMiriamTypeForQuery() throws Exception {
+ try {
+ MiriamData md = new SearchService().getMiriamTypeForQuery("hgnc:SNCA");
+ assertNotNull(md);
+ assertEquals(MiriamType.HGNC, md.getDataType());
+ assertEquals("SNCA", md.getResource());
+
+ md = new SearchService().getMiriamTypeForQuery("reactome:REACT_15128");
+ assertNotNull(md);
+ assertEquals(MiriamType.REACTOME, md.getDataType());
+ assertEquals("REACT_15128", md.getResource());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testSearchByMiriamInSubmap() throws Exception {
+ try {
+ String query = "HGNC_SYMBOL:SNCA";
+ Model model = new ModelFullIndexed(null);
+ Model submodel = new ModelFullIndexed(null);
+ GenericProtein protein = new GenericProtein("s1");
+ protein.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
+ submodel.addElement(protein);
+ model.addSubmodelConnection(new ModelSubmodelConnection(submodel, SubmodelType.UNKNOWN));
+
+ List<BioEntity> result = searchService.searchByQuery(model, query, 50, null, "127.0.0.1");
+
+ assertEquals(1, result.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetMiriamTypeForQuery2() throws Exception {
+ try {
+ MiriamData md = new SearchService().getMiriamTypeForQuery("UNKNOWN_HGNC:SNCA");
+ assertNull(md);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/UserServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/UserServiceTest.java
index 227edfbc2f..64bc23211d 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/UserServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/UserServiceTest.java
@@ -1,229 +1,229 @@
-package lcsb.mapviewer.services.impl;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-import org.mockito.invocation.InvocationOnMock;
-import org.mockito.stubbing.Answer;
-import org.springframework.test.annotation.Rollback;
-
-import com.unboundid.ldap.listener.InMemoryDirectoryServer;
-import com.unboundid.ldap.listener.InMemoryDirectoryServerConfig;
-import com.unboundid.ldap.sdk.LDAPConnection;
-import com.unboundid.ldap.sdk.LDAPException;
-
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.user.BasicPrivilege;
-import lcsb.mapviewer.model.user.ConfigurationElementType;
-import lcsb.mapviewer.model.user.ObjectPrivilege;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.services.ServiceTestFunctions;
-import lcsb.mapviewer.services.interfaces.ILdapService;
-
-@Rollback(true)
-public class UserServiceTest extends ServiceTestFunctions {
- static Logger logger = Logger.getLogger(UserServiceTest.class);
-
- @Before
- public void setUp() throws Exception {
- createUser();
- logService.setLoggedUser(user);
- }
-
- @After
- public void tearDown() throws Exception {
- userDao.delete(user);
- }
-
- @Test
- public void testLogin() {
- try {
- assertNull(userService.login("john.doe", "incorrect password"));
- assertNotNull(userService.login("john.doe", "passwd"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testLoginFromLdap() throws Exception {
- ILdapService originalLdapService = userService.getLdapService();
- try {
- String login = "john.doe.test";
- String passwd = "test_passwd";
-
- assertNull(userService.getUserByLogin(login));
-
- LdapService ldapService = createMockLdapService("testFiles/ldap/john-doe-test-example.ldif", login, passwd);
-
- userService.setLdapService(ldapService);
- assertNull(userService.login(login, "incorrect password"));
- assertNotNull("User from LDAP wasn't authenticated", userService.login(login, passwd));
-
- User user = userService.getUserByLogin(login);
- assertNotNull("After authentication from LDAP user is not present in the system", user);
- assertTrue(user.isConnectedToLdap());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- userService.setLdapService(originalLdapService);
- }
- }
-
- private LdapService createMockLdapService(String filename, String login, String passwd) throws LDAPException {
- configurationService.setConfigurationValue(ConfigurationElementType.LDAP_BASE_DN, "dc=uni,dc=lu");
- configurationService.setConfigurationValue(ConfigurationElementType.LDAP_OBJECT_CLASS, "person");
- configurationService.setConfigurationValue(ConfigurationElementType.LDAP_FILTER, "memberof=cn=gitlab,cn=groups,cn=accounts,dc=uni,dc=lu");
-
- LdapService ldapService = Mockito.spy(LdapService.class);
- ldapService.setConfigurationService(configurationService);
- Mockito.when(ldapService.getConnection()).thenAnswer(new Answer<LDAPConnection>() {
-
- @Override
- public LDAPConnection answer(InvocationOnMock invocation) throws Throwable {
- // Create the configuration to use for the server.
- InMemoryDirectoryServerConfig config = new InMemoryDirectoryServerConfig("dc=uni,dc=lu");
- config.addAdditionalBindCredentials("uid=" + login + ",cn=users,cn=accounts,dc=uni,dc=lu", passwd);
- config.setSchema(null);
-
- // Create the directory server instance, populate it with data from the
- // "test-data.ldif" file, and start listening for client connections.
- InMemoryDirectoryServer ds = new InMemoryDirectoryServer(config);
- ds.importFromLDIF(true, filename);
- ds.startListening();
- return ds.getConnection();
- }
- });
- return ldapService;
- }
-
- @Test
- public void testLoginWithNull() {
- try {
- assertNull(userService.login("john.doe", null));
- assertNull(userService.login(null, "passwd"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUserHasPrivilegeUserPrivilegeType1() {
- try {
- assertFalse(userService.userHasPrivilege(user, PrivilegeType.ADD_MAP));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUserHasPrivilegeUserPrivilegeType3() {
- try {
- userService.userHasPrivilege(user, PrivilegeType.VIEW_PROJECT);
- fail("An exception should occure. VIEW_MAP must be connected with object");
- } catch (Exception e) {
-
- }
- }
-
- @Test
- public void testUserHasPrivilegeUserPrivilegeType2() {
- try {
- BasicPrivilege privilege = new BasicPrivilege();
- privilege.setLevel(1);
- privilege.setType(PrivilegeType.ADD_MAP);
- userService.setUserPrivilege(user, privilege);
- assertTrue(userService.userHasPrivilege(user, PrivilegeType.ADD_MAP));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
- @Test
- public void testUserHasPrivilegeUserPrivilegeTypeObject() {
- try {
- Project project = new Project();
- projectDao.add(project);
-
- assertFalse(userService.userHasPrivilege(user, PrivilegeType.VIEW_PROJECT, project));
- try {
- userService.userHasPrivilege(user, PrivilegeType.ADD_MAP, project);
- fail("An exception should occure. ADD_MAP must not be connected with object");
- } catch (Exception e) {
-
- }
-
- try {
- userService.userHasPrivilege(user, PrivilegeType.VIEW_PROJECT, user);
- fail("An exception should occure. VIEW_MAP must be connected with Model type");
- } catch (Exception e) {
-
- }
-
- ObjectPrivilege privilege = new ObjectPrivilege();
- privilege.setLevel(1);
- privilege.setType(PrivilegeType.VIEW_PROJECT);
- privilege.setIdObject(project.getId());
- userService.setUserPrivilege(user, privilege);
-
- assertTrue(userService.userHasPrivilege(user, PrivilegeType.VIEW_PROJECT, project));
-
- privilege = new ObjectPrivilege(project, 0, PrivilegeType.VIEW_PROJECT, user);
- userService.setUserPrivilege(user, privilege);
-
- assertFalse(userService.userHasPrivilege(user, PrivilegeType.VIEW_PROJECT, project));
-
- projectDao.delete(project);
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknown exception");
- }
- }
-
- @Test
- public void testUserHasPrivilegeForDefaultProjectWithoutSetting() {
- assertFalse(userService.userHasPrivilege(user, PrivilegeType.VIEW_PROJECT, null));
- }
-
- @Test
- public void testAddUser() throws Exception {
- try {
- long logCount = logDao.getCount();
- User user2 = new User();
- user2.setLogin("login");
- userService.addUser(user2);
- assertNotNull(user2.getId());
- long logCount2 = logDao.getCount();
- assertEquals("Log entry is missing for add user event", logCount + 1, logCount2);
- userDao.evict(user2);
- User user3 = userService.getUserByLogin(user2.getLogin());
- assertNotNull(user3);
- userService.deleteUser(user3);
- user3 = userService.getUserByLogin(user2.getLogin());
- assertNull(user3);
-
- long logCount3 = logDao.getCount();
- assertEquals("Log entry is missing for remove user event", logCount2 + 1, logCount3);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-}
+package lcsb.mapviewer.services.impl;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+import org.mockito.invocation.InvocationOnMock;
+import org.mockito.stubbing.Answer;
+import org.springframework.test.annotation.Rollback;
+
+import com.unboundid.ldap.listener.InMemoryDirectoryServer;
+import com.unboundid.ldap.listener.InMemoryDirectoryServerConfig;
+import com.unboundid.ldap.sdk.LDAPConnection;
+import com.unboundid.ldap.sdk.LDAPException;
+
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.user.BasicPrivilege;
+import lcsb.mapviewer.model.user.ConfigurationElementType;
+import lcsb.mapviewer.model.user.ObjectPrivilege;
+import lcsb.mapviewer.model.user.PrivilegeType;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.services.ServiceTestFunctions;
+import lcsb.mapviewer.services.interfaces.ILdapService;
+
+@Rollback(true)
+public class UserServiceTest extends ServiceTestFunctions {
+ static Logger logger = Logger.getLogger(UserServiceTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ createUser();
+ logService.setLoggedUser(user);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ userDao.delete(user);
+ }
+
+ @Test
+ public void testLogin() {
+ try {
+ assertNull(userService.login("john.doe", "incorrect password"));
+ assertNotNull(userService.login("john.doe", "passwd"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testLoginFromLdap() throws Exception {
+ ILdapService originalLdapService = userService.getLdapService();
+ try {
+ String login = "john.doe.test";
+ String passwd = "test_passwd";
+
+ assertNull(userService.getUserByLogin(login));
+
+ LdapService ldapService = createMockLdapService("testFiles/ldap/john-doe-test-example.ldif", login, passwd);
+
+ userService.setLdapService(ldapService);
+ assertNull(userService.login(login, "incorrect password"));
+ assertNotNull("User from LDAP wasn't authenticated", userService.login(login, passwd));
+
+ User user = userService.getUserByLogin(login);
+ assertNotNull("After authentication from LDAP user is not present in the system", user);
+ assertTrue(user.isConnectedToLdap());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ userService.setLdapService(originalLdapService);
+ }
+ }
+
+ private LdapService createMockLdapService(String filename, String login, String passwd) throws LDAPException {
+ configurationService.setConfigurationValue(ConfigurationElementType.LDAP_BASE_DN, "dc=uni,dc=lu");
+ configurationService.setConfigurationValue(ConfigurationElementType.LDAP_OBJECT_CLASS, "person");
+ configurationService.setConfigurationValue(ConfigurationElementType.LDAP_FILTER, "memberof=cn=gitlab,cn=groups,cn=accounts,dc=uni,dc=lu");
+
+ LdapService ldapService = Mockito.spy(LdapService.class);
+ ldapService.setConfigurationService(configurationService);
+ Mockito.when(ldapService.getConnection()).thenAnswer(new Answer<LDAPConnection>() {
+
+ @Override
+ public LDAPConnection answer(InvocationOnMock invocation) throws Throwable {
+ // Create the configuration to use for the server.
+ InMemoryDirectoryServerConfig config = new InMemoryDirectoryServerConfig("dc=uni,dc=lu");
+ config.addAdditionalBindCredentials("uid=" + login + ",cn=users,cn=accounts,dc=uni,dc=lu", passwd);
+ config.setSchema(null);
+
+ // Create the directory server instance, populate it with data from the
+ // "test-data.ldif" file, and start listening for client connections.
+ InMemoryDirectoryServer ds = new InMemoryDirectoryServer(config);
+ ds.importFromLDIF(true, filename);
+ ds.startListening();
+ return ds.getConnection();
+ }
+ });
+ return ldapService;
+ }
+
+ @Test
+ public void testLoginWithNull() {
+ try {
+ assertNull(userService.login("john.doe", null));
+ assertNull(userService.login(null, "passwd"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUserHasPrivilegeUserPrivilegeType1() {
+ try {
+ assertFalse(userService.userHasPrivilege(user, PrivilegeType.ADD_MAP));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUserHasPrivilegeUserPrivilegeType3() {
+ try {
+ userService.userHasPrivilege(user, PrivilegeType.VIEW_PROJECT);
+ fail("An exception should occure. VIEW_MAP must be connected with object");
+ } catch (Exception e) {
+
+ }
+ }
+
+ @Test
+ public void testUserHasPrivilegeUserPrivilegeType2() {
+ try {
+ BasicPrivilege privilege = new BasicPrivilege();
+ privilege.setLevel(1);
+ privilege.setType(PrivilegeType.ADD_MAP);
+ userService.setUserPrivilege(user, privilege);
+ assertTrue(userService.userHasPrivilege(user, PrivilegeType.ADD_MAP));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+ @Test
+ public void testUserHasPrivilegeUserPrivilegeTypeObject() {
+ try {
+ Project project = new Project();
+ projectDao.add(project);
+
+ assertFalse(userService.userHasPrivilege(user, PrivilegeType.VIEW_PROJECT, project));
+ try {
+ userService.userHasPrivilege(user, PrivilegeType.ADD_MAP, project);
+ fail("An exception should occure. ADD_MAP must not be connected with object");
+ } catch (Exception e) {
+
+ }
+
+ try {
+ userService.userHasPrivilege(user, PrivilegeType.VIEW_PROJECT, user);
+ fail("An exception should occure. VIEW_MAP must be connected with Model type");
+ } catch (Exception e) {
+
+ }
+
+ ObjectPrivilege privilege = new ObjectPrivilege();
+ privilege.setLevel(1);
+ privilege.setType(PrivilegeType.VIEW_PROJECT);
+ privilege.setIdObject(project.getId());
+ userService.setUserPrivilege(user, privilege);
+
+ assertTrue(userService.userHasPrivilege(user, PrivilegeType.VIEW_PROJECT, project));
+
+ privilege = new ObjectPrivilege(project, 0, PrivilegeType.VIEW_PROJECT, user);
+ userService.setUserPrivilege(user, privilege);
+
+ assertFalse(userService.userHasPrivilege(user, PrivilegeType.VIEW_PROJECT, project));
+
+ projectDao.delete(project);
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknown exception");
+ }
+ }
+
+ @Test
+ public void testUserHasPrivilegeForDefaultProjectWithoutSetting() {
+ assertFalse(userService.userHasPrivilege(user, PrivilegeType.VIEW_PROJECT, null));
+ }
+
+ @Test
+ public void testAddUser() throws Exception {
+ try {
+ long logCount = logDao.getCount();
+ User user2 = new User();
+ user2.setLogin("login");
+ userService.addUser(user2);
+ assertNotNull(user2.getId());
+ long logCount2 = logDao.getCount();
+ assertEquals("Log entry is missing for add user event", logCount + 1, logCount2);
+ userDao.evict(user2);
+ User user3 = userService.getUserByLogin(user2.getLogin());
+ assertNotNull(user3);
+ userService.deleteUser(user3);
+ user3 = userService.getUserByLogin(user2.getLogin());
+ assertNull(user3);
+
+ long logCount3 = logDao.getCount();
+ assertEquals("Log entry is missing for remove user event", logCount2 + 1, logCount3);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/service/src/test/java/lcsb/mapviewer/services/overlay/AllOverlayTests.java b/service/src/test/java/lcsb/mapviewer/services/overlay/AllOverlayTests.java
index ceb35a663b..4812f764fd 100644
--- a/service/src/test/java/lcsb/mapviewer/services/overlay/AllOverlayTests.java
+++ b/service/src/test/java/lcsb/mapviewer/services/overlay/AllOverlayTests.java
@@ -1,14 +1,14 @@
-package lcsb.mapviewer.services.overlay;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AnnotatedObjectTreeRowTest.class, //
- ChebiTreeRowTest.class,//
- IconManagerTest.class, //
-})
-public class AllOverlayTests {
-
-}
+package lcsb.mapviewer.services.overlay;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AnnotatedObjectTreeRowTest.class, //
+ ChebiTreeRowTest.class,//
+ IconManagerTest.class, //
+})
+public class AllOverlayTests {
+
+}
diff --git a/service/src/test/java/lcsb/mapviewer/services/overlay/AnnotatedObjectTreeRowTest.java b/service/src/test/java/lcsb/mapviewer/services/overlay/AnnotatedObjectTreeRowTest.java
index bbb1ce76ef..f8e6609b5e 100644
--- a/service/src/test/java/lcsb/mapviewer/services/overlay/AnnotatedObjectTreeRowTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/overlay/AnnotatedObjectTreeRowTest.java
@@ -1,31 +1,31 @@
-package lcsb.mapviewer.services.overlay;
-
-import lcsb.mapviewer.modelutils.map.ClassTreeNode;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class AnnotatedObjectTreeRowTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new AnnotatedObjectTreeRow(new ClassTreeNode(Object.class)));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.services.overlay;
+
+import lcsb.mapviewer.modelutils.map.ClassTreeNode;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class AnnotatedObjectTreeRowTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new AnnotatedObjectTreeRow(new ClassTreeNode(Object.class)));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/service/src/test/java/lcsb/mapviewer/services/overlay/ChebiTreeRowTest.java b/service/src/test/java/lcsb/mapviewer/services/overlay/ChebiTreeRowTest.java
index 1b77de9f2d..5c3f1795f2 100644
--- a/service/src/test/java/lcsb/mapviewer/services/overlay/ChebiTreeRowTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/overlay/ChebiTreeRowTest.java
@@ -1,29 +1,29 @@
-package lcsb.mapviewer.services.overlay;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ChebiTreeRowTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new ChebiTreeRow(null,null,null,null));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.services.overlay;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ChebiTreeRowTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new ChebiTreeRow(null,null,null,null));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/service/src/test/java/lcsb/mapviewer/services/overlay/IconManagerTest.java b/service/src/test/java/lcsb/mapviewer/services/overlay/IconManagerTest.java
index fa49a795aa..d030a8f1c4 100644
--- a/service/src/test/java/lcsb/mapviewer/services/overlay/IconManagerTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/overlay/IconManagerTest.java
@@ -1,47 +1,47 @@
-package lcsb.mapviewer.services.overlay;
-
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class IconManagerTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void test() {
- IconManager im = IconManager.getInstance();
- assertNotNull(im);
- String icon1 = im.getIconForIndex(0, IconType.SEARCH, 0);
- String icon2 = im.getIconForIndex(1, IconType.SEARCH, 0);
- assertFalse(icon1.equals(icon2));
- }
-
- @Test
- public void test1() {
- IconManager im = IconManager.getInstance();
- assertNotNull(im);
- String icon1 = im.getIconForIndex(0, IconType.SEARCH, 0);
- String icon2 = im.getIconForIndex(0, IconType.DRUG, 0);
- assertFalse(icon1.equals(icon2));
- }
-
- @Test
- public void test2() {
- IconManager im = IconManager.getInstance();
- assertNotNull(im);
- String icon1 = im.getIconForIndex(0, IconType.SEARCH, 0);
- String icon2 = im.getIconForIndex(0, IconType.SEARCH, 1);
- assertFalse(icon1.equals(icon2));
- }
-
-}
+package lcsb.mapviewer.services.overlay;
+
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class IconManagerTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void test() {
+ IconManager im = IconManager.getInstance();
+ assertNotNull(im);
+ String icon1 = im.getIconForIndex(0, IconType.SEARCH, 0);
+ String icon2 = im.getIconForIndex(1, IconType.SEARCH, 0);
+ assertFalse(icon1.equals(icon2));
+ }
+
+ @Test
+ public void test1() {
+ IconManager im = IconManager.getInstance();
+ assertNotNull(im);
+ String icon1 = im.getIconForIndex(0, IconType.SEARCH, 0);
+ String icon2 = im.getIconForIndex(0, IconType.DRUG, 0);
+ assertFalse(icon1.equals(icon2));
+ }
+
+ @Test
+ public void test2() {
+ IconManager im = IconManager.getInstance();
+ assertNotNull(im);
+ String icon1 = im.getIconForIndex(0, IconType.SEARCH, 0);
+ String icon2 = im.getIconForIndex(0, IconType.SEARCH, 1);
+ assertFalse(icon1.equals(icon2));
+ }
+
+}
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/AllSearchTests.java b/service/src/test/java/lcsb/mapviewer/services/search/AllSearchTests.java
index 8aa6d16f47..d3350d52e7 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/AllSearchTests.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/AllSearchTests.java
@@ -1,20 +1,20 @@
-package lcsb.mapviewer.services.search;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-import lcsb.mapviewer.services.search.chemical.ChemicalServiceTest;
-import lcsb.mapviewer.services.search.drug.AllSearchDrugTests;
-import lcsb.mapviewer.services.search.mirna.MiRNAServiceTest;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AllSearchDrugTests.class, //
- ChemicalServiceTest.class, //
- DbSearchServiceTest.class, //
- ElementMatcherTest.class, //
- MiRNAServiceTest.class, //
-})
-public class AllSearchTests {
-
-}
+package lcsb.mapviewer.services.search;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+import lcsb.mapviewer.services.search.chemical.ChemicalServiceTest;
+import lcsb.mapviewer.services.search.drug.AllSearchDrugTests;
+import lcsb.mapviewer.services.search.mirna.MiRNAServiceTest;
+
+@RunWith(Suite.class)
+@SuiteClasses({ AllSearchDrugTests.class, //
+ ChemicalServiceTest.class, //
+ DbSearchServiceTest.class, //
+ ElementMatcherTest.class, //
+ MiRNAServiceTest.class, //
+})
+public class AllSearchTests {
+
+}
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/chemical/ChemicalServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/search/chemical/ChemicalServiceTest.java
index f7bf0eb096..d5d3cd553d 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/chemical/ChemicalServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/chemical/ChemicalServiceTest.java
@@ -1,70 +1,70 @@
-package lcsb.mapviewer.services.search.chemical;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.annotation.data.Chemical;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.services.ServiceTestFunctions;
-import lcsb.mapviewer.services.search.DbSearchCriteria;
-
-public class ChemicalServiceTest extends ServiceTestFunctions {
- Logger logger = Logger.getLogger(ChemicalServiceTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testgetPDChemicalByName2() throws Exception {
- try {
- MiriamData pdDiseaseID = new MiriamData(MiriamType.MESH_2012, "D010300");
- String name = "Amphetamine";
- Chemical result = chemicalService.getByName(name, new DbSearchCriteria().disease(pdDiseaseID));
- assertNotNull(result);
- assertEquals("D000661", result.getChemicalId().getResource());
-
- assertEquals("No warnings expected.", 0, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSearchByElements4() throws Exception {
- try {
- List<Element> elements = new ArrayList<>();
- Rna protein = new Rna("id");
- protein.setName("GDNF");
- elements.add(protein);
-
- List<Chemical> chemicals = chemicalService.getForTargets(elements, new DbSearchCriteria().disease(new MiriamData(MiriamType.MESH_2012, "D010300")));
- assertNotNull(chemicals);
- assertTrue(chemicals.size() > 0);
-
- assertEquals("No warnings expected.", 0, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
-}
+package lcsb.mapviewer.services.search.chemical;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.annotation.data.Chemical;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.services.ServiceTestFunctions;
+import lcsb.mapviewer.services.search.DbSearchCriteria;
+
+public class ChemicalServiceTest extends ServiceTestFunctions {
+ Logger logger = Logger.getLogger(ChemicalServiceTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testgetPDChemicalByName2() throws Exception {
+ try {
+ MiriamData pdDiseaseID = new MiriamData(MiriamType.MESH_2012, "D010300");
+ String name = "Amphetamine";
+ Chemical result = chemicalService.getByName(name, new DbSearchCriteria().disease(pdDiseaseID));
+ assertNotNull(result);
+ assertEquals("D000661", result.getChemicalId().getResource());
+
+ assertEquals("No warnings expected.", 0, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSearchByElements4() throws Exception {
+ try {
+ List<Element> elements = new ArrayList<>();
+ Rna protein = new Rna("id");
+ protein.setName("GDNF");
+ elements.add(protein);
+
+ List<Chemical> chemicals = chemicalService.getForTargets(elements, new DbSearchCriteria().disease(new MiriamData(MiriamType.MESH_2012, "D010300")));
+ assertNotNull(chemicals);
+ assertTrue(chemicals.size() > 0);
+
+ assertEquals("No warnings expected.", 0, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+}
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/drug/AllSearchDrugTests.java b/service/src/test/java/lcsb/mapviewer/services/search/drug/AllSearchDrugTests.java
index f98b3cd957..bd40b9629d 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/drug/AllSearchDrugTests.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/drug/AllSearchDrugTests.java
@@ -1,13 +1,13 @@
-package lcsb.mapviewer.services.search.drug;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ DrugServiceTest.class, //
-
-})
-public class AllSearchDrugTests {
-
-}
+package lcsb.mapviewer.services.search.drug;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ DrugServiceTest.class, //
+
+})
+public class AllSearchDrugTests {
+
+}
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/drug/DrugServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/search/drug/DrugServiceTest.java
index 104a58f28d..683b9c1ae5 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/drug/DrugServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/drug/DrugServiceTest.java
@@ -1,300 +1,300 @@
-package lcsb.mapviewer.services.search.drug;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.annotation.data.Drug;
-import lcsb.mapviewer.annotation.data.Target;
-import lcsb.mapviewer.annotation.services.TaxonomyBackend;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.persist.dao.map.species.ElementDao;
-import lcsb.mapviewer.services.ServiceTestFunctions;
-import lcsb.mapviewer.services.search.DbSearchCriteria;
-
-public class DrugServiceTest extends ServiceTestFunctions {
- Logger logger = Logger.getLogger(DrugServiceTest.class);
-
- @Autowired
- ElementDao elementDao;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetEmpty() throws Exception {
- try {
- Drug drug = drugService.getByName("blablablabla", new DbSearchCriteria());
- assertNull(drug);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetTargets() throws Exception {
- try {
- long count = searchHistoryDao.getCount();
- Model model = new ModelFullIndexed(null);
- Project project = new Project();
- project.setProjectId("TesT");
- project.addModel(model);
- Drug drug = drugService.getByName("Diazoxide", new DbSearchCriteria().project(project).ipAddress("ip"));
- assertNotNull(drug);
- assertNotNull(drug.getName());
- assertFalse(drug.getName().trim().equals(""));
- assertNotNull(drug.getDescription());
- assertFalse(drug.getDescription().trim().equals(""));
-
- String hgnc1 = "SLC12A3";
- String hgnc2 = "KCNJ8";
-
- boolean hgnc1Exists = false;
- boolean hgnc2Exists = false;
-
- for (Target target : drug.getTargets()) {
- for (MiriamData row : target.getGenes()) {
- if (row.getResource().equalsIgnoreCase(hgnc1))
- hgnc1Exists = true;
- if (row.getResource().equalsIgnoreCase(hgnc2))
- hgnc2Exists = true;
- }
- }
-
- assertTrue("Target " + hgnc1 + " doesn't exist in target list but should", hgnc1Exists);
- assertTrue("Target " + hgnc2 + " doesn't exist in target list but should", hgnc2Exists);
-
- long count2 = searchHistoryDao.getCount();
-
- assertEquals(count + 1, count2);
-
- assertEquals("YES", drug.getBloodBrainBarrier());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetTargetsBySynonym() throws Exception {
- try {
- // search by synonym
- Drug drug = drugService.getByName("Amantidine", new DbSearchCriteria().ipAddress("ip"));
- // search by name
- Drug drug2 = drugService.getByName("Amantadine", new DbSearchCriteria().ipAddress("ip"));
- assertNotNull(drug);
- assertNotNull(drug.getName());
- assertFalse(drug.getName().trim().equals(""));
- assertNotNull(drug.getDescription());
- assertFalse(drug.getDescription().trim().equals(""));
-
- // number of targets should be the same
- assertEquals(drug.getTargets().size(), drug2.getTargets().size());
- assertTrue(drug.getTargets().size() > 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testFindDrugSelegiline() throws Exception {
- try {
- Drug test = drugService.getByName("Selegiline",
- new DbSearchCriteria().ipAddress("ip").organisms(TaxonomyBackend.HUMAN_TAXONOMY));
- assertNotNull(test);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAnnotationsInDrug() throws Exception {
- try {
- Drug test = drugService.getByName("Selegiline", new DbSearchCriteria().organisms(TaxonomyBackend.HUMAN_TAXONOMY));
- assertNotNull(test);
- for (Target target : test.getTargets()) {
- for (MiriamData md : target.getGenes()) {
- assertNull(md.getAnnotator());
- }
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDornaseAplha() throws Exception {
- try {
- Drug drug = drugService.getByName("Dornase alpha", new DbSearchCriteria());
- assertNotNull(drug.getName());
- assertEquals("N/A", drug.getBloodBrainBarrier());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testRapamycin() throws Exception {
- try {
- Drug drug = drugService.getByName("Rapamycin", new DbSearchCriteria());
- assertNotNull(drug.getName());
- assertEquals("NO", drug.getBloodBrainBarrier());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testSearchByElements() throws Exception {
- try {
- List<Element> elements = new ArrayList<>();
- List<Drug> drugs = drugService.getForTargets(elements, new DbSearchCriteria());
- assertNotNull(drugs);
- assertEquals(0, drugs.size());
-
- Protein protein = new GenericProtein("id");
- protein.setName("DRD2");
- protein.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "DRD2"));
- elements.add(protein);
-
- drugs = drugService.getForTargets(elements, new DbSearchCriteria());
- assertNotNull(drugs);
- assertTrue(drugs.size() > 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testSearchByElements2() throws Exception {
- try {
- List<Element> elements = new ArrayList<>();
- Protein protein = new GenericProtein("id");
- protein.setName("DRD2");
- protein.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "DRD2"));
- elements.add(protein);
- List<Drug> drugs = drugService.getForTargets(elements,
- new DbSearchCriteria().organisms(TaxonomyBackend.HUMAN_TAXONOMY));
-
- assertNotNull(drugs);
- assertTrue(drugs.size() > 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testSearchByElements3() throws Exception {
- try {
- List<Element> elements = new ArrayList<>();
- Protein protein = new GenericProtein("id");
- protein.setName("GLUD1");
- protein.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "GLUD1"));
- protein.addMiriamData(new MiriamData(MiriamType.ENTREZ, "2746"));
- elements.add(protein);
- List<Drug> drugs = drugService.getForTargets(elements, new DbSearchCriteria());
-
- assertNotNull(drugs);
- assertTrue(drugs.size() > 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testObjectToDrugTargetList() throws Exception {
- try {
- Drug drug = drugService.getByName("AMANTADINE", new DbSearchCriteria());
- Drug drug2 = drugBankHTMLParser.findDrug("AMANTADINE");
-
- assertTrue(drug2.getTargets().size() <= drug.getTargets().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAspirinToDrugTargetList() throws Exception {
- try {
- Drug drug = drugService.getByName("Aspirin", new DbSearchCriteria());
- Drug drug2 = drugBankHTMLParser.findDrug("Aspirin");
-
- assertTrue(drug2.getTargets().size() <= drug.getTargets().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAspirinSynonyms() throws Exception {
- try {
- Drug drug = drugService.getByName("Aspirin", new DbSearchCriteria());
-
- Set<String> synonyms = new HashSet<String>();
- for (String string : drug.getSynonyms()) {
- assertFalse("Duplicate entry in drug synonym: " + string, synonyms.contains(string));
- synonyms.add(string);
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetSuggestedQueryList() throws Exception {
- try {
- List<String> result = drugService.getSuggestedQueryList(new Project(), null);
- assertEquals(0, result.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.services.search.drug;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.annotation.data.Drug;
+import lcsb.mapviewer.annotation.data.Target;
+import lcsb.mapviewer.annotation.services.TaxonomyBackend;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.persist.dao.map.species.ElementDao;
+import lcsb.mapviewer.services.ServiceTestFunctions;
+import lcsb.mapviewer.services.search.DbSearchCriteria;
+
+public class DrugServiceTest extends ServiceTestFunctions {
+ Logger logger = Logger.getLogger(DrugServiceTest.class);
+
+ @Autowired
+ ElementDao elementDao;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetEmpty() throws Exception {
+ try {
+ Drug drug = drugService.getByName("blablablabla", new DbSearchCriteria());
+ assertNull(drug);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetTargets() throws Exception {
+ try {
+ long count = searchHistoryDao.getCount();
+ Model model = new ModelFullIndexed(null);
+ Project project = new Project();
+ project.setProjectId("TesT");
+ project.addModel(model);
+ Drug drug = drugService.getByName("Diazoxide", new DbSearchCriteria().project(project).ipAddress("ip"));
+ assertNotNull(drug);
+ assertNotNull(drug.getName());
+ assertFalse(drug.getName().trim().equals(""));
+ assertNotNull(drug.getDescription());
+ assertFalse(drug.getDescription().trim().equals(""));
+
+ String hgnc1 = "SLC12A3";
+ String hgnc2 = "KCNJ8";
+
+ boolean hgnc1Exists = false;
+ boolean hgnc2Exists = false;
+
+ for (Target target : drug.getTargets()) {
+ for (MiriamData row : target.getGenes()) {
+ if (row.getResource().equalsIgnoreCase(hgnc1))
+ hgnc1Exists = true;
+ if (row.getResource().equalsIgnoreCase(hgnc2))
+ hgnc2Exists = true;
+ }
+ }
+
+ assertTrue("Target " + hgnc1 + " doesn't exist in target list but should", hgnc1Exists);
+ assertTrue("Target " + hgnc2 + " doesn't exist in target list but should", hgnc2Exists);
+
+ long count2 = searchHistoryDao.getCount();
+
+ assertEquals(count + 1, count2);
+
+ assertEquals("YES", drug.getBloodBrainBarrier());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetTargetsBySynonym() throws Exception {
+ try {
+ // search by synonym
+ Drug drug = drugService.getByName("Amantidine", new DbSearchCriteria().ipAddress("ip"));
+ // search by name
+ Drug drug2 = drugService.getByName("Amantadine", new DbSearchCriteria().ipAddress("ip"));
+ assertNotNull(drug);
+ assertNotNull(drug.getName());
+ assertFalse(drug.getName().trim().equals(""));
+ assertNotNull(drug.getDescription());
+ assertFalse(drug.getDescription().trim().equals(""));
+
+ // number of targets should be the same
+ assertEquals(drug.getTargets().size(), drug2.getTargets().size());
+ assertTrue(drug.getTargets().size() > 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testFindDrugSelegiline() throws Exception {
+ try {
+ Drug test = drugService.getByName("Selegiline",
+ new DbSearchCriteria().ipAddress("ip").organisms(TaxonomyBackend.HUMAN_TAXONOMY));
+ assertNotNull(test);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotationsInDrug() throws Exception {
+ try {
+ Drug test = drugService.getByName("Selegiline", new DbSearchCriteria().organisms(TaxonomyBackend.HUMAN_TAXONOMY));
+ assertNotNull(test);
+ for (Target target : test.getTargets()) {
+ for (MiriamData md : target.getGenes()) {
+ assertNull(md.getAnnotator());
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDornaseAplha() throws Exception {
+ try {
+ Drug drug = drugService.getByName("Dornase alpha", new DbSearchCriteria());
+ assertNotNull(drug.getName());
+ assertEquals("N/A", drug.getBloodBrainBarrier());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testRapamycin() throws Exception {
+ try {
+ Drug drug = drugService.getByName("Rapamycin", new DbSearchCriteria());
+ assertNotNull(drug.getName());
+ assertEquals("NO", drug.getBloodBrainBarrier());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testSearchByElements() throws Exception {
+ try {
+ List<Element> elements = new ArrayList<>();
+ List<Drug> drugs = drugService.getForTargets(elements, new DbSearchCriteria());
+ assertNotNull(drugs);
+ assertEquals(0, drugs.size());
+
+ Protein protein = new GenericProtein("id");
+ protein.setName("DRD2");
+ protein.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "DRD2"));
+ elements.add(protein);
+
+ drugs = drugService.getForTargets(elements, new DbSearchCriteria());
+ assertNotNull(drugs);
+ assertTrue(drugs.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testSearchByElements2() throws Exception {
+ try {
+ List<Element> elements = new ArrayList<>();
+ Protein protein = new GenericProtein("id");
+ protein.setName("DRD2");
+ protein.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "DRD2"));
+ elements.add(protein);
+ List<Drug> drugs = drugService.getForTargets(elements,
+ new DbSearchCriteria().organisms(TaxonomyBackend.HUMAN_TAXONOMY));
+
+ assertNotNull(drugs);
+ assertTrue(drugs.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testSearchByElements3() throws Exception {
+ try {
+ List<Element> elements = new ArrayList<>();
+ Protein protein = new GenericProtein("id");
+ protein.setName("GLUD1");
+ protein.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "GLUD1"));
+ protein.addMiriamData(new MiriamData(MiriamType.ENTREZ, "2746"));
+ elements.add(protein);
+ List<Drug> drugs = drugService.getForTargets(elements, new DbSearchCriteria());
+
+ assertNotNull(drugs);
+ assertTrue(drugs.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testObjectToDrugTargetList() throws Exception {
+ try {
+ Drug drug = drugService.getByName("AMANTADINE", new DbSearchCriteria());
+ Drug drug2 = drugBankHTMLParser.findDrug("AMANTADINE");
+
+ assertTrue(drug2.getTargets().size() <= drug.getTargets().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAspirinToDrugTargetList() throws Exception {
+ try {
+ Drug drug = drugService.getByName("Aspirin", new DbSearchCriteria());
+ Drug drug2 = drugBankHTMLParser.findDrug("Aspirin");
+
+ assertTrue(drug2.getTargets().size() <= drug.getTargets().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAspirinSynonyms() throws Exception {
+ try {
+ Drug drug = drugService.getByName("Aspirin", new DbSearchCriteria());
+
+ Set<String> synonyms = new HashSet<String>();
+ for (String string : drug.getSynonyms()) {
+ assertFalse("Duplicate entry in drug synonym: " + string, synonyms.contains(string));
+ synonyms.add(string);
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetSuggestedQueryList() throws Exception {
+ try {
+ List<String> result = drugService.getSuggestedQueryList(new Project(), null);
+ assertEquals(0, result.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/service/src/test/java/lcsb/mapviewer/services/search/mirna/MiRNAServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/search/mirna/MiRNAServiceTest.java
index 224e138b44..8049360871 100644
--- a/service/src/test/java/lcsb/mapviewer/services/search/mirna/MiRNAServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/search/mirna/MiRNAServiceTest.java
@@ -1,48 +1,48 @@
-package lcsb.mapviewer.services.search.mirna;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.services.ServiceTestFunctions;
-import lcsb.mapviewer.services.search.mirna.IMiRNAService;
-
-public class MiRNAServiceTest extends ServiceTestFunctions {
- Logger logger = Logger.getLogger(MiRNAServiceTest.class);
-
- @Autowired
- protected IMiRNAService miRNAService;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testCacheStub() throws Exception {
- try {
- // CellDesignerXmlParser parser = new CellDesignerXmlParser();
- // Model model = parser.createModel(new
- // ConverterParams().filename("testFiles/pd_full/PD_130909.xml"));
- Model model = new ModelFullIndexed(null);
- miRNAService.cacheDataForModel(model, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- logger.debug("Progress: " + progress);
- }
- });
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.services.search.mirna;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.services.ServiceTestFunctions;
+import lcsb.mapviewer.services.search.mirna.IMiRNAService;
+
+public class MiRNAServiceTest extends ServiceTestFunctions {
+ Logger logger = Logger.getLogger(MiRNAServiceTest.class);
+
+ @Autowired
+ protected IMiRNAService miRNAService;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testCacheStub() throws Exception {
+ try {
+ // CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ // Model model = parser.createModel(new
+ // ConverterParams().filename("testFiles/pd_full/PD_130909.xml"));
+ Model model = new ModelFullIndexed(null);
+ miRNAService.cacheDataForModel(model, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ logger.debug("Progress: " + progress);
+ }
+ });
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/service/src/test/java/lcsb/mapviewer/services/utils/AllUtilsTests.java b/service/src/test/java/lcsb/mapviewer/services/utils/AllUtilsTests.java
index e966305a09..3d06600136 100644
--- a/service/src/test/java/lcsb/mapviewer/services/utils/AllUtilsTests.java
+++ b/service/src/test/java/lcsb/mapviewer/services/utils/AllUtilsTests.java
@@ -1,15 +1,15 @@
-package lcsb.mapviewer.services.utils;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ ColorSchemaReaderTest.class, //
- ColorSchemaReaderXlsTest.class, //
- ColorSchemaReaderXlsxTest.class, //
- EmailSenderTest.class,//
-})
-public class AllUtilsTests {
-
-}
+package lcsb.mapviewer.services.utils;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+@RunWith(Suite.class)
+@SuiteClasses({ ColorSchemaReaderTest.class, //
+ ColorSchemaReaderXlsTest.class, //
+ ColorSchemaReaderXlsxTest.class, //
+ EmailSenderTest.class,//
+})
+public class AllUtilsTests {
+
+}
diff --git a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderXlsTest.java b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderXlsTest.java
index bcca8eab38..6b4bab84fd 100644
--- a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderXlsTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderXlsTest.java
@@ -1,135 +1,135 @@
-package lcsb.mapviewer.services.utils;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import java.awt.Color;
-import java.util.Collection;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
-import lcsb.mapviewer.services.ServiceTestFunctions;
-import lcsb.mapviewer.services.utils.ColorSchemaXlsxReader;
-
-public class ColorSchemaReaderXlsTest extends ServiceTestFunctions {
- Logger logger = Logger.getLogger(ColorSchemaReaderXlsTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testReadSchema() throws Exception {
- try {
- ColorSchemaXlsxReader reader = new ColorSchemaXlsxReader();
-
- Collection<ColorSchema> schemas = null;
-
- schemas = reader.readColorSchema("testFiles/enricoData/enricoData.xls", "ageing" );
-
- assertNotNull(schemas);
- assertEquals(412, schemas.size());
-
- schemas = reader.readColorSchema("testFiles/enricoData/enricoData.xls", "ge001");
-
- assertNotNull(schemas);
- assertEquals(3057, schemas.size());
-
- schemas = reader.readColorSchema("testFiles/enricoData/enricoData.xls", "ge005");
-
- assertNotNull(schemas);
- assertEquals(4338, schemas.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReadSchema2() throws Exception {
- try {
- ColorSchemaXlsxReader reader = new ColorSchemaXlsxReader();
-
- Collection<ColorSchema> schemas = reader.readColorSchema("testFiles/coloring/coloring.xls", "goodSchema");
-
- assertNotNull(schemas);
- assertEquals(3, schemas.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReadSchema3() throws Exception {
- try {
- try {
- ColorSchemaXlsxReader reader = new ColorSchemaXlsxReader();
- reader.readColorSchema("testFiles/coloring/coloring.xls", "wrongSchema");
- fail("Excepion expected");
- } catch (InvalidColorSchemaException e) {
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProblematicStephanSchema3() throws Exception {
- try {
- ColorSchemaXlsxReader reader = new ColorSchemaXlsxReader();
- Collection<ColorSchema> schemas = reader.readColorSchema("testFiles/coloring/coloring.xls", "problematicSchema");
- assertNotNull(schemas);
- assertEquals(329, schemas.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReadReactionSchema() throws Exception {
- try {
- ColorSchemaXlsxReader reader = new ColorSchemaXlsxReader();
- Collection<ColorSchema> collection = reader.readColorSchema("testFiles/coloring/coloring.xls", "reactionSchema");
- assertEquals(1, collection.size());
- ColorSchema schema = collection.iterator().next();
- assertEquals("re1", schema.getElementId());
- assertEquals(3.0, schema.getLineWidth(), EPSILON);
- assertEquals(Color.RED, schema.getColor());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test(timeout=15000)
- public void testNextVersionReadSchema() throws Exception {
- try {
- ColorSchemaXlsxReader reader = new ColorSchemaXlsxReader();
-
- Collection<ColorSchema> schemas = reader.readColorSchema("testFiles/coloring/coloring.xls", "goodLayout.v=1.0");
-
- assertNotNull(schemas);
- assertEquals(3, schemas.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.services.utils;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import java.awt.Color;
+import java.util.Collection;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
+import lcsb.mapviewer.services.ServiceTestFunctions;
+import lcsb.mapviewer.services.utils.ColorSchemaXlsxReader;
+
+public class ColorSchemaReaderXlsTest extends ServiceTestFunctions {
+ Logger logger = Logger.getLogger(ColorSchemaReaderXlsTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testReadSchema() throws Exception {
+ try {
+ ColorSchemaXlsxReader reader = new ColorSchemaXlsxReader();
+
+ Collection<ColorSchema> schemas = null;
+
+ schemas = reader.readColorSchema("testFiles/enricoData/enricoData.xls", "ageing" );
+
+ assertNotNull(schemas);
+ assertEquals(412, schemas.size());
+
+ schemas = reader.readColorSchema("testFiles/enricoData/enricoData.xls", "ge001");
+
+ assertNotNull(schemas);
+ assertEquals(3057, schemas.size());
+
+ schemas = reader.readColorSchema("testFiles/enricoData/enricoData.xls", "ge005");
+
+ assertNotNull(schemas);
+ assertEquals(4338, schemas.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReadSchema2() throws Exception {
+ try {
+ ColorSchemaXlsxReader reader = new ColorSchemaXlsxReader();
+
+ Collection<ColorSchema> schemas = reader.readColorSchema("testFiles/coloring/coloring.xls", "goodSchema");
+
+ assertNotNull(schemas);
+ assertEquals(3, schemas.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReadSchema3() throws Exception {
+ try {
+ try {
+ ColorSchemaXlsxReader reader = new ColorSchemaXlsxReader();
+ reader.readColorSchema("testFiles/coloring/coloring.xls", "wrongSchema");
+ fail("Excepion expected");
+ } catch (InvalidColorSchemaException e) {
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProblematicStephanSchema3() throws Exception {
+ try {
+ ColorSchemaXlsxReader reader = new ColorSchemaXlsxReader();
+ Collection<ColorSchema> schemas = reader.readColorSchema("testFiles/coloring/coloring.xls", "problematicSchema");
+ assertNotNull(schemas);
+ assertEquals(329, schemas.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReadReactionSchema() throws Exception {
+ try {
+ ColorSchemaXlsxReader reader = new ColorSchemaXlsxReader();
+ Collection<ColorSchema> collection = reader.readColorSchema("testFiles/coloring/coloring.xls", "reactionSchema");
+ assertEquals(1, collection.size());
+ ColorSchema schema = collection.iterator().next();
+ assertEquals("re1", schema.getElementId());
+ assertEquals(3.0, schema.getLineWidth(), EPSILON);
+ assertEquals(Color.RED, schema.getColor());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test(timeout=15000)
+ public void testNextVersionReadSchema() throws Exception {
+ try {
+ ColorSchemaXlsxReader reader = new ColorSchemaXlsxReader();
+
+ Collection<ColorSchema> schemas = reader.readColorSchema("testFiles/coloring/coloring.xls", "goodLayout.v=1.0");
+
+ assertNotNull(schemas);
+ assertEquals(3, schemas.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderXlsxTest.java b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderXlsxTest.java
index e80d01d43b..42be532cd5 100644
--- a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderXlsxTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderXlsxTest.java
@@ -1,135 +1,135 @@
-package lcsb.mapviewer.services.utils;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import java.awt.Color;
-import java.util.Collection;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
-import lcsb.mapviewer.services.ServiceTestFunctions;
-import lcsb.mapviewer.services.utils.ColorSchemaXlsxReader;
-
-public class ColorSchemaReaderXlsxTest extends ServiceTestFunctions {
- Logger logger = Logger.getLogger(ColorSchemaReaderXlsxTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testReadSchema() throws Exception {
- try {
- ColorSchemaXlsxReader reader = new ColorSchemaXlsxReader();
-
- Collection<ColorSchema> schemas = null;
-
- schemas = reader.readColorSchema("testFiles/enricoData/enricoData.xlsx", "ageing" );
-
- assertNotNull(schemas);
- assertEquals(412, schemas.size());
-
- schemas = reader.readColorSchema("testFiles/enricoData/enricoData.xlsx", "ge001");
-
- assertNotNull(schemas);
- assertEquals(3057, schemas.size());
-
- schemas = reader.readColorSchema("testFiles/enricoData/enricoData.xlsx", "ge005");
-
- assertNotNull(schemas);
- assertEquals(4338, schemas.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReadSchema2() throws Exception {
- try {
- ColorSchemaXlsxReader reader = new ColorSchemaXlsxReader();
-
- Collection<ColorSchema> schemas = reader.readColorSchema("testFiles/coloring/coloring.xlsx", "goodSchema");
-
- assertNotNull(schemas);
- assertEquals(3, schemas.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReadSchema3() throws Exception {
- try {
- try {
- ColorSchemaXlsxReader reader = new ColorSchemaXlsxReader();
- reader.readColorSchema("testFiles/coloring/coloring.xlsx", "wrongSchema");
- fail("Excepion expected");
- } catch (InvalidColorSchemaException e) {
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProblematicStephanSchema3() throws Exception {
- try {
- ColorSchemaXlsxReader reader = new ColorSchemaXlsxReader();
- Collection<ColorSchema> schemas = reader.readColorSchema("testFiles/coloring/coloring.xlsx", "problematicSchema");
- assertNotNull(schemas);
- assertEquals(329, schemas.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReadReactionSchema() throws Exception {
- try {
- ColorSchemaXlsxReader reader = new ColorSchemaXlsxReader();
- Collection<ColorSchema> collection = reader.readColorSchema("testFiles/coloring/coloring.xlsx", "reactionSchema");
- assertEquals(1, collection.size());
- ColorSchema schema = collection.iterator().next();
- assertEquals("re1", schema.getElementId());
- assertEquals(3.0, schema.getLineWidth(), EPSILON);
- assertEquals(Color.RED, schema.getColor());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test(timeout=15000)
- public void testNextVersionReadSchema() throws Exception {
- try {
- ColorSchemaXlsxReader reader = new ColorSchemaXlsxReader();
-
- Collection<ColorSchema> schemas = reader.readColorSchema("testFiles/coloring/coloring.xlsx", "goodLayout.v=1.0");
-
- assertNotNull(schemas);
- assertEquals(3, schemas.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.services.utils;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import java.awt.Color;
+import java.util.Collection;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
+import lcsb.mapviewer.services.ServiceTestFunctions;
+import lcsb.mapviewer.services.utils.ColorSchemaXlsxReader;
+
+public class ColorSchemaReaderXlsxTest extends ServiceTestFunctions {
+ Logger logger = Logger.getLogger(ColorSchemaReaderXlsxTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testReadSchema() throws Exception {
+ try {
+ ColorSchemaXlsxReader reader = new ColorSchemaXlsxReader();
+
+ Collection<ColorSchema> schemas = null;
+
+ schemas = reader.readColorSchema("testFiles/enricoData/enricoData.xlsx", "ageing" );
+
+ assertNotNull(schemas);
+ assertEquals(412, schemas.size());
+
+ schemas = reader.readColorSchema("testFiles/enricoData/enricoData.xlsx", "ge001");
+
+ assertNotNull(schemas);
+ assertEquals(3057, schemas.size());
+
+ schemas = reader.readColorSchema("testFiles/enricoData/enricoData.xlsx", "ge005");
+
+ assertNotNull(schemas);
+ assertEquals(4338, schemas.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReadSchema2() throws Exception {
+ try {
+ ColorSchemaXlsxReader reader = new ColorSchemaXlsxReader();
+
+ Collection<ColorSchema> schemas = reader.readColorSchema("testFiles/coloring/coloring.xlsx", "goodSchema");
+
+ assertNotNull(schemas);
+ assertEquals(3, schemas.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReadSchema3() throws Exception {
+ try {
+ try {
+ ColorSchemaXlsxReader reader = new ColorSchemaXlsxReader();
+ reader.readColorSchema("testFiles/coloring/coloring.xlsx", "wrongSchema");
+ fail("Excepion expected");
+ } catch (InvalidColorSchemaException e) {
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProblematicStephanSchema3() throws Exception {
+ try {
+ ColorSchemaXlsxReader reader = new ColorSchemaXlsxReader();
+ Collection<ColorSchema> schemas = reader.readColorSchema("testFiles/coloring/coloring.xlsx", "problematicSchema");
+ assertNotNull(schemas);
+ assertEquals(329, schemas.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReadReactionSchema() throws Exception {
+ try {
+ ColorSchemaXlsxReader reader = new ColorSchemaXlsxReader();
+ Collection<ColorSchema> collection = reader.readColorSchema("testFiles/coloring/coloring.xlsx", "reactionSchema");
+ assertEquals(1, collection.size());
+ ColorSchema schema = collection.iterator().next();
+ assertEquals("re1", schema.getElementId());
+ assertEquals(3.0, schema.getLineWidth(), EPSILON);
+ assertEquals(Color.RED, schema.getColor());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test(timeout=15000)
+ public void testNextVersionReadSchema() throws Exception {
+ try {
+ ColorSchemaXlsxReader reader = new ColorSchemaXlsxReader();
+
+ Collection<ColorSchema> schemas = reader.readColorSchema("testFiles/coloring/coloring.xlsx", "goodLayout.v=1.0");
+
+ assertNotNull(schemas);
+ assertEquals(3, schemas.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/service/src/test/java/lcsb/mapviewer/services/utils/EmailSenderTest.java b/service/src/test/java/lcsb/mapviewer/services/utils/EmailSenderTest.java
index 1226c4dd30..78051d1aa7 100644
--- a/service/src/test/java/lcsb/mapviewer/services/utils/EmailSenderTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/utils/EmailSenderTest.java
@@ -1,39 +1,39 @@
-package lcsb.mapviewer.services.utils;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Ignore;
-import org.junit.Test;
-
-import lcsb.mapviewer.services.ServiceTestFunctions;
-
-public class EmailSenderTest extends ServiceTestFunctions {
- Logger logger = Logger.getLogger(EmailSenderTest.class);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- @Ignore("This is just a showcase")
- public void test() throws Exception {
- try {
- EmailSender emailSender = new EmailSender(configurationService);
- List<String> recipients = new ArrayList<>();
- recipients.add("piotr.gawron@uni.lu");
- emailSender.sendEmail(recipients, new ArrayList<>(), "Test subject", "Test content");
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.services.utils;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Ignore;
+import org.junit.Test;
+
+import lcsb.mapviewer.services.ServiceTestFunctions;
+
+public class EmailSenderTest extends ServiceTestFunctions {
+ Logger logger = Logger.getLogger(EmailSenderTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ @Ignore("This is just a showcase")
+ public void test() throws Exception {
+ try {
+ EmailSender emailSender = new EmailSender(configurationService);
+ List<String> recipients = new ArrayList<>();
+ recipients.add("piotr.gawron@uni.lu");
+ emailSender.sendEmail(recipients, new ArrayList<>(), "Test subject", "Test content");
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/utils/CssContentTypeFilter.java b/web/src/main/java/lcsb/mapviewer/bean/utils/CssContentTypeFilter.java
index 2cce945990..42af8c57c7 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/utils/CssContentTypeFilter.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/utils/CssContentTypeFilter.java
@@ -1,52 +1,52 @@
-package lcsb.mapviewer.bean.utils;
-
-import java.io.IOException;
-
-import javax.servlet.Filter;
-import javax.servlet.FilterChain;
-import javax.servlet.FilterConfig;
-import javax.servlet.ServletException;
-import javax.servlet.ServletRequest;
-import javax.servlet.ServletResponse;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
-import lcsb.mapviewer.common.MimeType;
-
-import org.apache.log4j.Logger;
-
-/**
- * This class sets content type for requests accessing css files. We have to do
- * it as sometimes JSF forgets to set content type and Internet Explorer is
- * going crazy because of that.
- *
- * @author Piotr Gawron
- *
- */
-public class CssContentTypeFilter implements Filter {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(CssContentTypeFilter.class);
-
- @Override
- public void init(FilterConfig config) throws ServletException {
- }
-
- @Override
- public void doFilter(ServletRequest req, ServletResponse res, FilterChain chain) throws IOException, ServletException {
- HttpServletRequest request = (HttpServletRequest) req;
- HttpServletResponse response = (HttpServletResponse) res;
- if (request.getContentType() == null && request.getRequestURL().toString().contains("css.xhtml")) {
- response.setContentType(MimeType.CSS.getTextRepresentation());
- response.setHeader("Content-Type", MimeType.CSS.getTextRepresentation());
- }
- chain.doFilter(req, response);
- }
-
- @Override
- public void destroy() {
- }
-
-}
+package lcsb.mapviewer.bean.utils;
+
+import java.io.IOException;
+
+import javax.servlet.Filter;
+import javax.servlet.FilterChain;
+import javax.servlet.FilterConfig;
+import javax.servlet.ServletException;
+import javax.servlet.ServletRequest;
+import javax.servlet.ServletResponse;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import lcsb.mapviewer.common.MimeType;
+
+import org.apache.log4j.Logger;
+
+/**
+ * This class sets content type for requests accessing css files. We have to do
+ * it as sometimes JSF forgets to set content type and Internet Explorer is
+ * going crazy because of that.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CssContentTypeFilter implements Filter {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(CssContentTypeFilter.class);
+
+ @Override
+ public void init(FilterConfig config) throws ServletException {
+ }
+
+ @Override
+ public void doFilter(ServletRequest req, ServletResponse res, FilterChain chain) throws IOException, ServletException {
+ HttpServletRequest request = (HttpServletRequest) req;
+ HttpServletResponse response = (HttpServletResponse) res;
+ if (request.getContentType() == null && request.getRequestURL().toString().contains("css.xhtml")) {
+ response.setContentType(MimeType.CSS.getTextRepresentation());
+ response.setHeader("Content-Type", MimeType.CSS.getTextRepresentation());
+ }
+ chain.doFilter(req, response);
+ }
+
+ @Override
+ public void destroy() {
+ }
+
+}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/utils/CustomFilter.java b/web/src/main/java/lcsb/mapviewer/bean/utils/CustomFilter.java
index 193f7a3146..664a441cba 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/utils/CustomFilter.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/utils/CustomFilter.java
@@ -1,51 +1,51 @@
-package lcsb.mapviewer.bean.utils;
-
-import java.io.IOException;
-
-import javax.servlet.Filter;
-import javax.servlet.FilterChain;
-import javax.servlet.FilterConfig;
-import javax.servlet.ServletException;
-import javax.servlet.ServletRequest;
-import javax.servlet.ServletResponse;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
-import org.apache.log4j.Logger;
-
-/**
- * This class should be used only for debug purpose. It wrapps
- * {@link ServletResponse} into {@link CustomHttpServletResponseWrapper} which
- * allows to follow what is going on in {@link Filter filters} and how data is
- * obtained by JSF.
- *
- * @author Piotr Gawron
- *
- */
-public class CustomFilter implements Filter {
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(CustomFilter.class);
-
- @Override
- public void init(FilterConfig config) throws ServletException {
- }
-
- @Override
- public void doFilter(ServletRequest req, ServletResponse res, FilterChain chain) throws IOException, ServletException {
- HttpServletRequest request = (HttpServletRequest) req;
- HttpServletResponse response = (HttpServletResponse) res;
-
- logger.debug("URI: " + request.getRequestURI());
- logger.debug("URL: " + request.getRequestURL());
- logger.debug("val: " + response.getBufferSize());
- chain.doFilter(req, new CustomHttpServletResponseWrapper(response));
- logger.debug("Content after: " + response.getContentType());
- }
-
- @Override
- public void destroy() {
- }
-
-}
+package lcsb.mapviewer.bean.utils;
+
+import java.io.IOException;
+
+import javax.servlet.Filter;
+import javax.servlet.FilterChain;
+import javax.servlet.FilterConfig;
+import javax.servlet.ServletException;
+import javax.servlet.ServletRequest;
+import javax.servlet.ServletResponse;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import org.apache.log4j.Logger;
+
+/**
+ * This class should be used only for debug purpose. It wrapps
+ * {@link ServletResponse} into {@link CustomHttpServletResponseWrapper} which
+ * allows to follow what is going on in {@link Filter filters} and how data is
+ * obtained by JSF.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CustomFilter implements Filter {
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(CustomFilter.class);
+
+ @Override
+ public void init(FilterConfig config) throws ServletException {
+ }
+
+ @Override
+ public void doFilter(ServletRequest req, ServletResponse res, FilterChain chain) throws IOException, ServletException {
+ HttpServletRequest request = (HttpServletRequest) req;
+ HttpServletResponse response = (HttpServletResponse) res;
+
+ logger.debug("URI: " + request.getRequestURI());
+ logger.debug("URL: " + request.getRequestURL());
+ logger.debug("val: " + response.getBufferSize());
+ chain.doFilter(req, new CustomHttpServletResponseWrapper(response));
+ logger.debug("Content after: " + response.getContentType());
+ }
+
+ @Override
+ public void destroy() {
+ }
+
+}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/utils/CustomHttpServletResponseWrapper.java b/web/src/main/java/lcsb/mapviewer/bean/utils/CustomHttpServletResponseWrapper.java
index 75b1cd48d7..d856d8a4aa 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/utils/CustomHttpServletResponseWrapper.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/utils/CustomHttpServletResponseWrapper.java
@@ -1,248 +1,248 @@
-package lcsb.mapviewer.bean.utils;
-
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.util.Locale;
-
-import javax.servlet.ServletOutputStream;
-import javax.servlet.http.Cookie;
-import javax.servlet.http.HttpServletResponse;
-import javax.servlet.http.HttpServletResponseWrapper;
-
-import org.apache.log4j.Logger;
-
-/**
- * This class should be used only for debugging. It's a wrapper to standard JSF
- * {@link HttpServletResponse} which logs all activity in the servlet response.
- * To use it properly one can create a {@link javax.servlet.Filter Filter} that
- * will only encapsulate response with this class and ass it via
- * {@link javax.servlet.Filter#doFilter(javax.servlet.ServletRequest, javax.servlet.ServletResponse, javax.servlet.FilterChain)}
- * method.
- *
- * @author Piotr Gawron
- *
- */
-public class CustomHttpServletResponseWrapper extends HttpServletResponseWrapper {
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(CustomHttpServletResponseWrapper.class);
-
- /**
- * Default constructor.
- *
- * @param response
- * {@link HttpServletResponse} that should be encapsluated
- */
- public CustomHttpServletResponseWrapper(HttpServletResponse response) {
- super(response);
- logger.debug("Constructor: " + response);
- }
-
- @Override
- public PrintWriter getWriter() throws IOException {
- logger.debug("getWriter");
- return this.getWriter();
- }
-
- @Override
- public ServletOutputStream getOutputStream() throws IOException {
- logger.debug("getOutputStream");
- logger.debug(new Exception(), new Exception());
- return this.getOutputStream();
- }
-
- @Override
- public String getCharacterEncoding() {
- logger.debug("getCharacterEncoding");
- return this.getCharacterEncoding();
- }
-
- @Override
- public String getContentType() {
- logger.debug("getContentType");
- return this.getContentType();
- }
-
- @Override
- public void setCharacterEncoding(String charset) {
- logger.debug("setCharacterEncoding");
- this.setCharacterEncoding(charset);
- }
-
- @Override
- public void setContentLength(int len) {
- logger.debug("setContentLength");
- this.setContentLength(len);
- }
-
- @Override
- public void setContentType(String type) {
- logger.debug("setContentType: " + type);
- logger.debug(new Exception(), new Exception());
- this.setContentType(type);
- }
-
- @Override
- public void setBufferSize(int size) {
- logger.debug("setBufferSize");
- this.setBufferSize(size);
- }
-
- @Override
- public int getBufferSize() {
- logger.debug("getBufferSize");
- return this.getBufferSize();
- }
-
- @Override
- public void flushBuffer() throws IOException {
- logger.debug("flushBuffer");
- this.flushBuffer();
- }
-
- @Override
- public void resetBuffer() {
- logger.debug("resetBuffer");
- this.resetBuffer();
- }
-
- @Override
- public boolean isCommitted() {
- logger.debug("isCommitted");
- return this.isCommitted();
- }
-
- @Override
- public void reset() {
- logger.debug("reset");
- this.reset();
- }
-
- @Override
- public void setLocale(Locale loc) {
- logger.debug("setLocale");
- this.setLocale(loc);
- }
-
- @Override
- public Locale getLocale() {
- logger.debug("getLocale");
- return this.getLocale();
- }
-
- @Override
- public void addCookie(Cookie cookie) {
- logger.debug("addCookie");
- this.addCookie(cookie);
- }
-
- @Override
- public boolean containsHeader(String name) {
- logger.debug("containsHeader");
- return this.containsHeader(name);
- }
-
- @Override
- public String encodeURL(String url) {
- logger.debug("encodeURL");
- return this.encodeURL(url);
- }
-
- @Override
- public String encodeRedirectURL(String url) {
- logger.debug("encodeRedirectURL");
- return this.encodeRedirectURL(url);
- }
-
- @Override
- public String encodeUrl(String url) {
- logger.debug("encodeUrl");
- return this.encodeUrl(url);
- }
-
- @Override
- public String encodeRedirectUrl(String url) {
- logger.debug("encodeRedirectUrl");
- return this.encodeRedirectUrl(url);
- }
-
- @Override
- public void sendError(int sc, String msg) throws IOException {
- logger.debug("sendError");
- this.sendError(sc);
-
- }
-
- @Override
- public void sendError(int sc) throws IOException {
- logger.debug("sendError");
- this.sendError(sc);
-
- }
-
- @Override
- public void sendRedirect(String location) throws IOException {
- logger.debug("sendRedirect");
- this.sendRedirect(location);
-
- }
-
- @Override
- public void setDateHeader(String name, long date) {
- logger.debug("setDateHeader");
- this.setDateHeader(name, date);
-
- }
-
- @Override
- public void addDateHeader(String name, long date) {
- logger.debug("addDateHeader");
- this.addDateHeader(name, date);
-
- }
-
- @Override
- public void setHeader(String name, String value) {
- logger.debug("setHeader");
- this.setHeader(name, value);
-
- }
-
- @Override
- public void addHeader(String name, String value) {
- logger.debug("addHeader: " + name + " - " + value);
- this.addHeader(name, value);
-
- }
-
- @Override
- public void setIntHeader(String name, int value) {
- logger.debug("setIntHeader");
- this.setIntHeader(name, value);
-
- }
-
- @Override
- public void addIntHeader(String name, int value) {
- logger.debug("addIntHeader");
- this.addIntHeader(name, value);
-
- }
-
- @Override
- public void setStatus(int sc) {
- logger.debug("setStatus: " + sc);
- this.setStatus(sc);
-
- }
-
- @Override
- public void setStatus(int sc, String sm) {
- logger.debug("setStatus");
- this.setStatus(sc, sm);
-
- }
-
-}
+package lcsb.mapviewer.bean.utils;
+
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.Locale;
+
+import javax.servlet.ServletOutputStream;
+import javax.servlet.http.Cookie;
+import javax.servlet.http.HttpServletResponse;
+import javax.servlet.http.HttpServletResponseWrapper;
+
+import org.apache.log4j.Logger;
+
+/**
+ * This class should be used only for debugging. It's a wrapper to standard JSF
+ * {@link HttpServletResponse} which logs all activity in the servlet response.
+ * To use it properly one can create a {@link javax.servlet.Filter Filter} that
+ * will only encapsulate response with this class and ass it via
+ * {@link javax.servlet.Filter#doFilter(javax.servlet.ServletRequest, javax.servlet.ServletResponse, javax.servlet.FilterChain)}
+ * method.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CustomHttpServletResponseWrapper extends HttpServletResponseWrapper {
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(CustomHttpServletResponseWrapper.class);
+
+ /**
+ * Default constructor.
+ *
+ * @param response
+ * {@link HttpServletResponse} that should be encapsluated
+ */
+ public CustomHttpServletResponseWrapper(HttpServletResponse response) {
+ super(response);
+ logger.debug("Constructor: " + response);
+ }
+
+ @Override
+ public PrintWriter getWriter() throws IOException {
+ logger.debug("getWriter");
+ return this.getWriter();
+ }
+
+ @Override
+ public ServletOutputStream getOutputStream() throws IOException {
+ logger.debug("getOutputStream");
+ logger.debug(new Exception(), new Exception());
+ return this.getOutputStream();
+ }
+
+ @Override
+ public String getCharacterEncoding() {
+ logger.debug("getCharacterEncoding");
+ return this.getCharacterEncoding();
+ }
+
+ @Override
+ public String getContentType() {
+ logger.debug("getContentType");
+ return this.getContentType();
+ }
+
+ @Override
+ public void setCharacterEncoding(String charset) {
+ logger.debug("setCharacterEncoding");
+ this.setCharacterEncoding(charset);
+ }
+
+ @Override
+ public void setContentLength(int len) {
+ logger.debug("setContentLength");
+ this.setContentLength(len);
+ }
+
+ @Override
+ public void setContentType(String type) {
+ logger.debug("setContentType: " + type);
+ logger.debug(new Exception(), new Exception());
+ this.setContentType(type);
+ }
+
+ @Override
+ public void setBufferSize(int size) {
+ logger.debug("setBufferSize");
+ this.setBufferSize(size);
+ }
+
+ @Override
+ public int getBufferSize() {
+ logger.debug("getBufferSize");
+ return this.getBufferSize();
+ }
+
+ @Override
+ public void flushBuffer() throws IOException {
+ logger.debug("flushBuffer");
+ this.flushBuffer();
+ }
+
+ @Override
+ public void resetBuffer() {
+ logger.debug("resetBuffer");
+ this.resetBuffer();
+ }
+
+ @Override
+ public boolean isCommitted() {
+ logger.debug("isCommitted");
+ return this.isCommitted();
+ }
+
+ @Override
+ public void reset() {
+ logger.debug("reset");
+ this.reset();
+ }
+
+ @Override
+ public void setLocale(Locale loc) {
+ logger.debug("setLocale");
+ this.setLocale(loc);
+ }
+
+ @Override
+ public Locale getLocale() {
+ logger.debug("getLocale");
+ return this.getLocale();
+ }
+
+ @Override
+ public void addCookie(Cookie cookie) {
+ logger.debug("addCookie");
+ this.addCookie(cookie);
+ }
+
+ @Override
+ public boolean containsHeader(String name) {
+ logger.debug("containsHeader");
+ return this.containsHeader(name);
+ }
+
+ @Override
+ public String encodeURL(String url) {
+ logger.debug("encodeURL");
+ return this.encodeURL(url);
+ }
+
+ @Override
+ public String encodeRedirectURL(String url) {
+ logger.debug("encodeRedirectURL");
+ return this.encodeRedirectURL(url);
+ }
+
+ @Override
+ public String encodeUrl(String url) {
+ logger.debug("encodeUrl");
+ return this.encodeUrl(url);
+ }
+
+ @Override
+ public String encodeRedirectUrl(String url) {
+ logger.debug("encodeRedirectUrl");
+ return this.encodeRedirectUrl(url);
+ }
+
+ @Override
+ public void sendError(int sc, String msg) throws IOException {
+ logger.debug("sendError");
+ this.sendError(sc);
+
+ }
+
+ @Override
+ public void sendError(int sc) throws IOException {
+ logger.debug("sendError");
+ this.sendError(sc);
+
+ }
+
+ @Override
+ public void sendRedirect(String location) throws IOException {
+ logger.debug("sendRedirect");
+ this.sendRedirect(location);
+
+ }
+
+ @Override
+ public void setDateHeader(String name, long date) {
+ logger.debug("setDateHeader");
+ this.setDateHeader(name, date);
+
+ }
+
+ @Override
+ public void addDateHeader(String name, long date) {
+ logger.debug("addDateHeader");
+ this.addDateHeader(name, date);
+
+ }
+
+ @Override
+ public void setHeader(String name, String value) {
+ logger.debug("setHeader");
+ this.setHeader(name, value);
+
+ }
+
+ @Override
+ public void addHeader(String name, String value) {
+ logger.debug("addHeader: " + name + " - " + value);
+ this.addHeader(name, value);
+
+ }
+
+ @Override
+ public void setIntHeader(String name, int value) {
+ logger.debug("setIntHeader");
+ this.setIntHeader(name, value);
+
+ }
+
+ @Override
+ public void addIntHeader(String name, int value) {
+ logger.debug("addIntHeader");
+ this.addIntHeader(name, value);
+
+ }
+
+ @Override
+ public void setStatus(int sc) {
+ logger.debug("setStatus: " + sc);
+ this.setStatus(sc);
+
+ }
+
+ @Override
+ public void setStatus(int sc, String sm) {
+ logger.debug("setStatus");
+ this.setStatus(sc, sm);
+
+ }
+
+}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/utils/IPrimefacesUtils.java b/web/src/main/java/lcsb/mapviewer/bean/utils/IPrimefacesUtils.java
index 16f55d2cba..2311151db3 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/utils/IPrimefacesUtils.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/utils/IPrimefacesUtils.java
@@ -1,132 +1,132 @@
-package lcsb.mapviewer.bean.utils;
-
-import java.util.Map;
-
-import javax.faces.component.UIComponent;
-
-/**
- * Intefrace of the class that access data about connection and PF framework in
- * general.
- *
- * @author Piotr Gawron
- *
- */
-public interface IPrimefacesUtils {
- /**
- * Returns value of the request parameter.
- *
- * @param name
- * name of the parameter
- * @return value of the request parameter
- */
- String getRequestParameter(String name);
-
- /**
- * Returns path on hard drive to the project.
- *
- * @return path where the projest is run
- */
- String getPath();
-
- /**
- * Returns ip address of current client.
- *
- * @return IP addresss of the client
- */
- String getClientIpAddress();
-
- /**
- * Sends an error message to the client.
- *
- * @param message
- * error message to be sent
- */
- void error(String message);
-
- /**
- * Sends an info message to client.
- *
- * @param message
- * info message to be sent
- */
- void info(String message);
-
- /**
- * Returns version of primefaces.
- *
- * @return version of primefaces library
- */
- String getVersion();
-
- /**
- * Returns a {@link UIComponent} corresponding to the client side component
- * with the identifier given in the parameter.
- *
- * @param id
- * identifier of a component
- * @return {@link UIComponent} corresponding to the client side component with
- * the identifier given in the parameter
- */
- UIComponent findComponent(String id);
-
- /**
- * Adds parameter to a ajax response.
- *
- * @param key
- * name of the parameter
- * @param value
- * value of the parameter
- */
- void addCallbackParam(String key, Object value);
-
- /**
- * Returns request parameters map.
- *
- * @return request parameters map
- */
- Map<String, String> getRequestParameterMap();
-
- /**
- * Adds a parameter that will be stored in user session.
- *
- * @param key
- * name of the parameter
- * @param value
- * value of the parameter
- */
- void addSessionParam(String key, Object value);
-
- /**
- * Gets a value of the parameter stored in user session.
- *
- * @param key
- * name of the parameter
- * @return value of the user session parameter
- */
- Object getSessionParam(String key);
-
- /**
- * Creates http session if session hasn't been created yet.
- */
- void createSession();
-
- /**
- * Returns bean identified by {@link Class}.
- *
- * @param clazz
- * class of the bean
- * @param <T>
- * class of the bean
- * @return bean identified by {@link Class}
- */
- <T> T findBean(Class<T> clazz);
-
- /**
- * Executes javascript code on client.
- *
- * @param javascript
- * code to execute
- */
- void executeJavascript(String javascript);
-
+package lcsb.mapviewer.bean.utils;
+
+import java.util.Map;
+
+import javax.faces.component.UIComponent;
+
+/**
+ * Intefrace of the class that access data about connection and PF framework in
+ * general.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface IPrimefacesUtils {
+ /**
+ * Returns value of the request parameter.
+ *
+ * @param name
+ * name of the parameter
+ * @return value of the request parameter
+ */
+ String getRequestParameter(String name);
+
+ /**
+ * Returns path on hard drive to the project.
+ *
+ * @return path where the projest is run
+ */
+ String getPath();
+
+ /**
+ * Returns ip address of current client.
+ *
+ * @return IP addresss of the client
+ */
+ String getClientIpAddress();
+
+ /**
+ * Sends an error message to the client.
+ *
+ * @param message
+ * error message to be sent
+ */
+ void error(String message);
+
+ /**
+ * Sends an info message to client.
+ *
+ * @param message
+ * info message to be sent
+ */
+ void info(String message);
+
+ /**
+ * Returns version of primefaces.
+ *
+ * @return version of primefaces library
+ */
+ String getVersion();
+
+ /**
+ * Returns a {@link UIComponent} corresponding to the client side component
+ * with the identifier given in the parameter.
+ *
+ * @param id
+ * identifier of a component
+ * @return {@link UIComponent} corresponding to the client side component with
+ * the identifier given in the parameter
+ */
+ UIComponent findComponent(String id);
+
+ /**
+ * Adds parameter to a ajax response.
+ *
+ * @param key
+ * name of the parameter
+ * @param value
+ * value of the parameter
+ */
+ void addCallbackParam(String key, Object value);
+
+ /**
+ * Returns request parameters map.
+ *
+ * @return request parameters map
+ */
+ Map<String, String> getRequestParameterMap();
+
+ /**
+ * Adds a parameter that will be stored in user session.
+ *
+ * @param key
+ * name of the parameter
+ * @param value
+ * value of the parameter
+ */
+ void addSessionParam(String key, Object value);
+
+ /**
+ * Gets a value of the parameter stored in user session.
+ *
+ * @param key
+ * name of the parameter
+ * @return value of the user session parameter
+ */
+ Object getSessionParam(String key);
+
+ /**
+ * Creates http session if session hasn't been created yet.
+ */
+ void createSession();
+
+ /**
+ * Returns bean identified by {@link Class}.
+ *
+ * @param clazz
+ * class of the bean
+ * @param <T>
+ * class of the bean
+ * @return bean identified by {@link Class}
+ */
+ <T> T findBean(Class<T> clazz);
+
+ /**
+ * Executes javascript code on client.
+ *
+ * @param javascript
+ * code to execute
+ */
+ void executeJavascript(String javascript);
+
}
\ No newline at end of file
diff --git a/web/src/main/java/lcsb/mapviewer/bean/utils/JsfAjaxAccessControlAllowFilter.java b/web/src/main/java/lcsb/mapviewer/bean/utils/JsfAjaxAccessControlAllowFilter.java
index f4e265dd9b..71020b035e 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/utils/JsfAjaxAccessControlAllowFilter.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/utils/JsfAjaxAccessControlAllowFilter.java
@@ -1,44 +1,44 @@
-package lcsb.mapviewer.bean.utils;
-
-import java.io.IOException;
-
-import javax.servlet.Filter;
-import javax.servlet.FilterChain;
-import javax.servlet.FilterConfig;
-import javax.servlet.ServletException;
-import javax.servlet.ServletRequest;
-import javax.servlet.ServletResponse;
-import javax.servlet.http.HttpServletResponse;
-
-import org.apache.log4j.Logger;
-
-/**
- * This filter enables ajax queries from all domains. It should be used for
- * restfull API.
- *
- * @author Piotr Gawron
- *
- */
-public class JsfAjaxAccessControlAllowFilter implements Filter {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(JsfAjaxAccessControlAllowFilter.class);
-
- @Override
- public void init(FilterConfig config) throws ServletException {
- }
-
- @Override
- public void doFilter(ServletRequest req, ServletResponse res, FilterChain chain) throws IOException, ServletException {
- HttpServletResponse response = (HttpServletResponse) res;
- response.addHeader("Access-Control-Allow-Origin", "*");
- chain.doFilter(req, response);
- }
-
- @Override
- public void destroy() {
- }
-
-}
+package lcsb.mapviewer.bean.utils;
+
+import java.io.IOException;
+
+import javax.servlet.Filter;
+import javax.servlet.FilterChain;
+import javax.servlet.FilterConfig;
+import javax.servlet.ServletException;
+import javax.servlet.ServletRequest;
+import javax.servlet.ServletResponse;
+import javax.servlet.http.HttpServletResponse;
+
+import org.apache.log4j.Logger;
+
+/**
+ * This filter enables ajax queries from all domains. It should be used for
+ * restfull API.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class JsfAjaxAccessControlAllowFilter implements Filter {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(JsfAjaxAccessControlAllowFilter.class);
+
+ @Override
+ public void init(FilterConfig config) throws ServletException {
+ }
+
+ @Override
+ public void doFilter(ServletRequest req, ServletResponse res, FilterChain chain) throws IOException, ServletException {
+ HttpServletResponse response = (HttpServletResponse) res;
+ response.addHeader("Access-Control-Allow-Origin", "*");
+ chain.doFilter(req, response);
+ }
+
+ @Override
+ public void destroy() {
+ }
+
+}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/utils/PrimefacesUtils.java b/web/src/main/java/lcsb/mapviewer/bean/utils/PrimefacesUtils.java
index 42e75d73ce..127c796069 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/utils/PrimefacesUtils.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/utils/PrimefacesUtils.java
@@ -1,124 +1,124 @@
-package lcsb.mapviewer.bean.utils;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.Map;
-
-import javax.faces.application.FacesMessage;
-import javax.faces.component.UIComponent;
-import javax.faces.context.FacesContext;
-import javax.servlet.http.HttpServletRequest;
-
-import org.apache.log4j.Logger;
-import org.primefaces.context.RequestContext;
-import org.springframework.web.jsf.FacesContextUtils;
-
-/**
- * Util class containing some useful methods in Primefaces.
- *
- * @author Piotr Gawron
- *
- */
-public class PrimefacesUtils implements IPrimefacesUtils {
- /**
- * Default class logger.
- */
- private final transient Logger logger = Logger.getLogger(PrimefacesUtils.class);
-
- /**
- * Default constructor.
- */
- public PrimefacesUtils() {
-
- }
-
- @Override
- public String getRequestParameter(final String name) {
- return FacesContext.getCurrentInstance().getExternalContext().getRequestParameterMap().get(name);
- }
-
- @Override
- public String getPath() {
- FacesContext context = FacesContext.getCurrentInstance();
- if (context != null) {
- return context.getExternalContext().getRealPath("/");
- } else {
- String path;
- try {
- path = new File(".").getCanonicalPath() + "/";
- } catch (IOException e) {
- logger.warn("Problem with detecting current path", e);
- path = "";
- }
- return path;
- }
-
- }
-
- @Override
- public String getClientIpAddress() {
- HttpServletRequest httpServletRequest = (HttpServletRequest) FacesContext.getCurrentInstance().getExternalContext().getRequest();
- String ipAddress = httpServletRequest.getRemoteAddr();
- if (ipAddress == null) {
- ipAddress = FacesContext.getCurrentInstance().getExternalContext().getRequestHeaderMap().get("X-FORWARDED-FOR");
- }
- return ipAddress;
- }
-
- @Override
- public void error(final String message) {
- logger.debug("Error sent to PF: " + message);
- FacesContext.getCurrentInstance().addMessage(null, new FacesMessage(FacesMessage.SEVERITY_ERROR, "Error!", message));
- }
-
- @Override
- public void info(final String message) {
- FacesContext.getCurrentInstance().addMessage(null, new FacesMessage(FacesMessage.SEVERITY_INFO, "Info", message));
- }
-
- @Override
- public String getVersion() {
- return RequestContext.getCurrentInstance().getApplicationContext().getConfig().getBuildVersion();
- }
-
- @Override
- public UIComponent findComponent(String id) {
- return FacesContext.getCurrentInstance().getViewRoot().findComponent(id);
- }
-
- @Override
- public void addCallbackParam(String key, Object value) {
- RequestContext.getCurrentInstance().addCallbackParam(key, value);
- }
-
- @Override
- public Map<String, String> getRequestParameterMap() {
- return FacesContext.getCurrentInstance().getExternalContext().getRequestParameterMap();
- }
-
- @Override
- public void addSessionParam(String key, Object value) {
- FacesContext.getCurrentInstance().getExternalContext().getSessionMap().put(key, value);
- }
-
- @Override
- public Object getSessionParam(String key) {
- return FacesContext.getCurrentInstance().getExternalContext().getSessionMap().get(key);
- }
-
- @Override
- public void createSession() {
- FacesContext.getCurrentInstance().getExternalContext().getSession(true);
- }
-
- @Override
- public <T> T findBean(Class<T> clazz) {
- return FacesContextUtils.getWebApplicationContext(FacesContext.getCurrentInstance()).getBean(clazz);
- }
-
- @Override
- public void executeJavascript(String javascript) {
- RequestContext.getCurrentInstance().execute(javascript);
- }
-
-}
+package lcsb.mapviewer.bean.utils;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.Map;
+
+import javax.faces.application.FacesMessage;
+import javax.faces.component.UIComponent;
+import javax.faces.context.FacesContext;
+import javax.servlet.http.HttpServletRequest;
+
+import org.apache.log4j.Logger;
+import org.primefaces.context.RequestContext;
+import org.springframework.web.jsf.FacesContextUtils;
+
+/**
+ * Util class containing some useful methods in Primefaces.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class PrimefacesUtils implements IPrimefacesUtils {
+ /**
+ * Default class logger.
+ */
+ private final transient Logger logger = Logger.getLogger(PrimefacesUtils.class);
+
+ /**
+ * Default constructor.
+ */
+ public PrimefacesUtils() {
+
+ }
+
+ @Override
+ public String getRequestParameter(final String name) {
+ return FacesContext.getCurrentInstance().getExternalContext().getRequestParameterMap().get(name);
+ }
+
+ @Override
+ public String getPath() {
+ FacesContext context = FacesContext.getCurrentInstance();
+ if (context != null) {
+ return context.getExternalContext().getRealPath("/");
+ } else {
+ String path;
+ try {
+ path = new File(".").getCanonicalPath() + "/";
+ } catch (IOException e) {
+ logger.warn("Problem with detecting current path", e);
+ path = "";
+ }
+ return path;
+ }
+
+ }
+
+ @Override
+ public String getClientIpAddress() {
+ HttpServletRequest httpServletRequest = (HttpServletRequest) FacesContext.getCurrentInstance().getExternalContext().getRequest();
+ String ipAddress = httpServletRequest.getRemoteAddr();
+ if (ipAddress == null) {
+ ipAddress = FacesContext.getCurrentInstance().getExternalContext().getRequestHeaderMap().get("X-FORWARDED-FOR");
+ }
+ return ipAddress;
+ }
+
+ @Override
+ public void error(final String message) {
+ logger.debug("Error sent to PF: " + message);
+ FacesContext.getCurrentInstance().addMessage(null, new FacesMessage(FacesMessage.SEVERITY_ERROR, "Error!", message));
+ }
+
+ @Override
+ public void info(final String message) {
+ FacesContext.getCurrentInstance().addMessage(null, new FacesMessage(FacesMessage.SEVERITY_INFO, "Info", message));
+ }
+
+ @Override
+ public String getVersion() {
+ return RequestContext.getCurrentInstance().getApplicationContext().getConfig().getBuildVersion();
+ }
+
+ @Override
+ public UIComponent findComponent(String id) {
+ return FacesContext.getCurrentInstance().getViewRoot().findComponent(id);
+ }
+
+ @Override
+ public void addCallbackParam(String key, Object value) {
+ RequestContext.getCurrentInstance().addCallbackParam(key, value);
+ }
+
+ @Override
+ public Map<String, String> getRequestParameterMap() {
+ return FacesContext.getCurrentInstance().getExternalContext().getRequestParameterMap();
+ }
+
+ @Override
+ public void addSessionParam(String key, Object value) {
+ FacesContext.getCurrentInstance().getExternalContext().getSessionMap().put(key, value);
+ }
+
+ @Override
+ public Object getSessionParam(String key) {
+ return FacesContext.getCurrentInstance().getExternalContext().getSessionMap().get(key);
+ }
+
+ @Override
+ public void createSession() {
+ FacesContext.getCurrentInstance().getExternalContext().getSession(true);
+ }
+
+ @Override
+ public <T> T findBean(Class<T> clazz) {
+ return FacesContextUtils.getWebApplicationContext(FacesContext.getCurrentInstance()).getBean(clazz);
+ }
+
+ @Override
+ public void executeJavascript(String javascript) {
+ RequestContext.getCurrentInstance().execute(javascript);
+ }
+
+}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/utils/StartupBean.java b/web/src/main/java/lcsb/mapviewer/bean/utils/StartupBean.java
index a2502c47c5..f42489f214 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/utils/StartupBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/utils/StartupBean.java
@@ -1,192 +1,192 @@
-package lcsb.mapviewer.bean.utils;
-
-import java.io.IOException;
-
-import javax.annotation.PostConstruct;
-import javax.faces.bean.ApplicationScoped;
-import javax.faces.bean.ManagedBean;
-import javax.faces.bean.ManagedProperty;
-import javax.faces.context.FacesContext;
-import javax.servlet.ServletContext;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.ProjectStatus;
-import lcsb.mapviewer.model.map.layout.ReferenceGenome;
-import lcsb.mapviewer.model.user.ConfigurationElementType;
-import lcsb.mapviewer.persist.DbUtils;
-import lcsb.mapviewer.services.interfaces.IConfigurationService;
-import lcsb.mapviewer.services.interfaces.IProjectService;
-import lcsb.mapviewer.services.interfaces.IReferenceGenomeService;
-
-/**
- * Bean where init script of the application is placed. The method in this bean
- * should be called only once, during application start.
- *
- * @author Piotr Gawron
- *
- */
-@ManagedBean(eager = true)
-@ApplicationScoped
-public class StartupBean {
-
- /**
- * Default class logger.
- */
- private final transient Logger logger = Logger.getLogger(StartupBean.class);
-
- /**
- * Dao used to access information about projects.
- *
- */
- @ManagedProperty(value = "#{ProjectService}")
- private transient IProjectService projectService;
-
- /**
- * Service used to access configuration params from db.
- *
- * @see IProjectService
- */
- @ManagedProperty(value = "#{ConfigurationService}")
- private transient IConfigurationService configurationService;
-
- /**
- * Service used to access information about reference genomes.
- *
- * @see IReferenceGenomeService
- */
- @ManagedProperty(value = "#{ReferenceGenomeService}")
- private transient IReferenceGenomeService referenceGenomeService;
-
- @ManagedProperty(value = "#{DbUtils}")
- private transient DbUtils dbUtils;
-
- /**
- * Method that process initial script of application.
- */
- @PostConstruct
- public void init() {
- logger.debug("Application startup script starts");
- ServletContext servletContext = (ServletContext) FacesContext.getCurrentInstance().getExternalContext()
- .getContext();
- Configuration.setWebAppDir(servletContext.getRealPath(".") + "/../");
-
- setInterruptedProjectsStatuses();
- modifyXFrameDomain();
- removeInterruptedReferenceGenomeDownloads();
- logger.debug("Application startup script ends");
- }
-
- private void modifyXFrameDomain() {
- try {
- for (String domain : configurationService.getConfigurationValue(ConfigurationElementType.X_FRAME_DOMAIN)
- .split(";")) {
- Configuration.getxFrameDomain().add(domain);
- }
- } catch (Exception e) {
- logger.error("Problem with modyfing x frame domain...", e);
- }
- }
-
- /**
- * Removes downloads of reference genomes that were interrupted by tomcat
- * restart.
- */
- private void removeInterruptedReferenceGenomeDownloads() {
- try {
- for (ReferenceGenome genome : referenceGenomeService.getDownloadedGenomes()) {
- if (genome.getDownloadProgress() < IProgressUpdater.MAX_PROGRESS) {
- logger.warn("Removing genome that was interrupted: " + genome);
- try {
- referenceGenomeService.removeGenome(genome);
- } catch (IOException e) {
- logger.error("Problem with removing genome: " + genome);
- }
- }
- }
- } catch (Exception e) {
- logger.error("Problem with removing interrupted downloads...", e);
- }
-
- }
-
- /**
- * Set {@link ProjectStatus#FAIL} statuses to projects that were uploading when
- * application was shutdown.
- */
- private void setInterruptedProjectsStatuses() {
- try {
- for (Project project : projectService.getAllProjects()) {
- if (!ProjectStatus.DONE.equals(project.getStatus()) && !ProjectStatus.FAIL.equals(project.getStatus())) {
- String errors = project.getErrors();
- if (errors == null || errors.trim().isEmpty()) {
- errors = "";
- } else {
- errors = errors.trim() + "\n";
- }
- errors += "Project uploading was interrupted by application restart (at the stage: " + project.getStatus()
- + ").";
- project.setStatus(ProjectStatus.FAIL);
- project.setErrors(errors);
- projectService.updateProject(project, null);
- logger.info("Status of project: " + project.getProjectId() + " changed to fail. Errors: " + errors);
- }
- }
- } catch (Exception e) {
- logger.error("Problem with changing project status ...", e);
- }
- }
-
- /**
- * @return the configurationService
- * @see #configurationService
- */
- public IConfigurationService getConfigurationService() {
- return configurationService;
- }
-
- /**
- * @param configurationService
- * the configurationService to set
- * @see #configurationService
- */
- public void setConfigurationService(IConfigurationService configurationService) {
- this.configurationService = configurationService;
- }
-
- /**
- * @return the referenceGenomeService
- * @see #referenceGenomeService
- */
- public IReferenceGenomeService getReferenceGenomeService() {
- return referenceGenomeService;
- }
-
- /**
- * @param referenceGenomeService
- * the referenceGenomeService to set
- * @see #referenceGenomeService
- */
- public void setReferenceGenomeService(IReferenceGenomeService referenceGenomeService) {
- this.referenceGenomeService = referenceGenomeService;
- }
-
- public IProjectService getProjectService() {
- return projectService;
- }
-
- public void setProjectService(IProjectService projectService) {
- this.projectService = projectService;
- }
-
- public DbUtils getDbUtils() {
- return dbUtils;
- }
-
- public void setDbUtils(DbUtils dbUtils) {
- this.dbUtils = dbUtils;
- }
-}
+package lcsb.mapviewer.bean.utils;
+
+import java.io.IOException;
+
+import javax.annotation.PostConstruct;
+import javax.faces.bean.ApplicationScoped;
+import javax.faces.bean.ManagedBean;
+import javax.faces.bean.ManagedProperty;
+import javax.faces.context.FacesContext;
+import javax.servlet.ServletContext;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.ProjectStatus;
+import lcsb.mapviewer.model.map.layout.ReferenceGenome;
+import lcsb.mapviewer.model.user.ConfigurationElementType;
+import lcsb.mapviewer.persist.DbUtils;
+import lcsb.mapviewer.services.interfaces.IConfigurationService;
+import lcsb.mapviewer.services.interfaces.IProjectService;
+import lcsb.mapviewer.services.interfaces.IReferenceGenomeService;
+
+/**
+ * Bean where init script of the application is placed. The method in this bean
+ * should be called only once, during application start.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@ManagedBean(eager = true)
+@ApplicationScoped
+public class StartupBean {
+
+ /**
+ * Default class logger.
+ */
+ private final transient Logger logger = Logger.getLogger(StartupBean.class);
+
+ /**
+ * Dao used to access information about projects.
+ *
+ */
+ @ManagedProperty(value = "#{ProjectService}")
+ private transient IProjectService projectService;
+
+ /**
+ * Service used to access configuration params from db.
+ *
+ * @see IProjectService
+ */
+ @ManagedProperty(value = "#{ConfigurationService}")
+ private transient IConfigurationService configurationService;
+
+ /**
+ * Service used to access information about reference genomes.
+ *
+ * @see IReferenceGenomeService
+ */
+ @ManagedProperty(value = "#{ReferenceGenomeService}")
+ private transient IReferenceGenomeService referenceGenomeService;
+
+ @ManagedProperty(value = "#{DbUtils}")
+ private transient DbUtils dbUtils;
+
+ /**
+ * Method that process initial script of application.
+ */
+ @PostConstruct
+ public void init() {
+ logger.debug("Application startup script starts");
+ ServletContext servletContext = (ServletContext) FacesContext.getCurrentInstance().getExternalContext()
+ .getContext();
+ Configuration.setWebAppDir(servletContext.getRealPath(".") + "/../");
+
+ setInterruptedProjectsStatuses();
+ modifyXFrameDomain();
+ removeInterruptedReferenceGenomeDownloads();
+ logger.debug("Application startup script ends");
+ }
+
+ private void modifyXFrameDomain() {
+ try {
+ for (String domain : configurationService.getConfigurationValue(ConfigurationElementType.X_FRAME_DOMAIN)
+ .split(";")) {
+ Configuration.getxFrameDomain().add(domain);
+ }
+ } catch (Exception e) {
+ logger.error("Problem with modyfing x frame domain...", e);
+ }
+ }
+
+ /**
+ * Removes downloads of reference genomes that were interrupted by tomcat
+ * restart.
+ */
+ private void removeInterruptedReferenceGenomeDownloads() {
+ try {
+ for (ReferenceGenome genome : referenceGenomeService.getDownloadedGenomes()) {
+ if (genome.getDownloadProgress() < IProgressUpdater.MAX_PROGRESS) {
+ logger.warn("Removing genome that was interrupted: " + genome);
+ try {
+ referenceGenomeService.removeGenome(genome);
+ } catch (IOException e) {
+ logger.error("Problem with removing genome: " + genome);
+ }
+ }
+ }
+ } catch (Exception e) {
+ logger.error("Problem with removing interrupted downloads...", e);
+ }
+
+ }
+
+ /**
+ * Set {@link ProjectStatus#FAIL} statuses to projects that were uploading when
+ * application was shutdown.
+ */
+ private void setInterruptedProjectsStatuses() {
+ try {
+ for (Project project : projectService.getAllProjects()) {
+ if (!ProjectStatus.DONE.equals(project.getStatus()) && !ProjectStatus.FAIL.equals(project.getStatus())) {
+ String errors = project.getErrors();
+ if (errors == null || errors.trim().isEmpty()) {
+ errors = "";
+ } else {
+ errors = errors.trim() + "\n";
+ }
+ errors += "Project uploading was interrupted by application restart (at the stage: " + project.getStatus()
+ + ").";
+ project.setStatus(ProjectStatus.FAIL);
+ project.setErrors(errors);
+ projectService.updateProject(project, null);
+ logger.info("Status of project: " + project.getProjectId() + " changed to fail. Errors: " + errors);
+ }
+ }
+ } catch (Exception e) {
+ logger.error("Problem with changing project status ...", e);
+ }
+ }
+
+ /**
+ * @return the configurationService
+ * @see #configurationService
+ */
+ public IConfigurationService getConfigurationService() {
+ return configurationService;
+ }
+
+ /**
+ * @param configurationService
+ * the configurationService to set
+ * @see #configurationService
+ */
+ public void setConfigurationService(IConfigurationService configurationService) {
+ this.configurationService = configurationService;
+ }
+
+ /**
+ * @return the referenceGenomeService
+ * @see #referenceGenomeService
+ */
+ public IReferenceGenomeService getReferenceGenomeService() {
+ return referenceGenomeService;
+ }
+
+ /**
+ * @param referenceGenomeService
+ * the referenceGenomeService to set
+ * @see #referenceGenomeService
+ */
+ public void setReferenceGenomeService(IReferenceGenomeService referenceGenomeService) {
+ this.referenceGenomeService = referenceGenomeService;
+ }
+
+ public IProjectService getProjectService() {
+ return projectService;
+ }
+
+ public void setProjectService(IProjectService projectService) {
+ this.projectService = projectService;
+ }
+
+ public DbUtils getDbUtils() {
+ return dbUtils;
+ }
+
+ public void setDbUtils(DbUtils dbUtils) {
+ this.dbUtils = dbUtils;
+ }
+}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/utils/VersionResourceHandler.java b/web/src/main/java/lcsb/mapviewer/bean/utils/VersionResourceHandler.java
index 6f8e06e38d..4dd92e96ff 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/utils/VersionResourceHandler.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/utils/VersionResourceHandler.java
@@ -1,112 +1,112 @@
-package lcsb.mapviewer.bean.utils;
-
-import javax.faces.application.Resource;
-import javax.faces.application.ResourceHandler;
-import javax.faces.application.ResourceHandlerWrapper;
-import javax.faces.application.ResourceWrapper;
-
-import lcsb.mapviewer.services.impl.ConfigurationService;
-
-import org.apache.log4j.Logger;
-
-/**
- * This class is used to provide url for jsf resource files with "?v=version"
- * addition that will make sure that when we update files from git repository
- * browser will reload them.
- *
- * @author Piotr Gawron
- *
- */
-public class VersionResourceHandler extends ResourceHandlerWrapper {
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(VersionResourceHandler.class);
-
- /**
- * SVN version of the system.
- */
- private static String version = null;
-
- /**
- * Resource for which we generate modified url.
- */
- private ResourceHandler wrapped;
-
- /**
- * Default constructor.
- *
- * @param wrapped
- * {@link #wrapped}
- */
- public VersionResourceHandler(ResourceHandler wrapped) {
- this.wrapped = wrapped;
- }
-
- @Override
- public Resource createResource(String resourceName) {
- return createResource(resourceName, null, null);
- }
-
- @Override
- public Resource createResource(String resourceName, String libraryName) {
- return createResource(resourceName, libraryName, null);
- }
-
- @Override
- public Resource createResource(String resourceName, String libraryName, String contentType) {
- final Resource resource = super.createResource(resourceName, libraryName, contentType);
-
- if (resource == null) {
- return null;
- }
-
- return new ResourceWrapper() {
-
- @Override
- public String getRequestPath() {
- return super.getRequestPath() + "&m_version=" + getVersion();
- }
-
- @Override
- public Resource getWrapped() {
- return resource;
- }
- @Override
- public String getContentType() {
- return getWrapped().getContentType();
- }
- @Override
- public String getResourceName() {
- return getWrapped().getResourceName();
- }
- @Override
- public String getLibraryName() {
- return getWrapped().getLibraryName();
- }
- };
- }
-
- @Override
- public ResourceHandler getWrapped() {
- return wrapped;
- }
-
- /**
- * This method returns git version of the framework.
- *
- * @return git version of the framework
- */
- private String getVersion() {
- if (version == null) {
- try {
- version = new ConfigurationService().getSystemGitVersion(new PrimefacesUtils().getPath());
- } catch (Exception e) {
- logger.error(e, e);
- version = "UNKNOWN";
- }
- }
- return version;
- }
-
+package lcsb.mapviewer.bean.utils;
+
+import javax.faces.application.Resource;
+import javax.faces.application.ResourceHandler;
+import javax.faces.application.ResourceHandlerWrapper;
+import javax.faces.application.ResourceWrapper;
+
+import lcsb.mapviewer.services.impl.ConfigurationService;
+
+import org.apache.log4j.Logger;
+
+/**
+ * This class is used to provide url for jsf resource files with "?v=version"
+ * addition that will make sure that when we update files from git repository
+ * browser will reload them.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class VersionResourceHandler extends ResourceHandlerWrapper {
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(VersionResourceHandler.class);
+
+ /**
+ * SVN version of the system.
+ */
+ private static String version = null;
+
+ /**
+ * Resource for which we generate modified url.
+ */
+ private ResourceHandler wrapped;
+
+ /**
+ * Default constructor.
+ *
+ * @param wrapped
+ * {@link #wrapped}
+ */
+ public VersionResourceHandler(ResourceHandler wrapped) {
+ this.wrapped = wrapped;
+ }
+
+ @Override
+ public Resource createResource(String resourceName) {
+ return createResource(resourceName, null, null);
+ }
+
+ @Override
+ public Resource createResource(String resourceName, String libraryName) {
+ return createResource(resourceName, libraryName, null);
+ }
+
+ @Override
+ public Resource createResource(String resourceName, String libraryName, String contentType) {
+ final Resource resource = super.createResource(resourceName, libraryName, contentType);
+
+ if (resource == null) {
+ return null;
+ }
+
+ return new ResourceWrapper() {
+
+ @Override
+ public String getRequestPath() {
+ return super.getRequestPath() + "&m_version=" + getVersion();
+ }
+
+ @Override
+ public Resource getWrapped() {
+ return resource;
+ }
+ @Override
+ public String getContentType() {
+ return getWrapped().getContentType();
+ }
+ @Override
+ public String getResourceName() {
+ return getWrapped().getResourceName();
+ }
+ @Override
+ public String getLibraryName() {
+ return getWrapped().getLibraryName();
+ }
+ };
+ }
+
+ @Override
+ public ResourceHandler getWrapped() {
+ return wrapped;
+ }
+
+ /**
+ * This method returns git version of the framework.
+ *
+ * @return git version of the framework
+ */
+ private String getVersion() {
+ if (version == null) {
+ try {
+ version = new ConfigurationService().getSystemGitVersion(new PrimefacesUtils().getPath());
+ } catch (Exception e) {
+ logger.error(e, e);
+ version = "UNKNOWN";
+ }
+ }
+ return version;
+ }
+
}
\ No newline at end of file
diff --git a/web/src/main/java/lcsb/mapviewer/bean/utils/XFrameAccessControlFilter.java b/web/src/main/java/lcsb/mapviewer/bean/utils/XFrameAccessControlFilter.java
index eaedccd574..619f75d8cd 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/utils/XFrameAccessControlFilter.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/utils/XFrameAccessControlFilter.java
@@ -1,61 +1,61 @@
-package lcsb.mapviewer.bean.utils;
-
-import java.io.IOException;
-import java.util.List;
-
-import javax.servlet.Filter;
-import javax.servlet.FilterChain;
-import javax.servlet.FilterConfig;
-import javax.servlet.ServletException;
-import javax.servlet.ServletRequest;
-import javax.servlet.ServletResponse;
-import javax.servlet.http.HttpServletResponse;
-
-import org.apache.commons.validator.routines.UrlValidator;
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Configuration;
-
-/**
- * This filter enables x-frames from another domain if necessary.
- *
- * @author Piotr Gawron
- *
- */
-public class XFrameAccessControlFilter implements Filter {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(XFrameAccessControlFilter.class);
-
- @Override
- public void init(FilterConfig config) throws ServletException {
- }
-
- @Override
- public void doFilter(ServletRequest req, ServletResponse res, FilterChain chain)
- throws IOException, ServletException {
- HttpServletResponse response = (HttpServletResponse) res;
- List<String> domains = Configuration.getxFrameDomain();
-
- String value = "frame-ancestors ";
- for (String domain : domains) {
- if (new UrlValidator().isValid(domain) || (domain != null && domain.contains("localhost"))) {
- value += domain + " ";
- }
- }
-
- if (!value.equals("frame-ancestors ")) {
- response.addHeader("Content-Security-Policy", value);
- } else {
- response.addHeader("X-Frame-Options", "DENY");
- }
- chain.doFilter(req, response);
- }
-
- @Override
- public void destroy() {
- }
-
-}
+package lcsb.mapviewer.bean.utils;
+
+import java.io.IOException;
+import java.util.List;
+
+import javax.servlet.Filter;
+import javax.servlet.FilterChain;
+import javax.servlet.FilterConfig;
+import javax.servlet.ServletException;
+import javax.servlet.ServletRequest;
+import javax.servlet.ServletResponse;
+import javax.servlet.http.HttpServletResponse;
+
+import org.apache.commons.validator.routines.UrlValidator;
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Configuration;
+
+/**
+ * This filter enables x-frames from another domain if necessary.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class XFrameAccessControlFilter implements Filter {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(XFrameAccessControlFilter.class);
+
+ @Override
+ public void init(FilterConfig config) throws ServletException {
+ }
+
+ @Override
+ public void doFilter(ServletRequest req, ServletResponse res, FilterChain chain)
+ throws IOException, ServletException {
+ HttpServletResponse response = (HttpServletResponse) res;
+ List<String> domains = Configuration.getxFrameDomain();
+
+ String value = "frame-ancestors ";
+ for (String domain : domains) {
+ if (new UrlValidator().isValid(domain) || (domain != null && domain.contains("localhost"))) {
+ value += domain + " ";
+ }
+ }
+
+ if (!value.equals("frame-ancestors ")) {
+ response.addHeader("Content-Security-Policy", value);
+ } else {
+ response.addHeader("X-Frame-Options", "DENY");
+ }
+ chain.doFilter(req, response);
+ }
+
+ @Override
+ public void destroy() {
+ }
+
+}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/utils/package-info.java b/web/src/main/java/lcsb/mapviewer/bean/utils/package-info.java
index dd8178c3d4..32f3712033 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/utils/package-info.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/utils/package-info.java
@@ -1,5 +1,5 @@
-/**
- * Provides util classes used by the web interface.
- */
-package lcsb.mapviewer.bean.utils;
-
+/**
+ * Provides util classes used by the web interface.
+ */
+package lcsb.mapviewer.bean.utils;
+
diff --git a/web/src/main/java/lcsb/mapviewer/converter/MiriamTypeConverter.java b/web/src/main/java/lcsb/mapviewer/converter/MiriamTypeConverter.java
index b30e114700..535a4e8a20 100644
--- a/web/src/main/java/lcsb/mapviewer/converter/MiriamTypeConverter.java
+++ b/web/src/main/java/lcsb/mapviewer/converter/MiriamTypeConverter.java
@@ -1,59 +1,59 @@
-package lcsb.mapviewer.converter;
-
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.UUID;
-import java.util.WeakHashMap;
-
-import javax.faces.component.UIComponent;
-import javax.faces.context.FacesContext;
-import javax.faces.convert.Converter;
-import javax.faces.convert.FacesConverter;
-
-import org.apache.log4j.Logger;
-
-/**
- * Converter used for {@link lcsb.mapviewer.model.map.MiriamType} in primefaces
- * pick list.
- *
- * @author Piotr Gawron
- *
- */
-@FacesConverter(value = "miriamTypeConverter")
-public class MiriamTypeConverter implements Converter {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(MiriamTypeConverter.class);
-
- /**
- * Map between custom uuid and MiriamType object.
- */
- private static Map<Object, String> entities = new WeakHashMap<Object, String>();
-
- @Override
- public String getAsString(FacesContext context, UIComponent component, Object entity) {
- synchronized (entities) {
- if (!entities.containsKey(entity)) {
- String uuid = UUID.randomUUID().toString();
- entities.put(entity, uuid);
- return uuid;
- } else {
- return entities.get(entity);
- }
- }
- }
-
- @Override
- public Object getAsObject(FacesContext context, UIComponent component, String uuid) {
- for (Entry<Object, String> entry : entities.entrySet()) {
- if (entry.getValue().equals(uuid)) {
- return entry.getKey();
- }
- }
- return null;
- }
-
-}
+package lcsb.mapviewer.converter;
+
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.UUID;
+import java.util.WeakHashMap;
+
+import javax.faces.component.UIComponent;
+import javax.faces.context.FacesContext;
+import javax.faces.convert.Converter;
+import javax.faces.convert.FacesConverter;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Converter used for {@link lcsb.mapviewer.model.map.MiriamType} in primefaces
+ * pick list.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@FacesConverter(value = "miriamTypeConverter")
+public class MiriamTypeConverter implements Converter {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(MiriamTypeConverter.class);
+
+ /**
+ * Map between custom uuid and MiriamType object.
+ */
+ private static Map<Object, String> entities = new WeakHashMap<Object, String>();
+
+ @Override
+ public String getAsString(FacesContext context, UIComponent component, Object entity) {
+ synchronized (entities) {
+ if (!entities.containsKey(entity)) {
+ String uuid = UUID.randomUUID().toString();
+ entities.put(entity, uuid);
+ return uuid;
+ } else {
+ return entities.get(entity);
+ }
+ }
+ }
+
+ @Override
+ public Object getAsObject(FacesContext context, UIComponent component, String uuid) {
+ for (Entry<Object, String> entry : entities.entrySet()) {
+ if (entry.getValue().equals(uuid)) {
+ return entry.getKey();
+ }
+ }
+ return null;
+ }
+
+}
diff --git a/web/src/main/java/lcsb/mapviewer/converter/package-info.java b/web/src/main/java/lcsb/mapviewer/converter/package-info.java
index 68d2cc5eae..7a4cdc3873 100644
--- a/web/src/main/java/lcsb/mapviewer/converter/package-info.java
+++ b/web/src/main/java/lcsb/mapviewer/converter/package-info.java
@@ -1,6 +1,6 @@
-/**
- * Provides {@link javax.faces.convert.Converter converters} for components used
- * by primefaces.
- */
-package lcsb.mapviewer.converter;
-
+/**
+ * Provides {@link javax.faces.convert.Converter converters} for components used
+ * by primefaces.
+ */
+package lcsb.mapviewer.converter;
+
diff --git a/web/src/main/java/lcsb/mapviewer/events/Event.java b/web/src/main/java/lcsb/mapviewer/events/Event.java
index 81abf754fa..4292645f1f 100644
--- a/web/src/main/java/lcsb/mapviewer/events/Event.java
+++ b/web/src/main/java/lcsb/mapviewer/events/Event.java
@@ -1,11 +1,11 @@
-package lcsb.mapviewer.events;
-
-
-/**
- * Abstract event object that might be handled by {@link Listener} class.
- *
- * @author Piotr Gawron
- *
- */
-public abstract class Event {
-}
+package lcsb.mapviewer.events;
+
+
+/**
+ * Abstract event object that might be handled by {@link Listener} class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public abstract class Event {
+}
diff --git a/web/src/main/java/lcsb/mapviewer/events/Listener.java b/web/src/main/java/lcsb/mapviewer/events/Listener.java
index 771ebd60db..eaa8aa5ea6 100644
--- a/web/src/main/java/lcsb/mapviewer/events/Listener.java
+++ b/web/src/main/java/lcsb/mapviewer/events/Listener.java
@@ -1,60 +1,60 @@
-package lcsb.mapviewer.events;
-
-import java.io.Serializable;
-
-/**
- * Abstract class that handles {@link Event events}.
- *
- * @author Piotr Gawron
- *
- * @param <T>
- */
-public abstract class Listener<T extends Event> implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Class of event handled by this listener.
- */
- private Class<T> eventClass;
-
- /**
- * Default constructor.
- *
- * @param clazz
- * class of events handled by this listener
- */
- public Listener(Class<T> clazz) {
- this.eventClass = clazz;
- }
-
- /**
- * This method handle the event.
- *
- * @param event
- * event to be handled
- */
- protected abstract void handle(T event);
-
- /**
- * Handle the event.
- *
- * @param event
- * event to be handled
- */
- @SuppressWarnings("unchecked")
- public void handleEvent(Event event) {
- this.handle((T) event);
- }
-
- /**
- * @return the eventClass
- * @see #eventClass
- */
- public Class<T> getEventClass() {
- return eventClass;
- }
-}
+package lcsb.mapviewer.events;
+
+import java.io.Serializable;
+
+/**
+ * Abstract class that handles {@link Event events}.
+ *
+ * @author Piotr Gawron
+ *
+ * @param <T>
+ */
+public abstract class Listener<T extends Event> implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Class of event handled by this listener.
+ */
+ private Class<T> eventClass;
+
+ /**
+ * Default constructor.
+ *
+ * @param clazz
+ * class of events handled by this listener
+ */
+ public Listener(Class<T> clazz) {
+ this.eventClass = clazz;
+ }
+
+ /**
+ * This method handle the event.
+ *
+ * @param event
+ * event to be handled
+ */
+ protected abstract void handle(T event);
+
+ /**
+ * Handle the event.
+ *
+ * @param event
+ * event to be handled
+ */
+ @SuppressWarnings("unchecked")
+ public void handleEvent(Event event) {
+ this.handle((T) event);
+ }
+
+ /**
+ * @return the eventClass
+ * @see #eventClass
+ */
+ public Class<T> getEventClass() {
+ return eventClass;
+ }
+}
diff --git a/web/src/main/java/lcsb/mapviewer/events/ObjectAddedEvent.java b/web/src/main/java/lcsb/mapviewer/events/ObjectAddedEvent.java
index 15f809a15b..a531b2d02f 100644
--- a/web/src/main/java/lcsb/mapviewer/events/ObjectAddedEvent.java
+++ b/web/src/main/java/lcsb/mapviewer/events/ObjectAddedEvent.java
@@ -1,40 +1,40 @@
-package lcsb.mapviewer.events;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-
-/**
- * Event called when object was removed.
- *
- * @author Piotr Gawron
- *
- */
-public class ObjectAddedEvent extends Event {
-
- /**
- * Object that was removed.
- */
- private Object object;
-
- /**
- * Default constructor.
- *
- * @param object
- * {@link #object}
- */
- public ObjectAddedEvent(Object object) {
- if (object == null) {
- throw new InvalidArgumentException("object cannot be null");
- }
-
- this.object = object;
- }
-
- /**
- * @return the object
- * @see #object
- */
- public Object getObject() {
- return object;
- }
-
-}
+package lcsb.mapviewer.events;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+
+/**
+ * Event called when object was removed.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ObjectAddedEvent extends Event {
+
+ /**
+ * Object that was removed.
+ */
+ private Object object;
+
+ /**
+ * Default constructor.
+ *
+ * @param object
+ * {@link #object}
+ */
+ public ObjectAddedEvent(Object object) {
+ if (object == null) {
+ throw new InvalidArgumentException("object cannot be null");
+ }
+
+ this.object = object;
+ }
+
+ /**
+ * @return the object
+ * @see #object
+ */
+ public Object getObject() {
+ return object;
+ }
+
+}
diff --git a/web/src/main/java/lcsb/mapviewer/events/ObjectModifiedEvent.java b/web/src/main/java/lcsb/mapviewer/events/ObjectModifiedEvent.java
index 1e6bb47278..69e4e61223 100644
--- a/web/src/main/java/lcsb/mapviewer/events/ObjectModifiedEvent.java
+++ b/web/src/main/java/lcsb/mapviewer/events/ObjectModifiedEvent.java
@@ -1,39 +1,39 @@
-package lcsb.mapviewer.events;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-
-/**
- * Event called when object was modified.
- *
- * @author Piotr Gawron
- *
- */
-public class ObjectModifiedEvent extends Event {
-
- /**
- * Object that was modified.
- */
- private Object object;
-
- /**
- * Default constructor.
- *
- * @param object
- * {@link #object}
- */
- public ObjectModifiedEvent(Object object) {
- if (object == null) {
- throw new InvalidArgumentException("object cannot be null");
- }
- this.object = object;
- }
-
- /**
- * @return the object
- * @see #object
- */
- public Object getObject() {
- return object;
- }
-
-}
+package lcsb.mapviewer.events;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+
+/**
+ * Event called when object was modified.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ObjectModifiedEvent extends Event {
+
+ /**
+ * Object that was modified.
+ */
+ private Object object;
+
+ /**
+ * Default constructor.
+ *
+ * @param object
+ * {@link #object}
+ */
+ public ObjectModifiedEvent(Object object) {
+ if (object == null) {
+ throw new InvalidArgumentException("object cannot be null");
+ }
+ this.object = object;
+ }
+
+ /**
+ * @return the object
+ * @see #object
+ */
+ public Object getObject() {
+ return object;
+ }
+
+}
diff --git a/web/src/main/java/lcsb/mapviewer/events/ObjectRemovedEvent.java b/web/src/main/java/lcsb/mapviewer/events/ObjectRemovedEvent.java
index 953cf0086c..a79341833f 100644
--- a/web/src/main/java/lcsb/mapviewer/events/ObjectRemovedEvent.java
+++ b/web/src/main/java/lcsb/mapviewer/events/ObjectRemovedEvent.java
@@ -1,40 +1,40 @@
-package lcsb.mapviewer.events;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-
-/**
- * Event called when object was removed.
- *
- * @author Piotr Gawron
- *
- */
-public class ObjectRemovedEvent extends Event {
-
- /**
- * Object that was removed.
- */
- private Object object;
-
- /**
- * Default constructor.
- *
- * @param object
- * {@link #object}
- */
- public ObjectRemovedEvent(Object object) {
- if (object == null) {
- throw new InvalidArgumentException("object cannot be null");
- }
-
- this.object = object;
- }
-
- /**
- * @return the object
- * @see #object
- */
- public Object getObject() {
- return object;
- }
-
-}
+package lcsb.mapviewer.events;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+
+/**
+ * Event called when object was removed.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ObjectRemovedEvent extends Event {
+
+ /**
+ * Object that was removed.
+ */
+ private Object object;
+
+ /**
+ * Default constructor.
+ *
+ * @param object
+ * {@link #object}
+ */
+ public ObjectRemovedEvent(Object object) {
+ if (object == null) {
+ throw new InvalidArgumentException("object cannot be null");
+ }
+
+ this.object = object;
+ }
+
+ /**
+ * @return the object
+ * @see #object
+ */
+ public Object getObject() {
+ return object;
+ }
+
+}
diff --git a/web/src/main/java/lcsb/mapviewer/events/package-info.java b/web/src/main/java/lcsb/mapviewer/events/package-info.java
index 657dcab4cd..79e964e62c 100644
--- a/web/src/main/java/lcsb/mapviewer/events/package-info.java
+++ b/web/src/main/java/lcsb/mapviewer/events/package-info.java
@@ -1,5 +1,5 @@
-/**
- * Provides events and listeners functionality.
- */
-package lcsb.mapviewer.events;
-
+/**
+ * Provides events and listeners functionality.
+ */
+package lcsb.mapviewer.events;
+
diff --git a/web/src/main/java/lcsb/mapviewer/security/MvAuthenticationFailureHandler.java b/web/src/main/java/lcsb/mapviewer/security/MvAuthenticationFailureHandler.java
index 9f7347cff1..8f6a943c20 100644
--- a/web/src/main/java/lcsb/mapviewer/security/MvAuthenticationFailureHandler.java
+++ b/web/src/main/java/lcsb/mapviewer/security/MvAuthenticationFailureHandler.java
@@ -1,36 +1,36 @@
-package lcsb.mapviewer.security;
-
-import java.io.IOException;
-
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
-import org.springframework.security.core.AuthenticationException;
-import org.springframework.security.web.authentication.SimpleUrlAuthenticationFailureHandler;
-
-/**
- * Implementation of Spring Authentication Failure Handler. When authentication
- * fail, it will redirect user to the webpage defined in configuration xml.
- *
- * @author Piotr Gawron
- *
- */
-public class MvAuthenticationFailureHandler extends SimpleUrlAuthenticationFailureHandler {
-
- /**
- * Constructor with the redirect url.
- *
- * @param defaultFailureUrl
- * default redirect url
- */
- public MvAuthenticationFailureHandler(String defaultFailureUrl) {
- super(defaultFailureUrl);
- }
-
- @Override
- public void onAuthenticationFailure(HttpServletRequest request, HttpServletResponse response, AuthenticationException exception) throws IOException,
- ServletException {
- super.onAuthenticationFailure(request, response, exception);
- }
-}
+package lcsb.mapviewer.security;
+
+import java.io.IOException;
+
+import javax.servlet.ServletException;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import org.springframework.security.core.AuthenticationException;
+import org.springframework.security.web.authentication.SimpleUrlAuthenticationFailureHandler;
+
+/**
+ * Implementation of Spring Authentication Failure Handler. When authentication
+ * fail, it will redirect user to the webpage defined in configuration xml.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class MvAuthenticationFailureHandler extends SimpleUrlAuthenticationFailureHandler {
+
+ /**
+ * Constructor with the redirect url.
+ *
+ * @param defaultFailureUrl
+ * default redirect url
+ */
+ public MvAuthenticationFailureHandler(String defaultFailureUrl) {
+ super(defaultFailureUrl);
+ }
+
+ @Override
+ public void onAuthenticationFailure(HttpServletRequest request, HttpServletResponse response, AuthenticationException exception) throws IOException,
+ ServletException {
+ super.onAuthenticationFailure(request, response, exception);
+ }
+}
diff --git a/web/src/main/java/lcsb/mapviewer/security/MvAuthenticationSuccessHandler.java b/web/src/main/java/lcsb/mapviewer/security/MvAuthenticationSuccessHandler.java
index 4ded409599..0f36741781 100644
--- a/web/src/main/java/lcsb/mapviewer/security/MvAuthenticationSuccessHandler.java
+++ b/web/src/main/java/lcsb/mapviewer/security/MvAuthenticationSuccessHandler.java
@@ -1,68 +1,68 @@
-package lcsb.mapviewer.security;
-
-import java.io.IOException;
-
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
-import lcsb.mapviewer.common.Configuration;
-
-import org.springframework.security.core.Authentication;
-import org.springframework.security.web.authentication.SavedRequestAwareAuthenticationSuccessHandler;
-import org.springframework.security.web.savedrequest.HttpSessionRequestCache;
-import org.springframework.security.web.savedrequest.SavedRequest;
-
-/**
- * Implementation of Spring Authentication Success Handler. When authentication
- * is success, it will redirect user to the web page that had accessed before
- * authentication took place.
- *
- * @author Piotr Gawron
- */
-
-public class MvAuthenticationSuccessHandler extends SavedRequestAwareAuthenticationSuccessHandler {
- /**
- * Default session expire time in seconds (120 minutes).
- */
- private static final Integer MAX_INACTIVE_INTERVAL = 120 * 60;
-
- @Override
- public void onAuthenticationSuccess(HttpServletRequest request, HttpServletResponse response, Authentication authentication) throws IOException,
- ServletException {
-
- request.getSession().setMaxInactiveInterval(MAX_INACTIVE_INTERVAL);
-
- SavedRequest savedRequest = new HttpSessionRequestCache().getRequest(request, response);
- String url = request.getParameter("from");
-
-
- // if we are not redirecting from somewhere then
- if ((url != null && !url.isEmpty())) {
- logger.debug("Found redirect URL");
- } else if (savedRequest == null) {
- logger.debug(request.getRequestURL());
- //redirect to the main page
- url = request.getRequestURL().toString().replace(request.getServletPath(), "") + Configuration.MAIN_PAGE;
-
- String queryString = request.getQueryString();
- // and don't forget about parameters
- if (queryString != null) {
- url += "?" + queryString;
- }
- } else {
- url = savedRequest.getRedirectUrl();
- }
-
- logger.debug("Redirecting: " + url);
-
- if (!response.isCommitted()) {
- response.sendRedirect(url);
- return;
- } else {
- logger.warn("If you see this then something is wrong...");
- }
-
- super.onAuthenticationSuccess(request, response, authentication);
- }
-}
+package lcsb.mapviewer.security;
+
+import java.io.IOException;
+
+import javax.servlet.ServletException;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import lcsb.mapviewer.common.Configuration;
+
+import org.springframework.security.core.Authentication;
+import org.springframework.security.web.authentication.SavedRequestAwareAuthenticationSuccessHandler;
+import org.springframework.security.web.savedrequest.HttpSessionRequestCache;
+import org.springframework.security.web.savedrequest.SavedRequest;
+
+/**
+ * Implementation of Spring Authentication Success Handler. When authentication
+ * is success, it will redirect user to the web page that had accessed before
+ * authentication took place.
+ *
+ * @author Piotr Gawron
+ */
+
+public class MvAuthenticationSuccessHandler extends SavedRequestAwareAuthenticationSuccessHandler {
+ /**
+ * Default session expire time in seconds (120 minutes).
+ */
+ private static final Integer MAX_INACTIVE_INTERVAL = 120 * 60;
+
+ @Override
+ public void onAuthenticationSuccess(HttpServletRequest request, HttpServletResponse response, Authentication authentication) throws IOException,
+ ServletException {
+
+ request.getSession().setMaxInactiveInterval(MAX_INACTIVE_INTERVAL);
+
+ SavedRequest savedRequest = new HttpSessionRequestCache().getRequest(request, response);
+ String url = request.getParameter("from");
+
+
+ // if we are not redirecting from somewhere then
+ if ((url != null && !url.isEmpty())) {
+ logger.debug("Found redirect URL");
+ } else if (savedRequest == null) {
+ logger.debug(request.getRequestURL());
+ //redirect to the main page
+ url = request.getRequestURL().toString().replace(request.getServletPath(), "") + Configuration.MAIN_PAGE;
+
+ String queryString = request.getQueryString();
+ // and don't forget about parameters
+ if (queryString != null) {
+ url += "?" + queryString;
+ }
+ } else {
+ url = savedRequest.getRedirectUrl();
+ }
+
+ logger.debug("Redirecting: " + url);
+
+ if (!response.isCommitted()) {
+ response.sendRedirect(url);
+ return;
+ } else {
+ logger.warn("If you see this then something is wrong...");
+ }
+
+ super.onAuthenticationSuccess(request, response, authentication);
+ }
+}
diff --git a/web/src/main/java/lcsb/mapviewer/security/MvUsernamePasswordAuthenticationFilter.java b/web/src/main/java/lcsb/mapviewer/security/MvUsernamePasswordAuthenticationFilter.java
index c63e3b96a6..c9e253b2ac 100644
--- a/web/src/main/java/lcsb/mapviewer/security/MvUsernamePasswordAuthenticationFilter.java
+++ b/web/src/main/java/lcsb/mapviewer/security/MvUsernamePasswordAuthenticationFilter.java
@@ -1,43 +1,43 @@
-package lcsb.mapviewer.security;
-
-import java.io.IOException;
-
-import javax.servlet.FilterChain;
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
-import org.apache.log4j.Logger;
-import org.springframework.security.core.Authentication;
-import org.springframework.security.core.AuthenticationException;
-import org.springframework.security.web.authentication.UsernamePasswordAuthenticationFilter;
-
-
-/**
- * No idea about the reason why this class is put here...
- *
- * @author Piotr Gawron
- *
- */
-public class MvUsernamePasswordAuthenticationFilter extends UsernamePasswordAuthenticationFilter {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(MvUsernamePasswordAuthenticationFilter.class);
-
- @Override
- protected void successfulAuthentication(HttpServletRequest request, HttpServletResponse response, FilterChain chain, Authentication authResult)
- throws IOException, ServletException {
- super.successfulAuthentication(request, response, chain, authResult);
- logger.info("successfulAuthentication");
-
- }
-
- @Override
- protected void unsuccessfulAuthentication(HttpServletRequest request, HttpServletResponse response, AuthenticationException failed) throws IOException,
- ServletException {
- super.unsuccessfulAuthentication(request, response, failed);
- logger.info("unsuccessfulAuthentication");
- }
-
-}
+package lcsb.mapviewer.security;
+
+import java.io.IOException;
+
+import javax.servlet.FilterChain;
+import javax.servlet.ServletException;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import org.apache.log4j.Logger;
+import org.springframework.security.core.Authentication;
+import org.springframework.security.core.AuthenticationException;
+import org.springframework.security.web.authentication.UsernamePasswordAuthenticationFilter;
+
+
+/**
+ * No idea about the reason why this class is put here...
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class MvUsernamePasswordAuthenticationFilter extends UsernamePasswordAuthenticationFilter {
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(MvUsernamePasswordAuthenticationFilter.class);
+
+ @Override
+ protected void successfulAuthentication(HttpServletRequest request, HttpServletResponse response, FilterChain chain, Authentication authResult)
+ throws IOException, ServletException {
+ super.successfulAuthentication(request, response, chain, authResult);
+ logger.info("successfulAuthentication");
+
+ }
+
+ @Override
+ protected void unsuccessfulAuthentication(HttpServletRequest request, HttpServletResponse response, AuthenticationException failed) throws IOException,
+ ServletException {
+ super.unsuccessfulAuthentication(request, response, failed);
+ logger.info("unsuccessfulAuthentication");
+ }
+
+}
diff --git a/web/src/main/java/lcsb/mapviewer/security/package-info.java b/web/src/main/java/lcsb/mapviewer/security/package-info.java
index 999132d5da..39315f1e00 100644
--- a/web/src/main/java/lcsb/mapviewer/security/package-info.java
+++ b/web/src/main/java/lcsb/mapviewer/security/package-info.java
@@ -1,6 +1,6 @@
-/**
- * This package contains implementation of Spring interfaces used during
- * authentication process.
- */
-package lcsb.mapviewer.security;
-
+/**
+ * This package contains implementation of Spring interfaces used during
+ * authentication process.
+ */
+package lcsb.mapviewer.security;
+
--
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